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  1. Sep 2025
    1. Document d'Information : Synthèse de la 18ème Journée du Refus de l'Échec Scolaire

      Résumé

      La 18ème Journée du Refus de l'Échec Scolaire (JRES), organisée par l'AFEV, a porté sur le thème "Jeunesses populaires rurales et urbaines : même combat face aux inégalités éducatives ?".

      L'événement a mis en lumière les convergences et les divergences entre ces deux jeunesses, souvent opposées dans le discours public via la formule "jeunesse des tours, jeunesse des bourgs".

      Les débats ont révélé que, bien que confrontées à des défis spécifiques liés à leur territoire (mobilité pour les ruraux, discriminations pour les urbains), ces jeunesses partagent des problématiques communes profondément ancrées dans les inégalités sociales.

      Une enquête exclusive de Trajectoires Réflex, menée auprès de 1500 lycéens, a démontré la prépondérance du milieu social sur le lieu de vie dans la détermination des parcours scolaires et des aspirations.

      Les jeunes des classes populaires, qu'ils soient ruraux ou urbains, s'orientent davantage vers des filières courtes, tandis que les jeunes de classes supérieures visent des études longues. L'étude souligne également une anxiété partagée face à l'orientation, notamment à cause de Parcoursup.

      Les intervenants, incluant le sociologue Benoît Coquard, des élus locaux, des acteurs associatifs et des chercheurs, ont unanimement appelé à dépasser les oppositions stériles.

      Ils ont souligné l'importance de reconnaître les réalités diverses des territoires, les dynamiques d'autocensure, la complexité de la mobilité (partir, rester, revenir) et l'impact de l'isolement.

      Un consensus s'est dégagé sur l'urgence de refonder des politiques publiques décloisonnées, de repenser le modèle de la méritocratie et de valoriser toutes les formes de réussite et d'engagement pour reconstruire un "destin commun" et garantir une véritable égalité des chances pour tous les jeunes.

      1. Thématique Centrale : Dépasser l'Opposition "Tours vs. Bourgs"

      La 18ème JRES a été initiée pour analyser l'articulation entre les jeunesses populaires rurales et urbaines, un parallèle popularisé par la formule "jeunesse des tours, jeunesse des bourgs".

      Les intervenants ont largement critiqué l'instrumentalisation politique et médiatique de cette opposition.

      Origine de la réflexion (Eunice Mangado-Lunetta, AFEV) : L'AFEV, historiquement ancrée dans les Quartiers Prioritaires de la politique de la Ville (QPV), a constaté que "la France qui va mal, on la retrouve partout".

      L'association a remis en question le discours opposant un "bloc métropolitain" riche à un "bloc périphérique" en difficulté, discours souvent utilisé pour critiquer l'investissement public dans les QPV au détriment d'une "France qui souffre silencieusement dans les campagnes".

      Perspective sociologique (Benoît Coquard) : Le sociologue, parrain de l'événement, a souligné que cette formule est un slogan efficace mais "en partie trompeur".

      Il a expliqué que l'enjeu politique actuel est de se réclamer de la ruralité, devenue un "faire-valoir" et un "écran de fumée" masquant les questions sociales.

      Il insiste sur la nécessité de parler des "ruralités" au pluriel, car il existe des écarts de richesse et des dynamiques démographiques très variés entre les campagnes, tout comme dans les villes.

      Objectif de la journée : L'objectif n'était pas d'opposer ces jeunesses ni de mettre un signe égal entre elles, mais de "chercher du commun" tout en reconnaissant ce qui diffère, afin d'éviter les "oppositions stériles". L'enquête présentée visait spécifiquement à superposer le filtre territorial et le filtre social pour une analyse plus juste.

      2. Enquête Trajectoires Réflex : Données Clés sur les Lycéens

      Une enquête a été réalisée de mai à juillet 2025 auprès de plus de 1500 lycéens de filières générales, technologiques et professionnelles.

      L'échantillon comprenait 41% de jeunes de communes rurales et 26% de jeunes de petites villes. L'analyse croise le lieu de vie avec le milieu social (défini par le diplôme et la CSP des parents).

      2.1 Orientation et Projections d'Études Le milieu social apparaît comme le facteur prépondérant dans les choix d'orientation, plus que le lieu de vie.

      Rapport au lycée :

      ◦ 94% des jeunes disent avoir choisi leur filière.

      ◦ 70% ressentent de la pression liée aux cours et aux résultats.

      ◦ Plus d'un tiers déclare avoir des difficultés d'apprentissage, une part plus importante chez les jeunes de classes populaires.

      Orientation post-bac : ◦ 61% se sentent bien informés, mais 58% sont inquiets.

      ◦ Le stress est principalement causé par les démarches Parcoursup et le flou du projet d'orientation.

      Aspirations :

      ◦ 80% souhaitent poursuivre des études supérieures.

      ◦ L'influence du milieu social est nette : les jeunes urbains de classe supérieure privilégient les études longues (Master, Grande École), tandis que les jeunes ruraux de classe populaire ciblent davantage les filières courtes pour une insertion plus rapide sur le marché du travail.

      Type d'études Jeunes de classe populaire RURALE Jeunes de classe populaire URBAINE Filière courte (BTS/BUT) 32% 16% Niveau Master 38% 55%

      Sens donné aux études : Pour les jeunes de classe supérieure, la "réussite personnelle" prime. Pour ceux des milieux populaires, c'est avant tout le fait de "gagner de l'argent".

      2.2 Mobilité, Attachement et Avenir

      Attachement au territoire : 82% des jeunes partagent un fort attachement à leur lieu de vie. Cet attachement est plus marqué chez les jeunes ruraux (85%) et encore plus chez les jeunes ruraux de classe populaire (90%).

      Projet de départ : ◦ 69% se préparent à partir de chez leurs parents pour leurs études.

      ◦ Ce sont les jeunes de milieux favorisés et les jeunes ruraux qui sont les plus nombreux à se préparer à partir.

      ◦ Cependant, le départ est plus souvent subi par les ruraux : 17% des jeunes ruraux parlent d'une "contrainte à quitter le domicile familial", contre seulement 9% des jeunes citadins.

      Bien-être et difficultés :

      ◦ 84% se sentent bien au quotidien, mais 64% témoignent de leur anxiété.
      

      ◦ 1 jeune sur 5 se sent isolé. Ce sentiment est plus prononcé chez les jeunes de classe populaire rurale (21%) que chez les urbains (15%).

      ◦ Les difficultés financières sont plus fréquentes chez les jeunes de milieu populaire (40% vs 14% chez les enfants de Bac+5).

      • Projection sociale :

      ◦ Seuls 36% des citadins et 25% des ruraux pensent avoir une meilleure vie que leurs parents. 45% ne savent pas.

      ◦ Les jeunes de milieu populaire semblent plus optimistes, espérant une ascension sociale. Cependant, un clivage territorial existe : 42% des citadins de milieu populaire ont une image positive de leur avenir, contre 31% des ruraux de milieu populaire.

      2.3 Mobilité Quotidienne et Déplacements Les difficultés de déplacement sont significativement plus marquées pour les jeunes ruraux.

      • Seule la moitié (50%) des jeunes de classe populaire rurale déclare qu'il est facile pour eux de se déplacer, contre 90% des jeunes de classe populaire urbaine.

      Dépendance à la voiture : 53% des jeunes ruraux utilisent la voiture au quotidien (contre 12% des citadins). Le permis est jugé indispensable pour 80% des ruraux (contre 55% des citadins).

      2.4 Rapport aux Institutions et à l'Engagement

      Discriminations :

      ◦ 36% des jeunes déclarent en avoir été victimes, principalement à l'école (94% des cas).

      ◦ Le sentiment est plus marqué chez les jeunes urbains (43% vs 31% des ruraux).

      ◦ Les motifs varient : pour les citadins de classe populaire, les discriminations sont liées à l'origine, l'apparence et les convictions. Pour les ruraux de classe populaire, elles sont liées à l'apparence, la classe sociale et l'état de santé.

      Confiance dans les institutions : La confiance est plus forte chez les jeunes de classe supérieure et les jeunes ruraux.

      ◦ Police : 83% des jeunes ruraux de milieu modeste font confiance à la police, contre 58% des jeunes urbains de milieu modeste.

      ◦ Une méfiance généralisée est partagée envers les médias (42% de confiance), les réseaux sociaux (21%) et surtout la classe politique (16%).

      Rapport au vote et à l'engagement : ◦ Le rapport au vote est socialement inégal : 60% des jeunes de milieu favorisé pensent voter, contre 46% des enfants de non-diplômés.

      ◦ 44% des jeunes ne savent pas s'ils comptent s'engager plus tard. Ce doute est plus fort chez les jeunes ruraux.

      3. Parcours de Vie et Analyses Croisées

      3.1 Le Témoignage de Benoît Coquard : Du Rural à la Sociologie

      Le sociologue Benoît Coquard a partagé son parcours personnel, emblématique des barrières et des aléas qui façonnent les destins.

      Origines : Vient d'un village de Haute-Marne, un département avec très peu de cadres. Ses parents, "petits fonctionnaires", ont quitté l'école à 14-15 ans. Il n'avait "pas de modèle estudiantin".

      Bifurcation : Doit sa mobilité sociale à "l'intervention un peu divine, un peu aléatoire" de sa sœur qui l'a poussé vers les études supérieures.

      Il souligne que sans l'inexistence de Parcoursup à l'époque, il n'aurait pas pu s'inscrire à l'université avec son "mauvais dossier scolaire".

      Rapport à l'école : Mauvais élève, il a raté son bac. L'école était pour lui "la seule scène sociale sur laquelle [il était] parfois dévalorisé". Il décrit la construction d'une "culture anti-école" où l'on développe des modèles de reconnaissance alternatifs (sport, sociabilité locale).

      Analyse sociologique : Son travail de recherche, notamment Ceux qui restent, l'a amené à étudier son propre milieu.

      Il met en évidence que les jeunes ruraux croient davantage en leurs "ressources d'autochtonie" (réseau local, piston) pour s'en sortir, ce qui peut les détourner de l'école.

      À l'inverse, les jeunes des quartiers, souvent issus de l'immigration, surinvestissent l'école car leurs parents n'ont pas ce capital d'autochtonie.

      3.2 Le Témoignage d'Yvon Atonga : Destins Divergents en Banlieue

      Yvon Atonga, co-auteur de Petit frère, a raconté son histoire et celle de son frère Wilfried, qui a grandi dans le même environnement à Villiers-le-Bel mais a connu un destin tragique.

      Points de bifurcation : Il identifie plusieurs moments clés qui ont séparé leurs trajectoires :

      1. L'intervention de sa mère : Un jour, alors que ses amis venaient le chercher, sa mère leur a dit qu'il n'était pas là car il faisait ses devoirs. Ses amis sont partis commettre un braquage et ont été condamnés à de lourdes peines.

      2. Un voyage au Congo : À 15 ans, un voyage dans son pays d'origine a été un "électrochoc", lui faisant prendre conscience des opportunités qu'il avait en France.

      La loyauté au quartier : Il décrit une "loyauté indiscutable" au groupe d'amis et au quartier, qui représente une "deuxième famille". Partir est souvent perçu comme une "trahison".

      Il insiste sur le fait qu'il revient aujourd'hui au quartier via son association pour "ne pas trahir" et "transmettre aux petits frères et aux petites sœurs".

      3.3 Regards des Acteurs de Terrain

      Élus locaux (Fabrice Bossui, Driss Étaoui) : Ils dénoncent le manque de concertation sur des sujets cruciaux comme la carte scolaire, qui impose des temps de transport démesurés aux jeunes ruraux.

      Ils soulignent l'évitement scolaire massif vers le privé qui accentue la ségrégation et la concentration de la pauvreté dans certains établissements publics.

      • ANCT (Corine de la Maîtrise) : Rappelle que si le milieu social reste un "déterminant majeur", le territoire module les trajectoires.

      L'objectif est de "lutter contre les inégalités de destin territorial".

      Elle souligne que 30% des QPV se situent aujourd'hui dans des petites ou moyennes villes, brouillant la frontière traditionnelle entre politique de la ville et ruralité.

      Elle alerte sur le fait qu'il faut "12 générations pour sortir de la pauvreté quand on vient d'un QPV", contre 9 en moyenne en France.

      Acteurs associatifs (Salomé Berlou, Ashraf Manar) : Ils appellent à dépasser une vision "victimaire" des jeunes des territoires populaires.

      Ces jeunes sont des acteurs engagés dans leurs localités, même si cet engagement n'est pas toujours formalisé ou reconnu.

      Leurs associations (Rura, Destins Liés) visent à outiller ces jeunes pour qu'ils aient le "choix" de leur parcours, en luttant contre l'autocensure et en créant des ponts entre les territoires.

      4. Conclusions et Perspectives • Le primat du social : La journée a réaffirmé que la question sociale est le fil rouge qui relie les difficultés des différentes jeunesses populaires, bien au-delà des spécificités territoriales.

      La complexité du "partir/rester" : Le départ n'est pas toujours un choix émancipateur mais souvent une contrainte, notamment pour les ruraux.

      Rester n'est pas forcément un échec mais peut correspondre à un attachement profond, tout en étant parfois synonyme d'assignation à résidence.

      L'isolement et la santé mentale : La solitude, que ce soit dans un village éloigné ou dans une cité universitaire après le départ, est une problématique centrale et croissante qui impacte lourdement les parcours.

      La crise de la méritocratie : Les intervenants ont critiqué le modèle méritocratique qui invisibilise les déterminismes sociaux et territoriaux, et qui génère de la frustration.

      La promesse "travaille bien à l'école et tu réussiras" n'est plus tenue.

      L'urgence de refonder du commun : La conclusion, portée par Benoît Coquard et Christophe Paris (AFEV), est un appel à dépasser l'individualisme et la concurrence entre territoires.

      Il est crucial de reconstruire des "consciences collectives" et un "sentiment du nous" pour s'attaquer collectivement aux inégalités systémiques.

      Cela passe par des politiques publiques qui valorisent toutes les formes de contribution au bien commun et qui garantissent à chaque jeune les moyens d'une "vraie autodétermination de son parcours".

    1. Annotations on “An Antidote to Injustice” by Jennifer M. Morton

      [Annotation 1]
 Line: “This is your gruelling daily routine. Now, ask yourself: what could philosophy do for you?”
 → Morton paints a vivid picture of hardship to ground philosophy in lived experience. The rhetorical question links abstract theory with real-life struggles, making philosophy feel practical and relevant.

      [Annotation 2]
 Line: “They are strivers, seeking an education…while holding onto jobs and taking care of families.”
 → The word strivers highlights perseverance and determination. Morton emphasizes the resilience of her students, portraying their pursuit of education as a meaningful effort despite heavy responsibilities.

      [Annotation 3]
 Line: “Philosophy is the antidote to the uncritical acceptance of the world and ourselves as we are.”
 → The metaphor of antidote frames philosophy as medicine for the mind. Morton presents philosophy not as abstract luxury, but as a tool that helps people resist passivity and question harmful assumptions.

      [Annotation 4]
 Line: “Consider the questions our protagonist could ask herself: Why should she have to take out student loans…?”
 → Morton uses a series of rapid questions to model critical inquiry. The barrage challenges the reader to reflect and destabilizes passive acceptance, encouraging independent thought.

      [Annotation 5]
 Line: “Imagine that an evil demon is controlling your every thought.”
 → Descartes’ “evil demon” thought experiment pushes doubt to its extreme. By imagining complete deception, students are forced to question how much of their knowledge can truly be trusted.

      [Annotation 6]
 Line: “Philosophers…are failing as citizens if they turn their back on those in the cave who are less fortunate.”
 → By invoking Plato’s Allegory of the Cave, Morton reframes philosophy as a moral duty. Knowledge is shown to carry responsibility: those who understand more are obligated to help others see beyond ignorance.

      [Annotation 7]
 Line: “If the groups over-fish, famine ensues and all of the families will die.”
 → The classroom exercise dramatizes the challenge of limited resources. It highlights how individual greed can harm the whole community, teaching lessons about foresight, cooperation, and restraint.

      [Annotation 8]
 Line: “Rawls asks his readers to imagine a hypothetical social contract…”
 → Rawls’ “veil of ignorance” is a thought experiment designed to remove bias. It forces people to think about justice from a neutral position, encouraging fairness and equality.

      [Annotation 9] 
Line: “She will be indignant because many of them are the product of unjust political institutions…”
 → Morton frames indignation as a productive moral response. Philosophy helps people recognize injustice clearly and articulate why unfair systems provoke anger.

      [Annotation 10]
 Line: “The way injustice often undermines our agency is by shrinking the horizons of what we think is possible.”
 → Morton explains how injustice limits imagination and hope. Philosophy works to expand possibilities, giving people vision and confidence to seek change.

      [Annotation 11]
 Line: “Dogmatism is an enemy to peace, and an insuperable barrier to democracy.”
 → Russell critiques rigid certainty as harmful to progress. Morton uses this to emphasize how philosophy promotes open-mindedness, tolerance, and democratic dialogue.

      [Annotation 12]
 Line: “Martin Luther King Jr…held up hope in the form of a dream.”
 → Morton concludes by connecting philosophy with imagination and justice. King’s dream is used as an example of how ideas can inspire hope and collective action against injustice.

    1. Synthèse sur la Sexualité et la Contraception

      Résumé

      Ce document de synthèse résume les points clés d'une discussion sur la sexualité et la contraception, menée par des intervenantes du Planning Familial d'Indre-et-Loire.

      Les thèmes centraux incluent l'importance d'une éducation sexuelle et affective précoce et progressive, fondée sur les connaissances des jeunes pour déconstruire les idées reçues.

      Un accent particulier est mis sur la notion de consentement, détaillée à travers l'acronyme "REELS" (Réversible, Éclairé, Enthousiaste, Libre, Spécifique), qui sert de guide pratique pour des relations respectueuses.

      Le document présente un panorama exhaustif des méthodes de contraception existantes, classées en cinq catégories (hormonales, mécaniques, naturelles, définitives, d'urgence), en soulignant la responsabilité partagée et la possibilité de changer de méthode au cours de la vie.

      Enfin, il aborde la prévention des Infections Sexuellement Transmissibles (IST), l'importance cruciale du dépistage, et les modalités de l'Interruption Volontaire de Grossesse (IVG) en France, tout en listant les structures ressources locales pour les jeunes et les parents.

      1. L'Approche du Planning Familial en Matière d'Éducation Sexuelle

      Le Planning Familial d'Indre-et-Loire, une association loi 1901 fondée en 1967 localement, a pour mission la prévention, l'information et l'orientation sur la vie affective, relationnelle et la santé sexuelle. Ses interventions sont gratuites, anonymes, confidentielles et basées sur un accueil inconditionnel.

      1.1. Méthodologie : L'Éducation Populaire

      L'approche de l'association repose sur le principe de l'éducation populaire, qui considère que chaque individu possède des savoirs. Les interventions partent des représentations et des connaissances du public pour ensuite apporter des informations complémentaires.

      Outils utilisés : Le "brainstorming" est un outil central pour recueillir les mots et les idées des participants sur un thème donné (ex: la puberté).

      Objectifs :

      ◦ Déconstruire les idées reçues et les fausses informations, notamment celles issues d'internet.

      ◦ Rassurer les jeunes sur les changements corporels et les différences de développement, luttant ainsi contre les complexes. ◦ Adapter le contenu à l'âge des participants.

      1.2. Le Programme National d'Éducation à la Sexualité

      Un programme gouvernemental, en accord avec une loi de 2002 prévoyant trois séances annuelles de la maternelle au lycée (bien que peu appliquée), structure l'éducation à la vie affective et sexuelle. Ce programme, jugé pertinent par le Planning Familial, propose une approche progressive :

      Maternelle et Primaire : Aborde les émotions, le consentement non-sexuel ("je ne veux pas jouer avec toi"), les stéréotypes de genre et les relations aux autres.

      Collège (à partir de la 4ème) et Lycée : Introduction de la thématique de la sexualité au sens large. L'école est considérée comme le lieu idéal pour une information égalitaire.

      2. Puberté et Connaissance du Corps

      La puberté est une période de transition majeure, marquée par une "tempête hormonale" qui influence à la fois le corps et les émotions.

      2.1. Changements Physiques et Émotionnels

      Émotionnels : Humeur changeante (colère, tristesse), fatigue, susceptibilité. C'est une période de découverte de soi, de ses goûts et de ses limites.

      Physiques : Pilosité, développement des seins, mue de la voix, acné, croissance. Les intervenantes soulignent l'importance de rassurer sur le fait que chaque corps se développe à son propre rythme. La puberté survient en moyenne entre 11 et 16 ans, mais peut être plus précoce (dès 9-10 ans) ou plus tardive.

      2.2. Le Cycle Menstruel

      Le cycle menstruel est un sujet essentiel abordé avec tous les jeunes, garçons et filles.

      Fonctionnement : Un cycle moyen dure 28 jours, avec une ovulation survenant 14 jours avant le début du cycle suivant.

      Période de Fertilité : Un ovule est viable 24 à 48 heures, tandis qu'un spermatozoïde peut survivre jusqu'à 5 jours dans l'utérus, ce qui définit une fenêtre de fertilité de plusieurs jours.

      Idées Reçues : Il est possible de tomber enceinte dès les premières règles. Des ovulations spontanées peuvent survenir en dehors de la période théorique de fertilité.

      Douleurs : Il est rappelé que des douleurs de règles invalidantes ne sont pas normales et doivent motiver une consultation médicale.

      2.3. Ressources Pédagogiques pour les Parents et les Jeunes

      Une sélection d'ouvrages est présentée comme support pour aborder ces sujets en famille.

      Titre de l'Ouvrage

      Public Cible

      Thèmes Abordés

      Le petit illustré de l'intimité (4 tomes)

      Enfants, Adolescents, Parents

      Anatomie (pénis, vulve), famille, contraception, genre, orientation sexuelle.

      Le petit guide de la foufoune sexuelle

      Tous publics

      Sexualité, consentement, anatomie, puberté, fausses idées.

      Le parcours de Polo Jeunes enfants

      Reproduction (comment on fait les bébés) sous forme d'album jeunesse.

      Comment on fait les bébés

      Jeunes enfants

      Reproduction, avec un point de vue humoristique sur les non-dits des parents.

      Les règles, Quelle aventure

      Adolescents

      Les menstruations, sous forme d'histoire.

      Rouge

      Jeunes enfants

      Les émotions (la timidité, le fait de rougir).

      Corps, amour et sexualité Parents (Guide)

      Encyclopédie par tranche d'âge (5-12 ans) pour répondre aux questions des enfants.

      3. Le Consentement : Un Pilier des Relations

      Le consentement est un sujet de plus en plus évoqué par les jeunes. Le Planning Familial utilise un moyen mnémotechnique pour en définir les composantes essentielles.

      R - Réversible : Un "oui" peut être retiré à tout moment. L'absence de participation active équivaut à un retrait du consentement.

      E - Éclairé : La personne doit être en pleine capacité de comprendre ce qui est proposé. Le consentement n'est pas valide si la personne est endormie, sous l'influence de l'alcool ou de drogues.

      E - Enthousiaste : Le consentement doit être actif et joyeux, exprimé verbalement et non-verbalement. Une participation passive ou hésitante n'est pas un consentement enthousiaste.

      L - Libre : Le "oui" doit être donné sans pression, chantage, menace ou rapport de hiérarchie.

      S - Spécifique : Le consentement est donné pour un acte précis, à un moment précis. Il n'est pas valable pour d'autres actes ou pour d'autres moments.

      4. Panorama des Moyens de Contraception La contraception est présentée comme une responsabilité partagée, les hommes étant fertiles toute l'année. Aucune méthode n'est efficace à 100% et il est possible d'en changer tout au long de sa vie.

      4.1. Contraceptions Hormonales

      Elles agissent en faisant croire au corps qu'une grossesse est en cours, bloquant ainsi l'ovulation.

      • La Pilule : Comprimé quotidien à heure fixe. Efficace à 99%. Peut ne pas convenir à un mode de vie irrégulier.

      • L'Implant : Bâtonnet inséré sous la peau du bras, efficace 3 ans.

      • Le Patch : À coller sur la peau et à changer chaque semaine. Non remboursé.

      • Le Dispositif Intra-Utérin (DIU) Hormonal : Placé dans l'utérus, diffuse des hormones localement. Efficace 5 ans.

      • L'Anneau Vaginal : Anneau flexible placé dans le vagin pour 3 semaines. Non remboursé.

      • Les Injections d'Hormones : Tous les 3 mois pour les femmes, toutes les semaines pour les hommes.

      4.2. Contraceptions Mécaniques

      Elles créent une barrière physique pour empêcher la rencontre des spermatozoïdes et de l'ovule.

      • Préservatifs (Externe et Interne) : Seul moyen de contraception protégeant également des IST. Le préservatif interne peut être mis jusqu'à 8 heures avant le rapport.

      • Le Diaphragme / La Cape Cervicale : Dômes en silicone placés au fond du vagin. Efficacité renforcée avec des spermicides.

      • Le DIU au Cuivre : Le cuivre crée une inflammation qui rend l'utérus "hostile" à la nidation. Efficace 5 ans, sans hormones.

      • L'Andro-Switch (Anneau) / Le Slip Thermique : Méthodes masculines qui remontent les testicules contre le corps.

      La chaleur annule le pouvoir fécondant des spermatozoïdes. Nécessite d'être porté 15h/jour et un suivi médical (spermogrammes).

      4.3. Méthodes Naturelles (Contrôle des Naissances)

      Leur efficacité est jugée relative et moins fiable.

      • Le Retrait : Efficacité limitée car le liquide pré-séminal peut contenir des spermatozoïdes.

      • Méthode des Températures : Suivi de la température corporelle pour détecter l'ovulation.

      • Méthode de l'Allaitement : L'allaitement peut bloquer le retour de couches, mais reste très peu fiable.

      • Méthode Ogino (Calendrier) : Calcul de la période de fertilité, peu fiable en raison des ovulations spontanées.

      4.4. Contraceptions Définitives

      Elles sont accessibles dès 18 ans, après un délai de réflexion légal.

      • La Vasectomie (Homme) : Opération sous anesthésie locale pour sectionner les canaux déférents. L'éjaculation persiste mais sans spermatozoïdes. Considérée comme irréversible.

      • La Ligature des Trompes (Femme) : Opération plus lourde, sous anesthésie générale, pour bloquer le passage des ovules.

      4.5. Contraception d'Urgence • "Pilule du lendemain" : Comprimé à prendre le plus tôt possible après un rapport à risque (efficace jusqu'à 3-5 jours). Gratuite pour les mineurs et accessible en pharmacie sans avancer de frais pour les majeurs. Un homme peut aller la chercher pour sa partenaire.

      5. Infections Sexuellement Transmissibles (IST)

      • Protection : Le préservatif est le seul moyen de s'en protéger.

      • Dépistage : C'est un acte de responsabilité essentiel pour se protéger soi-même et ses partenaires. La plupart des IST sont asymptomatiques.

      ◦ Il est possible de se faire dépister sans ordonnance en laboratoire.

      ◦ Un délai (généralement 6 semaines à 3 mois après le rapport à risque) est nécessaire pour que le test soit fiable.

      • Traitement : La majorité des IST se soignent bien si elles sont prises à temps. Le VIH, bien qu'incurable, se traite efficacement, permettant une vie normale et une charge virale indétectable (et donc intransmissible).

      6. L'Interruption Volontaire de Grossesse (IVG)

      L'IVG est un droit en France, encadré par la loi. • Deux méthodes : 1. IVG médicamenteuse : Jusqu'à 7 semaines de grossesse (9 semaines d'aménorrhée). 2. IVG chirurgicale : Jusqu'à 14 semaines de grossesse (16 semaines d'aménorrhée). • Accompagnement : ◦ Pour une personne mineure, l'accompagnement par une personne majeure de confiance (pas obligatoirement un parent) est obligatoire. ◦ La démarche inclut des entretiens d'information pour permettre un choix éclairé. ◦ Les centres spécialisés (centres d'orthogénie) disposent d'équipes pluridisciplinaires (médecins, psychologues) pour accompagner les personnes.

      7. Lieux et Structures Ressources

      Plusieurs structures offrent information, accompagnement et soins de manière gratuite et confidentielle en Indre-et-Loire. • Le Planning Familial : Pour l'information, l'écoute et l'orientation. • Le CEGIDD (Centre Gratuit d'Information, de Dépistage et de Diagnostic) : Pour le dépistage des IST. • Les Centres de Santé Sexuelle : Pour le suivi gynécologique, la contraception, le dépistage et l'accompagnement global. • L'Espace Santé Jeunes (ESJ) : Pour les jeunes et les parents sur des questions de santé globale, y compris les addictions. • La Maison des Adolescents : Lieu ressource avec des professionnels variés (psychologues, pédiatres, etc.).

    1. La Cohérence Éducative : Synthèse et Analyse

      Résumé

      La cohérence éducative constitue le socle d'un développement sain pour l'enfant, en lui offrant un cadre stable, prévisible et sécurisant.

      Elle se définit par l'harmonisation des discours, des pratiques et des valeurs entre les différents adultes qui entourent l'enfant.

      Cette cohérence ne se limite pas au couple parental, mais s'étend sur cinq sphères interdépendantes : la cohérence interne de chaque adulte avec ses propres valeurs, le couple parental, la famille élargie et l'entourage, les professionnels (école, crèche), et la société dans son ensemble.

      Le principal risque de l'incohérence chronique est l'insécurité affective, qui peut entraver la construction de la confiance en soi et pousser l'enfant à tester constamment les limites.

      Il est crucial de distinguer la simple différence, qui peut être une source de richesse et d'ouverture d'esprit lorsqu'elle est expliquée, de l'incohérence conflictuelle et de la disqualification d'un adulte par un autre devant l'enfant, qui sont particulièrement préjudiciables.

      Les stratégies fondamentales pour cultiver cette cohérence reposent sur la communication, la souplesse et le respect mutuel.

      Il s'agit de dialoguer sur les désaccords, de comprendre les besoins sous-jacents aux positions de chacun, de chercher des compromis et d'expliquer les règles à l'enfant.

      L'objectif n'est pas une rigidité absolue, mais la construction d'un cadre général fiable qui prépare l'enfant à naviguer sereinement dans un monde où les incohérences font partie de la vie.

      1. Le Concept de Cohérence et ses Fondements

      1.1. Définition de la Cohérence

      La cohérence est définie comme l'adéquation et la logique entre les pensées, les paroles et les actes d'un individu.

      Cette harmonie interne est un besoin fondamental ; son absence génère un inconfort psychologique.

      1.2. La Dissonance Cognitive

      Théorisée par le psychologue Leon Festinger, la dissonance cognitive décrit l'état d'inconfort ressenti lorsqu'il y a un décalage entre les croyances et les comportements.

      Pour réduire cette tension, les individus ont tendance à modifier leurs pensées ou à trouver des justifications plutôt que de changer un comportement ancré.

      Exemples concrets :

      ◦ Un parent qui passe beaucoup de temps sur son écran tout en limitant celui de son enfant.

      ◦ Un parent qui fume tout en interdisant à son adolescent de le faire.

      Perception par l'enfant : Les enfants sont particulièrement habiles à détecter ces incohérences, ce qui peut miner la crédibilité des règles et des adultes qui les édictent.

      2. Les Cinq Sphères de la Cohérence Éducative Le document source structure l'analyse de la cohérence éducative autour d'un schéma central représentant cinq sphères d'influence concentriques, allant de l'individu à la société.

      2.1. La Cohérence Interne : La Base Individuelle

      Avant de pouvoir être cohérent avec d'autres adultes, il est nécessaire de l'être avec soi-même.

      Cette cohérence personnelle est un alignement entre les comportements visibles et les niveaux plus profonds que sont les règles, les croyances et les valeurs fondamentales, souvent héritées de sa propre éducation, de sa culture et de son histoire familiale.

      • Questionnement personnel : Il est essentiel pour un adulte de s'interroger sur l'origine de ses valeurs ("Est-ce que finir son assiette est une valeur qui me correspond vraiment ou est-ce un héritage familial que je transmets sans y réfléchir ?").

      • Gestion de ses propres incohérences : Nul n'est parfait.

      Lorsqu'un parent agit de manière incohérente (par exemple, crier alors que la règle est de ne pas crier), il est bénéfique de le reconnaître devant l'enfant.

      Nommer l'incohérence ("Je suis désolé, je me suis emporté") permet de donner du sens, de valider le ressenti de l'enfant et de renforcer la sécurité affective en montrant que les adultes peuvent admettre leurs erreurs.

      2.2. Le Couple Parental : Le Premier Cercle de Cohérence

      Qu'ils soient ensemble ou séparés, les parents forment le premier duo d'adultes dont la cohérence est primordiale.

      L'objectif commun est de protéger l'enfant et de lui offrir un cadre propice à son développement.

      • Métaphore de "L'oiseau à deux becs" : Cet album jeunesse illustre deux parents (les deux becs) qui nourrissent un même enfant (le ventre).

      Si les becs se disputent, le ventre en pâtit et peut même être "empoisonné". La coopération est donc vitale.

      • Sources de conflit : Les désaccords peuvent provenir de modèles éducatifs différents, de tensions conjugales ou de simples divergences de points de vue.

      • Stratégies de résolution :

      ◦ Identifier les besoins : Derrière une émotion comme la colère ou une position rigide se cache souvent un besoin non satisfait (besoin de respect, de sécurité, d'être écouté).

      Comprendre le besoin de l'autre permet de dépasser le conflit de surface.

      ◦ La disqualification : Le risque majeur est de disqualifier l'autre parent devant l'enfant ("De toute façon, toi, tu laisses tout faire").

      Cela consiste à nier sa compétence et place l'enfant dans une position intenable de loyauté.

      2.3. La Famille et l'Entourage : L'Élargissement du Cadre

      Cette sphère inclut les grands-parents, oncles, tantes, amis et voisins. L'enfant évolue dans différents lieux avec des règles potentiellement différentes.

      Différence vs. Incohérence : Avoir des règles différentes chez les grands-parents (plus de bonbons, par exemple) n'est pas une incohérence en soi et peut enrichir l'enfant.

      Cela devient problématique lorsque ces différences vont à l'encontre de valeurs fondamentales ou de règles de sécurité non négociables pour les parents.

      • Conflit et Clivage de Loyauté :

      Conflit de loyauté : L'enfant est partagé entre deux attentes différentes. C'est une situation courante et gérable.

      ◦ Clivage de loyauté : Situation plus grave où choisir un camp signifie être contre l'autre.

      Cela se produit lorsque des adultes dénigrent les autres, forçant l'enfant à prendre parti.

      Exemple : un enfant n'ose pas dire qu'il a passé un bon week-end chez un parent par peur de blesser l'autre.

      2.4. Les Professionnels : La Collaboration Éducative

      Cette sphère concerne les acteurs de la crèche, de l'école, des loisirs ou du secteur médical.

      • Légitimité parentale : Les parents sont les premiers éducateurs de leur enfant.

      Même face à des experts, ils ont la légitimité de questionner les pratiques qui ne leur semblent pas cohérentes avec leurs valeurs.

      • Importance du dialogue : Il est essentiel d'oser interroger les professionnels pour comprendre le sens de leurs pratiques (ex: la "motricité libre" en crèche qui autorise les enfants à monter sur des meubles sécurisés).

      Cet échange permet de créer une continuité éducative et de rassurer les parents.

      L'enfant est capable de comprendre que les règles peuvent varier selon le contexte (maison vs. crèche), à condition que ce contexte soit clair.

      2.5. La Société : Le Contexte Global

      C'est la sphère la plus diffuse et la plus difficile à influencer. Elle englobe les codes sociaux, les injonctions médiatiques, les évolutions culturelles et le cadre législatif.

      • Pression sociale : Le regard des autres peut pousser un parent à agir contre ses propres principes (ex: gérer une crise de colère d'un enfant dans un magasin).

      • Évolution des normes : Des concepts comme "l'éducation bienveillante" ou les apports des neurosciences modifient les attentes sociales envers les parents.

      • Le cadre légal : La loi impose un cadre non négociable, comme l'interdiction de la fessée en France depuis 2019, qui s'impose à toutes les pratiques éducatives.

      3. Les Risques de l'Incohérence et le Cadre Sécurisant

      3.1. L'Impact sur la Sécurité Affective de l'Enfant

      La cohérence est un pilier de la sécurité affective. Le chercheur québécois Georges Tarabulsy identifie trois facteurs clés de la sécurité de l'attachement : la chaleur, la prévisibilité et la cohérence.

      • La "jauge à sécurité" : Une métaphore est utilisée pour décrire la sécurité interne de l'enfant comme un réservoir.

      Des pratiques cohérentes, stables et harmonieuses remplissent cette jauge. Des incohérences chroniques la vident, ce qui peut affecter durablement le développement de l'enfant.

      3.2. Conséquences Comportementales et Psychologiques

      Un manque de cohérence peut entraîner :

      • Une recherche constante des limites pour comprendre un cadre flou.

      • Une perte de sens et une atteinte à la confiance en soi.

      • Des difficultés à construire son propre système de valeurs, car il n'y a pas eu de base stable à partir de laquelle se différencier.

      4. Stratégies Pratiques pour Cultiver la Cohérence

      Stratégie Description Exemple

      Adapter le cadre à l'enfant Ajuster les règles et les consignes à l'âge, au rythme de développement, aux compétences et aux besoins de l'enfant.

      Ne pas proposer à un enfant de 3 ans de sortir seul de l'école. Offrir un choix limité ("le pantalon bleu ou le rouge ?") plutôt qu'un choix trop vaste et insécurisant.

      Préciser les consignes

      Donner des instructions claires et s'assurer de leur compréhension. Expliquer le "pourquoi" derrière une règle.

      Au lieu de "ne dessine pas sur les murs", expliquer : "Je ne veux pas que tu abîmes la peinture. Si tu veux décorer, utilisons des post-it".

      Communiquer entre adultes

      Dialoguer ouvertement sur les désaccords, loin de la présence de l'enfant si le ton monte. Viser la compréhension mutuelle et le compromis.

      Un parent veut que l'enfant marche pieds nus pour sa motricité, l'autre s'inquiète de l'hygiène. Le compromis : pieds nus dans la maison, mais chaussons dans le garage.

      Faire preuve de souplesse

      Accepter que l'autre puisse avoir un point de vue différent sans que cela ne constitue une attaque personnelle.

      Métaphore du livre Quatre petits coins de rien du tout : parfois, il ne faut pas chercher à changer l'enfant (le carré) mais à adapter le cadre (la porte ronde).

      Pratiquer la "métacommunication"

      Communiquer sur la manière de communiquer : "Quand tu me parles sur ce ton, j'ai l'impression que tu penses que je suis une mauvaise mère."

      Permet de clarifier les malentendus et de comprendre l'impact de ses paroles sur l'autre.

      5. Conclusion : Viser un Équilibre Dynamique

      L'incohérence fait partie de la vie ; l'objectif n'est pas de l'éradiquer, mais de la minimiser et de la gérer.

      La clé est de construire un cadre éducatif globalement stable et sécurisant.

      Comme le disait le pédagogue Célestin Freinet, il s'agit moins d'éviter les incohérences que de "préparer l'enfant à pouvoir les vivre sereinement".

      En dialoguant, en s'ajustant et en faisant preuve de souplesse, les adultes peuvent transformer les différences en une richesse et offrir à l'enfant les repères solides dont il a besoin pour grandir et construire sa propre cohérence.

    1. Dossier d'Information : Consommation et Addiction à l'Adolescence

      Résumé

      Ce document synthétise les perspectives et données clés issues d'une discussion entre expertes sur la consommation de substances et l'addiction durant l'adolescence. Les points essentiels à retenir sont les suivants :

      1. Baisse de la Consommation : Contrairement à une perception médiatique souvent anxiogène, les données épidémiologiques (enquêtes ESCAPAD) montrent une baisse constante et significative de l'expérimentation et de la consommation régulière de tabac, d'alcool et de cannabis chez les adolescents en France depuis plus de dix ans.

      2. Distinction Cruciale : Il est impératif de ne pas confondre consommation, expérimentation et addiction.

      L'expérimentation est un comportement exploratoire fréquent et même jugé "presque nécessaire" au développement de l'adolescent pour tester ses limites.

      L'addiction, caractérisée par une perte de contrôle, reste un phénomène rare à cet âge. Le terme "conduite à risque" est souvent plus approprié.

      3. Signaux d'Alerte : L'inquiétude doit naître non pas d'une consommation isolée, mais d'un cumul de plusieurs facteurs : précocité de l'usage, cumul de produits, consommation à visée "autothérapeutique" (pour s'apaiser), recherche systématique d'excès et répétition fréquente. L'évaluation doit être globale, incluant le contexte scolaire, social et familial.

      4. Prévention Efficace : Les stratégies de prévention modernes ont abandonné l'approche basée sur la peur et l'information brute, jugée contre-productive. L'accent est désormais mis sur le renforcement des compétences psychosociales (CPS) : estime de soi, gestion des émotions, esprit critique et capacité à dire non.

      5. Rôle Parental Fondamental : Les parents sont des acteurs de prévention de premier plan. Leur rôle est de maintenir un dialogue ouvert, d'éviter les jugements hâtifs, de poser un cadre clair sans fermer la communication, et d'être une ressource fiable en cas de difficulté. Discuter des sensations et des limites est plus constructif que la seule répression.

      6. Ressources Disponibles : Des structures gratuites, confidentielles et accessibles existent pour les jeunes (12-25 ans) et leur entourage. Les Consultations Jeunes Consommateurs (CJC), hébergées par des entités comme le CSAPA 37 ou l'Espace Santé Jeune, offrent un lieu d'écoute et d'évaluation sans jugement.

      1. Définitions Clés : De la Substance Psychoactive à l'Addiction

      Selon les intervenantes, il est essentiel de clarifier les termes employés pour aborder sereinement le sujet.

      • Drogue / Substance Psychoactive : Une drogue est définie comme tout produit, licite ou illicite, qui modifie le fonctionnement du cerveau et du psychisme. Cette définition inclut donc l'alcool et le tabac, qui sont les substances les plus consommées et les principaux enjeux de santé publique.

      • Mécanismes Cérébraux : Le corps humain produit naturellement des substances psychoactives (endogènes) comme la dopamine ou les endorphines, qui génèrent du plaisir suite à des actions comme manger ou faire du sport.

      Les substances externes (exogènes) stimulent ces mêmes circuits de récompense de manière beaucoup plus rapide et intense, ce qui peut inciter le cerveau à privilégier cette voie pour obtenir une satisfaction immédiate.

      • Consommation vs. Addiction : Toute consommation n'est pas une addiction. L'addiction est un processus qui s'installe dans le temps et se caractérise par une "perte de la liberté de s'abstenir". Pour les adolescents, les professionnelles préfèrent parler de conduites à risque plutôt que d'addiction, cette dernière étant rare dans cette tranche d'âge.

      2. La Réalité de la Consommation chez les Adolescents : Données et Tendances

      Les intervenantes insistent sur la nécessité de dédramatiser le phénomène en s'appuyant sur des données objectives issues d'enquêtes nationales (ESCAPAD, menée par l'OFDT).

      Tendance Observée Détails

      Baisse Générale

      Une baisse constante des expérimentations et des consommations régulières de tabac, d'alcool et de cannabis est observée chez les collégiens et lycéens depuis plus de 10 ans.

      Recul de l'Âge

      Contrairement aux idées reçues, l'âge des premières consommations ne baisse pas ; il a même tendance à reculer.

      Les premières expérimentations ont souvent lieu vers 16-17 ans.

      Exemple du Tabac

      Le pourcentage de fumeurs réguliers à 17 ans est passé de 40% en 2002 à moins de 16% en 2022.

      Hiérarchie des Produits

      Les produits les plus consommés restent, de loin, le tabac et l'alcool, suivis par le cannabis. Les autres substances illicites ne représentent qu'une part mineure des consommations (environ 5%).

      Première Initiation

      L'initiation à l'alcool, produit très normalisé et culturellement ancré en France, se fait très souvent dans le cadre familial lors d'événements festifs.

      Cette perspective factuelle est cruciale pour éviter deux écueils : l'inquiétude parentale excessive et l'incitation paradoxale des jeunes qui, se croyant en décalage, pourraient être tentés d'expérimenter pour se conformer à une norme perçue.

      3. Identifier les Signes d'Alerte : Quand Faut-il s'Inquiéter ?

      Une consommation devient une conduite à risque préoccupante non pas à cause d'un seul acte, mais lorsque plusieurs signaux s'accumulent et indiquent un changement de comportement global. L'évaluation se base sur un faisceau d'indices.

      Les cinq indicateurs principaux à surveiller :

      1. La Précocité des Consommations : Un usage commencé très jeune (collège) est un facteur de risque majeur en raison de l'immaturité du cerveau.

      2. Le Cumul des Consommations : L'utilisation simultanée ou alternée de plusieurs produits (alcool, tabac, cannabis...).

      3. Les Consommations Autothérapeutiques : L'usage d'un produit pour s'apaiser, gérer une angoisse ou fuir une difficulté. Le produit devient alors une sorte de "médicament".

      4. La Recherche d'Excès : La volonté systématique d'atteindre des états extrêmes.

      5. La Répétition des Consommations : Une fréquence élevée qui peut entraîner une accoutumance et un besoin d'augmenter les doses.

      En parallèle, il faut observer le contexte général de l'adolescent :

      • Scolarité : Y a-t-il un désintérêt, un décrochage ?

      • Vie Sociale : L'adolescent s'isole-t-il ? Change-t-il de cercle d'amis ?

      • Centres d'Intérêt : Abandonne-t-il des activités qui lui procuraient du plaisir auparavant ?

      • Communication Familiale : Le dialogue est-il rompu ? Le comportement de consommation est souvent le symptôme d'un mal-être sous-jacent. L'analyse doit donc être systémique, en prenant en compte l'individu, la substance et son environnement.

      4. Le Processus Addictif Illustré : L'Allégorie "Nuggets" Le court-métrage d'animation "Nuggets" (Andreas Hykade, 2014) est utilisé pour décomposer le cheminement qui peut mener d'une expérimentation à une addiction.

      1. La Lune de Miel : La première rencontre avec le produit est une expérience positive, une recherche de plaisir pur. Il n'y a pas encore d'envie irrépressible de consommer (craving).

      2. L'Apparition des Dommages : La consommation apporte toujours du plaisir, mais les premières conséquences négatives apparaissent (physiques, sociales, financières). La tonalité devient plus sombre.

      3. La Compulsion et la Tolérance : L'envie devient pressante, compulsive. Les effets positifs durent moins longtemps et sont moins intenses. Une tolérance s'installe, obligeant à augmenter les doses pour retrouver les effets initiaux. C'est l'étape de la "perte de la liberté de s'abstenir".

      4. La Perte de Contrôle : Le comportement devient obsessionnel. La consommation se poursuit de manière frénétique malgré la dégradation de l'état du sujet et l'absence quasi totale de plaisir. Le but n'est plus de ressentir du plaisir, mais de soulager la souffrance du manque.

      Ce processus montre que l'addiction ne s'installe pas du jour au lendemain et que la continuité de la consommation est un facteur déterminant.

      5. L'Adolescence : Une Période de Vulnérabilité et d'Expérimentation La consommation de produits doit être comprise dans le contexte unique de l'adolescence, une période de profonds bouleversements.

      • Une Quête Nécessaire : L'expérimentation, y compris avec des produits, fait partie du processus normal de construction de l'identité. C'est une manière pour l'adolescent de tester ses limites, de se connaître, de développer son estime de soi et de s'autonomiser (processus d'individuation).

      • Fonctions Sociales : La consommation peut être un rite de passage, un moyen d'intégration dans un groupe de pairs, ou un acte d'imitation.

      • Vulnérabilité Psychique : Pour les adolescents plus fragiles, la substance peut devenir un "support" pour gérer des difficultés, notamment le détachement des parents ou un mal-être profond.

      • Le Danger de l'Identification : Le discours ambiant qui associe systématiquement adolescence et consommation problématique peut créer une identification négative. L'adolescent, en quête de modèles, peut se conformer à cette image et adopter le comportement attendu.

      6. Stratégies de Prévention Efficaces L'approche de la prévention a radicalement évolué, s'éloignant des méthodes jugées inefficaces pour se concentrer sur l'outillage de l'adolescent.

      Ce qui ne fonctionne pas :

      • Le Discours de Peur : Agiter les menaces ("tu vas mourir", "tu iras en prison") génère du stress (cortisol) et peut avoir un effet inverse, incitant l'adolescent à chercher une substance pour apaiser cette angoisse.

      • L'Apport de Connaissances Brutes : Le cerveau adolescent est dominé par l'impulsivité et le système émotionnel. La connaissance des risques ne suffit pas à empêcher le passage à l'acte.

      Ce qui fonctionne : le Renforcement des Compétences Psychosociales (CPS)

      L'objectif est de donner à l'adolescent les outils pour faire des choix éclairés et se protéger.

      Cela inclut le travail sur :

      • • L'estime de soi.
      • • La gestion des émotions et du stress.
      • • L'esprit critique et la prise de distance.
      • • La capacité à s'affirmer et à dire non.
      • • La connaissance de ses propres limites.

      Le rôle des parents et de l'entourage est central : • Maintenir la Communication : Laisser la porte du dialogue ouverte est la clé.

      L'adolescent doit savoir qu'il peut appeler un parent en cas de difficulté, même après une consommation excessive, sans craindre une punition disproportionnée.

      • Accueillir et Discuter : Face à une première ivresse, il est plus constructif d'ouvrir une discussion sur les sensations ressenties (positives et négatives) plutôt que de réprimer uniquement.

      • Poser un Cadre : L'échange ne signifie pas la permission. Il est du rôle du parent de rappeler les règles et la loi (ex: le cannabis est illégal).

      • Prévention Collective : La prévention est l'affaire de tous (parents, enseignants, éducateurs). Créer un environnement bienveillant et sécurisant, où le jeune se sent bien, est un facteur de protection puissant.

      Les adolescents eux-mêmes développent des stratégies de réduction des risques, comme le "capitaine de soirée" (celui qui ne boit pas) ou le fait de dormir sur place après une fête, montrant une prise de conscience des dangers.

      7. Ressources et Soutien Disponibles Un réseau de structures professionnelles existe pour accompagner les jeunes et leur entourage.

      • Les Consultations Jeunes Consommateurs (CJC) :

      Public : Jeunes de 12 à 25 ans, mais aussi leur entourage (parents, amis, grands-parents).

      Principes : Accueil gratuit, confidentiel et potentiellement anonyme. Il n'est pas nécessaire d'être en situation d'addiction ; toute question sur la consommation est légitime.

      Mission : Offrir un lieu d'écoute pour faire le point, évaluer une situation, obtenir de l'information, apprendre à réduire les risques et, si besoin, être orienté.

      Lieux : Elles sont implantées dans des structures spécialisées (comme le CSAPA - Centre de Soins, d'Accompagnement et de Prévention en Addictologie) et des lieux plus généralistes pour éviter la stigmatisation (Espace Santé Jeune, Maison des Adolescents).

      • Programmes de Prévention : ◦ En Milieu Scolaire : Des programmes probants comme "Unplugged" sont déployés dans les établissements pour travailler sur les compétences psychosociales en co-animation avec les enseignants. ◦ Soutien à la Parentalité : Des groupes de parole pour parents, comme "Mon Ado et Moi", permettent d'échanger sur les inquiétudes et de dédramatiser les situations.

      8. Nouvelles Tendances de Consommation

      Bien que la consommation des produits "classiques" soit en baisse, de nouveaux produits émergent et suscitent des inquiétudes :

      La "Puff" : Une cigarette électronique jetable, très attractive pour les jeunes par son design coloré et ses goûts sucrés. Elle constitue une nouvelle porte d'entrée vers la consommation de nicotine pour des jeunes qui n'auraient pas commencé à fumer autrement.

      Le Protoxyde d'Azote : Gaz hilarant contenu dans des cartouches. Sa consommation, perçue à tort comme inoffensive, peut entraîner des dommages neurologiques et physiques importants.

      La Chicha : Narguilé dont l'usage reste populaire et qui est également nocif.

    1. 1. a >L b: if and only if there is a trace σ =⟨t1,t2,t3,...,tn⟩ and i ∈{1,...,n−1} such that σ ∈ L and ti = a and ti+1 = b; 2. a →L b if and only if a > L and b >/ L a; 3. a #L b if and only if a >/ b and b >/ a; and 4. a ∥L b if and only if a > L b and b > L a.
      1. a >L b → a komt voor en daarna komt b.
      2. a →L b → a leidt tot b (a voor b, maar b niet voor a).
      3. a #L b → a en b komen nooit direct na elkaar.
      4. a ||L b → a en b kunnen beide kanten op (ze kunnen tegelijk of in willekeurige volgorde gebeuren).
    1. Reviewer #1 (Public review):

      Summary:

      It is well known that autophagosomes/autolysosomes move along microtubules. However, as these previous studies did not distinguish between autophagosomes and autolysosomes, it remains unknown whether autophagosomes begin to move after fusion with lysosomes or even before fusion. In this manuscript, the authors show using fusion-deficient vps16a RNAi cells that both pre-fusion autophagosomes and lysosomes can move along the microtubules towards the minus end. This was confirmed in snap29 RNAi cells. By screening motor proteins and Rabs, the authors found that autophagosomal traffic is primarily regulated by the dynein-dynactin system and can be counter-regulated by kinesins. They also show that Rab7-Epg5 and Rab39-ema interactions are important for autophagosome trafficking.

      Strengths:

      This study uses reliable Drosophila genetics and high-quality fluorescence microscopy. The data are properly quantified and statistically analyzed. It is a reasonable hypothesis that gathering pre-fusion autophagosomes and lysosomes in close proximity improves fusion efficiency.

      Weaknesses:

      (1) This study investigates the behavior of pre-fusion autophagosomes and lysosomes using fusion-incompetent cells (e.g., vps16a RNAi cells). However, the claim that these cells are truly fusion-incompetent relies on citations from previous studies. Since this is a foundational premise of the research, it should be rigorously evaluated before interpreting the data. It's particularly awkward that the crucial data for vps16a RNAi is only presented at the very end of Figure 10-S1; this should be among the first data shown (the same for SNAP29). It would be important to determine the extent to which autophagosomes and lysosomes are fusing (or tethered in close proximity), within each of these cell lines.

      (2) In the new Figures 8 and 9, the authors analyze autolysosomes without knocking down Vps16A (i.e., without inhibiting fusion). However, as this reviewer pointed out in the previous round, it is highly likely that both autophagosomes and autolysosomes are present in these cells. This is particularly relevant given that the knockdown of dynein-dynactin, Rab7, and Epg5 only partially inhibits the fusion of autophagosomes and lysosomes (Figure 10H). If the goal is to investigate the effects of fusion, it would be more appropriate to analyze autolysosomes and autophagosomes separately. The authors mention that they can differentiate these two structures based on the size of mCherry-Atg8a structures. If this is the case, they should perform separate analyses for both autophagosomes and autolysosomes.

      (3) This is also a continued Issue from the previous review. The authors suggest that autophagosome movement is crucial for fusion, based on the observed decrease in fusion rates in Rab7 and Epg5 knockdown cells (Fig. 10). However, this conclusion is not well supported. It is known that Rab7 and Epg5 are directly involved in the fusion process itself. Therefore, the possibility that the observed decrease is simply due to a direct defect in fusion, rather than an impairment of movement, has not been ruled out.

      (4) The term "autolysosome maturation" appears multiple times, yet its meaning remains unclear. Does it refer to autolysosome formation (autophagosome-lysosome fusion), or does it imply a further maturation process occurring after autolysosome formation? This is not a commonly used term in the field, so it requires a clear definition.

      (5) In Figure 1-S1D, the authors state that the disappearance of the mCherry-Atg8a signal after atg8a RNAi indicates that the observed structures are not non-autophagic vacuoles. This reasoning is inappropriate. Naturally, knocking down Atg8 will abolish its signal, regardless of the nature of the vacuoles. This does not definitively distinguish autophagic from non-autophagic structures.

    2. Author response:

      The following is the authors’ response to the original reviews.

      Reviewer #1 (Public review):  

      (1) To distinguish autophagosomes from autolysosomes, the authors used vps16 RNAi cells, which are supposed to be fusion deficient. However, the extent to which fusion is actually inhibited by knockdown of Vps16A is not shown. The co-localization rate of Atg8 and Lamp1 should be shown (as in Figure 8). Then, after identifying pre-fusion autophagosomes and lysosomes, the localization of each should be analyzed.

      Thank you for this insightful comment. We analyzed the colocalization of 3xmCherry-Atg8a and GFP-Lamp1, which label autophagic structures and lysosomes, respectively, in Vps16A RNAi fat body cells. As expected, Vps16A silencing markedly reduced the overlap between these two signals, indicating a strong block in autophagosome–lysosome fusion. Moreover, both 3xmCherry-Atg8a and GFP-Lamp1 became more perinuclearly localized compared to the control (luciferase RNAi) cells.

      It is also possible that autophagosomes and lysosomes are tethered by factors other than HOPS (even if they are not fused). If this is the case, autophagosomal trafficking would be affected by the movement of lysosomes.  

      Thank you for raising this possibility. While we cannot fully exclude that autophagosomes might be indirectly transported via tethering to lysosomes, we consider this unlikely. We believe that in Drosophila fat cells, autophagosomes and lysosomes rapidly fuse once in close proximity. Therefore, even if alternative tethering mechanisms exist, they are unlikely to permit prolonged joint trafficking without fusion.

      (2) The authors analyze autolysosomes in Figures 6 and 7. This is based on the assumption that autophagosome-lysosome fusion takes place in cells without vps16A RNAi. However, even in the presence of Vps16A, both pre-fusion autophagosomes and autolysosomes should exist. This is also true in Figure 8H, where the fusion of autophagosomes and lysosomes is partially suppressed in knockdown cells of dynein, dynactin, Rab7, and Epg5. If the effect of fusion is to be examined, it is reasonable to distinguish between autophagosomes and autolysosomes and analyze only autolysosomes.  

      Thank you for this careful observation. The 3xmCherry-Atg8a reporter is well suited to identify both autophagosomes and autolysosomes, as the mCherry fluorophore is resistant to degradation in the acidic environment of autolysosomes. Notably, mCherry-Atg8a–positive autolysosomes appear larger and brighter than pre-fusion autophagosomes, which are typically smaller and dimmer, especially under fusion-deficient conditions (e.g., Figure 4). Therefore, we use these morphological differences as a proxy to distinguish between the two.

      To improve structural assignment, we incorporated endogenous Lamp1 staining (Figure 10) and a Lamp1-GFP reporter (Figure 10—figure supplement 1). Vesicles positive for mCherryAtg8a but negative for Lamp1 are considered pre-fusion autophagosomes. Structures double-positive for mCherry-Atg8a and Lamp1 represent autolysosomes, while Lamp1positive, Atg8a-negative vesicles correspond to non-autophagic lysosomes. To clarify these interpretations, we revised the Results section and explained these reporters in more detail.

      (3) In this study, only vps16a RNAi cells were used to inhibit autophagosome-lysosome fusion. However, since HOPS has many roles besides autophagosome-lysosome fusion, it would be better to confirm the conclusion by knockdown of other factors (e.g., Stx17 RNAi).  

      Thank you for this valuable suggestion. We initially considered using Syntaxin17 RNAi; however, our recent findings indicate that loss of Syx17 results in a HOPS-dependent tethering lock between autophagosomes and lysosomes (DOI: 10.1126/sciadv.adu9605). In this case, tethered vesicles would likely move together, confounding the interpretation of autophagosome-specific trafficking.

      Therefore, we turned to other SNAREs such as Vamp7 and Snap29. One Snap29 RNAi was located on the appropriate chromosome needed for our genetic experiments. We generated a transgenic fly line expressing both Snap29 RNAi and the mCherry-Atg8a reporter under a fat body-specific R4 promoter. When we tested our key trafficking hits in this background, we observed similar autophagosome localization phenotypes as in Vps16A RNAi cells. These results, now included in the revised manuscript (see Figure 6), confirm that the observed transport phenotypes are not specific to Vps16A or HOPS complex loss.

      (4) Figure 8: Rab7 and Epg5 are also known to be directly involved in autophagosomelysosome tethering/fusion. Even if the fusion rate is reduced in the absence of Rab7 and Epg5, it may not be the result of defective autophagosome movement, but may simply indicate that these molecules are required for fusion itself. How do the authors distinguish between the two possibilities?

      Thank you for this important point. While Rab7 and Epg5 indeed participate in autophagosome–lysosome tethering and fusion, our data suggest they also contribute to autophagosome movement. This is evident from the distinct phenotypes observed upon Rab7 or Epg5 RNAi compared to Vps16A or SNARE RNAi. Depletion of Vps16A, Syx17, Vamp7, or Snap29 (factors involved specifically in fusion) results in perinuclear accumulation of autophagosomes. In contrast, Rab7 or Epg5 RNAi leads to a dispersed autophagosome pattern throughout the cytoplasm.

      These differences suggest that Rab7 and Epg5 play additional roles in positioning autophagosomes. Supporting this, our co-immunoprecipitation experiments show that Epg5 interacts with dynein motors. Therefore, we propose that Rab7 and Epg5 influence both autophagosome fusion and their microtubule-based transport.

      Reviewer #2 (Public review):  

      One limitation of the study is the genetic background that serves as the basis for the screening. In addition to preventing autophagosome-lysosome fusion, disruption of Vps16A has been shown to inhibit endosomal maturation and block the trafficking of components to the lysosome from both the endosome and Golgi apparatus. Additional effects previously reported by the authors include increased autophagosome production and reduced mTOR signaling. Thus Vps16A-depleted cells have a number of endosome, lysosome, and autophagosome-related defects, with unknown downstream consequences. Additionally, the cause and significance of the perinuclear localization of autophagosomes in this background is unclear. Thus, interpretations of the observed reversal of this phenotype are difficult, and have the caveat that they may apply only to this condition, rather than to normal autophagosomes. Additional experiments to observe autophagosome movement or positioning in a more normal environment would improve the manuscript.  

      Thank you for highlighting this limitation. We have tried to conduct time-lapse imaging of live fat body cells expressing 3xmCherry-Atg8a and GFP-Lamp1 to visualize the movement and fusion events of pre-fusion autophagosomes (3xmCherry-Atg8a positive and GFP-Lamp1 negative) and lysosomes (GFP-Lamp1 positive). Despite different experimental setups and durations of starvation, no vesicle movement was observed at all, so live imaging of larval Drosophila fat tissue will require time-consuming optimizations of in vitro culture conditions. Consistent with this, we did not find any literature data where organelle motility in fat body cells was successfully observed. Nuclear positioning in fat body cells was investigated in detail in an excellent study, however the authors were able to observe only very little movement of the nuclei by live imaging (Zheng et al. Nat Cell Biol. 2020 Mar;22(3):297-309. doi: 10.1038/s41556-020-0470-7), further highlighting the technical difficulties of live or timelapse imaging in this tissue type.

      Specific comments  

      (1) Several genes have been described that when depleted lead to perinuclear accumulation of Atg8-labeled vesicles. There seems to be a correlation of this phenotype with genes required for autophagosome-lysosome fusion; however, some genes required for lysosomal fusion such as Rab2 and Arl8 apparently did not affect autophagosome positioning as reported here. Thus, it is unclear whether the perinuclear positioning of autophagosomes is truly a general response to disruption of autophagosome-lysosome fusion, or may reflect additional aspects of Vps16A/HOPS function. A few things here would help. One would be an analysis of Atg8a vesicle localization in response to the depletion of a larger set of fusionrelated genes. Another would be to repeat some of the key findings of this study (effects of specific dynein, dynactin, rabs, effectors) on Atg8a localization when Syx17 is depleted, rather than Vps16A. This should generate a more autophagosome-specific fusion defect.  

      Thank you for this insightful suggestion. We recently discovered that Syx17 depletion induces a HOPS-dependent tethering lock between autophagosomes and lysosomes (DOI: 10.1126/sciadv.adu9605), making it unsuitable for modeling autophagosome-specific fusion defects. In contrast, Vamp7 and Snap29 knockdowns do not appear to cause such tethering lock. We were able to generate a suitable Drosophila line using a Snap29 RNAi transgene located on a compatible chromosome. Upon testing key hits from our screen in this background, we found that autophagosomes redistributed similarly, supporting our conclusions. These new results have been included in the revised manuscript (see Figure 6)

      Third, it would greatly strengthen the findings to monitor pre-fusion autophagosome localization without disrupting fusion. Such vesicles could be identified as Atg8a-positive Lamp-negative structures. The effects of dynein and rab depletion on the tracking of these structures in a post-induction time course would serve as an important validation of the authors' findings.  

      Thank you for this helpful suggestion. As described above, we attempted time-lapse imaging of 3xmCherry-Atg8a and GFP-Lamp1-expressing fat body cells under various conditions to identify motile pre-fusion autophagosomes. However, we did not observe any vesicle movement, regardless of the starvation duration or experimental setup. As this likely reflects technical limitations of ex vivo fat body imaging, we were unable to achieve live tracking of autophagosome dynamics without introducing perturbations. This limitation is now discussed in the revised manuscript.

      (2) The authors nicely show that depletion of Shot leads to relocalization of Atg8a to ectopic foci in Vps16A-depleted cells; they should confirm that this is a mislocalized ncMTOC by colabeling Atg8a with an MTOC component such as MSP300. The effect of Shot depletion on Atg8a localization should also be analyzed in the absence of Vps16A depletion.  

      Thank you for this positive comment. We co-labeled Atg8a with the minus-end microtubule marker Khc-nod-LacZ in both shot single knockdown and shot; vps16A double knockdown cells. Ectopic Khc-nod-LacZ-positive MTOC foci were clearly visible in both conditions, and Atg8a-positive autophagosomes accumulated around these structures. These findings confirm that Shot depletion induces ectopic MTOC formation, which correlates with autophagosome relocalization. The new data have been incorporated into the revised manuscript (see Figure 1O-S).

      (3) The authors report that depletion of Dynein subunits, either alone (Figure 6) or codepleted with Vps16A (Figure 2), leads to redistribution of mCherry-Atg8a punctae to the "cell periphery". However, only cell clones that contact an edge of the fat body tissue are shown in these figures. Furthermore, in these cells, mCherry-Atg8a punctae appear to localize only to contact-free regions of these cells, and not to internal regions of clones that share a border with adjacent cells. Thus, these vesicles would seem to be redistributed to the periphery of the fat body itself, not to the periphery of individual cells. Microtubules emanating from the perinuclear ncMTOC have been described as having a radial organization, and thus it is unclear that this redistribution of mCherry-Atg8a punctae to the fat body edge would reflect a kinesin-dependent process as suggested by the authors.  

      Thank you for this detailed observation. We frequently observe autophagosomes accumulating in contact-free peripheral regions of dynein-depleted cells, resulting in an asymmetric distribution. While previous studies describe a radial microtubule organization in fat body cells, none of them directly label MT plus ends, the direction of kinesin-based transport.

      To further explore this, we overexpressed a HA-tagged kinesin, Klp98A-3xHA, in both control and Vps16A RNAi backgrounds. Immunolabeling revealed that Klp98A localizes to the contact-free peripheral regions in both conditions, consistent with the distribution of autophagosomes in dynein knockdown cells. This supports our interpretation that kinesindependent transport drives autophagosome redistribution in the absence of dynein, and that fat body cells exhibit subtle asymmetries in MT polarity that influence this transport. These new results have been included in the revised manuscript (see Figure 3G, H).

      (4) To validate whether the mCherry-Atg8a structures in Vps16A-depleted cells were of autophagic origin, the authors depleted Atg8a and observed a loss of mCherry- Atg8a signal from the mosaic cells (Figure S1D, J). A more rigorous experiment would be to deplete other Atg genes (not Atg8a) and examine whether these structures persist.  

      Thank you for the suggestion to further validate our reporter. We depleted Atg1, a key kinase required for phagophore initiation, in the Vps16A RNAi background. This completely abolished the punctate mCherry-Atg8a distribution in knockdown cells (see Figure 1—figure supplement 1E, K), confirming that the labeled structures are indeed of autophagic origin.

      (5) The authors found that only a subset of dynein, dynactin, rab, and rab effector depletions affected mCherry-Atg8a localization, leading to their suggestion that the most important factors involved in autophagosome motility have been identified here. However, this conclusion has the caveat that depletion efficiency was not examined in this study, and thus any conclusions about negative results should be more conservative.  

      Thank you for this constructive feedback. We agree that negative results must be interpreted conservatively due to potential differences in knockdown efficiency. We have revised our conclusions accordingly, clarifying that the factors identified are key for autophagosome motility, while acknowledging the possibility of false negatives.

      Reviewer #3 (Public review):  

      Major concerns:

      (1) The localization of EPG5 should be determined. The authors showed that EPG5 colocalizes with endogenous Rab7. Rab7 labels late endosomes and lysosomes. Previous studies in mammalian cells have shown that EPG5 is targeted to late endosomes/lysosomes by interacting with Rab7. EPG5 promotes the fusion of autophagosomes with late endosomes/lysosomes by directly recognizing LC3 on autophagosomes and also by facilitating the assembly of the SNARE complex for fusion. In Figure 5I, the EPG5/Rab7colocalized vesicles are large and they are likely to be lysosomes/autolysosomes.

      Thank you for suggesting to improve our Epg5 localization data. We performed triple immunostaining for Atg8a, Lamp1-3xmCherry, and Epg5-9xHA in S2R+ cells. In addition to triple-positive structures—likely representing autolysosomes—we observed Atg8a and Epg59xHA double-positive vesicles that lacked Lamp1-3xmCherry signal, which likely correspond to pre-fusion autophagosomes. Based on these results, we propose that in addition to arriving via the endocytic route, Epg5 may also reach lysosomes through autophagosomes. These findings have been included in the revised manuscript (see Figure 5K).

      (2) The experiments were performed in Vps16A RNAi KD cells. Vps16A knockdown blocks fusion of vesicles derived from the endolysosomal compartments such as fusion between lysosomes. The pleiotropic effect of Vps16A RNAi may complicate the interpretation. The authors need to verify their findings in Stx17 KO cells, as it has a relatively specific effect on the fusion of autophagosomes with late endosomes/lysosomes.  

      Thank you for this valuable suggestion. We initially considered Syntaxin17 for validation; however, we recently found that loss of Syx17 leads to a HOPS-dependent tethering lock between autophagosomes and lysosomes, which would confound interpretation, as autophagosomes remain tethered to lysosomes (DOI: 10.1126/sciadv.adu9605). Therefore, Syntaxin17 loss is not suitable for our purpose. Among the remaining fusion SNAREs, one RNAi line targeting Snap29 was available on a compatible chromosome for generating Drosophila lines equivalent to those used in the screen. We established this Snap29 RNAicontaining tester line and crossed it with our top hits. We observed that autophagosome motility was comparable to that in the Vps16A RNAi background, further supporting our conclusions. These results have been incorporated into the revised manuscript (see Figure 6)

      (3) Quantification should be performed in many places such as in Figure S4D for the number of FYVE-GFP labeled endosomes and in Figures S4H and S4I for the number and size of lysosomes.  

      Thank you for pointing this out. We performed the suggested quantifications and statistical analyses for FYVE-GFP labeled endosomes, as well as for the number and size of lysosomes. The updated data are now presented in the revised Figure 5—figure supplement 1.

      (4) In this study, the transport of autophagosomes is investigated in fly fat cells. In fat cells, a large number of large lipid droplets accumulate and the endomembrane systems are distinct from that in other cell types. The knowledge gained from this study may not apply to other cell types. This needs to be discussed.

      Thank you for raising this important point. We agree that our findings may not be fully generalizable to all cell types. Given that the organization of the microtubule network depends on both cell function and developmental stage, it is plausible that the molecular machinery described here operates differently elsewhere. We now mention this limitation in the Discussion.

      Minor concerns:  

      (5) Data in some panels are of low quality. For example, the mCherry-Atg8a signal in Figure 5C is hard to see; the input bands of Dhc64c in Figure 5L are smeared.  

      Thank you for pointing this out. We repeated the experiment shown in Figure 5C and replaced the panel with a clearer image. The smeared Dhc64C input bands in Figure 5L result from the unusually large size of this protein, which affects its electrophoretic migration. We mentioned this point in the corresponding figure legend.

      (6) In this study, both 3xmCherry-Atg8a and mCherry-Atg8a were used. Different reporters make it difficult to compare the results presented in different figures.  

      Thank you for this comment. Both 3xmCherry-Atg8a and mCherry-Atg8a are well-established reporters that behave similarly as autophagic markers. Nevertheless, to avoid confusion, we ensured that each figure uses only one type of reporter consistently, which is now clearly indicated in the revised manuscript.

      (7) The small autophagosomes presented in Figures such as in Figure 1D and 1E are not clear. Enlarged images should be presented.  

      Thank you for your suggestion. We repeated these experiments and replaced the relevant panels with higher-quality images, including enlarged insets to better visualize small autophagosomes. These updated figures are now included in the revised manuscript.

      (8) The authors showed that Epg5-9xHA coprecipitates with the endogenous dynein motor Dhc64C. Is Rab7 required for the interaction?  

      Thank you for this insightful question. We tested this by co-transfecting S2R+ cells with Epg5-9xHA and different forms of Rab7: wild-type, GTP-locked (constitutively active), and GDP-locked (dominant-negative). Our results indicate that the strength of Epg5-Dhc interaction does not change in the presence of either GTP-locked or GDP-locked Rab7. However, we believe that Epg5 and dynein are recruited to the vesicle membranes via Rab7 in vivo, so we did not include these results in the revised manuscript.

      (9) The perinuclear lysosome localization in Epg5 KD cells has no indication that Epg5 is an autophagosome-specific adaptor.

      Thank you for this important comment. Accordingly, we have toned down our statements about Epg5 functions throughout the revised manuscript.

      Reviewer #1 (Recommendations for the authors):  

      (1) Figure 6: What do "autolysosome maturation" and "small autolysosomes" mean? Do different numbers of lysosomes fuse to a single autophagosome?

      Thank you for highlighting this point. We concluded that the formation of smaller autolysosomes—compared to controls—is likely due to a defect in autolysosome maturation, as is often the case. We had not explicitly considered whether a different number of lysosomes fuse with each autophagosome during this process. We clarified this issue in the revised manuscript.

      (2) Figure 5A shows that the localization of endogenous Atg8 requires Epg5, but the data is not as clear as for mCherry-Atg8 (Figure 4B). Why the difference?  

      Thank you for this question. The difference arises because the mCherry-Atg8a reporter strongly labels autolysosomes, as the mCherry fluorophore remains stable in acidic compartments. As a result, mCherry-Atg8a labels both autophagosomes and autolysosomes, but the strong autolysosomal signal originating from the surrounding GFP negative, nonRNAi cells can make accumulated autophagosomes appear fainter in fusion-defective cells (as in Figure 4). In contrast, endogenous Atg8a is degraded in lysosomes, and therefore labels only autophagosomes. This means that the appearance of these two experiments can be slightly different, but since in both cases autophagosomes no longer accumulate in the perinuclear region of Vps16A,Epg5 double RNAi cells we can conclude that Epg5 is required for autophagosome positioning. We explained this difference of the two methods in the revised manuscript where it first appears (Figure 1B and Figure 1—figure supplement 1A).

      (3) Blue letters on the black micrographs are hard to see. Some of the other letters are also small and hard to read.  

      Thank you for this suggestion. We improved the visibility and readability of the labels in the revised figures.

    1. Reviewer #3 (Public review):

      Summary:

      In their revised manuscript, the authors addressed most of the reviewers' concerns. One concern was the emphasis on increased MLEC-OST interactions during infection, which the authors toned down in the revision. They clarified that MLEC interaction with OST is maintained-rather than increased-during infection, while its interaction with other QC factors decreases. They also added context and discussion of the co-localization of viral proteins with ER and mitochondrial proteins, noting that both nsp2 and MLEC localize to mitochondria-associated membranes (MAMs), providing a plausible explanation for these interactions.

      Another concern involved the effects of MLEC KD on the cellular environment. To address this, the authors analyzed stress pathway activation and glycosylation of endogenous proteins in MLEC KD cells. They found only modest upregulation of the HSF1 pathway and no changes in the UPR or other stress responses, suggesting MLEC KD does not broadly disrupt ER proteostasis. Additionally, glycopeptide profiling showed only minor changes in host protein glycosylation, supporting a more direct role for MLEC in viral replication rather than general host glycoprotein disruption.

      However, some weaknesses remain. Direct interaction between MLEC and nsp2 during infection was not detected, and the identified viral glycopeptides were limited to only five Spike sites. Furthermore, the mechanism by which MLEC promotes viral replication is still unclear.

      In summary, the authors strengthened the manuscript by addressing reviewers' concerns through additional data, clarified language, and expanded discussion. While the overall support for MLEC's pro-viral role is solid, its precise mechanism of action remains speculative. Future work will be needed to directly link MLEC's activity to specific steps in viral protein biogenesis and replication.

      Original summary: In this study, Davies and Plate set out to discover conserved host interactors of coronavirus non-structural proteins (Nsp). They used 293T cells to ectopically express flag-tagged Nsp2 and Nsp4 from five human and mouse coronaviruses, including SARS-CoV-1 and 2, and analyzed their interaction with host proteins by affinity purification mass-spectrometry (AP-MS). To confirm whether such interactors play a role in coronavirus infection, the authors measured the effects of individual knockdowns on replication of murine hepatitis virus (MHV) in mouse Delayed Brain Tumor cells. Using this approach, they identified a previously undescribed interactor of Nsp2, Malectin (Mlec), which is involved in glycoprotein processing and shows a potent pro-viral function in both MHV and SARS-CoV-2. Although the authors were unable to confirm this interaction in MHV-infected cells, they show that infection remodels many other Mlec interactions, recruiting it to the ER complex that catalyzes protein glycosylation (OST). Mlec knockdown reduced viral RNA and protein levels during MHV infection, although such effects were not limited to specific viral proteins. However, knockdown reduced the levels of five viral glycopeptides that map to Spike protein, suggesting it may be affected by Mlec.

      Strengths:

      This is an elegant study that uses a state-of-the-art quantitative proteomic approach to identify host proteins that play critical roles in viral infection. Instead of focusing on a single protein from a single virus, it compares the interactomes of two viral proteins from five related viruses, generating a high confidence dataset. The functional follow-ups using multiple live and reporter viruses, including MHV and CoV2 variants, convincingly depict a pro-viral role for Mlec, a protein not previously implicated in coronavirus biology.

      Weaknesses:

      Although a commonly used approach, AP-MS of ectopically expressed viral proteins may not accurately capture infection-related interactions. The authors observed Mlec-Nsp2 interactions in transfected 293T cells (1C) but were unable to reproduce those in mouse cells infected with MHV (3C). EIF4E2/GIGYF2, two bonafide interactors of CoV2 Nsp2 from previous studies, are listed as depleted compared to negative controls (S1D). Most other CoV2 Nsp2 interactors are also depleted by the same analysis (S1D). Previously reported MERS Nsp2 interactors, including ASCC1 and TCF25, are also not detected (S1D). Furthermore, although GIGYF2 was not identified as an interactor of MHV Nsp2/4 in human cells (S1D), its knockdown in mouse cells reduced MHV titers about 1000 fold (S4). The authors should attempt to explain these discrepancies.

      More importantly, the authors were unable to establish a direct link between Mlec and the biogenesis of any viral or host proteins, by mass-spectrometry or otherwise. Although it is clear that Mlec promotes coronavirus infection, the mechanism remains unclear. Its knockdown does not affect the proteome composition of uninfected cells (S15B), suggesting it is not required for proteome maintenance under normal conditions. The only viral glycopeptides detected during MHV infection originated from Spike (5D), although other viral proteins are also known to be glycosylated. Cells depleted for Mlec produce ~4-fold less Spike protein (4E) but no more than 2-fold less glycosylated spike peptides (5D), compounding the interpretation of Mlec effects on viral protein biogenesis. Furthermore, Spike is not essential for the pro-viral role of Mlec, given that Mlec knockdown reduces replication of SARS-CoV-2 replicons that express all viral proteins except for Spike (6A/B).

      Any of the observed effects on viral protein levels could be secondary to multiple other processes. Interventions that delay infection for any reason could lead to imbalance of viral protein levels, because Spike and other structural proteins are produced at a much higher rate than non-structural proteins due to the higher abundance of their cognate subgenomic RNAs. Similarly, the observation that Mlec depletion attenuates MHV-mediated changes to the host proteome (S15C/D) can also be attributed to indirect effects on viral replication, regardless of glycoprotein processing. In the discussion, the authors acknowledge that Mlec may indirectly affect infection through modulation of replication complex formation or ER stress, but do not offer any supporting evidence. Interestingly, plant homologs of Mlec are implicated in innate immunity, favoring a more global role for Mlec in mammalian coronavirus infections.

      Finally, the observation that both Nsp2 (3C) and Mlec (3E/F) are recruited to the OST complex during MHV infection neither support nor refute any of these alternate hypotheses, given that Mlec is known to interact with OST in uninfected cells and that Nsp2 may interact with OST as part of the full length unprocessed Orf1a, as it co-translationally translocates into the ER.

      Therefore, the main claims about the role of Mlec in coronavirus protein biogenesis are only partially supported.

      Comments on revisions:

      Figure 7B should be revised to show that MLEC maintains interactions with rather than recruited to the OST.

    2. Author response:

      The following is the authors’ response to the original reviews.

      Reviewer #1 (Public Review):

      In this manuscript, the authors employ a combined proteomic and genetic approach to identify the glycoprotein QC factor malectin as an important protein involved in promoting coronavirus infection. Using proteomic approaches, they show that the non-structural protein NSP2 and malectin interact in the absence of viral infection, but not in the presence of viral infection. However, both NSP2 and malectin engage the OST complex during viral infection, with malectin also showing reduced interactions with other glycoprotein QC proteins. Malectin KD reduce replication of coronaviruses, including SARS-COV2. Collectively, these results identify Malectin as a glycoprotein QC protein involved in regulating coronavirus replication that could potentially be targeted to mitigate coronavirus replication.

      Overall, the experiments described appear well performed and the interpretations generally reflect the results. Moreover, this work identifies Malectin as an important pro-viral protein whose activity could potentially be therapeutically targeted for the broad treatment of coronavirus infection. However, there are some weaknesses in the work that, if addressed, would improve the impact of the manuscript.

      Notably, the mechanism by which malectin regulates viral replication is not well described. It is clear from the work that malectin is a pro-viral protein in the work presented, but the mechanistic basis of this activity is not pursued. Some potential mechanisms are proposed in the discussion, but the manuscript would be strengthened if additional insight was included. For example, does the UPR activated to higher levels in infected cells depleted of malectin? Do glycosylation patterns of viral (or non-viral) proteins change in malectindepleted cells? Additional insight into this specific question would significantly improve the manuscript.

      We concur with the reviewer that the mechanism by which Malectin regulates viral replication is an important point to elucidate further. Our proteomics data were able to offer additional insight into the questions posed here. We examined the upregulation of protein markers of the UPR and other stress response pathways in cells depleted of MLEC (Fig. S15D). We find that the UPR pathways are moderately but insignificantly upregulated, while the Heat Shock Factor 1 (HSF1) pathway is moderately and significantly upregulated. The fold change increase of these marker proteins are relatively small, so while upregulation of this pathway may contribute to the suppression of CoV replication, it may not fully explain the phenotype.

      In addition, to address the second question, we compared the glycosylation patterns of endogenous proteins in MLEC-KD cells (Fig. S15E-G). We found that there is a small increase in abundance of glycopeptides associated with LAMP2, SERPHINH1, RDX, RPL3/5, CADM4, and ITGB1, however these fold changes are small and tested to be insignificant. These results indicate there is relatively little modification of endogenous glycoproteins upon MLEC-depletion. These findings support a more direct role for MLEC in regulating viral replication.

      We added the following section to the manuscript text to discuss these results:

      “In uninfected cells, MLEC KD leads to relatively little proteome-wide changes, with MLEC being the only protein significantly downregulated and no other proteins significantly upregulated, supporting the specificity of MLEC KD in MHV suppression (Fig.  S15C). To determine whether MLEC KD alters general host proteostasis, we further examined the levels of protein markers of stress pathways based on previous gene pathway definitions(Davies et al., 2023; Grandjean et al., 2019; Shoulders et al., 2013) (Fig. S15D). We find that there are modest but significant increases in protein levels associated with the Heat Shock Factor 1 (HSF1) pathway, while the Unfolded Protein Response (UPR) pathways are largely unmodified. 

      We also probed the effect of MLEC KD on endogenous protein glycosylation. We find that there is only a small increase in abundance of glycopeptides, including those associated with the ribosome (Rpl3, Rpl5), a cytoskeletal protein (Rdx), the integrin Itgb1, and the ER-resident chaperone Serphinh1 (Fig. S15E-G).”

      “Our proteomics data reveals that there is only a modest increase in the Heat Shock Factor 1 (HSF1) pathway, while the Unfolded Protein Response is relatively unchanged (Fig. S15D). In addition, there are only minor increases in endogenous glycopeptide levels (Fig. S15E-G). Together, these results indicate that while MLEC KD leads to some alterations in ER proteostasis and host glycosylation, these changes are modest and may not be the primary mechanism by which MLEC KD hinders CoV replication.”

      Further, the evidence for increased interactions between OST and malectin during viral infection is fairly weak, despite being a major talking point throughout the manuscript. The reduced interactions between malectin and other glycoproteostasis QC factors is evident, but the increased interactions with OST are not well supported. I'd recommend backing off on this point throughout the text, instead, continuing to highlight the reduced interactions.

      We agree that the fold change increase of OST interactions with malectin are small compared to the fold change decrease of other glycoproteostasis factors We have modified the text to less emphasize this point and instead highlight the reduced interactions:

      “Further, MHV infection retains the association of MLEC with the OST complex while titrating off other interactors, potentially leading to more efficient glycoprotein biogenesis.”

      I was also curious as to why non-structural proteins, nsp2 and nsp4, showed robust interactions with host proteins localized to both the ER and mitochondria? Do these proteins localize to different organelles or do these interactions reflect some other type of dysregulation? It would be useful to provide a bit of speculation on this point.

      We also find these ER and mitochondrial protein interactions curious, which we initially reported on (Davies, Almasy et al. 2020 ACS Infectious Diseases). In this prior report, we found that when expressed in HEK293T cells, SARS-CoV-2 nsp2 and nsp4 have partial localization to mitochondrial-associated ER membranes (MAMs), as determined by subcellular fractionation. Given that malectin has also been shown to have MAMs localization (Carreras-Sureda, et al. 2019 Nature Cell Biology), we have added additional text in the Discussion to speculate on this point:

      “Additionally, MLEC has also been shown to localize to ER-mitochondria contact sites (MAMs)(Carreras-Sureda et al., 2019), which regulate mitochondrial bioenergetics. We have previously shown that SARS-CoV-2 nsp2 and nsp4 can partially localize to MAMs(Davies et al., 2020), so these viral proteins may also dysregulate MLEC and MAMs activity to promote infection.”

      Again, the overall identification of malectin as a pro-viral protein involved in the replication of multiple different coronaviruses is interesting and important, but additional insights into the mechanism of this activity would strengthen the overall impact of this work.

      Thank you for this endorsement. We hope the additional analyses and discussion points in the revised manuscript further homed in on a direct mechanistic function for MLEC in modulating viral replication.

      Reviewer #2 (Public Review):

      Summary:

      A strong case is presented to establish that the endoplasmic reticulum carbohydrate binding protein malectin is an important factor for coronavirus propagation. Malectin was identified as a coronavirus nsp2 protein interactor using quantitative proteomics and its importance in the viral life cycle was supported by using a functional genetic screen and viral assays. Malectin binds diglucosylated proteins, an early glycoform thought to transiently exist on nascent chains shortly after translation and translocation; yet a role for malectin has previously been proposed in later quality control decisions and degradation targeting. These two observations have been difficult to reconcile temporally. In agreement with results from the Locher lab, the malectininteractome shown here includes a number of subunits of the oligosaccharyltransferase complex (OST). These results place malectin in close proximity to both the co-translational (STT3A or OST-A) and post-translational (STT3B or OST-B) complexes. It follows that malectin knockdown was associated with coronavirus Spike protein hypoglycosylation.

      Strengths:

      Strengths include using multiple viruses to identify interactors of nsp2 and quantitative proteomics along with multiple viral assays to monitor the viral life cycle.

      Weaknesses:

      Malectin knockdown was shown to be associated with Spike protein hypoglycosylation. This was further supported by malectin interactions with the OSTs. However, no specific role of malectin in glycosylation was discussed or proposed.

      We have emphasized our hypotheses on this point in the discussion and added a summary figure to highlight the specific role of malectin.

      Given the likelihood that malectin plays a role in the glycosylation of heavily glycosylated proteins like Spike, it is unfortunate that only 5 glycosites on Spike were identified using the MS deamidation assay when Spike has a large number of glycans (~22 sites). The mass spec data set would also include endogenous proteins. Were any heavily glycosylated endogenous proteins hypoglycosylated in the MS analysis in Fig 5D?

      Thank you for this suggestion. We compared the glycosylation patterns of endogenous proteins in MLEC-KD cells (Fig. S15E-G). We found that there is a small increase in abundance of glycopeptides associated with LAMP2, SERPHINH1, RDX, RPL3/5, CADM4, and ITGB1, however these fold changes are small and tested insignificant. These results indicate there is relatively little modification of endogenous glycoproteins upon MLEC-depletion. We added the following sections:

      “We also probed the effect of MLEC KD on endogenous protein glycosylation. We find that there is only a small increase in abundance of glycopeptides, including those associated with the ribosome (Rpl3, Rpl5), a cytoskeletal protein (Rdx), the integrin Itgb1, and the ER-resident chaperone Serphinh1 (Fig. S15E-G).”

      “Our proteomics data reveals that there is only a modest increase in the Heat Shock Factor 1 (HSF1) pathway, while the Unfolded Protein Response is relatively unchanged (Fig. S15D). In addition, there are only minor increases in endogenous glycopeptide levels (Fig. S15E-G). Together, these results indicate that while MLEC KD leads to some alterations in ER proteostasis and host glycosylation, these changes are modest and may not be the primary mechanism by which MLEC KD hinders CoV replication.”

      The inclusion of the nsp4 interactome and its partial characterization is a distraction from the storyline that focuses on malectin and nsp2.

      We believe the nsp4 comparative interactome and functional genomics data offers a rich resource for further functional investigation by others, if made public. While we found the malectin and nsp2 storyline the most compelling to pursue, we believe the inclusion of the nsp4 data strengthens the overall approach, in agreement with Reviewer #3’s comments.

      Reviewer #3 (Public Review):

      Summary:

      In this study, Davies and Plate set out to discover conserved host interactors of coronavirus non-structural proteins (Nsp). They used 293T cells to ectopically express flag-tagged Nsp2 and Nsp4 from five human and mouse coronaviruses, including SARS-CoV-1 and 2, and analyzed their interaction with host proteins by affinity purification mass-spectrometry (AP-MS). To confirm whether such interactors play a role in coronavirus infection, the authors measured the effects of individual knockdowns on replication of murine hepatitis virus (MHV) in mouse Delayed Brain Tumor cells. Using this approach, they identified a previously undescribed interactor of Nsp2, Malectin (Mlec), which is involved in glycoprotein processing and shows a potent pro-viral function in both MHV and SARS-CoV-2. Although the authors were unable to confirm this interaction in MHVinfected cells, they show that infection remodels many other Mlec interactions, recruiting it to the ER complex that catalyzes protein glycosylation (OST). Mlec knockdown reduced viral RNA and protein levels during MHV infection, although such effects were not limited to specific viral proteins. However, knockdown reduced the levels of five viral glycopeptides that map to Spike protein, suggesting it may be affected by Mlec.

      Strengths:

      This is an elegant study that uses a state-of-the-art quantitative proteomic approach to identify host proteins that play critical roles in viral infection. Instead of focusing on a single protein from a single virus, it compares the interactomes of two viral proteins from five related viruses, generating a high confidence dataset. The functional follow-ups using multiple live and reporter viruses, including MHV and CoV2 variants, convincingly depict a pro-viral role for Mlec, a protein not previously implicated in coronavirus biology.

      Weaknesses:

      Although a commonly used approach, AP-MS of ectopically expressed viral proteins may not accurately capture infection-related interactions. The authors observed Mlec-Nsp2 interactions in transfected 293T cells (1C) but were unable to reproduce those in mouse cells infected with MHV (3C). EIF4E2/GIGYF2, two bonafide interactors of CoV2 Nsp2 from previous studies, are listed as depleted compared to negative controls (S1D). Most other CoV2 Nsp2 interactors are also depleted by the same analysis (S1D). Previously reported MERS Nsp2 interactors, including ASCC1 and TCF25, are also not detected (S1D). Furthermore, although GIGYF2 was not identified as an interactor of MHV Nsp2/4 in human cells (S1D), its knockdown in mouse cells reduced MHV titers about 1000 fold (S4). The authors should attempt to explain these discrepancies.

      We acknowledge these limitations in AP-MS from ectopically expressed viral proteins and have addressed these discrepancies with further elaboration in the text:

      “A limitation of our study is the initial overexpression of individual proteins for AP-MS, in which we find some variation between our data with other AP-MS studies. We sought to overcome these variations by focusing on conserved interactors and testing interactions in a live infection context.”

      “We also found GIGYF2-KD strongly suppressed MHV infection, despite GIGYF2 not interacting with MHV nsp2 (Fig. S1D), highlighting the importance of proteostasis factors in infection regardless of direct PPIs.”

      More importantly, the authors were unable to establish a direct link between Mlec and the biogenesis of any viral or host proteins, by mass-spectrometry or otherwise. Although it is clear that Mlec promotes coronavirus infection, the mechanism remains unclear. Its knockdown does not affect the proteome composition of uninfected cells (S15B), suggesting it is not required for proteome maintenance under normal conditions. The only viral glycopeptides detected during MHV infection originated from Spike (5D), although other viral proteins are also known to be glycosylated. Cells depleted for Mlec produce ~4-fold less Spike protein (4E) but no more than 2-fold less glycosylated spike peptides (5D), compounding the interpretation of Mlec effects on viral protein biogenesis. Furthermore, Spike is not essential for the pro-viral role of Mlec, given that Mlec knockdown reduces replication of SARS-CoV-2 replicons that express all viral proteins except for Spike (6A/B).

      Thank you, these are all important points. We have acknowledged these compounding factors in the Discussion:

      “Concurrently, knockdown of MLEC leads to impediment of nsp production and aberrant glycosylation of other viral proteins like Spike, though it should be noted that the decrease in Spike glycopeptides is compounded by the overall decrease in Spike protein. Given that MLEC is pro-viral in a SARS-CoV-2 replicon model lacking Spike (Fig. 6), MLEC can promote CoV replication independent of Spike production.”

      Any of the observed effects on viral protein levels could be secondary to multiple other processes.Interventions that delay infection for any reason could lead to an imbalance of viral protein levels because Spike and other structural proteins are produced at a much higher rate than non-structural proteins due to the higher abundance of their cognate subgenomic RNAs. Similarly, the observation that Mlec depletion attenuates MHV-mediated changes to the host proteome (S15C/D) can also be attributed to indirect effects on viral replication, regardless of glycoprotein processing. In the discussion, the authors acknowledge that Mlec may indirectly affect infection through modulation of replication complex formation or ER stress, but do not offer any supporting evidence. Interestingly, plant homologs of Mlec are implicated in innate immunity, favoring a more global role for Mlec in mammalian coronavirus infections.

      We examined the upregulation of protein markers of the UPR and other stress response pathways in cells depleted of MLEC (Fig. S15D). We find that the UPR pathways are moderately but insignificantly upregulated, while the Heat Shock Factor 1 (HSF1) pathway is moderately and significantly upregulated. The fold change increase of these marker proteins are relatively small, so while upregulation of this pathway may contribute to the suppression of CoV replication, it may not fully explain the phenotype. Please all see similar points brought up by reviewer 1 (comment 1). We added the following section to the manuscript text to discuss these results:

      “In uninfected cells, MLEC KD leads to relatively little proteome-wide changes, with MLEC being the only protein significantly downregulated and no other proteins significantly upregulated, supporting the specificity of MLEC KD in MHV suppression (Fig.  S15C). To determine whether MLEC KD alters general host proteostasis, we further examined the levels of protein markers of stress pathways based on previous gene pathway definitions(Davies et al., 2023; Grandjean et al., 2019; Shoulders et al., 2013) (Fig. S15D). We find that there are modest but significant increases in protein levels associated with the Heat Shock Factor 1 (HSF1) pathway, while the Unfolded Protein Response (UPR) pathways are largely unmodified. 

      “Our proteomics data reveals that there is only a modest increase in the Heat Shock Factor 1 (HSF1) pathway, while the Unfolded Protein Response is relatively unchanged (Fig. S15D). […] Together, these results indicate that while MLEC KD leads to some alterations in ER proteostasis and host glycosylation, these changes are modest and may not be the primary mechanism by which MLEC KD hinders CoV replication.”

      Finally, the observation that both Nsp2 (3C) and Mlec (3E/F) are recruited to the OST complex during MHV infection neither support nor refute any of these alternate hypotheses, given that Mlec is known to interact with OST in uninfected cells and that Nsp2 may interact with OST as part of the full length unprocessed Orf1a, as it co-translationally translocates into the ER. Therefore, the main claims about the role of Mlec in coronavirus protein biogenesis are only partially supported.

      We have acknowledged this point in the Discussion. 

      “We find that nsp2 interacts with several OST complex members, including DDOST, STT3A, and RPN1, though whether this is as part of the uncleaved Orf1a polyprotein during co-translational ER translocation or as an individual protein is unclear.”

      Reviewer #2 (Recommendations For The Authors):

      What is the proof that MLEC is a type I membrane protein? If it is strictly sequence analysis, this conclusion should be tapered in the text.

      Our response: We have added appropriate evidence on the biochemical characterization of MLEC topology from Galli et al., 2011, and cryo-EM structural characterization by Ramírez et al., 2019.

      “As it was surprising that nsp2, a non-glycosylated, cytoplasmic protein, would interact with MLEC, an integral ER membrane protein with a short two amino acid cytoplasmic tail(Galli et al., 2011; Ramírez et al., 2019), we assessed a broader genetic interaction between nsp2 and MLEC.”

      Validation of some of the nsp2 and malectin interactome components by pulldowns should be included.

      Our response: The interactions between nsp2 and Ddost, Stt3A, and Rpn1 passed a stringent confidence filter in our AP-MS experiment (Fig. 3C) based on several replication. For this reason, we do not believe additional validation by Western blotting will offer much useful information.

      NGI-1 inhibition of glycosylation looks to be very weak in Fig. 5B and Fig. S14B.

      Our response: It is important to note that the NGI-1 inhibition assay used a suboptimal NGI-1 concentration to prevent full suppression of MHV infection, which we have found previously. We have added this justification in the Methods section and associated figure legend (Fig. S14A).

      “The 5 uM NGI-1 dosage was chosen as it resulted in partial inhibition of glycosylation while not completely blocking MHV infection.”

      “This dosage and timing were chosen to partially inhibit the OST complex without fully ablating viral infection, as NGI-1 has been shown previously to be a potent positive-sense RNA virus inhibitor(Puschnik et al., 2017)  (Fig. S14)”

      Summary model figure at the end would help to communicate the conclusions.

      Our response: Thank you for this suggestion. We agree and have added a summary model figure at the end as suggested.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Reviewer #1 (Public Review):

      Given that there are different mutations identified at different CDK12 sites as illustrated in Figure 1B it would be nice to know which ones have been functionally classified as pathogenic and for which ones that the pathogenicity has not been determined. This would be especially interesting to perform in light of the differences in the LOH scores and WES data presented - specifically, are the pathogenic mutations vs the mutations for which true pathogenicity is unknown more likely to display LOH or TD?

      Alterations were classified as pathogenic when resulting in frameshift, nonsense, or cause an aminoacid change likely to alter function (according to ANNOVAR).  Four patients were called CDK12<sup>BAL</sup> but were negative for TDP signatures. Three of these had CDK12 mutations downstream of the kinase domain, which may be less likely to ablate protein activity. Most functionally validated pathogenic mutations include disruption of the kinase domain (PMID: 25712099). We added a sentence to the Results section (under “Identification of genomic characteristics that associate with CDK12 loss in prostate cancer”) to highlight this caveat on pathogenic mutation calls.

      For the cell inhibition studies with the CDK12/13 inhibitor, more details characterizing the specificity of this molecule to these targets would be useful. Additionally, could the authors perform short-term depletion studies with a PROTAC to the target or short shRNA or non-selected pool CRISPR deletion studies of CDK12 in these same cell lines to complement their pharmacological studies with genetic depletion studies? Also perhaps performing these same inhibitor studies in CDK12/13 deleted cells to test the specificity of the molecule would be useful.

      We are not aware of a CDK12-specific PROTAC, and generate such as reagent is beyond the scope of the present study. Regarding the specificity of the CDK12/13 inhibitor molecules, additional information on the specificity and in vivo dose selection were added to the Results section (under “CDK13 is synthetic lethal in cells with biallelic CDK12 loss”). Cells with CDK12-KO did not tolerate CDK13-KO, so we were unable to generate double knockouts to test for CDK12/13 inhibitor non-specific effects. 

      Additionally, expanding these studies to additional prostate cancer cell lines or organdies models would strengthen the conclusions being made. More information should be provided about the dose and schedule chosen and the rationale for choosing those doses and schedules for the in vivo studies proposed should be presented and discussed. Was there evidence for maximal evidence of inhibition of the target CDK12/13 at the dose tested given the very modest tumor growth inhibition noted in these studies.

      With respect to additional acute CDK12 loss models, our Tet-inducible shCDK12 models show only minor growth slowdown and do not appear to phenocopy the strong arrest or apoptosis seen with CDK12 KO or inhibition, respectively. Future work is ongoing to generate CDK12-degron regulated cell lines. We added a new immunoblot panel showing that acute CRISPR/sgRNA targeting of CDK12 does indeed lead to BRCA2 and ATM protein decrease (Fig. S4g), providing some orthogonal genomic targeting evidence of the acute HR gene effect.  We are continuing efforts to collect and generate additional CDK12<sup>BAL</sup> cell models, in both 2D and 3D culture systems, but none are presently available. We added a 3D culture drug dose curve with LuCaP189.4 exposed to THZ531 (Fig. S7m), which confirms heightened sensitivity vs two CDK12-intact lines. 

      Regarding assessments of CDK12 targets; as we are not aware of any unique CDK12 substrates, it is fair to ask but difficult to measure precise CDK12 inhibition by the compounds in tumors. We dosed mice using the same protocol as detailed in the original report testing SR4835 in mice (PMID: 31668947). We performed immunoblots on lysates from 3 and 28 day treated PDX tumors and did not see any consistent decreases in pRBP1(Ser2) or ATM or increases in γH2A.X (data not shown). However, we did see increases in APA usage and downregulation of DNA repair transcripts with three day treatment (Fig. 6k-l), as would be expected from on target acute effects.

      Reviewer #2 (Public review)

      One caveat that continues to be unclear as presented, is the uncoupling of cell cycle/essentiality of CDK12/13 from HR-directed mechanisms. Is this purely a cell cycle arrest phenotype acutely with associated down-regulation of many genes?

      In regard to untangling the effects of cell arrest on HR gene expression, this is a difficult question given that many HR genes, including BRCA2, are S/G2 linked. We attempted to account for those effects in the acute CDK12 inhibition experiment by including a palbociclib (CDK4/6i) control, which caused cell arrest and decreased BRCA1/2 RNA expression with no apparent 5/3’ transcript imbalance determined by qPCR (Fig. 4e,g). Though overall BRCA1 and BRCA2 mRNA levels are lower in the stable 22Rv1-CDK12-KO2 and KO5 lines, they do not show selective 3’ loss (Fig. 5c), suggesting the downregulation in these lines is mostly due to their slower growth (Fig. S4k) and not intronic polyA usage.

      While the RAD51 loading ssRNA experiments are informative, the Tet-inducible knockdown of BRCA2 and CDK12 is confusing as presented in Figure 5, shBRCA2 + and -dox are clearly shown. However, were the CDK12_K02 and K05 also knocked down using inducible shRNA or a stable knockout? The importance of this statement is the difference between acute and chronic deletion of CDK12. Previously, the authors showed that acute knockdown of CDK12 led to an HR phenotype, but here it is unclear whether CDK12K02/05 are acute knockdowns of CDK12 or have been chronically adapted after single cell cloning from CRISPR-knockout. 

      As a clarification, the 22Rv1-CDK12-KO2 and 22Rv1-CDK12-KO5 are stable CRISPR knockout clonal lines that were expanded from single cells. We added a new figure to include more validation of these lines (Fig. S5). We tried multiple times to reproduce the HRd phenotype and PARPi sensitivity with siRNA and inducible shRNA lines but were unable to see clear sensitivity differences, despite seeing the expected shifts with shBRCA2 controls (data not shown). It is possible the degree of knockdown (~80%), timing (8 days), or specific cell lines used in our experiments were not sufficient to expose the acute phenotype by this method.

      However, we were able to see acute HR gene decreases by inhibitor treatment (Fig. 4) or acute CRISPR (Fig. S4g).

      Given the multitude of lines, including some single-cell clones with growth inhibitory phenotypes and ex-vivo derived xenografts, the variability of effects with SR4835, ATM, ATR, and WEE1 inhibitors in different models can be confusing to follow. Overall, the authors suggest that the cell lines differ in therapeutic susceptibility as they may have alternate and diverse susceptibilities. It may be possible that the team could present this more succinctly and move extraneous data to the supplement.  

      We appreciate the complexity of the data and attempted to use multiple models to report consistency and variability. We are not able to ascertain what data would be extraneous, and elected to present data we view as relevant in the main figures while moving supporting data in the supplement.

      The in-vitro data suggests that SR4835 causes growth inhibition acutely in parental lines such as 22RV1. However, in vivo, tumor attenuation appears to be observed in both CDK12 intact and deficient xenografts, LuCAP136 and LuCaP 189.4 (albeit the latter is only nominally significant). Is there an effect of PARPi inhibition specifically in either model? What about the 22RV1-K02/05? Do these engraft? Given the role of CDK12/13 in RNAP II, these data might suggest that the window of susceptibility in CDK12 (mutant) tumors may not be that different from CDK12 intact tumors (or intact tissue) when using dual CDK12/13 inhibitors but rather represent more general canonical essential functions of CDK12 and CDK13 in transcription. From a therapeutic development strategy, the authors may want to comment in the discussion on the ability to target CDK13 specifically.

      Though the response of the CDK12<sup>BAL</sup> models to some compounds is variable, we believe those mixed results are important and future studies may be able to better explain why some show shifts in sensitivity while others do not. We hope future studies with additional models will help determine which sensitivities are more consistently true, and perhaps provide explanations for differences between models.

      Regarding SR4835, we find, and others have reported, a toxic (i.e. apoptotic) effect for in vitro treatment with dual CDK12/13 inhibitors (Fig. 4f, S4e,f); in fact, that may be why previous studies have used short timepoints in cell culture assays with these dual inhibitors. In mice, SR4835 was tolerated well but only LuCaP 189.4 showed statistically significant decreases in tumor volume and weight (Fig. 6j). We did not test PARPi responses in the PDX models, nor did we attempt engrafting the 22Rv1-CDK12-KO cell lines, but both would be worthwhile experiments in the future. Beyond CDK12<sup>BAL</sup> tumors, we agree that CDK12/13 inhibitors could be effective in cancer therapies more generally (e.g. triggering acute HRd, loss of RNAP2 phosphorylation). We added a line to the discussion section about ongoing efforts to combine PARPi and CDK12/13i, which we expect to be synergistic in CDK12-intact tumors due to the acute loss phenotype. We certainly agree that development of a specific CDK13 inhibitor would be the ideal therapeutic option for CDK12<sup>BAL</sup> tumors. However, CDK12 and CDK13 are 43% conserved at the protein level (PMID: 26748711), with 92% conservation in the active site (PMID: 30319007), and there are no available pharmacologic inhibitors that discriminate between CDK12 and CDK13.

      Reviewer #3 (Public review):

      It is generally assumed that CDK12 alterations are inactivating, but it is noteworthy that homozygous deletions are comparatively uncommon (Figure 1a). Instead many tumors show missense mutations on either one or both alleles, and many of these mutations are outside of the kinase domain (Figure 1b). It remains possible that the CDK12 alterations that occur in some tumors may retain residual CDK12 function, or may confer some other neomorphic function, and therefore may not be accurately modeled by CDK12 knockout or knockdown in vitro. This would also reconcile the observation that knockout of CDK12 is cell-essential while the human genetic data suggest that CDK12 functions as a tumor suppressor gene.

      Thank you for the feedback. It is a keen observation that homozygous deletions of CDK12 are not typical, though many mutations are upstream frameshifts that are expected to lead to loss of functional protein and mRNA via nonsense mediated decay. LuCaP189.4, our only natural mutant model, has two upstream frameshifts leading to complete protein loss (Fig 5b, S4h-i). We also added a caveat previously mentioned (in response to Reviewer 1) that mutations downstream of the kinase domain may be less likely to be fully pathogenic. For upstream missense mutations, the possibility of neuromorphic function remains an intriguing possibility that cannot be ruled out and would not be captured in our current models. Hopefully additional models can be developed, both natural and engineered, to help dissect that question in future studies.  

      It is not entirely clear whether CDK12 altered tumors may require a co-occurring mutation to prevent loss of fitness, either in vitro or in vivo (e.g. perhaps one or more of the alterations that occur as a result of the TDP may mitigate against the essentiality of CDK12 loss).

      We concur. Another caveat with the CRISPR models, beyond reliance on upstream frameshift mutations, is the simultaneous loss of alleles. In human tumors, there may be a period of single copy loss before the second hit that may provide a window for adaptation. It is possible that sequential loss is far easier for a cell to tolerate than acute bi-allelic inactivation. We agree that the question of what (if any) cooperating genetic alterations are required to tolerate CDK12 loss is an important one that we plant to further explore in future work.

      Recommendations for Authors:

      Reviewer #1 (Recommendations for Authors):

      The authors have thoroughly addressed all issues of data availability, reagents, in vivo protocols, and animal approvals associated with the studies presented in this manuscript. Specific comments and experimental suggestions that in my opinion would strengthen the conclusions of this interesting and compelling manuscript are included above

      Reviewer #2 (Recommendations for the authors):

      The authors were thorough in their studies. As a general note, switching between the cell lines is often overwhelming in interpreting the data given cell-to-cell variability in response. If possible, consolidating the text/conclusions in results would improve the readability of the manuscript.

      The variety of cell lines and models is perhaps expansive at times, but we hope the inclusion of these different models helps support the conclusions. 

      Is it possible to knockout CDK12 acutely using a degron-based approach, instead of utilizing an inhibitor that targets both CDK12/13?

      There is a HeLa cell line made with analog-sensitive CDK12 (Bartkowiak, Yan, and Greenleaf 2016) but we were unaware of any such prostate lines at the time of this work. We are attempting to develop engineered prostate lines with specific CDK12 degradation but do not yet have them available.

      How do the authors address a lower BRCA1/2 level in for example 22RV1-K05, does this cell line have increased sensitivity to PARPi over its parental 22RV1 line? Could this be added to Figure 5h/i?

      The lower BRCA2 levels in 22Rv1CDK12-KO5 is likely due to the slower growth rate (Fig. S4k), as BRCA2 expression is S/G2 linked. While the mRNA level of BRCA2 overall is lower in the KO5 line, we do not observe the 5’/3’ transcript imbalance (Fig. 5c). The 22Rv1-CDK12-KO lines did not show increased sensitivity to carboplatin, while inducible shBRCA2 did (Fig. S7a), so we do not believe this lower BRCA2 confers functional HRd. We did test the KO lines with olaparib (Fig. S7d) and saw a modest increased sensitivity compared to parental 22Rv1, but not to the extent measured in the BRCA1 mutant line UWB1.289.

      What is the clonality of the LuCAP 189.4 lines upon derivation? Is biallelic CDK12 loss seen in all cells?

      We do not know the exact clonality of the LuCAP 189.4 PDX or CL model, but we do see highly uniform CDK12 protein loss in these cells (quantified by IHC staining, data not shown).

      The authors state that 22RV1-K02/05 has an increased growth arrest to CDK13 inhibition. However, in Figure 6h, it appears the viability is not significantly different compared to the parental 22RV1 line. Similar aspects noted in 189.4-vec/CDK12?

      We found that 22Rv1 KO2/KO5 have growth arrest with sgCDK13 and cell death with CDK12/13 inhibitor. We did notice that SR4835 did not show the differential effects we anticipated (Fig. 6h), as was seen with THZ531 (Fig. 6i). SR4835 is a non-covalent inhibitor, while THZ531 is a covalent binder, so there are some functional differences between these compounds that might explain the lack of differential effects in the isogenic lines in a 4 day in vitro assay. We included the SR4835 in vitro data because it was used for the in vivo experiment. THZ531 is not suited for animal use.

      Could the authors comment on SR4835 response in vivo as a function of tumor growth rate?

      The in vivo SR4835 treated LuCaP189.4 did show signs of reduced proliferation with decreased Cell Cycle and DNA Replication in the RNA-seq signatures, but a more detailed investigation into cell cycle arrest vs apoptotic response has yet to be fully explored. We plan to conduct additional PDX experiments if we can obtain a selective CDK13 inhibitor. 

      Do the authors explore TDPs in their isogenic cell lines?

      We performed low coverage WGS on the 22Rv1 KO clones and added that to the paper (Fig. S5c). We did not see any obvious signs of TDP. We suspect the phenotype takes longer to accumulate and is not apparent within the ~20 passages our clones underwent in culture. This would be consistent with the tumor analysis (Fig. 2b) showing increase in TDs from primary to metastatic tumors, suggesting TDs accumulate over time.

      A future study may allow for screening synthetic lethals in the context of CDK12 loss in the presence or absence of SR4835 inhibition.

      We are actively pursuing experiments to identify new synthetic lethal targets by CRISPR and drug screens in CDK12 loss models and hope to report those in a future study.

      Reviewer #3 (Recommendations for the authors):

      As discussed above, the authors may wish to adjust their terminology to "CDK12-altered" rather than "CDK12 lost" or "CDK12-inactivated" to leave open the possibility that some tumors may retain residual CDK12 function or adopt neomorphic functions.

      Thank you for the additional comments and feedback. The possibility of neomorphic CDK12 allele function is important. As our models were all complete protein loss mutations, we decided to retain “biallelic loss” as our preferred nomenclature, but the note is well taken.

      The plots in Figures 1f-h are interesting and suggest that certain cancer genes (especially oncogenes) are recurrently gained in CDK12-altered tumors. It may be interesting to look at this on the individual level rather than the cohort level to see whether any groups of oncogenes tend to be gained together in an individual patient - this could inform whether certain combinations of cancer drivers cooperate with CDK12 alteration to drive oncogenesis.

      Thank you for the idea of looking at the patient-level for TDP-enriched oncogenes. A preliminary assessment did not identify recurrent co-gained oncogenes. We will continue these analyses as additional patient tumors with CDK12 alterations are identified. 

      The finding that AR gene or enhancer are recurrently gained with TDP is interesting and I am curious whether the authors have thoughts on whether these alterations can also be seen in the 1-2% of CDK12altered primary prostate cancers that are treatment naïve, and where AR pathway alterations are not as frequently seen.

      We did not focus on CDK12 altered primary prostate cancers, but we did check if there is AR amplification enrichment in the 6 CDK12<sup>BAL</sup> cases of the TCGA-PRAD dataset and did not identify enrichment. However, with such small numbers we would hesitate to draw any hard conclusions. 

      It could be interesting to more comprehensively characterize some of the CDK12 KO-adapted lines in Figure 5 (e.g. by WES or WGS) to determine whether they exhibit the TDP and/or whether they have acquired any secondary mutations that allow them to adapt to CDK12 loss.

      We are planning to do further genomics characterization of the CDK12-KO lines and will hopefully include that in a future study. Genomic analyses of the 22Rv1 clones (see copy number plots in Fig. S5c) did not identify a TDP. We plan to repeat the genomic assessments over additional cell passages and we have planned additional experiments designed to understand why some cells tolerate CDK12 loss and others do not.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Reviewer #1 (Public review):

      Hurtado et al. show that Sox9 is essential for retinal integrity, and its null mutation causes the loss of the outer nuclear layer (ONL). The authors then show that this absence of the ONL is due to apoptosis of photoreceptors and a reduction in the numbers of other retinal cell types such as ganglion cells, amacrine cells, and horizontal cells. They also describe that Müller Glia undergoes reactive gliosis by upregulating the Glial Fibrillary Acidic Protein. The authors then show that Sox9+ progenitors proliferate and differentiate to generate the corneal cells through Sox9 lineage-tracing experiments. They validate Sox9 expression and characterize its dynamics in limbal stem cells using an existing single-cell RNA sequencing dataset. Finally, the authors argue that Sox9 deletion causes progenitor cells to lose their clonogenic capacity by comparing the sizes of control and Sox9-null clones. Overall, Hurtado et al. underline the importance of Sox9 function in retinal and corneal cells.

      Strengths:

      The authors have characterized a myriad of striking phenotypes due to Sox9 deletion in the retina and limbal stem cells which will serve as a basis for future studies.

      Weaknesses:

      Hurtado et al. investigate the importance of Sox9 in the retina and limbal stem cells. However, the overall experimental narrative appears dispersed.

      (1) The authors begin by characterizing the phenotype of Sox9 deletion in the retina and show that the absence of the ON layer is due to photoreceptor apoptosis and a reduction in other retinal cell types. The authors also note that Müller glia undergoes gliosis in the Sox9 deletion condition. These striking observations are never investigated further, and instead, the authors switch to lineage-tracing experiments in the limbus that seem disconnected from the first three figures of the paper. Another example of this disconnect is the comparison of Sox9 high and Sox9 low populations using an existing scRNA-seq dataset and the subsequent GO term analysis, which does not directly tie in with the lineage-tracing data of the succeeding Sox9∆/∆ experiments.

      We thank the reviewer for their thoughtful observations. We would like to clarify the rationale behind the structure of our study and how the different parts are conceptually connected.

      Our central aim was to investigate the role of Sox9 in the adult eye. Given that Sox9 has been extensively studied during embryonic development, we specifically chose to use an inducible conditional knockout strategy (CAG-CreERTM) in order to assess its function postnatally, in the adult eye. This approach revealed a severe retinal phenotype, whereas the cornea showed no overt phenotype. A major strength of our experimental design is that it allowed us to examine the role of Sox9 specifically in the adult eye, avoiding confounding effects from embryonic development. Nevertheless, this approach entails an inherent limitation: the mosaic nature of the CAG-CreERTM system leads to substantial variability in both the extent and distribution of Sox9 inactivation among individual animals. We invested considerable effort over extended periods to obtain reliable and biologically meaningful data despite this variability. We did not proceed further because this mosaicism poses a significant limitation when attempting to dissect downstream mechanisms in a consistent and reproducible manner, making it extremely challenging to perform in-depth mechanistic studies.

      Regarding the cornea, given the absence of a clear phenotype upon Sox9 deletion, we expanded our investigation by adding lineage-tracing and transcriptomic analyses to better understand Sox9’s potential role in adult limbal epithelial stem cells. These additional experiments provided valuable insight into Sox9 function in the adult cornea, even in the absence of gross morphological changes. Thus, while the retinal and corneal data stem from different experimental approaches, they are unified by a shared goal: understanding the celltype-specific and tissue-specific functions of Sox9 in the adult eye.

      To ensure that other readers do not perceive this apparent disconnect, and overstate our conclusions, we have modified the manuscript.  In the Introduction section, we have included the main findings from studies conducted to date on the role of Sox9 in the cornea and retina, and we have removed the corresponding section from the Discussion. We believe it is now clear that our study focuses on the role of Sox9 in the adult eye, in contrast to previous studies, which focused on the developing eye.

      In the Discussion section, we have added a new paragraph at the beginning and end that explicitly addresses the relationship between the retinal and limbal findings, illustrating how a single transcription factor can play distinct roles in different tissues within the same organ.

      Regarding the reviewer’s comment that the scRNA-seq analyses appear disconnected from the lineage-tracing data, we respectfully disagree. These analyses provide independent transcriptional confirmation that Sox9 is a marker of limbal stem cells, reinforcing the conclusions drawn from our in vivo experiments. These approaches are complementary and they converge on the same biological insight: Sox9 marks a population with stem-like properties in the adult limbus. Nevertheless, we acknowledge the reviewer’s concern and have moderated the tone of our statements in the revised version of the manuscript to better reflect the supporting nature of the scRNA-seq data, without overstating its functional implications.

      (2) A major concern is that a single Sox9∆/∆ limbal clone has a sufficiently large size, comparable to wild-type clones, as seen in Figure 6D. This singular result is contrary to their conclusion, which states that Sox9-deficient stem cells minimally contribute to the maintenance of the cornea.

      We thank the reviewer for this important observation.

      Ligand-independent activity of Cre-ER fusion proteins has been repeatedly reported in various mouse models (Vooijs et al., 2001; Kemp et al., 2004; Haldar et al., 2009). This basal recombinase activity is thought to arise from inappropriate nuclear translocation or proteolysis of the Cre-ER fusion protein, leading to low-level recombination even in the absence of tamoxifen. Consistent with this, prior studies using the same CAGG-CreERTM; R26R-LacZ system for clonal analysis in the cornea have observed sparse reporter expression before tamoxifen administration (Dorà et al., 2015).

      In line with these findings, we also detected minimal background LacZ staining in Sox9Δ/ΔLacZ corneas (mean surface area: 0.85%; n = 8 eyes). This low-level staining likely reflects recombination events in transient amplifying or more differentiated cells, which are not expected to generate long-lived clones. However, in the rare instance of a large clone, as shown in Figure 6D, we believe that a spontaneous recombination event may have occurred in a bona fide limbal stem cell, giving rise to a sustained contribution. To rigorously address this potential artefact and assess the true contribution of Sox9-deficient stem cells, we conducted a comparative analysis of 8 control (Sox9Δ/+-LacZ) and 5 mutant (Sox9Δ/ΔLacZ) corneas. This analysis revealed a highly significant 8-fold reduction in the LacZpositive surface area in mutant samples (Sox9Δ/+-LacZ: 6.65 ± 1.77%; Sox9Δ/Δ-LacZ: 0.85 ± 0.85%; paired t-test, p = 0.00017; Figs. 6E and F; Table S12).

      We chose to include the image of the large clone in the main figure precisely because it does not align with our working hypothesis. We believe that showing such exceptions transparently is scientifically important and may be valuable for other researchers using similar inducible systems. Nonetheless, based on previous literature, the number of samples analyzed, and the statistically significant reduction in clonal contribution, we maintain that the observed phenotype reflects a true biological effect of Sox9 loss, supporting our conclusion that Sox9-deficient stem cells contribute minimally to corneal maintenance. To make that point clearer, we have introduced the following sentence in lines 462-464 of the revised version of the manuscript.

      “A possible explanation for this clone may be that spontaneous ligand-independent activity of Cre-ER fusion may have occurred in a bona fide limbal stem cell, as previously reported (Vooijs et al., 2001; Kemp et al., 2004; Haldar et al., 2009, Dorà et al., 2015).”

      Reviewer #2(Public revciew):

      Sox9 is a transcription factor crucial for development and tissue homeostasis, and its expression continues in various adult eye cell types, including retinal pigmented epithelium cells, Müller glial cells, and limbal and corneal basal epithelia. To investigate its functional roles in the adult eye, this study employed inducible mouse mutagenesis. Adult-specific Sox9 depletion led to severe retinal degeneration, including the loss of Müller glial cells and photoreceptors. Further, lineage tracing revealed that Sox9 is expressed in a basal limbal stem cell population that supports stem cell maintenance and homeostasis. Mosaic analysis confirmed that Sox9 is essential for the differentiation of limbal stem cells. Overall, the study highlights that Sox9 is critical for both retinal integrity and the differentiation of limbal stem cells in the adult mouse eye.

      Strengths:

      In general, inducible genetic approaches in the adult mouse nervous system are rare and difficult to carry out. Here, the authors employ tamoxifen-inducible mouse mutagenesis to uncover the functional roles of Sox9 in the adult mouse eye.

      Careful analysis suggests that two degeneration phenotypes (mild and severe) are detected in the adult mouse eye upon tamoxifen-dependent Sox9 depletion. Phenotype severity nicely correlates with the efficiency of Cre-mediated Sox9 depletion.

      Molecular marker analysis provides strong evidence of Mueller cell loss and photoreceptor degeneration.

      A clever genetic tracing strategy uncovers a critical role for Sox9 in limbal stem cell differentiation.

      Weaknesses:

      (1) The Introduction can be improved by explaining clearly what was previously known about Sox9 in the eye. A lot of this info is mentioned in a single, 3-page long paragraph in the Discussion. However, the current study's significance and novelty would become clearer if the authors articulated in more detail in the Introduction what was already known about Sox9 in retina cell types (in vitro and in vivo).

      We appreciate this insightful comment. Following the reviewer`s suggestion, we have reorganized the manuscript to provide a clearer scientific context in the Introduction. Specifically, we have moved the relevant background information on Sox9 in different retinal cell types—previously included in a single, extended paragraph in the Discussion—into the Introduction. This helps to better frame our study within the context of existing knowledge.

      Additionally, we have emphasized more explicitly that our work does not focus on embryonic development, as most previous studies on Sox9 have done, but instead investigates its role in the adult mouse retina and limbus/cornea. We believe this represents an important and novel aspect of our study, as the mechanisms of retinal maintenance and limbal stem cell differentiation in the adult have been less extensively studied.

      (2) Because a ubiquitous tamoxifen-inducible CreER line is employed, non-cell autonomous mechanisms possibly contribute to the observed retina degeneration. There is precedence for this in the literature. For example, RPE-specific ablation of Otx2 results in photoreceptor degeneration (PMID: 23761884). Have the authors considered the possibility of non-cell autonomous effects upon ubiquitous Sox9 deletion?

      Given the similar phenotypes between animals lacking Otx2 and Sox9 in specific cell types of the eye, the authors are encouraged to evaluate Otx2 expression in the tamoxifen-induced Sox9 adult retina.

      We appreciate the insightful comment of the reviewer regarding the potential contribution of non-cell autonomous mechanisms to the retinal degeneration observed upon ubiquitous Sox9 deletion. We agree that this is an important consideration, particularly in the context of findings showing that RPE-specific deletion of Otx2 results in secondary photoreceptor degeneration.

      However, we would like to emphasize that RPE-specific deletion of Sox9 does not lead to photoreceptor loss or retinal degeneration, as previously shown (Masuda et al., 2014; Goto et al., 2018; Cohen-Tayar et al., 2018) [PMID: 24634209; PMID: 29609731; PMID: 29986868]. In addition, it was shown that Sox9 deletion in the RPE caused downregulation of visual cycle genes but did not compromise photoreceptor integrity or survival. Interestingly, Otx2 expression was found to be upregulated in the absence of Sox9, further supporting the view that Sox9 is not a simple upstream regulator of Otx2 in the adult RPE (Matsuda, 2014). These findings suggest that RPE dysfunction alone cannot account for the severe retinal phenotype we observe in our model.

      In our study, we observed that photoreceptor degeneration correlates strongly with the depletion of Sox9 Müller glial cells. Given the well-established supportive and neuroprotective roles of Müller glia, we interpret the retinal degeneration in our model to be primarily a consequence of Müller cell dysfunction (confirmed by the loss of Müller glia markers, such as SOX8 and S100). This interpretation is further supported by previous studies showing that selective ablation of Müller glia can lead to photoreceptor degeneration through cell-autonomous mechanisms (Shen et al., 2012) [PMID: 23136411].

      Nevertheless, we agree that this possibility deserves further investigation, and we have acknowledged it in the following paragraph that has been added to the Discussion section (lines 511-523 of the revised ms):

      “An important consideration in our model is the potential contribution of non-cell autonomous mechanisms to photoreceptor degeneration. Sox9 is expressed in both MG and RPE cells, and both cell types are known to support photoreceptor viability (Poché et al., 2008; Masuda et al., 2014). Notably, Sox9 and Otx2 cooperate to regulate visual cycle gene expression in the RPE (Masuda et al., 2014), and loss of Otx2 specifically in the adult RPE leads to secondary photoreceptor degeneration through non-cell autonomous mechanisms (Housset et al., 2013). However, RPE-specific deletion of Sox9 does not induce retinal degeneration and in fact results in Otx2 upregulation (Masuda et al., 2014; Goto et al., 2018; Cohen-Tayar et al., 2018), suggesting that Sox9 is not an upstream regulator of Otx2 in this context. Further investigation into the molecular and cellular interactions between MG, RPE, and photoreceptors may help to clarify the indirect pathways contributing to degeneration in the absence of Sox9.”

      Consistent with the above, a new citation has been included:

      Housset M, Samuel A, Ettaiche M, Bemelmans A, Béby F, Billon N, Lamonerie T. 2013. Loss of Otx2 in the adult retina disrupts retinal pigment epithelium function, causing photoreceptor degeneration. J Neurosci 33:9890–904. doi:10.1523/JNEUROSCI.1099-13.2013.

      (3) The most parsimonious explanation for the dual role of Sox9 in retinal cell types and limbal stem cells is that the cell context is different. For example, Sox9 may cooperate with TF1 in photoreceptors, TF2, in Mueller cells, and TF3 in limbal stem cells, and such cell typespecific cooperation may result in different outcomes (retinal integrity, stem cell differentiation). The authors are encouraged to add a paragraph to the discussion and share their thoughts on the dual role of Sox9.

      We thank the reviewer for this thoughtful and constructive suggestion. In , we have added a paragraph at the end of the Discussion addressing the potential dual role of Sox9 in the cornea and retina. In this new section, we discuss how Sox9 might exert distinct functions depending on the cellular context, possibly through interactions with different transcriptional partners in specific cell types. This may help explain the contrasting roles of Sox9 in maintaining retinal integrity versus regulating stem cell differentiation in the limbal epithelium.

      (4) One more molecular marker for Mueller glial cells would strengthen the conclusion that these cells are lost upon Sox9 deletion.

      We thank the reviewer for this constructive suggestion. To reinforce our conclusion that most Müller glial cells are lost following Sox9 deletion, we analysed the expression of S100, a well-established cytoplasmic marker of Müller glia. As S100 is primarily localized to the innermost Müller cell processes and not restricted to cell bodies, direct cell counting was not feasible. Instead, we quantified the S100+ signal intensity across defined retinal surface areas. This analysis revealed a statistically significant reduction in S100 signal in Sox9<sup>Δ/Δ</sup> retinas compared to controls. These new data, included in the revised Figure 1 (panels F and G), support and extend our previous observations using SOX8, further confirming the loss of Müller glial cells in Sox9-deficient retinas.

      We have also modified the manuscript based on this new evidences as follows:

      In the Results section, lines 168-177 of the revised ms, we have added the following paragraph: “To independently validate the loss of MG cells in Sox9-deficient retinas, we examined the expression of S100, a cytoplasmic marker that labels the processes of adult Müller cells. In control retinas, strong S100 immunoreactivity was observed across the inner retina, outlining the typical radial projections of Müller glia (Fig. 1F). In contrast, Sox9Δ/Δ retinas with an extreme phenotype exhibited a marked reduction in S100 signal (Fig. 1G). Given the diffuse cytoplasmic localization of S100, we quantified its expression by measuring the fluorescence signal within a defined surface area of the retina. This analysis revealed a statistically significant reduction in S100 signal intensity in mutant samples (including both mild and extreme phenotypes) compared to controls (Fig. 1G; Table S4), further supporting the loss of MG cells upon Sox9 deletion.”

      In Methods, line 684 of the revised ms, the anti-S100 antibody reference and its working dilution have been added.

      (5) Using opsins as markers, the authors conclude that the photoreceptors are lost upon Sox9 deletion. However, an alternate possibility is that the photoreceptors are still present and that Sox9 is required for the transcription of opsin genes. In that case, Sox9 (like Otx2) may act as a terminal selector in photoreceptor cells. This point is particularly important because vertebrate terminal selectors (e.g., Nurr1, Otx2, Brn3a) initially affect neuron type identity and eventually lead to cell loss.

      We perfectly understand the reviewer’s point. However, we believe that the possibility that Sox9 regulates opsin gene expression without affecting photoreceptor survival is very unlikely in our model. The primary evidence comes from the histological analysis shown in Figure 1B, where hematoxylin and eosin staining clearly demonstrates the complete loss of the ONL in Sox9<sup>Δ/Δ</sup> retinas exhibiting the extreme phenotype. Similarly, DAPI counterstain also evidences the lack of the ONL in many of our immunofluorescence images of these samples.  This morphological disappearance of the ONL strongly supports the conclusion that photoreceptor cells are not merely transcriptionally silent but are physically absent.

      Furthermore, TUNEL assays in two retinas with a mild phenotype revealed extensive apoptosis within the ONL, suggesting a progressive degeneration process rather than a selective transcriptional effect. While we acknowledge that transcriptional regulation of opsin genes by Sox9 cannot be entirely ruled out, the observed phenotype is more consistent with a structural loss of photoreceptors rather than a change in their molecular identity alone. Therefore, our data support the interpretation that Sox9 is required for photoreceptor survival, likely through non-cell autonomous mechanisms related to Müller glia dysfunction, rather than acting as a terminal selector within photoreceptor cells themselves.

      (6) Quantification is needed for the TUNEL and GFAP analysis in Figure 3.

      We have quantified the GFAP immunofluorescence signal across defined surface areas of the retina and found a statistically significant increase in GFAP expression in Sox9<sup>Δ/Δ</sup> mutants compared to controls (Mann-Whitney U test, P = 0.0240; n = 4 controls, 10 mutants). These quantification data are now included in the revised Figure 3.

      Regarding the TUNEL assay, although extensive apoptosis was clearly observed in two Sox9<<sup>Δ/Δ</sup> retinas with a mild phenotype (as shown in Figure 3A), this pattern was not consistent across the full study mouse cohort. Out of 15 mutant samples analyzed (5 of them previously analyzed and 10 additional ones that have been newly analyzed), only two exhibited this pronounced apoptotic pattern. However, in the remaining 13 mutants, we did observe a small but statistically significant increase in the number of TUNEL+ cells compared to controls (zero-inflated Poisson test, P = 0.028, n = 5 controls, 13 mutants). These results are now included in Figure 3 and in Tables S7 and S8.

      This pattern likely reflects the transient nature of apoptosis in the degenerative process, which may occur rapidly and thus be difficult to capture consistently at a single time point. Nevertheless, the quantification supports our conclusion that Sox9 loss is associated with increased photoreceptor cell death.

      Based on the above, we have included the following paragraphs in the Results section of the manuscript:

      In lines 224-252 of the revised ms, the final version of the paragraph is as follows: “Since photoreceptors are absent in severely affected Sox9-mutant retinas, we conducted TUNEL assays to study the role of cell death in the process of retinal degeneration. In control samples (n=5), almost no TUNEL signal was observed in the retina. In contrast, Sox9<sup>Δ/Δ</sup> mice (n=15) showed numerous TUNEL+ cells, mainly located in the persisting ONL, indicating that photoreceptor cells were dying (Fig. 3A). Although extensive TUNEL staining in the ONL was clearly observed in two Sox9<sup>Δ/Δ</sup> retinas with mild phenotypes, this pattern was not consistently present across the full cohort. In the remaining 13 mutant retinas, we observed a modest but noticeable increase in the number of apoptotic cells compared to controls (Fig. 3B; Table S7). Despite a high frequency of zero counts (particularly among controls), the difference between groups reached statistical significance when analyzed using a zeroinflated Poisson model (P = 0.028; n = 5 controls, 13 mutants). These findings suggest that photoreceptor apoptosis following Sox9 deletion may occur acutely and within a narrow temporal window, making it challenging to capture the full degenerative process at a single time point”.

      Lines 263-269 of the revised ms: “To support these observations quantitatively, we measured GFAP fluorescence intensity across defined retinal surface areas in control and Sox9<sup>Δ/Δ</sup> mice (Fig. 3D; Table S8). This analysis revealed a statistically significant increase in GFAP signal in mutant retinas compared to controls (Mann-Whitney U test, P = 0.0240; n = 4 controls, 10 mutants). These results are consistent with a progressive gliotic  following Sox9 deletion and provide further evidence that MG cells become reactive in the absence of Sox9”.

      Similarly, the section “Estimation of the percentage of tamoxifen-induced, Cre-mediated recombination” has been expanded as follows:

      Lines 660-665 of the revised ms: “In parallel, to quantify GFAP expression as a measure of MG reactivity, we analyzed GFAP immunofluorescence intensity across defined retinal surface areas. Given the cytoplasmic distribution of GFAP within glial processes, direct cell counting was not feasible. Instead, fluorescence intensity was measured using ImageJ, within full-thickness retinal regions in 20x microphotographs of a retinal sections stained for GAFP. The total GFAP signal was normalized to the measured area for each section”.

      (7) Line 269-320: The authors examined available scRNA-Seq data on adult retina. This data provides evidence for Sox9 expression in distinct cell types. However, the dataset does not inform about the functional role of Sox9 because Sox9 mutant cells were not analyzed with RNA-Seq. Hence, all the data that claim that this experiment provides insights into possible Sox9 functional roles must be removed. This includes panels F, G, and H in Figure 5. In general, this section of the paper (Lines 269-320) needs a major revision. Similarly, lines 442-454 in the Discussion should be removed.

      We thank the reviewer for this important observation. We agree that the scRNA-Seq dataset used in this section does not include Sox9 mutant cells and therefore does not allow us to assess the consequences of Sox9 loss-of-function. However, we believe that this analysis still provides valuable complementary information. Specifically, it confirms that Sox9 is expressed in a distinct population of limbal stem cells, and that its expression dynamically changes along differentiation trajectories. Although we do not infer causality or phenotypic consequences, the ability to observe how gene expression programs shift as Sox9 is downregulated offers insights into potential transcriptional programs associated with Sox9 activity.

      We have carefully revised Lines 269–320 to remove any overinterpretations, and eliminated the corresponding lines in the Discussion (Lines 442–454). However, we have retained Panels G, and H in Figure 5 with updated text that reflect the descriptive nature of these findings, specifically to illustrate that the Sox9-positive cell signature is consistent with a stem cell genetic program, and that when Sox9 is downregulated some gene pathways involved in stem cell differentiation are upregulated.

      Reviewer #1 (Recommendations for the authors):

      Major points

      (1) Figure 1C shows the proportions of Sox9+cells that express Sox8 in control, mild and extreme phenotypes. However, as no quantitative classification of mild and extreme phenotypes is reported along with Figure 1A, the large standard deviation for Sox9∆/∆ mild retina might be due to a misclassification of the sample. Therefore, the authors must ascribe each sample to "mild" or "extreme" based on a quantitative metric.

      We appreciate the reviewer’s suggestion to clarify the classification criteria used to distinguish “mild” and “extreme” phenotypes in Sox9<sup>Δ/Δ</sup> retinas. As noted, our classification was based on a qualitative, phenotypic assessment of retinal morphology in hematoxylin/eosin-stained sections. Specifically, retinas were classified as “extreme” when the outer nuclear layer (ONL) was completely absent, and as “mild” when the ONL was present, although often reduced in thickness. This classification reflects the observable structural depletion of the ONL and aligns well with the extent of Sox9 loss in Müller glial cells, as shown in Figure 1. We acknowledge that some variability exists within the “mild” group, likely due to differences in recombination efficiency and the mosaic nature of tamoxifen-induced deletion.

      The phenotypic classification of each individual sample is explicitly provided in Supplementary Table S1. We have also added a statement in the Results section clarifying that this classification was based on qualitative histological criteria rather than a numerical threshold.

      Lines 104-113 of the revised ms: “We categorized Sox9<sup>Δ/Δ</sup> retinas into “mild” and “extreme” phenotypes in order to facilitate interpretation of our data. Clasification was based on a qualitative assessment of ONL integrity in histological sections. Specifically, samples were classified as “extreme” when the ONL was completely depleted, and as “mild” when the ONL persisted, albeit variably reduced in thickness. This phenotypic classification reflects observable structural differences rather than a fixed quantitative threshold. Some variability exists within the “mild” group, likely due to differences in recombination efficiency and the mosaic nature of tamoxifen-induced Cre-mediated Sox9 deletion”

      (2) The authors infer Sox9 high and Sox9 low groups of limbal stem cells using an existing scRNA-seq dataset. However, an immunohistology-based validation of this difference is missing. Given that limbal stem cells express Sox9, the authors must examine the heterogeneity in Sox9 levels within the Sox8+ population to demonstrate their claim: "...Sox9 expression decreases as transiently amplifying progenitors undergo progressive differentiation from limbal to peripheral corneal cells." in Line 292. Ideally, this must be further validated using differentiation markers corresponding to CB and ILB populations that show lower Sox9 expression according to the pseudotime graph.

      To validate the Sox9 expression results obtained with scRNA-seq, we performed double immunofluorescence for Sox9 and P63, the latter expressed by the basal cells of the limbal epithelium, but not by transient amplifying cells covering the corneal surface (Pellegrini et al., 2001, https://www.pnas.org/doi/abs/10.1073/ pnas.061032098). These results can be observed in the new panel 5F. Accordingly we have included a new paragraph in lines 369-396 of the revised version of the ms:

      “To validate these results, we decided to closely examine Sox9 expression in the limbus using immunofluorescence. Previous analyses revealed that the outer limbus is approximately 100 μm wide, while the inner limbus is wider, around 240 μm (Altshuler 2021). We observed that in the region corresponding to the OLB, most cells showed strong Sox9 expression. In the area corresponding to the ILB, this immunoreactivity appeared weaker in the basal layer (corresponding to the ILB proper), and no expression was detected in the suprabasal layers (flattened cells; Fig 5F left). Double immunofluorescence for SOX9 and P63, which is expressed in basal cells of the limbal epithelium, but not by transient amplifying cells covering the corneal surface (Pellegrini et al., 2001) revealed that Sox9 expression was restricted to P63-positive cells (Fig 5F right). These observations confirm that Sox9 is expressed in a basal cell population within both the OLB and ILB, and that its expression decreases in differentiated transient amplifying cells. ”

      We also have deleted  “This expression pattern is consistent with our immunofluorescence observations" from line 356 of the revised ms.

      (3) The authors' claim of "...Sox9-null cells cannot survive or proliferate as well as their wildtype neighbors, and are hence outcompeted over time, leading to an essentially wild-type cornea" does not seem very convincing in the light of Fig.6D and S3B where Sox9 deletion can still allow for a large LacZ+ clone. Their claim of wild-type cornea due to out-competing neighbors must be validated by increasing the number of Sox9-null progenitors, which can be tested by administering tamoxifen for a significantly longer duration, leading to a majority Sox9 deficient progenitor population, and then examining limbal and corneal defects.

      As previously discussed, we observed only one instance of a large LacZ+ clone across 8 Sox9<sup>Δ/Δ</sup>-LacZ eyes. Based on prior reports of ligand-independent Cre activity (Vooijs et al., 2001; Kemp et al., 2004; Haldar et al., 2009; Dorà et al., 2015), we believe this rare event likely resulted from spontaneous recombination in a bona fide limbal stem cell, independent of tamoxifen administration. For this reason, we do not expect that increasing the dose or duration of tamoxifen would eliminate such rare events. Furthermore, due to the mosaic and highly variable recombination efficiency of the CAGG-CreERTM system in the adult eye (see McMahon et al., 2008), attempting to increase the TX dosage would likely lead to systemic toxicity or lethality, without guaranteeing full inactivation of the gene in the limbus. Thus, this system is not well-suited for generating a fully Sox9-deficient limbal epithelium. To overcome this limitation, we crossed our mice with the R26R-LacZ reporter line to track the clonal behavior of Sox9-deficient cells. In control animals (Sox9Δ/+-LacZ), LacZ+ stripes originating from limbal stem cells are readily observed. In contrast, in Sox9Δ/Δ-LacZ mutants, these clones are either absent or drastically reduced. This suggests that Sox9-null cells have a severely impaired ability to form and sustain clones. To rigorously quantify this effect, we compared 8 control and 5 mutant corneas, revealing a highly significant 8-fold reduction in LacZ-positive area in the mutants (6.65 ± 1.77% vs. 0.85 ± 0.85%; p = 0.00017; Fig. 6F; Table S12; Supp. Fig. X???), supporting our claim that Sox9null cells cannot survive or proliferate as well as their wild-type neighbors, and are hence outcompeted over time, leading to an essentially wild-type cornea.

      Minor points

      (1) Quantification for Figure 2C and 2D is missing.

      We have now included quantification of BRN3A+ retinal ganglion cells (Figure 2E) across control and Sox9<sup>Δ/Δ</sup> retinas. Cell counts were performed on matched retinal sections, and the difference between groups was found to be statistically significant through Mann–Whitney U test (Table S5).

      Regarding PAX6/AP2a, we quantified inner retinal neurons by analyzing AP2α+ amacrine cells and PAX6+/AP2α- horizontal cells as distinct subpopulations, rather than simply comparing total PAX6 or AP2α immunoreactivity. This approach allowed us to better resolve specific neuronal subtype changes. Both populations showed a statistically significant reduction in Sox9-deficient retinas relative to controls. The quantification for these analyses has now been incorporated into the revised Figure 2F and G (Table S6).

      Consequently with the above, the following paragraph of the Results section (line 210 of the revised ms:

      “We also studied the status of other retinal cell types. The transcription factor BRN3A was used to identify ganglion cells (Nadal-Nicolás et al., 2009), which were shown to decrease in number in the mutant retinas, compared to control ones (Fig. 2C). Similarly, double immunodetection of the transcription factors PAX6 and AP2A was used to identify both amacrine and horizontal cells, as previously described (Marquardt et al., 2001; Barnstable et al., 1985; Edqvist and Hallböök, 2004), showing a similar reduction in both cell types in degenerated retinas (Fig. 2D).”

      Has been modified as follows:

      “We also studied the status of other retinal cell types. The transcription factor BRN3A was used to identify ganglion cells (Nadal-Nicolás et al., 2009), which were shown to decrease in number in the mutant retinas, compared to control ones (Figs. 2C and 2D and Table S5; n = 5 controls, n = 12 mutants; Mann-Whitney U test, P = 3 × 10<sup>-4</sup>). Similarly, double immunodetection of the transcription factors PAX6 and AP2A was used to identify both amacrine and horizontal cells (Fig. 2E), as previously described (Marquardt et al., 2001; Barnstable et al., 1985; Edqvist and Hallböök, 2004), showing a similar reduction in both cell types in degenerated retinas (Figs. 2F and 2G and Table S6; AP2α+ amacrine cells: n = 3 controls, n = 8 mutants;  2-sample T-tests P = 0.029; PAX6+/AP2α− horizontal cells: n = 3 controls, n = 8 mutants; Mann-Whitney U test P = 0.021). These findings indicate that the loss of Sox9 in the adult retina ultimately leads to the degeneration of multiple inner retinal neuronal populations, beyond the previously described effects on photoreceptors and Müller glia.

      (2) Figure 4G & H: The authors must mention that the dashed lines enclose the limbal area.

      Done

      (3) The authors infer from an existing scRNA-seq dataset that OLB cells have high Sox9 expression as compared to ILB and corneal populations. However, Figures 4A and B do not indicate the anatomical positions of these cell types. The authors must label these for the reader's reference as they state that "[Sox9] expression pattern is consistent with our immunofluorescence observations" in Line 280.

      As previously indicated, we have generated a new panel 5F and a corresponding paragraph to illustrate Sox9 expression pattern in the limbus. Accordingly, we have removed the sentence from line 280.

      (4) Quantification for Figures 6A and 6B is missing.

      We have quantified the number of Sox9 and P63 positive cells in the limbus between mutant and control corneas and found no difference in the number of positive cells. We have included these data in new panel 6C and Table S11.

      Reviewer #2 (Recommendations for the authors):

      Line 24: "synapsis" should be "synapses".

      Done

      (1) Consider starting a new paragraph after line 30.

      Done

      (2) Lines 42-48: make clear that this paragraph provides information only for HUMAN SOX9.

      We now distinguish which studies were conducted in humans and which in mice.

      (3) Line 55: explain to the non-expert reader what the "visual cycle" is.

      Done (lines 64-65 of the revised ms)

      (4) Line 66: consider "inactivate" instead of "suppress".

      We substituted “suppress” with “inactivate”

      (5) Line 90-92: ONLY PCR for the cGMP will provide formal evidence that this is not present in the mouse line.

      We agree with the reviewer that PCR genotyping is the most straightforward method to exclude the presence of the Pde6<sup>brd</sup>1 allele. Although retinal degeneration was never observed in untreated or control animals in our study, we have now removed the term “formal possibility” from the text to better reflect this limitation.

      We have modified the following paragraph (page 116 in the revised version of the manuscript): “Retinal degeneration was never observed in mice that had not been tamoxifen-treated, nor any other controls, eliminating the formal possibility that the retinal degeneration allele of photoreceptor cGMP phosphodiesterase 6b (Pde6brd1) was present in our mice (Bowes et al., 1990).”

      As follows: “Retinal degeneration was never observed in mice that had not been tamoxifentreated, nor any other control groups, making the presence of the retinal degeneration allele of photoreceptor cGMP phosphodiesterase 6b (Pde6<sup>brd1</sup>) unlikely in our mice (Bowes et al., 1990). However, we acknowledge that definitive exclusion of this possibility would require PCR-based genotyping.”

      (6) Line 160-166: This paragraph needs a conclusion.

      We agree with the reviewer and have added the following sentence at the end of the paragraph:

      “These findings indicate that the loss of Sox9 in the adult retina ultimately leads to the degeneration of multiple inner retinal neuronal populations, beyond the previously described effects on photoreceptors and Müller glia”

      (7) Line: 240-265: This paragraph ends without a conclusion.

      We have include the following conclusion:

      “Thus, Sox9 is expressed in a basal limbal stem cell population with the ability to form two types of long-lived cell clones involved in stem cell maintenance and homeostasis.”

      (8) In Results, it needs to be specified when exactly in adulthood the tamoxifen treatment started. This information is only provided in the Methods.

      We have specified the age of the mice at the onset of tamoxifen treatment (two months)  and included it in the schemes of Figs 1A, 4C, 4H, 6E.

      (9) Line 250: Because live imaging is not conducted, the word "dynamics" is not suitable.

      We substituted “dynamics” with “contribution”

      (10) Panel C in Figure 6 is nice and helpful. Consider adding a similar panel in Figure 1.

      Done.

      (11) Line 420: is this the human Sox9 enhancer?

      Yes. It is a human enhancer. We have indicated it in the text.

      (12) Line 459: typo "detected tissue".

      Corrected

      (13) Line 448 and 468: citations are needed.

      Line 448 is deleted in the revised version of the ms.

      (14) 479: typo "clones clones'.

      Corrected.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Reviewer #1 (Public review):

      This work computationally characterized the threat-reward learning behavior of mice in a  recent study (Akiti et al.), which had prominent individual differences. The authors  constructed a Bayes-adaptive Markov decision process model and fitted the behavioral data  by the model. The model assumed (i) hazard function starting from a prior (with free mean  and SD parameters) and updated in a Bayesian manner through experience (actually no real  threat or reward was given in the experiment), (ii) risk-sensitive evaluation of future  outcomes (calculating lower 𝛼 quantile of outcomes with free 𝛼 parameter), and (iii) heuristic  exploration bonus. The authors found that (i) brave animals had more widespread hazard  priors than timid animals and thereby quickly learned that there was in fact little real threat,  (ii) brave animals may also be less risk-aversive than timid animals in future outcome  evaluation, and (iii) the exploration bonus could explain the observed behavioral features,  including the transition of behavior from the peak to steady-state frequency of bout. Overall,  this work is a novel interesting analysis of threat-reward learning, and provides useful  insights for future experimental and theoretical work. However, there are several issues that I  think need to be addressed.

      Strengths:

      (1) This work provides a normative Bayesian account for individual differences in  braveness/timidity in reward-threat learning behavior, which complements the analysis by  Akiti et al. based on model-free threat reinforcement learning.

      (2) Specifically, the individual differences were characterized by (i) the difference in the  variance of hazard prior and potentially also (ii) the difference in the risk-sensitivity in the  evaluation of future returns.

      Weakness:

      (1) Theoretically the effect of prior is diluted over experience whereas the effect of biased  (risk-aversive) evaluation persists, but these two effects could not be teased apart in the  fitting analysis of the current data.

      (2) It is currently unclear how (whether) the proposed model corresponds to neurobiological ( rather than behavioral) findings, different from the analysis by Akiti et al.

      We thank reviewer #1 for their useful feedback which we’ve used to improve the discussion,  formatting and clarity of the paper, and for highlighting important questions for future  extensions of our work.

      Major points:

      (1) Line 219

      It was assumed that the exploration bonus was replenished at a steady rate when the animal  was at the nest. An alternative way would be assuming that the exploration bonus slowly  degraded over time or experience, and if doing so, there appears to be a possibility that the  transition of the bout rate from peak to steady-state could be at least partially explained by  such a decrease in the exploration bonus.

      Section 2.2.3 explains the mechanism of the exploration bonus which motivates approach.  We think that the mechanism suggested by the reviewer is, in essence, what is happening in  the model. The exploration pool is indeed depleted over time or bouts of experience at the  object. In the peak confident phase for brave animals and the peak cautious phase for timid  animals, the rate of depletion exceeds the rate of regeneration, since the agent spends only  a single turn at the nest between bouts. In the steady-state phase, the exploration pool has  depleted so much previously that the agent must wait multiple turns at the nest for the pool  to regenerate to a sufficiently high value to justify approaching the object again.

      We have updated section 2.2.3 to explain that agents spend one turn at the nest during peak  phase but multiple turns during steady-state phase. Hopefully, this makes our mechanism  clear:

      “In simulations, when 𝐺(𝑡) is high, the agent has a high motivation to explore the object,  spending only a single turn in the nest state between bouts. In other words, the depletion  from 𝐺0 substantially influences the time point at which approach makes a transition from  peak to steady-state; the steady-state time then depends on the dynamics of depletion  (when at the object) and replenishment (when at the nest). In particular, in the steady-state  phases, the agent must wait multiple turns at the nest for 𝐺(𝑡)  to regenerate so that  informational reward once again exceeds the potential cost of hazard.“

      (2) Line 237- (Section 2.2.6, 2.2.7, Figures 7, 9)

      I was confused by the descriptions about nCVaR. I looked at the cited original literature  Gagne & Dayan 2022, and understood that nCVaR is a risk-sensitive version of expected  future returns (equation 4) with parameter α (α-bar) (ranging from 0 to 1) representing risk  preference. Line 269-271 and Section 4.2 of the present manuscript described (in my  understanding) that α was a parameter of the model. Then, isn't it more natural to report  estimated values of α, rather than nCVaR, for individual animals in Section 2.2.6, 2.2.7,  Figures 7, 9 (even though nCVaR monotonically depends on α)? In Figures 7 and 9, nCVaR  appears to be upper-bounded to 1. The upper limit of α is 1 by definition, but I have no idea why nCVaR was also bounded by 1. So I would like to ask the authors to add more detailed  explanations on nCVaR. Currently, CVaR is explained in Lines 237-243, but actually, there is  no explanation about nCVaR rather than its formal name 'nested conditional value at risk' in  Line 237.

      Thank you for pointing out this error. We have corrected the paper to use nCVaR to refer to  the objective and nCVaR's α, or sometimes just α, to refer to the risk sensitivity parameter  and thus the degree of risk sensitivity.

      (3) Line 333 (and Abstract)

      Given that animals' behaviors could be equally well fitted by the model having both nCVaR ( free α) and hazard prior and the alternative model having only hazard prior (with α = 1), may  it be difficult to confidently claim that brave (/timid) animals had risk-neutral (/risk-aversive)  preference in addition to widespread (/low-variance) hazard prior? Then, it might be good to  somewhat weaken the corresponding expression in the Abstract (e.g., add 'potentially also'  to the result for risk sensitivity) or mention the inseparability of risk sensitivity and prior belief  pessimism (e.g., "... although risk sensitivity and prior belief pessimism could not be teased  apart").

      Thank you for this suggestion, we have duly weakened the wording in the Abstract to say  “potentially more risk neutral”:

      “Some animals begin with cautious exploration, and quickly transition to confident approach  to maximize exploration for reward; we classify them as potentially more risk neutral, and  enjoying a flexible hazard prior. By contrast, other animals only ever approach in a cautious  manner and display a form of  self-censoring; they are characterized by potential risk  aversion and high and inflexible hazard priors.”

      Reviewer #2 (Public Review):

      Shen and Dayan build a Bayes adaptive Markov decision process model with three key  components: an adaptive hazard function capturing potential predation, an intrinsic reward  function providing the urge to explore, and a conditional value at risk (CvaR, closely related  to probability distortion explanations of risk traits). The model itself is very interesting and  has many strengths including considering different sources of risk preference in generating  behavior under uncertainty. I think this model will be useful to consider for those studying  approach/avoid behaviors in dynamic contexts.

      The authors argue that the model explains behavior in a very simple and unconstrained  behavioral task in which animals are shown novel objects and retreat from them in various  manners (different body postures and patterns of motor chunks/syllables). The model itself  does capture lots of the key mouse behavioral variability (at least on average on a  mouse-by-mouse basis) which is interesting and potentially useful. However, the variables in  the model - and the internal states it implies the mice have during the behavior - are  relatively unconstrained given the wide range of explanations one can offer for the mouse  behavior in the original study (Akiti et al). This reviewer commends the authors on an original  and innovative expansion of existing models of animal behaviour, but recommends that the  authors  revise their study to reflect the obvious  challenges . I would also recommend a  reduction in claiming that this exercise gives a normative-like or at least quantitative account  of mental disorders.

      We thank reviewer #2 for highlighting some of the strengths of our paper as well as pointing  out important limitations of Akiti et al’s original study which we’ve inherited as well as some  limitations of our own method. We address their concerns below.

      We have added a paragraph to the discussion discussing the limitations of the state  representation we adopted from Akiti’s study.

      (Reviewer #1 had the same concern, see above) “Motivated by tail-behind versus  tail-exposed in Akiti et al. (2022), we model approach using a dichotomy between cautious  and confident approach states [...]”

      We have reduced the suggestion that our model provides an account of mental disorders in  the abstract.

      Before:

      “On the other hand, “timid” animals, characterized by risk aversion and high and inflexible  hazard priors, display self-censoring that leads to the sort of asymptotic maladaptive  behavior that is often associated with psychiatric illnesses such as anxiety and depression.”

      After:

      “By contrast, other animals only ever approach in a cautious manner and display a form of  self-censoring; they are characterized by potential risk aversion and high and inflexible  hazard priors. “

      My main comment is that this paper is a very nice model creation that can characterize the  heterogeneity rodent behavior in a very simple approach/avoid context (Akiti et al; when a  novel object is placed in an arena) that itself can be interpreted in a multitude of ways. The  use of terms like "exploration", "brave", etc in this context is tricky because the task does not  allow the original authors (Akiti et al) to quantify these "internal states" or "traits" with the  appropriate level of quantitative detail to say whether this model is correct or not in capturing  the internal states that result in the rodent behavior. That said, the original behavioral setup  is so simple that one could imagine capturing the behavioral variability in multiple ways ( potentially without evoking complex computations that the original authors never showed  the mouse brain performs). I would recommend reframing the paper as a new model that  proposes a set of internal states that could give rise to the behavioral heterogeneity  observed in Akiti et al, but nonetheless is at this time only a hypothesis. Furthermore, an  explanation of what would be really required to test this would be appreciated to make the  point clearer.

      We thought very hard about using terms that might be considered to be anthropomorphic  such as ‘timid’ and ‘brave’. We are, of course, aware, of the concerns articulated by  investigators such as LeDoux about this. However, we think that, provided that we are clear  on the first appearance (using ‘scare’ quotes) that we are using them as indeed labels for  latent characteristics that capture correlations in various aspects of behaviour, they are more  helpful than harmful in making our descriptions understandable.

      Reviewer #3 (Public Review):

      Summary:

      The manuscript presents computational modelling of the behaviour of mice during  encounters with novel and familiar objects, originally reported by Akiti et al. (Neuron 110, 2022)          . Mice typically perform short bouts of approach followed by a retreat to a safe  distance, presumably to balance exploration to discover possible rewards with the potential  risk of predation. However, there is considerable heterogeneity in this exploratory behaviour,  both across time as an individual subject becomes more confident in approaching the object,  and across subjects; with some mice rapidly becoming confident to closely explore the  object, while other timid mice never become fully confident that the object is safe. The  current work aims to explain both the dynamics of adaptation of individual animals over time,  and the quantitative and qualitative differences in behaviour between subjects, by modelling  their behaviour as arising from model-based planning in a Bayes adaptive Markov Decision  Process (BAMDP) framework, in which the subjects maintain and update probabilistic  estimates of the uncertain hazard presented by the object, and rationally balance the  potential reward from exploring the object with the potential risk of predation it presents.

      In order to fit these complex models to the behaviour the authors necessarily make  substantial simplifying assumptions, including coarse-graining the exploratory behaviour into  phases quantified by a set of summary statistics related to the approach bouts of the animal.  Inter-individual variation between subjects is modelled both by differences in their prior  beliefs about the possible hazard presented by the object and by differences in their risk  preference, modelled using a conditional value at risk (CVaR) objective, which focuses the  subject's evaluation on different quantiles of the expected distribution of outcomes.  Interestingly these two conceptually different possible sources of inter-subject variation in  brave vs timid exploratory behaviour turn out not to be dissociable in the current dataset as  they can largely compensate for each other in their effects on the measured behaviour.  Nonetheless, the modelling captures a wide range of quantitative and qualitative differences  between subjects in the dynamics of how they explore the object, essentially through  differences in how subject's beliefs about the potential risk and reward presented by the  object evolve over the course of exploration, and are combined to drive behaviour.

      Exploration in the face of risk is a ubiquitous feature of the decision-making problem faced  by organisms, with strong clinical relevance, yet remains poorly understood and  under-studied, making this work a timely and welcome addition to the literature.

      Strengths:

      (1) Individual differences in exploratory behaviour are an interesting, important, and  under-studied topic.

      (2) Application of cutting-edge modelling methods to a rich behavioural dataset, successfully  accounting for diverse qualitative and qualitative features of the data in a normative  framework.

      (3) Thoughtful discussion of the results in the context of prior literature.

      Limitations:

      (1) The model-fitting approach used of coarse-graining the behaviour into phases and fitting  to their summary statistics may not be applicable to exploratory behaviours in more complex  environments where coarse-graining is less straightforward.

      (2) Some aspects of the work could be more usefully clarified within the manuscript.

      We thank reviewer #3 for their positive feedback and helping us to improve the clarity of our  paper. We have added discussion they thought was missing.

      Reviewer #1 (Recommendations for the authors):

      (1) Line 25-28

      This part of the Abstract might give an impression that timidity (but not braveness) is  potentially associated with psychiatric illness and even that timidity is thus inferior to  braveness. However, even though extreme timidity might indeed be associated with anxiety  or depression, extreme braveness could also be associated with other psychiatric or  behavioral problems. Moreover, as a population, the existence of both timid and brave  individuals could be advantageous, and it could be a reason why both types of individuals  evolutionarily survived in the case of wild animals (although Akiti et al. used mice, which may  have no or very limited genetic varieties, and so things may be different). So I would like to  encourage the authors to elaborate on the expression of this part of the Abstract and/or  enrich the related discussion in the Discussion.

      This is an important point. We note on line 38 that excessive novelty seeking (potentially  caused by excessive braveness) could also be maladaptive.

      Additionally, we have added a paragraph to the discussion discussing heterogeneity in risk  sensitivity within a population.

      “Our data show that there is substantial variation in the degrees of risk sensitivity across the  mice.  Previous works have reported substantial interpopulation and intrapopulation  differences in risk-sensitivity in humans which depend on gender, age, socioeconomic  status, personality characteristics, wealth and culture (Rieger et al., 2015; Frey et al., 2017).  Despite the normative appeal of 𝛼 = 1, it is possible that a population may benefit from  including individuals with $\alpha$ different from 1.0 or highly negative priors. For example,  more cautious individuals could learn from merely observing the risky behavior of less  cautious individuals. Furthermore, we have only considered risk-sensitivity under epistemic  uncertainty in our work. Risk averse individuals, for instance with 𝛼 < 1 may be more  successful than risk-neutral agents in environments where there are unexpected dangers ( unknown unknowns). Risk-aversion is thus a temperament of ecological and evolutionary  significance (Réale et al., 2007).”

      (2) Line 149

      Section 2.2 consists of eight subsections. I think this organization may not be very  appealing, because there are a bit too many subsections, and their relations are not  immediately clear to readers. So I would like to encourage the authors to make an  elaboration. For example, since 2.2.1 - 2.2.5 describes a summary of model construction  and model fitting whereas 2.2.6-2.2.8 shows the results, it could be good to divide these into  separate sections (2.2.1 - 2.2.5 and 2.3.1 - 2.3.3).

      Thank you for pointing this out. We’ve renumbered the sections as you’ve suggested.

      (3) Line 347-8

      Theoretically, the effect of prior is diluted over experience whereas the effect of biased  (risk-aversive) evaluation persists, as the authors mentioned in Lines 393-394. Then isn't it  possible to consider environments/conditions in which the two effects can be separated?

      We appreciate this suggestion. Indeed, our original thought in modeling this experiment was  that this would be exactly the case here - with epistemic uncertainty reducing as the object  became more familiar. However, proving to an animal that a single environment is  completely stationary/fixed is hard - reflected in our conclusion here that the exploration  bonus pool replenishes. Thus, we argued in the discussion that a series of environments  would be necessary to separate risk sensitivity from priors.

      (4) Line 407

      It would be nice to add a brief phrase explaining how (in what sense) this model's  assumption was consistent with the reported behavior. Also, should the assumption of  having two discrete approach states (cautious and confident) itself be regarded as a  limitation of the model? If the tail-behind and tail-exposure approaches were not merely  operationally categorized but were indicated to be two qualitatively distinct behaviors in the  experiment by Akiti et al., it is reasonable to model them as two discrete states, but  otherwise, the assumption of two discrete states would need to be mentioned as a  simplification/limitation.

      We have now removed line 407, and now have an additional  paragraph in the discussion  discussing the limitations of the tail-behind and tail-exposure state representation: “Motivated by tail-behind versus tail-exposed in Akiti et al. (2022), we model approach using  a dichotomy between cautious and confident approach states. This is likely a crude  approximation to the continuous and multifaceted nature of animal approach behavior. For  example, during approach animals likely adjust their levels of vigilance continuously (or  discretely; Lloyd and Dayan (2018)) to  monitor threat, and choose different velocities for  movement, and different attentional strategies for inspecting the novel object. We hope  future works will model these additional behavioral complexities, perhaps with additional  internal states, and corroborate these states with neurobiological data.”

      (5) Line 418

      The authors contrasted their model-based analyses with the model-free analyses of Akiti et  al. Another aspect of differences between the authors' model and the model of Akiti et al. is  whether it is normative or mechanistic: while how the model of Akiti et al. can be biologically  implemented appears to be clear (TS dopamine represents threat TD error, and TS  dopamine-dependent cortico-striatal plasticity implements TD error-based update of  model-free threat prediction), biological implementation of the authors' model seems more  elusive. Given this, it might be a fruitful direction to explore how these two models can be  integrated in the future.

      We enthusiastically agree that it would be most interesting in the future to explore the  integration of the two models - and, in the discussion ( Lines 537-548, 454-461) , point to  some first steps that might be fruitful along these lines. There are two separate  considerations here: one is that our account is mostly computational and algorithmic,  whereas Akiti’s model is mostly algorithmic and implementational; the second is, as noted by  the reviewer, that our account is model-based, whereas Akiti’s model is model-free (in the  sense of reinforcement learning; RL). These are related - thanks in no small part to the work  from the group including Akiti, we know a lot more about the implementation of model-free  than model-based RL. However, our model-based account does reach additional features of  behavior not captured in Akiti et al.’s model such as bout duration, frequency, and approach  type. Thus, the temptation of unification.

      (6) Line 426

      Related to the previous point, it would be nice to more specifically describe what variable TS  dopamine can represent in the authors' model if possible.

      In the discussion  (Lines 454-461) , we speculate that  TS dopamine could still respond to the  physical salience of the novel object and affect choices by determining the potential cost of  the encountered threat or the prior on the hazard function. For example, perhaps ablating TS  dopamine reduces the hazard priors which leads to faster transition from cautious to  confident approach and longer bout durations, consistent with the optogenetics behavioral  data reported in Akiti et al.

      Reviewer #2 (Recommendations for the authors):

      My guess is simpler versions of the model would not fit the data well. But this does not mean  for example that the mice have probability distortions (CvaR) or that even probabilistic  reasoning and the internal models necessary to support them are acting in the behavioral  context studied by Akiti. So related to the above, I would ask what other models would fit and  would not fit the data? And what does this mean?

      These are good points. Our model provides an approximately normative account of the  animals’ behavior  in terms of what it achieves relative to a utility function. In practice, the  animals could deploy a precompiled model-free policy (which does not rely on probabilistic  computations) that is exactly equivalent to our model-based policy. With the current  experiment, we cannot conclude whether or not the animals are performing the prospective  calculations in an online manner. Of course, the extent to which animals or humans are  performing probabilistic computations online and have internal models are on-going  questions of study.

      Model comparison is difficult because currently we do not know of any other risk-sensitive  exploration models. We cannot directly compare to the model in Akiti et al. since our model  explains additional features of behavior: bout duration, frequency, and approach type.  Indeed, our model is as simple as it can be in the sense with the exception of nCVaR,  removing any of the other parameters makes it difficult to fit some animals in our dataset. In the future, our model could be used to fit other datasets of risk-sensitive exploration and,  ideally,  be compared to other models.

      Explaining why animals avoid the novel object in what the offers call benign environment is a  very tricky issue. In Akiti et al, the readers are not yet convinced that the mice know that this  environment is benign. Being placed in an arena with a novel object presents mice with a  great uncertainty and we do not know whether they treat this as benign. Therefore, the  alternative explanations in this study need to be carefully discussed in lieu of the limitations  of the initial study.

      It is certainly true that it is unclear if the arena is  completely  benign to the animals. However,  the amount of time the animal spends in the center of the arena decreases significantly from  habituation to novelty days. This suggests that the animals avoid the novel object largely  because of the object itself, rather than the potential danger associated with the arena.  Furthermore, the animals are not reported as exhibiting more extreme behaviours such as  freezing. In any case, our account is relative in the sense that we are comparing the time the  animal spends at the object versus elsewhere in the environment, driven by the relative  novelty and relative risk of the environment versus the object. Trying to get more absolute  measures of these quantities would require a richer experimental set-up, for instance with  different degree of habituation or experience of the occurrence of (other) novel objects, in  general.

      We added a short note to the discussion to explain this:

      “Fourth, we modeled the relative amount of time the animal spends at the object versus  elsewhere in the environment which depends on the differential risk in the two states.  However, it is likely the animals avoid the novel object largely because of the object itself,  rather than the potential danger associated with the arena since they spend much less time  at the center of the arena during novelty than habituation days.”

      Figure 2 - how confident are the authors that each mouse differs from y=1? Related to this,  the behavior in Akiti is very noisy and changes across time. I am not sure if the authors fully  describe at what levels their model captures the behavior vs not in a detailed enough  fashion.

      We have performed a random permutation test on the minute-to-minute data. We have  updated Figure 2 so that brave animals that pass the Benjamini–Hochberg procedure y>1 at  level q=0.05 are represented with solid green dots and animals that don’t pass are  represented with hollow dots. 8 out of 11 brave animals passed Benjamini–Hochberg.

      Reviewer #3 (Recommendations for the authors):

      (1) I could not find information in the preprint about code availability. Please consider making  the code public to help others apply these modelling methods.

      We have released code and included the url in the paper in the Methods section.

      (2) Though the manuscript was generally clearly written, there were a number of places  where some additional information or clarification would be useful:

      a) Please define and explain the terms 'tail-behind' and 'tail-exposed' (used to describe  approach bout types) when first used.

      We have added definitions when we first mention these terms:

      “[...] 'tail-behind' (bouts where the animal's nose was closer to the object than the tail for the  entire bout) and 'tail-exposed' (bouts where the animal's tail is closer to the object than the  nose at some point during the bout), associated respectively with cautious risk-assessment  and engagement”

      b) At lines 57-58 when contrasting the 'model-free' account of Akiti et al with the 'model-based' account of the current work, it would be worth clarifying that these terms are  being used in the RL sense rather than e.g. a model-based analysis of the data.  

      We have updated the relevant lines to say “model-free/based reinforcement learning”.

      c) Line 61, the phrase 'the significant long-run approach of timid animals despite having  reached the "avoid" state' is unclear as the 'avoid' state has not been defined.

      We updated the terminology to “avoidance behavior” to be consistent with Akiti et al.  Avoidance refers to the animal routinely avoiding the object and therefore being unable to  learn whether it is safe.

      d) It was not completely clear to me how the coarse-graining of the behaviour was  implemented. Specifically, how were animals assigned to the brave, intermediate, or timid  group, and how were the parameters of the resulting behavioural phases fit?

      Sorry that this was not clear. Section 2.1 explains how the minute-to-minute behavioral data  was coarse-grained and how animal groups were assigned. We have added further  explanation of Figure 2 to the main text:

      “Fig 2 summarizes our categorization of the animals into the three groups: brave,  intermediate, and timid based on the phases identified in the animal's exploratory  trajectories. Timid animals spend no time in confident approach and are plotted in orange at  the origin of Fig 2. Brave animals differ from intermediate animals in that their approach time  during the first ten minutes of the confident phase is greater than the last ten minutes ( steady-state phase). Brave animals are plotted in green above and intermediate animals  are plotted in black below the y=1 line in Fig 2.”

      We also added extra information to outline the goal, and methodology of coarse-graining and  animal grouping:

      “We sought to capture  these qualitative differences (cautious versus confident) as well as  aspects of the quantitative changes in bout durations and frequencies as the animal learns  about their environment. To make this readily possible, we abstracted the data in two ways:

      averaging  bout statistics over time, and clustering the animals into three groups with  operationally distinct behaviors.”

      e) What purpose does the 'retreat' state serve in the BAMDP model (as opposed to  transitioning directly from 'object' to 'nest' states), and why do subjects not pass through it  following 'detect' states?

      Thank you for pointing this out. We have updated Figure 3 to note that the two “detected  states” also point to the “retreat” state. The reviewer is correct that there could be alternative  versions of the state diagram, and the ‘retreat’ state could indeed have been eliminated.  However, we thought that it was helpful to structure the animal’s progress through state  space.

      f) Why was the hazard function parameterised via the mean and SD at each time step rather  than with a parametric form of the mean and SD as a function of time?

      Since the agent can only spend 2, 3, or 4 turns at the object states, we didn’t see a need to  parameterize the mean and SD as a function of time. Doing so is a good solution to scaling  up the hazard function to more time-steps.

      (3) There were also a couple of points that could potentially be usefully touched on in the  discussion:

      a) What, if any, is the relationship between the CVaR objective and distributional RL? They  seem potentially related due to both focussing on quantiles of the outcome distribution.

      We have added a paragraph to the discussion discussing the connection between  distributional RL and CVaR:

      “CVaR is known to come in different flavors in the case of temporally-extended behavior.  Gagne and Dayan (2021) introduces two alternative time-consistent formulations of CVaR:  nested CVaR (nCVaR) and precommitted CVaR (pCVaR). nCVaR and pCVaR both enjoy  Bellman equations which make it possible to compute approximately optimal policies without  directly computing whole distributions of the outcomes. We use nCVaR in this study for its  computational efficiency. There is, of course, great current interest in distributional  reinforcement learning (Bellemare et al., 2023b) which does acquire such whole  distributions, not the least because of prominent observations linking non-linearities in the  response functions of dopamine neurons to methods for learning distributions of outcomes ( Dabney et al., 2020; Masset et al., 2023; Sousa et al., 2023). One functional motivation for  considering entire outcome distributions is the possibility of using them to determine  risk-sensitive policies (Gagne and Dayan, 2021).

      While it is possible to compute CVaR directly from return distributions, Gagne and Dayan  (2021) showed that this can lead to temporally inconsistent policies where the agent  deviates from its original plans (the authors called this the fixed CVaR or fCVaR measure).

      Rather further removed from our model-based methods is work from Antonov and Dayan  (2023), who consider a model-free exploration strategy which exploits full return distributions  to compute the value of perfect information which is used as a heuristic for trying actions  with uncertain consequences. Future works can examine risk-sensitive versions of Antonov  and Dayan (2023)'s computationally efficient model-free algorithm as one solution to the  burdensome computations in our model-based method.”

      b) Why normatively might subjects have non-neutral risk preference as captured by the  CvaR?

      We also added a paragraph to the discussion discussing the advantage of heterogeneity in  risk sensitivity within a population:

      (Reviewer #1 had the same question, see above) “Our data show that there is substantial  variation in the degrees of risk sensitivity across the mice.  Previous works have reported  substantial interpopulation and intrapopulation differences in risk-sensitivity in humans which  depend on gender, age, socioeconomic status, personality characteristics, wealth and culture [...]”

      c) Relevance of the current modelling work to clinical conditions characterised by  dysregulation of risk assesment (e.g. anxiety or PTSD).

      We’ve added a paragraph to the discussion:

      “Inter-individual differences in risk sensitivity are also of critical importance in psychiatry,  reflected in a panoply of anxiety disorders (Butler and Mathews, 1983; Giorgetta et al., 2012;  Maner et al., 2007; Charpentier et al., 2017), along with worry and rumination (Gagne and  Dayan, 2022). Understanding the spectrum of   extreme priors and extreme values of 𝛼  could have therapeutic implications, adding significance to the search for tasks that can  more cleanly separate them.”

      d) Is it surprising to see differences in risk preference (nCVaR) between the familiar object  and novel object condition, given that risk preference might be conceptualised as a trait  rather than a state variable?

      Thank you for raising this point. You are right that we expected risk sensitivity (nCVaR alpha)  to be the same between FONC and UONC animals on average. It is difficult to know if alpha  is higher for FONC than UONC animals due to the non-identifiability between alpha and  hazard priors. We have added this discussion to the paper:

      “This is surprising if we interpret 𝛼 as a trait that is stable through time. Unfortunately, due to  the non-identifiability between 𝛼 and hazard priors, we cannot verify whether 𝛼 is actually  higher for FONC animals than UONC animals.”

    1. Editorial note: To ensure a thorough evaluation of the revised manuscript, we invited a third reviewer to assess whether the authors had sufficiently addressed the concerns raised in the initial round of peer review. This additional reviewer confirmed that the authors responded partially to the original reviewers requests. While he/she also provided a set of new comments, these do not alter the original assessment or editorial decision regarding the manuscript. For transparency and completeness, the additional comments are included below.

      Reviewer #3 (Public Review):

      Summary:

      In this manuscript, Li and coworkers present experiments generated with human induced pluripotent stem cells (iPSCs) differentiated to astrocytes through a three-step protocol consisting of neural induction/midbrain patterning, switch to expansion of astrocytic progenitors, and terminal differentiation to astroglial cells. They used lineage tracing with a LMX1A-Cre/AAVS1-BFP iPSCs line, where the initial expression of LMX1A and Cre allows the long-lasting expression of BFP, yielding BFP+ and BFP- populations, that were sorted when in the astrocytic progenitor expansion. BFP+ showed significantly higher number of cells positive to NFIA and SOX9 than BFP- cells, at 45 and 98 DIV. However, no significant differences in other markers such as AQP4, EAAT2, GFAP (which show a proportion of less than 10% in all cases) and S100B were found between BFP-positive or -negative, at these differentiation times. Intriguingly, non-patterned astrocytes produced higher proportions of GFAP positive cells than the midbrain-induced and then sorted populations. BFP+ cells have enhanced calcium responses after ATP addition, compared to BFP- cells. Single-cell RNA-seq of early and late cells from BFP- and BFP+ populations were compared to non-patterned astrocytes and neurons differentiated from iPSCs. Bioinformatic analyses of the transcriptomes resulted in 9 astrocyte clusters, 2 precursor clusters and one neuronal cluster. DEG analysis between BFP+ and BFP- populations showed some genes enriched in each population, which were subject to GO analysis, resulting in biological processes that are different for BFP+ or BFP- cells.

      Strengths:

      The manuscript tries to tackle an important aspect in Neuroscience, namely the importance of patterning in astrocytes. Regionalization is crucial for neuronal differentiation and the presented experiments constitute a trackable system to analyze both transcriptional identities and functionality on astrocytes.

      Weaknesses:

      The presented results have several fundamental issues, to be resolved, as listed in the following major points:

      (1) It is very intriguing that GFAP is not expressed in late BFP- nor in BFP+ cultures, when authors designated them as mature astrocytes.<br /> (2) In Fig. 2D, authors need to change the designation "% of positive nuclei".<br /> (3) In Fig. 2E, the text describes a decrease caused by 2APB on the rise elicited by ATP, but the graph shows an increase with ATP+2APB. However, in Fig. 2F, the peak amplitude for BFP+ cells is higher in ATP than in ATP+2APD, which is mentioned in the text, but this is inconsistent with the graph in 2E.<br /> (4) The description of Results in the single-cell section is confusing, particularly in the sorted CD49 and unsorted cultures. Where do these cells come from? Are they BFP-, BFP+, unsorted for BFP, or non-patterned? Which are the "all three astrocyte populations"? A more complete description of the "iPSC-derived neurons" is required in this section to allow the reader to understand the type and maturation stage of neurons, and if they are patterned or not.<br /> (5) A puzzling fact is that both BFP- and BFP- cells have similar levels of LMX1A, as shown in Fig. S6F. How do authors explain this observation?<br /> (6) In Fig. 3B, the non-patterned cells cluster away from the BFP+ and BFP-; on the other hand, early and late BFP- are close and the same is true for early and late BFP+. A possible interpretation of these results is that patterned astrocytes have different paths for differentiation, compared to non-patterned cells. If that can be implied from these data, authors should discuss the alternative ways for astrocytes to differentiate.<br /> (7) Fig. 3D shows that cluster 9 is the only one with detectable and coincident expression of both S100B and GFAP expression. Please discuss why these widely-accepted astrocyte transcripts are not found in the other astrocytes clusters. Also, Sox9 is expressed in neurons, astrocyte precursors and astrocytes. Why is that?<br /> (8) Line 337, Why authors selected a log2 change of 0.25? Typically, 1 or a higher number is used to ensure at least a 2-fold increase, or a 50% decrease. A volcano plot generated by the comparison of BFP+ with BFP- cells would be appropriate. The validation of differences by immunocytochemistry, between BFP+ and BFP-, is inconclusive. The staining is blur in the images presented in Fig. S8C. Quantification of the positive cells, without significant background signal, in both populations is required.<br /> (9) Lines 349-351: BFP+ cells did not show higher levels of transcripts for LMX1A nor FOXA2. This fact jeopardizes the claim that these cells are still patterned. In the same line, there are not significant differences with cortical astrocytes, indicating a wider repertoire of the initially patterned cells, that seems to lose the midbrain phenotype. Furthermore, common DGE shared by BFP- and BFP+ cells when compared to non-patterned cells indicate that after culture, the pre-pattern in BFP+ cells is somehow lost, and coincides with the progression of BFP- cells.<br /> (10) For the GO analyses, How did authors select 1153 genes? The previous section mentioned 287 genes unique for BFP+ cells. The Results section should include a rationale for performing a wider search for the enriched processes.<br /> (11) For Fig. 4C and 4D, both p values and the number of genes should be indicated in the graph. I would advise to select the 10 or 15 most significant categories, these panels are very difficult to read. Whereas the listed processes for BFP+ have a relation to Parkinson disease, the ones detected for BFP- cells are related to extracellular matrix and tissue development. Does it mean that BFP+ cells have impaired formation of this matrix, or defective tissue development? This is in contradiction of enhanced calcium responses of BFP+ cells compared to BFP- cells.<br /> (12) Both the comparison between midbrain and cortical astrocytes in Fig. S8A, and the volcano plot in S8B do not show consistent changes. For example, RCAN2 in Fig. S8A has the same intensity for cortical and midbrain cells, but is marked as an enriched gene in midbrain in the p vs log2FC graph in Fig. S8B.

    2. Author response:

      The following is the authors’ response to the current reviews.

      Response to Reviewer #3:

      We thank reviewer 3 for spending their valuable time on commenting on our revised paper.

      We would like to reiterate the central conclusion of this work, which appears to have been missed by Reviewer 3. Using a BFP-expressing lineage tracer hPSC line for tracking LMX1A+ midbrain-patterned neural progenitors and their differentiated progeny, we discovered a loss of the LMX1A lineage during pluripotent stem cell differentiation into astrocytes, despite BFP+ neural progenitors were the dominant population at the onset of astrocyte induction.

      Hence, the take-home message of this study is, as summarized in the abstract, ‘ the lineage composition of iPSC-derived astrocytes may not accurately recapitulate the founder progenitor population’ and that one should not take for granted that in vitro/stem cell-derived astrocytes are the descendants of the dominant starting neural progenitors (which is a general assumption in PSC publications as described in the paper and our response to reviewers).

      Please find below our point-by-point response to reviewer comments. We have re-ordered the points according to their relative importance to our main conclusions.

      ‘ the lineage composition of iPSC-derived astrocytes may not accurately recapitulate the founder progenitor population’ and that one should not take for granted that in vitro/stem cell derived astrocytes are the descendants of the dominant starting neural progenitors (which is a general assumption in PSC publications as described in the paper and our response to reviewers).

      Please find below our point-by-point response to their comments. We have re-ordered the points according to their relative importance to our main conclusions.

      …. They used lineage tracing with a LMX1A-Cre/AAVS1-BFP iPSCs line, where the initial expression of LMX1A and Cre allows the long-lasting expression of BFP, yielding BFP+ and BFP- populations, that were sorted when in the astrocytic progenitor expansion. BFP+ showed significantly higher number of cells positive to NFIA and SOX9 than BFP- cells …

      This is a misunderstanding by reviewer 3. As indicated in the first sentence of the second section, BFP- populations used for functional and transcriptomic analysis was not sorted BFP<sup>-</sup> cells, but those derived from unsorted, BFP<sup>+</sup> enriched populations. Our scRNAseq analysis indicated that they were transcriptomically aligned to human midbrain astrocytes. This finding is consistent with the fact that they are derived from midbrain-patterned neural progenitors, presumably minority LMX1A- progenitors.

      Reviewer 3’s comments indicate that they misunderstood the primary aims of our study as a mere functional and transcriptomic comparison of the two astrocyte populations.

      (9) BFP+ cells did not show higher levels of transcripts for LMX1A nor FOXA2. This fact jeopardizes the claim that these cells are still patterned. In the same line, there are not significant differences with cortical astrocytes, indicating a wider repertoire of the initially patterned cells, that seems to lose the midbrain phenotype. Furthermore, common DGE shared by BFP- and BFP+ cells when compared to non-patterned cells indicate that after culture, the pre-pattern in BFP+ cells is somehow lost, and coincides with the progression of BFP- cells.

      The reviewer seems to assume that astrocytes derived from LMX1A+ ventral midbrain progenitors must retain LMX1A expression. We do not take this view and do not claim this in this study. Moreover, we have discussed in the paper that due to a lack of transcriptomic studies of in vivo track regional progenitors (such as LMX1A), it remains unknown whether and to what extent patterning gene expression is maintained in astrocytes of different brain regions.

      Our findings on the lack of LMX1A and FOXA2 in BFP+ astrocytes are supported by several published single-cell transcriptomic studies of human midbrain astrocytes (La Manno et al. 2016; Agarwal et al. 2020; Kamath et al. 2022). We have a paragraph of discussion on this topic in both the original and updated versions of the paper with the relevant publications cited.

      Other points raised by reviewer 3

      (1) It is very intriguing that GFAP is not expressed in late BFP- nor in BFP+ cultures, when authors designated them as mature astrocytes.

      We did not designate our cells as ‘mature’ astrocytes but ‘astrocytes’ based on their global gene expression with the human fetal and adult brain astrocytes as references.

      Moreover, ‘mature’ only appeared once in the paper indicating that our cells lie in between the fetal and adult astrocytes in maturity.

      (2) In Fig. 2D, authors need to change the designation "% of positive nuclei".

      To be corrected in the version of record.

      (3) In Fig. 2E, the text describes a decrease caused by 2APB on the rise elicited by ATP, but the graph shows an increase with ATP+2APB. However, in Fig. 2F, the peak amplitude for BFP+ cells is higher in ATP than in ATP+2APD, which is mentioned in the text, but this is inconsistent with the graph in 2E.

      To be corrected in the version of record.

      (4) The description of Results in the single-cell section is confusing, particularly in the sorted CD49 and unsorted cultures. Where do these cells come from? Are they BFP-, BFP+, unsorted for BFP, or non-patterned? Which are the "all three astrocyte populations"? A more complete description of the "iPSC-derived neurons" is required in this section to allow the reader to understand the type and maturation stage of neurons, and if they are patterned or not.

      As previously reported in the reference cited, CD49 is a novel human astrocyte marker. This is independent of BFP expression. For all three astrocyte populations studied here (BFP+, BFP-, and non-patterned astrocytes), we included both CD49f+ sorted and unsorted samples to account for selection bias caused by FACS. iPSC-derived neurons were included in the sequencing study to provide a reference for cell-type annotation. They were generated following a GABAergic neuron differentiation protocol. However, their maturation stages and/or regional characteristics are not relevant to astrocytes.

      (5) A puzzling fact is that both BFP- and BFP- cells have similar levels of LMX1A, as shown in Fig. S6F. How do authors explain this observation?

      This figure panel shows that LMX1A, LMX1B and FOXA2 are essentially NOT expressed in these astrocytes.

      (6) In Fig. 3B, the non-patterned cells cluster away from the BFP+ and BFP-; on the other hand, early and late BFP- are close and the same is true for early and late BFP+. A possible interpretation of these results is that patterned astrocytes have different paths for differentiation, compared to non-patterned cells. If that can be implied from these data, authors should discuss the alternative ways for astrocytes to differentiate.

      Both BFP+ and BFP- astrocyte are from ventral midbrain patterned neural progenitors, while non-patterned neural progenitors are more akin to that of forebrain. Figure 3B is expected and confirms the patterning effect.

      (7) Fig. 3D shows that cluster 9 is the only one with detectable and coincident expression of both S100B and GFAP expression. Please discuss why these widely-accepted astrocyte transcripts are not found in the other astrocytes clusters. Also, Sox9 is expressed in neurons, astrocyte precursors and astrocytes. Why is that?

      S100B and GFAP are classic astrocyte markers in certain states. We are not relying only on two markers but the genome-wide expression profile as the criteria for astrocytes. As shown in the unbiased reference mapping to multiple human brain astrocyte scRNA-seq datasets, all our astrocyte clusters were mapped with high confidence to human astrocytes.

      SOX9 is an important regulator for astrogenesis, so its expression is expected in precursors (doi.org/10.1016/j.neuron.2012.01.024). In addition, recent studies have uncovered that SOX9 expression is also reported in foetal striatal projection neurons and early postnatal cortical neurons, where SOX9 regulates neuronal synaptogenesis and morphogenesis (dois:10.1016/j.fmre.2024.02.019; 10.1016/j.neuron.2018.10.008). Therefore, the expression of SOX9 in multiple cell types was expected. Instead of using a few selected markers for cell-type annotation, we employed a genomic approach relying on an unbiased reference mapping approach and a combination of various markers to ascertain our annotation results.

      (8) Line 337, Why authors selected a log2 change of 0.25? Typically, 1 or a higher number is used to ensure at least a 2-fold increase, or a 50% decrease. A volcano plot generated by the comparison of BFP+ with BFP- cells would be appropriate. The validation of differences by immunocytochemistry, between BFP+ and BFP-, is inconclusive. The staining is blur in the images presented in Fig. S8C. Quantification of the positive cells, without significant background signal, in both populations is required.

      We used a lenient threshold owing to the following considerations: 1) High FC does not necessarily mean biological relevance, as gene expression does not necessarily translate to protein expression. Therefore, a smaller FC value could also be biologically meaningful. 2) Balance between noise and biological differences. Any threshold was chosen arbitrarily. 3) We are identifying a trend rather than pinpointing a specific set of

      The quality was unfortunately reduced due to restrictions on file size upon submission. A high resolution Fig. S8C is available.

      (10) For the GO analyses, How did authors select 1153 genes? The previous section mentioned 287 genes unique for BFP+ cells. The Results section should include a rationale for performing a wider search for the enriched processes.

      GO enrichment using unique DEGS may not capture the wider landscape of the transcriptomic characteristics of BFP<sup>+</sup> astrocytes. The 287 unique genes were only differentially expressed in BFP<sup>+</sup> astrocytes. However, apart from these 287 genes, other genes among the 1187 DEGs were differentially expressed in BFP<sup>+</sup> astrocytes and in one other population.

      (11) For Fig. 4C and 4D, both p values and the number of genes should be indicated in the graph. I would advise to select the 10 or 15 most significant categories, these panels are very difficult to read. Whereas the listed processes for BFP+ have a relation to Parkinson disease, the ones detected for BFP- cells are related to extracellular matrix and tissue development. Does it mean that BFP+ cells have impaired formation of this matrix, or defective tissue development? This is in contradiction of enhanced calcium responses of BFP+ cells compared to BFP- cells.

      Information on all DEGs, including p values and numbers, is provided in Supplementary data 1-5.

      BFP+ astrocytes do have enrichment for GO terms related to extracellular matrix and tissue development, although not as obvious as BFP- astrocytes. Previous work have shown that both in vitro and in vivo derived astrocytes are functionally heterogeneous, containing functionally distinct subtypes exhibiting different GO enrichment profiles (doi: 10.1016/j.ygeno.2021.01.008; 10.1038/s41598-024-74732-7).

      (12) Both the comparison between midbrain and cortical astrocytes in Fig. S8A, and the volcano plot in S8B do not show consistent changes. For example, RCAN2 in Fig. S8A has the same intensity for cortical and midbrain cells, but is marked as an enriched gene in midbrain in the p vs log2FC graph in Fig. S8B.

      These are integrated analyses of published human datasets. S8A and S8B show the same data in different formats. The differences are better shown in the volcano plot/easier detected by the human eye.

      These are integrated analysis of published human datasets. S8A and S8B are the same data shown in different format. Differences are better shown in volcano plot /easier detected by the human eye. RCAN2 had a higher average expression in the midbrain than in the telencephalon, albeit small, and the difference was statistically significant (as shown in the volcano plot).


      The following is the authors’ response to the original reviews

      Reviewer 1:

      In vitro nature of this work being the fundamental weakness of this paper

      We disagree with this statement. As explained in the provisional response, the aim of this study was to test the validity of a general concept applied in pluripotent stem cell research that pluripotent stem cell-derived astrocytes faithfully represent the lineage heterogeneity of their ancestral neural progenitors and hence preserve the regionality of such progenitors. Our genetic lineage study is justified for addressing this in vitro-driven question. However, we have highlighted the rationale where appropriate in the revised paper.

      If regional identity is not maintained, so what? Don't we already know that this can happen? The authors acknowledge that this is known in the discussion.

      Importance of regional identity: Growing evidence demonstrates the functional heterogeneity of brain astrocytes in health and disease. Therefore, for in vitro disease modeling, it is believed that one should use astrocytes represent the anatomy of disease pathology; for example, midbrain astrocytes for studying dopamine neurodegeneration and Parkinson’s disease. Understanding the dynamics of stem cell-derived astrocytes and identifying astrocyte subtypes is important for their biomedical applications.

      Regional identity change/Discussion: It seems that the reviewer misunderstood the context in which the ‘identity change’ was discussed. The literature referred to (in the Discussion) concerns shifts in regional gene expression in bulk-cultured cells. In the days of pre-single-cell analysis/lineage tracking, one cannot distinguish whether this was due to a change in the transcriptomic landscape in progenies of the same lineage or alterations in lineage heterogeneity, but to interpret at face value as regional identity was not maintained. In the revised paper, we have made an effort to indicate that ‘regional identity’ is used broadly to refer to lineage relationships and/or traits rather than static gene expressioin.

      validation of the markers/additional work

      The scNAseq analysis performed in this study compared the profiles of astrocytes derived from LMX1A+ and LMX1A- ventral midbrain-patterned neural progenitors. Since it is not possible to perform genetic lineage tracking in humans and an analogous mouse lineage tracer line is not available, in vivo validation of these markers with respect to their lineage relationship is not currently feasible. However, we took advantage of abundant single-cell human astrocyte transcriptomic datasets and validated our genes in silico. We also validated the differential expression of selected markers in late BFP+ and BFP- astrocytes using immunocytochemistry, where reliable antibodies are available. The results of the additional analyses are presented in Figure S8 and Supplemental Data 5.

      Knowledge gaps concerning astrocyte development

      Reviewer 1 pointed out a number of knowledge gaps concerning astrocyte development, such as the transcriptomic landscape trajectories of midbrain floor plate cells as they progress towards astrocytes. Indeed, the limited knowledge on regional astrocyte molecule heterogeneity restricts the objective validation of in vitro-derived astrocyte subtypes and the development of novel approaches for their generation in vitro. We agree with the need for in-depth in vivo studies using model organisms, although these are beyond the scope of the current work.

      Reviewer 2:

      (1) The authors argue that the depletion of BFP seen in the unsorted population immediately after the onset of astrogenic induction is due to the growth advantage of the derivatives of the residual LMX1A- population. However, no objective data supporting this idea is provided, and one could also hypothesize that the residual LMX1A- cells could affect the overall LMX1A expression in the culture through negative paracrine regulation.

      We acknowledge the lack of evidence-based explanation for the depletion of BFP+ cells in mixed cultures. We were unable to perform additional experiments because of resource limitations. The design of the LMX1A-Cre/AAVS1-BFP lineage tracer line determines that BFP is expressed irreversibly in LMX1A-expressing cells or their derivatives regardless of their LMX1A expression status. Therefore, the potential negative paracrine regulation of LMX1A by residual LMX1A- cells should not affect cells that have already turned on BFP. We have highlighted the working principles of the LMX1A tracer line in the revised manuscript.

      (2) Furthermore, on line 124 it is stated that: "Interestingly, the sorted BFP+ cells exhibited similar population growth rate to that of unsorted cultures...". In the face of the suggested growth disadvantage of those cells, this statement needs clarification.

      To avoid confusion, we have removed the statement.

      (3) Regarding the fidelity of the model system, it is not clear to me how the TagBFP expression was detected in the BFP+ population supposedly in d87 and d136 pooled astrocytes (Fig S6C) while no LMX1A expression was observed in the same cells (Fig S6F).

      The TagBFP tracer is expressed in the progenies of LMX1A+ cells, regardless of their LMX1A expression status. We have gone through the MS text to ensure that this information has been provided.

      (4) The generated single-cell RNASeq dataset is extremely valuable. However, given the number of conditions included in this study (i.e. early vs late astrocytes, BFP+ vs BFP-, sorted vs unsorted, plus non-patterned and neuronal samples) the resulting analysis lacks detail. For instance, from a developmental perspective and to better grasp the functional significance of astrocytic heterogeneity, it would be interesting to map the identified clusters to early vs late populations and to the BFP status.

      We performed additional bioinformatics analysis, which provided independent support for the relative developmental maturity suggested by functional assays. The additional data are now provided in the revised Figure 3B, C, E.

      Moreover, although comprehensive, Figure S7 is complex to understand given that citations rather than the reference populations are depicted.

      The information provided in the revised Figure S7.

      (5) Do the authors have any consideration regarding the morphology of the astrocytes obtained in this study? None of the late astrocyte images depict a prototypical stellate morphology, which is reported in many other studies involving the generation of iPSC-derived astrocytes and which is associated with the maturity status of the cell.

      The morphology of our astrocytes was not unique to the present study. Many factors may influence the morphology of astrocytes, such as the culture media and supplements used, and maturity status. Based on the functional assays and limited GFAP expression, our astrocytes were relatively immature.

    1. Reviewer #2 (Public review):

      Summary:

      This paper presents a novel transformer-based neural network model, termed the epistatic transformer, designed to isolate and quantify higher-order epistasis in protein sequence-function relationships. By modifying the multi-head attention architecture, the authors claim they can precisely control the order of specific epistatic interactions captured by the model. The approach is applied to both simulated data and ten diverse experimental deep mutational scanning (DMS) datasets, including full-length proteins. The authors argue that higher-order epistasis, although often modest in global contribution, plays critical roles in extrapolation and capturing distant genotypic effects, especially in multi-peak fitness landscapes.

      Strengths:

      (1) The study tackles a long-standing question in molecular evolution and protein engineering: "how significant are epistatic interactions beyond pairwise effects?" The question is relevant given the growing availability of large-scale DMS datasets and increasing reliance on machine learning in protein design.

      (2) The manuscript includes both simulation and real-data experiments, as well as extrapolation tasks (e.g., predicting distant genotypes, cross-ortholog transfer). These well-rounded evaluations demonstrate robustness and applicability.

      (3) The code is made available for reproducibility.

      Weaknesses:

      (1) The paper mainly compares its transformer models to additive models and occasionally to linear pairwise interaction models. However, other strong baselines exist. For example, the authors should compare baseline methods such as "DANGO: Predicting higher-order genetic interactions". There are many works related to pairwise interaction detection, such as: "Detecting statistical interactions from neural network weights", "shapiq: Shapley interactions for machine learning", and "Error-controlled non-additive interaction discovery in machine learning models".

      (2) While the transformer architecture is cleverly adapted, the claim that it allows for "explicit control" and "interpretability" over interaction order may be overstated. Although the 2^M scaling with MHA layers is shown empirically, the actual biological interactions captured by the attention mechanism remain opaque. A deeper analysis of learned attention maps or embedding similarities (e.g., visualizations, site-specific interaction clusters) could substantiate claims about interpretability.

      (3) The distinction between nonspecific (global) and specific epistasis is central to the modeling framework, yet it remains conceptually underdeveloped. While a sigmoid function is used to model global effects, it's unclear to what extent this functional form suffices. The authors should justify this choice more rigorously or at least acknowledge its limitations and potential implications.

      (4) The manuscript refers to "pairwise", "3-4-way", and ">4-way" interactions without always clearly defining the boundaries of these groupings or how exactly the order is inferred from transformer layer depth. This can be confusing to readers unfamiliar with the architecture or with statistical definitions of interaction order. The authors should clarify terminology consistently. Including a visual mapping or table linking a number of layers to the maximum modeled interaction order could be helpful.

    2. Reviewer #3 (Public review):

      Summary:

      Sethi and Zou present a new neural network to study the importance of epistatic interactions in pairs and groups of amino acids to the function of proteins. Their new model is validated on a small simulated data set and then applied to 10 empirical data sets. Results show that epistatic interactions in groups of amino acids can be important to predict the function of a protein, especially for sequences that are not very similar to the training data.

      Strengths:

      The manuscript relies on a novel neural network architecture that makes it easy to study specifically the contribution of interactions between 2, 3, 4, or more amino acids. The study of 10 different protein families shows that there is variation among protein families.

      Weaknesses:

      The manuscript is good overall, but could have gone a bit deeper by comparing the new architecture to standard transformers, and by investigating whether differences between protein families explain some of the differences in the importance of interactions between amino acids. Finally, the GitHub repository needs some more information to be usable.

    1. 15 College 4 – Designs: (quasi-)experimentele designs

      Een causaal verband kan alleen worden aangetoond als buitenexperimentele factoren uitgeschakeld zijn dan wel onder controle Maatregelen: 1a. Manipulatie van de onafhankelijke variabele 1b. Vergelijkingsbasis creëren 2. Zorg voor een eerlijke vergelijking: randomiseren, matchen of counterbalancen

    1. contexture, n Etymology: < French contexture (Montaigne, 1572–80), = Italian contestura (Florio), probably representing a medieval Latin *contextūra , < context– participial stem of contexĕre : compare Latin textūra texture n. Very common in 17th cent.; now rare. 1.  a. The action or process of weaving together or intertwining; the fact of being woven together; the manner in which this is done, texture.  [….] 2.  a. transferred. The linking together of materials or elements, so as to form a connected structure (natural or artificial); the manner in which the parts of a thing are thus united.  […] 1662 E. Stillingfleet Origines Sacræ iii. ii. §14 Without this there cannot be imagined any concourse of Atoms at all, much less any such contexture of bodyes out of them.  [….] b. figurative of things non-material. 1672 A. Marvell Rehearsal Transpros’d i. 29 The Roman Church, having by a regular Contexture of continued Policy..interwoven itself with the Secular Interest. [….] 3. The structure, composition, or texture of anything made up by the combination of elements. Now chiefly figurative from 1.  [….] 1749 H. Fielding Tom Jones VI. xvi. vii. 59 Women are of a nice Contexture, and our Spirits when disordered are not to be recomposed in a Moment.  [….] 4.  That which is put together or constructed by the intertwining of parts. a. quasi-concrete. A mass of things interwoven together.  [….] 1667 Philos. Trans. (Royal Soc.) 2 491 The Corpus Callosum is nothing but a Contexture of small Fibres.  [….] b. An interwoven structure, a fabric.  [….] 1664 H. Power Exper. Philos. i. 17 How many thousand parts of Matter must go to make up this heterogeneous Contexture? [….] 5.  a. The weaving together of words, sentences, etc. in connected composition; the construction or composition of a writing as consisting of connected and coherent members.  […] b. The connected structure or ‘body’ of a literary composition; a connected passage or composition. c. = context n. 4.  [OED second edition (1989)] The first four definitions relate to weaving in material and immaterial forms.  Only the fifth definition relates to writing or literary composition … but that’s where the confusion comes in.  A common interpretation associates context with text (as in language), rather than with texture (as with weaving).
    1. learning to freeze-dry potatoes and detoxify cassava, and identifying wheat and rice as valuable plants, was probably done by women. Other farm work, such as yoking water buffalo or oxen to plows and building irrigation dikes and canals, was probably men's work.

      each gender has certain jobs/roles.

    2. The shift to representing sounds was important because it allowed cuneiform to represent abstract concepts and to be used by speakers of different languages.

      Cool that this made cuneiform versatile, kind of like an early universal communication tool.

    3. The earliest examples of cuneiform so far discovered date back about 5,300 years. They were images known as pictographs made on clay tokens; the earliest purpose seems to have been accounting tasks such as tallying grain or livestock.

      I find it extremely interesting they used tally marks before pictures. I also thought they would be older than that since the Earth is so old.

    1. Group G Ben Braniff, Kim Maynard, Nick Devic, Maria Echeverri Solis, Sam Yalda

      1. Design has a major impact on the world and society. Even the little things can add up to a lot. Sustainability is a revolutionary Idea that should be at the core of every design now.

      2. Society is another bottom line meaning all design inherently affects humans and/or is designed for humans. It's important to design for the extremes and the edge cases like people with disabilities.

      3. Corporations output a lot of waste. When they make small changes to be more sustainable, it results in big changes and saving a lot of material. Small changes can include anything from using 2% less plastic per water bottle to using wood buttons instead of plastic ones.

      4. A lot of people don't consider themselves disabled, but it's very common at some point in people's lives to have a certain level of impairment. It's important to keep this in mind when designing as you're designing for the general population--not just a specific individual.

      5. Addressing issues like world hunger may require rethinking the way we design food production. As they stated for example, choosing kangaroo meat over beef as a more environmentally sustainable option.

      6. Thoughtful design choices per the example in the video such as adding white circles inside letters to reduce ink use, can improve efficiency and conserve resources.

      7. It is interesting how he opens up his discussion to slowly introduce that design isn't just about doing it for marketing or 'profit' as he pointed out. When watching this it helps a person realize that design is so much more powerful than that if you put it towards another cause. Design could end up being the solution to some of the biggest problems in society.

      8. A very important point he made was that improving accessibility is beneficial to many more people than just the people that initially needed it such as people with disabilities. From this i think a good takeaway is that design should always be considerate of any disabilities/needs that the audience might have because sometimes that design is just better for everyone in general.

      9. My first take is design should go beyond money and aesthetics. By thinking about sustainability and accessibility the designers can create solutions that are socially responsible and environmentally friendly.

      10. My second take is when you design with people with disabilities you end up with solutions that are more usable and inclusive

    2. Group C:

      1.) Canada and Norway both depend on exporting natural resources. We need to build sustainable value locally not just send raw goods elsewhere.

      2.) Designers cannot just follow orders. They are responsible for what their work does in society. Every design choice affects people.

      3.) Design is not decoration. It is about safety fairness access and improving lives for all users regardless of their condition.

      4.) Designing for people with special needs often improves the product for everyone. Accessibility is not only for some but for all.

      5.) Our design work affects future generations. We must think about the full life of what we create and the culture we leave behind.

      6.) Whether a disability is permanent, temporary, or situational almost everyone will experience it. Accessible design should be normal for all.

      7.) We all design in some way through how we communicate organize spaces or build systems. With that power comes responsibility to shape better experiences.

      8.) Designers today have bigger reach and tools than ever before. That means their decisions matter more than ever for how we treat each other and our planet.

      9.) A product is not just its production and launch. It has sourcing use reuse and disposal. We should design with all those phases in mind and aim to leave positive outcomes.

      10.) Tiny design decisions like choice of material font or layout can multiply into big environmental and social effects when many people use them.

    3. David Berman on Sustainable Design Thinking Strategy

      Group B 1. In the 20th century, designers helped make profit, which is how design emerged as a means to a capitalist outcome.

      1. Accessibility and universal design are framed as having a core to people. Making products and services usable for everyone is a central social responsibility.

      2. People tend to think of design as “life and death,” with colors used in modern signage to depict warnings, danger, etc. While other times the same colors will depict guidance and help.

      3. Harlem Bruntland invented the idea of sustainability and Norway contributed to the growth of this idea. She is considered a “design thinker”.

      4. As mentioned, designers and design thinking has evolved from profit lead design, to environmental sustainability design. Design thinking evolves with the times and depends on the designers, society, and the environment.

      5. “Over the next 10 to 15 years, technology has the capacity to virtually eliminate barriers faced by people with disabilities in the workplace.” This quote was said by Steve Ballmer. We already see this with the way workplaces are designed, such as flexible workstations with adjustable desks, multisensory alarms, high-contrast color palettes for people with visual impairments, and many more.

      6. Culture is presented as the fourth bottom line, highlighting what makes humans unique is that we don’t just evolve alone. Humans design their responses to challenges; sustaining a culture means sustaining adaptability.

      7. The closing of the digital divide has liberated more people through information access, elevating the importance of ethics in design choices and accessible methodologies.

      8. The quadruple bottom line is designed to include profit, planet, people, and culture. It is aimed to ensure a holistic approach to design.

      9. Even small changes, like changing/thinning a font, can have positive impacts on safety, sustainability, and accessibility.

    4. David Berman on Sustainable Design Thinking Strategy
      1. 4x bottom line nowadays: profit, environment, people, and ???.
      2. Small changes in design result in a big impact.
      3. The way things are designed can make their argument more convincing, even if what they are arguing for is outlandish.
      4. Designers, through strategic thinking, can find a way to a better world.
      5. When designers design for the extreme, it benefits all. (a) Examples of small changes like these can benefit many people, For example the colorblind traffic light changes in canada would not only save those with the disability but those who get in car accidents due to a color blinded individual.
      6. Designers should focus more on doing good than on making good designs.
      7. Profit only firms may win short term, but sustainable first firms gain long term reliance, loyalty, and savings.
      8. “Over the next 10 to 15 years, technology has the capacity to virtually eliminate barriers faced by people with disabilities in the workplace” (24:57)
      9. Sustainable design must entwine with strategic thinking: especially at the early stages. (a) One company focused on defining their success solely off profit will lead to companies chasing efficiency and aesthetics. (b) Another company designing for accessibility and sustainability, may not be profitable in the start as much as the other company, but in the long term, generally speaking the will be more successful than those other companies who now have to catch up and focus on accessibility and sustainability.
      10. There is a fear of a divide of people, those with technology and those without. This is called the digital divide.
    5. Group A:

      1) We live in a world today where everyone is a designer.

      2) Every design speaker will always mention about the environment.

      3) In todays world it is easier to create ideas.

      4) A design can help change how we can change the world.

      5) A subtle design can have a huge impact such as traffic lights

      6) The Ghana medical problem being a simple fix with just a website saying if it was a real or fake medicine

      7) designers are beginning to consider ethics and necessity instead of just profit

      8) The events of September 22, 2011 are a lot worse now, the numbers would be astronomically higher than it was before

      9) Well designed solutions can solve more than one problem at a time - trees for clients and fish for employees

      10) When we design to increase accessibility, we are helping everyone, not just people with obvious disabilities

    6. David Berman on Sustainable Design Thinking Strategy

      GROUP D:

      1.everyone needs to have empathy, especially in today’s world where mostly everything is online. designers can use accessibility to help people. like the example with the girl and the tube in her mouth. she can now go on the internet, like everyone else, because someone designed the tube for her

      1. I think the eco fonts are a great idea. he said that using them, it can use 25% less ink and toner. this is great for companies and regular people. they will be able to save money, since the ink and toner won’t be used up as fast.

      2. "Designers must be cognizant of their power and impact on the world"

      3. "Small changes executed on a large scale can contribute massively to sustainability"

      4. sustainability isn't just about people, profit, and planet culture also matters, should be treated as a fourth bottom line

      5. accessibility helps many people and hurts nobody"

      6. Ethical codes matter. Berman emphasizes aligning design practice with professional ethics, similar to medicine or law, to reduce harm and increase trust.

      7. Profit isn’t the only measure of success. Good design must be judged by social benefit and long-term impact, not just short-term financial gain.

      8. Global perspective is essential. Designers must think beyond local markets, recognizing how their work contributes to worldwide challenges such as climate change and inequality.

      9. Designers as change agents. Berman encourages professionals to see themselves as leaders who can steer society toward justice, sustainability, and fairness through thoughtful design.

    7. GROUP D: 1. everyone needs to have empathy, especially in today’s world where mostly everything is online. designers can use accessibility to help people. like the example with the girl and the tube in her mouth. she can now go on the internet, like everyone else, because someone designed the tube for her

      1. I think the eco fonts are a great idea. he said that using them, it can use 25% less ink and toner. this is great for companies and regular people. they will be able to save money, since the ink and toner won’t be used up as fast.

      2. "Designers must be cognizant of their power and impact on the world"

      3. "Small changes executed on a large scale can contribute massively to sustainability"

      4. sustainability isn't just about people, profit, and planet culture also matters, should be treated as a fourth bottom line

      5. accessibility helps many people and hurts nobody"

      6. Ethical codes matter. Berman emphasizes aligning design practice with professional ethics, similar to medicine or law, to reduce harm and increase trust.

      7. Profit isn’t the only measure of success. Good design must be judged by social benefit and long-term impact, not just short-term financial gain.

      8. Global perspective is essential. Designers must think beyond local markets, recognizing how their work contributes to worldwide challenges such as climate change and inequality.

      9. Designers as change agents. Berman encourages professionals to see themselves as leaders who can steer society toward justice, sustainability, and fairness through thoughtful design.

    8. Group B 1. In the 20th century, designers helped make profit, which is how design emerged as a means to a capitalist outcome.

      1. Accessibility and universal design are framed as having a core to people. Making products and services usable for everyone is a central social responsibility.

      2. People tend to think of design as “life and death,” with colors used in modern signage to depict warnings, danger, etc. While other times the same colors will depict guidance and help.

      3. Harlem Bruntland invented the idea of sustainability and Norway contributed to the growth of this idea. She is considered a “design thinker”.

      4. As mentioned, designers and design thinking has evolved from profit lead design, to environmental sustainability design. Design thinking evolves with the times and depends on the designers, society, and the environment.

      5. “Over the next 10 to 15 years, technology has the capacity to virtually eliminate barriers faced by people with disabilities in the workplace.” This quote was said by Steve Ballmer. We already see this with the way workplaces are designed, such as flexible workstations with adjustable desks, multisensory alarms, high-contrast color palettes for people with visual impairments, and many more.

      6. Culture is presented as the fourth bottom line, highlighting what makes humans unique is that we don’t just evolve alone. Humans design their responses to challenges; sustaining a culture means sustaining adaptability.

      7. The closing of the digital divide has liberated more people through information access, elevating the importance of ethics in design choices and accessible methodologies.

      8. The quadruple bottom line is designed to include profit, planet, people, and culture. It is aimed to ensure a holistic approach to design.

      9. Even small changes, like changing/thinning a font, can have positive impacts on safety, sustainability, and accessibility.

    9. GROUP E: 1. Design has to move beyond profit. Whereas before, it was tied to mostly just to increasing profit. 2. Sustainability is now a mainstream thing that you need to think about, whereas just a decade ago, it was questioned as even being necessary. 3. Design things with accessibility in mind. By ensuring that your design is accessible to all people, it can often even improve the experience for everyone. 4. The internet can either feed into consumerism and insecurity or, help spread knowledge.

      5.Design should be about culture, and innovating and adapting, which creates meaning.

      6.accessibility is very important design to consider. The video talks about a trafic light example where fixing traffic lights for colorblind people made them clearer for everyone else as well.

      7.design should cater to everyone as caring and fairness is a part of a good design.

      8.before planning, think about goals and sustainability to insure the correct results.

      9.everyone can be a designer, by our choices we all shape the world.

      10.even tiny changes make a difference like using different font sizes and color choices.

      1. If you manufacture a problem and then create a solution, people will buy the solution to your artificial problem

      2.Double bottom lines, financial (profit) + environmental (planet)

      3.It's never been easier for us to create an d share ideas than today

      1. Simple innovations to previous designs can change things tremendously, for example a dutch font has tiny white dots goign through the letters, which saves companies 25% percent on ink and toner, however the result is still legible

      2. Designers, as humans, want to create projects that are sustainable and can be innovated, as it helps leave a legacy, something every person wants

      3. Simply following orders is not enough, designers must fight for innovation and creativity, especially to innovate or invent

      4. Baerekraft = sustainability, a term coined by Gro Harlem Brundtland, a Norwegian designer show pushed for this to be a major focus if design

      5. Carteret Islands was the first civilization to be completely wiped out, due to not being sustainable, showing sustainability is a key component to design

      6. Events, whether good or bad, are caused by designs and designers creating and innovating

      7. Designs are integral to sustaining life, to the point that it can determine life and death, such as traffic lights using distinct colors as well as shapes to save the lives of colorblind drivers

    1. Reviewer #1 (Public review):

      The authors tried to quantify the difference between human complex traits by calculating genetic overlap scores between a pair of traits. Sherlock-II was devised to integrate GWAS with eQTL signals. The authors claim that Sherlock-II is superior to the previous version (robustness, accuracy, etc). It appears that their framework provides a reasonable solution to this important question, although the study needs further clarification and improvements.

      (1) Sherlock-II incorporates GWAS and eQTL signals to better quantify genetic signals for a given complex trait. However, this approach is based on the hypothesis that "all GWAS signals confer association to complex trait via eQTL", which is not true (PMID: 37857933). This should be acknowledged (through mentioning in the text) and incorporated into the current setup (through differential analysis - for example, with or without eQTL signals, or with strong colocalization only).

      (2) When incorporating eQTL, why did the authors use the top p-value tissues for eQTL? This approach seems simpler and probably more robust. But many eQTLs are tissue-specific. Therefore, it would also be important to know if eQTLS from appropriate tissues were incorporated instead.

      (3) One of the main examples is the novel association between Alzheimer's disease and breast cancer. Although the authors provided a molecular clue underlying the association, it is still hard to comprehend the association easily, as the two diseases are generally known to be exclusive to each other. This is probably because breast cancer GWAS is performed for germline variants and does not consider the contribution of somatic variants.

      (4) It would help readers understand the story better if a summary figure of the entire process were provided. The current Figure 1 does not fulfil that role.

      (5) Figure 2 is not very informative. The readers would want to know more quantitative information rather than a heatmap-style display. Is there directionality to the relationship, or is it always unidirectional?

      (6) In Figure 3, readers may want to know more specific information. For example, what gene signals are really driving the hypoxia signal in Alzheimer's disease vs breast cancer? And what SNP signals are driving these gene-level signals?

    2. Reviewer #2 (Public review):

      Summary:

      The authors introduce a gene-level framework to detect shared genetic architecture between complex traits by integrating GWAS summary statistics with eQTL data via a new algorithm, Sherlock-II, which aggregates signals from multiple (cis/trans) eSNPs to produce gene-phenotype p-values. Shared pathways are identified with Partial-Pearson-Correlation Analysis (PPCA).

      Strengths:

      The authors show the gene-based approach is complementary and often more sensitive than SNP-level methods, and discuss limitations (in terms of no directionality, dependence on eQTL coverage).

      Weaknesses:

      (1) How do the authors explain data where missing tissues or sparse eQTL mapping are available? Would that bias as to which genes/traits can be linked and may produce false negatives or tissue-specific false positives?

      (2) Aggregating SNP-level signals into gene scores can be confounded by LD; for example, a nearby causal variant for a different gene or non-expression mechanism may drive a gene's score, producing spurious gene-trait links. How do the authors prevent this?

      (3) How the SNPs are assigned to genes would affect results, this is because different choices can change which genes appear shared between traits. The authors can expand on these.

      (4) Many reported novel trait links remain speculative without functional or orthogonal validation (e.g., colocalization, perturbation data). Thus, the manuscript's claims are inconclusive and speculative.

      (5) It would be best to run LD-aware colocalization and power-matched simulations to check for robustness.

    3. Author response:

      Reviewer #1 (Public review):

      The authors tried to quantify the difference between human complex traits by calculating genetic overlap scores between a pair of traits. Sherlock-II was devised to integrate GWAS with eQTL signals. The authors claim that Sherlock-II is superior to the previous version (robustness, accuracy, etc). It appears that their framework provides a reasonable solution to this important question, although the study needs further clarification and improvements.

      (1) Sherlock-II incorporates GWAS and eQTL signals to better quantify genetic signals for a given complex trait. However, this approach is based on the hypothesis that "all GWAS signals confer association to complex trait via eQTL", which is not true (PMID: 37857933). This should be acknowledged (through mentioning in the text) and incorporated into the current setup (through differential analysis - for example, with or without eQTL signals, or with strong colocalization only). 

      The reviewer is correct that in this version of the tool, we focused on SNPs with effect on gene expression, as the majority of the SNPs identified by GWASs are non-coding SNPs. In the future improvement, we should also include coding SNPs that change the amino acid sequence of genes. We will discuss this point more in the revised manuscript.

      (2) When incorporating eQTL, why did the authors use the top p-value tissues for eQTL? This approach seems simpler and probably more robust. But many eQTLs are tissue-specific. Therefore, it would also be important to know if eQTLS from appropriate tissues were incorporated instead. 

      This is a simple scheme to incorporate eQTL data from multiple tissues, assuming that the tissue that gives the strongest association is most relevant, or mainly mediates the effect from the SNP to the phenotype. This is a reasonable approach given that the tissues of origin for most of the phenotypes are unknown. In the future improvement, we should incorporate eQTL data from the appropriate tissue(s) if that is known.

      (3) One of the main examples is the novel association between Alzheimer's disease and breast cancer. Although the authors provided a molecular clue underlying the association, it is still hard to comprehend the association easily, as the two diseases are generally known to be exclusive to each other. This is probably because breast cancer GWAS is performed for germline variants and does not consider the contribution of somatic variants. 

      This is due to one of the limitations of the current algorithm: no direction of association is predicted explicitly. It could be that increasing the expression of a gene reduced the risk of one disease but increase the risk of another. Currently we have to analyze the details of the SNPs to infer direction once overlapping genes are found. This needs improvement in the future.  

      (4) It would help readers understand the story better if a summary figure of the entire process were provided. The current Figure 1 does not fulfil that role. 

      We plan to incorporate reviewer's suggestion in the revised manuscript.

      (5) Figure 2 is not very informative. The readers would want to know more quantitative information rather than a heatmap-style display. Is there directionality to the relationship, or is it always unidirectional? 

      We will consider a different presentation in the revised manuscript.

      (6) In Figure 3, readers may want to know more specific information. For example, what gene signals are really driving the hypoxia signal in Alzheimer's disease vs breast cancer? And what SNP signals are driving these gene-level signals? 

      We will add these information in the revised manuscript.

      Reviewer #2 (Public review):

      Summary:

      The authors introduce a gene-level framework to detect shared genetic architecture between complex traits by integrating GWAS summary statistics with eQTL data via a new algorithm, Sherlock-II, which aggregates signals from multiple (cis/trans) eSNPs to produce gene-phenotype p-values. Shared pathways are identified with Partial-Pearson-Correlation Analysis (PPCA).

      Strengths:

      The authors show the gene-based approach is complementary and often more sensitive than SNP-level methods, and discuss limitations (in terms of no directionality, dependence on eQTL coverage).

      Weaknesses:

      (1) How do the authors explain data where missing tissues or sparse eQTL mapping are available? Would that bias as to which genes/traits can be linked and may produce false negatives or tissue-specific false positives?

      Missing tissues or sparse eQTL certainly can produce false negatives as the signals linking the two phenotypes are simply not captured in the data. It is less likely to produce false positives as long as the statistical test is well controlled.   

      (2) Aggregating SNP-level signals into gene scores can be confounded by LD; for example, a nearby causal variant for a different gene or non-expression mechanism may drive a gene's score, producing spurious gene-trait links. How do the authors prevent this? 

      When there are multiple SNPs in LD with multiple genes nearby, it is generally difficult to map the causal SNP and the causal gene it affected, and thus there will be spurious gene-trait links. When we calculate the global similarity based on the gene-trait association profiles,  we tried to control this by simulating with random GWASs that have the same power as the real GWAS and preserve the LD structure, as the spurious links will also be present in the simulated data (but may appear in different loci) that are used to calibrate the statistical significance. 

      (3) How the SNPs are assigned to genes would affect results, this is because different choices can change which genes appear shared between traits. The authors can expand on these. 

      We assign SNPs to genes based on their strongest eQTL association from the available data. Improvement can be made if the relevant tissues for a trait are known (see response to Reviewer 1 above).

      (4) Many reported novel trait links remain speculative without functional or orthogonal validation (e.g., colocalization, perturbation data). Thus, the manuscript's claims are inconclusive and speculative. 

      We agree with the reviewer that the reported trait links are speculative, and they should be treated as hypotheses generated from the computational analyses. To truly validate some of these proposed relationships, deeper functional analyses and experimental tests are needed.

      (5) It would be best to run LD-aware colocalization and power-matched simulations to check for robustness. 

      We agree more control on LD and power-matched simulations will be important for testing the robustness of the predictions.

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      In this review, the author covered several aspects of the inflammation response, mainly focusing on the mechanisms controlling leukocyte extravasation and inflammation resolution.

      Strengths:

      This review is based on an impressive number of sources, trying to comprehensively present a very broad and complex topic.

      Weaknesses:

      (1) This reviewer feels that, despite the title, this review is quite broad and not centred on the role of the extracellular matrix.

      (2) The review will benefit from a stronger focus on the specific roles of matrix components and dynamics, with more informative subheadings.

      (3) The macrophage phenotype section doesn't seem well integrated with the rest of the review (and is not linked to the ECM).

      (4) Table 1 is difficult to follow. It could be reformatted to facilitate reading and understanding

      (5) Figure 2 appears very complex and broad.

      (6) Spelling and grammar should be thoroughly checked to improve the readability.

      This review focuses on the whole extravasation journey of leukocyte and highlights involvement of extracellular matrix (ECM) in multiple phases of the process. ECM may exert their roles either as a collective structure or as individual components. In the revision, for those functions involving specific matrix components, we will emphasize the matrix components and incorporate this information to subheadings as suggested. The parts of macrophage phenotype (Section 10-11) are included for its pivotal roles on deciding the tissue fate following inflammation (ie. to resolve / to regenerate damages incurred or to sustain inflammation), which is an important aspect of this review. ECM could modify macrophage phenotypes either directly (section 10) or indirectly via modulations of tissue stiffness or other cell types like fibroblasts (section 9). However, as pointed out by other reviewers as well, we acknowledge that Section 11 does not integrate well enough to the rest of the review. We plan to reorganize this part and to emphasize its link to ECM during the revision for better integration. We will reformat Table 1 for easier comprehension. We will consider restructuring Figure 2, which outlines various events influencing tissue decision of resolution/inflammation, perhaps by breaking up into two separate figures, to better focus the message. We will also check the language to improve readability.

      Reviewer #2 (Public review):

      Summary:

      The manuscript is a timely and comprehensive review of how the extracellular matrix (ECM), particularly the vascular basement membrane, regulates leukocyte extravasation, migration, and downstream immune function. It integrates molecular, mechanical, and spatial aspects of ECM biology in the context of inflammation, drawing from recent advances. The framing of ECM as an active instructor of immune cell fate is a conceptual strength.

      Strengths:

      (1) Comprehensive synthesis of ECM functions across leukocyte extravasation and post-transmigration activity.

      (2) Incorporation of recent high-impact findings alongside classical literature.

      (3) Conceptually novel framing of ECM as an active regulator of immune function.

      (4) Effective integration of molecular, mechanical, and spatial perspectives.

      Weaknesses:

      (1) Insufficient narrative linkage between the vascular phase (Sections 2-6) and the in-tissue phase (Sections 7-10).

      (2) Underrepresentation of lymphocyte biology despite mention in early sections.

      (3) The MIKA macrophage identity framework is only loosely tied to ECM mechanisms.

      (4) Limited discussion of translational implications and therapeutic strategies.

      (5) Overly dense figure insets and underdeveloped links between ECM carryover and downstream immune phenotypes.

      (6) Acronyms and some mechanistic details may limit accessibility for a broader readership.

      We will add a transition paragraph between Section 6 and Section 7 to provide a narrative that the extravasation processes affect downstream leukocyte functions. While lymphocytes follow a similar extravasation principle, their in-tissue activities differ from innate leukocytes. We will thus include discussion of lymphocyte-ECM crosstalk to Section 8 and/or 9 in the revision. We will restructure Section 11 and Figure 3 to better integrate to the rest of the review: In the current manuscript, we merely describe the capability of the MIKA framework to describe identity of any tissue macrophages and thus the framework could serve as a roadmap to facilitate identity normalization of pathological macrophages. We plan, in the revision, by employing the MIKA framework, to discuss and demonstrate linkage between macrophage identities and expression/production of modulators to functional ECM effectors described in Section 8-9. Regarding the comment of limited discussion of translational implications / therapeutic strategies, we will try to enrich this aspect throughout the manuscript where appropriate, in addition to the existing ones (eg. line 293-297; 388-391; 460-463; 512-517) We will also revise figure structure in general to avoid too dense information and to improve clarity. We will consider to provide a glossary explaining specialized terms to expand readership accessibility.

      Reviewer #3 (Public review):

      Summary & Strengths:

      This review by Yu-Tung Li sheds new light on the processes involved in leukocyte extravasation, with a focus on the interaction between leukocytes and the extracellular matrix. In doing so, it presents a fresh perspective on the topic of leukocyte extravasation, which has been extensively covered in numerous excellent reviews. Notably, the role of the extracellular matrix in leukocyte extravasation has received relatively little attention until recently, with a few exceptions, such as a study focusing on the central nervous system (J Inflamm 21, 53 (2024) doi.org/10.1186/s12950-024-00426-6) and another on transmigration hotspots (J Cell Sci (2025) 138 (11): jcs263862 doi.org/10.1242/jcs.263862). This review synthesizes the substantial knowledge accumulated over the past two decades in a novel and compelling manner.

      The author dedicates two sections to discussing the relevant barriers, namely, endothelial cell-cell junctions and the basement membrane. The following three paragraphs address how leukocytes interact with and transmigrate through endothelial junctions, the mechanisms supporting extravasation, and how minimal plasma leakage is achieved during this process. The subsequent question of whether the extravasation process affects leukocyte differentiation and properties is original and thought-provoking, having received limited consideration thus far. The consequences of the interaction between leukocytes and the extracellular matrix, particularly regarding efferocytosis, macrophage polarization, and the outcome of inflammation, are explored in the subsequent three chapters. The review concludes by examining tissue-specific states of macrophage identity.

      Weaknesses:

      Firstly, the first ten sections provide a comprehensive overview of the topic, presenting logical and well-formulated arguments that are easily accessible to a general audience. In stark contrast, the final section (Chapter 11) fails to connect coherently with the preceding review and is nearly incomprehensible without prior knowledge of the author's recent publication in Cell. Mol. Life Sci. CMLS 772 82, 14 (2024). This chapter requires significantly more background information for the general reader, including an introduction to the Macrophage Identity Kinetics Archive (MIKA), which is not even introduced in this review, its basis (meta-analysis of published scRNA-seq data), its significance (identification of major populations), and the reasons behind the revision of the proposed macrophage states and their further development. Secondly, while the attempt to integrate a vast amount of information into fewer figures is commendable, it results in figures that resemble a complex puzzle. The author may consider increasing the number of figures and providing additional, larger "zoom-in" panels, particularly for the topics of clot formation at transmigration hotspots and the interaction between ECM/ECM fragments and integrins. Specifically, the color coding (purple for leukocyte α6-integrins, blue for interacting laminins, also blue for EC α6 integrins, and red for interacting 5-1-1 laminins) is confusing, and the structures are small and difficult to recognize.

      We agree with and appreciate the specific and helpful suggestions by the reviewer. During the revision, we will provide the requested background description of MIKA to enhance accessibility of general readership. As pointed out by other reviewers, since this part (Section 11) is less well-integrated to the rest of the review, we will restructure this part by linking tissue macrophage identities under MIKA framework to modulation of functional ECM effectors described in previous sections (Section 8-9). We acknowledge the current figure organization might be overly information-dense and will consider breaking down the contents to multiple figures. The size and color-coding issues will also be addressed.

    2. Reviewer #1 (Public review):

      Summary:

      In this review, the author covered several aspects of the inflammation response, mainly focusing on the mechanisms controlling leukocyte extravasation and inflammation resolution.

      Strengths:

      This review is based on an impressive number of sources, trying to comprehensively present a very broad and complex topic.

      Weaknesses:

      (1) This reviewer feels that, despite the title, this review is quite broad and not centred on the role of the extracellular matrix.

      (2) The review will benefit from a stronger focus on the specific roles of matrix components and dynamics, with more informative subheadings.

      (3) The macrophage phenotype section doesn't seem well integrated with the rest of the review (and is not linked to the ECM).

      (4) Table 1 is difficult to follow. It could be reformatted to facilitate reading and understanding

      (5) Figure 2 appears very complex and broad.

      (6) Spelling and grammar should be thoroughly checked to improve the readability.

    3. Reviewer #2 (Public review):

      Summary:

      The manuscript is a timely and comprehensive review of how the extracellular matrix (ECM), particularly the vascular basement membrane, regulates leukocyte extravasation, migration, and downstream immune function. It integrates molecular, mechanical, and spatial aspects of ECM biology in the context of inflammation, drawing from recent advances. The framing of ECM as an active instructor of immune cell fate is a conceptual strength.

      Strengths:

      (1) Comprehensive synthesis of ECM functions across leukocyte extravasation and post-transmigration activity.

      (2) Incorporation of recent high-impact findings alongside classical literature.

      (3) Conceptually novel framing of ECM as an active regulator of immune function.

      (4) Effective integration of molecular, mechanical, and spatial perspectives.

      Weaknesses:

      (1) Insufficient narrative linkage between the vascular phase (Sections 2-6) and the in-tissue phase (Sections 7-10).

      (2) Underrepresentation of lymphocyte biology despite mention in early sections.

      (3) The MIKA macrophage identity framework is only loosely tied to ECM mechanisms.

      (4) Limited discussion of translational implications and therapeutic strategies.

      (5) Overly dense figure insets and underdeveloped links between ECM carryover and downstream immune phenotypes.

      (6) Acronyms and some mechanistic details may limit accessibility for a broader readership.

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This work aims to elucidate the molecular mechanisms affected in hypoxic conditions, causing reduced cortical interneuron migration. They use human assembloids as a migratory assay of subpallial interneurons into cortical organoids and show substantially reduced migration upon 24 hours of hypoxia. Bulk and scRNA-seq show adrenomedullin (ADM) up-regulation, as well as its receptor RAMP2, confirmed atthe protein level. Adding ADM to the culture medium after hypoxic conditions rescues the migration deficits, even though the subtype of interneurons affected is not examined. However, the authors demonstrate very clearly that ineffective ADM does not rescue the phenotype, and blocking RAMP2 also interferes with the rescue. The authors are also applauded for using 4 different cell lines and using human fetal cortex slices as an independent method to explore the DLXi1/2GFP-labelled iPSC-derived interneuron migration in this substrate with and without ADM addition (after confirming that also in this system ADM is up-regulated). Finally, the authors demonstrate PKA-CREB signalling mediating the effect of ADM addition, which also leads to up-regulation of GABAreceptors. Taken together, this is a very carefully done study on an important subject - how hypoxia affects cortical interneuron migration. In my view, the study is of great interest.

      Strengths:

      The strengths of the study are the novelty and the thorough work using several culture methods and 4 independent lines.

      Weaknesses:

      The main weakness is that other genes regulated upon hypoxia are not confirmed, such that readers will not know until which fold change/stats cut-off data are reliable.

      Reviewer #2 (Public review):

      Summary

      The manuscript by Puno and colleagues investigates the impact of hypoxia on cortical interneuron migration and downstream signaling pathways. They establish two models to test hypoxia, cortical forebrain assembloids, and primary human fetal brain tissue. Both of these models provide a robust assay for interneuron migration. In addition, they find that ADM signaling mediates the migration deficits and rescue using exogenous ADM.

      Strengths:

      The findings are novel and very interesting to the neurodevelopmental field, revealing new insights into how cortical interneurons migrate and as well, establishing exciting models for future studies. The authors use sufficient iPSC lines including both XX and XY, so the analysis is robust. In addition, the RNAseq data with re-oxygenation is a nice control to see what genes are changed specifically due to hypoxia. Further, the overall level of validation of the sequencing data and involvement of ADM signaling is convincing, including the validation of ADM at the protein level. Overall, this is a very nice manuscript.

      Weaknesses:

      I have a few comments and suggestions for the authors. See below.

      Reviewer #3 (Public review):

      Summary:

      The authors aimed to test whether hypoxia disrupts the migration of human cortical interneurons, a process long suspected to underlie brain injury in preterm infants but previously inaccessible for direct study. Using human forebrain assembloids and ex vivo developing brain tissue, they visualized and quantified interneuron migration under hypoxic conditions, identified molecular components of the response, and explored the effect of pharmacological intervention (specifically ADM) on restoring the migration deficits.

      Strengths:

      The major strength of this study lies in its use of human forebrain assembloids and ex vivo prenatal brain tissue, which provide a direct system to study interneuron migration under hypoxic conditions. The authors combine multiple approaches: long-term live imaging to directly visualize interneuron migration, bulk and single-cell transcriptomics to identify hypoxia-induced molecular responses, pharmacological rescue experiments with ADM to establish therapeutic potential, and mechanistic assays implicating the cAMP/PKA/pCREB pathway and GABA receptor expression in mediating the effect. Together, this rigorous and multifaceted strategy convincingly demonstrates that hypoxia disrupts interneuron migration and that ADM can restore this defect through defined molecular mechanisms.

      Overall, the authors achieve their stated aims, and the results strongly support their  conclusions. The work has a significant impact by providing the first direct evidence of hypoxia-induced interneuron migration deficits in the human context, while also nominating a candidate therapeutic avenue. Beyond the specific findings, the methodological platform - particularly the combination of assembloids and live imaging - will be broadly useful to the community for probing neurodevelopmental processes in health and disease.

      Weaknesses:

      The main weakness of the study lies in the extent to which forebrain assembloids

      recapitulate in vivo conditions, as the migration of interneurons from hSO to hCO does not fully reflect the native environment or migratory context of these cells. Nevertheless, this limitation is tempered by the fact that the work provides the first direct observation of human interneuron migration under hypoxia, representing a major advance for the field. In addition, while the transcriptomic analyses are valuable and highlight promising candidates, more in-depth exploration will be needed to fully elucidate the molecular mechanisms governing neuronal migration and maturation under hypoxic conditions.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) The authors should examine if all cortical interneurons are affected by ADM or only subtypes (Parvalbumin/Somatostatin).

      We thank the reviewer for raising this important question. In our study, we utilized the Dlx1/2b::eGFP reporter to broadly label cortical interneurons; however, this system does not distinguish specific interneuron subtypes. To address this, in the revised version of the manuscript we will use the single-cell RNA sequencing data and immunostainings to provide this information. Based on previous analyses from Birey et al (Cell Stem Cell, 2022), we expect interneurons within assembloids to express mostly calbindin (CALB2) and somatostatin (SST) at this in vitro stage of development; parvalbumin subtype appears later based on data from Birey et al (Nature, 2017) and more recently from Varela et al, (bioRxiv, 2025).

      In parallel, we will analyze available scRNA-seq data from developing human primary brain tissue a similar age as the one used in the manuscript, and check whether these subtypes of interneurons are similar to the ones within assembloids.

      (2) The authors should test more candidates from their bulk RNA-seq data with different fold changes for regulation after hypoxia, to allow the reader to judge at which cut-off the DEGs may be reproducible. This would make this database much more valuable for the field of hypoxia research.

      We appreciate the reviewers’ thoughtful suggestion. In addition to the bulk RNA-seq analysis, we did validate several upregulated hypoxia-responsive genes with varying fold changes by qPCR; these include PDK1, PFKP, VEGFA (Figure S1). 

      We go agree that in-depth investigation of specific cut-offs would be interesting, however, this could be the focus of a different manuscript.

      Reviewer #2 (Recommendations for the authors):

      (1) Can the authors comment on the possibility of inflammatory response pathways being activated by hypoxia? Has this been shown before? While not the focus of the manuscript, it could be discussed in the Discussion as an interesting finding and potential involvement of other cells in the Hypoxic response.

      We thank the reviewer this important comment about inflammation. Indeed, hypoxia has been shown to activate the inflammatory response pathways. In various studies, it was found that HIF-1a can interact with NF-κB signaling, leading to the upregulation of pro-inflammatory cytokines such as IL-1β, IL-6, and TNF-α (Rius et al., Cell, 2008; Hagberg et al., Nat Rev Neurol, 2015).

      In our transcriptomics data (Figure 2D), and to the reviewers’ point, we identified enrichment of inflammatory signaling response following the hypoxic exposure. Since hSO at the time of analyses do contain astrocytes, we think these glia contribute to the observed pro-inflammatory changes. Based on these results and because ADM is known to have strong anti-inflammatory properties, the effects of ADM on hypoxic astrocytes should be investigated in future studies focused on hypoxia-induced inflammation. In the revision, we will address this comment in the discussion section and cite the appropriate papers.

      (2) Could the authors comment on the mechanism at play here with respect to ADM and binding to RAMP2 receptors - is this a potential autocrine loop, or is the source of ADM from other cell types besides inhibitory neurons? Given the scRNA-seq data, what cell-to-cell mechanisms can be at play? Since different cells express ADM, there could be different mechanisms in place in ventral vs dorsal areas.

      Based on our scRNA-seq data in hSOs showing significant upregulation of ADM expression in astrocytes and progenitors, we speculate that the primary mechanism is likely to involve paracrine interactions. However, we cannot exclude autocrine mechanisms with the included experiments. Dissecting these interactions in a cell-type specific manner could be an important focus for future ADM-related studies.

      To address the question about the possible different mechanisms in ventral versus dorsal areas, in the revision we will plot and include in the figures the data about the cell-type expression of ADM and its receptors in hCOs.

      (3) For data from Figure 6 - while the ELISA assays are informative to determine which pathways (PKA, AKT, ERK) are active, there is no positive control to indicate these assays are "working" - therefore, if possible, western blot analysis from assembloid tissue could be used (perhaps using the same lysates from Figure 3) as an alternative to validate changes at the protein level (however, this might prove difficult); further to this, is P-CREB activated at the protein level using WB?

      We thank the reviewer for this comment and the observation. Although we did not include a traditional positive control in these ELISA assays, several lines of evidence indicate that the measurements are reliable. First, the standard curves behaved as expected, and all sample values fell within the assay’s dynamic range. Second, technical replicates showed low variability, and the observed changes across experimental conditions (e.g., hypoxia vs. control) were consistent with the expected biological responses based on previous literature. We agree that including western blot validation would strengthen the findings, and we will note this for our future studies focused on CREB and ADM.

      (4) Could the authors comment further on the mechanism and what biological pathways and potential events are downstream of ADM binding to RAMP2 in inhibitory neurons? What functional impact would this have linked to the CREB pathway proposed? While the link to GABA receptors is proposed, CREB has many targets beyond this.

      We appreciate the reviewers’ insightful question. Currently, not much is known about the molecular pathways and downstream cellular events triggered by ADM binding to RAMP2 in inhibitory neurons, and in general in brain cells. The data from our study brings the first information about the cell-type specific expression of ADM in baseline and hypoxic conditions and is one of the key novelties of our study.

      While the signaling landscape of ADM in interneurons is largely unexplored, several studies in other (non-brain) cell types have demonstrated that ADM binding to RAMP2 can activate downstream cascades such as the cAMP/PKA/CREB pathway, PI3K/AKT, and ERK/MAPK, all of which are also known to be critical regulators of neuronal development and survival. These previously published data along with our CREB-targeted findings in hypoxic interneurons, suggest ADM–RAMP2 signaling could influence multiple aspects of interneuron biology, but these remain to be evaluated in future studies.

      We agree with the reviewer that CREB has a wide range of transcriptional targets. We decided to focus on GABA as a target of CREB for two main reasons, including: (i) GABA signaling has been previously shown to play an important role in the migration of cortical interneurons, and (ii) a previous study by Birey et al. (Cell Stem Cell, 2022) demonstrated that CREB pathway activity is essential for regulating interneuron migration in assembloid models of Timothy Syndrom, thus further providing evidence that dysregulation of CREB activity disrupts migration dynamics.

      While our study provides a first step toward uncovering the mechanisms of interneuron migration protection by ADM, we fully acknowledge that future work will be needed to delineate the full spectrum of ADM–RAMP2 downstream signaling events in inhibitory neurons and other brain cells.

      (5) Does hypoxia cause any changes to inhibitory neurogenesis (earlier stages than migration?) - this might always be known, but was not discussed.

      We appreciate this question from the reviewer; however, this was not something that we focused on in this manuscript due to the already large amount of data included. A separate study focusing on neurogenesis defects and the molecular mechanisms of injury for that specific developmental process would be an important next step.

      (6) In the Discussion section, it might be worth detailing to the readers what the functional impact of delayed/reduced migration of inhibitory neurons into the cortex might result in, in terms of functional consequences for neural circuit development.

      We thank the Reviewer for the suggestion of detailing the functional impact of reduced inhibitory neuron migration. We will revise the manuscript by incorporating a paragraph about this in the Discussion section.

      Reviewer #3 (Recommendations for the authors):

      Most of the evidence presented is convincing in supporting the conclusions, and I have only minor suggestions for improvement:

      (1) The bulk RNA-seq was performed in hSOs only, which may not fully capture the phenotypes of migrating or migrated interneurons. It would be valuable, if feasible, to sort migrated cells from hSO-hCO assembloids and specifically examine their molecular mediators.

      We thank the reviewer for this suggestion. While it is likely that the cellular environment will have some influence on a subset of the molecular changes, based on all the data from the manuscript and our specific target, the RNA-sequencing on hCOs was sufficient to capture essential changes like ADM upregulation. The in-depth exploration on differential responses of migrated versus non-migrated interneurons to hypoxia could be the focus of a different project.

      (2) In Figure 3, it is striking that cell-type heterogeneity dominates over hypoxia vs. control conditions. A joint embedding of hSO and hCO cells could provide further insight into molecular differences between migrated and non-migrated interneurons.

      We thank the reviewer for this observation and opportunity to clarify. Since we manually separated the assembloids before the analyses, we processed these samples separately. That is why they separate like this. In the revision, we will add data about ADM expression and its receptors’ expression in the hCOs.

      (3) It would be helpful to expand the discussion on how closely the migration observed in hSO-hCO assembloids reflects in vivo conditions, and what environmental aspects are absent from this model. This would better frame the interpretation and translational relevance of the findings.

      We thank the Reviewer for bringing up this important point. Although the assembloid model offers the unique advantage of allowing the direct investigation of migration patterns of hypoxic interneurons, we fully agree it does not fully recapitulate the in vivo environment. While there are multiple aspects that cannot be recapitulated in vitro at this time (e.g. cellular complexity, vasculature, immune response, etc), we are encouraged by the validation of our main findings in ex vivo developing human brain tissue, which strongly supports the validity of our findings for in vivo conditions.

      We will expand our discussion to include more details and the need to validate these findings using in vivo models, while also acknowledging that different species (e.g. rodents versus non-human primates versus humans) might have different responses to hypoxia.

      (4) The authors suggest that hypoxia is also associated with delayed interneuron maturation, yet the bulk RNA-seq data primarily reveal stress and hypoxia-related genes. A more detailed discussion of why genes linked to interneuron maturation and function were not strongly affected would clarify this point.

      We thank the Reviewer for the opportunity to clarify.

      The RNAseq data was performed during the acute stages of hypoxia/reoxygenation and we think a maturation phenotype might be difficult to capture at this point and would require analysis at later in vitro assembloid maturation stages.

      Our speculation about a possible maturation defect is based on data from previous studies from developmental biology that showed failure of interneurons to reach their final cortical location within a specified developmental window will impair their integration within the neuronal network, and thus lead to maturation defects and possible elimination by apoptosis.

      Since preterm infants suffer from countless hypoxic events over multiple months, we suggest these repetitive events are likely to induce cumulative delays in migration, inability of interneurons to reach their target in time, followed by abnormal integration within the excitatory network, and eventual elimination of some of these interneurons through apoptosis. However, the direct demonstration of this effect following a hypoxic insult would require prolonged in vivo experiments in rodents to follow the migration, network integration and apoptosis of interneurons; to our knowledge this experimental design is not technically feasible at this time.

      (5) Relatedly, while the focus on interneuron migration is well justified, acknowledging how hypoxia might also impact other aspects of cortical development (e.g., progenitor proliferation, neuronal maturation, or circuit integration) would place the findings in a broader developmental framework and strengthen their relevance.

      We appreciate the Reviewer’s suggestion to discuss the role of hypoxia on other processes during cortical development. In the revised manuscript, we will include citations about the effects of hypoxia on interneuron proliferation, maturation and circuit integration as available, and also expand to other cell types known to be affected.

      (6) Very minor: in Figure S3C and D, it was not stated what the colors mean (grey: control, yellow: hypoxia)

      Thank you for pointing out this error and we will correct it in our revision.

    2. Reviewer #2 (Public review):

      Summary

      The manuscript by Puno and colleagues investigates the impact of hypoxia on cortical interneuron migration and downstream signaling pathways. They establish two models to test hypoxia, cortical forebrain assembloids, and primary human fetal brain tissue. Both of these models provide a robust assay for interneuron migration. In addition, they find that ADM signaling mediates the migration deficits and rescue using exogenous ADM. The findings are novel and very interesting to the neurodevelopmental field, revealing new insights into how cortical interneurons migrate and as well, establishing exciting models for future studies. The authors use sufficient iPSC line,s including both XX and XY, so the analysis is robust. In addition, the RNAseq data with re-oxygenation is a nice control to see what genes are changed specifically due to hypoxia. Further, the overall level of validation of the sequencing data and involvement of ADM signaling is convincing, including the validation of ADM at the protein level. Overall, this is a very nice manuscript. I have a few comments and suggestions for the authors.

      Strengths and Weaknesses:

      (1) Can the authors comment on the possibility of inflammatory response pathways being activated by hypoxia? Has this been shown before? While not the focus of the manuscript, it could be discussed in the Discussion as an interesting finding and potential involvement of other cells in the Hypoxic response.

      (2) Could the authors comment on the mechanism at play here with respect to ADM and binding to RAMP2 receptors - is this a potential autocrine loop, or is the source of ADM from other cell types besides inhibitory neurons? Given the scRNA-seq data, what cell-to-cell mechanisms can be at play? Since different cells express ADM, there could be different mechanisms in place in ventral vs dorsal areas.

      (3) For data from Figure 6 - while the ELISA assays are informative to determine which pathways (PKA, AKT, ERK) are active, there is no positive control to indicate these assays are "working" - therefore, if possible, western blot analysis from assembloid tissue could be used (perhaps using the same lysates from Figure 3) as an alternative to validate changes at the protein level (however, this might prove difficult); further to this, is P-CREB activated at the protein level using WB?

      (4) Could the authors comment further on the mechanism and what biological pathways and potential events are downstream of ADM binding to RAMP2 in inhibitory neurons? What functional impact would this have linked to the CREB pathway proposed? While the link to GABA receptors is proposed, CREB has many targets beyond this.

      (5) Does hypoxia cause any changes to inhibitory neurogenesis (earlier stages than migration?) - this might always be known, but was not discussed.

      (6) In the Discussion section, it might be worth detailing to the readers what the functional impact of delayed/reduced migration of inhibitory neurons into the cortex might result in, in terms of functional consequences for neural circuit development.

    1. Note: This response was posted by the corresponding author to Review Commons. The content has not been altered except for formatting.

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      Reply to the reviewers

      Reviewer #1 (Evidence, reproducibility and clarity (Required)):

      The manuscript by Xu et al. investigated split gene drive systems by targeting multiple female essential genes involved in fertility and viability in Drosophila. The authors evaluate the suppression efficiency through individual corsses and cage trials. Resistance allele formation and fitness costs are explored by examining the sterility and fertility of each line. Overall, the experimental design is sound and methods are feasible. The work is comprehensive, and conclusions are well supported by the data. This work offers informative insights that could guide the design of suppression gene drive systems in other invasive disease vectors or agricultural pests.

      However, several points requiring clarification or improvement:

      1 Methodological clarity: Some experimental details are indufficiently described, for example, regarding the setup of genetic crosses involving different Cas9 derivatives. In line 197-198, "the mated females, together with females that were mated with Cas9 only males", it is unclear whether the latter group refers to gRNA-females.

      -We thank the reviewer for pointing out this ambiguity. The latter group refers to Cas9 females crossed to Cas9 males. We have clarified this both in the methods (line 207) and results (line 505-509).

      2.Regarding the inheritance rates, you included the reverse orientation of CG4415-Cas9, as I understood, it means this component is in reverse orientation with fluorescent marker. Since it is standard to design adjacent components in opposite direction to avoid transcriptional interference, the rationale for including this comparison should be better justified.

      • In our construct, ‘CG4415 (reverse orientation)’ indicates that Cas9 was oriented in the same direction as the fluorescent marker, while the other Cas9 constructs (nanos-Cas9 and CG4415-Cas9) places them in opposite directions. “reverse” just indicates a change from a “standard” in another study. Our previous publication showed that Cas9 orientation relative to the marker had little apparent effect on drive performance at the yellow-G locus. In this study, we compared both orientations in a fertility gene and again observed similar results, suggesting that orientation relative to the marker does not substantially affect drive efficiency in our system. We have clarified this in the figure legend text.

      Embryo resistance is inferred from the percentage of sterile drive females derived from drive mothers. How many female individuals were analysed per line and why deep sequencing was not employed to directly detect resistance alleles.

      -Embryo resistance can mean slightly different things for different applications. The most important is probably the fraction of females that have little to no fertility due to embryo resistance. Some of these may not have complete embryo resistance alleles, but instead, have mosaicism, with a sufficient level of resistance to still cause sterility. It is unclear exactly what proportion of resistance to wild-type may cause this, and thus, proportions from pooled sequencing, which could include both complete and all levels of mosaicism, may not be sufficient to measure this parameter. Another relevant parameter that we did not measure is the fraction of males rendered unable to do drive conversion (this value should be closer to the complete resistance rate, but probably still lower because of the multiple gRNAs). Even in this case, deep sequencing would not allow us to determine exactly what is happening in males, making individual sequencing a preferred approached. It is very nice, of course, for characterizing which resistance alleles are present overall, but in this study, we wanted to put a bit more emphasis on the effect of resistance, rather than its sequence characterizing.

      We analyzed 30 females per line for lines targeting nox, oct, dec and stl, 9 females for ndl and 276 individuals for line tra-v2 (Data Set S4). We believe such individual analyses sufficiently detected embryo resistance causing sterility within reasonable error. Note that we did also randomly genotype several sterile females and found mutations at target sites that disrupted gene functions.

      In response to this comment, we have added some text to justify our measurement of resistance alleles and include some of this discussion:

      “Note also that this defines embryo resistance as sufficient to induce sterility, but these may be mosaic rather than complete resistance. Further, note that the multiplex gRNA design in males may allow for continued drive conversion with a complete (as opposed to mosaic) embryo resistance allele, if some sites remain wild-type.”

      Masculinisation phenotypes were observed upon disruption of tra gene. How strong intersexes were distinguished from males? What molecular markers were used to determine genetic sex. This information should be clearly provided.

      -We observed two types of strong masculinisation phenotypes (Figure S2), one with bigger body size than wildtype males, and the other was identical to wildtype males. The homozygosity of the drive allele could be assessed by the brightness of red fluorescence in the eyes. However, we also randomly genotyped these masculinized females (as part of a batch that included males) to confirm their sex using primers for the Y-linked gene PP1Y2. A specific band was detected in wild-type males but not in masculinized females, confirming their genetic sex. This information has been added to the manuscript (lines 477-480).

      It would be more appropriate to use "hatchability"rather than "fertility" when referring to egg-to-larva viability.

      -Thank you for the suggestion. We used egg-to-adult survival rates as a proxy for the fertility of their parents because they usually laid similar number of eggs. However, it still technically incorrect language. We have fixed this in line 582 and elsewhere in the section.

      In cage trials, a complete gene drive is mimicked by introducing Cas9 to the background population, but this differs from actual complete gene drive, due to potential effects from separate insertion sites (different chromosome or loci). These difference could impact the system's performance and should be discussed.

      -We appreciate this point and have added discussion on the limitations of mimicking a complete gene drive using split components (line 766-779).

      7.Given the large amount of data presented, it would improve readability and interpretation if each result section concluded with a concise summary highlighting the key findings and implications.

      -Thank you for the suggestion. We have added brief summaries at the end of each results section to highlight the key findings and their significance.

      Reviewer #1 (Significance (Required)):

      The authors evaluate suppression efficiency through individual courses and cage trials. Resistance allele formation and fitness costs are explored by examining the sterility and fertility of each line. Overall, the experimental design is sound and methods are feasible. The work is comprehensive, and conclusions are well supported by the data. This work offers informative insights that could guide the design of suppression gene drive systems in other invasive disease vectors or agricultural pests.

      -We appreciate the reviewer’s positive assessment of our work.

      Reviewer #2 (Evidence, reproducibility and clarity (Required)):

      Paper summary

      The manuscript by Xu. et al presents an insightful and valuable contribution to the field of gene drive research. The manuscript by Xu et al. presents an insightful and valuable contribution to the field of gene drive research. The strategy of targeting and disrupting female fertility genes using selfish homing genetic elements was first proposed by Burt in 2003. However, for this approach to be effective, the phenotypic constraints associated with gene disruption have meant that the pool of suitable target genes remains relatively small - notwithstanding the significant expansion in accessible targets enabled by CRISPR-based genome editing nucleases. Population suppression gene drives are well developed as proof-of-principle systems, with some now in the late stages of development as genetic control strains. However, advancing the pipeline will require a broader set of validated target genes - both to ensure effectiveness across diverse species and to build redundancy into control strategies, reducing reliance on any single genetic target.

      In their paper, the authors conduct a systematic review of nine female fertility genes in Drosophila melanogaster to assess their potential as targets for homing-based suppression gene drives. The authors first conduct a thorough bioinformatic review to select candidate target genes before empirically testing candidates through microinjection and subsequent in vivo analyses of drive efficiency, population dynamics, and fitness costs relating to fecundity and fertility. After finalising their results, the authors identify two promising candidate target genes - oct and stl - which both demonstrate high gene conversion rates and, regarding the latter, can successfully suppress a cage population at a high release frequency. However, the manuscript suffers from a lack of in-depth discussion of a key limitation in its experimental design - namely, that the authors utilise a split-drive design to assess population dynamics and fitness effects when such a drive will not reflect release scenarios in the field. The review below highlights some major strengths and weaknesses of the paper, with suggestions for improvement.

      Key strengths

      The study's most significant strength is in its systematic selection and empirical testing of nine distinct genes as targets for homing-based gene drive, hence providing a valuable resource that substantially expands the pool of potential targets beyond the more commonly studied target genes (e.g. nudel, doublesex, among others). The identification of suitable target genes presents a significant bottleneck in the development of gene drives and the work presented here provides a foundational dataset for future research. The authors bolster the utility of their results by assessing the conservation of candidate genes across a range of pest species, suggesting the potential for broader application.

      A key finding in the paper is the successful suppression of a cage population using a stl-targeting gene drive (albeit at a high release frequency). This provides a critical proof-of-principal result demonstrating that stl is a viable target for a suppression drive. While in the paper suppression was not possible at lower release frequencies, together, the results provide evidence for complex population dynamics and threshold effects that may govern the success or failure of a gene drive release strategy - hence moving the conversation from a technical perspective ("can it work") to how a gene drive may be implemented. Moreover, the authors also employ a multiplexed gRNA strategy for all their gene drive designs and in particular their population suppressive gene drive targeting stl. This provides further proof-of-principal evidence for multiplexed gRNAs in order to combat the evolution of functional resistance following gene drive deployment.

      Finally, a further strength of this paper is in the clever dissection of fitness effects resulting from maternal Cas9 deposition. The authors design and perform a robust set of crosses to elucidate the parental source of fitness effects (i.e. maternally, paternally, or biparentally derived Cas9), finding (as they and others have before) that embryonic fitness was significantly reduced when Cas9 was inherited from a maternal source. As discussed, the authors conclude that maternal deposition is particularly pronounced in the context of split drives as opposed to complete drives, with the implication being that a complete drive might succeed where a split-drive has failed; thus providing a key directive for future study.

      Concerns

      The manuscript's central weakness lies in its interpretation of the results from the cage experiments - namely that a split-drive system was used to "mimic the release of a complete drive". In the study, mosquitoes carrying the drive element (i.e. the gRNA) were introduced into a population homozygous for the Cas9 element over several generations. This design is likely not representative of a real-world scenario and, as the authors state, likely exaggerates fitness costs. This is because the females carrying Cas9 will maternally deposit Cas9 protein into her eggs, with activity spanning several generations. When mated with a drive-carrying male the gRNA will immediately co-exist with maternally deposited Cas9, leading to early somatic cleavage and significant fitness costs (reflected in the author's own fertility crosses). This is fundamentally different to how a complete drive would function in a real-world release, where complete-drive males would mate with wild-type females not carrying Cas9. Their offspring would carry the drive element but would not be exposed to maternally deposited cas9, thus deleterious maternal effects would only begin to appear in the subsequent generation from females carrying the drive. Fitness costs measured from split-drive designs are therefore likely substantially overestimated compared to what would occur during the initial but critical release phase of a complete drive. This flaw weakens the paper's ability to predict the failure or success of the screened targets in a complete drive design, thus weakening the interpretation of the results from the cage trials. As a suggestion for improvement, the authors should explicitly and more prominently discuss the limitations of their split-drive model compared to complete drive models, both in the Results and Discussion. It is also recommended to include a schematic for both strategies that contrasts the experimental setup design (i.e. release of the drive into a Cas9 homozygous background) with a complete-drive release, clearly illustrating differences in maternal deposition pathways. This will not only contextualise the results and support the author's conclusion that observed fitness costs are likely an overestimate but will further strengthen the arguments that the candidate target genes found in this study may still be viable in a complete-drive system.

      -We sincerely appreciate the thoughtful review and the valuable comments and suggestions provided, which have helped improve both the clarity and readability of this study. We have revised several parts in the discussion of the manuscript and hope that these changes adequately address the concerns raised. We have also made Figure S5 to illustrate the differences between two release strategies (biparental-Cas9 split drive in our study and complete drive in real release).

      Please note that this type of fitness cost may have partially undermined our cage study (the fitness effect is notable, but still small compared to total fitness costs), but this is also among the first studies to propose and investigate this phenomenon in the first place (it is also noted in another preprint from our lab but to our knowledge not proposed elsewhere). Thus, part of the impact of our manuscript is showing that this is important, which may inform future cage studies in our lab and elsewhere.

      A second weakness in the manuscript relates to its limited explanation and discussion of key concepts. For example, the manuscript reports a stark difference in outcome of the two stl-targeting drives, where a high initial release in cage 1 led to population elimination versus a failure of the drive to spread in cage 2. The authors attribute this to vague "allele effects" and stochastic factors such as larval competition; however the results appear reminiscent of the Allee effect, which is a well-characterised phenomenon describing the correlation of population size (or density) and individual fitness (or per capita population growth rate). Using their results as an example, is it plausible that the high-frequency initial release in cage 1 imposed enough genetic load to quickly drive the population density below the Allee threshold thus quickly leading to population eradication. In cage 2, the low-frequency at initial release was insufficient to cross the Allee threshold. Omitting mention of this ecological principal greatly weakens the Discussion, and further presents a missed opportunity to discuss one of the more crucial strengths of the paper - that is, in providing a deeper insight into the practical requirements for successful field implementation.

      -While we do indeed mention this Allee effect (the “allele effect” noted above is a misspelling that we have corrected), we were hesitant to give it much discussion, considering that the specific Allee effect in our cages is likely of a very different nature than one would find in nature (we explain that it is likely due to bacterial growth that occurs when fewer larvae are present). However, it is perhaps still a good excuse to cover it in the discussion, while still noting that the specific Allee effect in our cage may not be representative. We have added the following text: “Nonetheless, the successful result in the cage with high release study may point to a potential field strategy for a drive that is less efficient (perhaps even one found to be less efficient in initial field tests compared to laboratory tests). If the initial release frequency of the drive is sufficiently high and widespread, then short-term high genetic load may substantially reduce the population, perhaps enough for Allee effects to become important. At this point, even if average genetic load is slowly declining without additional drive releases, persistent moderate genetic load coupled with the Allee effect may be sufficient to ensure population elimination.”

      In a similar vein, the authors provide only a superficial mechanistic discussion into the fitness costs associated with drives targeting key candidate genes. The paper would benefit from a deeper discussion regarding the specific molecular functions of top-performing genes (stl, oct, nox) and how unintended Cas9 activity could disrupt their activity, integrating known molecular functions with observed fitness costs. For instance, oct encodes a G-protein coupled receptor essential for ovulation and oviduct muscle relaxation, thus disruption to the oct gene would directly impair egg-laying which would account for the observed phenotypic effects. A deeper discussion linking unintended Cas9 activity to the specific, sensitive functions of target genes would elevate the paper from a descriptive screen to a more insightful mechanistic study.

      -We appreciate the reviewer’s comment. We have added a discussion to further explain fitness cost caused by unintended Cas9 activity disrupting target gene functions. However, keep in mind that the exact timing of Cas9 cleavage and the exact timing of these gene’s essential functions is still somewhat uncertain, which may limit insights from this line of analysis compared to a situation where ideal, high quality data is available for both of these. Here is the new material in the discussion:

      “The functions of the top-performing genes suggests a mechanistic basis for the observed fitness costs. Aside from germline cells, nanos has expression in other ovary cells as well. CG4415 lacks this expression, but our Cas9 construct with this promoter may have a different expression pattern that the native gene, as evidenced by its support for good drive conversion in females. stl is essential for ovarian follicle development, and its disruption likely in non-germline ovary cells could compromise egg chamber development and fertility. oct encodes the octopamine β2 receptor, a G-protein coupled receptor critical for ovulation and fertilization, so if it were similarly lost, egg-laying would be directly impaired. nox, which encodes NADPH oxidase, contributes to calcium flux and smooth muscle contraction during ovulation, so its disruption may prevent egg laying. tra is needed in the whole body for sexual development, but may also play an important role in ovary function. Thus, unintended Cas9 activity at these non-germline ovary cells can directly interfere with sensitive reproductive functions, potentially explaining the fertility costs observed in drive carriers. This issue could potentially be overcome if promoters were available that were truly restricted to germline cells rather than other reproductive cells, though it remains unclear if such promoters both exist and would retain their expression pattern at a non-native locus.”

      It is curious that the authors chose two genes on the X chromosome as targets. In insects (such as Drosophila here) that have heterogametic sex chromosomes, homing is not possible in the heterogametic sex as there is no chromosome to home to - so there will be no homing in males. On top of that, there is usually some fitness effect in carrier (heterozygous) females, so in a population these are nearly always bad targets for drives - unless there is some other compelling reason to choose that target?

      -Our rationale for testing X-linked targets is twofold. First, these genes are likely to play important roles in sex-specific functions and may have a different expression pattern (which is why specifically Dec was included), potentially reducing fitness costs. Although homing cannot occur in males, if drive conversion at these sites in females is very high and fitness costs are minimal, the resulting genetic load could still be sufficient to suppress populations (thus, such candidates could be superior even in diploids if they happen to have a lower fitness costs). Second, X-linked targets may have broader relevance for suppression drives in haplodiploid pests (e.g., fire ants), which has the same population dynamics as an X-linked target in a diploid populations. Our results therefore could have provided useful insights for such scenarios (such as for fire ants: Liu et al., bioRxiv 2025) if drive performance was sufficient for followup testing.

      Minor comments

      • Enhanced clarity in the Figures and data presentation would greatly improve readability. For example, Figure 5 is critical yet difficult to interpret; consider changing x-axis labels from icons to explicit text (e.g. "biparental Cas9", "maternal cas9", "paternal Cas9"). Similarly, Figure 4 is difficult to read and the y-axis label "population size" is ambiguous; consider adding shapes or dashes (rather than relying solely on colour) and clarifying the y-axis (e.g. no. adults collected) in the legend.

      -We appreciate the reviewer’s comment and have revised Figure 4 as suggested. Regarding Figure 5, we attempted to replace the icons with text labels; however, this was not possible because there is very little horizontal space and two generations to specify. Instead, we have revised the figure legend to provide a clearer explanation, which can hopefully improve clarity..

      • Expand on or include a schematic to show the differences in construction between the tra-v1 and tra-v2 constructs to better contextualise the discrepancies in results (e.g. inheritance rates of 61%-66% for tra-v1 and 81%-83% for tra-v2 between the two.

      -We have expanded Figure 2 to compare the constructs of tra-v1 and tra-v2. The further explanation of these two constructs was added into the result section: ‘When targeting tra, we originally tested the 4-gRNA construct tra-v1. However, the drive inheritance rate was relatively low (61%-66%), and sequencing revealed that only the middle two gRNAs were active (Table S3). Lack of cleavage at the outmost sites is particularly detrimental to achieving high drive conversion. Therefore, a second construct tra-v2 was tested that retained the two active gRNAs and included two new gRNAs. It showed substantially improved drive inheritance (81%-83%). ’

      • Minor typos e.g.:

      o Line 87: "form" to "from"

      o Line 484: "expended" to "expanded

      o Line 560: "foor" to "for"

      o Line 732: "conversed" to "conserved

      -We have revised these typos.

      • Clarify the split drive system: the authors introduce split drive for the first time in Line 118. They should at least give a clear definition and explanation of split drive and complete drive in the introduction.

      -We have included an introduction of split drive and complete drive in the introduction (line 47-53).

      • Line 237-238., The fitness evaluation lacks a clear description of controls. How were non-drive flies generated and validated as controls?

      -Drive heterozygotes were crossed with Cas9 homozygotes to generate the flies used for fitness evaluation. From the same cross, non-drive progeny were obtained and used as controls, ensuring they shared a comparable genetic background and rearing conditions with the drive-carrying individuals. We have now clarified in the manuscript results that “these served as the controls because they had the same environment and parents as the drive flies”.

      • Line 409-412.,line 423.,The high inheritance rates of stl and oct drives are impressive; however, variation in results across Cas9 promoters should be explained further in the discussion.

      -In the discussion section (lines 751-765), we included a dedicated paragraph addressing the variation observed between the nanos and CG4415 promoters. We have now expanded it to briefly note some differences:

      “Our previous works showed that both nanos and CG4415 have high drive conversion rates8, but nanos failed to suppress target populations in a homing drive targeting the female fertility gene yellow-G due to its fitness cost in drive females27. CG4415 had much lower maternal deposition, which allowed the elimination of cage populations by targeting yellow-G8. Here, we tested both promoters with drives targeting oct and stl, with both showing slightly higher drive efficiency than the drive targeting yellow-G in small-scale crosses. CG4415 has slightly worse though still good performance in females, likely due to male-biased expression compared to nanos.”

      • Line 414: The CG4415 promoter yielded reduced drive conversion rates in females, yet is still referred to as a promising promoter. This conclusion seems optimistic and should be clarified/more justified.

      -Based on our previous study cited in this context, CG4415 shows relatively lower germline conversion rates compared to nanos, although still remaining at a high level. Importantly, CG4415 also exhibits reduced maternal deposition relative to nanos, which could help mitigate fitness costs associated with maternal deposition—an important consideration for suppression systems. Taken together, while its conversion efficiency is lower (but only slightly), the potential benefits of reduced maternal deposition and perhaps even fitness costs provide a rationale for regarding CG4415 as a promising promoter. We state this when first introducing the promoter in the “Drive efficiency assessment” results subsection.

      • Specify the number of flies released, sex ratio, and cage size per generation (Line 466). This is essential for reproducibility.

      -We appreciate the reviewer’s comment and have revised the text to clarify our release approach, which differed from that used in other studies (which tend to have substantial fitness differences between lines in the first generation that can complicate analysis and change results). Rather than directly releasing drive males or females into cages, we first crossed drive males with non-drive females and then mixed them with non-drive females mated to non-drive males. The offspring (including males and females) from these crosses were recorded as the G0 generation, and their ratios were recorded as release frequency. We have specified the release ratio adult numbers in the following paragraph and supplementary file.

      Reviewer #2 (Significance (Required)):

      Overall the manuscript presents a valuable and timely resource for gene drive research, in particular for its systematic appraisal of potential target genes for population suppression drives and its rigorous assessment of the impact of maternal Cas9 deposition. The value in the generation and empirical testing of a novel multiplexed stl-targeting gene drive that led to population eradication in a cage trial should not be understated. While several key aspects of the discussion of the manuscript should be strengthened, the study presents a meaningful contribution to the field, extending previous work and and outlines important considerations for the design and implementation of effective gene drive systems.

      -We thank the reviewer for their encouraging and constructive comments. We are pleased that the systematic evaluation of target genes, the analysis of maternal Cas9 deposition, and the multiplexed stl-targeting drive were recognized as valuable contributions. We have strengthened the discussion as suggested, and we believe these revisions further enhance the manuscript as an aid for the design and implementation of future gene drive systems.

      Reviewer #3 (Evidence, reproducibility and clarity (Required)):

      In this study, Xu and colleagues explored how CRISPR-based homing gene drives could be used to suppress insect populations by targeting female fertility genes in Drosophila melanogaster. They engineered split gene drives with multiplexed guide RNAs to target nine candidate genes, seeking to prevent functional resistance and achieve high drive conversion with minimal fitness costs.

      Here my comments about this work:

      Abstract: While the stated aim of the study on line 16 is to "maintain high drive conversion efficiency with low fitness costs in female drive carriers," the conclusion in lines 29-31 shifts focus toward the broader challenges and future optimization of gene drive systems. This conclusion does not clearly highlight the specific results of the study or how they relate directly to the original objective. It would be more effective to emphasize the actual findings, such as which target genes performed best and under what conditions, and how these findings support or contradict the stated goals. The study primarily aimed to assess the efficiency of specific female fertility genes and to evaluate strategies for minimizing the formation of functional resistance alleles, rather than proposing a protocol for optimization. Therefore, better alignment is needed between the study's aim, experimental design, and concluding statements. Clarifying this alignment would also help refine the paper's focus and more accurately communicate its contribution, including whether it is exploratory, comparative, or methodologically driven.

      -We have revised the abstract to clarify the alignment as suggested by the reviewer. We note that this discrepancy is due to the initial aim of our study being different than some of the important lessons learned along the way regarding fitness effects from Cas9 deposition in split drives. Still, we agree that it would be better to be more consistent in our wording and conclusions.

      Introduction: One of the key design elements in this study is the use of multiplexed gRNAs. It is reasonable to assume that this strategy may influence fitness costs, potentially in more than one way. Given that assessing fitness cost is a major focus of the study, it would be helpful to include a brief discussion of previous research examining how multiplexed gRNAs may impact fitness in gene drive systems. A short review of relevant studies, if available, would provide important context for interpreting the results and could help clarify whether any observed fitness costs might be attributed, at least in part, to the multiplexing strategy itself. This addition could be appropriately placed around line 102, where gRNA design is discussed.

      -We have added an explanation in the Discussion to mention this. However, it has not been conclusively shown that multiplexed gRNAs have any effect on fitness. Indeed, there have been some multiplexed constructs that seem to have no fitness effect, and some that have high fitness costs. This doesn’t rule out the potential for multiplexed gRNAs to influence fitness itself, but it means that the mechanism may be complex. The new text reads:

      “Another potential though unconfirmed source of fitness cost arises from increased cleavage events associated with multiplexed gRNAs, where the greater number of gRNAs can enhance the overall cut rate compared to single-gRNA designs.”

      Line 42: Cas12a also showed efficacy using gene drives in yeast and Drosophila.

      -We now mention Cas12a at the beginning of the introduction.

      Line 133: The paragraph begins by stating that homologs of the target genes were identified and aligned. To improve clarity, especially for readers who are new to gene drive research, it would be helpful to begin the paragraph with a brief introductory sentence explaining the purpose of this step. For example, you could state the importance of identifying and aligning homologs to assess the conservation of target sites across species, which is critical for evaluating the broader applicability of gene drive strategies. This context would guide the reader and clarify the relevance of the analysis.

      -We have added the explanation as suggested.

      Lines 144-145: You mention that "the exception was tra, for which two constructs containing different gRNA sets were generated." For clarity, it would be helpful to provide a brief explanation of why two different gRNA sets were used for tra, and whether this differs from the approach taken with the other target genes. It's currently unclear whether all other genes were targeted using a single, standardized set of gRNAs, and this should be explicitly stated here for consistency, even though it is mentioned later in the plasmid construction section. Additionally, I suggest combining the sections on gRNA target design and plasmid construction. Since these components are closely related and sequential in the experimental workflow, presenting them together would improve the logical flow and help readers follow the methodology more smoothly.

      -We have combined both the gRNA target design and plasmid construction sections. We also discuss the two tra constructs early in the results section (see response to reviewer 2).

      Line 210: The analysis of the cage experiments was based on models from previous studies that used a simplified assumption of a single gRNA at the target site. While I understand this approach has precedent, it raises important questions about potential limitations. Specifically, could simplifying the analysis to one gRNA affect the conclusions of this study, given that the experimental design involves multiplexed gRNAs with four distinct target sites? The implications of using this simplified model should be clearly addressed, as the dynamics of drive efficiency, resistance formation, and fitness effects may differ when multiple gRNAs are employed. Additionally, while I am not a statistician, it is worth asking whether more sophisticated modeling approaches could be applied to account for all four gRNAs, rather than reducing the system to a single-gRNA framework. A discussion of the modeling choices and their potential consequences would strengthen the interpretation of the results.

      -We have clarified this. While we have modeled multiple gRNAs with high fidelity in SLiM, the maximum likelihood method is not very amenable to such treatment. It may cause our fitness estimate to be a small overestimate, but give the low fitness inferences, would certainly not have a large enough effect to fundamentally change any conclusion (and should be of a consistent level across all cages). We now discuss this in the methods section.

      Lines 297-300: Your results show that the expression of all target genes was higher in females, except for oct, which had higher expression in males. Additionally, oct expression decreased in adults. Given that oct is functionally important for ovulation and fertilization, processes that are primarily required in adult females, this pattern is somewhat unexpected. Could there be a possible explanation for the lower expression of oct, particularly in females and especially in adults, where its function would presumably be most critical? A brief discussion or hypothesis addressing this discrepancy would help clarify the biological relevance and interpretation of the expression data.

      -Based on transcriptome data from FlyBase, derived from Graveley et al. (2011), Oct is indeed expressed slightly higher in adult males than in adult females. This difference may be attributed to the fact that the female flies used in the study were virgins; Oct expression could be upregulated post-mating to mediate ovulation. Additionally, Oct is expressed not only in reproductive tissues but also in other organs such as the nervous system, where sex-specific differences in cell type composition or neural activity may contribute to the observed expression bias. However, high expression does not necessarily correlate with essential expression. Though Oct could have multiple functions, it’s still possible that the only apparent phenotype upon knockout is female sterility. We have added the following text: “This male-biased expression may result from the use of virgin females in the dataset, as oct is likely upregulated after mating. Moreover, oct is also expressed in non-reproductive tissues such as the nervous system, which may contribute to sex-specific differences in expression38. While oct may have multiple functions, it is possible that it is only essential for female fertility.”

      Lines 346-347: What is the distance between the gRNA target sites within each gene? Are all of the gRNAs confirmed to be active? It would be valuable to include a table summarizing the distance between target sites for each gene, the activity levels of the individual gRNAs, and the corresponding homing rates. This would help determine whether there is a correlation between gRNA spacing and drive efficiency. For example, Lopez del Amo et al. (Nature Communications, 2020) demonstrated that even a 20-nucleotide mismatch at each homology arm can significantly reduce drive conversion. Including such a comparative analysis in your study could provide important insights into how gRNA arrangement influences overall drive performance and would be incredibly helpful for future multiplexing designs.

      -We have showed previously that close spacing of gRNAs should help maintain high drive conversion efficiency, and this is alluded to indirectly in the introduction (we now mention it more directly). In our study, gRNAs were positioned in close proximity without overlap, with the general distance between the outermost cut sites within each gene being We have added a summary table (Table S3) presenting the sequencing results, which also showed gRNA activity levels. Notably, most but not all gRNAs were active, at least for embryo resistance (low to moderate activity may still be present in the germline). Coupled with varying activity levels for those that were active, this likely contributed to reduced drive conversion due to mismatches at the homology arms. This observation supports the notion that drive performance could be optimized by selecting and arranging more active gRNAs. Consistent with this, our second construct targeting tra (tra-v2) exhibited a higher inheritance rate than the original construct, suggesting that gRNA arrangement and activity critically influence drive efficiency. Testing the activity of every single gRNA requires the construction of multiple gRNA lines, since in vitro or ex vivo tests will not be accurate as in vivo transformation test. However, in our study, as long as drive conversion rates were reasonably high, further optimization was not needed. Therefore, the multiplexing gRNA design can not only maximize drive conversion, but also reduce labor filtering an increased number of 1-gRNA designs with lower performance.

      Line 434: I was not able to find any sequencing data. This is important to evaluate gRNA activities and establish correlations with drive efficiency.

      -We have added a summary of the sequencing results in Table S3, though these are for embryo resistance alleles. Note that while high gRNA activity is correlated with high drive inheritance, these are not directly related. For suppression drives, germline resistance rates are usually of low importance compared to drive inheritance, so we did not assess these in detail (and pessimistically assumed complete germline resistance in our cage models).

      Line 482: Did the authors test Cas9-only individuals (without the drive) against a wild-type population? This would help determine whether Cas9 alone has any unintended fitness effects. Additionally, is Cas9 expression stable over time and across generations? It would be helpful to include any observations or thoughts on the long-term stability and potential fitness impact of Cas9 in the absence of the drive element.

      -We did not perform a direct comparison of Cas9-only individuals and wild-type flies in this study. However, previous studies (Champer et al., Nature Communications, 2020 - Langmuller et al., eLife 2022), which we now cite in the discussion, found no significant fitness difference between very similar Cas9-expressing lines and wild type in the absence of a drive element, indicating no significant fitness impact from Cas9 alone (though we cannot exclude a small effect, it certainly could not come close to explaining our results). In our experiments, Cas9 expression was generally stable across generations, as indicated by consistent drive inheritance and fertility test results obtained from independent batches. Separate from this study, we did observe rare instability in one nanos-Cas9 line, which had remained stable for over five years but recently became inactive (low population maintenance size may have caused stochastic removal of the functional allele). It is something to watch out for, but probably not on the timescale of a single study.

      Discussion: I would appreciate a more direct and clearly stated conclusion that summarizes the key findings of the study. While the discussion addresses the main outcomes in depth, presenting a concise concluding paragraph, either at the end of the discussion or as a standalone conclusion section, would provide a stronger and more definitive closing statement. This would help reinforce what the study ultimately achieved and ensure the main takeaways are clearly communicated to the reader.

      -We have revised and expanded the last paragraph of the discussion section to make our findings more direct and clear.

      Overall, I believe this is an important study that offers valuable insights for advancing the design of CRISPR-based gene drives. The findings contribute to the development of more efficient and practical gene drive prototypes, bringing the field closer to real-world applications.

      Reviewer #3 (Significance (Required)):

      In this study, Xu and colleagues explored how CRISPR-based homing gene drives could be used to suppress insect populations by targeting female fertility genes in Drosophila melanogaster. They engineered split gene drives with multiplexed guide RNAs to target nine candidate genes, seeking to prevent functional resistance and achieve high drive conversion with minimal fitness costs. Among the targets, the stall (stl) and octopamine β2 receptor (oct) genes performed better, showing the highest inheritance rates in lab crosses. When tested in population cages, the stl drive was able to completely eliminate a fly population, but only when released at a high enough frequency, while other cages failed. These failures were traced and explained by fitness cost in drive-carrying females, caused largely by maternally deposited Cas9, which led to embryo resistance and reduced fertility. Through additional fertility assays and modeling, the team confirmed that the origin and timing of Cas9 expression, particularly from mothers, significantly impacted drive success. Surprisingly, even when Cas9 was driven by promoters with supposedly low somatic activity, such as nanos, fitness still persisted. The study revealed that while gene drives can be powerful, their effectiveness relies on finely balanced factors like promoter choice, drive architecture, and gene function. Overall, the research offers valuable lessons for designing robust, next-generation gene drives aimed at ecological pest control.

      -We sincerely appreciate the reviewer’s positive and thoughtful comments. We agree that the points raised highlight the importance of our findings and hope that our revisions have further improved both the clarity and overall content of the manuscript.

    2. Note: This preprint has been reviewed by subject experts for Review Commons. Content has not been altered except for formatting.

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      Referee #2

      Evidence, reproducibility and clarity

      Paper summary

      The manuscript by Xu. et al presents an insightful and valuable contribution to the field of gene drive research. The manuscript by Xu et al. presents an insightful and valuable contribution to the field of gene drive research. The strategy of targeting and disrupting female fertility genes using selfish homing genetic elements was first proposed by Burt in 2003. However, for this approach to be effective, the phenotypic constraints associated with gene disruption have meant that the pool of suitable target genes remains relatively small - notwithstanding the significant expansion in accessible targets enabled by CRISPR-based genome editing nucleases. Population suppression gene drives are well developed as proof-of-principle systems, with some now in the late stages of development as genetic control strains. However, advancing the pipeline will require a broader set of validated target genes - both to ensure effectiveness across diverse species and to build redundancy into control strategies, reducing reliance on any single genetic target. In their paper, the authors conduct a systematic review of nine female fertility genes in Drosophila melanogaster to assess their potential as targets for homing-based suppression gene drives. The authors first conduct a thorough bioinformatic review to select candidate target genes before empirically testing candidates through microinjection and subsequent in vivo analyses of drive efficiency, population dynamics, and fitness costs relating to fecundity and fertility. After finalising their results, the authors identify two promising candidate target genes - oct and stl - which both demonstrate high gene conversion rates and, regarding the latter, can successfully suppress a cage population at a high release frequency. However, the manuscript suffers from a lack of in-depth discussion of a key limitation in its experimental design - namely, that the authors utilise a split-drive design to assess population dynamics and fitness effects when such a drive will not reflect release scenarios in the field. The review below highlights some major strengths and weaknesses of the paper, with suggestions for improvement.

      Key strengths

      The study's most significant strength is in its systematic selection and empirical testing of nine distinct genes as targets for homing-based gene drive, hence providing a valuable resource that substantially expands the pool of potential targets beyond the more commonly studied target genes (e.g. nudel, doublesex, among others). The identification of suitable target genes presents a significant bottleneck in the development of gene drives and the work presented here provides a foundational dataset for future research. The authors bolster the utility of their results by assessing the conservation of candidate genes across a range of pest species, suggesting the potential for broader application. A key finding in the paper is the successful suppression of a cage population using a stl-targeting gene drive (albeit at a high release frequency). This provides a critical proof-of-principal result demonstrating that stl is a viable target for a suppression drive. While in the paper suppression was not possible at lower release frequencies, together, the results provide evidence for complex population dynamics and threshold effects that may govern the success or failure of a gene drive release strategy - hence moving the conversation from a technical perspective ("can it work") to how a gene drive may be implemented. Moreover, the authors also employ a multiplexed gRNA strategy for all their gene drive designs and in particular their population suppressive gene drive targeting stl. This provides further proof-of-principal evidence for multiplexed gRNAs in order to combat the evolution of functional resistance following gene drive deployment. Finally, a further strength of this paper is in the clever dissection of fitness effects resulting from maternal Cas9 deposition. The authors design and perform a robust set of crosses to elucidate the parental source of fitness effects (i.e. maternally, paternally, or biparentally derived Cas9), finding (as they and others have before) that embryonic fitness was significantly reduced when Cas9 was inherited from a maternal source. As discussed, the authors conclude that maternal deposition is particularly pronounced in the context of split drives as opposed to complete drives, with the implication being that a complete drive might succeed where a split-drive has failed; thus providing a key directive for future study.

      Concerns

      The manuscript's central weakness lies in its interpretation of the results from the cage experiments - namely that a split-drive system was used to "mimic the release of a complete drive". In the study, mosquitoes carrying the drive element (i.e. the gRNA) were introduced into a population homozygous for the Cas9 element over several generations. This design is likely not representative of a real-world scenario and, as the authors state, likely exaggerates fitness costs. This is because the females carrying Cas9 will maternally deposit Cas9 protein into her eggs, with activity spanning several generations. When mated with a drive-carrying male the gRNA will immediately co-exist with maternally deposited Cas9, leading to early somatic cleavage and significant fitness costs (reflected in the author's own fertility crosses). This is fundamentally different to how a complete drive would function in a real-world release, where complete-drive males would mate with wild-type females not carrying Cas9. Their offspring would carry the drive element but would not be exposed to maternally deposited cas9, thus deleterious maternal effects would only begin to appear in the subsequent generation from females carrying the drive. Fitness costs measured from split-drive designs are therefore likely substantially overestimated compared to what would occur during the initial but critical release phase of a complete drive. This flaw weakens the paper's ability to predict the failure or success of the screened targets in a complete drive design, thus weakening the interpretation of the results from the cage trials. As a suggestion for improvement, the authors should explicitly and more prominently discuss the limitations of their split-drive model compared to complete drive models, both in the Results and Discussion. It is also recommended to include a schematic for both strategies that contrasts the experimental setup design (i.e. release of the drive into a Cas9 homozygous background) with a complete-drive release, clearly illustrating differences in maternal deposition pathways. This will not only contextualise the results and support the author's conclusion that observed fitness costs are likely an overestimate but will further strengthen the arguments that the candidate target genes found in this study may still be viable in a complete-drive system.

      A second weakness in the manuscript relates to its limited explanation and discussion of key concepts. For example, the manuscript reports a stark difference in outcome of the two stl-targeting drives, where a high initial release in cage 1 led to population elimination versus a failure of the drive to spread in cage 2. The authors attribute this to vague "allele effects" and stochastic factors such as larval competition; however the results appear reminiscent of the Allee effect, which is a well-characterised phenomenon describing the correlation of population size (or density) and individual fitness (or per capita population growth rate). Using their results as an example, is it plausible that the high-frequency initial release in cage 1 imposed enough genetic load to quickly drive the population density below the Allee threshold thus quickly leading to population eradication. In cage 2, the low-frequency at initial release was insufficient to cross the Allee threshold. Omitting mention of this ecological principal greatly weakens the Discussion, and further presents a missed opportunity to discuss one of the more crucial strengths of the paper - that is, in providing a deeper insight into the practical requirements for successful field implementation. In a similar vein, the authors provide only a superficial mechanistic discussion into the fitness costs associated with drives targeting key candidate genes. The paper would benefit from a deeper discussion regarding the specific molecular functions of top-performing genes (stl, oct, nox) and how unintended Cas9 activity could disrupt their activity, integrating known molecular functions with observed fitness costs. For instance, oct encodes a G-protein coupled receptor essential for ovulation and oviduct muscle relaxation, thus disruption to the oct gene would directly impair egg-laying which would account for the observed phenotypic effects. A deeper discussion linking unintended Cas9 activity to the specific, sensitive functions of target genes would elevate the paper from a descriptive screen to a more insightful mechanistic study.

      It is curious that the authors chose two genes on the X chromosome as targets. In insects (such as Drosophila here) that have heterogametic sex chromosomes, homing is not possible in the heterogametic sex as there is no chromosome to home to - so there will be no homing in males. On top of that, there is usually some fitness effect in carrier (heterozygous) females, so in a population these are nearly always bad targets for drives - unless there is some other compelling reason to choose that target?

      Minor comments

      • Enhanced clarity in the Figures and data presentation would greatly improve readability. For example, Figure 5 is critical yet difficult to interpret; consider changing x-axis labels from icons to explicit text (e.g. "biparental Cas9", "maternal cas9", "paternal Cas9"). Similarly, Figure 4 is difficult to read and the y-axis label "population size" is ambiguous; consider adding shapes or dashes (rather than relying solely on colour) and clarifying the y-axis (e.g. no. adults collected) in the legend.
      • Expand on or include a schematic to show the differences in construction between the tra-v1 and tra-v2 constructs to better contextualise the discrepancies in results (e.g. inheritance rates of 61%-66% for tra-v1 and 81%-83% for tra-v2 between the two.
      • Minor typos e.g.:
        • Line 87: "form" to "from"
        • Line 484: "expended" to "expanded
        • Line 560: "foor" to "for"
        • Line 732: "conversed" to "conserved
      • Clarify the split drive system: the authors introduce split drive for the first time in Line 118. They should at least give a clear definition and explanation of split drive and complete drive in the introduction.
      • Line 237-238., The fitness evaluation lacks a clear description of controls. How were non-drive flies generated and validated as controls?
      • Line 409-412.,line 423.,The high inheritance rates of stl and oct drives are impressive; however, variation in results across Cas9 promoters should be explained further in the discussion.
      • Line 414: The CG4415 promoter yielded reduced drive conversion rates in females, yet is still referred to as a promising promoter. This conclusion seems optimistic and should be clarified/more justified.
      • Specify the number of flies released, sex ratio, and cage size per generation (Line 466). This is essential for reproducibility.

      Significance

      Overall the manuscript presents a valuable and timely resource for gene drive research, in particular for its systematic appraisal of potential target genes for population suppression drives and its rigorous assessment of the impact of maternal Cas9 deposition. The value in the generation and empirical testing of a novel multiplexed stl-targeting gene drive that led to population eradication in a cage trial should not be understated. While several key aspects of the discussion of the manuscript should be strengthened, the study presents a meaningful contribution to the field, extending previous work and and outlines important considerations for the design and implementation of effective gene drive systems.

    3. Note: This preprint has been reviewed by subject experts for Review Commons. Content has not been altered except for formatting.

      Learn more at Review Commons


      Referee #1

      Evidence, reproducibility and clarity

      The manuscript by Xu et al. investigated split gene drive systems by targeting multiple female essential genes involved in fertility and viability in Drosophila. The authors evaluate the suppression efficiency through individual corsses and cage trials. Resistance allele formation and fitness costs are explored by examining the sterility and fertility of each line. Overall, the experimental design is sound and methods are feasible. The work is comprehensive, and conclusions are well supported by the data. This work offers informative insights that could guide the design of suppression gene drive systems in other invasive disease vectors or agricultural pests.

      However, several points requiring clarification or improvement:

      1. Methodological clarity: Some experimental details are indufficiently described, for example, regarding the setup of genetic crosses involving different Cas9 derivatives. In line 197-198, "the mated females, together with females that were mated with Cas9 only males", it is unclear whether the latter group refers to gRNA-females.
      2. Regarding the inheritance rates, you included the reverse orientation of CG4415-Cas9, as I understood, it means this component is in reverse orientation with fluorescent marker. Since it is standard to design adjacent components in opposite direction to avoid transcriptional interference, the rationale for including this comparison should be better justified.
      3. Embryo resistance is inferred from the percentage of sterile drive females derived from drive mothers. How many female individuals were analysed per line and why deep sequencing was not employed to directly detect resistance alleles.
      4. Masculinisation phenotypes were observed upon disruption of tra gene. How strong intersexes were distinguished from males? What molecular markers were used to determine genetic sex. This information should be clearly provided.
      5. It would be more appropriate to use "hatchability"rather than "fertility" when referring to egg-to-larva viability.
      6. In cage trials, a complete gene drive is mimicked by introducing Cas9 to the background population, but this differs from actual complete gene drive, due to potential effects from separate insertion sites (different chromosome or loci). These difference could impact the system's performance and should be discussed.
      7. Given the large amount of data presented, it would improve readability and interpretation if each result section concluded with a concise summary highlighting the key findings and implications.

      Significance

      The authors evaluate suppression efficiency through individual courses and cage trials. Resistance allele formation and fitness costs are explored by examining the sterility and fertility of each line. Overall, the experimental design is sound and methods are feasible. The work is comprehensive, and conclusions are well supported by the data. This work offers informative insights that could guide the design of suppression gene drive systems in other invasive disease vectors or agricultural pests.

    1. We would like to thank Najko Jahn and Mikael Laakso for their very positive and thoughtful reviews, which significantly improved our article. In response to the reviewers' specific comments, we have corrected all identified errors and made a number of improvements. In particular, regarding the presentation of results (Figure 3) and a more comprehensive speculation on the role of national and international infrastructure providers for unlocking article level metadata on transformative agreements. These are the changes we made in response to the reviewer’s comments:

      Response to Reviewer #1: Najko Jahn

      We agree that a broader discussion of transformative agreement complexity would be valuable, and this paper provides important insights—particularly regarding author opt-out possibilities, contract caps, and exclusion of non-research articles. However, we believe such discussion extends beyond the scope of this paper which we have meant primarily as a study to validate a method for tracking / analysing transformative agreements using open data.

      Following the reviewer's advice, we have updated the concluding section to include discussion of how various national and international infrastructures could facilitate more open availability of article-level transformative agreement data.

      We have implemented the reviewer's suggestion to present main results earlier in the paper. The key findings regarding matched and unmatched articles are now introduced on pages 3-4.

      The reviewer correctly identified our imprecise description of journal identification methodology. We have corrected both the figure and text to accurately reflect our use of ISSN (obtained from Crossref) rather than ISSN-L.

      Response to Reviewer #2: Mikael Laakso

      We thank the reviewer for their insightful feedback. We have implemented all suggested improvements to our results presentation, enhancing the Venn diagram in Figure 3 by: 1) making areas proportional to data, 2) improving label clarity, 3) providing clearer caption explanations, and 4) revising the accompanying text to follow the figure's label sequence.

      The revised version of the article is available here.

    1. This manuscript examines preprint review services and their role in the scholarly communications ecosystem.  It seems quite thorough to me. In Table 1 they list many peer-review services that I was unaware of e.g. SciRate and Sinai Immunology Review Project.

      To help elicit critical & confirmatory responses for this peer review report I am trialling Elsevier’s suggested “structured peer review” core questions, and treating this manuscript as a research article.

      Introduction

      1. Is the background and literature section up to date and appropriate for the topic?

        Yes.

      2. Are the primary (and secondary) objectives clearly stated at the end of the introduction?

        No. Instead the authors have chosen to put the two research questions on page 6 in the methods section. I wonder if they ought to be moved into the introduction – the research questions are not methods in themselves. Might it be better to state the research questions first and then detail the methods one uses to address those questions afterwards? [as Elsevier’s structured template seems implicitly to prefer.

      Methods

      1. Are the study methods (including theory/applicability/modelling) reported in sufficient detail to allow for their replicability or reproducibility?

        I note with approval that the version number of the software they used (ATLAS.ti) was given.

        I note with approval that the underlying data is publicly archived under CC BY at figshare.

        The Atlas.ti report data spreadsheet could do with some small improvement – the column headers are little cryptic e.g. “Nº  ST “ and “ST” which I eventually deduced was Number of Schools of Thought and Schools of Thought (?)   

        Is there a rawer form of the data that could be deposited with which to evidence the work done? The Atlas.ti report spreadsheet seemed like it was downstream output data from Atlas.ti. What was the rawer input data entered into Atlas.ti? Can this be archived somewhere in case researchers want to reanalyse it using other tools and methods.

        I note with disapproval that Atlas.ti is proprietary software which may hinder the reproducibility of this work. Nonetheless I acknowledge that Atlas.ti usage is somewhat ‘accepted’ in social sciences despite this issue.

        I think the qualitative text analysis is a little vague and/or under-described: “Using ATLAS.ti Windows (version 23.0.8.0), we carried out a qualitative analysis of text from the relevant sites, assigning codes covering what they do and why they have chosen to do it that way.” That’s not enough detail. Perhaps an example or two could be given? Was inter-rater reliability performed when ‘assigning codes’ ? How do we know the ‘codes’ were assigned accurately?

      2. Are statistical analyses, controls, sampling mechanism, and statistical reporting (e.g., P-values, CIs, effect sizes) appropriate and well described?

        This is a descriptive study (and that’s fine) so there aren’t really any statistics on show here other than simple ‘counts’ (of Schools of Thought) in this manuscript. There are probably some statistical processes going on within the proprietary qualitative analysis of text done in ATLAS.ti but it is under described and so hard for me to evaluate. 

      Results

      1. Is the results presentation, including the number of tables and figures, appropriate to best present the study findings?

        Yes. However, I think a canonical URL to each service should be given.  A URL is very useful for disambiguation, to confirm e.g. that the authors mean this Hypothesis (www.hypothes.is) and NOT this Hypothesis (www.hyp.io). I know exactly which Hypothesis is the one the authors are referring to but we cannot assume all readers are experts 😊

        Optional suggestion: I wonder if the authors couldn’t present the table data in a slightly more visual and/or compact way? It’s not very visually appealing in its current state. Purely as an optional suggestion, to make the table more compact one could recode the answers given in one or more of the columns 2, 3 and 4 in the table e.g. "all disciplines = ⬤ , biomedical and life sciences = ▲, social sciences =  ‡  , engineering and technology = † ". I note this would give more space in the table to print the URLs for each service that both reviewers have requested.

        ———————————————————————————————

        | Service name | Developed by | Scientific disciplines | Types of outputs |

        | Episciences | Other | ⬤ | blah blah blah. |

        | Faculty Opinions | Individual researcher | ▲ | blah blah blah. |

        | Red Team Market | Individual researcher | ‡ | blah blah blah. |

        ———————————————————————————————

        The "Types of outputs" column might even lend themselves to mini-colour-pictograms (?) which could be more concise and more visually appealing? A table just of text, might be scientifically 'correct' but it is incredibly dull for readers, in my opinion.

      2. Are additional sub-analyses or statistical measures needed (e.g., reporting of CIs, effect sizes, sensitivity analyses)?

        No / Not applicable. 

      Discussion

      1. Is the interpretation of results and study conclusions supported by the data and the study design?

        Yes.

      2. Have the authors clearly emphasized the limitations of their study/theory/methods/argument?

        No. Perhaps a discussion of the linguistic/comprehension bias of the authors might be appropriate for this manuscript. What if there are ‘local’ or regional Chinese, Japanese, Indonesian or Arabic language preprint review services out there? Would this authorship team really be able to find them?

      Additional points:

      • Perhaps the points made in this manuscript about financial sustainability (p24) are a little too pessimistic. I get it, there is merit to this argument, but there is also some significant investment going on there if you know where to look. Perhaps it might be worth citing some recent investments e.g. Gates -> PREreview (2024) https://content.prereview.org/prereview-welcomes-funding/  and Arcadia’s $4 million USD to COAR for the Notify Project which supports a range of preprint review communities including Peer Community In, Episciences, PREreview and Harvard Library.  (source: https://coar-repositories.org/news-updates/coar-welcomes-significant-funding-for-the-notify-project/

      • Although I note they are mentioned, I think more needs to be written about the similarity and overlap between ‘overlay journals’ and preprint review services. Are these arguably not just two different terms for kinda the same thing? If you have Peer Community In which has it’s overlay component in the form of the Peer Community Journal, why not mention other overlay journals like Discrete Analysis and The Open Journal of Astrophysics.   I think Peer Community In (& it’s PCJ) is the go-to example of the thin-ness of the line the separates (or doesn’t!) overlay journals and preprint review services. Some more exposition on this would be useful.

    1. In "Researchers Are Willing to Trade Their Results for Journal Prestige: Results from a Discrete Choice Experiment", the authors investigate researchers’ publication preferences using a discrete choice experiment in a cross-sectional survey of international health and medical researchers. The study investigates publishing decisions in relation to negotiation of trade-offs amongst various factors like journal impact factor, review helpfulness, formatting requirements, and usefulness for promotion in their decisions on where to publish. The research is timely; as the authors point out, reform of research assessment is currently a very active topic. The design and methods of the study are suitable and robust. The use of focus groups and interviews in developing the attributes for study shows care in the design. The survey instrument itself is generally very well-designed, with important tests of survey fatigue, understanding (dominant choice task) and respondent choice consistency (repeat choice task) included. Respondent performance was good or excellent across all these checks. Analysis methods (pMMNL and latent class analysis) are well-suited to the task. Pre-registration and sharing of data and code show commitment to transparency. Limitations are generally well-described.

      In the below, I give suggestions for clarification/improvement. Except for some clarifications on limitations and one narrower point (reporting of qualitative data analysis methods), my suggestions are only that – the preprint could otherwise stand, as is, as a very robust and interesting piece of scientific work.

      1. Respondents come from a broad range of countries (63), with 47 of those countries represented by fewer than 10 respondents. Institutional cultures of evaluation can differ greatly across nations. And we can expect variability in exposure to the messages of DORA (seen, for example, in level of permeation of DORA as measured by signatories in each country, https://sfdora.org/signers/)..%3B!!NVzLfOphnbDXSw!HdeyeHHei6yWQHFjhN3deSSfp82ur9i9JNOLEVOYZN0BvyslUO2S8DlvjBbautmafJEvlUsxQZbT0JLQX7lO8EcOYtZsJkA%24&data=05%7C02%7Ca.l.brasil.varandas.pinto%40cwts.leidenuniv.nl%7C9f47a111adec49d04bb608dd0614ae94%7Cca2a7f76dbd74ec091086b3d524fb7c8%7C0%7C0%7C638673408085242099%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=by5mhPfSM0MFFG9LE2iiYjdtSs5IhvpuukqVv%2FLak2s%3D&reserved=0 "https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsfdora.org%2Fsigners%2F).%3B!!NVzLfOphnbDXSw!HdeyeHHei6yWQHFjhN3deSSfp82ur9i9JNOLEVOYZN0BvyslUO2S8DlvjBbautmafJEvlUsxQZbT0JLQX7lO8EcOYtZsJkA%24&data=05%7C02%7Ca.l.brasil.varandas.pinto%40cwts.leidenuniv.nl%7C9f47a111adec49d04bb608dd0614ae94%7Cca2a7f76dbd74ec091086b3d524fb7c8%7C0%7C0%7C638673408085242099%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=by5mhPfSM0MFFG9LE2iiYjdtSs5IhvpuukqVv%2FLak2s%3D&reserved=0") In addition, some contexts may mandate or incentivise publication in some venues using measures including IF, but also requiring journals to be in certain databases like WoS or Scopus, or having preferred journal lists). I would suggest the authors should include in the Sampling section a rationale for taking this international approach, including any potentially confounding factors it may introduce, and then adding the latter also in the limitations.

      2. Reporting of qualitative results: In the introduction and methods, the role of the focus groups and interviews seems to have been just to inform the design of the experiment. But then, results from that qualitative work then appear as direct quotes within the discussion to contextualise or explain results. In this sense though, the qualitative results are being used as new data. Given this, I feel that the methods section should include description of the methods and tools used for qualitative data analysis (currently it does not). But in addition, to my understanding (and this may be a question of disciplinary norms – I’m not a health/medicine researcher), generally new data should not be introduced in the discussion section of a research paper. Rather the discussion is meant to interpret, analyse, and provide context for the results that have already been presented. I personally hence feel that the paper would benefit from the qualitative results being reported separately within the results section.

      3. Impact factors – Discussion section: While there is interesting new information on the relative trade-offs amongst other factors, the most emphasised finding, that impact factors still play a prominent role in publication venue decisions, is hardly surprising. More could perhaps be done to compare how the levels of importance reported here differ with previous results from other disciplines or over time (I know a like-for-like comparison is difficult but other studies have investigated these themes, e.g., https://doi.org/10.1177/01655515209585). In addition, beyond the question of whether impact factors are important, a more interesting question in my view is why they still persist. What are they used for and why are they still such important “driver[s] of researchers’ behaviour”? This was not the authors’ question, and they do provide some contextualisation by quoting their participants, but still I think they could do more to contextualise what is known from the literature on that to draw out the implications here. The attribute label in the methods for IF is “ranking”, but ranking according of what and for what? Not just average per-article citations in a journal over a given time frame. Rather, impact factors are used as a proxy indicators of less-tangible desirable qualities – certainly prestige (as the title of this article suggests), but also quality, trust (as reported by one quoted focus group member “I would never select a journal without an impact factor as I always publish in journals that I know and can trust that are not predatory”, p.6), journal visibility, importance to the field, or improved chances of downstream citations or uptake in news media/policy/industry etc. Picking apart the interactions of these various factors in researchers’ choices to make use of IFs (which is not in all cases bogus or unjustified) could add valuable context. I’d especially recommend engaging at least briefly with more work from Science and Technology Studies - especially Müller and de Rijcke’s excellent Thinking with Indicators study (doi: 10.1093/reseval/rvx023), but also those authors other work, as well as work from Ulrike Felt, Alex Rushforth (esp https://doi.org/10.1007/s11024-015-9274-5), Björn Hammerfelt and others.

      4. Disciplinary coverage: (1) A lot of the STS work I talk about above emphasises epistemic diversity and the ways cultures of indicator use differ across disciplinary traditions. For this reason, I think it should be pointed out in the limitations that this is research in Health/Med only, with questions on generalisability to other fields. (2) Also, although the abstract and body of the article do make clear the disciplinary focus, the title does not. Hence, I believe the title should be slightly amended (e.g., “Health and Medical Researchers Are Willing to Trade …”)

    1. Reviewer #3 (Public review):

      Summary:

      This is an exciting, comprehensive paper that demonstrates the role of GATA4 on OA-like changes in chondrocytes. The authors present elegant reverse translational experiments that justify this mechanism and demonstrate the sufficiency of GATA4 in a mouse model of osteoarthritis (DMM), where GATA4 drove cartilage degeneration and pain in a manner that was significantly worse than DMM alone. This could pave the way for new therapies for OA that account for both structural changes and pain.

      Strengths:

      (1) GATA4 was identified from human chondrocytes.

      (2) IHC and sequencing confirmed GATA4 presence.

      (3) Activation of SMADs is clearly shown in vitro with GATA4 overexpression.

      (4) The role of GATA4 was functionally assessed in vivo using the mouse DMM model, where the authors uncovered that GATA4 worsens OA structure and hyperalgesia in male mice.

      (5) It is interesting that GATA4 is largely known to be found in cardiac cells and to have a role in cardiac repair, metabolism, and inflammation, among other things listed by the authors in the discussion (in liver, lung, pancreas). What could this new knowledge of GATA4 mean for OA as a potentially systemically mediated disease, where cardiac disease and metabolic syndrome are often co-morbid?

      Weaknesses:

      I do not have further comments. Thank you for addressing the previously mentioned concerns.

    1. Reviewer #2 (Public review):

      This study uses all atom MD simulation to explore the mechanics of channel opening for the NOMPC mechanosensitive channel. Previously the authors used MD to show that external forces directed along the long-axis of the protein (normal to the membrane) results in AR domain compression and channel opening. This force causes two changes to the key TRP domains adjacent to the channel gate: 1) a compressive force pushes the TRP domain along the membrane normal, while 2) a twisting torque induces a clock-wise rotation on the TRP domain helix when viewing the bottom of the channel from the cytoplasm. Here, the authors wanted to understand which of those two changes are responsible for increasing the inner pore radius, and they show that it is the torque. The simulations in Figure 2 probe this question with different forces, and we can see the pore open with parallel forces in the membrane, but not with the membrane-normal forces. I believe this result as it is reproducible, the timescales are reaching 1 microsecond, and the gate is clearly increasing diameter to about 4 Å. This seems to be the most important finding in the paper, but the impact is limited since the authors already shows how forces lead to channel opening, and this is further teasing apart the forces and motions that are actually the ones that cause the opening.

    1. Reviewer #2 (Public review):

      In this work Thapliyal and Glauser tried to provide mechanistic understanding by which animals modulate their neural circuit responses to control nociceptive behavior on the basis of the dynamic internal feeding state. It is an important study that adds to growing body of evidences coming from multiple model systems. They have used elegant genetics, behavioral and Ca-imaging experiments to demonstrate how the auxiliary thermosensory neuron pair, AWC and one of the internal state sensing interneuron pair, ASI, respond to dynamic internal starvation-state to modulate behavioral response to noxious heat. Interestingly, these neuron pairs use distinct molecular mechanisms along with some other unidentified neurons to suppress heat-indued reversal response under short-term and prolonged starvations. The experiments are well performed that support most of the claims and provide important framework for future studies.

      I have some queries that if answered, will certainly enhance the study,

      (1) The results suggests that ASI is one of the primary drivers for the starvation-evoked behavioral plasticity, which regulates AWC activity under prolonged starvation. It raises many important questions including, a) how starvation modulates ASI response to heat? b) under prolonged starvation, whether ASI also promotes other, non-AWC, glutamatergic inhibitory neurons to suppress heat-induced reversal and how?

      (2) How does ASI regulate AWC activity? In the proposed model (figure 8) authors suggested an independent, unknown signal, other than INS-32 and NLP-18, from ASI to regulate AWC activity. However, from the results the existence of another signal is not very clear.

      (3) Previously, Takeishi et. al., showed that ins-1 dynamically modulates AWC-AIA mediated thermotaxis behavior based on the feeding state of the animal. It raises questions whether ins-1 also contributes to noxious heat-induced reversal behavior.

      (4) Experiments with AWC fate conversion mutants (nsy-1 and nsy-7) were very good ideas, however the results obtained were confusing. flp-6 mutant data suggests AWCoff would be essential for heat induced reversal, especially at the low intensity stimulus level. However, nsy-1 mutant forming two AWCon neurons showed complete rescue at the low heat level, which is quite opposite. Similarly, although less prominent, eat-4 rescue experiments suggested both nsy-1 and nsy-7 should behave normally at high heat condition, which was not the result observed.

    2. Reviewer #3 (Public review):

      Summary:

      Thapliyal and Glauser show that hunger alters how C. elegans respond to noxious thermal stimuli. Using targeted neural ablation, mutant analysis, and live-cell functional imaging the authors demonstrate that hunger changes the properties of AWC sensory neurons, which sense noxious heat. The authors further show that effects of hunger on nociception require ASI neurons, which are known to respond to hunger and mediate effects of food deprivation on behavior. Finally, the study uses mutant analysis to implicate glutamate and specific neuropeptides in thermal nociception and in modulation of nociceptors by hunger-responsive neurons.

      Strengths:

      The study clearly shows a strong effect of hunger on nociception and documents a striking effect of hunger on the intrinsic properties of AWC sensory neurons, which respond to noxious heat. The study also clearly and compellingly demonstrates that ablation of hunger-responsive ASI neurons blocks effects of hunger on nociceptive AWCs. These data, which constitute the kernel of the manuscript, are striking and exciting.

      Weaknesses:

      The study has some weaknesses that the authors should address.

      (1) Ablation of AWC neurons alters the basal sensitivity to noxious heat stimuli. This should be clearly noted in the description of the result and warrants some discussion.

      (2) Throughout the study it seems that data are replotted in multiple figure panels. The authors should clearly indicate in figure legends when this occurs. Also, the authors should ensure that statistical tests requiring multiple comparisons are correctly implemented and reflect the number of times experimental data are compared to a single set of control data.

      (3) How ASIs modulate AWCs remains unclear. The authors find that loss of INS-6, an insulin-like peptide provided by ASIs, partially recapitulates the effect of ASI ablation. This is observation is not further developed and instead the authors characterize other secreted factors that seem to mediate sensitization of animals to noxious heat stimuli. While it is interesting that there are multiple opposing inputs into the nociceptor circuit, the essential connection between ASIs and AWCs that underlies the foundational observations in figures 1 and 2 is not sufficiently characterized.

      (4) The assertion that 'starvation reshapes AWC responses from deterministic to stochastic' is not clearly supported by the data. AWC neurons seem capable of showing different responses to thermal stimuli, and the probabilities associated with these responses change after fasting. The different kinds of responses are seen under basal and fasted conditions.

    1. Author response:

      Reviewer #1 (Public review):

      (1) The strength of the relationship between the different transcriptional parameters and the mean expression output is displayed visually in Figures 5 and 7, but is not formally quantified. Given that the tau_off times seem more correlated to mean activity for some enhancers (e.g., rho) than others (e.g., sna SE), the quantification might be useful.

      We re-plot Figure 5 and Figure 7 to present the correlation between the studied burst parameters. As the reviewer suggested, after quantifying the correlation we can better study the correlation between the cells averaged tau-off and the cell-averaged fluorescence signal in some of the selected enhancers. As a result of these findings we decide to change our message and instead of claiming that the burst statistics are homogeneous over the embryo domain, to claim that these statistics have weak but significant correlations with the cell-averaged mean gene fluorescence.  

      (2) There are some mechanistic details that are not discussed in depth. For example, the authors observe that the accumulation and degradation of the MS2 signal have similar slopes. However, given that the accumulation represents the transcription of MS2 loops, while the degradation represents diffusion of nascent transcripts away from the site of transcription, there is no mechanistic expectation for this. The degradation of signal seems likely to be a property of the mRNA itself, which shouldn't vary between cells or enhancer reporters, but the accumulation rate may be cell- or enhancer-specific. Similarly, the activity time depends both on the time of transcription onset and the time of transcription cessation. These two processes may be controlled by different transcription factor properties or levels and may be interesting to disentangle.

      The accumulation slope represents the rate of nascent transcript production, which depends on transcription initiation frequency and RNA polymerase elongation rate. While transcription initiation rates can vary between enhancers, our results show that the loading rates are relatively comparable across different enhancer sequences (Figure 5D). Instead, the primary difference observed was in activity time and burst frequency, consistent with previous findings that enhancers predominantly modulate burst frequency (Fukaya et al., 2016). The degradation slope represents the diffusion of completed transcripts away from the transcription site, which should be an intrinsic property of the mRNA molecule and therefore independent of the regulatory sequences driving transcription.

      (3) There are previous analyses of the eve stripe dynamics, which the authors cite, but do not compare the results of their work to the previous work in depth.

      The goal of this manuscript is to compare transcriptional bursting properties across different enhancers, rather than to provide an in-depth analysis of eve stripe dynamics specifically. We analyzed four transgenic constructs with different enhancers alongside an endogenous eve construct, focusing on comparative bursting parameters rather than detailed eve expression patterns. Additionally, the previously published eve stripe dynamics data came from BAC constructs, whereas our data comes from the endogenous eve locus. This methodological difference makes direct comparison of stripe dynamics less straightforward and less relevant to our central research question about enhancer-driven bursting variability.

      Reviewer #2 (Public review):

      (1) The manuscript does not clearly delineate how this analysis extends beyond the prior landmark study (citation #40: Fukaya et al., 2016). While the current manuscript offers new modeling and statistics, more explicit clarification of what is novel in terms of biological conclusions and methodological advancement would help position the work.

      The prior study (Fukaya et al., 2016) characterized transcriptional bursting qualitatively, focusing on average burst properties per nucleus without systematic mathematical modeling or statistical analysis of burst-to-burst variability. While they demonstrated that enhancer strength correlates with burst frequency, no quantitative framework was developed to dissect the molecular mechanisms underlying these differences or to connect burst dynamics to spatial gene expression patterns.

      (1) We developed an explicit mathematical model with rigorous inference algorithms to quantify transcriptional states from fluorescence trajectories; (2) We performed comprehensive statistical analysis of burst timing distributions, revealing that inter-burst intervals follow exponential distributions while burst durations are hypo-exponentially distributed; (3) Most importantly, we discovered that burst kinetics (τON, τOFF) remain remarkably consistent across different genes and spatial locations, while spatial expression gradients arise primarily through modulation of activity time - the temporal window during which bursting occurs. This mechanistic insight reveals that enhancers regulate spatial patterning not by changing intrinsic burst properties, but by controlling the duration of transcriptionally permissive periods.

      (2) While the methods are explained in detail in the Supplementary Information, the manuscript would benefit from including a diagrammatic model and explicitly clarifying whether the model is descriptive or predictive in scope.

      We plan to prepare the diagrammatic model in the formal response. 

      (3) The interpretation that fluorescence decay reflects RNA degradation could be confounded by polymerase runoff or transcript diffusion from the transcription site. These potential limitations are not thoroughly discussed. (Write few lines in the discussion)

      This concern, related to the interpretation of the predictive model will be addressed in a future work. The decay in the fluorescence signal can be biologically related to the transcription termination, polymerase detachment, and diffusion. A key limitation of the approach is that the model is phenomenological and does not these capture processes that can be addressed with a more mechanistic model.

      (4) The so-called loading rate is used as an empirical parameter in fitting fluorescence traces, but is not convincingly linked to distinct biological processes. The manuscript would benefit from a more precise definition or reframing of this term.

      We modify the language of our definition of loading rate as follows: Loading rate is defined as the rate of increase of fluorescence signal following promoter activation. This quantity is a proxy measurement for the rate of RNA Polymerase II transcription initiation.” The full transcription process has multiple mechanisms including chromatin dynamics, 3D enhancer-promoter interactions, transcription factor binding, mRNA polymerase pausing, and interactions between developmental promoter motifs and associated proteins. We did not have access to specific measurements of these mechanisms and therefore cannot provide a solid biological meaning of the model behind the inference algorithm. However, the fact that we have reproducible results in biological replicas can support the robustness of our method at predicting the promoter state in the studied datasets. In the formal response we will compare the performance of our method with other available ones.

      Reviewer #3 (Public review):

      (1)The algorithm is not benchmarked against previously used algorithms in the field to infer ON and OFF times, for example, those based on Hidden Markov models. A comparison would help strengthen the support for this algorithm (if it really works well) or show at which point one must be careful when interpreting this data.

      We are implementing a benchmarking protocol to compare our results with the proposed and already published models. We expect to present this comparison in the formal response.

      (2) More broadly, the novelty of the findings and how those fit within the knowledge of the field is not super clear. A better account of previous findings that have already quantified ON, OFF times and so on, and how the current findings fit within those, would help better appreciate the significance of the work.

      To have a better clarity of the new findings we modified the title from “Regulation of Transcriptional Bursting and Spatial Patterning in Early Drosophila Embryo Development” to “Temporal Duration of Gene Activity is the main Regulator of Spatial Expression Patterns in Early Drosophila Embryos”.

      In short, (1) We developed an explicit mathematical model with rigorous inference algorithms to quantify transcriptional states from fluorescence trajectories; (2) We performed comprehensive statistical analysis of burst timing distributions, revealing that inter-burst intervals follow exponential distributions while burst durations are hypo-exponentially distributed; (3) Most importantly, we discovered that burst kinetics (τON, τOFF) remain remarkably consistent across different genes and spatial locations, while spatial expression gradients arise primarily through modulation of activity time - the temporal window during which bursting occurs. This mechanistic insight reveals that enhancers regulate spatial patterning not by changing intrinsic burst properties, but by controlling the duration of transcriptionally permissive periods.

    1. Reviewer #1 (Public review):

      Summary:

      The authors state the study's goal clearly: "The goal of our study was to understand to what extent animal individuality is influenced by situational changes in the environment, i.e., how much of an animal's individuality remains after one or more environmental features change." They use visually guided behavioral features to examine the extent of correlation over time and in a variety of contexts. They develop new behavioral instrumentation and software to measure behavior in Buridan's paradigm (and variations thereof), the Y-maze, and a flight simulator. Using these assays, they examine the correlations between conditions for a panel of locomotion parameters. They propose that inter-assay correlations will determine the persistence of locomotion individuality.

      Strengths:

      The OED defines individuality as "the sum of the attributes which distinguish a person or thing from others of the same kind," a definition mirrored by other dictionaries and the scientific literature on the topic. The concept of behavioral individuality can be characterized as: (1) a large set of behavioral attributes, (2) with inter-individual variability, that are (3) stable over time. A previous study examined walking parameters in Buridan's paradigm, finding that several parameters were variable between individuals, and that these showed stability over separate days and up to 4 weeks (DOI: 10.1126/science.aaw718). The present study replicates some of those findings, and extends the experiments from temporal stability to examining correlation of locomotion features between different contexts.

      The major strength of the study is using a range of different behavioral assays to examine the correlations of several different behavior parameters. It shows clearly that the inter-individual variability of some parameters is at least partially preserved between some contexts, and not preserved between others. The development of high-throughput behavior assays and sharing the information on how to make the assays is a commendable contribution.

      Weaknesses:

      The definition of individuality considers a comprehensive or large set of attributes, but the authors consider only a handful. In Supplemental Fig. S8, the authors show a large correlation matrix of many behavioral parameters, but these are illegible and are only mentioned briefly in Results. Why were five or so parameters selected from the full set? How were these selected? Do the correlation trends hold true across all parameters? For assays in which only a subset of parameters can be directly compared, were all of these included in the analysis, or only a subset?

      The correlation analysis is used to establish stability between assays. For temporal re-testing, "stability" is certainly the appropriate word, but between contexts it implies that there could be 'instability'. Rather, instead of the 'instability' of a single brain process, a different behavior in a different context could arise from engaging largely (or entirely?) distinct context-dependent internal processes, and have nothing to do with process stability per se. For inter-context similarities, perhaps a better word would be "consistency".

      The parameters are considered one-by-one, not in aggregate. This focuses on the stability/consistency of the variability of a single parameter at a time, rather than holistic individuality. It would appear that an appropriate measure of individuality stability (or individuality consistency) that accounts for the high-dimensional nature of individuality would somehow summarize correlations across all parameters. Why was a multivariate approach (e.g. multiple regression/correlation) not used? Treating the data with a multivariate or averaged approach would allow the authors to directly address 'individuality stability', along with the analyses of single-parameter variability stability.

      The correlation coefficients are sometimes quite low, though highly significant, and are deemed to indicate stability. For example, in Figure 4C top left, the % of time walked at 23{degree sign}C and 32{degree sign}C are correlated by 0.263, which corresponds to an R2 of 0.069 i.e. just 7% of the 32{degree sign}C variance is predictable by the 23{degree sign}C variance. Is it fair to say that 7% determination indicates parameter stability? Another example: "Vector strength was the most correlated attention parameter... correlations ranged... to -0.197," which implies that 96% (1 - R2) of Y-maze variance is not predicted by Buridan variance. At what level does an r value not represent stability?

      The authors describe a dissociation between inter-group differences and inter-individual variation stability, i.e. sometimes large mean differences between contexts, but significant correlation between individual test and retest data. Given that correlation is sensitive to slope, this might be expected to underestimate the variability stability (or consistency). Is there a way to adjust for the group differences before examining correlation? For example, would it be possible to transform the values to in-group ranks prior to correlation analysis?

      What is gained by classifying the five parameters into exploration, attention, and anxiety? To what extent have these classifications been validated, both in general, and with regard to these specific parameters? Is increased walking speed at higher temperature necessarily due to increased 'explorative' nature, or could it be attributed to increased metabolism, dehydration stress, or a heat-pain response? To what extent are these categories subjective?

      The legends are quite brief and do not link to descriptions of specific experiments. For example, Figure 4a depicts a graphical overview of the procedure, but I could not find a detailed description of this experiment's protocol.

      Using the current single-correlation analysis approach, the aims would benefit from re-wording to appropriately address single-parameter variability stability/consistency (as distinct from holistic individuality). Alternatively, the analysis could be adjusted to address the multivariate nature of individuality, so that the claims and the analysis are in concordance with each other.

      The study presents a bounty of new technology to study visually guided behaviors. The Github link to the software was not available. To verify successful transfer or open-hardware and open-software, a report would demonstrate transfer by collaboration with one or more other laboratories, which the present manuscript does not appear to do. Nevertheless, making the technology available to readers is commendable.

      The study discusses a number of interesting, stimulating ideas about inter-individual variability, and presents intriguing data that speaks to those ideas, albeit with the issues outlined above.

      While the current work does not present any mechanistic analysis of inter-individual variability, the implementation of high-throughput assays sets up the field to more systematically investigate fly visual behaviors, their variability, and their underlying mechanisms.

      Comments on revisions:

      While the incorporation of a hierarchical mixed model (HMM) appears to represent an improvement over their prior single-parameter correlation approach, it's not clear to me that this is a multivariate analysis. They write that "For each trait, we fitted a hierarchical linear mixed-effects model in Matlab (using the fit lme function) with environmental context as a fixed effect and fly identity (ID) as a random intercept... We computed the intraclass correlation coefficient (ICC) from each model as the between-fly variance divided by total variance. ICC, therefore, quantified repeatability across environmental contexts."

      Does this indicate that HMM was used in a univariate approach? Can an analysis of only five metrics of several dozen total metrics be characterized as 'holistic'?

      Within Figure 10a, some of the metrics show high ICC scores, but others do not. This suggests that the authors are overstating the overall persistence and/or consistency of behavioral individuality. It is clear from Figure S8 that a large number of metrics were calculated for each fly, but it remains unclear, at least to me, why the five metrics in Figure 10a are justified for selection. One is left wondering how rare or common is the 0.6 repeatability of % time walked among all the other behavioral metrics. It appears that a holistic analysis of this large data set remains impossible.

      The authors write: "...fly individuality persists across different contexts, and individual differences shape behavior across variable environments, thereby making the underlying developmental and functional mechanisms amenable to genetic dissection." However, presumably the various behavioral features (and their variability) are governed by different brain regions, so some metrics (high ICC) would be amenable to the genetic dissection of individuality/variability, while others (low ICC) would not. It would be useful to know which are which, to define which behavioral domains express individuality, and could be targets for genetic analysis, and which do not. At the very least, the Abstract might like to acknowledge that inter-context consistency is not a major property of all or most behavioral metrics.

      I hold that inter-trial repeatability should rightly be called "stability" while inter-context repeatability should be called "consistency". In the current manuscript, "consistency" is used throughout the manuscript, except for the new edits, which use "stability". If the authors are going to use both terms, it would be preferable if they could explain precisely how they define and use these terms.

    2. Author response:

      The following is the authors’ response to the previous reviews.

      Reviewer #1 (Public review):  

      Summary:  

      The authors state the study's goal clearly: "The goal of our study was to understand to what extent animal individuality is influenced by situational changes in the environment, i.e., how much of an animal's individuality remains after one or more environmental features change." They use visually guided behavioral features to examine the extent of correlation over time and in a variety of contexts. They develop new behavioral instrumentation and software to measure behavior in Buridan's paradigm (and variations thereof), the Y-maze, and a flight simulator. Using these assays, they examine the correlations between conditions for a panel of locomotion parameters. They propose that inter-assay correlations will determine the persistence of locomotion individuality.

      Strengths:  

      The OED defines individuality as "the sum of the attributes which distinguish a person or thing from others of the same kind," a definition mirrored by other dictionaries and the scientific literature on the topic. The concept of behavioral individuality can be characterized as: (1) a large set of behavioral attributes, (2) with inter-individual variability, that are (3) stable over time. A previous study examined walking parameters in Buridan's paradigm, finding that several parameters were variable between individuals, and that these showed stability over separate days and up to 4 weeks (DOI: 10.1126/science.aaw718). The present study replicates some of those findings and extends the experiments from temporal stability to examining correlation of locomotion features between different contexts.  

      The major strength of the study is using a range of different behavioral assays to examine the correlations of several different behavior parameters. It shows clearly that the inter-individual variability of some parameters is at least partially preserved between some contexts, and not preserved between others. The development of high-throughput behavior assays and sharing the information on how to make the assays is a commendable contribution.

      Weaknesses:  

      The definition of individuality considers a comprehensive or large set of attributes, but the authors consider only a handful. In Supplemental Fig. S8, the authors show a large correlation matrix of many behavioral parameters, but these are illegible and are only mentioned briefly in Results. Why were five or so parameters selected from the full set? How were these selected? Do the correlation trends hold true across all parameters? For assays in which only a subset of parameters can be directly compared, were all of these included in the analysis, or only a subset?  

      The correlation analysis is used to establish stability between assays. For temporal re-testing, "stability" is certainly the appropriate word, but between contexts it implies that there could be 'instability'. Rather, instead of the 'instability' of a single brain process, a different behavior in a different context could arise from engaging largely (or entirely?) distinct context-dependent internal processes, and have nothing to do with process stability per se. For inter-context similarities, perhaps a better word would be "consistency".  

      The parameters are considered one-by-one, not in aggregate. This focuses on the stability/consistency of the variability of a single parameter at a time, rather than holistic individuality. It would appear that an appropriate measure of individuality stability (or individuality consistency) that accounts for the high-dimensional nature of individuality would somehow summarize correlations across all parameters. Why was a multivariate approach (e.g. multiple regression/correlation) not used? Treating the data with a multivariate or averaged approach would allow the authors to directly address 'individuality stability', along with the analyses of single-parameter variability stability.

      The correlation coefficients are sometimes quite low, though highly significant, and are deemed to indicate stability. For example, in Figure 4C top left, the % of time walked at 23{degree sign}C and 32{degree sign}C are correlated by 0.263, which corresponds to an R2 of 0.069 i.e. just 7% of the 32{degree sign}C variance is predictable by the 23{degree sign}C variance. Is it fair to say that 7% determination indicates parameter stability? Another example: "Vector strength was the most correlated attention parameter... correlations ranged... to -0.197," which implies that 96% (1 - R2) of Y-maze variance is not predicted by Buridan variance. At what level does an r value not represent stability?

      The authors describe a dissociation between inter-group differences and inter-individual variation stability, i.e. sometimes large mean differences between contexts, but significant correlation between individual test and retest data. Given that correlation is sensitive to slope, this might be expected to underestimate the variability stability (or consistency). Is there a way to adjust for the group differences before examining correlation? For example, would it be possible to transform the values to in-group ranks prior to correlation analysis?

      What is gained by classifying the five parameters into exploration, attention, and anxiety? To what extent have these classifications been validated, both in general, and with regard to these specific parameters? Is increased walking speed at higher temperature necessarily due to increased 'explorative' nature, or could it be attributed to increased metabolism, dehydration stress, or a heat-pain response? To what extent are these categories subjective?

      The legends are quite brief and do not link to descriptions of specific experiments. For example, Figure 4a depicts a graphical overview of the procedure, but I could not find a detailed description of this experiment's protocol.

      Using the current single-correlation analysis approach, the aims would benefit from re-wording to appropriately address single-parameter variability stability/consistency (as distinct from holistic individuality). Alternatively, the analysis could be adjusted to address the multivariate nature of individuality, so that the claims and the analysis are in concordance with each other.

      The study presents a bounty of new technology to study visually guided behaviors. The Github link to the software was not available. To verify successful transfer or open-hardware and open-software, a report would demonstrate transfer by collaboration with one or more other laboratories, which the present manuscript does not appear to do. Nevertheless, making the technology available to readers is commendable.

      The study discusses a number of interesting, stimulating ideas about interindividual variability and presents intriguing data that speaks to those ideas, albeit with the issues outlined above.

      While the current work does not present any mechanistic analysis of interindividual variability, the implementation of high-throughput assays sets up the field to more systematically investigate fly visual behaviors, their variability, and their underlying mechanisms.  

      Comments on revisions:  

      I want to express my appreciation for the authors' responsiveness to the reviewer feedback. They appear to have addressed my previous concerns through various modifications including GLM analysis, however, some areas still require clarification for the benefit of an audience that includes geneticists.  

      (1) GLM Analysis Explanation (Figure 9)  

      While the authors state that their new GLM results support their original conclusions, the explanation of these results in the text is insufficient. Specifically:

      The interpretation of coefficients and their statistical significance needs more detailed explanation. The audience includes geneticists and other nonstatistical people, so the GLM should be explained in terms of the criteria or quantities used to assess how well the results conform with the hypothesis, and to what extent they diverge.

      The criteria used to judge how well the GLM results support their hypothesis are not clearly stated.

      The relationship between the GLM findings and their original correlationbased conclusions needs better integration and connection, leading the reader through your reasoning.

      We thank the reviewer for highlighting this important point. We have revised the Results section in the reviseed manuscript to include a more detailed explanation of the GLM analysis. Specifically, we now clarify the interpretation of the model coefficients, including the direction and statistical significance, in relation to the hypothesized effects. We also outline the criteria we used to assess how well the GLM supports our original correlation-based conclusions—namely, whether the sign and significance of the coefficients align with the expected relationships derived from our prior analysis. Finally, we explicitly describe how the GLM results confirm or extend the patterns observed in the correlation-based analysis, to guide readers through our reasoning and the integration of both approaches.

      (2) Documentation of Changes  

      One struggle with the revised manuscript is that no "tracked changes" version was included, so it is hard to know exactly what was done. Without access to the previous version of the manuscript, it is difficult to fully assess the extent of revisions made. The authors should provide a more comprehensive summary of the specific changes implemented, particularly regarding:

      We thank the reviewer for bringing this to our attention. We were equally confused to learn that the tracked-changes version was not visible, despite having submitted one to eLife as part of our revision. 

      Upon contacting the editorial office, they confirmed that we did submit a trackedchanges version, but clarified that it did not contain embedded figures (as they were added manually to the clean version).  The editorial response said in detail: “Regarding the tracked-changes file: it appears the version with markup lacked figures, while the figure-complete PDF had markup removed, which likely caused the confusion mentioned by the reviewers.” We hope this answer from eLife clarifies the reviewers’ concern.

      (2)  Statistical Method Selection  

      The authors mention using "ridge regression to mitigate collinearity among predictors" but do not adequately justify this choice over other approaches. They should explain:

      Why ridge regression was selected as the optimal method  

      How the regularization parameter (λ) was determined  

      How this choice affects the interpretation of environmental parameters' influence on individuality

      We appreciate the reviewer’s thoughtful question regarding our choice of statistical method. In response, we have expanded the Methods section in the revised manuscript to provide a more detailed justification for the use of a GLM, including ridge regression. Specifically, we explain that ridge regression was selected to address collinearity and to control for overfitting.

      We now also describe how the regularization parameter (λ) was selected: we used 5-fold cross-validation over a log-spaced grid (10<sup>⁻⁶</sup> - 10<sup>⁶</sup) to identify the optimal value that minimized the mean squared error (MSE).

      Finally, we clarify in both the Methods and Results sections how this modeling choice affects the interpretation of our findings. 

      Reviewer #2 (Public review):  

      Summary:  

      The authors repeatedly measured the behavior of individual flies across several environmental situations in custom-made behavioral phenotyping rigs.

      Strengths:  

      The study uses several different behavioral phenotyping devices to quantify individual behavior in a number of different situations and over time. It seems to be a very impressive amount of data. The authors also make all their behavioral phenotyping rig design and tracking software available, which I think is great, and I'm sure other folks will be interested in using and adapting to their own needs.

      Weaknesses/Limitations:  

      I think an important limitation is that while the authors measured the flies under different environmental scenarios (i.e. with different lighting, temperature) they didn't really alter the "context" of the environment. At least within behavioral ecology, context would refer to the potential functionality of the expressed behaviors so for example, an anti-predator context, or a mating context, or foraging. Here, the authors seem to really just be measuring aspects of locomotion under benign (relatively low risk perception) contexts. This is not a flaw of the study, but rather a limitation to how strongly the authors can really say that this demonstrates that individuality is generalized across many different contexts. It's quite possible that rank-order of locomotor (or other) behaviors may shift when the flies are in a mating or risky context.  

      I think the authors are missing an opportunity to use much more robust statistical methods It appears as though the authors used pearson correlations across time/situations to estimate individual variation; however far more sophisticated and elegant methods exist. The problem is that pearson correlation coefficients can be anti-conservative and additionally, the authors have thus had to perform many many tests to correlate behaviors across the different trials/scenarios. I don't see any evidence that the authors are controlling for multiple testing which I think would also help. Alternatively, though, the paper would be a lot stronger, and my guess is, much more streamlined if the authors employ hierarchical mixed models to analyse these data, which are the standard analytical tools in the study of individual behavioral variation. In this way, the authors could partition the behavioral variance into its among- and within-individual components and quantify repeatability of different behaviors across trials/scenarios simultaneously. This would remove the need to estimate 3 different correlations for day 1 & day 2, day 1 & 3, day 2 & 3 (or stripe 0 & stripe 1, etc) and instead just report a single repeatability for e.g. the time spent walking among the different strip patterns (eg. figure 3). Additionally, the authors could then use multivariate models where the response variables are all the behaviors combined and the authors could estimate the among-individual covariance in these behaviors. I see that the authors state they include generalized linear mixed models in their updated MS, but I struggled a bit to understand exactly how these models were fit? What exactly was the response? what exactly were the predictors (I just don't understand what Line404 means "a GLM was trained using the environmental parameters as predictors (0 when the parameter was not changed, 1 if it was) and the resulting individual rank differences as the response"). So were different models run for each scenario? for different behaviors? Across scenarios? What exactly? I just harp on this because I'm actually really interested in these data and think that updating these methods can really help clarify the results and make the main messages much clearer!

      I appreciate that the authors now included their sample sizes in the main body of text (as opposed to the supplement) but I think that it would still help if the authors included a brief overview of their design at the start of the methods. It is still unclear to me how many rigs each individual fly was run through? Were the same individuals measured in multiple different rigs/scenarios? Or just one?

      I really think a variance partitioning modeling framework could certainly improve their statistical inference and likely highlight some other cool patterns as these methods could better estimate stability and covariance in individual intercepts (and potentially slopes) across time and situation. I also genuinely think that this will improve the impact and reach of this paper as they'll be using methods that are standard in the study of individual behavioral variation

      Reviewer #3 (Public review):  

      This manuscript is a continuation of past work by the last author where they looked at stochasticity in developmental processes leading to inter-individual behavioural differences. In that work, the focus was on a specific behaviour under specific conditions while probing the neural basis of the variability. In this work, the authors set out to describe in detail how stable individuality of animal behaviours is in the context of various external and internal influences. They identify a few behaviours to monitor (read outs of attention, exploration, and 'anxiety'); some external stimuli (temperature, contrast, nature of visual cues, and spatial environment); and two internal states (walking and flying).

      They then use high-throughput behavioural arenas - most of which they have built and made plans available for others to replicate - to quantify and compare combinations of these behaviours, stimuli, and internal states. This detailed analysis reveals that:

      (1) Many individualistic behaviours remain stable over the course of many days.  

      (2) That some of these (walking speed) remain stable over changing visual cues. Others (walking speed and centrophobicity) remain stable at different temperatures.

      (3) All the behaviours they tested fail to remain stable over spatially varying environment (arena shape).

      (4) and only angular velocity (a read out of attention) remains stable across varying internal states (walking and flying)

      Thus, the authors conclude that there is a hierarchy in the influence of external stimuli and internal states on the stability of individual behaviours.

      The manuscript is a technical feat with the authors having built many new high-throughput assays. The number of animals are large and many variables have been tested - different types of behavioural paradigms, flying vs walking, varying visual stimuli, different temperature among others.  

      Comments on revisions:'  

      The authors have addressed my previous concerns.  

      We thank the reviewer for the positive feedback and are glad our revisions have satisfactorily addressed the previous concerns. We appreciate the thoughtful input that helped us improve the clarity and rigor of the manuscript.

      Reviewer #1 (Recommendations for the authors):  

      Comment on Revised Manuscript  

      Recommendations for Improvement  

      (1) Expand the Results section for Figure 9 with a more detailed interpretation of the GLM coefficients and their biological significance

      (2) Provide explicit criteria (or at least explain in detail) for how the GLM results confirm or undermine their original hypothesis about environmental context hierarchy

      While the claims are interesting, the additional statistical analysis appears promising. However, clearer explanation of these new results would strengthen the paper and ensure that readers from diverse backgrounds can fully understand how the evidence supports the authors' conclusions about individuality across environmental contexts. 

      We thank the reviewer for these constructive suggestions. In response to these suggestions, we have expanded both the Methods and Results sections to provide a more detailed explanation of the GLM coefficients, including their interpretation and how they relate to our original correlation-based findings.

      We now clarify how the direction, magnitude, and statistical significance of specific coefficients reflect the influence of different environmental factors on the persistence of individual behavioral traits. To make this accessible to readers from diverse backgrounds, we explicitly outline the criteria we used to evaluate whether the GLM results support our hypothesis about the hierarchical influence of environmental context, namely, whether the structure and strength of effects align with the patterns predicted from our prior correlation analysis.

      These additions improve clarity and help readers understand how the new statistical results reinforce our conclusions about the context-dependence of behavioral individuality.

      Reviewer #2 (Recommendations for the authors):  

      Thanks for the revision of the paper! I updated my review to try and provide a little more guidance by what I mean about updating your analyses. I really think this is a super cool data set and I genuinely wish this were MY dataset so that way I could really dig into it to partition the variance. These variance partitioning methods are standard in my particular subfield (study of individual behavioral variation in ecology and evolution) and so I think employing them is 1) going to offer a MUCH more elegant and holistic view of the behavioral variation (e.g. you can report a single repeatability estimate for each behavior rather than 3 different correlations) and 2) improve the impact and readership for your paper as now you'll be using methods that a whole community of researchers are very familiar with. It's just a suggestion, but I hope you consider it!

      We sincerely thank the reviewer for the insightful and encouraging feedback and for introducing us to this modeling approach. In response to this suggestion, we have incorporated a hierarchical linear mixed-effects model into our analysis (now presented in Figure 10), accompanied by a new supplementary table (Table T3). We also updated the Methods, Results, and Discussion sections to describe the rationale, implementation, and implications of the mixed-model analysis.

      We agree with the reviewer that this approach provides a more elegant way to quantify behavioral variation and individual consistency across contexts. In particular, the ability to estimate repeatability directly aligns well with the core questions of our study. It facilitates improved communication of our findings to ecology, evolution, and behavior researchers. We greatly appreciate the suggestion; it has significantly strengthened both the analytical framework and the interpretability of the manuscript.

    1. Reviewer #1 (Public review):

      Summary:

      In this manuscript, Mahajan et.al introduce two innovative macroscopic measures-intrachromosomal gene correlation length (𝓁∗) and transition energy barrier-to investigate chromatin structural dynamics associated with aging and age-related syndromes such as Hutchinson-Gilford Progeria Syndrome (HGPS) and Werner Syndrome (WRN). The authors propose a compelling systems-level approach that complements traditional biomarker-driven analyses, offering a more holistic and quantitative framework to assess genome-wide dysregulation. The concept of 𝓁∗ as a spatial correlation metric to capture chromatin disorganization is novel and well-motivated. The use of autocorrelation on distance-binned gene expression adds depth to the interpretation of chromatin state shifts. The energy landscape framework for gene state transitions is an elegant abstraction, with the notion of "irreversibility" providing a thermodynamic interpretation of transcriptional dysregulation. The application to multiple datasets (Fleischer, Line-1) and pathological states adds robustness to the analysis. The consistency of chromosome 6 (and to some extent chromosomes 16 and X) emerging as hotspots aligns well with known histone cluster localization and disease-relevant pathways. The manuscript does an excellent job of integrating transcriptomic trends with known epigenetic hallmarks of aging, and the proposed metrics can be used in place of traditional techniques like PCA in capturing structural transcriptome features. However, a direct correlation with ATACseq/ HiC data with the present analysis will be more informative.

      Strengths:

      Novel inclusion of statistical metrics that can help in systems-level studies in aging and chromatin biology.

      Weaknesses:

      (1) In the manuscript, the authors mention "While it may be intuitive to assume that highly expressed genes originate from euchromatin, this cannot be conclusively stated as a complete representation of euchromatin genes, nor can LAT be definitively linked to heterochromatin". What percentage of LAT can be linked to heterochromatin? What is the distribution of LAT and HAT in the euchromatin?

      (2) In Figure 2, the authors observe "that the signal from the HAT class is the stronger between two and the signal from the LAT class, being mostly uniform, can be constituted as background noise." Is this biologically relevant? Are low-abundance transcripts constitutively expressed? The authors should discuss this in the Results section.

      (3) The authors make a very interesting observation from Figure 3: that ASO-treated LINE-1 appears to be more effective in restoring HGPS cell lines closer to wild-type compared to WRN.. This can be explained by the difference in the basal activity of L1 elements in the HGPS vs WRN cell types. The authors should comment on this.

      (4) The authors report that "from the results on Fleicher dataset is the magnitude of the difference in similarity distance is more pronounced in 𝓁∗ than in gene expression." Does this mean that the alterations in gene distance and chromatin organization do not result in gene expression change during aging?

      (5) "In Fleischer dataset, as evident in Figure 4a, although changes in the heterochromatin are not identical for all chromosomes shown by the different degrees of variation of 𝓁∗ in each age group." The authors should present a comprehensive map of each chromosome change in gene distance to better explain the above statement.

      (6) While trends in 𝓁∗ are discussed at both global and chromosome-specific levels, stronger statistical testing (e.g., permutation tests, bootstrapping) would lend greater confidence, especially when differences between age groups or treatment states are modest.

      (7) While the transition energy barrier is an insightful conceptual addition, further clarification on the mathematical formulation and its physical assumptions (e.g., energy normalization, symmetry conditions) would improve interpretability. Also, in between Figures 7 and 8, the authors first compare the energy barrier of Chromosome 1 and then for all other chromosomes. What is the rationale for only analyzing chromosome 1? How many HAT or LAT are present there?

    2. Reviewer #2 (Public review):

      The authors report that intra-chromosomal gene correlation length (spatial correlations in gene expressions along the chromosome) serves as a proxy of chromatin structure and hence gene expression. They further explore changes in these metrics with aging. These are interesting and important findings. However, there are fundamental problems at this time.

      (1) The basic method lacks validation. There is no validation of the method by approaches that directly measure chromatin structure, for example ATAC-seq, ChIP-seq, or CUT n RUN.

      (2) There is no validation by interventions that directly probe chromatin structure, such as HDAC inhibitors. The authors employ datasets with knockdown of LINE-1 for validation. However, this is not a specific chromatin intervention.

      (3) There is no statistical analysis, e.g., in Figures 4 and 5.

      (4) The authors state, "in Figure 4a changes in the heterochromatin are not identical for all chromosomes shown...." I do not see the data for individual chromosomes.

      (5) In comparisons of WT vs HGPS NT or HGPS SCR (Figure S6), is this a fair comparison? The WT and HGPS are presumably from different human donors, so they have genetic and epigenetic differences unrelated to HGPS.

    3. Author response:

      Reviewer #1 (Public review):

      Summary:

      In this manuscript, Mahajan et. al. introduce two innovative macroscopic measures-intrachromosomal gene correlation length (𝓁∗) and transition energy barrier-to investigate chromatin structural dynamics associated with aging and age-related syndromes such as Hutchinson-Gilford Progeria Syndrome (HGPS) and Werner Syndrome (WRN). The authors propose a compelling systems-level approach that complements traditional biomarker-driven analyses, offering a more holistic and quantitative framework to assess genome-wide dysregulation. The concept of 𝓁∗ as a spatial correlation metric to capture chromatin disorganization is novel and well-motivated. The use of autocorrelation on distance-binned gene expression adds depth to the interpretation of chromatin state shifts. The energy landscape framework for gene state transitions is an elegant abstraction, with the notion of "irreversibility" providing a thermodynamic interpretation of transcriptional dysregulation. The application to multiple datasets (Fleischer, Line-1) and pathological states adds robustness to the analysis. The consistency of chromosome 6 (and to some extent chromosomes 16 and X) emerging as hotspots aligns well with known histone cluster localization and disease-relevant pathways. The manuscript does an excellent job of integrating transcriptomic trends with known epigenetic hallmarks of aging, and the proposed metrics can be used in place of traditional techniques like PCA in capturing structural transcriptome features. However, a direct correlation with ATACseq/HiC data with the present analysis will be more informative.

      (1) In the manuscript, the authors mention "While it may be intuitive to assume that highly expressed genes originate from euchromatin, this cannot be conclusively stated as a complete representation of euchromatin genes, nor can LAT be definitively linked to heterochromatin". What percentage of LAT can be linked to heterochromatin? What is the distribution of LAT and HAT in the euchromatin?

      Thank you for this insightful question. In the revision we will add chromatin state annotations using ChromHMM to identify overlap between HAT/LAT and corresponding chromatin state. This should provide the specific percentages and distributions you requested.

      We would like to take this opportunity to clarify that based on the plots Fig S1, and differential gene expressions, HAT is most likely a subset of euchromatin and LAT may contain both euchromatin and heterochromatin. The HAT/LAT cutoff occurs around the knee point in the log-log plot (Figure S1), where the linear portion indicates scale-invariant behavior with similar relative changes across expression ranks. The non-linear portion represents departure from power-law scaling, where low-expression genes exhibit sharper decline than expected. This suggests potential biological mechanisms such as chromatin silencing, detection limits, or technical artifacts related to sequencing depth.

      We will provide detailed chromatin state analysis in the revision. For reference, HAT gene lists per chromosome are available in our GitHub repository at: https://github.com/altoslabs/papers-2025-rnaseq-chrom-aging/tree/main/data/Preprocessed_dat a under /<dataset>/chromosome_{}/data_hi.

      (2) In Figure 2, the authors observe "that the signal from the HAT class is the stronger between two and the signal from the LAT class, being mostly uniform, can be constituted as background noise." Is this biologically relevant? Are low-abundance transcripts constitutively expressed? The authors should discuss this in the Results section.

      We apologize for the confusion arising from the usage of the term “background noise”. We agree that the distinction between high-abundance transcripts (HATs) and low-abundance transcripts (LATs) deserves more explicit discussion in the Results.

      Our intention is to say that HAT has a higher signal-to-noise ratio (SNR) compared to LAT. This is coming from the power law graph of FigS1.  Our intention is to state that the HAT class provides a strong, robust signal, consistent across chromosomes and the LAT class exhibits lower SNR and a more uniform background-like distribution in the context of the problem we are solving and not rather a generic biological statement. The experiment result that led to this statement is presented in FigS3. This does not imply that low-abundance transcripts lack biological relevance, but rather that they contribute less to the spatial organization patterns we measure.

      (3) The authors make a very interesting observation from Figure 3: that ASO-treated LINE-1 appears to be more effective in restoring HGPS cell lines closer to wild-type compared to WRN.. This can be explained by the difference in the basal activity of L1 elements in the HGPS vs WRN cell types. The authors should comment on this.

      We thank the reviewer for this incisive biological observation. While the differential effectiveness of ASO-treated LINE-1 in HGPS versus WRN cell lines is indeed an interesting phenomenon that may relate to basal L1 activity differences, this biological mechanism falls outside the scope of our current study.

      Our paper focuses on demonstrating that the 𝓁∗ metric can sensitively detect chromatin structural changes that have been independently validated. We utilize the Della Valle et al. (2022) dataset specifically because it provides experimentally confirmed chromatin structural differences (Progeroid vs wild-type vs ASO-treated Progeriod), allowing us to validate that 𝓁∗ correlates with these established changes.

      For detailed discussion of the biological mechanisms underlying differential LINE-1 ASO effectiveness between progeroid syndromes, we would direct readers to Della Valle et al. (2022) and related LINE-1 biology literature. Our contribution lies in demonstrating that 𝓁∗ can capture these chromatin organizational changes with enhanced sensitivity compared to traditional expression-based approaches. We are reluctant, without further experimentation, to venture into over-interpreting these results from a biology perspective.  

      (4) The authors report that "from the results on Fleischer dataset is the magnitude of the difference in similarity distance is more pronounced in 𝓁∗ than in gene expression." Does this mean that the alterations in gene distance and chromatin organization do not result in gene expression change during aging?

      Thank you for this important clarification request. This observation, illustrated in Figure 3, highlights two key points: (1) 𝓁∗ shows similar trends to PCA analysis, and (2) 𝓁∗ demonstrates higher sensitivity than traditional gene expression analysis.

      This enhanced sensitivity enables better discrimination between aging states, particularly in the Fleischer dataset representing natural aging where changes are more gradual. The higher sensitivity stems from 𝓁∗'s ability to capture transcriptional spatial organization through spatial autocorrelation, which can detect subtle organizational changes that may precede or accompany expression changes rather than replacing them.

      We will clarify in the revision that chromatin organizational changes and gene expression changes are complementary rather than mutually exclusive phenomena during aging.

      (5) "In Fleischer dataset, as evident in Figure 4a, although changes in the heterochromatin are not identical for all chromosomes shown by the different degrees of variation of 𝓁∗ in each age group." The authors should present a comprehensive map of each chromosome change in gene distance to better explain the above statement.

      Thank you for the feedback. If we understand your comment correctly, we need to provide a chromosome-wise distribution for Fig3c. We will update the paper and the supplementary.

      (6) While trends in 𝓁∗ are discussed at both global and chromosome-specific levels, stronger statistical testing (e.g., permutation tests, bootstrapping) would lend greater confidence, especially when differences between age groups or treatment states are modest.

      Thank you for the helpful suggestion. In the revision, we will incorporate permutation-based significance testing by shuffling the gene annotation and count table to generate a null distribution for our 𝓁∗ calculation. This will allow us to more rigorously assess whether the observed differences across age groups or treatment states deviate from chance expectations and thereby lend greater statistical confidence to our findings.

      (7) While the transition energy barrier is an insightful conceptual addition, further clarification on the mathematical formulation and its physical assumptions (e.g., energy normalization, symmetry conditions) would improve interpretability. Also, in between Figures 7 and 8, the authors first compare the energy barrier of Chromosome 1 and then for all other chromosomes.

      What is the rationale for only analyzing chromosome 1? How many HAT or LAT are present there?

      Regarding chromosome 1 focus: we initially presented chromosome 1 as a representative example, but we will include energy landscape analysis for all chromosomes in the supplementary materials

      We use the same HATs that were extracted during 𝓁∗ for the energy landscape as well. The HAT details are present in the github repo, the link provided in response to 1st feedback.

      The normalization of the energy barrier ensures comparability across chromosomes of different sizes and across samples with different absolute expression scales. Specifically, we normalize with respect to the total area under the two-dimensional energy landscape while using the thermal energy (k_B T) as a scaling factor to place transition energy barriers on the scale of thermal fluctuations. This is formally expressed as in Eq. (1). 

      The physical consequences of symmetry in the energy landscape are discussed in lines 472-491 of the manuscript, where we also introduce the concept of irreversibility. In brief, the chromatin energy landscape (Figure 8) is constructed by quantifying the energy contributions of genes that are upregulated (lower triangular matrix) and downregulated (upper triangular matrix) between two states. If the integrated energy contributions of upregulated and downregulated genes are equal, the landscape is symmetric, representing a thermodynamically reversible process, for example, nucleosome repositioning between euchromatic and heterochromatic regions without net gain or loss of nucleosomes. However, in cases where epigenetic modifications alter nucleosome density (e.g., disease states that reduce nucleosome numbers), the integrated energies are unequal, reflecting an irreversible energy cost. In this case, restoring chromatin requires additional energy input (e.g., to replace “missing” nucleosomes), which manifests as asymmetry in the landscape.

      Reviewer #2 (Public review):

      The authors report that intra-chromosomal gene correlation length (spatial correlations in gene expressions along the chromosome) serves as a proxy of chromatin structure and hence gene expression. They further explore changes in these metrics with aging. These are interesting and important findings. However, there are fundamental problems at this time.

      (1) The basic method lacks validation. There is no validation of the method by approaches that directly measure chromatin structure, for example ATAC-seq, ChIP-seq, or CUT n RUN.

      We appreciate the reviewer’s point that direct measurements such as ATAC-seq and ChIP-seq remain the gold standard for characterizing chromatin structure. Our method is designed to complement, not replace, these approaches by leveraging RNA-seq data to detect large-scale transcriptional patterns that correlate with chromatin dynamics.

      We agree that integrating datasets with paired RNA-seq and chromatin accessibility assays would strengthen the manuscript and plan to include one such dataset in the revision.

      Based on this feedback, we will also take the opportunity during revision to clarify and soften certain statements. Specifically, we will reposition ℓ∗ as a sensitive, computational proxy for detecting transcriptional signatures that are suggestive of chromatin structural changes. In other words, ℓ∗ provides an indirect window into chromatin dynamics through transcriptional spatial organization, allowing detection of patterns that may precede or accompany structural changes. Direct assays such as ATAC-seq or ChIP-seq remain essential for confirming the underlying physical modifications. To make this scope clear, we will revise the title to: “Macroscopic RNA-seq Analysis to Detect Transcriptional Patterns Associated with Chromatin State Changes,” and adjust the main text.  

      We would like to take this opportunity to clarify why our initial version focused on the Della Valle and Fleischer datasets rather than including new paired datasets with direct chromatin measurements. The primary objective of our paper is to introduce two macroscopic RNA-seq–based measures, ℓ∗ and the energy landscape, that are designed to detect transcriptional signatures suggestive of chromatin structural changes in the context of aging and age-related diseases. These measures explicitly model transcriptional spatial organization and provide a sensitive, scalable way to analyze RNA-seq data in domains where direct chromatin assays may not be readily available.

      The datasets we used (Della Valle et al., Fleischer et al.) have been rigorously validated and independently demonstrated differences in chromatin structure between conditions. Our goal was to show that ℓ∗ and the energy landscape align with and extend these established findings, offering a more sensitive measure of transcriptional spatial organization. Specifically, in the Della Valle dataset, chromatin structural differences between progeroid and healthy donors — and their partial rescue by LINE-1 ASO treatment — were experimentally confirmed, providing a strong foundation for testing whether our metrics reflect these known changes. Similarly, the Fleischer dataset captures natural, in vivo aging, which has also been linked to chromatin alterations in prior studies.

      Thus, our approach builds on this well-established biological context rather than attempting to re-demonstrate these chromatin differences from scratch. Finally, we emphasize that our current focus is aging and age-related diseases. While the framework could potentially be applied to other chromatin modification contexts, we have not tested it outside this domain and do not claim general applicability at this stage.

      (2) There is no validation by interventions that directly probe chromatin structure, such as HDAC inhibitors. The authors employ datasets with knockdown of LINE-1 for validation. However, this is not a specific chromatin intervention.

      We request the reviewer to refer to our response to (1) as it includes the rationale behind the selection of LINE-1 and Fleischer dataset. We would also like to state that while the focus of Della Valle et al. was LINE-1 treated ASO to show rescue of progeroid samples, it also contains data for non-treated as well as healthy samples. Importantly, untreated progeroid samples show distinctly different chromatin structure compared to healthy samples, with substantial differences detectable by both PCA and our 𝓁∗ metric.

      Our 𝓁∗ method provides additional interpretability by capturing transcriptional spatial organization, resulting in shorter correlation lengths for healthy patients and longer lengths for progeroid patients.

      But as mentioned in our response to (1) we will try to add an additional dataset with paired rna-seq and one of ATAC, ChIP-seq or CUT n RUN in the revision

      (3) There is no statistical analysis, e.g., in Figures 4 and 5.

      We have provided statistical analysis for Fig 4 (lines 237-241). We will do a similar analysis for Fig. 5. 

      (4) The authors state, "in Figure 4a changes in the heterochromatin are not identical for all chromosomes shown...." I do not see the data for individual chromosomes.

      The data for individual chromosomes is available in supplementary Fig. S11 – references at line 425. We will make this cross-reference clearer in the main text and consider whether some of this chromosome-specific information should be elevated to the main figures for better accessibility.

      (5) In comparisons of WT vs HGPS NT or HGPS SCR (Figure S6), is this a fair comparison? The WT and HGPS are presumably from different human donors, so they have genetic and epigenetic differences unrelated to HGPS.

      Figure S6 demonstrates that 𝓁∗ analysis identifies chromosome 6 as most affected, consistent with differential gene expression patterns.

      Regarding donor differences in WT vs HGPS comparisons, we defer to the experimental design of Della Valle et al., which follows standard practices in progeroid research. Our review of the literature indicates that progeroid studies typically use either parent/child samples or different donor comparisons (as individuals cannot simultaneously represent both WT and HGPS states).

      Importantly, the LINE-1 ASO treatment comparisons use the same cell lines, eliminating donor variability concerns. This experimental design allows us to validate that 𝓁∗ can detect rescue effects within genetically identical samples, supporting the method's sensitivity to chromatin structural changes  

      Reviewing Editor Comments:

      You'll note that both reviewers were very thoughtful in their comments, and in principle are supportive and excited by the work. However, their evaluation of the strength of evidence diverged substantially. I'm inclined to suggest that finding a way to support the novel method with an alternative approach would greatly improve the impact of this work. I encourage you to consider a revision that provides such data, in the context of technology currently available to the field.

      We sincerely thank the editor for their thoughtful and encouraging assessment of our work. We are grateful for their recognition of the novelty of our macroscopic measures (ℓ∗ and the transition energy barrier) and their potential to provide a systems-level understanding of chromatin structural dynamics in aging and age-related syndromes. In response to the editor’s suggestion for direct validation with chromatin accessibility data, we plan to integrate an additional dataset containing paired RNA-seq and ATAC-seq or related measurements in our revision. This will help strengthen the link between our RNA-seq–based metrics and direct chromatin assays. We have also clarified and softened the manuscript text to ensure it is clear that ℓ∗ serves as a complementary, computational proxy, not a replacement, for direct experimental approaches. Very specifically, to make this scope clear, we will revise the title to: “Macroscopic RNA-seq Analysis to Detect Transcriptional Patterns Associated with Chromatin State Changes,” and adjust the main text. We thank the editor for the feedback. We have provided additional details in response to specific comments made by the reviewers.

    1. Reviewer #1 (Public review):

      Summary

      This manuscript presents an updated version of rsatoolbox, a Python package for performing Representational Similarity Analysis (RSA) on neural data. The authors provide a comprehensive and well-integrated framework that incorporates a range of state-of-the-art methodological advances. The updated version extends the toolbox's capabilities.

      The paper outlines a typical RSA workflow in five steps:

      (1) Importing data and estimating activity patterns.

      (2) Estimating representational geometries (computing RDMs).

      (3) Comparing RDMs.

      (4) Performing inferential model comparisons.

      (5) Handling multiple testing across space and time.

      For each step, the authors describe methodological advances and best practices implemented in the toolbox, including improved measures of representational distances, evaluators for representational models, and statistical inference methods.

      While the relative impact of the manuscript is somewhat limited to the new contributions in this update (which are nonetheless very useful), the general toolbox - here thoroughly described and discussed - remains an invaluable contribution to the field and is well-received by the cognitive and computational neuroscience communities.

      Strengths:

      A key strength of the work is the breadth and integration of the implemented methods. The updated version introduces several new features, such as additional comparators and dissimilarity estimators, that closely follow recent methodological developments in the field. These enhancements build on an already extensive set of functionalities, offering seamless support for RSA analyses across a wide variety of data sources, including deep neural networks, fMRI, EEG, and electrophysiological recordings.

      The toolbox also integrates effectively with the broader open-source ecosystem, providing compatibility with BIDS formats and outputs from widely used neuroscience software. This integration will make it easier for researchers to incorporate rsatoolbox into existing workflows. The documentation is extensive, and the scope of functionality - from dissimilarity estimation to statistical inference - is impressive.

      For researchers already familiar with RSA, rsatoolbox offers a coherent environment that can streamline analyses, promote methodological consistency, and encourage best practices.

      Weaknesses:

      While I enjoyed reading the manuscript - and even more so exploring the toolbox - I have some comments for the authors. None of these points is strictly major, and I leave it to the authors' discretion whether to act on them, but addressing them could make the manuscript an even more valuable resource for those approaching RSA.

      (1) While several estimators and comparators are implemented, Figure 4 appears to suggest that only a subset should be used in practice. This raises the question of whether the remaining options are necessary, and under what circumstances they might be preferable. Although it is likely that different measures are suited to different scenarios, this is not clearly explained in the manuscript. As presented, a reader following the manuscript's guidance might rely on only a few of the available comparators and estimators without understanding the rationale. It would be helpful if the authors could provide practical examples illustrating when one measure might be preferred over another, and how different measures behave under varying conditions-for instance, in what situations the user should choose manifold similarity versus Bures similarity?

      (2) The comparison to other RSA tools is minimal, making it challenging to place rsatoolbox in the broader landscape of available resources. Although the authors mention some existing RSA implementations, they do not provide a detailed comparison of features or performance between their toolbox and alternatives.

      (3) Finally, given the growing interest in comparing neural network models with brain data, a more detailed discussion of how the toolbox can be applied to common questions in this area would be a valuable addition.

    1. Reviewer #1 (Public review):

      This is an interesting and timely computational study using molecular dynamics simulation as well as quantum mechanical calculation to address why tyrosine (Y), as part of an intrinsically disordered protein (IDP) sequence, has been observed experimentally to be stronger than phenylalanine (F) as a promoter for biomolecular phase separation. Notably, the authors identified the aqueous nature of the condensate environment and the corresponding dielectric and hydrogen bonding effects as a key to understand the experimentally observed difference. This principle is illustrated by the difference in computed transfer free energy of Y- and F-containing pentapeptides into solvent with various degrees of polarity. The elucidation offered by this work is important. The computation appears to be carefully executed, the results are valuable, and the discussion is generally insightful. However, there is room for improvement in some parts of the presentation in terms of accuracy and clarity, including, e.g., the logic of the narrative should be clarified with additional information (and possibly additional computation), and the current effort should be better placed in the context of prior relevant theoretical and experimental works on cation-π interactions in biomolecules and dielectric properties of biomolecular condensates. Accordingly, this manuscript should be revised to address the following, with added discussion as well as inclusion of references mentioned below.

      (1) Page 2, line 61: "Coarse-grained simulation models have failed to account for the greater propensity of arginine to promote phase separation in Ddx4 variants with Arg to Lys mutations (Das et al., 2020)". As it stands, this statement is not accurate, because the cited reference to Das et al. showed that although some coarse-grained model, namely the HPS model of Dignon et al., 2018 PLoS Comput did not capture the Arg to Lys trend, the KH model described in the same Dignon et al. paper was demonstrated by Das et al. (2020) to be capable of mimicking the greater propensity of Arg to promote phase separation than Lys. Accordingly, a possible minimal change that would correct the inaccuracy of this statement in the manuscript would be to add the word "Some" in front of "coarse-grained simulation models ...", i.e., it should read "Some coarse-grained simulation models have failed ...". In fact, a subsequent work [Wessén et al., J Phys Chem B 126: 9222-9245 (2022)] that applied the Mpipi interaction parameters (Joseph et al., 2021, already cited in the manuscript) showed that Mpipi is capable of capturing the rank ordering of phase separation propensity of Ddx4 variants, including a charge scrambled variant as well as both the Arg to Lys and the Phe to Ala variants (see Fig.11a of the above-cited Wessén et al. 2022 reference). The authors may wish to qualify their statements in the introduction to take note of these prior results. For example, they may consider adding a note immediately after the next sentence in the manuscript "However, by replacing the hydrophobicity scales ... (Das et al., 2020)" to refer to these subsequent findings in 2021-2022.

      (2) Page 8, lines 285-290 (as well as the preceding discussion under the same subheading & Fig.4): "These findings suggest that ... is not primarily driven by differences in protein-protein interaction patterns ..." The authors' logic in terms of physical explanation is somewhat problematic here. In this regard, "Protein-protein interaction patterns" appears to be a straw man, so to speak. Indeed, who (reference?) has argued that the difference in the capability of Y and F in promoting phase separation should be reflected in the pairwise amino acid interaction pattern in a condensate that contains either only Y (and G, S) and only F (and G, S) but not both Y and F? Also, this paragraph in the manuscript seems to suggest that the authors' observation of similar contact patterns in the GSY and GSF condensates is "counterintuitive" given the difference in Y-Y and F-F potentials of mean force (Joseph et al., 2021); but there is nothing particularly counterintuitive about that. The two sets of observations are not mutually exclusive. For instance, consider two different homopolymers, one with a significantly stronger monomer-monomer attraction than the other. The condensates for the two different homopolymers will have essentially the same contact pattern but very different stabilities (different critical temperatures), and there is nothing surprising about it. In other words, phase separation propensity is not "driven" by contact pattern in general, it's driven by interaction (free) energy. The relevant issue here is total interaction energy or critical point of the phase separation. If it is computationally feasible, the authors should attempt to determine the critical temperatures for the GSY condensate versus the GSF condensate to verify that the GSY condensate has a higher critical temperature than the GSF condensate. That would be the most relevant piece of information for the question at hand.

      (3) Page 9, lines 315-316: "...Our ε [relative permittivity] values ... are surprisingly close to that derived from experiment on Ddx4 condensates (45{plus minus}13) (Nott et al., 2015)". For accuracy, it should be noted here that the relative permittivity provided in the supplementary information of Nott et al. was not a direct experimental measurement but based on a fit using Flory-Huggins (FH), but FH is not the most appropriate theory for polymer with long-spatial-range Coulomb interactions. To this reviewer's knowledge, no direct measurement of relative permittivity in biomolecular condensates has been made to date. Explicit-water simulation suggests that relative permittivity of Ddx4 condensate with protein volume fraction ≈ 0.4 can have relative permittivity ≈ 35-50 (Das et al., PNAS 2020, Fig.7A), which happens to agree with the ε = 45{plus minus}13 estimate. This information should be useful to include in the authors' manuscript.

      (4) As for the dielectric environment within biomolecular condensates, coarse-grained simulation has suggested that whereas condensates formed by essentially electric neutral polymers (as in the authors' model systems) have relative permittivities intermediate between that of bulk water and that of pure protein (ε = 2-4, or at most 15), condensates formed by highly charge polymers can have relative permittivity higher than that of bulk water [Wessén et al., J Phys Chem B 125:4337-4358 (2021), Fig.14 of this reference]. In view of the role of aromatic residues (mainly Y and F) in the phase separation of IDPs such as A1-LCD and LAF-1 that contain positively and negatively charged residues (Martin et al., 2020; Schuster et al., 2020, already cited in the manuscript), it should be useful to address briefly how the relationship between the relative phase-separation promotion strength of Y vs F and dielectric environment of the condensate may or may not be change with higher relative permittivities.

      (5) The authors applied the dipole moment fluctuation formula (Eq.2 in the manuscript) to calculate relative permittivity in their model condensates. Does this formula apply only to an isotropic environment? The authors' model condensates were obtained from a "slab" approach (p.4) and thus the simulation box has a rectangular geometry. Did the authors apply their Eq.2 to the entire simulation box or only to the central part of the box with the condensate (see, e.g., Fig.3C in the manuscript). If the latter is the case, is it necessary to use a different dipole moment formula that distinguishes between the "parallel" and "perpendicular" components of the dipole moment (see, e.g., Eq.16 in the above-cited Wessén et al. 2021 paper). A brief added comments will be useful.

      (6) With regard to the general role of Y and F in the phase separation of biomolecules containing positively charged Arg and Lys residues, the relative strength of cation-π interactions (cation-Y vs cation-F) should be addressed (in view of the generality implied by the title of the manuscript), or at least discussed briefly in the authors' manuscript if a detailed study is beyond the scope of their current effort. It has long been known that in the biomolecular context, cation-Y is slightly stronger than cation-F, whereas cation-tryptophan (W) is significantly stronger than either cation-Y and cation-F [Wu & McMahon, JACS 130:12554-12555 (2008)]. Experimental data from a study of EWS (Ewing sarcoma) transactivation domains indicated that Y is a slightly stronger promoter than F for transcription, whereas W is significantly stronger than either Y or F [Song et al., PLoS Comput Biol 9:e1003239 (2013)]. In view of the subsequent general recognition that "transcription factors activate genes through the phase-separation capacity of their activation domain" [Boija et al., Cell 175:1842-1855.e16 (2018)] which is applicable to EWS in particular [Johnson et al., JACS 146:8071-8085 (2024)], the experimental data in Song et al. 2013 (see Fig.3A of this reference) suggests that cation-Y interactions are stronger than cation-F interactions in promoting phase separation, thus generalizing the authors' observations (which focus primarily on Y-Y, Y-F and F-F interactions) to most situations in which cation-Y and cation-F interactions are relevant to biomolecular condensation.

      (7) Page 9: The observation of a weaker effective F-F (and a few other nonpolar-nonpolar) interaction in a largely aqueous environment (as in an IDP condensate) than in a nonpolar environment (as in the core of a folded protein) is intimately related to (and expected from) the long-recognized distinction between "bulk" and "pair" as well as size dependence of hydrophobic effects that have been addressed in the context of protein folding [Wood & Thompson, PNAS 87:8921-8927 (1990); Shimizu & Chan, JACS 123:2083-2084 (2001); Proteins 49:560-566 (2002)]. It will be useful to add a brief pointer in the current manuscript to this body of relevant resource in protein science.

      Comments on revisions:

      The authors have largely addressed my previous concerns and the manuscript has been substantially improved. Nonetheless, it will benefit the readers more if the authors had included more of the relevant references provided in my previous review so as to afford a broader and more accurate context to the authors' effort. This deficiency is particularly pertinent for point number 6 in my previous report about cation-pi interactions. The authors have now added a brief discussion but with no references on the rank ordering of Y, F, and W interactions. I cannot see how providing additional information about a few related works could hurt. Quite the contrary, having the references will help readers establish scientific connections and contribute to conceptual advance.

    2. Author response:

      The following is the authors’ response to the original reviews.

      Reviewer #1 (Public review):

      This is an interesting and timely computational study using molecular dynamics simulation as well as quantum mechanical calculation to address why tyrosine (Y), as part of an intrinsically disordered protein (IDP) sequence, has been observed experimentally to be stronger than phenylalanine (F) as a promoter for biomolecular phase separation. Notably, the authors identified the aqueous nature of the condensate environment and the corresponding dielectric and hydrogen bonding effects as a key to understanding the experimentally observed difference. This principle is illustrated by the difference in computed transfer free energy of Y- and F-containing pentapeptides into a solvent with various degrees of polarity. The elucidation offered by this work is important. The computation appears to be carefully executed, the results are valuable, and the discussion is generally insightful. However, there is room for improvement in some parts of the presentation in terms of accuracy and clarity, including, e.g., the logic of the narrative should be clarified with additional information (and possibly additional computation), and the current effort should be better placed in the context of prior relevant theoretical and experimental works on cation-π interactions in biomolecules and dielectric properties of biomolecular condensates. Accordingly, this manuscript should be revised to address the following, with added discussion as well as inclusion of references mentioned below.

      We are grateful for the referee’s assessment of our work and insightful suggestions, which we address point by point below.

      (1) Page 2, line 61: "Coarse-grained simulation models have failed to account for the greater propensity of arginine to promote phase separation in Ddx4 variants with Arg to Lys mutations (Das et al., 2020)". As it stands, this statement is not accurate, because the cited reference to Das et al. showed that although some coarse-grained models, namely the HPS model of Dignon et al., 2018 PLoS Comput did not capture the Arg to Lys trend, the KH model described in the same Dignon et al. paper was demonstrated by Das et al. (2020) to be capable of mimicking the greater propensity of Arg to promote phase separation than Lys. Accordingly, a possible minimal change that would correct the inaccuracy of this statement in the manuscript would be to add the word "Some" in front of "coarse-grained simulation models ...", i.e., it should read "Some coarse-grained simulation models have failed ...". In fact, a subsequent work [Wessén et al., J Phys Chem B 126: 9222-9245 (2022)] that applied the Mpipi interaction parameters (Joseph et al., 2021, already cited in the manuscript) showed that Mpipi is capable of capturing the rank ordering of phase separation propensity of Ddx4 variants, including a charge scrambled variant as well as both the Arg to Lys and the Phe to Ala variants (see Figure 11a of the above-cited Wessén et al. 2022 reference). The authors may wish to qualify their statements in the introduction to take note of these prior results. For example, they may consider adding a note immediately after the next sentence in the manuscript "However, by replacing the hydrophobicity scales ... (Das et al., 2020)" to refer to these subsequent findings in 2021-2022.

      We agree with the referee that the wording used in the original version was inaccurate. We did not want to expand too much on the previous results on Lys/Arg, to avoid overwhelming our readers with background information that was not directly relevant to the aromatic residues Phe and Tyr. We have now introduced some of the missing details in the hope that this will provide a more accurate account of what has been achieved with different versions of coarse-grained models. In the revised version, we say the following:

      Das and co-workers attempted to explain arginine’s greater propensity to phase separate in Ddx4 variants using coarse-grained simulations with two different energy functions (Das et al., 2020). The model was first parametrized using a hydrophobicity scale, aimed to capture the “stickiness” of different amino acids (Dignon et al., 2018), but this did not recapitulate the correct rank order in the stability of the simulated condensates (Das et al., 2020). By replacing the hydrophobicity scale with interaction energies from amino acid contact matrices —derived from a statistical analysis of the PDB (Dignon et al., 2018; Miyazawa and Jernigan, 1996; Kim and Hummer, 2008)— they recovered the correct trends (Das et al., 2020). A key to the greater propensity for LLPS in the case of Arg may derive from the pseudo-aromaticity of this residue, which results in a greater stabilization relative to the more purely cationic character of Lys (Gobbi and Frenking, 1993; Wang et al., 2018; Hong et al., 2022).

      (2) Page 8, lines 285-290 (as well as the preceding discussion under the same subheading & Figure 4): "These findings suggest that ... is not primarily driven by differences in protein-protein interaction patterns ..." The authors' logic in terms of physical explanation is somewhat problematic here. In this regard, "Protein-protein interaction patterns" appear to be a straw man, so to speak. Indeed, who (reference?) has argued that the difference in the capability of Y and F in promoting phase separation should be reflected in the pairwise amino acid interaction pattern in a condensate that contains either only Y (and G, S) and only F (and G, S) but not both Y and F? Also, this paragraph in the manuscript seems to suggest that the authors' observation of similar contact patterns in the GSY and GSF condensates is "counterintuitive" given the difference in Y-Y and F-F potentials of mean force (Joseph et al., 2021); but there is nothing particularly counterintuitive about that. The two sets of observations are not mutually exclusive. For instance, consider two different homopolymers, one with a significantly stronger monomer-monomer attraction than the other. The condensates for the two different homopolymers will have essentially the same contact pattern but very different stabilities (different critical temperatures), and there is nothing surprising about it. In other words, phase separation propensity is not "driven" by contact pattern in general, it's driven by interaction (free) energy. The relevant issue here is total interaction energy or the critical point of the phase separation. If it is computationally feasible, the authors should attempt to determine the critical temperatures for the GSY condensate versus the GSF condensate to verify that the GSY condensate has a higher critical temperature than the GSF condensate. That would be the most relevant piece of information for the question at hand.

      We are grateful for this very insightful comment by the referee. We have followed this suggestion to address whether, despite similar interaction patterns in GSY and GSF condensates, their stabilities are different. As in our previous work (De Sancho, 2022), we have run replica exchange MD simulations for both condensates and derived their phase diagrams. Our results, shown in the new Figure 5 and supplementary Figs. S6-S7, clearly indicate that the GSY condensate has a lower saturation density than the GSF condensate. This result is consistent with the trends observed in experiments on mutants of the low-complexity domain of hnRNPA1, where the relative amounts of F and Y determine the saturation concentration (Bremer et al., 2022).

      (3) Page 9, lines 315-316: "...Our ε [relative permittivity] values ... are surprisingly close to that derived from experiment on Ddx4 condensates (45{plus minus}13) (Nott et al., 2015)".  For accuracy, it should be noted here that the relative permittivity provided in the supplementary information of Nott et al. was not a direct experimental measurement but based on a fit using Flory-Huggins (FH), but FH is not the most appropriate theory for a polymer with long-spatial-range Coulomb interactions. To this reviewer's knowledge, no direct measurement of relative permittivity in biomolecular condensates has been made to date. Explicit-water simulation suggests that the relative permittivity of Ddx4 condensate with protein volume fraction ≈ 0.4 can have a relative permittivity ≈ 35-50 (Das et al., PNAS 2020, Fig.7A), which happens to agree with the ε = 45{plus minus}13 estimate. This information should be useful to include in the authors' manuscript.

      We thank the referee for this useful comment. We are aware that the estimate we mentioned is not direct. We have now clarified this point and added the additional estimate from Das et al. In the new version of the manuscript, we say:

      Our 𝜀 values for the condensates (39 ± 5 for GSY and 47 ± 3 for GSF) are surprisingly close to that derived from experiments on Ddx condensates using Flory-Huggins theory (45±13) (Nott et al., 2015) and from atomistic simulations of Ddx4 (∼35−50 at a volume fraction of 𝜙 = 0.4) (Das et al., 2020).

      (4) As for the dielectric environment within biomolecular condensates, coarse-grained simulation has suggested that whereas condensates formed by essentially electric neutral polymers (as in the authors' model systems) have relative permittivities intermediate between that of bulk water and that of pure protein (ε=2-4, or at most 15), condensates formed by highly charged polymers can have relative permittivity higher than that of bulk water [Wessén et al., J Phys Chem B 125:4337-4358 (2021), Fig.14 of this reference]. In view of the role of aromatic residues (mainly Y and F) in the phase separation of IDPs such as A1-LCD and LAF-1 that contain positively and negatively charged residues (Martin et al., 2020; Schuster et al., 2020, already cited in the manuscript), it should be useful to address briefly how the relationship between the relative phase-separation promotion strength of Y vs F and dielectric environment of the condensate may or may not be change with higher relative permittivities.

      We thank the referee for their comment regarding highly charged polymers. However, we have chosen not to address these systems in our manuscript, as they are significantly different from the GSY/GSF peptide condensates under investigation. In polyelectrolyte systems, condensate formation is primarily driven by electrostatic interactions and counterion release, while we highlight the role of transfer free energies. At high dielectric constants (and dielectrics even higher than that of water), the strength of electrostatic interactions will be greatly reduced. In our approach to estimate differences between Y and F, the transfer free energy should plateau at a value of ΔΔG=0 in water. At greater values of ε>80, it becomes difficult to predict whether additional effects might become relevant. As this lies beyond the scope of our current study, we prefer not to speculate further.

      (5) The authors applied the dipole moment fluctuation formula (Eq.2 in the manuscript) to calculate relative permittivity in their model condensates. Does this formula apply only to an isotropic environment? The authors' model condensates were obtained from a "slab" approach (page 4 and thus the simulation box has a rectangular geometry. Did the authors apply Equation 2 to the entire simulation box or only to the central part of the box with the condensate (see, e.g., Figure 3C in the manuscript). If the latter is the case, is it necessary to use a different dipole moment formula that distinguishes between the "parallel" and "perpendicular" components of the dipole moment (see, e.g., Equation 16 in the above-cited Wessén et al. 2021 paper). A brief added comment will be useful.

      We have calculated the relative permittivity from dense phases only. These dense phases were sliced from the slab geometry and then re-equilibrated. Long simulations were then run to converge the calculation of the dielectric constant. We have clarified this in the Methods section of the paper. We say:

      For the calculation of the dielectric constant of condensates, we used the simulations of isolated dense phases mentioned above.

      (6) Concerning the general role of Y and F in the phase separation of biomolecules containing positively charged Arg and Lys residues, the relative strength of cation-π interactions (cation-Y vs cation-F) should be addressed (in view of the generality implied by the title of the manuscript), or at least discussed briefly in the authors' manuscript if a detailed study is beyond the scope of their current effort. It has long been known that in the biomolecular context, cation-Y is slightly stronger than cation-F, whereas cation-tryptophan (W) is significantly stronger than either cation-Y and cation-F [Wu & McMahon, JACS 130:12554-12555 (2008)]. Experimental data from a study of EWS (Ewing sarcoma) transactivation domains indicated that Y is a slightly stronger promoter than F for transcription, whereas W is significantly stronger than either Y or F [Song et al., PLoS Comput Biol 9:e1003239 (2013)]. In view of the subsequent general recognition that "transcription factors activate genes through the phase-separation capacity of their activation domain" [Boija et al., Cell 175:1842-1855.e16 (2018)] which is applicable to EWS in particular [Johnson et al., JACS 146:8071-8085 (2024)], the experimental data in Song et al. 2013 (see Figure 3A of this reference) suggests that cation-Y interactions are stronger than cation-F interactions in promoting phase separation, thus generalizing the authors' observations (which focus primarily on Y-Y, Y-F and F-F interactions) to most situations in which cation-Y and cation-F interactions are relevant to biomolecular condensation.

      We thank our referee for this insightful comment. While we restrict our analysis to aromatic pairs in this work, the observed crossover will certainly affect other pairs where tyrosine or phenylalanine are involved. We now comment on this point in the discussions section of the revised manuscript. This topic will be explored in detail in a follow-up manuscript we are currently completing. We say:

      We note that, although we have not included in our analysis positively charged residues that form cation-π interactions with aromatics, the observed crossover will also be relevant to Arg/Lys contacts with Phe and Tyr. Following the rationale of our findings, within condensates, cation-Tyr interactions are expected to promote phase separation more strongly than cation-Phe pairs.

      (7) Page 9: The observation of weaker effective F-F (and a few other nonpolar-nonpolar) interactions in a largely aqueous environment (as in an IDP condensate) than in a nonpolar environment (as in the core of a folded protein) is intimately related to (and expected from) the long-recognized distinction between "bulk" and "pair" as well as size dependence of hydrophobic effects that have been addressed in the context of protein folding [Wood & Thompson, PNAS 87:8921-8927 (1990); Shimizu & Chan, JACS 123:2083-2084 (2001); Proteins 49:560-566 (2002)]. It will be useful to add a brief pointer in the current manuscript to this body of relevant resources in protein science.

      We thank the referee for bringing this body of work to our attention. In the revised version of our work, we briefly mention how it relates to our results. We also note that the suggested references have pointed to another of the limitations of our study, that of chain connectivity, addressed in the work by Shimizu and Chan. While we were well aware of these limitations, we had not mentioned them in our manuscript. Concerning the distinction between pair and bulk hydrophobicities, we include the following in the concluding lines of our work:

      The observed context dependence has deep roots in the concepts of “pair” and “bulk” hydrophobicity (Wood and Thompson, 1990; Shimizu and Chan, 2002). While pair hydrophobicity is connected to dimerisation equilibria (i.e. the second step in Figure 2B), bulk hydrophobicity is related to transfer processes (the first step). Our work stresses the importance of considering both the pair contribution that dominates at high solvation, and the transfer free energy contribution, which overwhelms the interaction strength at low dielectrics.

      Reviewer #2 (Public review):

      Summary:

      In this preprint, De Sancho and López use alchemical molecular dynamics simulations and quantum mechanical calculations to elucidate the origin of the observed preference of Tyr over Phe in phase separation. The paper is well written, and the simulations conducted are rigorous and provide good insight into the origin of the differences between the two aromatic amino acids considered.

      We thank the referee for his/her positive assessment of our work. Below, we address all the questions raised one by one.

      Strengths:

      The study addresses a fundamental discrepancy in the field of phase separation where the predicted ranking of aromatic amino acids observed experimentally is different from their anticipated rankings when considering contact statistics of folded proteins. While the hypothesis that the difference in the microenvironment of the condensed phase and hydrophobic core of folded proteins underlies the different observations, this study provides a quantification of this effect. Further, the demonstration of the crossover between Phe and Tyr as a function of the dielectric is interesting and provides further support for the hypothesis that the differing microenvironments within the condensed phase and the core of folded proteins is the origin of the difference between contact statistics and experimental observations in phase separation literature. The simulations performed in this work systematically investigate several possible explanations and therefore provide depth to the paper.

      Weaknesses:

      While the study is quite comprehensive and the paper well written, there are a few instances that would benefit from additional details. In the methods section, it is unclear as to whether the GGXGG peptides upon which the alchemical transforms are conducted are positioned restrained within the condensed/dilute phase or not. If they are not, how would the position of the peptides within the condensate alter the calculated free energies reported? 

      The peptides are not restrained in our simulations and can therefore diffuse out of the condensate given sufficient time. Although the GGXGG peptide can, given sufficient time, leave the peptide condensate, we did not observe any escape event in the trajectories we used to generate starting points for switching. Hence, the peptide environment captured in our calculations reflects, on average, the protein-protein and protein-solvent interactions inside the model condensate. We believe this is the right way of performing the calculation of transfer free energy differences into the condensate. We have clarified this point when we describe the equilibrium simulation results in the revised manuscript. We say:

      Also, the peptide that experiences the transformation, which is not restrained, must remain buried within the condensate for all the snapshots that we use as initial frames, to avoid averaging the work in the dilute and dense phases.

      On the referee’s second point of whether there would be differences if the peptide visited the dilute phase, the answer is that, indeed, we would. We expect that the behaviour of the peptide would approach ΔΔG=0, considering the low protein concentration in the dilute phase. For mixed trajectories with sampling in both dilute and dense phases, our expectation would be a bimodal distribution in the free energy estimates from switching (see e.g. Fig. 8 in DOI:10.1021/acs.jpcb.0c10263). Because we are exclusively interested in the transfer free energies into the condensate, we do not pursue such calculations in this work.

      It would also be interesting to see what the variation in the transfer of free energy is across multiple independent replicates of the transform to assess the convergence of the simulations. 

      Upon submission of our manuscript, we were confident that the results we had obtained would pass the test of statistical significance. We had, after all, done many more simulations than those reported, plus the comparable values of ΔΔG<sub>Transfer</sub> for both GSY and GSF pointed in the right direction. However, we acknowledge that the more thorough test of running replicates recommended by the referee is important, considering the slow diffusion within the Tyr peptide condensates due to its stickiness. Also, the non-equilibrium switching method had not been tested before for dense phases like the ones considered here.

      We have hence followed our referee's suggestion and done three different replicates, 1 μs each, of the equilibrium runs starting from independent slab configurations, for both the GSY and GSF condensates (see the new supporting figures Fig. S1, S2 and S5). We now report the errors from the three replicates as the standard error of the mean (bootstrapping errors remain for the rest of the solvents). Our results are entirely consistent with the values reported originally, confirming the validity of our estimates.

      Additionally, since the authors use a slab for the calculation of these free energies, are the transfer free energies from the dilute phase to the interface significantly different from those calculated from the dilute phase to the interior of the condensate? 

      We thank the referee for this valuable comment, as it has pointed us in the direction of a rapidly increasing body of work on condensate interfaces, for example, as mediators of aggregation, that we may consider for future study with the same methodology. However, as discussed above, we have not considered this possibility in our work, as we decided to focus on the condensate environment, rather than its interface.

      The authors mention that the contact statistics of Phe and Tyr do not show significant difference and thereby conclude that the more favorable transfer of Tyr primarily originates from the dielectric of the condensate. However, the calculation of contacts neglects the differences in the strength of interactions involving Phe vs. Tyr. Though the authors consider the calculation of energy contact formation later in the manuscript, the scope of these interactions are quite limited (Phe-Phe, Tyr-Tyr, Tyr-Amide, Phe-Amide) which is not sufficient to make a universal conclusion regarding the underlying driving forces. A more appropriate statement would be that in the context of the minimal peptide investigated the driving force seems to be the difference in dielectric. However, it is worth mentioning that the authors do a good job of mentioning some of these caveats in the discussion section.

      We thank the referee for this important comment. Indeed, the similar contact statistics and interaction patterns that we reported originally do not necessarily imply identical interaction energies. In other words, similar statistics and patterns can still result in different stabilities for the Phe and Tyr condensates if the energetics are different. Hence, we cannot conclude that the GSF and GSY condensate environments are equivalent.

      To address this point, we have run new simulations for the revised version of our paper, using the temperature-replica exchange method, as before. From the new datasets, we derive the phase diagrams for both the GSF and GSY condensates (see the new Fig. 5). We find that the tyrosine-containing condensate is more stable than that of phenylalanine, as can be inferred from the lower saturation density in the low-density branch of the phase diagram. In consequence, despite the similar contact statistics, the energetics differ, making the saturation density of the GSY slightly lower than that of GSF. This result is consistent with experimental data by Bremer et al (Nat. Chem. 2022). 

      Reviewer #3 (Public review):

      Summary:

      In this study, the authors address the paradox of how tyrosine can act as a stronger sticker for phase separation than phenylalanine, despite phenylalanine being higher on the hydrophobicity scale and exhibiting more prominent pairwise contact statistics in folded protein structures compared to tyrosine.

      We are grateful for the referee’s favourable opinion on the paper. Below, we address all of the issues raised.

      Strengths:

      This is a fascinating problem for the protein science community with special relevance for the biophysical condensate community. Using atomistic simulations of simple model peptides and condensates as well as quantum calculations, the authors provide an explanation that relies on the dielectric constant of the medium and the hydration level that either tyrosine or phenylalanine can achieve in highly hydrophobic vs. hydrophilic media. The authors find that as the dielectric constant decreases, phenylalanine becomes a stronger sticker than tyrosine. The conclusions of the paper seem to be solid, it is well-written and it also recognises the limitations of the study. Overall, the paper represents an important contribution to the field.

      Weaknesses:

      How can the authors ensure that a condensate of GSY or GSF peptides is a representative environment of a protein condensate? First, the composition in terms of amino acids is highly limited, second the effect of peptide/protein length compared to real protein sequences is also an issue, and third, the water concentration within these condensates is really low as compared to real experimental condensates. Hence, how can we rely on the extracted conclusions from these condensates to be representative for real protein sequences with a much more complex composition and structural behaviour?

      We agree with the main weakness identified by the referee. In fact, all these limitations had already been stated in our original submission. Our ternary peptide condensates are just a minimal model system that bears reasonable analogies with condensates, but definitely is not identical to true LCR condensates. The analogies between peptide and protein condensates are, however, worth restating: 

      (1) The limited composition of the peptide condensates is inspired by LCR sequences (see Fig. 4 in Martin & Mittag, 2018).

      (2) The equilibrium phase diagram, showing a UCST, is consistent with that of LCRs from Ddx4 or hnRNPA1.

      (3) The dynamical behaviour is intermediate between liquid and solid (De Sancho, 2022). 

      (4) The contact patterns are comparable to those observed for FUS and LAF1 (Zheng et al, 2020).

      The third issue pointed out by the referee requires particular attention. Indeed, the water content in the model condensates is low (~200 mg/mL for GSY) relative to the experiment (e.g. ~600 mg/mL for FUS and LAF-1 from simulations). Considering that both interaction patterns and solvation contribute to the favorability of Tyr relative to Phe, we speculate that a greater degree of solvation in the true protein condensates will further reinforce the trends we observe.

      In any case, in the revised version of the manuscript, we have made an effort to insist on the limitations of our results, some of which we plan to address in future work.

      Reviewer #3 (Recommendations for the authors):

      (1) The fact that protein density is so high within GSY or GSF peptide condensates may significantly alter the conclusions of the paper. Can the authors show that for condensates in which the protein density is ~0.2-0.3 g/cm3, the same conclusions hold? Could the authors use a different peptide sequence that establishes a more realistic protein concentration/density inside the condensate?

      Unfortunately, recent work with a variety of peptide sequences suggests that finding peptides in the density range proposed by the referee may be very challenging. For example, Pettit and his co-workers have extensively studied the behaviour of GGXGG peptides. In a recent work, using the CHARMM36m force field and TIP3P water, they report densities of ~1.2-1.3 g/mL for capped pentapeptide condensates (Workman et al, Biophys. J. 2024; DOI: 10.1016/j.bpj.2024.05.009). Brown and Potoyan have recently run simulations of zwitterionic GXG tripeptides with the Amber99sb-ILDNQ force field and TIP3P water, starting with a homogenous distribution in cubic simulation boxes (Biophys. J. 2024, DOI: 10.1016/j.bpj.2023.12.027). In a box with an initial concentration of 0.25 g/mL, upon phase separation, the peptide ends up occupying what would seem to be ~1/3 of the box, although we could not find exact numbers. This would imply densities of ~0.75 g/mL in the dense phase, with the additional problem of many charges. Finally, Joseph and her co-workers have recently simulated a set of hexapeptide condensates with varied compositions using a combination of atomistic and coarse-grained simulations. For the atomistic simulations, the Amber03ws force field and TIP4P water were used (see BioRxiv reference 10.1101/2025.03.04.641530). They have found values of the protein density in the dense phase ranging between 0.8 and 1.2 g/mL.  The consistency in the range of densities reported in these studies suggests that short peptides, at least up to 7-residues long, tend to form quite dense condensates, akin to those investigated in our work. While the examples mentioned do not comprehensively span the full range of peptide lengths, sequences, and force fields, they nonetheless support the general behaviour we observe. A systematic exploration of all these variables would require an extensive search in parameter space, which we believe falls outside the scope of the present study.

      (2) Do the conclusions hold for phase-separating systems that mostly rely on electrostatic interactions to undergo LLPS, like protein-RNA complex coacervates? In other words, could the authors try the same calculations for a binary mixture composed of polyR-polyE, or polyK-polyE?

      This is an excellent idea that we may attempt in future work, but the remit of the current work is aromatic amino acids Phe and Tyr only. Hence, we do not include calculations or discussion on polyR-polyE systems in our revised manuscript.

      (3) One of the major approximations made by the authors is the length of the peptides within the condensates, which is not realistic, or their density. Specifically, could they double or triple the length of these peptides while maintaining their composition so it can be quantified the impact of sequence length in the transfer of free energies?

      We thank the referee for this comment and agree with the main point, which was stated as a limitation in our original submission. The suggested calculations anticipate research that we are planning but will not include in the current work. One of the advantages of our model systems is that the small size of the peptides allows for small simulation boxes and relatively rapid sampling. Longer peptide sequences would require conformational sampling beyond our current capabilities, if done systematically. An example of these limitations is the amount of data that we had to discard from the new simulations we report, which amounts to up to 200 ns of our replica exchange runs in smaller simulation boxes (i.e. >19 μs in total for the 48 replicas of the two condensates!). As stated in the answer to point 1, we have found in the literature work on peptides in the range of 1-7 residues with consistent densities. Additionally, a recent report using alchemical transformations using equilibrium techniques with tetrapeptide condensates, pointing to the role of transfer free energy as driving force for condensate formation, further supports the observations from our work.

      Minor issues:

      (1) The caption of Figure 3B is not clear. It can only be understood what is depicted there once you read the main text a couple of times. I encourage the authors to clarify the caption.

      We have rewritten the caption for greater clarity. Now it reads as follows:

      Time evolution of the density profiles calculated across the longest dimension of the simulation box (L) in the coexistence simulations. In blue we show the density of all the peptides, and in dark red that of the F/Y residue in the GGXGG peptide.

      (2) Why was the RDF from Figure 5A cut at such a short distance? Can the authors expand the figure to clearly show that it has converged?

      In the updated Figure 5 (now Fig. 6), we have extended the g(r) up to r=1.75 nm so that it clearly plateaus at a value of 1.

    1. Reviewer #1 (Public review):

      Summary

      In the presented paper, Lu and colleagues focus on how items held in working memory bias someone's attention. In a series of three experiments, they utilized a similar paradigm in which subjects were asked to maintain two colored squares in memory for a short and variable time. After this delay, they either tested one of the memory items or asked subjects to perform a search task.

      In the search task, items could share colors with the memory items, and the authors were interested in how these would capture attention, using reaction time as a proxy. The behavioral data suggest that attention oscillates between the two items. At different maintenance intervals, the authors observed that items in memory captured different amounts of attention (attentional capture effect).

      This attentional bias fluctuates over time at approximately the theta frequency range of the EEG spectrum. This part of the study is a replication of Peters and colleagues (2020).

      Next, the authors used EEG recordings to better understand the neural mechanisms underlying this process. They present results suggesting that this attentional capture effect is positively correlated with the mean amplitude of alpha power. Furthermore, they show that the weighted phase lag index (wPLI) between the alpha and theta bands across different electrodes also fluctuates at the theta frequency.

      Strengths

      The authors focus on an interesting and timely topic: how items in working memory can bias our attention. This line of research could improve our understanding of the neural mechanisms underlying working memory, specifically how we maintain multiple items and how these interact with attentional processes. This approach is intriguing because it can shed light on neuronal mechanisms not only through behavioral measures but also by incorporating brain recordings, which is definitely a strength.<br /> Subjects performed several blocks of experiments, ranging from 4 to 30, over a few days depending on the experiment. This makes the results - especially those from behavioral experiments 2 and 3, which included the most repetitions - particularly robust.

      Weaknesses

      One of the main EEG results is based on the weighted phase lag index (wPLI) between oscillations in the alpha and theta bands. In my opinion, this is problematic, as wPLI measures the locking of oscillations at the same frequency. It quantifies how reliably the phase difference stays the same over time. If these oscillations have different frequencies, the phase difference cannot remain consistent. Even worse, modeling data show that even very small fluctuations in frequency between signals make wPLI artificially small (Cohen, 2015).

      In response authors stated : "Additionally, the present study referenced previous research by using the wPLI index as a measure of cross-frequency coupling strength31,64-66"<br /> Unfortunately, after checking those publications, we can see that in paper 31 there is no mention of "wPLI" or "PLV." In 64 and 65, the authors use wPLI, but only to measure same-frequency coherence, whereas cross-frequency coupling is computed by phase-amplitude coupling or cross-frequency coupling also known as n:m-PS. In 66, I cannot find any cross-frequency results, only cross-species analysis. This is very problematic, as it indicates that the authors included references in their rebuttal without verifying their relevance.<br /> 31 de Vries, I. E. J., van Driel, J., Karacaoglu, M. & Olivers, C. N. L. Priority Switches in Visual Working Memory are Supported by Frontal Delta and Posterior Alpha Interactions. Cereb Cortex 28, 4090-4104, doi:10.1093/cercor/bhy223 (2018).64 Delgado-Sallent, C. et al. Atypical, but not typical, antipsychotic drugs reduce hypersynchronized prefrontal-hippocampal circuits during psychosis-like states in mice: Contribution of 5-HT2A and 5-HT1A receptors. Cerebral Cortex 32, 870 3472-3487 (2022). 65 Siebenhühner, F. et al. Genuine cross-frequency coupling networks in human resting-state electrophysiological recordings. PLoS Biology 18, e3000685 (2020). 66 Zhang, F. et al. Cross-Species Investigation on Resting State Electroencephalogram. Brain Topogr 32, 808-824, doi:10.1007/s10548-019-00723-x (2019).

      Another result from the electrophysiology data shows that the attentional capture effect is positively correlated with the mean amplitude of alpha power. In the presented scatter plot, it seems that this result is driven by one outlier. Unfortunately, Pearson correlation is very sensitive to outliers, and the entire analysis can be driven by an extreme case. I extracted data from the plot and obtained a Pearson correlation of 0.4, similar to what the authors report. However, the Spearman correlation, which is robust against outliers, was only 0.13 (p = 0.57) indicating a non-significant relationship.

      Cohen, M. X. (2015). Effects of time lag and frequency matching on phase based connectivity. Journal of Neuroscience Methods, 250, 137-146

    2. Author response:

      The following is the authors’ response to the original reviews.

      Reviewer #1 (Public review):

      Thank you very much for your recognition of our work and for pointing out the shortcomings. We have made revisions one by one and provided corresponding explanations regarding the issues you raised.

      Weaknesses:

      One of the main EEG results is based on the weighted phase lag index (wPLI) between oscillations in the alpha and theta bands. In my opinion, this is problematic, as wPLI measures the locking of oscillations at the same frequency. It quantifies how reliably the phase difference stays the same over time. If these oscillations have different frequencies, the phase difference cannot remain consistent. Even worse, modeling data show that even very small fluctuations in frequency between signals make wPLI artificially small (Cohen, 2015).

      thank you for raising the question regarding the application of wPLI between the alpha and theta bands, which indeed deserves further explanation. In our study, we referred to some relevant previous literatures and adopted their approach of using wPLI to measure cross-frequency coupling strength, as this index itself can reflect the stability of phase differences. We have also considered the point you mentioned that the phase differences of oscillations with different frequencies are difficult to remain consistent. However, in this study, the presentation times of the two memory items are the same, which is fair to both from this perspective. Moreover, the study observed that the wPLI values of these two items alternately dominate over time, and this changing pattern is consistent with the regularity of behavioral data. It seems hard to explain this as a mere coincidence. 

      The corresponding discussion has been added to the revised part of the paper:“the present study referenced previous research by using the wPLI index as a measure of cross-frequency coupling strength31,64-66 (this index quantifies the stability of phase differences), yet the phases of different oscillations inherently change over time. However, this is fair to the two memory items in the present study, as their presentation times were balanced. The study found that the wPLI values of the two items alternately dominated over time, consistent with the pattern of behavioral data, which is hardly explicable by coincidence”

      Another result from the electrophysiology data shows that the attentional capture effect is positively correlated with the mean amplitude of alpha power. In the presented scatter plot, it seems that this result is driven by one outlier. Unfortunately, Pearson correlation is very sensitive to outliers, and the entire analysis can be driven by an extreme case. I extracted data from the plot and obtained a Pearson correlation of 0.4, similar to what the authors report. However, the Spearman correlation, which is robust against outliers, was only 0.13 (p = 0.57), indicating a non-significant relationship.

      you mentioned that the correlation between the attentional capture effect and the mean amplitude of alpha power in the electrophysiological data might be influenced by an outlier, and you also compared the results of Pearson and Spearman correlation coefficients, which we fully agree with.

      It is true that the small sample size of the current study makes the results vulnerable to interference from extreme data. Regarding this point, I have already explained it in the limitations section of the discussion in the revised manuscript:“the sample size of the current study is small, which may render the results vulnerable to interference from extreme cases”

      The behavioral data are interesting, but in my opinion, they closely replicate Peters and colleagues (2020) using a different paradigm. In that study, participants memorized four spatial positions that formed the endpoints of two objects, and one object was cued. Similarly, reaction times fluctuated at theta frequency, and there was an anti-phase relationship between the two objects. The main novelty of the present study is that this bias can be transferred to an unrelated task. While the current study extends Peters and colleagues' findings to a different task context, the lack of a thorough, direct comparison with Peters et al. limits the clarity of the novel insights provided.

      thank you very much for your attention to the behavioral data and its relevance to the study by Peters et al. (2020). We have noticed that there are similarities in some results between the two studies, which also indicates the stability of the relevant phenomena from one aspect.

      However, we would also like to further explain the differences between this study and the study by Peters et al. In the study by Peters et al., participants memorized four spatial positions that formed the endpoints of two objects (one of which was cued), and their results showed that after the two objects disappeared, attention fluctuated at the theta rhythm between their original positions with an inverse correlation. In contrast, the present study explores the manner of memory maintenance indirectly by leveraging the guiding effect of working memory on attention, effectively avoiding the influence of spatial positions.

      The study by Peters et al. directly examined differences in probe positions, clearly demonstrating that attention undergoes rhythmic changes at the two spatial locations and persists after the objects vanish, but it hardly clarifies the rhythmicity of working memory performance. Whereas the present study directly investigates such performance using the attention-capture effect of working memory, revealing that when maintaining multiple memory items, their attention-capturing capabilities alternate in dominance, i.e., multiple working memory items alternately become priority templates in a rhythmic manner. This is also some new attempts in the research perspective and method of this study.

      The corresponding discussion has been added to the revised part of the paper

      “Similar to the present study, Peters et al. had participants memorize four spatial positions forming the endpoints of two objects (one cued), and their results showed that after the two objects disappeared, attention fluctuated at the theta rhythm between their original positions with an inverse correlation; in contrast, the present study explores the manner of memory maintenance indirectly by leveraging the guiding effect of working memory on attention, effectively avoiding the influence of spatial positions—while Peters et al.’s study, which directly examined differences in probe positions, clearly demonstrates that attention undergoes rhythmic changes at the two spatial locations and persists after the objects vanish, it hardly clarifies the rhythmicity of working memory performance, whereas the present study directly investigates such performance using the attention-capture effect of working memory, revealing that when maintaining multiple memory items, their attention-capturing capabilities alternate in dominance, i.e., multiple working memory items alternately become priority templates in a rhythmic manner.”

      Reviewer #2 (Public review):

      The information provided in the current version of the manuscript is not sufficient to assess the scientific significance of the study.

      thank you very much for pointing out the multiple issues in our manuscript. Due to several revisions of this work, including experimental adjustments, there have been some inconsistencies in details. We appreciate you identifying them one by one.  We have made corresponding revisions based on your comments:

      (1) In many cases, the details of the experiments or behavioral tasks described in the main text are not consistent with those provided in the Materials and Methods section. Below, I list only a few of these discrepancies as examples:

      a) For Experiment 1, the Methods section states that the detection stimulus was presented for 2000 ms (lines 494 and 498), but Figure 1 in the main text indicates a duration of 1500 ms.

      we greatly appreciate you catching this inconsistency. We have made unified revisions by referring to the final implemented experimental procedures.  Corresponding revisions have been made in the paper:

      b) For Experiment 2, not only is the range of SOAs mentioned in the Methods section inconsistent with that shown in the main text and the corresponding figure, but the task design also differs between sections.

      Thank you for bringing this discrepancy to our attention. We have made unified revisions by referring to the final implemented experimental procedures. The correct SOAs are 233:33:867 ms.

      Corresponding revisions have been made in the paper:

      c) For Experiment 3, the main text indicates that EEG recordings were conducted, but in the Methods section, the EEG recording appears to have been part of Experiment 2 (lines 538-540).

      we’re grateful for you noticing this mix-up. In fact, only Experiment 3 is an EEG experiment, and we have made corresponding corrections in the "Methods" section. Corresponding revisions have been made in the paper: “The remaining components after this process were then projected back into the channel space. We extracted data from -500 ms to 2000 ms relative to cue stimulus presentation in Experiment 3.”  

      (2) The results described in the text often do not match what is shown in the corresponding figure. For example:

      a) In lines 171-178, the SOAs at which a significant difference was found between the two conditions do not appear to match those shown in Figure 2A.

      Many thanks for spotting this error. The previous results missed one SOA time, namely 33 ms, leading to a 33 ms difference in time. We have corrected it in the revised manuscript.

      Corresponding revisions have been made in the paper:“Specifically, the capture effect of cued items was significantly greater than that of uncued items at SOAs of 267ms (t(24) = 2.72, p = 0.03, Cohen's d = 1.11), 667ms (t(24) = 2.37, p = 0.03, Cohen's d= 0.97) and 833ms (t(24) = 3.53, p = 0.002, Cohen's d = 1.44), while the capture effect of uncued items was significantly greater than that of cued items at SOAs of 333ms (t(24) = 2.97, p = 0.007, Cohen's d = 1.21), 367ms (t(24) = 2.14, p = 0.04, Cohen's d = 0.87), 433ms (t(24 )= 2.49, p = 0.02, Cohen's d = 1.02), 467ms (t(24)=2.37, p = 0.03, Cohen's d = 0.97) and 567ms (t(24)=2.72, p = 0.02, Cohen's d = 1.11). ”

      (b) In Figure 4, the figure legend (lines 225-228) does not correspond to the content shown in the figure.

      we appreciate you pointing out this oversight. When adjusting the color scheme during the revision of the manuscript, we neglected to revise the legend, which has now been corrected in the revised manuscript.

      Corresponding revisions have been made in the paper:“Figure 4. The red line represents the average across all participants of the Fourier transforms of the differences in capture effects between left and right memory items at the individual level. The gray area represents values below the group average of medians derived from 1000 permutations, with each permutation involving Fourier transforms for each participant. *: p < 0.05.”

      (c) In Figure 9, not sufficient information is provided within the figure or in the text, making it difficult to understand. Consequently, the results described in the text cannot be clearly linked to the figure.

      Thank you for drawing our attention to this issue. We have revised Figure 9 and its legend in the revised manuscript to make them clearer and easier to understand.

      Corresponding revisions have been made in the paper

      (3) Insufficient information is provided regarding the data analysis procedures, particularly the permutation tests used for the data presented in Figures 2B, 4, and 10. The results shown in these figures are critical for the main conclusions drawn in the manuscript.

      we’re thankful for you highlighting this gap. In the revised manuscript, we have provided a more detailed explanation in the "Methods" section, especially regarding the content related to frequency analysis, to make the expression clearer.

      Corresponding revisions have been made in the paper:“As shown in Figure 8, the alpha power (8-14 Hz) induced by cued and uncued items alternated in dominance during the memory retention phase. To quantify this rhythmic alternation, we conducted a spectral analysis following these steps: First, we computed the power difference between cued and uncued items within the 8-14 Hz range during the retention phase. These differences were then downsampled to 100 Hz using a 10 ms window for averaging, generating a one-dimensional time series spanning the 0-2000 ms retention period. This time series was subsequently subjected to amplitude spectrum analysis across frequencies from 1 Hz to 50 Hz using Fourier transformation.

      To assess the statistical significance of the observed spectral features, we employed a permutation test. Specifically, we randomly shuffled the temporal order of the time series of power differences between cued and uncued items—thereby preserving the amplitude distribution of the data while eliminating temporal correlations in the original sequence—and repeated the Fourier transform and spectral analysis for each shuffled time series. This permutation process was replicated 1000 times to generate a null distribution of spectral power values. A frequency component in the original data was considered statistically significant if its power ranked within the top 5% of the corresponding null distribution (p < 0.05).

      We applied the same analytical pipeline to investigate differences in the weighted phase-lag index (wPLI) between the contralateral regions of the two items and the prefrontal cortex during the retention phase. Specifically, wPLI differences (i.e., the difference between the two conditions) were computed, downsampled to 100 Hz using a 10 ms window for averaging to generate a time series spanning 0-2000 ms, and then subjected to amplitude spectrum analysis (1-50 Hz) using Fourier transformation. Significance was assessed via the identical permutation test procedure described above (randomly shuffling the temporal order of the difference time series).”

    1. Joint Public Review:

      Marshall et al describe the effects of altering metabotropic glutamate receptor 5 activity on activity of D1 receptor expressing spiny projection neurons in dorsolateral striatum focusing on two states - locomotion and rest. The authors examine effects of dSPN-specific constitutive mGlu5 deletion in several motor tests to arrive at this finding. Effects of inhibiting the degradation of the endocannabinoid 2-arachidonoyl glycerol are also examined. Overall, this is a valuable study that provides solid new information of relevance to movement disorders and possibly psychosis.

      The combination of in vivo cellular calcium imaging, pharmacology, receptor knockout and movement analysis is effectively used. The main findings do not involve gross firing rates or numbers of active neurons, but rather are revealed by specialized measures involving Jaccard coefficient and an assessment of coactivity. The authors conclude that mGlu5 expressed in dSPNs contributes to movement through effects on clustered spatial coactivity of dSPNs. More specifically, reduced mGluR5 increases coactivity during rest (defined as low velocity periods) but not during locomotion periods. The authors observe a role for mGlu5 expression in dSPNs in modulating the frequency of mEPSCs, suggesting a role in presynaptic neurotransmitter release. Some data suggesting the story may be different in the other major SPN subpopulation (iSPNs) are also presented but these studies are relatively underdeveloped leaving some ambiguity as to how cell-selective the findings are. In addition, an occlusion experiment in which the pharmacological mGluR5 agents are delivered to the dSPN mGluR5 KO to clarify if other sites of action are involved beyond the proposed D1-expressing neurons is missing. Finally, the authors present a working model that sets the stage for future experimentation. Overall, this study provides an important and detailed assessment of mGluR5 contributions to striatal circuit function and behavior.

      Remaining concerns include:

      (1) To clarify that dSPNs are sole site of action, it is necessary to examine effects of the mGlu5 NAM in the dSPN mGlu5 cKO mice. If the effects of the two manipulations occluded one another this would certainly support the hypothesis that the drug effects are mediated by receptors expressed in dSPNs. A similar argument can be made for examining effects of the JNJ PAM in the cKO mice.

      (2) There is a concern that the D1 Cre line used (Ey262), which may also target cortical neurons expands the interpretation of the study beyond the striatal populations. Further discussion of this point, particularly in the interpretation of the mGluR5 cKO experiments, would provide a better understanding of the contribution of the paper.

      (3) The use of CsF-based whole-cell internal solutions has caused concern in some past studies due to possible interference with G-protein, phosphatase and channel function (https://www.sciencedirect.com/science/article/abs/pii/S1044743104000296, https://www.jneurosci.org/content/jneuro/6/10/2915.full.pdf). It is reassuring the DHPG-induced LTD was still observable with this solution. However, it might be worth examining this plasticity with a different internal to ensure that the magnitude of the agonist effect is not altered by this manipulation.

      (4) Behavioral resolution of actions at low velocity that are termed "rest" are not explored in this study. Thus, a remaining ambiguity is whether the activities in rest include only periods of immobility or other low-velocity activities such as grooming or rearing.

    2. Author response:

      The following is the authors’ response to the original reviews.

      Reviewer #1 (Public review):

      “Can the authors offer a hypothesis as to how decreased coactivity promotes increased movement velocity.” 

      In our revision we have added an additional metric measuring how spatial coactivity changes during movement onset, the spatial correlation index, which replicates a previous finding that co-activity among proximal neurons is statistically greater surrounding movement onset. We did not find, as outlined in the revision, that mGluR5 manipulations significantly altered this relationship. Our data therefore shows, consistent with that shown previously, that ensembles of dSPNs that are co-active during movement onset, in particular ambulatory movement, are more likely to contain neurons that are closer together and the neurons are highly active. In contrast, rest ensembles contain neurons that are less active but have more highly correlated activity, across all pairwise distances. Additionally, mGluR5 inhibition, genetic or pharmacological, promotes the activation of rest ensembles but does not affect the properties of movement ensembles. Previous studies (e.g. Klaus A. et al., 2017) have shown that neurons in rest ensembles are, in general, unlikely to also be members of movement ensembles, We therefore hypothesize that corticostriatal synapses onto SPNs of rest ensembles are more likely, during spontaneous behavior, to have reduced synaptic weight due to mGluR5 signaling, potentially due to eCB mediated inhibition of neurotransmitter release. Therefore, when we inhibit mGluR5 at these synapses, we increase synaptic weight and increase the probability of activation of this coordinated rest ensemble, which suppresses movement. If, on the other hand, the synapses that govern activation of neurons in movement ensembles have a higher weight, they may be unaffected by mGluR5 inhibition. 

      The use of the Jaccard similarity index in this study is not intuitive and not fully explained by the methods or the diagram in Figure 1. 

      We have added more detail to the paper to explain the methodology of the jaccard similarity measure. The advantage of this method is that is specifically captures cells that are jointly active, as opposed to jointly inactive and is therefore useful for capturing co-activity in our sparsely active Ca<sup>2+</sup> imaging data. 

      The analysis of a possible 2-AG role in the mGlu5 mediated processes is incomplete. 

      We agree that, as an experiment to outline which endocannabinoids are involved in modulating synaptic strength through mGluR5, this experiment alone is not sufficient.

      However, our main focus in this paper is how manipulations of mGluR5 affect the spatiotemporal dynamics of dSPNs and we chose not to focus on specific mechanisms of endocannabinoid signaling, though these would certainly be interesting to investigate further in vivo.

      It would seem to be a simple experiment to examine effects of the mGlu5 NAM in the dSPN mGlu5 cKO mice. If effects of the two manipulations occluded one another this would certainly support the hypothesis that the drug effects are mediated by receptors expressed in dSPNs. A similar argument can be made for examining effects of the JNJ PAM in the cKO mice. 

      We agree that this experiment would be valuable and extend our findings presented in the paper, however, it has practically been outside the scope of the current work. 

      Reviewer #2 (Public review):

      Pharmacological and genetic manipulations of mGluR5 do not differentially/preferentially modulate the activity of proximal vs distal dSPNs, therefore, it could also be interpreted that mGluR5 is blanketly boosting/suppressing all dSPN activity as opposed to differential proximal/distal spatial relationships. 

      As in the response to reviewer 1 above, we have added additional clarification to the text explaining that our manipulations do not differentially affect the co-activity of proximal vs distal dSPNs, this is also quantified throughout the text using the spatial coordination index. However, we disagree that “it could also be interpreted that mGluR5 is blanketly boosting/suppressing all dSPN activity” as we do not observe statistically significant changes in the event rate following either pharmacological or genetic manipulations of mGluR5. Rather, we consistently observe statistically significant changes in co-activity among neurons, the extent to which activity of active neurons during either rest or movement are correlated with each other. This is the central finding of our manuscript, inhibiting or potentiating mGluR5 signaling alters behavior, not by blanket suppression or enhancement of the activity as measured using the event rate, of dSPNs, but by affecting their ensemble dynamic properties.  Co-activity during rest versus ambulatory movement is statistically greater in both proximal and distal cells and inhibiting mGluR5 increases this co-activity and decreases movement. 

      For these analyses of prox vs distal and all others, please include the detail of how many proximal vs distal cells were involved and per subject. 

      We have added a supplemental table that details the number of cells included per subject in all analyses

      Ln. 151-152: Please provide data concerning how volumes of infectivity differ between injecting AAV vs. coating the lens? If these numbers are very different, this could impact the number of Jaccard pairings and bias results. 

      While viral injection may lead to a larger volume of expression, with this one photon imaging method only those cells within ~200 microns of the edge of the lens will be able to be resolved, therefore practically, if there is an additional volume of infected tissue outside of the field of view of the lens, it would not affect the results as these neurons will not be resolved by the endoscope camera. Accordingly, the average number of cells detected per session is very similar following each approach (mean # of cells per session with coating 90.93 ± 23.69 cells, with viral injection 90.03 ± 29.29 cells)

      Is mGluR5 affecting dSPN activity in other measures beyond co-activity and rate? Does the amplitude of events change?

      We have added supplemental data for figures 2, 3, and 5 demonstrating that manipulations of mGluR5 do not affect the amplitude or length of Ca<sup>2+</sup> events included in the analysis. 

      What is the model of mGluR5 signaling in a resting state vs. movement? What other behaviors are occurring when the mouse is in a low velocity "resting state" (0-0.5 cm/s). If this includes other forms of movement (i.e. rearing, grooming) then the animal really isn't in a resting state. This is not mentioned in the open field behavior section of the methods and should be described (Ln. 486) in addition to greater explanation of what behavior measures were obtained from the video tracking software (only locomotion?)

      It would be very interesting to determine if during “rest,” when the animals is not engaged in ambulatory behavior, it may be engaged in some fine motor behavior. However, the resolution of the cameras used to measure locomotor activity in this dataset does not allow us to do this. 

      There is large variability in co-activity in proximal dSPNs when animals are "resting" (2j). Could this be explained by different behavior states within your definition of "rest"?

      We agree that if the animal is engaging in fine motor behavior that we cannot resolve with our behavior setup, this could produce some variability in coactivity. However, as shown previously (e.g. Klaus A. et al., 2017), ensembles active when the animal is not moving (our definition of “resting”), regardless of additional fine motor behaviors the animal may be engaged in when not moving, are substantially different that those ensembles that are active when the animal is moving. We therefore expect that this may limit, although potentially not eliminate, variability due to different behavioral states we may have grouped into our “resting” category. Unfortunately, as mentioned above, we are not able resolve variations in fine motor output in this behavioral data. 

      Have you performed IHC, ISH or another measure to validate D1 cell specific cKO?

      The mGluR5<sup>loxP/loxP</sup> mice used in this study were characterized previously by our lab (Xu et al., 2009), we used the same mice here with a different, but also published and characterized Cre-driver line, Drd1a-Cre Ey262 (Gerfen et al., 2013).

      Why are the "Mean Norm Co-activity" values in 5e so high in this experiment relative to figures 2-4?  

      In experiments where we treated the same animal with vehicle and a drug (i.e., experiments in Figure 2 and 3), we normalized the values for each animal in the drug treatment group to the distal bin of that animal following vehicle treatment. This allowed us to more clearly resolve the changes within each animal due to drug treatment. As comparisons in the data in figure 5 d–f are between different animals (rather than different treatments of the same animal) we could not perform this normalization procedure.  

      Reviewer #3 (Public review):

      Some D1 Cre lines have expression in the cortex. Which specific Cre line was used in this study? 

      We used, Drd1a-Cre Ey262. This is included in methods. 

      The text says JNJ treatment .... increased locomotor speed (Figure 3b) and increased the duration but not frequency of movement bouts (Figure 3c, d). However, the statistics of the figure legends say: however the change in mean velocity (3b) is not significant (p=0.060, U=3, Mann-Whitney U test), nor is the mean bout length during vehicle and JNJ (p=0.060, U=3, Mann-Whitney U test) (3d) Comparison of mean number of bouts of each animal during vehicle and JNJ (p=0.403, U=8, Mann-Whitney U test). 

      This has been corrected to indicate only the change in time spend at rest is statistically significant.

      This effect was most pronounced during periods of rest (Figure 3i, j). The decrease was only in rest? Are the colors in Figure 3J inverted? Therefore, JNJ treatment had effects that were qualitatively the inverse to the effects of fenobam on locomotion and dSPN activity. 

      We have corrected the text to state that, overall, and during periods of rest but not movement, JNJ had effects that were qualitatively the opposite of fenobam.

    1. Author response:

      The following is the authors’ response to the original reviews

      Reviewer #1 (Public review):

      Summary: 

      This study provides compelling evidence suggesting that ghrelin, a molecule released in the surroundings of the major adult brain neurogenic niche (V-SVZ) by blood vessels with high blood flow, controls the migration of newborn interneurons towards the olfactory bulbs. 

      Strengths:

      This study is a tour de force as it provides a solid set of data obtained by time-lapse recordings in vivo. The data demonstrate that the migration and guidance of newborn neurons rely on factors released by selective types of blood vessels. 

      Weaknesses:

      Some intermediate conclusions are weak and may be reinforced by additional experiments. 

      We thank the reviewer for the thoughtful evaluation and constructive comments outlined in the “Recommendations for The Authors”. In response, we have incorporated additional data, revised relevant figures, and clarified explanations in the revised manuscript.

      Reviewer #2 (Public review)

      Summary: 

      The authors establish a close spatial relationship between RMS neurons and blood vessels. They demonstrated that high blood flow was correlated with migratory speed. In vitro, they demonstrate that Ghrelin functions as a motogen that increases migratory speed through augmentation of actin cup formation. The authors proceed to demonstrate through the knockdown of the Ghrelin receptor that fewer RMS neurons reach the OB.

      They show the opposite is true when the animal is fasted. 

      Strengths: 

      Compelling evidence of close association of RMS neurons with blood vessels (tissue clearing 3D), preferentially arterioles. Good use of 2-photon imaging to demonstrate migratory speed and its correlation with blood flow. In vitro analysis of Ghrelin administration to cultured RMS neurons, actin visualization, Ghsr1KD, is solid and compelling. 

      We sincerely thank the reviewer for the encouraging comments and helpful suggestions. As noted, our original manuscript lacked sufficient in vivo evidence connecting blood flow with ghrelin signaling. To address this, we have added new data and revised the explanations throughout the manuscript as described below.

      Weaknesses: 

      (1) Novelty of findings attenuated due to prior work, especially Li et al., Experimental Neurology 2014. Here, the authors demonstrated that Ghrelin enhances migration in adultborn neurons in the SVZ and RMS. 

      We agree with the reviewer that the idea that ghrelin enhances migration of new neurons is not entirely novel. The study by Li et al. (2014) provided critical insights that guided our investigation into ghrelin as a blood-derived factor promoting neuronal migration. However, our study expands on this by demonstrating that ghrelin directly stimulates migration via GHSR1a in cultured new neurons, and we further identified the cellular and cytoskeletal mechanisms involved. Specifically, we showed that ghrelin enhances somal translocation by activating actin dynamics at the rear of the cell soma. We have revised the Results and Discussion sections accordingly to emphasize these novel aspects as follows:

      “A previous study demonstrated that the migration of V-SVZ-derived new neurons was attenuated in ghrelin knockout mice (Li et al., 2014). In our study, we found that the migration of cultured new neurons was enhanced by the application of ghrelin to the culture medium, and this effect was abolished by Ghsr1a knockdown (KD). These findings suggest that ghrelin directly stimulates neuronal migration through its receptor, GHSR1a, on new neurons. A previous study showed that GHSR1a is expressed in various regions of the brain (Zigman et al., 2006). In our experiments, new neuron-specific KD of Ghsr1a indicated that ghrelin signaling acts in a cell-autonomous manner to regulate neuronal migration.” (Discussion, page 13, lines 10–18)

      “Furthermore, we identified the cellular and cytoskeletal mechanisms underlying this effect on migration. The results indicate that ghrelin enhances somal translocation during migration by activating actin cytoskeletal dynamics at the rear of the neuronal soma.” (Discussion, page 13, lines 24–26)

      (2) The evidence for blood delivery of Ghrelin is not very convincing. Fluorescently-labeled Ghrelin appears to be found throughout the brain parenchyma, irrespective of the distance from vessels. It is also not clear from the data whether there is a link between increased blood flow and Ghrelin delivery. 

      We agree that the correlation between blood flow and ghrelin transcytosis is not very convincing in our study. As the reviewer pointed out, Figure 3A gives the impression that fluorescent-labeled ghrelin is uniformly distributed throughout the brain parenchyma. However, high-magnification images newly added in Figure 3 show that some, but not all, vessels have particularly strong fluorescent signals in the parenchymal area adjacent to the abluminal side of vascular endothelial cells, visualized by CD31 immunostaining (Feng et al., 2004) (Figure 3A′, A′′). To quantify these observations, we defined two regions: Area I (perivascular area), within 10 μm of the abluminal surface of CD31-positive endothelium; and Area II (distant area), located 10–20 μm away (Figure 3E). Of note, Area I corresponds to the perivascular region where new neurons are frequently observed (Figure 1).

      Importantly, we found strong ghrelin signals in vascular endothelial cells of endomucin-negative high-flow vessels (Figure 3C, D). This suggests that transcytosis of blood-derived ghrelin may occur more frequently in high-flow vessels due to increased endocytosis at the endothelium. To test this, we quantified signal gradients in the extra-vessel regions as fold changes (Area I / Area II), as illustrated in Figure 3E. The proportion of vessel segments with >1.5-fold increases was significantly higher in endomucin-negative vessels than in endomucin-positive ones (Figure 3F). Furthermore, vessels with >2-fold increases were observed exclusively in the endomucinnegative group (6.48% ± 1.18%). 

      These data suggest that, in high-flow vessels, blood-derived ghrelin accumulates more in the immediate perivascular region than in areas further away. This supports the possibility that elevated blood flow delivers a larger amount of ghrelin to the vascular endothelium, enhancing its transcytosis into adjacent brain parenchyma. This mechanism may underlie the preferential migration of new neurons along perivascular regions with high blood flow, as shown in Figure 1.  We have incorporated this new data in Figure 3 and corresponding explanations into the Results, Figure legend and Methods

      (3) The in vivo link between Ghsr1KD and migratory speed is not established. Given the strong work to open the study on blood flow and migratory speed and the in vitro evidence that migratory speed is augmented by Ghrelin, the paper would be much stronger with direct measurement of migration speed upon Ghsr1KD. Indeed, blood flow should also be measured in this experiment since it would address concerns in 2. If blood flow and ghrelin delivery are linked, one would expect that Ghsr1KD neurons would not exhibit increased migratory speed when associated with slow or fast blood flow vessels. 

      In Figure 3, we showed that ghrelin transcytosis occurs preferentially in high-flow vessels, suggesting a role for ghrelin in mediating the effects of blood flow on neuronal migration. However, whether this dependence is solely attributable to ghrelin signaling remains unclear. 

      To address this, we tested whether Ghsr1a-KD modifies the impact of reduced blood  flow on neuronal migration by combining Ghsr1a-KD with bilateral common carotid artery stenosis (BCAS), a chronic cerebral hypoperfusion model (Figure S9A). We found that BCAS decreased the percentage of Ghsr1a-KD new neurons reaching the OB, similar to the effect seen in control neurons (Figure S9B, see also Figure 2A–C). This suggests that blood flow influences neuronal migration even under Ghsr1a-KD conditions. 

      Furthermore, we analyzed the distribution of Ghsr1a-KD neurons with respect to vessel flow characteristics. Even under Ghsr1a-KD, a higher proportion of new neurons were located in the area of endomucin-negative (high-flow) vessels compared with endomucin-positive (low-flow) vessels (Figure S9C), indicating that Ghsr1a-KD does not abolish the preferential association of migrating neurons with high flow vessels. These findings suggest that although ghrelin signaling contributes to blood flow-dependent migration, it is not the sole factor. Other blood-derived signals may also mediate this effect. We have included these new data in Figure S9 and updated the corresponding sections in the Results

      Reviewer #1 (Recommendations for the authors) :

      Major 

      Page 6, Line 13. Please provide in the result section some explanation about how photothrombic clot is induced.  

      We added the following explanation to the Results section to clarify the method used to induce photothrombotic clot formation.

      “For clot formation, a restricted area of selected vessels was irradiated by a two-photon laser immediately after intravenous injection of rose bengal.” (Results, Page 7, lines 27–28)

      Page 6, Line 18. The authors use the marmoset as an additional experimental model. Here, V-SVZ-derived newborn neurons migrate in other brain regions as compared to rodents. Please provide a clear rationale for moving from rodents to "common marmosets" as an experiment model. And why use marmosets only for this set of experiments? 

      We clarified the rationale for using common marmosets in addition to mice as follows:

      “Because blood vessel-guided neuronal migration in the adult brain is a conserved phenomenon across species (Kishimoto et al., 2011; Akter et al., 2021; Shvedov et al., 2024), we hypothesized that blood flow may also influence neuronal migration in other brain regions of primates. The neocortex, which supports higher-order brain functions and has undergone evolutionary expansion in primates, was selected as a target region. In common marmosets, but not in mice, V-SVZ-derived new neurons migrate toward the neocortex and ventral striatum (Akter et al., 2021) (Supplemental Movies S4 and S5).” (Results, Page 6, lines 19–25)

      Figure 2B. The experimental setup is possibly problematic as the lentiviral tracing measurement does not take into consideration the rate of neurogenesis or newborn neuron survival. Can authors assess the rate of proliferation and survival in the VSVZ/RMS upon BCAS to decipher whether the reduced number of cells observed in the OB only results from migration changes? (comparable remark stands for Figure 5) 

      To evaluate whether the reduction in the number of new neurons observed in the OB after BCAS (Figure 2B, C) is due solely to impaired migration, we assessed cell proliferation and survival in the V-SVZ and RMS. Specifically, we quantified the density of Ki67+ proliferating cells and cleaved caspase-3+ apoptotic cells in the sham and BCAS groups. BCAS significantly decreased cell proliferation and increased cell death in both the V-SVZ and RMS (Figure S4), suggesting that reduced neurogenesis and/or survival may contribute to the decreased neuronal distribution in the OB. 

      Although we cannot exclude the possibility that changes in cell proliferation or survival contributed to this effect, our photothrombotic clot formation experiments are better suited to directly examine how acute reduction in blood flow affects neuronal migration. These experiments allowed us to measure the migration speed of new neurons shortly after inducing localized blood flow inhibition. We found that clot formation significantly reduced the migration speed of new neurons (Figure 2E, H), indicating that blood flow changes directly impair neuronal migration in the adult brain. 

      We have included these new data in Figure S4 and updated the corresponding text in the Results, Discussion, Figure legend, and Methods as follows:

      Figure 3. About ghrelin signaling. It is unclear whether its transcytosis occurs in endomucin-negative because of the high bloodstream flow. How can this be explained? What happens upon BCAS, is there still a close relation between ghrelin transcytosis, blood flow, and neuron migration? 

      As correctly noted, our initial explanation and data did not provide sufficient evidence that higher blood flow delivers a larger amount of ghrelin into the brain parenchyma. We found that some vessels had particularly strong fluorescent signals in the parenchymal area adjacent to the abluminal surface of vascular endothelial cells, as visualized by CD31 immunostaining (Feng et al., 2004) (Figure 3A′, A′′). On the basis of our observation that strong fluorescent signals were detected in vascular endothelial cells of endomucin-negative (high-flow) vessels (Figure 3C, D), we hypothesized that ghrelin transcytosis may occur more frequently in high-flow vessels due to increased endocytosis at the vessel endothelium. 

      To test this hypothesis, we quantified signal gradients in the extra-vessel regions by calculating fold changes in fluorescent intensity between two zones: Area I (0–10 μm from the abluminal surface of the endothelium) and Area II (10–20 μm away), as illustrated in Figure 3E. Area I corresponds to the perivascular region where new neurons are frequently found (Figure 1). We found that the proportion of vessel segments with >1.5-fold signal increase in Area I relative to Area II was significantly higher in endomucin-negative vessels than endomucin-positive ones (Figure 3F). Furthermore, vessel segments with >2-fold increases were observed exclusively in the endomucin-negative group (6.48% ± 1.18%). These results support the idea that higher blood flow increases the amount of ghrelin that reaches the luminal surface of vascular endothelial cells, thereby increasing the possibility of ghrelin transcytosis into the brain parenchyma.

      We also examined whether blood flow inhibition–induced by BCAS or photothrombotic clot formation–affects the relationship between ghrelin transcytosis, blood flow, and neuronal migration. The above results suggest that blood flow reduction may decrease ghrelin transcytosis, thereby contributing to impaired neuronal migration. To further explore this, we analyzed the distribution of new neurons around high- versus low-flow vessels under BCAS conditions. In the BCAS group, we still observed a higher density of new neurons in the region of high-flow (endomucin-negative) vessels compared with in low-flow (endomucin-positive) ones (Figure S9C). This suggests that even under reduced blood flow, neuronal migration preferentially occurs near high-flow vessels. Taken together, these results suggest that ghrelin transcytosis, blood flow and neuronal migration are connected, and that this relationship persists under conditions of blood flow reduction.

      Figure 4. Is ghrelin controlling both individual Dcx+ neuron migration as well as chain migration (cells moving more together)? This should be assessed and clarified. 

      How is ghrelin controlling actin dynamics in newborn migrating neurons? Since somal translocation speed and somal stride length are both modulated by ghrelin, this factor may also control MT remodeling, could that be checked? 

      We have revised the manuscript to better explain the role of ghrelin in both modes of neuronal migration–chain and individual. Initially, we demonstrated that ghrelin enhances the migration of new neurons in V-SVZ culture (Figure 4A, B), where these neurons migrate outward as chains, indicating that ghrelin facilitates chain migration. In subsequent in vitro experiments (Figure 4C–M), we showed that ghrelin also enhances the migration of individual neurons. To examine this in vivo, we injected Ghsr1a-KD and control lentiviruses into two different anatomical regions: the V-SVZ, where chain migration originates, and the OB core, where new neurons migrate individually. These experiments enabled us to assess the role of ghrelin signaling in each mode of migration independently. We found that ghrelin enhanced both chain migration in the RMS and individual migration in the OB. These results indicate that ghrelin signaling facilitates both forms of neuronal migration. We added the following text in the Results section:

      “To assess the direct effect of ghrelin on neuronal migration, we applied recombinant ghrelin to V-SVZ cultures, in which new neurons emerge and migrate as chains (Figure 4A). Ghrelin significantly increased the migration distance of these neurons (Figure 4B), indicating enhanced chain migration. We then used super-resolution time-lapse imaging to examine individually migrating neurons with or without knockdown (KD) of growth hormone secretagogue receptor 1a (GHSR1a), a ghrelin receptor expressed in V-SVZ-derived new neurons (Li et al., 2014) (Figure 4C). Ghrelin enhanced the migration speed of control cells (lacZ-KD) cells, indicating that it also facilitates individual migration (Figure 4D).” (Results, Page 9, lines 5–12)

      “Of the total labeled Dcx+ cells, the percentage of Dcx+ cells reaching the GL was significantly lower in the Ghsr1a-KD group than in the control group (Figure 5B, C), suggesting that ghrelin enhances individual radial migration of new neurons in the OB.” (Results, Page 10, lines 5–8) “These data indicate that ghrelin signaling facilitates both individual migration in the OB and chain migration in the RMS.” (Results, Page 10, lines 17–18)

      We also added discussion on how ghrelin may regulate cytoskeletal dynamics in migrating neurons. Ghrelin signaling has been reported to control actin cytoskeletal remodeling in astrocytoma cells (Dixit et al., 2006), which led us to investigate similar effects in migrating neurons. Rac, a member of the Rho GTPase family, was shown to mediate this actin remodeling in astrocytoma migration, suggesting it may also be involved in ghrelin-induced actin cup formation in new neurons. Furthermore, because somal translocation depends not only on actin but also on microtubule dynamics (Kaneko et al., 2017), it is possible that ghrelin influences both systems. Supporting this idea, ghrelin signaling was shown to modulate microtubule behavior via SFK-dependent phosphorylation of α-tubulin (Slomiany and Slomiany, 2017). These findings suggest that ghrelin may enhance somal translocation through coordinated regulation of both the actin and microtubule systems. We added following text in the Results and Discussion sections:

      “Ghrelin signaling has been reported to regulate actin cytoskeletal dynamics in astrocytoma cells (Dixit et al., 2006), which led us to examine whether a similar mechanism operates in migrating neurons.”(Results, Page 9, lines 23–25)

      “Further studies are needed to elucidate how ghrelin promotes actin cup formation in migrating neurons. Given that Rac, a Rho family GTPase, mediates actin remodeling downstream of ghrelin in astrocytoma cells (Dixit et al., 2006), it is possible that Rac may also be involved in ghrelininduced cytoskeletal regulation in new neurons.” (Discussion, Page 13, lines 28–31)

      “In addition to actin remodeling, ghrelin may regulate microtubule dynamics. Ghrelin signaling was shown to modulate microtubules via SFK-dependent phosphorylation of α-tubulin (Slomiany and Slomiany, 2017), raising the possibility that ghrelin promotes somal translocation of new neurons through coordinated regulation of both actin and microtubule networks (Kaneko et al., 2017).” (Discussion, Page 13, line 31–Page 14, line 2)

      It would also be informative to provide immunolabeling of Ghsr1 in the V-SVZ / RMS/ OB to have a clear picture of the expression pattern of this receptor. Newborn neurons migrate along blood vessels, which are surrounded by astrocytes that have also been reported to express Ghsr1, thus could newborn neuron migration change may also arise from activation of Ghsr1 in their surrounding astrocytes? 

      A previous study reported that GHSR1a is expressed in DCX+ new neurons in the RMS and OB, and in V-SVZ neural progenitor cells (Li et al., 2014). To visualize the spatial expression pattern of Ghsr1a, we performed RNAscope in situ hybridization because specific anti-GHSR1a antibodies suitable for immunohistochemistry were not available. Consistent with the previous report, we detected Ghsr1a mRNA in DCX+ new neurons in the VSVZ, RMS, and OB (Figure S5A), indicating that new neurons directly receive ghrelin signaling. 

      Moreover, our KD experiments demonstrated that ghrelin enhanced the migration of new neurons in a cell-autonomous manner via GHSR1a (Figure 4, 5). Nevertheless, a recent study (Stark et al., 2024) showed that GHSR1a was expressed in various cell types, including glutamatergic and GABAergic neurons, suggesting that ghrelin may also exert non-cellautonomous effects on neuronal migration. Given the presence of diverse cell types, including neurons, microglia, pericytes, and astrocytes, along the migratory route, it remains possible that GHSR1a activation in these neighboring cells contributes to the overall regulation of neuronal migration. 

      Figure 5. About the in vivo knockdown of Ghsr1a. The results section (page 9, line 3) mentioned that mice were either injected with one or the other construct but Figure 5 shows coincidence of GFP and dsRed positive cells. Were control and Ghsr1a shRNAs injected together into the same mouse? Could you quantify the number of cells in green (control), red (Ghsr1a KD), and yellow (both)? Won't they mostly be yellow? Have you tried injecting control and Ghsr1a separately? If yes, do you get the same result? Such analysis would be important to separate cell autonomous from noncell autonomous effects. 

      To minimize variability in injection conditions, we initially coinjected control and Ghsr1a-KD lentiviruses into the same mice and analyzed their migration using a paired design. As the reviewer correctly noted, some cells were coinfected and expressed both EmGFP and DsRed (18.7% ± 2.86% of EmGFP+ cells and 10.8% ± 0.533% of DsRed+ cells). To ensure that this overlap did not affect our analysis, we excluded EmGFP+/DsRed+ double-positive cells and focused solely on EmGFP+/DsRed− (control) and EmGFP−/DsRed+ (Ghsr1a-KD) single-positive cells. 

      We agree with the reviewer that coinjection could lead to reciprocal interactions between control and Ghsr1a-KD cells, potentially masking cell-autonomous effects. To address this, we performed an independent experiment in which control and Ghsr1a-KD lentiviruses were injected separately into different mice (Figure S7A), as suggested. Consistent with the results of the coinjection experiment, we found that the Ghsr1a-KD cells showed significantly reduced distribution in the GL compared with that in control cells (Figure S7B). Although we cannot exclude the possibility of a non-cell-autonomous effect of ghrelin, this result supports the conclusion that ghrelin signaling enhances neuronal migration in a cell-autonomous manner. 

      Who is expressing Ghsr1a, newborn neurons, and or their progenitors? The production and survival of newborn V-ZVS cells should be assessed upon knockdown of the ghrelin receptor too. 

      To determine whether the altered distribution of new neurons observed upon Ghsr1aKD is due to impaired migration rather than decreased cell production or survival, we examined the effects of Ghsr1a-KD on the proliferation and survival of new neurons and their progenitors, which express GHSR1a (Li et al., 2014). 

      We compared the proportion of cleaved caspase-3+ cells and Ki67+ cells from the total labeled cells in the V-SVZ and RMS between the control and Ghsr1a-KD groups. There was no significant difference in the proportion of cleaved caspase-3+ cells between the groups (Control: 874 cells from 5 mice; Ghsr1a-KD: 678 cells from 7 mice), suggesting that ghrelin signaling does not affect the survival of new neurons and their progenitors. 

      Similarly, the proportion of Ki67+ cells in the RMS did not differ significantly between the two groups (Figure S8), indicating that Ghsr1a-KD does not impair cell proliferation in the RMS. However, it remains technically difficult to evaluate whether Ghsr1a-KD affects proliferation in the VSVZ, because lentivirus injection into the VSVZ may interfere with GHSR1a expression not only in new neurons and neural progenitors, but also in other cell types known to express GHSR1a (Zigman et al., 2006). A previous study reported that ghrelin signaling promoted cell proliferation in the V-SVZ (Li et al., 2014), thus we cannot exclude the possibility that Ghsr1a-KD may affect V-SVZ proliferation.

      To overcome this limitation, we assessed the effects of Ghsr1a-KD on neuronal migration using in vitro KD experiments (Figure 4C–J) and in vivo OB-core lentivirus injections (Figure 5A–C), both of which did not interfere with proliferation in the V-SVZ. These complementary approaches consistently demonstrated that Ghsr1a-KD reduces the migration speed of new neurons. 

      “To determine whether the altered distribution of new neurons after Ghsr1a-KD is due to impaired migration rather than changes in cell production or survival, we assessed the effects of Ghsr1aKD on the proliferation and survival of new neurons and their progenitors, which express GHSR1a (Li et al., 2014). We quantified the proportion of cleaved caspase-3+ cells and Ki67+ cells from the total labeled cells in the V-SVZ and RMS in both control and Ghsr1a-KD groups. We found no significant difference in cleaved caspase-3+ cell proportions between the groups (Control: 874 cells from 5 mice; Ghsr1a-KD: 678 cells from 7 mice), suggesting that ghrelin signaling does not influence the survival of new neurons and their progenitors. Similarly, the percentage of Ki67+ cells in the RMS was similar between the two groups (Figure S8), indicating that Ghsr1a-KD does not impair cell proliferation in the RMS. However, technical limitations prevented a reliable evaluation of proliferation in the V-SVZ, as lentivirus injection into this region may interfere with GHSR1a expression in not only neural progenitors and new neurons, but also other GHSR1aexpressing cell types (Zigman et al., 2006). Although ghrelin signaling has been reported to promote cell proliferation in the V-SVZ (Li et al., 2014), our complementary in vitro KD experiments (Figure 4C–J) and in vivo OB-core lentivirus injections (Figure 5A–C), which did not affect the V-SVZ, consistently demonstrated that Ghsr1a-KD reduces neuronal migration. Taken together, our results suggest that blood-derived ghrelin enhances neuronal migration in the RMS and OB by stimulating actin cytoskeleton contraction in the cell soma, rather than by altering cell proliferation or survival.” (Results, Page 10, line 19–Page 11, line 4)

      “rat anti-Ki67 (1:500, #14-5698-82, eBioscience); and rabbit anti-cleaved caspase-3 (1:200, #9661, Cell Signaling Technology)” (Methods, Page 48, lines 14–16)

      How much is ghrelin/Ghsr1 signaling conserved in marmosets? 

      How ghrelin signaling is conserved between mice and common marmosets is important to clarify. A previous study reported the existence of a ghrelin homolog in common marmoset, which shares high sequence similarity with that in mice (Takemi et al., 2016). Moreover, the GHSR1a homolog in the common marmoset (https://www.ncbi.nlm.nih.gov/protein/380748978) shares 95.36% amino acid identity with its mouse counterpart. These findings suggest that blood-derived ghrelin may similarly promote neuronal migration in the marmoset brain, as observed in mice. 

      We have added the following text in the Discussion section:

      “Our data showed that new neurons preferentially migrate along arteriole-side vessels rather than venule-side vessels in both mouse and common marmoset brains, suggesting that the mechanism of blood flow-dependent neuronal migration is conserved across rodent and primate species, as well as across brain regions. A previous study identified a ghrelin homolog in the common marmoset with high sequence similarity to the murine version (Takemi et al., 2016). In addition, the marmoset GHSR1a homolog shares 95.36% amino acid identity with that of the mouse (https://www.ncbi.nlm.nih.gov/protein/380748978). These findings suggest that bloodderived ghrelin promotes neuronal migration in the common marmoset brain in a manner similar to that in mice.” (Discussion, Page 15, lines 8–16)

      Page 9. Starvation has been shown to boost ghrelin blood levels. What is the exact protocol used in this experiment and is this indeed increasing Ghrelin release from blood vessels in the V-SVZ? What about Ghsr1 expression level in newborn neurons? 

      We have clarified the calorie restriction (CR) protocol used in our experiments. We adopted a 70% CR protocol, which was previously shown to enhance hippocampal neurogenesis when administered for 14 days (Hornsby et al., 2016). In our study, the daily food intake under ad libitum (AL) conditions was first measured, and CR mice were then fed 70% of that amount for 5 consecutive days (see Figure 5I and Figure S10A). 

      To assess whether CR enhances ghrelin transcytosis into the brain parenchyma, we performed ELISA to quantify ghrelin levels in the OB and RMS. However, ghrelin concentrations were below the detection limit in both groups, precluding a direct comparison.

      We also considered whether CR modulates the expression level of the ghrelin receptor GHSR1a. A recent study reported that fasting increased GHSR1a expression in the OB (Stark et al., 2024), raising the possibility that CR may exert a similar effect. To test this, we performed in situ hybridization and quantified Ghsr1a mRNA puncta in Dcx+ cells in the OB. No significant difference was found between the AL and CR groups (Figure S5B), suggesting that CR does not alter GHSR1a expression levels in new neurons. 

      Although we cannot exclude the possibility that CR increases GHSR1a expression in other OB cell types, our combined CR and Ghsr1a-KD experiments strongly support a cellautonomous contribution of ghrelin signaling to the enhanced neuronal migration observed under CR conditions. Corresponding data and text have been added to Figure S5 and the Results, Discussion, and the Figure legend sections as follows:

      Minor 

      Page 4 

      Line 19 In Supplemental movies 1 and 2, it is unclear where to see the GFP+ new neurons interact with BV. Can you add arrows as an indication for the readers? It will be better to add the anatomy term for orientation, caudal, or rostral in the video. (The same for Supplemental movies 3, 4, and 5).  

      To clarify the regions of interest in Supplemental Movies 1 and 2, where neuron–vessel interactions in the RMS are highlighted, we added dotted lines indicating the RMS boundaries. In addition, we created a new movie (Supplemental Movie S1′) showing a high-magnification view of Supplemental Movie S1, in which arrows mark EGFP+ new neurons interacting with blood vessels. We also added orientation indicators (e.g., caudal and rostral) and arrows to highlight new neuron–vessel interactions in Supplemental Movies S1–S5. 

      The following descriptions have been added to the Figure legends:

      “Supplemental Movie S1′ 

      High-magnification view extracted from Supplemental Movie S1. Arrows indicate EGFP+ cells interacting with blood vessels.” (Figure legend, Page 46, lines 6–8)

      “Arrows indicate EGFP+ cells interacting with blood vessels.” (Figure legend, Supplemental Movie S3, Page 46, lines 16–17)

      “Arrows indicate Dcx+ cells interacting with blood vessels.” (Figure legend, Supplemental Movies S4 and S5, Page 46, lines 21–22, 26–27)

      Blood vessels are labeled in the Supplemental movies 2 and 3 by employing Flt1DsRed transgenic mice instead of RITC-Dex-GMA. However, Flt1-DsRed transgenic mice are not mentioned in the results section. 

      We have now included an explanation regarding the use of Flt1-DsRed mice, in which vascular endothelial cells were labeled with DsRed.

      “To visualize blood vessels, we also used Flt1-DsRed transgenic mice, in which vascular endothelial cells were specifically labeled with DsRed (Matsumoto et al., 2012). Using DcxEGFP/Flt1-DsRed double transgenic mice, we observed close spatial relationships between new neurons and blood vessels (Supplemental Movies S2 and S3).” (Results, Page 4, lines 22– 26)

      Figure 5. Can you indicate (in the figure legend and the result section) the stage of the adult brain used for this experiment? 

      We used 6- to 12-week-old adult male mice in all experiments in this study. To specify this, we have added the age of animals to both the Results and the relevant Figure legends as follows:

      “Therefore, we first studied blood vessel-guided neuronal migration in the RMS and OB using three-dimensional imaging in 6- to 12-week-old adult mice, which enabled analysis of the in vivo spatial relationship between new neurons and blood vessels.” (Results, Page 4, lines 14–16)

      “Figure 1 New neurons migrate along blood vessels with abundant flow in the adult brain.” (Figure legend, Page 25, line 4)

      “(B, C) Three-dimensional reconstructed images of a new neuron (green) and blood vessels (red) in the rostral migratory stream (RMS) (B) and glomerular layer (GL) (C) of 6- to 12-weekold adult mice.” (Figure legend, Page 25, lines 6–8)

      “(E) Transmission electron microscopy image of a new neuron (green) in close contact with a blood vessel (red) in the GL of a 6- to 12-week-old adult mouse.” (Figure legend, Page 26, lines 4–5)

      “(F) Time-lapse images of a migrating neuron (indicated by asterisks) in the GL of a 6- to 12week-old Dcx-EGFP mouse.” (Figure legend, Page 26, lines 6–7)

      “Figure 3 Ghrelin is delivered from the bloodstream to the RMS and OB in the adult brain (A) Representative images of the OB and cortex of a fluorescent ghrelin-infused mouse (6 to 12 weeks old).” (Figure legend, Page 30, lines 1–3)

      “Lentivirus injection into the OB core (A) and the VSVZ (D) was performed in 6- to 12-week-old adult mice.” (Figure legend, Page 33, lines 3–4)

      Reviewer #2 (Recommendations for author):

      Major:

      Ghsr1KD and blood flow 2-photon experiments to directly measure migratory speed. Could also do the same with fasting with or without Ghsr1KD.  

      We thank the reviewer for the valuable suggestion to strengthen our study. As pointed out in the Public Review, we agree that direct in vivo measurement of neuronal migration speed under Ghsr1a-KD conditions is important to clarify the link between ghrelin signaling and blood flow. 

      Two-photon imaging is the most suitable method for this purpose. Although we attempted two-photon imaging of Ghsr1a-KD new neurons, the number of virus-infected cells observed in vivo was too low to yield reliable data. Therefore, we chose an alternative strategy, combining Ghsr1a-KD with blood flow reduction using the BCAS model (Figure S9A), in which migration speed can be quantified based on the percentage of labeled cells reaching the OB. As stated in the Public Review response, BCAS significantly decreased the migration speed of Ghsr1a-KD new neurons (Figure S9B), indicating that Ghsr1a-KD does not abolish the influence of blood flow reduction. These findings suggest that ghrelin signaling is involved, but is not essential, for blood flow-dependent neuronal migration. 

      As suggested by the reviewer, direct observation of migration dynamics (e.g., somal translocation, leading process extension, stationary and migratory phases) is needed, especially in calorie restriction experiments. Although our data indicate that ghrelin signaling is required for fasting-induced increases in migration speed of new neurons, calorie restriction could also change concentrations of other factors in blood (Bonnet et al., 2020; Wu et al., 2024; Alogaiel et al., 2025), which may independently affect behavior of migrating neurons. Given that ghrelin is not the sole factor contributing to blood flow-dependent neuronal migration, other circulating factors could affect behavior of migrating neurons in a different manner during fasting. In vivo twophoton imaging would be a powerful approach to determine whether fasting-induced neuronal migration is caused by upregulated somal translocation speed, which would further support a role for ghrelin in this process.

      We have added the following text in the Discussion:

      “Although our data indicate that ghrelin signaling is essential for fasting-induced acceleration of neuronal migration, calorie restriction may also alter the concentrations of other circulating factors (Bonnet et al., 2020; Wu et al., 2024; Alogaiel et al., 2025), which could independently influence the behavior of migrating neurons.” (Discussion, Page 14, lines 25–29)

      Minor: 

      (1) Show fluorescent Ghreliin in Figure 3 for all brain areas measured in Figure 1 (GL, EPL, GCL, and RMS) for direct comparison.  

      To allow for direct comparison across brain regions, we added a new Supplemental figure showing the distribution of fluorescently labeled ghrelin in the OB, including the GL, EPL, GCL and RMS. This comprehensive view highlights ghrelin localization relative to vasculature and migrating neurons in the regions analyzed in Figure 1.

      (1) Figure 1, panel I is presented in a confusing manner. High blood flow points to 0 degrees, low blood flow to 180 degrees. It implies (unintentionally, I am sure) that low blood flow results in migration away from OB. Maybe plot separately?

      We agree that the original presentation of Figure 1I could be misinterpreted as referring to anatomical orientation (i.e., toward or away from the OB). To avoid confusion, we revised the figure to categorize new neuron–vessel interactions into four groups according to (1) the angle between the migration direction and vessel axis (small or large), and (2) whether the new neuron is migrating toward or away from the direction of higher blood flow. This new presentation avoids implying a fixed anatomical direction and better reflects the relationship between local blood flow and neuronal migration behavior. The revised figure is presented as Supplemental Figure S1.

    1. Reviewer #1 (Public review):

      Summary:

      LRRK2 protein is familially linked to Parkinson's disease by the presence of several gene variants that all confer a gain-of-function effect on LRRK2 kinase activity.

      The authors examine the effects of BDNF stimulation in immortalized neuron-like cells, cultured mouse primary neurons, hIPSC-derived neurons, and brain tissue from genetically modified mice. They examine a LRRK2 regulatory phosphorylation residue, LRRK2 binding relationships, and measures of synaptic structure and function.

      Strengths:

      The study addresses an important research question: how does a PD-linked protein interact with other proteins, and contribute to responses to a well-characterized neuronal signalling pathway involved in the regulation of synaptic function and cell health.

      They employ a range of good models and techniques to fairly convincingly demonstrate that BDNF stimulation alters LRRK2 phosphorylation and binding to many proteins. IN this revised manuscript, aspects are well validated e.g., drebrin binding, but there is a disconnect between these findings and alterations to LRRK2 substrates. A convincing phosphoproteomic analysis of PD mutant Knock-in mouse brain is included. Overall the links between LRRK2, LRRK2 activity, and the changes to synaptic molecules, structures, and activity are intriguing.

      Weaknesses:

      The data sets remain disjointed, conclusions are sweeping, and not always in line with what the data is showing. Validation of 'omics' data is light. Some inconsistencies with the major conclusions are ignored. Several of the assays employed (western blotting especially) are underpowered, findings key to their interpretation are addressed in only one or other of the several models employed, and supporting observations are lacking.

      Main Conclusions of Abstract:

      (1) Increase in pLRRK2 Ser935 and pRAB after BDNF in SH-SY5Y & mouse neurons

      Well supported, but only for pLRRK2 in neurons, why not pERK pAkt & pRab?

      (2) Omics Proteome remodelling of LRRK2 interactome with BDNF & different in G2019S mouse neurons.

      Supports that the phosphoproteome of G2019S is different. Drebrin interaction with LRRK2 very well supported. Link between drebrin and LRRK2 activity somewhat supported (pS935 site), but the consequence (non-specific pRab8) not supported, as there is no evidence of a change in LRRK2 substrate(s).

      (3) Golgi 1 month LKO mouse altered dendritic spines, transient at 1m not older.

      Supported but very small transient change in spines, disconnected to other results (e.g., drebrin).

      (4) iPSC-derived neurons BDNF increases mEPSC frequency (transient at 70 not 50 or 90 days) in WT not KO "which appear to bypass this regulation through developmental compensation"

      Weak, not clear what is being bypassed.

      Main Conclusions Based on Old and New Figure / Data:

      (1) Increase in pLRRK2 Ser935 and pRAB after BDNF in SH-SY5Y & mouse neurons

      Well supported, but only for pLRRK2 in neurons, why not ERK Akt & Rab?

      (2) BDNF promotes LRRK2 interaction with "post-synaptic actin cytoskeleton components"

      Tone down, only one postsynaptic validated - drebrin strong BUT CONTRADICTORY; link between drebrin and LRRK2 activity (pS935 site) supported, consequence (non-specific pRab8) broken, no evidence of change in LRRK2 substrate.

      (3) LRRK2 G2019S striatal phosphoproteome is different from WT.

      It is different. Where is link to BDNF or Drebrin?

      (4) BDNF signaling is impaired in Lrrk2 knockout neurons

      TrkB changes seem higher in SHSY5Y. pAKT impaired, pERK not convincing. Primary neurons Akt slower but it and Erk mostly intact. MLi-2 did not block pAkt or pErk in WT or KO (higher in latter). Whatever is happening in KO, Mli-2 not really blocking effect in WT. If we are to assume that studying the KO was a means to understand LRRK2 function, the authors data should explain why we care if an effect is absent in LKO, if LRRK2 isn't doing the same job in WT?

      BDNF increases synaptic puncta in WT not LKO (which start higher?). Is this BDNF increase blocked by LRRK2 inhibition?

      (5) Postsynaptic structural changes in Lrrk2 knockout neurons

      Golgi impregnation shows some very small spine changes at 1m. Not sustained over age. mRNA changes are very small (10% not even a fold... very weak and should be written as so). Derbrin levels reduced clearly at 1m, but probably also at 4 & 18. Underpowered, disconnected time course from the spine changes.

      (6) An effect on "spontaneous electrical activity" at Div70

      Weak. What is so special at 70 days that means we should be confident in the differences, or be satisfied that the other time points are legitimately ignored? These are 10-11 cells from 3 cultures assayed at 3 time points but only one is presented (rest in supplement). This should be a 2 (time) or 3 way (+culture RM) ANOVA. As it stands, in WT there is a little - no activity at 50 days, little to no at 70 days, and variable to lots or none at 90. BDNF did nothing at 50 or 90 but may have at 70. In KO low activity stable at 50 & 70, tanks at 90. BDNF would seem to have a similar effect on KO at 90 as WT at 70, but as there are only 7 cells it remains inconclusive. Thus the conclusion that BDNF signalling is broken in LKO is not well supported by the ephys data, nor is the BDNF effect in WT cells (even at the 70 day time point) shown to be susceptible to LRRK2 inhibition.

    1. Reviewer #1 (Public review):

      The manuscript by Zhang et al describes the use of a protein language model (pLM) to analyse disordered regions in proteins, with a focus on those that may be important in biological phase separation. While the paper is relatively easy to read overall, my main comment is that the authors could perhaps make it clearer which observations are new, and which support previous work using related approaches. Further, while the link to phase separation is interesting, it is not completely clear which data supports the statements made, and this could also be made clearer.

      Major comments:

      (1) With respect to putting the work in a better context of what has previously been done before, this is not to say that there is not new information in it, but what the authors do is somewhat closely related to work by others. I think it would be useful to make those links more directly. Some examples:

      (1a) Alderson et al (reference 71) analysed in detail the conservation of IDRs (via pLDDT, which is itself related to conservation) to show, for example, that conserved residues fold upon binding. This analysis is very similar to the analysis used in the current study (using ESM2 as a different measure of conservation). Thus, the approach (pages 7-8) described as "This distinction allows us to classify disordered regions into two types: "flexible disordered" regions, which show high ESM2 scores and greater mutational tolerance, and "conserved disordered" regions, which display low ESM2 scores, indicating varying levels of mutational constraint despite a lack of stable folding." is fundamentally very similar to that used by Alderson et al. Thus, the result that "Given that low ESM2 scores generally reflect mutational constraint in folded proteins, the presence of region a among disordered residues suggests that certain disordered amino acids are evolutionarily conserved and likely functionally significant" is in some ways very similar to the results of that paper.

      (1b) Dasmeh et al (https://doi.org/10.1093/genetics/iyab184), Lu et al (https://doi.org/10.1371/journal.pcbi.1010238) and Ho & Huang (https://doi.org/10.1002/pro.4317) analysed conservation in IDRs, including aromatic residues and their role in phase separation

      (1c) A number of groups have performed proteomewide saturation scans using pLMs, including variants of the ESM family, including Meier (reference 89, but cited about something else) and Cagiada et al (https://doi.org/10.1101/2024.05.21.595203) that analysed variant effects in IDRs using a pLM. Thus, I think statements such as "their applicability to studying the fitness and evolutionary pressures on IDRs has yet to be established" should possibly be qualified.

      (2) On page 4, the authors write, "The conserved residues are primarily located in regions associated with phase separation." These results are presented as a central part of the work, but it is not completely clear what the evidence is.

      (3) It would be useful with an assessment of what controls the authors used to assess whether there are folded domains within their set of IDRs.

    1. Reviewer #3 (Public Review):

      Summary:

      In this article, Barnett examines a pressing question regarding citing behavior of authors during the peer review process. In particular, the author studies the interaction between reviewers and authors, focusing on the odds of acceptance, and how this may be affected by whether or not the authors cited the reviewers' prior work, whether the reviewer requested such citations be added, and whether the authors complied/how that affected the reviewer decision-making.

      Strengths:

      The author uses a clever analytical design, examining four journals that use the same open peer review system, in which the identities of the authors and reviewers are both available and linkable to structured data. Categorical information about the approval is also available as structured data. This design allows a large scale investigation of this question.

      Weaknesses:

      My concerns pertain to the interpretability of the data as presented and the overly terse writing style.

      Regarding interpretability, it is often unclear what subset of the data are being used both in the prose and figures. For example, the descriptive statistics show many more Version 1 articles than Version 2+. How are the data subset among the different possible methods?

      Likewise, the methods indicate that a matching procedure was used comparing two reviewers for the same manuscript in order to control for potential confounds. However, the number of reviews is less than double the number of Version 1 articles, making it unclear which data were used in the final analysis. The methods also state that data were stratified by version. This raises a question about which articles/reviews were included in each of the analyses. I suggest spending more space describing how the data are subset and stratified. This should include any conditional subsetting as in the analysis on the 441 reviews where the reviewer was not cited in Version 1 but requested a citation for Version 2. Each of the figures and tables, as well as statistics provided in the text should provide this information, which would make this paper much more accessible to the reader. [Note from editor: Please see "Editorial feedback" for more on this]

      Finally, I would caution against imputing motivations to the reviewers, despite the important findings provided here. This is because the data as presented suggest a more nuanced interpretation is warranted. First, the author observes similar patterns of accept/reject decisions whether the suggested citation is a citation to the reviewer or not (Figs 3 and 4). Second, much of the observed reviewer behavior disappears or has much lower effect sizes depending on whether "Accept with Reservations" is considered an Accept or a Reject. This is acknowledged in the results text, but largely left out of the discussion. The conditional analysis on the 441 reviews mentioned above does support a more cautious version of the conclusion drawn here, especially when considered alongside the specific comments left by reviewers that were mentioned in the results and information in Table S.3. However, I recommend toning the language down to match the strength of the data.

    1. April is the cruellest month, breeding Lilacs out of the dead land, mixing Memory and desire, stirring Dull roots with spring rain.

      “April Showers bring May flowers” is a popular saying, encouraging us to push through the cruelest month (ie. April), to enjoy the flowers of May. It gives us hope that the rain will end and that blooms will grow, a reason to hate April just a little less. TWL begins, “April is the cruellest month, breeding/ Lilacs out of the dead land, mixing/ Memory and desire, stirring/ Dull roots with spring rain” (TWL, 1–4), an opening that does not reflect, but refracts the opening to Chaucer’s Canterbury Tales: “When April with its sweet-smelling showers/ Has pierced the drought of March to the root,/ And bathed every vein (of the plants) in such liquid/ By which power the flower is created.” Hollow reminiscences of Chaucer’s structure and content appear in TWL, but where did the hope go? Or rather, where was it in the Canterbury Tales? And where is it not in The Waste Land? In Chaucer, water carries the cleansing power of spring; April’s showers wash away the dryness of March and stir new life, a natural image that resonates with baptism and spiritual renewal, setting pilgrims on the road to Canterbury. In Eliot, however, water loses this redemptive quality. Rain does not cleanse but unsettles, dragging up memory and desire rather than washing them away– creating sin, not absolving them. The “spring rain” becomes a burden, a reminder of the impossibility of purification in a modern world which in Eliot's time was plagued by war and spiritual desolation. Where Chaucer’s showers signify the promise of divine grace and renewal, Eliot’s water is cruel as it exposes an inability of renewal and regrowth. Has the human race gone too far to go back and live in hope?

    2. The Burial of the Dead

      The Greek Orthodox “Burial of the Dead” asks, in the service of the death of an Orthodox member of the laity, “What delight of life continueth unmixed with sorrow?” (pg. 19). In titling the first part of “The Waste Land” the same, Eliot ties his work to demise: whether that be of the land (turning into a Waste Land), the demise of one’s life, or more largely, to the demise of fighting soldiers and innocents in The Great War (also referencing The “Burial of the Dead” on Armistice Day). In Tone 4 of the Greek Orthodox death service, as the Priest lays the dead Christian to rest, he asks “Where is the yearning for the world? Where is the pomp of things temporal? Where the gold and the silver? Where the tumult and rush of servers? All is dust, all is ashes, a shadow” (pg. 21). In death, as suggested by the “modern Christian book of funeral rites” , humans lose the “yearning for the world,” ending finally the cycles between day and night, and the disorderly “tumult” of everyday life. We lose the quintessential chaos and the anguish of pain and heartbreak. At the end of one’s life, they lose “the gold and the silver,” leaving the world with only “a shadow” of their impact on the lives that surrounded them. Eliot’s lines: “Your shadow at morning striding behind you/Or your shadow at evening rising to meet you,” ties the soul and the body to the “shadow” that is left behind (ln, 28-9). The “shadow behind you” acts as a nod to “your” soul and eventual death lagging behind you, in the early days/”morning” of your life. Further, with the shadow behind you, “striding,” the sun’s position is straight ahead, suggesting movement towards enlightenment. Conversely, “the shadow at evening rising to meet you” is the acceptance and joining of soul and body in death, whether or not you are ready. This idea of regret is further explored in the line “I will show you fear in a handful of dust” (ln 30). The “dust” represents all that is left, a world or an existence after (or in the absence of) life. The fear exists two-fold: a singular fear of a life left behind or forgotten, or a larger fear of a world in the wake of destruction (like the war), where all signs of life and civilization turn to dust.

    3. ‘Nam Sibyllam quidem Cumis ego ipse oculis meis vidi in ampulla pendere, et cum illi pueri dicerent: Σίβυλλα τί θέλεις; respondebat illa: ἀποθανεῖν θέλω.’

      Beyond the differences between the working and final title of “The Wasteland,” I found the change the epigraph used noteworthy. In most circumstances, an epigraph suggests the general theme or tone of a certain piece– second to the title, it is the first impression a reader has when encountering a work of writing. This implies that the change in the epigraph likely reflected a significant shift in Eliot’s perception of his poem and the message he hoped it to convey.

      The working epigraph draws from Heart of Darkness, an 1899 novella by Joseph Conrad. In the moment of this excerpt, the narrator, Charles Marlow, stumbled upon Kurtz, a successful former station chief, on the brink of death. Just as Marlow encounters Kurtz “lying on his back with closed eyes,” Marlow hears him mumble: “‘Live rightly, die, die’” (3). In his nearly unconscious state, Kurtz reveals a newfound clarity in the purpose of one’s life: to live virtuously (likely following Christian values), so that he may die peacefully and move weightlessly into the next realm of existence. However, just before Kurtz passes, and just before he exclaims “‘The horror! the horror!”, Marlow notes a significant turn of expression on the dying man’s face: an “expression of sombre pride, of ruthless power, of craven terror– of an intense and hopeless despair” (4). This moment illustrates a the process of realization undergone by Kurtz in his final moments: first, his satisfaction in his life’s achievements; then, a surge of power and authority in remembering his esteemed working position; and terror in realizing that his life and choices have not been so righteous as he formerly believed them to be. This leads to his final statement: “‘the horror, the horror!’” (4). While the new version of the epigraph suggests a kind of longing for death after enduring the consequences of a youthless immortality, the old epigraph expresses a different kind of anguish: the despair and horror when one comes to the realization of living a wasted, and in some ways dishonest, life.

    4. THE WASTE LAND

      The Waste Land suggests a desolate place, a barren landscape devoid of life. The waste land that appears in Le Morte D’Arthur fits this description, when “sithen increased neither corn, nor grass, nor well-nigh no fruit, nor in the water was no fish.” (4) This land is lacking, defined by “nor,” known for what it does not have. While the war-torn context of the poem lends itself to an understanding of a waste land solely defined by depravity, a careful inspection of the texts that inspired this title reveals a different, and more hopeful, interpretation.

      In her work From Ritual to Romance, Jessie L. Weston identifies a cycle maintained across the variations of the myth of the Holy Grail. In this cycle, a land goes from paradise to waste land and back to paradise again, with the health of the land tied directly to the health of its King. Though the waste land is barren and bleak, the stories of the Holy Grail carry with them a level of hope, a promise that on the other side of the waste land is a restoration to what was. In this sense, a waste land must not simply be defined by its fall from previous glory, and instead must take into account a promise of a better future. The story of the Bible and the vegetation ceremonies studied in The Golden Bough mirror this understanding of a waste land, sharing a similar progression from paradise to barren waste land, followed by a resurrection.

      The story of the fall, referenced explicitly in Le Morte D’Arthur (“When sinful Eve came to gather fruit, for which Adam and she were put out of paradise,” (6), is potentially the most well-known example of a transition from paradise to waste land. The biblical waste land, though full of human sin and suffering, is also full of hope, hope for the coming of the messiah and a return to the paradise of Eden. Similarly, ancient vegetation ceremonies occur in a waste land, the barren time between the fertility of the spring and fall, reflecting the “yearly decay and revival of life.” (Frazer, 7) The death and resurrection in both these stories (albeit one is of the gods and one is of mankind), is similar to that found in the quest for the Holy Grail, and is essential to understanding the title The Waste Land.

      The title of Eliot’s poem places the poem in a sort of limbo, having fallen from a paradise that was before yet not having reached a paradise that is to come. This imparts upon the poem a tension between the loss of what came before and the hope for a future restoration. Like the Israelites in the Old Testament and the ancient civilizations in winter, the waste land is waiting for a better future, for a resurrection and restoration that is still to come.

    5. THE WASTE LAND

      In each of the iterations of the quest for the Holy Grail, the vigor and fertility of the King is intrinsically tied to the health of the natural world. In a belief system that has appeared in countless cultures and traditions worldwide, the theme of human and natural codependence manifests itself into the image of a “Wasteland” and the Grail legend– a string of narratives surrounding the quest for a Christian relic (often described as the chalice used by Jesus at the Last Supper and by Saint Joseph of Arimathea to gather Jesus’s blood at his crucifixion) thought to bestow youth, healing, and/or divine grace upon those chosen to drink from it. In Malory’s Le Morte D’Arthur, the story ensues with the description of two warring kings, wherein the King Labor—father to the Maimed King—was struck by King Hurlame using a sword of great power and sanctity. In doing so, “the waste land” is created, reaping harm and disease for both sides; at the stroke of the sword and the fall of King Labor, the land is left without vegetation and fish. It is only when the Maimed King (King Pelles/the Fisher King) is asked a certain question that he is brought back to health and the land is restored.

      The tale of the Holy Grail is woven in accordance with a formula familiar to many Biblical stories. At the first stage, humanity condemns itself to ruin, often in the execution of some extraordinary sin or betrayal: in the Le Morte D’Arthur, it is when “King Hurlame saw King Labor… and smote him upon the helm so hard that he clave him and his horse to the earth with the first stroke of his sword” (4); in the New Testament of the Bible, the comparable event is the Judas’s betrayal of Jesus Christ and his crucifixion. The following stage further elaborates on the current condition of the world: the struggle and despair of humanity, and the ruin of the Earth (“for sithen increased neither corn, nor grass, nor well-nigh no fruit, nor in the water was no fish; wherefore men call it the lands of the two marches, the waste land”) (4). The third and final stage comes in the redemption of the humanity, or in the Holy Grail, and fulfillment of the quest, for when the quest is completed, its paladins have thus completed their life’s purpose and willingly ascend into Heaven: Galahad dies not long after his completion of his god-appointed task, with Sir Percivale following a year and two months after (19, 21). However, Eliot’s The Wasteland reaches no such conclusion, however, the absence of a conclusion does not renounce any opportunity for a better future. Rather, humanity must, and will, take upon itself the task of its redemption, and the world shall be restored once more.

    1. Advanced Context Engineering for Agents - Summary

      Overview

      • Source: https://www.youtube.com/watch?v=IS_y40zY-hc
      • Type: Technical Conference Talk
      • Length: ~14 minutes (YC Root Access)
      • Speaker: Dexter Horthy, Founder of Human Layer (YC Fall 24)
      • Key Focus: Advanced context engineering techniques for scaling coding agents in production environments

      Executive Summary

      Dexter Horthy presents a systematic approach to context engineering that transforms AI coding from prototyping to production-ready development. He demonstrates how spec-first development, intentional context management, and structured workflows enable teams to ship complex code in large repositories while maintaining quality and team alignment.

      Key Insights

      • Context as Core Constraint: "LLMs are pure functions. The only thing that improves the quality of your outputs is the quality of what you put in, which is your context window." - Context management is the fundamental lever for agent performance
      • Spec-First Development: "In the future where AI is writing more and more of our code, the specs, the description of what we want from our software is the important thing." - Specifications become the source code equivalent in AI-driven development
      • Hierarchy of Impact: "A bad line of research, a misunderstanding of how the system works and how data flows and where things happen can be thousands of bad lines of code." - Early-stage errors compound exponentially through the development process

      Key Elements (CRITICAL FOR LOOKUP)

      Key Concepts

      • Context Engineering: "Everything that makes agents good is context engineering" - [Core philosophy throughout talk]
      • Intentional Compaction: "Be very intentional with what you commit to the file system and the agents memory" - [08:48 timestamp]
      • Spec-First Development: "We were forced to adopt spec first development because it was the only way for everyone to stay on the same page" - [03:12 timestamp]
      • 40% Context Rule: "Our goal all the time is to keep context utilization under 40%" - [11:00 timestamp]
      • Research-Plan-Implement Workflow: "We have three phases research, plan and implement" - [11:00 timestamp]

      Key Personalities

      • Dexter Horthy: "My name is Dex. I'm the founder of a company called Human Layer" - [Speaker, YC Fall 24]
      • Sean Grove: "Sean Grove, the new code. He talked about how we're all vibe coding wrong" - [Referenced expert on coding practices]
      • Jeff Huntley: "Jeff Huntley works on source AMP... he wrote this thing called Ralph Wigum as a software engineer" - [Context optimization expert]
      • Vibbov: "I do a podcast with another YC founder named Vibbov. He built Bam" - [Collaboration partner, BAML creator]

      Key Tools/Technologies

      • Human Layer: "I'm the founder of a company called Human Layer" - [Dexter's company focused on context engineering]
      • BAML: "He built Bam... has anyone here you used BAML before?" - [Programming language/tool for AI workflows]
      • Sub Agents: "A lot of people saw cloud code sub aents and they jumped in... but they're really about context control" - [Context management technique]
      • MCP Tools: "If you have MCP tools that return big blobs of JSON, that's going to flood your context window" - [Tool integration consideration]

      Key References

      • 12 Factor Agents: "We wrote a weird little manifesto called 12actor agents um principles of reliable LLM applications" - [April 22nd foundational work]
      • Stanford Study: "The Stanford study... they ingested data from 100,000 developers... AI engineering and software leads to a lot of rework" - [Research on AI coding effectiveness]
      • Ralph Wigum Article: "He wrote this thing called Ralph Wigum as a software engineer" - [Context optimization methodology]
      • Open Source Prompts: "This is our research prompt. It's really long. It's open source. You can go find it" - [Available implementation resources]

      Detailed Analysis

      The Problem with Current AI Coding

      • Naive Approach Fails: "The most naive way to use a coding agent, which is to shout back and forth with it until you run out of context or you give up or you cry" - [04:48]
      • Complex Systems Challenge: "Doesn't work in big repos, doesn't work for complex systems" - [02:44]
      • Rework Problem: "AI engineering and software leads to a lot of rework. So even if you get benefits, you're actually throwing half of it away" - [01:45]

      Context Engineering Solutions

      • Intentional Compaction Strategy: "Even if we're on the right track, if we're starting to run out of context, be very intentional with what you commit to the file system and the agents memory" - [05:45]
      • Sub-Agent Context Control: "The parent agent can get right to work without having to have the context burden of all of that reading and searching" - [07:27]
      • Frequent Compaction Workflow: "Building your entire development workflow around context management" - [08:48]

      Three-Phase Implementation

      • Research Phase: "Understand how the system works and all the files that matter and perhaps like where a problem is located" - [11:00]
      • Planning Phase: "Tell me every single change you're going to make. not line by line, but like include the files and the snippets" - [11:12]
      • Implementation Phase: "If the plan is good, I'm never shouting at cloud cloud anymore. And if I'm shouting at cloud, it's because the plan was bad" - [11:59]

      Actionable Takeaways

      1. Implement Spec-First Development: Start with detailed specifications before any code generation
      2. Maintain 40% Context Utilization: Keep context windows under 40% capacity for optimal performance
      3. Use Three-Phase Workflow: Structure all development as Research → Plan → Implement
      4. Review Plans, Not Code: Focus human review on specifications and plans rather than generated code
      5. Implement Intentional Compaction: Regularly compress context with structured progress files

      Technical Details

      • Tools/Technologies: Human Layer, BAML, Sub-agents, MCP tools, Context compaction systems
      • Requirements: ~170,000 token context windows, structured prompt engineering, team workflow transformation
      • Implementation Notes: Open-source prompts available, requires significant team process changes

      Case Study Results

      • BAML Rust Codebase: "We decided to see if we could oneshot a fix to a 300,000 line RS codebase... The PR was so good the CTO did not know I was doing it as a bit and he had merged it" - [11:12]
      • Boundary CEO Session: "For 7 hours we sat down and we shipped 35,000 lines of code... he estimated that was 1 to two weeks of work roughly" - [12:44]
      • Team Productivity: "Our intern Sam... shipped two PRs on his first day. on his eighth day, he shipped like 10 in a day" - [13:30]

      Open-Source Prompts Discovery

      FOUND! The research and planning prompts Dexter mentioned are available in Human Layer's GitHub repository:

      Research Prompt

      • Location: https://github.com/humanlayer/humanlayer/blob/main/.claude/commands/research_codebase.md
      • Purpose: Comprehensive codebase research using parallel sub-agents
      • Key Features:
      • Spawns specialized agents (codebase-locator, codebase-analyzer, thoughts-locator, etc.)
      • Structured research document generation with YAML frontmatter
      • File path and line number references for developer navigation
      • Integration with thoughts directory for historical context

      Planning Prompt

      • Location: https://github.com/humanlayer/humanlayer/blob/main/.claude/commands/create_plan.md
      • Purpose: Interactive implementation plan creation through iterative process
      • Key Features:
      • 5-step process: Context Gathering → Research & Discovery → Plan Structure → Detailed Writing → Sync & Review
      • Automated vs Manual success criteria separation
      • Phase-based implementation with specific file changes and verification steps
      • Integration with specialized research agents

      Implementation Methodology

      These prompts demonstrate the practical application of Dexter's three-phase workflow:

      1. Research Phase: Uses research_codebase.md to understand system architecture
      2. Planning Phase: Uses create_plan.md to create detailed implementation specifications
      3. Implementation Phase: Structured execution with clear success criteria

      References & Follow-up

    1. Document d'Information : Synthèse sur le TDAH et l'Anxiété

      Résumé Analytique

      • Ce document synthétise les liens complexes entre le trouble du déficit de l'attention avec ou sans hyperactivité (TDAH) et l'anxiété, en se basant sur l'idée que de nombreux symptômes anxieux peuvent être mieux expliqués par des déficits sous-jacents de la fonction exécutive liés au TDAH. Jusqu'à 50 % des personnes atteintes de TDAH souffrent également d'un trouble anxieux, et le chevauchement des symptômes, tels que les pensées rapides, les troubles du sommeil et les problèmes de concentration, rend le diagnostic complexe.
      • La distinction fondamentale réside dans la cause première des symptômes.

      L'anxiété est généralement enracinée dans une réponse de peur exacerbée et des comportements d'évitement habituels, souvent liés à une suractivité de l'amygdale.

      En revanche, lorsque les symptômes de type anxieux proviennent du TDAH, ils découlent principalement d'un déficit prédisposé de la fonction exécutive — la capacité du cerveau à planifier, organiser, réguler les émotions et contrôler les impulsions. Ce déficit est souvent lié à des différences dans le cortex préfrontal. * Un concept neurologique clé, la "dispersion du profil cognitif", illustre cette différence. Les personnes atteintes de TDAH présentent souvent des écarts importants entre leurs différentes capacités cognitives, comme une vitesse de traitement très élevée associée à une mémoire de travail faible.

      Cette disparité, décrite comme un "moteur de voiture de course avec des freins de vélo", crée des difficultés de régulation émotionnelle qui alimentent l'anxiété. * Par conséquent, une approche efficace pour traiter l'anxiété chez les personnes atteintes de TDAH consiste à soutenir et à renforcer la fonction exécutive. Cela implique des stratégies pratiques visant à "ralentir la voiture de course" (améliorer l'inhibition), "renforcer les freins" (soutenir la mémoire de travail) et "obtenir une équipe de soutien" (utiliser des ressources externes), offrant ainsi une voie pour gérer l'anxiété en s'attaquant à sa racine neurodéveloppementale.


      1. Le Chevauchement Symptomatique entre TDAH et Anxiété

      • La relation entre le TDAH et l'anxiété peut être illustrée par la métaphore d'un arbre qui semble unique mais possède en réalité deux systèmes racinaires distincts. Bien que les "feuilles" — les symptômes visibles — soient identiques (inquiétude, surmenage, troubles du sommeil), les "racines" — les causes sous-jacentes — diffèrent. Une racine représente l'anxiété découlant d'une réponse de peur, tandis que l'autre représente des symptômes de type anxieux alimentés par un déficit de la fonction exécutive lié au TDAH.

      De nombreux symptômes sont communs aux deux conditions, mais leur origine et leur mécanisme diffèrent.

      • Symptôme
      • Origine dans l'Anxiété
      • Origine dans le TDAH
      • Inquiétude
      • Une habitude inadaptée visant à prévenir les événements négatifs, renforçant un cycle où l'anxiété mène à l'inquiétude, qui prévient (par coïncidence) le résultat redouté, ce qui renforce l'anxiété.
      • Le cerveau active son "réseau du mode par défaut" en l'absence de stimulation, se tournant vers l'inquiétude. L'hyperfocalisation rend difficile le désengagement des pensées anxiogènes.

      Hyperactivité * Une manifestation de la réponse combat-fuite-figer (fight/flight/freeze). Le corps est inondé d'hormones de stress, le préparant à fuir un danger perçu (par exemple, des e-mails). * Décrite comme être "propulsé par un moteur", résultant d'un surplus d'énergie physique combiné à une faible inhibition.

      Difficulté de Concentration

      • Le cerveau est constamment en état d'alerte, balayant l'environnement à la recherche de dangers. Il est difficile de se concentrer sur des tâches (par exemple, les devoirs) lorsqu'on se sent menacé.
      • Une difficulté inhérente à maintenir l'attention sur des tâches qui ne fournissent pas le niveau de stimulation adéquat pour le cerveau TDAH.

      Troubles du Sommeil

      • Les pensées anxieuses et l'inquiétude préventive maintiennent le système nerveux sympathique actif (état d'alerte élevé), empêchant le corps et l'esprit de se détendre.
      • Le cerveau a des difficultés avec le contrôle des impulsions et la régulation comportementale. Il déteste l'ennui et génère donc un flot d'idées aléatoires au moment de s'endormir pour se stimuler.

      2. La Différence Fondamentale : La Fonction Exécutive

      • La distinction la plus cruciale entre l'anxiété et les symptômes de type anxieux liés au TDAH réside dans le rôle de la fonction exécutive. Il s'agit de la capacité du cerveau à gérer les pensées, les émotions et les actions pour atteindre un objectif, englobant des compétences comme la planification, la concentration, la mémorisation et la régulation des impulses.
      • • Racine du TDAH : Déficit de la Fonction Exécutive
      • ◦ Le TDAH est caractérisé par un déficit prédisposé de la fonction exécutive, localisée principalement dans le cortex préfrontal.
      • ◦ Ce déficit rend difficile le traitement des émotions. Par exemple, face à une grande quantité de devoirs, une faible fonction exécutive entrave la priorisation des tâches, diminue la motivation et rend difficile l'initiation du travail. Ce cycle peut mener au stress, au manque de sommeil, à l'anxiété concernant les notes et à un sentiment de surmenage.
      • • Racine de l'Anxiété : Réponse de Peur et Évitement
      • ◦ Les troubles anxieux sont souvent associés à une amygdale ou un axe HPA (hypothalamo-hypophyso-surrénalien) suractif, créant une réponse de peur accrue face à un danger perçu.
      • ◦ Lorsque le cerveau est en mode survie, il détourne l'énergie du cortex préfrontal (la pensée rationnelle) vers des réponses réactives. Cela mène à des comportements d'évitement (par exemple, éviter les devoirs par peur de l'échec ou, à l'inverse, viser la perfection pour éviter l'échec), qui alimentent et renforcent le cycle de l'anxiété.
      • Ce lien crée un cercle vicieux : la faible fonction exécutive (TDAH) alimente la dérégulation émotionnelle et l'anxiété. En retour, l'état émotionnel intense de l'anxiété inhibe davantage la fonction exécutive, rendant la pensée claire encore plus difficile.

      3. Les Bases Neurologiques : La "Dispersion du Profil Cognitif"

      • La "dispersion du profil cognitif" est un phénomène fréquemment observé chez les personnes atteintes de TDAH qui explique la déconnexion entre l'intelligence apparente et les difficultés fonctionnelles.
      • Un score de QI est une moyenne de plusieurs sous-tests mesurant différentes compétences (par exemple, raisonnement verbal, mémoire de travail, vitesse de traitement). Chez une personne neurotypique, ces scores sont généralement groupés. Chez une personne atteinte de TDAH, il peut y avoir un écart significatif entre les scores.
      • • L'Analogie de la Voiture de Course : Le Dr Russell Barkley décrit un schéma courant dans le TDAH comme ayant "un moteur de voiture de course avec des freins de vélo".
      • ◦ Moteur de voiture de course : Vitesse de traitement élevée. Le cerveau génère des idées et des émotions à un rythme extrêmement rapide.
      • ◦ Freins de vélo : Faible mémoire de travail. La mémoire de travail est la capacité de retenir et de manipuler plusieurs informations simultanément. Elle est essentielle pour la régulation émotionnelle, car elle permet de comparer l'expérience actuelle à des souvenirs passés ("J'ai déjà traversé cela, ça va aller") et de se calmer.
      • Lorsque la vitesse de traitement dépasse de loin la capacité de la mémoire de travail, le cerveau est inondé d'émotions et de pensées catastrophiques sans avoir les outils internes pour ralentir, organiser ou apaiser ces sentiments. Cela peut entraîner des explosions émotionnelles impulsives, un sentiment de surmenage et une anxiété chronique.
      • Cette disparité conduit souvent à des malentendus. Un enfant ou un adulte peut paraître "très intelligent" en raison de sa fluidité verbale (vitesse de traitement élevée), mais avoir du mal à initier des tâches ou à se réguler (faible mémoire de travail). Ils sont alors perçus à tort comme "non motivés" ou "paresseux", ce qui peut entraîner des punitions, une faible estime de soi et une peur de l'échec.

      4. Stratégies Pratiques : Aborder l'Anxiété via la Fonction Exécutive

      Si l'anxiété est alimentée par un déficit de la fonction exécutive, la solution consiste à construire des systèmes de soutien ("échafaudages") pour ces fonctions. L'objectif n'est pas d'appliquer plus de "discipline", mais de fournir des outils adaptés.

      Stratégie 1 : Ralentir la Voiture de Course (Améliorer l'Inhibition)

      • • Exercice physique : Soutient directement la fonction exécutive et l'inhibition.
      • • Méditation : Considérée comme une compétence d'entraînement pour le cerveau afin de ralentir et d'améliorer l'attention, plutôt qu'une simple technique de relaxation.
      • • Médicaments : Les stimulants pour le TDAH activent les parties du cerveau responsables de la fonction exécutive, aidant à ralentir les processus de pensée.
      • • Écriture : Journaliser ou simplement écrire ses sentiments est un moyen efficace de ralentir le cerveau, de clarifier le chaos mental et d'activer les parties organisatrices du cerveau.
      • ◦ Exemple : Le témoignage de Sean, coach en fonction exécutive, qui gère le surmenage en écrivant chaque jour : "Si je ne faisais qu'une seule chose aujourd'hui, quelle serait-elle ?" Cette approche minimise la pression et définit un critère de réussite unique et réalisable.
      • • Faire une Pause : Pour contrer l'impulsivité, il est utile de s'entraîner à faire une pause avant de réagir.
      • ◦ Exemple : Mettre en place une "règle de 48 heures" avant de prendre des décisions importantes (par exemple, démissionner, faire un achat coûteux).
      • • Faire Moins de Choses : Le surbooking est une cause majeure de désorganisation et d'anxiété. Il est essentiel de planifier activement du temps pour le repos et l'organisation.

      Stratégie 2 : Renforcer les Freins (Soutenir la Mémoire de Travail et l'Organisation)

      • Rappels Visuels : Pour les personnes atteintes de TDAH, "loin des yeux, loin du cœur" est une réalité. Utiliser des post-it, des tableaux blancs et des listes visibles pour les routines, les stratégies d'adaptation et les objectifs.
      • Systèmes et Routines : Les systèmes de planification (calendriers visuels, listes de contrôle) sont souvent plus efficaces que les approches cognitives comme la TCC pour gérer l'anxiété liée au TDAH.
      • Rappels Numériques : Utiliser des alarmes et des rappels sur son téléphone pour les tâches importantes, les pauses ou même les gestes relationnels (par exemple, "faire un câlin à son conjoint").
      • Traitement Physique des Émotions : Au lieu de traiter les émotions uniquement mentalement, utiliser des supports physiques comme dessiner un schéma de ses sentiments, faire un "brain dump" (décharge mentale) ou une carte mentale.

      Stratégie 3 : Obtenir une Équipe de Soutien (Support Externe)

      • Aide Professionnelle : Un thérapeute ou un coach spécialisé en fonction exécutive peut aider à ralentir, à être moins impulsif et à renforcer les stratégies de régulation.
      • "Body Doubling" : Accomplir des tâches difficiles en présence d'une autre personne. La présence d'un ami peut fournir la structure et la motivation nécessaires.
      • Verbaliser ses Pensées : Exprimer ses pensées à voix haute — que ce soit à un ami, dans un mémo vocal ou même à une IA — les empêche de tourner en boucle et les rend plus faciles à analyser.

      En conclusion, lorsque l'anxiété et le TDAH sont liés, soutenir la fonction exécutive en premier lieu permet de mieux résoudre les problèmes et d'apaiser les émotions.

      Cette approche permet de construire les fondations nécessaires pour que la pensée claire et les choix alignés avec ses valeurs deviennent plus accessibles.

    1. How long does a typical benchmarking study take?

      What are the typical turnaround times for transfer pricing analyses and reports? A standard benchmarking study is usually completed within around 4 business days. Simple financial data updates can be finalized in as little as 48 hours, while a complete documentation update typically takes about 1 week. Master Files are also delivered within 1 week, and Local Files usually require 2–3 weeks depending on complexity and the number of transactions involved.

    1. FeatureTP Doc UpdateBenchmark StudyFull TP ReportPrior Year Comparison✓✗✓Database SearchLimitedComprehensiveComprehensiveStatistical AnalysisBasicDetailedCompleteNACE Code Filtering✗✓✓OECD CompliancePartial✓FullExpert Review✗✓✓Industry Expert Consultation✗BasicComprehensiveDocumentationUpdate onlyBenchmark reportComplete setTurnaround Time48 hours48 hours7-10 daysPrice€250€500Custom

      illetve a featureeket is frissíteni, a 48 órás delivery date az jó a csak pénzügyi adatok frissítésére. ha a komplett doksit frissítjük (kieg. szolgáltatás) akkor 1 hét, benchmark study 4 nap, local file és master file komplexitástól függően 2, maximum 3 hét.

    1. чи можна у вскоді збергіти блокнот юпітер з усіма розрахованими змінними, щоб не перезапускати розрахунок6:04amТак, ти можеш зберегти стан Jupyter Notebook разом зі всіма розрахованими змінними, щоб не перезапускати код з нуля. Ось кілька способів це зробити: 1. Збереження всього середовища (рекомендовано) а) Зберегти ноутбук з вихідними даними Автоматично: Jupyter зберігає стан ядра (змінні, моделі, результати) поки ноутбук відкритий. Просто закрий ноутбук без виходу з Jupyter (не закривай браузер/вкладку повністю). При повторному відкритті ноутбука всі змінні залишаться в пам’яті (якщо ядро не було перезавантажене). Увага: Якщо ти закриєш браузер або перезапустиш ядро (Kernel → Restart), всі змінні зникнуть. Якщо ти вимкнеш комп’ютер, дані теж втратяться. б) Зберегти змінні в файл (наприклад, .pkl або .npz) Використовуй бібліотеку pickle або numpy для збереження важливих змінних на диск: Copyimport pickle # Зберегти всі потрібні змінні в файл with open('notebook_variables.pkl', 'wb') as f: pickle.dump({ 'model': model, # Навчена модель 'history': vers_4.history, # Історія тренування 'train_generator': train_generator, # Генератори даних (якщо потрібно) 'valid_generator': valid_generator, # Додай інші змінні, які потрібно зберегти }, f) Щоб завантажити пізніше: Copywith open('notebook_variables.pkl', 'rb') as f: saved_data = pickle.load(f) model = saved_data['model'] history = saved_data['history'] # Віднови інші змінні в) Зберегти модель окремо (якщо вона найважливіша) Copymodel.save('my_model.h5') # Зберігає модель у форматі HDF5 Завантаження: Copyfrom tensorflow.keras.models import load_model model = load_model('my_model.h5') 2. Автоматичне збереження стану ноутбука а) Використовуй розширення nbautosave Встановіть розширення: Copyjupyter contrib nbextension install --user jupyter nbextensions_configurator enable --user Увімкніть автоматичне збереження в Jupyter: Перейдіть у вкладку Nbextensions (з’являється після встановлення). Увімкніть Autosave Notebook. б) Зберегти ноутбук з вихідними даними (Checkpoints) Jupyter автоматично створює checkpoints (точки відновлення) кожні кілька хвилин. Якщо ноутбук "злетить", можна відновити останню версію: File → Revert to Checkpoint. 3. Збереження всього середовища Python (для складних випадків) Якщо у тебе багато змінних і складне середовище, можна зберегти весь простір імен за допомогою %store (магічна команда Jupyter): Copy# Зберегти всі змінні %store -r model %store -r history %store -r train_generator Щоб завантажити пізніше (в тому ж ноутбуці або іншому): Copy%store -r model # Відновити модель %store -r history # Відновити історію 4. Збереження в формат .ipynb з вихідними даними Jupyter Notebook не зберігає змінні безпосередньо в .ipynb, але можна додати комірку з збереженням даних на початку ноутбука: Copy# Комірка 1: Завантаження даних (якщо файл існує) try: with open('notebook_variables.pkl', 'rb') as f: saved_data = pickle.load(f) model = saved_data['model'] history = saved_data['history'] print("Дані завантажено!") except FileNotFoundError: print("Файл не знайдено. Починаємо з нуля.") 5. Альтернатива: Використовуй joblib для великих об’єктів Якщо у тебе великі об’єкти (наприклад, великі масиви даних), joblib працює швидше за pickle: Copyfrom joblib import dump, load # Зберегти dump({'model': model, 'history': history}, 'notebook_data.joblib') # Завантажити saved_data = load('notebook_data.joblib') model = saved_data['model'] 6. Як уникнути проблем? Не зберігай зайве: Не зберігай генератори даних (train_generator, valid_generator), якщо вони створюються швидко. Зберігай тільки те, що довго обчислюється (наприклад, навчену модель, історію тренування). Перевіряй сумісність версій: Якщо ти оновлюєш бібліотеки (наприклад, tensorflow), збережені файли можуть стати несумісними. Коментуй код: Додай комірку на початку ноутбука з поясненням, як відновити дані. Питання до тебе Які саме змінні тобі потрібно зберегти? (Модель, історія тренування, генератори даних, інші?) Чи плануєш ти перезапускати ноутбук на іншому комп’ютері? (Тоді краще зберігати в файли .pkl/.h5.) Чи хочеш ти автоматизувати збереження (наприклад, щоб файл оновлювався після кожної епохи)? (Можна додати колбек для цього.)

      Збереження стану змінних у Jupiter

    1. On this website, there are many examples of good practices regarding accessibility.

      1) There is a link that says "Skip to main content" which is accessible by pressing the tab key. For users who are unable to use a mouse, this makes the website a lot easier to navigate.

      2) Another thing that this website does well is large and easily readable text. Having large font size is crucial for people who are visually impaired.

      3) Similar to the second point, there is good amount of spacing between the lines which improves readability. Having these features also improve perceivability and make them more understandable according to POUR principles.

      4) Another thing I noticed when navigating this site was the contrast of colours. The text stands out really well, and would meet perceivability standards.

      5) Finally, this site has a very well structured page making it easy to operate and navigate. It utilizes clear, bold headings to state key topics. They also integrate landmark regions into headings which makes it even easier for readers to navigate

    1. Are you sure you want to mark the task as complete? This will trigger your solution to be graded and you won't be able to make any further corrections. If so, include "task_complete": true in your JSON response again.

      this is another comment on this site

    1. زها حديد

      تسليم على كانفاس

      After preparing the lesson and reading the text, annotate the paragraph assigned to you on

      Hypothesis as follows:

      1- Write a summary in your own words for the paragraph assigned to you in Arabic. 

      2- Highlight and annotate the new vocabulary and expressions from this unit in your paragraph, and write one example sentence for each highlighted word.

      3- Highlight and annotate any grammatical rules that you studied so far, for example, passive, masdar, verb forms, قد, etc. Just highlight it and comment, what rule it is. 

      4- Post Questions you have on the article as a whole. 

      Alp من البداية حتى نهاية فقرة الوظائف والمسؤوليات

      Yousef التجربة الهندسية

      Sophia الأوسمة والجوائز

      Doaa الوفاة

  2. teacher.imperial-english.com teacher.imperial-english.com
    1. ps of words below to describe appearance. Write the word which does not belong in each group.

      1) slim / skinny / curvy / thin 👉 Odd one out: curvy Why: slim, skinny, and thin describe people who are not fat. Curvy describes someone (usually a woman) with more shape, not thin.

      2) good-looking / ugly / attractive / beautiful 👉 Odd one out: ugly Why: the others are positive words to describe appearance, but ugly is negative.

      3) short / brunette / blonde / dark-haired 👉 Odd one out: short Why: brunette, blonde, and dark-haired all describe hair colour, while short describes height.

      4) beard / pale / moustache / clean-shaven 👉 Odd one out: pale Why: beard, moustache, and clean-shaven describe facial hair, while pale describes skin colour/complexion.

      5) well-built / stocky / slender / fair 👉 Odd one out: fair Why: well-built, stocky, and slender describe body shape/size, while fair describes hair or skin colour.

    1. There are 12 pairs of ribs, each connected to the thoracic vertebrae (the bones of the spine) at the back.

      This shows the rib cage is connected to our vertebrae’s

    2. bony framework that protects the vital organs within the chest, such as the heart and lungs. It’s composed of three main elements:

      the rib cage is held together with ligaments and costal cartilage

    3. Furthermore, the thoracic cage provides essential support for the shoulder girdle and upper limbs, enabling a wide range of movement and activities.

      The thoracic cage provides support for other muscles and limbs

    4. Conversely, during exhalation, the ribs move downwards and inwards, reducing the chest cavity volume and expelling air from the lungs.

      This expansion of the chest cavity is essential for your lungs to fill with air

    5. nose and mouth, the entry points for air, and the pharynx, which is further divided into the oropharynx (located behind the oral cavity) and nasopharynx (located behind the nasal cavity).

      Nose, mouth are entry points for air and the pharynx is divided by oropharynx and nasopharynx.

    6. Understanding the basic functions and interdependencies of these systems is fundamental for healthcare professionals to effectively diagnose, treat, and prevent various health conditions.

      Knowing dependencies helps with preventing health conditions.

    7. The nervous system is broadly divided into two major components: the central nervous system (CNS) and the peripheral nervous system (PNS).

      Nervous System made of 2 components named the central nervous and peripheral nerves.

    8. PNS, on the other hand, encompasses all the nerves that branch out from the CNS, connecting it to the rest of the body

      PNS supports nerves to the CNS and connects to rest of body.

    1. Reviewer #4 (Public review):

      Summary:

      In this study Tateishi et al. used TnSeq to identify 131 shared essential or growth defect-associated genes in eight clinical MAC-PD isolates and the type strain ATCC13950 of Mycobacterium intracellulare which are proposed as potential drug targets. Genes involved in gluconeogenesis and the type VII secretion system which are required for hypoxic pellicle-type biofilm formation in ATCC13950 also showed increased requirement in clinical strains under standard growth conditions. These findings were further confirmed in a mouse lung infection model.

      Strengths:

      This study has conducted TnSeq experiments in reference and 8 different clinical isolates of M. intracellulare thus producing large number of datasets which itself is a rare accomplishment and will greatly benefit the research community.

      Weaknesses:

      (1) A comparative growth study of pure and mixed cultures of clinical and reference strains under hypoxia will be helpful in supporting the claim that clinical strains adapt better to such conditions. This should be mentioned as future directions in the discussion section along with testing the phenotype of individual knockout strains.<br /> (2) Authors should provide the quantitative value of read counts for classifying a gene as "essential" or "non-essential" or "growth-defect" or "growth-advantage". Merely mentioning "no insertions in all or most of their TA sites" or "unusually low read counts" or "unusually high low read counts" is not clear.<br /> (3) One of the major limitations of this study is the lack of validation of TnSeq results with individual gene knockouts. Authors should mention this in the discussion section.

    1. Author response:

      Reviewer #1 (Public Review):

      Summary:

      The present study evaluates the role of visual experience in shaping functional correlations between extrastriate visual cortex and frontal regions. The authors used fMRI to assess "resting-state" temporal correlations in three groups: sighted adults, congenitally blind adults, and neonates. Previous research has already demonstrated differences in functional correlations between visual and frontal regions in sighted compared to early blind individuals. The novel contribution of the current study lies in the inclusion of an infant dataset, which allows for an assessment of the developmental origins of these differences.

      The main results of the study reveal that correlations between prefrontal and visual regions are more prominent in the blind and infant groups, with the blind group exhibiting greater lateralization. Conversely, correlations between visual and somato-motor cortices are more prominent in sighted adults. Based on these data, the authors conclude that visual experience plays an instructive role in shaping these cortical networks. This study provides valuable insights into the impact of visual experience on the development of functional connectivity in the brain.

      Strengths:

      The dissociations in functional correlations observed among the sighted adult, congenitally blind, and neonate groups provide strong support for the study's main conclusion regarding experience-driven changes in functional connectivity profiles between visual and frontal regions.

      In general, the findings in sighted adult and congenitally blind groups replicate previous studies and enhance the confidence in the reliability and robustness of the current results.

      Split-half analysis provides a good measure of robustness in the infant data.

      Weaknesses:

      There is some ambiguity in determining which aspects of these networks are shaped by experience.

      This uncertainty is compounded by notable differences in data acquisition and preprocessing methods, which could result in varying signal quality across groups. Variations in signal quality may, in turn, have an impact on the observed correlation patterns.

      The study's findings could benefit from being situated within a broader debate surrounding the instructive versus permissive roles of experience in the development of visual circuits.

      Reviewer #2 (Public Review):

      Summary:

      Tian et al. explore the developmental organs of cortical reorganization in blindness. Previous work has found that a set of regions in the occipital cortex show different functional responses and patterns of functional correlations in blind vs. sighted adults. In this paper, Tian et al. ask: how does this organization arise over development? Is the "starting state" more like the blind pattern, or more like the adult pattern? Their analyses reveal that the answer depends on the particular networks investigated; some functional connections in infants look more like blind than sighted adults; other functional connections look more like sighted than blind adults; and others fall somewhere in the middle, or show an altogether different pattern in infants compared with both sighted and blind adults. 

      Strengths:

      The question raised in this paper is extremely important: what is the starting state in development for visual cortical regions, and how is this organization shaped by experience? This paper is among the first to examine this question, particularly by comparing infants not only with sighted adults but also blind adults, which sheds new light on the role of visual (and cross-modal) experience. Another clear strength lies in the unequivocal nature of many results. Many results have very large effect sizes, critical interactions between regions and groups are tested and found, and infant analyses are replicated in split halves of the data. 

      Weaknesses:

      A central claim is that "infant secondary visual cortices functionally resemble those of blind more than sighted adults" (abstract, last paragraph of intro). I see two potential issues with this claim. First, a minor change: given the approaches used here, no claims should be made about the "function" of these regions, but rather their "functional correlations". Second (and more importantly), the claim that the secondary visual cortex in general resembles blind more than sighted adults is still not fully supported by the data. In fact, this claim is only true for one aspect of secondary visual area functional correlations (i.e., their connectivity to A1/M1/S1 vs. PFC). In other analyses, the infant secondary visual cortex looks more like sighted adults than blind adults (i.e., in within vs. across hemisphere correlations), or shows a different pattern from both sighted and blind adults (i.e., in occipito-frontal subregion functional connectivity). It is not clear from the manuscript why the comparison to PFC vs. non-visual sensory cortex is more theoretically important than hemispheric changes or within-PFC correlations (in fact, if anything, the within-PFC correlations strike me as the most important for understanding the development and reorganization of these secondary visual regions). It seems then that a more accurate conclusion is that the secondary visual cortex shows a mix of instructive effects of vision and reorganizing effects of blindness, albeit to a different extent than the primary visual cortex.

      Relatedly, group differences in overall secondary visual cortex connectivity are particularly striking as visualized in the connectivity matrices shown in Figure S1. In the results (lines 105-112), it is noted that while the infant FC matrix is strongly correlated with both adult groups, the infant group is nonetheless more strongly correlated with the blind than sighted adults. I am concerned that these results might be at least partially explained by distance (i.e., local spread of the bold signal), since a huge portion of the variance in these FC matrices is driven by stronger correlations between regions within the same system (e.g., secondary-secondary visual cortex, frontal-frontal cortex), which are inherently closer together, relative to those between different systems (e.g., visual to frontal cortex). How do results change if only comparisons between secondary visual regions and non-visual regions are included (i.e., just the pairs of regions within the bold black rectangle on the figure), which limits the analysis to long-rang connections only? Indeed, looking at the off-diagonal comparisons, it seems that in fact there are three altogether different patterns here in the three groups. Even if the correlation between the infant pattern and blind adult pattern survives, it might be more accurate to claim that infants are different from both adult groups, suggesting both instructive effects of vision and reorganizing effects of blindness. It might help to show the correlation between each group and itself (across independent sets of subjects) to better contextualize the relative strength of correlations between the groups. 

      It is not clear that differences between groups should be attributed to visual experience only. For example, despite the title of the paper, the authors note elsewhere that cross-modal experience might also drive changes between groups. Another factor, which I do not see discussed, is possible ongoing experience-independent maturation. The infants scanned are extremely young, only 2 weeks old. Although no effects of age are detected, it is possible that cortex is still undergoing experience-independent maturation at this very early stage of development. For example, consider Figure 2; perhaps V1 connectivity is not established at 2 weeks, but eventually achieves the adult pattern later in infancy or childhood. Further, consider the possibility that this same developmental progression would be found in infants and children born blind. In that case, the blind adult pattern may depend on blindness-related experience only (which may or may not reflect "visual" experience per se). To deal with these issues, the authors should add a discussion of the role of maturation vs. experience and temper claims about the role of visual experience specifically (particularly in the title). 

      The authors measure functional correlations in three very different groups of participants and find three different patterns of functional correlations. Although these three groups differ in critical, theoretically interesting ways (i.e., in age and visual/cross-modal experience), they also differ in many uninteresting ways, including at least the following: sampling rate (TR), scan duration, multi-band acceleration, denoising procedures (CompCor vs. ICA), head motion, ROI registration accuracy, and wakefulness (I assume the infants are asleep).

      Addressing all of these issues is beyond the scope of this paper, but I do feel the authors should acknowledge these confounds and discuss the extent to which they are likely (or not) to explain their results. The authors would strengthen their conclusions with analyses directly comparing data quality between groups (e.g., measures of head motion and split-half reliability would be particularly effective).

      Response #1: We appreciate the reviewer’s comments. In response, we have revised the paper to provide a more balanced summary of the data and clarified in the introduction which signatures the paper focuses on and why. Additionally, we have included several control analyses to account for other plausible explanations for the observed group differences. Specifically, we randomly split the infant dataset into two halves and performed split-half cross-validation. Across all comparisons, the results from the two halves were highly similar, suggesting that the effects are robust (see Supplementary Figures S3 and S4).

      Furthermore, we compared the split-half noise ceiling across the groups (infants, sighted adults, and blind adults) and found no significant differences between them (details in response #6). Finally, we repeated our analysis after excluding infants with a radiology score of 4 or 5, and the results remained consistent, indicating that our findings are not confounded by potential brain anomalies (details in response #2).

      We hope these control analyses help strengthen our conclusions.

      Reviewer #3 (Public Review):

      Summary:

      This study aimed to investigate whether the differences observed in the organization of visual brain networks between blind and sighted adults result from a reorganization of an early functional architecture due to blindness, or whether the early architecture is immature at birth and requires visual experience to develop functional connections. This question was investigated through the comparison of 3 groups of subjects with resting-state functional MRI (rs-fMRI). Based on convincing analyses, the study suggests that: 1) secondary visual cortices showed higher connectivity to prefrontal cortical regions (PFC) than to non-visual sensory areas (S1/M1 and A1) in sighted infants like in blind adults, in contrast to sighted adults; 2) the V1 connectivity pattern of sighted infants lies between that of sighted adults (stronger functional connectivity with non-visual sensory areas than with PFC) and that of blind adults (stronger functional connectivity with PFC than with non-visual sensory areas); 3) the laterality of the connectivity patterns of sighted infants resembled those of sighted adults more than those of blind adults, but sighted infants showed a less differentiated fronto-occipital connectivity pattern than adults.

      Strengths:

      The question investigated in this article is important for understanding the mechanisms of plasticity during typical and impaired development, and the approach considered, which compares different groups of subjects including, neonates/infants and blind adults, is highly original.

      -Overall, the analyses considered are solid and well-detailed. The results are quite convincing, even if the interpretation might need to be revised downwards, as factors other than visual experience may play a role in the development of functional connections with the visual system.

      Weaknesses:

      While it is informative to compare the "initial" state (close to birth) and the "final" states in blind and sighted adults to study the impact of post-natal and visual experience, this study does not analyze the chronology of this development and when the specialization of functional connections is completed. This would require investigating when experience-dependent mechanisms are important for the setting- establishment of multiple functional connections within the visual system. This could be achieved by analyzing different developmental periods in the same way, using open databases such as the Baby Connectome Project. Given the early, "condensed" maturation of the visual system after birth, we might expect sighted infants to show connectivity patterns similar to those of adults a few months after birth.

      The rationale for mixing full-term neonates and preterm infants (scanned at term-equivalent age) from the dHCP 3rd release is not understandable since preterms might have a very different development related to prematurity and to post-natal (including visual) experience. Although the authors show that the difference between the connectivity of visual and other sensory regions, and the one of visual and PFC regions, do not depend on age at birth, they do not show that each connectivity pattern is not influenced by prematurity. Simply not considering the preterm infants would have made the analysis much more robust, and the full-term group in itself is already quite large compared with the two adult groups. The current study setting and the analyses performed do not seem to be an adequate and sufficient model to ascertain that "a few weeks of vision after birth is ... insufficient to influence connectivity".

      In a similar way, excluding the few infants with detected brain anomalies (radiological scores higher or equal to 4) would strengthen the group homogeneity by focusing on infants supposed to have a rather typical neurodevelopment. The authors quote all infants as "sighted" but this is not guaranteed as no follow-up is provided.

      Response #2: We appreciate the reviewer’s suggestion. We re-analyzed the infant cohort after excluding all cases with radiological scores ≥4 (n =39 infants excluded). The revised analysis confirmed that the connectivity patterns reported in the main text remain statistically unchanged (see Supplementary Fig. S11). This demonstrates the robustness of our findings to potential confounding effects from potential brain anomalies. We have explicitly clarified this in the revised Methods section (page 14, line 391in the manuscript).

      In our dataset, newborns (average age at scan = 2.79 weeks) have very limited and immature vision. We agree with the reviewer that long-term visual outcomes cannot be guaranteed without follow-up data. The term "sighted infants" was used operationally to distinguish this cohort from congenitally blind populations.

      The post-menstrual age (PMA) at scan of the infants is also not described. The methods indicate that all were scanned at "term-equivalent age" but does this mean that there is some PMA variability between 37 and 41 weeks? Connectivity measures might be influenced by such inter-individual variability in PMA, and this could be evaluated.

      The rationale for presenting results on the connectivity of secondary visual cortices before one of the primary cortices (V1) was not clear to understand. Also, it might be relevant to better justify why only the connectivity of visual regions to non-visual sensory regions (S1-M1, A1) and prefrontal cortex (PFC) was considered in the analyses, and not the ones to other brain regions.

      In relation to the question explored, it might be informative to reposition the study in relation to what others have shown about the developmental chronology of structural and functional long-distance and short-distance connections during pregnancy and the first postnatal months.

      The authors acknowledge the methodological difficulties in defining regions of interest (ROIs) in infants in a similar way as adults. The reliability and the comparability of the ROIs positioning in infants is definitely an issue. Given that brain development is not homogeneous and synchronous across brain regions (in particular with the frontal and parietal lobes showing delayed growth), the newborn brain is not homothetic to the adult brain, which poses major problems for registration. The functional specialization of cortical regions is incomplete at birth. This raises the question of whether the findings of this study would be stable/robust if slightly larger or displaced regions had been considered, to cover with greater certainty the same areas as those considered in adults. And have other cortical parcellation approaches been considered to assess the ROIs robustness (e.g. MCRIB-S for full-terms)?

      Recommendations for the Authors:

      Reviewer #1(Recommendations for the authors):

      Further consideration should be given to the underlying changes in network architecture that may account for differences in functional correlations across groups. An increase (or decrease) in correlation between two regions could signify an increase (decrease) in connection or communication between those regions. Alternatively, it might reflect an increase in communication or connection with a third region, while the physical connections/interactions between the two original regions remain unchanged. These possibilities lead to distinct mechanistic interpretations. For example, there are substantial changes in connectivity during early visual (e.g. Burkhalter A. 1993, Cerebral Cortex) and visuo-motor development (e.g., Csibra et al. 2000 Neuroreport). It's not clear whether increases in communication within the visual network and improvements in visuo-motor behavior (e.g., Yizhar et al. 2023 Frontiers in Neuroscience) wouldn't produce a qualitatively similar pattern of results.

      Relatedly, the within-network correlation patterns between visual ROIs and frontal ROIs appear markedly different between sighted adults and infants (Supplementary Figure S1). To what extent do the differences in long-range correlations between visual and frontal regions reflect these within-network differences in functional organization?

      Response #3: The reviewer is raising some interesting questions about possible mechanisms and network changes. Resting state studies are indeed always subject to possibility that some effects are mediated by a third, unobserved region. Prior whole-cortex connectivity analyses have observed primarily changes in occipito-frontal connectivity in blindness, so there is not a clear cortical ‘third region’ candidate (Deen et al., 2015). However, some thalamic affects have also been observed and could contribute to the phenomenon (Bedny et al., 2011). Resting state changes in correlation between two areas do not imply changes in strength of long-range anatomical connectivity. Indeed, in the current case they may well reflect differential functional coupling, rather than strengthening or weakening of anatomical connections. We now discuss this in the Discussion section on page 12, line 301 as follows:

      “Despite these insights, many questions remain regarding the neurobiological mechanisms underlying experience-based functional connectivity changes and their relationship to anatomical development. Long-range anatomical connections between brain regions are already present in infants—even prenatally—though they remain immature (Huang et al., 2009; Kostović et al., 2019, 2021; Takahashi et al., 2012; Vasung, 2017). Functional connectivity changes may stem from local synaptic modifications within these stable structural pathways, consistent with findings that functional connectivity can vary independently of structural connection strength (Fotiadis et al., 2024). Moreover, functional connectivity has been shown to outperform structural connectivity in predicting individual behavioral differences, suggesting that experience-based functional changes may reflect finer-scale synaptic or network-level modulations not captured by macrostructural measures (Ooi et al., 2022). Prior studies also suggest that, even in adults, coordinated sensory-motor experience can lead to enhancement of functional connectivity across sensory-motor systems, indicating that large-scale changes in functional connectivity do not necessarily require corresponding changes in anatomical connectivity (Guerra-Carrillo et al., 2014; Li et al., 2018).”

      It is not clear how changes in correlation patterns among visual areas would produce the connectivity between visual areas and prefrontal areas reported in the current study. Activity in visual areas drives correlations both among visual areas and between visual and prefrontal areas and the same is true of prefrontal corticies.

      The findings from this study should be more closely linked to the extensive literature surrounding the debate on whether experience plays an instructive or permissive role in visual development (e.g., Crair 1999 Current Opin Neurobiol; Sur et al. 1999 J Neurobiol; Kiorpes 2016 J Neurosci; Stellwagen & Shatz 2002 Neuron; Roy et al. 2020 Nature Communications).

      Response #4: The instructive role suggests that specific experiences or patterns of neural activity directly shape and organize neural circuitry, while the permissive role indicates that such experiences or activity merely enable other factors, such as molecular signals, to influence neural circuit formation(Crair, 1999; Sur et al., 1999). To distinguish whether experience plays an instructive or permissive role, it is essential to manipulate the pattern or information content of neural activity while maintaining a constant overall activity level (Crair, 1999; Roy et al., 2020; Stellwagen & Shatz, 2002). However, both the sighted and blind adult groups have had extensive experience and neural activity in the visual cortices. For the sighted group, activity in the visual cortex is partly driven by bottom-up input from the external environment, through the retina, LGN, and ultimately to the cortex. In contrast, the blind group’s visual cortex activity is partially driven by top-down input from non-visual networks. The precise role of this activity in shaping the observed connectivity patterns remains unclear. Although our study cannot speak to this issue directly, we now link to the relevant literature on page 12,line 320 of the manuscript in the Discussion section as follows:

      “The current findings reveal both effects of vision and effects of blindness on the functional connectivity patterns of the visual cortex. A further open question is whether visual experience plays an instructive or permissive role in shaping neural connectivity patterns. An instructive role suggests that specific sensory experiences or patterns of neural activity directly shape and organize neural circuitry. In contrast, a permissive role implies that sensory experience or neural activity merely facilitates the influence of other factors—such as molecular signals—on the formation and organization of neural circuits (Crair, 1999; Sur et al., 1999). Studies with animals that manipulate the pattern or informational content of neural activity while keeping overall activity levels constant could distinguish between these hypotheses (Crair, 1999; Roy et al., 2020; Stellwagen & Shatz, 2002).”

      The assertion that a few weeks of vision after birth is insufficient to influence connectivity is provocative. Though supported by the study's results, it would benefit from integration with research in animal models showing considerable malleability of networks from early experience (e.g., Akerman et al. 2002 Neuron; Li et al. 2006 Nature Neuroscience; Stacy et al. 2023 J Neuroscience).

      Response #5: We thank the reviewer for their suggestion. The present study found that several weeks of postnatal visual experience is insufficient to significantly alter the long-term connectivity patterns of the visual cortices. While animal studies have shown that acute visual experience, or even exposure to visual stimuli through unopened eyelids, can robustly influence visual system development(Akerman et al., 2002; Li et al., 2008; Van Hooser et al., 2012). We think this discrepancy may be attributed to the substantial differences in developmental timelines between species. The human lifespan is much longer, and so is the human critical period, making it unclear how to map duration from one species to another. We briefly touched upon the time course issue in page 11 line 289 in the Discussion section as follows:

      “The present results reveal the effects of experience on development of functional connectivity between infancy and adulthood, but do not speak to the precise time course of these effects. Infants in the current sample had between 0 and 20 weeks of visual experience. Comparisons across these infants suggests that several weeks of postnatal visual experience is insufficient to produce a sighted-adult connectivity profile. The time course of development could be anywhere between a few months and years and could be tested by examining data from children of different ages.”

      Substantial differences between the groups are evident in several key aspects of the study, including the number of subjects, brain sizes, imaging parameters, and data preprocessing, all of which are likely to have an impact on the overall signal quality. To clarify how these differences might have impacted correlation differences between groups, it would be essential to include information on the noise ceilings for each correlation analysis within each group.

      Response #6: We thank the reviewer for their suggestion. We now report the split-half noise ceiling for adult and infant groups. For each participant, we first split the rs-fMRI time series into two halves, then calculated the ROI-wise rsFC pattern from the two splits. The split-half noise ceiling was estimated according to Lage-Castellanos et al (2019). The noise ceilings of the three groups (infants: 0.90 ± 0.056,blind adults: 0.88 ± 0.041, sighted adults: 0.90 ± 0.055) showed no significant difference (One-way ANOVA<sub>,</sub> F(2,552) = 2.348, p = 0.097). Therefore, we believe that overall signal quality is unlikely to impact our results. We also add the relevant context in the Method section in page 16 Line 447 as follows:

      “Substantial differences between the groups exist in this study, including the number of subjects, brain sizes, imaging parameters, and data preprocessing, all of which are likely to have an impact on the overall signal quality. To address this concern, we compared the split-half noise ceiling across the groups (infants, sighted adults, and blind adults). For each participant, we first split the rs-fMRI time series into two halves, then calculated the ROI-wise rsFC pattern from the two splits. The split-half noise ceiling was estimated according to Lage-Castellanos et al (Lage-Castellanos et al., 2019). The noise ceilings of the three groups (infants: 0.90 ± 0.056, blind adults: 0.88 ± 0.041, sighted adults: 0.90 ± 0.055) showed no significant difference (One-way ANOVA, F (2,552) = 2.348, p = 0.097). Therefore, overall signal quality is unlikely to impact our results.”

      In general, it appears that the infant correlations are stronger compared to the other groups. While this could reflect increased coherence or lack of differentiation, it is also possible that it is simply due to the presence of a non-neuronal global signal. Such a signal has the potential to substantially limit the effective range of functional correlations and comparisons with adults. To address this, it is advisable to conduct control analyses aimed at assessing and potentially removing global signals.

      Response #7: We agree with the reviewer that global signal regression (GSR) may help reduce non-neuronal artifacts, such as motion, cardiac, and respiratory signals, which are known to correlate with the global signal. However, the global signal also contains neural signals from gray matter, and removing it can introduce unwanted artifacts, especially for the current study. First, GSR can reduce the physiological accuracy of functional connectivity (FC); second, GSR may have differential effects across groups, potentially introducing additional artifacts in between-group comparisons, as noted by Murphy et al (Murphy & Fox, 2017). The CompCor method (Behzadi et al., 2007; Whitfield-Gabrieli & Nieto-Castanon, 2012) is capble to estimate the global non-neuronal artifacts like the GSR method. Meanwhile as it estimate global non-neuronal artifacts from signals within the white matter (WM) and cerebrospinal fluid (CSF) masks, but not the gray matter (GM), CompCor could introduce minimal unwanted bias to the GM signal.

      Was there a difference in correlations for preterm vs term neonates? Recent research has suggested that preterm births can have an impact on functional networks, particularly in frontal cortices. e.g., Tokariev et al. 2019, Li et al. 2021 elife; Zhang et al. 2022 Fronteirs in Neuroscience.

      Response #8: We have compared preterm and term neonates for all the main results, including the connectivity from the secondary visual cortex/V1 to non-visual sensory cortices versus prefrontal cortices, the laterality of occipito-frontal connectivity, and the specialization across different fronto-occipital networks. This information is reported in Page 6 line 169 and Supplementary Figure S7. The connectivities of full-term infants are generally higher than those of preterm infants. However, the connectivity patterns of term and preterm infants are very similar.

      The consistency between the current results and prior work (e.g., Burton et al. 2014) is notable, particularly in the observed greater correlations in prefrontal regions and weaker correlations in somato-motor regions for early blind individuals compared to sighted. However, almost all visual-frontal correlations in both groups were negative in that prior study. Some discussion on why positive correlations were found in the current study could help to clarify.

      Response #9: Many other papers have reported positive correlations similar to those found in our study (e.g., Deen et al., 2015; Kanjlia et al., 2021). In contrast, Burton's study identified predominantly negative visual-frontal correlations, we think this is likely because the global signal was regressed out during preprocessing. This methodological choice can lead to an increase in negative connections (Murphy & Fox, 2017).

      The term "secondary visual areas" used throughout the paper lacks specificity, and its usage in terms of underlying anatomical and functional areas has been inconsistent in the literature. It would be advisable to adopt a more precise characterization based on functional and/or anatomical criteria.

      Response #10: We specified in the article that Tthe occipital ROIs were defined in the current study are functional areas in people born blind identified in prior studies as regions that respond to three non-visual tasks such as language, math, or executive function, and show functional connectivity changes in blind adults in previous studies (Kanjlia et al., 2016, 2021; Lane et al., 2015). These regions respond to language, math and executivie function in the congenitally blind population (see Figure 1.) The are refered collectively as ‘secondary visual areas’ to destinguish them from V1. Anatomically, these three regions cover the majority of the lateral occipital cortex and part of the ventral occipital cortex, providing a good sample of the connectivity profile of higher-order visual areas. Thus, we are using the term "secondary visual areas" to refer to these regions. In blind individuals, although these regions respond to non-visual tasks, their exact functions are unknown.

      The inclusion of the ventral temporal cortex in the visual ROIs is currently only depicted in Supplementary Figure S7. To enhance the clarity of the areas of interest analyzed, it would be advisable to illustrate the ventral temporal areas in the main text. Were there notable differences in the frontal correlations between the lateral occipital visual areas and ventral temporal areas?

      Response #11: We thank the reviewer for pointing out this issue. We added a statement about the ventral visual cortex in describing the location of the ROI and added the ventral view of ROIs in the Figure 1. The language-responsive and math -responsive ROIs covers both the lateral and ventral visual cortex, whereas executive function (response-conflict) regions cover only the lateral visual cortex. We compared the connectivity patterns of these three regions and found no differences (see supplementary Fig S2).

      The blind group results are characterized as reflecting a reorganization in comparison to sighted adults while the results for sighted adults compared to infants are discussed more as a maturation ("adult pattern isn't default but requires experience to establish"). Both the sighted and blind adult groups showed differences from the infant group, and these differences are attributed to the role of experience. Why use "reorganization" for one result and maturation for another?

      Response #12: We agree with the reviewer that both of the adult groups should be thought of as equal in relation to the infants. In other words, the brain develops under one set of experiential conditions or another. We do not think that the adult sighted pattern reflects maturation. Rather, the sighted adult pattern reflects the combined influence of maturation and visual experience. The adult blind pattern reflects the combined influence of maturation and blindness. We use the term ‘reorganization’ to label differences in the blind adults relative to sighted infants. We do so for the purpose of clarity and to remain consistent with terminology in prior liaterature. However, we agree with the reviewer that the blind group does not reflect ‘reorganization’ intrinsically any more than the sighted adult group.

      The statement that "visual experience is required to set up long-range functional connectivity" is unclear, especially since the infant and blind groups showed stronger long-range functional correlations with PFC.

      Response #13: We revised this sentence to specifically as “visual experience establishes elements of the sighted-adult long-range connectivity” in tha Abstract line 17.

      The statement that the visual ROIS roughly correspond to "the anatomical location of areas such as V5/MT+, LO, V3a, and V4v" appears imprecise. From Supplementary Figure S7, these areas cover anterior portions of ventral temporal cortex (do these span the anatomical location of putative category-selective areas?) and into the intraparietal sulcus.

      Response #14: Thanks to the reviewer for the clarification. The ventral ROIs cover the middle and part of the anterior portion of the ventral temporal lobe, including the putative category-selective areas. Additionally, the dorsal ROIs extend beyond the occipital lobe to the intraparietal sulcus and superior parietal lobule. We have added a more detailed description of the anatomical location of the ROI in the Methods section Page 17 line 489 as follows:

      “Each functional ROI spans multiple anatomical regions and together the secondary visual ROIs tile large portions of lateral occipital, occipito-temporal, dorsal occipital and occipito-parietal cortices. In sighted people, the secondary visual occipital ROIs include the anatomical locations of functional regions such as motion area V5/MT+, the lateral occipital complex (LO), category specific ventral occipitotemporal cortices and dorsally, V3a and V4v.  The occipital ROI also covers the middle of the ventral temporal lobe. Dorsally, it extended to the intraparietal sulcus and superior parietal lobule.”

      The motivation for assessing correlations with motor and frontal regions was briefly discussed in the introduction. It would be helpful to reiterate this motivation when first introducing the analyses in the results.

      Response #15: Thank you for the thoughtful suggestion. Upon reflection, we chose to substantially revise the Introduction to more clearly and comprehensively explain the rationale for examining the couplings with motor and frontal regions, rather than reiterating it in the Results section. We believe this revised framing provides a stronger foundation for the analyses that follow, while avoiding redundancy across sections. We hope this addresses the reviewer’s concern.

      Reviewer #2 (Recommendations for the authors):

      Congratulations on a well-written paper and an interesting set of results.

      Reviewer #3 (Recommendations for the authors):

      Abstract:

      Mentioning "sighted infants" does not seem adequate.

      Response #16: In our dataset, newborns (average age at scan = 2.79 weeks) have very limited and immature vision. We agree with the reviewer that long-term visual outcomes cannot be guaranteed without follow-up data. The term "sighted infants" was used operationally to distinguish this cohort from congenitally blind populations.

      In sentences after "Specifically...", it was not clear whether the authors referred to V1 connectivity.

      Response #17: We thank the reviewer for this comment. In the revised abstract, we have removed the original "Specifically..." phrasing and clarified the results.

      Introduction

      Talking about the "instructive effects" of vision might be confusing or misleading. Visual experiences like exposure to oral language are part of the normal/spontaneous environment that allows the infant behavioral acquisitions (contrarily with learnings that occur later during development with instruction like for reading).

      Response #18: We appreciate the reviewer’s concern and would like to clarify that the term “instructive effect” is used here derived from neurodevelopmental studies (Crair, 1999; Sur et al., 1999). In this context, “instructive” refers to activity-dependent mechanisms where patterns of neural activity actively guide the organization of synaptic connectivity, emphasizing that spontaneous or sensory-driven activity (e.g., retinal waves, visual experience) can directly shape circuit refinement, as seen in ocular dominance column formation. In the context of our study, we emphasize that vision plays an instructive role in setting up the balance of connectivity between occipital cortex and non-visual networks.

      For references on the development of connectivity, I would advise citing MRI studies but also studies based on histological approaches (see for example the detailed review by Kostovic et al, NeuroImage 2019).

      Response #19: We thank the reviewer for this suggestion. We have incorporated a discussion on the long-range anatomical connections that emerge as early as infancy, referencing studies that employed diffusion MR imaging and histological methods, as detailed below.

      “Many long-range anatomical connections between brain regions are already established in infants, even before birth, although they are not yet mature (Huang et al., 2009; Kostović et al., 2019, 2021; Takahashi et al., 2012; Vasung, 2017).” (Page 12, line 303 in the manuscript)

      Results

      P7 l170: It might be helpful to be precise that this is "compared with inter-hemispheric connectivity".

      Response #20: We thank the reviewer for this suggestion. To align with our established terminology, we have revised the statement to explicitly contrast within-hemisphere connectivity with between-hemisphere connectivity. The modified text now reads (page 7, line 183 in the manuscript):

      “Compared to sighted adults, blind adults exhibited a stronger dominance of within-hemisphere connectivity over between-hemisphere connectivity. That is, in people born blind, left visual networks are more strongly connected to left PFC, whereas right visual networks are more strongly connected to right PFC.

      L176-181: It was not clear to me what was the difference between "across" and "between hemisphere connectivity". Would it be informative to test the difference between blind and sighted adults?

      Response #21: We clarify that there is no distinction between the terms “across” and “between hemisphere connectivity”—they refer to the same concept. To ensure consistency, we have revised the text to exclusively use “between hemisphere connectivity” throughout the manuscript. Regarding the comparison between blind and sighted adults, we conducted statistical comparisons between these groups in our analysis, and the results have been incorporated into the revised version (Page 7, line 187 in the manuscript).

      Adding statistics on Figure 3, but also on Figures 1 and 2 might help the reading.

      Response #22: We have added the statistics in Figure 1-4.

      Adding the third comparison in Figure 4 would be possible in my view.

      Response #23: We explored integrating the response-conflict region into Figure 4, but this would require a 3x3 bar chart with pairwise statistical significance markers, which introduced excessive visual complexity that hindered readers’ ability to grasp our intended message. To ensure clarity, we retained the original Figure 4 while providing the complete three-region analysis (including all statistical comparisons) in Supplementary Figure S8 to ensure completeness.

      Methods

      The authors might have to specify ages at birth, and ages at scan (median + range?).

      Response #24: We have added that information in the Methods section as follows:

      “The average age from birth at scan = 2.79 weeks (SD = 3.77, median = 1.57, range = 0 – 19.71); average gestational age at scan = 41.23 weeks (SD = 1.77, median = 41.29, range = 37 – 45.14); average gestational age at birth = 38.43 weeks (SD = 3.73, median = 39.71, range = 23 – 42.71).” (Page 14, line 379 in the manuscript)

      It might be relevant to comment on the range of available fMRI volumes, and the fact that connectivity measures might then be less robust in infants.

      Response #25: We report the range of fMRI volumes in the Methods section (Page 16, Line 449). Adult participants (blind and sighted) underwent 1–4 scanning sessions, each containing 240 volumes (mean scan duration: 710.4 seconds per participant). For infants, all subjects had 2300 fMRI volumes, and we retained a subset of 1600 continuous volumes per subject with the minimum number of motion outliers. While infant connectivity measures may inherently exhibit lower robustness due to developmental and motion-related factors, our infant cohort’s large sample size (n=475) and stringent motion censoring criteria enhance the reliability of group-level inferences. We have integrated this clarification into the Methods section (Page 16, Line 444) as follows:

      "While infant connectivity estimates may be less robust at the individual level compared to adults due to shorter scan durations and higher motion, our cohort’s large sample size (n=475) and rigorous motion censoring mitigate these limitations for group-level analyses. "

      The mention of dHCP 2nd release should be removed from the paragraph on data availability.

      Response #26: We have removed it.

    1. Author response:

      Response to Comments from reviewer #1

      Many thanks for appreciating that SZN-043 can promote hepatocyte proliferation via the Wnt-signaling pathway.

      (1) The reviewer is concerned with using only CYP1A2 expression as an endpoint to make a conclusion about the effect of SZN-043 on Wnt activity in human ALD samples. The reviewer raises a good point as the more commonly used Wnt target gene, AXIN2, is not consistantly changed in both cohorts. We were at first also surprised by this finding. However, upon closer analysis we found that the expression of hepatocyte-specific target genes such as CYP1A2 (Figure 2), CYP2E1, OAT, LGR5, GLUL (Table 1) and ZNRF3 were mostly expressed in hepatocytes and ductal cells were all down-regulated in ALD samples. Others Wnt target genes expressed in epithelial and mesenchymal liver cell populations, such as AXIN2, CCND1 and NOTUM are indeed not consistently and significantly changed. Given that SZN-043 is not active on mesenchymal cells, this discrepancy could be best explained by the large increase in mesenchymal cells in ALD tissue samples, thereby confounding the results. We have now clarified this in the discussion. Another method to assess Wnt activity is to measure b-catenin phosphorylation and nuclear transfer. In our hands, this method was found to be better suited for tissue culture than histological sections from in vivo studies. We have also amended the manuscript title to refer to expression of Wnt target genes, rather than Wnt activity.

      (2) We have now added a supplemental figure to show the lack of Ki-67+ human hepatocytes in the cirrhotic tissue samples to confirm the absence of hepatocyte proliferation (Figure S1).

      (3) The differences in amino acid sequence between SZN-043 and its precursor, αASGR1-RSPO2-RAIgG, can be found in the material and method section. These changes in amino acid sequences improved the biophysical properties of the final clinical candidate, such as oxidation and nonspecific binding. The biochemical analysis of those differences exceeds the scope of the current manuscript. We present here the pharmacokinetic properties of SZN-043 only, as this was the only molecule advanced to clinical trial and used in the studies presented here.

      (4) The reviewer suggests to assess the effect of SZN-043 in Ctnnb1-KO mice to confirm that SZN043 acts via a canonical Wnt pathway. Indeed, there were several reports on the ability of Rspondin to act on other pathways besides the Wnt signaling pathway (for recent review, Niehrs et al, 2024, Bioessays). However, while an interesting suggestion, this line of investigation belongs to MOA studies and exceeds the scope of the current manuscript. An additional manuscript presenting MOA studies for SZN-043 was recently submitted elsewhere. Still, we have added this possibility in the discussion section.

      (5) The reviewer is asking how SZN-043 is affecting liver functions in general. Indeed, we have observed a consistent reduction in the international normalized ratio of prothrombin time using the thioacetamide (TAA)-induced fibrosis model and previously published those findings (Zhang, 2020). In our hands, the TAA is the only liver injury model that significantly increases INR. This increase is modest compared to that observed in clinical patients. Therefore, we do not report INR findings for other models. We have not seen any effects of SZN-043 on hepatocyte differentiation markers such as HNF4A (data not shown) and the hepatocyte specific ASGR1/2 as shown in Figure 5. Rather we focused on proliferation as the main potentially beneficial endpoint, to restore the parenchymal mass in injured livers. Finally, consistent with what was reported in the literature, we have observed a transient and reciprocal effect on albumin and alfa-fetoprotein expression during the proliferative phase of liver regeneration. These results are detailed in an additional manuscript presenting MOA studies for SZN-043, which was recently submitted elsewhere.

      (6) We have used females only in the ethanol-induced injury models because there are numerous reports in the literature stating that males are not as susceptible to those injuries.  

      (7) The reviewer questions the relevance of the ethanol-induced injury model used to evaluate SZN043 efficacy. Indeed, none of the disease model developed to date reproduce the severity and complexity of alcohol-associated liver diseases, although some, such as the ethanol supplemented Lieber DeCarli diet, are more commonly used than others – which is the reason why this model was selected. 

      (8) The reviewer questions the relevance of the fibrosis model used to evaluate SZN-043 efficacy. Indeed, none of the fibrosis models developed to date reproduce the severity and complexity of cirrhosis in human livers. While combining ethanol with CCl4 would lead to more severe fibrotic livers, CCl4 itself is not involved in ALD in humans. Both models are likely to result in similar pericentral fibrosis with central-to-central bridging. In this study, we were mostly interested in addressing the effects of SZN-043 in a tissue affected by fibrotic scars.  

      (9) The sex of CCl4-treated mice is male. We added this information in the methods section.

      (10) A summary of histology and fibrosis assessment data for alcohol-fed mice was added in supplemental Table S3. In our hands, the use of aging mice did not induce the presence of fibrosis, in contrast to published results.  

      (11) The rationale for using 13.5-month-old mice in the alcohol studies and scid mice in the CCl4 studies has been clarified in the results and discussion sections. 

      a. Briefly, aging mice were reported to be more susceptible to ethanol-induced injury than young mice and to include induction of fibrosis. However, we were unable to reproduce the presence of fibrosis reported in the literature.  

      b. Scid mice were used in the CCl4 studies to test whether a stronger response could be observed in the absence of a potential anti-drug antibodies response. While a modest reduction in fibrosis was observed in both B6 and scid mice following the SZN-043 treatment, the effect size did not seem affected by the mouse strain. 

      Response to Comments from reviewer #2

      Many thanks for appreciating that the use of multiple disease models to identify SZN-043 as a potential novel drug for liver regeneration.

      (1) The importance of restoring liver regeneration capacity to reduce the need for liver transplantation had been emphasized in the introduction.

      (2) There is continuous damage to the mouse hepatocytes in the FRG mice, due to the Fah mutation. They undergo repair mechanisms favoring the proliferation of human hepatocytes during the production period. Injury models that affect the human hepatocytes population have been developed in these mice. However, the primary goal of this study was to confirm that SZN043 was efficacious in inducing human hepatocytes proliferation, a feature difficult to reproduce in primary hepatocyte cultures. Given the artefactual nature of the chimeric liver in FRG mice and the high cost of these mice, further studies were not judged to be necessary.

      (3) Corrected

      (4) A figure including DAPI staining has now been included in supplemental Figure S2.

      (5) Clarification that the 8 weeks alcohol feeding used in our study design is a modification of the NIAAA model. While some ASGR1 has been reported on the surface of macrophages, additional data from MOA studies strongly suggest that the effect of SZN-043 is mediated via a hepatocytespecific mechanism (submitted manuscript).

      (6) The reviewer inquired about the potential role of macrophages in promoting an antiinflammatory state in response to SZN-043. While a direct effect is unlikely, a potential effect of macrophages in response to SZN-043 is plausible. Wnt activation is known to induce the secretion of hepatokines, such as LECT2, which in turn can influence macrophage activity. This possibility is discussed in the discussion section.

      (7) The potential off-target effects of SZN-043 such as stellate cell activation is discussed in the discussion section.

      (8) The discussion of the limitations of current models has been included in the discussion section of the manuscript.

      (9) We have now included a discussion of prior RSPO-based therapies, such as OMP-131R10. We explain why the hepatocyte-targeting of RSPO activity minimizes undesired effects.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Reviewer #1 (Public review):

      Summary:

      The work from this paper successfully mapped transcriptional landscape and identified EA-responsive cell types (endothelial, microglia). Data suggest EA modulates BBB via immune pathways and cell communication. However, claims of "BBB opening" are not directly proven (no permeability data).

      (1) No in vivo/in vitro assays confirm BBB permeability changes (e.g., Evans blue leakage, TEER).

      (2) Only male rats were used, ignoring sex-specific BBB differences.

      (3) Pericytes and neurons, critical for the BBB, were not captured, likely due to dissociation artifacts.

      (4) Protein-level validation (Western blot, IHC) absent for key genes (e.g., LY6E, HSP90).

      (5) Fixed stimulation protocol (2/100 Hz, 40 min); no dose-response or temporal analysis.

      We sincerely apologize for the oversight regarding the description of changes in blood-brain barrier permeability. In fact, our team conducted a series of preliminary studies that verified this aspect, and we hace provided a more detailed introduction in the introduction section, in lines 60-71 of the manuscript.

      We are very grateful to the reviewers for pointing out the important and meaningful issue of "gender-specific BBB differences." We will make this a focal point in our future research.

      As for pericytes and neurons, we acknowledge their importance in the function of the blood-brain barrier. We acknowledge the importance of pericytes and neurons in the blood-brain barrier. However, neurons are absent because our sample processing method involves dissociation. During the dissociation procedure, neuronal axons, which are relatively long, are filtered out during the frequent cell suspension steps and cannot enter the downstream microfluidic system for analysis, so they are not present in our data. Since this experiment is primarily focused on non-neuronal cells, we did not choose to use nucleus extraction for sample processing. As for pericytes, we believe they are not captured because their proportion in our samples is extremely low, which is why they are not present in the data. Further research may require single-nucleus transcriptomics or the separate isolation of these two cell types for study. Of course, in our current mechanistic studies, we are also fully considering the important roles these two cell types play in BBB function.

      In addition, to validate the results at the protein level, we have recently conducted some experiments. However, as several proteins are currently at a critical stage of further experimental validation, it is not appropriate to present them in the manuscript at this time. Instead, we have uploaded the relevant data as an appendix for your review. This includes a figure of several protein markers we examined, as well as a table of the antibodies used.

      This section is also further elaborated in the introduction and its references.

      Reviewer #2 (Public review):

      Summary:

      This study uses single-cell RNA sequencing to explore how electroacupuncture (EA) stimulation alters the brain's cellular and molecular landscape after blood-brain barrier (BBB) opening. The authors aim to identify changes in gene expression and signaling pathways across brain cell types in response to EA stimulation using single-cell RNA sequencing. This direction holds promise for understanding the consequences of noninvasive methods of BBB opening for therapeutic drug delivery across the BBB.

      (1) The work falls short in its current form. The experimental design lacks a clear justification, and readers are not provided with sufficient background information on the extent, timing, or regional specificity of BBB opening in this EA model. These details, established in prior work, are critical to understanding the rationale behind the current transcriptomic analyses.

      (2) Further, the results are often presented with minimal context or interpretation. There is no model of intercellular or molecular coordination to explain the BBB-opening process, despite the stated goal of identifying such mechanisms. The statement that EA induces a "unique frontal cortex-specific transcriptome signature" is not supported, as no data from other brain regions are presented. Biological interpretation is at times unclear or inaccurate - for instance, attributing astrocyte migration effects to endothelial cell clusters or suggesting microglial tight junction changes without connecting them meaningfully to endothelial function.

      (3) The study does include analyses of receptor-ligand signaling and cell-cell communication, which could be among its most biologically rich outputs. However, these are relegated to supplementary material and not shown in the leading figures. This choice limits the utility of the manuscript as a hypothesis-generating resource.

      (4) Overall, while the dataset may be of interest to BBB researchers and those developing technologies for drug delivery across the BBB, the manuscript in its current form does not yet fulfill its interpretive goals. A more integrated and biologically grounded analysis would be beneficial.

      This section is also further elaborated in the introduction and its references.

      Our current study is actually based on previous findings that electroacupuncture can open the BBB, with a more pronounced effect observed in the frontal lobe (this aspect should be further described in the research background). Building on this foundation, our aim is to delineate the potential biological mechanisms involved. Therefore, we selected frontal lobe tissue as our primary choice for sequencing and have not yet investigated differences across other brain regions, although this may become a focus of future research. Additionally, we recognize that the mechanism underlying BBB opening is complex, and at present, we cannot determine whether it is driven by a single direct factor or by coordinated actions between cells or molecules. As such, our results are presented only briefly for now, and we will carefully consider whether to supplement our findings by incorporating insights from other studies.

      Considering the overall data layout and the length of the article, we ultimately decided not to make any changes to the presentation of the article's data. The images included in the supplementary materials are also thoroughly described and referenced in the manuscript, allowing readers to selectively view any data they are interested in.

      Indeed, our current dataset and analysis tend to present objective data results. We are also conducting a series of validations that may be related to the biology of the blood-brain barrier, and we look forward to sharing and discussing any future research findings with you and everyone.

      Reviewer #1 (Recommendations for the authors):

      (1) Figures 3-7: Label treatment groups (CON vs. EA) consistently in legends.

      (2) Methods: Specify rat strain (Sprague-Dawley) in the abstract.

      (3) Clarify Limitations: Explicitly state that BBB opening is inferred, not proven.

      This section has been revised at lines 743-733, 748, 949, 754-755, and 759-760 of the manuscript.

      Revised at line 31 of the manuscript.

      Thank you for your feedback. The background information on the open evidence of BBB has been added to the introduction.

      Reviewer #2 (Recommendations for the authors):

      (1) Abstract and Introduction

      • Include specific key findings in the abstract to improve clarity and reader engagement.

      • Expand the introduction to situate this work in the context of other BBB-opening methods (e.g., ultrasound) and the known consequences of BBB disruption.

      • Clarify the rationale for choosing electroacupuncture.

      • Include information (perhaps summarized from previous studies) about the extent, timeline, and functional assessment of BBB opening in this model to help justify the single-cell RNA-seq design.

      (2) Experimental Rationale and Context

      • Reiterate experimental design and rationale in each results section, rather than relying exclusively on the Methods section.

      • Specify the time point of tissue collection relative to the EA intervention.

      • Describe the anatomical sites of acupuncture stimulation and their physiological relevance.

      (3) Data Presentation

      • Replace the human brain cartoon in Figure 1 with an anatomically appropriate rat brain schematic.

      • Reevaluate which data are presented in the main versus supplementary figures. Highlight biologically meaningful results, such as cell-cell communication and ligand-receptor interactions, in the main figures rather than supplementary data.

      (4) Interpretation and Modeling

      • More carefully link transcriptional changes (e.g., Wnt signaling in microglia) to biologically plausible mechanisms of BBB regulation-e.g., microglial signaling to endothelial cells.

      • Clarify whether the presence of granulocytes and T cells might result from a lack of perfusion prior to brain dissection.

      • Consider proposing a model (even speculative) of how EA leads to BBB opening based on observed transcriptional changes.

      First, for the sake of brevity in the abstract, we did not present specific results in this section. Second, since BBB opening via EA is a unique strategy, our previous studies have examined the opening time window and the recovery of the BBB after EA intervention (as mentioned in the introduction). We believe its characteristics differ from those of ultrasound-induced BBB opening and BBB disruption, so we did not conduct comparative discussions, but objectively presented our research findings. In further functional validation experiments, we may consider integrating other opening strategies in our studies. Additionally, the choice of electroacupuncture was based on our previous series of studies, which have already been outlined in the research background. Finally, we did indeed determine the experimental design of this study based on prior research, as described in the background section of the introduction.

      We decided not to make changes to this section in the manuscript after careful consideration. The setup of electroacupuncture intervention and controls has been thoroughly discussed in our previous studies (as referenced in the introduction), so we have not repeated it in this manuscript. Overall, building on all our previous findings, this study focuses primarily on the potential mechanisms of EA intervention. The anatomical sites of acupuncture stimulation and their physiological relevance are another key area of our research, and we are currently conducting a series of related studies. We look forward to sharing these findings with you in the future.

      We have already changed the human brain diagram in Figure 1 to a rat brain diagram, and have replaced Figure 1 in the files with the revised version. However, considering the overall data layout and the length of the article, we ultimately decided not to make changes to the data presentation in the manuscript. The images in the supplementary materials are also thoroughly described and referenced in the manuscript, allowing readers to selectively view the data they are interested in.

      This section has provided us with excellent suggestions for further exploration, although no changes have been made to the manuscript at this time. In the future, we may conduct more detailed transcriptomic studies focusing on sex differences and different brain regions, which will allow for a more comprehensive analysis of the biological mechanisms involved in BBB regulation.

    1. Reviewer #3 (Public review):

      Summary:

      The authors generated knockout mice for Atad2, a conserved bromodomain-containing factor expressed during spermatogenesis. In Atad2 KO mice, HIRA, a chaperone for histone variant H3.3, was upregulated in round spermatids, accompanied by an apparent increase in H3.3 levels. Furthermore, the sequential incorporation and removal of TH2B and PRM1 during spermiogenesis were partially disrupted in the absence of ATAD2, possibly due to delayed histone removal. Despite these abnormalities, Atad2 KO male mice were able to produce offspring normally.

      Strengths:

      The manuscript addresses the biological role of ATAD2 in spermatogenesis using a knockout mouse model, providing a valuable in vivo framework to study chromatin regulation during male germ cell development. The observed redistribution of H3.3 in round spermatids is clearly presented and suggests a previously unappreciated role of ATAD2 in histone variant dynamics. The authors also document defects in the sequential incorporation and removal of TH2B and PRM1 during spermiogenesis, providing phenotypic insight into chromatin transitions in late spermatogenic stages. Overall, the study presents a solid foundation for further mechanistic investigation into ATAD2 function.

      Weaknesses:

      While the manuscript reports the gross phenotype of Atad2 KO mice, the findings remain largely superficial and do not convincingly demonstrate how ATAD2 deficiency affects chromatin dynamics. Moreover, the phenotype appears too mild to elucidate the functional significance of ATAD2 during spermatogenesis.

      (1) Figures 4-5: The analyses of differential gene expression and chromatin organization should be more comprehensive. First, Venn diagrams comparing the sets of significantly differentially expressed genes between this study and previous work should be shown for each developmental stage. Second, given the established role of H3.3 in MSCI, the effect of Atad2 knockout on sex chromosome gene expression should be analyzed. Third, integrated analysis of RNA-seq and ATAC-seq data is needed to evaluate how ATAD2 loss affects gene expression. Finally, H3.3 ChIP-seq should be performed to directly assess changes in H3.3 distribution following Atad2 knockout.

      (2) Figure 3: The altered distribution of H3.3 is compelling. This raises the possibility that histone marks associated with H3.3 may also be affected, although this has not been investigated. It would therefore be important to examine the distribution of histone modifications typically associated with H3.3. If any alterations are observed, ChIP-seq analyses should be performed to explore them further.

      (3) Figure 7: While the authors suggest that pre-PRM2 processing is impaired in Atad2 KO, no direct evidence is provided. It is essential to conduct acid-urea polyacrylamide gel electrophoresis (AU-PAGE) followed by western blotting, or a comparable experiment, to substantiate this claim.

      (4) HIRA and ATAD2: Does the upregulation of HIRA fully account for the phenotypes observed in Atad2 KO? If so, would overexpression of HIRA alone be sufficient to phenocopy the Atad2 KO phenotype? Alternatively, would partial reduction of HIRA (e.g., through heterozygous deletion) in the Atad2 KO background be sufficient to rescue the phenotype?

      (5) The mechanism by which ATAD2 regulates HIRA turnover on chromatin and the deposition of H3.3 remains unclear from the manuscript and warrants further investigation.

    2. Author response:

      Reviewer #1 (Public review): 

      Summary: 

      The authors analyzed the expression of ATAD2 protein in post-meiotic stages and characterized the localization of various testis-specific proteins in the testis of the Atad2 knockout (KO). By cytological analysis as well as the ATAC sequencing, the study showed that increased levels of HIRA histone chaperone, accumulation of histone H3.3 on post-meiotic nuclei, defective chromatin accessibility and also delayed deposition of protamines. Sperm from the Atad2 KO mice reduces the success of in vitro fertilization. The work was performed well, and most of the results are convincing. However, this manuscript does not suggest a molecular mechanism for how ATAD2 promotes the formation of testis-specific chromatin. 

      We would like to take this opportunity to highlight that the present study builds on our previously published work, which examined the function of ATAD2 in both yeast S. pombe and mouse embryonic stem (ES) cells (Wang et al., 2021). In yeast, using genetic analysis we showed that inactivation of HIRA rescues defective cell growth caused by the absence of ATAD2. This rescue could also be achieved by reducing histone dosage, indicating that the toxicity depends on histone over-dosage, and that HIRA toxicity, in the absence of ATAD2, is linked to this imbalance.

      Furthermore, HIRA ChIP-seq performed in mouse ES cells revealed increased nucleosome-bound HIRA, particularly around transcription start sites (TSS) of active genes, along with the appearance of HIRA-bound nucleosomes within normally nucleosome-free regions (NFRs). These findings pointed to ATAD2 as a major factor responsible for unloading HIRA from nucleosomes. This unloading function may also apply to other histone chaperones, such as FACT (see Wang et al., 2021, Fig. 4C).

      In the present study, our investigations converge on the same ATAD2 function in the context of a physiologically integrated mammalian system—spermatogenesis. Indeed, in the absence of ATAD2, we observed H3.3 accumulation and enhanced H3.3-mediated gene expression. Consistent with this functional model of ATAD2— unloading chaperones from histone- and non-histone-bound chromatin—we also observed defects in histone-toprotamine replacement.

      Together, the results presented here and in Wang et al. (2021) reveal an underappreciated regulatory layer of histone chaperone activity. Previously, histone chaperones were primarily understood as factors that load histones. Our findings demonstrate that we must also consider a previously unrecognized regulatory mechanism that controls assembled histone-bound chaperones. This key point was clearly captured and emphasized by Reviewer #2 (see below).

      Strengths: 

      The paper describes the role of ATAD2 AAA+ ATPase in the proper localization of sperm-specific chromatin proteins such as protamine, suggesting the importance of the DNA replication-independent histone exchanges with the HIRA-histone H3.3 axis. 

      Weaknesses: 

      (1) Some results lack quantification. 

      We will consider all the data and add appropriate quantifications where necessary.

      (2) The work was performed well, and most of the results are convincing. However, this manuscript does not suggest a molecular mechanism for how ATAD2 promotes the formation of testis-specific chromatin. 

      Please see our comments above.

      Reviewer #2 (Public review): 

      Summary: 

      This manuscript by Liakopoulou et al. presents a comprehensive investigation into the role of ATAD2 in regulating chromatin dynamics during spermatogenesis. The authors elegantly demonstrate that ATAD2, via its control of histone chaperone HIRA turnover, ensures proper H3.3 localization, chromatin accessibility, and histone-toprotamine transition in post-meiotic male germ cells. Using a new well-characterized Atad2 KO mouse model, they show that ATAD2 deficiency disrupts HIRA dynamics, leading to aberrant H3.3 deposition, impaired transcriptional regulation, delayed protamine assembly, and defective sperm genome compaction. The study bridges ATAD2's conserved functions in embryonic stem cells and cancer to spermatogenesis, revealing a novel layer of epigenetic regulation critical for male fertility. 

      Strengths: 

      The MS first demonstration of ATAD2's essential role in spermatogenesis, linking its expression in haploid spermatids to histone chaperone regulation by connecting ATAD2-dependent chromatin dynamics to gene accessibility (ATAC-seq), H3.3-mediated transcription, and histone eviction. Interestingly and surprisingly, sperm chromatin defects in Atad2 KO mice impair only in vitro fertilization but not natural fertility, suggesting unknown compensatory mechanisms in vivo. 

      Weaknesses:

      The MS is robust and there are not big weaknesses 

      Reviewer #3 (Public review): 

      Summary: 

      The authors generated knockout mice for Atad2, a conserved bromodomain-containing factor expressed during spermatogenesis. In Atad2 KO mice, HIRA, a chaperone for histone variant H3.3, was upregulated in round spermatids, accompanied by an apparent increase in H3.3 levels. Furthermore, the sequential incorporation and removal of TH2B and PRM1 during spermiogenesis were partially disrupted in the absence of ATAD2, possibly due to delayed histone removal. Despite these abnormalities, Atad2 KO male mice were able to produce offspring normally. 

      Strengths: 

      The manuscript addresses the biological role of ATAD2 in spermatogenesis using a knockout mouse model, providing a valuable in vivo framework to study chromatin regulation during male germ cell development. The observed redistribution of H3.3 in round spermatids is clearly presented and suggests a previously unappreciated role of ATAD2 in histone variant dynamics. The authors also document defects in the sequential incorporation and removal of TH2B and PRM1 during spermiogenesis, providing phenotypic insight into chromatin transitions in late spermatogenic stages. Overall, the study presents a solid foundation for further mechanistic investigation into ATAD2 function. 

      Weaknesses:

      While the manuscript reports the gross phenotype of Atad2 KO mice, the findings remain largely superficial and do not convincingly demonstrate how ATAD2 deficiency affects chromatin dynamics. Moreover, the phenotype appears too mild to elucidate the functional significance of ATAD2 during spermatogenesis. 

      We respectfully disagree with the statement that our findings are largely superficial. Based on our investigations of this factor over the years, it has become evident that ATAD2 functions as an auxiliary factor that facilitates mechanisms controlling chromatin dynamics (see, for example, Morozumi et al., 2015). These mechanisms can still occur in the absence of ATAD2, but with reduced efficiency, which explains the mild phenotype we observed.

      This function, while not essential, is nonetheless an integral part of the cell’s molecular biology and should be studied and brought to the attention of the broader biological community, just as we study essential factors. Unfortunately, the field has tended to focus primarily on core functional actors, often overlooking auxiliary factors. As a result, our decade-long investigations into the subtle yet important roles of ATAD2 have repeatedly been met with skepticism regarding its functional significance, which has in turn influenced editorial decisions.

      We chose eLife as the venue for this work specifically to avoid such editorial barriers and to emphasize that facilitators of essential functions do exist. They deserve to be investigated, and the underlying molecular regulatory mechanisms must be understood.

      (1) Figures 4-5: The analyses of differential gene expression and chromatin organization should be more comprehensive. First, Venn diagrams comparing the sets of significantly differentially expressed genes between this study and previous work should be shown for each developmental stage. Second, given the established role of H3.3 in MSCI, the effect of Atad2 knockout on sex chromosome gene expression should be analyzed. Third, integrated analysis of RNA-seq and ATAC-seq data is needed to evaluate how ATAD2 loss affects gene expression. Finally, H3.3 ChIP-seq should be performed to directly assess changes in H3.3 distribution following Atad2 knockout.  

      (1) In the revised version, we will include Venn diagrams to illustrate the overlap in significantly differentially expressed genes between this study and previous work. However, we believe that the GSEAs presented here provide stronger evidence, as they indicate the statistical significance of this overlap (p-values). In our case, we observed p-value < 0.01 (**) and p < 0.001 (***).

      (2) Sex chromosome gene expression was analyzed and is presented in Fig. 5C.

      (3) The effect of ATAD2 loss on gene expression is shown in Fig. 4A, B, and C as histograms, with statistical significance indicated in the middle panels.

      (4) Although mapping H3.3 incorporation across the genome in wild-type and Atad2 KO cells would have been informative, the available anti-H3.3 antibody did not work for ChIP-seq, at least in our hands. The authors of Fontaine et al., 2022, who studied H3.3 during spermatogenesis in mice, must have encountered the same problem, since they tagged the endogenous H3.3 gene to perform their ChIP experiments.

      (2) Figure 3: The altered distribution of H3.3 is compelling. This raises the possibility that histone marks associated with H3.3 may also be affected, although this has not been investigated. It would therefore be important to examine the distribution of histone modifications typically associated with H3.3. If any alterations are observed, ChIP-seq analyses should be performed to explore them further.  

      Based on our understanding of ATAD2’s function—specifically its role in releasing chromatin-bound HIRA—in the absence of ATAD2 the residence time of both HIRA and H3.3 on chromatin increases. This results in the detection of H3.3 not only on sex chromosomes but across the genome. Our data provide clear evidence of this phenomenon. The reviewer is correct in suggesting that the accumulated H3.3 would carry H3.3-associated histone PTMs; however, we are unsure what additional insights could be gained by further demonstrating this point.

      (3) Figure 7: While the authors suggest that pre-PRM2 processing is impaired in Atad2 KO, no direct evidence is provided. It is essential to conduct acid-urea polyacrylamide gel electrophoresis (AU-PAGE) followed by western blotting, or a comparable experiment, to substantiate this claim. 

      Figure 7 does not suggest that pre-PRM2 processing is affected in Atad2 KO; rather, this figure—particularly Fig. 7B—specifically demonstrates that pre-PRM2 processing is impaired, as shown using an antibody that recognizes the processed portion of pre-PRM2. ELISA was used to provide a more quantitative assessment; however, in the revised manuscript we will also include a western blot image.

      (4) HIRA and ATAD2: Does the upregulation of HIRA fully account for the phenotypes observed in Atad2 KO? If so, would overexpression of HIRA alone be sufficient to phenocopy the Atad2 KO phenotype? Alternatively, would partial reduction of HIRA (e.g., through heterozygous deletion) in the Atad2 KO background be sufficient to rescue the phenotype? 

      These are interesting experiments that require the creation of appropriate mouse models, which are not currently available.

      (5)The mechanism by which ATAD2 regulates HIRA turnover on chromatin and the deposition of H3.3 remains unclear from the manuscript and warrants further investigation. 

      The Reviewer is absolutely correct. In addition to the points addressed in response to Reviewer #1’s general comments (see above), it would indeed have been very interesting to test the segregase activity of ATAD2 (likely driven by its AAA ATPase activity) through in vitro experiments using the Xenopus egg extract system described by Tagami et al., 2004. This system can be applied both in the presence and absence (via immunodepletion) of ATAD2 and would also allow the use of ATAD2 mutants, particularly those with inactive AAA ATPase or bromodomains. However, such experiments go well beyond the scope of this study, which focuses on the role of ATAD2 in chromatin dynamics during spermatogenesis

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      Fontaine E, Papin C, Martinez G, Le Gras S, Nahed RA, Héry P, Buchou T, Ouararhni K, Favier B, Gautier T, Sabir JSM, Gerard M, Bednar J, Arnoult C, Dimitrov S, Hamiche A. Dual role of histone variant H3.3B in spermatogenesis: positive regulation of piRNA transcription and implication in X-chromosome inactivation. Nucleic Acids Res. 2022 Jul 22;50(13):7350-7366. doi: 10.1093/nar/gkac541. PMID: 35766398; PMCID: PMC9303386.

      Tagami H, Ray-Gallet D, Almouzni G, Nakatani Y. Histone H3.1 and H3.3 complexes mediate nucleosome assembly pathways dependent or independent of DNA synthesis. Cell. 2004 Jan 9;116(1):51-61. doi:10.1016/s0092-8674(03)01064-x. PMID: 14718166.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Reviewer #1 (Public review):

      Summary:

      Desveaux et al. describe human mAbs targeting protein from the Pseudomonas aeruginosa T3SS, discovered by employing single cell B cell sorting from cystic fibrosis patients. The mAbs were directed at the proteins PscF and PcrV. They particularly focused on two mAbs binding the T3SS with the potential of blocking activity. The supplemented biochemical analysis was crystal structures of P3D6 Fab complex. They also compared the blocking activity with mAbs that were described in previous studies, using an assay that evaluated the toxin injection. They conducted mechanistic structure analysis and found that these mAbs might act through different mechanisms by preventing PcrV oligomerization and disrupting PcrVs scaffolding function.

      Strengths:

      The antibiotic resistance crisis requires the development of new solutions to treat infections caused by MDR bacteria. The development of antibacterial mAbs holds great potential. In that context, this report is important as it paves the way for the development of additional mAbs targeting various pathogens that harbor the T3SS. In this report, the authors present a comparative study of their discovered mAbs vs. a commercial mAb currently in clinical testing resulting in valuable data with applicative implications. The authors investigated the mechanism of action of the mAbs using advanced methods and assays for the characterization of antibody and antigen interaction, underlining the effort to determine the discovered mAbs suitability for downstream application.

      Weaknesses:

      Although the information presented in this manuscript is important, previous reports regarding other T3SS structures complexed with antibodies, reduce the novelty of this report. Nevertheless, we provide several comments that may help to improve the report. The structural analysis of the presented mAbs is incomplete and unfortunately, the authors did not address any developability assessment. With such vital information missing, it is unclear if the proposed antibodies are suited for diagnostic or therapeutic usage. This vastly reduces the importance of the possibly great potential of the authors' findings. Moreover, the structural information does not include the interacting regions on the mAb which may impede the optimization of the mAb if it is required to improve its affinity.

      As described in the manuscript (Fig. 6), our mAbs are markedly less effective in every in vitro T3SS inhibition assay than the mAbs recently described by Simonis et al. They are therefore very unlikely to outperform these mAbs in in vivo animal models of P. aeruginosa infection. Considering the high cost of animal experiments and ethical concerns-and in accordance with the Reduction principal of the 3Rs guidelines-we chose not to pursue in vivo experiments. Instead, we focused on leveraging the new isolated mAbs to investigate the mechanisms of action and structural features of anti-PcrV mAbs.

      Following the reviewer's suggestion, we have now added mAb interaction features into the structural data presented in the manuscript. However, based on the efficiency data, the structural analysis and the mechanistic insights presented, we do not consider further therapeutic use and optimization of our mAbs to be warranted.

      Reviewer #2 (Public review):

      Summary:

      Desveaux et al. performed Elisa and translocation assays to identify among 34 cystic fibrosis patients which ones produced antibodies against P. aeruginosa type three secretion system (T3SS). The authors were especially interested in antibodies against PcrV and PcsF, two key components of the T3SS. The authors leveraged their binding assays and flow cytometry to isolate individual B cells from the two most promising sera, and then obtained monoclonal antibodies for the proteins of interest. Among the tested monoclonal antibodies, P3D6 and P5B3 emerged as the best candidates due to their inhibitory effect on the ExoS-Bla translocation marker (with 24% and 94% inhibition, respectively). The authors then showed that P5B3 binds to the five most common variants of PcrV, while P3D6 seems to recognize only one variant. Furthermore, the authors showed that P3D6 inhibits translocon formation, measured as cell death of J774 macrophages. To get insights into the P3D6PcrV interaction, the authors defined the crystal structure of the P3D6-PcrV complex. Finally, the authors compared their new antibodies with two previous ones (i.e., MEDI3902 and 30-B8).

      Strengths:

      (1) The article is well written.

      (2) The authors used complementary assays to evaluate the protective effect of candidate monoclonal antibodies.

      (3) The authors offered crystal structure with insights into the P3D6 antibody-T3SS interaction (e.g., interactions with monomer vs pentamers).

      (4) The authors put their results in context by comparing their antibodies with respect to previous ones.

      Weaknesses:

      The authors used a similar workflow to the one previously reported in Simonis et al. 2023 (antibodies from cystic fibrosis patients that included B cell isolation, antibody-PcrV interaction modeling, etc.) but the authors do not clearly explain how their work and findings differentiate from previous work.   

      We employed a similar mAb isolation pipeline to that used by Simonis et al., beginning with the screening of a cohort of cystic fibrosis patients chronically infected with P. aeruginosa. As in Simonis et al., we isolated specific B cells using a recombinant PcrV bait, followed by single-cell PCR amplification of immunoglobulin genes. The main differences in methodology between the two studies are as follows: i) the use of individuals from different cohorts, and therefore having different Ab repertoires; ii) the nature of the screening assays, although in both cases the screening was focused on the inhibition of T3SS function; iii) the PcrV labeling strategy, with Simonis et al. employing direct labeling, whereas we used a biotinylated tag combined with streptavidin;

      The number of specific mAbs obtained and produced was higher in Simonis et al. (47 versus 9 in our study). They sorted B cells from three individuals compared to two in our work and possibly started with a larger amount of PBMCs per donor, which may account for the higher number of specific B cells and mAbs isolated. Considering that the strategies were overall very similar, the greater number of mAbs isolated in Simonis et al. likely explains, to a large extent, why they identified mAbs targeting different epitopes compared to ours, including highly potent mAbs that we did not recover. 

      Our modeling study, unlike that of Simonis et al., which relied on an AlphaFold prediction of the multimeric structure of P. aeruginosa PcrV, was based on the experimentally determined structure of the homologous Salmonella SipD pentamer, as described in the manuscript. Furthermore, we compared our mAb P3D6 not only with 30-B8 from Simonis et al., but also with MEDI3902. Finally, in contrast to the approach of Simonis et al., we used functional assays to investigate the differences in mechanisms of action among these mAbs, which target three distinct epitopes.

      (2) Although new antibodies against P. aeruginosa T3SS expand the potential space of antibodybased therapies, it is unclear if P3D6 or P5B3 are better than previous antibodies. In fact, in the discussion section authors suggested that the 30-B8 antibody seems to be the most effective of the tested antibodies.  

      As explained above and shown in the Results section (Figure 6), the 30-B8 mAb is markedly more effective at inhibiting T3SS activity in both in vitro assays used.

      (3) The authors should explain better which of the two antibodies they have discovered would be better suited for follow-up studies. It is confusing that the authors focused the last sections of the manuscript on P3D6 despite P3D6 having a much lower ExoS-Bla inhibition effect than P5B3 and the limitation in the PcrV variant that P3D6 seems to recognize. A better description of this comparison and the criteria to select among candidate antibodies would help readers identify the main messages of the paper. 

      The P3D6 mAb shows stronger inhibitory activity than P5B3 in the two assays used, as shown in Supplementary Figure 1. An error in the table in Figure 2B was corrected and this table now reflects the results presented in Supplementary Figure 1. 

      The final sections of the manuscript focus on P3D6, which is more potent than P5B3, and for which we successfully determined a co-crystal structure with PcrV*. All parallel attempts to obtain a structure of P5B3 in complex with PcrV* failed. The P3D6-PcrV* structure was used to analyze epitope recognition and mechanisms of action in comparison to previously described mAbs. As previously mentioned, we do not consider further studies aimed at therapeutic development and optimization of our mAbs to be justified given the current data. Therefore, we believe that the main message of the paper is adequately captured in the title.

      (4) This work could strongly benefit from two additional experiments:

      (a) In vivo experiments: experiments in animal models could offer a more comprehensive picture of the potential of the identified monoclonal antibodies. Additionally, this could help to answer a naïve question: why do the patients that have the antibodies still have chronic P. aeruginosa infections? 

      As explained above, the mAbs we isolated are significantly less potent than those described by Simonis et al., and are therefore unlikely to outperform the best anti-PcrV candidates in vivo. In light of the data, and considering ethical concerns related to animal use in research and budgetary constraints, we decided not to proceed with in vivo experiments.

      There are a number of reasons that may explain why patients with anti-PcrV Abs blocking the T3SS can still be chronically infected with Pa. First these Abs may be at limiting concentration, particularly in sites where Pa replicates, and thus unable to clear infection. in addition, it has been described that the T3SS is downregulated in chronic infection in cystic fibrosis patients. This suggests that a therapeutic intervention with T3SS inhibiting Abs may be more efficient if done early in cystic fibrosis patients to prevent colonization when Pa possesses an active T3SS. Finally, T3SS is not the only virulence mechanism employed by P. aeruginosa during infection. Indeed, multiple protein adhesins and polysaccharides are important factors facilitating the formation of bacterial biofilms that are crucial for establishing chronic persistent infection. In this regard, a combination of Abs targeting different factors on the P. aeruginosa surface may be needed to treat chronic infections.  

      (b) Multi-antibody T3SS assays (i.e., a combination of two or more monoclonal antibodies evaluated with the same assays used for characterization of single ones). This could explore the synergistic effects of combinatorial therapies that could address some of the limitations of individual antibodies. 

      Given the high potency of the Simonis mAbs and the mechanisms of action highlighted by our analysis, it is unlikely that our mAbs would synergize with those described by Simonis. Additionally, since our two mAbs cross-compete for binding, synergy between them is also improbable.

      Reviewer #1 (Recommendations for the authors):

      Line 166: How was the serum-IgG purified? (e.g., protein A, protein G). 

      Protein A purification was used, as now mentioned in the manuscript. Purified Igs were thus predominantly IgG1, IgG2 and IgG4, as indicated.

      (2) Line 196: When mentioning affinities, it is preferable to present in molar units. 

      To facilitate comparisons, Ab concentrations were presented in µg/mL as in Simonis et al.

      (3) Line 206: The author states that P3D6 displays significantly reduced ExoS-Bla injection (Figure 2B), but according to the presented table, ExoS-Bla inhibition was higher for P5B3. Additionally, when using "significantly", what was the statistical test that was used to evaluate the significance? Please clarify.

      We thank the reviewer for pointing out this inconsistency. Indeed, the names of P3D6 and P5B3 were exchanged when building the table related to Figure 2B. The corrected version of this figure is now presented in the new version of the manuscript. An ANOVA was performed to evaluate the significance of the observed difference (adjusted p-values < 0.001) and it is now mentioned in the figure caption.  

      (4) Line 215: "P3B3" typo.

      This was corrected.

      (5) Figure 3B: Could the author explain the higher level of ExoS-Bla injection when using VRCO1 antibody compared to no antibody.  

      A slightly higher level of the median is observed in the case of three variants out of five. However, this difference is not statistically significant (p-value > 0.05).

      (6) Supplement Figure 1: the presented grey area is not clear (is it the 95%CI?) and how was the IC50 calculated? With what model was it projected? Are the values for IC50 beyond the 100µg/mL mark a projection? It seems that projecting such greater values (such as the IC50 of over 400µg/mL for variant 5) is prone to high error probability.

      The grey area represents the 95% confidence interval (95% CI) and it is now mentioned in the figure caption. The IC50 and 95% CI were both inferred by the dose-response drc R package based on a three-parameters log-logistic model and it is now explained in the Materials & Methods section. The p-values for IC50 beyond the 100µg/mL were below 0.05 but we agree that such extrapolation should be considered with precaution (see below our response to comment number 7).

      (7) Line 227: The author describes that P5B3 has similar IC50 values towards variants 1-4, but the  IC50 towards variant 5 is substantially higher with 400µg/mL, albeit the only difference between variant 4 and 5 is the switch position 225 Arg -> Lys which are very similar in their properties. Please provide an explanation. 

      As explained in our response to comment number 6, we agree that the comparison of IC50 that are estimated to be close or higher than the highest experimental concentration is somehow speculative. Indeed, we performed further statistical analysis that showed no significant difference between the IC50 toward the five PcrV variants of mAb P5B3. In contrast, the difference between the IC50 of mAbs P5B3 and P3D6 toward variant 1 is statistically significant. This is now explained in the manuscript.

      (8) Line 233: Pore assembly: It is not clear how the data was normalized. The authors mention the methods normalization against the wildtype strain in the absence of antibodies, but did not elaborate clearly if the mutant strain has the same base cytotoxicity as the wild type. It would be helpful to show the level of cytotoxicity of the wild type compared to the mutant in the absence of antibodies to understand the baseline of cytotoxicity of both strains.  

      In these experiments we did not use the wild-type strain. As explained, the only strain that allows the measurement of pore formation by translocators PopB/PopD is the one lacking all effectors. All the experiments were done with this strain, and all the measurements were normalized accordingly. 

      (9) Figure 4: The explanation is redundant as it is clearly stated in the results. It would be better for the caption to describe the figure and leave interpretation to the results section. Overall, this comment is relevant to all figure captions, as it will reduce redundancy. My suggestion is to keep the figure caption as a road map to understand what is shown in the figure. For example, the Figure 4 caption should include that the concentration is presented in logarithmic scale, what is the dashed line, what is the grey area (what interval does it represent?), what each circle represents, and what is the regression model used? 

      Figure captions have been improved as suggested. 

      (10) Line 432: The authors apparently misquoted the original article describing the chimeric form PcrV* by describing the fusion of amino acids 1-17 and 136-249. I quote the original article by Tabor et al. "[...] we generated a truncated PcrV fragment (PcrVfrag) comprising PcrV amino acids 1-17 fused to amino acids 149-236 [...]". Additionally, how does the absence of amino acid 21 in the variant affect the conclusion? 

      Our construct was inspired by the one described in Tabor et al. but was not identical. We have therefore replaced "was constructed based on a construct by Tabor et al." for "whose design was inspired by the construct described in Tabor et al."

      Amino acid 21 is only absent in the construct used for crystallization experiments; all other experiments looking at Ab activity were performed with bacteria bearing full-length PcrV. The difference in P3D6 activity between variants V1 and V2-appears to be explained by the nature of the residue at position 225, according to the structural data, as explained now in more detail in the manuscript. Accordingly, the difference in efficiency of P3D6 against the V1 and V2  variants is explained by the residue at position 225, as both variants have the same residue at position 21. However, while the nature of the residue at position 225 appears to explain the absence of efficiency of the Ab for the variants studied, an impact of residue 21 could not be totally ruled out in putative variants with a Ser at 225 but different amino acids at 21.

      (11) Line 569: Missing word - ESRF stands for European Synchrotron Radiation Facility. 

      This has been corrected.

      (12) Line 268-269 (Figure 5A): The description of the alpha helices in relation to the figure is incomplete. Helices 2,3 and 5 are not indicated. 

      Indeed, since the structure is well-known and in the interest of visibility and simplicity, we only included the most relevant secondary structure features.

      (13) Line 271-272: It would be good to elaborate on the exact binding platform between LC and HC of the Fab and the residues on the PcrV side. For example, the author could apply the structure to PDBePISA (EMBL-EBI) which will provide details about the interface between the PcrV and the antibody. It is very interesting to learn what regions of the antibody are in charge of the binding, such as: is the H-CDR3 the major contributor of the binding or are other CDRs more involved? Additionally, in line 275 they state that the substitution of Ser 225 with Arg or Lys is consistent with the P3D6 insufficient binding. What contributed to this result on the antibodies side? 

      In order to address this question, we are now providing a LigPlot figure (supplementary Figure 3) in which specific interactions between PcrV* and the Fab are shown.

      (14) Line 291: It is unclear from what data the authors concluded that anti-PscF targets 3 distinct regions of PscF. 

      The data are shown in Supplementary Table 2, as mentioned in the manuscript. We have now modified the order of the anti-PcrV mAbs in the table to better illustrate the three identified epitope clusters (Sup table 2). Similarly, the anti-PscF mAbs appear to group into three clusters as P3G9 and P5E10 only compete with themselves, while mabs P3D6 and P5B3 compete with themselves and each other.

      (15) Line 315: It is preferable to introduce results in the results section instead of the discussion. 

      While preparing the manuscript, we initially included these results as a separate paragraph in the Results section, but ultimately chose the current format to improve flow and avoid redundancy.

      (16) Supplement Figure 2: What was the regression model used to evaluate IC50, and what is presented in the graph? What is the dashed line (see comment for Figure 4 above)? 

      The regression is based on a three-parameters log-logistic model and the light-colors area correspond to the 95% IC. The dashed lines visually represents 100% of ExoS-Bla injection. These information are now mentioned in the figure caption.

      (17) Figure 6B: It would be better to show an additional rotation of the PcrV bound by Fab 30-B8 that corresponds to the same as the one represented with Fab MEDI3092. This would clear up the differences in binding regions. Same for Fab P3D6. 

      Figure 6 already depicts two orientations. Despite the fact that we agree that additional orientations could be of interest, we believe that this would add unnecessary complexity to the figure, and would prefer to maintain the figure as is, if possible.

      (18) Line 356-358: The author proposes an experiment to support the suggested mechanism of P3D6, it would follow up with a bio-chemical analysis showing the prevention of PcrV oligomerization in its presence. 

      We understand the reviewers’ comment regarding the potential use of biochemical approaches to test our hypothesis. However, this not currently feasible as we have been unable to achieve in vitro oligomerization of PcrV alone, possibly due to the absence of other T3SS components, such as the polymerized PscF needle.

      (19) Line 456: Missing details about how the ELISA was conducted including temperature, how the antigen was absorbed, plate type, etc. 

      Experimental details have been added.

      (20) Line 460: Missing substrate used for alkaline phosphatase. 

      The nature of the substrate was added to the methods.

    1. Toronto Climate chart (explanation) J F M A M J J A S O N D     65     0 −7     54     1 −6     53     5 −2     78     12 4     76     19 10     82     24 15     77     27 18     72     26 18     69     22 14     69     15 8     71     8 2     58     3 −3 █ Average max. and min. temperatures in °C █ Precipitation totals in mmSource: Environment Canada[131] showImperial conversion

      Bad: Low contrast in parts of the climate chart (pale colours and small labels). For people with low vision or colour-vision issues, pale colours + small text make reading hard. The chart needs stronger contrast and legible fonts.

  3. mathieubcd.github.io mathieubcd.github.io
    1. Another tool that is useful for teams is a gap analysis, which provides aformat to compare best practices with existing processes. This comparisonis then used, in conjunction with identified barriers to implementation, asa driver to move the organization to where it needs to be in terms of per-formance. Gap analysis can help an organization by informing the needsassessment process and helping to focus its goals. The steps in conductinggap analysis are:1. Identify what is currently happening in the organization.2. Define the best practice (aka, gold standard) or desired practice for theprocess/project.3. Clarify the gap or discrepancy between current reality and desired state.4. Determine objectives for the organization based on the identified gaps.Implementing a gap analysis requires gathering data related to the pro-cess/project to be studied. Examples of data to consider include: outcomesfrom literature review, customer data (e.g., hospital admissions), governmen-tal policies, and clinical care guidelines. A simple table can be constructed foreach process/project to assist in decision making (Table 4.3)

      At Ontario Health we use Gap Analysis quite often, one example is the Home First Resource Guide/toolkit. Our current state was a fragmented toolkit with outdated content from 2011. The desired state was a modern, equity-informed guide aligned with ALC Leading Practices and the Transitions Quality Standard. By laying the two side by side, we could see the gaps, missing caregiver engagement tools, outdated role definitions, and lack of standardized discharge planning templates. That gap analysis has been driving the work of our cross-regional planning teams.

    1. Note: This preprint has been reviewed by subject experts for Review Commons. Content has not been altered except for formatting.

      Learn more at Review Commons


      Referee #2

      Evidence, reproducibility and clarity

      Summary: The manuscript by Valdivieso-Rivera et al. investigated the role of a transcription factor, E4BP4, in brown fat functions. Using in vivo AAV gain-of-function studies, in vitro primary cultured brown adipocytes, and transcription regulation studies, authors identified that E4BP4 works together with PRDM16 to suppress Cers6 transcriptions and its derived ceramide C16:0 production. The resulted decreasing C16:0 prevents diet-induced mitochondrial fragmentation within brown adipocytes, thereby promoting brown fat functions. Overall, this study employed state-of-the-art methodologies and the collected evidence generally supported the conclusion. However, there are issues remaining to be addressed.

      Major Comments:

      1. The evidence of mitochondrial fragmentation is not convincing. In the reviewer's opinion, Figures 3E, 3G, 4F, and 5M demonstrated a decrease in mitochondrial quantity, but not fragmentation.
      2. Whether E4BP4-OE affects cold tolerance in mice is now shown.
      3. A key experiment is missing: does adding C16:0 block the mitochondrial benefits of E4BP4-OE?
      4. Whether PRDM16-OE mimics the effects of E4BP4 to induce p-Drp1 is not shown.

      Minor points:

      1. It is confusing whether the association shown in Figure 1C is a positive or an inverse association.
      2. Results from the PRDM16-OE model were mostly obtained in cultured brown adipocytes. It would be worthwhile to investigate whether in vivo knockdown of E4BP4 blunts the Cers6-suppressing effects of PRDM16-OE.

      Cross-commenting

      Reviewer #1's comments are all solid, and I agree with all of them.

      Significance

      Key strengths include state-of-the-art methodologies and detailed mechanistic studies. Key limitations include some unconvincing staining data, lack of key "rescue" experiments, and less novelty in molecular mechanisms (the ceramide-Drp1 pathway).

      Overall, this study uncovers a critical role of E4BP4 in maintaining brown adipocyte mitochondrial integrity and function, advancing our understanding of TFs in brown fat biology. This study well fits readers' interests in the adipose biology and metabolism field.

    2. Note: This preprint has been reviewed by subject experts for Review Commons. Content has not been altered except for formatting.

      Learn more at Review Commons


      Referee #1

      Evidence, reproducibility and clarity

      Summary of the key results:

      Valdivieso-Rivera and colleagues present a novel regulatory mechanism by which E4BP4 modulates C16:0 ceramide production in brown adipocytes. Several points warrant clarification or additional data.

      Suggested improvements:

      1) Figure 1F: There is an unexpected dip in gene expression at cold exposure days 3 and 7, followed by a rebound at day 14. Is this fluctuation biologically meaningful or technical?

      2) Figures B: Sample size of EE experiments is too low to draw any meaningful conclusions or to know for certain if the data are reproducible. Small sample sizes, likely coming from one litter and one batch of AAV are prone to type I error.

      3) Figures 2H and 2I (GTT): How was the AUC calculated? The GTT and ITT curves appear largely parallel aside from fasting differences. If total AUC was used instead of incremental AUC, it may overstate group differences. The recommended method is outlined in [DOI: 10.1038/s42255-021-00414-7]. Also, since insulin's half-life is ~10 minutes, later differences in the ITT curve likely reflect counterregulatory responses driven by hepatic gluconeogenesis.

      4) Figure 3I: Why do cells (none of the groups) show no response to NE stimulation? Please clarify or provide potential mechanistic insight. Perhaps the cells were not differentiated well.

      5) Figure 4F: How was mitochondrial fragmentation quantified? Please ensure that the ROI boxes shown in zoomed panels match the same region in size and shape - this applies throughout the manuscript.

      5) Figures 3I vs 5N: There is a striking discrepancy between these panels. In both, cells were treated with palmitate for 6 h, yet the NE and CCCP responses differ significantly. Are these the same cell types and conditions? Please reconcile the differences.

      6) Figure 3A: The claim that one group contains smaller mitochondria is not convincing. Both small and elongated mitochondria appear in each group. Moreover, it is unclear whether these minor differences are of any physiological relevance or whether they drive phenotypes.

      7) Figure 3E: The claim that confocal microscopy reveals palmitate-induced mitochondrial fragmentation is difficult to discern. The images lack clear morphological differences.

      8) Figure 3G: Dendra2-labeled mitochondria appear unaffected by palmitate, raising concern about the robustness of the effect across readouts.

      9) Figure 5H: Were E4BP4 expression levels equivalent between WT and mutant cells? Quantification should be shown. Figure 5H: Were E4BP4 expression levels equivalent between WT and mutant cells? Quantification should be shown.

      Cross-commenting

      I agree with R2's points

      Significance

      This advance is incremental for the basic science community.

    1. Reviewer #3 (Public review):

      A bias in how people infer the amount of control they have over their environment is widely believed to be a key component of several mental illnesses including depression, anxiety, and addiction. Accordingly, this bias has been a major focus in computational models of those disorders. However, all of these models treat control as a unidimensional property, roughly, how strongly outcomes depend on action. This paper proposes---correctly, I think---that the intuitive notion of "control" captures multiple dimensions in the relationship between action and outcome. In particular, the authors identify one key dimension: the degree to which outcome depends on how much *effort* we exert, calling this dimension the "elasticity of control". They additionally argue that this dimension (rather than the more holistic notion of controllability) may be specifically impaired in certain types of psychopathology. This idea has the potential to change how we think about several major mental disorders in a substantial way, and can additionally help us better understand how healthy people navigate challenging decision-making problems. More concisely, it is a *very good idea*.

      The more concrete contributions, however, are not as strong. In particular, evidence for the paper's most striking claims is weak. Quoting the abstract, these claims are (1) "the elasticity of control [is] a distinct cognitive construct guiding adaptive behavior" and (2) "overestimation of elasticity is associated with elevated psychopathology involving an impaired sense of control."

      Main issues

      I'll highlight the key points.

      - The task cannot distinguish elasticity inference from general learning processes

      - Participants were explicitly instructed about elasticity, with labeled examples

      - The psychopathology claims rely on an invalid interpretation of CCA, and are contradicted by simple correlations (elasticity bias and the sense of agency scale is r=0.03)

      Distinct construct

      Starting with claim 1, there are three subclaims here. (1A) People's behavior is sensitive to differences in elasticity; (1B) there are mental processes specific to elasticity inference, i.e., not falling out of general learning mechanisms; and, implicitly, (1C) people infer elasticity naturally as they go about their daily lives. The results clearly support 1A. However, 1B and 1C are not well supported.

      (1B) The data cannot support the "distinct cognitive construct" claim because the task is too simple to dissociate elasticity inference from more general learning processes (also raised by Reviewer 1). The key behavioral signature for elasticity inference (vs. generic controllability inference) is the transfer across ticket numbers, illustrated in Fig 4. However, this pattern is also predicted by a standard Bayesian learner equipped with an intuitive causal model of the task. Each ticket gives you another chance to board and the agent infers the probability that each attempt succeeds. Crucially, this logic is not at all specific to elasticity or even control. An identical model could be applied to inferring the bias of a coin from observations of whether any of N tosses were heads-a task that is formally identical to this one (at least, the intuitive model of the task; see first minor comment).

      Importantly, this point cannot be addressed by showing that the author's model fits data better than this or any other specific Bayesian model. It is not a question of whether one particular updating rule explains data better than another. Rather, it is a question of whether the task can distinguish between biases in *elasticity* inference versus biases in probabilistic inference more generally. The present task cannot make this distinction because it does not make separate measurements of the two types of inference. To provide compelling evidence that elasticity inference is a "distinct cognitive construct", one would need to show that there are reliable individual differences in elasticity inference that generalize across contexts but do not generalize to computationally similar types of probabilistic inference (e.g. the coin flipping example).

      (1C) The implicit claim that people infer elasticity outside of the experimental task is undermined by the experimental design. The authors explicitly tell people about the two notions of control as part of the training phase: "To reinforce participants' understanding of how elasticity and controllability were manifested in each planet, [participants] were informed of the planet type they had visited after every 15 trips."

      In the revisions, the authors seem to go back and forth on whether they are claiming that people infer elasticity without instruction (I won't quote it here). I'll just note that the examples they provide in the most recent rebuttal are all cases in which one never receives explicit labels about elasticity. If people only infer elasticity when it is explicitly labeled, I struggle to see its relevance for understanding human cognition and behavior.

      Psychopathology

      Finally, I turn to claim 2, that "overestimation of elasticity is associated with elevated psychopathology involving an impaired sense of control." The CCA analysis is in principle unable to support this claim. As the authors correctly note in their latest rebuttal, the CCA does show that "there is a relationship between psychopathology traits and task parameters". The lesion analysis further shows that "elasticity bias specifically contributes to this relationship" (and similarly for the Sense of Agency scale). Crucially, however, this does *not* imply that there is a relationship between those two variables. The most direct test of that relationship is the simple correlation, which the authors report only in a supplemental figure: there is no relationship (r=0.03). Although it is of course possible that there is a relationship that is obscured by confounding variables, the paper provides no evidence-statistical or otherwise-that such a relationship exists.

      Minor comments

      The statistical structure of the task is inconsistent with the framing. In the framing, participants can make either one or two second boarding attempts (jumps) by purchasing extra tickets. The additional attempt(s) will thus succeed with probability p for one ticket and 2p - p^2 for two tickets; the p^2 captures the fact that you only take the second attempt if you fail on the first. A consequence of this is buying more tickets has diminishing returns. In contrast, in the task, participants always jumped twice after purchasing two tickets, and the probability of success with two tickets was exactly double that with one ticket. Thus, if participants are applying an intuitive causal model to the task, the researcher could infer "biases" in elasticity inference that are probably better characterized as effective use of prior information (encoded in the causal model).

      The model is heuristically defined and does not reflect Bayesian updating. For example, it over-estimates maximum control by not using losses with less than 3 tickets (intuitively, the inference here depends on what your beliefs about elasticity). Including forced three-ticket trials at the beginning of each round makes this less of an issue; but if you want to remove those trials, you might need to adjust the model. The need to introduce the modified model with kappa is likely another symptom of the heuristic nature of the model updating equations.

    1. Reviewer #2 (Public review):

      Summary:

      This manuscript presents a tactile categorization task in head-fixed mice to test whether Fmr1 knockout mice display differences in vibrotactile discrimination using the forepaw. Tactile discrimination differences have been previously observed in humans with Fragile X Syndrome, autistic individuals, as well as mice with loss of Fmr1 across multiple studies. The authors show that during training, Fmr1 mutant mice display subtle deficits in perceptual learning of "low salience" stimuli, but not "high salience" stimuli, during the task. Following training, Fmr1 mutant mice displayed an enhanced tactile sensitivity under low-salience conditions but not high-salience stimulus conditions. The authors suggest that, under 'high cognitive load' conditions, Fmr1 mutant mouse performance during the lowest indentation stimuli presentations was affected, proposing an interplay of sensory and cognitive system disruptions that dynamically affect behavioral performance during the task.

      Strengths:

      The study employs a well-controlled vibrotactile discrimination task for head-fixed mice, which could serve as a platform for future mechanistic investigations. By examining performance across both training stages and stimulus "salience/difficulty" levels, the study provides a more nuanced view of how tactile processing deficits may emerge under different cognitive and sensory demands.

      Weaknesses:

      The study is primarily descriptive. The authors collect behavioral data and fit simple psychometric functions, but provide no neural recordings, causal manipulations, or computational modeling. Without mechanistic evidence, the conclusions remain speculative. Second, the authors repeatedly make strong claims about "categorical priors," "attention deficits," and "choice biases," but these constructs are inferred indirectly from secondary behavioral measures. Many of the effects are based on non-significant trends, and alternative explanations (such as differences in motivation, fatigue, satiety, stereotyped licking, and/or reward valuation) are not considered. Third, the mapping of the behavioral results onto high-level cognitive constructs is tenuous and overstated. The authors' interpretations suggest that they directly tested cognitive theories such as Load Theory, Adaptive Resonance Theory, or Weak Central Coherence. However, the experiments do not manipulate or measure variables that would allow such theories to be tested. More specific comments are included below.

      (1) The authors employ a two-choice behavioral task to assess forepaw tactile sensitivity in Fmr1 knockout mice. The data provide an interesting behavioral observation, but it is a descriptive study. Without mechanistic experiments, it is difficult to draw any conclusions, especially regarding top-down or bottom-up pathway dysfunctions. While the task design is elegant, the data remain correlational and do not advance our mechanistic understanding of Fmr1-related sensory and/or cognitive alterations.

      (2) The conclusions hinge on speculative inferences about "reduced top-down categorization influence" or "choice consistency bias," but no neural, circuit-level, or causal manipulations (e.g., optogenetics, pharmacology, targeted lesions, modeling) are used to support these claims. Without mechanistic data, the translational impact is limited.

      (3) Statistical analysis:

      (a) Several central claims are based on "trends" rather than statistically significant effects (e.g., reduced task sensitivity, reduced across-category facilitation). Building major interpretive arguments on non-significant findings undermines confidence in the conclusions.

      (b) The n number for both genotypes should be increased. In several experiments (e.g., Figure 1D, 2E), one animal appears to be an outlier. Considering the subtle differences between genotypes, such an outlier could affect the statistical results and subsequent interpretations.

      (c) The large number of comparisons across salience levels, categories, and trial histories raises concern for false positives. The manuscript does not clearly state how multiple comparisons were controlled.

      (d) The data in Figure 5, shown as separate panels per indentation value, are analyzed separately as t-tests or Mann-Whitney tests. However, individual comparisons are inappropriate for this type of data, as these are repeated stimulus applications across a given session. The data should be analyzed together and post-hoc comparisons reported. Given the very subtle difference in miss rates across control and mutant mice for 'low-salience' stimulus trials, this is unlikely to be a statistically meaningful difference when analyzed using a more appropriate test.

      (4) Emphasis on theoretical models:

      The paper leans heavily on theories such as Adaptive Resonance Theory, Load Theory of Attention, and Weak Central Coherence, but the data do not actually test these frameworks in a rigorous way. The discussion should be reframed to highlight the potential relevance of these frameworks while acknowledging that the current data do not allow them to be assessed.

    2. Author response:

      Reviewer #1 (Public review): 

      Summary: 

      This study addresses the important question of how top-down cognitive processes affect tactile perception in autism - specifically, in the Fmr1-/y genetic mouse model of autism. Using a 2AFC tactile task in behaving mice, the study investigated multiple aspects of perceptual processing, including perceptual learning, stimulus categorization and discrimination, as well as the influence of prior experience and attention.  

      We appreciate the reviewer’s statement highlighting the importance of our study. 

      Strengths: 

      The experiments seem well performed, with interesting results. Thus, this study can/will advance our understanding of atypical tactile perception and its relation to cognitive factors in autism. 

      We thank the reviewer for recognizing the quality of our experiments and the relevance of our findings for understanding tactile perception and cognition in autism.

      Weaknesses: 

      Certain aspects of the analyses (and therefore the results) are unclear, which makes the manuscript difficult to understand. Clearer presentation, with the addition of more standard psychometric analyses, and/or other useful models (like logistic regression) would improve this aspect. The use of d' needs better explanation, both in terms of how and why these analyses are appropriate (and perhaps it should be applied for more specific needs rather than as a ubiquitous measure). 

      We thank the reviewer for the helpful comments. We understand that the analyses were difficult to follow, and we will work on the clarity of the Results section. However, we would like to emphasize that every d′ measure is accompanied by analyses of response rates (i.e., correct and incorrect choice rates). In addition, we applied standard psychometric analyses whenever possible. Specifically, psychometric functions were fitted to the data using logistic regression. We will rework the text to clarify these points.

      During training, only two stimulus amplitudes were presented, which precluded the construction of psychometric curves. For the categorization task, however, psychometric analyses were feasible and conducted (Figure 2). These analyses revealed no evidence of categorization bias (as measured by threshold) or accuracy (as measured by the slope) across stimulus strengths.

      The calculation of d’ is included in the Methods, but we will also report and explain its use in each part of the Results section where it has been included.

      Reviewer #2 (Public review): 

      Summary: 

      This manuscript presents a tactile categorization task in head-fixed mice to test whether Fmr1 knockout mice display differences in vibrotactile discrimination using the forepaw. Tactile discrimination differences have been previously observed in humans with Fragile X Syndrome, autistic individuals, as well as mice with loss of Fmr1 across multiple studies. The authors show that during training, Fmr1 mutant mice display subtle deficits in perceptual learning of "low salience" stimuli, but not "high salience" stimuli, during the task. Following training, Fmr1 mutant mice displayed an enhanced tactile sensitivity under low-salience conditions but not high-salience stimulus conditions. The authors suggest that, under 'high cognitive load' conditions, Fmr1 mutant mouse performance during the lowest indentation stimuli presentations was affected, proposing an interplay of sensory and cognitive system disruptions that dynamically affect behavioral performance during the task. 

      Strengths: 

      The study employs a well-controlled vibrotactile discrimination task for head-fixed mice, which could serve as a platform for future mechanistic investigations. By examining performance across both training stages and stimulus "salience/difficulty" levels, the study provides a more nuanced view of how tactile processing deficits may emerge under different cognitive and sensory demands. 

      We thank the reviewer for emphasizing the strengths of our task design and analysis approach, and we appreciate that the potential of this platform for future mechanistic investigations is recognized.

      Weaknesses: 

      The study is primarily descriptive. The authors collect behavioral data and fit simple psychometric functions, but provide no neural recordings, causal manipulations, or computational modeling. Without mechanistic evidence, the conclusions remain speculative. 

      We thank the reviewer for the careful reading of our manuscript and for the constructive feedback. The reviewer raises a valid point. We agree that our study is primarily descriptive and focused on behavioral data, and we appreciate the opportunity to clarify the scope and interpretation of our findings. Our primary goal was to characterize behavioral patterns during tactile discrimination and categorization, and the psychometric analyses were intended to provide a detailed description of these patterns. We do not claim to provide direct neural, causal, or computational evidence. 

      Second, the authors repeatedly make strong claims about "categorical priors," "attention deficits," and "choice biases," but these constructs are inferred indirectly from secondary behavioral measures. Many of the effects are based on non-significant trends, and alternative explanations (such as differences in motivation, fatigue, satiety, stereotyped licking, and/or reward valuation) are not considered. 

      Alternative explanations of our findings, such as differences in motivation, fatigue, satiety, stereotyped licking, and reward valuation have indeed been considered. We will revise the manuscript to present these points more clearly. 

      Third, the mapping of the behavioral results onto high-level cognitive constructs is tenuous and overstated. The authors' interpretations suggest that they directly tested cognitive theories such as Load Theory, Adaptive Resonance Theory, or Weak Central Coherence. However, the experiments do not manipulate or measure variables that would allow such theories to be tested. More specific comments are included below.

      This was not done intentionally. We do not claim to have tested the Load Theory; rather, inspired by it, we assessed behavioral patterns in our tactile categorization task. We agree that referring to the Adaptive Resonance Theory, which is based on artificial neural network models, might be misleading since we focus on behavioral results, and we will revise the text accordingly. However, our task allowed us to examine the impact of categorization on discrimination, confirming that Fmr1<sup>-/y</sup>ation can amplify perceptual differences between stimuli belonging to different categories and reduce perceived differences within a category in WT mice but not in the mice when low-salience stimuli were experienced. Finally, we do not claim to have tested the Weak Central Coherence theory, although our results suggest reduced use of categories in low-salience tactile discrimination. 

      (1) The authors employ a two-choice behavioral task to assess forepaw tactile sensitivity in Fmr1 knockout mice. The data provide an interesting behavioral observation, but it is a descriptive study. Without mechanistic experiments, it is difficult to draw any conclusions, especially regarding top-down or bottom-up pathway dysfunctions. While the task design is elegant, the data remain correlational and do not advance our mechanistic understanding of Fmr1-related sensory and/or cognitive alterations. 

      We agree with the reviewer that our current experiments are behavioral in nature and do not provide direct mechanistic evidence for top-down pathway dysfunction. Our goal was to carefully characterize tactile responses and behavioral patterns in Fmr1<sup>-/y</sup> mice. The notion of “top-down” is used at the behavioral level, referring to the influence of higher-level cognitive processes (e.g., categorization, attention) on perception, rather than to underlying neural circuits. We will revise the manuscript to more clearly emphasize that our conclusions are based on behavioral observations, and we will frame mechanistic inferences as hypotheses rather than established findings. We will also explicitly note that future work using neural recordings or causal manipulations will be required to directly test these hypotheses.

      We also note that identifying the precise top-down circuits involved will require extensive additional experimentation. For example, one would first need to pinpoint the specific top-down pathway that modulates the influence of categorization on discrimination without directly altering categorization itself. After such a circuit is identified, further work would then be needed to rescue or manipulate this pathway in the Fmr1<sup>-/y</sup> model. These steps represent a substantial program of mechanistic research that, while important, goes well beyond the scope of the present study.

      (2) The conclusions hinge on speculative inferences about "reduced top-down categorization influence" or "choice consistency bias," but no neural, circuit-level, or causal manipulations (e.g., optogenetics, pharmacology, targeted lesions, modeling) are used to support these claims. Without mechanistic data, the translational impact is limited. 

      We recognize that “reduced top-down categorization influence” and “choice consistency bias” are based on behavioral observations. However, we respectfully disagree that this makes these constructs inherently speculative. Similar behavioral inferences have been applied in previous clinical studies to characterize cognitive tendencies (Soulières et al., 2007; Feigin et al., 2021). The translational impact of our work lies in the highly translational platform we have developed – and in highlighting the complexity of tactile measures and additional analyses that can be conducted in clinical studies.

      We agree with the reviewer that the neural-based experiments would indeed provide valuable mechanistic insight into our observed behavioral alterations, and we believe future studies should therefore focus on their underlying neurobiological substrate.

      We will revise the language throughout the manuscript to clarify that all conclusions are based on behavioral measures.  

      (3) Statistical analysis: 

      (a) Several central claims are based on "trends" rather than statistically significant effects (e.g., reduced task sensitivity, reduced across-category facilitation). Building major interpretive arguments on nonsignificant findings undermines confidence in the conclusions.  

      Several trends are evident in complex measures, such as d’ analyses on task sensitivity or responses pooled across different amplitudes. Additional analyses revealed which component of these measures showed a statistically significant difference across genotypes, namely the low-salience incorrect choices accounting for low task sensitivity. We chose to present all analyses to be transparent and to highlight that commonly used complex measures (like d’ analyses) may mask important findings. In the text, we described p-values between 0.05 and 0.1 as observed trends without over-interpreting their significance. 

      (b) The n number for both genotypes should be increased. In several experiments (e.g., Figure 1D, 2E), one animal appears to be an outlier. Considering the subtle differences between genotypes, such an outlier could affect the statistical results and subsequent interpretations. 

      The number of mice used in each genotype group is consistent with standard practices in behavioral studies using mice and sensory tasks. We have performed effect size measures (e.g., Cohen’s d) alongside some of the statistical comparisons, showing a medium effect size (>0.5). 

      As the reviewer correctly noted, no mice were excluded based on outlier analyses, since the observed variability reflects true biological differences rather than experimental or technical errors. We will reexamine our dataset for potential outliers. If any are identified, we will perform analyses both with and without the outlier and report any effects that are sensitive to single animals. These procedures and results will be explicitly described in the Methods and Results sections.

      (c) The large number of comparisons across salience levels, categories, and trial histories raises concern for false positives. The manuscript does not clearly state how multiple comparisons were controlled.  

      We thank the reviewer for raising this important point and we will include a clear statement on multiple comparisons in the Methods section. 

      (d) The data in Figure 5, shown as separate panels per indentation value, are analyzed separately as ttests or Mann-Whitney tests. However, individual comparisons are inappropriate for this type of data, as these are repeated stimulus applications across a given session. The data should be analyzed together and post-hoc comparisons reported. Given the very subtle difference in miss rates across control and mutant mice for 'low-salience' stimulus trials, this is unlikely to be a statistically meaningful difference when analyzed using a more appropriate test. 

      We thank the reviewer for raising this point. This was not done intentionally. A repeated-measures ANOVA on miss rates for low-salience stimuli during categorization confirmed that there are statistically significant differences both across stimulus amplitudes and between genotypes. Additional correction for multiple comparisons will be performed and explained in the Methods section.  

      (4) Emphasis on theoretical models: The paper leans heavily on theories such as Adaptive Resonance Theory, Load Theory of Attention, and Weak Central Coherence, but the data do not actually test these frameworks in a rigorous way. The discussion should be reframed to highlight the potential relevance of these frameworks while acknowledging that the current data do not allow them to be assessed. 

      As mentioned above, our goal was not to directly test these theories but rather to apply them within our translational framework. The Discussion section will be reframed to highlight that our findings are consistent with predictions from certain cognitive theories rather than implying that these frameworks were directly tested.

      Reviewer #3 (Public review): 

      Summary: 

      Developing consistent and reliable biomarkers is critically important for developing new pharmacological therapies in autism spectrum disorders (ASDs). Altered sensory perception is one of the hallmarks of autism and has been recently added to DSM-5 as one of the core symptoms of autism. Touch is one of the fundamental sensory modalities, yet it is currently understudied. Furthermore, there seems to be a discrepancy between different studies from different groups focusing on tactile discrimination. It is not clear if this discrepancy can be explained by different experimental setups, inconsistent terminology, or the heterogeneity of sensory processing alterations in ASDs. The authors aim to investigate the interplay between tactile discrimination and cognitive processes during perceptual decisions. They have developed a forepaw-based 2-alternative choice task for mice and investigated tactile perception and learning in Fmr1-/y mice 

      Strengths: 

      There are several strengths of this task: translational relevance to human psychophysical protocols, including controlled vibrotactile stimulation. In addition to the experimental setup, there are also several interesting findings: Fmr1-/y mice demonstrated choice consistency bias, which may result in impaired perceptual learning, and enhanced tactile discrimination in low-salience conditions, as well as attentional deficits with increased cognitive load. The increase in the error rates for low salience stimuli is interesting. These observations, together with the behavioral design, may have a promising translational potential and, if confirmed in humans, may be potentially used as biomarkers in ASD. 

      We appreciate the reviewer’s positive assessment of our study’s translational value and the importance of our behavioral findings.

      Weaknesses: 

      Some weaknesses are related to the lack of the original raster plots and density plots of licks under different conditions, learning rate vs time, and evaluation of the learning rate at different stages of learning. Overall, these data would help to answer the question of whether there are differences in learning strategies or neural circuit compensation in Fmr1-/y mice. It is also not clear if reversal learning is impaired in Fmr1-/y mice.  

      We thank the reviewer for these helpful suggestions. We agree that visualizing behavioral patterns, such as raster and density plots of licks, as well as learning rate over time, could provide additional insights into learning dynamics. This analysis will be conducted and added into the revised manuscript.

      There was no assessment of reversal learning in Fmr1<sup>-/y</sup> mice in this study. While it is an interesting and important question based on previous findings in preclinical and clinical studies, it falls outside the scope of the current manuscript.    

      Feigin H, Shalom-Sperber S, Zachor DA, Zaidel A (2021) Increased influence of prior choices on perceptual decisions in autism. Elife 10.

      Soulières I, Mottron L, Saumier D, Larochelle S (2007) At ypical categorical perception in autism: Autonomy of discrimination? J Autism Dev Disord 37:481–490.

    1. Does
      1. Pplateau= Lung Compliance, the higher the pressure, the lower the compliance. The Plateau Pressure is an estimate of LUNG COMPLIANCE. As you give more volume to the lungs you can cause overdistension of the lungs. That can create more alveolar damage; It is elevated because the part of the lung that is being ventilated is minimal (only the undamaged part of the lung; so you are workign wiht lower lung volume for ventilation

      2. Treatment:

      3. Respiraotry Support (PEEP > 5)
      4. Treat Inciting Event
      5. +/- steroids
      6. Prone Positioning More severe Cases:
      7. Consider ECMO
      8. Pulmonary Vasodialators
    1. Author response:

      Reviewer #1 (Public review):

      Cognitive Load and Task-Switching Components:

      We agree that cognitive load is multi-faceted and encompasses dimensions not fully captured in our present models, including domain and rule switching. For the revision, we will explicitly model these components in the statistical analyses by incorporating predictors reflecting attended domain switching and rule complexity, as suggested. We will also explain our inclusion of n-back reaction predictors and justify their relationship with theoretical constructs of executive function. Full details of coding schemes will be provided.

      Modeling Entropy and Surprisal:

      We appreciate the reviewer’s suggestion to further explain the distinction between entropy (predictive uncertainty) and surprisal (integration difficulty), and acknowledge that our treatment of entropy warrants extension. In the revision, we will expand the results and discussion on entropy, providing clearer theoretical motivation for its inclusion and conducting supplementary analyses to examine its role alongside surprisal.

      Replicability of Findings:

      We note the concern regarding two-way vs. three-way interactions in model replication. In the revised manuscript, we will report robustness analyses on subsets of our data (e.g., matched age and education groups), clarify degrees of freedom and group sizes, and transparently report any discrepancies.

      Predictors and Statistical Modeling:

      We will add clarifications on predictor selection, data structure, and rationale for model hierarchy. The functions of d-prime, comprehension accuracy, and performance modeling will be described in more detail, including discussion of block-level vs. participant-level effects.

      Reviewer #2 (Public review):

      Distinction Between Prediction and Predictability:

      We recognize the importance of clearly communicating the difference between prediction and predictability, as well as integration-based vs. prediction-based effects. We will clarify these distinctions throughout the introduction, methods, and discussion sections, citing the relevant theoretical literature (e.g., Pickering & Gambi 2018; Federmeier 2007; Staub 2015; Frisson 2017).

      Aging, Corpus Predictability, and Individual Differences:

      We appreciate the critical point regarding age, corpus-based predictability, and potential cohort effects in language model estimates. In the revision, we will provide conceptual clarifications on how surprisal and entropy might differ for different age groups and discuss limitations in extrapolating these metrics to participant-specific predictions. The limitations inherent in relying on LLM-derived estimates and text materials will be more directly addressed.

      Coverage of Literature and Paradigms:

      We will broaden the literature review as requested, particularly on the N400 effects and behavioral traditions in prediction research. These additions should help contextualize the present work within both neuroscience and psycholinguistics.

      Experimental Context and Predictability Metrics:

      We will address concerns regarding the context window for prediction estimation, describing more precisely how context was defined and whether broader textual cues may improve predictability metrics.

      References

      Pickering, M.J. & Gambi, C. (2018). Predicting while comprehending language: A theory and review. Psychol. Bull., 144(10), 1002–1044.

      Federmeier, K.D. (2007). Thinking ahead: The role and roots of prediction in language comprehension. Psychophysiology, 44(4), 491–505.

      Frisson, S. (2017). Can prediction explain the lexical processing advantage for short words? J. Mem. Lang., 95, 121–138.\

      Staub, A. (2015). The effect of lexical predictability on eye movements in reading: Critical review and theoretical interpretation. Lang. Linguist. Compass, 9(8), 311–327.Huettig, F. & Mani, N. (2016). Is prediction necessary to understand language? Probably not. Trends Cogn. Sci., 20(10), 484–492.We appreciate the reviewers’ constructive comments and believe their suggestions will meaningfully strengthen the paper. Our planned revisions will address each of the above points with additional analyses, clarifications, and expanded discussion.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Reviewer #1 (Public review):

      (1) The manuscript is quite dense, with some concepts that may prove difficult for the non-specialist. I recommend spending a few more words (and maybe some pictures) describing the difference between task-relevant and task-irrelevant planes. Nice technique, but not instantly obvious. Then we are hit with "stimulus-related", which definitely needs some words (also because it is orthogonal to neither of the above). 

      We agree that the original description of the planes was too terse and have expanded on this in the revised manuscript.

      Line 85 - To test the influence of attention, trials were sorted according to two spatial reference planes, based on the location of the stimulus: task-related and task-unrelated (Fig. 1b). The task-related plane corresponded to participants’ binary judgement (Fig 1b, light cyan vertical dashed line) and the task-unrelated plane was orthogonal to this (Fig 1b, dark cyan horizontal dashed line). For example, if a participant was tasked with performing a left-or-right of fixation judgement, then their task-related plane was the vertical boundary between the left and right side of fixation, while their task-unrelated plane was the horizontal boundary. The former (left-right) axis is relevant to their task while the latter (top-bottom) axis is orthogonal and task irrelevant. This orthogonality can be leveraged to analyze the same data twice (once according to the task-related plane and again according to the taskunrelated plane) in order to compare performance when the relative location of an event is either task relevant or irrelevant.

      Line 183 - whereas task planes were constant, the stimulus-related plane was defined by the location of the stimulus on the previous trial, and thus varied from trial to trial. That is, on each trial, the target is considered a repeat if it changes location by <|90°| relative to its location on the previous trial, and an alternate if it moves by >|90°|.

      (2) While I understand that the authors want the three classical separations, I actually found it misleading. Firstly, for a perceptual scientist to call intervals in the order of seconds (rather than milliseconds), "micro" is technically coming from the raw prawn. Secondly, the divisions are not actually time, but events: micro means one-back paradigm, one event previously, rather than defined by duration. Thirdly, meso isn't really a category, just a few micros stacked up (and there's not much data on this). And macro is basically patterns, or statistical regularities, rather than being a fixed time. I think it would be better either to talk about short-term and long-term, which do not have the connotations I mentioned. Or simply talk about "serial dependence" and "statistical regularities". Or both. 

      We agree that the temporal scales defined in the current study are not the only way one could categorize perceptual time. We also agree that by using events to define scales, we ignore the influence of duration. In terms of the categories, we selected these for two reasons: 1) they conveniently group previous phenomena, and 2) they loosely correspond to iconic-, short- and long-term memory. We agree that one could also potentially split it up into two categories (e.g., short- and long-term), but in general, we think any form of discretization will have limitations. For example, Reviewer 1 suggests that the meso category is simply a few micros stacked together. However, there is a rich literature on phenomena associated with sequences of an intermediate length that do not appear to be entirely explained by stacking micro effects (e.g., sequence learning and sequential dependency). We also find that when controlling for micro level effects, there are clear meso level effects. Also, by the logic that meso level effects are just stacked micro effects, one could also argue the same for macro effects. We don’t think this argument is incorrect, rather we think it exemplifies the challenge of discretising temporal scales. Ultimately, the current study was aimed to test whether seemingly disparate phenomena identified in previous work could be captured by unifying principles. To this end we found that these categories were the most useful. However, we have included a “Limitations and future directions” section in the Discussion of the revised manuscript that acknowledges both the alternative scheme proposed by Reviewer 1, and the value of extending this work to consider the influence of duration (as well as events).

      Line 488 - Limitations and future directions. One potential limitation of the current study is the categorization of temporal scales according to events, independent of the influence of event duration. While this simplification of time supports comparison between different phenomena associated with each scale (e.g., serial dependence, sequential dependencies, statistical learning), future work could investigate the role of duration to provide a more comprehensive understanding of the mechanisms identified in the current study.

      Related to this, while the temporal scales applied here conveniently categorized known sensory phenomena, and partially correspond to iconic-, short-, and long-term memory, they are but one of multiple ways to delineate time. For example, temporal scales could alternatively be defined simply as short- and long-term (e.g., by combining micro and meso scale phenomena). However, this could obscure meaningful differences between phenomena associated with sensory persistence and short-term memory, or qualitative differences in the way that shortsequences of events are processed.

      (3) More serious is the issue of precision. Again, this is partially a language problem. When people use the engineering terms "precision" and "accuracy" together, they usually use the same units, such as degrees. Accuracy refers to the distance from the real position (so average accuracy gives bias), and precision is the clustering around the average bias, usually measured as standard deviation. Yet here accuracy is percent correct: also a convention in psychology, but not when contrasting accuracy with precision, in the engineering sense. I suggest you change "accuracy" to "percent correct". On the other hand, I have no idea how precision was defined. All I could find was: "mixture modelling was used to estimate the precision and guess rate of reproduction responses, based on the concentration (k) and height of von Mises and uniform distributions, respectively". I do not know what that means.

      In the case of a binary decision, is seems reasonable to use the term “accuracy” to refer to the correspondence between the target state and the response on a task. However, we agree that while our (main) task is binary, the target is not and nor is the secondary task. We thank the reviewer for bringing this to our attention, as we agree that this will be a likely cause of confusion. To avoid confusion we have specifically referred to “task accuracy” throughout the revised manuscript.

      With regards to precision, our measure of precision is consistent with what Reviewer 1 describes as such, i.e., the clustering of responses. In particular, the von Mises distribution is essentially a Gaussian distribution in circular space, and the kappa parameter defines the width of the distribution, regardless of the mean, with larger values of kappa indicating narrower (more precise) distributions. We could have used standard deviation to assess precision; however, this would incorrectly combine responses on which participants failed to encode the target (e.g., because of a blink) and were simply guessing. To account for these trials, we applied mixture modelling of guess and genuine responses to isolate the precision of genuine responses, as is standard in the visual working memory literature. However, we agree that this was not sufficiently described in the original manuscript and have elaborated on this method in the revised version.

      Line 598 - From the reproduction task, we sought to estimate participant’s recall precision. It is likely that on some trials participants failed to encode the target and were forced to make a response guess. To isolate the recall precision from guess responses, we used mixture modelling to estimate the precision and guess rate of reproduction responses, based on the concentration (k) and height of von Mises and uniform distributions, respectively (Bays et al., 2009). The k parameter of the von Mises distribution reflects its width, which indicates the clustering of responses around a common location.

      (4) Previous studies show serial dependence can increase bias but decrease scatter (inverse precision) around the biased estimate. The current study claims to be at odds with that. But are the two measures of precision relatable? Was the real (random) position of the target subtracted from each response, leaving residuals from which the inverse precision was calculated? (If so, the authors should say so..) But if serial dependence biases responses in essentially random directions (depending on the previous position), it will increase the average scatter, decreasing the apparent precision. 

      Previous studies have shown that when serial dependence is attractive there is a corresponding increase in precision around small offsets from the previous item (citations). Indeed, attractive biases will lead to reduced scattering (increased precision) around a central attracter. Consistent with previous studies, and this rational, we also found an attractive bias coupled with increased precision. To clarify, for the serial dependency analysis, we calculated bias and precision by binning reproduction responses according to the offset between the current and previous target and then performing the same mixture modelling described above to estimate the mean (bias) and kappa (precision) parameters of the von Mises distribution fit to the angular errors. This was not explained in the original manuscript, so we thank Reviewer 1 for bringing this to our attention and have clarified the analysis in the revised version.

      Line 604 - For the serial dependency analysis, we calculated bias and precision by binning reproduction responses according to the angular offset between the current and previous target and then performing mixture modelling to estimate the mean (bias) and k (precision) parameters of the von Mises distribution.

      (5) I suspect they are not actually measuring precision, but location accuracy. So the authors could use "percent correct" and "localization accuracy". Or be very clear what they are actually doing. 

      As explained in our response to Reviewer 1’s previous comment, we are indeed measuring precision.

      Reviewer #2 (Public review):

      (1) The abstract should more explicitly mention that conclusions about feedforward mechanisms were derived from a reanalysis of an existing EEG dataset. As it is, it seems to present behavioral data only.

      It is not clear what relevance the fact that the data has been analyzed previously has to the results of the current study. However, we do think that it is important to be clear that the EEG recordings were collected separately from the behavioural and eyetracking data, so we have clarified this in the revised abstract.

      Line 7 - By integrating behavioural and pupillometry recordings with electroencephalographical recordings from a previous study, we identify two distinct mechanisms that operate across all scales.

      (2) The EEG task seems quite different from the others, with location and color changes, if I understand correctly, on streaks of consecutive stimuli shown every 100 ms, with the task involving counting the number of target events. There might be different mechanisms and functions involved, compared to the behavioral experiments reported. 

      As stated above, we agree that it is important that readers are aware that the EEG recordings were collected separately to the behavioural and eyetracking data. We were forthright about this in the original manuscript and how now clarified this in the revised abstract. We agree that collecting both sets of data in the same experiment would be a useful validation of the current results and have acknowledged this in a new Limitations and future directions section of the Discussion of the revised manuscript.

      Line 501 - Another limitation of the current study is that the EEG recordings were collected in the separate experiment to the behavioural and pupillometry data. The stimuli and task were similar between experiments, but not identical. For example, the EEG experiment employed coloured arc stimuli presented at a constant rate of ~3.3 Hz and participants were tasked with counting the number of stimuli presented at a target location. By contrast, in the behavioural experiment, participants viewed white blobs presented at an average rate of ~2.8 Hz and performed a binary spatial task coupled with an infrequent reproduction task. An advantage of this was that the sensory responses to stimuli in the EEG recordings were not conflated with motor responses; however, future work combining these measures in the same experiment would serve as a validation for the current results.

      (3) How is the arbitrary choice of restricting EEG decoding to a small subset of parieto-occipital electrodes justified? Blinks and other artifacts could have been corrected with proper algorithms (e.g., ICA) (Zhang & Luck, 2025) or even left in, as decoders are not necessarily affected by noise. Moreover, trials with blinks occurring at the stimulus time should be better removed, and the arbitrary selection of a subset of electrodes, while reducing the information in input to the decoder, does not account for trials in which a stimulus was missed (e.g., due to blinks).

      Electrode selection was based on several factors: 1) reduction of eye movement/blink artifacts (as noted in the original manuscript), 2) consistency with the previous EEG study (Rideaux, 2024) and other similar decoding studies (Buhmann et al., 2024; Harrison et al., 2023; Rideaux et al., 2023), 3) improved signal-to-noise by including only sensors that carry the most position information (as shown in Supplementary Figure 1a and the previous EEG study). We agree that this was insufficiently explained in the original manuscript and have clarified our sensor selection in the revised version.

      Line 631 - We only included the parietal, parietal-occipital, and occipital sensors in the analyses to i) reduce the influence of signals produced by eye movements, blinks, and non-sensory cortices, ii) for consistency with similar previous decoding studies (Buhmann et al., 2024; Rideaux, 2024; Rideaux et al., 2025), and iii) to improve decoding accuracy by restricting sensors to those that carried spatial position information (Supplementary Fig. 1a).

      (4) The artifact that appears in many of the decoding results is puzzling, and I'm not fully convinced by the speculative explanation involving slow fluctuations. I wonder if a different high-pass filter (e.g., 1 Hz) might have helped. In general, the nature of this artifact requires better clarification and disambiguation.

      We agree that the nature of this artifact requires more clarification and disambiguation. Due to relatively slow changes in the neural signal, which are not stimulus-related, there is a degree of temporal autocorrelation in the recordings. This can be filtered out, for example, by using a stricter high-pass filter; however, we tried a range of filters and found that a cut-off of at least 0.7 Hz is required to remove the artifact, and even a filter of 0.2 Hz introduces other (stimulus-related) artifacts, such as above-chance decoding prior to stimulus onset. These stimulus-related artifacts are due to the temporal smearing of data, introduced by the filtering, and have a more pronounced and complex influence on the results and are more difficult to remove through other means, such as the baseline correction applied in the original manuscript.

      The temporal autocorrelation is detected by the decoder during training and biases it to classify/decode targets that are presented nearby in time as similar. That is, it learns the neural pattern for a particular stimulus location based on the activity produced by the stimulus and the temporal autocorrelation (determined by slow stimulus unrelated fluctuations). The latter only accounts for a relatively smaller proportion of the variance in the neural recordings under normal circumstances and would typically go undetected when simply plotting decoding accuracy as a function of position. However, it becomes weakly visible when decoding accuracy is plotted as a function of distance from the previous target, as now the bias (towards temporally adjacent targets) aligns with the abscissa. Further, it becomes highly visible when the stimulus labels are shuffled, as now the decoder can only learn from the variance associated with the temporal autocorrelation (and not from the activity produced by the stimulus).

      In the linear discriminant analysis, this led to temporally proximal items being more likely to be classified as on the same side. This is why there is above-chance performance for repeat trials (Supplementary Figure 2b), and below-chance performance for alternate trials, even when the labels are shuffled – the temporal autocorrelation produces a general bias towards classifying temporally proximate stimuli as on the same side, which selectively improves the classification accuracy of repeat trials. Fortunately, the bias is relatively constant as a function of time within the epoch and is straightforward to estimate by shuffling the labels, which means that it can be removed through a baseline correction. However, to further demonstrate that the autocorrelation confound cannot account for the differences observed between repeat and alternate trials in the micro classification analysis, we now additionally show the results from a more strictly filtered version of the data (0.7 Hz). These results show a similar pattern as the original, with the additional stimulusrelated artifacts introduced by the strict filter, e.g., above chance decoding prior to stimulus onset.

      In the inverted encoding analysis, the same temporal autocorrelation manifests as temporally proximal trials being decoded as more similar locations. This is why there is increased decoding accuracy for targets with small angular offsets from the previous target, even when the labels are shuffled (Supplementary Figure 3c), because it is on these trials that the bias happens to align with the correct position. This leads to an attractive bias towards the previous item, which is most prominent when the labels are shuffled.

      To demonstrate the phenomenon, we simulated neural recordings from a population of tuning curves and performed the inverted encoding analysis on a clean version of the data and a version in which we introduced temporal autocorrelation. We then repeated this after shuffling the labels. The simulation produced very similar results to those we observed in the empirical data, with a single exception: while precision in the simulated shuffled data was unaffected by autocorrelation, precision in the unshuffled data was clearly affected by this manipulation. This may explain why we did not find a correlation between the shuffled and unshuffled precision in the original manuscript. 

      These results echo those from the classification analysis, albeit in a more continuous space. However, whereas in the classification analysis it was straightforward to perform a baseline correction to remove the influence of general temporal dependency, the more complex nature of the accuracy, precision, and bias parameters over the range of time and delta location makes this approach less appropriate. For example, the bias in the shuffled condition ranged from -180 to 180 degrees, which when subtracted from the bias in the unshuffled condition would produce an equally spurious outcome, i.e., the equal opposite of this extreme bias. Instead for the inverted encoding analysis, we used the data high-pass filtered at 0.7 Hz. As with the classification analysis, this removed the influence of general temporal dependencies, as indicated by the results of the shuffled data analysis (Supplementary Figure 3f), but it also temporally smeared the stimulus-related signal, resulting in above chance decoding accuracy prior to stimulus onset (Supplementary Figure 3d). However, given thar we were primarily interested in the pattern of accuracy, precision, and bias as a function of delta location, and less concerned with the precise temporal dynamics of these changes, which appeared relatively stable in the filtered data. Thus, this was the more suitable approach to removing the general temporal dependencies in the inverted encoding analysis and the one that is presented in Figure 3.

      We have updated the revised manuscript in light of these changes, including a fuller description of the artifact and the results from the abovementioned control analyses.

      Figure 3 updated.

      Figure 3 caption - e) Decoding accuracy for stimulus location, from reanalysis of previously published EEG data (17). Inset shows the EEG sensors included in the analysis (blue dots), and black rectangles indicate the timing of stimulus presentations (solid: target stimulus, dashed: previous and subsequent stimuli). f) Decoding accuracy for location, as a function of time and D location. Bright colours indicate higher decoding accuracy; absolute accuracy values can be inferred from (e). g-i) Average location decoding  (g) accuracy, (h) precision, and (h) bias from 50 – 500 ms following stimulus onset. Horizontal bar in (e) indicates cluster corrected periods of significance; note, all time points were significantly above chance due to temporal smear introduced by strict high-pass filtering (see Supplementary Figure 3 for full details). Note, the temporal abscissa is aligned across (e & f). Shaded regions indicate ±SEM.

      Line 218 - To further investigate the influence of serial dependence, we applied inverted encoding modelling to the EEG recordings to decode the angular location of stimuli. We found that decoding accuracy of stimulus location sharply increased from ~60 ms following stimulus onset (Fig. 3e). Note, to reduce the influence of general temporal dependencies, we applied a 0.7 Hz high-pass filter to the data, which temporally smeared the stimulus-related information, resulting in above chance decoding accuracy prior to stimulus presentation (for full details, see Supplementary Figure 3). To understand how serial dependence influences the representation of these features, we inspected decoding accuracy for location as a function of both time and D location (Fig. 3f). We found that decoding accuracy varied depending not only as a function of time, but also as a function of D location. To characterise this relationship, we calculated the average decoding accuracy from 50 ms until the end of the epoch (500 ms), as a function of D location (Fig. 3g). This revealed higher accuracy for targets with larger D location. We found a similar pattern of results for decoding precision (Fig. 3h). These results are consistent with the micro temporal context (behavioural) results, showing that targets that alternated were recalled more precisely. Lastly, we calculated the decoding bias as a function of D location and found a clear repulsive bias away from the previous item (Fig. 3i). While this result is inconsistent with the attractive behavioural bias, it is consistent with recent studies of serial dependence suggesting an initial pattern of repulsion followed by an attractive bias during the response period (20–22).

      Line 726 - As shown in Supplementary Figure 3, we found the same general temporal dependencies in the decoding accuracy computed using inverted encoding that were found using linear discriminant classification. However, as a baseline correction would not have been appropriate or effective for the parameters decoded with this approach, we instead used a high-pass filter of 0.7 Hz to remove the confound, while being cautious about interpreting the timing of effects produced by this analysis due to the temporal smear introduced by the filter.

      Supplementary Figure 2 updated.

      Supplementary Figure 2 caption - Removal of general micro temporal dependencies in EEG responses. We found that there were differences in classification accuracy for repeat and alternate stimuli in the EEG data, even when stimulus labels were shuffled. This is likely due to temporal autocorrelation within the EEG data due to low frequency signal changes that are unrelated to the decoded stimulus dimension. This signal trains the decoder to classify temporally proximal stimuli as the same class, leading to a bias towards repeat classification. For example, in general, the EEG signal during trial one is likely to be more similar to that during trial two than during trial ten, because of low frequency trends in the recordings. If the decoder has been trained to classify the signal associated with trial one as a leftward stimulus, then it will be more likely to classify trial two as a leftward stimulus too. These autocorrelations are unrelated to stimulus features; thus, to isolate the influence of stimulus-specific temporal context, we subtracted the classification accuracy produced by shuffling the stimulus labels from the unshuffled accuracy (as presented in Figure 2e, f). We confirmed that using a stricter high-pass filter (0.7 Hz) removes this artifact, as indicated by the equal decoding accuracy between the two shuffled conditions. However, the stricter high-pass filter temporally smears the stimulus-related signal, which introduces other (stimulus-related) artifacts, e.g., above-chance decoding accuracy prior to stimulus presentation, that are larger and more complex, i.e., changing over time. Thus, we opted to use the original high pass filter (0.1 Hz) and apply a baseline correction. a) The uncorrected classification  accuracy along task related and unrelated planes. Note that these results are the same as the corrected version shown in Figure 2e, because the confound is only apparent when accuracy is grouped according to temporal context.

      b) Same as (a), but split into repeat and alternate stimuli, along (left) task-related and (right) unrelated planes. Classification  accuracy when labels are shuffled is also shown. Inset in (a) shows the EEG sensors included in the analysis (blue dots). (c, d) Same as (a, b), but on data filtered using a 0.7 Hz high-pass filter. Black rectangles indicate the timing of stimulus presentations (solid: target stimulus, dashed: previous and subsequent stimuli). Shaded regions indicate ±SEM.

      Supplementary Figure 3 updated.

      Supplementary Figure 3 caption - Removal of general temporal dependencies in EEG responses for inverted encoding analyses. As described in Methods - Neural Decoding, we used inverted encoding modelling of EEG recordings to estimate the decoding accuracy, precision, and bias of stimulus location. Just as in the linear discriminant classification analysis, we also found the influence of general temporal dependencies in the results produced by the inverted encoding analysis. In particular, there was increased decoding accuracy for targets with low D location. This was weakly evident in the period prior to stimulus presentation, but clearly visible when the labels were shuffled. These results are mirror those from the classification analysis, albeit in a more continuous space. However, whereas in the classification analysis it was straightforward to perform a baseline correction to remove the influence of general temporal dependency, the more complex nature of the accuracy, precision, and bias parameters over the range of time and D location makes this approach less appropriate. For example, the bias in the shuffled condition ranged from -180° to 180°, which when subtracted from the bias in the unshuffled condition would produce an equally spurious outcome, i.e., the equal opposite of this extreme bias. Instead for the inverted encoding analysis, we used the data high-pass filtered at 0.7 Hz. As with the classification analysis, this significantly reduced the influence of general temporal dependencies, as indicated by the results of the shuffled data analysis, but it also temporally smeared the stimulus-related signal, resulting in above chance decoding accuracy prior to stimulus onset. However, we were primarily interested in the pattern of accuracy, precision, and bias as a function of D location, and less concerned with the precise temporal dynamics of these changes. Thus, this was the more suitable approach to removing the general temporal dependencies in the inverted encoding analysis and the one that is presented in Figure 3. (a) Decoding accuracy as a function of time for the EEG data filtered using a 0.1 Hz high-pass filter. Inset shows the EEG sensors included in the analysis (blue dots), and black rectangles indicate the timing of stimulus presentations (solid: target stimulus, dashed: previous and subsequent stimuli). (b, c) The same as (a), but as a function of time and D location for (b) the original data and (c) data with shuffled labels. (d-f) Same as (a-c), but for data filtered using a 0.7 Hz high-pass filter. Shaded regions in (a, d) indicate ±SEM. Horizontal bars in (a, d) indicate cluster corrected periods of significance; note, all time points in (d) were significantly above chance. Note, the temporal abscissa is vertically aligned across plots (a-c & d-f).

      In the process of performing these additional analyses and simulations, we became aware that the sign of the decoding bias in the inverted encoding analyses had been interpreted in the wrong direction. That is, where we previously reported an initial attractive bias followed by a repulsive bias relative to the previous target, we have in fact found the opposite, an initial repulsive bias followed by an attractive bias relative to the previous target. Based on the new control analyses and simulations, we think that the latter attractive bias was due to general temporal dependencies. That is, in the filtered data, we only observe a repulsive bias. While the bias associated with serial dependence was not a primary feature of the study, this (somewhat embarrassing) discovery has led to reinterpretation of some results relating to serial dependence. However, it is encouraging to see that our results now align with those of recent studies (Fischer et al., 2024; Luo et al., 2025; Sheehan et al. 2024).

      Line 385 - Our corresponding EEG analyses revealed better decoding accuracy and precision for stimuli preceded by those that were different and a bias away from the previous stimulus. These results are consistent with finding that alternating stimuli are recalled more precisely. Further, while the repulsive pattern of biases is inconsistent with the observed behavioural attractive biases, it is consistent with recent work on serial dependence indicating an initial period of repulsion, followed by an attractive bias during the response period (20–22). These findings indicate that serial dependence and first-order sequential dependencies can be explained by the same underlying principle.

      (5) Given the relatively early decoding results and surprisingly early differences in decoding peaks, it would be useful to visualize ERPs across conditions to better understand the latencies and ERP components involved in the task.

      A rapid presentation design was used in the EEG experiment, and while this is well suited to decoding analyses, unfortunately we cannot resolve ERPs because the univariate signal is dominated by an oscillation at the stimulus presentation frequency (~3 Hz). We agree that this could be useful to examine in future work.

      (6) It is unclear why the precision derived from IEM results is considered reliable while the accuracy is dismissed due to the artifact, given that both seem to be computed from the same set of decoding error angles (equations 8-9).

      This point has been addressed in our response to point (4).

      (7) What is the rationale for selecting five past events as the meso-scale? Prior history effects have been shown to extend much further back in time (Fritsche et al., 2020). 

      We used five previous items in the meso analyses to be consistent with previous research on sequential dependencies (Bertelson, 1961; Gao et al., 2009; Jentzsch & Sommer, 2002; Kirby, 1976; Remington, 1969). However, we agree that these effects likely extend further and have acknowledged this in the revied version of the manuscript.

      Line 240 - Higher-order sequential dependences are an example of how stimuli (at least) as far back as five events in the past can shape the speed and task accuracy of responses to the current stimulus (9, 10); however, note that these effects have been observed for more than five events (20).

      (8) The decoding bias results, particularly the sequence of attraction and repulsion, appear to run counter to the temporal dynamics reported in recent studies (Fischer et al., 2024; Luo et al., 2025; Sheehan & Serences, 2022). 

      This point has been addressed in our response to point (4).

      (9) The repulsive component in the decoding results (e.g., Figure 3h) seems implausibly large, with orientation differences exceeding what is typically observed in behavior. 

      As noted in our response to point (4), this bias was likely due to the general temporal dependency confound and has been removed in the revised version of the manuscript.

      (10) The pattern of accuracy, response times, and precision reported in Figure 3 (also line 188) resembles results reported in earlier work (Stewart, 2007) and in recent studies suggesting that integration may lead to interference at intermediate stimulus differences rather than improvement for similar stimuli (Ozkirli et al., 2025).

      Thank you for bringing this to our attention, we have acknowledged this in the revised manuscript.

      Line 197 - Consistent with our previous binary analysis, and with previous work (19), we also found that responses were faster and more accurate when D location was small (Fig. 3b, c).

      (11) Some figures show larger group-level variability in specific conditions but not others (e.g., Figures 2b-c and 5b-c). I suggest reporting effect sizes for all statistical tests to provide a clearer sense of the strength of the observed effects. 

      Yes, as noted in the original manuscript, we find significant differences between the variance task-related and -unrelated conditions. We think this is due to opposing forces in the task-related condition: 

      “The increased variability of response time differences across the taskrelated plane likely reflects individual differences in attention and prioritization of responding either quickly or accurately. On each trial, the correct response (e.g., left or right) was equally probable. So, to perform the task accurately, participants were motivated to respond without bias, i.e., without being influenced by the previous stimulus. We would expect this to reduce the difference in response time for repeat and alternate stimuli across the taskrelated plane, but not the task-unrelated plane. However, attention may amplify the bias towards making faster responses for repeat stimuli, by increasing awareness of the identity of stimuli as either repeats or alternations (17). These two opposing forces vary with task engagement and strategy and thus would be expected produce increased variability across the task-related plane.” We agree that providing effect sizes may provided a clearer sense of the observed effects and have done so in the revised version of the manuscript.

      Line 739 - For Wilcoxon signed rank tests, the rank-biserial correlation (r) was calculated as an estimate of effect size, where 0.1, 0.3, and 0.5 indicate small, medium, and large effects, respectively (54). For Friedman’s ANONA tests, Kendal’s W was calculated as an estimate of effect size, where 0.1, 0.3, and 0.5 indicate small, medium, and large effects, respectively (55).

      (12) The statement that "serial dependence is associated with sensory stimuli being perceived as more similar" appears inconsistent with much of the literature suggesting that these effects occur at post-perceptual stages (Barbosa et al., 2020; Bliss et al., 2017; Ceylan et al., 2021; Fischer et al., 2024; Fritsche et al., 2017; Sheehan & Serences, 2022). 

      In light of the revised analyses, this statement has been removed from the manuscript.

      (13) If I understand correctly, the reproduction bias (i.e., serial dependence) is estimated on a small subset of the data (10%). Were the data analyzed by pooling across subjects?

      The dual reproduction task only occurred on 10% of trials. There were approximately 2000 trials, so ~200 reproduction responses. For the micro and macro analyses, this was sufficient to estimate precision within each of the experimental conditions (repeat/alternate, expected/unexpected). However, it is likely that we were not able to reproduce the effect of precision at the meso level across both experiments because we lacked sufficient responses to reliably estimate precision when split across the eight sequence conditions. Despite this, the data was always analysed within subjects.

      (14) I'm also not convinced that biases observed in forced-choice and reproduction tasks should be interpreted as arising from the same process or mechanism. Some of the effects described here could instead be consistent with classic priming. 

      We agree that the results associated with the forced-choice task (response time task accuracy) were likely due to motor priming, but that a separate (predictive) mechanism may explain the (precision) results associated with the reproduction task. These are two mechanisms we think are operating across the three temporal scales investigated in the current study.

      Reviewing Editor Comments:

      (1) Clarify task design and measurement: The dense presentation makes it difficult to understand key design elements and their implications. Please provide clearer descriptions of all task elements, and how they relate to each other (EEG vs. behaviour, stimulus plane vs. TR and TU plane, reproduction vs. discrimination and role of priming), and clearly explain how key measures were computed for each of these (e.g., precision, accuracy, reproduction bias).

      In the revised manuscript, we have expanded on descriptions of the source and nature of the data (behavioural and EEG), the different planes analyzed in the behavioural task, and how key metrics (e.g., precision) were computed.

      (2) Offer more insight into underlying data, including original ERP waveforms to aid interpretation of decoding results and the timing of effects. In particular, unpack the decoding temporal confound further.

      In the revised manuscript, we have considerably offered more insight into the decoding results, in particular, the nature of the temporal confound. We were unable to assess ERPs due to the rapid presentation design employed in the EEG experiment.

      (3) Justify arbitrary choices such as electrode selection for EEG decoding (e.g., limiting to parieto-occipital sensors), number of trials in meso scale, and the time terminology itself.

      In the revised manuscript, we have clarified the reasons for electrode selection.

      (3) Discuss deviations from literature: Several findings appear to contradict or diverge from previous literature (e.g., effects of serial dependence). These discrepancies could be discussed in more depth. 

      Upon re-analysis of the serial dependence bias and removal of the temporal confound, the results of the revised manuscript now align with those from previous literature, which has been acknowledged.

      Reviewer #1 (Recommendations for the authors):

      (1) would like to use my reviewer's prerogative to mention a couple of relevant publications. 

      Galluzzi et al (Journal of Vision, 2022) "Visual priming and serial dependence are mediated by separate mechanisms" suggests exactly that, which is relevant to this study.

      Xie et al. (Communications Psychology, 2025) "Recent, but not long-term, priors induce behavioral oscillations in peri-saccadic vision" also seems relevant to the issue of different mechanisms. 

      Thank you for bringing these studies to our attention. We agree that they are both relevant have referenced both appropriately in the revised version of the manuscript.

      Reviewer #2 (Recommendations for the authors): 

      (1) I find the discussion on attention and awareness (from line 127 onward) somewhat vague and requiring clarification.

      We agree that this statement was vague and referred to “awareness” without operationation. We have revised this statement to improve clarity.

      Line 135 - However, task-relatedness may amplify the bias towards making faster responses for repeat stimuli, by increasing attention to the identity of stimuli as either repeats or alternations (17).

      (2) Line 140: It's hard to argue that there are expectations that the image of an object on the retina is likely to stay the same, since retinal input is always changing. 

      We agree that retinal input is often changing, e.g., due to saccades, self-motion, and world motion. However, for a prediction to be useful, e.g., to reduce metabolic expenditure or speed up responses, it must be somewhat precise, so a prediction that retinal input will change is not necessarily useful, unless it can specify what it will change to. Given retinal input of x at time t, the range of possible values of x at time t+1 (predicting change) is infinite. By contrast, if we predict that x=x at time t+1 (no change), then we can make a precise prediction. There is, of course, other information that could be used to reduce the parameter space of predicted change from x at time t, e.g., the value of x at time t-1, and we think this drives predictions too. However, across the infinite distribution of changes from x, zero change will occur more frequently than any other value, so we think it’s reasonable to assert that the brain may be sensitive to this pattern.

      (3) Line 564: The gambler's fallacy usually involves sequences longer than just one event.

      Yes, we agree that this phenomenon is associated with longer sequences. This section of the manuscript was in regards to previous findings that were not directly relevant to the current study and has been removed in the revised version.

      (4) In the shared PDF, the light and dark cyan colors used do not appear clearly distinguishable. 

      I expect this is due to poor document processing or low-quality image embeddings. I will check that they are distinguishable in the final version.

      References: 

      Barbosa, J., Stein, H., Martinez, R. L., Galan-Gadea, A., Li, S., Dalmau, J., Adam, K. C. S., Valls-Solé, J., Constantinidis, C., & Compte, A. (2020). Interplay between persistent activity and activity-silent dynamics in the prefrontal cortex underlies serial biases in working memory. Nature Neuroscience, 23(8), Articolo 8. https://doi.org/10.1038/s41593-020-0644-4

      Bliss, D. P., Sun, J. J., & D'Esposito, M. (2017). Serial dependence is absent at the time of perception but increases in visual working memory. Scientific reports, 7(1), 14739. 

      Ceylan, G., Herzog, M. H., & Pascucci, D. (2021). Serial dependence does not originate from low-level visual processing. Cognition, 212, 104709. https://doi.org/10.1016/j.cognition.2021.104709

      Fischer, C., Kaiser, J., & Bledowski, C. (2024). A direct neural signature of serial dependence in working memory. eLife, 13. https://doi.org/10.7554/eLife.99478.1

      Fritsche, M., Mostert, P., & de Lange, F. P. (2017). Opposite effects of recent history on perception and decision. Current Biology, 27(4), 590-595. 

      Fritsche, M., Spaak, E., & de Lange, F. P. (2020). A Bayesian and efficient observer model explains concurrent attractive and repulsive history biases in visual perception. eLife, 9, e55389. https://doi.org/10.7554/eLife.55389

      Gekas, N., McDermott, K. C., & Mamassian, P. (2019). Disambiguating serial effects of multiple timescales. Journal of vision, 19(6), 24-24. 

      Luo, M., Zhang, H., Fang, F., & Luo, H. (2025). Reactivation of previous decisions repulsively biases sensory encoding but attractively biases decision-making. PLOS Biology, 23(4), e3003150. https://doi.org/10.1371/journal.pbio.3003150

      Ozkirli, A., Pascucci, D., & Herzog, M. H. (2025). Failure to replicate a superiority effect in crowding. Nature Communications, 16(1), 1637. https://doi.org/10.1038/s41467025-56762-5

      Sheehan, T. C., & Serences, J. T. (2022). Attractive serial dependence overcomes repulsive neuronal adaptation. PLoS biology, 20(9), e3001711. 

      Stewart, N. (2007). Absolute identification is relative: A reply to Brown, Marley, and

      Lacouture (2007).  Psychological  Review, 114, 533-538. https://doi.org/10.1037/0033-295X.114.2.533

      Treisman, M., & Williams, T. C. (1984). A theory of criterion setting with an application to sequential dependencies. Psychological review, 91(1), 68. 

      Zhang, G., & Luck, S. J. (2025). Assessing the impact of artifact correction and artifact rejection on the performance of SVM- and LDA-based decoding of EEG signals. NeuroImage, 316, 121304. https://doi.org/10.1016/j.neuroimage.2025.121304

    1. Document de Synthèse : L'Emprise du Numérique et les Dangers des Réseaux Sociaux

      Introduction : Une Lutte "David contre Goliath"

      Ce briefing expose la problématique alarmante de l'impact des réseaux sociaux sur la santé mentale et la sécurité des enfants et adolescents.

      Il met en lumière les témoignages poignants de victimes et de leurs familles, les actions en justice, le manque de régulation et les tactiques des géants de la technologie.

      La lutte est présentée comme un combat "David contre Goliath" entre des familles endeuillées et des entreprises multimillionnaires.

      Thèmes Principaux et Faits Importants :

      1. Addiction et Impact sur la Santé Mentale des Adolescents :

      Témoignage d'Alexis Spence : Alexis a développé de l'anorexie, de la dépression et s'est scarifiée à partir de 11 ans après avoir téléchargé Instagram.

      L'algorithme l'a submergée de contenus sur la minceur, puis de photos de personnes anorexiques, de contenus tristes et déprimants.

      Elle décrit comment elle s'est enfermée dans sa souffrance, devenant "une personne qu'on ne reconnaissait plus".

      Citation : "J'avais 11 ans quand j'ai téléchargé Instagram pour la première fois et c'est là que tout a commencé. [...]

      À force de regarder de la fitness, l'application a commencé à me montrer des mannequins. [...] Les mannequins étaient de plus en plus minces jusqu'à ce que ce ne soient plus des mannequins mais des personnes anorexiques."

      Citation : "Mon compte est devenu rempli de ces contenus. C'était des photos tristes en noir et blanc avec des textes déprimants."

      Citation : "Je pense vraiment qu'Instagram a une grande part de responsabilité dans les problèmes de santé mentale dont j'ai souffert, surtout si on prend en compte mon Je n'avais que 13 ans."

      Idées Suicidaires et Automutilation : Plusieurs témoignages de parents évoquent les scarifications et les tentatives de suicide de leurs enfants, directement liées aux contenus diffusés par les algorithmes.

      Citation : "J'ai posté une photo qui disait que j'avais l'intention de me suicider ce soir-là. [...] J'ai reçu un appel de l'assistante sociale. Vous devez venir à l'école immédiatement. Votre fille a tenté de se suicider."

      Citation : "On avait mis en place des scarifications un peu contrôlées. Donc lorsqu'il allait pas bien, il me demandait ses lames. J'attendais derrière la porte de sa chambre et voir se scarifier."

      Déni des Plateformes : Les dirigeants des Big Tech ont longtemps nié le lien entre leurs plateformes et les problèmes de santé mentale.

      Citation d’un sénateur interrogeant Mark Zuckerberg : "everyone knows that kids who spend a lot of time too much time on your platforms are at risk and it's not just the mental health issues. I mean let me ask you a question is your platform safe for kids I believe it is but there's a difference between country if we don't start honest."

      2. Cyberpédocriminalité et Manque de Sécurité :

      Prolifération de Contenus Dangereux : Les plateformes sont des vecteurs de cyberpédocriminalité, avec des prédateurs sexuels qui exploitent les algorithmes et les fonctionnalités pour cibler les enfants. Interpol Europe est "débordé par la cyberpédocriminalité".

      Citation : "on est quand même un moment assez crucial où Interpol Europe on est débordé par la cyberpédocriminalité et les plateformes elles sont vraiment utilisées par les prédateurs sexuels."

      Citation : "Plus de 80 % des cas de sextorsion, c'est sur Instagram et Snapchat. Urgence à ce qu'elles fassent le ménage."

      Algorithmes Complices : Une expérience avec un avatar de 13 ans, "Lili", démontre que les algorithmes proposent très rapidement des contenus sombres, des scènes d'automutilation, du vampirisme, des scènes sexualisées, et même l'apologie du suicide, même sans recherche préalable de l'utilisateur.

      Citation : "Sur TikTok, l'algorithme est encore plus rapide. En moins de 5 minutes, la plateforme met en avant des vidéos faisant l'apologie du suicide."

      Citation : "En quelques clics, la petite Lili se retrouve témoin de plusieurs viols sur mineurs."

      Techniques de Manipulation des Prédateurs : Des modes d'emploi pour piéger les enfants sont disponibles en ligne. Les prédateurs utilisent des tactiques psychologiques comme le "love bombing" et la sexualisation progressive des conversations, détournant des codes familiers (personnages de dessins animés) pour normaliser des comportements abusifs.

      Citation : "Ils vont vraiment jouer sur plein de ressorts psychologiques différents au niveau des enfants."

      Citation : "Le fait de reprendre des codes par exemple de la Reine des Neiges, enfin des des différents personnages comme ça, il y a il y a des choses qui sont familières qui font pas forcément heurté comme un cohite frontal de de pornographie."

      Réponse Insuffisante des Plateformes : Malgré les signalements, les plateformes ne suppriment pas toujours les contenus illicites et les comptes de prédateurs. Leurs efforts de sécurité sont jugés insuffisants.

      Citation d’un sénateur : "Mr. Zuckerberg, what the hell were you thinking? [...] In what I understand get resources in what saying universe is there a link for se results anyway?" (concernant un message d'avertissement offrant l'option "voir les résultats quand même" pour des contenus problématiques).

      Citation d’un représentant de l’office de lutte contre la cyberpédocriminalité : "On a très très peu de signalement qui parviennent par exemple WhatsApp."

      3. Le Rôle des Entreprises de Technologie et leur Responsabilité :

      Le "Business Model" des Big Tech : Les documents internes de Meta révélés par Frances Haugen (une lanceuse d'alerte) montrent que l'entreprise était consciente des vulnérabilités des enfants et des impacts négatifs, mais a privilégié les profits.

      Citation : "Ces documents montrent que depuis 20 ans mett à enquête sur les vulnérabilités des enfants."

      Citation : "Facebook repeatedly encounter conflicts between its own profits and our safety."

      Citation d’un sénateur : "Children are not your priority. Children are your product. Children you see as a way to make money."

      L'Article 230 comme Bouclier : Les entreprises se cachent derrière l'article 230 du droit américain, qui leur confère une immunité en tant qu'hébergeurs de contenu, les protégeant des poursuites judiciaires pour le contenu publié par leurs utilisateurs.

      Citation : "Ces entreprises se cachent derrière l'article 230 qui est vraiment archaïque. Ils utilisent cette loi comme bouclier pour dire vous ne pouvez pas nous attaquer."

      Citation d’un sénateur : "It's an astonishing benefit that your industry has that no other industry has. They just don't have to worry about being held in court if they're negligent."

      Lobbying Intense : Pour contrer les projets de loi visant à lever leur immunité et à les responsabiliser, les Big Five ont dépensé près de 100 millions de dollars en lobbying, plus de la moitié provenant du groupe Meta.

      Citation : "Ils ont dépensé près de 100 millions de dollars pour faire renoncer les députés et les sénateur, plus de la moitié de cette somme provient du seul groupe métablill."

      4. Mobilisation Collective et Actions en Justice :

      Mouvement Mondial des Parents : Des parents et des familles du monde entier se mobilisent pour exiger des changements et une meilleure protection des enfants.

      Citation d’un père : "Nous en tant que père Tant que mer nous ne faisons rien, personne ne le fera à notre place. C'est notre lutte."

      Citation d’une mère : "Nous sommes des milliers de pères et de mères qui pensons que les smartphones et les réseaux sociaux ne sont pas bons pour nos fils et nos filles."

      Collectif Algos Victima : Fondé par l'avocate Maître Laure Bouttron Marmion, ce collectif rassemble des familles d'adolescents dont le suicide est lié aux réseaux sociaux, notamment l'affaire de Marie, une jeune fille décédée en 2021.

      Le collectif vise à faire reconnaître la responsabilité des entreprises.

      Citation de Maître Bouttron Marmion : "On souhaite la régulation cette plateforme qui aujourd'hui est au degré zéro de la régulation."

      Citation de Maître Bouttron Marmion : "On ne peut pas ne pas considérer que le réseau social n'a pas sa part de responsabilité dans le suicide de Marie."

      Actions Judiciaires aux États-Unis et en Europe : Plus de 1000 familles et 44 États américains sur 50 poursuivent les géants de la technologie. Des avocats cherchent des bases juridiques solides pour les attaquer.

      Citation d’Alexis : "Depuis, plus de 1000 familles nous ont rejoint et maintenant 44 États américains sur 50 attaquent en justice les grandes entreprises technologiques pour qu'ils soient tenu responsable." Initiatives de Réglementation : Des projets de loi comme le "Kids Online Safety Act", le "EARN IT Act" et le "STOP CSAM Act" visent à rendre les entreprises responsables de l'exploitation des enfants et à supprimer leur immunité.

      Citation d’un sénateur : "We have bills that have passed through this incredibly diverse committee when it comes to our political views. Kids online safety act earned act stopam act."

      5. Solutions et Espoirs :

      Interdiction des Smartphones avant un certain âge : En Espagne, un mouvement de parents a réussi à réglementer l'utilisation des téléphones portables dans les collèges et milite pour une interdiction totale avant 16 ans.

      Citation d’une mère : "Nous souhaitons que les smartphones ne puissent pas être utilisés avant 16 ans."

      Citation : "Maintenant, dans les classes et dans la cour, ils ne peuvent plus utiliser leur téléphone portable, sauf si le professeur le demande à un moment précis."

      Désactivation des Algorithmes pour les Mineurs : Une demande clé est la désactivation des algorithmes pour les mineurs afin de les protéger des contenus inappropriés.

      Citation : "Nous devons veiller à ce que l'algorithme soit désactivé pour les mineurs."

      Espoir dans la Lutte "d'en bas" : L'espoir réside dans la mobilisation des familles et des citoyens face à l'inaction des entreprises et des législateurs.

      Citation : "J'ai beaucoup plus d'espoir dans les familles, dans la lutte qui vient d'en bas plutôt que d'en haut."

      L'excuse de Zuckerberg : Lors d'une audition au Sénat, Mark Zuckerberg a été contraint de s'excuser devant les victimes, bien que ses excuses aient été perçues comme insincères et non liées à la nature de son produit.

      Citation de Mark Zuckerberg : "I'm sorry for everything that you all gone through terrible. No one should have to go through the things that your families have have suffered."

      Citation d’Alexis : "Ses excuses n'étaient pas sincères. Il s'est excusé mais il ne s'est pas excusé à cause de son produit qu'il appelle lui-même un produit et qui fait du mal."

      Conclusion : Un Monde Post-Écran pour les Enfants ?

      Le briefing souligne que le consensus sur la menace profonde que représentent les réseaux sociaux pour la santé mentale et la sécurité des enfants est désormais établi.

      La persévérance des victimes et des familles est cruciale pour obliger les entreprises et les législateurs à agir, avec l'espoir qu'un jour, "ça nous semblera tout aussi horrible qu'un enfant possède un téléphone portable et soit déconnecté de la vie".

    1. Briefing : L'Alcoolisme au Féminin – Briser le Tabou

      Objectif : Ce briefing vise à synthétiser les principaux thèmes, idées et faits marquants concernant l'alcoolisme au féminin, tels qu'abordés dans les extraits sonores de "Alcool au féminin, elles brisent le tabou".

      Résumé Exécutif

      L'alcoolisme au féminin est une maladie complexe, souvent invisible et entourée d'une honte et d'une culpabilité profondes, rendant sa détection et sa prise en charge plus difficiles que chez les hommes.

      Les femmes sont physiologiquement plus vulnérables à l'alcool et l'utilisent souvent comme une "béquille" pour gérer un mal-être, une anxiété, une dépression, ou des traumatismes passés, notamment des violences sexuelles.

      L'industrie de l'alcool cible activement les femmes avec des produits et des stratégies marketing spécifiques.

      Le chemin vers la sobriété est long, marqué par des rechutes possibles, et nécessite un soutien indispensable de l'entourage, des groupes de parole, et des structures spécialisées.

      Briser le tabou et reconnaître l'alcoolisme comme une maladie est crucial pour aider les femmes à s'en sortir.

      Thèmes et Idées Principales

      1. L'Alcoolisme Féminin : Une Réalité Invisible et Sous-Estimée

      Prévalence incertaine : Le nombre de femmes dépendantes à l'alcool est difficile à estimer, oscillant entre 100 000 et 1,5 million, en raison du silence imposé par la honte et la culpabilité.

      Honte et Culpabilité Accrues pour les Femmes : "Une femme qui boit tout d'un coup, c'est une honte. C'est deux fois plus dur qu'un homme.

      Une femme alcoolique, c'est vraiment on nous le pardonne pas." Ce jugement social conduit à l'isolement et au déni, retardant la consultation de 10 ans en moyenne par rapport aux hommes.

      Stratégies de Dissimulation : Les femmes mettent souvent en place des stratagèmes pour cacher leur consommation, comme planquer des bouteilles dans des endroits inattendus (ex: "planquer la bouteille dans le landau de ma fille").

      2. Vulnérabilité Physiologique et Conséquences Spécifiques

      Métabolisme et Dilution : "Quand on donne la même quantité d'alcool à un homme et une femme du même poids, l'alcoolémie sera plus élevée chez la femme."

      Cela est dû à un métabolisme plus lent et une moindre proportion d'eau dans le corps féminin.

      Impacts Accrus sur la Santé : Les maladies (cirrhose, maladies cardiovasculaires, troubles cognitifs comme la mémoire et la concentration) se développent plus rapidement et sont plus violentes chez les femmes.

      Un lien fort existe avec le risque de cancer du sein, "quelque chose qui est très peu connu".

      Signes Visibles : L'alcool "abîme énormément et chez les femmes, ça se voit. Une femme alcoolique, ça se voit au visage, aux yeux. Les yeux sont tristes souvent. La peau est abîmée."

      3. Les Racines Psychologiques de l'Addiction chez les Femmes

      Alcool comme Béquille ou Auto-Médication : Contrairement aux hommes dont la consommation "part d'une consommation plus festive qui dérape", les femmes "le plus souvent consomment pour traiter quelque chose, pour traiter un mal-être, une dépression, une anxiété."

      Noémilovski témoigne : "j'ai bu de l'alcool comme j'aurais pris des médicaments pour pour apaiser et l'angoisse et la dépression."

      Traumatismes d'Enfance et Violences Sexuelles : Derrière l'addiction se cachent souvent des "traumatismes d'enfance, des drames intimes".

      Le vécu d'une agression sexuelle peut multiplier "jusqu'à 36 le risque de développer une addiction".

      L'alcool permet "d'économiser, d'avoir à se confronter à ces horreurs". Laurence, par exemple, a découvert que son alcoolisme masquait un inceste.

      Sentiment de Solitude et Différence : Muriel Robin a ressenti : "je me sentais tellement différente que j'étais très seule. Donc j'étais en souffrance."

      L'alcool est alors apparu comme une solution pour "masquer tout", "penser à rien" et "se perdre".

      L'Illusion du Plaisir et du "Soi-Même" : Beaucoup croient que l'alcool est une source de plaisir ou qu'il permet d'être "soi-même".

      Noémilovski réfute cette idée : "on n'est pas soi-même. On est l'alcool, on est l'effet de l'alcool."

      L'alcool crée une "chaleur, une douceur, un calme", mais mène à un "cercle vicieux" où l'on est "encore plus déprimé que la veille, encore plus angoissé".

      4. L'Influence de la Société et du Marketing de l'Alcool

      Normalisation de la Consommation Féminine : Boire est devenu "courant" pour les femmes, une manière de "s'intégrer", de décompresser, ou de faire la fête.

      Lucille Woodward souligne : "on a toujours eu l'impression que c'était cool de boire et normal et plutôt une démonstration de force de la femme et on se rend pas compte en fait que finalement ça nous affaiblit."

      Ciblage Marketing Spécifique : L'industrie de l'alcool cible les femmes avec des produits et des packagings "ultra girly" (ex: "tube de rouge à lèvres géant qui en fait contient une bouteille de champagne") et des saveurs aromatisées (mangue, litchi, cerise, pamplemousse) pour des alcools "moins forts".

      Ces stratégies "associent un univers positif à un produit qui est quand même problématique pour la santé."

      La "Zone Grise" : De nombreuses femmes se situent dans une "zone grise" où elles dépassent les limites recommandées (10 verres/semaine) sans se considérer comme dépendantes.

      Le critère n'est pas le nombre de verres, mais "quand on ne peut pas s'en séparer et quand on a le sentiment d'avoir perdu la liberté de s'abstenir" et l'impact sur la santé et l'environnement.

      5. Le Chemin vers la Sobriété : Un Combat Difficile mais Possible

      Reconnaître la Maladie : L'alcoolisme est une maladie, non un manque de volonté.

      C'est "une maladie que l'on peut soigner à condition d'oser la regarder en face."

      L'Importance du Soutien : "L'alcool, on ne peut pas s'en sortir seul. Il faut demander de l'aide."

      Groupes de parole : Les Alcooliques Anonymes ont été une "révélation" pour Noémilovski grâce à l'absence de jugement.

      Des groupes spécifiques aux femmes permettent de reconnaître une "consommation autothérapeutique" commune.

      Entraide et Témoignages : Des initiatives comme celle de Sylvie, qui aide d'autres femmes via internet, sont cruciales. "À force d'en parler, de déculpabiliser, d'avoir moins honte, j'ai pu tomber le masque en fait."

      L'Entourage Aimant : Le soutien du conjoint est fondamental, comme pour Fiona Géin et Muriel Robin. Leurs partenaires ont cessé de boire et ont posé des limites claires pour leur relation.

      La Reconstruction Personnelle :Deuil de l'Alcool :

      L'arrêt peut être vécu comme un deuil, "comme si ma meilleure amie était morte", laissant un sentiment de vide.

      Accepter les Rechutes : Les rechutes sont fréquentes et "ne remettent pas tout en cause". La mémoire de l'alcool reste présente ("l'image de Pac-Man dans mon cerveau").

      Se Réconcilier avec Soi-Même : Le processus de reconstruction inclut la réappropriation de son image, de son corps, et de son estime de soi, souvent perdus pendant l'addiction.

      Des ateliers d'art-thérapie ou de socio-esthétique aident à "se redonner une dignité" et à "adoucir le regard sur soi-même".

      Trouver de Nouveaux Plaisirs : Remplacer l'alcool par d'autres sources de joie, comme le thé pour Sylvie, est une stratégie efficace.

      6. L'Impact sur l'Entourage, en Particulier les Enfants

      Souffrance Familiale : Pour chaque personne alcoolique, "en moyenne sept personnes qui souffrent autour d'elle", les enfants étant souvent en première ligne.

      Les Enfants Observateurs : Charlotte, fille d'une mère alcoolique, mesurait le niveau des bouteilles et comprenait l'ambiance "sordide" de la maison.

      Le Paradoxe de l'Amour et de la Haine : Les enfants d'alcooliques doivent gérer un paradoxe : "Je pouvais beaucoup l'aimer mais je pouvais la haïr en même temps parce que je ne la reconnaissais pas quand elle était ivre."

      Nécessité de se Sauver Soi-Même : Malgré les tentatives de "réparer" le parent, le chemin est souvent de "sauver notre peau" et "abandonner cette famille dysfonctionnelle".

      Citations Clés

      "J'ai senti que dans mon disque dur, il y avait quelque chose qui était là et que et boire était normal." – Muriel Robin, sur l'installation de sa dépendance.

      "Moi je buvais je buvais un litre de champagne quand je quand j'étais dehors. Je buvais un litre de champagne tous les soirs minimum." – Muriel Robin, sur la quantité consommée.

      "L'alcool, j'allais dire c'est la récompense. Ce n'est pas une récompense. C'est quelque c'est c'est quelque chose qui qui vous veut du mal." – Muriel Robin, sur la nature trompeuse de l'alcool.

      "Oui, j'étais alcoolique. Ouais, j'étais alcoolique pendant 30 ans." – Muriel Robin, sur la durée de son addiction. "L'alcool dérobe des années de vie de manière insidieuse et pour les femmes en particulier de façon invisible. C'est un poison qui s'instille à l'abri des regards." – Narratrice.

      "Une femme qui boit tout d'un coup, c'est une honte. C'est deux fois plus dur qu'un homme. Une femme alcoolique, c'est vraiment on nous le pardonne pas." – Témoignage.

      "Les hommes, ça part d'une consommation plus festive qui dérape. Les femmes le plus souvent consomment pour traiter quelque chose, pour traiter un mal-être, une dépression, une anxiété." – Experte.

      "J'ai commencé à boire suite à un viol." – Anaïs. "Mon engagement, j'ai un problème avec l'alcool. Je bois, je bois trop." – Lucille Woodward, brisant le tabou en ligne.

      "On a un problème d'alcool lorsqu'on ne peut pas s'en séparer et quand on a le sentiment d'avoir perdu la liberté de s'abstenir." – Définition de l'addiction.

      "J'ai pris de l'alcool comme on prendrait des anxiolytiques." – Noémilovski.

      "Tu n'es pas toi-même quand tu bois et moi je veux être avec toi quand tu es toi-même." – Proche de Noémilovski. "L'alcool, c'est sans faim. Vous voyez le matin, vous vous dites, je vais arrêter de boire et puis le soir, vous remettez ça." – Sylvie.

      "Le pire que j'ai fait, je crois que c'était dans le landau de ma fille. J'avais planqué la bouteille dans le landau de ma fille." – Sylvie, sur la dissimulation.

      "Il y a un gros pourcentage de risque de cancer du sein lié à l'alcool et ça vraiment c'est quelque chose qui est très peu connu." – Dr. Sarah Coscas, psychiatre addictologue. "Ma petite me disait : 'Maman, tu sens la bière ?'" – Témoignage d'une mère.

      "Le vécu d'une agression sexuelle par une femme pouvait multiplier jusqu'à 36 le risque de développer une addiction." – Dr. Sarah Coscas.

      "La personne, elle préfère préfère dire non, j'ai pas bu pour ne pas passer la soirée à se disputer avec son conjoint ou sa conjointe alors que elle peut pas aligner trois mots parce que elle a passé sa soirée ou sa journée à à boire." – Richard Baudouin, compagnon de Fiona Géin.

      "Écoute moi si tu veux boire une bouteille de champagne tous les soirs c'est ta vie mais moi je j'ai trop peur de te perdre et entre la cigarette et l'alcool je peux pas voir quelqu'un qui se détruit donc on arrête l'histoire." – Anne Le Nen à Muriel Robin, un ultimatum salvateur.

      Conclusion

      Le document met en lumière la spécificité de l'alcoolisme au féminin, caractérisé par une invisibilité sociale, une vulnérabilité physiologique accrue, et des origines souvent liées à des traumatismes ou un mal-être profond.

      Il souligne l'importance cruciale de la reconnaissance de cette maladie, de la brisure du tabou, et du soutien collectif pour permettre aux femmes de se reconstruire et de retrouver une vie digne et sobre.

      Le chemin est long, mais le témoignage de ces femmes courageuses montre que la sortie est possible.

    1. Briefing Détaillé : La Relation des Français à l'Alcool – Entre Héritage Culturel et Lutte Personnelle

      Ce document de briefing explore la relation complexe et souvent paradoxale des Français à l'alcool, à partir d'un enregistrement audio riche en témoignages et analyses.

      Il met en lumière comment l'alcool est profondément ancré dans la culture française, ses différentes fonctions sociales et personnelles, les dangers sous-estimés, les défis de la sobriété et l'influence des lobbies.

      Thèmes Principaux

      L'Alcool comme Héritage Culturel et Art de Vivre Français : L'alcool est présenté comme une tradition séculaire, un "art de vivre" fait de rituels et de moments de convivialité.

      L'Alcool, Rite de Passage et Quête d'Identité : De l'enfance à l'âge adulte, l'alcool marque les étapes de la vie, offrant un sentiment de liberté, de socialisation et de performance.

      Les Illusions et Dangers de l'Alcool : Malgré sa valorisation, l'alcool est une drogue qui masque les problèmes, conduit à des comportements risqués (violences, blackouts) et a des conséquences dévastatrices sur la santé et les relations.

      La Lutte pour la Sobriété : Le parcours vers l'abstinence est semé d'embûches, confronté à la pression sociale, au déni et à la nécessité d'une reconstruction profonde.

      L'Influence des Lobbies et les Croyances Tenaces : Les campagnes de santé publique se heurtent à la puissante influence des lobbies de l'alcool et à des mythes persistants comme le "French Paradoxe".

      Idées et Faits Importants

      1. L'Alcool comme Héritage Culturel et Art de Vivre Français

      Ancrage Profond : L'alcool est "une histoire profondément ancrée dans nos mémoires. C'est la France, une bonne bouteille." Il est omniprésent lors des rencontres entre amis ("on va boire un coup"), symbolisant la convivialité.

      Rituels Sociaux : L'expression "il y a toujours une bonne bouteille sur la table" souligne l'aspect ritualisé de la consommation.

      Initiation Précoce : De nombreux témoignages révèlent une initiation à l'alcool dès la petite enfance, souvent en famille.

      Charlotte se souvient d'avoir "fini la soupe avec le vin" avec son grand-père à 6 ans, et David d'un "fond de Sauternes" à un repas de Noël. Cette initiation est vécue avec fierté, comme un partage du "patrimoine".

      Traditions Institutionnelles : Jusqu'en novembre 1956, les écoles primaires servaient de l'eau coupée au vin à la cantine, ce qui témoigne de la normalisation de l'alcool dès le jeune âge.

      2. L'Alcool, Rite de Passage et Quête d'Identité

      Adolescence et Transgression : Pour les adolescents, "boire est alors un rite de passage pour rentrer dans l'âge adulte." C'est une manière de "faire comme les grands", de "faire partie d'un groupe", même si le goût n'est pas apprécié au début.

      Libération et Communication : Le premier verre est un "déclic" qui permet de "vivre différemment", de "se libérer de quelque chose", de "communiquer avec les autres et avec soi-même".

      Sentiment de Puissance et de Liberté : Baptiste décrit l'alcool comme des "super pouvoirs", de "l'essence dans [son] moteur", le "breuvage magique qui va [lui] permettre d'être pleinement [lui]-même".

      Il procure un sentiment de "liberté" et de "rébellion", où "la nuit nous appartient, on est les rois du monde."

      Performance et Compétition : L'ivresse est associée à des notions de "performance" et de "compète" : "bien tenir l'alcool", "accepter les défis", "pas savoir dire non". Le "binge drinking" (cinq verres en moins de deux heures) est courant chez les jeunes.

      Séduction et Désirabilité : L'alcool est perçu comme un moyen de devenir "quelqu'un", de "plaire", d'avoir des "premières expériences avec les filles". Charlotte buvait "pour me sentir désirable.

      Draguer sans alcool me paraissait inconcevable." Près d'un jeune sur trois confie avoir besoin de boire avant un rapport sexuel.

      Valorisation de l'Excès : "Boire c'est rentrer dans la norme, boire c'est s'émanciper." La "valorisation de l'ivresse et de la transgression et des excès" est perçue comme faisant "partie de la jeunesse."

      Désinhibition et Faux Courage : L'alcool "désinhibe les timides", "décoince les coincés" et sert de "petite dose de courage liquide" pour Charlotte, qui a du mal à aborder des inconnus sobre.

      3. Les Illusions et Dangers de l'Alcool

      Une "Drogue Plaisir" aux Conséquences Néfastes : L'alcool est une "molécule plaisir qui va dès le premier verre agir dans le cerveau et puis euh donner un petit peu d'effets euphorisant, plaisant, relaxant", mais il conduit à l'illusion. Perte de Mémoire et Blackouts :

      L'alcool peut "détruire mes souvenirs" ("Je sais où je suis allé mais je me rappelle plus de ce que j'y ai fait"). Marie décrit des "trous noirs" fréquents où elle ne se souvenait de rien, y compris comment elle était rentrée chez elle.

      Violences et Agressions Sexuelles : L'alcool est impliqué dans 40% des condamnations pour violence familiale en France. Plus d'un jeune sur cinq (18-24 ans) déclare avoir eu un rapport sexuel non consenti à cause de l'alcool.

      Le témoignage de Marie, violée par un ami de son père pendant un confinement alcoolisé, est particulièrement frappant.

      Elle affirme : "pour moi, le problème c'est pas l'alcool, c'est qu'il faut éduquer les garçons". Son père, dévasté, reconnaît : "Et l'alcool a une part de une part de responsabilité là-dedans".

      Baptiste raconte son propre viol, "J'aurais aussi aimé qu'on me dise que qu'on peut me faire du mal quand je suis bourré. On peut aussi me faire du mal parce que je suis bourré."

      La discussion met en évidence la culture du viol persistante : "encore aujourd'hui, si une femme a bu trop, qu'elle a perdu le contrôle, qu'en plus elle avait mis une mini jupe, bah s'il lui arrive quelque chose, elle a un petit peu cherché." Le responsable est l'agresseur.

      Impact sur la Santé : L'alcool multiplie les risques de cancer, d'AVC hémorragique et de troubles du rythme cardiaque.

      Il cause 41 000 décès par an en France, étant la deuxième cause de mort évitable après le tabac.

      Détérioration des Relations : David explique comment l'alcool a détruit son couple et son lien avec ses enfants. Sa femme décrit son regard "dans le vide, fuyant, vitreux" et le sentiment qu'il ne faisait "pas d'efforts pour moi."

      L'alcool le rend agressif et manipulateur verbalement, au point d'une altercation physique avec sa femme devant leurs enfants.

      L'Alcool comme Béquille face à l'Ennui et l'Angoisse : Jean-François a commencé à boire seul après sa carrière sportive, pour combler "la petite mort du sportif" et "accompagner l'ennui".

      Il buvait ses "émotions", son "salaire", "tout". Rose utilisait l'alcool pour "tuer l'ennui et défier la mort".

      4. La Lutte pour la Sobriété Pression Sociale et Jugement : Refuser de boire, surtout jeune, expose à des jugements : "tu te crains", "celle qui l'emmerdeuse", "celle qui n'est pas marrante".

      Pour Lou, qui ne boit pas du tout à 21 ans, la pression sociale est "quasiment en permanence sur [ses] épaules". Arrêter de boire suscite la réaction "Ah, vous êtes devenu chiant", ou "tu es malade".

      Le Déni : Les personnes dépendantes sont souvent dans le déni, se croyant capables de contrôler leur consommation. Jean-François et Baptiste décrivent des "pauses" pour se rassurer, avant de reprendre de plus belle.

      L'addiction est une "pathologie de la liberté", la "perte de la liberté de s'abstenir."

      Le Chemin Difficile de la Reconstruction : La sobriété n'est pas un "glamour instantané". C'est un processus long et douloureux, car le système de plaisir est "endormi". Il faut "apprendre à vivre sans cette béquille là".

      Le Rôle du Soutien : Le soutien des proches est crucial. La lettre des amis de Baptiste l'a aidé à "ouvrir les yeux". Coluche soulignait l'importance d'"avoir des copains qui vous aident".

      Bénéfices de la Sobriété : Pour David, la sobriété lui a permis de "redevenir acteur de [sa] vie", d'"être présent" pour ses enfants et sa femme, de "répondre au téléphone quand les gens [l']appellent".

      C'est une source de fierté et de bonheur retrouvé.

      5. L'Influence des Lobbies et les Croyances Tenaces Publicités et Mythes : Pendant des décennies, l'alcool a été promu comme un bienfait, voire un médicament ("le bon grog picon chaud tue la grippe", "soignez-vous par le vin"). Un livre de 1974 "Soignez-vous par le vin" a connu un immense succès.

      Le "French Paradoxe" : La croyance que le vin rouge protège des maladies cardiaques, popularisée par le "French Paradoxe" dans les années 90, a "fait du mal" car elle est "restée très ancrée".

      Cette "corrélation" n'a jamais été réellement prouvée comme un lien de causalité.

      Le slogan "consommer avec modération" a été judicieusement introduit par les lobbies pour atténuer les messages de prévention.

      Loi Evain (1991) : Cette loi a marqué un tournant en interdisant la publicité à la télévision et au cinéma et en imposant un message de prévention. Cependant, elle a été rapidement "attaquée" par les lobbies.

      Influence Politique : Le président de la République est "sous influence des lobbies de l'alcool", ce qui se traduit par des annulations de campagnes de prévention jugées trop "prohibitionnistes" par l'industrie.

      La campagne de 2023 "C'est pas un peu absurde de se souhaiter une bonne santé avec de l'alcool ?" a provoqué une réaction virulente des lobbies.

      L'attitude des hommes politiques, comme le président qui "va boire une bière avec les joueurs", "brouille vraiment tous les messages."

      En conclusion, l'alcool en France est un phénomène culturel complexe, intriqué dans l'histoire, les rituels sociaux et les parcours individuels.

      Si son rôle dans la convivialité et la libération est souvent mis en avant, les témoignages révèlent les dangers profonds sur la santé physique et mentale, les relations humaines, et la dignité individuelle.

      La lutte pour la sobriété est un combat personnel et collectif, exacerbé par la pression sociale et la puissante influence des lobbies qui perpétuent des mythes favorables à la consommation.

      Le défi est de reconsidérer une culture où "boire était aussi naturel que respirer" pour une société plus consciente et en meilleure santé.

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      • Users with cognitive impairments may struggle to distinguish important from unimportant information.
    1. Planning the learning activity (orienting part) involvesidentifying the following aspects: (1) the outcome of the action with its particularcharacteristics (e.g. what concept are the students to learn?), (2) the units/parts of theoutcome of the action and the order in which they will have to be developed (what arethe essential characteristics of the target concept and in which order should thesecharacteristics be presented for students?), (3) tools that are available for the students(what resources and tools are useful for the students?) and (4) the overview of the entireactivity – the scheme of action as a whole is termed as an operational scheme ofthinking (Engeness 2020) (how will the students engage in learning?).

      I never realized that the reasoning behind the typical lesson plan template was science/research backed.

    1. Art. 163-A
      • ADI 7688 MC-Ref
      • Órgão julgador: Tribunal Pleno
      • Relator(a): Min. FLÁVIO DINO
      • Julgamento: 19/08/2024
      • Publicação: 16/10/2024

      DIREITO CONSTITUCIONAL. AÇÃO DIRETA DE INCONSTITUCIONALIDADE. ART 166-A, INCISO I E PARÁGRAFOS DA CONSTITUIÇÃO. DISPOSITIVOS QUE TRATAM DAS TRANSFERÊNCIAS ESPECIAIS CONHECIDAS COMO “EMENDAS PIX”. INADEQUAÇÃO DOS MECANISMOS DE TRANSPARÊNCIA E RASTREABILIDADE DAS TRANSFERÊNCIAS ESPECIAIS. RISCO DE GRAVE DANO AO ERÁRIO. CAUTELAR DEFERIDA EM PARTE.

      • 1. A transparência requer a ampla divulgação sobre a origem e o destino dos recursos públicos, conforme decidido pelo STF na ADPF 854. Imperativo assegurar o controle institucional e social sobre o orçamento público. A probabilidade do direito está demonstrada mediante dados que apontam para a inexistência dos instrumentos de planejamento, bem como para a inadequação de mecanismos de controle quanto às transferências especiais (“emendas PIX”).

      • 2. Há risco de dano ao erário e à ordem constitucional caso a realização das transferências especiais (“emendas PIX”), previstas no art. 166-A da Constituição, continue a ocorrer sem mecanismos que assegurem a transparência e a rastreabilidade dos dados (art. 163-A da Constituição).

      • 3. Decisão liminar obriga a existência prévia de planos de trabalho, com o registro em plataforma eletrônica sobre a destinação e aplicação de parcela muito expressiva do Orçamento da União. No mesmo sentido de obediência à Constituição Federal, a decisão liminar dispõe sobre a incidência plena dos controles externo e interno constantes dos artigos 70, 71 e 74 da Carta Magna.

      • 4. Tutela liminar deferida não é impeditiva de realização de transferências especiais (“emendas PIX”), desde que observados os trilhos constantes da Constituição Federal.

      • 5. Medida cautelar referendada.


      • ADPF 854 Ref
      • Órgão julgador: Tribunal Pleno
      • Relator(a): Min. FLÁVIO DINO
      • Julgamento: 04/12/2024
      • Publicação: 14/03/2025

      DIREITO CONSTITUCIONAL. ARGUIÇÃO DE DESCUMPRIMENTO DE PRECEITO FUNDAMENTAL E AÇÕES DIRETAS DE INCONSTITUCIONALIDADE. TRANSPARÊNCIA E RASTREABILIDADE NO PROCESSO ORÇAMENTÁRIO. ARTS. 163 E SEGUINTES DA CF. SUPERVENIÊNCIA DA LC Nº. 210/2024. INEXISTÊNCIA DE BLOQUEIO GENERALIZADO À EXECUÇÃO DE EMENDAS PARLAMENTARES. MEDIDA CAUTELAR REFERENDADA.

      • 1. A execução de recursos oriundos de emendas parlamentares exige o cumprimento dos pressupostos constitucionais da transparência e da rastreabilidade (163-A da CF).
      • 2. A LC nº. 210/2024 constitui avanço no cumprimento das determinações do Plenário desta Corte, ao estabelecer regras acerca da proposição e execução de emendas parlamentares. A referida lei complementar deve ser aplicada em consonância com a Constituição, interpretada pelas decisões do Plenário do STF.
      • 3. Inexiste bloqueio generalizado à execução de emendas parlamentares, cabendo ao ordenador de despesas competente a análise e deliberação motivada, caso a caso, acerca do cumprimento das determinações desta Corte e da LC nº. 210/2024 para a continuidade da execução das emendas.
      • 4. Medida cautelar referendada.
      1. He believes that if he discredits all belief, he can disregard falsified beliefs and mitigate their influence on the “good” or true beliefs that he strived for.
      2. The action of doubting demonstrates that there is a doubter, therefore because he thinks, he is.
      3. Substance dualism, that his mind and body that differentiate as a thinking substance and a physical substance.
      4. After going through methodological doubt, ensuring that any idea depredations as true has already passed the test of being clear.
      5. Yes, as senses are notorious for misleading individuals, Descartes reasoning is more trustworthy.
      6. Rationalism and Empiricism differ by justifying existence in two very different ways- one using sensory experiences and the other using reasoning as the basis of understanding.
    1. Author response:

      The following is the authors’ response to the previous reviews.

      Reviewer #1 (Recommendations for the authors):

      Although this study is rigorous and the paper is well-written, I have a few concerns that the authors should address before publication.

      (1) Cellular levels of protein ADP-ribosylation should be analyzed using anti-ADPR antibodies following infection, both with and without Mac1 and AVI-4206 treatment. While the authors have provided impressive in vivo data, these experiments could ideally be conducted in mice. However, I would be amenable to these analyses being performed in human airway organoids, as they demonstrate clear phenotypes following AVI-4206 treatment post-infection. For a more in-depth exploration, the authors could consider affinity purifying ADP-ribosylated proteins and identifying them via mass spectrometry. I would find it particularly compelling if this approach revealed components of the NF-kB signaling pathway, given the intriguing results presented in Fig. 5. I am also curious if there are differences in ADP ribosylated proteins when comparing Mac1 KO SARS-C0V-2 to AVI-4206 treatment.

      We note that despite the recent flurry of activity around Mac1, there is a surprising lack of public data on overall ADPr levels or targets. While we will address the literature precedence for PARP14 signals specifically below (Reviewer 2 point (h)) by immunofluorescence, we note that overall levels have not been characterized biochemically previously. Recent PARP14 papers and the ASAP AViDD preprint show changes by immunofluorescence only: and the evidence in that preprint is quite modest - see Figure 7B - https://pmc.ncbi.nlm.nih.gov/articles/PMC11370477/.

      We suspect the difficulty in tracking changes biochemically is due to multiple factors that influence the overall detectability and reproducibility. First, with regard to detectability - it is quite possible that only a small change in the ADPr status of a small number of targets is responsible for the phenotypes in vivo. Virus levels are very low in the organoid system and the variability in ADPr levels from tissue samples from in vivo experiments is high. Given the difficulty in translating back to cellular models, this problem is therefore magnified further. Second, with regard to reproducibility - we observe a great deal of reagent dependence on ADPr signals by Western blot+/- Mac1 expression in both cellular and tissue lysates (including when stimulated with H2O2, interferon, or during viral infection). Similarly, we do not observe reproducible proteins that pulldown with Mac1 when assayed by mass spectrometry. It is quite likely that these issues are a result of tissue/sample preparation that results in a loss of the ADPr modification during preparation (especially for acidic residue modifications). This also explains the reliance on IF assays in the PARP14 literature. A very good discussion of these issues is also contained in this paper: https://doi.org/10.1042/BSR20240986.

      Nonetheless we have attempted one final experiment. Here, we have measured ADPr modification of cellular lysates upon uninfected conditions as well as upon infection with either WT or N40D mutant virus. For all conditions, this was done with or without treatment of cells with 100 μM of AVI-4206. Measurement of ADPr modifications by western blot using a  pan-ADPr antibody revealed a single prominent band with a molecular weight of ~130kDa, that showed a uniform increase in signal upon treatment of cells with AVI-4206 regardless of infection status. While this general trend was also observed with the mono-ADPr antibody, it was not statistically significant in its regulation upon AVI-4206 treatment. We suspect that the major band observed in these western blots is PARP1, as upon enrichment of ADPr proteins from these lysates by Af1521 immunoprecipitation, we find PARP1 to be among the most abundant proteins detected within this molecular weight range. We note that there is a baseline increase in polyADPr detection upon infection of virus with WT Mac1 (relative to uninfected and virus with N40D) and further increase when treated with AVI-4206. This compound-dependent increase is paralleled in the uninfected and N40D conditions. The counterintuitive increase upon WT Mac1 virus infection, which should erase ADPr marks, and the compound-dependent increase in the uninfected condition suggest that there are many indirect effects on ADPr signalling dynamics in this experiment. These results are difficult to reconcile with the specificity profiling of AVI-4206 (Supplementary Figure5: Thermal proteome profiling in A549 cellular lysates). As mentioned above, the lack of consistent signal across reagents for ADPr detection and the timing of monitoring ADPr levels are additional complicating factors.

      We added to the results:

      “However, we observed no strong consistent signals of global pan-ADP-ribose (panADPr) or mono-ADP-ribose (monoADPr) accumulation in infected cells treated with AVI-4206 in immunoblot analyses (Supplementary Figure 8).”

      Methods for experiment:

      Calu3 cells were obtained from ATCC and cultured in Advanced DMEM (Gibco) supplemented with 2.5% FBS, 1x GlutaMax, and 1x Penicillin-Streptomycin at 37°C and 5% CO<sub>2</sub>. 5x10<sup>6</sup> cells were plated in 15-cm dishes and media was changed every 2-3 days until the cells were 80% confluent. The cells were treated with INFy 50 ng/mL (R&D Systems) w/without AVI-4206 100 μM. After 6 hours, the cells were infected with WA1 or WA1 NSP3 Mac1 N40D at a multiplicity of infection (MOI) of 1 for 36 hours. The cells were washed with PBS x 3 and scraped in Pierce IP Lysis Buffer (ThermoFisher) containing 1x HALT protease and phosphatase inhibitor mix (ThermoFisher) on ice. The lysate was stored at -80C until further processing.

      The cell lysate was incubated for 5 minutes at room temperature with recombinant benzonase. Following incubation, the lysate was centrifuged at 13,000 rpm at 4°C for 20 minutes, and the supernatant was collected. The samples were then boiled for 5 minutes at 95°C in 1x NuPAGE LDS sample buffer (Invitrogen) with a final concentration of 1X NuPAGE sample reducing agent (Invitrogen). For the detection of ADPr levels in whole-cell lysates, the samples were subjected to SDS-PAGE and Immunoblotting. All primary and secondary antibodies (pan-ADP-ribose antibody (MABE1016, Millipore), Mono-ADP-ribose antibody (AbD33204, Bio-Rad), HRP-conjugated (Cell signaling), used at a 1:1000 dilution were diluted in 5% non-fat dry milk in TBST. Signals were detected by chemiluminescence (Thermo) and visualized using the ChemiDoc XRS+ System (Bio-Rad). Densitometric analysis was performed using Image Lab (Bio-Rad). Quantification was normalized to Actin. The data are expressed as mean ± SD. Statistical differences were determined using an unpaired t-test in GraphPad Prism 10.3.1.

      (2) SARS-CoV-2 escape mutants for AVI-4206 should be generated, sequenced, and evaluated for both ADP-ribosyl hydrolase activity and their susceptibility to inhibition by AVI-4206.

      We thank the reviewer for this suggestion. These are indeed key experiments which are currently hampered by the lack of a cell line that is fully responsive to drug treatment. Although infected organoids and macrophages show an effect in response to AVI-4206, viral levels are ~3 logs lower than in cell lines and difficult to sequence. In the absence of a system that would allow meaningful screening for outgrowth of resistant viruses, we have conducted mass spectrometry studies that showed that Mac1 is the only significant hit for AVI-4206 (SupplementaryFigure 5). The suggested outgrowth experiments will be conducted once a responsive cell line model has been established.

      (3) Given that Mac1 is found in several coronaviruses, it would be insightful for the authors to test a selection of Mac1 homologs from divergent coronaviruses to assess whether AVI-4206 can inhibit their activity in vitro.

      As mentioned above, inconsistencies in ADPr staining limit our ability to directly measure cellular activity. As an alternative approach to measure AVI-4206 selectivity in cells, we have adapted our CETSA assay for SARS-1 and MERs macrodomain proteins and find evidence that AVI-4206 can shift the melting temperature of both proteins, albeit to a lesser degree than that seen for Mac1. In line with MERS being more structurally divergent than SARS-1 from SARS CoV2, the ΔTagg for SARS-1 and MERS are 4℃ and 1℃, respectively, compared to 9℃ for Mac1.  These data have been added as Supplementary Fig S3C. Development of broader spectrum pan-inhibitors is on our radar for future work which will more thoroughly assess homologs from divergent coronaviruses.

      We added the following sentence to the main results:

      “Encouragingly, we were also able to adapt our CETSA assay for SARS-1 and MERs macrodomain proteins and find that AVI-4206 can shift the melting temperature of both proteins, albeit to a lesser degree than that seen for Mac1 (Supplementary Figure 3C).”

      We also added this supplementary figure 3:

      Minor

      (1) Line 88, "respectively.heir potency"

      Fixed, thank you!

      (2) Line 149 add a period after proteome

      Fixed, thank you!

      Reviewer #2 (Recommendations for the authors):

      (a) The authors assess inhibition of MacroD2 and Targ1 as of-targets for AVI-4206. However, Mac1 belongs to the MacroD-type class of macrodomains of which MacroD1, MacroD2 and MOD1s of PARP9 and PARP14 are the human members. In contrast Targ1 belongs to the ALC1-like class, which is only very distantly related to Mac1. Furthermore, recent studies have shown that the first macrodomains of PARP9 and PARP4 (MOD1 of PARP9/14) are much closer related to Mac1 and PARP9/14 were implicated in antiviral immunity. As such the authors should include assays showing the activity of their compounds against MacroD1 and MOD1s of PARP9/14.

      We emphasize that we detect no significant shift for any protein other than Mac1 in A549 cells by CETSA-MS (Supplementary Figure 6). For Mac1 CESTA, we see an average of 6 PARP14 spectral counts across conditions and did not detect PARP9.  In addition, for separate work in MPro, we ran similar CETSA experiments where we observed an average of 2 PARP9 and 15 PARP14 spectral counts across conditions. Although PARP9 and PARP14 massively increase expression upon IFN treatment in A549 cells, both proteins have been detected by Western Blot in A549 cells previously at baseline.

      Nonetheless, we have included modeling of more diverse macrodomains as a supplemental figure and added to the text:

      Modeling of other diverse macrodomains, including those within human PARP9 and PARP14 further suggests that AVI-4206 is selective for Mac1 (Supplementary Figure 4)

      (b) In the context of SARS-CoV-2 superinfection are a known major complication of infections. These superinfections are associated with lung damage and therefore it would be good if the authors could assess lung damage, e.g. by histology, to see if their treatment has a positive impact on lung damage and thus may help to suppress complications.

      We performed histology and the results are inconclusive, but suggest that AVI-4206 treatment could lower apoptosis.There is no difference in pathology between the N40D cohort and vehicle with these markers. This could suggest that AVI-4206 provides an additional mechanism that results in protection.  We added to the results:

      Caspase 3 staining shows that AVI-4206 treatment reduces apoptosis in the lungs compared to vehicle controls. Additionally, Masson's Trichrome staining reveals  a significant reduction in collagen deposition, a surrogate for lung pathology, in the lungs of AVI-4206 treated animals.(Supplementary Figure 9).

      Histology:

      Mouse lung tissues were fixed in 4% PFA (Sigma Aldrich, Cat #47608) for 24 hours, washed three times with PBS and stored in 70% ethanol. All the stainings were performed at Histo-Tec Laboratory (Hayward, CA). Samples were processed, embedded in paraffin, and sectioned at 4μm. The slides were dewaxed using xylene and alcohol-based dewaxing solutions. Epitope retrieval was performed by heat-induced epitope retrieval (HIER) of the formalin-fixed, paraffin-embedded tissue using citrate-based pH 6 solution (Leica Microsystems, AR9961) for 20 mins at 95°C. The tissues were stained for H&E, caspase-3 (Biocare #CP229c 1:100), and trichrome, dried, coverslipped (TissueTek-Prisma Coverslipper), and visualized using Axioscan 7 slide scanner (ZEISS) at 40X. Image quantification was performed with Image J software and GraphPad Prism.

      (c) Fig. 1D labelling is wrong

      Thank you - fortunately the data were plotted correctly and it was just the inset table of values that was incorrect. This is now fixed!

      (d) Line 88: "T" missing at start of sentence

      Fixed, thank you!

      (e) Line 118: NudT5/AMP-Glo assay was developed in https://doi.org/10.1021/acs.orglett.8b01742

      We have added this foundational reference, thank you!

      (f) Line 147ff: It would be good if the authors could highlight that the TPP methodology has known limitations (e.g. detection of low abundance proteins and low thermal shift of some binders) and thus is not an absolute proof that AVI-4206 "engage with high specificity for Mac1"

      We added this important context to the concluding sentence of this paragraph:

      “While this assay may not be sensitive to detection of proteins with low abundance proteins or low thermal shift upon ligand binding, collectively, these results indicate that AVI-4206 can cross cellular membranes and engage with high specificity for Mac1.”

      (g) The authors use their well established in vitro Mac1 model as well as the SARS-CoV-2 WA strain. Given the ongoing diversification of SARS-CoV-2 and the current prevalence of the Omicron VOC it would be good if the authors could investigate whether alteration in Mac1 occurred or are detected which could influence the efficacy of their inhibitor. Similarly, it would be interesting to know how effective their drug is on other clinically relevant beta-CoV Mac1, e.g. from MERS or SARS1.

      We thank the reviewer for the suggestion. Mac1 is one of the more conserved areas of the SARS-CoV-2 genome as there has only been one nonsynonymous mutation V34L (Orf1a:V1056L) that recently emerged in the BA.2.86 lineage and is now in all of the JN.1 derivatives. Currently, the mutation is only ~80% penetrant in circulating SARS-CoV-2 sequences suggesting that it might revert to wild-type and is not associated with a fitness benefit. Based on our structural analysis (shown in Supplementary Figure4D above), we do not believe this mutation affects AVI-4206 binding, but we are including this variant in our future in vitro and in vivo studies as well as other beta-CoV.  For SARS and MERS, see response to Reviewer 1 using CETSA to show that these targets are engaged by AVI-4206.

      (h) As methods to detect PARP14-derived ADP-ribosylation are available and it was shown that Mac1 can reverse this modification in cells. It would be good if the authors could investigate the impact of AVI-4206 on ADP-ribosylation in vivo.

      To test this idea we adapted the IF assay used by others in the field and show an effect of AVI-4206. We have added to the text:

      Although the IFN response was not sufficient to control viral replication, it is possible that the changes in ADP-ribosylation, in particular marks catalyzed by PARP14, downstream of IFN treatment could serve as a marker for Mac1 efficacy  (Ribeiro et al. 2025). To investigate whether downstream signals from PARP14 were specifically erased by Mac1, we used an immunofluorescence assay that showed that Mac1 could remove IFN-γ-induced ADP-ribosylation that is mediated by PARP14 (Kar et al. 2024).  We stably expressed wild-type Mac1 and the N40D mutant Mac1 in A549 cells. The data showed that Mac1 expression decreased IFN-γ-induced ADP-ribosylation, whereas the Mac1-N40D mutant did not (Figure 3E, F), indicating that Mac1 mediates the hydrolysis of IFN-γ-induced ADP-ribosylation. The PARP14 inhibitor RBN012759 completely blocked IFN-γ-induced ADP-ribosylation (Figure 3E, F), further confirming that IFN-γ-induced ADP-ribosylation is mediated by PARP14. AVI-4206 reversed the Mac1-induced hydrolysis of ADP-ribosylation and enhanced the ADP-ribosylation signal in Mac1-overexpressing cells (Figure 3E, F), further demonstrating its ability to inhibit the hydrolase activity of Mac1. We further validated this result using different ADP-ribosylation antibodies for immunofluorescence (Supplementary Figure 7). However, we observed no strong consistent signals of global pan-ADP-ribose (panADPr) or mono-ADP-ribose (monoADPr) accumulation in infected cells treated with AVI-4206 in immunoblot analyses (Supplementary Figure 8). Collectively, these results provide further evidence that simple cellular models are insufficient to explore the effects of Mac1 inhibition and that monitoring specific PARP14-mediated ADP-ribosylation patterns can provide an accessible biomarker for the efficacy of Mac1 inhibition.

      A549 Mac1 expression cell construction

      Mac1 wild-type (Mac1) and N1062D mutant (Mac1 N1062D) gene fragments were loaded into pLVX-EF1α-IRES-Puro (empty vector, EV) using Gibson cloning kit (NEB E5510). Lentivirus was prepared as previously described (PMID: 30449619; DOI: 10.1016/j.cell.2018.10.024). Briefly, 15 million HEK293T cells were grown overnight on 15 cm poly-L-Lysine coated dishes and then transfected with 6 ug pMD2.G (Addgene plasmid # 12259 ; http://n2t.net/addgene:12259 ; RRID:Addgene_12259), 18 ug dR8.91 (since replaced by second generation compatible pCMV-dR8.2, Addgene plasmid #8455) and 24 ug pLVX-EF1α-IRES-Puro (EV, Mac1, Mac1-N1062D) plasmids using the lipofectamine 3000 transfection reagent per the manufacturer’s protocol (Thermo Fisher Scientific, Cat #L3000001). pMD2.G and dR8.91 were a gift from Didier Trono. The following day, media was refreshed with the addition of viral boost reagent at 500x as per the manufacturer’s protocol (Alstem, Cat #VB100). Viral supernatant was collected 48 hours post transfection and spun down at 300 g for 10 minutes, to remove cell debris. To concentrate the lentiviral particles, Alstem precipitation solution (Alstem, Cat #VC100) was added, mixed, and refrigerated at 4°C overnight. The virus was then concentrated by centrifugation at 1500 g for 30 minutes, at 4°C. Finally, each lentiviral pellet was resuspended at 100x of original volume in cold DMEM+10%FBS+1% penicillin-streptomycin and stored until use at -80°C. To generate Mac1 overexpressing cells, 2 million A549 cells were seeded in 10 cm dishes and transduced with lentivirus in the presence of 8 μg/mL polybrene (Sigma, TR-1003-G). The media was changed after 24h and, after 48 hours, media containing 2μg/ml puromycin was added. Cells were selected for 72 hours and then expanded without selection. The expression of Mac1 was confirmed by Western Blot.

      Immunofluorescence assay:

      To assess the effect of Mac1 on IFN-induced ADP-ribosylation. A549-pLVX-EV, A549-pLVX-Mac1 and A549-pLVX-Mac1-N1062D cells were seeded in 96-well plate (10,000 cells/well). Cells were pre-treated with medium or 100 unit/mL IFN-γ (Sigma, SRP3058) for 24 hours to induce the expression of ADP-ribosylation. These 3 cell lines were then treated the next day with the indicated concentrations of AVI-4206 or RBN012759 (Medchemexpress, HY-136979). After 24 hours of exposure to drugs, treated cells were fixed in pre-cooled methanol at -20°C for 20 min, blocked in 3% bovine serum albumin for 15 min, incubated with Poly/Mono-ADP Ribose (E6F6A) Rabbit mAb (CST, 83732S) or Poly/Mono-ADP Ribose (D9P7Z) Rabbit mAb (CST, 89190S) antibodies for 1 h, and then incubated with Goat anti-Rabbit IgG Secondary Antibody, Alexa Fluor 488 (ThermoFisher, A-11008) secondary antibodies for 30 min and stained with DAPI for 10 minutes. Fluorescent cells were imaged with an IN Cell Analyzer 6500 System (Cytiva) and analyzed using IN Carta software (Cytiva).

      Reviewer #3 (Recommendations for the authors):

      Just a couple of observations/details that might help strengthen the article:

      (1) The caco-1 data for AVI4206 would suggest that there is some sort of efflux going on, yet there is no mention of it in the paper. This might be useful in the optimization paradigm moving forward.

      We thank the reviewer for this observation and suggestion.  Indeed, we believe that efflux is behind the low oral bioavailability of AVI-4206.  We are working specifically to remove this liability in next-generation analogs, using the caco2 assay to guide this ongoing effort. Keep an eye out for a preprint on this soon!  We have added to the discussion:

      “In addition to dissecting such molecular mechanisms of macrodomain function and inhibition, future efforts will focus on improving pharmacokinetic properties, including a cellular efflux liability that results in low oral bioavailability of AVI-4206. ”

      (2) There are some spectroscopic anomalies/mistakes in the NMR data. The carbon NMR for 1-((8-amino-9H-pyrimido[4,5-b]indol-4-yl)amino)pyrrolidin-2-one should only have 14 unique carbons, but the authors report 15. The HNMR for AVI1500 should only have 19 H's, but the authors list 20. The HNMR data for AVI3762/3763 should have 16 H's, but the authors only report 13. The CNMR for AVI4206 should only have 19 unique carbons, but the authors report 20.

      Thank you for noting these inconsistencies regarding the reported NMR spectra. We have rectified them by more closely examining the spectra and in some cases acquiring new data. We identified one peak (47.9) in the 13C NMR of 1-((8-amino-9H-pyrimido[4,5-b]indol-4-yl)amino)pyrrolidin-2-one that is apparently an artifact of the automated peak picking in the data analysis software.  In the 1H NMR of AVI-1500, the triplet peak at 7.20 integrates to 1H, but was erroneously reported as 2H in the original manuscript.  This error has been corrected.  Spectra were re-acquired for AVI-3762, AVI-3763, and AVI-4206 with longer acquisition times, and/or on a 600 MHz spectrometer to afford the complete line lists now reported in the revised manuscript. Please note AVI-4206 has 18 distinct 13C resonances due to the equivalence of the gem-dimethyl methyl groups.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Reviewer #1 (Public review):

      (1) The use of single-cell RNA and TCR sequencing is appropriate for addressing potential relationships between gene expression and dual TCR.

      Thank you for your detailed review and suggestions. The main advantages of scRNA+TCR-seq are as follows: (1) It enables comparative analysis of features such as the ratio of single TCR paired T cells to dual TCR paired T cells at the level of a large number of individual T cells, through mRNA expression of the α and β chains. In the past, this analysis was limited to a small number of T cells, requiring isolation of single T cells, PCR amplification of the α and β chains, and Sanger sequencing; (2) While analyzing TCR paired T cell characteristics, it also allows examination of mRNA expression levels of transcription factors in corresponding T cells through scRNA-seq.

      (2) The data confirm the presence of dual TCR Tregs in various tissues, with proportions ranging from 10.1% to 21.4%, aligning with earlier observations in αβ T cells.

      Thank you very much for your detailed review and suggestions. Early studies on dual TCR αβ T cells have been very limited in number, with reported proportions of dual TCR T cells ranging widely from 0.1% to over 30%. In contrast, scRNA+TCR-seq can monitor over 5,000 single and paired TCRs, including dual paired TCRs, in each sample, enabling more precise examination of the overall proportion of dual TCR αβ T cells. It is important to note that our analysis focuses on T cells paired with functional α and β chains, while T cells with non-functional chain pairings and those with a single functional chain without pairing were excluded from the total cell proportion analysis. Previous studies generally lacked the ability to determine expression levels of specific chains in T cells without dual TCR pairings.

      (3) Tissue-specific patterns of TCR gene usage are reported, which could be of interest to researchers studying T cell adaptation, although these were more rigorously analyzed in the original works.

      Thank you very much for your detailed review and suggestions. T cell subpopulations exhibit tissue specificity; thus, we conducted a thorough investigation into Treg cells from different tissue sites. This study builds upon the original by innovatively analyzing the differences in VDJ rearrangement and CDR3 characteristics of dual TCR Treg cells across various tissues. This provides new insights and directions for the potential existence of “new Treg cell subpopulations” in different tissue locations. The results of this analysis suggest the necessity of conducting functional experiments on dual TCR Treg cells at both the TCR protein level and the level of effector functional molecules.

      (4) Lack of Novelty: The primary findings do not substantially advance our understanding of dual TCR expression, as similar results have been reported previously in other contexts.

      Thank you for your detailed review and suggestions. Early research on dual TCR T cells primarily relied on transgenic mouse models and in vitro experiments, using limited TCR alpha chain or TCR beta chain antibody pairings. Flow cytometry was used to analyze a small number of T cells to estimate dual TCR T cell proportion. No studies have yet analyzed dual TCR Treg cell proportion, V(D)J recombination, and CDR3 characteristics at high throughput in physiological conditions. The scRNA+TCR-seq approach offers an opportunity to conduct extensive studies from an mRNA perspective. With high-throughput advantages of single-cell sequencing technology, researchers can analyze transcriptomic and TCR sequence characteristics of all dual TCR Treg cells within a study sample, providing new ideas and technical means for investigating dual TCR T cell proportions, characteristics, and origins under different physiological and pathological states.

      (5) Incomplete Evidence: The claims about tissue-specific differences lack sufficient controls (e.g., comparison with conventional T cells) and functional validation (e.g., cell surface expression of dual TCRs).

      Thank you for your detailed review and suggestions. This study indeed only analyzed dual  TCR Treg cells from different tissue locations based on the original manuscript, without a comparative analysis of other dual TCR T cell subsets corresponding to these tissue locations. The main reason for this is that, in current scRNA+TCR-seq studies of different tissue locations, unless specific T cell subsets are sorted and enriched, the number of T cells obtained from each subset is very low, making a detailed comparative analysis impossible. In the results of the original manuscript, we observed a relatively high proportion of dual TCR Treg cell populations in various tissues, with differences in TCR composition and transcription factor expression. Following the suggestions, we have included additional descriptions in R1, citing the study by Tuovinen et al., which indicates that the proportion of dual TCR Tregs in lymphoid tissues is higher than other T cell types. This will help understand the distribution characteristics of dual TCR Treg cells in different tissues and provide a basis for mRNA expression levels to conduct functional experiments on dual TCR Treg cells in different tissue locations.

      (6) Methodological Weaknesses: The diversity analysis does not account for sample size differences, and the clonal analysis conflates counts and clonotypes, leading to potential misinterpretation.

      We thank you for your review and suggestions. In response to your question about whether the diversity analysis considered the sample size issue, we conducted a detailed review and analysis. This study utilized the inverse Simpson index to evaluate TCR diversity of Treg cells. A preliminary analysis compared the richness and evenness of single TCR Treg cell and dual TCR Treg cell repertoires. The two datasets analyzed were from four mouse samples with consistent processing and sequencing conditions. However, when analyzing single TCR Tregs and dual TCR Tregs from various tissues, differences in detected T cell numbers by sequencing cannot be excluded from the diversity analysis. Following recommendations, we provided additional explanations in R1: CDR3 diversity analysis indicates TCR composition of dual TCR Treg cells exhibits diversity, similar to single TCR Treg cells; however, diversity indices of single TCR Tregs and dual TCR Tregs are not suitable for statistical comparison. Regarding the "clonal analysis" you mentioned, we define clonality based on unique TCR sequences; cells with identical TCR sequences are part of the same clone, with ≥2 counts defined as expansion. For example, in Blood, there are 958 clonal types and 1,228 cells, of which 449 are expansion cells. In R1, we systematically verified and revised clonal expansion cells across all tissue samples according to a unified standard.

      (7) Insufficient Transparency: The sequence analysis pipeline is inadequately described, and the study lacks reproducibility features such as shared code and data.

      Thank you for your review and suggestions. Based on the original manuscript, we have made corresponding detailed additions in R1, providing further elaboration on the analysis process of shared data, screening methods, research codes, and tools. This aims to offer readers a comprehensive understanding of the analytical procedures and results.

      (8) Weak Gene Expression Analysis: No statistical validation is provided for differential gene expression, and the UMAP plots fail to reveal meaningful clustering patterns.

      Thank you very much for your review and suggestions. Based on your recommendations, we conducted an initial differential expression analysis of the top 10 mRNA molecules in single TCR Treg and dual TCR Treg cells using the DESeq2 R package in R1, with statistical significance determined by Padj < 0.05. Regarding the clustering patterns in the UMAP plots, since the analyzed samples consisted of isolated Treg cell subpopulations that highly express immune suppression-related genes, we did not perform a more detailed analysis of subtypes and expression gene differences. This study primarily aims to explore the proportions of single TCR and dual TCR Treg cells from different tissue sources, as well as the characteristics of CDR3 composition, with a focus on showcasing the clustering patterns of samples from different tissue origins and various TCR pairing types.

      (9) A quick online search reveals that the same authors have repeated their approach of reanalysing other scientists' publicly available scRNA-VDJ-seq data in six other publications,In other words, the approach used here seems to be focused on quick re-analyses of publicly available data without further validation and/or exploration.

      Thank you for your review and suggestions. Most current studies utilizing scRNA+TCR-seq overlook analysis of TCR pairing types and related research on single TCR and dual TCR T cell characteristics. Through in-depth analysis of shared scRNA+TCR-seq data from multiple laboratories, we discovered a significant presence of dual TCR T cells in high-throughput T cell research results that cannot be ignored. In this study, we highlight the higher proportion of dual TCR Tregs in different tissue locations, which exhibits a certain degree of tissue specificity, suggesting these cells may participate in complex functional regulation of Tregs. This finding provides new ideas and a foundation for further research into dual TCR Treg functions. However, as reviewers pointed out, findings from scRNA+TCR-seq at the mRNA level require additional functional experiments on dual TCR T cells at the protein level. We have supplemented our discussion in R1 based on these suggestions.

      Reviewer #2 (Public review):

      (1) The existence of dual TCR expression by Tregs has previously been demonstrated in mice and humans (Reference #18 and Tuovinen. 2006. Blood. 108:4063; Schuldt. 2017. J Immunol. 199:33, both omitted from references). The presented results should be considered in the context of these prior important findings.

      Thank you very much for your review and suggestions. Based on the original manuscript, we have supplemented our reading, understanding, and citation of closely related literature (Tuovinen, 2006, Blood, 108:4063 (line 44,line175 in R1); Schuldt, 2017, J Immunol, 199:33 (line 44,line178 in R1)). We once again appreciate the valuable comments from the reviewers, and we will refer to these in our subsequent dual TCR T cell research.

      (2) This demonstration of dual TCR Tregs is notable, though the authors do not compare the frequency of dual TCR co-expression by Tregs with non-Tregs. This limits interpreting the findings in the context of what is known about dual TCR co-expression in T cells.

      Thank you very much for your review and suggestions. This analysis is primarily based on the scRNA+TCR-seq study of sorted Treg cells, where we found the proportions and distinguishing features of dual TCR Treg cells in different tissue sites. Given the diversity and complexity of Treg function, conducting a comparative analysis of the origins of dual TCR Treg cells and non-T cells with dual TCRs will be a meaningful direction. Currently, peripheral induced Treg cells can originate from the conversion of non-Treg cells; however, little is known about the sources and functions of dual TCR Treg cell subsets in both central and peripheral sites. In R1, we have supplemented the discussion regarding the possible origins and potential applications of the "novel dual TCR Treg" subsets.

      (3) Comparison of gene expression by single- and dual TCR Tregs is of interest, but as presented is difficult to interpret. Statistical analyses need to be performed to provide statistical confidence that the observed differences are true.

      Thank you very much for your review and suggestions. Based on your recommendations, we performed an initial differential expression analysis of the top 10 mRNA molecules in single TCR Treg and dual TCR Treg cells using the DESeq2 R package in R1, with a statistical significance threshold of Padj<0.05 for comparisons.

      (4) The interpretations of the gene expression analyses are somewhat simplistic, focusing on the single-gene expression of some genes known to have a function in Tregs. However, the investigators miss an opportunity to examine larger patterns of coordinated gene expression associated with developmental pathways and differential function in Tregs (Yang. 2015. Science. 348:589; Li. 2016. Nat Rev Immunol. Wyss. 2016. 16:220; Nat Immunol. 17:1093; Zenmour. 2018. Nat Immunol. 19:291).

      Thank you for your review and suggestions. This study is based on publicly available scRNA+TCR-seq data from different organ sites generated by the original authors, focusing on sorted and enriched Treg cells within each tissue sample. However, there was no corresponding research on other cell types in each tissue sample, preventing analysis of other cells and factors involved in development and differentiation of single TCR Treg and dual TCR Treg. The literature suggested by the reviewer indicates that development, differentiation, and function of Treg cells have been extensively studied, resulting in significant advances. It also highlights complexity and diversity of Treg origins and functions. This research aims to investigate "novel dual TCR Treg cell subpopulations" that may exhibit tissuespecific differences found in the original authors' studies of Treg cells across different organ sites. This suggests further experimental research into their development, differentiation, origin, and functional gene expression as an important direction, which we have supplemented in the discussion section of R1.

      Reviewer #3 (Public review):

      (1) Definition of Dual TCR and Validity of Doublet Removal:This study analyzes Treg cells with Dual TCR, but it is not clearly stated how the possibility of doublet cells was eliminated. The authors mention using DoubletFinder for detecting doublets in scRNA-seq data, but is this method alone sufficient?We strongly recommend reporting the details of doublet removal and data quality assessment in the Supplementary Data.

      Thank you very much for your review and suggestions. In the analysis of the shared scRNA+TCR-seq data across multiple laboratories, as you mentioned, this study employed the DoubletFinder R package to exclude suspected doublets. Additionally, we used the nCount values of individual cells (i.e., the total sequencing reads or UMI counts for each cell) as auxiliary parameters to further optimize the assessment of cell quality. Generally, due to the possibility that doublet cells may contain gene expression information from two or more cells, their nCount values are often abnormally high. In this study, all cells included in the analysis had nCount values not exceeding 20,000. Among the five tissue sample datasets, we further utilized hashtag oligonucleotide (HTO) labeling (where HTO labeling provides each cell with a unique barcode to differentiate cells from different tissue sources. By analyzing HTO labels, doublets and negative cells can be accurately identified) to eliminate doublets and negative cells.After the removal of chimeric cells, all samples exhibited T cells that possessed two or more TCR clones. This phenomenon validates the reliability of the methodological approach employed in this study and indicates that the analytical results accurately reflect the proportion of dual TCR T cells. Based on the recommendations of the reviewers, we have supplemented and clarified the methods and discussion sections in the manuscript. It is particularly noteworthy that in our analysis, the discussed dual TCR Treg cells and single TCR Treg cells specifically refer to those T cells that possess both functional α and β chains, which are capable of forming TCR. We have excluded from this analysis any Treg cells that possess only a single functional α or β chain and do not form TCR pairs, as well as those Treg cells in which the α or β chains involved in TCR pairing are non-functional.

      (2) In Figure 3D, the proportion of Dual TCR T cells (A1+A2+B1+B2) in the skin is reported to be very high compared to other tissues. However, in Figure 4C, the proportion appears lower than in other tissues, which may be due to contamination by non-Tregs. The authors should clarify why it was necessary to include non-Tregs as a target for analysis in this study. Additionally, the sensitivity of scRNA-seq and TCR-seq may vary between tissues and may also be affected by RNA quality and sequencing depth in skin samples, so the impact of measurement bias should be assessed.

      We deeply appreciate your review and constructive comments. Based on the original manuscript, we have further supplemented and elaborated on the uniqueness and relative proportions of double TCR T cell pairs in skin tissue samples in Section R1. Due to the scarcity of T cells in skin samples, we included some non-Treg cells during single-cell RNA sequencing and TCR sequencing to obtain a sufficient number of cells for effective analysis. The presence of non-regulatory T cells may indeed impact the statistical representation of double TCR T cells as well as the related comparative analyses, as noted by the reviewer. T cells with A1+A2+B1+B2 type double TCR pairings are primarily found within the non-regulatory T cell population in the skin. In response to this point, we have provided a detailed explanation of this analytical result in the revised manuscript R1. Furthermore, concerning the two datasets included in the study, we conducted a comparative analysis in R1, exploring how factors such as sequencing depth at different tissue sites might introduce biases in our findings, which we have thoroughly elaborated upon in the discussion section. We thank you once again for your valuable suggestions. 

      (3) Issue of Cell Contamination:In Figure 2A, the data suggest a high overlap between blood, kidney, and liver samples, likely due to contamination. Can the authors effectively remove this effect? If the dataset allows, distinguishing between blood-derived and tissue-resident Tregs would significantly enhance the reliability of the findings. Otherwise, it would be difficult to separate biological signals from contamination noise, making interpretation challenging.

      We thank you for your review and suggestions. We have carefully verified data sources for tissues such as blood, kidneys, and liver. In the study by Oliver T et al., various techniques were employed to differentiate between leukocytes from blood and those from tissues, ensuring accurate identification of leukocytes from tissue samples. First, anti-CD45 antibody was injected intravenously to label cells in the vasculature, verifying that analyzed cells were indeed resident in the tissue. Second, prior to dissection and cell collection, authors performed perfusion on anesthetized mice to reduce contamination of tissue samples by leukocytes from the vasculature. Additionally, during single-cell sequencing, authors utilized HTO technology to avoid overlap between cells from different tissues.

      Analysis of the scRNA+TCR-seq data shared by the original authors revealed highly overlapping TCR sequences in blood, kidney, and liver, despite distinct cell labels associated with each tissue. While these techniques minimize overlap of cells from different sources, they cannot completely rule out the potential impact of this technical issue. As suggested, we have provided additional clarification in R1 of the manuscript regarding this phenomenon of high overlap in the kidney, liver, and blood, indicating that the possibility of Treg migration from blood to kidney and liver cannot be entirely excluded.

      (4) Inconsistency Between CDR3 Overlap and TCR Diversity:The manuscript states that Single TCR Tregs have a higher CDR3 overlap, but this contradicts the reported data that Dual TCR Tregs exhibit lower TCR diversity (higher 1/DS score). Typically, when TCR diversity is low (i.e., specific clones are concentrated), CDR3 overlap is expected to increase. The authors should carefully address this discrepancy and discuss possible explanations.

      Thank you for your review and suggestions. Regarding the potential relationship between CDR3 overlap and TCR diversity, in samples with consistent sequencing depth, lower diversity indeed corresponds to a higher proportion of CDR3 overlap. In our analysis of scRNA+TCR-seq data, we found that single TCR Tregs exhibit both higher diversity and CDR3 overlap, seemingly presenting contradictory analytical results (i.e., dual TCR Tregs show lower TCR diversity and CDR3 overlap). In R1, we supplemented the analysis of possible reasons: the presence of multiple TCR chains in dual TCR Treg cells may lead to a higher uniqueness of CDR3 due to multiple rearrangements and selections, resulting in lower CDR3 overlap; the lower diversity of dual TCR Tregs may be related to the number of T cells sequenced in each sample. The CDR3 diversity analysis in this study merely suggests that the TCR composition of dual TCR Treg cells is diverse, similar to that of single TCR Tregs. However, the diversity indices of single TCR Tregs and dual TCR Tregs are not suitable for statistical comparative analysis. A more in-depth and specific analysis of the diversity and overlap of the VDJ recombination mechanisms and CDR3 composition in dual TCR Tregs during development will be an important technical means to elucidate the function of dual TCR Treg cells.

      (5) Functional Evaluation of Dual TCR Tregs:This study indicates gene expression differences among tissue-resident Dual TCR T cells, but there is no experimental validation of their functional significance. Including functional assays, such as suppression assays or cytokine secretion analysis, would greatly enhance the study's impact.

      We sincerely appreciate your review and suggestions: In this analysis of scRNA+TCR-seq data, we innovatively discovered a higher proportion of dual TCR Treg cells in different tissue sites, which exhibited differences in tissue characteristics. Furthermore, we conducted a comparative analysis of the homogeneity and heterogeneity between single TCR Treg and dual TCR Treg cells. This result provides a foundation for further research on the origin and characteristics of dual TCR Treg cells in different tissue sites, offering new insights for understanding the complexity and functional diversity of Treg cells. Based on your suggestions, we have supplemented R1 with the feasibility of further exploring the functions of tissue-resident dual TCR T cells and the necessity for potential application research.

      (6) Appropriateness of Statistical Analysis:When discussing increases or decreases in gene expression and cell proportions (e.g., Figure 2D), the statistical methods used (e.g., t-test, Wilcoxon, FDR correction) should be explicitly described. They should provide detailed information on the statistical tests applied to each analysis.

      Thank you for your review and suggestions: Based on the original manuscript, we have supplemented the specific statistical methods for the differences in cell proportions and gene expression in R1.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Reviewer #1 (Public review):

      “Alternative possibilities are discussed regarding the prior and likelihood of the model. Given that the second case study inspired the introduction of the zero-inflation likelihood, it is not clear how applicable the general methodology is to various datasets. If every unique dataset requires a tailored prior or likelihood to produce the best results, the methodology will not easily replace more traditional statistical analyses that can be applied in a straightforward manner. Furthermore, the differences between the results produced by the two Bayesian models in case study 2 are not discussed. In specific regions, the models provide conflicting results (e.g., regions MH, VPMpc, RCH, SCH, etc.), which are not addressed by the authors. A third case study would have provided further evidence for the generalizability of the methodology.”

      We hope in this paper to propose a ‘standard workflow’ for these data; this standard workflow uses the horseshoe prior and we propose that this is the approach used to describe cell count data instead of the better established, but to our thinking, inefficient, t-testing approach.

      The horseshoe prior is robust and allows a partially-pooled model to used while weighing-up the contribution of different data points. This is an analogue of excluding outliers and, in any analysis it is normal to investigate further if there are points being excluded as outliers. Often this reveals a particular challenge with the data, in the case of the data here, there are a lot of zeros, indicating that some samples should be excluded because the preparation failed to tag cells rather than because there were no cells to tag. This idea behind the ZIP example is to show that the Bayesian method can allow for this sort of further investigation and, indeed, as the reviewer notes this sort of extended analysis is often bespoke, tailored to the data.

      We have clearly failed to explain that the ‘standard workflow’ we propose replace the more traditional methods is the first one we describe, with the horseshoe prior; this produces better results on both datasets than the traditional approach. However, we also feel it is useful to show how a more tailored follow-on can be useful; we need to make it clear that this is intended as an illustration of an ‘optional extra’ rather than a part of the more straightforward ‘standard workflow’.

      To make this clearer we have made altered the text in several locations:

      • end of Introduction: added clarifying sentence “Here, our aim is to introduce a ‘standard’ Bayesian model for cell count data. We illustrate the application of this model to two datasets, one related to neural activation and the other to developmental lineage. For the second dataset, we also demonstrate a second example extension Bayesian model.”

      • Section Hierarchical modeling: “Our goal in both cases is to quantify group differences in the data. We present a ‘standard’ hierarchical model. This model reflects the experimental features common to cell count experiments and reflects the hierarchical structure of cell count data; the standard model is designed to deal robustly and efficiently with noise. On some occasions, to reflect a specific hypotheses, the structure of a particular experiment or an observed source of noise, this model can be further refined or changed to target the analysis. We will give an example of this for our second dataset.”

      • Section Horseshoe prior: “The alternative is via a flexible prior such as the horseshoe Carvalho et al., 2010; Piironen and Vehtari, 2017. This more generic option may be suitable as a default ‘standard’ approach in the typical case where outliers are poorly understood.”

      • Discussion: word ‘standard’ added to sentence: “Our standard workflow uses a horseshoe prior, along with the partial pooling, this allows our model to deal effectively with outliers.”

      • Discussion: modified sentence “The horseshoe prior model workflow we have exhibited here is intended as a standard approach.”

      Indeed, because the horseshoe prior deals robustly with outliers, whereas the ZIP is intended to model the outliers, any substantial difference between the two should be examined carefully. The referee is right to point out that we have not explained this in any detail and has helpfully listed a few brain regions were there are differences. This is useful, particularly since the examples listed illustrate in a useful way the opportunities and hazards this sort of data presents. To address this, we have added a new version of Figure 6 to the revised manuscript

      Previously Figure 6 showed two example brain regions: MPN and TMd. We have now added MH and SCH to the figure, and new text commenting on the insights the plots provide, both in the Results and Discussion.

      Reviewer #2 (Public review):

      “A clearer link between the experimental data and model-structure terminology would be a benefit to the non-expert reader.”

      This is a very good point and we are acutely aware through our own work how difficult it can be moving between fields with different research goals, different scientific cultures and different technical vocabularies. Just as it can be difficult translating from one language to another without losing nuance and meaning, it can be a real challenge finding technical terms that are useful for the non-expert reader while retaining the precision the application requires! In the long run, we hope that, just as some of the very specialized vocabulary that surrounds frequentist statistics has become familiar to to the working experimental scientists, the precise terminology involved in Bayesian modelling will become familiar and transparent. However, in advance of that day, we have included a glossary of terms at the end of the main text, and have made numerous small tweaks to make sure that link between data and model terminology is clearer and better explained.

      Reviewer #1 (Recommendations fro the authors):

      (1) “I would strongly recommend that the authors include more case studies in the manuscript, and address the qualitative differences between the different versions of the model.”

      We agree that our method will only become established when it is applied to more datasets, we hope to contribute to further analysis and we know other people are already using the approach on their own data. We do, however, feel that adding more datasets to this paper will make it longer and more complex; the plan, instead, is to use the method on novel datasets to test specific hypotheses, so that the results will include novel scientific findings as well as adding another illustration of the Bayesian approach applied to data that is already well studied.

      (2) “Figure 6 is not discussed in the main text.”

      We had discussed the results presented in Figure 6 in the second paragraph of the section “Case study two – Ontogeny of inhibitory interneurons of the mouse thalamus”, however the reviewer is right in that we did not directly refer to the Figure – this was an oversight. In any case, in the revised manuscript we present a new version of Figure 6 (in response to above comment), which is now explicitly cited in the text.

      Revised Figure 6: Example data and inferences highlighting model discrepancies. On the left under ‘data’: boxplots with medians and interquartile ranges for the raw data for four example brain regions. The shape of each point pairs left and right hemisphere readings in each of the five animals. On the right under ‘inference’: HDIs and confidence intervals are plotted. Purple is the Bayesian horseshoe model, pink is the Bayesian ZIP model, and orange is the sample mean. The Bayesian estimates are not strongly influenced by the zero-valued observations (MPN, SCH, TMd) or large-valued outliers (MH) and have means close to the data median. This explains the advantage of the Bayesian results over the confidence interval.

      Reviewer #2 (Recommendations from the authors):

      (1) “This is a generally well-written methodology paper that also provides the underlying code as a resource. As a reviewer outside both cell-count modelling and hierarchical-Bayesian approaches (though with a general interest in the topics) I found the method a little difficult to follow and would have liked to have been left with a better understanding of how the method is applied to the data. For example, in Figure 1 we are introduced to brain region count, animal count, and “items”. Then in the next line: pooling, model, structure, population and etc in subsequent lines. It is not clear what the subscripts (the pools?) are referring to: are they different regions R or animals N? These terms need to be better linked to the data and/or trimmed. Having said that, the later results look like a solid contribution to the field with a significant reduction in uncertainty from the Bayesian approach over the frequentist one. A future version of the manuscript, therefore, would benefit from greater precision of language as well as an economy and greater focus of terms linking the method to the biology. This is particularly the case around the exposition parts in Figure 1, Figure 2, and the “Hierarchical modelling” section.”

      This is another important point. We have now made numerous small changes to tighten up the text in the paper, in response to both this point and the next point.

      (2) “Language throughout could be sharpened. Subjectivity like “surprising outliers” could be removed and quirky grammar like “often small, ten is a typical” improved. There are also typos “an rate” etc that should be tidied up.”

      As per previous response, we have made numerous tweaks and small improvements and feel that the paper is stronger in this respect.

      (3) “Figure 1 caption. “It is a spectrum that depends” Is spectrum the right word here? Also, “thicker stroke” what does this refer to? Wasn’t immediately clear. In A, why is the whole animal within the R bracket that signifies brain regions, and then the brain regions are within the N bracket that signifies whole animals? Apart from the teal colouring, what are the other coloured regions in the image referring to? Improving this first figure would greatly help a reader unfamiliar with the context of the approach.”

      We have replaced the word “spectrum” with “continuum”. We have replaced “ Observed quantities have been highlighted with a thicker stroke in the graphical model.” with “The observed data quantities, y<sub>i</sub> to y<sub>n</sub>, are highlighted with a thick line in the model diagrams”. We have added the following text to describe the red and green lines in panel A: “green and red lines indicate regions labeled as damaged”.

      (4) “On P2 there is no discussion of priors when running through the advantage of the Bayesian approach. Is this a choice or an oversight? Priors do have a role in the later analysis.”

      A short additional paragraph has been added to the introduction outlining the advantage of having a prior, but also noting that the obligation to pick a prior can be intimidating and that suggesting priors is one of the contributions of our paper: “A Bayesian model also includes a set of probability distributions, referred to as the prior, which represent those beliefs it is reasonable to hold about the statistical model parameters before actually doing the experiment. The prior can be thought of as an advantage, it allows us to include in our analysis our understanding of the data based on previous experiments. The prior also makes explicit in a Bayesian model assumptions that are often implicit in other approaches. However, having to design priors is often considered a challenge and here we hope to make this more straightforward by suggesting priors that are suitable for this class of data.”

      (5) “On P4 more explanation would help greatly. Formulas like 23*10*4 or 50*6+50*4 are presented without explanation. What are the various numbers being multiplied? Regions, animals? Again, a clearer link between biological data and model structure would be advantageous.”

      We have now modified this line to clearly state the numbers’ sources: “The index i runs over the full set of samples, which in this case comprises 23 brain regions ×10 animals ×4 groups ≈920 datapoints in the first study, and 50 brain regions × 6 HET animals + 50 brain regions × 4 KO animals ≈500 datapoints in the second.”

      (6) “P6 and Results. Is it possible to show examples of the data set sampled from? Perhaps an image or two for the two experiments. Both Figures 4 and 5 as they currently are could be made slightly smaller to provide space for a small explanatory sub-panel. This would help ground the results.”

      This is a good idea. We have now added heatmap visualisations of both entire datasets to revised versions of Figures 4 and 5 (assuming that this is what the reviewer was suggesting).

    1. Reviewer #1 (Public review):

      Summary

      Xu et al. use transcriptomic comparisons of mouse cochlear and vestibular hair to show that the vestibular hair cells alone are enriched in gene expression for proteins necessary for cilia motility and to further argue that such motility is a normal function of the kinocilia.

      Background:

      Cilia are prominent in sensory receptors, including vertebrate photoreceptors, olfactory neurons, and mechanosensitive hair cells of the inner ear and lateral line. Cilia can be motile or nonmotile depending on their axonemal structure: motile cilia require dynein and the inner 2 singlet microtubules of the 9+2 array. Primary cilia, present early in development, are considered to have sensory functions and to be nonmotile (Mill et al., Nature Rev Gen 2023).

      In hair cells, the kinocilium anchors and polarizes the mechanosensitive hair bundle of specialized microvilli. The kinocilium matures from the primary cilium of a newborn hair cell; behind it, the bundle of mechanosensory microvilli rises in a descending staircase of rows. During maturation of the mammalian cochlea, all hair cells lose the kinocilium, though not the associated basal body. The consensus for many years has been that most vertebrate kinocilia, and especially mammalian kinocilia, are nonmotile, based largely on the lack of spontaneous motility in excised mammalian vestibular organs, but also on the impression that the rare examples of spontaneous beating motility even in non-mammalian hair cells are associated with deterioration of the preparation (Rüsch & Thurm 1990).

      Strengths

      In comparing RNA expression across the 4 major types of mouse hair cells - 2 cochlear and 2 vestibular - Xu et al. noted that some ciliary genes related to motility are expressed by vestibular but not cochlear hair cells. They curated the ciliary genes into types known to be associated with different aspects of beating motility, and also investigated the expression of genes typical of primary cilia, which are considered to have sensory and cell signaling functions and to be nonmotile. They add immunostaining to back up some of the RNA data, and also evaluate relative expression by neonatal mouse cochlear and vestibular hair cells from a published dataset. The focus on kinociliary genes is an appropriate use of the comparative expression data for cochlear and vestibular hair cells, and the paper overall is readable and interesting. The transcriptome data are rounded off by comparing the authors' results in adult hair cells with published neonatal mouse cochlear and vestibular transcriptomes.

      Weaknesses:

      (1) Data:

      a) The main weakness in the data is the lack of functional and anatomical data from mouse hair bundles. While the authors compensate in part for this difficulty with bullfrog crista bundles, those data are also fragmentary - one TEM and 2 exemplar videos. Much of the novelty of the EM depends on the different appearance of stretches of a single kinocilium - can we be sure of the absence of the central microtubule singlets at the ends?

      b) While it was a good idea to compare ciliary motility expression in published P2 datasets for mouse cochlear and vestibular hair cells for comparison with the authors' adult hair cell data, the presentation is too superficial to assess (Figure 6C-E; text from line 336) - it is hard to see the basis for concluding that motility genes are specifically lower in P2 cochlear hair cells than vestibular hair cells. Visually, it is striking that CHCs have much darker bands for about 10 motility-related genes.

      (2) Interpretation:

      The authors take the view that kinociliary motility is likely to be normally present but is rare in their observations because the conditions are not right. But while others have described some (rare) kinociliary motility in fish organs (Rusch & Thurm 1990), they interpreted its occurrence as a sign of pathology. Indeed, in this paper, it is not clear, or even discussed, how kinociliary motility would help with mechanosensitivity in mature hair bundles. Rather, the presence of an autonomous rhythm would actively interfere with generating temporally faithful representations of the head motions that drive vestibular hair cells.

      Could kinociliary beating play other roles, possibly during development - for example, by interacting with forming accessory structures (but see Whitfield 2020) or by activating mechanosensitivity cell-autonomously, before mature stimulation mechanisms are in place? Then a latent capacity to beat in mature vestibular hair cells might be activated by stressful conditions, as speculated regarding persistent Piezo channels that are normally silent in mature cochlear hair cells but may reappear when TMC channel gating is broken (Beurg and Fettiplace 2017). While these are highly speculative thoughts, there is a need in the paper for more nuanced consideration of whether the observed motility is normal and what good it would do.

    2. Reviewer #2 (Public review):

      Summary:

      In this study, the authors compared the transcriptomes of the various types of hair cells contained in the sensory epithelia of the cochlea and vestibular organs of the mouse inner ear. The analysis of their transcriptomic data led to novel insights into the potential function of the kinocilium.

      Strengths:

      The novel findings for the kinocilium gene expression, along with the demonstration that some kinocilia demonstrate rhythmic beating as would be seen for known motile cilia, are fascinating. It is possible that perhaps the kinocilium, known to play a very important role in the orientation of the stereocilia, may have a gene expression pattern that is more like a primary cilium early in development and later in mature hair cells, more like a motile cilium. Since the kinocilium is retained in vestibular hair cells, it makes sense that it is playing a different role in these mature cells than its role in the cochlea.

      Another major strength of this study, which cannot be overstated, is that for the transcriptome analysis, they are using mature mice. To date, there is a lot of data from many labs for embryonic and neonatal hair cells, but very little transcriptomic data on the mature hair cells. They do a nice job in presenting the differences in marker gene expression between the 4 hair cell types. This information is very useful to those labs studying regeneration or generation of hair cells from ES cell cultures. One of the biggest questions these labs confront is what type of hair cells develop in these systems. The more markers available, the better. These data will also allow researchers in the field to compare developing hair cells with mature hair cells to see what genes are only required during development and not in later functioning hair cells.

    3. Author response:

      Reviewer #1 (Public review):

      Weaknesses:

      (1) Data:

      a) The main weakness in the data is the lack of functional and anatomical data from mouse hair bundles. While the authors compensate in part for this difficulty with bullfrog crista bundles, those data are also fragmentary - one TEM and 2 exemplar videos. Much of the novelty of the EM depends on the different appearance of stretches of a single kinocilium - can we be sure of the absence of the central microtubule singlets at the ends?

      Our single-cell RNA-seq findings show that genes related to motile cilia are specifically expressed in vestibular hair cells. This has not been demonstrated before. We have also provided supporting evidence using electrophysiology and imaging from bullfrogs and mice. Although no ultrastructural images of mouse vestibular kinocilia were provided in our study, transmission electron micrograph of mouse vestibular kinocilia has been published (O’Donnell and Zheng, 2022). The mouse vestibular kinocilia have a “9+2” microtubule configuration with nine doublet microtubules surrounding two central singlet microtubules. This finding contrasts with a previous study, which demonstrated that the vestibular kinocilia from guinea pigs lack central singlet microtubules and inner dynein arms, whereas outer dynein arms and radial spokes are present (Kikuchi et al., 1989). The central pair of microtubules is absent at the end of the bullfrog saccular kinocilium (Fig. 7A).  We would like to point out that the dual identity of primary and motile cilia is not just based on the TEM images. The kinocilium has long been considered a specialized cilium, and its role as a primary cilium during development has been demonstrated before (Moon et al., 2020; Shi et al., 2022).  

      In most motile cilia, the central pair complex (CPC) does not originate directly from the basal body; instead, it begins a short distance above the transition zone, a feature that already illustrates variation in CPC assembly across systems (Lechtreck et al., 2013). The CPC can also show variation in its spatial extent: for example, in mammalian sperm axonemes, it can terminate before reaching the distal end of the axoneme (Fawcett and Ito, 1965). In addition, CPC orientation differs across organisms: in metazoans and Trypanosoma, the CPC is fixed relative to the outer doublets, whereas in Chlamydomonas and ciliates it twists within the axoneme (Lechtreck et al., 2013). Such variation has been described in multiple motile cilia and flagella and is therefore not unique to vestibular kinocilia. What appears more unusual in our data is the organization at the distal tip, where a distinct distal head is present, similar to cilia tip morphologies recently described in human islet cells (Polino et al., 2023). Although this feature is intriguing, we interpret it primarily as a structural signature rather than as evidence for a specialized motile adaptation, and we will moderate our interpretation accordingly in the revision.

      b) While it was a good idea to compare ciliary motility expression in published P2 datasets for mouse cochlear and vestibular hair cells for comparison with the authors' adult hair cell data, the presentation is too superficial to assess (Figure 6C-E; text from line 336) - it is hard to see the basis for concluding that motility genes are specifically lower in P2 cochlear hair cells than vestibular hair cells. Visually, it is striking that CHCs have much darker bands for about 10 motility-related genes.

      We aimed to show that kinocilia in neonatal cochlear and vestibular hair cells are largely similar, except that neonatal cochlear hair cells lack key genes and proteins required for the motile apparatus. While these genes (e.g., Dynll1, Dynll2, Dynlrb1, Cetn2, and Mdh1) appear more highly expressed in P2 cochlear hair cells, they are not uniquely associated with the axoneme. For example, Dynll1/2 and Dynlrb1 are components of the cytoplasmic dynein-1 complex (Pfister et al., 2006), Cetn2 has multiple basic cellular functions beyond cilia (e.g., centrosome organization, DNA repair), and Mdh1 encodes a cytosolic malate dehydrogenase involved in central metabolic pathways such as the citric acid cycle and malate–aspartate shuttle. This contrasts with axonemal dyneins, which are uniquely required for cilia motility. To avoid ambiguity, we will mark such cytoplasmic or multifunctional genes with stars in both Figure 5G and Figure 6D together with legend in the revised manuscript.

      Although those genes (i.e., Dynll1, Dynll2, Dynlrb1, Cetn2, and Mdh1) are highly expressed in neonatal cochlear hair cells, key genes for motile machinery are not detected. For example, Dnah6, Dnah5, and Wdr66 are not expressed in the P2 cochlear hair cells.  Dnah6 and Dnah5 encode axonemal dynein and are part of inner and outer dynein arms while Wdr66 is a component of radial spokes. Importantly, we did not detect the expression of CCDC39 and CCDC40 in kinocilia of P2 cochlear hair cells.  Axonemal CCDC39 and CCDC40 are the molecular rulers that organize the axonemal structure in the 96-nm repeating interactome and are required for the assembly of IDAs and N-DRC for ciliary motility (Becker-Heck et al., 2011; Merveille et al., 2011; Oda et al., 2014). We will modify Figure 6D to highlight the key difference between P2 cochlear and vestibular hair cells in the revised manuscript. We will also revise the text so that the key differences will clearly be described.

      (2) Interpretation:

      The authors take the view that kinociliary motility is likely to be normally present but is rare in their observations because the conditions are not right. But while others have described some (rare) kinociliary motility in fish organs (Rusch & Thurm 1990), they interpreted its occurrence as a sign of pathology. Indeed, in this paper, it is not clear, or even discussed, how kinociliary motility would help with mechanosensitivity in mature hair bundles. Rather, the presence of an autonomous rhythm would actively interfere with generating temporally faithful representations of the head motions that drive vestibular hair cells.

      Spontaneous flagella-like rhythmic beating of kinocilia in vestibular HCs in frogs and eels (Flock et al., 1977; Rüsch and Thurm, 1990) and in zebrafish early otic vesicle (Stooke-Vaughan et al., 2012; Wu et al., 2011) has been reported previously. Based on Rüsch and Thurm (1990), spontaneous kinocilia motility occurred under non-physiological conditions and was interpreted as a sign of cellular deterioration rather than a normal feature. We speculate that deterioration under non-physiological conditions may lead to the disruption of lateral links between the kinocilium and the stereociliary bundle, effectively unloading the kinocilium and allowing it to move more freely. Additionally, fluctuations in intracellular ATP levels may contribute, as ciliary motility is highly ATP-dependent; when ATP is depleted, beating ceases. Similar phenomena have been documented in respiratory epithelia, where ciliary activity can temporarily pause. Nevertheless, the fact that kinocilia can exhibit spontaneous motility under these conditions indicates that they possess the motile machinery necessary for such beating. Irrespective of the condition, cilia without the molecular machinery required for motility will not be able to move.

      We agree with the reviewer that, based on the present data, it is difficult to know the functional role of kinocilia and whether the presence of such autonomous rhythm would interfere with temporal fidelity. Spontaneous bundle motion, driven by the active process associated with mechanotransduction, was observed in bullfrog saccular hair cells (Benser et al., 1996; Martin et al., 2003). We will revise the discussion to clarify this important point of the reviewer. Specifically, we will emphasize that our observations of ciliary beating in the ex vivo conditions may not reflect its properties in the mature in vivo context, but rather a byproduct of motile machinery clearly present in the kinocilia. We speculate that this machinery in mature hair cells could operate in a more subtle mode—modulating the rigor state of dynein arms or related axonemal structures to influence kinociliary mechanics and, in turn, bundle stiffness in response to stimuli or signaling cues. Such a mechanism could either enhance sensitivity or introduce filtering properties, thereby contributing to the fine control of mechanosensory function without compromising temporal fidelity. Future studies using loss-of-function approach will be needed to reveal the unexplored role(s) of kinocilia for vestibular hair cells in vertebrates. 

      Could kinociliary beating play other roles, possibly during development - for example, by interacting with forming accessory structures (but see Whitfield 2020) or by activating mechanosensitivity cell-autonomously, before mature stimulation mechanisms are in place? Then a latent capacity to beat in mature vestibular hair cells might be activated by stressful conditions, as speculated regarding persistent Piezo channels that are normally silent in mature cochlear hair cells but may reappear when TMC channel gating is broken (Beurg and Fettiplace 2017). While these are highly speculative thoughts, there is a need in the paper for more nuanced consideration of whether the observed motility is normal and what good it would do.

      We thank the reviewer for these excellent suggestions. We agree that kinociliary motility could plausibly serve roles during development, for example by guiding hair bundle formation or by contributing to early mechanosensitivity and spontaneous activity before mature stimulation mechanisms are established. It is also possible that the motility machinery represents a latent capacity in mature vestibular hair cells that could be reactivated under stress or pathological conditions. We will revise the Discussion to address these possibilities and to provide a more nuanced consideration of whether the observed motility is normal and what potential functions it might serve.

      Reviewer #2 (Public review):

      Summary:

      In this study, the authors compared the transcriptomes of the various types of hair cells contained in the sensory epithelia of the cochlea and vestibular organs of the mouse inner ear. The analysis of their transcriptomic data led to novel insights into the potential function of the kinocilium.

      Strengths:

      The novel findings for the kinocilium gene expression, along with the demonstration that some kinocilia demonstrate rhythmic beating as would be seen for known motile cilia, are fascinating. It is possible that perhaps the kinocilium, known to play a very important role in the orientation of the stereocilia, may have a gene expression pattern that is more like a primary cilium early in development and later in mature hair cells, more like a motile cilium. Since the kinocilium is retained in vestibular hair cells, it makes sense that it is playing a different role in these mature cells than its role in the cochlea.

      Another major strength of this study, which cannot be overstated, is that for the transcriptome analysis, they are using mature mice. To date, there is a lot of data from many labs for embryonic and neonatal hair cells, but very little transcriptomic data on the mature hair cells. They do a nice job in presenting the differences in marker gene expression between the 4 hair cell types. This information is very useful to those labs studying regeneration or generation of hair cells from ES cell cultures. One of the biggest questions these labs confront is what type of hair cells develop in these systems. The more markers available, the better. These data will also allow researchers in the field to compare developing hair cells with mature hair cells to see what genes are only required during development and not in later functioning hair cells.

      We would like to thank reviewer 2 for his/her comments and hope that the datasets provided in this manuscript will be a useful resource for researchers in the auditory and vestibular neuroscience community.

      Joint Recommendations:

      We will make changes in the revision based on the joint recommendations of the two reviewers.

      References

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      Benser, M.E., Marquis, R.E., Hudspeth, A.J., 1996. Rapid, Active Hair Bundle Movements in Hair Cells from the Bullfrog’s Sacculus. J. Neurosci. 16, 5629–5643. https://doi.org/10.1523/JNEUROSCI.16-18-05629.1996

      Fawcett, D.W., Ito, S., 1965. The fine structure of bat spermatozoa. American Journal of Anatomy 116, 567–609. https://doi.org/10.1002/aja.1001160306

      Flock, Å., Flock, B., Murray, E., 1977. Studies on the Sensory Hairs of Receptor Cells in the Inner Ear. Acta Oto-Laryngologica 83, 85–91. https://doi.org/10.3109/00016487709128817

      Kikuchi, T., Takasaka, T., Tonosaki, A., Watanabe, H., 1989. Fine structure of guinea pig vestibular kinocilium. Acta Otolaryngol 108, 26–30.https://doi.org/10.3109/00016488909107388

      Lechtreck, K.-F., Gould, T.J., Witman, G.B., 2013. Flagellar central pair assembly in Chlamydomonas reinhardtii. Cilia 2, 15. https://doi.org/10.1186/2046-2530-2-15

      Martin, P., Bozovic, D., Choe, Y., Hudspeth, A.J., 2003. Spontaneous Oscillation by Hair Bundles of the Bullfrog’s Sacculus. J. Neurosci. 23, 4533–4548. https://doi.org/10.1523/JNEUROSCI.23-11-04533.2003

      Merveille, A.-C., Davis, E.E., Becker-Heck, A., Legendre, M., Amirav, I., Bataille, G., Belmont, J., Beydon, N., Billen, F., Clément, A., Clercx, C., Coste, A., Crosbie, R., de Blic, J., Deleuze, S., Duquesnoy, P., Escalier, D., Escudier, E., Fliegauf, M., Horvath, J., Hill, K., Jorissen, M., Just, J., Kispert, A., Lathrop, M., Loges, N.T., Marthin, J.K., Momozawa, Y., Montantin, G., Nielsen, K.G., Olbrich, H., Papon, J.-F., Rayet, I., Roger, G., Schmidts, M., Tenreiro, H., Towbin, J.A., Zelenika, D., Zentgraf, H., Georges, M., Lequarré, A.-S., Katsanis, N., Omran, H., Amselem, S., 2011. CCDC39 is required for assembly of inner dynein arms and the dynein regulatory complex and for normal ciliary motility in humans and dogs. Nat Genet 43, 72–78. https://doi.org/10.1038/ng.726

      Moon, K.-H., Ma, J.-H., Min, H., Koo, H., Kim, H., Ko, H.W., Bok, J., 2020. Dysregulation of sonic hedgehog signaling causes hearing loss in ciliopathy mouse models. eLife 9, e56551. https://doi.org/10.7554/eLife.56551

      Oda, T., Yanagisawa, H., Kamiya, R., Kikkawa, M., 2014. A molecular ruler determines the repeat length in eukaryotic cilia and flagella. Science 346, 857–860. https://doi.org/10.1126/science.1260214

      O’Donnell, J., Zheng, J., 2022. Vestibular Hair Cells Require CAMSAP3, a Microtubule Minus-End Regulator, for Formation of Normal Kinocilia. Front Cell Neurosci 16, 876805. https://doi.org/10.3389/fncel.2022.876805

      Pfister, K.K., Shah, P.R., Hummerich, H., Russ, A., Cotton, J., Annuar, A.A., King, S.M., Fisher, E.M.C., 2006. Genetic Analysis of the Cytoplasmic Dynein Subunit Families. PLOS Genetics 2, e1. https://doi.org/10.1371/journal.pgen.0020001

      Polino, A.J., Sviben, S., Melena, I., Piston, D.W., Hughes, J.W., 2023. Scanning electron microscopy of human islet cilia. Proceedings of the National Academy of Sciences 120, e2302624120. https://doi.org/10.1073/pnas.2302624120

      Rüsch, A., Thurm, U., 1990. Spontaneous and electrically induced movements of ampullary kinocilia and stereovilli. Hearing Research 48, 247–263. https://doi.org/10.1016/0378-5955(90)90065-W

      Shi, H., Wang, H., Zhang, C., Lu, Y., Yao, J., Chen, Z., Xing, G., Wei, Q., Cao, X., 2022. Mutations in OSBPL2 cause hearing loss associated with primary cilia defects via sonic hedgehog signaling [WWW Document]. https://doi.org/10.1172/jci.insight.149626

      Stooke-Vaughan, G.A., Huang, P., Hammond, K.L., Schier, A.F., Whitfield, T.T., 2012. The role of hair cells, cilia and ciliary motility in otolith formation in the zebrafish otic vesicle. Development 139, 1777–1787. https://doi.org/10.1242/dev.079947

      Wu, D., Freund, J.B., Fraser, S.E., Vermot, J., 2011. Mechanistic Basis of Otolith Formation during Teleost Inner Ear Development. Developmental Cell 20, 271–278. https://doi.org/10.1016/j.devcel.2010.12.00

  4. teacher.imperial-english.com teacher.imperial-english.com
    1. Use one of the phrasal verbs from the box to complete each sentence. The meaning has been given in brackets.

      1) I’ve decided to _____ a new hobby this year in my free time. (start to learn)

      👉 take up

      Meaning: to start doing a new activity or hobby. ✔️ Sentence: I’ve decided to take up a new hobby this year in my free time.

      2) The plane will _____ in about 10 minutes I think. (leave the ground and fly)

      👉 take off

      Meaning: when an airplane leaves the ground and begins to fly. ✔️ Sentence: The plane will take off in about 10 minutes I think.

      3) Really the business needs to _____ 2 or 3 new members of staff. (recruit / employ)

      👉 take on

      Meaning: to employ or accept responsibility for new people/tasks. ✔️ Sentence: Really the business needs to take on 2 or 3 new members of staff.

      4) That new coffee shop has been _____ by a big chain company. (buy / get control of)

      👉 take over

      Meaning: to gain control of something (a company, a shop, etc.). ✔️ Sentence: That new coffee shop has been taken over by a big chain company.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Reviewer #1 (Public review):

      Summary:

      The authors aim to explore the effects of the electrogenic sodium-potassium pump (Na<SUP>+</SUP>/K<SUP>+</SUP>ATPase) on the computational properties of highly active spiking neurons, using the weakly-electric fish electrocyte as a model system. Their work highlights how the pump's electrogenicity, while essential for maintaining ionic gradients, introduces challenges in neuronal firing stability and signal processing, especially in cells that fire at high rates. The study identifies compensatory mechanisms that cells might use to counteract these effects, and speculates on the role of voltage dependence in the pump's behavior, suggesting that Na<SUP>+</SUP>/K<SUP>+</SUP>-ATPase could be a factor in neuronal dysfunctions and diseases

      Strengths:

      (1) The study explores a less-examined aspect of neural dynamics-the effects of Na<SUP>+</SUP>/K<SUP>+</SUP>-ATPase electrogenicity. It offers a new perspective by highlighting the pump's role not only in ion homeostasis but also in its potential influence on neural computation.

      (2) The mathematical modeling used is a significant strength, providing a clear and controlled framework to explore the effects of the Na<SUP>+</SUP>/K<SUP>+</SUP>-ATPase on spiking cells. This approach allows for the systematic testing of different conditions and behaviors that might be difficult to observe directly in biological experiments.

      (3) The study proposes several interesting compensatory mechanisms, such as sodium leak channelsand extracellular potassium buffering, which provide useful theoretical frameworks for understanding how neurons maintain firing rate control despite the pump's effects.

      Weaknesses:

      (1) While the modeling approach provides valuable insights, the lack of experimental data to validate the model's predictions weakens the overall conclusions.

      (2)The proposed compensatory mechanisms are discussed primarily in theoretical terms without providing quantitative estimates of their impact on the neuron's metabolic cost or other physiological parameters.

      Comments on revisions:

      The revised manuscript is notably improved.

      We thank the reviewer for their concise and accurate summary and appreciate the constructive feedback on the article’s strengths and weaknesses. Experimental work is beyond the scope of our modeling-based study. However, we would like our work to serve as a framework for future experimental studies into the role of the electrogenic pump current (and its possible compensatory currents) in disease, and its role in evolution of highly specialized excitable cells (such as electrocytes).

      Quantitative estimates of metabolic costs in this study are limited to the ATP that is required to fuel the Na<SUP>+</SUP>/K<SUP>+</SUP> pump. By integrating the net pump current over time and dividing by one elemental charge, one can find the rate of ATP that is consumed by the Na<SUP>+</SUP>/K<SUP>+</SUP> pump for either compensatory mechanism. The difference in net pump current is thus proportional to ATP consumption, which allows for a direct comparison of the cost efficiency of the Na<SUP>+</SUP>/K<SUP>+</SUP> pump for each proposed compensatory mechanism. The Na<SUP>+</SUP>/K<SUP>+</SUP> pump is however not the only ATP-consuming element in the electrocyte, and some of the compensatory mechanisms induce other costs related to cell ‘housekeeping’ or presynaptic processes. We now added a section in the appendix titled ‘Considerations on metabolic costs of compensatory mechanisms’ (section 11.4), where we provide rough estimates on the influence of the compensatory mechanisms on the total metabolic costs of the cell and membrane space occupation. Although we argue that according these rough estimates, the impact of discussed compensatory mechanisms could be significant, due to the absence of more detailed experimental quantification, a plausible quantitative cost estimate on the whole cell level remains beyond the scope of this article.

      Reviewer #1 (Recommendations for the authors):

      I just have a few recommendations on the updated manuscript.

      (1) When exploring the different roles of Na<SUP>+</SUP>/K<SUP>+</SUP>-ATPase in the Results section, the authors employed many different models. For instance, the voltage equation on page 15, voltage equation (2) on page 22, voltage equation (12) on page 24, voltage equation (30) on page 32, and voltage equation (38) on page 35 are presented as the master equations for their respective biophysical models. Meanwhile, the phase models are presented on page 29 and page 33. I would recommend that the authors clearly specify which equations correspond to each subsection of the Results section and explicitly state which equations were used to generate the data in each figure. This would help readers more easily follow the connections between the models, the results, and the figures.

      We thank the reviewer for pointing out that the links of the different voltage equations to the results could be expressed more explicitly in the article. All simulations were done using the ‘master equation’  expressed in Eq. 2, and the other voltage equations that are specified in the article (in the new version of the article Eqs. 13, 31, and 39) are reformulations of Eq. 2 to analytically show different properties of the voltage equation (Eq. 2). This has now been mentioned in the article when formulating the voltage equations, and the equation for the total leak current (in the new version Eq. 3) has been added for completeness.

      (2) The authors may want to revisit their description and references concerning Eigenmannia virescens. For example, wave-type weakly electric fish (e.g., Eigenmannia) and pulse-type weakly electric fish (e.g., Gymnotus carapo) exhibit large differences, making references 52-55 may be inappropriate for subsection 4.3.1, as these studies focus on Gymnotus carapo. Additionally, even within wave-type species, chirp patterns vary. For example, Eigenmannia can exhibit short "pauses"-type chirps, whereas Apteronotus leptorhynchus (another waver-form fish) does not (https://pubmed.ncbi.nlm.nih.gov/14692494/).

      We thank the reviewer for pointing this out. The citations and phrasing in sections 4.3.1 and 4.3.2 have been updated to specifically refer to the weakly electric fish e. Virescens.

      (3) Table on page 21: Please explain why the parameter value (13.5mM) of [Na<SUP>^</SUP>+]_{in} is 10 timeslarger than its value (1.35mM) in reference [26]? How does this value (13.5mM) compare with the range of variable [Na<SUP>^</SUP>+]_{in} in equation (6)?

      The intracellular sodium concentration in reference [26] was reported to be 1.35 mM, but the authors also reported an extracellular sodium concentration of 120 mM, and a sodium reversal potential of 55 mV. Upon calculating the sodium reversal potential, we found that an intracellular sodium concentration of 1.35 mM would give a sodium reversal potential of 113 mV. An intracellular sodium concentration of 13.5 mM, on the other hand, leads to the reported and physiological reversal potential of 55 mV. This has now been clarified in the article, and the connection between this value and Eq. 6 (Eq. 7 in the new version) has also been clarified.

      Reviewer #2 (Public review):

      Summary:

      The paper by Weerdmeester, Schleimer, and Schreiber uses computational models to present the biological constraints under which electrocytes - specialized, highly active cells that facilitate electro-sensing in weakly electric fish-may operate. The authors suggest potential solutions that these cells could employ to circumvent these constraints.

      Electrocytes are highly active or spiking (greater than 300Hz) for sustained periods (for minutes to hours), and such activity is possible due to an influx of sodium and efflux of potassium ions into these cells after each spike. The resulting ion imbalance must be restored, which in electrocytes, as with many other biological cells, is facilitated by the Na-K pumps at the expense of biological energy, i.e., ATP molecules. For each ATP molecule the pump uses, three positively charged sodium ions from the intracellular space are exchanged for two positively charged potassium ions from the extracellular space. This creates a net efflux of positive ions into the extracellular space, resulting in hyperpolarized potentials for the cell over time. For most cells, this does not pose an issue, as their firing rate is much slower, and other compensatory mechanisms and pumps can effectively restore the ion imbalances. However, in the electrocytes of weakly electric fish, which spike at exceptionally high rates, the net efflux of positive ions presents a challenge. Additionally, these cells are involved in critical communication and survival behaviors, underscoring their essential role in reliable functioning.

      In a computational model, the authors test four increasingly complex solutions to the problem of counteracting the hyperpolarized states that occur due to continuous NaK pump action to sustain baseline activity. First, they propose a solution for a well-matched Na leak channel that operates in conjunction with the NaK pump, counteracting the hyperpolarizing states naturally. Their model shows that when such an orchestrated Na leak current is not included, quick changes in the firing rates could have unexpected side effects. Secondly, they study the implications of this cell in the context of chirps-a means of communication between individual fish. Here, an upstream pacemaking neuron entrains the electrocyte to spike, which ceases to produce a so-called chirp - a brief pause in the sustained activity of the electrocytes. In their model, the authors demonstrate that including the extracellular potassium buffer is necessary to obtain a reliable chirp signal. Thirdly, they tested another means of communication in which there was a sudden increase in the firing rate of the electrocyte, followed by a decay to the baseline. For this to occur reliably, the authors emphasize that a strong synaptic connection between the pacemaker neuron and the electrocyte is necessary. Finally, since these cells are energy-intensive, they hypothesize that electrocytes may have energy-efficient action potentials, for which their NaK pumps may be sensitive to the membrane voltages and perform course correction rapidly.

      Strengths:

      The authors extend an existing electrocyte model (Joos et al., 2018) based on the classical Hodgkin and Huxley conductance-based models of sodium and potassium currents to include the dynamics of the sodium-potassium (NaK) pump. The authors estimate the pump's properties based on reasonable assumptions related to the leak potential. Their proposed solutions are valid and may be employed by weakly electric fish. The authors explore theoretical solutions to electrosensing behavior that compound and suggest that all these solutions must be simultaneously active for the survival and behavior of the fish. This work provides a good starting point for conducting in vivo experiments to determine which of these proposed solutions the fish employ and their relative importance. The authors include testable hypotheses for their computational models.

      Weaknesses:

      The model for action potential generation simplifies ion dynamics by considering only sodium and potassium currents, excluding other ions like calcium. The ion channels considered are assumed to be static, without any dynamic regulation such as post-translational modifications. For instance, a sodium-dependent potassium pump could modulate potassium leak and spike amplitude (Markham et al., 2013).

      This work considers only the sodium-potassium (NaK) pumps to restore ion gradients. However, in many cells, several other ion pumps, exchangers, and symporters are simultaneously present and actively participate in restoring ion gradients. When sodium currents dominate action potentials, and thus when NaK pumps play a critical role, such as the case in Eigenmannia virescens, the present study is valid. However, since other biological processes may find different solutions to address the pump's non-electroneutral nature, the generalizability of the results in this work to other fast-spiking cell types is limited. For example, each spike could include a small calcium ion influx that could be buffered or extracted via a sodium-calcium exchanger.

      We thank the reviewer for the detailed summary and the updated identified strengths and weaknesses. The current article indeed focuses on and isolates the interplay between sodium currents, potassium currents, and sodium-potassium pump currents. As discussed in section 5.1, in excitable cells where these currents are the main players in action-potential generation, the results presented in this article are applicable. The contribution of post-translational effects of ion channels, other ionic currents, and other active transporters and pumps, could be exciting avenues for further studies

      .

      Reviewer #2 (Recommendations for the authors):

      Thank you for addressing my comments.

      All the figures are now consistent. The color schema used is clear.

      The methods and discussions expansions improve the paper.

      Including the model assumptions and simplifications is appreciated.

      Including internal references is helpful.

      The equations are clear, and the references have been fixed.

      I am content with the changes. I have updated my review accordingly.

      We thank the reviewer for their initial constructive comments that lead to the significant improvement of the article.

      Page : 3 Line : 113 Author : Unknown Author 07/24/2025 

      Although this is technically correct, the article is about electrocommunication signals and does not focus on sensing.

      Page : 3 Line : 153 Author : Unknown Author 07/24/2025

      electrocommunication

      Page : 4 Line : 164 Author : Unknown Author 07/24/2025 

      Judging from the cited article, I think this should be a sodium-dependent potassium current.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Reviewer #1 (Public review):

      Summary:

      The authors developed a sequence-based method to predict drug-interacting residues in IDP, based on their recent work, to predict the transverse relaxation rates (R2) of IDP trained on 45 IDP sequences and their corresponding R2 values. The discovery is that the IDPs interact with drugs mostly using aromatic residues that are easy to understand, as most drugs contain aromatic rings. They validated the method using several case studies, and the predictions are in accordance with chemical shift perturbations and MD simulations. The location of the predicted residues serves as a starting point for ligand optimization.

      Strengths:

      This work provides the first sequence-based prediction method to identify potential druginteracting residues in IDP. The validity of the method is supported by case studies. It is easy to use, and no time-consuming MD simulations and NMR studies are needed.

      Weaknesses:

      The method does not depend on the information of binding compounds, which may give general features of IDP-drug binding. However, due to the size and chemical structures of the compounds (for example, how many aromatic rings), the number of interacting residues varies, which is not considered in this work. Lacking specific information may restrict its application in compound optimization, aiming to derive specific and potent binding compounds.

      We fully recognize that different compounds may have different interaction propensity profiles along the IDP sequence. In future studies, we will investigate compound-specific parameter values. The limiting factor is training data, but such data are beginning to be available.

      Reviewer #2 (Public review):

      Summary:

      In this work, the authors introduce DIRseq, a fast, sequence-based method that predicts druginteracting residues (DIRs) in IDPs without requiring structural or drug information. DIRseq builds on the authors' prior work looking at NMR relaxation rates, and presumes that those residues that show enhanced R2 values are the residues that will interact with drugs, allowing these residues to be nominated from the sequence directly. By making small modifications to their prior tool, DIRseq enables the prediction of residues seen to interact with small molecules in vivo.

      Strengths:

      The preprint is well written and easy to follow

      Weaknesses:

      (1) The DIRseq method is based on SeqDYN, which itself is a simple (which I do not mean as a negative - simple is good!) statistical predictor for R2 relaxation rates. The challenge here is that R2 rates cover a range of timescales, so the physical intuition as to what exactly elevated R2 values mean is not necessarily consistent with "drug interacting". Presumably, the authors are not using the helix boost component of SeqDYN here (it would be good to explicitly state this). This is not necessarily a weakness, but I think it would behove the authors to compare a few alternative models before settling on the DIRseq method, given the somewhat ad hoc modifications to SeqDYN to get DIRseq.

      Actually, the factors that elevate R2 are well-established. These are local interactions and residual secondary structures (if any). The basic assumption of our method is that intra-IDP interactions that elevate R2 convert to IDP-drug interactions. This assumption was supported by our initial observation that the drug interaction propensity profiles predicted using the original SeqDYN parameters already showed good agreement with CSP profiles. We only made relatively small adjustments to the parameters to improve the agreement. Indeed we did not apply the helix boost portion of SeqDYN to DIRseq, and now state as such (p. 4, second last paragraph). We now also compare DIRseq with several alternative models, as summarized in new Table S2.

      Specifically, the authors previously showed good correlation between the stickiness parameter of Tesei et al and the inferred "q" parameter for SeqDYN; as such, I am left wondering if comparable accuracy would be obtained simply by taking the stickiness parameters directly and using these to predict "drug interacting residues", at which point I'd argue we're not really predicting "drug interacting residues" as much as we're predicting "sticky" residues, using the stickiness parameters. It would, I think, be worth the authors comparing the predictive power obtained from DIRseq with the predictive power obtained by using the lambda coefficients from Tesei et al in the model, local density of aromatic residues, local hydrophobicity (note that Tesei at al have tabulated a large set of hydrophobicity scores!) and the raw SeqDYN predictions. In the absence of lots of data to compare against, this is another way to convince readers that DIRseq offers reasonable predictive power.

      We now compare predictions of these various parameter sets, and report the results in Table S2.  In short, among all the tested parameter sets, DIRseq has the best performance as measured by (1) strong correlations between prediction scores and CSPs and (2) high true positives and low false positives (p. 7-9).

      (2) Second, the DIRseq is essentially SeqDYN with some changes to it, but those changes appear somewhat ad hoc. I recognize that there is very limited data, but the tweaking of parameters based on physical intuition feels a bit stochastic in developing a method; presumably (while not explicitly spelt out) those tweaks were chosen to give better agreement with the very limited experimental data (otherwise why make the changes?), which does raise the question of if the DIRseq implementation of SeqDYN is rather over-parameterized to the (very limited) data available now? I want to be clear, the authors should not be critiqued for attempting to develop a model despite a paucity of data, and I'm not necessarily saying this is a problem, but I think it would be really important for the authors to acknowledge to the reader the fact that with such limited data it's possible the model is over-fit to specific sequences studied previously, and generalization will be seen as more data are collected.

      We have explained the rationale for the parameter tweaks, which were limited to q values for four amino-acid types, i.e., to deemphasize hydrophobic interactions and slightly enhance electrostatic interactions (p. 4-5). We now add that these tweaks were motivated by observations from MD simulations of drug interactions with a-syn (ref 13). As already noted in the response to the preceding comment, we now also present results for the original parameter values as well as for when the four q values are changed one at a time.

      (3) Third, perhaps my biggest concern here is that - implicit in the author's assumptions - is that all "drugs" interact with IDPs in the same way and all drugs are "small" (motivating the change in correlation length). Prescribing a specific length scale and chemistry to all drugs seems broadly inconsistent with a world in which we presume drugs offer some degree of specificity. While it is perhaps not unexpected that aromatic-rich small molecules tend to interact with aromatic residues, the logical conclusion from this work, if one assumes DIRseq has utility, is that all IDRs bind drugs with similar chemical biases. This, at the very least, deserves some discussion.

      The reviewer raises a very important point. In Discussion, we now add that it is important to further develop DIRseq to include drug-specific parameters when data for training become available (p. 12-13). To illustrate this point, we use drug size as a simple example, which can be modeled by making the b parameter dependent on drug molecule size.

      (4) Fourth, the authors make some general claims in the introduction regarding the state of the art, which appear to lack sufficient data to be made. I don't necessarily disagree with the author's points, but I'm not sure the claims (as stated) can be made absent strong data to support them. For example, the authors state: "Although an IDP can be locked into a specific conformation by a drug molecule in rare cases, the prevailing scenario is that the protein remains disordered upon drug binding." But is this true? The authors should provide evidence to support this assertion, both examples in which this happens, and evidence to support the idea that it's the "prevailing view" and specific examples where these types of interactions have been biophysically characterized.

      We now cite nine studies showing that IDPs remain disordered upon drug binding.

      Similarly, they go on to say:

      "Consequently, the IDP-drug complex typically samples a vast conformational space, and the drug molecule only exhibits preferences, rather than exclusiveness, for interacting with subsets of residues." But again, where is the data to support this assertion? I don't necessarily disagree, but we need specific empirical studies to justify declarative claims like this; otherwise, we propagate lore into the scientific literature. The use of "typically" here is a strong claim, implying most IDP complexes behave in a certain way, yet how can the authors make such a claim? 

      Here again we add citations to support the statement.

      Finally, they continue to claim:

      "Such drug interacting residues (DIRs), akin to binding pockets in structured proteins, are key to optimizing compounds and elucidating the mechanism of action." But again, is this a fact or a hypothesis? If the latter, it must be stated as such; if the former, we need data and evidence to support the claim.

      We add citations to both compound optimization and mechanism of action.

      Reviewer #1 (Recommendations for the authors):

      (1) The authors should compare the sequences of the IDPs in the case studies with the 45 IDPs in training the SeqDYN model to make sure that they are not included in the training dataset or are highly homologous.

      Please note that the data used for training SeqDYN were R2 rates, which are independent of the property being studied here, i.e., drug interacting residues. Therefore whether the IDPs studied here were in the training set for SeqDYN is immaterial.

      (2) The authors manually tuned four parameters in SeqDYN to develop the model for predicting drug-interacting residues without giving strict testing or explanations. More explanations, testing of more values, and ablation testing should be given.

      As responded above, we now both expand the explanation and present more test results.

      (3) The authors changed the q values of L, I, and M to the value of V. What are the results if these values are not changed?

      These results are shown in Table S2 (entry named SeqDYN_orig).

      (4) Only one b value is chosen based on the assumption that a drug molecule interacts with 3-4 residues at a time. However, the number of interacting residues is related to the size of the drug molecule. Adjusting the b value with the size of the ligand may provide improvement. It is better to test the influence of adjusting b values. At least, this should be discussed.

      Good point! We now state that b potentially can be adjusted according to ligand size (p. 12-13). In addition, we also show the effect of varying b on the prediction results (Table S2; p. 8, last paragraph).

      (5) The authors add 12 Q to eliminate end effects. However, explanations on why 12 Qs are chosen should be given. How about other numbers of Q or using other residues (e.g., the commonly used residues in making links, like GS/PS or A?

      As we already explained, “Gln was selected because its 𝑞 value is at the middle of the 20 𝑞 values.” (p. 5, second paragraph). Also, 12 Qs are sufficient to remove any end effects; a higher number of Qs does not make any difference.

      Reviewer #2 (Recommendations for the authors):

      (1) The authors make reference to the "C-terminal IDR" in cMyc, but the region they note is found in the bHLH DNA binding domain (which falls from residue ~370-420).

      We now clarify that this region is disordered on its own but form a helix-loop-loop structure upon heterodimerization with Max (p. 11, last paragraph).

      (2) Given the fact that X-seq names are typically associated with sequencing-based methods, it's perhaps confusing to name this method DIRseq?

      We appreciate the reviewer’s point, but by now the preprint posted in bioRxiv is in wide circulation, and the DIRseq web server has been up for several months, so changing its name would cause a great deal of confusion.

      (3) I'd encourage the authors just to spell out "drug interacting residues" and retain an IDR acronym for IDRs. Acronyms rarely make writing clearer, and asking folks to constantly flip between IDR and DIR is asking a lot of an audience (in this reviewer's opinion, anyway).

      The reviewer makes a good point; we now spell out “drug-interacting residues”.

      (4) The assumption here is that CSPs result from direct drug:IDR interactions. However, CSPs result from a change in the residue chemical environment, which could in principle be an indirect effect (e.g., in the unbound state, residues A and B interact; in the bound state, residue A is now free, such that it experiences a CSP despite not engaging directly). While I recognize such assumptions are commonly made, it behoves the authors to explicitly make this point so the reader understands the relationship between CSPs and binding.

      We did add caveats of CSP in Introduction (p. 3, second paragraph).

      (5) On the figures, please label which protein is which figure, as well as provide a legend for the annotations on the figures (red line, blue bar, cyan region, etc.)

      We now label protein names in Fig. 1. For annotation of display items, it is also made in the Figs. 2 and 3 captions; we now add it to the Fig. 4 caption.

      (6) abstract: "These successes augur well for deciphering the sequence code for IDP-drug binding." - This is not grammatically correct, even if augur were changed to agree. Suggest rewriting.

      “Augur well” means to be a good sign (for something). We use this phrase here in this meaning.

      (6) page 5: "we raised the 𝑞 value of Asp to be the same as that of Glu" → suggested "increased" instead of raised.

      We have made the suggested change.

      (7) The authors should consider releasing the source code (it is available via the .js implementation on the server, but this is not very transferable/shareable, so I'd encourage the authors to provide a stand-alone implementation that's explicitly shareable).

      We have now added a link for the user to download the source code.

    1. Author response:

      The following is the authors’ response to the current reviews.

      eLife Assessment

      The authors examine the effect of cell-free chromatin particles (cfChPs) derived from human serum or from dying human cells on mouse cells in culture and propose that these cfChPs can serve as vehicles for cell-to-cell active transfer of foreign genetic elements. The work presented in this paper is intriguing and potentially important, but it is incomplete. At this stage, the claim that horizontal gene transfer can occur via cfChPs is not well supported because it is only based on evidence from one type of methodological approach (immunofluorescence and fluorescent in situ hybridization (FISH)) and is not validated by whole genome sequencing.

      We disagree with the eLife assessment that our study is incomplete because we did not perform whole genome sequencing. Tens of thousands of genomes have been sequenced, and yet they have failed to detect the presence of the numerous “satellite genomes” that we describe in our paper. To that extent whole genome sequencing has proved to be an inappropriate technology. Rather, eLife should have commended us for the numerous control experiments that we have done to ensure that our FISH probes and antibodies are target specific and do not cross-react.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Horizontal gene transfer is the transmission of genetic material between organisms through ways other than reproduction. Frequent in prokaryotes, this mode of genetic exchange is scarcer in eukaryotes, especially in multicellular eukaryotes. Furthermore, the mechanisms involved in eukaryotic HGT are unknown. This article by Banerjee et al. claims that HGT occurs massively between cells of multicellular organisms. According to this study, the cell free chromatin particles (cfChPs) that are massively released by dying cells are incorporated in the nucleus of neighboring cells.

      The reviewer is mistaken. We do not claim that the internalized cfChPs are incorporated into the nucleus. We show throughout the paper that the cfChPs perform their novel functions autonomously outside the genome without being incorporated into the nucleus. This is clearly seen in all our chromatin fibre images, metaphase spreads and our video abstract. Occasionally, when the cfChPs fluorescent signal overlie the chromosomes, we have been careful to state that the cfChPs are associated with the chromosomes without implying that they have integrated.

      These cfChPs are frequently rearranged and amplified to form concatemers, they are made of open chromatin, expressed, and capable of producing proteins. Furthermore, the study also suggests that cfChPs transmit transposable elements (TEs) between cells on a regular basis, and that these TEs can transpose, multiply, and invade receiving cells. These conclusions are based on a series of experiments consisting in releasing cfChPs isolated from various human sera into the culture medium of mouse cells, and using FISH and immunofluorescence to monitor the state and fate of cfChPs after several passages of the mouse cell line.

      Strengths:

      The results presented in this study are interesting because they may reveal unsuspected properties of some cell types that may be able to internalize free-circulating chromatin, leading to its chromosomal incorporation, expression, and unleashing of TEs. The authors propose that this phenomenon may have profound impacts in terms of diseases and genome evolution. They even suggest that this could occur in germ cells, leading to within-organism HGT with long-term consequences.

      Again the reviewer makes the same mistake. We do not claim that the internalized cfChPs are incorporated into the chromosomes. We have addressed this issue above.

      We have a feeling that the reviewer has not understood our work – which is the discovery of “satellite genomes” which function autonomously outside the nuclear genome.

      Weaknesses:

      The claims of massive HGT between cells through internalization of cfChPs are not well supported because they are only based on evidence from one type of methodological approach: immunofluorescence and fluorescent in situ hybridization (FISH) using protein antibodies and DNA probes. Yet, such strong claims require validation by at least one, but preferably multiple, additional orthogonal approaches. This includes, for example, whole genome sequencing (to validate concatemerization, integration in receiving cells, transposition in receiving cells), RNA-seq (to validate expression), ChiP-seq (to validate chromatin state).

      We disagree with the reviewer that our study is incomplete because we did not perform whole genome sequencing. Tens of thousands of genomes have been sequenced, and yet they have failed to detect the presence of the numerous “satellite genomes” that we describe in our paper. To that extent whole genome sequencing has proved to be an inappropriate approach. Rather, the reviewer should have commended us for the numerous control experiments that we have done to ensure that our FISH probes and antibodies are target specific and do not cross-react.

      Should HGT through internalization of circulating chromatin occur on a massive scale, as claimed in this study, and as illustrated by the many FISH foci observed on Fig 3 for example, one would expect that the level of somatic mosaicism may be so high that it would prevent assembling a contiguous genome for a given organism. Yet, telomere-to-telomere genomes have been produced for many eukaryote species, calling into question the conclusions of this study.

      The reviewer has raised a related issue below and we have responded to both of them together.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      I thank the authors for taking my comments and those of the other reviewer into account and for adding new material to this new version of the manuscript. Among other modifications/additions, they now mention that they think that NIH3T3 cells treated with cfChPs die out after 250 passages because of genomic instability which might be caused by horizontal transfer of cfChPs DNA into the genome of treated cells (pp. 45-46, lines 725-731). However, no definitive formal proof of genomic instability and horizontal transfer is provided.

      We mention that the NIH3T3 cells treated with cfChPs die out after 250 passages in response to the reviewer’s earlier comment “Should HGT through internalization of circulating chromatin occur on a massive scale, as claimed in this study, and as illustrated by the many FISH foci observed in Fig 3 for example, one would expect that the level of somatic mosaicism may be so high that it would prevent assembling a contiguous genome for a given organism”.

      We have agreed with the reviewer and have simply speculated that the cells may die because of extreme genomic instability. We have left it as a speculation without diverting our paper in a different direction to prove genomic instability.

      The authors now refer to an earlier study they conducted in which they Illumina-sequenced NIH3T3 cells treated with cfChPs (pp. 48, lines. 781-792). This study revealed the presence of human DNA in the mouse cell culture. However, it is unclear to me how the author can conclude that the human DNA was inside mouse cells (rather than persisting in the culture medium as cfChPs) and it is also unclear how this supports horizontal transfer of human DNA into the genome of mouse cells. Horizontal transfer implies integration of human DNA into mouse DNA, through the formation of phosphodiester bounds between human nucleotides and mouse nucleotides. The previous Illumina-sequencing study and the current study do not show that such integration has occured. I might be wrong but I tend to think that DNA FISH signals showing that human DNA lies next to mouse DNA does not necessarily imply that human DNA has integrated into mouse DNA. Perhaps such signals could result from interactions at the protein level between human cfChPs and mouse chromatin?

      With due respect, our earlier genome sequencing study that the reviewer refers to was done on two single cell clones developed following treatment with cfChPs. So, the question of cfChPs lurking in the culture medium does not arise.

      The authors should be commended for doing so many FISH experiments. But in my opinion, and as already mentioned in my earlier review of this work, horizontal transfer of human DNA into mouse DNA should first be demonstrated by strong DNA sequencing evidence (multiple long and short reads supporting human/mouse breakpoints; discarding technical DNA chimeras) and only then eventually confirmed by FISH.

      As mentioned earlier, we disagree with the reviewer that our study is incomplete because we did not perform whole genome sequencing. Tens of thousands of genomes have been sequenced, and yet they have failed to detect the presence of the numerous “satellite genomes” that we describe in our paper. To that extent whole genome sequencing has proved to be an inappropriate approach. Rather, the reviewer should have commended us for the numerous control experiments that we have done to ensure that our FISH probes and antibodies are target specific and do not cross-react.

      Regarding my comment on the quantity of human cfChPs that has been used for the experiments, the authors replied that they chose this quantity because it worked in a previous study. Could they perhaps explain why they chose this quantity in the earlier study? Is there any biological reason to choose 10 ng and not more or less? Is 10 ng realistic biologically? Could it be that 10 ng is orders of magnitude higher than the quantity of cfChPs normally circulating in multicellular organisms and that this could explain, at least in part, the results obtained in this study?

      The reviewer again raises the same issue to which we have already addressed in our revised manuscript. To quote “We chose to use 10ng based on our earlier report in which we had obtained robust biological effects such as activation of DDR and activation of apoptotic pathways using this concentration of cfChPs (Mittra I et. al., 2015)”.

      It is also mentioned in the response that RNA-seq has been performed on mouse cells treated with cfChPs, and that this confirms human-mouse fusion (genomic integration). Since these results are not included in the manuscript, I cannot judge how robust they are and whether they reflect a biological process rather than technical issues (technical chimeras formed during the RNA-seq protocol is a well-known artifact). In any case, I do not think that genomic integration can be demonstrated through RNA-seq as junction between human and mouse RNA could occur at the RNA level (i.e. after transcription). RNA-seq could however show whether human-mouse chimeras that have been validated by DNA-sequencing are expressed or not.

      We did perform transcriptome sequencing as suggested earlier by the reviewer, but realized that the amount of material required to be incorporated into the manuscript to include “material and methods”, “results”, “discussion”, “figures” and “legends to figures” and “supplementary figures and tables” would be so massive that it will detract from the flow of our work and hijack it in a different direction. We have, therefore, decided to publish the transcriptome results as a separate manuscript.

      Given these comments, I believe that most of the weaknesses I mentioned in my review of the first version of this work still hold true.

      An important modification is that the work has been repeated in other cell lines, hence I removed this criticism from my earlier review.

      Additional changes made

      (1) We have now rewritten the “Abstract” to 250 words to fit in eLife’s instructions. (It was not possible to reduce the word count further.

      (2) We have provided the Video 1 as separate file instead of link.

      (3) Some of Figure Supplements (which were stand-alone) are now given as main figures. We have re-arranged Figures and Figure Supplements in accordance with eLife’s instructions.

      (4) We have now provided a list of the various cell lines used in this study, their tissue origin and procurement source in Supplementary File 3.


      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Horizontal gene transfer is the transmission of genetic material between organisms through ways other than reproduction. Frequent in prokaryotes, this mode of genetic exchange is scarcer in eukaryotes, especially in multicellular eukaryotes. Furthermore, the mechanisms involved in eukaryotic HGT are unknown. This article by Banerjee et al. claims that HGT occurs massively between cells of multicellular organisms. According to this study, the cell free chromatin particles (cfChPs) that are massively released by dying cells are incorporated in the nucleus of neighboring cells. These cfChPs are frequently rearranged and amplified to form concatemers, they are made of open chromatin, expressed, and capable of producing proteins. Furthermore, the study also suggests that cfChPs transmit transposable elements (TEs) between cells on a regular basis, and that these TEs can transpose, multiply, and invade receiving cells. These conclusions are based on a series of experiments consisting in releasing cfChPs isolated from various human sera into the culture medium of mouse cells, and using FISH and immunofluorescence to monitor the state and fate of cfChPs after several passages of the mouse cell line.

      Strengths:

      The results presented in this study are interesting because they may reveal unsuspected properties of some cell types that may be able to internalize free-circulating chromatin, leading to its chromosomal incorporation, expression, and unleashing of TEs. The authors propose that this phenomenon may have profound impacts in terms of diseases and genome evolution. They even suggest that this could occur in germ cells, leading to within-organism HGT with long-term consequences.

      Weaknesses:

      The claims of massive HGT between cells through internalization of cfChPs are not well supported because they are only based on evidence from one type of methodological approach: immunofluorescence and fluorescent in situ hybridization (FISH) using protein antibodies and DNA probes. Yet, such strong claims require validation by at least one, but preferably multiple, additional orthogonal approaches. This includes, for example, whole genome sequencing (to validate concatemerization, integration in receiving cells, transposition in receiving cells), RNA-seq (to validate expression), ChiP-seq (to validate chromatin state).

      We have responded to this criticism under “Reviewer #1 (Recommendations for the authors, item no. 1-4)”.

      Another weakness of this study is that it is performed only in one receiving cell type (NIH3T3 mouse cells). Thus, rather than a general phenomenon occurring on a massive scale in every multicellular organism, it could merely reflect aberrant properties of a cell line that for some reason became permeable to exogenous cfChPs. This begs the question of the relevance of this study for living organisms.

      We have responded to this criticism under “Reviewer #1 (Recommendations for the authors, item no. 6)”.

      Should HGT through internalization of circulating chromatin occur on a massive scale, as claimed in this study, and as illustrated by the many FISH foci observed in Fig 3 for example, one would expect that the level of somatic mosaicism may be so high that it would prevent assembling a contiguous genome for a given organism. Yet, telomere-to-telomere genomes have been produced for many eukaryote species, calling into question the conclusions of this study.

      The reviewer is right in expecting that the level of somatic mosaicism may be so high that it would prevent assembling a contiguous genome. This is indeed the case, and we find that beyond ~ 250 passages the cfChPs treated NIH3T3 cells begin to die out apparently become their genomes have become too unstable for survival. This point will be highlighted in the revised version (pp. 45-46, lines 725-731).

      Reviewer #2 (Public review):

      I must note that my comments pertain to the evolutionary interpretations rather than the study's technical results. The techniques appear to be appropriately applied and interpreted, but I do not feel sufficiently qualified to assess this aspect of the work in detail.

      I was repeatedly puzzled by the use of the term "function." Part of the issue may stem from slightly different interpretations of this word in different fields. In my understanding, "function" should denote not just what a structure does, but what it has been selected for. In this context, where it is unclear if cfChPs have been selected for in any way, the use of this term seems questionable.

      We agree. We have removed the term “function” wherever we felt we had used it inappropriately.

      Similarly, the term "predatory genome," used in the title and throughout the paper, appears ambiguous and unjustified. At this stage, I am unconvinced that cfChPs provide any evolutionary advantage to the genome. It is entirely possible that these structures have no function whatsoever and could simply be byproducts of other processes. The findings presented in this study do not rule out this neutral hypothesis. Alternatively, some particular components of the genome could be driving the process and may have been selected to do so. This brings us to the hypothesis that cfChPs could serve as vehicles for transposable elements. While speculative, this idea seems to be compatible with the study's findings and merits further exploration.

      We agree with the reviewer’s viewpoint. We have replaced the term “predatory genome” with a more realistic term “satellite genome” in the title and throughout the manuscript. We have also thoroughly revised the discussion section and elaborated on the potential role of LINE-1 and Alu elements carried by the concatemers in mammalian evolution. (pp. 46-47, lines 743-756).

      I also found some elements of the discussion unclear and speculative, particularly the final section on the evolution of mammals. If the intention is simply to highlight the evolutionary impact of horizontal transfer of transposable elements (e.g., as a source of new mutations), this should be explicitly stated. In any case, this part of the discussion requires further clarification and justification.

      As mentioned above, we have revised the “discussion” section taking into account the issues raised by the reviewer and highlighted the potential role of cfChPs in evolution by acting as vehicles of transposable elements.

      In summary, this study presents important new findings on the behavior of cfChPs when introduced into a foreign cellular context. However, it overextends its evolutionary interpretations, often in an unclear and speculative manner. The concept of the "predatory genome" should be better defined and justified or removed altogether. Conversely, the suggestion that cfChPs may function at the level of transposable elements (rather than the entire genome or organism) could be given more emphasis.

      As mentioned above, we have replaced the term “predatory genome” with “satellite genome” and revised the “discussion” section taking into account the issues raised by the reviewer.

      Reviewer #1 (Recommendations for the authors):

      (1) I strongly recommend validating the findings of this study using other approaches. Whole genome sequencing using both short and long reads should be used to validate the presence of human DNA in the mouse cell line, as well as its integration into the mouse genome and concatemerization. Breakpoints between mouse and human DNA can be searched in individual reads. Finding these breakpoints in multiple reads from two or more sequencing technologies would strengthen their biological origin. Illumina and ONT sequencing are now routinely performed by many labs, such that this validation should be straightforward. In addition to validating the findings of the current study, it would allow performance of an in-depth characterization of the rearrangements undergone by both human cfChPs and the mouse genome after internalization of cfChPs, including identification of human TE copies integrated through bona fide transposition events into the mouse genome. New copies of LINE and Alu TEs should be flanked by target site duplications. LINE copies should be frequently 5' truncated, as observed in many studies of somatic transposition in human cells.

      (2) Furthermore, should the high level of cell-to-cell HGT detected in this study occur on a regular basis within multicellular organisms, validating it through a reanalysis of whole genome sequencing data available in public databases should be relatively easy. One would expect to find a high number of structural variants that for some reason have so far gone under the radar.

      (3) Short and long-read RNA-seq should be performed to validate the expression of human cfChPs in mouse cells. I would also recommend performing ChIP-seq on routinely targeted histone marks to validate the chromatin state of human cfChPs in mouse cells.

      (4) The claim that fused human proteins are produced in mouse cells after exposing them to human cfChPs should be validated using mass spectrometry.

      The reviewer has suggested a plethora of techniques to validate our findings. Clearly, it is neither possible to undertake all of them nor to incorporate them into the manuscript. However, as suggested by the reviewer, we did conduct transcriptome sequencing of cfChPs treated NIH3T3 cells and were able to detect the presence of human-human fusion sequences (representing concatemerisation) as well as human-mouse fusion sequences (representing genomic integration). However, we realized that the amount of material required to be incorporated into the manuscript to include “material and methods”, “results”, “discussion”, “figures” and “legends to figures” and “supplementary figures and tables” would be so massive that it will detract from the flow of our work and hijack it in a different direction. We have, therefore, decided to publish the transcriptome results as a separate manuscript. However, to address the reviewer’s concerns we have now referred to results of our earlier whole genome sequencing study of NIH3T3 cells similarly treated with cfChPs wherein we had conclusively detected the presence of human DNA and human Alu sequences in the treated mouse cells. These findings have now been added as an independent paragraph (pp. 48, lines. 781-792).

      (5) It is unclear from what is shown in the paper (increase in FISH signal intensity using Alu and L1 probes) if the increase in TE copy number is due to bona fide transposition or to amplification of cfChPs as a whole, through mechanisms other than transposition. It is also unclear whether human TEs end up being integrated into the neighboring mouse genome. This should be validated by whole genome sequencing.

      Our results suggest that TEs amplify and increase their copy number due to their association with DNA polymerase and their ability to synthesize DNA (Figure 14a and b). Our study design cannot demonstrate transposition which will require real time imaging.

      The possibility of incorporation of TEs into the mouse genome is supported by our earlier genome sequencing work, referred to above, wherein we detected multiple human Alu sequences in the mouse genome (pp. 48, lines. 781-792).

      (6) In order to be able to generalize the findings of this study, I strongly encourage the authors to repeat their experiments using other cell types.

      We thank the reviewer for this suggestion. We have now used four different cell lines derived from four different species and demonstrated that horizontal transfer of cfChPs occur in all of them suggesting that it is a universal phenomenon. (pp. 37, lines 560-572) and (Supplementary Fig. S14a-d).

      We have also mentioned this in the abstract (pp. 3, lines 52-54).

      (7) Since the results obtained when using cfChPs isolated from healthy individuals are identical to those shown when using cfChPs from cancer sera, I wonder why the authors chose to focus mainly on results from cancer-derived cfChPs and not on those from healthy sera.

      Most of the experiments were conducted using cfChPs isolated from cancer patients because of our especial interest in cancer, and our earlier results (Mittra et al., 2015) which had shown that cfChPs isolated from cancer patients had significantly greater activity in terms of DNA damage and activation of apoptotic pathways than those isolated from healthy individuals. We have now incorporated the above justification on (pp. 6, lines. 124-128).

      (8) Line 125: how was the 10-ng quantity (of human cfChPs added to the mouse cell culture) chosen and how does it compare to the quantity of cfChPs normally circulating in multicellular organisms?

      We chose to use 10ng based on our earlier report in which we had obtained robust biological effects such as activation of DDR and apoptotic pathways using this concentration of cfChPs (Mittra I et. al. 2015). We have now incorporated the justification of using this dose in our manuscript (pp. 51-52, lines. 867-870).

      (9) Could the authors explain why they repeated several of their experiments in metaphase spreads, in addition to interphase?

      We conducted experiments on metaphase spreads in addition to those on chromatin fibres because of the current heightened interest in extra-chromosomal DNA in cancer, which have largely been based on metaphase spreads. We were interested to see how the cfChP concatemers might relate to the characteristics of cancer extrachromosomal DNA and whether the latter in fact represent cfChPs concatemers acquired from surrounding dying cancer cells. We have now mentioned this on pp. 7, lines 150-155.

      (10) Regarding negative controls consisting in checking whether human probes cross-react with mouse DNA or proteins, I suggest that the stringency of washes (temperature, reagents) should be clearly stated in the manuscript, such that the reader can easily see that it was identical for controls and positive experiments.

      We were fully aware of these issues and were careful to ensure that washing steps were conducted meticulously. The careful washing steps have been repeatedly emphasized under the section on “Immunofluorescence and FISH” (pp. 54-55, lines. 922-944).

      (11) I am not an expert in Immuno-FISH and FISH with ribosomal probes but it can be expected that ribosomal RNA and RNA polymerase are quite conserved (and thus highly similar) between humans and mice. A more detailed explanation of how these probes were designed to avoid cross-reactivity would be welcome.

      We were aware of this issue and conducted negative control experiment to ensure that the human ribosomal RNA probe and RNA polymerase antibody did not cross-react with mouse. Please see Supplementary Fig. S4c.

      (12) Finally, I could not understand why the cfChPs internalized by neighboring cells are called predatory genomes. I could not find any justification for this term in the manuscript.

      We agree and this criticism has also been made by #Reviewer 2. We have now replaced the term “predatory” genomes with “satellite” genomes.

      Reviewer #2 (Recommendations for the authors):

      (1) P2 L34: The term "role" seems to imply "what something is supposed to do" (similar to "function"). Perhaps "impact" would be more neutral. Additionally, "poorly defined" is vague-do you mean "unknown"?

      We thank the reviewer for this suggestion. We have now rephrased the sentence to read “Horizontal gene transfer (HGT) plays an important evolutionary role in prokaryotes, but it is thought to be less frequent in mammals.” (pp. 2, lines. 26-27).

      (2) P2 L35: It seems that the dash should come after "human blood."

      Thank you, we have changed the position of the dash (pp. 2, line. 29).

      (3) P2 L37: Must we assume these structures have a function? Could they not simply be side effects of other processes?

      We think this is a matter of semantics, especially since we show that cfChPs once inside the cell perform many functions such as replication, DNA synthesis, RNA synthesis, protein synthesis etc. We, therefore, think the word “function” is not inappropriate.

      (4) Abstract: After reading the abstract, I am unclear on the concept of a "predatory genome." Based on the summarized results, it seems one cannot conclude that these elements provide any adaptive value to the genome.

      We agree. We have now replaced the term “predatory” genomes with a more realistic term viz. “satellite” genomes.

      (5) Video abstract: The video abstract does not currently stand on its own and needs more context to be self-explanatory.

      Thank you for pointing this out. We have now created a new and much more professional video with more context which we hope will meet with the reviewer’s approval.

      (6) P4 L67: Again, I am uncertain that HGT should be said to have "a role" in mammals, although it clearly has implications and consequences. Perhaps "role" here is intended to mean "consequence"?

      We have now changed the sentence to read as follows “However, defining the occurrence of HGT in mammals has been a challenge” (pp. 4, line. 73).

      (7) P6 L111: The phrase "to obtain a new perspective about the process of evolution" is unclear. What exactly is meant by this statement?

      We have replaced this sentence altogether which now reads “The results of these experiments are presented in this article which may help to throw new light on mammalian evolution, ageing and cancer” (pp. 5-6, lines 116-118).

      (8) P38 L588: The term "predatory genome" has not been defined, making it difficult to assess its relevance.

      This issue has been addressed above.

      (9) P39 L604: The statement "transposable elements are not inherent to the cell" suggests that some TEs could originate externally, but this does not rule out that others are intrinsic. In other words, TEs are still inherent to the cell.

      This part of the discussion section has been rewritten and the above sentence has been deleted.

      (10) P39 L609: The phrase "may have evolutionary functions by acting as transposable elements" is unclear. Perhaps it is meant that these structures may serve as vehicles for TEs?

      This sentence has disappeared altogether in the revised discussion section.

      (11) P41 L643: "Thus, we hypothesize ... extensively modified to act as foreign genetic elements." This sentence is unclear. Are the authors referring to evolutionary changes in mammals in general (which overlooks the role of standard mutational processes)? Or is it being proposed that structural mutations (including TE integrations) could be mediated by cfChPs in addition to other mutational mechanisms?

      We have replaced this sentence which now reads “Thus, “within-self” HGT may occur in mammals on a massive scale via the medium of cfChP concatemers that have undergone extensive and complex modifications resulting in their behaviour as “foreign” genetic elements” (pp. 47, lines 763-766).

      (12) P41 L150: The paragraph beginning with "It has been proposed that extreme environmental..." transitions too abruptly from HGT to adaptation. Is it being proposed that cfChPs are evolutionary processes selected for their adaptive potential? This idea is far too speculative at this stage and requires clarification.

      We agree. This paragraph has been removed.

      (13) P43 L681: This summary appears overly speculative and unclear, particularly as the concept of a "predatory genome" remains undefined and thus cannot be justified. It suggests that cfChPs represent an alternative lifestyle for the entire genome, although alternative explanations seem far more plausible at this point.

      We have now replaced the term “predatory” genome with “satellite” genome. The relevant part of the summary section has also been partially revised (pp. 49-50, lines 817-831).

      Changes independent of reviewers’ comments.

      We have made the following additions / modifications.

      (1) The abstract has been modified and it’s “conclusion” section has been rewritten.

      (2) Section 1.14 has been newly added together with accompanying Figures 15 a,b and c.

      (3) The “Discussion” section has been greatly modified and parts of it has been rewritten.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Reviewer #1 (Public review): 

      Summary: 

      In this study, the authors explore a novel mechanism linking aging to chromosome mis-segregation and aneuploidy in yeast cells. They reveal that, in old yeast mother cells, chromosome loss occurs through asymmetric partitioning of chromosomes to daughter cells, a process coupled with the inheritance of an old Spindle Pole Body. Remarkably, the authors identify that remodelling of the nuclear pore complex (NPC), specifically the displacement of its nuclear basket, triggers these asymmetric segregation events. This disruption also leads to the leakage of unspliced pre-mRNAs into the cytoplasm, highlighting a breakdown in RNA quality control. Through genetic manipulation, the study demonstrates that removing introns from key chromosome segregation genes is sufficient to prevent chromosome loss in aged cells. Moreover, promoting pre-mRNA leakage in young cells mimics the chromosome mis-segregation observed in old cells, providing further evidence for the critical role of nuclear envelope integrity and RNA processing in aging-related genome instability. 

      Strengths: 

      The findings presented are not only intriguing but also well-supported by robust experimental data, highlighting a previously unrecognized connection between nuclear envelope integrity, RNA processing, and genome stability in aging cells, deepening our understanding of the molecular basis of chromosome loss in aging. 

      We thank the reviewer for this very positive assessment of our work

      Weaknesses: 

      Further analysis of yeast aging data from microfluidic experiments will provide important information about the dynamic features and prevalence of the key aging phenotypes, e.g. pre-mRNA leakage and chromosome loss, reported in this work. 

      We thank the reviewer for bringing this point, which we have addressed in the revised version of the manuscript.  In short, chromosome loss is an abrupt, late event in the lifespan of the cells. To examine its prevalence, we have quantified the combined loss frequency of two chromosomes when both are labelled in the same cell. Whereas single chromosomes are lost at a frequency of 10-15% per cell, less than 5% of the cells lose both at the same time.  Thus, the different chromosomes are lost largely but not fully independently from each other. Based on these data, and on the fact that yeast cells have 16 chromosomes, we evaluate that about half of the cells lose at least one chromosome in their final cell cycle.

      We also tried to estimate the prevalence of the pre-mRNA leakage phenotype, based on the increased mCherry to GFP ratio observed between 0h and 24 hours of aging for 146 individual cells. For this analysis, we compared the mCherry/GFP ratio at 0 and 24h for the same individual cell. This analysis indicates that 81% of the cells show a fold change strictly above 1 as they age. Furthermore, the data appears to be unimodal. Thus, we can conservatively conclude that a majority of the cells show premRNA leakage at 24 hours.  Since not all cells are at the end of their life at that time, this is possibly an underestimate.

      In addition, a discussion would be needed to clarify the relationship between "chromosome loss" in this study and "genomic missegregation" reported previously in yeast aging. 

      Genomic mis-segregation is characterized by the entry of both SPBs and all the chromosomes into the daughter cell compartment (PMID: 31714209).  We have observed these events in our movies as well.  However, the chromosome loss phenotype that we are focusing on affects only some chromosomes (as discussed above) and takes place under proper elongation of the spindle, with one SPB remaining in the mother cell whereas the other one goes to the bud, as shown in the manuscript’s Figure 2.  In our movies, chromosome loss is at least three-fold more frequent (for a single chromosome) than full genome mis-segregation (Sup Fig 1A-B). Furthermore, whereas chromosome loss is alleviated by the removal of the introns of MCM21, NBL1 and GLC7, genomic mis-segregation is not (Sup Fig 1B).  Thus, genomic mis-segregation mentioned by the reviewer is a process distinct from the chromosome loss that we report.  This discussion and the relevant data have been added to the manuscript.

      We thank the reviewer for bringing up the possible confusion between these two phenotypes, allowing us to clarify this point.

      Reviewer #2 (Public review): 

      Summary: 

      The authors make the interesting discovery of increased chromosome non-dysjunction in aging yeast mother cells. The phenotype is quite striking and well supported with solid experimental evidence. This is quite significant to a haploid cell (as used here) - loss of an essential chromosome leads to death soon thereafter. The authors then work to tie this phenotype to other age-associated phenotypes that have been previously characterized: accumulation of extrachromosomal rDNA circles that then correlate with compromised nuclear pore export functions, which correlates with "leaky" pores that permit unspliced mRNA messages to be inappropriately exported to the cytoplasm. They then infer that three intron containing mRNAs that encode portions in resolving sister chromatid separation during mitosis, are unspliced in this age-associated defect and thus lead to the non-dysjunction problem. 

      Strengths: The discovery of age-associated chromosome non-dysjunction is an interesting discovery, and it is demonstrated in a convincing fashion with "classic" microscopy-based single cell fluorescent chromosome assays that are appropriate and seem robust. The correlation of this phenotype with other age-associated phenotypes - specifically extrachromosomal rDNA circles and nuclear pore dysfunction - is supported by in vivo genetic manipulations that have been well-characterized in the past. 

      In addition, the application of the single cell mRNA splicing defect reporter showed very convincingly that general mRNA splicing is compromised in aged cells. Such a pleiotropic event certainly has big implications. 

      We thank the reviewer for this assessment of our work.  To avoid confusion, we would like to stress out, however, that our data do not show that splicing per se is defective in old cells.  Actually, we specifically show that the cells are unlikely to show splicing defect (last figure of the original and the revised version of the manuscript). Our data specifically show that unspliced mRNAs tend to leak out of the nucleus of old cells.

      Weaknesses: 

      The biggest weakness is "connecting all the dots" of causality and linking the splicing defect to chromosome disjunction. I commend the authors for making a valiant effort in this regard, but there are many caveats to this interpretation. While the "triple intron" removal suppressed the non-dysjunction defect in aged cells, this could simply be a kinetic fix, where a slowdown in the relevant aspects of mitosis, could give the cell time to resolve the syntelic attachment of the chromatids.  

      The possibility that intron-removal leads to a kinetic fix is an interesting idea that we have now considered.  In the revised manuscript, we now provide measurements of mitotic duration in the “triple intron” mutant compared to wild type cells and the duration of their last cell cycle (See supplementary figure 3A-D). There is no evidence that removing these introns slows down mitosis.  Thus, the kinetic fix hypothesis is unlikely to explain our observation about the effect of intron removal.

      To this point, I note that the intron-less version of GLC7, which affects the most dramatic suppression of the three genes, is reported by one of the authors to have a slow growth rate (Parenteau et al, 2008 - https://doi.org/10.1091/mbc.e07-12-1254)

      The reviewer is right, removing the intron of GLC7 reduces the expression levels of the gene product (PMID: 16816425) to about 50% of the original value and causes a slow growth phenotype.  However, the cells revert fairly rapidly through duplication of the GLC7-∆i gene (see supplementary Figure 3EF).  As a consequence, neither the GLC7-∆i nor the 3x∆i mutant strains show noticeable growth phenotypes by spot assays.  We now document these findings in supplementary figure 3.  

      Lastly, the Herculean effort to perform FISH of the introns in the cytoplasm is quite literally at the statistical limit of this assay. The data were not as robust as the other assays employed through this study. The data show either "no" signal for the young cells or a signal of 0, 1, or 2 FISH foci in the aged cells. In a Poisson distribution, which this follows, it is improbable to distinguish between these differences. 

      This is correct, this experiment was not the easiest of the manuscript... However, despite the limitations of the assay, the data presented in figure 7B are very clear.  300 cells aged by MEP were analysed, divided in the cohorts of 100 each, and the distribution of foci (nuclear vs cytoplasmic) in these aged cells were compared to the distribution in three cohorts of young cells.  For all 3 aged cohorts, over 70% of the visible foci were cytoplasmic, while in the young cells, this figure was around 3%.  A t-test was conducted to compare these frequencies between young and old cells (Figure 7B). The difference is highly significant.  Therefore, we are clearly not at the statistical limit.

      What the reviewer refers to is the supplementary Figure 4, where we were simply asking i) is the signal lost in cells lacking the intron of GLC7 (the response is unambiguously yes) and ii) what is the general number of dots per cell between young and old wild type cells (without distinguishing between nuclear and cytoplasmic) and the information to be taken from this last quantification is indeed that there is no clearly distinguishable difference between these two population of cells, as the reviewer rightly concludes.  In other word, the reason why there are more dots in the cytoplasm of the old cells in the Figure 7B is not because the old cells have much more dots in general (see supplementary Figure 4C).  We hope that these clarifications help understand the data better.  We have edited the manuscript to avoid confusion.

      Reviewer #3 (Public review): 

      Summary: 

      Mirkovic et al explore the cause underlying development of aneuploidy during aging. This paper provides a compelling insight into the basis of chromosome missegregation in aged cells, tying this phenomenon to the established Nuclear Pore Complex architecture remodelling that occurs with aging across a large span of diverse organisms. The authors first establish that aged mother cells exhibit aberrant error correction during mitosis. As extrachromosomal rDNA circles (ERCs) are known to increase with age and lead to NPC dysfunction that can result in leakage of unspliced pre-mRNAs, Mirkovic et al search for intron-containing genes in yeast that may be underlying chromosome missegregation, identifying three genes in the aurora B-dependent error correction pathway: MCM21, NBL1, and GLC7. Interestingly, intron-less mutants in these genes suppress chromosome loss in aged cells, with a significant impact observed when all three introns were deleted (3x∆i). The 3x∆i mutant also suppresses the increased chromosome loss resulting from nuclear basket destabilization in a mlp1∆ mutant. The authors then directly test if aged cells do exhibit aberrant mRNA export, using RNA FISH to identify that old cells indeed leak intron-containing pre-mRNA into the cytoplasm, as well as a reporter assay to demonstrate translation of leaked pre-mRNA, and that this is suppressed in cells producing less ERCs. Mutants causing increased pre-mRNA leakage are sufficient to induce chromosome missegregation, which is suppressed by the 3x∆i. 

      Strengths: 

      The finding that deleting the introns of 3 genes in the Aurora B pathway can suppress age-related chromosome missegregation is highly compelling. Additionally, the rationale behind the various experiments in this paper is well-reasoned and clearly explained. 

      We thank the reviewer for their very positive assessment of our work

      Weaknesses:  

      In some cases, controls for experiments were not presented or were depicted in other figures. 

      We are sorry about this confusion.  We have improved our presentation of the controls, bringing them back each time they are relevant.  We have also added those that were missing (such as those mentioned by reviewer 2, see above). Note that the frequencies of centromeric plasmid loss at 0h in Figure 1C is not meaningful and therefore not presented. Since the cells were grown on selective medium before loading on to the ageing chip, we cannot report a plasmid loss frequency here. The ageing experiments themselves were subsequently conducted in full medium, to allow for centromeric plasmid loss without killing the cell. We explain this in the materials and methods section.

      High variability was seen in chromosome loss data, leading to large error bars. 

      We thank the reviewer for this comment. The variance in those two figures (3A and 5D) comes from the suboptimal plotting of this data. This is now corrected as follows.  We divided the available data into 4 cohorts and then plotted the average loss frequency across these cohorts for the indicated age groups.  This filters out much of the noise and improves the statistical resolution.

      The text could have been more polished. 

      Thank you for this comment.  We have gone through the manuscript again in detail.

      Reviewer #1 (Recommendations for the authors):

      (1) A previous study (PMID: 31714209). showed that aging yeast cells undergo genomic missegregation in which material was abnormally segregated to the daughter cells, leading to cell cycle arrest. After that, the missegregation is either corrected by returning aberrantly segregated genetic material to the mother cells so that they can resume cell cycles, or if not corrected, the mother cells will terminally exist the cell cycle and eventually die. That paper also showed that this agedependent genomic missegregation is related to rDNA instability. Is the chromosome loss in this work related to the genomic missegregation reported before? Is it partially reversible like genomic missegregation? Are all the chromosomes lost in one cell division, like in the case of genomic missegregation? Some additional characterization and a discussion would be helpful. 

      As mentioned above, indeed the phenotype of full genome mis-segregation described by Crane et al. (2019) is observable in our data as well. At 24h ~3% of the cells segregate both SPBs to the bud, as they previously described (Supp Figure 1A and B).  This phenomenon is clearly distinct from asymmetric chromosome partition, where cells undergo anaphase, separate the SPBs and segregate one to the mother cell and one to the bud (Figure 2A).  Also, asymmetric chromosome partitioning affects only a subset of the chromosomes (see below), not the entire genome. Finally, unlike asymmetric chromosome partitioning, the frequency of genome mis-segregation in ageing was not alleviated by intron removal (Supp Figure 1B). Thus, these two processes are clearly distinct and driven by different mechanisms. Note that asymmetric chromosome partitioning appears 3 to 5 times more frequently than genomic mis-segregation.

      Supporting further the notion that these two processes are distinct, chromosome loss seals the end of the life of the cell, as we reported, indicating that this is not a reversible event.  Also, it does not involve all chromosomes at once. Cells that contain the labelled versions of both chromosome II and IV at the same time, the loss frequency of both chromosomes is less than 5%, whereas each chromosome is lost in 10-15% of the cells (Figure 1C). Thus, most cells lose one and keep the other. Furthermore, this indicates that there are many more cells losing at least one chromosome than the 15% that lose chromosome IV for example, probably 50% or more.  Thus, chromosome loss by asymmetric segregation is much more frequent than the partly transient transfer of the entire nucleus to the bud.

      (2) What percentage of aging WT cells undergo pre-mRNA leakage (using the GFP/mCherry reporter) during their entire lifespan? Is it a sporadic, reversible process or an accumulative, one-way deterioration? Previous studies (PMID: 32675375; PMID: 24332850; PMID: 36194205; PMID: 31291577) showed that only a fraction of yeast cells age with rDNA instability and ERC accumulation, as indicated by excessive rRNA transcription and nucleolar enlargement. Are they the same fraction of aging cells that undergo pre-mRNA leakage and chromosome loss? This information will indicate the prevalence of the key aging phenotypes reported in this work and should be readily obtainable from microfluidic experiments. In addition, a careful discussion would be helpful. 

      Pre-mRNA leakage is relatively widespread in the population, but it is difficult to put a precise number on it. Analysis of how the mCherry/GFP ratio changes in 146 individual cells between 0 and 24 hours and imaging in our microfluidics platform indicates that ~80% show an increase and 50% of the cells show an increase above 1.5-fold. Therefore, the frequencies of pre-mRNA leakage and chromosome loss are probably similar.  We have modified the discussion to account for these considerations.  This would be in the same range as the frequency of aging by ERC accumulation (mode 1) estimated by PMID: 32675375. 

      Reviewer #2 (Recommendations for the authors)

      The manuscript could use a bit of editing in places - please go through it once more. 

      Editing suggestions: 

      Line 80 – irrespective

      Corrected.

      Line 97 - these are not "rates" but frequencies. Please correct this error throughout. 

      Replaced “rate” with “frequency throughout the manuscript and the figures, when pertaining to chromosome loss

      Line 328 - increase in chromosome... 

      Corrected.

      Line 379 - tampering 

      Reviewer #3 (Recommendations for the authors):

      Specific Feedback to Authors 

      (a) Major Points 

      (i) While the proposed connection between ERC-mediated nuclear basket removal and erroneous error correction was clearly stated, this connection is correlative and was not directly tested. Specifically, although mutants impacting ERC levels were tested for missegregation, it was not directly tested if increased missegregation levels occurred due to ERC tethering to the NPC and subsequent nuclear basket removal. It is possible that the increased ERCs may be driving missegregation via a different pathway. Authors should consider experiments to strengthen this idea, such as looking at chromosome loss frequency in a sir2∆ 3x∆i double mutant, or a sir2∆ sgf73∆ double mutant. 

      This connection is addressed in the original version of the manuscript, where we show that preventing attachment of ERCs to the NPC, by removing the linker protein Sgf73, alleviates chromosome loss.  The link is further substantiated by the fact that removing the basket on its own promote chromosome loss and that in both cases, namely during normal aging, i.e., upon ERC accumulation, and upon basket removal the mechanism of chromosome loss is the same.  In both cases, it depends on the introns of the GLC7, MCM21 and NBL1 genes.  

      However, we acknowledge that the mutants tested have pleiotropic effects, making interpretation somewhat difficult, even when examining chromosome loss in multiple mutants that affect ERC formation and NPC remodelling, as we have done.  As recommended by the reviewer, we have characterized the phenotype of the sir2∆ 3x∆i mutant strain. Intron removal in the sir2∆ mutant cells largely rescued the elevated chromosome loss frequency of these cells and slightly extended their replicative lifespan (Figure 6D-E). We conclude that intron removal can remedy the chromosome loss phenotype of the sir2∆. Although clearly significant, the effect on the replicative lifespan was not very strong, likely due to the sir2∆ affecting other ageing processes.

      Touching on this question, we added a new set of experiments asking whether any accumulating DNA circle causes chromosome loss in an intron-dependent manner.  Thus, we have introduced a noncentromeric replicative plasmid in wild type and 3x∆i mutant strains carrying the labelled version of chromosome II (Figure 6A-C).  These studies show that these cells age much faster than wild type cells, as expected, and lose chromosomes at a higher frequency than non-transformed cells.  Finally, the effect is at least in part alleviated by removing the introns of NBL1, MCM21 and GLC7.

      Therefore, after adding this new and more direct test of the role of DNA circles in chromosome loss, we are confidently concluding that ERC-mediated basket removal is the trigger of chromosome loss in old cells.

      (b) Minor Points 

      (i) In Figure 1C, the text (lines 91-92) argues that chromosome loss happens abruptly as cells age; however the data only show loss at young and old time points, not an intermediate, which leaves open the possibility that chromosome loss is occurring gradually. While cells that lost chromosomes should fail to divide further, we don't know if these events happened and were simply excluded.

      We agree with the reviewer that formally the conclusion drawn in the lines 91-92 (of the original manuscript), namely that chromosome loss takes place abruptly as cells age, cannot be drawn from the Figure 1C alone but only from subsequent observations. However, since chromosome loss is lethal in haploid, as we mention in the text and the reviewer notes as well, it is difficult to envision how cells could lose chromosomes before the end of their lifespan and must therefore increase abruptly as the cells reach that point.  This is now underlined in the revised version of the manuscript. Accordingly, the frequency of chromosome loss per age group, which is depicted in Figure 3A, shows that the wild type cells that have budded less than 10 times show no chromosome loss. The chromosome loss frequency starts to ramp up only pass that point. Therefore, chromosome loss does not increase linearly with age.

      Additionally, cells that lost minichromosome should not arrest. We suggest that the interpretation of these data should be softened in the text, or that chromosome loss fraction could be more effectively portrayed as a Kaplan-Meier survival curve depicting cells that have not lost chromosomes, if these data are easily available. Or, chromosome loss at an intermediate time point could be depicted. 

      Since we cannot visualize more than 2 chromosomes at a time, it is not possible to plot the KaplanMeier curve of cells that have not lost chromosomes. However, as mentioned above, the chromosome loss frequencies at intermediate time points are depicted in Figure 3A and Figure 4B and shows that it increases with age.

      (ii) Also regarding Figure 1, it would be helpful to expound on the purpose of the minichromosomes, as well as how the Ubi-GFP minichromosome is constructed. 

      We now explained why we tested the loss of minichromosome, namely, as a mean to test whether the centromere is necessary and sufficient to drive the loss of the genetic material linked to it, i.e., chromosomes, in old cells.  Concerning the Ubi-GFP minichromosome, the Materials and methods section is now updated and reports plasmid construction, backbone used, primers as well as the plasmid sequence being available in the supplementary data.

      The purpose of the minichromosome initially appears to be the engineering of an eccDNA (ERC) with a CEN to demonstrate distinct behaviour, but it is unclear whether this was actually conducted or if the minichromosome are simply CEN plasmids and/or if this was the intended goal. Furthermore, lines 102-103 state that the presence of a centromere was necessary and sufficient for minichromosome loss. However, since no constructs lacking a centromere were tested, necessity cannot be concluded. Please clarify this in the text and include experimental details to help readers understand what was tested. 

      We apologize for having been too short here. The behaviour of the CEN-less version of this plasmid has been characterized in detail in previous studies (Shcheprova et al., 2008; Denoth-Lippuner 2014, Meinema et al 2022). Here we focused on the behaviour of the CEN+ version of an otherwise Identical plasmid.  We now clarify in the text that this plasmid is retained in the mother cell when CEN-less and cite the relevant literature. 

      (iii) It is unclear how cells at 0-3 budding events were identified in assays using the microfluidics platform. Can the authors clarify the known "age" of the cells once captured, i.e. how do the authors know how many divisions a cell has undergone prior to capture? 

      The reviewer is right; we do not know the exact age of these cells.  However, in any asynchronous population of yeast cells, which is what we start from, 50% of the cells are newborn daughters, 25% have budded once, 12.5 have budded twice, 6.25 % have budded three times…  Therefore, at the time of loading, 93% of the cells have budded between 0 and 3 times.  For this reason, we report to this population as cells age 0-3 CBE. We acknowledge that this is an approximation, but it remains a relatively safe one.  

      (iv) While the schematic in Figure 2D is generally helpful, a different depiction of the old and new SPBs would be beneficial in cases where the new SPB and TetR-GFP are depicted as colocalized, it is difficult to see that the red is fainter for the new SPB. 

      We have corrected this issue by completely separating the SPB and the Chromosome signals in the Figure 2D.

      (v) In Figure 2F, the grey colour of the 12h Ipl1-321 data bar did not have high enough contrast when the manuscript was printed-would recommend changing this to a darker shade. 

      We have corrected this issue by using a darker shade of grey.

      (vi) In Figure 3A, 'Budding' is misspelled on X-axis label  

      We have corrected this error.

      (vii) In Figure 4, the authors should clarify the differences between the analyses in panels B and C. The distinction is not immediately clear and may be difficult to grasp upon initial reading. 

      We have corrected this issue in the main text as well as figure legend.

      (viii) In Figure 5, It would aid comparisons to depict the 3x∆i only as well on panels B, D, and E. 

      We have added 3x∆i data to Figure 5,6 and 8.

      (ix) In Figure 6D, it is unclear why there was an appreciable level of unspliced RNA in the wild-type and sir2∆ young cells. Additionally, it is unclear why there is so much signal observed in the Merge image for the old wild-type cell, especially regarding the apparent bright spot. Is that nuclear signal? Please clarify. 

      The pre-mRNA processing reporter is not very efficiently spliced. It was selected as such during design (Sorenson et al 2014; DOI: 10.1261/rna.042663.113) to provide sensitivity. As for the bright spot occurring, translation of the unspliced reporter produces the N-terminal part of a ribosomal protein, a fraction of which forms some sort of nuclear aggregate in a fraction of the population. 

      (x) In Figure 6E, why does the sir2∆ exhibit higher mCherry/GFP than the wild-type and fob1∆ at "young age"? Is this due to disrupted proteostasis in the sir2∆, or a different pleiotropic effect of sir2∆? Please comment on this observation in the text.

      Indeed, as we have stated in the text the sir2∆ mutation already perturbs pre-mRNA processing in young cells. We do not know the reason of this but indeed it is most probably reflective of its pleiotropic function. Following the reviewer’s request, we now state this in the text. For example, Sir2 may regulate the acetylation state of the basket itself.  The genetic interactions observed between sir2∆ and quite a few nucleoporin mutations seem to support this possibility. 

      (xi) Throughout, the authors switch between depicting aging in Completed Budding Events versus hours, which made it difficult to compare data across figures

      Ideally, all the data in this manuscript should be plotted according to the CBE age of the cell. To ensure that the major findings are plotted in such a way, we have done so for over ~3000 combined cells and thousands of replicative divisions in Figures 3,5-7. All the measurements of chromosome loss at a specific CBE had to be done manually, due to the absence of algorithms that would be able to accurately detect chromosome loss and replicative age. Therefore, doing this for the entirety of our dataset, encompassing well over 50 ageing chips and tens of thousands of cells is not easily doable at this stage. 

      (xii) Typo on line 12 (Sindle Pole Body) 

      We have corrected this error.

      (xiii) The phrase should be 'chromosome partitioning' rather than 'chromosome partition', throughoutfor example, line 17 

      Replaced “chromosome partition” with “chromosome partitioning” throughout the text.

      (xiv) There are inconsistencies between plural and singular references throughout sentences-example, lines 35-37, and lines 44-45. 

      We carefully combed through the manuscript again and hope that we caught all inconsistencies.

    1. Reviewer #1 (Public review):

      Summary:

      The authors demonstrate with a simple stochastic model that the initial composition of the community is important in achieving a target frequency during the artificial selection of a community.

      Strengths:

      To my knowledge, the intra-collective selection during artificial selection has not been seriously theoretically considered. However, in many cases, the species dynamics during the incubation of each selection cycle is important and relevant to the outcome of the artificial selection experiment. Stochasticity from birth and death (demographic stochasticity) plays a big role in these species' abundance dynamics. This work uses a simple framework to tackle this idea meticulously.

      This work may or may not be related to hysteresis (path dependency). If this is true, maybe it would be nice to have a discussion paragraph talking about how this may be the case. Then, this work would even attract the interest of people studying dynamical systems.

      Weaknesses:

      (1) Connecting structure and function.<br /> In typical artificial selection literature, most of them select the community based on collective function. Here in this paper, the authors are selecting a target composition. Although there is a schematic cartoon illustrating the relationship between collective function (y-axis) and the community composition in the main figure 1, there is no explicit explanation or justification of what may be the origin of this relationship. I think giving the readers a naïve idea about how this structure-function relationship arises in the introduction section would help. This is because the conclusion of this paper is that the intra-collective selection makes it hard to artificially select for a community that has an intermediate frequency of f (or s). If there is really evidence or theoretical derivation from this framework that indeed the highest function comes from the intermediate frequency of f, then the impact of this paper would increase because the conclusions of this stochastic model could allude to the reasons for the prevalent failures of artificial selection in literature.

      (2) Explain intra-collective and inter-collective selection better for readers.<br /> The abstract, the introduction, and the result section use these terms or intra-collective and inter-collective selection without much explanation. For the wide readership of eLife, a clear definition in the beginning would help the audience grasp the importance of this paper, because these concepts are at the core of this work.

      (3) Achievable target frequency strongly depending on the degree of demographic stochasticity.<br /> I would expect that the experimentalists would find these results interesting and would want to consider these results during their artificial selection experiments. The main figure 4 indicates that the Newborn size N0 is a very important factor to consider during the artificial selection experiment. This would be equivalent to how much bottleneck you impose on the artificial selection process in every iteration step (i.e., the ratio of serial dilution experiment). However, with a low population size, all target frequencies can be achieved, and therefore in these regimes, the initial frequency now does not matter much. It would be great for the authors to provide what the N0 parameter actually means during the artificial selection experiments. Maybe relative to some other parameter in the model. I know this could be very hard. But without this, the main result of this paper (initial frequency matters) cannot be taken advantage of by the experimentalists.

      (4) Consideration of environmental stochasticity.<br /> The success (gold area of Figure 2d) in this framework mainly depends on the size of the demographic stochasticity (birth-only model) during the intra-collective selection. However, during experiments, a lot of environmental stochasticity appears to be occurring during artificial selection. This may be out of the scope of this study. But it would definitely be exciting to see how much environmental stochasticity relative to the demographic stochasticity (variation in the Gaussian distribution of F and S) matters in succeeding in achieving the target composition from artificial selection.

      (5) Assumption about mutation rates<br /> If setting the mutation rates to zero does not change the result of the simulations and the conclusion, what is the purpose of having the mutation rates \mu? Also, is the unidirectional (S -> F -> FF) mutation realistic? I didn't quite understand how the mutations could fit into the story of this paper.

      (6) Minor points<br /> In Figure 3b, it is not clear to me how the frequency difference for the Intra-collective and the Inter-collective selection is computed.<br /> In Figure 5b, the gold region (success) near the FF is not visible. Maybe increase the size of the figure or have an inset for zoom-in. Why is the region not as big as the bottom gold region?

      Comments on revisions:

      I thank the authors for addressing many points raised by the reviewers. Overall, the readability of the manuscript has improved with more context provided around why they were solving this specific problem. However, I've found many of the responses to be too terse. It would have been nicer if there had been more discussion and description of the thought process that led up to the conclusions they made for each comment or question. Instead, many of the responses only showed the screenshot of the text they added.

      Most of my comments or questions were answered. Below are my comments on some of the authors' responses.

      (2) Explain intra-collective and inter-collective selection better for readers.<br /> In the Abstract and Introduction, you've added more sentences about the intra-collective or inter-collective selection. However, these are either making analogies to the waterfall or just describing the result of the intra/inter-collective selection. I would still appreciate a proper definition of those terms, which is paramount for readers to understand the entire paper.

      (4) Consideration of environmental stochasticity.<br /> I think providing the reason 'why' the paper focuses on demographic stochasticity and not environmental stochasticity will greatly justify the paper's work. For example, citing papers that actually performed artificial selection and pointing out that your model captures the stochasticity from those kinds of experiments would be great.

      (5) Assumption about mutation rates.<br /> It would be great if you could add a citation in the added sentence to support your claim: "This scenario is encountered in biotechnology: .....".

    1. Author response:

      The following is the authors’ response to the original reviews.

      Reviewer #1 (Public review):

      Summary:

      The present work studies the coevolution of HIV-1 and the immune response in clinical patient data. Using the Marginal Path Likelihood (MPL) framework, they infer selection coefficients for HIV mutations from time-series data of virus sequences as they evolve in a given patient.

      Strengths:

      The authors analyze data from two human patients, consisting of HIV population sequence samples at various points in time during the infection. They infer selection coefficients from the observed changes in sequence abundance using MPL. Most beneficial mutations appear in viral envelop proteins. The authors also analyze SHIV samples in rhesus macaques, and find selection coefficients that are compatible with those found in the corresponding human samples.

      Weaknesses:

      The MPL method used by the authors considers only additive effects of mutations, thus ignoring epistasis.

      As suggested, we have now addressed this limitation by inferring epistatic fitness landscapes for CH505, CH848, SHIV.CH505, and SHIV.CH848. Indeed, the computational burden of the epistasis inference procedure was one constraint that motivated us to consider only additive fitness in the previous version of our paper. The original approach developed by Sohail et al. (2022) tested only sequences with <50 sites due to this limitation, far smaller than the ones we consider. Beyond this computational constraint, we also believed that 1) an additive fitness model may suffice to capture local fitness landscapes, and practically, 2) epistatic interactions are more challenging to validate than the effects of individual mutations, making the interpretation of the model more complex.

      However, after performing the analyses described in this paper, we developed a new approach for identifying epistatic interactions that can scale to much longer sequences (Shimagaki et al., Genetics, in press). We therefore applied this method to infer an epistatic fitness landscape for the HIV and SHIV data sets that we studied. As in that work, we focused on short-range (<50 bp) interactions which we could more confidently estimate from data. We have added a section in the SI describing the epistatic fitness model and our analysis. 

      Overall, we found substantial agreement between the epistatic and purely additive models in terms of the estimated fitness effects of individual mutations (new Supplementary Fig. 8) and overall fitness (Supplementary Fig. 9). Consistent with our prior work, we did not find substantial evidence for very strong epistatic interactions (Supplementary Fig. 10). This does not necessarily mean that strong epistatic interactions do not exist; rather, this shows that strong interactions don’t substantially improve the fit of the model to data, and thus many are regularized toward zero. While the biological validation of epistatic interactions is challenging, we found that the largest epistatic interactions, which we defined as the top 1% of all shortrange interactions, were modestly but significantly enriched in the CD4 binding site, V1 and V5 regions for CH505 and in the CD4 binding site, V4, and V5 for CH848. In addition, mutation pairs N280S/V281A and E275K/V281G, which confer resistance to CH235, ranked in the top 15% of all epistatic interactions in CH505.

      We have now included an additional section in the Results, “Robustness of inferred selection to changes in the fitness model and finite sampling”, which discusses our epistatic analyses (page 6, lines 415-464), along with the above Supplementary Figures and a technical section in the SI summarizing the epistasis inference approach.

      Although the evolution of broadly neutralizing antibodies (bnAbs) is a motivating question in the introduction and discussion sections (and the title), the relevance of the analysis and results to better understanding how bnAbs arise is not clear. The only result presented in direct connection to bnAbs is Figure 6.

      It is true that, while bnAb development is a major motivator of our study, our analysis focuses on HIV-1 and does not directly consider antibody evolution. We have now brought attention to this point as a limitation directly in the Discussion. Following the suggestion below in the “Recommendations for the authors,” we have edited our manuscript to place more emphasis on viral fitness and somewhat reduce the emphasis on bnAbs, though this remains an important motivating factor. Specifically, the Abstract now begins

      Human immunodeficiency virus (HIV)-1 evolves within individual hosts to escape adaptive immune responses while maintaining its capacity for replication. Coevolution between the HIV-1 and the immune system generates extraordinary viral genetic diversity. In some individuals, this process also results in the development of broadly neutralizing antibodies (bnAbs) that can neutralize many viral variants, a key focus of HIV-1 vaccine design. However, a general understanding of the forces that shape virusimmune coevolution within and across hosts remains incomplete. Here we performed a quantitative study of HIV-1 evolution in humans and rhesus macaques, including individuals who developed bnAbs.

      We have similarly modified the Discussion to focus first on viral fitness. In response to comments from Reviewer 3, we have also more clearly articulated how our work might contribute to the understanding of bnAb development in the Discussion.

      Questions or suggestions for further discussion:

      I list here a number of points for which I believe the paper would benefit if additional discussion/results were included.

      The MPL method used by the authors considers only additive effects of mutations, thus ignoring epistasis. In Sohail et al (2022) MBE 39(10), p. msac199  (https://doi.org/10.1093/molbev/msac199) an extension of MPL is developed allowing one to infer epistasis. Can the authors comment on why this was not attempted here?

      I presume one possible reason is that epistasis inference requires considerably more computational effort (and more data). However, since the authors find most beneficial mutations occurring in Env, perhaps restricting the analysis to Env genes only (e.g. the trimer shown in Figure 2) can lead to tractable inference of epistasis within this segment (instead of the full genome).

      As described above, we have now addressed this comment by inferring epistatic fitness landscapes for the data sets that we consider. Our overall results using the epistatic fitness model are consistent with the ones that we previously obtained with an additive model.

      Do the authors find correlations in the inferred selection coefficients of the two samples CH505 and CH848? I could not find any discussion of this in the manuscript. Only correlations between Humans and RM are discussed.

      To address this question, we compared the fitness values and individual selection coefficients across CH505 and CH848 data sets. We found little correlation between CH505 and CH848 fitness values (shown in a new Supplementary Fig. 6) or selection coefficients. We found only 199 common mutations between HIV-1 amino acid sequences from CH505 and CH848 out of 868 and 1,406 total mutations, respectively. Thus, we were not surprised to find no strong relationship between fitness estimates from CH505 and CH848 data sets. 

      Reviewer #2 (Public review):

      Summary:

      This paper combines a biological topic of interest with the demonstration of important theoretical/methodological advances. Fitness inference is the foundation of the quantitative analysis of adapting systems. It is a hard and important problem and this paper highlights a compelling approach (MPL) first presented in (1) and refined in (2), roughly summarized in equation 12.

      (1) Sohail, M. S., Louie, R. H., McKay, M. R. & Barton, J. P. Mpl resolves genetic linkage in fitness inference from complex evolutionary histories. Nature biotechnology 39, 472-479 (2021).

      (2) Shimagaki, K. & Barton, J. P. Bézier interpolation improves the inference of dynamical models from data. Physical Review E 107, 024116 (2023).

      The authors find that positive selection shapes the variable regions of env in shared patterns across two patient donors. The patterns of positive selection are interesting in and of themselves, they confirm the intuition that hyper-variation in env is the result of immune evasion rather than a broadly neutral landscape (flatness). They show that the immune evasion patterns due to CD8 T and naive B-cell selection are shared across patients. Furthermore, they suggest that a particular evolutionary history (larger flux to high fitness states) is associated with bNAb emergence. Mimicking this evolutionary pattern in vaccine design may help us elicit bNAbs in patients in the future.

      There is a lot of information to be found in the full fitness landscape of env. The enormous strength of reversion-to-consensus in the patterns is a known pattern of HIV post-infection populations but they are nicely quantified here. Agreement between SHIV and HIV evolution is shown. They find selection is larger for autologous antibodies than the bNAbs themselves (perhaps bNAbs are just too small a component of the host response to drive the bulk of selection?), and that big fitness increases precede antibody breadth in rhesus macaques, suggesting that this fitness increase is the immune challenge required to draw forth a bNAb. This is all of high interest to HIV researchers.

      Strength of evidence:

      One limitation is, of course, that the fitness model is constant in time when the immune challenge is variable and changing. This simplification may complicate some interpretations.

      We agree that this is a limitation of our current approach. In prior work, we have found that the constant fitness effects of mutations that we infer typically reflect the time-averaged fitness effect when the selection changes over time (Gao and Barton, PNAS 2025; Lee et al., Nat Commun 2025). It could be difficult, however, to capture changes in selection that fluctuate rapidly with underlying immune responses. We have added a new paragraph in the Discussion that more clearly sets out some of the limitations of our analysis, including our assumption of constant selection coefficients.

      There are additional methodological and technical limitations that should be considered in the interpretation of our results. Most notably, we assume that the viral fitness landscape is static in time. While we do not expect selection for effective replication (“intrinsic” fitness) to change substantially over time, pressure for immune escape could vary along with the immune responses that drive them. In prior work, we have found that constant selection coefficients typically reflect the average fitness effect of a mutation when its true contribution to fitness is time-varying [42,43]. This may not adequately description mutational effects that undergo large or rapid shifts in time. Future work should also examine temporal patterns in selection for individual mutations.

      Equation 12 in the methods is really a beautiful tool because it is so simple, but accounts for linkage and can be solved precisely even in the presence of detailed mutational and selection models. However, the reliance on incomplete observations of the frequency leads to complications that must be carefully (re)addressed here.

      For instance, the consistent finding of strong selection in hypervariable regions is biologically intuitive but so striking, that I worry that it might be the result of a bias for selection in high entropy regions. 

      Thank you for this suggestion. We agree that it is important to carefully interrogate these results. To assess the effects of general sequence variability on inferred selection, we first computed a position-specific entropy measure, H<sub >i</sub >, for each site i. We first defined the time-dependent entropy H<sub >i</sub >(t) = - ∑<sub >a</sub> x<sub>i</sub> (a, t) log x<sub>i</sub> (a, t)), where x<sub>i</sub> (a, t) represents the frequency of amino acid/nucleotide a at position i and time t, at each sample time. We then computed H<sub>i</sub> as the average of H<sub>i</sub>(t) across all sample times. A new Supplementary Fig. 1 plots the entropy against the inferred selection coefficients. Although some sequence variation must be observed in order for us to infer that a mutation is beneficial, we did not find a systematic bias toward larger (more beneficial) selection coefficients at more variable sites. Overall, we found only a modest correlation between inferred selection coefficients and entropy (Pearson’s r = 0.33 and 0.29 for CH505 and CH848, respectively), which appears to be partly driven by the tendency for mutations inferred to be significantly deleterious to occur at sites with low entropy. In addition to the new Supplementary Figure, we have added a reference to this analysis in the main text:

      To test whether our results might be biased by overall sequence variability, we examined the relationship between our inferred selection coefficients and entropy, a common measure of sequence variability. Overall, we found only a modest correlation between selection and entropy, suggesting that the signs of selection that we observe are not due to increased sequence variability alone (Supplementary Fig. 1).

      Mutational and covariance terms in equation 12 might be underestimated, due to finite sampling effect in highly diverse populations. Sampling effects lead to zeros in x(t) when actual frequency zeros might be rare at the population sizes of HIV viral loads and mutation rates. Both mutational flux and C underestimation will bias selection upward in eq. 12. 

      The prior papers (1) and (2) seem to show robustness to finite sampling effects, but, again, more care needs to be shown that this robustness transfers to the amino acid inference under these conditions. That synonymous sites are rarely selected for in the nucleotide level is a good sign, and it may be a matter of simply fully explaining the amino-acid level model.

      As above, we agree that these tests are important. To assess the robustness of our results to finite sampling, we performed bootstrap sampling on the viral sequences and inferred selection coefficients using the resampled sequences. Specifically, we resampled the same number of sequences as in the original data at each time point and repeated this for all time points across all HIV-1 and SHIV data sets. A new Supplementary Fig. 11 shows a typical comparison of the original selection coefficients vs. those obtained through bootstrap resampling. Overall, we observe a high degree of consistency between the selection coefficients in each case, which is surely aided by the long time series in these data sets. As pointed out by the reviewer, uncertainty in low-frequency mutations is a particular concern, though the effects on inferred selection are mitigated by regularization. 

      We have added a section in the Results, “Robustness of inferred selection to changes in the fitness model and finite sampling”, which includes this analysis:

      Finite sampling of sequence data could also affect our analyses. To further test the robustness of our results, we inferred selection coefficients using bootstrap resampling, where we resample sequences from the original ensemble, maintaining the same number of sequences for each time point and subject. The selection coefficients from the bootstrap samples are consistent with the original data (see Supplementary Fig. 11), with Pearson’s r values of around 0.85 for HIV-1 data sets and 0.95 for SHIV data sets, respectively.

      Uncertainty propagates to the later parts of the paper, eg. HIV and SIV shared patterns might be the result of shared biases in the method application. However, this worry does not extend to the apples-to-apples comparison of fitness trajectories across individuals (Figures 5 and 6) which I think are robust (for these sample sizes). 

      One way to address this uncertainty is to compare the fitness values and individual selection coefficients across CH505 and CH848 data sets, which was also requested by Reviewer 1. Overall, we found little correlation between CH505 and CH848 fitness values (shown in a new Supplementary Fig. 6) or selection coefficients. This suggests that similarities between HIV-1 and SHIV landscapes are not solely determined by potential biases in the inference approach. We have now added a reference to this point in the main text:

      In contrast, the inferred fitness landscapes of CH505 and CH848, which share few mutations in common, are poorly correlated (Supplementary Fig. 6). This suggests that the similarities between viral fitness values in humans and RMs are not artifacts of the model, but rather stem from similarities in underlying evolutionary drivers.

      The timing evidence is slightly weakened by the fact that bNAb detection is different from bNAb presence and the possibility that fitness increases occurred after the bNAbs appeared remains. Still, their conclusion is plausible and fits in with the other observations which form a coherent and compelling picture.

      Yes, we agree that this is a limitation of our analysis — bNAbs may have been present at low levels before they were detected, and we cannot definitively reject selection by bNAbs. Nonetheless, in at least one case (RM5695), rapid fitness gains were substantially separated in time from bNAb detection (roughly 2 weeks after infection vs. 16 weeks, respectively). We have now added this point in a new paragraph in the Discussion:

      While we found a strong relationship between viral fitness dynamics and the emergence of bnAbs, it may not be true that the former stimulates the latter. For example, bnAbs may have been present within each host before they were experimentally detected. Rapid viral fitness gains within hosts that developed broad antibody responses could then have been driven by undetected bnAb lineages. However, we did not find strong selection for known bnAb resistance mutations, and in at least one case (RM5695), rapid fitness gains (roughly 2 weeks after infection) substantially preceded bnAb detection (16 weeks). Still, given the limited size of the data set that we studied, it is unclear the extent to which our results will transfer to larger and broader data sets.

      Overall thisrpretations could provide valuable insights into the broader significance of these results. is a convincing paper, part of a larger admirable project of accurately inferring complete fitness landscapes.

      Reviewer #3 (Public review):

      Summary:

      Shimagaki et al. investigate the virus-antibody coevolutionary processes that drive the development of broadly neutralizing antibodies (bnAbs). The study's primary goal is to characterize the evolutionary dynamics of HIV-1 within hosts that accompany the emergence of bnAbs, with a particular focus on inferring the landscape of selective pressures shaping viral evolution. To assess the generality of these evolutionary patterns, the study extends its analysis to rhesus macaques (RMs) infected with simianhuman immunodeficiency viruses (SHIV) incorporating HIV-1 Env proteins derived from two human individuals.

      Strengths:

      A key strength of the study is its rigorous assessment of the similarity in evolutionary trajectories between humans and macaques. This cross-species comparison is particularly compelling, as it quantitatively establishes a shared pattern of viral evolution using a sophisticated inference method. The finding that similar selective pressures operate in both species adds robustness to the study's conclusions and suggests broader biological relevance.

      Weaknesses:

      However, the study has some limitations. The most significant weakness is that the authors do not sufficiently discuss the implications of the observed similarities. While the identification of shared evolutionary patterns (e.g., Figure 5) is intriguing, the study would benefit from a more explicit discussion of what these findings mean for instance, in the context of HIV vaccine design, immunotherapy, or fundamental viral-host interactions. Even speculative inte

      Thank you for this suggestion. We have now clarified the potential implications of our work in several areas. While speculative, one possible application is in vaccine design: it may be beneficial to design sequential immunogens to mimic the patterns of viral evolution associated with rapid fitness gains. This “population-based” design principle is different from typical approaches, which have focused on molecular details of virus surface proteins. 

      We have extended our discussion of our results in the context of viral evolution within and across hosts and related host species. Overall, our work suggests that there may be relatively few paths to significantly higher viral fitness in vivo. Evolutionary “contingencies” such as shifting immune pressure or epistatic interactions could influence the direction of evolution, but not so dramatically that the dynamics that we see in different hosts are not comparable. We have also connected our work more broadly to the literature in evolutionary parallelism in HIV-1 in different contexts.

      A secondary, albeit less critical, limitation is the placement of methodological details in the Supplementary Information. While it is understandable that the authors focus on results in the main text - especially since the methodology is not novel and has been previously described in earlier publications - some readers might benefit from a more thorough presentation of the method within the main paper.

      We have now modified the main text to add a new section, “Model overview,” that lays out the key steps of our approach. While we reserve technical details for the Methods, we believe that this new section provides more intuition about how our results were obtained (including a discussion of the important Eq. 12, now Eq. 3 in the main text) and our underlying assumptions.

      Conclusions:

      Overall, the study presents a compelling analysis of HIV-1 evolution and its parallels in SHIV-infected macaques. While the quantitative comparison between species is a notable contribution, a deeper discussion of its broader implications would strengthen the paper's impact.

      Reviewer #1 (Recommendations for the authors):

      I suggest de-emphasizing bnAbs and focusing on selection landscape inference, which seems to be the actual focus of the paper.

      While we do not directly study antibody development in this work, bnAb development is certainly an important motivating factor. As described in the responses above, we have now modified the Abstract and Discussion to place relatively more emphasis on fitness comparisons and to relatively less focus on bnAb development.  

      Reviewer #2 (Recommendations for the authors):

      Please make sure that the MPL method is defined in this paper and its limitations are at least partially repeated.

      As noted in responses above, we have now included more methodological details in the main text of the paper, which we hope will make the intuition and assumptions involved in our analysis clearer.

      I'd like the code to better show or describe the model, I could not figure out the model details by looking at the code. It seems mostly just to be csv exporting for use with preexisting MPL code. A longer code readme would be helpful.

      We have now updated the README on GitHub to include a conceptual overview of our inference approach, which references how each step is implemented in the code.

      Reviewer #3 (Recommendations for the authors):

      Try to give some more details (not necessarily giving the full mathematical derivation) on the statistical method utilized.

      As noted above, we have now expanded our discussion of the statistical methods and assumptions in the main text.

      Figures 3 and 4 are somewhat 'messy'. Although I do not have a constructive suggestion here, I feel that with a little more effort maybe the authors could come up with something more clean.

      It is true that the mutation frequency dynamics are somewhat “choppy” and difficult to follow intuitively. To attempt to make these figures easier to parse visually, we have increased the transparency on the lines and added exponential smoothing to the mutation frequencies, resulting in smoother trajectories. The trajectories without smoothing are retained in Supplementary Fig. 3. Here we also note that this smoothing is for visual purposes only; we use the original frequency trajectories for inference, rather than the smoothed ones.

    1. Reviewer #1 (Public review):

      Summary:

      Ever since the surprising discovery of the membrane-associated Periodic Skeleton (MPS) in axons, a significant body of published work has been aimed at trying to understand its assembly mechanism and function. Despite this, we still lack a mechanistic understanding of how this amazing structure is assembled in neuronal cells. In this article, the authors report a "gap-and-patch" pattern of labelled spectrin in iPSC-derived human motor neurons grown in culture. The mid-sections of these axons exhibit patches with reasonably well-organized MPS that are separated by gaps lacking any detectable MPS and having low spectrin content. Further, they report that the intensity modulation of spectrin is correlated with intensity modulations of tubulin as well. However, neurofilament fluorescence does not show any correlation. Using DIC imaging, the authors show that often the axonal diameter remains uniform across segments, showing a patch-gap pattern. Gaps are seen more abundantly in the midsection of the axon, with the proximal section showing continuous MPS and the distal segment showing continuous spectrin fluorescence but no organized MPS. The authors show that spectrin degradation by caspase/calpain is not responsible for gap formation, and the patches are nascent MPS domains. The gap and patch pattern increases with days in culture and can be enhanced by treating the cells using the general kinase inhibitor staurosporine. Treatment with the actin depolymerizing agent Latrunculin A reduces gap formation. The reasons for the last two observations are not well understood/explained.

      Strengths:

      The claims made in the paper are supported by extensive imaging work and quantification of MPS. Overall, the paper is well written and the findings are interesting. Although much of the reported data are from axons treated with staurosporine, this may be a convenient system to investigate the dynamics of MPS assembly, which is still an open question.

      Weaknesses:

      Much of the analysis is on staurosporine-treated cells, and the effects of this treatment can be broad. The increase in patch-gap pattern with days in culture is intriguing, and the reason for this needs to be checked carefully. It would have been nice to have live cell data on the evolution of the patch and gap pattern using a GFP tag on spectrin. The evolution of individual patches and possible coalescence of patches can be observed even with confocal microscopy if live cell super-resolution observation is difficult.

      Some more comments:

      (1) Axons can undergo transient beading or regularly spaced varicosity formation during media change if changes in osmolarity or chemical composition occur. Such shape modulations can induce cytoskeletal modulations as well (the authors report modulations in microtubule fluorescence). The authors mention axonal enlargements in some instances. Although they present DIC images to argue that the axons showing gaps are often tubular, possible beading artefacts need to be checked. Beading can be transient and can be checked by doing media changes while observing the axons on a microscope.

      (2) Why do microtubules appear patchy? One would imagine the microtubule lengths to be greater than the patch size and hence to be more uniform.

      (3) Why do axons with gaps increase with days in culture? If patches are nascent MPS that progressively grow, one would have expected fewer gaps with increasing days in culture. Is this indicative of some sort of degeneration of axons?

      (4) It is surprising that Latrunculin A reduces gap formation induced by staurosporine (also seems to increase MPS correlation) while it decreases actin filament content. How can this be understood? If the idea is to block actin dynamics, have the authors tried using Jasplakinolide to stabilize the filaments?

      (5) The authors speculate that the patches are formed by the condensation of free spectrins, which then leaves the immediate neighborhood depleted of these proteins. This is an interesting hypothesis, and exploring this in live cells using spectrin-GFP constructs will greatly strengthen the article. Will the patch-gap regions evolve into continuous MPS? If so, do these patches expand with time as new spectrin and actin are recruited and merge with neighboring patches, or can the entire patch "diffuse" and coalesce with neighboring patches, thus expanding the MPS region?

    2. Author response:

      Reviewer #1 (Public review)

      Summary:

      Ever since the surprising discovery of the membrane-associated Periodic Skeleton (MPS) in axons, a significant body of published work has been aimed at trying to understand its assembly mechanism and function. Despite this, we still lack a mechanistic understanding of how this amazing structure is assembled in neuronal cells. In this article, the authors report a "gap-and-patch" pattern of labelled spectrin in iPSC-derived human motor neurons grown in culture. The mid-sections of these axons exhibit patches with reasonably well-organized MPS that are separated by gaps lacking any detectable MPS and having low spectrin content. Further, they report that the intensity modulation of spectrin is correlated with intensity modulations of tubulin as well. However, neurofilament fluorescence does not show any correlation. Using DIC imaging, the authors show that often the axonal diameter remains uniform across segments, showing a patch-gap pattern. Gaps are seen more abundantly in the midsection of the axon, with the proximal section showing continuous MPS and the distal segment showing continuous spectrin fluorescence but no organized MPS. The authors show that spectrin degradation by caspase/calpain is not responsible for gap formation, and the patches are nascent MPS domains. The gap and patch pattern increases with days in culture and can be enhanced by treating the cells using the general kinase inhibitor staurosporine. Treatment with the actin depolymerizing agent Latrunculin A reduces gap formation. The reasons for the last two observations are not well understood/explained.

      We thank the reviewer for the detailed and accurate description of the data shown and its relevance to further our understanding of MPS assembly mechanism and function.

      Strengths:

      The claims made in the paper are supported by extensive imaging work and quantification of MPS. Overall, the paper is well written and the findings are interesting. Although much of the reported data are from axons treated with staurosporine, this may be a convenient system to investigate the dynamics of MPS assembly, which is still an open question.

      We thank the reviewer for the positive comments on the manuscript, the techniques used and the proposed model.

      Weaknesses:

      Much of the analysis is on staurosporine-treated cells, and the effects of this treatment can be broad. The increase in patch-gap pattern with days in culture is intriguing, and the reason for this needs to be checked carefully. It would have been nice to have live cell data on the evolution of the patch and gap pattern using a GFP tag on spectrin. The evolution of individual patches and possible coalescence of patches can be observed even with confocal microscopy if live cell super-resolution observation is difficult.

      We will consider the inclusion of live imaging experiments using the expressión of C-terminus-tagged human beta2-spectrin in the revised version of the manuscript. We are familiar with live-imaging and FRAP experiments and we will explore how to develop these experiments to generate data for inclusion in a revised submission.

      Some more comments:

      (1) Axons can undergo transient beading or regularly spaced varicosity formation during media change if changes in osmolarity or chemical composition occur. Such shape modulations can induce cytoskeletal modulations as well (the authors report modulations in microtubule fluorescence). The authors mention axonal enlargements in some instances. Although they present DIC images to argue that the axons showing gaps are often tubular, possible beading artefacts need to be checked. Beading can be transient and can be checked by doing media changes while observing the axons on a microscope.

      We don´t discard the presence of “nano beads” in these axons. It was recently suggested that the normal morphology of axons is indeed resembling “pearls-on-a-string” (Griswold et al., 2025), with “nano beads” separated by thin tubular "connectors" (also referred to as NSV, for non-synaptic varicosities). However, it is unlikely that the gap-patch pattern of beta2-spectrin can be attributed to such a morphology, given we used formaldehyde as fixative, and Griswold and colleagues show that the use of aldehyde-based fixatives do not preserve NSVs. We are able to see scattered axonal enlargements (“micro beads”), as we described in distal portions in Fig. 1C(C2) and E. However, the number, appearance and staining of these are not compatible with the gap-patch pattern in beta2-spectrin. Moreover, we would have expected to see these NSVs in our extensive STED imaging, yet we did not. We will discuss this further in the resubmission.

      (2) Why do microtubules appear patchy? One would imagine the microtubule lengths to be greater than the patch size and hence to be more uniform.

      Our stainings are for tubulin protein isoforms beta-III and alpha-II. That is, they would label microtubules, but free tubulin as well. The slight decrease in intensity for tubulin within gaps is indeed something to investigate, but we don´t interpret this as “patchy microtubules”. If the Reviewer refers to Fig. 2C-D, it is actually difficult to anticipate the slight decrease in intensity by the naked eye. To further support this, we will consider including stainings and quantitative analyses for microtubules in the resubmission. We are familiar with the use of permeabilizing conditions during fixation (in protocols known as “cytoskeletal fixation” to label microtubules (and not free tubulin).

      (3) Why do axons with gaps increase with days in culture? If patches are nascent MPS that progressively grow, one would have expected fewer gaps with increasing days in culture. Is this indicative of some sort of degeneration of axons?

      We agree with the apparent discrepancy. However, one has to take into account that these axons are still elongating even at 2 weeks in culture. Hence, at any time point, there is a new axonal compartment recently added, and hence, with low beta2-spectrin and no MPS. Also, the dynamical evolution of the MPS has to take into account beta2-spectrin supply. If supply is somehow lower than a given threshold, it is expected that there will be more gaps, given the new, more distant parts of the axons have a lower supply of beta2-spectrin . To explore this formally, we are working on simulations of these multifactorial dynamic systems to better understand this, that together with key experimental observations would enhance our understanding into overall MPS assembly in growing axons. However, findings for this project will be the subject of another manuscript.

      (4) It is surprising that Latrunculin A reduces gap formation induced by staurosporine (also seems to increase MPS correlation) while it decreases actin filament content. How can this be understood? If the idea is to block actin dynamics, have the authors tried using Jasplakinolide to stabilize the filaments?

      The results with the co-treatment with Latrunculin A and Staurosporine are indeed intriguing, and provide clear evidence that the gap-and-patch pattern arises from local assembly of the MPS, requiring new actin filaments. However, the fact that F-actin within the pre-formed MPS seems unaffected is not surprising. There are many different populations of F-actin in axons (i.e. MPS rings, longitudinal filaments, actin patches, actin trails). Latrunculin A affects filaments indirectly. The target of Latrunculin A is not actin filaments, but free monomers. It ultimately affects actin filaments as they end up losing monomers, and devoid of new monomers, filaments get shorter and eventually disappear. The drastic decrease in F-actin in our axons reflects that. The fact that F-actin in the MPS is preserved only speaks to the fact that these filaments are stable -if they are not losing monomers in the time frame of the treatment, the filament remains unaffected. We will support this with more observations and imaging and with a more extensive discussion summarizing the literature on the matter in the resubmission.

      On the other hand, the use of F-actin stabilizing drugs (like Jasplakinolide) would have a different effect. We will study how an experiment with these drugs could be informative of the process under investigation for the resubmission

      (5) The authors speculate that the patches are formed by the condensation of free spectrins, which then leaves the immediate neighborhood depleted of these proteins. This is an interesting hypothesis, and exploring this in live cells using spectrin-GFP constructs will greatly strengthen the article. Will the patch-gap regions evolve into continuous MPS? If so, do these patches expand with time as new spectrin and actin are recruited and merge with neighboring patches, or can the entire patch "diffuse" and coalesce with neighboring patches, thus expanding the MPS region?

      We agree with the reviewer's interpretation. A virtue of our experimental model and our interpretations of the observations in fixed cells is that it gives rise to informative questions such as the ones posed by the reviewer. As stated above, we will consider the inclusion of live imaging experiments using the expressión of C-terminus tagged human beta2-spectrin in the revised version of the manuscript. We are familiar with live-imaging and FRAP experiments and we think we can provide the evidence suggested.

      Reviewer #2 (Public review):

      Summary:

      In this manuscript, Gazal et al. describe the presence of unique gaps and patches of BetaII-spectrin in medial sections of long human motor neuron axons. BII-spectrin, along with Alpha-spectrin, forms horizontal linkers between 180nm spaced F-actin rings in axons. These F-actin rings, along with the spectrin linkers, form membrane periodic structures (MPS) which are critical for the maintenance of the integrity, size, and function of axons. The primary goal of the authors was to address whether long motor axons, particularly those carrying familial mutations associated with the neurodegenerative disorder ALS, show defects in gaps and patches of BetaII-spectrin, ultimately leading to degradation of these neurons.

      We thank the reviewer for the detailed and accurate description of the data shown.

      Strengths:

      The experiments are well-designed, and the authors have used the right methods and cutting-edge techniques to address the questions in this manuscript. The use of human motor neurons and the use of motor neurons with different familial ALS mutations is a strength. The use of isogenic controls is a positive. The induction of gaps and patches by the kinase inhibitor staurosporine and their rescue by Latrunculin A is novel and well-executed. The use of biochemical assays to explore the role of calpains is appropriate and well-designed. The use of STED imaging to define the periodicity of MPS in the gaps and patches of spectrin is a strength.

      We thank the reviewer for the positive comments on the manuscript, the techniques used and the proposed model.

      Weaknesses:

      The primary weakness is the lack of rigorous evaluation to validate the proposed model of spectrin capture from the gaps into adjacent patches by the use of photobleaching and live imaging. Another point is the lack of investigation into how gaps and patches change in axons carrying the familial ALS mutations as they age, since 2 weeks is not a time point when neurodegeneration is expected to start.

      We will consider the inclusion of live imaging experiments using the expressión of tagged human beta2-spectrin in the revised version of the manuscript. We are familiar with live-imaging and FRAP experiments and we believe we can provide the evidence suggested. We don't discard the notion that axons carrying familial ALS mutations will show defects in MPS formation and/or stability when observed at longer culture times, or under culture conditions that promote neuronal aging (Guix et al., 2021). Thus, we will continue to work with these cells, but the goal of that project lies well beyond the primary message of the present manuscript, and we anticipate that the revised version will not include new data on this matter. 

      Reviewer #3 (Public review):

      Summary:

      Gazal et al present convincing evidence supporting a new model of MPS formation where a gap-and-patch MPS pattern coalesces laterally to give rise to a lattice covering the entire axon shaft.

      Strengths:

      (1) This is a very interesting study that supports a change in paradigm in the model of MPS lattice formation.

      (2) Knowledge on MPS organization is mainly derived from studies using rat hippocampal neurons. In the current manuscript, Gazal et al use human IPS-derived motor neurons, a highly relevant neuron type, to further the current knowledge on MPS biology.

      (3) The quality of the images provided, specifically of those involving super-resolution, is of a high standard. This adequately supports the conclusions of the authors.

      We thank the reviewer for the positive comments on the manuscript, the techniques used and the proposed model.

      Weaknesses:

      (1) The main concern raised by the manuscript is the assumption that staudosporine-induced gap and patch formation recapitulates the physiological assembly of gaps and patches of betaII-spectrin.

      We will further explore the inclusion of more measurements of other parameters and variables towards establishing whether these gaps-and-patches patterns are equivalent structures in control and staurosporine-treated cells. 

      (2) One technical challenge that limits a more compelling support of the new model of MPS formation is that fixed neurons are imaged, which precludes the observation of patch coalescence.

      As stated before regarding similar comments by other reviewers, we will consider the inclusion of live imaging experiments in the revised version of the manuscript.

      Nicolas Unsain, PhD, and Thomas Durcan, PhD.

      References

      Griswold, J.M., Bonilla-Quintana, M., Pepper, R. et al. Membrane mechanics dictate axonal pearls-on-a-string morphology and function. Nat Neurosci 28, 49–61 (2025). https://doi.org/10.1038/s41593-024-01813-1

      Guix F.X., Marrero Capitán A., Casadomé-Perales A., Palomares-Pérez .I, López Del Castillo I., Miguel V., Goedeke L., Martín M.G., Lamas S., Peinado H., Fernández-Hernando C., Dotti C.G. Increased exosome secretion in neurons aging in vitro by NPC1-mediated endosomal cholesterol buildup. Life Sci Alliance. 2021 Jun 28;4(8):e202101055. doi: 10.26508/lsa.202101055. Print 2021 Aug.

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      Reply to the reviewers

      Manuscript number: RC-2025-03098

      Corresponding author: Pedro Escoll

      1. General Statements

      Our study investigates the interplay between the metabolism of host cells and the intracellular replication of Salmonella enterica serovar Typhimurium (ST). Type III Secretion Systems (T3SSs) are considered essential for ST to replicate within macrophages. However, we found that restricting macrophages to different bioenergetic contexts, such as supplementing them with glycerol, modulates bacterial replication and remarkably, enables a T3SS-deficient ST mutant (ΔprgHssaV) to replicate intracellularly. This T3SS-independent replication occurs within the Salmonella-containing vacuole (SCV) and is driven by the capacity of the host cell to provide these preferred nutrients, rather than by the host glycolytic activity itself.

      2. Description of the planned revisions

      __Reviewer #1 (Evidence, reproducibility and clarity): __

      Summary:

      In this manuscript, the authors investigate how host cell metabolic heterogeneity influences the intracellular replication of Salmonella enterica serovar Typhimurium. They use live-cell imaging of infected human primary macrophages to reveal that bacterial replication does not occur uniformly across infected cells. They demonstrate that supplementation with specific carbon sources-used by Salmonella during infection-promotes bacterial replication and increases the proportion of macrophages supporting intracellular growth. These effects are seen even in the absence of functional Type III Secretion Systems (T3SS), using a ΔprgHssaV double mutant. The authors further suggest that this replication enhancement is not strictly dependent on host glycolytic activity but rather on the host cell's ability to import nutrients. Their findings imply that intracellular Salmonella can exploit host cell metabolism to grow, even without its canonical virulence secretion systems, under nutrient-favorable conditions.

      Major Concern:

      While the topic is potentially interesting, the novelty is not fully clear. The concept that nutrient availability impacts intracellular Salmonella replication, largely via T3SS2 function, has been addressed previously (e.g., Liss et al., 2017). The finding that added exogenous carbon sources can enhance bacterial growth is thus not unexpected. The key claim-that Salmonella can replicate intracellularly even in the absence of T3SS function-would be significantly strengthened by demonstrating whether this is specific to Salmonella, or whether similar effects are seen with non-intracellular organisms such as E. coli K-12. If the phenomenon is unique to Salmonella, this would suggest a pathogen-specific mechanism beyond general metabolic support.

      As acknowledged by the Reviewer, the novelty and key claim of our work is that Salmonella can replicate intracellularly even in the absence of T3SS. To experimentally sustain that claim, we showed evidence that providing macrophages with the preferred carbon sources used by Salmonella during infection, such as glycerol, bypass the requirement of both T3SS by Salmonella to grow, intravacuolarly, inside macrophages.

      With respect to the article mentioned by the Reviewer (Liss et al. 2017, ref 36 in the manuscript), there are three important novel insights provided by our work: i) we show that Salmonella can replicate intracellularly in the SCV even in the absence of T3SS if certain carbon sources are provided; ii) we show the preference of Salmonella for certain carbon sources intracellularly such as glycerol and galactose (but not preferentially glucose); and iii) we have extended our observations to primary human macrophages in addition to RAW cells.

      We are not convinced that the experiment suggested by the Reviewer to use E. coli K12 (ECK12) is necessary to support our findings for Salmonella, but we propose to add the requested experiment. Briefly, we will infect hMDMs and RAW macrophages with ST-WT-GFP, ST-ΔprgHΔssaV or ECK12-WT-GFP, while culturing macrophages on different carbon sources (glucose, glycerol, galactose, fructose). Then we will monitor intracellular bacterial growth. By comparing bacterial growth of ST double mutant with ECK12-WT-GFP under favorable carbon sources such as glycerol, the results will be definitive to answer whether this phenomenon is unique to Salmonella or not.

      Specific Comments:

      1. Figure 1H: The effect shown here is not compelling due to inconsistent y-axis scaling. Panels 1B, 1C, and 1D should use a unified axis range with 1H to allow direct visual comparison of growth dynamics.

      Thank you, we will change it as suggested.

      Figures 1B, 1C, 1G, 1H: The current presentation of individual growth traces makes it difficult to appreciate the population-level trend. A smoothed average line overlaid on these plots could better represent the average dynamics of replicative vs. non-replicative infections. Or alternatively the total fraction of cells that proliferate summarized as a segmented bar plot (possibly binned per time point).

      We will plot the results as suggested, the total fraction of infected cells harboring bacteria that proliferate as a segmented bar plot, binned per time point.

      Figure 2G: This panel would benefit from including a comparable condition with the SPI-1/SPI-2 double mutant to aid interpretation. Additionally, the authors should explore whether this nutrient-supported replication is seen in non-phagocytic cells such as HeLa or Caco-2, which would help delineate whether the observed phenomenon is macrophage-specific.

      The graph asked by Reviewer is Figure S1D. As we are representing ST growth in macrophages supporting Salmonella replication, some of the conditions, such as lactate, cannot be shown in the infection conditions using the double mutant because there are no cells supporting the replication of the double mutant, so there are no cells to plot.

      As suggested, we are also going to perform the same experiments in HeLa cells to investigate whether the observed phenomenon is macrophage specific.

      Line 117: The sentence stating that the double mutant can undergo "exponential intracellular growth even in the absence of T3SS-dependent secretion" is an overstatement. The data suggest only a modest improvement in growth, restricted to a minority of infected cells. This claim should be revised accordingly, as should similar overstatements in the discussion (e.g., lines 203-204).

      We will remove the term 'exponential' and revise the sentence at line 117 and those in the discussion. Line 203-204 will be: 'we demonstrated that providing macrophages with preferred nutrients allows a subpopulation of ST to replicate intracellularly without the need for a functional T3SS'.

      Line 162: The authors should clarify that glycerol had the strongest effect in primary macrophages, while multiple alternative carbon sources had notable effects primarily in RAW cells.

      We will add this clarification in the text.

      Lines 198-201: This relates to the major concern. The authors should assess whether the observed growth enhancement is unique to Salmonella by testing other bacteria not known for intracellular replication. This would clarify whether the effect is due to general nutrient-driven host cell permissivity or a pathogen-specific adaptation.

      As outlined above, we will perform the suggested experiment with E. coli K12 to answer whether this phenomenon is unique to Salmonella or not.

      RAW 264.7 Observations: The modest intracellular growth of SPI-1/SPI-2 double mutants in RAW cells is consistent with prior observations in the field. The idea that nutrient availability explains this is noteworthy. The authors might consider whether differences in standard culture media (e.g., glucose concentration) influence these outcomes. This could have broader implications for reproducibility in infection models.

      Thank you for the suggestion, we will include a paragraph discussing whether differences in standard culture media might influence bacterial replication. Indeed, to answer also a question from Reviewer #2, we will include a new supplementary Figure where we have already compared "no Glucose" (0 mM), "low Glucose" (2 mM) and standard culture media Glucose levels (10 mM). Our results show that differences in Glucose levels in the culture media influence Salmonella intracellular growth in hMDMs and RAW macrophages (see Figure below).

      Reviewer #1 (Significance):

      This manuscript highlights how host cell metabolism and nutrient availability can influence intracellular Salmonella replication. While the findings are intriguing, the current framing overstates their novelty and impact. Key revisions-such as comparative experiments with non-pathogenic bacteria and non-phagocytic cells, consistent figure scaling, and more measured language-would improve the clarity and significance of the work. If the authors can show Salmonella-specific mechanisms at play, the study could offer important insights into host-pathogen metabolic interactions.

      We believe that performing all experiments suggested by the Reviewers, as well as the requested changes in the text to avoid overstatements, will improve the manuscript and will offer readers new insights and details to better understand the metabolic interactions happening between host and pathogens and how they can shape bacterial virulence.

      Reviewer #2 (Evidence, reproducibility and clarity):

      Summary: In their study titled "Provision of Preferred Nutrients to Macrophages Enables Salmonella to Replicate Intracellularly Without Relying on Type III Secretion Systems", Dr. Garcia-Rodriguez et al. describe the influence of the host cell metabolism on the intracellular proliferation potential of Salmonella during infection. The authors investigate whether the supplementation of the media with different carbon sources has an impact on the intracellular lifestyle of Salmonella. By using single cell tracking in live-cell microscopy, including the use of different reporter strains, they describe that glycerol benefits Salmonella's ability to grow within its vacuolar niche, in part, interestingly, in a Type-3-Secretion System independent manner.

      They furthermore highlight the dependence on host background for this observation by showing that effects differ between cells of varying metabolic activity. Throughout their study, they use cutting-edge methodologies, as well as Salmonella strains that could be of versatile use in other investigations. This work, while limited to in vitro models for now, has implications for the better understanding of how pathogens and their host are intertwined. This, in turn, has significance for the development of new anti-infective strategies further down the line. I therefore believe that it should be disseminated to the research community. The following comments summarize ideas how the quality of the study could be improved:

      Major comments:

      1. Salmonella, especially when cultured to activate the SPI-1 T3SS, introduce rapid cell death in their host - most commonly through activation of the NLRC4 inflammasome and downstream pyroptotic signaling. The authors don't describe the effect of the infection in differently supplemented media on host cell death, yet it would be important to elucidate whether this cellular response is also altered.

      We have performed these experiments and tracked host cell death by measuring Annexin-V levels in single cells, during infection in the conditions using the different supplements. We will include these results in the revised version of the manuscript and main text. Please see the Figure below showing that the different carbon sources did not affect macrophages cell death significantly (future Figure S1E and S1F)

      The aspect of partially T3SS-independent growth enhancement by glycerol (and depending on the host background glucose) is most curious. The authors quantify this by determining the percentage of cells containing proliferating Salmonella and by tracking individual cells over the time course of the infection. I am missing a general statement on whether the initial infection rate (i.e. timepoint 0) is comparable across conditions and mutants, and whether possible discrepancies in the infection rate could have downstream effects on the statements and claims made in the manuscript. This is, to my mind, also important for the quantification of cytosolic and vacuolar bacteria. There, the authors always speak in "percent of infected cells", so it is relevant whether the number of infected cells varies among conditions (see e.g. Figure 3).

      We thank the reviewer for this comment. The initial infection rate at t=0 significantly differs between WT and mutants in RAW 264.7 macrophages, and carbon source supplementation has no effect. However, as we only analyze infected cells, this does not affect the final results. In any case, we are going to add the graphs of % of infected cells at t=0 as supplementary Figures S1G-K.

      The authors use a concentration of 10mM for all supplemented alternative carbon sources. It would be useful to discuss the rationale behind this approach, including whether all chemicals have the same ability to be taken up by the cell. A concentration series (at least for some of the tested compounds) may be beneficial to bolster the conclusions that the authors make.

      We use 10 mM as this is the concentration of Glucose in standard culture media. By using 10 mM for all the different carbon sources, we can thus compare them keeping concentration constant (10 mM). Indeed, to answer also Reviewer #1, we will include in the manuscript a paragraph discussing whether differences in standard culture media might influence bacterial replication. As this Reviewer suggested, we will include a new supplementary Figure comparing no Glucose (0 mM), low Glucose (2 mM) and standard culture media Glucose levels (10 mM), showing that the concentration of glucose has a gradual effect in supporting the replication of the T3SS-deficient strain in RAW macrophages (see Figure below).

      I think it would strengthen the study, if the authors used host cell mutants in certain metabolite transporters, or alternatively Salmonella mutants that are deficient in uptake or metabolism of some of the compounds used in this study. This point is alluded to in the discussion, and I believe if the authors could show that in certain host mutant backgrounds the impact of supplementation with alternative carbon sources can be reversed, it would immensely bolster the strength of the claims.

      Following Reviewer's suggestion, we generated ST metabolic mutants unable to metabolize glycerol, galactose or fructose. As seen in the Figures below, during infection, the supplementations with glycerol/galactose does not boost Salmonella replication in metabolic mutants as in WT conditions, demonstrating that supplemented carbon sources indeed arrive to bacteria within the SCV and are used by intracellular Salmonella to grow. This Figures will be now Future Figure 4J-N.

      I think it would be useful to include the meaning of this work for other intracellular pathogens in the discussion section: Do the authors believe that this phenotype is Salmonella-specific? If the pathogens are at hand, it might be interesting to infect with other intracellular bacteria, such as Shigella or Francisella to investigate if the boosting of growth by glycerol also holds true for these.

      We have performed experiments with Legionella pneumophila and galactose (see figure below), showing that this carbon source is specific of Salmonella (as shown in Figure 4F in the manuscript). We could perform experiments also with L. pneumophila and glycerol to answer the Reviewers question. However, we think that the results with Legionella might be out of the focus of this article and would constitute themselves a new article, as both pathogens have a very different, non-comparable intracellular metabolism. Thus, the experiment suggested by Reviewer #1 using E. coli K12 (ECK12) while culturing macrophages on different carbon sources (glucose, glycerol, galactose, fructose) is in our opinion a better fit. We will monitor intracellular bacterial growth and, by comparing bacterial growth of the ST-ΔprgHssaV double mutant with ECK12-WT-GFP under favorable carbon sources such as glycerol, the results will be definitive to answer whether this phenomenon is unique to Salmonella or not.

      Minor comments:

      • Line 41: The authors write "are required for", but given their findings, it might be more accurate to phrase this as "have previously been described to be required for" or "have previously been described essential for".

      We will change it.

      • Line 86: Is the referencing of Figure S1C correct or should it be S1A?

      Yes, thank you, it is S1A, we will change it.

      • Lines 119,120: Related to what is displayed in Figure 2G: Are these differences significant?

      Glucose, galactose and lactate curves are significantly different compared to control (p

      • Lines 126,127: What is the change for glycerol, and is the intracellular growth significantly higher compared to the control?

      6,2 {plus minus} 1.9% in glycerol vs. 2 {plus minus} 1% in control, p

      • Figure 1E&F: Related to one of the major comments: Would it be possible to quantify this at timepoint 0 to ensure that the initial infection rates are the same across conditions?

      As outlined above, we will add the graphs of % of infected cells at t=0 as supplementary Figures S1G-K (Major Comment number 2 from this Reviewer)

      • Figure 3E,F: Why does the sum of the curves not add up to 100% (especially in the beginning)? And related to that, why do both the percentage of cytosolic and vacuolar cells grow over time? Since this infection is performed with gentamycin present, re-infection should not be possible.

      The localization module of the SINA plasmid relies on transcriptional reporters, whose expression requires time for induction and detection. Therefore, at early time points, infected cells are not classified as vacuolar or cytoplasmic because the reporters have not yet been expressed (as described in PLoS Pathog. 2021;17(4):e1009550, PMID: 33930101).

      At later time points, a subset of cells harbors bacteria that do not express any of the reporters. These bacteria are considered dormant, representing about 10% of the population, as detailed in the same article. In addition, a small percentage of infected cells simultaneously contain both STvac and STcyt. Such cells are subclassified as harboring STcyt but also STvac. Consequently, the total proportion of infected cells carrying STvac and STcyt may also exceed 100%.

      • Figure S1A: While significance testing is described in the legend, there are no indications of significance in the figure panels.

      The Reviewer is right, there is no significant changes between conditions, we will change the significance testing to ns=non-significant.

      • Figure S1B: Due to the stark discrepancies between hMDMs and RAW264.7, it might make sense to plot them on two different y-axes. Furthermore, I would clarify the y-axis: In the legend, it seems as CFU counts are shown, while CFU/ml/t2 rather describes a change over time.

      We agree. However, we will maintain the scale of the Y-axis as it was required by Reviewer #1 to be consistent with Y-axis. We will change the legend to indicate that we plot CFU/ml/t2.

      • Figure S1C: The prgH-mutant seems to outperform the wildtype in intracellular proliferation, while the double mutant underperforms compared to the ssaV-mutant. Could you please discuss/explain how the prgH-deletion has seemingly opposite effects on intracellular proliferation, depending on whether it is introduced in a wildtype or ssaV-KO background?

      As T3SS-1 plays a role in inducing macrophage cell death via activation of the NLRC4 inflammasome, macrophages infected with bacteria carrying a functional T3SS-1 (such as WT), are more prone to undergo cell death at late time-points, which disrupts bacterial proliferation and reduces the proportion of infected cells. Thus, these dead cells were not considered in the analysis. Even if cell death of ST-WT-infected RAW macrophages remains below 5%, more ΔprgH-infected cells are considered in the analyses at late time-points, and ST-ΔprgH continue replicating (and growing in ST area).

      • Figure S2A: As for the comments related to Figure 3, I am unsure how the sum of STvac and STcyt can deviate from 100. This is especially puzzling for the red curve (glycerol) at e.g. 3hpi, when the sum of the two clearly seems to be larger than 100.

      At early time points, no infected cells are classified as vacuolar or cytoplasmic because the reporters have not yet been expressed. At later time points, a subset of cells harbor bacteria that do not express any of the reporters, which are considered dormant (10% of the population). Finally, a small percentage of infected cells simultaneously contain both STvac and STcyt, therefore the total proportion of infected cells carrying STvac and STcyt may also exceed 100%.

      **Cross-commenting** I agree in principle with the comments raised by Reviewer #1 - especially when it comes to the enhancement in significance if the authors assess the species specificity. Elucidating whether the growth enhancement is Salmonella-specific, occurs for other intracellular pathogens (e.g. Shigella, Francisella) or also for extracellular bacteria (e.g. E. coli, Yersinia), would definitely strengthen the study.

      As said before, for the revision we are going to perform the experiments suggested by Reviewer #1 of using E. coli K12 (ECK12) while culturing macrophages on different carbon sources (glucose, glycerol, galactose, fructose). And to satisfy this Reviewer's curiosity, we are going to perform experiments also with L. pneumophila and glycerol.

      Reviewer #2 (Significance):

      General assessment:

      As the authors write in their discussion, the strength of this study is also it's limitation: Using single cell tracking in microscopy is a very elegant and powerful approach, yet conversely, it limits the scope of the study to in vitro approaches. While it enables assessment of bacterial pathogenicity and host-dependence on a single-cell level, it remains to be investigated whether the conclusion that the authors draw from their work will hold in more complex or physiologically relevant models.

      During the preparation of this Revision Plan, we discovered the article published in PLoS Pathogens by Andrew Grant and Pietro Mastroni "Attenuated Salmonella Typhimurium Lacking the Pathogenicity Island-2 Type 3 Secretion System Grow to High Bacterial Numbers inside Phagocytes in Mice" (PLoS Pathog 2012 8(12): e1003070, PMID: 23236281). In this article, authors showed that our main conclusion is also relevant in vivo (Salmonella Typhimurium can replicate within macrophages in the absence of T3SS). This will be addressed in the Discussion of the revised manuscript. Our study provides a metabolic explanation, at the single cell level for those observations.

      A further small shortcoming of the study is the heavy focus on the bacterial aspect in this host-pathogen interaction. While the authors do link the proliferative potential of the intracellular bacteria to the metabolic status of the individual host cell, more could be done with respect to host responses in the varying media compositions, including investigating alterations to the cell cycle, induction of cell death, or the ability to activate inflammatory signaling.

      We agree, and we are actively investigating how restricting macrophages to specific carbon sources impact other host responses, such as cytokine production. For the revised manuscript, we will add the results on the induction of cell death.

      Nonetheless, this study is of large interest to the field and the systematic approach to addressing their hypotheses speaks to the scientific excellence of the investigators.

      Thank you.

      3. Description of the revisions that have already been incorporated in the transferred manuscript

      N/A

      • *

      4. Description of analyses that authors prefer not to carry out

      N/A

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      Referee #2

      Evidence, reproducibility and clarity

      Summary:

      In their study titled "Provision of Preferred Nutrients to Macrophages Enables Salmonella to Replicate Intracellularly Without Relying on Type III Secretion Systems", Dr. Garcia-Rodriguez et al. describe the influence of the host cell metabolism on the intracellular proliferation potential of Salmonella during infection. The authors investigate whether the supplementation of the media with different carbon sources has an impact on the intracellular lifestyle of Salmonella. By using single cell tracking in live-cell microscopy, including the use of different reporter strains, they describe that glycerol benefits Salmonella's ability to grow within its vacuolar niche, in part, interestingly, in a Type-3-Secretion System independent manner.

      They furthermore highlight the dependence on host background for this observation by showing that effects differ between cells of varying metabolic activity. Throughout their study, they use cutting-edge methodologies, as well as Salmonella strains that could be of versatile use in other investigations. This work, while limited to in vitro models for now, has implications for the better understanding of how pathogens and their host are intertwined. This, in turn, has significance for the development of new anti-infective strategies further down the line. I therefore believe that it should be disseminated to the research community. The following comments summarize ideas how the quality of the study could be improved:

      Major comments:

      1. Salmonella, especially when cultured to activate the SPI-1 T3SS, introduce rapid cell death in their host - most commonly through activation of the NLRC4 inflammasome and downstream pyroptotic signaling. The authors don't describe the effect of the infection in differently supplemented media on host cell death, yet it would be important to elucidate whether this cellular response is also altered.
      2. The aspect of partially T3SS-independent growth enhancement by glycerol (and depending on the host background glucose) is most curious. The authors quantify this by determining the percentage of cells containing proliferating Salmonella and by tracking individual cells over the time course of the infection. I am missing a general statement on whether the initial infection rate (i.e. timepoint 0) is comparable across conditions and mutants, and whether possible discrepancies in the infection rate could have downstream effects on the statements and claims made in the manuscript. This is, to my mind, also important for the quantification of cytosolic and vacuolar bacteria. There, the authors always speak in "percent of infected cells", so it is relevant whether the number of infected cells varies among conditions (see e.g. Figure 3).
      3. The authors use a concentration of 10mM for all supplemented alternative carbon sources. It would be useful to discuss the rationale behind this approach, including whether all chemicals have the same ability to be taken up by the cell. A concentration series (at least for some of the tested compounds) may be beneficial to bolster the conclusions that the authors make.
      4. I think it would strengthen the study, if the authors used host cell mutants in certain metabolite transporters, or alternatively Salmonella mutants that are deficient in uptake or metabolism of some of the compounds used in this study. This point is alluded to in the discussion, and I believe if the authors could show that in certain host mutant backgrounds the impact of supplementation with alternative carbon sources can be reversed, it would immensely bolster the strength of the claims.
      5. I think it would be useful to include the meaning of this work for other intracellular pathogens in the discussion section: Do the authors believe that this phenotype is Salmonella-specific? If the pathogens are at hand, it might be interesting to infect with other intracellular bacteria, such as Shigella or Francisella to investigate if the boosting of growth by glycerol also holds true for these.

      Minor comments:

      • Line 41: The authors write „are required for", but given their findings, it might be more accurate to phrase this as „have previously been described to be required for" or „have previously been described essential for".
      • Line 86: Is the referencing of Figure S1C correct or should it be S1A?
      • Lines 119,120: Related to what is displayed in Figure 2G: Are these differences significant?
      • Lines 126,127: What is the change for glycerol, and is the intracellular growth significantly higher compared to the control?
      • Figure 1E&F: Related to one of the major comments: Would it be possible to quantify this at timepoint 0 to ensure that the initial infection rates are the same across conditions?
      • Figure 3E,F: Why does the sum of the curves not add up to 100% (especially in the beginning)? And related to that, why do both the percentage of cytosolic and vacuolar cells grow over time? Since this infection is performed with gentamycin present, re-infection should not be possible.
      • Figure S1A: While significance testing is described in the legend, there are no indications of significance in the figure panels.
      • Figure S1B: Due to the stark discrepancies between hMDMs and RAW264.7, it might make sense to plot them on two different y-axes. Furthermore, I would clarify the y-axis: In the legend, it seems as CFU counts are shown, while CFU/ml/t2 rather describes a change over time.
      • Figure S1C: The prgH-mutant seems to outperform the wildtype in intracellular proliferation, while the double mutant underperforms compared to the ssaV-mutant. Could you please discuss / explain how the prgH-deletion has seemingly opposite effects on intracellular proliferation, depending on whether it is introduced in a wildtype or ssaV-KO background?
      • Figure S2A: As for the comments related to Figure 3, I am unsure how the sum of STvac and STcyt can deviate from 100. This is especially puzzling for the red curve (glycerol) at e.g. 3hpi, when the sum of the two clearly seems to be larger than 100.

      Cross-commenting

      I agree in principle with the comments raised by Reviewer #1 - especially when it comes to the enhancement in significance if the authors assess the species specificity. Elucidating whether the growth enhancement is Salmonella-specific, occurs for other intracellular pathogens (e.g. Shigella, Francisella) or also for extracellular bacteria (e.g. E. coli, Yersinia), would definitely strengthen the study.

      Significance

      General assessment:

      As the authors write in their discussion, the strength of this study is also it's limitation: Using single cell tracking in microscopy is a very elegant and powerful approach, yet conversely, it limits the scope of the study to in vitro approaches. While it enables assessment of bacterial pathogenicity and host-dependence on a single-cell level, it remains to be investigated whether the conclusion that the authors draw from their work will hold in more complex or physiologically relevant models.

      A further small shortcoming of the study is the heavy focus on the bacterial aspect in this host-pathogen interaction. While the authors do link the proliferative potential of the intracellular bacteria to the metabolic status of the individual host cell, more could be done with respect to host responses in the varying media compositions, including investigating alterations to the cell cycle, induction of cell death, or the ability to activate inflammatory signaling.

      Nonetheless, this study is of large interest to the field and the systematic approach to addressing their hypotheses speaks to the scientific excellence of the investigators.

      Advance:

      The advance this study makes is rather on the foundational than the applied side - which does not mean that conclusions drawn in this work are not of interest to a wider field. By investigating the intracellular lifestyle on a single-cell level, the authors were able to observe a striking and curious phenotype: that certain alternative carbon sources can enhance intracellular proliferation in a T3SS-independent manner. By further dissecting the reason for this observation, they create a stronger base for their conclusion in what can be described as an overall comprehensive study.

      Audience:

      As outlined in the description of the main advances, this study will be of largest interest to members of the basic research community in host-pathogen interactions. While the study so far focuses on Salmonella, a well-described and genetically accessible intracellular model pathogen, it could also be of interest to a broader community of researchers investigating bacterial pathogenicity, as well as those that are interested in the host metabolism.

      Describe your expertise:

      I have a background in bacterial pathogenicity in Salmonella infection, and have since expanded to other pathogens, as well as co-infections with viruses. In addition to investigating the pathogens, I have expertise in dissecting the host response, with a focus on innate immunity, inflammasome activation and host cell death. Overall, I am accustomed to unbiased screening approaches, which are followed by the formulation and assessment of hypotheses to unravel the molecular mechanisms underlying the host-pathogen interface.

    3. Note: This preprint has been reviewed by subject experts for Review Commons. Content has not been altered except for formatting.

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      Referee #1

      Evidence, reproducibility and clarity

      Summary:

      In this manuscript, the authors investigate how host cell metabolic heterogeneity influences the intracellular replication of Salmonella enterica serovar Typhimurium. They use live-cell imaging of infected human primary macrophages to reveal that bacterial replication does not occur uniformly across infected cells. They demonstrate that supplementation with specific carbon sources-used by Salmonella during infection-promotes bacterial replication and increases the proportion of macrophages supporting intracellular growth. These effects are seen even in the absence of functional Type III Secretion Systems (T3SS), using a ΔprgH/ΔssaV double mutant. The authors further suggest that this replication enhancement is not strictly dependent on host glycolytic activity but rather on the host cell's ability to import nutrients. Their findings imply that intracellular Salmonella can exploit host cell metabolism to grow, even without its canonical virulence secretion systems, under nutrient-favorable conditions.

      Major Concern:

      While the topic is potentially interesting, the novelty is not fully clear. The concept that nutrient availability impacts intracellular Salmonella replication, largely via T3SS2 function, has been addressed previously (e.g., Liss et al., 2017). The finding that added exogenous carbon sources can enhance bacterial growth is thus not unexpected. The key claim-that Salmonella can replicate intracellularly even in the absence of T3SS function-would be significantly strengthened by demonstrating whether this is specific to Salmonella, or whether similar effects are seen with non-intracellular organisms such as E. coli K-12. If the phenomenon is unique to Salmonella, this would suggest a pathogen-specific mechanism beyond general metabolic support.

      Specific Comments:

      1. Figure 1H: The effect shown here is not compelling due to inconsistent y-axis scaling. Panels 1B, 1C, and 1D should use a unified axis range with 1H to allow direct visual comparison of growth dynamics.
      2. Figures 1B, 1C, 1G, 1H: The current presentation of individual growth traces makes it difficult to appreciate the population-level trend. A smoothed average line overlaid on these plots could better represent the average dynamics of replicative vs. non-replicative infections. Or alternatively the total fraction of cells that proliferate summarized as a segmented barplot (possibly binned per time point).
      3. Figure 2G: This panel would benefit from including a comparable condition with the SPI-1/SPI-2 double mutant to aid interpretation. Additionally, the authors should explore whether this nutrient-supported replication is seen in non-phagocytic cells such as HeLa or Caco-2, which would help delineate whether the observed phenomenon is macrophage-specific.
      4. Line 117: The sentence stating that the double mutant can undergo "exponential intracellular growth even in the absence of T3SS-dependent secretion" is an overstatement. The data suggest only a modest improvement in growth, restricted to a minority of infected cells. This claim should be revised accordingly, as should similar overstatements in the discussion (e.g., lines 203-204).
      5. Line 162: The authors should clarify that glycerol had the strongest effect in primary macrophages, while multiple alternative carbon sources had notable effects primarily in RAW cells.
      6. Lines 198-201: This relates to the major concern. The authors should assess whether the observed growth enhancement is unique to Salmonella by testing other bacteria not known for intracellular replication. This would clarify whether the effect is due to general nutrient-driven host cell permissivity or a pathogen-specific adaptation.
      7. RAW 264.7 Observations: The modest intracellular growth of SPI-1/SPI-2 double mutants in RAW cells is consistent with prior observations in the field. The idea that nutrient availability explains this is noteworthy. The authors might consider whether differences in standard culture media (e.g., glucose concentration) influence these outcomes. This could have broader implications for reproducibility in infection models.

      Significance

      This manuscript highlights how host cell metabolism and nutrient availability can influence intracellular Salmonella replication. While the findings are intriguing, the current framing overstates their novelty and impact. Key revisions-such as comparative experiments with non-pathogenic bacteria and non-phagocytic cells, consistent figure scaling, and more measured language-would improve the clarity and significance of the work. If the authors can show Salmonella-specific mechanisms at play, the study could offer important insights into host-pathogen metabolic interactions.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Reviewer #1 (Public review):

      “In their current study, Cummings et al have approached this fundamental biochemical problem using a combination of purified enzyme-substrate reactions, MS/MS, and microscopy in vitro to provide key insights into the hierarchy of generating polyglycylation in cilia and flagella. They first establish that TTLL8 is a monoglycylase, with the potential to add multiple mono glycine residues on both α- and β-tubulin. They then go on to establish that monoglycylation is essential for TTLL10 binding and catalytic activity, which progressively reduces as the level of polyglycylation increases. This provides an interesting mechanism of how the level of polyglycylation is regulated in the absence of a deglycylase. Finally, the authors also establish that for efficient TTLL10 activity, it is not just monoglycylation, but also polyglutamylation that is necessary, giving a key insight into how both these modifications interact with each other to ensure there is a balanced level of PTMs on the axonemes for efficient cilia function.”

      Strengths: 

      The manuscript is well-written, and experiments are succinctly planned and outlined. The experiments were used to provide the conclusions to what the authors were hypothesising and provide some new novel possible mechanistic insights into the whole process of regulation of tubulin glycylation in motile cilia.”

      We thank the reviewer for their support of our study and recognition of its importance to understanding microtubule glycylation and its regulation.  

      “The initial part of the manuscript where the authors discuss about the requirement of monoglycylation by TTLL8 is not new. This was established back in 2009 when Rogowski et al (2009) showed that polyglycylation of tubulin by TTLL10 occurs only when co-expressed in cells with TTLL3 or TTLL8. So, this part of the study adds very little new information to what was known. “

      Our study provides the first in vitro evidence with purified recombinant components that human TTLL8 is exclusively a monoglycylase (Figure 1) and that polyglycylation by TTLL10 requires previous priming with monoglycylation (Figure 2). Studies with purified recombinant components are the gold standard for establishing the activity of an enzyme as cellular work can be obfuscated by the activity of other regulators. We did cite in our original submission the work by Rogowski, Gaertig and Janke from 2009 (reference 15 in the original submission) as well as that Ikegami and Setou 2009 work (reference 26 in the original submission) that established that TTLL10 polygyclylase activity requires co-expression with TTLL8 in cells. Specifically, we stated in our original submission and in the revised manuscript:

      “Cellular overexpression studies coupled with the use of antibodies that recognize mono- and polyglycylation indicate that TTLL8 is also a glycyl-initiase, while TTLL10 a glycyl-elongase (15, 26).  However, direct biochemical evidence with purified enzymes for segregated initiation and elongation activity for glyclases is still lacking as does knowledge of their substrate specificity and regulation.” 

      In addition to citing the Setou study, we now cite again the Rogowski, Gaertig and Janke 2009 study later in the manuscript when the cellular data are mentioned again.  Specifically, we state in the revised manuscript: 

      “This is consistent with cellular overexpression data which showed that polyglycylation signal was detected via antibody only in tubulin from cells that co-expressed TTLL8 and TTLL10, but not TTLL10 alone (15, 26).”

      “The study also fails to discuss the involvement of the other monoglycylase, TTLL3 in the entire study, which is a weakness as in vivo, in cells, both the monoglycylases act in concert and so, may play a role in regulating the activity of TTLL10. “

      We previously showed that purified recombinant TTLL3, like TTLL8, adds only monoglycines, with a preference for the b-tubulin tail (Garnham et al., PNAS 2017). Given that TTLL10 requires priming by monoglycylation, we expect that, similarly to TTLL8, TTLL3 will allow elongation of the initial monoglycyline chains by TTLL10. 

      (1) From the mass spec data, it appears that the Xaenopus Laevis TTLL10 can add up to 18 residues. However, the numbers indicated in Figure 2E seem to suggest that it is a maximum of 23 residues only at a particular position. Does this mean that the 13-18 residues observed are a collection of multiple short-chain polyglycylations or are there positions that the authors observed where there were chains of longer than 3 glycine residues? This would be an interesting point to note as when it was discovered in Paramecium, the polyglycyl chains were reported to be up to 34 residues (Redeker et al., Science 1994). If the authors could test the TTLL10 from Paramecium to observe if this is a consistent phenomenon across evolution or is there a biologically significant difference that is being developed, would be interesting to know.”

      Figure 2E shows a subset of the modified tails that we identified and where the position of the posttranslationally added glycine can be mapped to a specific position, or range of positions. Additional species exist. We note that the mass spectra in Figure 2B are intact LC/MS, while those in Figure 2E are MS/MS. The ionization of tubulin tail peptides with larger number of glycines is not as efficient as for shorter glycine chains, reducing the sensitivity of detection of species that have higher number of glycines. This is not as pronounced when the mass spectra are obtained from the intact protein (Figure 2B). In summary, our data supports the fact that TTLL10 elongates polyglycine chains at multiple positions in the tubulin tail (shown in Figure 2E), however, we cannot ascertain the maximum polyglycine chain length, only the total number of glycyines added.

      Testing the enzyme from Paramecium is an interesting proposal but outside the scope of this manuscript. 

      (2) While it is interesting to know that the TTLL10 binds to TTLL8-modified tubulin with a much higher affinity than unmodified tubulin, in vivo, the microtubules will be a mixture of both TTLL3- and TTLL8-modified tubulin. It would be good to see the binding of the enzyme to a tubulin that is modified by both TTLL3 and TTLL8 if the two have a greater influence on TTLL10 binding.”

      Our previous work showed that purified recombinant TTLL3 has purely monoglycylase activity, with a preference for b-tubulin (Garnham et al., PNAS 2017). The sites of monoglycylation by TTLL3 overlap with those introduced by TTLL8 on b-tubulin (the difference being mainly that TTLL3 is more selective towards b-tubulin and thus has lower activity on a-tubulin). TTLL8 introduces additional monoGlys on the a-tubulin tail. Therefore, it is unlikely that TTLL10 will have a different response to microtubules that carry similar numbers of Gly residues, regardless of whether introduced by TTLL8 or TTLL3 and 8. Our data show that TTLL10 binding increases with Gly number, but that the gains in affinity plateau as the density of glycine residues on the tails increases above a certain threshold, likely because one TTLL10 molecule recognizes one monoGly branch, and steric hindrance on the tubulin tail prevents further recruitment of additional TTLL10 molecules.  

      (3) The authors have always increased the number of monoglycines in beta-tubulin more than in alpha-tubulin. Is there a rationale for this? Since TTLL8 is known to predominantly modify alphatubulin (Rogowski et al., 2009; Gadadhar et al., 2017) why did the authors not check for the increased binding of the TTLL10 on dimers where the number of monoglycines on alpha-tubulin is higher than 1.1? Especially when they themselves observe in their mass spec that even on alphatubulin there are 1, 2, and 3 glycines added. I would like to see what happens if the ratio is high alpha-G + low beta-G”

      As our spectra in Figure 1 show, we find that TTLL8 is able to modify robustly in vitro both a- and b-tubulin but that it shows a slight preference for b-tubulin (Figure 1B). The work from the Janke group that the reviewer is referring to (Rogowski et al., 2009 and Gadahar et al., 2017) did not use recombinant, purified enzymes and unmodified microtubules as substrates and used axonemal tubulin (which carries many modifications), and so it is possible that the a-tubulin preference observed in that system when TTLL8 is overexpressed, is likely to other factors that do not reflect the biochemical property of the enzyme alone (for example, it could be because btubulin site are not available because they are already glutamylated). As can be seen from Figure 3D, the gain in affinity when increasing the number of glycines from one glycine is small, compared to the initial monoglycine added to the a- and the b-tubulin tail, likely reflecting that one tail cannot bind more than one TTLL10 at one time because of steric hindrance. Moreover, it is important here to note that glutamylation and glycylases compete for the same sites on the tubulin tails, as we have for example shown for TTLL3 and TTLL7 (Garnham et al., 2017), therefore the activity of these enzymes in vivo or with non-naïve substrates are context dependent and influences also what sites are available for TTLL10 to modify. In conclusion, by using recombinant enzymes and naïve tubulin we gain insight into the intrinsic property of these enzymes and therefore provide a framework for the interpretation of in vitro and in vivo observations. 

      (4) I wonder why the authors did not use the human TTLL10 to test if this also shows similar binding to the glycylated tubulin despite the fact that it is enzymatically inactive. If it does, then it would be interesting to see the kinetics of binding of this enzyme to see if the fall off of the enzyme from the tubulin is solely driven by the level of polyglycylation only, or if it has any other mechanism involved as well.”

      Work with human recombinant TTLL10, a TTLL10 homolog which was proposed to be inactive, will be an interesting future direction but outside the scope of this manuscript. We did note in our previous manuscript (Garnham et al., 2017, Figure S5) that the residues which are mutated in the human enzyme compared to other mammals are on the dorsal face of the enzyme, far away from the active site, raising an interesting question of how they inactivate the enzyme.   We need however to emphasize that our work clearly shows that it is polyglycylation on the microtubules that reduces binding of TTL10 to microtubules because experiments done in the absence of glycylating activity i.e. with enzyme that was incubated with microtubules that were pre-modified with polyglycline chains, but in the absence of glycyine substrate (precluding any glycylation activity during the binding assay) show that the binding decreases monotonically with the number of polyglycines  on the microtubule (Figures 4A, B).  

      (5) In Figure 5, the authors use monoglycylated tubulin that is either glutamylated or not to show that the activity of TTLL10 is enhanced by the extent of polyglutamylation present on the tubulin. However, there is no evidence of the enzyme binding to microtubules that are only glutamylated. It would be good to test this to determine if the binding is also dependent on both monoglycylation and glutamylation or is it only the enzyme activity.

      Figure 5E shows that TTLL10 binding increases with monoglycylation alone, and that glutamylation is additive and Figures 4A, B show that it is not the enzyme activity that affects the binding, but the glycylation state of the microtubule. We did not determine binding to microtubules that were only glutamylated, because TTLL10 would not be able to elongate polyglycine chains on those microtubules, even if it bound. 

      (6) The level of polyglycylation used in Figure 5 is quite low. It would be good to see how the length of the polyglycine chain impacts TTLL10 activity in the presence of polyglutamylation, and whether this has any cooperative effect leading to longer chain polyglycylation than what is seen with only monoglycylated tubulin.

      We expect longer chain polyglycylation to have an inhibitory effect as we show in Figure 4. 

      “(7) In the overall study, the authors fail to discuss whether the activity of both the glycylases at different sites on tubulin is sequential, or modifications at different residues happen all at once. If the authors were to do a sequential time course of the modification followed by MS/MS analysis, they could get some indications about this.”

      As the data in Figure 3D shows, the effect of adding more monoGly site on a tubulin tail has a muted effect on binding, indicating that the additional mono-Gly branches do not lead to more TTLL10 recruitment because of steric hindrance i.e. multiple TTLL10 enzymes cannot be accommodated on the same tail at the same time efficiently. This is consistent with the overall dimensions of the enzyme and the positions of its active site, which were modeled initially in our previous publication (Garnham et al., PNAS 2017).  The site of TTL10 action is pre-determined by the position of the mono-Gly branch introduced by TTLL3 or TTLL8. The length of the tubulin tail and the proximity of mono-Gly sites to each other precludes TTLL10 acting at multiple positions at once on the same tail.

      “(8) Do the modifications have any cooperative effect with respect to the sites of modification? Does modifying a particular site enhance the kinetics of modification of the other sites? Can the authors test this?”

      This would be an interesting line of future investigations.  

      “Minor points:

      (1’) The authors opine that the level of polyglycylation is regulated by the decreased binding of the TTLL10 to the polyglycylated tubulin. While this is an interesting argument, which could be a possibility based on the data they present, it would still not answer if this is a mechanism followed by TTLL10 of all species or not. If they could test the efficacy of TTLL10 from another species, to see the binding efficiency of that enzyme, it could potentially strengthen their argument of this possible mechanism.”

      The differences between the properties of TTLL10 from different organisms will be an interesting focus of future investigations, but outside the scope of this present study. However, we would like to point out that the level of sequence conservation between TTLL10 makes it unlikely that other TTLL10 do not follow a similar mechanism, albeit with possible differences in the extent of the response.  We also note that we have shown that polyglycylation also inhibits binding to the microtubule of the severing enzyme katanin (Szczesna et al., Dev. Cell 2022). Therefore, these studies suggests that polyglycylation might be a more general mechanism for reducing microtubule binding affinity since glycylation reduces the negative charge on the tubulin tails, which frequently interact with positively charged domains or interfaces in microtubule associated proteins.  

      “(2) The authors indicate that glycylases act on pre-glutamylated microtubules. However, in their assays, they use unmodified tubulin, which I would presume is also not glutamylated. If this is the case, how can they justify that the enzymes prefer pre-glutamylated microtubules? This is a bit unclear. Do they mean that their tubulin is already pre-glutamylated? Have they tested this?”

      The statement regarding the action of these enzymes on glutamylated microtubules refer to the in vivo situation where polyglycylated microtubules appear in cilia biogenesis after the microtubules in the axoneme are already glutamylated. In vitro, by using microtubules that are only monoglycylated and microtubules that are both glutamylated and monoglycylated, we show that glutamylation further increases recruitment of TTLL10 to microtubules that are monoglycyated. Therefore, glutamylated microtubules will be polyglycylated preferentially over those that are not glutamylated. 

      We state: “Axonemal microtubules are abundantly glutamylated. Glutamylation appears during cilia development first, followed by glycylation (12, 13), indicating that in this scenario glycylases act on pre-glutamylated microtubule substrates.”

      “(3) In continuation with the previous point, an immunoblot of their purified tubulin showing no reactivity to anti-glycylation or anti-glutamylation antibodies, which upon treatment with TTLL8 reacts to the anti-glycylation antibody would be confirmatory evidence to show that the isolated tubulin was indeed unmodified.”

      We have now included a Western blot of our TOG-purified tubulin as Figure S3 in our revised manuscript.  This shows a faint signal with the pep-G1 antibody and a very strong signal after TTLL8 treatment. We are not sure whether the low signal with the pep-G1 antibody for the unmodified tubulin is due to low bona fide monoglycylation-specific signal or a low affinity nonspecific interaction of this antibody (raised against mono-glycylated tubulin tail peptides) with the unmodified tubulin. We note that this signal is clearly visible only when loading at least 0.2 micrograms of the purified tubulin. At this loading level the signal for the glycylated species is saturated. It is also important to note that we have not detected glycylated species in this tubulin either by LC-MS or MS/MS. Therefore, our data strongly indicate that the tubulin purified from tsA201 cells is not glycylated or has at most extremely low levels of glycylation. Importantly, this potential trace level of monoglycylated tubulin does not affect any of the conclusions in this study. The Western blot also shows no detectable signal with the polyglycyation antibody in the unmodified tubulin and a very strong, saturated signal after the tubulin was treated with both TTLL8 and TTLL10.  We also added an additional Figure S8 that shows that the tSA201 tubulin does not give a detectable signal for glutamylation. Please see also Figure 3 from Vemu et al., Methods Enzymology 2017 where we also published a Western blot from our TOG-purified tubulin using anti-glutamylation antibodies. 

      “(4) In their study, the authors have used polyglycylation of up to 10-13 residues. This brings me to my first point that in the case of Paramecium, the number was identified to be up to 34, which would mean that this enzyme has higher binding or catalytic activity. I would like to know the authors' perspective on this, as to what could potentially determine the difference in the activities of TTLL10 across species.”

      The Xenopus TTLL10 enzyme can add more glycines than the 10-13 range that we show here if the enzyme is incubated for longer periods. The fact that glycine numbers as high as 34 were detected in Paramecium does not necessarily mean that the Paramecium enzyme is more active since there is no equivalent data to compare it with from Xenopus. The only way to address potential species differences in enzyme specific activity is to purify enzymes from different species and compare their activity side-by-side.  

      (5) How was the completion of the reaction of monoglycylation and polyglycylation determined? If the enzymes were left for more than 20 minutes, did TTLL8/ TTLL10 add more glycines? What is the reason for using less tubulin (1:20 enzyme:tubulin molar ratio) for monoglycylation by TTLL8, and more tubulin (1:50 enzyme:tubulin molar ratio) for polyglycylation by TTLL10?

      Yes, if the enzymes were incubated longer, they added more glycines. The extent of glycylation was determined from the LC-MS and the incubation time was varied to obtain samples with fewer or more glycines.   The lower ratio used for TTLL10 is because of the higher specific activity of that enzyme compared to TTLL8.  

      (6) Figure S2 A, b2 ion is not indicated in the peptide sequence, while it is shown in the m/z graph.

      We thank the reviewer for the careful reading. We have corrected this in our MS/MS spectrum. 

      Reviewer #2 (Public review):

      “In their manuscript, Cummings et al. focus on the enzymatic activities of TTLL3, TTLL8, and TTLL10, which catalyze the glycylation of tubulin, a crucial posttranslational modification for cilia maintenance and motility. The experiments are beautifully performed, with meticulous attention to detail and the inclusion of appropriate controls, ensuring the reliability of the findings. The authors utilized in vitro reconstitution to demonstrate that TTLL8 functions exclusively as a glycyl initiase, adding monoglycines at multiple positions on both α- and β-tubulin tails. In contrast, TTLL10 acts solely as a tubulin glycyl elongase, extending existing glycine chains. A notable finding is the differential substrate recognition between TTLL glycylases and TTLL glutamylases, highlighting a broader substrate promiscuity in glycylases compared to the more selective glutamylases. This observation aligns with the greater diversification observed among glutamylases. The study reveals a hierarchical mechanism of enzyme recruitment to microtubules, where TTLL10 binding necessitates prior monoglycylation by TTLL8. This binding is progressively inhibited by increasing polyglycine chain length, suggesting a self-regulatory mechanism for polyglycine chain length control. Furthermore, TTLL10 recruitment is enhanced by TTLL6mediated polyglutamylation, illustrating a complex interplay between different tubulin modifications. In addition, they uncover that polyglutamylation stimulates TTLL10 recruitment without necessarily increasing glycylation on the same tubulin dimer, due to the potential for TTLLs to interact with neighboring tubulin dimers. This mechanism could lead to an enrichment of glycylation on the same microtubule, contributing to the complexity of the tubulin code. The article also addresses a significant challenge in the field: the difficulty of generating microtubules with controlled posttranslational modifications for in vitro studies. By identifying the specific modification sites and the interplay between TTLL activities, the authors provide a valuable tool for creating differentially glycylated microtubules. This advancement will facilitate further studies on the effects of glycylation on microtubule-associated proteins and the broader implications of the tubulin code. In summary, this study substantially contributes to our knowledge of posttranslational enzymes and their regulation, offering new insights into the biochemical mechanisms underlying microtubule modifications. The rigorous experimental approach and the novel findings presented make this a pivotal addition to the field of cellular and molecular biology.”

      We thank the reviewer for their support of our work.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Reviewer #1 (Recommendations For The Authors):

      Minor:

      (1) In Figure 2, only the right or left selective neurons are presented for the comparison, it would be helpful to also compare these with the neurons that are not selective for any of the sides and maybe include them in the supplemental materials

      We have included all non-selective neurons in Figure 2D and supplemental Figure 2B. Their differences in firing rate between left and right sides are quantified by their selective indices (SIs). 

      (2) The authors should provide controls of speed during NMDA infusion and vehicle.

      We have quantified and compared the duration of running laps, which is equivalent to speed.

      (3) In Figure 1d, the trend shows that even during NMDA infusion, the animals learn as shown by a higher proportion of correct trials in the 3rd compared to the 1st trial

      We thank the reviewer for pointing that out. We noticed that NMDAlesioned ACC animal showed a trend of improved performance in the track, and we believe this is due to re-learning of the task, which we point out in the main text. However, we emphasize that, compared to the Vehicle control, the overall performance of NMDA-lesioned animals was significantly impaired.

      (4) Clarify the implications of the NMDA experiments, as it is not straightforward to interpret that an interplay between ACC-CA1 is involved in this task as per this experiment.

      Rather than stating the involvement of ACC-CA1 interplay, we use the results of NMDA lesion experiment to demonstrate that ACC is also required, besides CA1, for the task.

      (5) In Figure 4b, there seems to be a lag between CA1 and ACC correlations; the authors could provide a quantification of this temporal delay between CA1 and ACC.

      Figure 4B shows the cross-correlation between one example ACC cell and its associated CA1 ensembles on the left and opposite sides. There was a broad peak around time lag 0. Our further investigation did not identify a significant, systemic delay for all ACC cells, which led us to quantify the correlation at time lag 0 in Figure 4C and D.

      (6) The example correlation provided in 5c for the opposite, doesn't seem representative of the population trend as shown in 5d, since both the Same and the Opposite for the demo show a positive trend. It would be best to choose an example that represents the population better.

      Following the reviewer’s suggestion, we have replaced the original plot with another ACC cell in Figure 5C.

      (7) Almost the same can be applied to Figure 6.

      Following the reviewer’s suggestion, we have replaced the original plot with another ACC cell in Figure 6E.

      (8) The results in Figure 7 are convincing, in my opinion, as they show that the trend is lost for the opposite side (contrary to the coactivation shown in Figures 5 and 6 that showed the same trends for the same and opposite during Demo). Do the authors have any interpretation of this? Is it due to co-activity reflecting other task-relevant features different than the spatial trajectory being observed?

      The correlation on the opposite side between CA1 and ACC shown in Figure 5C-D and Figure 6E-F is likely due to a general interaction between CA1 activities around SWRs with prefrontal cortical areas including ACC, as shown in previous studies (Jadhav et al., 2016; Remondes and Wilson, 2015).  We would like to point out that this correlation only quantifies the coactivation between CA1 ensemble firing rates and individual ACC cells’ firing rate. This raw correlation does not consider the content of spikes generated by CA1 ensembles, neglecting the sequential firing patterns of CA1 cells. The replay analysis in Fig. 7 examines the order of spikes generated by individual CA1 cells. The result in Fig. 7 shows that the sequential activation of CA1 place cells more accurately reflects the distinction between the same- and opposite-side trajectories. We consider Fig. 7 is more refined analysis than Figs. 5 and 6.

      (9) For all the figures regarding SWR activities, the authors should provide average PSTH for CA1 as well as ACC, perhaps also examples of neurons that are selectively active during one side or the opposite side runs.

      Following the reviewer’s suggestion, we have added data to show PSTH for CA1 and ACC cells surrounding SWR peaks (Figure S5E, F). 

      Reviewer #2 (Recommendations For The Authors):

      Below are additional notes for improvements.

      (1) Figure 1C. Unclear what Time 0 indicates.

      We specify it (OB's poke time) in the figure legend. 

      (2) Figure 2C. Unclear what the numbers above datapoints mean.

      Those numbers are selection indices (SIs), as specified in the legend. 

      (3) Figure 5: Line 374-375. Given the repetitive nature of the task, it is unclear whether SWRs are encoding upcoming or past spatial trajectories or whether they are encoding trajectories at all. The authors would need to show that SWRs-ACC communication is predictive of task outcome to claim it is specifically necessary for future outcomes rather than consolidating past trajectories.

      We agree with the reviewer and have made changes to reflect that the ACC-CA1 correlation in Fig.5 is specific to the same side of their selectivity, not exactly to future trajectories. Regarding the repetitive nature of the task (same-side rule), we have specifically addressed the advantage and limitation of this task design in the discussion. Regarding the observer's own past vs. future trajectories, our past publication (Mou et al., 2022) shows that the CA1 replay in SWRs more likely encode the correct, future trajectories. 

      (4) Figure 7. It appears that the correlation was conducted between ACC activity and CA1 replays recorded at distinct time windows (delay period vs. water consumption). It is unclear how ACC activity could influence CA1 replays when they occur hundreds of milliseconds apart or even longer.

      We thank the reviewer for raising this important question. We have shown that the higher same-side ACC activity during observation continues during water consumption. However, our added data in Fig.S5E show that this enhancement did not occur precisely within SWRs. We thus propose a possibility that the overall enhanced activity of same-side ACC cells during water consumption provides an overall, background excitation boost to same-side CA1 cells to enhance their replay within SWRs. We have revised the discussion section to present this model. 

      (5) Abstract: lines 24-25 Discussion: lines 475-476 Based on the data there is no certainty whether ACC biases or coordinates CA1 replays. The data simply shows that they are correlated with one another.

      We have modified those sentences to clarify the non-causal nature of the interaction.

      Reviewer #3 (Recommendations For The Authors):

      Please see below for the list of minor corrections and suggestions:

      (1) Line 136-143: On the data shown in Figure 1D, I recommend using two-way mixed ANOVA with sessions as a within-subjects factor and groups as a between-subjects factor.

      We thank the reviewer for this point. We indeed use two-way ANOVA for those comparisons. We have specified out in the text.

      (2) Line 219-228: I recommend expanding the explanation of two control conditions here. It was written in the method section, but the readers would appreciate the gist of these conditions in the result section. In particular, it was unclear how box SI was calculated in the Empty condition. Also, the plots of poke rates in the control conditions will be useful to show that rats did not learn the correct choice from observation in these control conditions.

      We have added more explanation of the two control conditions in the text. The quantifications of poke rates for Demo and two control conditions (Object, Empty) are provided in our previous publication (Mou et al., 2022).

      (3) Line 610: Please specify the number of three types of sessions each rat underwent and the order of these session types.

      We revise the texts in the Method section and provide the numbers.

      (4) In Figure 2c legend, please specify what the number (e.g., -0.41) indicates.

      Those numbers are selection indices (SIs), as specified in the legend.

    1. Reviewer #2 (Public review):

      Summary:

      This paper presents a thoughtful and well-motivated strategy to address a major challenge in TCR-epitope binding prediction: data imbalance, particularly the scarcity of positive (binding) TCR, peptide pairs. The authors introduce a two-step pipeline combining data balancing, via undersampling and generative augmentation, and a supervised CNN-based classifier. Notably, the use of Restricted Boltzmann Machines (RBMs) and BERT-style transformer models to generate synthetic CDR3β sequences is shown to improve model performance. The proposed method is applied to both peptide-specific and pan-specific settings, yielding notable performance improvements, especially for in-distribution peptides. Generative augmentation also leads to measurable gains for out-of-distribution epitopes, particularly those with high sequence similarity to the training set.

      Strengths:

      (1) The authors tackle the well-known but under-addressed issue of class imbalance in TCR-epitope binding data, where negatives vastly outnumber positive (binding) pairs. This imbalance undermines classifier reliability and generalization.

      (2) The model is tested on both in-distribution (seen epitopes) and out-of-distribution (unseen epitopes) scenarios. Including a synthetic lattice protein benchmark allows the authors to dissect generalization behavior in a controlled environment.

      (3) The paper shows a measurable benefit of generative. For example, AUC improvements of up to +0.11 are observed for peptides closely related to those seen during training, demonstrating the method's practical impact.

      (4) A direct comparison between RBM- and Transformer-based sequence generators adds value, offering the community guidance on trade-offs between different generative architectures in TCR modeling applications.

      Weaknesses:

      (1) Generalization degrades with epitope dissimilarity

      The performance drops substantially as the test epitope becomes more dissimilar to the training set. This is expected, but it highlights an essential limitation of the generative models: they help only when the test epitope is similar to one already seen. Table 1 shows that the performance gain from generative augmentation decreases as the test epitope becomes more dissimilar to the training epitopes. For epitopes with a Levenshtein distance of 1 from the training set, the average AUC improvement is approximately +0.11. This gain drops to around +0.06 for epitopes at distance 2. It becomes minimal for those at distance 4, indicating an explicit limitation in the model's ability to generalize to more distant epitopes. The authors should quantify more explicitly how far the model can generalize effectively. What is the performance degradation threshold as a function of Levenshtein distance?

      (2) What is the minimal number of positive samples needed for data augmentation to help?

      The approach has an intrinsic catch-22: generative models require data to learn the underlying distribution and cannot be applied to epitopes with insufficient data. As a result, the method is unlikely to be effective for completely new epitopes. Could the authors quantify the minimum number of real binders needed for effective generative augmentation? This would be particularly relevant for zero-shot or few-shot prediction scenarios, where only 0-10 positive samples are available. Such experiments would help clarify the practical limits of the proposed strategy.

      (3) Lack of end-to-end evaluation on unseen epitopes as inputs

      The authors frame peptide-specific models as classification over a few known epitopes, a closed-set formulation. While this is useful for evaluating generation effects, it's not representative of the more practical open-set task of predicting binding to truly novel epitopes. A stronger test would include models that take peptides as input (e.g., pan-specific, peptide-conditioned classifiers), including unseen epitopes at test time. Could the authors attempt an evaluation on benchmarks like IMMREP25 or other datasets where test epitopes are excluded from training?

      (4) Focus on β-chain limits generalizability

      The current pipeline is trained exclusively on CDR3β sequences. However, the field is increasingly moving toward single-cell sequencing, which provides paired α/β TCR chain data. Understanding how the proposed approach performs when both chains are available would be valuable. Could the authors evaluate the performance gains on paired α/β information, even in a small subset of single-cell data?

      (5) Synthetic lattice proteins (LPs) have limited biological fidelity

      While the LP-based benchmark presented in Figure 5 is a clever and controlled tool for probing model generalization, it remains conceptually and biophysically distant from real TCR-peptide interactions. Its utility as a toy model is valid, but its limitations should be more explicitly acknowledged:

      a) Over-simplified binding landscape: The LP system is designed for tractability, with a simplified sequence-structure mapping and fixed lattice constraints. As shown in Figure 5c, the LP binding landscape is linearly separable, in stark contrast to the complex and often degenerate nature of real TCR-epitope interactions, where multiple structurally distinct TCRs can bind the same peptide and vice versa.

      b) Absence of immunological context: The LP model abstracts away key biological factors such as MHC restriction, α/β chain pairing, peptide presentation, and structural constraints of the TCR-pMHC complex. These are essential for understanding binding specificity in actual immune repertoires.

      c) Overestimation of generalization: While performance drops on more distant LP structures, even these are structurally and statistically more similar to the training data than truly novel biological epitopes. Thus, the LP benchmark likely underestimates the true difficulty of out-of-distribution generalization in real-world TCR prediction tasks.

      d) Simplified biophysics: The LP simulations rely on coarse-grained energy models and empirical potentials that do not capture conformational dynamics, side-chain flexibility, or realistic binding energetics of TCR-peptide interfaces.

      In summary, while the LP benchmark helps isolate specific generalization behaviors and for sanity-checking model performance under controlled perturbations, its biological relevance is limited. The authors should explicitly frame these assumptions and limitations to prevent overinterpreting results from this synthetic system.

    2. Author response:

      We would like to thank editors and reviewers for their time spent on our work, fair assessments and constructive criticism. We plan to address their concerns in the future revision as follows, detailed by topic.

      (1) Limitations of focusing on CDR3β only

      In its current state, our work tested the proposed pipeline of data augmentation for binding prediction on benchmark datasets limited to peptide+CDR3β sequence pairs only. As pointed out by all the reviewers, the TCR-peptide interaction is more complex and involves also other regions of the receptor (such as the CDR3α chain) and the MHC presenting the peptide as well. To investigate how the inclusion of additional information impacts results, we plan to apply our pipeline in a setting where the generative protocol is extended to generate paired α and β. The supervised classifier will then receive a concatenation of α+β chains as inputs. We will compare the performance of this classifier with the one using β chains only, and add this analysis to the revised manuscript.

      (1) Validation of generated sequences and interpretation of the features learned by the generative model

      The reliability of the generative model in augmenting the training set with biologically sensible sequences is a crucial assumption of our approach, and we agree with the reviewers raising this as a main concern. Before stating our strategy to improve the soundness of the method, let us first point out a few aspects already considered in the present manuscript:

      • The test set of the classifier is always composed of real sequences: in this way, an increase in performance due to data augmentation cannot be due to overfitting to synthetic, possibly unrealistic, sequences.

      • The generative protocol is initialized from real sequences, and used to generate sequences not too far from them. In this respect, it could be taken as a way to “regularize” the simplest strategy of data augmentation, random oversampling (taking multiple copies of sequences at random to rebalance the data). This procedure avoids generating “wildly hallucinated” sequences with unreliable models. We will better quantify this statement (see below).

      • The training protocol is tailored to push the generative model towards learning binding features between peptide and CDR3β sequences (and not merely fitting their local statistics separately). For example, in the pan-specific setting, during training of the generative model on peptide+CDR3β sequences, the masked language modeling task is modified to force the model to recover the missing amino acid using only the other sequence context.

      We will better stress these points in the revised manuscript. To further validate the generative protocol in the future revision, we will carry out additional sanity checks on the generated data to confirm that the synthetic sequences remain biologically plausible and comparable to real ones.

      (1) Assessment of the performance of the pan-specific protocol for out-of-distribution data:

      To better clarify how the degradation in performance of a classifier tested on out-of-distribution data is impacted by the dissimilarity between test and training data distribution, we will improve the synthetic analysis currently reported in Table 1, adding confidence intervals for accuracy, quantifying thresholds on the distance for the method to work, providing t-SNE embeddings of in- and out-of distribution data.

      (2) Quantification of the threshold for the number of examples per class in order to train the generative model and obtain a performance increase

      In the paper, we adopted an operative common-sense threshold of at least 100 sequences per class in order to apply our data augmentation pipeline. We will quantify this effect testing this threshold in the revised manuscript, in order to (i) emphasize the limits of this two-step generative protocol in the low-data regime and to (ii) assess if the generative model falls back to a random oversampling strategy (due to strong overfitting) when few data are available for training.

      (3) Motivation for the use of RBMs:

      While RBMs have known limitations, their use in our pipeline (together with the more modern TCR-BERT, that we also test) is mainly motivated by the fact that they provide measurable increases in performance with data augmentation despite their simple 2-layer architecture. We stress that simpler generative (profile) models are unable to show this increase, see Appendix 3. In this respect, the RBM provides a minimal generative model allowing us to augment data successfully, and a lower bound to the increase of performance with respect to more complex architectures trained on more data. We will report this point of view in the text.

      (4) Clarification on the role of lattice proteins as an oversimplified toy model for protein interaction

      We agree with the points raised by Reviewer #2 on the limitations of lattice proteins as a model for protein interaction. Indeed, we used it merely as a toy model for phenomenology, a strategy whose validity has been fairly acknowledged by the reviewer. We will report in the main text all the drastic simplifications and reasons why the reader should take the comparison to real data with great care.

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      Reply to the reviewers

      We thank the Reviewers for their kind and constructive comments. We are happy to read that the reviewers found our study methodologically robust and comprehensive in addressing the metabolic heterogeneity of endothelial cells.

      Reviewer 1, comment 1: Image quality in sprouting assays - The images presented for the sprouting assays (e.g., Figure 4) are of suboptimal resolution and quality, making it difficult to evaluate the effects of the various compounds on EC behavior. Even under control conditions, clear sprout-like structures are not readily discernible. Improved image resolution-preferably through high-quality bright-field microscopy-and the inclusion of immunofluorescence images of labeled endothelial spheroids are recommended to enhance interpretability.

      Response: We appreciate the reviewer’s concern and have revisited the sprouting assay images. Our approach is consistent with established methods in the field (Heiss et al., FASEB J, 2015), where brightfield imaging is routinely used for quantification without additional immunostaining. Hence, we believe that the brightfield images are of sufficient resolution to allow reproducible quantification of normalized total sprout length. All experiments were performed under identical imaging and analysis protocols, and thus we are confident that the quantification reflects true biological differences. We cite the reference in the revised manuscript and clarify it as well in the Methods section.

      Reviewer 1, comment 2: Validation of the quiescence model - The current approach to induce quiescence should be further substantiated. Beyond proliferation markers, additional hallmarks of quiescent cells-such as epigenetic signatures, protein quality control mechanisms, and translational activity-should be assessed to confirm that the EC subtypes achieve a bona fide resting state.

      Response: We acknowledge the value of proper phenotyping of quiescent cells. However, most studies involving quiescent (endothelial) cells rely on EdU incorporation or similar proliferation markers to confirm entry into a non-proliferative state (Kalucka et al., Cell Metabolism, 2018; Coloff et al., Cell Metabolism, 2016). In our study, we have used EdU staining and FACS analysis to establish cell cycle arrest. Moreover, we find clear proteomic patterns that support the case of a quiescent state. We have also demonstrated the reversibility of quiescence (see Suppl. Fig. 1c) via reseeding and proliferation recovery of all EC types, which is a defining functional hallmark of true quiescence. Together, the EdU, proteomic and reseeding/proliferation data provide strong evidence that our EC subtypes reach a physiologically quiescent, non-senescent state.

      Reviewer 1, comment 3: Reversibility of quiescence - It is important to demonstrate that the EC subtypes investigated can re-enter the cell cycle following release from contact inhibition. Without such evidence, the possibility remains that some of the observed metabolic features reflect a transition to senescence rather than reversible quiescence.

      Response: This is an excellent suggestion. We have included new data that shows that ECs regain proliferative capacity upon reseeding of quiescent ECs at lower confluency (Suppl. Fig. 1c). The results support the interpretation that the observed metabolic features reflect reversible quiescence rather than senescence.

      Reviewer 1, comment 4: Assessment of cell viability - While EC proliferation, migration, and sprouting were examined to infer functional roles of metabolic adaptations, analyses of cell viability and death are also necessary to evaluate potential homeostatic or survival-related functions of the observed metabolic changes.

      Response: We appreciate the Reviewer’s concern about cell viability in our experimental setup, and we agree that viability assessment is important. Using trypan blue staining and automated cell counting, we observed that >85% of ECs remained viable from day 1 through day 10 of the quiescence model and included these results in the manuscript (Suppl. Fig. 1b).

      Reviewer 1, comment 5: Validation of pharmacological findings - The pharmacological inhibition experiments are informative and constitute a central part of the study. However, given the possibility of off-target effects, key conclusions should be corroborated using alternative loss-of-function approaches, such as RNA interference (e.g., shRNA or siRNA).

      Response: We recognize the possibility of side effects for pharmacological inhibitors, but the inhibitors, including the ones that show the strongest different effects in HUVECs and iLECs (succinyl acetone and R162) in our study are well-established, selective inhibitors of glutamate dehydrogenase (Wang et al., Pharmacological Research, 2022) and δ-aminolevulinic acid dehydratase (Nauli et al., J Clin. Biochem. Nutr., 2023), respectively, and have not been reported to exhibit significant off-target activity in endothelial cells. Furthermore, the aim of our study was not to define specific mechanistic pathways, but to highlight phenotype-specific metabolic vulnerabilities in distinct endothelial states. Performing knockdown experiments would go beyond the scope and focus of this manuscript and introduce their own limitations, including off-target effects and, most importantly, timing mismatches relative to our long-term assays (e.g., sprouting assays assessed at day 3 versus transient RNAi effects lasting for only 1-2 days). We hope the Reviewer agrees that our current approach sufficiently supports the study’s conclusions.

      __Reviewer 2, comment 1: __it was not clear whether the authors worked with single donor endothelial cells or with mixed donors. This should be clarified as it is important for the statistical analyses (single donor based EC research typically uses n=4, while for the mixed donor, an n=3 is sufficient).

      Response: We thank Rreviewer 2 for highlighting that we did not include this information in the Methods section and we did so in the revised manuscript. HDBECs, HDLECs and iLECs are from single donors, HUVECs are from mixed donors. We acknowledge the reviewer’s concern about the power of statistical analyses, but we think that n=3 is sufficient with proper correction for statistical tests. Furthermore, previous in vitro studies with ECs are done with single donor cells and in biological triplicates (Wong et al., 2017; Kalucka et al., 2018; Simões-Faria et al., 2025 and more). Moreover, for sprouting assays, we have n > 3 for most conditions.

      Reviewer 2, comment 2: I would like to see a sentence on the importance of shear stress in EC behavior (metabolism) in the introduction. It was recently shown that the in vivo situation of ECs encountering wall shear stress (Faria et al, PMID: 39832080) affects the metabolic behavior switching to glutamine metabolism. This aligns with the research of the authors as well.

      Response: We thank Reviewer 2 for drawing our attention to this relevant and interesting study. We mention the study in the introduction and the discussion.

      Reviewer 2, comment 3: suggestion for the authors: it could be useful if a figure is introduced to show the "physiological" location of the 4 EC used and that a rationale is provided for this.

      Response: We have included this in Supplementary Figure 1 and in the text.

      Reviewer 2, comment 4: figures are of low quality, I found it very difficult to see the spheroid/sprouting images. This should be addressed in the final version prior publication.

      Response: The new version has higher quality sprouting images in figure 4 and 5. The images can also be found in high quality on BioStudies (Accession: S-BSST1716).

      Reviewer 2, comment 5: Fig 2 c: I'm not sure if this panel is very relevant, when looking into detail, opposite pathways are present (glycolysis - gluconeogenesis). As well, I'm not sure if galactose metabolism is truly relevant, unless the author managed to measure distinct hexose and hexose-phosphates? Given the flow injection analysis setup, I doubt this. Would suggest to move this to supplement or to simply leave it out.

      Response: The Reviewer is correct; the employed analytics cannot distinguish different hexoses and hexose-phosphates. We have moved figure 2c to supplementary figure 4c.

      Reviewer 2, comment 6: Fig 3 b: was there any statistics performed on these data to compare the different setups?

      Response: We performed statistical analyses on this data and included it in the figures and figure legends.

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      Referee #2

      Evidence, reproducibility and clarity

      By employing a proteomics and metabolomics approach the authors clarified the molecular landscape of 4 major EC types in quiescent and proliferating conditions. The study is extensive and adds novelty to the EC research

      Major comments:

      • it was not clear whether the authors worked with single donor endothelial cells or with mixed donors. This should be clarified as it is important for the statistical analyses (single donor based EC research typically uses n=4, while for the mixed donor, an n=3 is sufficient).
      • I would like to see a sentence on the importance of shear stress in EC behavior (metabolism) in the introduction. It was recently shown that the in vivo situation of ECs encountering wall shear stress (Faria et al, PMID: 39832080) affects the metabolic behavior switching to glutamine metabolism. This aligns with the research of the authors as well.
      • suggestion for the authors: it could be useful if a figure is introduced to show the "physiological" location of the 4 EC used and that a rationale is provided for this.
      • figures are of low quality, I found it very difficult to see the spheroid/sprouting images. This should be addressed in the final version prior publication.
      • Fig 2 c: I'm not sure if this panel is very relevant, when looking into detail, opposite pathways are present (glycolysis - gluconeogenesis). As well, I'm not sure if galactose metabolism is truly relevant, unless the author managed to measure distinct hexose and hexose-phosphates? Given the flow injection analysis setup, I doubt this. Would suggest to move this to supplement or to simply leave it out.
      • Fig 3 b: was there any statistics performed on these data to compare the different setups?

      Significance

      the study adds insights to the ongoing research on EC molecular behavior.

      using different types of ECs in both quiescent and proliferating mode, as well as the validation of pathways by introducing inhibitors combined with the sprouting assays is an asset.

      I would like to see stated the biological complexity of EC, it was recently shown that shear stress plays an important role in EC metabolism.

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      Referee #1

      Evidence, reproducibility and clarity

      Summary: 
 The study by Durot and colleagues explores the metabolic heterogeneity of endothelial cells (ECs) across distinct subtypes (blood vs. lymphatic) and growth states (proliferating vs. quiescent). Through integrated proteomic and metabolomic analyses, the authors demonstrate that quiescent ECs are not metabolically inactive but instead undergo subtype-specific metabolic reprogramming. Functional perturbation of key metabolic pathways using chemical inhibitors results in differential phenotypic responses in blood versus lymphatic ECs. Collectively, the findings underscore a critical, context-dependent role of metabolism in maintaining EC function and highlight metabolic specialization as a fundamental feature of endothelial diversity.

      General Comments: 
 This manuscript presents a comprehensive and methodologically robust investigation into the metabolic diversity of cultured ECs. By combining proteomic and metabolomic approaches, the authors provide novel insights into the distinct metabolic profiles of blood and lymphatic ECs, and how these profiles shift as ECs transition from a proliferative to a quiescent state. The observation that quiescent ECs exhibit active metabolic reprogramming, rather than simply entering a dormant state, is particularly compelling and challenges existing models of cellular quiescence.

      The work is timely, well-written and addresses a significant gap in our understanding of endothelial metabolism. The integration of large-scale omics data with functional perturbation experiments strengthens the overall conclusions and enhances the impact of the study.

      Nevertheless, while the data are largely convincing, certain experimental aspects-particularly those related to the in vitro sprouting assays-require further validation to solidify the mechanistic interpretations. Additionally, some findings would benefit from further validation using alternative approaches (e.g., chemical perturbation studies).

      Specific Comments:

      1. Image quality in sprouting assays - The images presented for the sprouting assays (e.g., Figure 4) are of suboptimal resolution and quality, making it difficult to evaluate the effects of the various compounds on EC behavior. Even under control conditions, clear sprout-like structures are not readily discernible. Improved image resolution-preferably through high-quality bright-field microscopy-and the inclusion of immunofluorescence images of labeled endothelial spheroids are recommended to enhance interpretability.
      2. Validation of the quiescence model - The current approach to induce quiescence should be further substantiated. Beyond proliferation markers, additional hallmarks of quiescent cells-such as epigenetic signatures, protein quality control mechanisms, and translational activity-should be assessed to confirm that the EC subtypes achieve a bona fide resting state.
      3. Reversibility of quiescence - It is important to demonstrate that the EC subtypes investigated can re-enter the cell cycle following release from contact inhibition. Without such evidence, the possibility remains that some of the observed metabolic features reflect a transition to senescence rather than reversible quiescence.
      4. Assessment of cell viability - While EC proliferation, migration, and sprouting were examined to infer functional roles of metabolic adaptations, analyses of cell viability and death are also necessary to evaluate potential homeostatic or survival-related functions of the observed metabolic changes.
      5. Validation of pharmacological findings - The pharmacological inhibition experiments are informative and constitute a central part of the study. However, given the possibility of off-target effects, key conclusions should be corroborated using alternative loss-of-function approaches, such as RNA interference (e.g., shRNA or siRNA).

      Significance

      In summary, this manuscript makes a substantial contribution to the field and is likely to stimulate further research into endothelial metabolic regulation. With additional experimental validation, the study has the potential to serve as a reference in both vascular and metabolic research.

    1. Résumé de la vidéo [00:00:00][^1^][1] - [00:35:42][^2^][2] :

      Cette vidéo est une conférence de Jean-Philippe Lachaux, directeur de recherche à l'INSERM et spécialiste du système attentionnel, sur l'attention et la concentration à l'école. Il présente les principes de base de l'attention, ses enjeux pour l'apprentissage, et les moyens de la développer chez les élèves. Il propose également des exemples d'activités et de programmes d'éducation de l'attention, comme Atol et Adolesc.

      Points forts : + [00:01:13][^3^][3] L'attention est sélective et limitée * Elle permet de choisir ce qui est important parmi les informations disponibles * Elle nécessite d'identifier la cible de son attention et de s'y connecter activement * Elle peut être perturbée par des distracteurs internes ou externes + [00:10:10][^4^][4] La concentration est différente de l'attention * Elle implique une intention claire et une seule à la fois * Elle demande de coupler la perception et l'action * Elle peut être facilitée par des stratégies mentales adaptées + [00:21:00][^5^][5] L'attention s'apprend et se développe * Elle peut être entraînée par des exercices spécifiques * Elle peut être renforcée par des habitudes de vie saines * Elle peut être stimulée par des situations pédagogiques variées et motivantes + [00:29:00][^6^][6] L'attention est au cœur de l'apprentissage * Elle permet de se connecter à son objet d'étude et d'en extraire le sens * Elle favorise la mémorisation et la compréhension * Elle contribue à la motivation et à la confiance en soi

    1. Résumé de la vidéo [00:00:00][^1^][1] - [00:07:06][^2^][2]:

      Cette vidéo explique comment améliorer l'apprentissage en utilisant des stratégies d'étude efficaces, en mettant l'accent sur la récupération en mémoire plutôt que sur la relecture passive.

      Points forts: + [00:00:00][^3^][3] Importance de la récupération en mémoire * Active les neurones * Renforce les connaissances + [00:01:22][^4^][4] Stratégies d'étude courantes * Lecture et relecture dominent * Peu utilisent la récupération en mémoire + [00:02:09][^5^][5] Inefficacité de la relecture * Stratégie la moins efficace * La récupération en mémoire est préférable + [00:04:00][^6^][6] Méthodes de récupération en mémoire * Poser des questions * Utiliser des fiches d'études * Refaire des problèmes + [00:05:29][^7^][7] Reformulation des contenus * Aide à la récupération en mémoire * Intégrer dans l'étude régulière

    1. Document de Synthèse : Effets d'Espacement et de Répétition dans l'Apprentissage

      Introduction

      Ce document de synthèse présente les principaux thèmes, idées et faits clés issus de la conférence "Effets d’espacement et de répétition".

      L'objectif est de définir l'apprentissage d'un point de vue édimétrique, d'explorer les effets liés à l'espacement et la répétition, et de proposer des applications concrètes pour optimiser l'enseignement.

      1. Définition Édimétrique de l'Apprentissage

      L'apprentissage est souvent mal évalué en milieu scolaire, où l'on se concentre davantage sur la performance que sur l'apprentissage lui-même.

      La psychométrie mesure des choses de manière rigoureuse, tandis que l'édimétrie, concept plus récent (première mention en français en 1988), est

      "l'étude quantitative des variables relatives aux apprentissages justement suscités par l'éducation."

      Pour observer minimalement un apprentissage d'un point de vue édimétrique, trois éléments sont nécessaires :

      • Une première observation.
      • Une activité positive visant l'apprentissage.
      • Une seconde observation.

      Cette nécessité d'une seconde observation implique que "la notion d’apprentissage est donc pratiquement indissociable de la notion de répétition."

      En effet, l'apprentissage n'est utile que si une situation identique ou équivalente se présente à nouveau dans le futur, ce qui constitue la motivation fondamentale de l'apprentissage.

      L'apprentissage peut être vu comme "une réaction adaptative à la répétition," permettant de s'adapter à son milieu.

      2. Les Effets Clés de l'Espacement et de la Répétition

      Plusieurs effets ont été identifiés par la recherche :

      2.1. Effet de l'Entraînement

      "Plus on s'entraîne, plus on réussit" et "plus on réussit rapidement."

      Cet effet est constaté dans diverses tâches, de l'apprentissage du piano à la lecture d'un nouvel alphabet ou la résolution de preuves en géométrie.

      La courbe de performance (temps pour effectuer une tâche) diminue avec l'entraînement, tandis que la courbe d'apprentissage (taux de réussite) augmente, prenant souvent une forme sigmoïdale avec des paliers aux extrémités (0% et 100%).

      2.2. Rétention (Courbe de l'Oubli)

      "Après un premier entraînement, plus le temps passe et moins on réussit."

      Cette observation, étudiée dès les années 1800, montre que la performance diminue avec le temps si l'apprentissage n'est pas réactivé.

      La forme exacte de cette courbe est toujours un sujet de recherche.

      2.3. Effet d'Espacement

      L'espacement des entraînements a un impact significatif :

      • Activation Cérébrale : Le cerveau est "plus activé lorsque les périodes sont espacées."

      Des recherches en neurosciences montrent que des entraînements massés (regroupés) peuvent entraîner une saturation de l'activité cérébrale, tandis que des entraînements espacés maintiennent une activité régulière et productive.

      • Mémoire à Long Terme : Des entraînements trop rapprochés sollicitent davantage la mémoire de travail (mémoire à court terme) plutôt que la mémoire à long terme, ce qui réduit l'efficacité de l'apprentissage durable.

      • Rôle du Sommeil : Le sommeil est un facteur important.

      Il peut "consolider l'apprentissage en réactivant les mêmes réseaux de neurones."

      Des expériences ont montré que des stimuli sonores pendant le sommeil peuvent renforcer l'apprentissage d'une tâche, et même sans stimuli, le simple fait de dormir entre deux périodes d'étude améliore la rétention à long terme.

      • Mécanismes Cellulaires et Moléculaires : Le renforcement des connexions synaptiques (l'apprentissage au niveau cellulaire) "demande du temps."

      Il existe différents mécanismes qui se déroulent sur des échelles de temps variées (secondes, minutes, heures, jours), ce qui limite l'efficacité d'entraînements trop rapprochés.

      2.4. Espacement Optimal

      "Il existe un espacement optimal" pour l'apprentissage, qui n'est "ni trop court ni trop long."

      Cet espacement optimal est souvent progressif, augmentant avec le temps. Les recherches montrent que l'utilisation de séquences d'espacement optimales peut "produire jusqu'à 150% plus d'apprentissage."

      L'espacement optimal dépend du délai jusqu'au test final, mais une proportion courante est de 10% à 30% du délai total (par exemple, pour un test dans 10 jours, un espacement d'un jour serait optimal ; pour un test dans 168 jours, 28 jours).

      Cet effet est généralisable à différents âges, sujets (vocabulaire, histoire, sciences, etc.) et types d'apprentissage (simples ou complexes), et même chez les animaux, suggérant un mécanisme fondamental du fonctionnement cérébral.

      2.5. Séquences Progressives d'Espacement

      "Les séquences progressives d'espacement semblent préférables."

      Plutôt que des intervalles réguliers, espacer progressivement les entraînements (par exemple, 1 jour, 4 jours, 9 jours, 16 jours – correspondant aux carrés des nombres naturels) permet non seulement de maintenir la performance au-dessus d'un seuil désiré à long terme, mais aussi de faire vivre aux apprenants "plus de succès" tout au long du chemin, renforçant leur sentiment de compétence.

      3. Applications Pédagogiques

      Les connaissances sur l'espacement et la répétition offrent des pistes concrètes pour améliorer les pratiques éducatives :

      3.1. Maintenir la Performance au-dessus d'un Seuil

      En espaçant progressivement les entraînements selon une règle (par exemple, les nombres carrés), il est possible de garantir que la performance des élèves reste au-dessus d'un seuil de réussite prédéfini sur une longue période.

      Cela permet d'introduire de nouveaux contenus sans sacrifier la rétention des précédents.

      3.2. Espacement Régulier pour Augmenter la Réussite

      Un espacement régulier peut être utilisé pour augmenter le taux de réussite jusqu'à un niveau désiré, avant de passer à un espacement progressif pour maintenir cette performance.

      3.3. Planification des Séquences Conceptuelles

      Il est crucial de "planifier les séquences conceptuelles" en tenant compte de l'espacement.

      Cela signifie organiser le contenu non pas en blocs isolés, mais en intégrant des rappels et des réactivations des notions antérieures.

      Rappels Réguliers : Intégrer des moments de révision au début des cours, en rappelant non seulement ce qui a été vu la veille, mais aussi des notions plus anciennes.

      Manuels Scolaires : Privilégier des manuels qui intègrent des retours sur les chapitres précédents plutôt que des chapitres distincts et isolés.

      Séquençage au niveau Ministériel : À terme, il serait bénéfique de "scénariser des séquences scolaires" au niveau systémique pour optimiser l'apprentissage.

      3.4. Éviter les Cours Intensifs

      Les cours intensifs produisent une bonne performance temporaire mais ne favorisent pas l'apprentissage à long terme. "Éviter les cours intensifs" est recommandé pour des objectifs d'apprentissage durable.

      3.5. Comparaison Massé vs. Espacé

      "L'idée de travailler avec un espacement qui est plus grand produit un effet plus grand à long terme."

      Un étudiant qui "bourre" son crâne juste avant un examen peut réussir, mais sa rétention à long terme sera bien inférieure à celle d'un étudiant qui a étudié la même quantité de matière de manière espacée.

      3.6. Stratégies Générales pour l'Apprentissage Durable

      Utiliser les Expériences des Élèves : Rendre l'apprentissage pertinent en se référant aux expériences passées des élèves, faisant en sorte que le nouveau contenu apparaisse comme la suite de quelque chose et non comme une nouveauté isolée.

      Contextes Pertinents et Authentiques : Choisir des contextes d'apprentissage qui ressemblent à ce que les élèves utiliseront ou ont déjà utilisé, renforçant la motivation intrinsèque et la perception de l'utilité future.

      Varier les Contextes et Situations : Exposer les élèves à des contextes variés élargit l'apprentissage et leur permet de mieux cerner les invariants conceptuels.

      Entremêler les Éléments (Interleaving) : Plutôt que d'étudier un sujet à la fois de manière exhaustive (par exemple, toute la géométrie, puis tout le numérique), entremêler les sujets permet d'augmenter l'espacement entre les révisions de chaque sujet et développe des "habiletés de plus haut niveau" en obligeant les élèves à choisir la bonne stratégie.

      Devoirs pour la Réactivation : Utiliser les devoirs comme une occasion de "réactiver les choses" déjà apprises, plutôt que d'introduire de nouvelles notions complexes. Le but est un "exercice qui est positif."

      Examens Cumulatifs : Bien que source de pression, les examens cumulatifs forcent la révision des notions antérieures, contribuant à un apprentissage plus durable.

      Nommer et Structurer : Donner des noms spécifiques aux catégories, regroupements ou étapes d'une méthode permet de créer un "pouvoir d'évocation" qui facilite la réactivation rapide et l'accès à l'information.

      Conclusion

      La conférence souligne l'importance capitale de la répétition et de l'espacement pour un apprentissage efficace et durable.

      En comprenant les mécanismes sous-jacents (activation cérébrale, consolidation synaptique, rôle du sommeil) et en appliquant des stratégies d'espacement progressif et d'entremêlement des contenus, les éducateurs peuvent significativement améliorer la rétention à long terme et la réussite de leurs élèves.

      La clé réside dans une planification consciente et systématique des interventions pédagogiques, transformant la répétition en un levier puissant d'apprentissage.

    2. Résumé de la vidéo [00:00:05][^1^][1] - [00:20:13][^2^][2]:

      La vidéo présente une conférence sur l'association pour la recherche en neuroéducation, mettant l'accent sur l'importance de l'espacement et de la répétition dans l'apprentissage. Elle explore les effets de l'espacement sur le cerveau et la rétention, et propose des applications pratiques pour améliorer l'efficacité de l'apprentissage.

      Points forts: + [00:00:17][^3^][3] Introduction de la conférence * Importance de petits changements + [00:01:27][^4^][4] Définition de l'apprentissage * Apprentissage comme adaptation + [00:03:09][^5^][5] Effets de l'entraînement * Plus d'entraînement, meilleure réussite + [00:11:00][^6^][6] Effets de la rétention * Diminution de la performance avec le temps + [00:17:19][^7^][7] Effet d'espacement sur le cerveau * Plus d'activité cérébrale avec espacement + [00:19:41][^8^][8] Applications pratiques * Recommandations pour l'espacement dans l'éducation Résumé de la vidéo [00:20:15][^1^][1] - [00:42:16][^2^][2]:

      La vidéo présente une conférence sur l'optimisation de l'apprentissage en neuroéducation. Elle aborde les effets de l'espacement des séances d'étude, le rôle du sommeil dans la consolidation de l'apprentissage, et propose des stratégies pour améliorer l'efficacité éducative.

      Points forts: + [00:20:15][^3^][3] L'espacement optimal * Importance de l'espacement * Impact sur l'activité cérébrale + [00:21:55][^4^][4] Le sommeil et l'apprentissage * Le sommeil consolide l'apprentissage * Réactivation des réseaux de neurones + [00:31:00][^5^][5] Mesure de l'espacement * Identification de l'espacement idéal * Influence sur la rétention à long terme + [00:36:54][^6^][6] Application en contexte éducatif * Adaptation des horaires scolaires * Optimisation de l'apprentissage Résumé de la vidéo [00:42:18][^1^][1] - [01:03:08][^2^][2]:

      La vidéo présente une conférence sur l'application des principes de neuroéducation dans l'enseignement, en mettant l'accent sur l'espacement progressif des séances d'apprentissage pour améliorer la rétention à long terme.

      Points forts: + [00:42:18][^3^][3] L'importance de l'espacement * L'espacement progressif favorise le succès en cours d'apprentissage + [00:45:00][^4^][4] Les séquences optimales * Des séquences d'apprentissage bien planifiées améliorent la rétention + [00:47:24][^5^][5] Maintenir la performance * Garder la performance au-dessus d'un seuil défini pour assurer le succès + [00:49:03][^6^][6] Planification des séquences * Utiliser des modèles pour espacer les séances et maintenir la rétention + [00:52:05][^7^][7] Éviter les cours intensifs * Les cours intensifs ne favorisent pas l'apprentissage à long terme + [00:57:00][^8^][8] Varier les contextes * Varier les contextes d'apprentissage pour créer des classes plus générales Résumé de la vidéo [01:03:11][^1^][1] - [01:05:26][^2^][2]:

      La partie 4 de la vidéo aborde l'utilisation des devoirs comme moyen d'apprentissage positif, en soulignant l'importance de nommer et de systématiser les méthodes d'enseignement pour faciliter la rétention et l'évocation des informations par les étudiants.

      Points forts: + [01:03:11][^3^][3] Les devoirs comme outil d'apprentissage * Vue comme une chance d'apprendre + [01:03:22][^4^][4] L'importance de la systématisation * Créer des catégories et les nommer * Utiliser ces noms systématiquement + [01:03:49][^5^][5] L'évocation par un seul mot * Évoque toute la situation * Aide les étudiants à se rappeler + [01:04:00][^6^][6] L'impact de la méthode d'enseignement * Les étudiants se souviennent des étapes * Ils entendent la voix de l'enseignant + [01:04:45][^7^][7] La révision progressive * Produit un effet à long terme * Favorise un apprentissage durable

    1. Résumé de la vidéo [00:00:00]¹[1] - [00:21:10]²[2]:

      La vidéo présente une discussion sur l'utilisation de la pensée visuelle pour améliorer l'autonomie des élèves et l'efficacité de l'enseignement. Jean-Luc Berthier et Sarah Jaoban expliquent comment la pensée visuelle peut être un outil puissant pour structurer les informations, résoudre des problèmes créatifs et renforcer la mémorisation chez les élèves.

      Points forts: + [00:00:15]³[3] Introduction à la pensée visuelle * Importance de la pensée visuelle dans l'éducation * Impact sur l'attention et la compréhension des élèves * Utilisation pour représenter des concepts complexes de manière simple + [00:07:00]⁴[4] Application pratique en classe * Gestion de l'hétérogénéité des élèves * Utilisation de la pensée visuelle pour différencier l'enseignement * Création d'un "buffet pédagogique" pour répondre aux besoins variés + [00:14:19]⁵[5] Avantages cognitifs de la pensée visuelle * Activation de la mémoire visuelle et de la compréhension spatiale * Amélioration de la rétention et de la compréhension des informations * Utilisation de métaphores visuelles pour ancrer les connaissances + [00:19:00]⁶[6] Démystification des idées fausses * Clarification des malentendus sur la pensée visuelle * Importance sérieuse de la pensée visuelle dans l'apprentissage * Distinction entre l'utilisation ludique et fonctionnelle de la pensée visuelle

      Source : conversation avec Bing, 17/03/2024 (1) undefined. https://www.education.gouv.fr/education-la-sexualite-en-milieu-scolaire-341103. (2) undefined. https://soseducation.org/docs/notes-etudes-entretiens-tribunes/education-a-la-sexualite-danger-ou-prevention-final.pdf. (3) undefined. https://www.planning-familial.org/sites/default/files/2023-11/LIVRE_BLANC_WEB.pdf. (4) undefined. https://www. Résumé de la vidéo [00:21:12][^1^][1] - [00:41:19][^2^][2]:

      Cette vidéo, présentée par Jean-Luc Berthier, explore comment construire l'autonomie des élèves en utilisant les sciences cognitives à travers la technique de la "Cogni'classe". Il discute de l'importance de la pensée visuelle dans l'éducation, en particulier comment les sketchnotes (notes visuelles) peuvent améliorer la mémorisation et la compréhension des élèves.

      Points forts: + [00:21:12][^3^][3] L'art de la sketchnote * Importance de la simplicité et de la fonctionnalité * Pas besoin d'être artiste pour créer des sketchnotes efficaces * L'objectif est d'organiser et de retenir l'information, pas de produire une œuvre d'art + [00:23:58][^4^][4] Les six usages quotidiens de la sketchnote * Préparation de la classe et des cours * Création de supports pédagogiques visuels * Animation de groupes et communication d'idées + [00:32:01][^5^][5] Les six dimensions à maîtriser * Maîtrise de la ligne, des formes, de l'espace, de la synthèse, du temps et du style * Importance de la rapidité et de la clarté pour l'application en classe + [00:39:55][^6^][6] Développer son propre style de sketchnote * Créer une charte graphique personnelle pour faciliter la création de sketchnotes * Utiliser des couleurs et des hiérarchies pour organiser l'information visuellement Résumé de la vidéo [00:41:21][^1^][1] - [00:49:54][^2^][2]: La partie 3 de la vidéo aborde la construction de l'autonomie des élèves à travers les sciences cognitives. Jean-Luc Berthier discute de l'importance de la cohérence dans les supports pédagogiques et de l'impact de la liberté pédagogique sur l'attention des élèves. Il souligne les défis rencontrés par les enseignants et présente l'Université du kif pédagogique, une plateforme conçue pour fournir des outils et un accompagnement aux professeurs souhaitant intégrer des méthodes d'enseignement innovantes et efficaces.

      Points forts: + [00:41:21][^3^][3] Cohérence des supports pédagogiques * Importance de la charte graphique uniforme * Facilitation de la compréhension des consignes * Impact sur l'attention des élèves, notamment ceux avec des troubles d'apprentissage + [00:43:58][^4^][4] L'Université du kif pédagogique * Créée pour accompagner les enseignants * Propose des outils pour une pédagogie différenciée * Offre un espace d'échange et de soutien entre collègues + [00:47:38][^5^][5] Atelier d'initiation à la pensée visuelle * Présentation d'un atelier pour créer des supports visuels * Jeux et défis pour développer son propre style * Techniques pour améliorer la mémorisation et l'entrée dans la tâche

    1. Résumé de la vidéo [00:00:00][^1^][1] - [00:04:28][^2^][2]:

      Cette vidéo présente des conseils sur l'apprentissage et l'éducation des enfants, en mettant l'accent sur l'importance de l'attention, de l'environnement enrichi, du sommeil et de la répétition. Elle souligne l'impact de la parole des parents et des activités stimulantes sur le développement cognitif des enfants.

      Points forts: + [00:00:00][^3^][3] L'importance de l'attention * Apprendre à se concentrer est crucial * Utiliser la tension exécutive pour sélectionner les pensées * La pratique quotidienne est essentielle + [00:01:00][^4^][4] Enrichir l'environnement cognitif * Le cerveau de l'enfant est une machine à apprendre * Utiliser un vocabulaire élevé et parler aux enfants * Fournir des jouets et des défis stimulants + [00:02:15][^5^][5] Encourager la curiosité naturelle * Les enfants explorent ce qu'ils peuvent apprendre * Éviter les sujets trop difficiles ou déjà connus * Le sommeil consolide les apprentissages + [00:03:08][^6^][6] Techniques d'enseignement efficaces * Captiver et canaliser l'attention des enfants * Alterner enseignement et mise à l'épreuve * Accepter les erreurs comme partie de l'apprentissage

    1. Voici les techniques d'étude efficaces expliquées dans la vidéo avec leurs timestamps :

      • Chunking [00:00:00][^1^][1] : Diviser les informations en morceaux gérables.
      • Mnémoniques [00:00:28][^2^][2] : Aides mémoire pour se souvenir des informations.
      • Visualisation [00:01:01][^3^][3] : Créer des images mentales de l'information étudiée.
      • Mind Mapping [00:01:27][^4^][4] : Organiser visuellement l'information autour d'une idée centrale.
      • Active Recall [00:02:00][^5^][5] : Se tester sur ce qu'on a appris.
      • Practice Tests [00:02:30][^6^][6] : Prendre des tests pratiques pour se préparer aux examens.
      • Pomodoro Technique [00:02:57][^7^][7] : Méthode de gestion du temps avec des sessions de 25 minutes.
      • SQ3R [00:03:23][^8^][8] : Méthode de lecture structurée (Survey, Question, Read, Recite, Review).
      • Dual Coding [00:03:55][^9^][9] : Combiner mots et visuels pour mieux apprendre.
      • Self-Explanation [00:04:18][^10^][10] : Expliquer le matériel à soi-même dans ses propres mots.
      • Retrieval Practice [00:04:40][^11^][11] : Pratique de récupération active de l'information.
      • Elaborative Interrogation [00:05:07][^12^][12] : Se poser des questions approfondies sur le matériel.
      • Spaced Repetition [00:05:32][^13^][13] : Étaler les sessions d'étude dans le temps.
      • Interleaved Practice [00:06:04][^14^][14] : Mélanger différents sujets pendant l'étude.
      • Feynman Technique [00:06:32][^15^][15] : Enseigner ce qu'on a appris à quelqu'un d'autre.

      Ces techniques sont conçues pour améliorer la rétention et la compréhension des informations étudiées.

      Timestamps : 00:00 - Chunking 00:20 - Mnemonics 01:01 - Visualization 01:28 - Mind Mapping 02:01 - Active Recall 02:29 - Practice Testing 02:54 - Pomodoro Technique 03:20 - SQ3R 03:53 - Dual Coding 04:17 - Self-Explanation 04:40 - Retrieval Practice 05:06 - Elaborative Interrogation 05:31 - Spaced Repetition 06:04 - Interleaved Practice 06:31 - Feynman Technique

    1. Résumé de la vidéo [00:00:01][^1^][1] - [00:22:42][^2^][2]:

      Cette vidéo présente des méthodes efficaces pour aider les enfants à apprendre et à se mettre au travail. Elle explique l'importance de se tester et d'espacer les révisions dans le temps pour une meilleure mémorisation et rétention à long terme.

      Points forts: + [00:00:30][^3^][3] Introduction au sujet * Importance d'apprendre à apprendre * Difficultés rencontrées par les enfants et les parents * Objectif de partager des conseils utiles + [00:01:36][^4^][4] Les méthodes d'apprentissage dans les programmes scolaires * Présence dans les programmes depuis 2016 * Manque de mise en pratique dans les salles de classe * Nécessité de transmettre ces compétences aux enseignants, parents et enfants + [00:03:24][^5^][5] Techniques d'apprentissage efficaces selon la recherche * Se tester et étaler les révisions dans le temps * Alternance des contenus et élaboration sur les apprentissages * Inefficacité de méthodes courantes comme surligner ou relire plusieurs fois + [00:07:44][^6^][6] Planification des révisions pour les examens * Comparaison entre apprentissage massé et distribué * Meilleure rétention à long terme avec des révisions espacées * Adaptation du calendrier de révision en fonction des objectifs d'apprentissage + [00:12:25][^7^][7] Messages clés pour les parents et les enfants * Importance de la récupération active en mémoire * Espacement des séances de révision pour un apprentissage à long terme * Utilisation de méthodes génératives et élaboratives pour renforcer la compréhension + [00:18:34][^8^][8] Aider les enfants à se mettre au travail * Mise en place d'une routine après l'école * Utilisation des récompenses plutôt que des punitions * Automatisation des comportements souhaités par la répétition et la récompense

      Résumé de la vidéo [00:19:00][^1^][1] - [00:22:42][^2^][2]:

      La vidéo aborde des stratégies pour aider les enfants à apprendre plus efficacement et à établir des routines pour les devoirs. Elle souligne l'importance de se tester et d'espacer les révisions dans le temps pour une meilleure mémorisation à long terme. Des méthodes comportementales pour encourager les bonnes habitudes chez les enfants sont également discutées.

      Points forts: + [00:19:00][^3^][3] Établir des routines pour les devoirs * Importance de commencer les devoirs juste après le goûter * Éviter de jouer avant les devoirs pour ne pas perturber la routine * Utiliser des récompenses pour encourager la bonne routine + [00:20:00][^4^][4] Utiliser des méthodes comportementales * Les punitions sont inefficaces et n'enseignent pas les bons comportements * Se concentrer sur les comportements souhaités et les récompenser * Renforcer positivement les bonnes habitudes jusqu'à ce qu'elles deviennent automatiques + [00:21:00][^5^][5] Transition vers l'autonomie * Passer progressivement de l'accompagnement à l'autonomie dans les devoirs * Rappeler à l'enfant la routine jusqu'à ce qu'il l'adopte de lui-même * L'objectif est d'automatiser le comportement souhaité + [00:22:00][^6^][6] Ressources supplémentaires * Présentation de livres et de blogs pour approfondir les techniques d'apprentissage * Suggestions de lectures pour mieux comprendre la gestion des comportements et l'apprentissage

    1. Briefing : Comprendre et Agir Face à l'Échec Scolaire : L'Approche par le "Point Nodal"

      Ce document de briefing synthétise les idées clés et les méthodologies présentées dans l'entretien "Échec scolaire : qu’est-ce qui empêche certains de réussir ?".

      Il met en lumière une approche solutionniste et systémique de la difficulté scolaire, rompant avec la focalisation exclusive sur les diagnostics de troubles et le rattrapage.

      1. Rejet de la Focalisation Exclusive sur la Cause et le Diagnostic

      L'expert, enseignant-chercheur et spécialiste de l'échec scolaire, met en garde contre la recherche prolongée des causes de la difficulté scolaire et une dépendance excessive aux diagnostics de troubles.

      • Approche solutionniste : Plutôt que de s'attarder sur les causes, l'accent doit être mis sur l'évaluation des besoins et des difficultés de l'élève pour "rapidement tendre vers des solutions possibles". La question "est-il crucial de trouver la cause de la difficulté scolaire ?" est jugée "plutôt faux" car elle peut immobiliser l'action.

      • Danger du sur-diagnostic : Il existe un "réel danger" à se reposer uniquement sur un diagnostic. Bien qu'il fournisse "un élément d'information", il ne doit pas être une fin en soi ni une "excuse". Le diagnostic, comme la dyslexie, peut même conduire l'élève à se "réfugier derrière l'étiquette", justifiant un abaissement des exigences et un décrochage.

      • Approche globale vs. "médicale" : L'expert prône une approche "un peu plus globale", critiquant la tendance à vouloir "identifier la maladie et puis avoir automatiquement le traitement".

      Les enseignants de classe régulière, n'étant pas des experts des troubles, ne devraient pas être exclus de l'aide aux élèves en difficulté.

      2. Le Principe d'Éducabilité et la Responsabilité de l'École

      Un principe fondamental est réaffirmé : "il y a toujours une solution pour aider un élève en difficulté, il faut chercher".

      Ce postulat, qualifié d' "absolument vrai, 100 % vrai", repose sur le "principe d'éducabilité".

      L'échec scolaire est l'échec de l'école : L'expert insiste sur la responsabilité de l'institution scolaire : "l'échec est scolaire donc c'est l'école qui crée de l'échec donc nécessairement l'école a des solutions par rapport à cet échec puisque c'est l'école qui crée de l'échec".

      Cette perspective vise à redonner du "pouvoir d'action" aux enseignants.

      Le rôle de la pédagogie : La plupart des situations (95 à 98%) relèvent du domaine pédagogique :

      "l'élève est en échec parce qu'il est en échec dans l'apprendre et et la question de l'apprendre c'est une question éminemment pédagogique".

      3. La Pyramide de Fox et la Nécessité d'Approches Alternatives

      S'appuyant sur l'approche de Fox, l'expert décrit une répartition des élèves face à la difficulté scolaire :

      • 80% réussissent normalement.
      • 15% nécessitent une différenciation de l'enseignant de classe régulière (ré-explication, exercices adaptés, etc.).

      Ces mesures relèvent du "bon sens".

      5-8% "bloquent" et nécessitent des "approches alternatives".

      Pour ces élèves, il ne suffit plus de "faire plus de la même chose". C'est pour eux que le concept de "point nodal" est particulièrement pertinent.

      4. Le Concept du "Point Nodal" et la Démarche d'Enquête

      Le "point nodal" est défini comme "l'identification d'un point d'appui qui est très rarement la discipline scolaire [elle-même]... mais qui est un point d'appui qu'on va trouver en faisant justement ce pas de côté et en prenant du temps pour une évaluation globale". Ce point permet de "débloquer la situation".

      • Rupture avec le rattrapage : L'expert a lui-même constaté l'inefficacité du "rattrapage scolaire" ("je faisais plus de lecture jusqu'au jour je me suis rendu compte que je me fatiguais beaucoup sans beaucoup de résultat").

      • La démarche "à la Colombo" : S'inspirant des sciences forensiques, la démarche d'enquête se décompose en quatre étapes :

      • Arriver sur le "lieu de l'échec" et prendre des traces (observation factuelle) : Recueillir des informations objectives sur l'élève, son comportement, ses difficultés, ses interactions.

      • Identifier le point nodal (clarification) : Cette étape est la plus délicate.

      Il s'agit de "poser les pièces [du puzzle], voir celles qui s'ajustent et puis progressivement se dessine l'image de la situation de l'élève et le point nodal".

      L'exemple de Léo, élève en difficulté de lecture avec une situation familiale complexe et des retards, a révélé que son point nodal était sa "disponibilité pour les apprentissages" et sa compréhension de son "métier d'élève".

      Le retard, initialement anecdotique, devient un "indice d'un manque d'investissement dans les apprentissages scolaires" une fois replacé dans le puzzle.

      • Mettre en œuvre le projet (intervention) : Une fois le point nodal et l'hypothèse explicative identifiés, un plan d'action est mis en place.

      Cela peut impliquer une collaboration avec les parents, d'autres professionnels (psychologue scolaire), ou un travail direct avec l'enfant sur la signification des apprentissages.

      • Faire le bilan : L'évaluation porte spécifiquement sur le point nodal et l'hypothèse explicative :

      "est-ce que c'était bien la bonne hypothèse ?".

      Cette étape doit être ouverte à la remise en question.

      • Confiance dans l'intuition et l'expérience de l'enseignant : Les enseignants de classe, par leur temps passé avec les élèves, disposent de nombreuses informations.

      Ce qui leur manque parfois est la "confiance qu'on peut avoir en ses capacités à faire ce pas de côté et à dire OK... quelle hypothèse explicative quel point de date je peux identifier". La formation doit cultiver cette confiance.

      • Choix d'un seul point d'appui : Bien que plusieurs hypothèses soient possibles, "il me paraît méthodologiquement indispensable de faire le choix d'une hypothèse".

      L'important est que "tout le monde soit d'accord d'appuyer aussi là", c'est-à-dire que l'hypothèse soit partagée par l'élève, les parents et les enseignants.

      La force de l'intervention vient alors de cet "appui collectif" sur le même levier.

      5. Implications et Bénéfices

      Décomplexer l'enseignant : L'approche permet à l'enseignant de "se décomplexer sur le fait d'aller chercher ailleurs que sur ce que je vois, c'est-à-dire mon élève qui n'entre pas dans la lecture" pour investiguer le "symptôme".

      Optimisme et pouvoir d'action : La démarche est fondamentalement optimiste, reposant sur le principe d'éducabilité et redonnant aux acteurs éducatifs, et notamment à l'enseignant, un "pouvoir d'action" face à la difficulté scolaire.

      Vision holistique de l'élève : Il s'agit de s'intéresser à la "globalité de la personne" et pas seulement aux symptômes, à l'image des "médecines qui prennent en compte la globalité de la personne".

      L'observation du comportement en classe ou à la récréation fournit des informations précieuses.

      Efficacité prouvée : Les progrès de Léo, par exemple, sont "spectaculaires".

      L'expert est "chaque fois impressionné à quel point certaines situations se débloquent en quelques semaines".

      L'école comme tiers et espace d'apprentissage : L'école a pour mission d'offrir un espace d'apprentissage (y compris comportemental) que certains élèves n'ont pas forcément à la maison.

      L'approche aide à surmonter l'excuse facile de la "famille" ("oui mais avec la famille qu'il a") en se concentrant sur ce que l'école peut faire en prenant en compte ces difficultés.

      En somme, cette approche invite à un changement de paradigme, passant d'une logique de diagnostic et de rattrapage à une démarche d'enquête collaborative et centrée sur l'identification d'un levier unique – le point nodal – pour catalyser le progrès de l'élève.

    1. Note: This response was posted by the corresponding author to Review Commons. The content has not been altered except for formatting.

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      Reply to the reviewers

      Reviewer #1 (Evidence, reproducibility and clarity (Required)):

      In this paper, the GFP-GBP system for mistargeting protein localization was used in fission yeast cells to discover new protein interactions involved in vesicular trafficking during cytokinesis. This approach uncovered a new association between the F-BAR protein Rga7 and its binding partner Rng10 with the Munc13 protein Ync13 at the cell division site. Additional associations were observed between Rga7-Rng10, Ync13 and the glucan synthases Ags1 and Bgs4, and the vesicle fusion protein Sec1. These interactions identified by the GFP-GBP system were further supported by co-immunoprecipitation experiments and by defining localization dependencies with live cell imaging in a variety of mutant strains. The imaging data are all of high quality and for the most part support the conclusions. However, in my opinion some of the interpretations are overstated, and the manuscript would benefit from providing additional mechanistic information. Major and minor recommendations are outlined below.

      Major suggestions 1. The co-IP data are interpreted to suggest that all the above-mentioned proteins form a single "big complex." However, as noted in the manuscript and reflected in the model, the multipass integral membrane proteins Bgs4 and Ags1 are embedded in the vesicle membrane and likely only indirectly associate with the scaffold Rga7-Rng10 via Ync13, without forming a 'complex'. One would expect the entirety of these vesicle contents to co-IP if the model is correct. The first paragraph of page 11 should be revised to more clearly reflect this scenario and to align with the proposed model.

      Response: We thank the reviewer for this thoughtful clarification. In the original manuscript, we stated “…indicating these proteins do interact or form big protein complexes… These results suggest that Rga7, Rng10, and Ync13 form a protein complex.” We agree that our initial wording may have unintentionally implied that all proteins detected in co-IP experiments assemble into a single, large physical complex. As the reviewer correctly noticed, the multipass integral membrane proteins Bgs4 and Ags1 are embedded within vesicle membranes and are more likely to associate indirectly with the Rga7-Rng10-Ync13 complex, rather than being part of one unified protein complex. To avoid overinterpretation, we have modified the last sentence of the first paragraph on the original page 11 as below: “These results suggest that Rga7, Rng10, and Ync13 do form a protein complex, although maybe dynamic and not super stable (see Discussion). Our data indicate that Rga7 interacts with both Ync13 and Rng10 to form a module on the plasma membrane for targeting of the vesicles containing cargos such as glucan synthases Bgs4 and Ags1. However, these glucan synthases are multipass integral membrane embedded proteins and likely only indirectly associate with the module Rng10-Rga7-Ync13, without forming a big protein complex.”

      Can Ync13 be artificially directed or tethered to the division site independently of Rga7-Rng10 (e.g., via Imp2)? If so, can this rescue the phenotypes of rga7Δ cells? This experiment could clarify whether Ync13 is the key functional effector of the Rga7-Rng10 complex.

      Response: We thank the reviewer for suggesting this interesting experiment. We agree that testing whether correctly localized Ync13 is sufficient to execute the division-site function of the Rga7–Rng10 complex would clarify its role. To test this, we artificially targeted Ync13 to the division site independently of Rga7 by tethering it to the scaffold protein Pmo25. Pmo25, an MO25 family protein, localizes to both the plasma membrane at the division site and the spindle pole body (mainly one of the SPBs) during mitosis and cytokinesis, enabling us to mislocalize Ync13 to these structures through GFP–GBP system. We did not use Imp2 because its localization pattern (mainly to the contractile ring [1, 2]) is different from Ync13. Microscopy revealed robust localization of Ync13 at the division site and the SPB in rga7Δ cells, and this tethered Ync13 persisted along the cleavage furrow throughout ring constriction. Importantly, enforced division-site localization of Ync13 significantly rescued the cytokinesis defects and cell lysis of rga7Δ. Consistently, growth assays on Phloxin B (PB) plate showed the elevated lysis/death in rga7Δ cells was rescued by Ync13 tethering to Pmo25-GBP. Together, these findings support that Ync13 is a key functional effector acting downstream of the Rga7–Rng10 scaffold at the division site. We have added these results in the new Figure 6 and associate text in the revised manuscript. We have also updated the model in Figure 8 to reflect this new result.

      1. Demeter J, Sazer S. imp2, a new component of the actin ring in the fission yeast Schizosaccharomyces pombe. J Cell Biol. 1998;143(2):415-27. PubMed PMID: 9786952.
      2. Martin-Garcia R, Coll PM, Perez P. F-BAR domain protein Rga7 collaborates with Cdc15 and Imp2 to ensure proper cytokinesis in fission yeast. J Cell Sci. 2014;127(Pt 19):4146-58. Epub 2014/07/24. doi: 10.1242/jcs.146233. PubMed PMID: 25052092.
      3. The authors should consider structural or computational modeling of the proposed Rga7-Rng10-Ync13 complex. Such analysis could offer insight into how these components interact and strengthen the proposed model. Response: We thank the reviewer for this valuable suggestion. Following the recommendation, we performed structural modeling of the Rga7–Rng10–Ync13 complex using AlphaFold3. Our previous work demonstrated that the F-BAR protein Rga7 forms a stable dimer and its F-BAR domain binds the C-terminal (aa751–1038) region of Rng10 [3]. Based on these findings, we constructed an input model consisting of two full-length Rga7 subunits, two Rng10(751–1038) subunits, and one full-length Ync13. The predicted structure revealed a modular organization in which Rng10(751–1038) associated strongly with the F-BAR domain of the Rga7 dimer, consistent with our prior biochemical data [3]. In addition, the model suggested that Ync13 interacted with the GAP domain of Rga7, positioning Ync13 in close proximity to the Rga7–Rng10 interface (Fig. S5, A, B, D and F). Further domain specific predictions confirmed the interactions between Rga7-GAP and Ync13 N-terminus (pTM: 0.63, ipTM: 0.64), two Rga7 F-BARs (pTM: 0.74, ipTM: 0.71), as well as Rga7 F-BAR and Rng10(751–1038) (pTM: 0.56, ipTM: 0.78) (Fig. S5, C-F). Overlay analyses revealed that the interacting domains align well with the structure of whole complex as the root mean square differences (RMSDs) are Liu Y, McDonald NA, Naegele SM, Gould KL, Wu J-Q. The F-BAR domain of Rga7 relies on a cooperative mechanism of membrane binding with a partner protein during fission yeast cytokinesis. Cell Rep. 2019;26(10):2540-8.e4. doi: 10.1016/j.celrep.2019.01.112. PubMed PMID: 30840879; PubMed Central PMCID: PMCPMC6425953.

      Minor text edits 1. Define "SIN" in the discussion section for clarity.

      Response: We defined the SIN pathway in the Discussion section as suggested: “At low restrictive temperatures, the lethality of mutant sid2, the most downstream kinase in the Septation Initiation Network, is partially rescued by upregulating Rho1. Thus, it has been suggested that the Septation Initiation Network activates Rho1, which in turn activates the glucan synthases [4].”

      Alcaide-Gavilán M, Lahoz A, Daga RR, Jimenez J. Feedback regulation of SIN by Etd1 and Rho1 in fission yeast. Genetics. 2014;196(2):455-70. Epub 2013/12/18. doi: 10.1534/genetics.113.155218. PubMed PMID: 24336750; PubMed Central PMCID: PMCPMC3914619.

      Figure S3, the protein schematics should start at residue "1" and not "0".

      Response: We apologize for the mistake. The schematics in revised figure (now Figure S4A) have been corrected to start at residue 1.

      Mass spectrometry data referenced in the text are not provided in the manuscript.

      __Response: __We apologize for the omission. The mass spectrometry data are now shown in Table S1. __

      __

      In Figure 4A. The Ags1 rim localization does not appear decreased as the authors claim.

      __Response: __After examining the data again, we agree with the reviewer’s assessment. So, we reworded the sentence as the following: “We also found that in ync13Δ cells, the Bgs4 intensity at the rim of the septum was much lower than in WT after ring constriction (Fig. 4B).”


      On page 13: "both Rga7 and Rng10 can mistarget Trs120 to mitochondria."

      Response: Thank you. The typo “mistargeting” has been corrected to “mistarget”.

      Minor figure edits 1. Consider inverting single-channel images to display fluorescence on a white background, which would improve visual clarity.

      Response: We appreciate the reviewer’s suggestion. However, we have chosen to retain the original display format with fluorescence shown in a black background, to be consistent with our (and some others’) previous publications. We believe this format preserves clarity while allowing easier comparison with the previously published works.

      The Figure 1 legend should describe the experimental setup rather than restating conclusions.

      Response: We thank the reviewer for this helpful suggestion. The Figure 1 legend has been revised to describe the experimental setup and imaging conditions rather than summarizing conclusions as the following:

      Fig. 1. Physical interactions among the key cytokinetic proteins in plasma membrane deposition and septum formation revealed by ectopic mistargeting to mitochondria by Tom20-GBP. __Arrowheads mark examples of colocalization at mitochondria. (A) Ync13 colocalizes with Rga7 and Rng10 at cell tips and the division site. (B-F) Tom20-GBP can ectopically mistarget Rga7/Rng10-mEGFP and their interacting partners tagged with tdTomato/RFP/mCherry to mitochondria. Tom20–GBP was used to recruit mEGFP-tagged Rga7 or Rng10 to mitochondria, and colocalization was assessed with tdTomato/RFP/mCherry-tagged candidate binding partners. Cells were grown at 25ºC in YE5S + 1.2 M sorbitol medium for ~36 to 48 h and then were washed with YE5S without sorbitol and grown in YE5S for 4 h before imaging. (B) Rga7/Rng10-Ync13. (C) Rga7/Rng10-Trs120. (D) Rga7/Rng10-Bgs4. (E) Rga7/Rng10-Ags1. (F)__ Rga7-Smi1. Bars, 5 μm.

      Reduce the number of arrows indicating co-localization in microscopy images; highlighting 1-2 representative examples is sufficient and less visually cluttered.

      Response: We appreciate the reviewer’s suggestion. We have revised the micrographs to reduce the number of arrowheads, highlighting several representative examples of co-localization per image. This improves clarity and reduces visual clutter while still guiding the reader to the key observations.

      Figure 3F, the scale bar is listed as 5 μm in the legend but it appears to my eye to be 2 μm.

      Response: We thank the reviewer for noticing this error. After rechecking the original imaging data, we have added a new 5 μm scale bar.

      The orientation of Bgs4/Smi1 should be inverted in the schematic within vesicles so that Smi1 is always on the cytoplasmic side.

      Response: We thank the reviewer for pointing out this error. The schematic has been corrected so that Bgs4 and Smi1 are oriented appropriately, with Smi1 consistently placed on the cytoplasmic side of vesicles because it does not have a transmembrane domain. The revised schematic is included in the updated Figure 8.

      6. Also in the schematic, Mid1 is not at the constricting CR and therefore needs to be removed.

      __Response: __Thank you for the suggestion. Mid1 has been removed from the model figure.

      Reviewer #1 (Significance (Required): From the data presented in the manuscript, it is proposed that Rga7 and Rng10 form a scaffold at the division site for delivery of exocytic vesicles marked by the TRAPPII complex but not the exocyst complex. Further, it is proposed that these vesicles deliver specifically the glucan synthases necessary for septation. Overall, this study builds on previous work from the Wu lab to clarify how the TRAPPII-decorated vesicles are specifically delivered to the cell division site, adding some new information about vesicle trafficking regulation during cytokinesis. It also provides new insight into the role of a F-BAR scaffold protein.

      This paper will be of interest to those studying cytokinesis and also those studying mechanisms of intracellular trafficking.

      Reviewer expertise: Cell division, signaling, membrane biology

      Reviewer #2 (Evidence, reproducibility and clarity (Required)):

      Summary:

      This paper provides a comprehensive analysis of the roles of Rng10, Rga7, and Ync13 in cytokinesis using fission yeast as a model system. The authors demonstrate that Ync13/Rna7/Rng10 not only interact with each other but also associate with components of glucan synthases, which are essential for secondary septum formation but not for the primary septum. They further show that Ync13 is involved in exocytosis through its interaction with Sec1 and plays a role in membrane trafficking via interaction with the TRAPP-II complex. Collectively, their findings reveal a coordinated mechanism that ensures the timely formation of the secondary septum during cytokinesis, as deletion of these proteins disrupts septum formation and leads to cell lysis.

      The conclusions drawn in this paper are well-supported by the data, with a clear methodology and robust statistical analyses that enhance reproducibility. However, I have the following major and minor comments:

      Major Comments - 1) The authors propose that Ync13, Rng10, and Rga7 interact to form a protein complex, supported by their mislocalization studies. While these findings are suggestive, additional co-immunoprecipitation (co-IP) data specifically demonstrating a direct interaction between Ync13 and Rng10 would strengthen the claim.

      Response: We thank the reviewer for this suggestion. The direct interaction between Rga7 with Rng10 has been already established and published by our group [3, 5]. Here we found that Rga7 and Ync13 directly interact by in vitro binding assay (Figure 2, D and E). While our current data do not suggest a direct physical interaction between Ync13 and Rng10, our mislocalization results and other data do provide strong support for their functional association. In particular, ectopic tethering of Ync13 to mitochondria recruits Rng10 to the same sites and vice versa (Figures. 1B and S2A). Additionally, division-site tethering of Ync13 by Pmo25-GBP rescues both the growth and cell-lysis phenotype of rga7Δ (Figure 6), consistent with the idea that Ync13 functions downstream of Rga7-Rng10 because Rga7 localization depends on Rng10 (Figure 8). Furthermore, our AlphaFold3 modeling predicts that Rng10 binds the BAR domain of Rga7, whereas Ync13 binds the GAP domain of Rga7, suggesting that Rng10 and Ync13 are positioned within the same complex through Rga7 without direct interaction (Figure S5).

              The predicted lack of direct interaction between Ync13 and Rng10(751–1038) is supported by the experiment mentioned below to answer the minor question from the Reviewer 3. We tested the mistargeting of mECitrine-Rng10(751–1038) in *rga7Δ tom20-GBP* cells and found that Ync13-tdTomato could not be recruited to mitochondria (Figure S4H). This indicates that Ync13 cannot interact with Rng10(751–1038) independently of Rga7, supporting our proposed model that Rga7 interacts with Rng10 through the BAR domain while with Ync13 through the GAP domain. We have added these clarifications to the revised manuscript (Results and Discussion) to better contextualize the evidence for the Rga7–Rng10–Ync13 assembly.
      

      Liu Y, McDonald NA, Naegele SM, Gould KL, Wu J-Q. The F-BAR Domain of Rga7 Relies on a Cooperative Mechanism of Membrane Binding with a Partner Protein during Fission Yeast Cytokinesis. Cell Rep. 2019;26(10):2540-8.e4. doi: 10.1016/j.celrep.2019.01.112. PubMed PMID: 30840879; PubMed Central PMCID: PMCPMC6425953. Liu Y, Lee I-J, Sun M, Lower CA, Runge KW, Ma J, et al. Roles of the novel coiled-coil protein Rng10 in septum formation during fission yeast cytokinesis. Mol Biol Cell. 2016;27(16):2528-41. Epub 2016/07/08. doi: 10.1091/mbc.E16-03-0156. PubMed PMID: 27385337; PubMed Central PMCID: PMCPMC4985255.

      2) It remains unclear whether Ync13 directly interacts with components of the glucan synthase complex (Bgs4/Ags1), or if this association is mediated through other factors (Rng10, Rga7). Clarifying the nature of this interaction would significantly enhance the mechanistic insight.

      Response: We thank the reviewer for this thoughtful clarification. As pointed out by Reviewer 1 in major comment 1, the multipass integral membrane proteins Bgs4 and Ags1 are embedded within vesicle membranes and are more likely to associate indirectly with the Rga7–Rng10-Ync13 complex rather than being part of one unified protein complex, although Rga7 Co-IPs with Bgs4 and its binding partner Smi1 (Figure 1, A-C). We would like to make it clear that our model or manuscript does not claim direct interactions between the Ync13-Rga7-Rng10 module and the glucan synthase complexes but suggest that the module aids in selection of vesicle targeting sites on the plasma membrane. To clarify, we have revised the text to more clearly state that our co-IP and in vitro binding results demonstrate that Rga7 physically associates with Ync13 and Rng10, and that vesicle-associated proteins such as Bgs4 and Ags1 are likely recruited through indirect interactions.

      __Minor comments: __1) The manuscript refers to mass spectrometry-based interaction data, but the corresponding dataset is not included. Providing this would enhance transparency and reproducibility.

      __Response: __We apologize for the omission. The mass spectrometry data are now shown in Table S1.

      2) In Figure 2D, the MBP-6x pull-down lane shows a faint band around 76 kDa. The authors should clarify what this band represents and whether it has any relevance to the study.

      Response: We thank the reviewer for noticing this faint band. The weak ~76 kDa band in the MBP-6x pull-down lane is non-specific background binding of MBP and Rga7. We added a note in the figure legend to clarify this point.


      3) A quantification graph corresponding to the data in Figure 3G would aid in better interpreting the results and assessing their significance.

      Response: We thank the reviewer for this suggestion. We have now added two quantification graphs corresponding to Figure 3G, showing the measured Rng10 signal intensities across the division site. Statistical analysis shows the full width at half maximum (FWHM) is significantly different between WT and ync13D cells, and the figure legend and text have been updated accordingly in the revised manuscript.

      4) Figure 4D appears to be missing time legends, which are essential for interpreting the dynamics of the experiment.

      Response: We thank the reviewer for noticing this. We apology for making this confusing statement in figure legend. We would like to clarify that the full width at half maximum (FWHM) was calculated from line scans using single time point images from cells at the end of contractile-ring constriction. Those line scans were fitted with the Gaussian distribution to calculate the mean and standard deviation of FWHM. We have updated the figure legend to make it clearer in the revised manuscript.

      Reviewer #2 (Significance (Required)):

      Nature and Significance of the Advance This study provides a conceptual and mechanistic advance in understanding the spatial and temporal regulation of membrane trafficking during cytokinesis. It identifies a conserved module-Ync13-Rga7-Rng10-that directs the selective tethering and fusion of secretory vesicles at the division site, functioning independently of the exocyst complex. This finding challenges the prevailing model that the exocyst is universally required for vesicle tethering during cytokinesis. While previous work has underscored the roles of TRAPP-II and vesicle trafficking in septum formation (Wang et al., 2016; Arellano et al., 1997; Gerien and Wu, 2018), the precise mechanism targeting vesicles to the division site remained unclear. This study fills that gap by elucidating how Ync13 and Rga7 coordinate vesicle delivery and glucan synthase localization (Liu et al., 2016; Zhu et al., 2018), thereby extending our understanding of septum biogenesis and membrane remodeling beyond actomyosin ring dynamics.

      Relevant Audience: This work is relevant to: • Cell biologists investigating cytokinesis, membrane trafficking, or vesicle fusion. • Yeast geneticists interested in conserved cell division pathways. • Researchers focused on SNARE-mediated membrane dynamics and trafficking regulation. • Biomedical scientists exploring analogous processes in mammalian systems, particularly those studying cell division defects linked to disease. The findings have implications across both basic and translational research in cell biology and membrane dynamics.

      My Expertise: My research focuses on membrane fusion, specifically the SNARE-mediated fusion process. I study the spatio-temporal regulation of fusion events and the coordinated action of regulatory proteins in determining the structural and functional outcomes of membrane fusion. This background provides me with the framework to critically evaluate studies investigating cytokinesis and trafficking mechanisms at the molecular level.

      Reviewer #3 (Evidence, reproducibility and clarity (Required)):

      Zhang et al. elucidate key roles of a conserved module the Ync13-Rga7-Rng10 complex in coordinating selective tethering, docking, and fusion of glucan synthases containing vesicles with the plasma membrane, a process crucial for cell wall synthesis and survival of fission yeast at division. Using methods including mistargeting proteins to mitochondria, co-immunoprecipitation, in vitro binding assays, genetic and cellular methods, electron microscopy, and live-cell confocal microscopy, the authors demonstrate that this module controls a vesicle targeting pathway mediated by the TRAPP-II complex and SM protein Sec1, which ensures glucan synthases Bgs4 and Ags1 are deposited at the division site in a spatiotemporal manner.

      Major comments: The authors report aberrant accumulation of Bgs4 and Ags1 in the center of the septum after actomyosin ring constriction in ync13del cells and detect no overall defects in Bgs1 distribution there (Figure 4). When similar experiments were analyzed in this paper ( https://pmc.ncbi.nlm.nih.gov/articles/PMC6249806/), Bgs1 distribution and level did change in cells lacking Ync13, although these phenotypes of Bgs1 appeared later that that of Bgs4. I wonder whether there could exist a second wave of Bgs1 arrival in ync13del cells at later time points after ring fully constricts. Could this late recruitment of Bgs1 depends on Rng7 and Rng10, since these protein complexes are enriched in the middle of septum of ync13del cells? Or as the authors mentioned in the Discussion, could Rho GTPase regulated by Rga7 GAP also play a role in Bgs1 accumulation or fusion with the septum in the above scenario, if no obvious accumulation of vesicles is observed in ync13del cells with electron microscopy? How does Bgs1 localize in ync13-19 rng10del double?

      Response: We thank the reviewer for this insightful observation. We repeated the experiment to observe the localization of Bgs1 in WT and ync13Δ cells. We confirmed our earlier observation reported in this manuscript that the localization of Bgs1 at rim of the division site and its distribution along the division plane in ync13Δ is not very different from WT, although its intensity is higher and has more variation in ync13Δ cells (Figure above) . As suggested by the reviewer, we did microscopy to test Bgs1 localization in ync13-19 temperature sensitive mutant, rng10Δ, ync13-19 rng10Δ, and WT (Fig. S7). While line scan curves for Bgs1 localization at the division site steep for ync13-19 rng10Δ double mutant, it has no statistically significant difference in FWHM as compared to control WT (Fig. S7). Please note that we used different confocal systems, cameras, and laser powers for Fig. 4, C and E (PerkinElmer UltraVIEW Vox CSUX1) and Fig. S7 (Nikon W1+SoRa), so the FWHMs are not comparable between the two figures.

      To test if there is any second wave of Bgs1 localization at the division site, we tracked the fluorescence intensity of Bgs1 throughout 2 h long movies and plotted the Bgs1 intensity profile at the division site over time. The data clearly show only one peak of Bgs1 and no later accumulation at the division site, although Bgs1 intensity has more variation in ync13-19 and ync13-19 rng10Δ cells and the intensity is higher in ync13-19 rng10Δ cells. All these experiments conclude that Ync13-Rga7-Rng10 module impacts the localization of glucan synthases essential for the secondary septum (Bgs4 and Ags1) but not the primary (Bgs1).

      Assessments of protein abundance by Western blotting (Figure 3C and 3D) can benefit from some quantifications.

      Response: We thank the reviewer for this suggestion. We have now quantified the Western blot bands in Figures 3C and 3D, which have been added as supplementary figures along with the Western blot for Rng10 (Fig. S6, A-C) in the revised figures.

      Minor comments: Based on a series of experiments in which mistargeting Rga7 and Rng10 truncations drive Ync13-tdTomato to mitochondria, the authors suggest that Rga7, Rng10, and Ync13 have multivalent interactions with each other. Previous study (https://pmc.ncbi.nlm.nih.gov/articles/PMC6425953/) demonstrated that in cells co-expressing Tom20-GBP mECitrine-Rng10(751-950), Rga7 was efficiently mistargeted to mitochondria. This raises a possibility that Ync13 mistargeted by mECitrine-Rng10(751-1038) could come from Rga7 that strongly associated with Rng10(751-1038) on mitochondria. I wonder whether the authors could compare some of their truncation mistargeting experiments in the original manuscript and the ones in which either Rga7 or Rng10 is deleted, e.g. Tom20-GBP mECitrine-Rng10(751-1038) experiments in rga7del cells, if cells are still viable in this genetic background.

      Response: We thank the reviewer for this insightful suggestion. We tested the mistargeting of mECitrine-Rng10(751–1038) in rga7Δ tom20-GBP cells and found that Ync13-tdTomato could not be recruited to mitochondria. This indicates that Ync13 cannot interact with Rng10 C-terminus independently of Rga7, supporting the Alphafold3 modeling and our proposed model that Rga7 interacts with Rng10 through the BAR domain while with Ync13 through the GAP domain. We have added the new data to the revised manuscript (Fig. S4H and associate text) and included a brief discussion highlighting that Rga7 is required for the Rng10–Ync13 interaction. We removed the mentioning of multivalent interactions in the manuscript to minimize confusion.

      It is interesting that rga7del rng10del double mutants can survive better in EMM or YES with sorbitol. I wonder this would allow the authors to test whether the interaction between Ync13 and Sec1 is modulated by the presence of Rga7 and Rng10 or even the entire vesicle? Does mistargeted Ync13 overexpressed using the 3nmt1 promoter is still capable of driving Sec1 to mitochondria in rga7del rng10del cells.

      Response: We thank the reviewer for this suggestion. While we did not succeed in constructing the pentamutant deleting both rga7 and rng10 and mislocalizing Ync13 to mitochondria, we were able to make a quadruple mutant deleting rng10 and mislocalizing Ync13 to mitochondria. We tested whether mistargeted Ync13 overexpressed using the 3nmt1 promoter can recruit Sec1 to mitochondria in rng10Δ cells. Our results show that overexpressed Ync13 is still able to drive Sec1 localization to mitochondria without Rng10 (Fig. S2G). This suggests that Rng10 (together with Rga7) primarily functions to recruit and position Ync13 at the division site rather than being strictly required for the interaction between Ync13 and Sec1. This is also consistent with our Pmo25-GBP mislocalization experiments where we found that rga7Δ 3nmt1-mECitrine-ync13 cells even under the repressed condition for the 3nmt1 promoter can partially rescue the lysis phenotype of rga7Δ cells (Figure 6).

      The endogenous level of Ync13 is not particular high. Is this low level of Ync13 crucial for its function? Does mildly elevated level of Ync1 promote vesicle fusion at the closing septum?

      Response: We thank the reviewer for this insightful question. To test if there is a correlation between Ync13 levels and vesicle fusion at the division site, we mildly overexpressed Ync13 from the 3nmt1 promoter in YE5S rich medium without additionally added thiamine to obtain cells with different Ync13 levels (the rich medium has some residual amount of thiamine, which partially represses the nmt1 promoter) and then tracked the Rab11 GTPase Ypt3 labeled vesicles. This resulted in increased levels of Ync13 as well as Ypt3 at the division site (Fig. S8B). We measured the Ync13 intensity at division site and counted the number of Ypt3 vesicles reaching the division site in 2-minute continuous movie at the middle focal plane. We observed that increasing Ync13 level promoted the tethering and accumulation of Ypt3 vesicles at the division site until it reached a plateau (Fig. S8B). Thus, the Ync13 level is important for vesicle fusion at the division site. Collectively, Ync13, working with Rga7 and Rng10, plays an important role in vesicle targeting and fusion on the plasma membrane at the division site during cytokinesis. This is consistent with our results that overexpressed Ync13 can mislocalize Sec1 to mitochondria in rng10Δ (Fig. S2G) and can rescue the rga7Δ (Fig. 6).

      Reviewer #3 (Significance (Required)):

      Most of conclusions are well supported by a combination of methods. Out of curiosity, I wonder how much of Bgs4 or Smi1 detected in Co-IP experiments exist in the vesicle-bound form. The authors propose a very interesting working model that addresses several key challenges in achieving vesicle targeting specificity when timely delivery of various enzymes to their respective spatial locations along the primary and secondary septum must be orchestrated. I think this manuscript will be of interest to a broad audience.

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      Referee #2

      Evidence, reproducibility and clarity

      Summary:

      This paper provides a comprehensive analysis of the roles of Rng10, Rga7, and Ync13 in cytokinesis using fission yeast as a model system. The authors demonstrate that Ync13/Rna7/Rng10 not only interact with each other but also associate with components of glucan synthases, which are essential for secondary septum formation but not for the primary septum. They further show that Ync13 is involved in exocytosis through its interaction with Sec1 and plays a role in membrane trafficking via interaction with the TRAPP-II complex. Collectively, their findings reveal a coordinated mechanism that ensures the timely formation of the secondary septum during cytokinesis, as deletion of these proteins disrupts septum formation and leads to cell lysis.

      The conclusions drawn in this paper are well-supported by the data, with a clear methodology and robust statistical analyses that enhance reproducibility. However, I have the following major and minor comments:

      Major Comments

      1. The authors propose that Ync13, Rng10, and Rga7 interact to form a protein complex, supported by their mislocalization studies. While these findings are suggestive, additional co-immunoprecipitation (co-IP) data specifically demonstrating a direct interaction between Ync13 and Rng10 would strengthen the claim.
      2. It remains unclear whether Ync13 directly interacts with components of the glucan synthase complex (Bgs4/Ags1), or if this association is mediated through other factors (Rng10, Rga7). Clarifying the nature of this interaction would significantly enhance the mechanistic insight.

      Minor comments:

      1. The manuscript refers to mass spectrometry-based interaction data, but the corresponding dataset is not included. Providing this would enhance transparency and reproducibility.
      2. In Figure 2D, the MBP-6x pull-down lane shows a faint band around 76 kDa. The authors should clarify what this band represents and whether it has any relevance to the study.
      3. A quantification graph corresponding to the data in Figure 3G would aid in better interpreting the results and assessing their significance.
      4. Figure 4D appears to be missing time legends, which are essential for interpreting the dynamics of the experiment.

      Significance

      Nature and Significance of the Advance

      This study provides a conceptual and mechanistic advance in understanding the spatial and temporal regulation of membrane trafficking during cytokinesis. It identifies a conserved module-Ync13-Rga7-Rng10-that directs the selective tethering and fusion of secretory vesicles at the division site, functioning independently of the exocyst complex. This finding challenges the prevailing model that the exocyst is universally required for vesicle tethering during cytokinesis. While previous work has underscored the roles of TRAPP-II and vesicle trafficking in septum formation (Wang et al., 2016; Arellano et al., 1997; Gerien and Wu, 2018), the precise mechanism targeting vesicles to the division site remained unclear. This study fills that gap by elucidating how Ync13 and Rga7 coordinate vesicle delivery and glucan synthase localization (Liu et al., 2016; Zhu et al., 2018), thereby extending our understanding of septum biogenesis and membrane remodeling beyond actomyosin ring dynamics.

      Relevant Audience:

      This work is relevant to:

      • Cell biologists investigating cytokinesis, membrane trafficking, or vesicle fusion.
      • Yeast geneticists interested in conserved cell division pathways.
      • Researchers focused on SNARE-mediated membrane dynamics and trafficking regulation.
      • Biomedical scientists exploring analogous processes in mammalian systems, particularly those studying cell division defects linked to disease. The findings have implications across both basic and translational research in cell biology and membrane dynamics.

      My Expertise:

      My research focuses on membrane fusion, specifically the SNARE-mediated fusion process. I study the spatio-temporal regulation of fusion events and the coordinated action of regulatory proteins in determining the structural and functional outcomes of membrane fusion. This background provides me with the framework to critically evaluate studies investigating cytokinesis and trafficking mechanisms at the molecular level.

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      Referee #1

      Evidence, reproducibility and clarity

      In this paper, the GFP-GBP system for mistargeting protein localization was used in fission yeast cells to discover new protein interactions involved in vesicular trafficking during cytokinesis. This approach uncovered a new association between the F-BAR protein Rga7 and its binding partner Rng10 with the Munc13 protein Ync13 at the cell division site. Additional associations were observed between Rga7-Rng10, Ync13 and the glucan synthases Ags1 and Bgs4, and the vesicle fusion protein Sec1. These interactions identified by the GFP-GBP system were further supported by co-immunoprecipitation experiments and by defining localization dependencies with live cell imaging in a variety of mutant strains. The imaging data are all of high quality and for the most part support the conclusions. However, in my opinion some of the interpretations are overstated, and the manuscript would benefit from providing additional mechanistic information. Major and minor recommendations are outlined below.

      Major suggestions

      1. The co-IP data are interpreted to suggest that all the above-mentioned proteins form a single "big complex." However, as noted in the manuscript and reflected in the model, the multipass integral membrane proteins Bgs4 and Ags1 are embedded in the vesicle membrane and likely only indirectly associate with the scaffold Rga7-Rng10 via Ync13, without forming a 'complex'. One would expect the entirety of these vesicle contents to co-IP if the model is correct. The first paragraph of page 11 should be revised to more clearly reflect this scenario and to align with the proposed model.
      2. Can Ync13 be artificially directed or tethered to the division site independently of Rga7-Rng10 (e.g., via Imp2)? If so, can this rescue the phenotypes of rga7Δ cells? This experiment could clarify whether Ync13 is the key functional effector of the Rga7-Rng10 complex.
      3. The authors should consider structural or computational modeling of the proposed Rga7-Rng10-Ync13 complex. Such analysis could offer insight into how these components interact and strengthen the proposed model.

      Minor text edits

      1. Define "SIN" in the discussion section for clarity.
      2. Figure S3, the protein schematics should start at residue "1" and not "0".
      3. Mass spectrometry data referenced in the text are not provided in the manuscript.
      4. In Figure 4A. The Ags1 rim localization does not appear decreased as the authors claim.
      5. On page 13: "both Rga7 and Rng10 can mistarget Trs120 to mitochondria."

      Minor figure edits

      1. Consider inverting single-channel images to display fluorescence on a white background, which would improve visual clarity.
      2. The Figure 1 legend should describe the experimental setup rather than restating conclusions.
      3. Reduce the number of arrows indicating co-localization in microscopy images; highlighting 1-2 representative examples is sufficient and less visually cluttered.
      4. Figure 3F, the scale bar is listed as 5 μm in the legend but it appears to my eye to be 2 μm.
      5. The orientation of Bgs4/Smi1 should be inverted in the schematic within vesicles so that Smi1 is always on the cytoplasmic side.
      6. Also in the schematic, Mid1 is not at the constricting CR and therefore needs to be removed.

      Significance

      From the data presented in the manuscript, it is proposed that Rga7 and Rng10 form a scaffold at the division site for delivery of exocytic vesicles marked by the TRAPPII complex but not the exocyst complex. Further, it is proposed that these vesicles deliver specifically the glucan synthases necessary for septation. Overall, this study builds on previous work from the Wu lab to clarify how the TRAPPII-decorated vesicles are specifically delivered to the cell division site, adding some new information about vesicle trafficking regulation during cytokinesis. It also provides new insight into the role of a F-BAR scaffold protein.

      This paper will be of interest to those studying cytokinesis and also those studying mechanisms of intracellular trafficking.

      Reviewer expertise: Cell division, signaling, membrane biology

  5. danm0nster.github.io danm0nster.github.io
    1. Lad en funktion f(x)f(x)f(x) være givet ved udtrykket f(x)=6x3−12x2−54x+108f(x) = 6x^3 - 12x^2 - 54x + 108f(x)=6x3−12x2−54x+108 for x>3x > 3x>3. Find differentialkvotienten for den inverse funktion, df−1dx\frac{\mathrm{d} f^{-1}}{\mathrm{d} x}dxdf−1​ i punktet x=f(4)=84x = f(4) = 84x=f(4)=84.

      Lidt svær

  6. teacher.imperial-english.com teacher.imperial-english.com
    1. ng in the city centre, th

      1) I hate driving in the city centre, there is always a lot of traffic.

      Why? “Traffic” is an uncountable noun, so we cannot use many.

      Much is grammatically correct, but it sounds unnatural in a positive statement. In everyday English, we usually say a lot of traffic.

      2) There aren’t many good restaurants in my town any more.

      Why? “Restaurants” is countable plural, so we need many.

      Much is for uncountable nouns, so it doesn’t fit.

      A few means “some, but not many,” and the sentence is negative, so many is the natural choice.

      3) I’m so bored, there isn’t much on TV tonight.

      Why? Here “much” means “a large amount,” and TV is considered uncountable in this context.

      Many is for plural countable nouns, which doesn’t fit.

      Some would make it positive, but the sentence is negative.

      4) Did we have a lot of homework today?

      Why? “Homework” is an uncountable noun.

      Much homework is possible, especially in formal English, but in questions, a lot of is more natural in everyday speech.

      Many doesn’t fit because homework is uncountable.

      5) My friends brought a lot of chocolate back from Switzerland for us to try.

      Why? “Chocolate” is usually uncountable when talking about it in general.

      Much chocolate is possible, but usually used in negatives or questions (e.g., I don’t eat much chocolate).

      A lot of is natural and correct in a positive statement.

    1. Two original annotation\ 1.The stacks for the story telling is getting people to the point of the main story itself.

      1. The changes i see in the storytelling is how people perceptively explain themselves when it get to a bad part in the story they stay on that topic

      2. The main theme is about how they feel in the story what type of emoticon triggers that feeling if it's sadness or joyfulness

      3. I find in the story that they change emotion when they feeling sad or scared they go from happy to worry..

      4. in the beginning of the story they get the main purpose of what gonna happened next after the Introduction they can be either scared or worried about the person telling the story

      5. At the end the story teller can be feeling nervous about this whole story or relief they got it out in public they don't have to image the story or tell the story again.

      I would pick " "What is Implicit Bias?" because they talking about Mexican coming from their country to American and board control telling them if they illegal in that country it not okay to say since they're immigrants that came from their hometown just to get peace but not be mock by the person who trying send him back to where eh came from that mean a lot to me and my parents as African myself getting kicked for not fitting in with the Americans. I know what that feel liked

    1. Reviewer #1 (Public review):

      Multiple waves of follicles have been proven to exist in multiple species, and different waves of follicles contribute differently to oogenesis and fertility. This work characterizes the wave 1 follicles in mouse comprehensively and compares different waves of follicles regarding their cellular and molecular features. Elegant mouse genetics methods are applied to provide lineage tracing of the wave 1 folliculogenesis, together with sophisticated microscopic imaging and analyses. Single-cell RNA-seq is further applied to profile the molecular features of cells in mouse ovaries from week 2 until week 6. While extensive details about the wave 1 follicles, especially the atresia process, are provided, the authors also identified another group of follicles located in the medullary-cortical boundary, which could also be labeled by the FoxL2-mediated lineage tracing method. The "boundary" or "wave 1.5" follicles are proposed by the authors to be the earliest wave 2 follicles, which contribute to the early fertility of puberty mice, instead of the wave 1 follicles, which undergo atresia with very few oocytes generated. The wave 1 follicle atresia, which degrades most oocytes, on the other hand, expands the number of theca cells and generates the interstitial gland cells in the medulla, where the wave 1 follicles are located. These gland cells likely contribute to the generation of androgen and estrogen, which shape oogenesis and animal development. By comparing scRNA-seq data from cells collected from week 2 until week 6 ovaries, the author profiled the changes in numbers of different cells and identified key genes that differ between wave 1 and wave 2 follicles, which could potentially be another driver of different waves of folliculogenesis. In summary, the authors provide a high amount of new results with good quality that illustrate the molecular and cellular features of different waves of mouse follicles, which could be further reused by other researchers in related fields. The findings related to the boundary follicles could potentially bring many new findings related to oogenesis.

      This paper is overall well-written with solid and intriguing conclusions that are well supported. The reviewer only has some minor comments for the authors' consideration that could potentially help with the readability of the paper.

      (1) The authors identify the wave 1.5 follicles at the medullary-cortex boundary, which begin to develop shortly after 2 weeks. Since the authors already collected scRNA-seq data from week 2 until week 6, could any special gene expression patterns be identified that make wave 1.5 follicle cells different from wave 1 and wave 2?

      (2) Are Figures 1C and 1E Z projections from multiple IF slices? If so, please provide representative IF slice(s) from Figures 1C and 1E and clearly label wave 1 and wave 2 follicles to better illustrate how the wave 1 follicles are clarified and quantified.

      (3) For Figure 3D, please also provide an image showing the whole ovary section, like in Figures 3A and 3C, to better illustrate the localization and abundance of different cells.

      (4) In Figure 4H, expressions of HSD3B1 and PLIN1 seem to be detected in almost all medulla cells. Does this mean all medulla cells gain gland cell features? Or there is only a subset of the medulla cells that are actively expressing these 2 proteins. Please provide image(s) with higher magnification to show more clearly how the expression of these 2 proteins differs among different cells.

      (5) Figure 5: The authors discussed cell number changes for different types of cells from week 2 to week 6. A table, or some plots, visualizing numbers of different cell types, instead of just providing original clusters in Dataset S6, at different time points, would make the changes easier to observe.

      (6) Figure S7: It would be more helpful to directly show the number of wave 1 follicles.

      (7) Did the fluorescence cryosection staining (Line 587 - 595) use the same buffers as in the whole-mount staining (Line 575 - 586)? Please clarify.

      (8) In Line 618, what tissue samples were collected? Please point out clearly.

    1. Reviewer #1 (Public review):

      Summary:

      The authors have conducted the largest to date Mendelian Randomization (MR) analysis of the association between genetically predicted measures of adiposity and risk of head and neck cancer (HNC) overall and by subsites within HNC. MR uses genetic predictors of an exposure, such as gene variants associated with high BMI or tobacco use, rather than data from individual physical exams or questionnaires and if it can be done in its idealized state, there should be no problems with confounding. Traditional epidemiologic studies have reported a variety of associations between BMI (and a few other measures of adiposity) and risk of HNC that typically differs by the smoking status of the subjects. Those findings are controversial given the complex relationship between tobacco and both BMI and HNC risk. Tobacco smokers are often thinner than no-smokers so this could create an artificial ('confounded') association that may not be fully adjusted away in risk models. The findings of a BMI-HNC association are often attributed to residual confounding and this seems ripe for an MR approach if suitable genetic instrumental variables can be created. Here the authors built a variety of genetic instrumental variables for BMI and other measures of adiposity as well as two instrumental variables for smoking habits and then tested their hypotheses in a large case-controls set of HNC and controls with genetic data.

      The authors found that the genetic model for BMI was associated with HNC risk in simple models, but this association disappeared when using models that better accounted for pleiotropy, the condition when genetic variants are associated with more than one trait such as both BMI and tobacco use. When they used both adiposity and tobacco use genetic instruments in a single model, there was a strong association with genetically predicted tobacco use (as is expected) but there was no remaining association with genetic predictors of adiposity. They conclude that high BMI/adiposity is not a risk factor for HNC.

      Strengths:

      The primary strength was the expansive use of a variety of different genetic instruments for BMI/adiposity/body size along with employing a variety of MR model types, several of which are known to be less sensitive to pleiotropy. They also used the largest case-control sample size to date.

      Weaknesses:

      The lack of pleiotropy is an unconfirmable assumption of MR and the addition of those models is therefore quite important as this is a primary weakness of the MR approach. Given that concern, I read the sensitivity analyses using pleiotropy-robust models as the main result and in that case, they are more limited in their ability to test their hypothesis as these models do not show a robust BMI instrumental variable association.

      Comments on the revised manuscript:

      After the first round of review, the authors have improved the manuscript by (1) adding the requested power calculations and adding text to help the reader integrate that additional information; (2) adding the main effects for the tobacco instruments; (3) updating the comparison of their results to the prior literature; (4) and some other edits to the text. They have declined to include the smoking stratified estimates and provide a rationale for this decision that references the potential for collider bias. While true that yet another bias might be introduced, that gets added to the list and the careful reader would know that. Many important questions in cancer etiology can only be addressed via observational approaches and each observational approach has the potential for a long list of biases. The best inference comes from integrating the totality of the data and realizing that most conclusions are subject to updating as we conduct more work and learn more.

    2. Author response:

      The following is the authors’ response to the original reviews.

      Joint Public Review:

      Weaknesses:

      The lack of pleiotropy is an unconfirmable assumption of MR, and the addition of those models is therefore quite important, as this is a primary weakness of the MR approach. Given that concern, I read the sensitivity analyses using pleiotropy-robust models as the main result, and in that case, they can't test their hypotheses as these models do not show a BMI instrumental variable association. The other weakness, which might be remedied, is that the power of the tests here is not described. When a hypothesis is tested with an under-powered model, the apparent lack of association could be due to inadequate sample size rather than a true null. Typically, when a statistically significant association is reported, power concerns are discounted as long as the study is not so small as to create spurious findings. That is the case with their primary BMI instrumental variable model - they find an association so we can presume it was adequately powered. But the primary models they share are not the pleiotropy-robust methods MR-Egger, weighted median, and weighted mode. The tests for these models are null, and that could mean a couple of things: (1) the original primary significant association between the BMI genetic instrument was due to pleiotropy, and they therefore don't have a robust model to explore the effects of the tobacco genetic instrument. (2) The power for the sensitivity analysis models (the pleiotropy-robust methods) is inadequate, and the authors share no discussion about the relative power of the different MR approaches. If they do have adequate power, then again, there is no need to explore the tobacco instrument.

      Reviewing Editor Comments:

      We suggest that the authors add power estimates to assess whether the sample size is sufficient, given the strength and variability of the genetic instruments. It would also be helpful to present effect estimates for the tobacco instruments alone, to clarify their independent contribution and improve the interpretation of the joint models. In addition, the role of pleiotropy should be addressed more clearly, including which model is considered primary. Stratified analyses by smoking status are encouraged, as prior studies indicate that BMI-HNC associations may differ between smokers and non-smokers. Finally, the comparison with previous studies should be revised, as most reported null findings without accounting for tobacco instruments. If this study finds an association, it should not be framed as a replication

      We would like to highlight that post-hoc power calculations are often considered redundant since the statistical power estimated for an observed association is directly related to its p-value[1]. In other words, the uncertainty of the association is already reflected in its 95% confidence interval. However, we understand power calculations may still be of interest to the reader, so we have incorporated them in the revised manuscript. We have edited the text as follows (lines 151-155):“Consequently, we used the total R<sup>2</sup> values to examine the statistical power in our study[42]. However, we acknowledge that the value of post-hoc power calculations is limited, since the statistical power estimated for an observed association is already reflected in the 95% confidence interval presented alongside the point estimate[43].” We have also added supplementary figures 1 and 2.

      We can see that when using the latest HEADSpAcE data we were able to detect BMI-HNC ORs as small as 1.16 with 80% power, while the GAME-ON dataset only permitted the detection of ORs as small as 1.26 using the same BMI instruments (Figure B). We have explained these figures in the results section as follows (lines 257-263): “Using the BMI genetic instruments (total R<sup>2</sup>= 4.8%) and an α of 0.05, we had 80% statistical power to detect an OR as small as 1.16 for HNC risk (Supplementary Figure 1). For WHR (total R<sup>2</sup>= 3.1%) and WC (total R<sup>2</sup>= 4.4%), we could detect odds ratios (ORs) as small as 1.20 and 1.17, respectively. This is an improvement in terms of statistical power compared to the GAME-ON analysis published by Gormley et al.[28], for which there was 80% power to detect an OR as small as 1.26 using the same BMI genetic instruments (Supplementary Figure 2).”

      The reason we use inverse variance weighted (IVW) Mendelian randomization (MR) to obtain our main results rather than the pleiotropy-robust methods mentioned by the reviewer/editors (i.e., MR-Egger, weighted median and weighted mode) is that the former has greater statistical power than the latter[2]. Hence, instead of focussing on the statistical significance of the pleiotropy-robust analyses, we consider it is of more value to compare the consistency of the effect sizes and direction of the effect estimates across methods. Any evidence of such consistency increases our confidence in our main findings, since each method relies on different assumptions. As we cannot be sure about the presence and nature of horizontal pleiotropy, it is useful to compare results across methods even though they are not equally powered. It is true that our results for the genetically predicted effects of body mass index (BMI) on the risk of head and neck cancer (HNC) differ across methods. This is precisely what led us to question the validity of our main finding (suggesting a positive effect of BMI on HNC risk). We have now clarified this in the methods section of the revised manuscript as advised. Lines 165-171:

      “Because the IVW method assumes all genetic variants are valid instruments[44], which is unlikely the case, three pleiotropy-robust two-sample MR methods (i.e., MR-Egger[45], weighted median[46] and weighted mode[47]) were used in sensitivity analyses. When the magnitude and direction of effect estimates are consistent across methods that rely on different assumptions, the main findings are more convincing. As we cannot be sure about the presence and nature of horizontal pleiotropy, it is useful to compare results across methods even if they are not equally powered.”

      We understand that the reviewer/editors are concerned that we do not have a robust model to explore the role of tobacco consumption in the link between BMI and HNC. However, we have a different perspective on the matter. If indeed, the main IVW finding for BMI and HNC is due to pleiotropy (since some of the pleiotropy-robust methods suggest conflicting results), then the IVW multivariable MR method is a way to explore the potential source of this bias[3]. We were particularly interested in exploring the role of smoking in the observed association because smoking and adiposity are known to influence each other [4-9] and share a genetic basis[10, 11].

      We agree that it would be useful to present the univariable MR effect estimates for smoking behaviour and HNC risk along those obtained using multivariable MR. We have now included the univariable MR estimates for both smoking behaviour variables as a note under Supplementary Table 11 and in the manuscript (lines 316-318): “In univariable IVW MR, both CSI and SI were linked to an increased risk of HNC (CSI OR=4.47 per 1-SD higher CSI, 95%CI 3.31–6.03, p<0.001; SI OR=2.07 per 1-SD higher SI 95%CI 1.60–2.68, p<0.001) (Additional File 2: note in Supplementary Table 11).”

      We understand the appeal of conducting stratified MR analyses by smoking status. However, we anticipate such analyses would hinder the interpretation of our findings as they can induce collider bias which could spuriously lead to different effect estimates across strata[12, 13].

      We thank the reviewer/editors for their comment regarding the way we frame of our findings. We have now edited the discussion section to highlight our study results are different to those obtained in studies that do not account for smoking behaviour. Lines 398-401: “With a much larger sample (N=31,523, including 12,264 cases), our IVW MR analysis suggested BMI may play a role in HNC risk, in contrast to previous studies. However, our sensitivity analyses implied that causality was uncertain.”

      Reviewer #1 (Recommendations for the authors):

      The authors do share a table of the percent variance explained of the different genetic instruments, which vary widely, and that table is very welcome because we can get some sense of their utility. The problem is that they don't translate that into a power estimate for the case-control study size that they use. They say that it is the biggest to date, which is good, but without some formal power estimate, it is not particularly reassuring. A framework for MR study power estimates was reported in PMID: 19174578, but that was using very simple MR constructs in use in 2009, and it isn't clear to me if that framework can be used here. That power paper suggests that weak genetic instruments need very large sample sizes, far larger than what is used in the current manuscript. I am unable to estimate the true strength of the instruments used here, and so I am unsure of whether power is an issue or not.

      We have now included power calculations in our manuscript to address the reviewer’s concerns. Nevertheless, as mentioned above, post-hoc power calculations are of limited value, as statistical power is already reflected in the uncertainty around the point estimates (the 95% confidence intervals). Hence, it is important to avoid drawing conclusions regarding the likelihood of true effects or false negatives based on these calculations.

      Although the hypothesis here is that smoking accounts for the apparent BMI association previously reported for HNC, it would have been preferable to see the estimates for their 2 genetic instruments for tobacco alone. The current results only show the BMI instruments alone and then with the tobacco instruments. I would like to see what the risk estimates are for the tobacco instrument alone, so that I can judge for myself what happens in the joint models. As presented, one can only do that for the BMI instruments.

      We thank the reviewer for this comment. The univariable IVW MR estimate of smoking initiation was OR=2.07 (95%CI 1.60 to 2.68, p<0.001), while the one for comprehensive smoking index was OR=4.47 (95%CI 3.31 to 6.03, p<0.001). We have included this information in the manuscript as requested (please see response to reviewing editor above).

      On line 319, they write that "We did not find evidence against bias due to correlated pleiotropy..." I find this difficult to parse, but I think it means that they should believe that correlated pleiotropy remains a problem. So again, they seem to see their primary model as compromised, and so do I. This limitation is again stated by the authors on lines 351-352.

      We apologise if the wording of the sentence was not easy to understand. When using the CAUSE method, we did not find evidence to reject the null hypothesis that the sharing (correlated pleiotropy) model fits the data at least as well as the causal model. In other words, our CAUSE finding and the inconsistencies observed across our other sensitivity analyses led us to believe that our main IVW MR estimate for BMI-HNC was likely biased by correlated pleiotropy. We believe it is important to explore the source of this bias, which is why we used multivariable MR to investigate the direct effect of BMI on HNC risk while accounting for smoking behaviour.

      In the following paragraphs (lines 358-369), the authors state that their findings are consistent with prior reports, but that doesn't seem to be the case if we take their primary BMI instrument as representing the outcome of this manuscript. Here, they find an association between the BMI instrument and HNC risk, but in each of the other papers they present the primary finding was null without the extensive model changes or the aim of accounting for tobacco with another instrument. I don't see that as replication.

      This is a good point. We have now edited the discussion of our manuscript to avoid giving the impression that our findings replicate those from studies that do not account for smoking behaviour in their analyses. We have edited lines 384-401 as follows:

      “Previous MR studies suggest adiposity does not influence HNC risk[27-29]. Gormley et al.[28] did not find a genetically predicted effect of adiposity on combined oral and oropharyngeal cancer when investigating either BMI (OR=0.89 per 1-SD, 95% CI 0.72–1.09, p=0.26), WHR (OR=0.98 per 1-SD, 95% CI 0.74–1.29, p=0.88) or waist circumference (OR=0.73 per 1-SD, 95% CI 0.52–1.02, p=0.07) as risk factors. Similarly, a large two-sample MR study by Vithayathil et al.[29] including 367,561 UK Biobank participants (of which 1,983 were HNC cases) found no link between BMI and HNC risk (OR=0.98 per 1-SD higher BMI, 95% CI 0.93–1.02, p=0.35). Larsson et al.[27] meta-analysed Vithayathil et al.’s[29] findings with results obtained using FinnGen data to increase the sample size even further (N=586,353, including 2,109 cases), but still did not find a genetically predicted effect of BMI on HNC risk (OR=0.96 per 1-SD higher BMI, 95% CI 0.77–1.19, p=0.69). With a much larger sample (N=31,523, including 12,264 cases), our IVW MR analysis suggested BMI may play a role in HNC risk, in contrast to previous studies. However, our sensitivity analyses implied that causality was uncertain.”

      We also deleted part of a sentence in the discussion section, so lines 416-418 now look as follows: “An important strength of our study was that the HEADSpAcE consortium GWAS used had a large sample size which conferred more statistical power to detect effects of adiposity on HNC risk compared to previous MR analyses[27-29].”

      On lines 384-386 they note a strength is that this is the largest study to date, but I would reiterate that larger and more powerful does not equate to adequately powered.

      This is true. We have included power calculations in the manuscript as requested.

      It's well known that different HNC subsites have different etiologies, as they mention on lines 391-392, and it is implicit in their use of data on HPV positive and negative oropharyngeal cancer. They say that they did not find evidence for heterogeneity in this study, but that would only be true for the null BMI instrument. The effect sizes for their smoking instruments are strikingly different between the subsites.

      We agree and are sorry for the confusion we may have caused by the way we worded our findings. We have edited the text to clarify that the lack of subsite heterogeneity only applied to our results for BMI/WHC/WC-HNC risk. Lines 418-424 now read as follows:

      “Furthermore, the availability of data on more HNC subsites, including oropharyngeal cancers by HPV status, allowed us to investigate the relationship between adiposity and HNC risk in more detail than previous MR studies which limited their subsite analyses to oral cavity and overall oropharyngeal cancers[28, 68]. This is relevant because distinct HNC subsites are known to have different aetiologies[69], although we did not find evidence of heterogeneity across subsites in our analyses investigating the genetically predicted effects of BMI, WHR and WC on HNC risk.”

      Finally, the literature on mutational patterns gives us strong reason to believe that HNC caused by tobacco are biologically distinct from tumors not caused by tobacco. The authors report in the introduction that traditional observational studies of BMI and HNC have reported different findings in smokers versus never smokers, so I would assume there is a possibility that the BMI instrument could have different associations with tumors of the tobacco-induced phenotype and tumors with a non-tobacco induced phenotype. I would assume that authors have access to the data on self-reported tobacco use behavior, even if they can't separate these tumors by molecular types. Stratifying their analysis by tobacco users or not might reveal different results with the BMI instrument.

      We appreciate the reviewer’s comment. We agree that it would have been interesting to present stratified analyses by smoking status along our main findings. However, we decided against this because of the risk of inducing collider bias in our MR analyses i.e., where stratifying on smoking status may induce spurious associations between the adiposity instruments and confounding factors. Multivariable MR is considered a better way of investigating the direct effects of an exposure (adiposity) on an outcome (HNC) accounting for a third variable (smoking)[14], which is why we opted for this method instead.

      References:

      (1) Heinsberg LW, Weeks DE: Post hoc power is not informative. Genet Epidemiol 2022, 46(7):390-394.

      (2) Burgess S, Butterworth A, Thompson SG: Mendelian randomization analysis with multiple genetic variants using summarized data. Genet Epidemiol 2013, 37(7):658-665.

      (3) Burgess S, Davey Smith G, Davies NM, Dudbridge F, Gill D, Glymour MM, Hartwig FP, Kutalik Z, Holmes MV, Minelli C et al: Guidelines for performing Mendelian randomization investigations: update for summer 2023. Wellcome Open Res 2019, 4:186.

      (4) Morris RW, Taylor AE, Fluharty ME, Bjorngaard JH, Asvold BO, Elvestad Gabrielsen M, Campbell A, Marioni R, Kumari M, Korhonen T et al: Heavier smoking may lead to a relative increase in waist circumference: evidence for a causal relationship from a Mendelian randomisation meta-analysis. The CARTA consortium. BMJ Open 2015, 5(8):e008808.

      (5) Taylor AE, Morris RW, Fluharty ME, Bjorngaard JH, Asvold BO, Gabrielsen ME, Campbell A, Marioni R, Kumari M, Hallfors J et al: Stratification by smoking status reveals an association of CHRNA5-A3-B4 genotype with body mass index in never smokers. PLoS Genet 2014, 10(12):e1004799.

      (6) Taylor AE, Richmond RC, Palviainen T, Loukola A, Wootton RE, Kaprio J, Relton CL, Davey Smith G, Munafo MR: The effect of body mass index on smoking behaviour and nicotine metabolism: a Mendelian randomization study. Hum Mol Genet 2019, 28(8):1322-1330.

      (7) Asvold BO, Bjorngaard JH, Carslake D, Gabrielsen ME, Skorpen F, Smith GD, Romundstad PR: Causal associations of tobacco smoking with cardiovascular risk factors: a Mendelian randomization analysis of the HUNT Study in Norway. Int J Epidemiol 2014, 43(5):1458-1470.

      (8) Carreras-Torres R, Johansson M, Haycock PC, Relton CL, Davey Smith G, Brennan P, Martin RM: Role of obesity in smoking behaviour: Mendelian randomisation study in UK Biobank. BMJ 2018, 361:k1767.

      (9) Freathy RM, Kazeem GR, Morris RW, Johnson PC, Paternoster L, Ebrahim S, Hattersley AT, Hill A, Hingorani AD, Holst C et al: Genetic variation at CHRNA5-CHRNA3-CHRNB4 interacts with smoking status to influence body mass index. Int J Epidemiol 2011, 40(6):1617-1628.

      (10) Thorgeirsson TE, Gudbjartsson DF, Sulem P, Besenbacher S, Styrkarsdottir U, Thorleifsson G, Walters GB, Consortium TAG, Oxford GSKC, consortium E et al: A common biological basis of obesity and nicotine addiction. Transl Psychiatry 2013, 3(10):e308.

      (11) Wills AG, Hopfer C: Phenotypic and genetic relationship between BMI and cigarette smoking in a sample of UK adults. Addict Behav 2019, 89:98-103.

      (12) Coscia C, Gill D, Benitez R, Perez T, Malats N, Burgess S: Avoiding collider bias in Mendelian randomization when performing stratified analyses. Eur J Epidemiol 2022, 37(7):671-682.

      (13) Hamilton FW, Hughes DA, Lu T, Kutalik Z, Gkatzionis A, Tilling K, Hartwig FP, Davey Smith G: Non-linear Mendelian randomization: evaluation of effect modification in the residual and doubly-ranked methods with simulated and empirical examples. Eur J Epidemiol 2025.

      (14) Sanderson E, Davey Smith G, Windmeijer F, Bowden J: An examination of multivariable Mendelian randomization in the single-sample and two-sample summary data settings. Int J Epidemiol 2019, 48(3):713-727.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Reviewer #1 (Public review):

      Summary:

      The authors use high-throughput gene editing technology in larval zebrafish to address whether microexons play important roles in the development and functional output of larval circuits. They find that individual microexon deletions rarely impact behavior, brain morphology, or activity, and raise the possibility that behavioral dysregulation occurs only with more global loss of microexon splicing regulation. Other possibilities exist: perhaps microexon splicing is more critical for later stages of brain development, perhaps microexon splicing is more critical in mammals, or perhaps the behavioral phenotypes observed when microexon splicing is lost are associated with loss of splicing in only a few genes.

      A few questions remain:

      (1) What is the behavioral consequence for loss of srrm4 and/or loss-of-function mutations in other genes encoding microexon splicing machinery in zebrafish?

      It has been established that srrm4 mutants exhibit no overt morphological phenotypes and are not visually impaired (Ciampi et al., 2022). We are coordinating our publication with Lopez-Blanch et al. (https://doi.org/10.1101/2024.10.23.619860), which shows that srrm4 mutants also have minimal behavioral phenotypes. In contrast, srrm3 mutants have severe vision loss, early mortality, and numerous neural and behavioral phenotypes (Ciampi et al., 2022; Lopez-Blanch et al., 2024). We now point out the phenotypes of srrm3/srrm4 mutants in the manuscript.

      We chose not to generate and characterize the behavior and brain activity of srrm3/srrm4 mutants for two reasons: 1) we were aware of two other labs in the zebrafish community that had generated srrm3 and/or srrm4 mutants (Ciampi et al., 2022 and Gupta et al., 2024, https://doi.org/10.1101/2024.11.29.626094; Lopez-Blanch et al., 2024, https://doi.org/10.1101/2024.10.23.619860), and 2) we were far more interested in determining the importance of individual microexons to protein function, rather than loss of the entire splicing program. Microexon inclusion can be controlled by different splicing regulators, such as srrm3 (Ciampi et al., 2022) and possibly other unknown factors. Genetic compensation in srrm4 mutants could also result in microexons still being included through actions of other splicing regulators, complicating the analysis of these regulators. We mention srrm4 in the manuscript to point out that some selected microexons are adjacent to regulatory elements expected of this pathway. We did not, however, choose microexons to mutate based on whether they were regulated by Srrm4, making the characterization of srrm3/srrm4 mutants disconnected from our overarching project goal.

      We have edited the Introduction as follows to clarify our goal: “Studies of splicing regulators such as srrm4 impact the entire splicing program, making it impossible to determine the importance of individual microexons to protein function. Further, microexons could still be differentially included in a regulatory mutant via compensation by other splicing factors ...”

      (2) What is the consequence of loss-of-function in microexon splicing genes on splicing of the genes studied (especially those for which phenotypes were observed).

      We are unclear whether “microexon splicing genes” refers to the splicing regulators srrm3/srrm4, which we choose not to study in this work (see response to point #1 above), or the genes that contain microexons. The severe visual phenotypes of srrm3 mutants confounds the study of microexon splicing in this line because altered splicing levels could be due to downstream changes in this significantly different developmental context. A detailed discussion of splicing consequences on removal of microexons from microexoncontaining genes is in the response to point #4 below.

      (3) For the microexons whose loss is associated with substantial behavioral, morphological, or activity changes, are the same changes observed in loss-of-function mutants for these genes?

      In the first version of the manuscript, we had included two explicit comparisons of microexon loss with a standard loss-of-function allele, one with a phenotype and one without, in Figure S1 (now Figures S3 and S4) of this manuscript. Beyond the two pairs we had included, Lopez-Blanch et al. (https://doi.org/10.1101/2024.10.23.619860) described mild behavioral phenotypes for a microexon removal for kif1b, and we showed developmental abnormalities for the kif1b loss-of-function allele (now Figure S3). We have now added a predicted protein-truncating allele for ppp6r3. This new line has phenotypes that are similar but slightly stronger in brain activity and structure than the mutant that lacks only the microexon. The prior Figure S1 (now Figures S3 and S4) was only briefly mentioned in the first version of the manuscript, and we now clarify this point in the Results: “Protein-truncating mutations in eleven additional genes that contain microexons revealed developmental and neural phenotypes in zebrafish (Figure S3, Figure S4), indicating that the genes themselves are involved in biologically relevant pathways. Three of these genes– tenm4, sptan1, and ppp6r3 – are also in our microexon line collection.”

      Additionally, we can draw expected conclusions from the literature, as some genes with our microexon mutations have been studied as typical mutants in zebrafish or mice. We have modified our manuscript to include a discussion of both loss-of-function zebrafish and mouse mutants. See the response to below point #4.

      (4) Do "microexon mutations" presented here result in the precise loss of those microexons from the mRNA sequence? E.g. are there other impacts on mRNA sequence or abundance?

      We acknowledge that unexpected changes to the mRNA of the tested mutants could occur following microexon removal. In particular, all regulatory elements should be removed from the region surrounding the microexon, as any remaining elements could drive the inclusion of unexpected exons that result in premature stop codons.

      First, we have clarified our generated mutant alleles by adding a figure (Figure S1) that details the location of the gRNA cut sites in relation to the microexon, its predicted regulatory elements, and its neighboring exons.

      Second, we have experimentally determined whether the mRNA was modified as expected for a subset of mutants with phenotypes. In all eight tested lines (Figure S2), the microexon was precisely eliminated without causing any other effects on the sequence of the transcript in the neighboring region. We did, however, observe an effect on transcript abundance for one homozygous mutant (vav2). It is possible that complex forms of genetic regulation are occurring that are not induced by unexpected isoforms or premature stop codons. Interestingly, Lopez-Blanch et al. (https://doi.org/10.1101/2024.10.23.619860) eliminated a different microexon in vav2 and also observed a subtle well center preference. If their allele from an entirely different intronic region also results in transcript downregulation, it would support the hypothesis of genetic compensation through atypical pathways. If not, it is likely this phenotype is due specifically to removal of the microexon protein sequence. Not all mutants with phenotypes could be assessed with qRT-PCR because some were no longer present in the lab. All lines were generated in a similar way, however, removing both the microexon and neighboring regulatory elements while avoiding the neighboring exons. Accordingly, we now also explicitly point out those where the clean loss of the microexon was confirmed (eif4g3b, ppp6r3, sptan1, vti1a, meaf6, nrxn1a, tenm3) and those with possibly interesting phenotypes that were not confirmed (ptprd-1, ptprd-2, rapgef2, dctn4, dop1a, mapk8ip3).

      Third, we have further emphasized in the manuscript that these observed phenotypes are extremely mild compared to those observed in over one hundred protein-truncating mutations we have assessed in previous (Thyme et al., 2019; Capps et al., 2024) and unpublished ongoing work. We showed data for one mutant, tcf7l2, which we consider to have moderately strong neural phenotypes, and we have extended this comparison in the revision (new Figure 3G). Additionally, loss-of-function alleles for some microexoncontaining genes have strong developmental phenotypes, as we showed in Figure S1 (now Figures S3 and S4) of this manuscript in addition to our published work (Thyme et al., 2019; Capps et al., 2024). It is known from the literature that the loss-of-function mutants for mapk8ip3 are stronger than we observed here (Tuttle., et al., 2019), suggesting that only the microexon is removed in our line. The microexons in Ptprd are also well-studied in mice, and we expect that only the microexon was removed in our lines. Both Dctn4 and Rapgef2 are completely lethal prior to weaning in mice (the International Mouse Phenotyping Consortium).

      (5) Microexons with a "canonical layout" (containing TGC / UC repeats) were selected based on the likelihood that they are regulated by srrm4. Are there other parallel pathways important for regulating the inclusion of microexons? Is it possible to speculate on whether they might be more important in zebrafish or in the case of early brain development?

      The microexons were not selected based on the likelihood that they were regulated by Srrm4. We have clarified the manuscript regarding this point. There are parallel pathways that can control the inclusion of microexons, such as Srrm3 (Ciampi et al., 2022). It is wellknown that loss of srrm3 has a stronger impact on zebrafish development than srrm4 (Ciampi et al., 2022). The goal of our work was not to investigate these splicing regulators but instead to determine the individual importance of these highly conserved protein changes.

      Strengths:

      (1) The authors provide a qualitative analysis of splicing plasticity for microexons during early zebrafish development.

      (2) The authors provide comprehensive phenotyping of microexon mutants, addressing the role of individual microexons in the regulation of brain morphology, activity, and behavior.

      We thank the reviewer for their support. The pErk brain activity mapping method is highly sensitive, significantly minimizing the likelihood that the field has simply not looked hard enough for a neural phenotype in these microexon mutants. In our published work (Thyme et al., 2019), we show that brain activity can be drastically impacted without manifesting in differences in those behaviors assessed in a typical larval screen (e.g., tcf4, cnnm2, and more).

      Weaknesses:

      (1) It is difficult to interpret the largely negative findings reported in this paper without knowing how the loss of srrm4 affects brain activity, morphology, and behavior in zebrafish.

      See response to point 1.

      (2) The authors do not present experiments directly testing the effects of their mutations on RNA splicing/abundance.

      See response to point 4.

      (3) A comparison between loss-of-function phenotypes and loss-of-microexon splicing phenotypes could help interpret the findings from positive hits.

      See response to points 3 and 4.

      Reviewer #2 (Public review):

      Summary:

      The manuscript from Calhoun et al. uses a well-established screening protocol to investigate the functions of microexons in zebrafish neurodevelopment. Microexons have gained prominence recently due to their enriched expression in neural tissues and misregulation in autism spectrum disease. However, screening of microexon functionality has thus far been limited in scope. The authors address this lack of knowledge by establishing zebrafish microexon CRISPR deletion lines for 45 microexons chosen in genes likely to play a role in CNS development. Using their high throughput protocol to test larval behaviour, brain activity, and brain structure, a modest group of 9 deletion lines was revealed to have neurodevelopmental functions, including 2 previously known to be functionally important.

      Strengths:

      (1) This work advances the state of knowledge in the microexon field and represents a starting point for future detailed investigations of the function of 7 microexons.

      (2) The phenotypic analysis using high-throughput approaches is sound and provides invaluable data.

      We thank the reviewer for their support.

      Weaknesses:

      (1) There is not enough information on the exact nature of the deletion for each microexon.

      To clarify the nature of our mutant alleles, we have added a figure (Figure S1) that details the location of the microexon in relation to its predicted neighboring exons, deletion boundaries, guide RNAs, and putative regulatory elements.

      (2) Only one deletion is phenotypically analysed, leaving space for the phenotype observed to be due to sequence modifications independent of the microexon itself.

      We have determined whether the mRNA is impacted in unanticipated ways for a subset of mutants with mild phenotypes (see point #4 responses to Reviewer 1 for details). Our findings for three microexon mutants (ap1g1, vav2, and vti1a) are corroborated by LopezBlanch et al. (https://doi.org/10.1101/2024.10.23.619860). We have also already compared the microexon removal to a loss-of-function mutant for two lines (Figures S3 and S4), and we have made this comparison more obvious as well as increasing the discussion of the expected phenotypes from typical loss-of-function mutants (see point #3 response to reviewer 1).

      Unlike protein-coding truncations, clean removal of the microexon and its regulatory elements is unlikely to yield different phenotypic outcomes if independent lines are generated (with the exception of genetic background effects). When generating a proteintruncating allele, the premature stop codon can have different locations and a varied impact on genetic compensation. In previous work (Capps et al., 2024), we have observed different amounts of nonsense-mediated decay-induced genetic compensation (El-Brolosy, et al., 2019) depending on the location of the mutation. As they lack variable premature stop codons (the expectation of a clean removal), two mutants for the same microexons should have equivalent impacts on the mRNA.

      We now address the concern of subtle genetic background effects in the Methods: “Even with using sibling controls and collecting multiple biological replicates from individual parents, the possibility remains that linked genetic variation may have contributed to the mild phenotypes we observed, as only a single line was generated.”

      Reviewer #3 (Public review):

      Summary:

      This paper sought to understand how microexons influence early brain function. By selectively deleting a large number of conserved microexons and then phenotyping the mutants with behavior and brain activity assays, the authors find that most microexons have minimal effects on the global brain activity and broad behaviors of the larval fish-- although a few do have phenotypes.

      Strengths:

      The work takes full advantage of the scale that is afforded in zebrafish, generating a large mutant collection that is missing microexons and systematically phenotyping them with high throughput behaviour and brain activity assays. The work lays an important foundation for future studies that seek to uncover the likely subtle roles that single microexons will play in shaping development and behavior.

      We thank the reviewer for their support.

      Weaknesses:

      The work does not make it clear enough what deleting the microexon means, i.e. is it a clean removal of the microexon only, or are large pieces of the intron being removed as well-- and if so how much? Similarly, for the microexon deletions that do yield phenotypes, it will be important to demonstrate that the full-length transcript levels are unaffected by the deletion. For example, deleting the microexon might have unexpected effects on splicing or expression levels of the rest of the transcript that are the actual cause of some of these phenotypes.

      To clarify the nature of our mutant alleles, we have added a figure (Figure S1) that details the location of the microexon in relation to its predicted neighboring exons, deletion boundaries, guide RNAs, and putative regulatory elements. We have determined whether the mRNA is impacted in unanticipated ways for a subset of mutants with mild phenotypes (see point #4 responses to Reviewer 1 for details).

      Reviewer #1 (Recommendations for the authors):

      (1) For most ME mutations, 4 guide sequences are provided. More description / a diagram could be helpful to interpret how ME mutations were generated.

      We have added diagrams to the Supplementary Materials (new Figure S1) to show where the guide RNAs, cut sites, and putative regulatory elements are in relationship to the microexon and its neighboring exons. We have also added the following point to the text: “Four guide RNAs were used, two on each side of the microexon (Table S2, Figure S1).”

      (2) Figure 1 indicates that there are 45 microexons (MEs) but the text initially indicates that there are 44 that exist in a canonical layout (the text later indicates there are 45). This could be made more clear.

      The 45 refers to the mutants that were generated, not the microexons with putative Srrm4 regulatory elements. We did not choose microexons to mutate based on whether they were regulated by Srrm4. We have clarified these points in the manuscript as follows: “Of these 95 microexons, 42 exist in a canonical layout in the zebrafish genome, with both a UGC and UC repeat – or similar polypyrimidine tract – directly upstream of the alternatively spliced exon (Gonatopoulos-Pournatzis et al., 2018) (Table S1), indicating that Srrm4 likely controls their inclusion. Of the remaining microexons, 44 are organized similarly to the canonical layout, typically with either a UGC or UC repeat. Thus, they may also be regulated by Srrm4.” and “Using CRISPR/Cas9, we generated lines that removed 45 conserved microexons  (Table S2) and assayed larval brain activity, brain structure, and behavior (Figure 1A). Four guide RNAs were used, two on each side of the microexon (Table S2, Figure S1). For microexons with upstream regulatory elements that are likely important for splicing, these elements were also removed (Figure S1).”

      (3) The description of the "canonical layout" as containing TGC / UC repeats could be rewritten as either "containing a UGC motif and UC repeats" or "containing a TGC motif and TC repeats."

      This error has been corrected.

      (4) Why was tcf7l2 selected as a control for MAP mapping?

      The mutant for tcf7l2 is an example of a moderately strong phenotype from a recent study we completed (Capps et al., 2025). This mutant was selected because it has both increased and decreased activity and structure and is ideal for setting the range of the graph. We now include a comparison to additional mutants from this study of autism genes (Capps et al., 2025) to further demonstrate how mild the phenotypes are in the microexon removal mutants (new Figure 3G). We also include the activity and structure maps of tcf7l2 mutants in Supplementary Figures 9 and 11.

      (5) What does it mean that of the remaining microexons, most are similar to canonical layout?

      Typically, they would have one of the two regulatory elements instead of both or the location of the possible elements would be slightly farther away than expected. We have clarified this point in the manuscript as follows: “Of these 95 microexons, 42 exist in a canonical layout in the zebrafish genome, with both a UGC and UC repeat  or similar polypyrimidine tract – directly upstream of the alternatively spliced exon (Gonatopoulos-Pournatzis et al., 2018) (Table S1), indicating that Srrm4 likely controls their inclusion. Of the remaining microexons, 44 are organized similarly to the canonical layout, typically with either a UGC or UC repeat. Thus, they may also be regulated by Srrm4.”

      (6) Figure 2A is very difficult to see - most are either up or down - suggest splitting into 2 figures - one = heat map, second can summarize values that were both up and down.

      We prefer to retain this information for accuracy. The bubble location is offset to effectively share the box between the orange (decreased) and purple (increased) measures. For example, and as noted in the methods and now expanded upon, a measure can change between 4 and 6 dpf or a measure such as bout velocity could be increased while the distance traveled is decreased (both are magnitude measures). The offset of the bubbles is consistently 0.2 data units in x and y from the center of the box.

      (7) The authors apply rigorous approaches to testing the importance of microexons. I especially appreciate the inclusion of separate biological replicates in the main figures!

      We thank the reviewer for their positive feedback.

      (8) Page 5 line 5 - suggest "compared to homozygous mutants".

      The change has been made.

      (9) For Eif5g3b dark flash phenotype, it's not clear what "p-values are not calculated for response plots" means. A p-value is provided in the plot for ppp6r3 response freq.

      The eif4g3b plot is the actual response trace measuring through pixel changes whereas the ppp6r3 is the frequency of response. While informative, the response plot is time-based data with a wide dynamic range, making the average signal across the entire time window meaningless. We include the p-values for a related measure, the latency for the first 10 dark flashes in block 1 (day6dpfdf1a_responselatency) in the legend.

      (10) The ptprd phenotype in 2D is not described in the text.

      The change has been made.

      (11) Page 7 line 7: "mild" is repeated.

      This error has been corrected.

      Reviewer #2 (Recommendations for the authors):

      Specific points for needed improvement:

      (1) The title should be adjusted to more accurately describe the results. The term 'minimal' is under-representing the findings. 9/45 (20%) of targets in their screen have some phenotype, indicating that a significant number have indeed an important function. Moreover, the phenotypic analysis is limited, leaving space for missed abnormalities (as discussed by the authors). I would therefore suggest a more neutral title such as 'Systematic genetic deletion of microexons uncovers their roles in zebrafish brain development and larval behaviour'.

      While some microexon mutants do have repeatable phenotypes, these phenotypes are far milder than phenotypes observed in other mutant sets. We now include a comparison to additional mutants from this study of autism genes (Capps et al.,2025) to further demonstrate how mild the phenotypes are in the microexon removal mutants (new Figure 3G). The title states that these microexons have a minimal impact on larval zebrafish brain morphology and function, leaving room for the possibility of adult phenotypes. Thus, we prefer to retain this title.

      (2) Do the 45 chosen microexons correspond to the 44 with a canonical layout with TGC and UC repeats? If so, it needs to be explicitly stated in the text that exons were chosen for mutation based on the potential for SRRM4 regulation. If not, then the rationale for the choice of the 45 mutants from the 95 highly conserved events needs to be explained further.

      The 45 refers to the mutants that were generated, not the microexons with putative Srrm4 regulatory elements. We did not choose microexons to mutate based on whether they were regulated by Srrm4. We have clarified these points in the manuscript as follows: “Of these 95 microexons, 42 exist in a canonical layout in the zebrafish genome, with both a UGC and UC repeat – or similar polypyrimidine tract – directly upstream of the alternatively spliced exon (Gonatopoulos-Pournatzis et al., 2018) (Table S1), indicating that Srrm4 likely controls their inclusion. Of the remaining microexons, 44 are organized similarly to the canonical layout, typically with either a UGC or UC repeat. Thus, they may also be regulated by Srrm4.” and “Using CRISPR/Cas9, we generated lines that removed 45 conserved microexons (Table S2) and assayed larval brain activity, brain structure, and behavior (Figure   1A). Four guide RNAs were used, two on each side of the microexon (Table S2, Figure S1). For microexons with upstream regulatory elements that are likely important for splicing, these elements were also removed (Figure S1).”

      There was no clear rationale for those that were selected. We attempted to generate all 95 and some mutants were not successfully generated in our initial attempt. As we found minimal phenotypes, we elected to not continue to make the remaining ones on the list.

      (3) More detail regarding the design of guides for CRISPR is required in the text in the methods section. From Table S2, 4 guides were used per microexon. Were these designed to flank the microexon? How far into the intronic sequence were the guides designed? Were the splicing regulatory sequences (polypyrimidine tract, branchpoint) also removed? The flanking sequences of each of the 45 deletion lines need to be provided.

      We have added diagrams to the Supplementary Materials (new Figure S1) to show where the guide RNAs, cut sites, and putative regulatory elements are in relationship to the microexon and its neighboring exons. We removed the microexon and the surrounding area that contains the putative regulatory elements.

      (4) Following on from the previous point, to ascertain that the phenotype observed is truly due to lack of microexon (rather than other event linked to removed intronic sequences) - for the 7 exons newly identified as functionally important, at least one added deletion line has to be shown, presenting the same phenotype. If making 7 more lines can't be achieved in a reasonable time (we are aware this is a big ask), a MO experiment blocking microexon splicing needs to be provided (may not be ideal for analysis at 6 dpf). For the existing mutants and the new ones (or morphants), sequencing of the mRNAs for the 7 genes in mutants and siblings also needs to be added to check any possible change in other variants.

      Unlike protein-coding truncations, clean removal of the microexon and its regulatory elements is unlikely to yield different phenotypic outcomes if independent lines are generated (with the exception of genetic background effects). When generating a protein-truncating allele, the premature stop codon can have different locations and a varied impact on genetic compensation. In previous work (Capps et al., 2024), we have observed different amounts of nonsense-mediated decay-induced genetic compensation (El-Brolosy, et al., 2019) depending on the location of the mutation. As they lack variable premature stop codons (the expectation of a clean removal), two mutants for the same microexons should have equivalent impacts on the mRNA. We acknowledge that we inadequately described the generation of these alleles, and we now provide Figure S1 to show the microexon’s relationship to possible regulatory elements that impact splicing in unexpected ways if they remain.

      We now acknowledge the concern of subtle genetic background effects in the Methods: “Even with using sibling controls and collecting multiple biological replicates from individual parents, the possibility remains that linked genetic variation may have contributed to the mild phenotypes we observed, as only a single line was generated.”

      Given the caveats of MOs and transient microinjection for the study of 6 dpf phenotypes, we disagree that this suggested experiment would provide value. The phenotypic assays we use are highly sensitive, and we would not even trust CRISPANTs to yield reliable data. We have added an additional loss-of-function allele for ppp6r3 from the Sanger knockout project, which has a similar but stronger size change to the ppp6r3 microexon-removal line. In addition, our findings for three microexon mutants (ap1g1, vav2, and vti1a) are corroborated by Lopez-Blanch et al. (https://doi.org/10.1101/2024.10.23.619860).

      To support that these we generated clean removal of these microexons, we experimentally determined whether the mRNA is impacted in unanticipated ways for a subset of mutants with mild phenotypes (see the point #4 public response to Reviewer 1). We also have already compared the microexon removal to a loss-offunction mutant for two lines (Figure S1), and we have made that outcome more obvious as well as increasing the discussion of the expected phenotypes from typical loss-of-function mutants (see point #3 public response to Reviewer 1).

      (5) Figure 3: An image of control tcf7l2 mutant brain activity as a reference should be included.

      We now include the activity and structure maps of tcf7l2 mutants in Supplementary Figures 9 and 11.

      (6) Figure 3a/b. The gene names on the y-axis of the pERK and structure comparisons should be reordered to be alphabetical so that phenotypes can be compared by the reader for the same microexon across the two assays.

      These data are clustered so that any similarities between maps can be recognized. We prefer to retain the clustering to compare lines to each other.

      (7) Figure S6 legend. Including graph titles like "day3msdf_dpix_numberofbouts_60" is not comprehensible to the reader so should be replaced with more descriptive text. As should jargon such as "combo plot" and"habituation_day5dpfhab1post_responsefrequency_1_a1f1000d5p" etc.

      The legend has been edited to describe the experiments. Subsections of the prior names are maintained in parentheses to enable the reader to connect the plots in this figure to the specific image and underlying data in Zenodo.

      (8) Page 2 line 21 "to enable proper".

      The change has been made.

      (9) Page 7 line 7. Repeatable phenotypes were mild mild.

      This error has been corrected.

      Reviewer #3 (Recommendations for the authors):

      (1) Figure 1B is confusingly laid out.

      We are unclear how to modify Figure 1B, as it is a bar plot. We have modified several figures to improve clarity.

      (2) Figure 1E-there are some pictures of zebrafish but to what end? They aren't labelled. The dark "no expression" looks really similar to the dark green, "high expression".

      The zebrafish images represent the ages assessed for microexon inclusion. We have added labels to clarify this point.

      (3) The main text says "microexons were removed by Crispr" but there is no detail in the main text about this at all-- and barely any in the methods. What does it mean to be removed? Cleanly? Or including part of the introns on either side? Etc. How selected, raised, etc? I can glean some of this from the Table S2 if I do a lot of extra work, but at least some notes about this would be important.

      We have added diagrams to the Supplementary Materials (new Figure S1) to show where the guide RNAs, cut sites, and putative regulatory elements are in relationship to the microexon and its neighboring exons. We removed the microexon and the surrounding area that contains the putative regulatory elements.

      (4) Figure 2 - There are no Ns, at least for the plots on the right. The reader shouldn't have to dig deep in Table S2 to find that. It is also unclear why heterozygous fish are not included in these analyses, since there are sibling data for all. Removed for readability of the plots might be warranted, but this should be made explicitly clear.

      The Ns for these plots have been added to the legend. The legend was also modified as follows: “Comparisons to the heterozygous larvae are removed for clarity and available in the Supplementary Materials, as they often have even milder phenotypes than homozygous.”

      (5) Needed data: for those with phenotypes, some evidence should be presented that the full-length transcripts that encode proteins without the microexons are still expressed at the same level and without splicing errors/NMD. Otherwise, some of these phenotypes that were found could be due to knockdown or LOF (or I suppose even overexpression) of the targeted gene.

      We have added a new Supplementary Figure S2 confirming clean removal of the microexons with RT-PCR for a subset of mutants with phenotypes. This figure also includes qRT-PCR for the same subset. We now discuss these findings: Results: “For eight mutant lines, we confirmed that the microexon was eliminated from the transcripts as expected (Figure S2). Although our genomic deletion did not yield unexpected isoforms, qRT-PCR on these eight lines revealed significant downregulation for the homozygous vav2 mutant (Figure S2), indicating possibly complex genetic regulation.”

    1. Reviewer #2 (Public review):

      Summary:

      This manuscript investigates the mechanism by which chronic stress induces degeneration of locus coeruleus (LC) neurons. The authors demonstrate that chronic stress leads to the internalization of α2A-adrenergic receptors (α2A-ARs) on LC neurons, causing increased cytosolic noradrenaline (NA) accumulation and subsequent production of the neurotoxic metabolite DOPEGAL via monoamine oxidase A (MAO-A). The study suggests a mechanistic link between stress-induced α2A-AR internalization, disrupted autoinhibition, elevated NA metabolism, activation of asparagine endopeptidase (AEP), and Tau pathology relevant to Alzheimer's disease (AD). The conclusions of this paper are well-supported mainly by the data, but some aspects of image acquisition require further examination.

      Strengths:

      This study clearly demonstrates the effects of chronic stimulation on the excitability of LC neurons using electrophysiological techniques. It also elucidates the role of α2-adrenergic receptor (α2-AR) internalization and the associated upstream and downstream signaling pathways of GIRK-1, using a range of pharmacological agents, highlighting the innovative nature of the work. Additionally, the study identifies the involvement of the MAO-A-DOPEGAL-AEP pathway in this process. The topic is timely, the proposed mechanistic pathway is compelling, and the findings have translational relevance, particularly in relation to therapeutic strategies targeting α2A-AR internalization in neurodegenerative diseases.

      Weaknesses:

      (1) The manuscript reports that chronic stress for 5 days increases MAO-A levels in LC neurons, leading to the production of DOPEGAL, activation of AEP, and subsequent tau cleavage into the tau N368 fragment, ultimately contributing to neuronal damage. However, the authors used wild-type C57BL/6 mice, and previous literature has indicated that AEP-mediated tau cleavage in wild-type mice is minimal and generally insufficient to cause significant behavioral alterations. Please clarify and discuss this apparent discrepancy.

      (2) It is recommended that the authors include additional experiments to examine the effects of different durations and intensities of stress on MAO-A expression and AEP activity. This would strengthen the understanding of stress-induced biochemical changes and their thresholds.

      (3) Please clarify the rationale for the inconsistent stress durations used across Figures 3, 4, and 5. In some cases, a 3-day stress protocol is used, while in others, a 5-day protocol is applied. This discrepancy should be addressed to ensure clarity and experimental consistency.

      (4) The abbreviation "vMAT2" is incorrectly formatted. It should be "VMAT2," and the full name (vesicular monoamine transporter 2) should be provided at first mention.

      Comments on revisions:

      The authors have addressed all of the reviewers' comments.

    2. Author response:

      The following is the authors’ response to the previous reviews

      Reviewer # 1 (Public review)

      This study aims to elucidate the mechanisms by which stress-induced α2A-adrenergic receptor (α2A-AR) internalization leads to cytosolic noradrenaline (NA) accumulation and subsequent neuronal dysfunction in the locus coeruleus (LC). While the manuscript presents an interesting but ambitious model involving calcium dynamics, GIRK channel rundown, and autocrine NA signaling, several key limitations undermine the strength of the conclusions. 

      (1) First, the revision does not include new experiments requested by reviewers to validate core aspects of the mechanism. Specifically, there is no direct measurement of cytosolic NA levels or MAO-A enzymatic activity to support the link between receptor internalization and neurochemical changes. The authors argue that such measurements are either not feasible or beyond the scope of the study, leaving a significant gap in the mechanistic chain of evidence. 

      Although the reviewer #1 commented that “The authors argue that such measurements are either not feasible or beyond the scope of the study, leaving a significant gap in the mechanistic chain of evidence”, we believe that this comment may be unfair. 

      It may be unfair for the reviewer #1 to neglect our responses to the original reviewer comments regarding the direct measurement of cytosolic NA levels. It is true that none of the recommended methods to directly measure cytosolic NA levels are not feasible as described in the original authors’ response (see the original authors’ response to the comment raised by the Reviewer #1 as Recommendations for the authors (2)). To measure extracellular NA with GRAB-NE photometry, α2A-ARs must be expressed in the cell membrane. GRAB-NE photometry is not applicable unless α2A-ARs are expressed, whereas increases in cytosolic NA levels are caused by internalization of α2A-ARs in our study.

      In our study, we elaborated to detect the change in MAO-A protein with Western blot method, instead of examining MAO-A enzymatic activity. Because the relative quantification of active AEP and Tau N368 proteins by Western blot analysis should accurately reflect the change in the MAO-A enzymatic activity, enzymatic assay may not be necessarily required while we admit the necessity of enzymatic assay to better demonstrate the MAO-A activities as discussed in the previously revised manuscript (R1, page 10, lines 314-315). 

      We used the phrase “beyond the scope of the current study” for “the mechanism how Ca<sup>2+</sup> activates MAO-A” as described in the original authors’ responses (see the original authors’ response to the comment raised by the Reviewer #1 as Weakness (3)). We do not think that this mechanism must be investigated in the present study because the Ca<sup>2+</sup> dependent nature of MAO-A activity is already known (Cao et al., 2007). 

      On the other hand, because it is not possible to measure cytosolic NA levels with currently available methods, the quantification of the connection between α2A-AR internalization and increased cytosolic NA levels must be considered outside the scope of the study. However, our study demonstrated the qualitative relationship between α2A-AR internalization and active-AEP/TauN-368 reflecting increased cytosolic NA levels, leaving “a small gap in the mechanistic chain of evidence.” Therefore, it may be unreasonable to criticize our study as “leaving a significant gap in the mechanistic chain of evidence” with the phrase “beyond the scope of the current study.” 

      (2) Second, the behavioral analysis remains insufficient to support claims of cognitive impairment. The use of a single working memory test following an anxiety test is inadequate to verify memory dysfunction behaviors. Additional cognitive assays, such as the Morris Water Maze or Novel Object Recognition, are recommended but not performed.

      As described in the original authors’ response (see the original authors’ response to the comment raised by the Reviewer #1 as Weakness (4)), we had already done another behavioral test using elevated plus maze (EPM) test. By combining the two tests, it may be possible to more accurately evaluate the results of Y-maze test by differentiating the memory impairment from anxiety. However, the results obtained by these behavioral tests showed that chronic RS mice displayed both anxiety-like and memory impairment-like behaviors. Accordingly, we have softened the implication of anxiety and memory impairment (page 13, lines 396-399) and revised the abstract (page 2, line 59) in the revised manuscript (R2).  

      (3) Third, concerns regarding the lack of rigor in differential MAO-A expression in fluorescence imaging were not addressed experimentally. Instead of clarifying the issue, the authors moved the figure to supplementary data without providing further evidence (e.g., an enzymatic assay or quantitative reanalysis of Western blot, or re-staining of IF for MAO-A) to support their interpretation.

      Because the quantification of MAO-A expression can be performed with greater accuracy by means of Western blot than by immunohistochemistry, we have moved the immunohistochemical results (shown in Figure 5) to the supplemental data (Figure S8) following the suggestion made by the Reviewer #3. As the relative quantification of active AEP and Tau N368 proteins by Western blot analysis may accurately reflect changes in the MAO-A enzymatic activity which is consistent with the result of Western blot analysis of MAO-A, enzymatic assay or re-staining of immunofluorescence for MAO-A may not be necessarily required. We do not think that a new experiment of Western blot analysis is necessary to re-evaluate MAO-A just because of the lack of the less-reliable quantification of immunohistochemical staining.

      (4) Fourth, concerns regarding TH staining remain unresolved. In Figure S7, the α2A-AR signal appears to resemble TH staining, and vice versa, raising the possibility of labeling errors. It is recommended that the authors re-examine this issue by either double-checking the raw data or repeating the immunostaining to validate the staining.

      The reviewer #3 is misunderstanding Figure S7. In Figure S7, there are two types of α2A-AR expressing neurons; one is TH-positive LC neuron and the other is TH-negative neuron in mesencephalic trigeminal nucleus (MTN). This clearly indicates that TH staining is specific. Furthermore, α2A-AR staining was much more extensive in MTN neurons than in LC neurons. Thus, α2A-AR signal is not similar to TH signal and there are no labeling errors, which is also evident in the merged image (Figure S7C).

      (5) Overall, the manuscript offers a potentially interesting framework but falls short in providing the experimental rigor necessary to establish causality. The reliance on indirect reasoning and reorganizing of existing data, rather than generating new evidence, limits the overall impact and interpretability of the study.

      Overall, the reviewer #1 was not satisfied with our revision regardless of the authors’ responses. As detailed above in our responses to the replies (1)~(4), we believe that in the original authors’ responses and in the above-described responses we effectively responded to the criticisms by the reviewer #1.

      Reviewer #2 (Public review): 

      Comments on revisions: 

      The authors have addressed all of the reviewers' comments.

      We appreciate constructive and helpful comments made by the reviewer #2.

      Reviewer #3 (Public review): 

      Weaknesses:  

      Nevertheless, the manuscript currently reads as a sequence of discrete experiments rather than a single causal chain. Below, I outline the key points that should be addressed to make the model convincing.

      Please see the responses to the recommendation for the authors made by reviewer #3.

      Reviewer #3 (Recommendations for the authors):

      (1) Causality across the pathway  

      Each step (α2A internalisation, GIRK rundown, Ca<sup>2+</sup> rise, MAO-A/AEP upregulation) is demonstrated separately, but no experiment links them in a single preparation. Consider in vivo Ca<sup>2+</sup> or GRAB NE photometry during restraint stress while probing α2A levels with i.p. clonidine injection or optogenetic over excitation coupled to biochemical readouts. Such integrated evidence would help to overcome the correlational nature of the manuscript to a more mechanistic study. 

      Authors response: It is not possible to measure free cytosolic NA levels with GRAB NE photometry when α2A AR is internalized as described above (see the response to the comment made by reviewer #1 as the recommendation for the authors).

      The core idea behind my comment, as well as that of Reviewer 1, was to encourage integrating your individual findings into a more cohesive in vivo experiment. Using GRAB-NE to measure extracellular NA could serve as an indirect readout of NA uptake via NAT, and ultimately, cytosolic NA levels. Connecting these experiments would significantly strengthen the manuscript and enhance its overall impact. 

      It may be true that the measurement of extracellular NA could serve as an indirect readout of NA uptake via NAT, and ultimately cytosolic NA levels. However, the reviewer #3 is still misunderstanding the applicability of GRAB-NE method to detect NE in our study. As described in the original authors’ response, there appeared to be no fluorescence probe to label cytosolic NA at present. Especially, the GRAB-NE method recommended by the reviewers #1 and #3 is limited to detect NA only when α2A-AR is expressed in the cell membrane.Therefore, when increases in cytosolic NA levels are caused by internalization of α2A-ARs, NA measurement with GRAB-NE photometry is not applicable.

      (2) Pharmacology and NE concentration  

      The use of 100 µM noradrenaline saturates α and β adrenergic receptors alike. Please provide ramp measurements of GIRK current in dose-response at 1-10 µM NE (blocked by atipamezole) to confirm that the rundown really reflects α2A activity rather than mixed receptor effects. 

      Authors response: It is true that 100 µM noradrenaline activates both α and β adrenergic receptors alike. However, it was clearly showed that enhancement of GIRK-I by 100 µM noradrenaline was completely antagonized by 10 µM atipamezole and the Ca<sup>2+</sup> dependent rundown of NA-induced GIRK-I was prevented by 10 µM atipamezole. Considering the Ki values of atipamezole for α2A AR (=1~3 nM) (Vacher et al., 2010, J Med Chem) and β AR (>10 µM) (Virtanen et al., 1989, Arch Int Pharmacodyn Ther), these results really reflect α2A AR activity but not β AR activity (Figure S5). Furthermore, because it is already well established that NA-induced GIRK-I was mediated by α2A AR activity in LC neurons (Arima et al., 1998, J Physiol; Williams et al., 1985, Neuroscience), it is not necessarily need to re-examine 1-10 µM NA on GIRK-I.

      While the milestone papers by Williams remain highly influential, they should be re-evaluated in light of more recent findings, given that they date back over 40 years. Advances in our understanding now allow for a more nuanced interpretation of some of their results. For example, see McKinney et al. (eLife, 2023). This study demonstrates that presynaptic β-adrenergic receptors-particularly β2-can enhance neuronal excitability via autocrine mechanisms. This suggests that your post-activation experiments using atipamezole may not fully exclude a contribution of β-adrenergic signaling. Such a role might become apparent when conducting more detailed titration experiments.

      The reviewer #3 may be misunderstanding the report by McKinney et al. (eLife, 2013). This paper did not demonstrate that presynaptic β-adrenergic receptors-particularly β2- can enhance neuronal excitability via autocrine mechanisms. It is impossible for LC neurons to increase their excitability by activating β-adrenergic receptors, as we have clearly shown that enhancement of GIRK-I by 100 µM noradrenaline was completely antagonized by 10 µM atipamezole. Considering the difference in Ki values of atipamezole for α2-AR (= 2~4 nM) (Vacher et al., 2010, J Med Chem) and β-AR (>10 µM) (Virtanen et al., 1989, Arch Int Pharmacodyn Ther), such a complete antagonization (of 100 µM NA-induced GIRK-I) by 10 µM atipamezole really reflect α2A-AR activity but not β-AR activity (Figure S5). Furthermore, it is already well established that NA-induced GIRK-I was mediated by α2-AR activity in LC neurons (Arima et al., 1998, J Physiol). McKinney et al. (eLife, 2023) have just found the absence of lateral inhibition on adjacent LC neurons by NA autocrine caused respective spike activity. This has nothing to do with autoinhibition.

      (4) Age mismatch and disease claims 

      All electrophysiology and biochemical data come from juvenile (< P30) mice, yet the conclusions stress Alzheimer-related degeneration. Key endpoints need to be replicated in adult or aged mice, or the manuscript should soften its neurodegenerative scope. 

      Authors response: As described in the section of Conclusion, we never stress Alzheimer-related degeneration, but might give such an impression. To avoid such a misunderstanding, we have added a description “However, the present mechanism must be proven to be valid in adult or old mice, to validate its involvement in the pathogenesis of AD.” (R1, page 14, lines 448-450).

      It would be great to see this experiment performed in aged mice-you are the one who has everything in place to do it right now! 

      In our future separate studies, we would like to prove that the present mechanism is valid in aged mice, to validate its involvement in the pathogenesis of AD. This is partly because the patch-clamp study in aged mice is extremely difficult and takes much time.

      Authors response: In the abstract, you suggest that internalization of α2A-adrenergic receptors could represent a therapeutic target for Alzheimer's disease. "...Thus, it is likely that internalization of α2A-AR increased cytosolic NA, as reflected in AEP increases, by facilitating reuptake of autocrine-released NA. The suppression of α2A-AR internalization may have a translational potential for AD treatment."

      α2A-AR internalization was involved in the degeneration of LC neurons. Because we confirmed that spike-frequency adaptation reflecting α2A-AR-mediated autoinhibition can be induced in adult mice as prominently as in juvenile mice (Figure S10), it is not inadequate to suggest that the suppression of α2A-AR internalization may have a translational potential for anxiety/AD treatment (see Discussion; R2, page 14, lines 445-449).

      (6) Quantitative histology  

      Figure 5 presents attractive images, but no numerical analysis is provided. Please provide ROI-based fluorescence quantification (with n values) or move the images to the supplement and rely on the Western blots. 

      Author response: We have moved the immunohistochemical results in Fig. 5 to the supplement, as we believe the quantification of immunohistochemical staining is not necessarily correct.   

      What do you mean by that " ...immunohistochemical staining is not necessarily correct."  

      It is evident that in terms of quantification, Western blot analysis is a more accurate method than immunohistochemical staining. In this sense, it is the contention of our study that the ROI-based fluorescence quantification of immunohistochemical staining is not necessarily an accurate or correct procedure, compared to the quantification by Western blot analysis.

    1. Reviewer #1 (Public review):

      The authors previously reported that Heliconius, one genus of the Heliconiini butterflies, evolved to be efficient foragers to feed pollen of specific plants and have massively expanded mushroom bodies. Using the same image dataset, the authors segmented the central complex and associated brain regions and found that the volume of the central complex relative to the rest of the brain is largely conserved across the Heliconiini butterflies. By performing immunostaining to label a specific subset of neurons, the authors found several potential sites of evolutionary divergence in the central complex neural circuits, including the number of GABAergic ellipsoid body ring neurons and the innervation patterns of Allatostatin A expressing neurons in the noduli. These neuroanatomical data will be helpful to guide future studies to understand the evolution of the neural circuits for vector-based navigation.

      Strengths:

      The authors used a sufficiently large scale of dataset from 307 individuals of 41 species of Heliconiini butterflies to solidify the quantitative conclusions and present new microscopy data for fine neuroanatomical comparison of the central complex.

      Weaknesses:

      (1) Although the figures display a concise summary of anatomical findings, it would be difficult for non-experts to learn from this manuscript to identify the same neuronal processes in the raw confocal stacks. It would be helpful to have instructive movies to show a step-by-step guide for identification of neurons of interest, segmentations, and 3D visualizations (rotation) for several examples, including ER neurons (to supplement texts in line 347-353) and Allatostatin A neurons.

      (2) Related to (1), it was difficult for me to assess if the data in Figure 7 support the author's conclusions that ER neuron number increased in Heliconius Melpomene. By my understanding, the resolution of this dataset isn't high enough to trace individual axons and therefore authors do not rule out that the portion of "ER ring neurons" in Heliconius may not innervate the ER, as stated in Line 635 "Importantly, we also found that some ER neurons bypass the ellipsoid body and give rise to dense branches within distinct layers in the fan-shaped body (ER-FB)". If they don't innervate the ellipsoid body, why are they named as "ER neurons"?

      (3) Discussions around the lines 577-584 require the assumption that each ellipsoid body (EB) ring neuron typically arborises in a single microglomerulus to form a largely one-to-one connection with TuBu neurons within the bulb (BU), and therefore, the number of BU microglomeruli should provide an estimation of the number of ER neurons. Explain this key assumption or provide an alternative explanation.

      (4) The details of antibody information are missing in the Key resource table. Instead of citing papers, list the catalogue numbers and identifier for commercially available antibodies, and describe the antigen, and whether they are monoclonal or polyclonal. Are antigens conserved across species?

      (5) I did not understand why authors assume that foraging to feed on pollens is a more difficult cognitive task than foraging to feed on nectar. Would it be possible that they are equally demanding tasks, but pollen feeding allows Heliconius to pass more proteins and nucleic acids to their offspring and therefore they can develop larger mushroom bodies?

    1. Reviewer #2 (Public review):

      Summary:

      This work provides a general theoretical framework for understanding molecular transport across liquid-liquid phase boundaries, focusing on interfacial resistance arising from deviations from local equilibrium. By bridging sharp and continuous interface descriptions, the authors demonstrate how distinct microscopic mechanisms can yield similar effective kinetics and propose practical experimental validation strategies.

      Strengths:

      (1) Conceptually rich and physically insightful interface resistance formulation in sharp and continuous limits.

      (2) Strong integration of non-equilibrium thermodynamics with biologically motivated transport scenarios.

      (3) Thorough numerical and analytical support, with thoughtful connection to current and emerging experimental techniques.

      (4) Relevance to various systems, including biomolecular condensates and engineered aqueous two-phase systems.

      Weaknesses:

      (1) The work remains theoretical, mainly, with limited direct comparison to quantitative experimental data.

      (2) The biological implications are only briefly explored; further discussion of specific systems where interface resistance might play a functional role would enhance the impact.

      (3) Some model assumptions (e.g., symmetric labeling or idealized diffusivity profiles) could be further contextualized regarding biological variability.