Case#: Case 2

DiseaseAssertion: APDS

FamilyInfo: no familial history of PID

CaseHPOFreeText: belongs to a family in which two siblings were reported as suffering from a CSR-D (data from the affected sister P7 “see Tables E1 and E2”). From the age of 5 months, he suffered recurrent upper (recurrent acute otitis media) and lower respiratory tract infections complicated by bronchiectasis, chronic non-infectious diarrhea with malabsorption syndrom and failure to thrive. Other infections were also noticed, including pericarditis caused by Echo virus infection and recurrent synovitis. The diagnosis of CSR-D was made, according to his familial history and IgG substitution was started. At 6 and 8 years of age, he displayed episodes of massive enlargement of lymph nodes (cervical and mesenteric) with no malignant feature at biopsy. Serum Ig levels revealed an increase of IgM (4.5g/L at 5 years and 13g/L at 11 years) and a decrease of IgG (<1.9g/L) and IgA (0.41 g/L). At 11 years of age, he had a new episode of cervical lymph nodes enlargement which led to the diagnosis of Hodgkin disease, histological type nodular sclerosis, stage III with localization to cervical, mediastinum, retroperitoneum and spleen (EBV status was unknown and could not be studied retrospectively) (Figure 1 g-i). Patient received chemotherapy and radiotherapy with irradiation of regions above and below diaphragma, which induced complete remission. He is now well on IgG substitution and prophylactic antibiotherapy with a follow-up of more than 10 years.

CasePreviousTesting: None. Genotyping only done at position c.3061 of PIK3CD

GenotypingMethod: We genotyped the PIK3CD gene at position c.3061G as described previously (1) in a cohort of 139 patients with immunological phenotype of Ig CSR-D. We found 8 new APDS patients with the E1021K heterozygous mutation in the PIK3CD gene

Variant: E1021K

CAID: CA145460

gnomAD: absent in gnomAD v2.1.1

SupplementalData: Clinical features of patients 3-8 in supplementary

Case#: 2 year old female

DiseaseAssertion: APDS (She was diagnosed with polymorphous B-cell lymphoproliferative disorder)

FamilyInfo: no family history suggestive of an immunodeficiency

CaseHPOFreeText: referred by pulmonary to clinical immunology for evaluation of her recurrent pneumonias and bronchiectasis. Work-up at that time revealed IgA < 6 (34–305 mg/dL), IgG 30 (572–1,474 mg/dL), IgM 1190 (31–208 mg/dL). In addition to low levels of IgG and IgA but elevated IgM levels, immune evaluation revealed T and B cell lymphopenia −827 (876–3,394 CU MM) and 28 (200–1,259/CU MM), respectively. Her CD4 count was 331 (412–2,095/CU MM) and CD8 count was 481 (236–995/CU MM). She had a normal response to lymphocyte mitogen and antigen stimulation. Due to these results and her clinical history, she was started on intravenous immunoglobulin replacement which helped decrease her incidence of infections. As she grew older she began to have increased hospitalizations for hemolytic anemia and recurrent pneumonias and sinusitis. She also developed lymphadenopathy and splenomegaly. She received rituximab with resultant improvement in her counts and decrease in size of her lymphadenopathy and hepatosplenomegaly. She was also started on trimethoprim/sufamethoxazole prophylaxis to help prevent infections, and though she continued to have intermittent respiratory infections the amount was improved. In addition to asymmetrical cervical lymphadenopathy and parotid gland enlargement Figures 2A,B, a CT neck/chest/abdomen and pelvis done at that time showed mediastinal, hilar, abdominal, and pelvic lymphadenopathy, impressive retroperitoneal lymphadenopathy, hepatosplenomegaly, and cecum and terminal ileum thickening Figures 2C,D.

CasePreviousTesting: Genetic testing revealed no mutation in AID, UNG, CD40, or CD40L but later gene sequencing discovered a dominant activating mutation in PIK3CD–c.3061G > A (p.Glu1021Lys).

GenotypingMethod:

Variant: PIK3CD–c.3061G > A (p.Glu1021Lys).

CAID: CA145460

gnomAD: absent in gnomAD v2.1.1

Case#: 19 year old, Indian, male

DiseaseAssertion: APDS

FamilyInfo: Neither parent carried this mutation, suggesting a de novo origin.

CaseHPOFreeText: referred for the evaluation of chronic active EBV disease. The patient’s medical history revealed congenital stenosis of the left bronchus, recurrent sinopulmonary infections, and autism spectrum disorder with an IQ of 80–86. EBV seroconversion was identified at 7 years of age when the patient presented idiopathic abdominal lymphadenopathy. Furthermore, a previous laboratory examination revealed IgA deficiency and low IgG2 and IgG4 levels without an overarching diagnosis. Four months before presentation, the patient developed fatigue, fever, night sweats, hepatosplenomegaly, anemia, hepatitis, weight loss of 10 kg, and lymphadenopathy (Fig. 1). Serum EBV copy numbers were repeatedly > 1500/mL. Histology of the three lymph nodes did not reveal any evidence of malignant lymphoma, but rather a markedly positive EBV-encoded RNA (EBER). Chronically active EBV was diagnosed, and rituximab therapy of 500 mg weekly during 4 weeks was initiated. A stable condition without any additional immunosuppressive drugs was achieved for 3 months after which he developed high spiking fever, pneumonia, progressive lymphadenopathy, severe unexplained cardiomyopathy with progressive anemia, thrombocytopenia, and hyperferritinemia (Table ​(Table1).1). Malignant lymphoma was excluded and hemophagocytosis was detected in the bone marrow (Fig. 3A, B). The patient therefore fulfilled six out of eight diagnostic HLH-04 criteria (Table ​(Table2)2) [7]. His clinical status quickly deteriorated, and he developed acute respiratory distress syndrome and multiple organ failure. Salvage therapy was initiated with high-dose steroids, sirolimus, and intravenous immunoglobulin. PI3K delta inhibitors were withheld due to heart and respiratory failure. Etoposide was withheld due to leucopenia and severe sepsis with systemic infection (hospital acquired pneumonia with H. influenza, not responding to treatment). Within 1 month, the patient died from cardiac failure with refractory pulmonary edema.

CasePreviousTesting: whole exome sequencing (confirmed by Sanger sequencing)

GenotypingMethod: whole exome sequencing (confirmed by Sanger sequencing)

Variant: heterozygous c.3074A > C, p.Glu1025Gly mutation in the PIK3CD gene (NM_005026.3)

CAID: CA16617216

gnomAD: absent from gnomAD v2.1.1

Case#: P7, diagnosed at age 7, female

DiseaseAssertion: APDS

FamilyInfo:

CaseHPOFreeText: recurrent respiratory tract infections, EBV viremia conjunctivitis, lymphadenopathy, hepatosplenomegaly, short stature, thrombocytopenia

GenotypingMethod: Unclear, possibly WES ("In a previous study (15), we reviewed clinical and routine immunological features of 15 APDS patients diagnosed in our center by next-generation sequencing (NGS). In the present study, we extended our previous study...")

Variant: Y524N

CAID: CA338303802

gnomAD: absent from gnomAD v2.1.1

SupplementalData: Table S1

Case#: 2 year old female, Albanian

DiseaseAssertion: APDS

FamilyInfo: The patient was the first of three children from a non-consanguineous family of Albanian origin

CaseHPOFreeText: presented with recurrent otitis media, respiratory infections, persistent splenomegaly and nonmalignant lymphadenopathy. In the first year of life, she had recurrent episodes of wheezing associated with viral infections. In four occasions, she developed otitis media. Clinical evaluation at 17 months of age revealed splenomegaly suggesting Autoimmune lymphoproliferative disease (ALPS), but analysis of CD4 − /CD8 − /TCR alpha/beta + T cells was normal. In addition, bone marrow morphology and karyotype were normal. At the age of 21 months, the patient was hospitalized due to an additional episode of otitis caused by multidrug resistant Pseudomonas aeruginosa . Since then, she suffered of recurrent otorrhea, due to Haemophilus influenzae and Moraxella catarrhalis . Virological testing ( Table 1 ) revealed chronic low-level Epstein–Barr virus (EBV) viraemia characterized by EBV-DNA persistence and elevated anti-VCA IgM (total viral load ranging from negative to 506 copies/ml; VCA IgM ranging from 43 AU/ml to 186 AU/ml).

CasePreviousTesting: No genotyping ot other genes

GenotypingMethod: Genetic analysis of PIK3CD by Sanger sequencing revealed a heterozygous G > A mutation at the position c.3061 resulting in E1021K substitution

Variant: heterozygous G > A mutation at the position c.3061 resulting in E1021K substitution

CAID: CA145460

gnomAD: variant is absent in gnomAD v2.1.1