Proliferation AnalysisKi67+ islet endocrine (synaptophysin), α-cell (glucagon), PP, SS, ghrelin, and cytoplasmic Sox9 (Sox9Cyt) proliferation were calculated as % total cells. A subset of high proliferators was quantified as % intra-islet Ki67+ cells for insulin and all other markers. High proliferation was defined as having an islet endocrine cell replication rate >0.71%, corresponding to z score of 0.5.

ImmunohistochemistryParaffin sections were incubated with primary antisera (Supplementary Table 3), followed by the appropriate secondary antisera conjugated to aminomethylcoumarin (AMCA), Cy2, Cy3, or Cy5 (Jackson ImmunoResearch) and DAPI (Molecular Probes, Eugene, OR) as previously described (1). Primary antisera were as follows: 1:100, ARX (AF7068; R&D Systems), β3 tubulin (NB100-1612; Novus Biologicals), CD3 (PA1-37282; Thermo Fisher Scientific), CD31 (ab28364; Abcam), chromagranin A (ab8204; Abcam), ghrelin (H-031-77; Phoenix Pharmaceuticals), GLUT1 (07-1401; Millipore), ISL1&2 (39.4D5; DSHB), INSM1 (sc-271408; Santa Cruz Biotechnology), NeuN (MAB377; Millipore), Nkx2.2 (ab191077; Abcam), Nkx6.1 (F55A12; DSHB), pancreatic polypeptide (PP) (18-0043; Invitrogen), PCNA (2586S; Cell Signaling Technology), PC1/3 (AB10553; Millipore), Pdx1 (NBP2-38865; Novus Biologicals), phospho-histone H3 (9701S; Cell Signaling Technology), proinsulin (GN-ID4; DSHB), SNAP25 (MAB331; Millipore), somatostatin (SS) (18-0078; Invitrogen), synaptotagmin 1A (ab133856; Abcam), Sox9 (AB5535; Millipore), Sox9 (pS181) (ab59252; Abcam), and synaptophysin (18-0130, Thermo Fisher Scientific, and AB6245, Abcam); 1:250, glucagon (ab8055 and ab10988; Abcam) and Ki67 (550609; BD Biosciences); and 1:1,500, insulin (A0564; Dako).

Islet MorphometryIslet endocrine and α-cell morphometry were assessed with Volocity 6.1.1 (PerkinElmer) as previously described (9). Zeiss AxioImager M1 (Carl Zeiss Microscopy) with automated X-Y stage and Orca ER camera (Hamamatsu) acquired images of tens of thousands of individual nuclei/sample (Supplementary Table 4).

TUNELApoptosis analysis was performed in a subset of available control and T1D samples as previously described (1). Total terminal deoxynucleotide TUNEL-positive islet endocrine cells were assessed in >85,000 islet cells/condition. Total TUNEL+ Sox9Cyt cells were assessed in 993 islet cells/condition. In every sample, TUNEL+ pancreatic ducts were imaged to ensure adequate TUNEL staining.