Total terminal deoxynucleotide transferase–mediated dUTP nick end labelingApoptosis analysis was performed in a random sampling of T1D cases, as previously described (30), with modification; sections were predigested in 0.004% trypsin and identified with Cy5-labeled reagents. Total terminal deoxynucleotide transferase–mediated dUTP nick end labeling (TUNEL)–positive β cells were assessed in >95,000 islet cells per condition. In every sample, TUNEL-positive pancreatic ducts were imaged to ensure adequate TUNEL staining.

Proliferation analysisKi-67+ cells were measured within insulin-stained slides or ×20 magnification colorimetric images from optimal cutting temperature compound (OCT)–embedded pancreas sections prepared by the nPOD core laboratory, available through the nPOD Datashare. Colorimetric insulin and DAPI were identified using a sample-specific red-green-blue color range, established through sampling of multiple data points. Ki-67+ β-cell and Ki-67+ acinar proliferation was calculated as percent total cell population. Acinar cells were identified as nonislet cells containing DAPI.

Slides were imaged to quantify β-cell morphometry using Volocity 6.1.1 (PerkinElmer, Waltham, MA), as previously described (29). Images were acquired with Zeiss Axio Imager M1 (Carl Zeiss Microscopy, Thornwood, NY) with an automated X-Y stage and captured with Orca ER camera (Hamamatsu, Bridgewater, NJ), resulting in images of tens of thousands of individual nuclei per sample (summarized in Supplemental Table 3).