Methods
Multiple islet sections were collected through laser microdissection of frozen pancreatic tissues of organ donors positive for islet autoantibodies (AAb+, n=5), compared to age/sex-matched nondiabetic controls (ND, n=5) obtained from the Network for Pancreatic Organ donors with Diabetes (nPOD). Islet sections were subjected to mass spectrometry-based proteomics and analyzed with label-free quantification followed by pathway and functional annotations.
Results
Analyses resulted in ~4,500 proteins identified with low false discovery rate (FDR) <1%, with 2,165 proteins reliably quantified in every islet sample. We observed large inter-donor variations that presented a challenge for statistical analysis of proteome changes between donor groups. We therefore focused on the three multiple AAb+ cases (mAAb+) with high genetic risk and their three matched controls for a final statistical analysis. Approximately 10% of the proteins (n=202) were significantly different between mAAb+ cases versus ND. The significant alterations clustered around major functions for upregulation in the immune response and glycolysis, and downregulation in endoplasmic reticulum (ER) stress response as well as protein translation and synthesis. The observed proteome changes were further supported by several independent published datasets, including proteomics dataset from in vitro proinflammatory cytokine-treated human islets and single cell RNA-seq data sets from AAb+ cases.