Characterization of the Secretome, Transcriptome, and Proteome of Human beta Cell Line EndoC-beta H1

Early diabetes research is hampered by limited availability, variable quality, and instability of human pancreatic islets in culture. Little is known about the human beta cell secretome, and recent studies question translatability of rodent beta cell secretory profiles. Here, we verify representativeness of EndoC-beta H1, one of the most widely used human beta cell lines, as a translational human beta cell model based on omics and characterize the EndoC beta H1 secretome. We profiled EndoC-beta H1 cells using RNAseq, data-independent acquisition, and tandem mass tag proteomics of cell lysate. Omics profiles of EndoC-beta H1 cells were compared to human beta cells and insulinomas. Secretome composition was assessed by data independent acquisition proteomics. Agreement between EndoC-beta H1 cells and primary adult human beta cells was ~90% for global omics profiles as well as for beta cell markers, transcription factors, and enzymes. Discrepancies in expression were due to elevated proliferation rate of EndoC-beta H1 cells compared to adult beta cells. Consistently, similarity was slightly higher with benign nonmetastatic insulinomas. EndoC-beta H1 secreted 783 proteins in untreated baseline state and 3135 proteins when stressed with nontargeting control siRNA, including known beta cell hormones INS, IAPP, and IGF2. Further, EndoC-beta H1 secreted proteins known to generate bioactive peptides such as granins and enzymes required for production of bioactive peptides. EndoC-beta H1 secretome contained an unexpectedly high proportion of predicted extracellular vesicle proteins. We believe that secretion of extracellular vesicles and bioactive peptides warrant further investigation with specialized proteomics workflows in future studies.