The Human Pancreatic Islet Transcriptome: Expression of Candidate Genes for Type 1 Diabetes and the Impact of Pro-Inflammatory Cytokines

Abstract

Type 1 diabetes (T1D) is an autoimmune disease in which pancreatic beta cells are killed by infiltrating immune cells and by cytokines released by these cells. Signaling events occurring in the pancreatic beta cells are decisive for their survival or death in diabetes. We have used RNA sequencing (RNA–seq) to identify transcripts, including splice variants, expressed in human islets of Langerhans under control conditions or following exposure to the pro-inflammatory cytokines interleukin-1β (IL-1β) and interferon-γ (IFN-γ). Based on this unique dataset, we examined whether putative candidate genes for T1D, previously identified by GWAS, are expressed in human islets. A total of 29,776 transcripts were identified as expressed in human islets. Expression of around 20% of these transcripts was modified by pro-inflammatory cytokines, including apoptosis- and inflammation-related genes. Chemokines were among the transcripts most modified by cytokines, a finding confirmed at the protein level by ELISA. Interestingly, 35% of the genes expressed in human islets undergo alternative splicing as annotated in RefSeq, and cytokines caused substantial changes in spliced transcripts. Nova1, previously considered a brain-specific regulator of mRNA splicing, is expressed in islets and its knockdown modified splicing. 25/41 of the candidate genes for T1D are expressed in islets, and cytokines modified expression of several of these transcripts. The present study doubles the number of known genes expressed in human islets and shows that cytokines modify alternative splicing in human islet cells. Importantly, it indicates that more than half of the known T1D candidate genes are expressed in human islets. This, and the production of a large number of chemokines and cytokines by cytokine-exposed islets, reinforces the concept of a dialog between pancreatic islets and the immune system in T1D. This dialog is modulated by candidate genes for the disease at both the immune system and beta cell level.

Author Summary

Pancreatic beta cells are destroyed by the immune system in type 1 diabetes mellitus, causing insulin dependence for life. Candidate genes for diabetes contribute to this process by acting both at the immune system and, as we suggest here, at the pancreatic beta cell level. We have utilized a novel technology, RNA sequencing, to define all transcripts expressed in human pancreatic islets under basal conditions and following exposure to cytokines, pro-inflammatory mediators that contribute to trigger diabetes. Our observations double the number of known genes present in human islets and indicate that >60% of the candidate genes for type 1 diabetes are expressed in beta cells. The data also show that pro-inflammatory cytokines modify alternative splicing in human islets, a process that may generate novel RNAs and proteins recognizable by the immune system. This, taken together with the findings that pancreatic beta cells themselves express and release many cytokines and chemokines (proteins that attract immune cells), indicates that early type 1 diabetes is characterized by a dialog between beta cells and the immune system. We suggest that candidate genes for diabetes function at least in part as “writers” for the beta cell words in this dialog.