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.

The genetic and regulatory architecture of ERBB3-type 1 diabetes susceptibility locus

“…ERBB3 has been reported to be expressed and down-regulated in response to pro-inflammatory cytokines in human islets at the transcriptional level (Eizirik et al, 2012). Using western blotting we confirmed that ERBB3 is expressed and down-regulated by a mixture of IL-1b, IFN-g and TNFa in human islets (p-value < 0.05, Fig.…”

“…S6). Intriguingly, members of the ERBB3 protein interactome included 6 bona-fide T1D candidate genes: ERBB2, GRB7, PA2G4, PTPN11, TENC1 and SH2B3, all known to be regulated by pro-inflammatory cytokines (Eizirik et al, 2012). All six genes were significantly enriched within the ERBB3 interactome (p-value ¼ 7.93e-04, binomial test).…”

IL-17A increases the expression of proinflammatory chemokines in human pancreatic islets

“…Beta cell purity, as evaluated by immunofluorescence for insulin (ESM Table 2), was 56%±4% (mean ± SEM). The islets were cultured in M199 culture medium containing 5.5 mmol/l glucose and sent to Brussels within 1 to 5 days after isolation, where they were dispersed and cultured in Ham's F-10 medium containing 6.1 mmol/l glucose (Invitrogen Life Technologies, Paisley, UK) as described [3,23].…”

“…Key steps of the beta cell-autonomous immune response are regulated by candidate genes for type 1 diabetes, including viral recognition, regulation of inflammation and cross-talk with the adaptive immune response [3][4][5]. Excessive pancreatic beta cell-autonomous immunity, in crosstalk with endoplasmic reticulum stress and other signals, exacerbates inflammation, beta cell apoptosis and the progression to type 1 diabetes [6].…”

Expression of Interferon-Stimulated Genes in Insulitic Pancreatic Islets of Patients Recently Diagnosed With Type 1 Diabetes

“…ISGs constitute a group of genes that are upregulated in response to IFN and put the surrounding cells in an antiviral state, protecting them from being infected. Being induced by virus infection (7), signs of their expression have been interpreted as "viral footprints," but, importantly, many of these genes are also overexpressed under other conditions, in the absence of viral infection (8,9).…”