The impact of pro-inflammatory cytokines on the β-cell regulatory landscape provides new insights into the genetics of type 1 diabetes

Abstract

Early stages of type 1 diabetes (T1D) are characterized by local autoimmune inflammation and progressive loss of insulin-producing pancreatic β cells.We show here that exposure to pro-inflammatory cytokines unmasks a marked plasticity of the β-cell regulatory landscape. We expand the repertoire of human islet regulatory elements by mapping stimulusresponsive enhancers linked to changes in the β-cell transcriptome, proteome and 3D chromatin structure. Our data indicates that the β cell response to cytokines is mediated by the induction of novel regulatory regions as well as the activation of primed regulatory elements pre-bound by islet-specific transcription factors. We found that T1D-associated loci are enriched of the newly mapped cis-regulatory regions and identify T1Dassociated variants disrupting cytokine-responsive enhancer activity in human β cells. Our study illustrates how β cells respond to a proinflammatory environment and implicate a role for stimulus-response islet enhancers in T1D.In type 1 diabetes (T1D) early inflammation of the pancreatic islets (insulitis) by T and B cells contributes to both the primary induction and secondary amplification of the immune assault, with inflammatory mediators such as the cytokines interleukin-1β (IL-1β) and interferon-γ (IFN-γ) contributing to the functional suppression and apoptosis of β cells 1-3 .Genome wide association studies (GWAS) have made a substantial contribution to the knowledge of T1D genetic architecture uncovering >60 regions containing thousands of associated genetic variants. Nevertheless, translating variants to function remains a main challenge for T1D and other complex diseases. Most of the associated variants do not reside in coding regions 4 suggesting that they may influence transcript regulation rather than altering protein coding sequences.Recent studies showed a primary enrichment of T1D association signals in T and B cells enhancers 4,5 . A secondary 5 , or a lack of enrichment, was instead observed in islet regulatory regions. While such observation point to a major role of the immune system, we hypothesize that a subset of T1D variants may also act at the β-cell level but only manifest upon islet-cell perturbation and are not captured by the current maps of islet regulatory elements.Ramos-Rodríguez et al. Pro-inflammatory Cytokines and β-cells Regulatory Changes 3We have now mapped inflammation-induced cis-regulatory networks, transcripts, proteins and 3D chromatin structure changes in human β cells ( Fig. 1a). We leverage these data to unmask functional T1D genetic variants as well as key candidate genes and regulatory pathways contributing to the β cell autoimmune destruction. Such analyses permit elucidation of the role of epigenetic gene regulation and its interaction with T1D genetics in the context of the autoimmune reaction that drives β cell death.Ramos-Rodríguez et al. . To characterize the effect of pro-inflammatory cytokines on the β-cell regulatory landscape we first mapped all accessible or open chromatin sites in human...

Molecular Footprints of the Immune Assault on Pancreatic Beta Cells in Type 1 Diabetes

“…We observed that the in vivo beta cell responses can be closely recapitulated using an in vitro system biology approach that combines exposure to cytokines putatively present at different stages of the disease and high coverage RNA-sequencing. This may be further improved by the parallel evaluation of cytokine-induced changes in human beta cells protein expression (10,95,96) and chromatin status (10,95). The validation of these models is an important finding, as the access to high quality beta cells from patients affected by T1D for multi-omics analysis is extremely difficult.…”

Multi-Omics Approaches in Immunological Research

“…As an example, the impact of cytokines was studied on the epigenome of insulin releasing cells (b cells) from type 1 diabetes pancreases. By measuring ATAC-seq, Chip-seq and RNA-seq, the authors identified proinflammatory cytokines induced neo/primed epigenetic events in human b cells (114). Moreover, in immune systems, the effects of epigenetic changes lead to long-term alterations in the metabolic and transcriptional pathways, and further induce immune memory (115) or immunological diseases (116).…”

Characterization of the secretome, transcriptome and proteome of human β cell line EndoC-βH1

“…Recently, EndoC-βH1 open chromatin, transcriptomics and miRNA landscapes were reported to be most similar to adult human β cells or islets compared to α cells, adipocytes, muscle and peripheral blood cells (17). Two proteomics studies investigated the response to interferons in EndoC-βH1 cells (18,19), but did not validate EndoC-βH1 as a β cell model. It remains…”