Abstract
Aims/hypothesisMost type 2 diabetes-associated genetic variants identified via genome-wide association studies (GWASs) appear to act via the pancreatic islet. Observed defects in insulin secretion could result from an impact of these variants on islet development and/or the function of mature islets. Most functional studies have focused on the latter, given limitations regarding access to human fetal islet tissue. Capitalising upon advances in in vitro differentiation, we characterised the transcriptomes of human induced pluripotent stem cell (iPSC) lines differentiated along the pancreatic endocrine lineage, and explored the contribution of altered islet development to the pathogenesis of type 2 diabetes.MethodsWe performed whole-transcriptome RNA sequencing of human iPSC lines from three independent donors, at baseline and at seven subsequent stages during in vitro islet differentiation. Differentially expressed genes (q < 0.01, log2 fold change [FC] > 1) were assigned to the stages at which they were most markedly upregulated. We used these data to characterise upstream transcription factors directing different stages of development, and to explore the relationship between RNA expression profiles and genes mapping to type 2 diabetes GWAS signals.ResultsWe identified 9409 differentially expressed genes across all stages, including many known markers of islet development. Integration of differential expression data with information on transcription factor motifs highlighted the potential contribution of REST to islet development. Over 70% of genes mapping within type 2 diabetes-associated credible intervals showed peak differential expression during islet development, and type 2 diabetes GWAS loci of largest effect (including TCF7L2; log2FC = 1.2; q = 8.5 × 10−10) were notably enriched in genes differentially expressed at the posterior foregut stage (q = 0.002), as calculated by gene set enrichment analyses. In a complementary analysis of enrichment, genes differentially expressed in the final, beta-like cell stage of in vitro differentiation were significantly enriched (hypergeometric test, permuted p value <0.05) for genes within the credible intervals of type 2 diabetes GWAS loci.Conclusions/interpretationThe present study characterises RNA expression profiles during human islet differentiation, identifies potential transcriptional regulators of the differentiation process, and suggests that the inherited predisposition to type 2 diabetes is partly mediated through modulation of islet development.Data availabilitySequence data for this study has been deposited at the European Genome-phenome Archive (EGA), under accession number EGAS00001002721.
Highlights
Our understanding of the genetic contribution to pathogenesis of type 2 diabetes has been greatly facilitated by genome-wide association studies (GWASs)
Characterising an in vitro-derived model of human beta-like cells To determine whether the differentiated cells followed normal islet development, we profiled gene expression patterns across induced pluripotent stem cell (iPSC) and seven subsequent developmental stages in lines from three independent donors (SB Ad2, SB Ad3 and SB Neo1) differentiated in parallel
Principal component analysis of the transcriptome showed that the beta-like cells generated in the current study clustered more closely with in vivo-matured islet-like cells [14] than cells from earlier differentiations [10] (Fig. 1, ESM Fig. 3)
Summary
Our understanding of the genetic contribution to pathogenesis of type 2 diabetes has been greatly facilitated by genome-wide association studies (GWASs). Characterising an in vitro-derived model of human beta-like cells To determine whether the differentiated cells followed normal islet development, we profiled gene expression patterns across iPSC and seven subsequent developmental stages in lines from three independent donors (SB Ad2, SB Ad3 and SB Neo1) differentiated in parallel.
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