Pancreatic progenitor epigenome maps prioritize type 2 diabetes risk genes with roles in development

Abstract

Genetic variants associated with type 2 diabetes (T2D) risk affect gene regulation in metabolically relevant tissues, such as pancreatic islets. Here, we investigated contributions of regulatory programs active during pancreatic development to T2D risk.Generation of chromatin maps from developmental precursors throughout pancreatic differentiation of human embryonic stem cells (hESCs) identifies enrichment of T2D variants in pancreatic progenitor-specific stretch enhancers that are not active in islets.Genes associated with progenitor-specific stretch enhancers are predicted to regulate developmental processes, most notably tissue morphogenesis. Through gene editing in hESCs, we demonstrate that progenitor-specific enhancers harboring T2D-associated variants regulate cell polarity genes LAMA1 and CRB2. Knockdown of lama1 or crb2 in zebrafish embryos causes a defect in pancreas morphogenesis and impairs islet cell development. Together, our findings reveal that a subset of T2D risk variants specifically affects pancreatic developmental programs, suggesting that dysregulation of developmental processes can predispose to T2D. This work was supported by grant T32 GM008666 (R.J.G.), grant P30 DK064391 (K.J.), R01 DK068471 and U01 DK105541 (M.S., B.R.).

eQTL mapping in fetal-like pancreatic progenitor cells reveals early developmental insights into diabetes risk

“…Variants without evidence of overlapping active regulatory elements in adult pancreatic islets may be functional only during pancreatic embryonic development. Supporting this hypothesis, it was recently shown that the T2D risk variants associated with LAMA1 and CRB2 overlap fetal-specific enhancers, suggesting that they affect pancreatic endocrine cells development, which may predispose to T2D later in life (Geusz et al, 2020). Here, we detected 208 T2D loci that overlap pancreatic regulatory elements that are active in iPSC-PPC, including 55 that are active only in iPSC-PPC and not in the adult pancreas.…”

“…While GWAS studies involving hundreds of thousands of individuals have identified 380 genomic loci associated with T2D (Mahajan et al, 2018), it is still complicated to determine the causal variant in each locus and to characterize the molecular mechanisms underlying the associations between each variant and the disease. The vast majority of T2D risk variants map to non-coding sequences, indicating that they likely affect the function of regulatory elements, rather than directly influencing transcription (Gaulton et al, 2015; Geusz et al, 2020; Greenwald et al, 2019; Pasquali et al, 2014; Varshney et al, 2017). Many T2D risk variants overlap regulatory elements that are functional in pancreatic endocrine cells and their function and disease association have been thoroughly characterized (Chiou et al, 2019; Mahajan et al, 2018; Spracklen et al, 2020; Vujkovic et al, 2020; Xue et al, 2018).…”

TGF-β modulates cell fate in human ES cell-derived foregut endoderm by inhibiting multiple endogenous signaling pathways

“…As we found TGF-β1 induced the OTX2/LHX1 GRN and OTX2 is able to directly activate cell cycle genes (Bunt et al, 2012), we examined publicly available ATAC-seq and ChIP-seq data for chromatin accessibility, Smad2 binding, and binding of selected TFs from the OTX2/LHX1 GRN to cell cycle genes in human ES cell cultures differentiating towards endoderm (Geusz et al, 2021;Tsankov et al, 2015). This analysis revealed that cell cycle genes upregulated by TGF-β1 all showed binding of OTX2 in their promoter regions at the DE stage (Figure S2), suggesting that OTX2 could be directly activating cell cycle genes in proliferating foregut progenitors.…”

“…Studies in mice, fish and frogs have found that genes encoding signaling antagonists such as Cer1, Sfrp1 and Shisa2 as well as the Wnt receptors Fzd2, Fzd5, Fzd7 and Fzd8 are activated by the concerted action of Otx2 and Lhx1 (Costello et al, 2015;Fossat et al, 2015;Sibbritt et al, 2018), while ligands such as Wnt8 and Wnt11 are repressed by Gsc in concert with Otx2 (Seiliez et al, 2006;Yao and Kessler, 2001;Yasuoka et al, 2014). Since these TFs were strongly induced by TGF-β1 (Figure S3E), we assessed chromatin accessibility and TF binding for these Wnt pathway genes in human ES cell cultures differentiating towards endoderm (Geusz et al, 2021;Tsankov et al, 2015). This revealed enhanced chromatin accessibility and binding of EOMES, FOXA2 and OTX2 at two putative cis-acting regions located ~65 and ~130 kb downstream of the SHISA2 gene at the DE stage (Figure 3F).…”

“…The ATAC-seq data (GSE149148, Geusz et al, 2021) and the ChIP-seq data (GSE61475, Tsankov et al, 2015) used in this study were downloaded from Gene Expression Omnibus (GEO) as processed data in bigwig and bed formats.…”