Human iPSC-Based Modeling Identifies Epigenetic Regulation at the KCNQ1 Locus During Early Islet Development That Contributes to Lower β-Cell Mass

The strongest type 2 diabetes signal in Indigenous Americans from Arizona is in intron 15 of KCNQ1. We previously identified a functional region in this intron that contained four type 2 diabetes–associated single nucleotide polymorphisms (SNPs) (rs2299620, rs2237896, rs2237897, and rs74046911) and demonstrated functionality of this fragment using Indigenous American induced pluripotent stem cell (iPSC)-derived pancreatic islets (SC-islets). In the current study, we used isogenic iPSCs with targeted edits at these four SNPs, and three additional SNPs (rs2237895, rs60808706, and rs234864), to generate SC-islets and study the effect of these variants during different developmental stages. We identify an 11% reduction in stem cell–derived β-cells (SC-β-cells) in SC-islets with the risk alleles, suggesting an effect of these variants on β-cell mass. We further show premature endocrine commitment in cells with the risk allele and lower rate of β-cell commitment during the endocrine progenitor stages, likely due to differences in H19 and INS gene expression dynamics. We also show that the differential expression may be attributable to lower CpG methylation and higher chromatin accessibility in cells with the risk alleles. In summary, the type 2 diabetes SNPs at KCNQ1 affect SC-β-cell generation, and this effect is manifested early during development, likely via an epigenomic effect on gene regulation.

• We previously developed an induced pluripotent stem cell–based model to study an intronic region of KCNQ1 that represents the strongest association signal with type 2 diabetes in Indigenous Americans from Arizona. The current study builds on this model by using CRISPR/Cas9-edited isogenic cells that differ only by targeted type 2 diabetes single nucleotide polymorphisms in this intronic region.
• The effect of KCNQ1 type 2 diabetes single nucleotide polymorphisms on pancreatic β-cell development and the probable mechanism of this effect were previously unknown. The current study shows an effect on INS and H19 gene expression dynamics specifically during the endocrine progenitor stage of pancreatic islet development likely via an epigenomic effect on gene regulation resulting in generation of lower β-like cells.
• Individuals carrying KCNQ1 risk alleles for type 2 diabetes will likely benefit from therapeutics that increase pancreatic β-cell mass.

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