Functional characterization of T2D-associated SNP effects on baseline and ER stress-responsive β cell transcriptional activation

Shubham Khetan, Susan Kales, Romy Kursawe, Alexandria Jillette, Jacob C. Ulirsch, Steven K. Reilly, Duygu Ucar, Ryan Tewhey () and Michael L. Stitzel ()
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Shubham Khetan: The Jackson Laboratory for Genomic Medicine
Susan Kales: The Jackson Laboratory for Mammalian Genetics
Romy Kursawe: The Jackson Laboratory for Genomic Medicine
Alexandria Jillette: The Jackson Laboratory for Genomic Medicine
Jacob C. Ulirsch: Program in Biological and Biomedical Sciences, Harvard Medical School
Steven K. Reilly: Broad Institute of MIT and Harvard
Duygu Ucar: The Jackson Laboratory for Genomic Medicine
Ryan Tewhey: The Jackson Laboratory for Mammalian Genetics
Michael L. Stitzel: The Jackson Laboratory for Genomic Medicine

Nature Communications, 2021, vol. 12, issue 1, 1-13

Abstract: Abstract Genome-wide association studies (GWAS) have linked single nucleotide polymorphisms (SNPs) at >250 loci in the human genome to type 2 diabetes (T2D) risk. For each locus, identifying the functional variant(s) among multiple SNPs in high linkage disequilibrium is critical to understand molecular mechanisms underlying T2D genetic risk. Using massively parallel reporter assays (MPRA), we test the cis-regulatory effects of SNPs associated with T2D and altered in vivo islet chromatin accessibility in MIN6 β cells under steady state and pathophysiologic endoplasmic reticulum (ER) stress conditions. We identify 1,982/6,621 (29.9%) SNP-containing elements that activate transcription in MIN6 and 879 SNP alleles that modulate MPRA activity. Multiple T2D-associated SNPs alter the activity of short interspersed nuclear element (SINE)-containing elements that are strongly induced by ER stress. We identify 220 functional variants at 104 T2D association signals, narrowing 54 signals to a single candidate SNP. Together, this study identifies elements driving β cell steady state and ER stress-responsive transcriptional activation, nominates causal T2D SNPs, and uncovers potential roles for repetitive elements in β cell transcriptional stress response and T2D genetics.

Date: 2021
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DOI: 10.1038/s41467-021-25514-6

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