Multiple genetic variants at the SLC30A8 locus affect a local super-enhancer cluster to influence pancreatic β-cell survival and function.

Variants at the SLC30A8 locus are associated with type 2 diabetes (T2D) risk. The lead variant, rs13266634, encodes an amino acid change, Arg325Trp (R325W), at the C-terminus of the secretory granule-enriched zinc transporter, ZnT8. Although this protein-coding variant was previously thought to be the sole driver of altered disease risk, recent studies have provided evidence for lowered expression of SLC30A8 mRNA in protective allele carriers. In the present study, combined allele-specific expression (cASE) analysis in human islets revealed that multiple variants affect the expression SLC30A8 . Chromatin accessibility and epigenomic analyses imply the existence at the SLC30A8 locus of an islet-selective super-enhancer cluster hosting multiple diabetes-associated variants. The variant region is spatially associated with both the SLC30A8 promoter and with the regulatory regions of the neighbouring RAD21, RAD21-AS1, UTP23 and other genes. Deletion of variant-bearing regions from human-derived EndoC-βH3 cells using CRISPR-Cas9 lowered the expression of SLC30A8 and several neighbouring genes, suggesting their co-regulation by this enhancer cluster. Whilst deletion of SLC30A8 had no effect on beta cell survival under the conditions examined, loss of RAD21 or UTP23 markedly reduced cell viability. Thus, the protective effects of variants that lower SLC30A8 activity may be modulated by the altered expression of nearby genes. Direct evidence for this possibility was not, however, obtained by cASE or eQTL analysis of human islet samples.