CRISPR Mediated Deletion of a Proxy 19.2kb Distal to the T2D GWAS-Implicated SLC30A8 R325W Variant Impacts RAD21 and UTP23 Gene Expression in HepG2 Cells

Abstract

Genome wide association studies (GWAS) have revealed multiple loci for type 2 diabetes (T2D). However, given that GWAS generally only reports genomic signals associated with a given trait, there is need for follow-up characterization. Despite key reports of missense variants within SLC30A8 conferring protection of T2D risk, there is still need to better understand the relationship between the GWAS signal and mechanism at this locus. The application of ’Assay for Transposase Accessible Chromatin combined with sequencing’ (ATAC-seq) to Endo-BH1, SGBS and HepG2 cell lines, representing models for pancreatic beta-cells, adipose and liver respectively, allowed us to filter for putatively informative proxy SNPs (r2>0.8) coinciding with open chromatin at this locus. Following sequencing on the Illumina Hi-Seq platform, the sentinel SNP itself coincided with open chromatin, namely rs13266634 (a missense R325W variant), in both Endo-BH1 and SGBS; however, in HepG2 this region was closed while proxy rs9650069 was open, situated 3’ to SLC30A8 and 19.2kb from rs13266634. We elected to generate CRISPR/Cas9 mediated deletions immediately around rs9650069 in a mixed cell setting. Following confirmation of deletion by sequencing, we assessed changes in expression for all genes in the corresponding topological associating domain (TAD), namely SLC30A8, AARD, EIF3H, RAD21, TRPS1 and UTP23. Two genes revealed a significant change in expression when normalized to beta-actin, namely RAD21 and UTP23, yielding 5.58 fold and 4.57 fold decreases, respectively. Given that according to GTEx the expression of SLC30A8 is largely contained to the pancreas, this gene was not expressed in this cell setting and thus the impact of this deletion on this gene could not be assessed. This effort implicates an enhancer element for these genes in a liver cell model as being a part of the machinery genetically controlling this locus. Disclosure K.M. Hodge: None. S. Lu: None. M. Leonard: None. J.A. Pippin: None. A. Chesi: None. A.D. Wells: None. M. Johnson: None. S.F. Grant: None.