Translation of GWAS-identified risk loci into functionally distinct mutations and molecular pathways is one of the major challenges of the post-GWAS era. Once a causal gene in a locus has been identified, all biological effects of the locus are usually ascribed to that one gene. However, complete attribution of a phenotypic effect of a GWAS-identified locus to a single functional DNA variant or gene may not be justified. Incomplete assignment of GWAS causality may hinder the discovery of key genetic influences on disease mechanisms. We propose to investigate a locus on chromosome 19p13.11 spanning 15 genes that is strongly associated with incidence of both cardiovascular and nonalcoholic fatty liver diseases (CVD and NAFLD), as a model of a GWAS locus whose phenotypic associations may be driven by more than one causal gene. Recent conditional analyses reported that the plasma cholesterol and hepatic triglyceride associations with rs10401969, the GWAS index SNP for the 19p13.11 locus, is explained by a very tightly linked (r2>0.95, D'=1 EUR) missense SNP in TM6SF2 (rs58542926, p.Glu167Lys). Functional studies confirmed a causal role for this SNP. However, if multiple DNA variants are in very high linkage disequilibrium, statistical analyses can neither distinguish whic variant(s) contributes to the genetic signal, nor resolve the underlying biology contributing to th phenotypic effects. We found that the 19p13.11 index SNP, rs10401969, which is located in an intron of SUGP1, disrupts its splicing, reducing SUGP1 protein levels. Notably, we observed that SUGP1 knock-down or overexpression in cellular and mouse models affected several measures of lipid metabolism, indicating that the 19p13.11 haplotype contains at least two highly linked functional SNPs that regulate two genes acting concordantly to affect lipid metabolism. These findings, together with preliminary evidence for effects of knockdown of other genes at this locus on cholesterol metabolism, lead us to hypothesize that the 19p13.11 locus functions as an extended multi-variant and multi-gene haplotype. Our overall goal is to identify and investigate the individual contributions of causal genes underlying the association between 19p13.11 with plasma and hepatic lipids.
In Aim 1, we will prioritize genes for functional assessment by identifying those with transcript and protein level variation associated with the 19p13.11 haplotype using publicly available datasets (e.g. GTEx) and a panel of ~650 human livers.
In Aim 2, we will examine the effects of in vivo hepatic knock- down of Tm6sf2 and Sugp1 singly and together, as well as genes identified in Aim 1, on measures of lipid metabolism.
In Aim 3, we will investigate the molecular mechanisms underlying effects of SUGP1 and other high-priority 19p13.11 genes on plasma and hepatic lipids through molecular and cellular biology approaches as well as tailored animal models. With its complex genetic structure and varied pathologic associations, the 19p13.11 locus is a particularly attractive model for re-assessing GWAS causality. Its thorough investigation could reveal new biology that may inform the development of diagnostics or drug targets for CVD and NAFLD.
Genome-wide association studies (GWAS) have identified a number of regions in the genome associated with various diseases; however, determining which specific gene or genes is responsible for the genetic signal remains a significant challenge. Here we propose to investigate a locus on chromosome 19p13.11, associated with plasma cholesterol and triglycerides and incidence of cardiovascular and non-alcoholic fatty liver diseases, as a model for evaluating causality within a GWAS-identified locus comprised of multiple functional DNA variants and multiple causal genes. The successful completion of this project will not only improve our understanding of how DNA variants and genes produce these GWAS signals, but also may lead to the discovery of new genes and pathways that may inform the development of novel drug targets for the prevention or treatment of cardiovascular disease and non-alcoholic fatty liver disease.
| Kim, Kyungpil; Theusch, Elizabeth; Kuang, Yu-Lin et al. (2018) ZNF542P is a pseudogene associated with LDL response to simvastatin treatment. Sci Rep 8:12443 |
