Multiple Hepatic Regulatory Variants at the GALNT2 GWAS Locus Associated with High-Density Lipoprotein Cholesterol
Year: 2015
Type: article
Abstract: Genome-wide association studies (GWASs) have identified more than 150 loci associated with blood lipid and cholesterol levels; however, the functional and molecular mechanisms for many associations are unknown. We examined the functional regulatory effects of candidate variants at the GALNT2 locus associated with high-density lipoprotein cholesterol (HDL-C). Fine-mapping and conditional analyses in the METSIM study identified a single locus harboring 25 noncoding variants (r(2) > 0.7 with the lead GWAS variants) strongly associated with total cholesterol in medium-sized HDL (e.g., rs17315646, p = 3.5 × 10(-12)). We used luciferase reporter assays in HepG2 cells to test all 25 variants for allelic differences in regulatory enhancer activity. rs2281721 showed allelic differences in transcriptional activity (75-fold [T] versus 27-fold [C] more than the empty-vector control), as did a separate 780-bp segment containing rs4846913, rs2144300, and rs6143660 (49-fold [AT(-) haplotype] versus 16-fold [CC(+) haplotype] more). Using electrophoretic mobility shift assays, we observed differential CEBPB binding to rs4846913, and we confirmed this binding in a native chromatin context by performing chromatin-immunoprecipitation (ChIP) assays in HepG2 and Huh-7 cell lines of differing genotypes. Additionally, sequence reads in HepG2 DNase-I-hypersensitivity and CEBPB ChIP-seq signals spanning rs4846913 showed significant allelic imbalance. Allelic-expression-imbalance assays performed with RNA from primary human hepatocyte samples and expression-quantitative-trait-locus (eQTL) data in human subcutaneous adipose tissue samples confirmed that alleles associated with increased HDL-C are associated with a modest increase in GALNT2 expression. Together, these data suggest that at least rs4846913 and rs2281721 play key roles in influencing GALNT2 expression at this HDL-C locus.
Authors: Tamara S. Roman, Amanda F. Marvelle, Marie P. Fogarty, Swarooparani Vadlamudi, Arlene J. Gonzalez, Martin L. Buchkovich, Jeroen R. Huyghe, Christian Fuchsberger, Anne U. Jackson, Ying Wu, Mete Civelek, Aldons J. Lusis, Kyle J. Gaulton, Praveen Sethupathy, Antti J. Kangas, Pasi Soininen, Mika Ala-Korpela, Johanna Kuusisto, Francis S. Collins, Markku Laakso, Michael Boehnke, Karen L. Mohlke
Institutions: University of North Carolina at Chapel Hill, University of Michigan, University of California, Los Angeles, University of Virginia, Centre for Human Genetics, University of Oxford, University of Oulu, University of Eastern Finland, Oulu University Hospital, University of Bristol, MRC Integrative Epidemiology Unit, Kuopio University Hospital, National Human Genome Research Institute
Language: English
Subfield: Genetics
Domain: Life Sciences
Open Access status: hybrid
Estimated APC paid: $5,150
Funders: American Heart Association, Bristol-Myers Squibb, Wellcome Trust, British Heart Foundation, Academy of Finland, Tekes, Novo Nordisk, Oulun Yliopisto, Diabetestutkimussäätiö, National Institutes of Health, Medical Research Council, National Heart, Lung, and Blood Institute, National Institute on Drug Abuse, National Human Genome Research Institute, National Institute of General Medical Sciences, National Institute of Diabetes and Digestive and Kidney Diseases, NHLBI Division of Intramural Research
Awards: G1218886914, Systems genetics analysis of cardiometabolic trait loci in humans , G2124545180, Targeted Genetic Analysis of T2D and Quantitative Traits, Genetic analysis of type II diabetes in Finnish population, Identifying Genes for Type 2 Diabetes: FUSION, NRSA in Genetics, Predoctoral Training Program in Bioinformatics and Computational Biology, G4474400647, Identifying disease-related functional regulatory variants in open chromatin, Systems genetics analysis of cardiometabolic trait loci in humans , Molecular Genetic Approaches in Atherosclerosis Research, Systems Genetics Dissection of Non-alcoholic Steatohepatitis, Michigan Diabetes Research Center (MDRC), Genetic epidemiology of rare and regulatory variants for metabolic traits, Pre-doctoral Training Program in Integrative Vascular Biology, Identifying Genes for Type 2 Diabetes: FUSION
OpenAlex ID: W2189622420