Trans-ancestry Fine Mapping and Molecular Assays Identify Regulatory Variants at the ANGPTL8 HDL-C GWAS Locus

Abstract

Recent genome-wide association studies (GWAS) have identified variants associated with high-density lipoprotein cholesterol (HDL-C) located in or near the ANGPTL8 gene. Given the extensive sharing of GWAS loci across populations, we hypothesized that at least one shared variant at this locus affects HDL-C. The HDL-C–associated variants are coincident with expression quantitative trait loci for ANGPTL8 and DOCK6 in subcutaneous adipose tissue; however, only ANGPTL8 expression levels are associated with HDL-C levels. We identified a 400-bp promoter region of ANGPTL8 and enhancer regions within 5 kb that contribute to regulating expression in liver and adipose. To identify variants functionally responsible for the HDL-C association, we performed fine-mapping analyses and selected 13 candidate variants that overlap putative regulatory regions to test for allelic differences in regulatory function. Of these variants, rs12463177-G increased transcriptional activity (1.5-fold, P = 0.004) and showed differential protein binding. Six additional variants (rs17699089, rs200788077, rs56322906, rs3760782, rs737337, and rs3745683) showed evidence of allelic differences in transcriptional activity and/or protein binding. Taken together, these data suggest a regulatory mechanism at the ANGPTL8 HDL-C GWAS locus involving tissue-selective expression and at least one functional variant.

Deciphering the Emerging Complexities of Molecular Mechanisms at GWAS Loci

“…Although chromatin interactions often suggest multiple plausible target genes, they can provide stronger evidence when observed with colocalized eQTLs or functional evidence. At the ARL15 locus (associated with insulin resistance traits and type 2 diabetes), HiC data in multiple cell types show significant interaction between the GWAS variant region and the FST (MIM: 136470) promoter, 108 500 kb away, and these data support evidence that the GWAS signals exhibit significant colocalized eQTLs for FST, 83 although functional studies support a role for ARL15 in insulin secretion. 123 At a schizophrenia-associated locus, variants were linked by both HiC and genome editing to FOXG1 (MIM: 164874) >700 kb away, 124 and at the TMEM106B (MIM: 613413) GWAS locus (associated with dementia), a variant in a CTCF binding site altered chromatin architecture to change TMEM106B expression and cell toxicity.…”

“…Methods make different assumptions about the contributions of underlying variants and apply different strategies incorporating genetic association, LD, and functional annotation. At the ANGPTL8 (MIM: 616223) locus, associated with high-density lipoprotein (HDL) cholesterol across populations, three fine-mapping methods (MANTRA, CAVIAR, and PAINTOR) of prioritizing candidate variants generated differing results; 83 MANTRA identified a credible set of ten variants, CAVIAR identified a credible set of 24 variants by using Finnish association data and a credible set of two variants by using African American association data, and PAINTOR identified ten, seven, and five variants in Finnish, African American, and the combined studies, respectively. Of the 39 variants identified by least one method, only 12 were identified in at least two analyses, and only four were identified in all three analyses.…”

Tractor: A framework allowing for improved inclusion of admixed individuals in large-scale association studies

“…ANGPTL8, also known as lipasin and betatrophin, has been shown to regulate plasma lipid levels in mice by inhibiting the enzyme lipoprotein lipase 93–96 . In humans, ANGPTL8 levels correlate with metabolic phenotypes including type 2 diabetes and obesity 97–100 and HDL-C expression levels across diverse ancestry groups have been demonstrated to better correlate with than DOCK6 101 . Together these make ANGPTL8 a more promising candidate gene than DOCK6, which has no clear tie to blood lipid phenotypes.…”

The negative effect of ANGPTL8 on HDL-mediated cholesterol efflux capacity

“…ANGPTL8 has been reported to present significant but contradictive relationship with various blood lipid markers. Genomic studies showed that ANGPTL8 gene variant was associated with HDL-C variant [ 16 , 25 ]. The relationship between ANGPTL8 and triglyceride has also been deeply excavated.…”