Abnormal serum lipid levels, or dyslipidemias, are risk factors for cardiovascular disease (CVD), the leading cause of death worldwide. The genetic factors underlying serum triglyceride (TG) levels are not well understood, despite this trait exhibiting ~50% heritability. Adipose tissue is an important endocrine organ for lipid homeostasis, and adipocytes are key players in energy intake and expenditure mediated through free fatty acid uptake and TG storage and mobilization. The goal of this project is to improve the current understanding of genomic regulatory mechanisms in gene expression and lipid processing pathways in adipocytes.
Aim 1 is targeted to identify serum TG-correlated, adipose-expressed genes that are under local genetic control by expression quantitative trait loci (cis-eQTLs) in the Finnish METabolic Syndrome In Men (METSIM) cohort. We will use promoter Capture Hi-C (pCHi-C) in primary human white adipocytes (HWA) to identify which adipose cis-eQTLs interact with the target gene promoter, as promoter-interacting regions are enriched for regulatory elements. Our preliminary data support this, showing that SNPs in open chromatin within promoter-interacting regions in HWA contribute significantly to the heritability of adipose gene expression and serum TG levels in the METSIM cohort. By further integrating lipid genome-wide association study (GWAS) loci into our analysis, we can find a target gene and underlying mechanism of the GWAS signal.
In Aim 2 we will perform RNA- sequencing, pCHi-C, and Assay for Transposase-Accessible Chromatin (ATAC)-seq in primary HWA after treating them with saturated or monounsaturated fatty acids, to investigate the genomic regulatory mechanisms altered in response to lipid challenge. This will facilitate detection of elements mediating gene expression changes, assayed through both pCHi-C and ATAC-seq. We hypothesize that genomic regulatory architecture uncovered in this system can be used across populations. We will thus use our data to examine Mexican-specific regions found to be associated with high serum TGs in our laboratory. One locus on chromosome 11 contains a risk haplotype for both high TGs and increased post-prandial TG levels after a fatty meal. The regulatory circuitry, identified in HWA both before and after lipid challenge, can be highly valuable for understanding how Mexican-specific variation might lead to genetic dysregulation at this locus.
Aim 2 will also use the UK Biobank (UKBB) for genotype-by-environment interaction analyses. Many systemic metabolic disturbances that are more likely to be present in obese and overweight individuals involve adipocyte function. The UKBB has so far collected genotypes and deep clinical phenotypes for ~150,000 humans, with measures including BMI, lipids, and other CVD risk factors. We will use BMI as an interaction term to test whether the variants within lipid challenge-responsive regions in primary HWA are more likely to affect TGs in the context of this common obesity measurement.
Aims 1 and 2 align with the mission of NHLBI to improve medical care for CVD and dyslipidemia through identification of mechanisms of trait-associated variants in diverse populations.
Abnormal lipid levels, or dyslipidemia, can cause cardiovascular disease, a leading cause of death worldwide. As dyslipidemia has a strong genetic component, it is important to understand how human genetic variation contributes to differences in levels of circulating lipids, ultimately helping inform about risk and prevention strategies to reduce medical and economic burdens. The goals of this project are to identify genomic regulatory mechanisms that contribute to lipid disorders, leading to advanced molecular and genetic understanding, and aiming to better diagnose, prevent, and treat individuals in a personalized manner.
| Freund, Malika Kumar; Burch, Kathryn S; Shi, Huwenbo et al. (2018) Phenotype-Specific Enrichment of Mendelian Disorder Genes near GWAS Regions across 62 Complex Traits. Am J Hum Genet 103:535-552 |
