Leveraging the transcriptome to further our understanding of GWAS findings: eQTLs associated with genes related to LDL and LDL subclasses, in a cohort of African Americans

Abstract

Background: GWAS discoveries often pose a significant challenge in terms of understanding their underlying mechanisms. Further research, such as an integration with expression quantitative trait locus (eQTL) analyses, are required to decipher the mechanisms connecting GWAS variants to phenotypes. An eQTL analysis was conducted on genes associated with low-density lipoprotein (LDL) cholesterol and its subclasses, with the aim of pinpointing genetic variants previously implicated in GWAS studies focused on lipid-related traits. Notably, the study cohort consisted of African Americans, a population characterized by a heightened prevalence of hypercholesterolemia. Methods: A comprehensive differential expression (DE) analysis was undertaken, with a dataset of 17,948 protein-coding mRNA transcripts extracted from the whole-blood transcriptomes of 416 samples to identify mRNA transcripts associated with LDL, with further granularity delineated between small LDL and large LDL subclasses. Subsequently, eQTL analysis was conducted with a subset of 242 samples for which whole-genome sequencing data were available to identify single-nucleotide polymorphisms (SNPs) associated with the LDL-related mRNA transcripts. Lastly, plausible functional connections were established between the identified eQTLs and genetic variants reported in the GWAS catalogue. Results: DE analysis revealed 1,048, 284, and 94 mRNA transcripts that exhibited differential expression in response to LDL, small LDL, and large LDL, respectively. The eQTL analysis identified a total of 9,950 significant SNP-mRNA associations involving 6,955 SNPs including a subset 101 SNPs previously documented in GWAS of LDL and LDL-related traits. Conclusion: Through comprehensive differential expression analysis, we identified numerous mRNA transcripts responsive to LDL, small LDL, and large LDL. Subsequent eQTL analysis revealed a rich landscape of eQTL-mRNA associations, including a subset of eQTL reported in GWAS studies of LDL and related traits. The study serves as a testament to the important role of integrative genomics in unraveling the enigmatic GWAS relationships between genetic variants and the complex fabric of human traits and diseases.

Keywords: African American (AA); GWAS; LDL; eQTL; transcriptome.

FIGURE 1

First, (1) mRNAs differentially expressed (DE) between the top and bottom tertiles of LDL, small LDL and large LDL are identified. Then, (2) eQTL analysis was conducted to identify cis-eQTLs associated with mRNAs DE by LDL, small and large LDL. Finally, cis-eQTLs reported in GWAS of LDL and LDL-related traits are identified.

FIGURE 2

Graphical summary of the (A) differential expression analysis results along with the (B) number of differentially expressed genes overlapping between the 3 lists.

FIGURE 3

Plots of CXCL5 and PF4, 2 of the 10 mRNAs differentially expressed between top and bottom tertiles of LDL, small LDL and large LDL in respectively column 1, 2 and 3 of the graph.

FIGURE 4

Plot of HLA-B and FCRL3 by respectively rs2247056 and rs3761959 associated with LDL cholesterol level in previous GWAS analyses.