Systems Genetics Analysis of Genome-Wide Association Study Reveals Novel Associations Between Key Biological Processes and Coronary Artery Disease

Abstract

Objective Genome-wide association (GWA) studies have identified multiple genetic variants affecting the risk of coronary artery disease (CAD). However, individually these explain only a small fraction of the heritability of CAD and for most, the causal biological mechanisms remain unclear. We sought to obtain further insights into potential causal processes of CAD by integrating large-scale GWA data with expertly curated databases of core human pathways and functional networks. Approaches and Results Employing pathways (gene sets) from Reactome, we carried out a two-stage gene set enrichment analysis strategy. From a meta-analyzed discovery cohort of 7 CADGWAS data sets (9,889 cases/11,089 controls), nominally significant gene-sets were tested for replication in a meta-analysis of 9 additional studies (15,502 cases/55,730 controls) from the CARDIoGRAM Consortium. A total of 32 of 639 Reactome pathways tested showed convincing association with CAD (replication p<0.05). These pathways resided in 9 of 21 core biological processes represented in Reactome, and included pathways relevant to extracellular matrix integrity, innate immunity, axon guidance, and signaling by PDRF, NOTCH, and the TGF-β/SMAD receptor complex. Many of these pathways had strengths of association comparable to those observed in lipid transport pathways. Network analysis of unique genes within the replicated pathways further revealed several interconnected functional and topologically interacting modules representing novel associations (e.g. semaphorin regulated axonal guidance pathway) besides confirming known processes (lipid metabolism). The connectivity in the observed networks was statistically significant compared to random networks (p<0.001). Network centrality analysis (‘degree’ and ‘betweenness’) further identified genes (e.g. NCAM1, FYN, FURIN etc.) likely to play critical roles in the maintenance and functioning of several of the replicated pathways. Conclusions These findings provide novel insights into how genetic variation, interpreted in the context of biological processes and functional interactions among genes, may help define the genetic architecture of CAD.

Genetics of Coronary Artery Disease

“…116 Thus, interrogation of molecular networks provides additional information on interactions among gene subsets within a given pathway and highlights potentially important interactions between components of different biological pathways. In the study of Ghosh et al, 105 network analysis of unique genes within the replicated pathways not only further confirmed the known processes, such as lipid metabolism, but also revealed many interconnected functional and topologically interacting modules representing novel associations, for example, the semaphorin-regulated axonal guidance pathway. The axon guidance pathways modulate diverse biological phenomena, including cellular adhesion, migration, proliferation, differentiation, survival, and synaptic plasticity, through the participation of highly conserved families of guidance molecules, including netrins, slits, semaphorins, and ephrins, and their cognate receptors 117 and members of these pathways have been highlighted in many recent reports related to macrophage migration, 118 expression of inflammatory markers and M2 signals in atherosclerotic plaque, 119 and chemokine-directed migration of human monocytes.…”

“…However, on the basis of the premise that clinically informative polymorphisms related to complex disease occur in systems of closely interacting genes, 104 even weakly associated variants may provide important information on the biological basis of disease when such variants cluster within a common functional module or a pathway. 105 Thus, novel insights into the genetic architecture of CAD can be obtained by interpreting genetic findings in the context of biological processes and functional interactions among genes.…”

“…[108][109][110][111][112] These analytic algorithms seek to identify a sets of genes whose variants collectively demonstrate strong association with a trait of interest even if the component SNPs individually exhibit relatively modest or nonsignificant association. 105 To identify novel associations between established biological mechanisms and CAD, we recently performed a 2-stage pathwaybased gene-set enrichment analysis of 16 GWAS data sets for CAD that included >25 000 subjects with CAD and >66 000 controls 105 using the i-GSEA4GWAS tool 112 and the Reactome pathway database. 113 A total of 32 of 639 Reactome pathways tested demonstrated convincing association with CAD.…”

Systems Analysis of Thrombus Formation

“…10 Several genome-wide association studies (GWAS) have focused on coronary artery disease (CAD) risk, typically identifying only small percentages of heritable risk such as polymorphisms in platelet derived growth factor (PDGF) pathways. 11 A population study ( Plateletomics.com ) 12 of platelet hyper-responsiveness to arachidonic acid, ADP, PAR1/4 activating petpides revealed: (1) 129 mRNAs and 15 miRNAs that were differentially expressed by age, (2) 54 mRNAs and 9 miRNA differentially expressed by gender, and (3) miR-376c differentially expressed by race (reduced in black subjects) and linked to increased platelet PAR4 signaling. 13 …”

Recent Advances in the Genetics of Atherothrombotic Disease and Its Determinants

“…16 Other studies further explored CAD GWAS data by working to annotate replicated CAD loci. In one such study, Ghosh et al 17 integrated large-scale GWA data with a large pathway database. Using network centrality analysis, they identified several novel gene candidates involved in CAD pathways.…”