Elucidating mechanisms of genetic cross-disease associations: an integrative approach implicates protein C as a causal pathway in arterial and venous diseases

Abstract

Genome-wide association studies have identified many individual genetic loci associated with multiple complex traits and common diseases. There are, however, few examples where the molecular basis of such pleiotropy has been elucidated. To address this challenge, we describe an integrative approach, focusing on the p.Ser219Gly (rs867186 A>G) variant in the PROCR gene (encoding the endothelial protein C receptor, EPCR), which has been associated with lower coronary artery disease (CAD) risk but higher venous thromboembolism (VTE) risk. In a phenome scan of 12 cardiometabolic diseases and 24 molecular factors, we found that PROCR-219Gly associated with higher plasma levels of zymogenic and activated protein C as well as coagulation factor VII. Using statistical colocalization and Mendelian randomization analyses, we uncovered shared genetic etiology across activated protein C, factor VII, CAD and VTE, identifying p.S219G as the likely causal variant at the locus. In a recall-by-genotype study of 52 healthy volunteers stratified by p.S219G, we detected 2.5-fold higher soluble EPCR levels and 1.2-fold higher protein C levels in plasma per effect allele, suggesting the allele induces EPCR shedding from the membrane of endothelial cells. Finally, in cell adhesion assays, we found that increasing concentrations of activated protein C, but not soluble EPCR, reduced leukocyte-endothelial cell adhesion, a marker for vascular inflammation. These results support a role for protein C as a causal factor in arterial and venous diseases, suggesting that PROCR-219Gly protects against CAD through anti-inflammatory mechanisms while it promotes VTE risk through pro-thrombotic mechanisms. Overall, our study illustrates a multi-modal approach that can help reveal molecular underpinnings of cross-disease associations.

Phenome-wide Mendelian randomization mapping the influence of the plasma proteome on complex diseases

“…For each of these examples, the direction of effect between circulating protein and disease risk was consistent with the therapeutic mechanism, except IL6R and PROC at first sight. However, for IL6R and PROC, the alleles associated with higher soluble protein levels have been shown to also lead to lower intracellular pathway activation 36 , 37 , indicating consistency of direction with the therapeutic approach. These examples highlight the importance of careful examination of the biological mechanisms underlying plasma pQTLs to enable translation.…”

“…In this study, we have estimated the role of protein measured in plasma on a range of complex human phenotypes but are unable to assess the relevance of protein levels in other tissues. WhileeQTL studies highlight a large proportion of eQTLs being shared across tissues 37 , there are many which show cell type and state specificity 49 , highlighting the potential value of applying the current approach to data from proteomics analyses in other cell types and tissues. We also hypothesize that, in instances with multiple conditionally distinct pQTLs but where we observe colocalization of only certain conditionally distinct pQTL-phenotype pairs, this may reflect underlying cell- and state-specific heterogeneity in bulk plasma pQTLs, among which only certain cell-types or states are causal 50 .…”

Balancing scientific interests and the rights of participants in designing a recall by genotype study

“…RbG studies are often conducted as sub-studies within the framework of a larger-scale research study, which can be longitudinal, long term, biobank based, and with broad aims. The most recently published RbG studies included in our literature review were conducted in Europe, mostly in the frame of population studies such as the Cambridge BioResource [25,26], the Avon Longitudinal Study of Parents and Children [27,28], the Exeter 10000 study [29], the Estonian Biobank of the Estonian Genome Center [30], the PPP-Botnia study [31], and other types of study [32,33]. These RbG studies were designed to understand a variety of diseases, conditions, and topics, such as inflammatory bowel disease [25], arterial and venous diseases [26], schizophrenia [27], cardiovascular disease [28], level of adiponectin [29], familial hypercholesterolaemia [30], type 2 diabetes [31], anxiety disorders [32], and predisposition to hypertriacylglycerolaemia [33].…”

“…The most recently published RbG studies included in our literature review were conducted in Europe, mostly in the frame of population studies such as the Cambridge BioResource [25,26], the Avon Longitudinal Study of Parents and Children [27,28], the Exeter 10000 study [29], the Estonian Biobank of the Estonian Genome Center [30], the PPP-Botnia study [31], and other types of study [32,33]. These RbG studies were designed to understand a variety of diseases, conditions, and topics, such as inflammatory bowel disease [25], arterial and venous diseases [26], schizophrenia [27], cardiovascular disease [28], level of adiponectin [29], familial hypercholesterolaemia [30], type 2 diabetes [31], anxiety disorders [32], and predisposition to hypertriacylglycerolaemia [33]. Where the variant(s) under study had clinical implications and treatment options for the participant and their relatives, genetic counselling, the disclosure of the carrier status, and further tests for family members were offered [30].…”

Antithrombin, protein C and protein S: Genome and transcriptome wide association studies identify 7 novel loci regulating plasma levels

“…After examination of pleiotropic effects, the variant at the PROCR gene (rs1799809) was excluded to avoid violations of MR assumptions. Moreover, additional evidence indicates that this variant is strongly associated with several hemostasis and thrombosis phenotypes and has opposite effect directions for venous and arterial thrombosis reflecting distinct pleiotropic biological mechanisms 18,46,47 . Details of selected genetic instruments can be found in Supplementary Table S12 .…”