Mapping disease-regulatory flux through eQTL-based causal gene networks: a complex-trait framework applied to coronary artery disease

Abstract

A substantial proportion of inherited susceptibility to common diseases is mediated through tissue-specific regulatory variation. The omnigenic model hypothesizes that much of this risk arises from distant (trans) regulatory effects that are propagated via gene-regulatory networks (GRNs) from numerous regulatory genes onto a relatively small set of core genes. Two major challenges have hindered an empirical assessment of this model. First, transcriptome-wide association studies primarily assess gene expression that is regulated locally (in cis), and thus miss trans-acting effects. Second, trans regulation has so far been examined only in aggregate, without identifying which regulatory genes transmit disease-associated signals to which target genes. Here, we present a framework that decomposes each gene's disease association into a local cis component and a set of trans components attributable to its upstream regulators, propagated along a directed causal GRN. For each gene, we estimate sparse Bayesian expression models and we assess model performance using out-of-sample prediction. Propagating trans signals through the inferred network yields a disease-regulatory flux map: a directed, signed representation that quantifies the contribution of each regulator to the disease association of each target gene. Applying this framework to seven tissues relevant to coronary artery disease, we demonstrate how genetic variation flows through the GRN to affect disease risk. Outgoing regulatory influences from individual genes are directionally heterogeneous, whereas disease-associated genes tend to integrate convergent input from multiple regulators; these convergent targets are enriched for cardiovascular-related biological processes. Consequently, each gene's disease association can be reinterpreted as a detailed allocation of the disease signal among its contributing regulators.