Innate Immune Activity Conditions the Effect of Regulatory Variants upon Monocyte Gene Expression

Abstract

To systematically investigate the impact of immune stimulation upon regulatory variant activity, we exposed primary monocytes from 432 healthy Europeans to interferon-γ (IFN-γ) or differing durations of lipopolysaccharide and mapped expression quantitative trait loci (eQTLs). More than half of cis-eQTLs identified, involving hundreds of genes and associated pathways, are detected specifically in stimulated monocytes. Induced innate immune activity reveals multiple master regulatory trans-eQTLs including the major histocompatibility complex (MHC), coding variants altering enzyme and receptor function, an IFN-β cytokine network showing temporal specificity, and an interferon regulatory factor 2 (IRF2) transcription factor-modulated network. Induced eQTL are significantly enriched for genome-wide association study loci, identifying contextspecific associations to putative causal genes including CARD9, ATM, and IRF8. Thus, applying pathophysiologically relevant immune stimuli assists resolution of functional genetic variants.Inappropriate immune activity and associated inflammation are involved in the pathogenesis of a broad range of common diseases including inflammatory bowel disease, atherosclerosis, rheumatoid arthritis, and cancer. Moreover, a significant proportion of common disease risk loci identified with genome-wide association studies (GWAS) implicate immune genes (1). Most GWAS loci consist of single-nucleotide polymorphisms (SNPs) within noncoding, putatively regulatory DNA, often at a distance from any gene coding regions (2). The identification of functional regulatory variants and associated modulated genes is key to interpreting GWAS findings and establishing how genes are associated with disease. This can be explored by mapping gene expression as a quantitative trait (eQTL mapping) (3-6).

The macrophage IRF8/IRF1 regulome is required for protection against infections and is associated with chronic inflammation

“…Indeed, different association studies have identified IRF8-and/or IRF1-associated variants as genetic risk factors for inflammatory bowel disease, multiple sclerosis, rheumatoid arthritis, and other chronic inflammatory diseases in humans (Jostins et al, 2012;Beecham et al, 2013;Okada et al, 2014). Of interest is a single nucleotide polymorphism near IRF8 (SNP accession number rs17445836) that regulates IRF8 mRNA expression (eSNP) in peripheral blood mononuclear cells and that is also the lead risk factor single nucleotide polymorphism associated with multiple sclerosis (Fairfax et al, 2014). Likewise, a similar regulatory single nucleotide polymorphism located near IRF1 behaves as a risk factor for Crohn's disease (Fairfax et al, 2014).…”

Characterizing the genetic basis of innate immune response in TLR4-activated human monocytes

“…However, future studies could test this hypothesis, as eQTL data for large numbers of different cell types become increasingly available. Recently two studies identified eQTLs under LPS stimulation in primary human monocytes 29 and dendritic cells 30 . Comparison of our study with these studies showed a significant overlap between our data and those of Fairfax et al 29 In all, 43 and 44% of our monocyte data under baseline and LPS stimulation, respectively, were found to be genome-wide significant in Fairfax et al (Supplementary Fig.…”

“…Recently two studies identified eQTLs under LPS stimulation in primary human monocytes 29 and dendritic cells 30 . Comparison of our study with these studies showed a significant overlap between our data and those of Fairfax et al 29 In all, 43 and 44% of our monocyte data under baseline and LPS stimulation, respectively, were found to be genome-wide significant in Fairfax et al (Supplementary Fig. 9a) and 55 (baseline) and 56% (LPS) of the data of Fairfax et al showed evidence of replication in our data set ( Supplementary Fig.…”

Effects of anti-inflammatory drugs on the expression of tryptophan-metabolism genes by human macrophages

“…Notably, the 7 h LPS samples were most distant (least correlated with) from the control samples. In keeping with evidence that LPS‐inducible genes in monocytes can be treated as quantitative traits with extensive variation between individuals,51 samples from the same donor tended to be in the same neighborhood.…”

“…LPS is itself known to induce type 1 IFNs (mainly IFNβ) in MDM, which act in an autocrine manner via IFNAR1, itself induced by LPS 27. Accordingly, the response to exogenous type 1 IFN (IFNα) was largely a subset of the LPS response, as reported in previous studies 24, 28, 50, 51, 54. None of the anti‐inflammatory agents we examined completely prevented the response to either challenge and, although prednisolone and anti‐TNFα both reduced expression of many genes that were up‐ or down‐regulated by the inflammatory challenges, each had a distinctive transcriptional effect.…”