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

By B. P. Fairfax, P. Humburg, S. Makino, V. Naranbhai, Daniel Wong, Evelyn Lau, L. Jostins, K. Plant, R. Andrews, C. McGee and 1 more. Science, 2014

792 citations recorded by the source corpus.

Introduction Many genetic variants associated with common disease susceptibility occur close to immune-related genes in noncoding DNA, suggestive of a regulatory function. The definition of functional variants and the specific genes that they regulate remains challenging and in many cases is unresolved. We hypothesized that a significant proportion of variants, including those implicated in disease, may show activity in a context-specific manner and therefore only be identifiable upon triggering of immune responses. Context-specific genetic association with differential gene expression in IFN-β signaling. (A) A local association (cis-eQTL) with IFNB1 expression for a single-nucleotide polymorphism (rs2275888) revealed after 2 hours of LPS stimulation of monocytes. (B) This genetic marker shows association with expression of 17 genes on different chromosomes (trans-eQTLs) after 24 hours of LPS stimulation, forming a gene network (C) consistent with the IFN-β signaling cascade. Methods We mapped interindividual variation in gene expression as a quantitative trait, defining expression quantitative trait loci (eQTLs). To investigate the effect of innate immune stimuli on eQTLs, we exposed primary CD14+ human monocytes from 432 European volunteers to the inflammatory proxies interferon-γ (IFN-γ) or differing durations (2 or 24 hours) of lipopolysaccharide (LPS). eQTL mapping was performed on a genome-wide basis with an additive linear model. A subset of 228 individuals with expression data available for all experimental conditions enabled cross-treatment comparisons. Results Stimulation with LPS or IFN-γ resulted in profound effects across monocyte eQTLs, with hundreds of genes and associated pathways demonstrating context-specific eQTLs dependent on the type and duration of stimulus. Context-specific eQTLs frequently intersected established canonical pathways of monocyte signaling and included key nodal genes and effector molecules. These eQTLs are typically more distal to the transcriptional start site and, in some cases, showed reversal of effect between conditions. We also found stimulation reveals novel eQTLs with simultaneous effects involving many genes (trans-eQTLs). Examples included coding polymorphisms in CYP1B1, P2RY11, and IDO2 that modulate activity and develop trans network effects upon stimulation; an LPS-specific IFN-β cytokine network response driven by a cis-eQTL for IFNB1 that was only revealed over time; an interferon regulatory factor 2 (IRF2) transcription factor modulated network up-regulated by IFN-γ involving a cis-eQTL for IRF2; and an IFN-γ–inducible trans gene network involving the transcription factor NFE2L3. We find trans associations to the major histocompatibility complex are dependent on context, paralleling the expression of class II genes. Induced eQTLs were enriched for disease-risk loci with context-specific associations to many putative causal genes, including at ATM, IRF8, and CCR3. Conditional analysis defined additional independent stimulus-specific peaks of association for a given gene. For CARD9 we observed, in addition to a constitutive eQTL informative for a genome-wide association study locus for Crohn’s disease, a stimulus-specific peak eQTL after IFN-γ, defining a further independent signal of disease association. Discussion Interindividual variation in immune responses is accompanied by diverging patterns of gene regulation dependent on underlying genotype. In human monocytes, many regulatory variants display functionality only after pathophysiologically relevant immune stimuli. By considering the cellular and environmental context relevant to disease, it is possible to more extensively resolve functional genetic variants and the specific modulated genes associated with disease. Immune Variation It is difficult to determine the mechanistic consequences of context-dependent genetic variants, some of which may be related to disease (see the Perspective by Gregersen). Two studies now report on the effects of stimulating immunological monocytes and dendritic cells with proteins that can elicit a response to bacterial or viral infection and assess the functional links between genetic variants and profiles of gene expression. M. N. Lee et al. (10.1126/science.1246980) analyzed the expression of more than 400 genes, in dendritic cells from 30 healthy subjects, which revealed how expression quantitative trait loci (eQTLs) affect gene expression within the interferon-β and the Toll-like receptor 3 and 4 pathways. Fairfax et al. (10.1126/science.1246949) performed a genome-wide analysis to show that many eQTLs affected monocyte gene expression in a stimulus- or time-specific manner. Analysis of the transcriptional responses during induced innate immune activity in primary human monocytes is explained. [Also see Perspective by Gregersen] 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 context-specific associations to putative causal genes including CARD9, ATM, and IRF8. Thus, applying pathophysiologically relevant immune stimuli assists resolution of functional genetic variants.

Subfields: Cancer Research, Genetics, Immunology

View Paper: https://www.semanticscholar.org/paper/d3ebdd64aa62f4d92444aef8e6504b1e04fbe260

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Cancer Research

In Genetics

In Immunology

Citations in the corpus

Altered Bile Acid Profile Associates with Cognitive Impairment in Alzheimer’s Disease – An Emerging Role for Gut Microbiome (2018, background): “Interestingly, both ABI3 and MEF2C are thought to be involved in immune reactions to proinflammatory stimuli that are partially secreted by microbes [64,65].”
Comprehensive analysis of single cell ATAC-seq data with SnapATAC (2021, methodology): “Signi ﬁ cant cis -eQTL associations are downloaded from supplementary material in Fairfax (2014) 29 .”
Genetics of circulating inflammatory proteins identifies drivers of immune-mediated disease risk and therapeutic targets (2023, positive): “By analogy, eQTL studies using human immune cells stimulated in vitro (for example, with lipopolysaccharide or interferon) have demonstrated eQTLs that are not present in resting cells but become apparent in the context of cellular activation 49,50 .”
GENETICS AND PATHOGENESIS OF INFLAMMATORY BOWEL DISEASE (2016, background): “Notably, induced eQTL were significantly enriched for GWAS loci, thus providing an independent signal for disease association (60).”
Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells (2016, background): “First, genetic effects on gene expression have been shown to be often context-specific (Kundaje et al., 2015) and thus are better captured in studies probing multiple primary cell types or experimental conditions (Bentham et al., 2015; Fairfax et al., 2014; Naranbhai et al., 2015).”
Modelling local gene networks increases power to detect trans-acting genetic effects on gene expression (2016, methodology): “We validated the results from the Cardiogenics Tran-scriptomic Study [68] in 414 independent monocyte expression arrays in an independent monocyte eQTL dataset [18]. eQTL replication was assessed on a set of 9106 overlapping probes, considering eQTLs down-stream of the locus 12q15.”
Integrated single-cell analysis maps the continuous regulatory landscape of human hematopoietic differentiation (2018, methodology): “We therefore collected previously published cis-eQTLs, derived from interferon-g and lipopolysaccharide stimulation of monocytes (Fairfax et al., 2014), and filtered for SNPswithin developmentally dynamic regulatory elements linked to dynamic genes (n = 370 peak-gene pairs).”
Impact of genetic polymorphisms on human immune cell gene expression (2018, positive): “Previous studies have reported that several genetic variants are associated with gene expression only following perturbation of resting immune cells by relevant environmental (extrinsic) stimuli (Fairfax et al., 2014; Lee et al., 2014).”