Common Genetic Variants Modulate Pathogen-Sensing Responses in Human Dendritic Cells

Introduction Variation in an individual’s response to environmental factors is likely to influence susceptibility to complex human diseases. The genetic basis of such variation is poorly understood. Here, we identify natural genetic variants that underlie variation in the host innate immune response to infection and analyze the mechanisms by which such variants alter these responses. Identifying the genetic basis of variability in the host response to pathogens. A cohort of 534 individuals donated blood for (a) genotyping of common DNA variants and (b) isolation of immune DCs. DCs were stimulated with viral and bacterial components, and the variability in individuals’ gene expression responses was mapped to specific DNA variants, which were then shown to affect binding of particular transcription factors. Methods We derived dendritic cells (DCs) from peripheral blood monocytes of healthy individuals (295 Caucasians, 122 African Americans, 117 East Asians) and stimulated them with Escherichia coli lipopolysaccharide (LPS), influenza virus, or the cytokine interferon-β (IFN-β) to generate 1598 transcriptional profiles. We genotyped each of these individuals at sites of common genetic variation and identified the genetic variants that best explain variation in gene expression and gene induction between individuals. We then tested mechanistic predictions from these associations using synthetic promoter constructs and genome engineering. Results We identified 264 loci containing genetic variants associated with variation in absolute gene expression in human DCs, of which 121 loci were associated with variation in the induction of gene expression by one or more stimuli. Fine-mapping identified candidate causal single-nucleotide polymorphisms (SNPs) associated with expression variance, and deeper functional experiments localized three of these SNPs to the binding sites of stimulus-activated transcription factors. We also identified a cis variant in the transcription factor, IRF7, associated in trans with the induction of a module of antiviral genes in response to influenza infection. Of the identified genetic variants, 35 were also associated with autoimmune or infectious disease loci found by genome-wide association studies. Discussion The genetic variants we uncover and the molecular basis for their action provide mechanistic explanations and principles for how the innate immune response to pathogens and cytokines varies across individuals. Our results also link disease-associated variants to specific immune pathways in DCs, which provides greater insight into mechanisms underlying complex human phenotypes. Extending our approach to many immune cell types and pathways will provide a global map linking human genetic variants to specific immunological processes. 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 534 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. Mapping of human host-pathogen gene-by-environment interactions identifies pathogen-specific loci. [Also see Perspective by Gregersen] Little is known about how human genetic variation affects the responses to environmental stimuli in the context of complex diseases. Experimental and computational approaches were applied to determine the effects of genetic variation on the induction of pathogen-responsive genes in human dendritic cells. We identified 121 common genetic variants associated in cis with variation in expression responses to Escherichia coli lipopolysaccharide, influenza, or interferon-β (IFN-β). We localized and validated causal variants to binding sites of pathogen-activated STAT (signal transducer and activator of transcription) and IRF (IFN-regulatory factor) transcription factors. We also identified a common variant in IRF7 that is associated in trans with type I IFN induction in response to influenza infection. Our results reveal common alleles that explain interindividual variation in pathogen sensing and provide functional annotation for genetic variants that alter susceptibility to inflammatory diseases.