Human genetic variation influences cellular response to Chlamydia trachomatis infection

Abstract

Human genetic diversity can have profound effects on health outcomes upon exposure to infectious agents. For infections with Chlamydia trachomatis (C. trachomatis), the wide range of genital and ocular disease manifestations are likely influenced by human genetic differences that regulate interactions between C. trachomatis and host cells. Using a cellular GWAS, we leveraged this diversity in cellular responses to demonstrate the importance of variation at the Toll-like Receptor 1 (TLR1), TLR6, and TLR10 gene locus to cytokine production in response to C. trachomatis. We determined that a single nucleotide polymorphism (SNP), rs1057807, located in a region that forms a loop with the TLR6 promoter, is associated with increased expression of TLR1, TLR6, and TLR10 and secreted levels of ten C. trachomatis-induced cytokines. Production of these C. trachomatis-induced cytokines is primarily dependent on MyD88 and TLR6 based on experiments using inhibitors, blocking antibodies, RNAi, and protein overexpression. Population genetic analyses further demonstrated that the mean IL-6 response of cells from two European populations were higher than the mean response of cells from three African populations and that this difference was partially attributable to variation in rs1057807 allele frequency. In contrast, a SNP associated with a different pro-inflammatory cytokine (rs2869462 associated with the chemokine CXCL10) exhibited an opposite response, underscoring the complexity of how different genetic variants contribute to an individual’s immune response. This multidisciplinary study has identified a long-range chromatin interaction and genetic variation that regulates TLR6 to broaden our understanding of how human genetic variation affects the C. trachomatis-induced immune response.The identification of host factors involved in infectious disease pathogenesis have the potential to lead to the clinical development of therapeutics or biomarkers of disease progression. Through the identification and characterization of a SNP associated with C. trachomatis-induced cytokine responses, we have elucidated a role for TLR6 in the host immune response to C. trachomatis. Further characterization of this genetic locus and the involvement of TLR6 in C. trachomatis infection will determine the clinical relevance of this association. As C. trachomatis is a disease with a wide range of clinical outcomes that are likely influenced by human genetic differences, other genetic loci beyond the TLR locus are also likely involved in C. trachomatis pathogenesis and host response. To broaden the tools available to study the role of human genetic variation in C. trachomatis cellular infection traits beyond the TLR10/TLR1/TLR6 locus, we developed single-cell Hi-HOST (scHi-HOST), a cellular single-cell RNA-sequencing-based variation of the original Hi-HOST cellular GWAS screen and applied the platform to C. trachomatis infection. Whereas Hi-HOST is powerful and has proved successful, the technique is time- and labor-intensive. scHi-HOST decreases the amount of time and labor required for cellular GWAS screening and introduces a cellular phenotype not assayed in Hi-HOST: host gene expression. As scHi-HOST replicates the original Hi-HOST phenotypes and introduces a new cellular phenotype measurement, this screen serves as a replication screen for previously identified associations and a discovery screen for new associations.