Myeloid cell genome-wide screen identifies variants associated with Mycobacterium tuberculosis–induced cytokine transcriptional responses
Joshua J. Ivie, Kimberly A. Dill-McFarland, Jason D. Simmons, Glenna J. Peterson, Penelope H. Benchek, Harriet Mayanja-Kizza, Lily E. Veith, Moeko Agata, Dang T.M. Ha, Ho D.T. Nghia, W. Henry Boom, Catherine M. Stein, Chiea C. Khor, Guy E. Thwaites, Hoang T. Hai, Nguyen T.T. Thuong, Xuling Chang, Sarah J. Dunstan, Thomas R. Hawn
Joshua J. Ivie, Kimberly A. Dill-McFarland, Jason D. Simmons, Glenna J. Peterson, Penelope H. Benchek, Harriet Mayanja-Kizza, Lily E. Veith, Moeko Agata, Dang T.M. Ha, Ho D.T. Nghia, W. Henry Boom, Catherine M. Stein, Chiea C. Khor, Guy E. Thwaites, Hoang T. Hai, Nguyen T.T. Thuong, Xuling Chang, Sarah J. Dunstan, Thomas R. Hawn
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Research Article Genetics Infectious disease

Myeloid cell genome-wide screen identifies variants associated with Mycobacterium tuberculosis–induced cytokine transcriptional responses

Abstract

Immune and clinical outcomes to Mycobacterium tuberculosis (Mtb) infection vary greatly between individuals, yet the underlying genetic and cellular mechanisms driving this heterogeneity remain poorly understood. We performed a cellular genome-wide association study to identify genetic variants associated with Mtb-induced monocyte transcriptional expression of IL1B, IL6, TNF, and IFNB1 via RNA-Seq in a Ugandan cohort. Significantly associated variants were assessed for transferability in an independent Seattle cohort, further validated in vitro, and assessed for clinical phenotype associations. We identified 77 loci suggestively associated with Mtb-induced cytokine expression in monocytes in Uganda. SNPs associated with Mtb-induced TNF were enriched within α-linolenic acid metabolism pathway genes, which was validated in vitro using PLA2 inhibitors. Four loci maintained significant associations in Seattle. We validated a cytokine effect with siRNA knockdown for two of these loci, which mapped to the genes SLIT3 and SLC1A1. Furthermore, exogenous treatment of macrophages with SLIT3 enhanced Mtb intracellular replication. Finally, SLC1A1 and SLIT3 variants were associated with susceptibility to tuberculous meningitis and subsequent survival, respectively, in a Vietnamese cohort. In summary, we identified multiple variants and pathways associated with Mtb-induced cytokine transcriptional responses that were validated in vitro and were associated with clinical tuberculosis susceptibility.

Authors

Joshua J. Ivie, Kimberly A. Dill-McFarland, Jason D. Simmons, Glenna J. Peterson, Penelope H. Benchek, Harriet Mayanja-Kizza, Lily E. Veith, Moeko Agata, Dang T.M. Ha, Ho D.T. Nghia, W. Henry Boom, Catherine M. Stein, Chiea C. Khor, Guy E. Thwaites, Hoang T. Hai, Nguyen T.T. Thuong, Xuling Chang, Sarah J. Dunstan, Thomas R. Hawn

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Figure 5

Evaluation of SNP-associated gene effect on other Mtb-response phenotypes reveals SLIT3 effect on intracellular Mtb.

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Evaluation of SNP-associated gene effect on other Mtb-response phenotype...
Intracellular Mtb replication in human macrophages assessed after hSLIT3 N- and C-terminal cotreatment using fluorescence microscopy to measure Mtb-mCherry surface area within each well over 72 hours. Four-hour time point quantifies differences in initial phagocytic uptake and shows no significant differences between groups. Results shown are from 6 biological replicates in 3 human donors. Significant differences were evaluated at each time point and show a significant increase in intracellular Mtb replication with cotreatment of N- and C-terminal SLIT3 at 48 and 72 hours. Significance was assessed using a linear mixed model adjusting for random effect of donor followed by ANOVA and pairwise comparisons for each time point. Individual data points were plotted according to model calculated values adjusted for donor intercept. *P < 0.05. Individual donor values are presented in Supplemental Figure 6E.