Project 1 will apply systems approaches to identify Host Regulatory Gene (HRG) networks that determine the balance between asymptomatic MTB infection and TB disease progression. Our strategy is centered on our recent identification of transcriptomic signatures that predict progression to active tuberculosis (TB) in humans. By integrating our human transcriptomic signatures for MTB disease progression with network models of macrophage innate immunity, we have identified nearly 200 candidate HRGs of MTB infection. Leveraging our access to a vast and expanding repository of mice harboring ENU-induced incidental mutations, we will screen the HRG mouse mutants for altered MTB-induced innate and adaptive immunity in vivo. HRG mutants that alter TB disease progression will be advanced for detailed mechanistic analysis. MTB-regulated innate immunity networks, and networks governing the interface between innate and adaptive immunity will be exhaustively characterized in vitro and in vivo through systems-level profiling. We will collect host and MTB transcriptomes, targeted protein level changes, condition-specific ChlP-seq, and proteomic enhanceosome profiles of key host regulators from within matched samples of infected macrophages. These data will fuel modeling of both the bacterial and host response networks, predictions from which will drive a new round of candidate HRG evaluation, omics-scale data collection and additional modeling. Our ultimate modeling Aim: a novel integrated host/MTB network model will be tested using samples from humans, with both candidate mutant bacteria and specific host genes modulated by RNAi. In recent years, we have contributed substantially to the infrastructure needed for systems biology, including the development of key tools for data generation, analysis and modeling. We have generated an extensive compendium of innate regulatory networks that will serve as a foundation for the MTB studies proposed here. This project combines separate advances in immunology, transcriptomics, molecular genetics, ChlPseq, proteomics and network modeling to produce an experimentally grounded and verifiable systems-level

Public Health Relevance

Mycobacterium tuberculosis causes ~9 million new cases of active disease and 1.4 million deaths each year, and our tools to combat tuberculosis (TB) disease are universally outdated and overmatched. This project combines separate advances in systems biology and network modeling to produce an experimentally grounded and verifiable systems-level model of the host regulatory networks that affect TB progression.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Research Program--Cooperative Agreements (U19)
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Special Emphasis Panel (ZAI1-EC-M (M1))
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Seattle Biomedical Research Institute
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Peterson, Eliza J R; Ma, Shuyi; Sherman, David R et al. (2016) Network analysis identifies Rv0324 and Rv0880 as regulators of bedaquiline tolerance in Mycobacterium tuberculosis. Nat Microbiol 1:16078
Rothchild, Alissa C; Sissons, James R; Shafiani, Shahin et al. (2016) MiR-155-regulated molecular network orchestrates cell fate in the innate and adaptive immune response to Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 113:E6172-E6181
Turkarslan, Serdar; Peterson, Eliza J R; Rustad, Tige R et al. (2015) A comprehensive map of genome-wide gene regulation in Mycobacterium tuberculosis. Sci Data 2:150010
Moguche, Albanus O; Shafiani, Shahin; Clemons, Corey et al. (2015) ICOS and Bcl6-dependent pathways maintain a CD4 T cell population with memory-like properties during tuberculosis. J Exp Med 212:715-28
Ma, Shuyi; Minch, Kyle J; Rustad, Tige R et al. (2015) Integrated Modeling of Gene Regulatory and Metabolic Networks in Mycobacterium tuberculosis. PLoS Comput Biol 11:e1004543
Andersen, Peter; Urdahl, Kevin B (2015) TB vaccines; promoting rapid and durable protection in the lung. Curr Opin Immunol 35:55-62
Minch, Kyle J; Rustad, Tige R; Peterson, Eliza J R et al. (2015) The DNA-binding network of Mycobacterium tuberculosis. Nat Commun 6:5829
Di Paolo, Nelson C; Shafiani, Shahin; Day, Tracey et al. (2015) Interdependence between Interleukin-1 and Tumor Necrosis Factor Regulates TNF-Dependent Control of Mycobacterium tuberculosis Infection. Immunity 43:1125-36
Zak, Daniel E; Aderem, Alan (2015) Systems integration of innate and adaptive immunity. Vaccine 33:5241-8
Urdahl, Kevin B (2014) Understanding and overcoming the barriers to T cell-mediated immunity against tuberculosis. Semin Immunol 26:578-87

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