This project will address the critical need for new and effective antitubercular drugs. Our primary objective is to elucidate the mechanisms by which Mycobacterium tuberculosis tolerates antitubercular drug treatment. Our motivating hypothesis is that M. tuberculosis tolerates drug induced stress by differentially regulating detoxification enzymes, efflux pumps, metabolic activity, pellicle-forming factors, and cell wall remodeling systems. Further, we postulate that a secondary drug targeting one or few regulators of these tolerance strategies will potentiate the primary drug-treatment, and potentially reduce the emergence of resistance. We propose a systems biology approach to generate a network perspective of drug-induced tolerance mechanisms and how they are coordinated by one or few regulators that could be targeted for overcoming drug-specific tolerance using combinatorial treatment regimens. Hence, the innovation of our proposed research emerges from integrating network characterization of drug- specific tolerance mechanisms into the rational discovery of novel drug combinations.
In Aim 1, we will transcriptionally profile M. tuberculosis following treatment with ten selected drugs (primary drugs). Using techniques developed in our laboratory, differentially expressed genes will be mapped onto a systems-scale gene regulatory network model of M. tuberculosis to infer drug-specific tolerance sub-networks and elucidate key regulators. We will also identify tolerance sub-networks by generating genome-wide fitness profiles in the presence of the selected primary drugs. Drug-associated fitness defects will reveal genes that are important for dealing with drug-induced stress and are hypothesized to cluster together in drug-specific tolerance sub-networks.
In Aim 2, we will transcriptionally profile ~250 secondary drugs and perform combination high-throughput screens of all primary and secondary drug combinations. Data from these studies will be used to iteratively refine the model and develop a machine learning algorithm to identify gene- and network-level features that are predictive of synergistic drug interactions. Finally, mechanism of synergistic drug combinations will be characterized by selectively perturbing the predicted regulators of the tolerance sub-networks. This project will propel the development of systems biology tools to accurately predict novel synergistic drug combinations, thereby guiding experimental assessment and accelerating the delivery of new treatments to patients with tuberculosis infection.

Public Health Relevance

Treatment of tuberculosis infection (responsible for 1.5 million deaths annually) is complicated by the impermeable cell wall structure of Mycobacterium tuberculosis and its intrinsic ability to adapt and withstand drug treatment, a phenomenon called tolerance. Thus, an urgent goal of antitubercular drug discovery is to overcome drug tolerance. This project will deepen our understanding of how M. tuberculosis responds to and thereby tolerates drug treatment and will use this systems-scale understanding to develop a predictive framework for identifying new synergistically acting drug combinations for the treatment of tuberculosis.

Agency
National Institute of Health (NIH)
Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Type
Research Project (R01)
Project #
5R01AI128215-05
Application #
10059161
Study Section
Drug Discovery and Mechanisms of Antimicrobial Resistance Study Section (DDR)
Program Officer
Lacourciere, Karen A
Project Start
2016-12-01
Project End
2021-11-30
Budget Start
2020-12-01
Budget End
2021-11-30
Support Year
5
Fiscal Year
2021
Total Cost
Indirect Cost
Name
Institute for Systems Biology
Department
Type
DUNS #
135646524
City
Seattle
State
WA
Country
United States
Zip Code
98109