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Network analysis identifies Rv0324 and Rv0880 as regulators of bedaquiline tolerance in Mycobacterium tuberculosis

Abstract

The resilience of Mycobacterium tuberculosis (MTB) emerges from its ability to effectively counteract immunological, environmental and antitubercular challenges. Here, we demonstrate that MTB can tolerate drug treatment by adopting a tolerant state that can be deciphered through systems analysis of its transcriptional responses. Specifically, we demonstrate how treatment with the antitubercular drug bedaquiline activates a regulatory network that coordinates multiple resistance mechanisms to push MTB into a tolerant state. Disruption of this network, by knocking out its predicted transcription factors, Rv0324 and Rv0880, significantly increased bedaquiline killing and enabled the discovery of a second drug, pretomanid, that potentiated killing by bedaquiline. We demonstrate that the synergistic effect of this combination emerges, in part, through disruption of the tolerance network. We discuss how this network strategy also predicts drug combinations with antagonistic interactions, potentially accelerating the discovery of new effective combination drug regimens for tuberculosis.

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Figure 1: Bedaquiline response networks regulated by Rv0324 and Rv0880.
Figure 2: Killing of ΔRv0324 and ΔRv0880 MTB strains by bedaquiline.
Figure 3: Influence of Rv0880 overexpression on EOB estimation of bedaquiline and pretomanid drug combination.

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Acknowledgements

The authors thank members of the Baliga and Sherman laboratories for discussions, T. Rustad, J. Winkler and S. Hobbs for generating knockout and overexpressing strains, and Z. Simon, M. Sarvothama and R. Liao for technical help. Funding was provided by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health (U19 AI10676, U19 AI111276 and ISBpilot-10135) and the National Institute of General Medical Sciences of the National Institutes of Health (P50GM076547).

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E.J.R.P. led the design and drafted the manuscript. E.J.R.P. and S.M. generated results and analysed data. S.M. helped design the study and helped draft online methods. D.R.S. helped designed the study, discussed results and commented on the manuscript. N.S.B. conceived of the study, discussed the results and drafted the manuscript.

Corresponding author

Correspondence to Nitin S. Baliga.

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The authors declare no competing financial interests.

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Supplementary Information

Supplementary Figures 1-8 and Supplementary Tables 4 and 5. (PDF 2195 kb)

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Supplementary Tables 1–3 (XLSX 58 kb)

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Peterson, E., Ma, S., Sherman, D. et al. Network analysis identifies Rv0324 and Rv0880 as regulators of bedaquiline tolerance in Mycobacterium tuberculosis. Nat Microbiol 1, 16078 (2016). https://doi.org/10.1038/nmicrobiol.2016.78

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