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Poonawala H, Zhang Y, Kuchibhotla S, Green AG, Cirillo DM, Di Marco F, Spitlaeri A, Miotto P, Farhat MR. Transcriptomic responses to antibiotic exposure in Mycobacterium tuberculosis. Antimicrob Agents Chemother 2024; 68:e0118523. [PMID: 38587412 PMCID: PMC11064486 DOI: 10.1128/aac.01185-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 03/06/2024] [Indexed: 04/09/2024] Open
Abstract
Transcriptional responses in bacteria following antibiotic exposure offer insights into antibiotic mechanism of action, bacterial responses, and characterization of antimicrobial resistance. We aimed to define the transcriptional antibiotic response (TAR) in Mycobacterium tuberculosis (Mtb) isolates for clinically relevant drugs by pooling and analyzing Mtb microarray and RNA-seq data sets. We generated 99 antibiotic transcription profiles across 17 antibiotics, with 76% of profiles generated using 3-24 hours of antibiotic exposure and 49% within one doubling of the WHO antibiotic critical concentration. TAR genes were time-dependent, and largely specific to the antibiotic mechanism of action. TAR signatures performed well at predicting antibiotic exposure, with the area under the receiver operating curve (AUC) ranging from 0.84-1.00 (TAR <6 hours of antibiotic exposure) and 0.76-1.00 (>6 hours of antibiotic exposure) for upregulated genes and 0.57-0.90 and 0.87-1.00, respectfully, for downregulated genes. This work desmonstrates that transcriptomics allows for the assessment of antibiotic activity in Mtb within 6 hours of exposure.
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Affiliation(s)
- Husain Poonawala
- Department of Medicine and Department of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, Massachusetts, USA
- Department of Medicine and Department of Anatomic and Clinical Pathology, Tufts University School of Medicine, Boston, Massachusetts, USA
- Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance, Boston, Massachusetts, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Yu Zhang
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Anna G. Green
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Federico Di Marco
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Andrea Spitlaeri
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy
| | - Paolo Miotto
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Maha R. Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
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Naidu A, Nayak SS, Lulu S S, Sundararajan V. Advances in computational frameworks in the fight against TB: The way forward. Front Pharmacol 2023; 14:1152915. [PMID: 37077815 PMCID: PMC10106641 DOI: 10.3389/fphar.2023.1152915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
Around 1.6 million people lost their life to Tuberculosis in 2021 according to WHO estimates. Although an intensive treatment plan exists against the causal agent, Mycobacterium Tuberculosis, evolution of multi-drug resistant strains of the pathogen puts a large number of global populations at risk. Vaccine which can induce long-term protection is still in the making with many candidates currently in different phases of clinical trials. The COVID-19 pandemic has further aggravated the adversities by affecting early TB diagnosis and treatment. Yet, WHO remains adamant on its "End TB" strategy and aims to substantially reduce TB incidence and deaths by the year 2035. Such an ambitious goal would require a multi-sectoral approach which would greatly benefit from the latest computational advancements. To highlight the progress of these tools against TB, through this review, we summarize recent studies which have used advanced computational tools and algorithms for-early TB diagnosis, anti-mycobacterium drug discovery and in the designing of the next-generation of TB vaccines. At the end, we give an insight on other computational tools and Machine Learning approaches which have successfully been applied in biomedical research and discuss their prospects and applications against TB.
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Affiliation(s)
| | | | | | - Vino Sundararajan
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, India
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Larkins-Ford J, Aldridge BB. Advances in the design of combination therapies for the treatment of tuberculosis. Expert Opin Drug Discov 2023; 18:83-97. [PMID: 36538813 PMCID: PMC9892364 DOI: 10.1080/17460441.2023.2157811] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Tuberculosis requires lengthy multi-drug therapy. Mycobacterium tuberculosis occupies different tissue compartments during infection, making drug access and susceptibility patterns variable. Antibiotic combinations are needed to ensure each compartment of infection is reached with effective drug treatment. Despite drug combinations' role in treating tuberculosis, the design of such combinations has been tackled relatively late in the drug development process, limiting the number of drug combinations tested. In recent years, there has been significant progress using in vitro, in vivo, and computational methodologies to interrogate combination drug effects. AREAS COVERED This review discusses the advances in these methodologies and how they may be used in conjunction with new successful clinical trials of novel drug combinations to design optimized combination therapies for tuberculosis. Literature searches for approaches and experimental models used to evaluate drug combination effects were undertaken. EXPERT OPINION We are entering an era richer in combination drug effect and pharmacokinetic/pharmacodynamic data, genetic tools, and outcome measurement types. Application of computational modeling approaches that integrate these data and produce predictive models of clinical outcomes may enable the field to generate novel, effective multidrug therapies using existing and new drug combination backbones.
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Affiliation(s)
- Jonah Larkins-Ford
- Department of Molecular Biology and Microbiology and Tufts University School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA
- Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance (CIMAR), Tufts University, Boston, MA, USA
- Current address: MarvelBiome Inc, Woburn, MA, USA
| | - Bree B. Aldridge
- Department of Molecular Biology and Microbiology and Tufts University School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA
- Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance (CIMAR), Tufts University, Boston, MA, USA
- Department of Biomedical Engineering, Tufts University School of Engineering, Medford, MA, USA
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Cooper C, Peterson EJR, Bailo R, Pan M, Singh A, Moynihan P, Nakaya M, Fujiwara N, Baliga N, Bhatt A. MadR mediates acyl CoA-dependent regulation of mycolic acid desaturation in mycobacteria. Proc Natl Acad Sci U S A 2022; 119:e2111059119. [PMID: 35165190 PMCID: PMC8872791 DOI: 10.1073/pnas.2111059119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 12/28/2021] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium tuberculosis has a lipid-rich cell envelope that is remodeled throughout infection to enable adaptation within the host. Few transcriptional regulators have been characterized that coordinate synthesis of mycolic acids, the major cell wall lipids of mycobacteria. Here, we show that the mycolic acid desaturase regulator (MadR), a transcriptional repressor of the mycolate desaturase genes desA1 and desA2, controls mycolic acid desaturation and biosynthesis in response to cell envelope stress. A madR-null mutant of M. smegmatis exhibited traits of an impaired cell wall with an altered outer mycomembrane, accumulation of a desaturated α-mycolate, susceptibility to antimycobacterials, and cell surface disruption. Transcriptomic profiling showed that enriched lipid metabolism genes that were significantly down-regulated upon madR deletion included acyl-coenzyme A (aceyl-CoA) dehydrogenases, implicating it in the indirect control of β-oxidation pathways. Electromobility shift assays and binding affinities suggest a unique acyl-CoA pool-sensing mechanism, whereby MadR is able to bind a range of acyl-CoAs, including those with unsaturated as well as saturated acyl chains. MadR repression of desA1/desA2 is relieved upon binding of saturated acyl-CoAs of chain length C16 to C24, while no impact is observed upon binding of shorter chain and unsaturated acyl-CoAs. We propose this mechanism of regulation as distinct to other mycolic acid and fatty acid synthesis regulators and place MadR as the key regulatory checkpoint that coordinates mycolic acid remodeling during infection in response to host-derived cell surface perturbation.
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Affiliation(s)
- Charlotte Cooper
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | | | - Rebeca Bailo
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Min Pan
- Institute for Systems Biology, Seattle, WA 98109
| | - Albel Singh
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Patrick Moynihan
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | | | - Nagatoshi Fujiwara
- Department of Food and Nutrition, Faculty of Contemporary Human Life Science, Tezukayama University, Nara 631-8585, Japan
| | - Nitin Baliga
- Institute for Systems Biology, Seattle, WA 98109;
- Department of Biology, University of Washington, Seattle, WA 98105
- Department of Microbiology, University of Washington, Seattle, WA 98105
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98105
- Lawrence Berkeley National Lab, Berkeley, CA 94720
| | - Apoorva Bhatt
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK;
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
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