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Guallar-Garrido S, Soldati T. Exploring host-pathogen interactions in the Dictyostelium discoideum-Mycobacterium marinum infection model of tuberculosis. Dis Model Mech 2024; 17:dmm050698. [PMID: 39037280 DOI: 10.1242/dmm.050698] [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] [Indexed: 07/23/2024] Open
Abstract
Mycobacterium tuberculosis is a pathogenic mycobacterium that causes tuberculosis. Tuberculosis is a significant global health concern that poses numerous clinical challenges, particularly in terms of finding effective treatments for patients. Throughout evolution, host immune cells have developed cell-autonomous defence strategies to restrain and eliminate mycobacteria. Concurrently, mycobacteria have evolved an array of virulence factors to counteract these host defences, resulting in a dynamic interaction between host and pathogen. Here, we review recent findings, including those arising from the use of the amoeba Dictyostelium discoideum as a model to investigate key mycobacterial infection pathways. D. discoideum serves as a scalable and genetically tractable model for human phagocytes, providing valuable insights into the intricate mechanisms of host-pathogen interactions. We also highlight certain similarities between M. tuberculosis and Mycobacterium marinum, and the use of M. marinum to more safely investigate mycobacteria in D. discoideum.
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Affiliation(s)
- Sandra Guallar-Garrido
- Department of Biochemistry, Faculty of Science, University of Geneva, 30 quai Ernest-Ansermet, Science II, 1211 Geneva-4, Switzerland
| | - Thierry Soldati
- Department of Biochemistry, Faculty of Science, University of Geneva, 30 quai Ernest-Ansermet, Science II, 1211 Geneva-4, Switzerland
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Al-Bari MAA, Peake N, Eid N. Tuberculosis-diabetes comorbidities: Mechanistic insights for clinical considerations and treatment challenges. World J Diabetes 2024; 15:853-866. [PMID: 38766427 PMCID: PMC11099355 DOI: 10.4239/wjd.v15.i5.853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/08/2024] [Accepted: 03/21/2024] [Indexed: 05/10/2024] Open
Abstract
Tuberculosis (TB) remains a leading cause of death among infectious diseases, particularly in poor countries. Viral infections, multidrug-resistant and ex-tensively drug-resistant TB strains, as well as the coexistence of chronic illnesses such as diabetes mellitus (DM) greatly aggravate TB morbidity and mortality. DM [particularly type 2 DM (T2DM)] and TB have converged making their control even more challenging. Two contemporary global epidemics, TB-DM behaves like a syndemic, a synergistic confluence of two highly prevalent diseases. T2DM is a risk factor for developing more severe forms of multi-drug resistant-TB and TB recurrence after preventive treatment. Since a bidirectional relationship exists between TB and DM, it is necessary to concurrently treat both, and promote recommendations for the joint management of both diseases. There are also some drug-drug interactions resulting in adverse treatment outcomes in TB-DM patients including treatment failure, and reinfection. In addition, autophagy may play a role in these comorbidities. Therefore, the TB-DM comorbidities present several health challenges, requiring a focus on multidisciplinary collaboration and integrated strategies, to effectively deal with this double burden. To effectively manage the comorbidity, further screening in affected countries, more suitable drugs, and better treatment strategies are required.
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Affiliation(s)
| | - Nicholas Peake
- Biosciences and Chemistry and Biomolecular Research Centre, Sheffield Hallam University, Sheffield S1 1WB, United Kingdom
| | - Nabil Eid
- Department of Anatomy, Division of Human Biology, School of Medicine, International Medical University, Kuala Lumpur 57000, Malaysia
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Sinha PR, Balasubramanian R, Hegde SR. Integrated sequence and -omic features reveal novel small proteome of Mycobacterium tuberculosis. Front Microbiol 2024; 15:1335310. [PMID: 38812687 PMCID: PMC11133741 DOI: 10.3389/fmicb.2024.1335310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 04/15/2024] [Indexed: 05/31/2024] Open
Abstract
Bioinformatic studies on small proteins are under-represented due to difficulties in annotation posed by their small size. However, recent discoveries emphasize the functional significance of small proteins in cellular processes including cell signaling, metabolism, and adaptation to stress. In this study, we utilized a Random Forest classifier trained on sequence features, RNA-Seq, and Ribo-Seq data to uncover small proteins (smORFs) in M. tuberculosis. Independent predictions for the exponential and starvation conditions resulted in 695 potential smORFs. We examined the functional implications of these smORFs using homology searches, LC-MS/MS, and ChIP-seq data, testing their expression in diverse growth conditions, and identifying protein domains. We provide evidence that some of these smORFs could be part of operons, or exist as upstream ORFs. This expanded data resource for the proteins of M. tuberculosis would aid in fine-tuning the existing protein and gene regulatory networks, thereby improving system-wide studies. The primary goal of this study was to uncover and characterize smORFs in M. tuberculosis through bioinformatic analysis, shedding light on their functional roles and genomic organization. Further investigation of these potential smORFs would provide valuable insights into the genome organization and functional diversity of the M. tuberculosis proteome.
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Affiliation(s)
| | | | - Shubhada R. Hegde
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, India
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Abstract
The global burden of tuberculosis (TB) is aggravated by the continuously increasing emergence of drug resistance, highlighting the need for innovative therapeutic options. The concept of host-directed therapy (HDT) as adjunctive to classical antibacterial therapy with antibiotics represents a novel and promising approach for treating TB. Here, we have focused on repurposing the clinically used anticancer drug tamoxifen, which was identified as a molecule with strong host-directed activity against intracellular Mycobacterium tuberculosis (Mtb). Using a primary human macrophage Mtb infection model, we demonstrate the potential of tamoxifen against drug-sensitive as well as drug-resistant Mtb bacteria. The therapeutic effect of tamoxifen was confirmed in an in vivo TB model based on Mycobacterium marinum infection of zebrafish larvae. Tamoxifen had no direct antimicrobial effects at the concentrations used, confirming that tamoxifen acted as an HDT drug. Furthermore, we demonstrate that the antimycobacterial effect of tamoxifen is independent of its well-known target the estrogen receptor (ER) pathway, but instead acts by modulating autophagy, in particular the lysosomal pathway. Through RNA sequencing and microscopic colocalization studies, we show that tamoxifen stimulates lysosomal activation and increases the localization of mycobacteria in lysosomes both in vitro and in vivo, while inhibition of lysosomal activity during tamoxifen treatment partly restores mycobacterial survival. Thus, our work highlights the HDT potential of tamoxifen and proposes it as a repurposed molecule for the treatment of TB. IMPORTANCE Tuberculosis (TB) is the world's most lethal infectious disease caused by a bacterial pathogen, Mycobacterium tuberculosis. This pathogen evades the immune defenses of its host and grows intracellularly in immune cells, particularly inside macrophages. There is an urgent need for novel therapeutic strategies because treatment of TB patients is increasingly complicated by rising antibiotic resistance. In this study, we explored a breast cancer drug, tamoxifen, as a potential anti-TB drug. We show that tamoxifen acts as a so-called host-directed therapeutic, which means that it does not act directly on the bacteria but helps the host macrophages combat the infection more effectively. We confirmed the antimycobacterial effect of tamoxifen in a zebrafish model for TB and showed that it functions by promoting the delivery of mycobacteria to digestive organelles, the lysosomes. These results support the high potential of tamoxifen to be repurposed to fight antibiotic-resistant TB infections by host-directed therapy.
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Pagán AJ, Lee LJ, Edwards-Hicks J, Moens CB, Tobin DM, Busch-Nentwich EM, Pearce EL, Ramakrishnan L. mTOR-regulated mitochondrial metabolism limits mycobacterium-induced cytotoxicity. Cell 2022; 185:3720-3738.e13. [PMID: 36103894 PMCID: PMC9596383 DOI: 10.1016/j.cell.2022.08.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 06/17/2022] [Accepted: 08/16/2022] [Indexed: 02/01/2023]
Abstract
Necrosis of macrophages in the granuloma, the hallmark immunological structure of tuberculosis, is a major pathogenic event that increases host susceptibility. Through a zebrafish forward genetic screen, we identified the mTOR kinase, a master regulator of metabolism, as an early host resistance factor in tuberculosis. We found that mTOR complex 1 protects macrophages from mycobacterium-induced death by enabling infection-induced increases in mitochondrial energy metabolism fueled by glycolysis. These metabolic adaptations are required to prevent mitochondrial damage and death caused by the secreted mycobacterial virulence determinant ESAT-6. Thus, the host can effectively counter this early critical mycobacterial virulence mechanism simply by regulating energy metabolism, thereby allowing pathogen-specific immune mechanisms time to develop. Our findings may explain why Mycobacterium tuberculosis, albeit humanity's most lethal pathogen, is successful in only a minority of infected individuals.
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Affiliation(s)
- Antonio J. Pagán
- Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge, Cambridge CB2 0AW, UK,MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK,Department of Microbiology, University of Washington, Seattle, WA 98195, USA,Corresponding author
| | - Lauren J. Lee
- Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge, Cambridge CB2 0AW, UK,MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Joy Edwards-Hicks
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Cecilia B. Moens
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - David M. Tobin
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Elisabeth M. Busch-Nentwich
- Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge, Cambridge CB2 0AW, UK
| | - Erika L. Pearce
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Lalita Ramakrishnan
- Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge, Cambridge CB2 0AW, UK,MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK,Department of Microbiology, University of Washington, Seattle, WA 98195, USA,Corresponding author
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Lenz SM, Ray NA, Lema T, Collins JH, Thapa R, Girma S, Balagon M, Bobosha K, Hagge DA, Williams DL, Scollard DM, Lahiri R, Adams LB. Utility of a Mycobacterium leprae molecular viability assay for clinical leprosy: An analysis of cases from the Philippines, Ethiopia, and Nepal. FRONTIERS IN TROPICAL DISEASES 2022. [DOI: 10.3389/fitd.2022.967351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Mycobacterium leprae is a slow-growing species of mycobacteria that cannot be cultured in axenic media. This presents a number of challenges for monitoring treatment efficacy and advancing new drugs and regimens for treating leprosy. We previously developed a molecular viability assay (MVA) which measures expression of hsp18 and esxA transcripts to determine viability of M. leprae directly from infected tissue. The objective of the current study was to determine the utility of the MVA for practical use on clinical specimens. Leprosy cases from the Philippines (N = 199), Ethiopia (N = 40), and Nepal (N = 200) were diagnosed by clinical examination, slit-skin smears (SSS) from index sites, and/or histopathology. Biopsy specimens for MVA were collected from an active lesion and stored in 70% ethanol. DNA and RNA were extracted from the tissue, and M. leprae were enumerated on the DNA fraction via RLEP qPCR. Based on this count, DNased RNA was normalized to the equivalent of 3x103M. leprae per reverse transcription reaction, and hsp18 and esxA transcripts were amplified by PCR on the resulting cDNA. There was a strong correlation between RLEP enumeration on the specific biopsy specimen for MVA and the average SSS bacterial index (BI) in all three cohorts (p < 0.001). The MVA could be performed on most biopsies with an average SSS BI ≥ 2 and showed a decrease in M. leprae viability with increasing duration of leprosy multidrug therapy (R2 = 0.81, p < 0.001). The MVA also detected viable M. leprae in relapse patients where it showed significant correlation with the mouse footpad assay (p = 0.018). The MVA is a M. leprae-specific, sensitive, and relatively quick test. Clinically, the MVA would likely be most useful to monitor treatment, confirm suspected relapse cases, and determine efficacy of new leprosy drugs in clinical trials.
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Dou Y, Xie Y, Zhang L, Liu S, Xu D, Wei Y, Li Y, Zhang XL. Host MKRN1-Mediated Mycobacterial PPE Protein Ubiquitination Suppresses Innate Immune Response. Front Immunol 2022; 13:880315. [PMID: 35603194 PMCID: PMC9114769 DOI: 10.3389/fimmu.2022.880315] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 04/11/2022] [Indexed: 11/17/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb), as an important intracellular pathogen, can invade and survive in macrophages and is capable of escaping the clearance of immune system. Despite decades of research efforts, the precise mechanism of immune escape and the virulence factors encoded by Mtb involved remain to be explored. Mtb-specific genomic regions of deletion (RD)-encoded proteins and PE/PPE family proteins have been implicated in immune evasion. Here, we screened more than forty RD-encoded proteins which might be involved in facilitating bacterial survival in macrophages, and found that a Mtb PPE68/Rv3873 protein, encoded by Mtb-RD1, is essential for efficient Mtb intracellular survival in macrophages. In terms of mechanism, we found that the ubiquitin ligase (E3) Makorin Ring Finger Protein 1 (MKRN1) of macrophage interacted with PPE68 and promoted the attachment of lysine (K)-63-linked ubiquitin chains to the K166 site of PPE68. K63-ubiquitination of PPE68 further bound src homology 2 domain-containing protein tyrosine phosphatase 1 (SHP1) to suppress K63-linked polyubiquitin chains of tumor necrosis factor receptor-associated factor 6 (TRAF6), and then remarkably suppressed TRAF6-driven NF-κB and AP-1 signaling and TNF-α, IL-6 and NO production. We demonstrate that the K63-linked ubiquitination of PPE68 by MKRN1 contributed to the PPE68-mediated mycobacterial immune escape. Our finding identifies a previously unrecognized mechanism by which host MKRN1-mediated-ubiquitination of mycobacterial PPE protein suppresses innate immune responses. Disturbing the interaction between host MKRN1 ubiquitin system and mycobacterial PPE protein might be a potential therapeutic target for tuberculosis.
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Affiliation(s)
- Yafeng Dou
- Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, Wuhan University TaiKang Medical School (School of Basic Medical Sciences), Wuhan, China
| | - Yan Xie
- Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, Wuhan University TaiKang Medical School (School of Basic Medical Sciences), Wuhan, China
| | - Lingyun Zhang
- Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, Wuhan University TaiKang Medical School (School of Basic Medical Sciences), Wuhan, China
| | - Sheng Liu
- Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, Wuhan University TaiKang Medical School (School of Basic Medical Sciences), Wuhan, China
| | - Dandan Xu
- Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, Wuhan University TaiKang Medical School (School of Basic Medical Sciences), Wuhan, China
| | - Yuying Wei
- Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, Wuhan University TaiKang Medical School (School of Basic Medical Sciences), Wuhan, China
| | - Yongshuai Li
- Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, Wuhan University TaiKang Medical School (School of Basic Medical Sciences), Wuhan, China
| | - Xiao-Lian Zhang
- Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, Wuhan University TaiKang Medical School (School of Basic Medical Sciences), Wuhan, China
- Department of Allergy of Zhongnan Hospital, Wuhan University, School of Medicine, Wuhan, China
- State Key Laboratory of Virology, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
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Osman MM, Shanahan JK, Chu F, Takaki KK, Pinckert ML, Pagán AJ, Brosch R, Conrad WH, Ramakrishnan L. The C terminus of the mycobacterium ESX-1 secretion system substrate ESAT-6 is required for phagosomal membrane damage and virulence. Proc Natl Acad Sci U S A 2022; 119:e2122161119. [PMID: 35271388 PMCID: PMC8931374 DOI: 10.1073/pnas.2122161119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 01/15/2022] [Indexed: 12/21/2022] Open
Abstract
SignificanceTuberculosis (TB), an ancient disease of humanity, continues to be a major cause of worldwide death. The causative agent of TB, Mycobacterium tuberculosis, and its close pathogenic relative Mycobacterium marinum, initially infect, evade, and exploit macrophages, a major host defense against invading pathogens. Within macrophages, mycobacteria reside within host membrane-bound compartments called phagosomes. Mycobacterium-induced damage of the phagosomal membranes is integral to pathogenesis, and this activity has been attributed to the specialized mycobacterial secretion system ESX-1, and particularly to ESAT-6, its major secreted protein. Here, we show that the integrity of the unstructured ESAT-6 C terminus is required for macrophage phagosomal damage, granuloma formation, and virulence.
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Affiliation(s)
- Morwan M. Osman
- Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge, CB2 OQH Cambridge, United Kingdom
- Cell Biology Division, Medical Research Council Laboratory of Molecular Biology, CB2 0QH Cambridge, United Kingdom
| | - Jonathan K. Shanahan
- Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge, CB2 OQH Cambridge, United Kingdom
- Cell Biology Division, Medical Research Council Laboratory of Molecular Biology, CB2 0QH Cambridge, United Kingdom
| | - Frances Chu
- Department of Microbiology, University of Washington, Seattle, WA 98105
| | - Kevin K. Takaki
- Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge, CB2 OQH Cambridge, United Kingdom
- Cell Biology Division, Medical Research Council Laboratory of Molecular Biology, CB2 0QH Cambridge, United Kingdom
| | - Malte L. Pinckert
- Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge, CB2 OQH Cambridge, United Kingdom
- Cell Biology Division, Medical Research Council Laboratory of Molecular Biology, CB2 0QH Cambridge, United Kingdom
| | - Antonio J. Pagán
- Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge, CB2 OQH Cambridge, United Kingdom
- Cell Biology Division, Medical Research Council Laboratory of Molecular Biology, CB2 0QH Cambridge, United Kingdom
| | - Roland Brosch
- Institut Pasteur, Université de Paris, CNRS UMR 3525, Unit for Integrated Mycobacterial Pathogenomics, 75724 Paris Cedex 15, France
| | - William H. Conrad
- Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge, CB2 OQH Cambridge, United Kingdom
- Cell Biology Division, Medical Research Council Laboratory of Molecular Biology, CB2 0QH Cambridge, United Kingdom
| | - Lalita Ramakrishnan
- Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge, CB2 OQH Cambridge, United Kingdom
- Cell Biology Division, Medical Research Council Laboratory of Molecular Biology, CB2 0QH Cambridge, United Kingdom
- Department of Microbiology, University of Washington, Seattle, WA 98105
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