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Nesakumar M, Luke EH, Vetrivel U. Next-Gen Dual Transcriptomics for Adult Extrapulmonary Tuberculosis Biomarkers and Host-Pathogen Interplay in Human Cells: A Strategic Review. Indian J Microbiol 2024; 64:36-47. [PMID: 38468742 PMCID: PMC10924812 DOI: 10.1007/s12088-023-01143-z] [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: 04/27/2023] [Accepted: 11/09/2023] [Indexed: 03/13/2024] Open
Abstract
Tuberculosis (TB) is a major public health concern that results in significant morbidity and mortality, particularly in middle- to low-income countries. Extra-pulmonary tuberculosis (EPTB) in adults is a form of TB that affects organs other than the lungs and is challenging to diagnose and treat due to a lack of accurate early diagnostic markers and inadequate knowledge of host immunity. Next-generation sequencing-based approaches have shown potential for identifying diagnostic biomarkers and host immune responses related to EPTB. This strategic review discusses on the significance using primary human cells and cell lines for in vitro transcriptomic studies on common forms of EPTB, such as lymph node TB, brain TB, bone TB, and endometrial TB to derive potential insights. While organoids have shown promise as a model system, primary cell lines still remain a valuable tool for studying host-pathogen interplay due to their conserved immune system, non-iPSC origin, and lack of heterogeneity in cell population. This review outlines a basic workflow for researchers interested in performing transcriptomics studies in EPTB, and also discusses the potential of cell-line based dual RNA-Seq technology for deciphering comprehensive transcriptomic signatures, host-pathogen interplay, and biomarkers from the host and Mycobacterium tuberculosis. Thus, emphasizing the implementation of this technique which can significantly contribute to the global anti-TB effort and advance our understanding of EPTB. Graphical Abstract
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Affiliation(s)
- Manohar Nesakumar
- Department of Virology and Biotechnology, Bioinformatics Division, Indian Council for Medical Research-National Institute for Research in Tuberculosis (ICMR-NIRT), Chennai, India
| | - Elizabeth Hanna Luke
- Department of Virology and Biotechnology, Bioinformatics Division, Indian Council for Medical Research-National Institute for Research in Tuberculosis (ICMR-NIRT), Chennai, India
| | - Umashankar Vetrivel
- Department of Virology and Biotechnology, Bioinformatics Division, Indian Council for Medical Research-National Institute for Research in Tuberculosis (ICMR-NIRT), Chennai, India
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Kaur K, Sharma S, Abhishek S, Kaur P, Saini UC, Dhillon MS, Karakousis PC, Verma I. Metabolic switching and cell wall remodelling of Mycobacterium tuberculosis during bone tuberculosis. J Infect 2023; 86:134-146. [PMID: 36549425 DOI: 10.1016/j.jinf.2022.12.014] [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: 04/13/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
OBJECTIVES Bone tuberculosis (TB) is the third most common types of extrapulmonary tuberculosis. It is critical to understand mycobacterial adaptive strategies within bone lesions to identify mycobacterial factors that may have role in disease pathogenesis. METHODS Whole genome microarray was used to characterize the in-vivo transcriptome of Mycobacterium tuberculosis (M.tb) within bone TB specimens. Mycobacterial virulent proteins were identified by bioinformatic software. An in vitro osteoblast cell line model was used to study the role of these proteins in bone TB pathogenesis. RESULTS 914 mycobacterial genes were significantly overexpressed and 1688 were repressed in bone TB specimens. Pathway analysis of differentially expressed genes demonstrated a non-replicative and hypometabolic state of M.tb, reinforcement of the mycobacterial cell wall and induction of DNA damage repair responses, suggesting possible survival strategies of M.tb within bone. Bioinformatics mining of microarray data led to identification of five virulence proteins. The genes encoding these proteins were also upregulated in the in vitro MC3T3 osteoblast cell line model of bone TB. Further, exposure of osteoblast cells to two of these virulence proteins (Rv1046c and Rv3663c) significantly inhibited osteoblast differentiation. CONCLUSION M.tb alters its transcriptome to establish infection in bone by upregulating certain virulence genes which play a key role in disturbing bone homeostasis.
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Affiliation(s)
- Khushpreet Kaur
- Department of Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Sumedha Sharma
- Department of Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Sudhanshu Abhishek
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Prabhdeep Kaur
- Department of Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Uttam Chand Saini
- Department of Orthopaedics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Mandeep Singh Dhillon
- Department of Orthopaedics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Petros C Karakousis
- Centers for Tuberculosis Research and Systems Approaches for Infectious Diseases, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Indu Verma
- Department of Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh, India.
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Shantal CJN, Juan CC, Lizbeth BUS, Carlos HGJ, Estela GPB. Candida glabrata is a successful pathogen: an artist manipulating the immune response. Microbiol Res 2022; 260:127038. [DOI: 10.1016/j.micres.2022.127038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 04/02/2022] [Accepted: 04/07/2022] [Indexed: 02/07/2023]
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Bhattacharya D, Danaviah S, Muema DM, Akilimali NA, Moodley P, Ndung'u T, Das G. Cellular Architecture of Spinal Granulomas and the Immunological Response in Tuberculosis Patients Coinfected with HIV. Front Immunol 2017; 8:1120. [PMID: 28955338 PMCID: PMC5601989 DOI: 10.3389/fimmu.2017.01120] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 08/25/2017] [Indexed: 12/30/2022] Open
Abstract
Mycobacterium tuberculosis (M.tb) and HIV are individually responsible for the most deaths worldwide among all infectious agents, and coinfection with M.tb and HIV is a significant public health challenge in the developing world. Although the lung is the primary target organ for tuberculosis (TB), M.tb can also cause extrapulmonary tuberculosis (EPTB) such as in the bones and joints. Treatment of EPTB is much more challenging than treatment of pulmonary TB. The hallmark of the host immune response against TB is the formation of organized structures called granulomas that are infiltrated with immune cells and are rich in cytokines and chemokines. Inside granulomas, the host confines the M.tb bacteria to a particular region of the organ and avoids dispersion. In this study, we analyzed immune cells in bone granulomas of patients with EPTB that are also coinfected with HIV. We found that HIV-infected TB patients have dispersed bone granulomas, with reduced T cell numbers and a concomitant increase in plasma cells. Additionally, HIV-infected patients exhibited dramatically increased serum levels of IgM and IgG1 antibodies, which is indicative of T-cell-independent B-cell activation and mucosal T-cell activation, respectively. Interestingly, we also observed that CD29+ stem cells are increased in HIV-TB coinfection, suggesting a link with HIV infection. Therefore, our work provides new insights into the architecture of spinal TB granulomas and the role of B-cells and humoral immunity against a highly infectious intracellular pathogen. We propose that our findings will inform biomarker identification for EPTB and possibly the development of related therapeutics and/or vaccines to protect HIV-infected patients against disseminated TB.
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Affiliation(s)
- Debapriya Bhattacharya
- Special Centre for Molecular Medicine (SCMM), Jawaharlal Nehru University, New Delhi, India.,Medical Microbiology Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Siva Danaviah
- Africa Health Research Institute, Durban, South Africa
| | | | | | - Prashini Moodley
- Medical Microbiology Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Thumbi Ndung'u
- Africa Health Research Institute, Durban, South Africa.,HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa.,Max Planck Institute for Infection Biology, Berlin, Germany.,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, Harvard University, Cambridge, MA, United States
| | - Gobardhan Das
- Special Centre for Molecular Medicine (SCMM), Jawaharlal Nehru University, New Delhi, India
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Cieślik AI. Evidence of tuberculosis among children in medieval (13th–15th century) Wrocław: A case study of hip joint tuberculosis in a juvenile skeleton excavated from the crypt of the St. Elizabeth church. ANTHROPOLOGICAL REVIEW 2017. [DOI: 10.1515/anre-2017-0014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Abstract
Paleopathological examinations of the skeletal remains of people who died centuries ago are material source of knowledge about health and diseases in the past. In this article, a case of skeletal tuberculosis from historical (13th-15th c.) Wrocław, Poland has been presented. The juvenile skeleton excavated from grave No 93, from the crypt located under the church of St. Elizabeth, displayed pathological lesions within the right hip joint resulting from a chronic inflammation, which might have been assigned to signs typical for skeletal tuberculosis. The results of macroscopic and radiological analyses appeared to be consistent, and allowed to determine a reliable diagnosis of this paleopathological case.
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Affiliation(s)
- Agata Izabela Cieślik
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Department of Anthropology in Wrocław, 75 Podwale St, 50-445 Wrocław , Poland
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Mikheecheva NE, Zaychikova MV, Melerzanov AV, Danilenko VN. A Nonsynonymous SNP Catalog of Mycobacterium tuberculosis Virulence Genes and Its Use for Detecting New Potentially Virulent Sublineages. Genome Biol Evol 2017; 9:887-899. [PMID: 28338924 PMCID: PMC5381574 DOI: 10.1093/gbe/evx053] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2017] [Indexed: 02/06/2023] Open
Abstract
Mycobacterium tuberculosis is divided into several distinct lineages, and various genetic markers such as IS-elements, VNTR, and SNPs are used for lineage identification. We propose an M. tuberculosis classification approach based on functional polymorphisms in virulence genes. An M. tuberculosis virulence genes catalog has been established, including 319 genes from various protein groups, such as proteases, cell wall proteins, fatty acid and lipid metabolism proteins, sigma factors, toxin–antitoxin systems. Another catalog of 1,573 M. tuberculosis isolates of different lineages has been developed. The developed SNP-calling program has identified 3,563 nonsynonymous SNPs. The constructed SNP-based phylogeny reflected the evolutionary relationship between lineages and detected new sublineages. SNP analysis of sublineage F15/LAM4/KZN revealed four lineage-specific mutations in cyp125, mce3B, vapC25, and vapB34. The Ural lineage has been divided into two geographical clusters based on different SNPs in virulence genes. A new sublineage, B0/N-90, was detected inside the Beijing-B0/W-148 by SNPs in irtB, mce3F and vapC46. We have found 27 members of B0/N-90 among the 227 available genomes of the Beijing-B0/W-148 sublineage. Whole-genome sequencing of strain B9741, isolated from an HIV-positive patient, was demonstrated to belong to the new B0/N-90 group. A primer set for PCR detection of B0/N-90 lineage-specific mutations has been developed. The prospective use of mce3 mutant genes as genetically engineered vaccine is discussed.
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Affiliation(s)
- Natalya E Mikheecheva
- Vavilov Institute of General Genetics, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | | | | | - Valery N Danilenko
- Vavilov Institute of General Genetics, Moscow, Russia.,Scientific Research Center of Biotechnology of Antibiotics BIOAN, Moscow, Russia
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