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Qin G, Liao X, Zhang B, Su Y, Yang H, Xie Y, Zhang R, Kong X, Liao S, Chen C, Mo Y, Dai J, Tang H, Duan Y, Jiang W. An individualized immune prognostic signature in nasopharyngeal carcinoma. Oral Oncol 2024; 157:106985. [PMID: 39126750 DOI: 10.1016/j.oraloncology.2024.106985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 07/28/2024] [Accepted: 08/06/2024] [Indexed: 08/12/2024]
Abstract
BACKGROUND Immune-related characteristics can serve as reliable prognostic biomarkers in various cancers. Herein, we aimed to construct an individualized immune prognostic signature in nasopharyngeal carcinoma (NPC). METHODS This study retrospectively included 455 NPC samples and 39 normal healthy nasopharyngeal tissue specimens. Samples from Gene Expression Omnibus (GEO) were obtained as discovery cohort to screen candidate prognostic immune-related gene pairs based on relative expression ordering of the genes. Quantitative real-time reverse transcription-PCR was used to detect the selected genes to construct an immune-related gene pair signature in training cohort, which comprised 118 clinical samples, and was then validated in validation cohort 1, comprising 92 clinical samples, and validation cohort 2, comprising 88 samples from GEO. RESULTS We identified 26 immune-related gene pairs as prognostic candidates in discovery cohort. A prognostic immune signature comprising 11 immune gene pairs was constructed in training cohort. In validation cohort 1, the immune signature could significantly distinguish patients with high or low risk in terms of progression-free survival (PFS) (hazard ratio [HR] 2.66, 95 % confidence interval (CI) 1.17-6.02, P=0.015) and could serve as an independent prognostic factor for PFS in multivariate analysis (HR 2.66, 95 % CI 1.17-6.02, P=0.019). Similar results were obtained using validation cohort 2, in which PFS was significantly worse in high risk group than in low risk group (HR 3.02, 95 % CI 1.12-8.18, P=0.022). CONCLUSIONS The constructed immune signature showed promise for estimating prognosis in NPC. It has potential for translation into clinical practice after prospective validation.
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Affiliation(s)
- Guanjie Qin
- Department of Radiation Oncology, Affiliated Hospital of Guilin Medical University, 15 Lequn Road, Guilin 541001, China; Key Laboratory of Oncology (Guilin Medical University), Education Department of Guangxi Zhuang Autonomous Region, Guilin 541001, China
| | - Xiaofei Liao
- Department of Radiation Oncology, Affiliated Hospital of Guilin Medical University, 15 Lequn Road, Guilin 541001, China; Key Laboratory of Oncology (Guilin Medical University), Education Department of Guangxi Zhuang Autonomous Region, Guilin 541001, China
| | - Bin Zhang
- Department of Radiation Oncology, Wuzhou Red Cross Hospital, Wuzhou 543002, China
| | - Yixin Su
- Department of Radiation Oncology, Lingshan People's Hospital, Zhongxiu Road, Lingshan 535400, China
| | - Huiyun Yang
- Department of Radiation Oncology, Affiliated Hospital of Guilin Medical University, 15 Lequn Road, Guilin 541001, China; Key Laboratory of Oncology (Guilin Medical University), Education Department of Guangxi Zhuang Autonomous Region, Guilin 541001, China
| | - Yuan Xie
- Department of Radiation Oncology, Wuzhou Red Cross Hospital, Wuzhou 543002, China
| | - Rongjun Zhang
- Department of Radiation Oncology, Affiliated Hospital of Guilin Medical University, 15 Lequn Road, Guilin 541001, China; Key Laboratory of Oncology (Guilin Medical University), Education Department of Guangxi Zhuang Autonomous Region, Guilin 541001, China
| | - Xiangyun Kong
- Department of Radiation Oncology, Affiliated Hospital of Guilin Medical University, 15 Lequn Road, Guilin 541001, China; Key Laboratory of Oncology (Guilin Medical University), Education Department of Guangxi Zhuang Autonomous Region, Guilin 541001, China
| | - Shufang Liao
- Department of Radiation Oncology, Affiliated Hospital of Guilin Medical University, 15 Lequn Road, Guilin 541001, China; Key Laboratory of Oncology (Guilin Medical University), Education Department of Guangxi Zhuang Autonomous Region, Guilin 541001, China
| | - Cancan Chen
- Department of Radiation Oncology, Affiliated Hospital of Guilin Medical University, 15 Lequn Road, Guilin 541001, China; Key Laboratory of Oncology (Guilin Medical University), Education Department of Guangxi Zhuang Autonomous Region, Guilin 541001, China
| | - Yunyan Mo
- Department of Radiation Oncology, Affiliated Hospital of Guilin Medical University, 15 Lequn Road, Guilin 541001, China; Key Laboratory of Oncology (Guilin Medical University), Education Department of Guangxi Zhuang Autonomous Region, Guilin 541001, China
| | - Jinxuan Dai
- Department of Oncology, Second Affiliated Hospital of Guilin Medical University, 212 Renmin Road, Guilin 541199, China
| | - Huaying Tang
- Department of Radiation Oncology, Affiliated Hospital of Guilin Medical University, 15 Lequn Road, Guilin 541001, China; Key Laboratory of Oncology (Guilin Medical University), Education Department of Guangxi Zhuang Autonomous Region, Guilin 541001, China
| | - Yuting Duan
- Department of Radiation Oncology, Affiliated Hospital of Guilin Medical University, 15 Lequn Road, Guilin 541001, China; Key Laboratory of Oncology (Guilin Medical University), Education Department of Guangxi Zhuang Autonomous Region, Guilin 541001, China
| | - Wei Jiang
- Department of Radiation Oncology, Affiliated Hospital of Guilin Medical University, 15 Lequn Road, Guilin 541001, China; Key Laboratory of Oncology (Guilin Medical University), Education Department of Guangxi Zhuang Autonomous Region, Guilin 541001, China.
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Vasiliu A, Martinez L, Gupta RK, Hamada Y, Ness T, Kay A, Bonnet M, Sester M, Kaufmann SHE, Lange C, Mandalakas AM. Tuberculosis prevention: current strategies and future directions. Clin Microbiol Infect 2024; 30:1123-1130. [PMID: 37918510 DOI: 10.1016/j.cmi.2023.10.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 10/20/2023] [Accepted: 10/22/2023] [Indexed: 11/04/2023]
Abstract
BACKGROUND An estimated one fourth of the world's population is infected with Mycobacterium tuberculosis, and 5-10% of those infected develop tuberculosis in their lifetime. Preventing tuberculosis is one of the most underutilized but essential components of curtailing the tuberculosis epidemic. Moreover, current evidence illustrates that tuberculosis manifestations occur along a dynamic spectrum from infection to disease rather than a binary state as historically conceptualized. Elucidating determinants of transition between these states is crucial to decreasing the tuberculosis burden and reaching the END-TB Strategy goals as defined by the WHO. Vaccination, detection of infection, and provision of preventive treatment are key elements of tuberculosis prevention. OBJECTIVES This review provides a comprehensive summary of recent evidence and state-of-the-art updates on advancements to prevent tuberculosis in various settings and high-risk populations. SOURCES We identified relevant studies in the literature and synthesized the findings to provide an overview of the current state of tuberculosis prevention strategies and latest research developments. CONTENT We present the current knowledge and recommendations regarding tuberculosis prevention, with a focus on M. bovis Bacille-Calmette-Guérin vaccination and novel vaccine candidates, tests for latent infection with M. tuberculosis, regimens available for tuberculosis preventive treatment and recommendations in low- and high-burden settings. IMPLICATIONS Effective tuberculosis prevention worldwide requires a multipronged approach that addresses social determinants, and improves access to tuberculosis detection and to new short tuberculosis preventive treatment regimens. Robust collaboration and innovative research are needed to reduce the global burden of tuberculosis and develop new detection tools, vaccines, and preventive treatments that serve all populations and ages.
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Affiliation(s)
- Anca Vasiliu
- Department of Pediatrics, Baylor College of Medicine, Global TB Program, Houston, TX, USA.
| | - Leonardo Martinez
- Department of Epidemiology, School of Public Health, Boston University, Boston, MA, USA
| | - Rishi K Gupta
- Institute of Health Informatics, University College London, London, United Kingdom
| | - Yohhei Hamada
- Institute for Global Health, University College London, London, United Kingdom
| | - Tara Ness
- Department of Pediatrics, Baylor College of Medicine, Global TB Program, Houston, TX, USA
| | - Alexander Kay
- Department of Pediatrics, Baylor College of Medicine, Global TB Program, Houston, TX, USA
| | - Maryline Bonnet
- University of Montpellier, TransVIHMI, IRD, INSERM, Montpellier, France
| | - Martina Sester
- Department of Transplant and Infection Immunology, Saarland University, Homburg, Germany
| | - Stefan H E Kaufmann
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany; Systems Immunology (Emeritus Group), Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany; Hagler Institute for Advanced Study, Texas A&M University, College Station, TX, USA
| | - Christoph Lange
- Department of Pediatrics, Baylor College of Medicine, Global TB Program, Houston, TX, USA; Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany; Respiratory Medicine and International Health, University of Lübeck, Lübeck, Germany
| | - Anna M Mandalakas
- Department of Pediatrics, Baylor College of Medicine, Global TB Program, Houston, TX, USA; Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
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Wang P, Yang GL, He YF, Shen YH, Hao XH, Liu HP, Shen HB, Wang L, Sha W. Single-cell transcriptomics of blood identified IFIT1 + neutrophil subcluster expansion in NTM-PD patients. Int Immunopharmacol 2024; 137:112412. [PMID: 38901242 DOI: 10.1016/j.intimp.2024.112412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 05/18/2024] [Accepted: 06/02/2024] [Indexed: 06/22/2024]
Abstract
OBJECTIVE Non-tuberculous mycobacterial pulmonary disease (NTM-PD) is caused by an imbalance between pathogens and impaired host immune responses. Mycobacterium avium complex (MAC) and Mycobacterium abscessus (MAB) are the two major pathogens that cause NTM-PD. In this study, we sought to dissect the transcriptomes of peripheral blood immune cells at the single-cell resolution in NTM-PD patients and explore potential clinical markers for NTM-PD diagnosis and treatment. METHODS Peripheral blood samples were collected from six NTM-PD patients, including three MAB-PD patients, three MAC-PD patients, and two healthy controls. We employed single-cell RNA sequencing (scRNA-seq) to define the transcriptomic landscape at a single-cell resolution. A comprehensive scRNA-seq analysis was performed, and flow cytometry was conducted to validate the results of scRNA-seq. RESULTS A total of 27,898 cells were analyzed. Nine T-cells, six mononuclear phagocytes (MPs), and four neutrophil subclusters were defined. During NTM infection, naïve T-cells were reduced, and effector T-cells increased. High cytotoxic activities were shown in T-cells of NTM-PD patients. The proportion of inflammatory and activated MPs subclusters was enriched in NTM-PD patients. Among neutrophil subclusters, an IFIT1+ neutrophil subcluster was expanded in NTM-PD compared to healthy controls. This suggests that IFIT1+ neutrophil subcluster might play an important role in host defense against NTM. Functional enrichment analysis of this subcluster suggested that it is related to interferon response. Cell-cell interaction analysis revealed enhanced CXCL8-CXCR1/2 interactions between the IFIT1+ neutrophil subcluster and NK cells, NKT cells, classical mononuclear phagocytes subcluster 1 (classical Mo1), classical mononuclear phagocytes subcluster 2 (classical Mo2) in NTM-PD patients compared to healthy controls. CONCLUSIONS Our data revealed disease-specific immune cell subclusters and provided potential new targets of NTM-PD. Specific expansion of IFIT1+ neutrophil subclusters and the CXCL8-CXCR1/2 axis may be involved in the pathogenesis of NTM-PD. These insights may have implications for the diagnosis and treatment of NTM-PD.
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Affiliation(s)
- Peng Wang
- Department of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China; Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Guo-Ling Yang
- Department of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China; Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Yi-Fan He
- Department of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China; Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Yan-Heng Shen
- Department of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China; Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Xiao-Hui Hao
- Department of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China; Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Hai-Peng Liu
- Clinical Translation Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
| | - Hong-Bo Shen
- Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Li Wang
- Department of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China; Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China.
| | - Wei Sha
- Department of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China; Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China; Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China.
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Balasingam S, Dheda K, Fortune S, Gordon SB, Hoft D, Kublin JG, Loynachan CN, McShane H, Morton B, Nambiar S, Sharma NR, Robertson B, Schrager LK, Weller CL. Review of Current Tuberculosis Human Infection Studies for Use in Accelerating Tuberculosis Vaccine Development: A Meeting Report. J Infect Dis 2024; 230:e457-e464. [PMID: 38709726 PMCID: PMC11326834 DOI: 10.1093/infdis/jiae238] [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: 10/26/2023] [Revised: 04/29/2024] [Accepted: 05/03/2024] [Indexed: 05/08/2024] Open
Abstract
Tools to evaluate and accelerate tuberculosis (TB) vaccine development are needed to advance global TB control strategies. Validated human infection studies for TB have the potential to facilitate breakthroughs in understanding disease pathogenesis, identify correlates of protection, develop diagnostic tools, and accelerate and de-risk vaccine and drug development. However, key challenges remain for realizing the clinical utility of these models, which require further discussion and alignment among key stakeholders. In March 2023, the Wellcome Trust and the International AIDS Vaccine Initiative convened international experts involved in developing both TB and bacillus Calmette-Guérin (BCG) human infection studies (including mucosal and intradermal challenge routes) to discuss the status of each of the models and the key enablers to move the field forward. This report provides a summary of the presentations and discussion from the meeting. Discussions identified key issues, including demonstrating model validity, to provide confidence for vaccine developers, which may be addressed through demonstration of known vaccine effects (eg, BCG vaccination in specific populations), and by comparing results from field efficacy and human infection studies. The workshop underscored the importance of establishing safe and acceptable studies in high-burden settings, and the need to validate >1 model to allow for different scientific questions to be addressed as well as to provide confidence to vaccine developers and regulators around use of human infection study data in vaccine development and licensure pathways.
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Affiliation(s)
| | - Keertan Dheda
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and University of Cape Town (UCT) Lung Institute and South African Medical Research Council/UCT Centre for the Study of Antimicrobial Resistance, University of Cape Town, South Africa
| | - Sarah Fortune
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Stephen B Gordon
- Clinical Experimental Medicine, Malawi Liverpool Wellcome Programme, Blantyre
| | - Daniel Hoft
- Departments of Internal Medicine and Molecular Microbiology & Immunology, Saint Louis University of Medicine, Missouri
| | - James G Kublin
- Cancer Center, Vaccine and Infectious Disease Division, Fred Hutchinson Institute, Seattle, Washington
| | | | - Helen McShane
- The Jenner Institute, University of Oxford, United Kingdom
| | - Ben Morton
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, United Kingdom
| | - Sujatha Nambiar
- TB Impact Area, International AIDS Vaccine Initiative, New York, New York
| | | | - Brian Robertson
- Department of Infectious Disease, Imperial College London, United Kingdom
| | - Lewis K Schrager
- TB Impact Area, International AIDS Vaccine Initiative, New York, New York
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5
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Sun M, Phan JM, Kieswetter NS, Huang H, Yu KKQ, Smith MT, Liu YE, Wang C, Gupta S, Obermoser G, Maecker HT, Krishnan A, Suresh S, Gupta N, Rieck M, Acs P, Ghanizada M, Chiou SH, Khatri P, Boom WH, Hawn TR, Stein CM, Mayanja-Kizza H, Davis MM, Seshadri C. Specific CD4 + T cell phenotypes associate with bacterial control in people who 'resist' infection with Mycobacterium tuberculosis. Nat Immunol 2024; 25:1411-1421. [PMID: 38997431 PMCID: PMC11291275 DOI: 10.1038/s41590-024-01897-8] [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: 08/09/2023] [Accepted: 06/13/2024] [Indexed: 07/14/2024]
Abstract
A subset of individuals exposed to Mycobacterium tuberculosis (Mtb) that we refer to as 'resisters' (RSTR) show evidence of IFN-γ- T cell responses to Mtb-specific antigens despite serially negative results on clinical testing. Here we found that Mtb-specific T cells in RSTR were clonally expanded, confirming the priming of adaptive immune responses following Mtb exposure. RSTR CD4+ T cells showed enrichment of TH17 and regulatory T cell-like functional programs compared to Mtb-specific T cells from individuals with latent Mtb infection. Using public datasets, we showed that these TH17 cell-like functional programs were associated with lack of progression to active tuberculosis among South African adolescents with latent Mtb infection and with bacterial control in nonhuman primates. Our findings suggested that RSTR may successfully control Mtb following exposure and immune priming and established a set of T cell biomarkers to facilitate further study of this clinical phenotype.
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Affiliation(s)
- Meng Sun
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA
| | - Jolie M Phan
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Nathan S Kieswetter
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Huang Huang
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA
| | - Krystle K Q Yu
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Malisa T Smith
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Yiran E Liu
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA
- Department of Epidemiology and Population Health, School of Medicine, Stanford University, Stanford, CA, USA
| | - Chuangqi Wang
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medicine Campus, Aurora, CO, USA
| | - Sanjana Gupta
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA
- Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Gerlinde Obermoser
- Human Immune Monitoring Center, Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA
| | - Holden Terry Maecker
- Human Immune Monitoring Center, Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA
| | - Akshaya Krishnan
- Human Immune Monitoring Center, Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA
| | - Sundari Suresh
- Human Immune Monitoring Center, Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA
| | - Neha Gupta
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA
- Human Immune Monitoring Center, Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA
| | - Mary Rieck
- Human Immune Monitoring Center, Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA
| | - Peter Acs
- Human Immune Monitoring Center, Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA
| | - Mustafa Ghanizada
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Shin-Heng Chiou
- Division of Medical Oncology, Rutgers Cancer Institute of New Jersey, Department of Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, USA
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA
- Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Sciences, School of Medicine, Stanford University, Stanford, CA, USA
| | - W Henry Boom
- Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Thomas R Hawn
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Catherine M Stein
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | | | - Mark M Davis
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA.
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
| | - Chetan Seshadri
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA.
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Andrews JR. Recasting resistance to Mycobacterium tuberculosis. Nat Immunol 2024; 25:1316-1318. [PMID: 39048789 DOI: 10.1038/s41590-024-01907-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Affiliation(s)
- Jason R Andrews
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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Rotundo S, Tassone MT, Serapide F, Russo A, Trecarichi EM. Incipient tuberculosis: a comprehensive overview. Infection 2024; 52:1215-1222. [PMID: 38589748 PMCID: PMC11289152 DOI: 10.1007/s15010-024-02239-4] [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: 02/27/2024] [Accepted: 03/13/2024] [Indexed: 04/10/2024]
Abstract
In the context of the evolving global health landscape shaped by the COVID-19 pandemic, tuberculosis (TB) is gaining renewed attention as a reemerging threat even in low-endemic countries. Immunological tests such as the tuberculin skin test (TST) and interferon-gamma release assay (IGRA) are pivotal in identifying tuberculosis infection (TBI). However, their inability to distinguish between past and ongoing infection poses a diagnostic challenge, possibly leading to the unnecessary treatment of a significant portion of the population with potential side effects. This review delves into the concept of incipient tuberculosis (ITB), a dynamic, presymptomatic stage characterized by heightened Mycobacterium tuberculosis complex (MTC) metabolic activity and replication that result in minimal radiological changes, signifying a transitional state between TBI and TB. Key focus areas include epidemiological factors, underlying pathogenesis, imaging findings, and the ongoing challenges in the identification of individuals with ITB through the development of new biomarkers and the use of whole-genome sequencing-based analyses to implement early treatment strategies.
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Affiliation(s)
- Salvatore Rotundo
- Department of Medical and Surgical Sciences, "Magna Graecia" University, Catanzaro, Italy.
| | - Maria Teresa Tassone
- Department of Medical and Surgical Sciences, "Magna Graecia" University, Catanzaro, Italy
| | - Francesca Serapide
- Department of Medical and Surgical Sciences, "Magna Graecia" University, Catanzaro, Italy
- Infectious and Tropical Disease Unit, "Renato Dulbecco" Teaching Hospital, Catanzaro, Italy
| | - Alessandro Russo
- Department of Medical and Surgical Sciences, "Magna Graecia" University, Catanzaro, Italy
- Infectious and Tropical Disease Unit, "Renato Dulbecco" Teaching Hospital, Catanzaro, Italy
| | - Enrico Maria Trecarichi
- Department of Medical and Surgical Sciences, "Magna Graecia" University, Catanzaro, Italy
- Infectious and Tropical Disease Unit, "Renato Dulbecco" Teaching Hospital, Catanzaro, Italy
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8
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Choudhary Balla S, Ali MH, Tyagi M, Basu S. Systemic and ocular outcomes in TB-immunoreactive patients receiving immunomodulatory therapy for non-infectious uveitis: a case-control study. Br J Ophthalmol 2024:bjo-2024-325625. [PMID: 39009421 DOI: 10.1136/bjo-2024-325625] [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: 04/01/2024] [Accepted: 06/30/2024] [Indexed: 07/17/2024]
Abstract
BACKGROUND Tuberculosis (TB)-immunoreactivity, measured in vivo (tuberculin skin test (TST)) or in vitro (interferon gamma release assay (IGRA)), can be found in latent, active or even following clearance of TB infection. In this case-control study, we compared the systemic and ocular outcomes between patients with or without TB-immunoreactivity, who received immunomodulatory therapy (IMT) for non-infectious uveitis. METHODS We retrospectively reviewed charts of patients with (cases) or without (controls) TB-immunoreactivity (TST±IGRA), who received conventional IMT for ≥6 months, for the treatment of non-infectious uveitis. Patients who received prior or concomitant anti-TB therapy were excluded. Systemic and ocular outcomes were compared between both groups. RESULTS 36 cases and 70 controls (gender-matched and age-matched) were included. New-onset pulmonary or extrapulmonary TB developed in one case and none of the controls. Based on this outcome, the absolute risk increase for systemic TB reactivation was noted to be 0.028 (95% CI 0.005 to 0.051) and the number needed to harm was 36. The incidence of persistent or recurrent (worsening ≥2 grades) intraocular inflammation during IMT was comparable between both groups (cases 18/36, controls 35/70, p=1.0). A change in anatomical site of presentation at recurrence was not seen in any case, but in six controls (p=0.15). No new focal chorio-retinal lesions were noted in either group. CONCLUSIONS Conventional IMT has a very low risk of systemic TB reactivation, and no additional detrimental effect on ocular outcomes, in TB-immunoreactive patients with non-infectious uveitis.
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Affiliation(s)
| | | | - Mudit Tyagi
- Saroja A Rao Center for Uveitis, LV Prasad Eye Institute, Hyderabad, Telangana, India
- Anant Bajaj Retina Institute, LV Prasad Eye Institute, Hyderabad, India
| | - Soumyava Basu
- Saroja A Rao Center for Uveitis, LV Prasad Eye Institute, Hyderabad, Telangana, India
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Krishnan P, Bobak CA, Hill JE. Sex-specific blood-derived RNA biomarkers for childhood tuberculosis. Sci Rep 2024; 14:16859. [PMID: 39039071 PMCID: PMC11263679 DOI: 10.1038/s41598-024-66946-6] [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: 04/07/2024] [Accepted: 07/05/2024] [Indexed: 07/24/2024] Open
Abstract
Confirmatory diagnosis of childhood tuberculosis (TB) remains a challenge mainly due to its dependence on sputum samples and the paucibacillary nature of the disease. Thus, only ~ 30% of suspected cases in children are diagnosed and the need for minimally invasive, non-sputum-based biomarkers remains unmet. Understanding host molecular changes by measuring blood-based transcriptomic markers has shown promise as a diagnostic tool for TB. However, the implication of sex contributing to disease heterogeneity and therefore diagnosis remains to be understood. Using publicly available gene expression data (GSE39939, GSE39940; n = 370), we report a sex-specific RNA biomarker signature that could improve the diagnosis of TB disease in children. We found four gene biomarker signatures for male (SLAMF8, GBP2, WARS, and FCGR1C) and female pediatric patients (GBP6, CELSR3, ALDH1A1, and GBP4) from Kenya, South Africa, and Malawi. Both signatures achieved a sensitivity of 85% and a specificity of 70%, which approaches the WHO-recommended target product profile for a triage test. Our gene signatures outperform most other gene signatures reported previously for childhood TB diagnosis.
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Affiliation(s)
- Preethi Krishnan
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, V6T 1Z3, Canada
| | - Carly A Bobak
- Department of Biomedical Data Science, Dartmouth College, Hanover, NH, 03755, USA
| | - Jane E Hill
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, V6T 1Z3, Canada.
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10
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Campo M, Dill-McFarland KA, Peterson GJ, Benson B, Skerrett SJ, Hawn TR. Human Alveolar and Monocyte-Derived Human Macrophage Responses to Mycobacterium tuberculosis. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 213:161-169. [PMID: 38836816 DOI: 10.4049/jimmunol.2300885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 04/29/2024] [Indexed: 06/06/2024]
Abstract
Alveolar macrophages (AMs) and recruited monocyte-derived macrophages (MDMs) mediate early lung immune responses to Mycobacterium tuberculosis. Differences in the response of these distinct cell types are poorly understood and may provide insight into mechanisms of tuberculosis pathogenesis. The objective of this study was to determine whether M. tuberculosis induces unique and essential antimicrobial pathways in human AMs compared with MDMs. Using paired human AMs and 5-d MCSF-derived MDMs from six healthy volunteers, we infected cells with M. tuberculosis H37Rv for 6 h, isolated RNA, and analyzed transcriptomic profiles with RNA sequencing. We found 681 genes that were M. tuberculosis dependent in AMs compared with MDMs and 4538 that were M. tuberculosis dependent in MDMs, but not AMs (false discovery rate [FDR] < 0.05). Using hypergeometric enrichment of DEGs in Broad Hallmark gene sets, we found that type I and II IFN Response were the only gene sets selectively induced in M. tuberculosis-infected AM (FDR < 0.05). In contrast, MYC targets, unfolded protein response and MTORC1 signaling, were selectively enriched in MDMs (FDR < 0.05). IFNA1, IFNA8, IFNE, and IFNL1 were specifically and highly upregulated in AMs compared with MDMs at baseline and/or after M. tuberculosis infection. IFNA8 modulated M. tuberculosis-induced proinflammatory cytokines and, compared with other IFNs, stimulated unique transcriptomes. Several DNA sensors and IFN regulatory factors had higher expression at baseline and/or after M. tuberculosis infection in AMs compared with MDMs. These findings demonstrate that M. tuberculosis infection induced unique transcriptional responses in human AMs compared with MDMs, including upregulation of the IFN response pathway and specific DNA sensors.
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Affiliation(s)
- Monica Campo
- Department of Medicine, University of Minnesota, Minneapolis, MN
| | | | | | - Basilin Benson
- Systems Immunology Program, Benaroya Research Institute, Seattle, WA
| | | | - Thomas R Hawn
- Department of Medicine, University of Washington, Seattle, WA
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11
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Anes E, Azevedo-Pereira JM, Pires D. Role of Type I Interferons during Mycobacterium tuberculosis and HIV Infections. Biomolecules 2024; 14:848. [PMID: 39062562 PMCID: PMC11275242 DOI: 10.3390/biom14070848] [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: 06/18/2024] [Revised: 07/10/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
Tuberculosis and AIDS remain two of the most relevant human infectious diseases. The pathogens that cause them, Mycobacterium tuberculosis (Mtb) and HIV, individually elicit an immune response that treads the line between beneficial and detrimental to the host. Co-infection further complexifies this response since the different cytokines acting on one infection might facilitate the dissemination of the other. In these responses, the role of type I interferons is often associated with antiviral mechanisms, while for bacteria such as Mtb, their importance and clinical relevance as a suitable target for manipulation are more controversial. In this article, we review the recent knowledge on how these interferons play distinct roles and sometimes have opposite consequences depending on the stage of the pathogenesis. We highlight the dichotomy between the acute and chronic infections displayed by both infections and how type I interferons contribute to an initial control of each infection individually, while their chronic induction, particularly during HIV infection, might facilitate Mtb primo-infection and progression to disease. We expect that further findings and their systematization will allow the definition of windows of opportunity for interferon manipulation according to the stage of infection, contributing to pathogen clearance and control of immunopathology.
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Affiliation(s)
- Elsa Anes
- Host-Pathogen Interactions Unit, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal; (J.M.A.-P.); (D.P.)
| | - José Miguel Azevedo-Pereira
- Host-Pathogen Interactions Unit, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal; (J.M.A.-P.); (D.P.)
| | - David Pires
- Host-Pathogen Interactions Unit, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal; (J.M.A.-P.); (D.P.)
- Center for Interdisciplinary Research in Health, Católica Medical School, Universidade Católica Portuguesa, Estrada Octávio Pato, 2635-631 Rio de Mouro, Portugal
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12
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Nwaneshiudu C, Girdhar K, Kleopoulos SP, Fullard JF, Butelman ER, Parvaz MA, Goldstein RZ, Alia-Klein N, Roussos P. Dynamic alterations in gene co-expression networks and gene-transcript associations characterize co-morbidities in cocaine use disorder. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.10.602908. [PMID: 39026764 PMCID: PMC11257536 DOI: 10.1101/2024.07.10.602908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Background- Individuals with cocaine use disorder (CUD) who attempt abstinence experience craving and relapse, which poses challenges in treatment. Longitudinal studies linking behavioral manifestations in CUD to the blood transcriptome in living individuals are limited. Therefore, we investigated the connection between drug use behaviors during abstinence with blood transcriptomics. Methods- We conducted a comprehensive longitudinal study involving 12 subjects (9 males, 3 females) with CUD and RNA sequencing on blood collected at a drug-free baseline, and 3, 6 & 9 months thereafter. We categorized subjects into 2 responder groups (high-low) based on scores of drug use variables, and 3 responder groups (low-intermediate-high) on days of abstinence. We investigated differential expression and gene-transcript associations across responder groups at each time point. Lastly, we examined genes that are both co-expressed and showed dynamic expression with time. Results- Genes with significant transcript associations between high and. intermediate days of abstinence at 9 months were notably enriched for cannabis use disorder, drinks weekly, and coronary artery disease risk genes. Time-specific gene co-expression analysis prioritized transcripts related to immune processes, cell cycle, RNA-protein synthesis, and second messenger signaling for days of abstinence. Conclusion- We demonstrate that abstinence reflects robust changes in drug use behaviors and the blood transcriptome in CUD. We also highlight the importance of longitudinal studies to capture complex biological processes during abstinence in CUD.
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Affiliation(s)
- Chinwe Nwaneshiudu
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Anesthesiology, Perioperative and Pain Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kiran Girdhar
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Steven P. Kleopoulos
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - John F. Fullard
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eduardo R. Butelman
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Muhammad A. Parvaz
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rita Z. Goldstein
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nelly Alia-Klein
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Panos Roussos
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Center for Precision Medicine and Translational Therapeutics, James J. Peters VA Medical Center, Bronx, New York, 10468, USA
- Mental Illness Research Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, New York, 10468, USA
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13
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Kreitmann L, D'Souza G, Miglietta L, Vito O, Jackson HR, Habgood-Coote D, Levin M, Holmes A, Kaforou M, Rodriguez-Manzano J. A computational framework to improve cross-platform implementation of transcriptomics signatures. EBioMedicine 2024; 105:105204. [PMID: 38901146 PMCID: PMC11245942 DOI: 10.1016/j.ebiom.2024.105204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 05/29/2024] [Accepted: 06/02/2024] [Indexed: 06/22/2024] Open
Abstract
The emergence of next-generation sequencing technologies and computational advances have expanded our understanding of gene expression regulation (i.e., the transcriptome). This has also led to an increased interest in using transcriptomic biomarkers to improve disease diagnosis and stratification, to assess prognosis and predict the response to treatment. Significant progress in identifying transcriptomic signatures for various clinical needs has been made, with large discovery studies accounting for challenges such as patient variability, unwanted batch effects, and data complexities; however, obstacles related to the technical aspects of cross-platform implementation still hinder the successful integration of transcriptomic technologies into standard diagnostic workflows. In this article, we discuss the challenges associated with integrating transcriptomic signatures derived using high-throughput technologies (such as RNA-sequencing) into clinical diagnostic tools using nucleic acid amplification (NAA) techniques. The novelty of the proposed approach lies in our aim to embed constraints related to cross-platform implementation in the process of signature discovery. These constraints could include technical limitations of amplification platform and chemistry, the maximal number of targets imposed by the chosen multiplexing strategy, and the genomic context of identified RNA biomarkers. Finally, we propose to build a computational framework that would integrate these constraints in combination with existing statistical and machine learning models used for signature identification. We envision that this could accelerate the integration of RNA signatures discovered by high-throughput technologies into NAA-based approaches suitable for clinical applications.
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Affiliation(s)
- Louis Kreitmann
- Section of Adult Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0NN, United Kingdom; Centre for Antimicrobial Optimisation, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0NN, United Kingdom
| | - Giselle D'Souza
- Section of Adult Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0NN, United Kingdom; Centre for Antimicrobial Optimisation, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0NN, United Kingdom; Section of Paediatric Infectious Disease, Faculty of Medicine, Imperial College London, London, W2 1NY, United Kingdom; Centre for Paediatrics and Child Health, Imperial College London, London, W2 1NY, United Kingdom
| | - Luca Miglietta
- Section of Adult Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0NN, United Kingdom; Centre for Antimicrobial Optimisation, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0NN, United Kingdom
| | - Ortensia Vito
- Section of Paediatric Infectious Disease, Faculty of Medicine, Imperial College London, London, W2 1NY, United Kingdom; Centre for Paediatrics and Child Health, Imperial College London, London, W2 1NY, United Kingdom
| | - Heather R Jackson
- Section of Paediatric Infectious Disease, Faculty of Medicine, Imperial College London, London, W2 1NY, United Kingdom; Centre for Paediatrics and Child Health, Imperial College London, London, W2 1NY, United Kingdom
| | - Dominic Habgood-Coote
- Section of Paediatric Infectious Disease, Faculty of Medicine, Imperial College London, London, W2 1NY, United Kingdom; Centre for Paediatrics and Child Health, Imperial College London, London, W2 1NY, United Kingdom
| | - Michael Levin
- Section of Paediatric Infectious Disease, Faculty of Medicine, Imperial College London, London, W2 1NY, United Kingdom; Centre for Paediatrics and Child Health, Imperial College London, London, W2 1NY, United Kingdom
| | - Alison Holmes
- Section of Adult Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0NN, United Kingdom; Centre for Antimicrobial Optimisation, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0NN, United Kingdom
| | - Myrsini Kaforou
- Section of Paediatric Infectious Disease, Faculty of Medicine, Imperial College London, London, W2 1NY, United Kingdom; Centre for Paediatrics and Child Health, Imperial College London, London, W2 1NY, United Kingdom
| | - Jesus Rodriguez-Manzano
- Section of Adult Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0NN, United Kingdom; Centre for Antimicrobial Optimisation, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0NN, United Kingdom.
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14
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Mahmoudi S, García MJ, Drain PK. Current approaches for diagnosis of subclinical pulmonary tuberculosis, clinical implications and future perspectives: a scoping review. Expert Rev Clin Immunol 2024; 20:715-726. [PMID: 38879875 DOI: 10.1080/1744666x.2024.2326032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 02/28/2024] [Indexed: 06/18/2024]
Abstract
INTRODUCTION Subclinical tuberculosis (TB) is the presence of TB disease among people who are either asymptomatic or have minimal symptoms. AREAS COVERED Currently, there are no accurate diagnostic tools and clear treatment approaches for subclinical TB. In this study, a comprehensive literature search was conducted across major databases. This review aimed to uncover the latest advancements in diagnostic approaches, explore their clinical implications, and outline potential future perspectives. While innovative technologies are in development to enable sputum-free TB tests, there remains a critical need for precise diagnostic tools tailored to the unique characteristics of subclinical TB. Given the complexity of subclinical TB, a multidisciplinary approach involving clinicians, microbiologists, epidemiologists, and public health experts is essential. Further research is needed to establish standardized diagnostic criteria and treatment guidelines specifically tailored for subclinical TB, acknowledging the unique challenges posed by this elusive stage of the disease. EXPERT OPINION Efforts are needed for the detection, diagnosis, and treatment of subclinical TB. In this review, we describe the importance of subclinical TB, both from a clinical and public health perspective and highlight the diagnostic and treatment gaps of this stage.
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Affiliation(s)
- Shima Mahmoudi
- Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Maria J García
- Department of Preventive Medicine and Public Health and Microbiology, Autonoma University of Madrid, Madrid, Spain
| | - Paul K Drain
- International Clinical Research Center, Department of Global Health, Schools of Medicine and Public Health, University of Washington, Seattle, WA, USA
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
- Division of Allergy and Infectious Diseases, Department of Medicine, School of Medicine, University of Washington, Seattle, WA, USA
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15
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Arya R, Shakya H, Chaurasia R, Kumar S, Vinetz JM, Kim JJ. Computational reassessment of RNA-seq data reveals key genes in active tuberculosis. PLoS One 2024; 19:e0305582. [PMID: 38935691 PMCID: PMC11210783 DOI: 10.1371/journal.pone.0305582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 05/31/2024] [Indexed: 06/29/2024] Open
Abstract
BACKGROUND Tuberculosis is a serious life-threatening disease among the top global health challenges and rapid and effective diagnostic biomarkers are vital for early diagnosis especially given the increasing prevalence of multidrug resistance. METHODS Two human whole blood microarray datasets, GSE42826 and GSE42830 were retrieved from publicly available gene expression omnibus (GEO) database. Deregulated genes (DEGs) were identified using GEO2R online tool and Gene Ontology (GO), protein-protein interaction (PPI) network analysis was performed using Metascape and STRING databases. Significant genes (n = 8) were identified using T-test/ANOVA and Molecular Complex Detection (MCODE) score ≥10, which was validated in GSE34608 dataset. The diagnostic potential of three biomarkers was assessed using Area Under Curve (AUC) of Receiver Operating Characteristic (ROC) plot. The transcriptional levels of these genes were also examined in a separate dataset GSE31348, to monitor the patterns of variation during tuberculosis treatment. RESULTS A total of 62 common DEGs (57 upregulated, 7 downregulated genes) were identified in two discovery datasets. GO functions and pathway enrichment analysis shed light on the functional roles of these DEGs in immune response and type-II interferon signaling. The genes in Module-1 (n = 18) were linked to innate immune response, interferon-gamma signaling. The common genes (n = 8) were validated in GSE34608 dataset, that corroborates the results obtained from discovery sets. The gene expression levels demonstrated responsiveness to Mtb infection during anti-TB therapy in GSE31348 dataset. In GSE34608 dataset, the expression levels of three specific genes, GBP5, IFITM3, and EPSTI1, emerged as potential diagnostic makers. In combination, these genes scored remarkable diagnostic performance with 100% sensitivity and 89% specificity, resulting in an impressive Area Under Curve (AUC) of 0.958. However, GBP5 alone showed the highest AUC of 0.986 with 100% sensitivity and 89% specificity. CONCLUSIONS The study presents valuable insights into the critical gene network perturbed during tuberculosis. These genes are determinants for assessing the effectiveness of an anti-TB response and distinguishing between active TB and healthy individuals. GBP5, IFITM3 and EPSTI1 emerged as candidate core genes in TB and holds potential as novel molecular targets for the development of interventions in the treatment of TB.
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Affiliation(s)
- Rakesh Arya
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, South Korea
| | - Hemlata Shakya
- Department of Biomedical Engineering, Shri G. S. Institute of Technology and Science, Indore, Madhya Pradesh, India
| | - Reetika Chaurasia
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, United States of America
| | - Surendra Kumar
- Department of Orthopaedic Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Joseph M. Vinetz
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, United States of America
| | - Jong Joo Kim
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, South Korea
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16
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Zielinski N, Baiceanu D, Dragomir A, Heyckendorf J, Ibraim E, Köhler N, Leschczyk C, Popa C, Rachow A, Sachsenweger J, Sanchez Carballo P, Schaub D, Zeeb H, Tulu B, DiNardo AR, Lange C, Reimann M. A Transcriptomic Biomarker Predicting Linezolid-Associated Neuropathy During Treatment of Drug-Resistant Tuberculosis. Pathog Immun 2024; 9:25-42. [PMID: 38939039 PMCID: PMC11210591 DOI: 10.20411/pai.v9i2.705] [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: 04/01/2024] [Accepted: 05/28/2024] [Indexed: 06/29/2024] Open
Abstract
Background Neuropathic adverse events occur frequently in linezolid-containing regimens, some of which remain irreversible after drug discontinuation. Objective We aimed to identify and validate a host RNA-based biomarker that can predict linezolid-associated neuropathy before multidrug-resistant/rifampicin-resistant tuberculosis (MDR/RR-TB) treatment initiation and to identify genes and pathways that are associated with linezolid-associated neuropathy. Methods Adult patients initiating MDR/RR-TB treatment including linezolid were prospectively enrolled in 3 independent cohorts in Germany. Clinical data and whole blood RNA for transcriptomic analysis were collected. The primary outcome was linezolid-associated optic and/or peripheral neuropathy. A random forest algorithm was used for biomarker identification. The biomarker was validated in an additional fourth cohort of patients with MDR/RR-TB from Romania. Results A total of 52 patients from the 3 identification cohorts received linezolid treatment. Of those, 24 (46.2%) developed peripheral and/or optic neuropathies during linezolid treatment. The majority (59.3%) of the episodes were of moderate (grade 2) severity. In total, the expression of 1,479 genes differed significantly at baseline of treatment. Suprabasin (SBSN) was identified as a potential biomarker to predict linezolid-associated neuropathy. In the validation cohort, 10 of 42 (23.8%) patients developed grade ≥3 neuropathies. The area under the curve for the biomarker algorithm prediction of grade ≥3 neuropathies was 0.63 (poor; 95% confidence interval: 0.42 - 0.84). Conclusions We identified and preliminarily validated a potential clinical biomarker to predict linezolid-associated neuropathies before the initiation of MDR/RR-TB therapy. Larger studies of the SBSN biomarker in more diverse populations are warranted.
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Affiliation(s)
- Nika Zielinski
- Division of Clinical Infectious Diseases, Research
Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Partner
Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Respiratory Medicine and International Health,
University of Lübeck, Lübeck, Germany
| | - Dragos Baiceanu
- Marius Nasta Institute of Pneumophtiziology (MNI),
Bucharest, Romania
- Eastern-European Study Site of DZIF in MNI,
Bucharest, Romania
| | - Antonela Dragomir
- Marius Nasta Institute of Pneumophtiziology (MNI),
Bucharest, Romania
- Eastern-European Study Site of DZIF in MNI,
Bucharest, Romania
- UMF Carol Davila, Bucharest, Romania
| | - Jan Heyckendorf
- Clinic for Internal Medicine I, Leibniz Lung Clinic,
University Hospital Schleswig-Holstein (UKSH) Campus Kiel, Kiel, Germany
| | - Elmira Ibraim
- Marius Nasta Institute of Pneumophtiziology (MNI),
Bucharest, Romania
- Eastern-European Study Site of DZIF in MNI,
Bucharest, Romania
| | - Niklas Köhler
- Division of Clinical Infectious Diseases, Research
Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Partner
Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Respiratory Medicine and International Health,
University of Lübeck, Lübeck, Germany
| | - Christoph Leschczyk
- German Center for Infection Research (DZIF) Partner
Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Division of Cellular Microbiology, Research Center
Borstel, Borstel, Germany
| | - Cristina Popa
- Marius Nasta Institute of Pneumophtiziology (MNI),
Bucharest, Romania
- Eastern-European Study Site of DZIF in MNI,
Bucharest, Romania
| | - Andrea Rachow
- Division of Infectious Diseases and Tropical
Medicine, Medical Centre of the University of Munich (LMU), Munich,
Germany
- German Centre for Infection Research (DZIF),
Partner Site Munich, Munich, Germany
- Unit Global Health, Helmholtz Zentrum
München, German Research Centre for Environmental Health (HMGU),
Neuherberg, Germany
| | - Jens Sachsenweger
- Department of Pneumology, Asklepios Clinic
Hamburg-Harburg, Hamburg, Germany
| | - Patricia Sanchez Carballo
- Division of Clinical Infectious Diseases, Research
Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Partner
Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Respiratory Medicine and International Health,
University of Lübeck, Lübeck, Germany
| | - Dagmar Schaub
- Division of Clinical Infectious Diseases, Research
Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Partner
Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Respiratory Medicine and International Health,
University of Lübeck, Lübeck, Germany
| | - Hajo Zeeb
- Department of Prevention and Evaluation, Leibniz
Institute for Prevention Research and Epidemiology – BIPS, Bremen,
Germany
- Faculty of Human and Health Sciences, University
of Bremen, Bremen, Germany
| | - Begna Tulu
- Division of Clinical Infectious Diseases, Research
Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Partner
Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Respiratory Medicine and International Health,
University of Lübeck, Lübeck, Germany
| | - Andrew R. DiNardo
- Baylor College of Medicine and Texas
Children's Hospital, Global TB Program, Houston, Texas
- Radboud University Medical Center, Internal
Medicine, Nijmegen, Netherlands
| | - Christoph Lange
- Division of Clinical Infectious Diseases, Research
Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Partner
Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Respiratory Medicine and International Health,
University of Lübeck, Lübeck, Germany
- Baylor College of Medicine and Texas
Children's Hospital, Global TB Program, Houston, Texas
| | - Maja Reimann
- Division of Clinical Infectious Diseases, Research
Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Partner
Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Respiratory Medicine and International Health,
University of Lübeck, Lübeck, Germany
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17
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Scherer J, Mukasa SL, Wolmarans K, Guler R, Kotze T, Song T, Dunn R, Laubscher M, Pape HC, Held M, Thienemann F. Comparing gene expression profiles of adults with isolated spinal tuberculosis to disseminated spinal tuberculosis identified by 18FDG-PET/CT at time of diagnosis, 6- and 12-months follow-up: classifying clinical stages of spinal tuberculosis and monitoring treatment response (Spinal TB X cohort study). J Orthop Surg Res 2024; 19:376. [PMID: 38918806 PMCID: PMC11202394 DOI: 10.1186/s13018-024-04840-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 06/07/2024] [Indexed: 06/27/2024] Open
Abstract
BACKGROUND Tuberculosis (TB) is one of the top ten causes of death worldwide, with approximately 10 million cases annually. Focus has been on pulmonary TB, while extrapulmonary TB (EPTB) has received little attention. Diagnosis of EPTB remains challenging due to the invasive procedures required for sample collection. Spinal TB (STB) accounts for 10% of EPTB and often leads to lifelong debilitating disease due to devastating spinal deformation and compression of neural structures. Little is known about the extent of disease, although both isolated STB and a disseminated form of STB have been described. In our Spinal TB X cohort study, we aim to describe the clinical phenotype of STB using whole-body 18FDG-PET/CT, identify a specific gene expression profile for different stages of dissemination and compare findings to previously described gene expression signatures for latent and active pulmonary TB. METHODS A single-centre, prospective cohort study will be established to describe the distributional pattern of STB detected by whole-body 18FDG-PET/CT and gene expression profile of patients with suspected STB on magnetic resonance imaging (MRI) at point of diagnosis, six months, and 12 months. Blood biobanking will be performed at these time points. Specimens for microbiology will be obtained from sputum/urine, from easily accessible sites of disease (e.g., lymph nodes, abscess) identified in the first 18FDG-PET/CT, from CT-guided biopsy and/or surgery. Clinical parameters and functional scores will be collected at every physical visit. Data will be entered into RedCap® database; data cleaning, validation and analysis will be performed by the study team. The University of Cape Town Ethics Committee approved the protocol (243/2022). DISCUSSION The Spinal TB X cohort study is the first prospective cohort study using whole-body 18FDG-PET/CT scans in patients with microbiologically confirmed spinal tuberculosis. Dual imaging techniques of the spine using 18FDG-PET/CT and magnetic resonance imaging as well as tissue diagnosis (microbiology and histopathology) will allow us to develop a virtual biopsy model. If successful, a distinct gene-expression profile will aid in blood-based diagnosis (point of care testing) as well as treatment monitoring and would lead to earlier diagnosis of this devastating disease. TRIAL REGISTRATION The study has been registered on ClinicalTrials.gov (NCT05610098).
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Affiliation(s)
- Julian Scherer
- General Medicine & Global Health (GMGH), Department of Medicine and Orthopaedic Research Unit (ORU), Division of Orthopaedic Surgery, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Department of Traumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Sandra L Mukasa
- Department of Medicine, Faculty of Health Science, General Medicine and Global Health (GMGH), University of Cape Town, 4Th Floor, Chris Barnard Building, Anzio Road, Observatory, Cape Town, 7925, South Africa
| | - Karen Wolmarans
- Department of Medicine, Faculty of Health Science, General Medicine and Global Health (GMGH), University of Cape Town, 4Th Floor, Chris Barnard Building, Anzio Road, Observatory, Cape Town, 7925, South Africa
| | - Reto Guler
- Institute of Infectious Diseases and Molecular Medicine (IDM), Department of Pathology, Division of Immunology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town Component, Cape Town, South Africa
| | - Tessa Kotze
- Department of Medicine, CUBIC, PETCT, University of Cape Town, Cape Town, South Africa
| | - Taeksun Song
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa
| | - Robert Dunn
- Orthopaedic Research Unit (ORU), Division of Orthopaedic Surgery, Faculty of Health Science, University of Cape Town, Cape Town, South Africa
| | - Maritz Laubscher
- Orthopaedic Research Unit (ORU), Division of Orthopaedic Surgery, Faculty of Health Science, University of Cape Town, Cape Town, South Africa
| | - Hans-Christoph Pape
- Department of Traumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Michael Held
- Orthopaedic Research Unit (ORU), Division of Orthopaedic Surgery, Faculty of Health Science, University of Cape Town, Cape Town, South Africa
| | - Friedrich Thienemann
- Department of Medicine, Faculty of Health Science, General Medicine and Global Health (GMGH), University of Cape Town, 4Th Floor, Chris Barnard Building, Anzio Road, Observatory, Cape Town, 7925, South Africa.
- Department of Internal Medicine, University Hospital Zurich, University of Zurich, Zurich, Switzerland.
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18
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Painter H, Larsen SE, Williams BD, Abdelaal HFM, Baldwin SL, Fletcher HA, Fiore-Gartland A, Coler RN. Backtranslation of human RNA biosignatures of tuberculosis disease risk into the preclinical pipeline is condition dependent. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.21.600067. [PMID: 38948876 PMCID: PMC11212953 DOI: 10.1101/2024.06.21.600067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
It is not clear whether human progression to active tuberculosis disease (TB) risk signatures are viable endpoint criteria for evaluations of treatments in clinical or preclinical development. TB is the deadliest infectious disease globally and more efficacious vaccines are needed to reduce this mortality. However, the immune correlates of protection for either preventing infection with Mycobacterium tuberculosis or preventing TB disease have yet to be completely defined, making the advancement of candidate vaccines through the pipeline slow, costly, and fraught with risk. Human-derived correlate of risk (COR) gene signatures, which identify an individual's risk to progressing to active TB disease, provide an opportunity for evaluating new therapies for TB with clear and defined endpoints. Though prospective clinical trials with longitudinal sampling are prohibitively expensive, characterization of COR gene signatures is practical with preclinical models. Using a 3Rs (Replacement, Reduction and Refinement) approach we reanalyzed heterogeneous publicly available transcriptional datasets to determine whether a specific set of COR signatures are viable endpoints in the preclinical pipeline. We selected RISK6, Sweeney3 and BATF2 human-derived blood-based RNA biosignatures because they require relatively few genes to assign a score and have been carefully evaluated across several clinical cohorts. Excitingly, these data provide proof-of-concept that human COR signatures seem to have high fidelity across several tissue types in the preclinical TB model pipeline and show best performance when the model most closely reflected human infection or disease conditions. Human-derived COR signatures offer an opportunity for high-throughput preclinical endpoint criteria of vaccine and drug therapy evaluations. One Sentence Summary Human-derived biosignatures of tuberculosis disease progression were evaluated for their predictive fidelity across preclinical species and derived tissues using available public data sets.
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19
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Wang X, VanValkenberg A, Odom AR, Ellner JJ, Hochberg NS, Salgame P, Patil P, Johnson WE. Comparison of gene set scoring methods for reproducible evaluation of tuberculosis gene signatures. BMC Infect Dis 2024; 24:610. [PMID: 38902649 PMCID: PMC11191245 DOI: 10.1186/s12879-024-09457-z] [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: 07/29/2023] [Accepted: 05/31/2024] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND Blood-based transcriptional gene signatures for tuberculosis (TB) have been developed with potential use to diagnose disease. However, an unresolved issue is whether gene set enrichment analysis of the signature transcripts alone is sufficient for prediction and differentiation or whether it is necessary to use the original model created when the signature was derived. Intra-method comparison is complicated by the unavailability of original training data and missing details about the original trained model. To facilitate the utilization of these signatures in TB research, comparisons between gene set scoring methods cross-data validation of original model implementations are needed. METHODS We compared the performance of 19 TB gene signatures across 24 transcriptomic datasets using both rrebuilt original models and gene set scoring methods. Existing gene set scoring methods, including ssGSEA, GSVA, PLAGE, Singscore, and Zscore, were used as alternative approaches to obtain the profile scores. The area under the ROC curve (AUC) value was computed to measure performance. Correlation analysis and Wilcoxon paired tests were used to compare the performance of enrichment methods with the original models. RESULTS For many signatures, the predictions from gene set scoring methods were highly correlated and statistically equivalent to the results given by the original models. In some cases, PLAGE outperformed the original models when considering signatures' weighted mean AUC values and the AUC results within individual studies. CONCLUSION Gene set enrichment scoring of existing gene sets can distinguish patients with active TB disease from other clinical conditions with equivalent or improved accuracy compared to the original methods and models. These data justify using gene set scoring methods of published TB gene signatures for predicting TB risk and treatment outcomes, especially when original models are difficult to apply or implement.
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Affiliation(s)
- Xutao Wang
- Department of Biostatistics, Boston University, Boston, MA, USA
- Division of Computational Biomedicine and Bioinformatics Program, Boston University, Boston, MA, USA
| | - Arthur VanValkenberg
- Division of Infectious Disease, Center for Data Science, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Aubrey R Odom
- Division of Computational Biomedicine and Bioinformatics Program, Boston University, Boston, MA, USA
| | - Jerrold J Ellner
- Department of Medicine, Center for Emerging Pathogens, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Natasha S Hochberg
- Boston Medical Center, Boston, MA, USA
- Section of Infectious Diseases, Boston University School of Medicine, Boston, MA, USA
| | - Padmini Salgame
- Department of Medicine, Center for Emerging Pathogens, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Prasad Patil
- Department of Biostatistics, Boston University, Boston, MA, USA
| | - W Evan Johnson
- Division of Infectious Disease, Center for Data Science, Rutgers New Jersey Medical School, Newark, NJ, USA.
- Department of Medicine, Center for Emerging Pathogens, Rutgers New Jersey Medical School, Newark, NJ, USA.
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20
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Chang A, Loy CJ, Eweis-LaBolle D, Lenz JS, Steadman A, Andgrama A, Nhung NV, Yu C, Worodria W, Denkinger CM, Nahid P, Cattamanchi A, De Vlaminck I. Circulating cell-free RNA in blood as a host response biomarker for detection of tuberculosis. Nat Commun 2024; 15:4949. [PMID: 38858368 PMCID: PMC11164910 DOI: 10.1038/s41467-024-49245-6] [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: 03/08/2023] [Accepted: 05/29/2024] [Indexed: 06/12/2024] Open
Abstract
Tuberculosis (TB) remains a leading cause of death from an infectious disease worldwide, partly due to a lack of effective strategies to screen and triage individuals with potential TB. Whole blood RNA signatures have been tested as biomarkers for TB, but have failed to meet the World Health Organization's (WHO) optimal target product profiles (TPP). Here, we use RNA sequencing and machine-learning to investigate the utility of plasma cell-free RNA (cfRNA) as a host-response biomarker for TB in cohorts from Uganda, Vietnam and Philippines. We report a 6-gene cfRNA signature, which differentiates TB-positive and TB-negative individuals with AUC = 0.95, 0.92, and 0.95 in test, training and validation, respectively. This signature meets WHO TPPs (sensitivity: 97.1% [95% CI: 80.9-100%], specificity: 85.2% [95% CI: 72.4-100%]) regardless of geographic location, sample collection method and HIV status. Overall, our results identify plasma cfRNA as a promising host response biomarker to diagnose TB.
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Affiliation(s)
- Adrienne Chang
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Conor J Loy
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | | | - Joan S Lenz
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | | | - Alfred Andgrama
- World Alliance for Lung and Intensive Care Medicine in Uganda, Kampala, Uganda
| | | | - Charles Yu
- De La Salle Medical and Health Sciences Institute, Dasmarinas, Philippines
| | - William Worodria
- World Alliance for Lung and Intensive Care Medicine in Uganda, Kampala, Uganda
| | - Claudia M Denkinger
- University Hospital Heidelberg & German Center of Infection Research, Heidelberg, Germany
| | - Payam Nahid
- UCSF Center for Tuberculosis, University of California San Francisco, San Francisco, CA, USA
| | - Adithya Cattamanchi
- UCSF Center for Tuberculosis, University of California San Francisco, San Francisco, CA, USA
- Division of Pulmonary and Critical Care Medicine, University of California Irvine, Orange, CA, USA
| | - Iwijn De Vlaminck
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.
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21
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Vu A, Glassman I, Campbell G, Yeganyan S, Nguyen J, Shin A, Venketaraman V. Host Cell Death and Modulation of Immune Response against Mycobacterium tuberculosis Infection. Int J Mol Sci 2024; 25:6255. [PMID: 38892443 PMCID: PMC11172987 DOI: 10.3390/ijms25116255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024] Open
Abstract
Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis (TB), a prevalent infectious disease affecting populations worldwide. A classic trait of TB pathology is the formation of granulomas, which wall off the pathogen, via the innate and adaptive immune systems. Some key players involved include tumor necrosis factor-alpha (TNF-α), foamy macrophages, type I interferons (IFNs), and reactive oxygen species, which may also show overlap with cell death pathways. Additionally, host cell death is a primary method for combating and controlling Mtb within the body, a process which is influenced by both host and bacterial factors. These cell death modalities have distinct molecular mechanisms and pathways. Programmed cell death (PCD), encompassing apoptosis and autophagy, typically confers a protective response against Mtb by containing the bacteria within dead macrophages, facilitating their phagocytosis by uninfected or neighboring cells, whereas necrotic cell death benefits the pathogen, leading to the release of bacteria extracellularly. Apoptosis is triggered via intrinsic and extrinsic caspase-dependent pathways as well as caspase-independent pathways. Necrosis is induced via various pathways, including necroptosis, pyroptosis, and ferroptosis. Given the pivotal role of host cell death pathways in host defense against Mtb, therapeutic agents targeting cell death signaling have been investigated for TB treatment. This review provides an overview of the diverse mechanisms underlying Mtb-induced host cell death, examining their implications for host immunity. Furthermore, it discusses the potential of targeting host cell death pathways as therapeutic and preventive strategies against Mtb infection.
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Affiliation(s)
| | | | | | | | | | | | - Vishwanath Venketaraman
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA (G.C.); (A.S.)
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22
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Nieto-Caballero VE, Reijneveld JF, Ruvalcaba A, Innocenzi G, Abeydeera N, Asgari S, Lopez K, Iwany SK, Luo Y, Nathan A, Fernandez-Salinas D, Chiñas M, Huang CC, Zhang Z, León SR, Calderon RI, Lecca L, Budzik JM, Murray M, Van Rhijn I, Raychaudhuri S, Moody DB, Suliman S, Gutierrez-Arcelus M. History of tuberculosis disease is associated with genetic regulatory variation in Peruvians. PLoS Genet 2024; 20:e1011313. [PMID: 38870230 PMCID: PMC11208071 DOI: 10.1371/journal.pgen.1011313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 06/26/2024] [Accepted: 05/21/2024] [Indexed: 06/15/2024] Open
Abstract
A quarter of humanity is estimated to have been exposed to Mycobacterium tuberculosis (Mtb) with a 5-10% risk of developing tuberculosis (TB) disease. Variability in responses to Mtb infection could be due to host or pathogen heterogeneity. Here, we focused on host genetic variation in a Peruvian population and its associations with gene regulation in monocyte-derived macrophages and dendritic cells (DCs). We recruited former household contacts of TB patients who previously progressed to TB (cases, n = 63) or did not progress to TB (controls, n = 63). Transcriptomic profiling of monocyte-derived DCs and macrophages measured the impact of genetic variants on gene expression by identifying expression quantitative trait loci (eQTL). We identified 330 and 257 eQTL genes in DCs and macrophages (False Discovery Rate (FDR) < 0.05), respectively. Four genes in DCs showed interaction between eQTL variants and TB progression status. The top eQTL interaction for a protein-coding gene was with FAH, the gene encoding fumarylacetoacetate hydrolase, which mediates the last step in mammalian tyrosine catabolism. FAH expression was associated with genetic regulatory variation in cases but not controls. Using public transcriptomic and epigenomic data of Mtb-infected monocyte-derived dendritic cells, we found that Mtb infection results in FAH downregulation and DNA methylation changes in the locus. Overall, this study demonstrates effects of genetic variation on gene expression levels that are dependent on history of infectious disease and highlights a candidate pathogenic mechanism through pathogen-response genes. Furthermore, our results point to tyrosine metabolism and related candidate TB progression pathways for further investigation.
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Affiliation(s)
- Victor E. Nieto-Caballero
- Division of Immunology, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Undergraduate Program in Genomic Sciences, Center for Genomic Sciences, Universidad Nacional Autónoma de México (UNAM), Morelos, Mexico
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Josephine F. Reijneveld
- Zuckerberg San Francisco General Hospital, Division of Experimental Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Angel Ruvalcaba
- Zuckerberg San Francisco General Hospital, Division of Experimental Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Gabriel Innocenzi
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Nalin Abeydeera
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Samira Asgari
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Data Sciences, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Kattya Lopez
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Socios En Salud Sucursal Peru, Lima, Peru
| | - Sarah K. Iwany
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Yang Luo
- Division of Immunology, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Data Sciences, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
| | - Aparna Nathan
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Data Sciences, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Daniela Fernandez-Salinas
- Division of Immunology, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Marcos Chiñas
- Division of Immunology, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Chuan-Chin Huang
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Zibiao Zhang
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Segundo R. León
- Socios En Salud Sucursal Peru, Lima, Peru
- Medical Technology School and Global Health Research Institute, San Juan Bautista Private University, Lima, Perú
| | | | | | - Jonathan M. Budzik
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Megan Murray
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Ildiko Van Rhijn
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Soumya Raychaudhuri
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Data Sciences, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - D. Branch Moody
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Sara Suliman
- Zuckerberg San Francisco General Hospital, Division of Experimental Medicine, University of California San Francisco, San Francisco, California, United States of America
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Gladstone-UCSF Institute of Genomic Immunology, University of California San Francisco, San Francisco, California, United States of America
- Chan Zuckerberg Initiative Biohub, San Francisco, California, United States of America
| | - Maria Gutierrez-Arcelus
- Division of Immunology, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Data Sciences, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
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23
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Dheda K, Migliori GB. New framework to define the spectrum of tuberculosis. THE LANCET. RESPIRATORY MEDICINE 2024; 12:426-428. [PMID: 38527483 DOI: 10.1016/s2213-2600(24)00085-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 03/12/2024] [Indexed: 03/27/2024]
Affiliation(s)
- Keertan Dheda
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute and South African MRC/UCT Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, 7700, South Africa; Faculty of Infectious and Tropical Diseases, Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, UK.
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24
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Davies LRL, Wang C, Steigler P, Bowman KA, Fischinger S, Hatherill M, Fisher M, Mbandi SK, Rodo M, Ottenhoff THM, Dockrell HM, Sutherland JS, Mayanja-Kizza H, Boom WH, Walzl G, Kaufmann SHE, Nemes E, Scriba TJ, Lauffenburger D, Alter G, Fortune SM. Age and sex influence antibody profiles associated with tuberculosis progression. Nat Microbiol 2024; 9:1513-1525. [PMID: 38658786 PMCID: PMC11153143 DOI: 10.1038/s41564-024-01678-x] [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: 10/12/2023] [Accepted: 03/20/2024] [Indexed: 04/26/2024]
Abstract
Antibody features vary with tuberculosis (TB) disease state. Whether clinical variables, such as age or sex, influence associations between Mycobacterium tuberculosis-specific antibody responses and disease state is not well explored. Here we profiled Mycobacterium tuberculosis-specific antibody responses in 140 TB-exposed South African individuals from the Adolescent Cohort Study. We identified distinct response features in individuals progressing to active TB from non-progressing, matched controls. A multivariate antibody score differentially associated with progression (SeroScore) identified progressors up to 2 years before TB diagnosis, earlier than that achieved with the RISK6 transcriptional signature of progression. We validated these antibody response features in the Grand Challenges 6-74 cohort. Both the SeroScore and RISK6 correlated better with risk of TB progression in adolescents compared with adults, and in males compared with females. This suggests that age and sex are important, underappreciated modifiers of antibody responses associated with TB progression.
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Affiliation(s)
- Leela R L Davies
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Chuangqi Wang
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Pia Steigler
- South African Tuberculosis Vaccine Initiative and Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Kathryn A Bowman
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | | | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative and Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Michelle Fisher
- South African Tuberculosis Vaccine Initiative and Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Stanley Kimbung Mbandi
- South African Tuberculosis Vaccine Initiative and Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Miguel Rodo
- South African Tuberculosis Vaccine Initiative and Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Tom H M Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Hazel M Dockrell
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Jayne S Sutherland
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Harriet Mayanja-Kizza
- Department of Medicine and Department of Microbiology, Makerere University, Kampala, Uganda
| | - W Henry Boom
- Tuberculosis Research Unit, Case Western Reserve University, Cleveland, OH, USA
| | - Gerhard Walzl
- Department of Science and Technology National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Stefan H E Kaufmann
- Max Planck Institute for Infection Biology, Berlin, Germany
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Hagler Institute for Advanced Study, Texas A&M University, College Station, TX, USA
| | - Elisa Nemes
- South African Tuberculosis Vaccine Initiative and Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative and Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | | | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA.
- Moderna Therapeutics, Cambridge, MA, USA.
| | - Sarah M Fortune
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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25
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Jaime-Sánchez E, Lara-Ramírez EE, López-Ramos JE, Ramos-González EJ, Cisneros-Méndez AL, Oropeza-Valdez JJ, Zenteno-Cuevas R, Martínez-Aguilar G, Bastian Y, Castañeda-Delgado JE, Serrano CJ, Enciso-Moreno JA. Potential molecular patterns for tuberculosis susceptibility in diabetic patients with poor glycaemic control: a pilot study. Mol Genet Genomics 2024; 299:60. [PMID: 38801463 DOI: 10.1007/s00438-024-02139-0] [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: 05/02/2022] [Accepted: 04/06/2024] [Indexed: 05/29/2024]
Abstract
Type 2 diabetes (DM2) is an increasingly prevalent disease that challenges tuberculosis (TB) control strategies worldwide. It is significant that DM2 patients with poor glycemic control (PDM2) are prone to developing tuberculosis. Furthermore, elucidating the molecular mechanisms that govern this susceptibility is imperative to address this problem. Therefore, a pilot transcriptomic study was performed. Human blood samples from healthy controls (CTRL, HbA1c < 6.5%), tuberculosis (TB), comorbidity TB-DM2, DM2 (HbA1c 6.5-8.9%), and PDM2 (HbA1c > 10%) groups (n = 4 each) were analyzed by differential expression using microarrays. We use a network strategy to identify potential molecular patterns linking the differentially expressed genes (DEGs) specific for TB-DM2 and PDM2 (p-value < 0.05, fold change > 2). We define OSM, PRKCD, and SOCS3 as key regulatory genes (KRGs) that modulate the immune system and related pathways. RT-qPCR assays confirmed upregulation of OSM, PRKCD, and SOCS3 genes (p < 0.05) in TB-DM2 patients (n = 18) compared to CTRL, DM2, PDM2, or TB groups (n = 17, 19, 15, and 9, respectively). Furthermore, OSM, PRKCD, and SOCS3 were associated with PDM2 susceptibility pathways toward TB-DM2 and formed a putative protein-protein interaction confirmed in STRING. Our results reveal potential molecular patterns where OSM, PRKCD, and SOCS3 are KRGs underlying the compromised immune response and susceptibility of patients with PDM2 to develop tuberculosis. Therefore, this work paved the way for fundamental research of new molecular targets in TB-DM2. Addressing their cellular implications, and the impact on the diagnosis, treatment, and clinical management of TB-DM2 could help improve the strategy to end tuberculosis for this vulnerable population.
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Affiliation(s)
- Elena Jaime-Sánchez
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa, Tamaulipas, México
- Área de Ciencias de La Salud, Universidad Autónoma de Zacatecas, Carretera Zacatecas-Guadalajara, Zacatecas, México
- Unidad de Investigación Biomédica de Zacatecas, IMSS, Zacatecas, México
| | - Edgar E Lara-Ramírez
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa, Tamaulipas, México
- Unidad de Investigación Biomédica de Zacatecas, IMSS, Zacatecas, México
| | - Juan Ernesto López-Ramos
- Academia de Ciencias Químico-Biológicas, Instituto Politécnico Nacional, Centro de Estudios Científicos y Tecnológicos No. 18, Zacatecas, México
| | | | | | - Juan José Oropeza-Valdez
- Human Systems Biology Laboratory. Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| | | | | | - Yadira Bastian
- Instituto de Física, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - Julio Enrique Castañeda-Delgado
- Unidad de Investigación Biomédica de Zacatecas, IMSS, Zacatecas, México
- Investigador por Mexico/Catedras CONAHCYT, Consejo nacional de Humanidades, Ciencias y Tecnologias, Ciudad de Mexico, México
- Consejo Nacional de Ciencia y Tecnologia, CONACYT, Ciudad de Mexico, México
| | | | - José Antonio Enciso-Moreno
- Unidad de Investigación Biomédica de Zacatecas, IMSS, Zacatecas, México.
- Facultad de Química, Cerro de Las Campanas S/N, Universidad Autónoma de Querétaro, Colonia Las Campanas, Centro Universitario, C.P. 76010, Querétaro, México.
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26
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Gupta A, Thirunavukkarasu S, Rangel-Moreno J, Ahmed M, Swanson RV, Mbandi SK, Smrcka AV, Kaushal D, Scriba TJ, Khader SA. Phospholipase C epsilon-1 (PLCƐ1) mediates macrophage activation and protection against tuberculosis. Infect Immun 2024; 92:e0049523. [PMID: 38451080 PMCID: PMC11003233 DOI: 10.1128/iai.00495-23] [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: 12/01/2023] [Accepted: 02/16/2024] [Indexed: 03/08/2024] Open
Abstract
Tuberculosis (TB) caused by Mycobacterium tuberculosis (Mtb) infects up to a quarter of the world's population. Although immune responses can control Mtb infection, 5%-10% of infected individuals can progress to active TB disease (progressors). A myriad of host factors regulate disease progression in TB and a better understanding of immune correlates of protection and disease is pivotal for the development of new therapeutics. Comparison of human whole blood transcriptomic metadata with that of macaque TB progressors and Mtb-infected diversity outbred mice (DO) led to the identification of differentially regulated gene (DEG) signatures, associated with TB progression or control. The current study assessed the function of Phospholipase C epsilon (PLCƐ1), the top downregulated gene across species in TB progressors, using a gene-specific knockout mouse model of Mtb infection and in vitro Mtb-infected bone marrow-derived macrophages. PLCƐ1 gene expression was downregulated in TB progressors across species. PLCε1 deficiency in the mouse model resulted in increased susceptibility to Mtb infection, coincident accumulation of lung myeloid cells, and reduced ability to mount antibacterial responses. However, PLCε1 was not required for the activation and accumulation of T cells in mice. Our results suggest an important early role for PLCƐ1 in shaping innate immune response to TB and may represent a putative target for host-directed therapy.
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Affiliation(s)
- Ananya Gupta
- Department of Microbiology, The University of Chicago, Chicago, Illinois, USA
| | | | - Javier Rangel-Moreno
- Division of Allergy, Immunology and Rheumatology, Department of Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | - Mushtaq Ahmed
- Department of Microbiology, The University of Chicago, Chicago, Illinois, USA
| | - Rosemary V. Swanson
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Stanley Kimbung Mbandi
- South African Tuberculosis Vaccine Initiative (SATVI), Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Alan V. Smrcka
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan, USA
| | - Deepak Kaushal
- Southwest National Primate Research Centre (SNPRC) at Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Thomas J. Scriba
- South African Tuberculosis Vaccine Initiative (SATVI), Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Shabaana A. Khader
- Department of Microbiology, The University of Chicago, Chicago, Illinois, USA
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27
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Bobba S, Chauhan KS, Akter S, Das S, Mittal E, Mathema B, Philips JA, Khader SA. A protective role for type I interferon signaling following infection with Mycobacterium tuberculosis carrying the rifampicin drug resistance-conferring RpoB mutation H445Y. PLoS Pathog 2024; 20:e1012137. [PMID: 38603763 PMCID: PMC11037539 DOI: 10.1371/journal.ppat.1012137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 04/23/2024] [Accepted: 03/19/2024] [Indexed: 04/13/2024] Open
Abstract
Interleukin-1 (IL-1) signaling is essential for controlling virulent Mycobacterium tuberculosis (Mtb) infection since antagonism of this pathway leads to exacerbated pathology and increased susceptibility. In contrast, the triggering of type I interferon (IFN) signaling is associated with the progression of tuberculosis (TB) disease and linked with negative regulation of IL-1 signaling. However, mice lacking IL-1 signaling can control Mtb infection if infected with an Mtb strain carrying the rifampin-resistance conferring mutation H445Y in its RNA polymerase β subunit (rpoB-H445Y Mtb). The mechanisms that govern protection in the absence of IL-1 signaling during rpoB-H445Y Mtb infection are unknown. In this study, we show that in the absence of IL-1 signaling, type I IFN signaling controls rpoB-H445Y Mtb replication, lung pathology, and excessive myeloid cell infiltration. Additionally, type I IFN is produced predominantly by monocytes and recruited macrophages and acts on LysM-expressing cells to drive protection through nitric oxide (NO) production to restrict intracellular rpoB-H445Y Mtb. These findings reveal an unexpected protective role for type I IFN signaling in compensating for deficiencies in IL-1 pathways during rpoB-H445Y Mtb infection.
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Affiliation(s)
- Suhas Bobba
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Kuldeep S. Chauhan
- Department of Microbiology, University of Chicago, Chicago, Illinois, United States of America
| | - Sadia Akter
- Department of Microbiology, University of Chicago, Chicago, Illinois, United States of America
| | - Shibali Das
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Ekansh Mittal
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Barun Mathema
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, New York, United States of America
| | - Jennifer A. Philips
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Shabaana A. Khader
- Department of Microbiology, University of Chicago, Chicago, Illinois, United States of America
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28
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Källenius G, Correia-Neves M, Sundling C. Diagnostic markers reflecting dysregulation of the host response in the transition to tuberculosis disease. Int J Infect Dis 2024; 141S:106984. [PMID: 38417614 DOI: 10.1016/j.ijid.2024.106984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 03/01/2024] Open
Abstract
Sustained control of Mycobacterium tuberculosis infection without evidence of disease is based on a finely tuned balance between pro- and anti-inflammatory responses. Loss of this balance leads to tuberculosis (TB) disease, in which exacerbated myeloid and neutrophil activation is common. Proteomic and transcriptomic assessment of the host response can detect increasing immune activation associated with TB disease progression several months before clinical disease. Future diagnostic methods based on measuring host response biomarkers that are able to detect this dysregulation could therefore be valuable in the early detection of TB disease progression.
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Affiliation(s)
- Gunilla Källenius
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden; Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden; Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Margarida Correia-Neves
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden; Life and Health Sciences Research Institute, School of Medicine, University of Minho, Braga, Portugal; ICVS/3B's, PT Government Associate Laboratory, Braga, Portugal
| | - Christopher Sundling
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden; Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden; Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden.
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29
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Arya R, Shakya H, Chaurasia R, Haque MA, Kim JJ. Exploring the Role of Extracellular Vesicles in the Pathogenesis of Tuberculosis. Genes (Basel) 2024; 15:434. [PMID: 38674369 PMCID: PMC11049626 DOI: 10.3390/genes15040434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
Tuberculosis (TB) remains a significant global health concern, necessitating accurate diagnosis and treatment monitoring. Extracellular vesicles (EVs), including exosomes, play crucial roles in disease progression, with their associated genes serving as potential biomarkers and therapeutic targets. Leveraging publicly available RNA-Seq datasets of TB patients and healthy controls (HCs), to identify differentially expressed genes (DEGs) and their associated protein-protein interaction networks and immune cell profiles, the common EV-related DEGs were identified and validated in the GSE42830 and GSE40553 datasets. We have identified nine common EV-related DEGs (SERPINA1, TNFAIP6, MAPK14, STAT1, ITGA2B, VAMP5, CTSL, CEACAM1, and PLAUR) upregulated in TB patients. Immune cell infiltration analysis revealed significant differences between TB patients and HCs, highlighting increased proportions of various immune cells in TB patients. These DEGs are involved in crucial cellular processes and pathways related to exocytosis and immune response regulation. Notably, VAMP5 exhibited excellent diagnostic performance (AUC-0.993, sensitivity-93.8%, specificity-100%), with potential as a novel biomarker for TB. The EV-related genes can serve as novel potential biomarkers that can distinguish between TB and HCs. VAMP5, which functions in exosome biogenesis and showed significant upregulation in TB, can be targeted for therapeutic interventions and treatment outcomes.
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Affiliation(s)
- Rakesh Arya
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea; (R.A.); (M.A.H.)
| | - Hemlata Shakya
- Department of Biomedical Engineering, Shri G. S. Institute of Technology and Science, Indore 452003, Madhya Pradesh, India;
| | - Reetika Chaurasia
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Md Azizul Haque
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea; (R.A.); (M.A.H.)
| | - Jong-Joo Kim
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea; (R.A.); (M.A.H.)
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30
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Lim J, Zhou S, Baek J, Kim AY, Valera E, Sweedler J, Bashir R. A Blood Drying Process for DNA Amplification. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2307959. [PMID: 37888793 DOI: 10.1002/smll.202307959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Indexed: 10/28/2023]
Abstract
The presence of numerous inhibitors in blood makes their use in nucleic acid amplification techniques difficult. Current methods for extracting and purifying pathogenic DNA from blood involve removal of inhibitors, resulting in low and inconsistent DNA recovery rates. To address this issue, a biphasic method is developed that simultaneously achieves inhibitor inactivation and DNA amplification without the need for a purification step. Inhibitors are physically trapped in the solid-phase dried blood matrix by blood drying, while amplification reagents can move into the solid nano-porous dried blood and initiate the amplification. It is demonstrated that the biphasic method has significant improvement in detection limits for bacteria such as Escherichia coli, Methicillin-resistant Staphylococcus aureus, Methicillin-Sensitive Staphylococcus aureus using loop-mediated isothermal amplification (LAMP) and recombinase polymerase amplification (RPA). Several factors, such as drying time, sample volume, and material properties are characterized to increase sensitivity and expand the application of the biphasic assay to blood diagnostics. With further automation, this biphasic technique has the potential to be used as a diagnostic platform for the detection of pathogens eliminating lengthy culture steps.
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Affiliation(s)
- Jongwon Lim
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Shuaizhen Zhou
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Janice Baek
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Alicia Yeaeun Kim
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Enrique Valera
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jonathan Sweedler
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Rashid Bashir
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Biomedical and Translational Science, Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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31
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Lai H, Lyu M, Ruan H, Liu Y, Liu T, Lei S, Xiao Y, Zhang S, Ying B. Large-scale analysis reveals splicing biomarkers for tuberculosis progression and prognosis. Comput Biol Med 2024; 171:108187. [PMID: 38402840 DOI: 10.1016/j.compbiomed.2024.108187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 02/07/2024] [Accepted: 02/18/2024] [Indexed: 02/27/2024]
Abstract
BACKGROUND Emerging evidence suggests that aberrant alternative splicing (AS) may play an important role in tuberculosis (TB). However, current knowledge regarding the value of AS in TB progression and prognosis remains unclear. METHOD Public RNA-seq datasets related to TB progression and prognosis were searched and AS analyses were conducted based on SUPPA2. Percent spliced in (PSI) was used for quantifying AS events and multiple machine learning (ML) methods were employed to construct predictive models. Area under curve (AUC), sensitivity and specificity were calculated to evaluate the model performance. RESULTS A total of 1587 samples from 7 datasets were included. Among 923 TB-progression related differential AS events (DASEs), 3 events (GET1-skipping exon (SE), TPD52-alternative first exons (AF) and TIMM10-alternative 5' splice site (A5)) were selected as candidate biomarkers; however, their predictive performance was limited. For TB prognosis, 5 events (PHF23-AF, KIF1B-SE, MACROD2-alternative 3' splice site (A3), CD55-retained intron (RI) and GALNT11-AF) were selected as candidates from the 1282 DASEs. Six ML methods were used to integrate these 5 events and XGBoost outperformed than others. AUC, sensitivity and specificity of XGBoost model were 0.875, 81.1% and 83.5% in training set, while they were 0.805, 68.4% and 73.2% in test set. CONCLUSION GET1-SE, TPD52-AF and TIMM10-A5 showed limited role in predicting TB progression, while PHF23-AF, KIF1B-SE, MACROD2-A3, CD55-RI and GALNT11-AF could well predict TB prognosis and work as candidate biomarkers. This work preliminarily explored the value of AS in predicting TB progression and prognosis and offered potential targets for further research.
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Affiliation(s)
- Hongli Lai
- Department of Laboratory Medicine/Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, PR China; West China Medical School/West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, PR China
| | - Mengyuan Lyu
- Department of Laboratory Medicine/Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, PR China; Sichuan Clinical Research Center for Laboratory Medicine, Chengdu, Sichuan Province, 610041, PR China
| | - Hongxia Ruan
- Department of Laboratory Medicine/Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, PR China; Sichuan Clinical Research Center for Laboratory Medicine, Chengdu, Sichuan Province, 610041, PR China
| | - Yang Liu
- Department of Laboratory Medicine/Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, PR China; West China Medical School/West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, PR China
| | - Tangyuheng Liu
- Department of Laboratory Medicine/Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, PR China; Sichuan Clinical Research Center for Laboratory Medicine, Chengdu, Sichuan Province, 610041, PR China
| | - Shuting Lei
- West China Medical School/West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, PR China
| | - Yuling Xiao
- Department of Laboratory Medicine/Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, PR China; Sichuan Clinical Research Center for Laboratory Medicine, Chengdu, Sichuan Province, 610041, PR China
| | - Shu Zhang
- Department of Emergency Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, PR China
| | - Binwu Ying
- Department of Laboratory Medicine/Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, PR China; Sichuan Clinical Research Center for Laboratory Medicine, Chengdu, Sichuan Province, 610041, PR China.
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32
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Feng S, McNehlan ME, Kinsella RL, Sur Chowdhury C, Chavez SM, Naik SK, McKee SR, Van Winkle JA, Dubey N, Samuels A, Swain A, Cui X, Hendrix SV, Woodson R, Kreamalmeyer D, Smirnov A, Artyomov MN, Virgin HW, Wang YT, Stallings CL. Autophagy promotes efficient T cell responses to restrict high-dose Mycobacterium tuberculosis infection in mice. Nat Microbiol 2024; 9:684-697. [PMID: 38413834 DOI: 10.1038/s41564-024-01608-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 01/16/2024] [Indexed: 02/29/2024]
Abstract
Although autophagy sequesters Mycobacterium tuberculosis (Mtb) in in vitro cultured macrophages, loss of autophagy in macrophages in vivo does not result in susceptibility to a standard low-dose Mtb infection until late during infection, leaving open questions regarding the protective role of autophagy during Mtb infection. Here we report that loss of autophagy in lung macrophages and dendritic cells results in acute susceptibility of mice to high-dose Mtb infection, a model mimicking active tuberculosis. Rather than observing a role for autophagy in controlling Mtb replication in macrophages, we find that autophagy suppresses macrophage responses to Mtb that otherwise result in accumulation of myeloid-derived suppressor cells and subsequent defects in T cell responses. Our finding that the pathogen-plus-susceptibility gene interaction is dependent on dose has important implications both for understanding how Mtb infections in humans lead to a spectrum of outcomes and for the potential use of autophagy modulators in clinical medicine.
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Affiliation(s)
- Siwei Feng
- Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Michael E McNehlan
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Rachel L Kinsella
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Chanchal Sur Chowdhury
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Sthefany M Chavez
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Sumanta K Naik
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Samuel R McKee
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Jacob A Van Winkle
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Neha Dubey
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Amanda Samuels
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Amanda Swain
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Xiaoyan Cui
- Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Skyler V Hendrix
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Reilly Woodson
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Darren Kreamalmeyer
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Asya Smirnov
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Maxim N Artyomov
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Herbert W Virgin
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ya-Ting Wang
- Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China.
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA.
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Shanxi Medical University, Taiyuan, Shanxi, China.
| | - Christina L Stallings
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA.
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Burel JG, Wang W, Wuhrer M, Dedicoat M, Fletcher TE, Cunningham AF, O'Shea MK. IgG glycosylation associates with risk of progression from latent to active tuberculosis. J Infect 2024; 88:106115. [PMID: 38309308 DOI: 10.1016/j.jinf.2024.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/23/2024] [Accepted: 01/28/2024] [Indexed: 02/05/2024]
Abstract
OBJECTIVES Glycosylation motifs shape antibody structure, stability and antigen affinity and play an important role in antibody localization and function. Serum IgG glycosylation profiles are significantly altered in infectious diseases, including tuberculosis (TB), but have not been studied in the context of progression from latent to active TB. METHODS We performed a longitudinal study of paired bulk IgG glycosylation and transcriptomic profiling in blood from individuals with active TB (ATB) or latent TB infection (LTBI) before and after treatment. RESULTS We identified that a combination of two IgG1 glycosylation traits were sufficient to distinguish ATB from LTBI with high specificity and sensitivity, prior to, and after treatment. Importantly, these two features positively correlated with previously defined cellular and RNA signatures of ATB risk in LTBI, namely monocyte to lymphocyte ratio and the expression of interferon (IFN)-associated gene signature of progression (IFN-risk signature) in blood prior to treatment. Additional glycosylation features at higher prevalence in LTBI individuals with high expression of the IFN-risk signature prior to treatment included fucosylation on IgG1, IgG2 and IgG3. CONCLUSIONS Together, our results demonstrate that bulk IgG glycosylation features could be useful in stratifying the risk of LTBI reactivation and progression to ATB.
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Affiliation(s)
- Julie G Burel
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Wenjun Wang
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Martin Dedicoat
- Department of Infection, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Thomas E Fletcher
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK; Academic Department of Military Medicine, Royal Centre for Defence Medicine, Birmingham, UK
| | - Adam F Cunningham
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Matthew K O'Shea
- Department of Infection, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK; Academic Department of Military Medicine, Royal Centre for Defence Medicine, Birmingham, UK; Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK.
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Serene LG, Webber K, Champion PA, Schorey JS. Mycobacterium tuberculosis SecA2-dependent activation of host Rig-I/MAVs signaling is not conserved in Mycobacterium marinum. PLoS One 2024; 19:e0281564. [PMID: 38394154 PMCID: PMC10889897 DOI: 10.1371/journal.pone.0281564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 11/02/2023] [Indexed: 02/25/2024] Open
Abstract
Retinoic acid inducible gene I (Rig-I) is a cytosolic pattern recognition receptor canonically described for its important role in sensing viral RNAs. Increasingly, bacterially-derived RNA from intracellular bacteria such as Mycobacterium tuberculosis, have been shown to activate the same host Rig-I/Mitochondrial antiviral sensing protein (MAVS) signaling pathway to drive a type-I interferon response that contributes to bacterial pathogenesis in vivo. In M. tuberculosis, this response is mediated by the protein secretion system SecA2, but little is known about whether this process is conserved in other pathogenic mycobacteria or the mechanism by which these nucleic acids gain access to the host cytoplasm. Because the M. tuberculosis and M. marinum SecA2 protein secretion systems share a high degree of genetic and functional conservation, we hypothesized that Rig-I/MAVS activation and subsequent induction of IFN-β secretion by host macrophages will also be conserved between these two mycobacterial species. To test this, we generated a ΔsecA2 M. marinum strain along with complementation strains expressing either the M. marinum or M. tuberculosis secA2 genes. Our results suggest that the ΔsecA2 strain has a growth defect in vitro but not in host macrophages. These intracellular growth curves also suggested that the calculation applied to estimate the number of bacteria added to macrophage monolayers in infection assays underestimates bacterial inputs for the ΔsecA2 strain. Therefore, to better examine secreted IFN-β levels when bacterial infection levels are equal across strains we plated bacterial CFUs at 2hpi alongside our ELISA based infections. This enabled us to normalize secreted levels of IFN-β to a standard number of bacteria. Applying this approach to both WT and MAVS-/- bone marrow derived macrophages we observed equal or higher levels of secreted IFN-β from macrophages infected with the ΔsecA2 M. marinum strain as compared to WT. Together our findings suggest that activation of host Rig-I/MAVS cytosolic sensors and subsequent induction of IFN-β response in a SecA2-dependent manner is not conserved in M. marinum under the conditions tested.
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Affiliation(s)
- Lindsay G. Serene
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States of America
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, United States of America
| | - Kylie Webber
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States of America
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, United States of America
| | - Patricia A. Champion
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States of America
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, United States of America
| | - Jeffrey S. Schorey
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States of America
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, United States of America
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Shaik J, Pillay M, Jeena P. A Review Of Host-Specific Diagnostic And Surrogate Biomarkers In Children With Pulmonary Tuberculosis. Paediatr Respir Rev 2024:S1526-0542(24)00018-6. [PMID: 38521643 DOI: 10.1016/j.prrv.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 03/25/2024]
Abstract
BACKGROUND Tuberculosis (TB) is one of the most common causes of mortality globally with a steady rise in paediatric cases in the past decade. Laboratory methods of diagnosing TB and monitoring response to treatment have limitations. Current research focuses on interrogating host- and/or pathogen-specific biomarkers to address this problem. METHODS We reviewed the literature on host-specific biomarkers in TB to determine their value in diagnosis and treatment response in TB infected and HIV/TB co-infected children on anti-tuberculosis treatment. RESULTS AND CONCLUSION While no single host-specific biomarker has been identified for diagnosis or treatment responses in children, several studies suggest predictive biosignatures for disease activity. Alarmingly, current data on host-specific biomarkers for diagnosing and assessing anti-tuberculosis treatment in TB/HIV co-infected children is inadequate. Various factors affecting host-specific biomarker responses should be considered in interpreting findings and designing future studies within specific clinical settings.
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Affiliation(s)
- Junaid Shaik
- Department of Paediatrics and Child Health, School of Clinical Medicine, College of Health Sciences, University of KwaZulu-Natal, 719 Umbilo Road, Durban, 4000, South Africa; Faculty of Health Sciences, Durban University of Technology, Steve Biko Road, Berea, Durban, 4000, South Africa.
| | - Manormoney Pillay
- Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, 719 Umbilo Road, Durban, 4000, South Africa
| | - Prakash Jeena
- Department of Paediatrics and Child Health, School of Clinical Medicine, College of Health Sciences, University of KwaZulu-Natal, 719 Umbilo Road, Durban, 4000, South Africa
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Alonso-Rodríguez N, Vianello E, van Veen S, Jenum S, Tonby K, van Riessen R, Lai X, Mortensen R, Ottenhoff THM, Dyrhol-Riise AM. Whole blood RNA signatures in tuberculosis patients receiving H56:IC31 vaccine as adjunctive therapy. Front Immunol 2024; 15:1350593. [PMID: 38433842 PMCID: PMC10904528 DOI: 10.3389/fimmu.2024.1350593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 01/25/2024] [Indexed: 03/05/2024] Open
Abstract
Introduction Therapeutic vaccination in tuberculosis (TB) represents a Host Directed Therapy strategy which enhances immune responses in order to improve clinical outcomes and shorten TB treatment. Previously, we have shown that the subunit H56:IC31 vaccine induced both humoral and cellular immune responses when administered to TB patients adjunctive to standard TB treatment (TBCOX2 study, NCT02503839). Here we present the longitudinal whole blood gene expression patterns in H56:IC31 vaccinated TB patients compared to controls receiving standard TB treatment only. Methods The H56:IC31 group (N=11) and Control group (N=7) underwent first-line TB treatment for 182 days. The H56:IC31 group received 5 micrograms of the H56:IC31 vaccine (Statens Serum Institut; SSI, Valneva Austria GmbH) intramuscularly at day 84 and day 140. Total RNA was extracted from whole blood samples collected in PAXgene tubes on days 0, 84, 98, 140, 154, 182 and 238. The expression level of 183 immune-related genes was measured by high-throughput microfluidic qPCR (Biomark HD system, Standard BioTools). Results The targeted gene expression profiling unveiled the upregulation of modules such as interferon (IFN) signalling genes, pattern recognition receptors and small nucleotide guanosine triphosphate (GTP)-ases in the vaccinated group compared to controls two weeks after administration of the first H56:IC31 vaccine. Additionally, the longitudinal analysis of the Adolescent Cohort Study-Correlation of Risk (ACS-COR) signature showed a progressive downregulation in both study arms towards the end of TB treatment, in congruence with reported treatment responses and clinical improvements. Still, two months after the end of TB treatment, vaccinated patients, and especially those developing both cellular and humoral vaccine responses, showed a lower expression of the ACS-COR genes compared to controls. Discussion Our data report gene expression patterns following H56:IC31 vaccination which might be interpreted as a lower risk of relapse in therapeutically vaccinated patients. Further studies are needed to conclude if these gene expression patterns could be used as prognostic biosignatures for therapeutic TB vaccine responses.
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Affiliation(s)
| | - Eleonora Vianello
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Suzanne van Veen
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Synne Jenum
- Department of Infectious Diseases, Oslo University Hospital, Oslo, Norway
| | - Kristian Tonby
- Department of Infectious Diseases, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Rosalie van Riessen
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Xiaoran Lai
- Oslo Centre for Biostatistics and Epidemiology, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Rasmus Mortensen
- Deptartment of Infectious Disease Immunology, Statens Serum Institut, Copenhagen, Denmark
| | - Tom H. M. Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Anne Ma Dyrhol-Riise
- Department of Infectious Diseases, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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Drain PK, Dalmat RR. The elusive allure of a rapid host blood signature for tuberculosis disease. J Clin Microbiol 2024; 62:e0128923. [PMID: 38270458 PMCID: PMC10865849 DOI: 10.1128/jcm.01289-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024] Open
Abstract
A rapid host transcriptional signature cartridge could be a major advancement for tuberculosis diagnosis and treatment monitoring. In a recent study, M. Li, Y. Qiu, M. Guo, R. Qu, et al. (J Clin Microbiol 61:e00911-23, 2023, https://doi.org/10.1128/jcm.00911-23) conducted an evaluation of the Cepheid 3-gene assay (Xpert-MTB-HR) within a diagnostic case-control study in China. While the study provides a strong contribution for determining the value of the Xpert-MTB-HR assay for diagnostic accuracy and treatment response, further assay optimization and more prospective studies are necessary before adaptation into clinical practice.
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Affiliation(s)
- Paul K. Drain
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Ronit R. Dalmat
- Department of Global Health, University of Washington, Seattle, Washington, USA
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Long R, Croxen M, Lee R, Doroshenko A, Lau A, Asadi L, Heffernan C, Paulsen C, Egedahl ML, Lloyd C, Li V, Tyrrell G. The association between phylogenetic lineage and the subclinical phenotype of pulmonary tuberculosis: A retrospective 2-cohort study. J Infect 2024; 88:123-131. [PMID: 38104727 DOI: 10.1016/j.jinf.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 12/01/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
BACKGROUND Subclinical pulmonary tuberculosis (PTB) is an asymptomatic disease state between established TB infection and symptomatic (clinical) TB disease. It is present in 20-25% of PTB patients in high-income countries. Mycobacterium tuberculosis complex (MTBC) genetic heterogeneity, and differential host immunological responses, have been implicated in its pathogenesis. METHODS To determine the association between MTBC lineage and PTB disease phenotype, we used two retrospective cohorts of PTB patients in Canada and two independent lineage attribution methods (DNA fingerprinting and genome sequencing). The first cohort, Cohort 1, consisted of consecutively diagnosed PTB patients between 2014 and 2020. The second, Cohort 2, consisted of newly-arrived foreign-born PTB patients who either were or were not referred for post-landing medical surveillance between 2004 and 2017. Univariable and multivariable logistic regression models were sequentially fitted to both cohorts, adjusting for age, sex, disease type, drug resistance and HIV. Evolution of radiographic features was correlated to lineage in Cohort 2. FINDINGS Cohort 1 and 2 included 874 (209 subclinical) and 111 (44 subclinical) patients, respectively. In both cohorts, subclinical patients were more likely than clinical patients to have relapse/retreatment disease, be smear-negative, have longer times-to-culture positivity and to harbor an ancestral MTBC lineage (Indo-Oceanic or Mycobacterium africanum). Relapse/retreatment disease and ancestral MTBC lineage were independent predictors of subclinical disease (ORs and 95% CIs in Cohort 1, 1.85 [1.07,3.28], p < 0.029 and 2.30 [1.66,3.18], p < 0.001, respectively, and Cohort 2, 5.74 [1.37-24.06], p < 0.017 and 3.21 (1.29,7.97], p < 0.012, respectively). The geographic distribution of Indo-Oceanic strains causing subclinical disease was uneven. Non-progressive lung disease was more common in patients infected with ancestral than modern lineages in Cohort 2, 56.0% vs 25.4%, p < 0.005. INTERPRETATION MTBC lineage is a strong predictor of PTB disease phenotype. The genetic drivers of this association, and the relative contribution of other explanatory variables, are unknown.
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Affiliation(s)
- Richard Long
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada.
| | - Matthew Croxen
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada; Alberta Precision Laboratories, Edmonton, Alberta, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada; Women and Children's Health Research Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Robyn Lee
- Department of Medicine, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
| | - Alexander Doroshenko
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Angela Lau
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Leyla Asadi
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Courtney Heffernan
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Catherine Paulsen
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Mary Lou Egedahl
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Colin Lloyd
- Alberta Precision Laboratories, Edmonton, Alberta, Canada; Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - Vincent Li
- Alberta Precision Laboratories, Edmonton, Alberta, Canada
| | - Gregory Tyrrell
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada; Alberta Precision Laboratories, Edmonton, Alberta, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada
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Olbrich L, Verghese VP, Franckling-Smith Z, Sabi I, Ntinginya NE, Mfinanga A, Banze D, Viegas S, Khosa C, Semphere R, Nliwasa M, McHugh TD, Larsson L, Razid A, Song R, Corbett EL, Nabeta P, Trollip A, Graham SM, Hoelscher M, Geldmacher C, Zar HJ, Michael JS, Heinrich N. Diagnostic accuracy of a three-gene Mycobacterium tuberculosis host response cartridge using fingerstick blood for childhood tuberculosis: a multicentre prospective study in low-income and middle-income countries. THE LANCET. INFECTIOUS DISEASES 2024; 24:140-149. [PMID: 37918414 PMCID: PMC10808504 DOI: 10.1016/s1473-3099(23)00491-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/22/2023] [Accepted: 07/25/2023] [Indexed: 11/04/2023]
Abstract
BACKGROUND Childhood tuberculosis remains a major cause of morbidity and mortality in part due to missed diagnosis. Diagnostic methods with enhanced sensitivity using easy-to-obtain specimens are needed. We aimed to assess the diagnostic accuracy of the Cepheid Mycobacterium tuberculosis Host Response prototype cartridge (MTB-HR), a candidate test measuring a three-gene transcriptomic signature from fingerstick blood, in children with presumptive tuberculosis disease. METHODS RaPaed-TB was a prospective diagnostic accuracy study conducted at four sites in African countries (Malawi, Mozambique, South Africa, and Tanzania) and one site in India. Children younger than 15 years with presumptive pulmonary or extrapulmonary tuberculosis were enrolled between Jan 21, 2019, and June 30, 2021. MTB-HR was performed at baseline and at 1 month in all children and was repeated at 3 months and 6 months in children on tuberculosis treatment. Accuracy was compared with tuberculosis status based on standardised microbiological, radiological, and clinical data. FINDINGS 5313 potentially eligible children were screened, of whom 975 were eligible. 784 children had MTB-HR test results, of whom 639 had a diagnostic classification and were included in the analysis. MTB-HR differentiated children with culture-confirmed tuberculosis from those with unlikely tuberculosis with a sensitivity of 59·8% (95% CI 50·8-68·4). Using any microbiological confirmation (culture, Xpert MTB/RIF Ultra, or both), sensitivity was 41·6% (34·7-48·7), and using a composite clinical reference standard, sensitivity was 29·6% (25·4-34·2). Specificity for all three reference standards was 90·3% (95% CI 85·5-94·0). Performance was similar in different age groups and by malnutrition status. Among children living with HIV, accuracy against the strict reference standard tended to be lower (sensitivity 50·0%, 15·7-84·3) compared with those without HIV (61·0%, 51·6-69·9), although the difference did not reach statistical significance. Combining baseline MTB-HR result with one Ultra result identified 71·2% of children with microbiologically confirmed tuberculosis. INTERPRETATION MTB-HR showed promising diagnostic accuracy for culture-confirmed tuberculosis in this large, geographically diverse, paediatric cohort and hard-to-diagnose subgroups. FUNDING European and Developing Countries Clinical Trials Partnership, UK Medical Research Council, Swedish International Development Cooperation Agency, Bundesministerium für Bildung und Forschung; German Center for Infection Research (DZIF).
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Affiliation(s)
- Laura Olbrich
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, Munich, Germany; German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany; Fraunhofer Institute ITMP, Immunology, Infection and Pandemic Research, Munich, Germany; Oxford Vaccine Group, Department of Paediatrics and the NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Valsan P Verghese
- Pediatric Infectious Diseases, Department of Pediatrics, Christian Medical College, Vellore, India
| | - Zoe Franckling-Smith
- Department of Paediatrics and Child Health, SA-MRC Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Issa Sabi
- Mbeya Medical Research Centre, National Institute for Medical Research, Mbeya, Tanzania
| | - Nyanda E Ntinginya
- Mbeya Medical Research Centre, National Institute for Medical Research, Mbeya, Tanzania
| | - Alfred Mfinanga
- Mbeya Medical Research Centre, National Institute for Medical Research, Mbeya, Tanzania
| | - Denise Banze
- Instituto Nacional de Saúde, Marracuene, Mozambique
| | - Sofia Viegas
- Instituto Nacional de Saúde, Marracuene, Mozambique
| | - Celso Khosa
- Instituto Nacional de Saúde, Marracuene, Mozambique
| | - Robina Semphere
- Helse Nord Tuberculosis Initiative, Department of Pathology, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Marriott Nliwasa
- Helse Nord Tuberculosis Initiative, Department of Pathology, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Timothy D McHugh
- Centre for Clinical Microbiology, University College London, London, UK
| | - Leyla Larsson
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, Munich, Germany; German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Alia Razid
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, Munich, Germany; German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Rinn Song
- Oxford Vaccine Group, Department of Paediatrics and the NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Elizabeth L Corbett
- Helse Nord Tuberculosis Initiative, Department of Pathology, Kamuzu University of Health Sciences, Blantyre, Malawi; Clinical Research Department, London School of Hygiene & Tropical Medicine, London, UK
| | - Pamela Nabeta
- Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland
| | - Andre Trollip
- Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland
| | - Stephen M Graham
- Department of Paediatrics, University of Melbourne and Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, Munich, Germany; CIHLMU Center for International Health, LMU University Hospital, LMU Munich, Munich, Germany; German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany; Fraunhofer Institute ITMP, Immunology, Infection and Pandemic Research, Munich, Germany; Unit Global Health, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Neuherberg, Germany
| | - Christof Geldmacher
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, Munich, Germany; German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany; Fraunhofer Institute ITMP, Immunology, Infection and Pandemic Research, Munich, Germany
| | - Heather J Zar
- Department of Paediatrics and Child Health, SA-MRC Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | | | - Norbert Heinrich
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, Munich, Germany; CIHLMU Center for International Health, LMU University Hospital, LMU Munich, Munich, Germany; German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany; Fraunhofer Institute ITMP, Immunology, Infection and Pandemic Research, Munich, Germany.
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Corrêa RDS, Leal-Calvo T, Mafort TT, Santos AP, Leung J, Pinheiro RO, Rufino R, Moraes MO, Rodrigues LS. Reanalysis and validation of the transcriptional pleural fluid signature in pleural tuberculosis. Front Immunol 2024; 14:1256558. [PMID: 38288122 PMCID: PMC10822927 DOI: 10.3389/fimmu.2023.1256558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 12/18/2023] [Indexed: 01/31/2024] Open
Abstract
Introduction Pleural tuberculosis (PlTB), the most common site of extrapulmonary TB, is characterized by a paucibacillary nature and a compartmentalized inflammatory response in the pleural cavity, both of which make diagnosis and management extremely challenging. Although transcriptional signatures for pulmonary TB have already been described, data obtained by using this approach for extrapulmonary tuberculosis and, specifically, for pleural tuberculosis are scarce and heterogeneous. In the present study, a set of candidate genes previously described in pulmonary TB was evaluated to identify and validate a transcriptional signature in clinical samples from a Brazilian cohort of PlTB patients and those with other exudative causes of pleural effusion. Methods As a first step, target genes were selected by a random forest algorithm with recursive feature elimination (RFE) from public microarray datasets. Then, peripheral blood (PB) and pleural fluid (PF) samples from recruited patients presenting exudative pleural effusion were collected during the thoracentesis procedure. Transcriptional analysis of the selected top 10 genes was performed by quantitative RT-PCR (RT-qPCR). Results Reanalysis of the public datasets identified a set of candidate genes (CARD17, BHLHE40, FCGR1A, BATF2, STAT1, BTN3A1, ANKRD22, C1QB, GBP2, and SEPTIN4) that demonstrated a global accuracy of 89.5% in discriminating pulmonary TB cases from other respiratory diseases. Our validation cohort consisted of PlTB (n = 35) patients and non-TB (n = 34) ones. The gene expressions of CARD17, GBP2, and C1QB in PF at diagnosis were significantly different between the two (PlTB and non-TB) groups (p < 0.0001). It was observed that the gene expressions of CARD17 and GBP2 were higher in PlTB PF than in non-TB patients. C1QB showed the opposite behavior, being higher in the non-TB PF. After anti-TB therapy, however, GBP2 gene expression was significantly reduced in PlTB patients (p < 0.001). Finally, the accuracy of the three above-cited highlighted genes in the PF was analyzed, showing AUCs of 91%, 90%, and 85%, respectively. GBP2 was above 80% (sensitivity = 0.89/specificity = 0.81), and CARD17 showed significant specificity (Se = 0.69/Sp = 0.95) in its capacity to discriminate the groups. Conclusion CARD17, GBP2, and C1QB showed promise in discriminating PlTB from other causes of exudative pleural effusion by providing accurate diagnoses, thus accelerating the initiation of anti-TB therapy.
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Affiliation(s)
- Raquel da Silva Corrêa
- Laboratory of Immunopathology, Medical Sciences Faculty, Rio de Janeiro State University (FCM/UERJ), Rio de Janeiro, Brazil
| | - Thyago Leal-Calvo
- Laboratory of Leprosy, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (IOC/FIOCRUZ), Rio de Janeiro, Brazil
| | - Thiago Thomaz Mafort
- Department of Pulmonary Care, Pedro Ernesto University Hospital, Rio de Janeiro State University (HUPE/UERJ), Rio de Janeiro, Brazil
| | - Ana Paula Santos
- Department of Pulmonary Care, Pedro Ernesto University Hospital, Rio de Janeiro State University (HUPE/UERJ), Rio de Janeiro, Brazil
| | - Janaína Leung
- Department of Pulmonary Care, Pedro Ernesto University Hospital, Rio de Janeiro State University (HUPE/UERJ), Rio de Janeiro, Brazil
| | - Roberta Olmo Pinheiro
- Laboratory of Leprosy, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (IOC/FIOCRUZ), Rio de Janeiro, Brazil
| | - Rogério Rufino
- Department of Pulmonary Care, Pedro Ernesto University Hospital, Rio de Janeiro State University (HUPE/UERJ), Rio de Janeiro, Brazil
| | - Milton Ozório Moraes
- Laboratory of Leprosy, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (IOC/FIOCRUZ), Rio de Janeiro, Brazil
| | - Luciana Silva Rodrigues
- Laboratory of Immunopathology, Medical Sciences Faculty, Rio de Janeiro State University (FCM/UERJ), Rio de Janeiro, Brazil
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Amaral EP, Namasivayam S, Queiroz ATL, Fukutani E, Hilligan KL, Aberman K, Fisher L, Bomfim CCB, Kauffman K, Buchanan J, Santuo L, Gazzinelli-Guimaraes PH, Costa DL, Teixeira MA, Barreto-Duarte B, Rocha CG, Santana MF, Cordeiro-Santos M, Barber DL, Wilkinson RJ, Kramnik I, Igarashi K, Scriba T, Mayer-Barber KD, Andrade BB, Sher A. BACH1 promotes tissue necrosis and Mycobacterium tuberculosis susceptibility. Nat Microbiol 2024; 9:120-135. [PMID: 38066332 PMCID: PMC10769877 DOI: 10.1038/s41564-023-01523-7] [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: 02/26/2023] [Accepted: 10/11/2023] [Indexed: 01/07/2024]
Abstract
Oxidative stress triggers ferroptosis, a form of cellular necrosis characterized by iron-dependent lipid peroxidation, and has been implicated in Mycobacterium tuberculosis (Mtb) pathogenesis. We investigated whether Bach1, a transcription factor that represses multiple antioxidant genes, regulates host resistance to Mtb. We found that BACH1 expression is associated clinically with active pulmonary tuberculosis. Bach1 deletion in Mtb-infected mice increased glutathione levels and Gpx4 expression that inhibit lipid peroxidation. Bach1-/- macrophages exhibited increased resistance to Mtb-induced cell death, while Mtb-infected Bach1-deficient mice displayed reduced bacterial loads, pulmonary necrosis and lipid peroxidation concurrent with increased survival. Single-cell RNA-seq analysis of lungs from Mtb-infected Bach1-/- mice revealed an enrichment of genes associated with ferroptosis suppression. Bach1 depletion in Mtb-infected B6.Sst1S mice that display human-like necrotic lung pathology also markedly reduced necrosis and increased host resistance. These findings identify Bach1 as a key regulator of cellular and tissue necrosis and host resistance in Mtb infection.
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Affiliation(s)
- Eduardo P Amaral
- Immunobiology Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD, USA.
| | | | - Artur T L Queiroz
- Laboratório de Inflamação e Biomarcadores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Bahia, Brazil
| | - Eduardo Fukutani
- Laboratório de Inflamação e Biomarcadores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Bahia, Brazil
| | - Kerry L Hilligan
- Immunobiology Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD, USA
| | - Kate Aberman
- Immunobiology Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD, USA
| | - Logan Fisher
- Immunobiology Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine Graduate School of Medical Sciences, New York, NY, USA
| | - Caio Cesar B Bomfim
- Immunobiology Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD, USA
| | - Keith Kauffman
- T lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Jay Buchanan
- T lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Leslie Santuo
- T lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Pedro Henrique Gazzinelli-Guimaraes
- Helminth Immunology Section, Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Diego L Costa
- Immunobiology Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD, USA
- Departmento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- Programa de Pós-Graduação em Imunologia Básica e Aplicada, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Mariane Araujo Teixeira
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Salvador, Brazil
| | - Beatriz Barreto-Duarte
- Laboratório de Inflamação e Biomarcadores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Bahia, Brazil
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Salvador, Brazil
- Curso de Medicina, Universidade Salvador (UNIFACS), Laureate Universities, Salvador, Bahia, Brazil
| | - Clarissa Gurgel Rocha
- Department of Pathology, School of Medicine of the Federal University of Bahia, Salvador, Bahia, Brazil
- Center for Biotechnology and Cell Therapy, D'Or Institute for Research and Education (IDOR), Sao Rafael Hospital, Salvador, Bahia, Brazil
| | - Monique Freire Santana
- Departmento de Ensino e Pesquisa, Fundação Centro de Controle de Oncologia do Estado do Amazonas-FCECON, Manaus, Amazonas, Brazil
- Fundação Medicina Tropical Doutor Heitor Vieira Dourado, Manaus, Amazonas, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas, Manaus, Amazonas, Brazil
| | - Marcelo Cordeiro-Santos
- Fundação Medicina Tropical Doutor Heitor Vieira Dourado, Manaus, Amazonas, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas, Manaus, Amazonas, Brazil
- Faculdade de Medicina, Universidade Nilton Lins, Manaus, Amazonas, Brazil
| | - Daniel L Barber
- T lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Robert J Wilkinson
- Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- The Francis Crick Institute, London, UK
- Department of Infectious Disease, Imperial College London, London, UK
| | - Igor Kramnik
- Boston University School of Medicine, Boston, MA, USA
| | - Kazuhiko Igarashi
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Thomas Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Katrin D Mayer-Barber
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD, USA
| | - Bruno B Andrade
- Laboratório de Inflamação e Biomarcadores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Bahia, Brazil
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Salvador, Brazil
- Curso de Medicina, Universidade Salvador (UNIFACS), Laureate Universities, Salvador, Bahia, Brazil
- Department of Pathology, School of Medicine of the Federal University of Bahia, Salvador, Bahia, Brazil
- Curso de Medicina, Escola Bahiana de Medicina e Saúde Pública, Salvador, Bahia, Brazil
- Faculdade de Medicina, Universidade Federal da Bahia, Salvador, Bahia, Brazil
- Curso de Medicina, Universidade Faculdade de Tecnologia e Ciências (UniFTC), Salvador, Bahia, Brazil
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Alan Sher
- Immunobiology Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD, USA.
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Mai D, Jahn A, Murray T, Morikubo M, Lim PN, Cervantes MM, Pham LK, Nemeth J, Urdahl K, Diercks AH, Aderem A, Rothchild AC. Exposure to Mycobacterium remodels alveolar macrophages and the early innate response to Mycobacterium tuberculosis infection. PLoS Pathog 2024; 20:e1011871. [PMID: 38236787 PMCID: PMC10796046 DOI: 10.1371/journal.ppat.1011871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/27/2023] [Indexed: 01/22/2024] Open
Abstract
Alveolar macrophages (AMs) play a critical role during Mycobacterium tuberculosis (Mtb) infection as the first cells in the lung to encounter bacteria. We previously showed that AMs initially respond to Mtb in vivo by mounting a cell-protective, rather than pro-inflammatory response. However, the plasticity of the initial AM response was unknown. Here, we characterize how previous exposure to Mycobacterium, either through subcutaneous vaccination with Mycobacterium bovis (scBCG) or through a contained Mtb infection (coMtb) that mimics aspects of concomitant immunity, impacts the initial response by AMs. We find that both scBCG and coMtb accelerate early innate cell activation and recruitment and generate a stronger pro-inflammatory response to Mtb in vivo by AMs. Within the lung environment, AMs from scBCG vaccinated mice mount a robust interferon-associated response, while AMs from coMtb mice produce a broader inflammatory response that is not dominated by Interferon Stimulated Genes. Using scRNAseq, we identify changes to the frequency and phenotype of airway-resident macrophages following Mycobacterium exposure, with enrichment for both interferon-associated and pro-inflammatory populations of AMs. In contrast, minimal changes were found for airway-resident T cells and dendritic cells after exposures. Ex vivo stimulation of AMs with Pam3Cys, LPS and Mtb reveal that scBCG and coMtb exposures generate stronger interferon-associated responses to LPS and Mtb that are cell-intrinsic changes. However, AM profiles that were unique to each exposure modality following Mtb infection in vivo are dependent on the lung environment and do not emerge following ex vivo stimulation. Overall, our studies reveal significant and durable remodeling of AMs following exposure to Mycobacterium, with evidence for both AM-intrinsic changes and contributions from the altered lung microenvironments. Comparisons between the scBCG and coMtb models highlight the plasticity of AMs in the airway and opportunities to target their function through vaccination or host-directed therapies.
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Affiliation(s)
- Dat Mai
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Ana Jahn
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Tara Murray
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Michael Morikubo
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Pamelia N. Lim
- Department of Veterinary and Animal Sciences, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
| | - Maritza M. Cervantes
- Department of Veterinary and Animal Sciences, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
| | - Linh K. Pham
- Department of Veterinary and Animal Sciences, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
- Animal Biotechnology and Biomedical Sciences Graduate Program, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
| | - Johannes Nemeth
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Kevin Urdahl
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Alan H. Diercks
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Alan Aderem
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Alissa C. Rothchild
- Department of Veterinary and Animal Sciences, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
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Silver RF, Xia M, Storer CE, Jarvela JR, Moyer MC, Blazevic A, Stoeckel DA, Rakey EK, Tennant JM, Goll JB, Head RD, Hoft DF. Distinct gene expression signatures comparing latent tuberculosis infection with different routes of Bacillus Calmette-Guérin vaccination. Nat Commun 2023; 14:8507. [PMID: 38129388 PMCID: PMC10739751 DOI: 10.1038/s41467-023-44136-8] [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: 12/17/2022] [Accepted: 12/01/2023] [Indexed: 12/23/2023] Open
Abstract
Tuberculosis remains an international health threat partly because of limited protection from pulmonary tuberculosis provided by standard intradermal vaccination with Bacillus of Calmette and Guérin (BCG); this may reflect the inability of intradermal vaccination to optimally induce pulmonary immunity. In contrast, respiratory Mycobacterium tuberculosis infection usually results in the immune-mediated bacillary containment of latent tuberculosis infection (LTBI). Here we present RNA-Seq-based assessments of systemic and pulmonary immune cells from LTBI participants and recipients of intradermal and oral BCG. LTBI individuals uniquely display ongoing immune activation and robust CD4 T cell recall responses in blood and lung. Intradermal BCG is associated with robust systemic immunity but only limited pulmonary immunity. Conversely, oral BCG induces limited systemic immunity but distinct pulmonary responses including enhanced inflammasome activation potentially associated with mucosal-associated invariant T cells. Further, IL-9 is identified as a component of systemic immunity in LTBI and intradermal BCG, and pulmonary immunity following oral BCG.
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Affiliation(s)
- Richard F Silver
- Division of Pulmonary, Critical Care and Sleep Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
- Pulmonary and Critical Care Medicine, The Louis Stokes Cleveland Department of Veterans' Affairs Medical Center, Cleveland, OH, USA.
| | - Mei Xia
- Division of Infectious Diseases, Allergy & Immunology, Saint Louis University School of Medicine, St. Louis, MO, USA
- Center for Vaccine Development, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Chad E Storer
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Jessica R Jarvela
- Division of Pulmonary, Critical Care and Sleep Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Pulmonary and Critical Care Medicine, The Louis Stokes Cleveland Department of Veterans' Affairs Medical Center, Cleveland, OH, USA
| | - Michelle C Moyer
- Division of Pulmonary, Critical Care and Sleep Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Pulmonary and Critical Care Medicine, The Louis Stokes Cleveland Department of Veterans' Affairs Medical Center, Cleveland, OH, USA
| | - Azra Blazevic
- Division of Infectious Diseases, Allergy & Immunology, Saint Louis University School of Medicine, St. Louis, MO, USA
- Center for Vaccine Development, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - David A Stoeckel
- Division of Pulmonary, Critical Care and Sleep Medicine, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Erin K Rakey
- Division of Pulmonary, Critical Care and Sleep Medicine, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Jan M Tennant
- Division of Infectious Diseases, Allergy & Immunology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | | | - Richard D Head
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Daniel F Hoft
- Division of Infectious Diseases, Allergy & Immunology, Saint Louis University School of Medicine, St. Louis, MO, USA.
- Center for Vaccine Development, Saint Louis University School of Medicine, St. Louis, MO, USA.
- Department of Molecular Microbiology & Immunology Saint Louis University School of Medicine, St. Louis, MO, USA.
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44
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Mutua F, Su RC, Mesa C, Lopez C, Ball TB, Kiazyk S. Type I interferons and Mycobacterium tuberculosis whole cell lysate induce distinct transcriptional responses in M. tuberculosis infection. Tuberculosis (Edinb) 2023; 143:102409. [PMID: 37729851 DOI: 10.1016/j.tube.2023.102409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/06/2023] [Accepted: 09/11/2023] [Indexed: 09/22/2023]
Abstract
Type I interferon (IFN)-induced genes have the potential for distinguishing active tuberculosis (ATB) from latent TB infection (LTBI) and healthy controls (HC), monitoring treatment, and detection of individuals at risk of progression to active disease. We examined the differential effects of IFN-α, IFN-β and Mycobacterium tuberculosis whole cell lysate (Mtb WCL) stimulation on the expression of selected IFN-stimulated genes in peripheral blood mononuclear cells from individuals with either LTBI, ATB, and healthy controls. Stimulation with IFN-α and IFN-β induced a higher expression of the interrogated genes while Mtb WCL stimulation induced expression similar to that observed at baseline, with the exception of IL-1A and IL-1B genes that were downregulated. The expression of IFN-α-induced FCGR1A gene, IFN-β-induced FCGR1A, FCGR1B, and SOCS3 genes, and Mtb WCL-induced IFI44, IFI44L, IFIT1, and IFITM3 genes differed significantly between LTBI and ATB. These findings suggest stimulation-driven gene expression patterns could potentially discriminate LTBI and ATB. Mechanistic studies are necessary to define the processes through which distinct type I IFNs and downstream ISGs determine infection outcomes and identify potential host-directed therapeutic strategies.
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Affiliation(s)
- Florence Mutua
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Canada; Department of Medical Microbiology and Immunology, Kenyatta National Hospital Campus, University of Nairobi, Kenya
| | - Ruey-Chyi Su
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Canada; JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Canada
| | - Christine Mesa
- JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Canada
| | - Carmen Lopez
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Canada; JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Canada
| | - T Blake Ball
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Canada; JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Canada
| | - Sandra Kiazyk
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Canada; JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Canada.
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45
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Kaufmann SHE. Vaccine development against tuberculosis before and after Covid-19. Front Immunol 2023; 14:1273938. [PMID: 38035095 PMCID: PMC10684952 DOI: 10.3389/fimmu.2023.1273938] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 10/16/2023] [Indexed: 12/02/2023] Open
Abstract
Coronavirus disease (Covid-19) has not only shaped awareness of the impact of infectious diseases on global health. It has also provided instructive lessons for better prevention strategies against new and current infectious diseases of major importance. Tuberculosis (TB) is a major current health threat caused by Mycobacterium tuberculosis (Mtb) which has claimed more lives than any other pathogen over the last few centuries. Hence, better intervention measures, notably novel vaccines, are urgently needed to accomplish the goal of the World Health Organization to end TB by 2030. This article describes how the research and development of TB vaccines can benefit from recent developments in the Covid-19 vaccine pipeline from research to clinical development and outlines how the field of TB research can pursue its own approaches. It begins with a brief discussion of major vaccine platforms in general terms followed by a short description of the most widely applied Covid-19 vaccines. Next, different vaccination regimes and particular hurdles for TB vaccine research and development are described. This specifically considers the complex immune mechanisms underlying protection and pathology in TB which involve innate as well as acquired immune mechanisms and strongly depend on fine tuning the response. A brief description of the TB vaccine candidates that have entered clinical trials follows. Finally, it discusses how experiences from Covid-19 vaccine research, development, and rollout can and have been applied to the TB vaccine pipeline, emphasizing similarities and dissimilarities.
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Affiliation(s)
- Stefan H. E. Kaufmann
- Max Planck Institute for Infection Biology, Berlin, Germany
- Systems Immunology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Hagler Institute for Advanced Study, Texas A&M University, College Station, TX, United States
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Wang L, Ma H, Wen Z, Niu L, Chen X, Liu H, Zhang S, Xu J, Zhu Y, Li H, Chen H, Shi L, Wan L, Li L, Li M, Wong KW, Song Y. Single-cell RNA-sequencing reveals heterogeneity and intercellular crosstalk in human tuberculosis lung. J Infect 2023; 87:373-384. [PMID: 37690670 DOI: 10.1016/j.jinf.2023.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 08/21/2023] [Accepted: 09/06/2023] [Indexed: 09/12/2023]
Abstract
Lung inflammation indicated by 18F-labeled fluorodeoxyglucose (FDG) in patients with tuberculosis is associated with disease severity and relapse risk upon treatment completion. We revealed the heterogeneity and intercellular crosstalk in lung tissues with 18F-FDG avidity and adjacent uninvolved tissues from 6 tuberculosis patients by single-cell RNA-sequencing. Tuberculous lungs had an influx of regulatory T cells (Treg), exhausted CD8 T cells, immunosuppressive myeloid cells, conventional DC, plasmacytoid DC, and neutrophils. Immune cells in inflamed lungs showed general up-regulation of ATP synthesis and interferon-mediated signaling. Immunosuppressive myeloid and Treg cells strongly displayed transcriptions of genes related to tuberculosis disease progression. Intensive crosstalk between IL4I1-expressing myeloid cells and Treg cells involving chemokines, costimulatory molecules, and immune checkpoints, some of which are specific in 18F-FDG-avid lungs, were found. Our analysis provides insights into the transcriptomic heterogeneity and cellular crosstalk in pulmonary tuberculosis and guides unveiling cellular and molecular targets for tuberculosis therapy.
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Affiliation(s)
- Lin Wang
- Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Shanghai, China
| | - Hui Ma
- Department of Scientific Research, Shanghai Public Health Clinical Center, Shanghai, China
| | - Zilu Wen
- Department of Scientific Research, Shanghai Public Health Clinical Center, Shanghai, China
| | - Liangfei Niu
- Department of Scientific Research, Shanghai Public Health Clinical Center, Shanghai, China
| | - Xinchun Chen
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, Shenzhen University School of Medicine, Shenzhen, China
| | - Haiying Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shulin Zhang
- Department of Scientific Research, Shanghai Public Health Clinical Center, Shanghai, China
| | - Jianqing Xu
- Department of Scientific Research, Shanghai Public Health Clinical Center, Shanghai, China
| | - Yijun Zhu
- Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Shanghai, China
| | - Hongwei Li
- Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Shanghai, China
| | - Hui Chen
- Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Shanghai, China
| | - Lei Shi
- Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Shanghai, China
| | - Laiyi Wan
- Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Shanghai, China
| | - Leilei Li
- Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Shanghai, China
| | - Meiyi Li
- Fudan Zhangjiang Institute, Fudan University, Shanghai, China.
| | - Ka-Wing Wong
- Department of Scientific Research, Shanghai Public Health Clinical Center, Shanghai, China.
| | - Yanzheng Song
- Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Shanghai, China.
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Bobba S, Howard NC, Das S, Ahmed M, Tang L, Thirunavukkarasu S, Larsen MH, Mathema B, Divangahi M, Khader SA. Mycobacterium tuberculosis carrying the rifampicin drug-resistance-conferring rpoB mutation H445Y is associated with suppressed immunity through type I interferons. mBio 2023; 14:e0094623. [PMID: 37682004 PMCID: PMC10653897 DOI: 10.1128/mbio.00946-23] [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: 05/08/2023] [Accepted: 06/22/2023] [Indexed: 09/09/2023] Open
Abstract
IMPORTANCE This study highlights the impact of specific rifampicin-resistance-conferring mutations on the host immune response to Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB). Clinical reports have previously suggested that multi-drug-resistant) TB patients exhibit altered peripheral immune responses as compared with their drug-sensitive TB counterparts. The murine model of infection with Mtb strains carrying drug-resistance-conferring mutations recapitulated these findings and allowed us to mechanistically interrogate the pathways responsible for driving the divergent immune responses. Our findings underscore the need for greater investigation into bacterial heterogeneity to better appreciate the diversity in host-pathogen interactions during TB disease.
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Affiliation(s)
- Suhas Bobba
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Nicole C. Howard
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Shibali Das
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Mushtaq Ahmed
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
| | - Linrui Tang
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, New York, USA
| | - Shyamala Thirunavukkarasu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Michelle H. Larsen
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Barun Mathema
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, New York, USA
| | - Maziar Divangahi
- Meakins-Christie Laboratories, Department of Medicine, McGill University, Montreal, Quebec, Canada
- Department of Microbiology and Immunology, McGill International TB Centre, Montreal, Quebec, Canada
- Department of Pathology, McGill University Health Centre, Montreal, Quebec, Canada
| | - Shabaana A. Khader
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
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48
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Cornell TR, Jobe D, Donkor S, Wootton DG, Pinchbeck G, Sutherland JS, Scantlebury CE. Histoplasma Seropositivity in TB Patients in The Gambia: Evidence to Drive Research on a High-Priority Fungal Pathogen. Open Forum Infect Dis 2023; 10:ofad510. [PMID: 37901120 PMCID: PMC10603589 DOI: 10.1093/ofid/ofad510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 10/11/2023] [Indexed: 10/31/2023] Open
Abstract
Background Inclusion of Histoplasma in the World Health Organization's first Fungal Priority Pathogens List under "high-priority" fungal species highlights the need for robust surveillance of Histoplasma spp. in endemic and underrepresented regions. Despite increasing reports of histoplasmosis in Africa, data on the burden of this fungal disease are sparse in The Gambia. This baseline study examined the human seroprevalence of anti-Histoplasma antibody in a TB patient group in The Gambia, explored associations between seropositivity and demographic and clinical variables, and proposes future research directions. Methods Biobanked plasma samples were selected from active TB cases with variable HIV infection status. Latex agglutination tests were performed on samples from 52 study participants to detect the presence of anti-Histoplasma antibodies. Potential risk factors for Histoplasma exposure were explored using logistic regression analysis. Results The sample seroprevalence of anti-Histoplasma antibody was 28.8% (n = 15/52; 95% CI, 17.1%-43.1%). Multivariable logistic regression analysis identified a statistically significant association between Histoplasma seropositivity and age (odds ratio, 0.91; 95% CI, 0.84-0.98; P = .008). Conclusions This baseline study provides evidence of Histoplasma seropositivity in TB patients in The Gambia and explores risk factors for exposure. The small sample size and use of the LAT in TB and HIV-positive patient groups are significant study limitations. Future research directions are proposed to ascertain the burden of Histoplasma in general and patient populations and explore the context-specific risk factors for exposure and infection in The Gambia.
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Affiliation(s)
- Tessa R Cornell
- Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, UK
| | - Dawda Jobe
- Vaccines and Immunity Theme, MRC Unit The Gambia, London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Simon Donkor
- Vaccines and Immunity Theme, MRC Unit The Gambia, London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Daniel G Wootton
- Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Diseases, University of Liverpool, Liverpool, UK
| | - Gina Pinchbeck
- Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, UK
| | - Jayne S Sutherland
- Vaccines and Immunity Theme, MRC Unit The Gambia, London School of Hygiene and Tropical Medicine, Fajara, The Gambia
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49
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Mayer-Barber KD. Granulocytes subsets and their divergent functions in host resistance to Mycobacterium tuberculosis - a 'tipping-point' model of disease exacerbation. Curr Opin Immunol 2023; 84:102365. [PMID: 37437471 PMCID: PMC10543468 DOI: 10.1016/j.coi.2023.102365] [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: 04/01/2023] [Revised: 05/29/2023] [Accepted: 06/14/2023] [Indexed: 07/14/2023]
Abstract
Granulocytes are innate immune effector cells with essential functions in host resistance to bacterial infections. I will discuss emerging evidence that during Mycobacterium tuberculosis infection, counter-intuitively, eosinophils are host-protective while neutrophils are host detrimental. Additionally, I will propose a 'tipping-point' model in which neutrophils are an integral part of a feedforward loop driving tuberculosis disease exacerbation.
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Affiliation(s)
- Katrin D Mayer-Barber
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, 20892, USA.
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50
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Gao Y, Sun F. Batch normalization followed by merging is powerful for phenotype prediction integrating multiple heterogeneous studies. PLoS Comput Biol 2023; 19:e1010608. [PMID: 37844077 PMCID: PMC10602384 DOI: 10.1371/journal.pcbi.1010608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/26/2023] [Accepted: 09/30/2023] [Indexed: 10/18/2023] Open
Abstract
Heterogeneity in different genomic studies compromises the performance of machine learning models in cross-study phenotype predictions. Overcoming heterogeneity when incorporating different studies in terms of phenotype prediction is a challenging and critical step for developing machine learning algorithms with reproducible prediction performance on independent datasets. We investigated the best approaches to integrate different studies of the same type of omics data under a variety of different heterogeneities. We developed a comprehensive workflow to simulate a variety of different types of heterogeneity and evaluate the performances of different integration methods together with batch normalization by using ComBat. We also demonstrated the results through realistic applications on six colorectal cancer (CRC) metagenomic studies and six tuberculosis (TB) gene expression studies, respectively. We showed that heterogeneity in different genomic studies can markedly negatively impact the machine learning classifier's reproducibility. ComBat normalization improved the prediction performance of machine learning classifier when heterogeneous populations are present, and could successfully remove batch effects within the same population. We also showed that the machine learning classifier's prediction accuracy can be markedly decreased as the underlying disease model became more different in training and test populations. Comparing different merging and integration methods, we found that merging and integration methods can outperform each other in different scenarios. In the realistic applications, we observed that the prediction accuracy improved when applying ComBat normalization with merging or integration methods in both CRC and TB studies. We illustrated that batch normalization is essential for mitigating both population differences of different studies and batch effects. We also showed that both merging strategy and integration methods can achieve good performances when combined with batch normalization. In addition, we explored the potential of boosting phenotype prediction performance by rank aggregation methods and showed that rank aggregation methods had similar performance as other ensemble learning approaches.
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Affiliation(s)
- Yilin Gao
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Fengzhu Sun
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California, United States of America
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