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Vinhaes CL, Fukutani ER, Santana GC, Arriaga MB, Barreto-Duarte B, Araújo-Pereira M, Maggitti-Bezerril M, Andrade AM, Figueiredo MC, Milne GL, Rolla VC, Kristki AL, Cordeiro-Santos M, Sterling TR, Andrade BB, Queiroz AT. An integrative multi-omics approach to characterize interactions between tuberculosis and diabetes mellitus. iScience 2024; 27:109135. [PMID: 38380250 PMCID: PMC10877940 DOI: 10.1016/j.isci.2024.109135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 01/02/2024] [Accepted: 02/01/2024] [Indexed: 02/22/2024] Open
Abstract
Tuberculosis-diabetes mellitus (TB-DM) is linked to a distinct inflammatory profile, which can be assessed using multi-omics analyses. Here, a machine learning algorithm was applied to multi-platform data, including cytokines and gene expression in peripheral blood and eicosanoids in urine, in a Brazilian multi-center TB cohort. There were four clinical groups: TB-DM(n = 24), TB only(n = 28), DM(HbA1c ≥ 6.5%) only(n = 11), and a control group of close TB contacts who did not have TB or DM(n = 13). After cross-validation, baseline expression or abundance of MMP-28, LTE-4, 11-dTxB2, PGDM, FBXO6, SECTM1, and LINCO2009 differentiated the four patient groups. A distinct multi-omic-derived, dimensionally reduced, signature was associated with TB, regardless of glycemic status. SECTM1 and FBXO6 mRNA levels were positively correlated with sputum acid-fast bacilli grade in TB-DM. Values of the biomarkers decreased during the course of anti-TB therapy. Our study identified several markers associated with the pathophysiology of TB-DM that could be evaluated in future mechanistic investigations.
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Affiliation(s)
- Caian L. Vinhaes
- Laboratório de Pesquisa Clínica e Translacional, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Salvador 41810-710, Brazil
- Programa de Pós-Graduação em Medicina e Saúde Humana, Escola Bahiana de Medicina e Saúde Pública (EBMSP), Salvador 40290-150, Brazil
- Departamento de Infectologia, Hospital Português da Bahia, Salvador 40140-901, Brazil
- Instituto de Pesquisa Clínica e Translacional, Faculdade de Tecnologia e Ciências, Salvador 41741-590, Brazil
| | - Eduardo R. Fukutani
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Salvador 41810-710, Brazil
- Instituto de Pesquisa Clínica e Translacional, Faculdade de Tecnologia e Ciências, Salvador 41741-590, Brazil
- Centro de Integração de Dados e Conhecimentos para Saúde, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
| | - Gabriel C. Santana
- Laboratório de Pesquisa Clínica e Translacional, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Salvador 41810-710, Brazil
- Curso de Medicina, Universidade Salvador, Salvador, Brazil
| | - María B. Arriaga
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Beatriz Barreto-Duarte
- Laboratório de Pesquisa Clínica e Translacional, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Salvador 41810-710, Brazil
- Instituto de Pesquisa Clínica e Translacional, Faculdade de Tecnologia e Ciências, Salvador 41741-590, Brazil
- Curso de Medicina, Universidade Salvador, Salvador, Brazil
- Programa Acadêmico de Tuberculose. Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mariana Araújo-Pereira
- Laboratório de Pesquisa Clínica e Translacional, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Salvador 41810-710, Brazil
- Instituto de Pesquisa Clínica e Translacional, Faculdade de Tecnologia e Ciências, Salvador 41741-590, Brazil
- Faculdade de Medicina, Univerdidade Federal da Bahia, Salvador, Brazil
| | - Mateus Maggitti-Bezerril
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Salvador 41810-710, Brazil
- Instituto de Pesquisa Clínica e Translacional, Faculdade de Tecnologia e Ciências, Salvador 41741-590, Brazil
| | - Alice M.S. Andrade
- Laboratório de Pesquisa Clínica e Translacional, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Salvador 41810-710, Brazil
- Instituto de Pesquisa Clínica e Translacional, Faculdade de Tecnologia e Ciências, Salvador 41741-590, Brazil
| | - Marina C. Figueiredo
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ginger L. Milne
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Valeria C. Rolla
- Instituto Nacional de Infectologia Evandro Chagas, Fiocruz, Rio de Janeiro, Brazil
| | - Afrânio L. Kristki
- Programa Acadêmico de Tuberculose. Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcelo Cordeiro-Santos
- Fundação Medicina Tropical Doutor Heitor Vieira Dourado, Manaus, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas, Manaus, Brazil
- Universidade Nilton Lins, Manaus, Brazil
| | - Timothy R. Sterling
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bruno B. Andrade
- Laboratório de Pesquisa Clínica e Translacional, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Salvador 41810-710, Brazil
- Programa de Pós-Graduação em Medicina e Saúde Humana, Escola Bahiana de Medicina e Saúde Pública (EBMSP), Salvador 40290-150, Brazil
- Instituto de Pesquisa Clínica e Translacional, Faculdade de Tecnologia e Ciências, Salvador 41741-590, Brazil
- Curso de Medicina, Universidade Salvador, Salvador, Brazil
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Faculdade de Medicina, Univerdidade Federal da Bahia, Salvador, Brazil
| | - Artur T.L. Queiroz
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Salvador 41810-710, Brazil
- Instituto de Pesquisa Clínica e Translacional, Faculdade de Tecnologia e Ciências, Salvador 41741-590, Brazil
- Centro de Integração de Dados e Conhecimentos para Saúde, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
| | - for the RePORT Brazil Consortium
- Laboratório de Pesquisa Clínica e Translacional, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Salvador 41810-710, Brazil
- Programa de Pós-Graduação em Medicina e Saúde Humana, Escola Bahiana de Medicina e Saúde Pública (EBMSP), Salvador 40290-150, Brazil
- Departamento de Infectologia, Hospital Português da Bahia, Salvador 40140-901, Brazil
- Instituto de Pesquisa Clínica e Translacional, Faculdade de Tecnologia e Ciências, Salvador 41741-590, Brazil
- Centro de Integração de Dados e Conhecimentos para Saúde, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
- Curso de Medicina, Universidade Salvador, Salvador, Brazil
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Programa Acadêmico de Tuberculose. Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Faculdade de Medicina, Univerdidade Federal da Bahia, Salvador, Brazil
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
- Instituto Nacional de Infectologia Evandro Chagas, Fiocruz, Rio de Janeiro, Brazil
- Fundação Medicina Tropical Doutor Heitor Vieira Dourado, Manaus, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas, Manaus, Brazil
- Universidade Nilton Lins, Manaus, Brazil
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Li A, Bao J, Gao S, He Y, Nie X, Hosyanto FF, He X, Li T, Xu L. MicroRNA hsa-miR-320a-3p and Its Targeted mRNA FKBP5 Were Differentially Expressed in Patients with HIV/TB Co-Infection. ACS Infect Dis 2023; 9:1742-1753. [PMID: 37624586 DOI: 10.1021/acsinfecdis.3c00211] [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] [Indexed: 08/26/2023]
Abstract
Among the PLWH (people living with HIV) population, the risk of developing active tuberculosis (TB) is increasing. Active TB also accelerates the deterioration of PLWH's immune function and is one of the leading causes of death in the PLWH population. So far, accurate diagnosis of active TB in the PLWH population remains challenging. Through data analysis of HIV/TB co-infection in the GEO database, the differentially expressed genes as well as their related microRNA (miRNA) were acquired and were further verified through clinical blood samples. Dual-luciferase assay was used to verify the mechanism of miRNA on mRNA. The enrichment of immune cells in database patient samples was analyzed by bioinformatics and finally verified by blood routine data. Our study found that FKBP5 (FK506 binding protein 5) was highly expressed in the HIV/TB co-infection group; hsa-miR-320a-3p was highly expressed in the HIV infection group but decreased in the HIV/TB co-infection group. Dual-luciferase assay results showed that hsa-miR-320a-3p mimics significantly reduced the relative luciferase activity of the WT-FKBP5 group; however, this phenomenon was not observed in the MUT-FKBP5 group. At the same time, as a key molecule of the immune-related pathway, FKBP5 is highly correlated with the amount of neutrophils, which provides a new suggestion for the treatment of the HIV/TB co-infection population. Our study found that hsa-miR-320a-3p can decrease FKBP5 expression, suggesting a potential regulatory role for FKBP5. The involvement of FKBP5 and its related molecule hsa-miR-320a-3p in HIV/TB co-infection proposes them as potential biomarkers for the diagnosis of active TB in the PLWH population.
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Affiliation(s)
- Anlong Li
- Department of Pathogenic Biology, School of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Jiajia Bao
- Department of Pathogenic Biology, School of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
- Hospital-Acquired Infection Control Department, First People's Hospital of Jintang County, Chengdu 610400, China
| | - Sijia Gao
- Department of Pathogenic Biology, School of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Ying He
- Central Laboratory, Chongqing Public Health Medical Center, Southwest University Public Health Hospital, Chongqing 400036, China
| | - Xiaoping Nie
- Central Laboratory, Chongqing Public Health Medical Center, Southwest University Public Health Hospital, Chongqing 400036, China
| | | | - Xintong He
- Department of Pathogenic Biology, School of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Tongxin Li
- Central Laboratory, Chongqing Public Health Medical Center, Southwest University Public Health Hospital, Chongqing 400036, China
| | - Lei Xu
- Department of Pathogenic Biology, School of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
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3
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Yu Y, Jiang XX, Li JC. Biomarker discovery for tuberculosis using metabolomics. Front Mol Biosci 2023; 10:1099654. [PMID: 36891238 PMCID: PMC9986447 DOI: 10.3389/fmolb.2023.1099654] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 02/06/2023] [Indexed: 02/22/2023] Open
Abstract
Tuberculosis (TB) is the leading cause of death among infectious diseases, and the ratio of cases in which its pathogen Mycobacterium tuberculosis (Mtb) is drug resistant has been increasing worldwide, whereas latent tuberculosis infection (LTBI) may develop into active TB. Thus it is important to understand the mechanism of drug resistance, find new drugs, and find biomarkers for TB diagnosis. The rapid progress of metabolomics has enabled quantitative metabolite profiling of both the host and the pathogen. In this context, we provide recent progress in the application of metabolomics toward biomarker discovery for tuberculosis. In particular, we first focus on biomarkers based on blood or other body fluids for diagnosing active TB, identifying LTBI and predicting the risk of developing active TB, as well as monitoring the effectiveness of anti-TB drugs. Then we discuss the pathogen-based biomarker research for identifying drug resistant TB. While there have been many reports of potential candidate biomarkers, validations and clinical testing as well as improved bioinformatics analysis are needed to further substantiate and select key biomarkers before they can be made clinically applicable.
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Affiliation(s)
- Yi Yu
- Center for Analyses and Measurements, College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, China
| | - Xin-Xin Jiang
- Clinical Research Laboratory, Shaoxing Seventh People's Hospital, Shaoxing, China
| | - Ji-Cheng Li
- Clinical Research Laboratory, Shaoxing Seventh People's Hospital, Shaoxing, China.,Institute of Cell Biology, Zhejiang University Medical School, Hangzhou, China
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4
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Nogueira BMF, Krishnan S, Barreto‐Duarte B, Araújo‐Pereira M, Queiroz ATL, Ellner JJ, Salgame P, Scriba TJ, Sterling TR, Gupta A, Andrade BB. Diagnostic biomarkers for active tuberculosis: progress and challenges. EMBO Mol Med 2022; 14:e14088. [PMID: 36314872 PMCID: PMC9728055 DOI: 10.15252/emmm.202114088] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/05/2022] [Accepted: 09/05/2022] [Indexed: 12/14/2022] Open
Abstract
Tuberculosis (TB) is a leading cause of morbidity and mortality from a single infectious agent, despite being preventable and curable. Early and accurate diagnosis of active TB is critical to both enhance patient care, improve patient outcomes, and break Mycobacterium tuberculosis (Mtb) transmission cycles. In 2020 an estimated 9.9 million people fell ill from Mtb, but only a little over half (5.8 million) received an active TB diagnosis and treatment. The World Health Organization has proposed target product profiles for biomarker- or biosignature-based diagnostics using point-of-care tests from easily accessible specimens such as urine or blood. Here we review and summarize progress made in the development of pathogen- and host-based biomarkers for active TB diagnosis. We describe several unique patient populations that have posed challenges to development of a universal diagnostic TB biomarker, such as people living with HIV, extrapulmonary TB, and children. We also review additional limitations to widespread validation and utilization of published biomarkers. We conclude with proposed solutions to enhance TB diagnostic biomarker validation and uptake.
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Affiliation(s)
- Betânia M F Nogueira
- Programa de Pós‐graduação em Ciências da SaúdeUniversidade Federal da BahiaSalvadorBrazil,Instituto Couto MaiaSalvadorBrazil,Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) InitiativeSalvadorBrazil
| | - Sonya Krishnan
- Division of Infectious Diseases, Department of MedicineJohns Hopkins University School of MedicineBaltimoreMDUSA
| | - Beatriz Barreto‐Duarte
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) InitiativeSalvadorBrazil,Curso de MedicinaUniversidade Salvador (UNIFACS)SalvadorBrazil,Programa de Pós‐Graduação em Clínica MédicaUniversidade Federal do Rio de JaneiroRio de JaneiroBrazil,Laboratório de Inflamação e Biomarcadores, Instituto Gonçalo MonizFundação Oswaldo CruzSalvadorBrazil
| | - Mariana Araújo‐Pereira
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) InitiativeSalvadorBrazil,Laboratório de Inflamação e Biomarcadores, Instituto Gonçalo MonizFundação Oswaldo CruzSalvadorBrazil,Faculdade de MedicinaUniversidade Federal da BahiaSalvadorBrazil
| | - Artur T L Queiroz
- Instituto Couto MaiaSalvadorBrazil,Center of Data and Knowledge Integration for Health (CIDACS), Instituto Gonçalo MonizFundação Oswaldo CruzSalvadorBrazil
| | - Jerrold J Ellner
- Department of Medicine, Centre for Emerging PathogensRutgers‐New Jersey Medical SchoolNewarkNJUSA
| | - Padmini Salgame
- Department of Medicine, Centre for Emerging PathogensRutgers‐New Jersey Medical SchoolNewarkNJUSA
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative and Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of PathologyUniversity of Cape TownCape TownSouth Africa
| | - Timothy R Sterling
- Division of Infectious Diseases, Department of MedicineVanderbilt University Medical CenterNashvilleTNUSA
| | - Amita Gupta
- Division of Infectious Diseases, Department of MedicineJohns Hopkins University School of MedicineBaltimoreMDUSA
| | - Bruno B Andrade
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) InitiativeSalvadorBrazil,Curso de MedicinaUniversidade Salvador (UNIFACS)SalvadorBrazil,Laboratório de Inflamação e Biomarcadores, Instituto Gonçalo MonizFundação Oswaldo CruzSalvadorBrazil,Faculdade de MedicinaUniversidade Federal da BahiaSalvadorBrazil,Curso de MedicinaFaculdade de Tecnologia e Ciências (FTC)SalvadorBrazil,Curso de MedicinaEscola Bahiana de Medicina e Saúde Pública (EBMSP)SalvadorBrazil
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6
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Olsson O, Tesfaye F, Søkilde R, Mazurek J, Abebe M, Yeba H, Aseffa A, Skogmar S, Balcha TT, Rovira C, Björkman P, Jansson M. Expression of MicroRNAs Is Dysregulated by HIV While Mycobacterium tuberculosis Drives Alterations of Small Nucleolar RNAs in HIV Positive Adults With Active Tuberculosis. Front Microbiol 2022; 12:808250. [PMID: 35295678 PMCID: PMC8920554 DOI: 10.3389/fmicb.2021.808250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 12/29/2021] [Indexed: 11/13/2022] Open
Abstract
HIV infection affects the course of tuberculosis (TB), and HIV and Mycobacterium tuberculosis (Mtb) synergize in disease progression through complex immunological interplay. To gain further understanding of these mechanisms, we compared the microRNA (miRNA) and small nucleolar RNA (snoRNA) expression patterns in whole blood of individuals with active TB, with and without HIV coinfection (HIV+/TB+ and HIV-/TB+), and HIV and TB-negative individuals (HIV-/TB-). We found that 218 miRNAs were differentially expressed between HIV+/TB+ and HIV-/TB+, while no statistically significant difference in snoRNA expression was observed between these groups. In contrast, both miRNA (n = 179) and snoRNA (n = 103) expression patterns were significantly altered in HIV+/TB+ individuals compared to those of the HIV-/TB- controls. Of note, 26 of these snoRNAs were also significantly altered between the HIV-/TB+ and HIV-/TB- groups. Normalization toward the miRNA and snoRNA expression patterns of the HIV-/TB- control group was noted during anti-TB and antiretroviral treatment in HIV+/TB+ participants. In summary, these results show that HIV coinfection influences miRNA expression in active TB. In contrast, snoRNA expression patterns differ between individuals with and without active TB, independently of HIV coinfection status. Moreover, in coinfected individuals, therapy-induced control of HIV replication and clearance of Mtb appears to normalize the expression of some small non-coding RNA (sncRNA). These findings suggest that dysregulation of miRNA is a mechanism by which HIV may modify immunity against TB, while active TB alters snoRNA expression. Improved understanding of how regulation of sncRNA expression influences the disease course in coinfected individuals may have implications for diagnostics, risk stratification, and host-directed therapy. Here, we propose a novel mechanism by which HIV alters the immune response to TB.
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Affiliation(s)
- Oskar Olsson
- Clinical Infection Medicine, Department of Translational Medicine, Lund University, Malmö, Sweden.,Department of Infectious Diseases, Skåne University Hospital, Malmö, Sweden
| | - Fregenet Tesfaye
- Clinical Infection Medicine, Department of Translational Medicine, Lund University, Malmö, Sweden.,Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Rolf Søkilde
- Breastca-Genetics, Cancer and Non-coding RNA, Lund University Cancer Centre, Lund University, Lund, Sweden
| | - Jolanta Mazurek
- Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Markos Abebe
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Habtamu Yeba
- Adama Public Health Research and Referral Center, Adama, Ethiopia
| | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Sten Skogmar
- Clinical Infection Medicine, Department of Translational Medicine, Lund University, Malmö, Sweden.,Department of Infectious Diseases, Skåne University Hospital, Malmö, Sweden
| | - Taye Tolera Balcha
- Clinical Infection Medicine, Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Carlos Rovira
- Breastca-Genetics, Cancer and Non-coding RNA, Lund University Cancer Centre, Lund University, Lund, Sweden
| | - Per Björkman
- Clinical Infection Medicine, Department of Translational Medicine, Lund University, Malmö, Sweden.,Department of Infectious Diseases, Skåne University Hospital, Malmö, Sweden
| | - Marianne Jansson
- Division of Medical Microbiology, Department of Laboratory Medicine, Lund University, Lund, Sweden
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