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Rocha EF, Vinhaes CL, Araújo-Pereira M, Mota TF, Gupte AN, Kumar NP, Arriaga MB, Sterling TR, Babu S, Gaikwad S, Karyakarte R, Mave V, Kulkarni V, Paradkar M, Viswanathan V, Kornfeld H, Gupta A, Andrade BB, Queiroz ATLD. The sound of silent RNA in tuberculosis and the lncRNA role on infection. iScience 2024; 27:108662. [PMID: 38205253 PMCID: PMC10777062 DOI: 10.1016/j.isci.2023.108662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/27/2023] [Accepted: 12/05/2023] [Indexed: 01/12/2024] Open
Abstract
Tuberculosis (TB) is one of the leading causes of death worldwide, and Diabetes Mellitus is one of the major comorbidities (TB/DM) associated with the disease. A total of 103 differentially expressed ncRNAs have been identified in the TB and TB/DM comparisons. A machine learning algorithm was employed to identify the most informative lncRNAs: ADM-DT, LINC02009, LINC02471, SOX2-OT, and GK-AS1. These lncRNAs presented substantial accuracy in classifying TB from HC (AUCs >0.85) and TB/DM from HC (AUCs >0.90) in the other three countries. Genes with significant correlations with the five lncRNAs enriched common pathways in Brazil and India for both TB and TB/DM. This suggests that lncRNAs play an important role in the regulation of genes related to the TB immune response.
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Affiliation(s)
- Eduardo Fukutani Rocha
- Centro de Integração de Dados e Conhecimentos para Saúde, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Salvador, Brazil
| | - Caian Leal Vinhaes
- Laboratório de Inflamação e Biomarcadores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Salvador, Brazil
- Escola Bahiana de Medicina e Saúde Pública (EBMSP), Salvador 40290-150, Brazil
| | - Mariana Araújo-Pereira
- Laboratório de Inflamação e Biomarcadores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Salvador, Brazil
- Escola Bahiana de Medicina e Saúde Pública (EBMSP), Salvador 40290-150, Brazil
- Faculdade de Tecnologia e Ciências, Instituto de Pesquisa Clínica e Translacional, Salvador, Brazil
| | - Tiago Feitosa Mota
- Centro de Integração de Dados e Conhecimentos para Saúde, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Salvador, Brazil
| | | | | | - Maria Belen Arriaga
- Laboratório de Inflamação e Biomarcadores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Salvador, Brazil
| | - Timothy R. Sterling
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA
| | - Subash Babu
- National Institutes of Health- NIRT - International Center for Excellence in Research, Chennai, India
| | - Sanjay Gaikwad
- Department of Pulmonary Medicine, Byramjee-Jeejeebhoy Government Medical College and Sassoon General Hospitals, Pune, India
| | - Rajesh Karyakarte
- Department of Microbiology, Byramjee-Jeejeebhoy Government Medical College and Sassoon General Hospitals, Pune, India
| | - Vidya Mave
- Byramjee-Jeejeebhoy Government Medical College-Johns Hopkins University Clinical Research Site, Pune, India
- Johns Hopkins Center for Infectious Diseases in India, Pune, India
| | - Vandana Kulkarni
- Byramjee-Jeejeebhoy Government Medical College-Johns Hopkins University Clinical Research Site, Pune, India
- Johns Hopkins Center for Infectious Diseases in India, Pune, India
| | - Mandar Paradkar
- Byramjee-Jeejeebhoy Government Medical College-Johns Hopkins University Clinical Research Site, Pune, India
- Johns Hopkins Center for Infectious Diseases in India, Pune, India
| | | | - Hardy Kornfeld
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA USA
- UMass Chan Medical School, Worcester, MA USA
| | - Amita Gupta
- Byramjee-Jeejeebhoy Government Medical College-Johns Hopkins University Clinical Research Site, Pune, India
| | - Bruno Bezerril Andrade
- Laboratório de Inflamação e Biomarcadores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Salvador, Brazil
- Escola Bahiana de Medicina e Saúde Pública (EBMSP), Salvador 40290-150, Brazil
- Faculdade de Tecnologia e Ciências, Instituto de Pesquisa Clínica e Translacional, Salvador, Brazil
| | - Artur Trancoso Lopo de Queiroz
- Centro de Integração de Dados e Conhecimentos para Saúde, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
- Laboratório de Inflamação e Biomarcadores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Salvador, Brazil
| | - RePORT Brazil
- Centro de Integração de Dados e Conhecimentos para Saúde, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
- Laboratório de Inflamação e Biomarcadores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Salvador, Brazil
- Escola Bahiana de Medicina e Saúde Pública (EBMSP), Salvador 40290-150, Brazil
- Boston University School of Public Health, Boston, MA USA
- National Institutes of Health- NIRT - International Center for Excellence in Research, Chennai, India
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA
- Department of Pulmonary Medicine, Byramjee-Jeejeebhoy Government Medical College and Sassoon General Hospitals, Pune, India
- Department of Microbiology, Byramjee-Jeejeebhoy Government Medical College and Sassoon General Hospitals, Pune, India
- Byramjee-Jeejeebhoy Government Medical College-Johns Hopkins University Clinical Research Site, Pune, India
- Johns Hopkins Center for Infectious Diseases in India, Pune, India
- Prof. M. Viswanathan Diabetes Research Centre, Chennai, India
- Faculdade de Tecnologia e Ciências, Instituto de Pesquisa Clínica e Translacional, Salvador, Brazil
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA USA
- UMass Chan Medical School, Worcester, MA USA
- ICMR-National Institute for Research in Tuberculosis, Chennai, India
| | - RePORT India Consortia
- Centro de Integração de Dados e Conhecimentos para Saúde, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
- Laboratório de Inflamação e Biomarcadores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Salvador, Brazil
- Escola Bahiana de Medicina e Saúde Pública (EBMSP), Salvador 40290-150, Brazil
- Boston University School of Public Health, Boston, MA USA
- National Institutes of Health- NIRT - International Center for Excellence in Research, Chennai, India
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA
- Department of Pulmonary Medicine, Byramjee-Jeejeebhoy Government Medical College and Sassoon General Hospitals, Pune, India
- Department of Microbiology, Byramjee-Jeejeebhoy Government Medical College and Sassoon General Hospitals, Pune, India
- Byramjee-Jeejeebhoy Government Medical College-Johns Hopkins University Clinical Research Site, Pune, India
- Johns Hopkins Center for Infectious Diseases in India, Pune, India
- Prof. M. Viswanathan Diabetes Research Centre, Chennai, India
- Faculdade de Tecnologia e Ciências, Instituto de Pesquisa Clínica e Translacional, Salvador, Brazil
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA USA
- UMass Chan Medical School, Worcester, MA USA
- ICMR-National Institute for Research in Tuberculosis, Chennai, India
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