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Yao S, Liu B, Hu X, Tan Y, Liu K, He M, Wu B, Ahmad N, Su X, Zhang Y, Yi M. Diagnostic value of microRNAs in active tuberculosis based on quantitative and enrichment analyses. Diagn Microbiol Infect Dis 2024; 108:116172. [PMID: 38340483 DOI: 10.1016/j.diagmicrobio.2024.116172] [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: 09/10/2023] [Revised: 12/31/2023] [Accepted: 01/02/2024] [Indexed: 02/12/2024]
Abstract
BACKGROUND Tuberculosis (TB) infection remains a crucial global health challenge, with active tuberculosis (ATB) representing main infection source. MicroRNA (miRNA) has emerged as a potential diagnostic tool in this context. This study aims to identify candidate miRNAs for ATB diagnosis and explore their possible mechanisms. METHODS Differentially expressed miRNAs in ATB were summarized in qualitative analysis. The diagnostic values of miRNAs for ATB subtypes were assessed by overall sensitivity, specificity, and area under the curve. Additionally, we conducted enrichment analysis on miRNAs and target genes. RESULTS Over 100 differentially expressed miRNAs were identified, with miR-29 family being the most extensively studied. The miR-29 family demonstrated sensitivity, specificity, and area under the curve of 80 %, 80 % and 0.86 respectively for active pulmonary TB (PTB). The differentially expressed miR-29-target genes in PTB were enriched in immune-related pathways. CONCLUSIONS The miR-29 family exhibits good diagnostic value for active PTB and shows association with immune process.
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Affiliation(s)
- Shuoyi Yao
- Department of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China; Xiangya School of Medicine, Central South University, Changsha, China
| | - Bin Liu
- Department of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Xinyue Hu
- Department of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yun Tan
- School of Medicine, Changsha Social Work College, Changsha, China
| | - Kun Liu
- School of Life Sciences, Central South University, Changsha, China
| | - Meng He
- Department of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Bohan Wu
- School of Life Sciences, Central South University, Changsha, China
| | - Namra Ahmad
- School of Life Sciences, Central South University, Changsha, China
| | - Xiaoli Su
- Department of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yuan Zhang
- Department of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Minhan Yi
- School of Life Sciences, Central South University, Changsha, China.
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Deng F, Xu P, Miao J, Jin C, Tu H, Zhang J. Pulmonary tuberculosis biomarker miR-215-5p inhibits autophagosome-lysosome fusion in macrophages. Tuberculosis (Edinb) 2023; 143:102422. [PMID: 37925930 DOI: 10.1016/j.tube.2023.102422] [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: 07/01/2023] [Revised: 09/17/2023] [Accepted: 10/15/2023] [Indexed: 11/07/2023]
Abstract
The normal autophagy flux is beneficial for the rapid elimination of phagocytic pathogens by macrophages. However, Mycobacterium tuberculosis interferes with the autophagy flux of macrophages to weaken their immune function and evade immune surveillance. In this study, we found that miRNA-215-5p was downregulated in tuberculosis patients. A potential diagnostic model for tuberculosis was established by combining miRNA-215-5p with three others differentially expressed microRNAs (miRNA-145-5p, miRNA-486-5p and miRNA-628-3p). Furthermore, we discovered that the up-regulated miRNA-215-5p could inhibit the maturation of autophagy by preventing the fusion of autophagosomes with lysosomes in macrophages. The role of TB-specific miRNA-215-5p in inhibiting auto-lysosome formation provides evidence of its potential role in Host-directed therapy for tuberculosis.
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Affiliation(s)
- Feng Deng
- School of Medicine, Shaoxing University, Shaoxing, Zhejiang, 312000, China
| | - Peng Xu
- Department of Clinical Laboratory, Affiliated Hospital of Shaoxing University, Shaoxing, Zhejiang, 312000, China
| | - Jiahong Miao
- School of Medicine, Shaoxing University, Shaoxing, Zhejiang, 312000, China
| | - Cheng Jin
- School of Medicine, Shaoxing University, Shaoxing, Zhejiang, 312000, China
| | - Huihui Tu
- School of Medicine, Shaoxing University, Shaoxing, Zhejiang, 312000, China.
| | - Jianhua Zhang
- School of Medicine, Shaoxing University, Shaoxing, Zhejiang, 312000, China.
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3
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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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4
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Davuluri KS, Chauhan DS. microRNAs associated with the pathogenesis and their role in regulating various signaling pathways during Mycobacterium tuberculosis infection. Front Cell Infect Microbiol 2022; 12:1009901. [PMID: 36389170 PMCID: PMC9647626 DOI: 10.3389/fcimb.2022.1009901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 10/03/2022] [Indexed: 11/22/2022] Open
Abstract
Despite more than a decade of active study, tuberculosis (TB) remains a serious health concern across the world, and it is still the biggest cause of mortality in the human population. Pathogenic bacteria recognize host-induced responses and adapt to those hostile circumstances. This high level of adaptability necessitates a strong regulation of bacterial metabolic characteristics. Furthermore, the immune reponse of the host virulence factors such as host invasion, colonization, and survival must be properly coordinated by the pathogen. This can only be accomplished by close synchronization of gene expression. Understanding the molecular characteristics of mycobacterial pathogenesis in order to discover therapies that prevent or resolve illness relies on the bacterial capacity to adjust its metabolism and replication in response to various environmental cues as necessary. An extensive literature details the transcriptional alterations of host in response to in vitro environmental stressors, macrophage infection, and human illness. Various studies have recently revealed the finding of several microRNAs (miRNAs) that are believed to play an important role in the regulatory networks responsible for adaptability and virulence in Mycobacterium tuberculosis. We highlighted the growing data on the existence and quantity of several forms of miRNAs in the pathogenesis of M. tuberculosis, considered their possible relevance to disease etiology, and discussed how the miRNA-based signaling pathways regulate bacterial virulence factors.
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Wang L, Xiong Y, Fu B, Guo D, Zaky MY, Lin X, Wu H. MicroRNAs as immune regulators and biomarkers in tuberculosis. Front Immunol 2022; 13:1027472. [PMID: 36389769 PMCID: PMC9647078 DOI: 10.3389/fimmu.2022.1027472] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/12/2022] [Indexed: 07/26/2023] Open
Abstract
Tuberculosis (TB), which is caused by Mycobacterium tuberculosis (Mtb), is one of the most lethal infectious disease worldwide, and it greatly affects human health. Some diagnostic and therapeutic methods are available to effectively prevent and treat TB; however, only a few systematic studies have described the roles of microRNAs (miRNAs) in TB. Combining multiple clinical datasets and previous studies on Mtb and miRNAs, we state that pathogens can exploit interactions between miRNAs and other biomolecules to avoid host mechanisms of immune-mediated clearance and survive in host cells for a long time. During the interaction between Mtb and host cells, miRNA expression levels are altered, resulting in the changes in the miRNA-mediated regulation of host cell metabolism, inflammatory responses, apoptosis, and autophagy. In addition, differential miRNA expression can be used to distinguish healthy individuals, patients with TB, and patients with latent TB. This review summarizes the roles of miRNAs in immune regulation and their application as biomarkers in TB. These findings could provide new opportunities for the diagnosis and treatment of TB.
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Affiliation(s)
- Lulu Wang
- Department of Biology, School of Life Sciences, Chongqing University, Chongqing, China
| | - Yan Xiong
- Department of Biology, School of Life Sciences, Chongqing University, Chongqing, China
| | - Beibei Fu
- Department of Biology, School of Life Sciences, Chongqing University, Chongqing, China
| | - Dong Guo
- Department of Biology, School of Life Sciences, Chongqing University, Chongqing, China
| | - Mohamed Y. Zaky
- Department of Zoology, Molecular Physiology Division, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Xiaoyuan Lin
- Department of Biology, School of Life Sciences, Chongqing University, Chongqing, China
| | - Haibo Wu
- Department of Biology, School of Life Sciences, Chongqing University, Chongqing, China
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6
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Xiao M, Yang S, Zhou A, Li T, Liu J, Chen Y, Luo Y, Qian C, Yang F, Tang B, Li C, Su N, Li J, Jiang M, Yang S, Lin H. MiR-27a-3p and miR-30b-5p inhibited-vitamin D receptor involved in the progression of tuberculosis. Front Microbiol 2022; 13:1020542. [PMID: 36304947 PMCID: PMC9593098 DOI: 10.3389/fmicb.2022.1020542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/20/2022] [Indexed: 11/28/2022] Open
Abstract
Background MicroRNAs (miRNAs) play a vital role in tuberculosis (TB). Vitamin D receptor (VDR), an miRNA target gene, and its ligand, vitamin D3 (VitD3), have been reported to exert protective effects against TB. However, whether miRNAs can affect the progression of TB by targeting VDR has not been reported. Materials and methods Research subjects were selected according to defined inclusion criteria. A clinical database of 360 samples was established, including the subjects’ demographic information, miRNA expression profiles and cellular experimental results. Two candidate miRNAs, miR-27a-3p, and miR-30b-5p, were identified by a high-throughput sequencing screen and validated by qRT–PCR assays. Univariate and multivariate statistical analyses were performed. VDR and NF-kB p65 protein levels were detected by Western blot assays. Proinflammatory cytokine expression levels were detected by enzyme-linked immunosorbent assay (ELISA). Luciferase assays and fluorescence-activated cell sorting (FACS) were further applied to elucidate the detailed mechanisms. Results Differential miRNA expression profiles were obtained, and miR-27a-3p and miR-30b-5p were highly expressed in patients with TB. These results showed that the two miRNAs were able to induce M1 macrophage differentiation and inhibit M2 macrophage differentiation. Further experiments showed that the two miRNAs decreased the VDR protein level and increased proinflammatory cytokine secretion by macrophages. Mechanistically, the miRNAs targeted the 3′ untranslated region (3′UTR) of the VDR mRNA and thereby downregulated VDR protein levels by post-transcriptional regulation. Then, due to the reduction in VDR protein levels, the NF-kB inflammatory cytokine signaling pathway was activated, thus promoting the progression of TB. Conclusion Our study not only identified differentially expressed miRNAs between the TB and control groups but also revealed that miR-27a-3p and miR-30b-5p regulate proinflammatory cytokine secretion and macrophage differentiation through VDR in macrophages. Thus, these two miRNAs influence the progression of TB.
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Affiliation(s)
- Min Xiao
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Song Yang
- Chongqing Public Health Medical Center, Southwest University, Chongqing, China
| | - An Zhou
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Tongxin Li
- Chongqing Public Health Medical Center, Southwest University, Chongqing, China
| | - Jingjing Liu
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Yang Chen
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Ya Luo
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Chunfang Qian
- Chongqing Public Health Medical Center, Southwest University, Chongqing, China
| | - Fuping Yang
- Chongqing Public Health Medical Center, Southwest University, Chongqing, China
| | - Bo Tang
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Chunhua Li
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Na Su
- Chongqing Public Health Medical Center, Southwest University, Chongqing, China
| | - Jing Li
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Mingying Jiang
- Chongqing Public Health Medical Center, Southwest University, Chongqing, China
- *Correspondence: Mingying Jiang,
| | - Shiming Yang
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, Chongqing, China
- Shiming Yang,
| | - Hui Lin
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, Chongqing, China
- Hui Lin,
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Hong GH, Guan Q, Peng H, Luo XH, Mao Q. Identification and validation of a T-cell-related MIR600HG/hsa-mir-21-5p competing endogenous RNA network in tuberculosis activation based on integrated bioinformatics approaches. Front Genet 2022; 13:979213. [PMID: 36204312 PMCID: PMC9531151 DOI: 10.3389/fgene.2022.979213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
Background: T cells play critical roles in the progression of tuberculosis (TB); however, knowledge regarding these molecular mechanisms remains inadequate. This study constructed a critical ceRNA network was constructed to identify the potentially important role of TB activation via T-cell regulation. Methods: We performed integrated bioinformatics analysis in a randomly selected training set from the GSE37250 dataset. After estimating the abundance of 18 types of T cells using ImmuCellAI, critical T-cell subsets were determined by their diagnostic accuracy in distinguishing active from latent TB. We then identified the critical genes associated with T-cell subsets in TB activation through co-expression analysis and PPI network prediction. Then, the ceRNA network was constructed based on RNA complementarity detection on the DIANA-LncBase and mirDIP platform. The gene biomarkers included in the ceRNA network were lncRNA, miRNA, and targeting mRNA. We then applied an elastic net regression model to develop a diagnostic classifier to assess the significance of the gene biomarkers in clinical applications. Internal and external validations were performed to assess the repeatability and generalizability. Results: We identified CD4+ T, Tr1, nTreg, iTreg, and Tfh as T cells critical for TB activation. A ceRNA network mediated by the MIR600HG/hsa-mir-21-5p axis was constructed, in which the significant gene cluster regulated the critical T subsets in TB activation. MIR600HG, hsa-mir-21-5p, and five targeting mRNAs (BCL11B, ETS1, EPHA4, KLF12, and KMT2A) were identified as gene biomarkers. The elastic net diagnostic classifier accurately distinguished active TB from latent. The validation analysis confirmed that our findings had high generalizability in different host background cases. Conclusion: The findings of this study provided novel insight into the underlying mechanisms of TB activation and identifying prospective biomarkers for clinical applications.
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Affiliation(s)
- Guo-Hu Hong
- Department of Infectious Disease, Guizhou Provincial People’s Hospital, Guiyang, China
| | - Qing Guan
- Department of Dermatology, The First People’s Hospital of Guiyang, Guiyang, China
| | - Hong Peng
- Department of Infectious Disease, Guizhou Provincial People’s Hospital, Guiyang, China
| | - Xin-Hua Luo
- Department of Infectious Disease, Guizhou Provincial People’s Hospital, Guiyang, China
- *Correspondence: Xin-Hua Luo, ; Qing Mao,
| | - Qing Mao
- Department of Infectious Disease, The First Hospital Affiliated to Army Medical University, Chongqing, China
- *Correspondence: Xin-Hua Luo, ; Qing Mao,
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Kameni C, Mezajou CF, Ngongang NN, Ngum JA, Simo USF, Tatang FJ, Nguengo SN, Nouthio APC, Pajiep MAW, Toumeni MH, Madjoumo EST, Tchinda MF, Ngangue RJEM, Koro Koro F, Wade A, Akami M, Ngono ARN, Tamgue O. p50-associated Cyclooxygenase-2 Extragenic RNA (PACER) and Long Non-coding RNA 13 (LNC13) as potential biomarkers for monitoring tuberculosis treatment. FRONTIERS IN TROPICAL DISEASES 2022. [DOI: 10.3389/fitd.2022.969347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Gaps in early and accurate diagnosis, effective drug control, and treatment monitoring are hindering the global eradication effort of tuberculosis. This infectious disease has become the deadliest worldwide before the outbreak of Covid-19. The search for new molecular biomarkers of tuberculosis will help to reverse this trend. Long non-coding RNAs (lncRNAs) have emerged as important regulators of the host immune response to infection, hence their link with the etiology and diagnosis of tuberculosis has attracted some attention from the research community. However, very little is known about their potential for the monitoring of tuberculosis treatment. This study aimed at assessing the potential of two lncRNAs: p50-associated Cyclooxygenase-2 Extragenic RNA (PACER) and Long Non-coding RNA 13 (LNC13) in the monitoring of tuberculosis treatment. This was a cross-sectional study carried out in Douala, Cameroon from December 2020 to August 2021. A quantitative real-time polymerase chain reaction followed by Cq analysis using the Livak method were performed to measure the relative expression levels of PACER and LNC13 in whole blood of healthy controls, patients with active pulmonary tuberculosis at the initiation of treatment, after two, five, and six months into treatment. Receiver Operating Characteristic curves analysis was used to assess the ability of targeted lncRNAs to discriminate among those groups. The study showed that the lncRNAs PACER and LNC13 were significantly upregulated in patients with active pulmonary tuberculosis at the initiation of treatment than in healthy controls. The expression levels of the two lncRNAs were significantly downregulated in patients during the treatment as compared to the active pulmonary tuberculosis patients. However, the expression levels of the lncRNAs PACER and LNC13 in whole blood of patients after six months of treatment were similar to those in healthy controls. Similarly, lncRNAs PACER and LNC13 showed very good performance in distinguishing between active tuberculosis patients and healthy controls as well as in differentiating between newly diagnosed active tuberculosis patients and those under treatment. Interestingly, those lncRNAs could not discriminate healthy controls from patients after six months of treatment. The lncRNAs PACER and LNC13 are therefore potential biomarkers for the monitoring of tuberculosis treatment.
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Chen YC, Hsiao CC, Wu CC, Chao TY, Leung SY, Chang YP, Tseng CC, Lee CP, Hsu PY, Wang TY, Wang PW, Chen TW, Lin MC. Next generation sequencing reveals miR-431-3p/miR-1303 as immune-regulating microRNAs for active tuberculosis. J Infect 2022; 85:519-533. [DOI: 10.1016/j.jinf.2022.08.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/22/2022] [Accepted: 08/27/2022] [Indexed: 11/29/2022]
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10
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Kelly E, Whelan SO, Harriss E, Murphy S, Pollard AJ, O' Connor D. Systematic review of host genomic biomarkers of invasive bacterial disease: Distinguishing bacterial from non-bacterial causes of acute febrile illness. EBioMedicine 2022; 81:104110. [PMID: 35792524 PMCID: PMC9256842 DOI: 10.1016/j.ebiom.2022.104110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 05/27/2022] [Accepted: 05/28/2022] [Indexed: 12/03/2022] Open
Abstract
Background Infectious diseases play a significant role in the global burden of disease. The gold standard for the diagnosis of bacterial infection, bacterial culture, can lead to diagnostic delays and inappropriate antibiotic use. The advent of high- throughput technologies has led to the discovery of host-based genomic biomarkers of infection, capable of differentiating bacterial from other causes of infection, but few have achieved validation for use in a clinical setting. Methods A systematic review was performed. PubMed/Ovid Medline, Ovid Embase and Scopus databases were searched for relevant studies from inception up to 30/03/2022 with forward and backward citation searching of key references. Studies assessing the diagnostic performance of human host genomic biomarkers of bacterial infection were included. Study selection and assessment of quality were conducted by two independent reviewers. A meta-analysis was undertaken using a diagnostic random-effects model. The review was registered with PROSPERO (ID: CRD42021208462). Findings Seventy-two studies evaluating the performance of 116 biomarkers in 16,216 patients were included. Forty-six studies examined TB-specific biomarker performance and twenty-four studies assessed biomarker performance in a paediatric population. The results of pooled sensitivity, specificity, negative and positive likelihood ratio, and diagnostic odds ratio of genomic biomarkers of bacterial infection were 0.80 (95% CI 0.78 to 0.82), 0.86 (95% CI 0.84 to 0.88), 0.18 (95% CI 0.16 to 0.21), 5.5 (95% CI 4.9 to 6.3), 30.1 (95% CI 24 to 37), respectively. Significant between-study heterogeneity (I2 77%) was present. Interpretation Host derived genomic biomarkers show significant potential for clinical use as diagnostic tests of bacterial infection however, further validation and attention to test platform is warranted before clinical implementation can be achieved. Funding No funding received.
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Affiliation(s)
- Eimear Kelly
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford. UK; NIHR Oxford Biomedical Research Centre, Oxford, UK.
| | - Seán Olann Whelan
- Department of Clinical Microbiology, Galway University Hospital, Galway, Ireland
| | - Eli Harriss
- Bodleian Health Care Libraries, University of Oxford
| | - Sarah Murphy
- Department of Paediatrics, Cork University Maternity Hospital, Wilton, Cork, Ireland
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford. UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Daniel O' Connor
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford. UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
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Pitaloka DAE, Syamsunarno MRAAA, Abdulah R, Chaidir L. Omics Biomarkers for Monitoring Tuberculosis Treatment: A Mini-Review of Recent Insights and Future Approaches. Infect Drug Resist 2022; 15:2703-2711. [PMID: 35664683 PMCID: PMC9160605 DOI: 10.2147/idr.s366580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/20/2022] [Indexed: 11/23/2022] Open
Abstract
Poor sensitivity of sputum conversion for monitoring tuberculosis (TB) treatment that makes identification of a non-sputum-based biomarker is urgently needed. Monitoring biomarkers in TB treatment is used to decide whether critical thresholds have been reached and helps clinicians to conclude the therapeutic success. In this mini review, we highlight recent studies on omics-related contributes to identifying of a novel biomarker as surrogate markers for the cure and predicting future reactivation risk following TB treatment. We catalogue the studies published to seek the progress made in transcriptomics, proteomics, and metabolomics in pulmonary TB. We also discuss how integrative multi-omics data will provide further understanding and effective TB treatment, such as revealing the interrelationships at multiple molecular levels, facilitating the identification of biologically interconnected processes, and accelerating precision medicine in TB treatment. However, proper validation in prospective longitudinal studies with long-term follow-up and outcome assessment must be conducted before the biomarkers are utilized in clinical practice.
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Affiliation(s)
- Dian Ayu Eka Pitaloka
- Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Sumedang, West Java, 45363, Indonesia
- Center for Translational Biomarker Research, Universitas Padjadjaran, Bandung, West Java, 40132, Indonesia
| | - Mas Rizky Anggun A A Syamsunarno
- Center for Translational Biomarker Research, Universitas Padjadjaran, Bandung, West Java, 40132, Indonesia
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Sumedang, West Java, 45363, Indonesia
| | - Rizky Abdulah
- Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Sumedang, West Java, 45363, Indonesia
- Center of Excellence in Higher Education for Pharmaceutical Care Innovation, Universitas Padjadjaran, Sumedang, West Java, 45363, Indonesia
| | - Lidya Chaidir
- Center for Translational Biomarker Research, Universitas Padjadjaran, Bandung, West Java, 40132, Indonesia
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Sumedang, West Java, 45363, Indonesia
- Correspondence: Lidya Chaidir, Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Sumedang, West Java, 45363, Indonesia, Tel +62-22-84288812, Email
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Almatroudi A. Non-Coding RNAs in Tuberculosis Epidemiology: Platforms and Approaches for Investigating the Genome's Dark Matter. Int J Mol Sci 2022; 23:ijms23084430. [PMID: 35457250 PMCID: PMC9024992 DOI: 10.3390/ijms23084430] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/05/2022] [Accepted: 04/14/2022] [Indexed: 02/07/2023] Open
Abstract
A growing amount of information about the different types, functions, and roles played by non-coding RNAs (ncRNAs) is becoming available, as more and more research is done. ncRNAs have been identified as potential therapeutic targets in the treatment of tuberculosis (TB), because they may be essential regulators of the gene network. ncRNA profiling and sequencing has recently revealed significant dysregulation in tuberculosis, primarily due to aberrant processes of ncRNA synthesis, including amplification, deletion, improper epigenetic regulation, or abnormal transcription. Despite the fact that ncRNAs may have a role in TB characteristics, the detailed mechanisms behind these occurrences are still unknown. The dark matter of the genome can only be explored through the development of cutting-edge bioinformatics and molecular technologies. In this review, ncRNAs' synthesis and functions are discussed in detail, with an emphasis on the potential role of ncRNAs in tuberculosis. We also focus on current platforms, experimental strategies, and computational analyses to explore ncRNAs in TB. Finally, a viewpoint is presented on the key challenges and novel techniques for the future and for a wide-ranging therapeutic application of ncRNAs.
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Affiliation(s)
- Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
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13
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Pattnaik B, Patnaik N, Mittal S, Mohan A, Agrawal A, Guleria R, Madan K. Micro RNAs as potential biomarkers in tuberculosis: A systematic review. Noncoding RNA Res 2022; 7:16-26. [PMID: 35128217 PMCID: PMC8792429 DOI: 10.1016/j.ncrna.2021.12.005] [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: 10/04/2021] [Revised: 12/24/2021] [Accepted: 12/29/2021] [Indexed: 12/15/2022] Open
Abstract
Tuberculosis (TB) remains a major infectious disease across the globe. With increasing TB infections and a rise in multi-drug resistance, rapid diagnostic modalities are required to achieve TB control. Radiological investigations and microbiological tests (microscopic examination, cartridge-based nucleic acid amplification tests, and cultures) are most commonly used to diagnose TB. Histopathological/cytopathological examinations are also required for an accurate diagnosis in many patients. The causative agent, Mycobacterium tuberculosis (Mtb), is known to circumvent the host's immune system. Circulating microRNAs (miRNAs) play a crucial role in biological pathways and can be used as a potential biomarker to detect tuberculosis. miRNAs are small non-coding RNAs and negatively regulate gene expression during post-transcriptional regulation. The differential expression of miRNAs in multiple clinical samples in tuberculosis patients may be helpful as potential disease biomarkers. This review summarizes the literature on miRNAs in various clinical samples as biomarkers for TB diagnosis.
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Affiliation(s)
- Bijay Pattnaik
- Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Niharika Patnaik
- Centre of Excellence in Asthma & Lung Disease, Molecular Immunogenetics Lab, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India
| | - Saurabh Mittal
- Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Anant Mohan
- Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Anurag Agrawal
- Centre of Excellence in Asthma & Lung Disease, Molecular Immunogenetics Lab, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India
| | - Randeep Guleria
- Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Karan Madan
- Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, India
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14
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Magdalena D, Magdalena G. Biological functions and diagnostic implications of microRNAs in Mycobacterium tuberculosis infection. Asian Pac J Trop Biomed 2022. [DOI: 10.4103/2221-1691.333208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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15
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Kundu M, Basu J. The Role of microRNAs and Long Non-Coding RNAs in the Regulation of the Immune Response to Mycobacterium tuberculosis Infection. Front Immunol 2021; 12:687962. [PMID: 34248974 PMCID: PMC8264550 DOI: 10.3389/fimmu.2021.687962] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/09/2021] [Indexed: 12/16/2022] Open
Abstract
Non-coding RNAs have emerged as critical regulators of the immune response to infection. MicroRNAs (miRNAs) are small non-coding RNAs which regulate host defense mechanisms against viruses, bacteria and fungi. They are involved in the delicate interplay between Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), and its host, which dictates the course of infection. Differential expression of miRNAs upon infection with M. tuberculosis, regulates host signaling pathways linked to inflammation, autophagy, apoptosis and polarization of macrophages. Experimental evidence suggests that virulent M. tuberculosis often utilize host miRNAs to promote pathogenicity by restricting host-mediated antibacterial signaling pathways. At the same time, host- induced miRNAs augment antibacterial processes such as autophagy, to limit bacterial proliferation. Targeting miRNAs is an emerging option for host-directed therapies. Recent studies have explored the role of long non-coding RNA (lncRNAs) in the regulation of the host response to mycobacterial infection. Among other functions, lncRNAs interact with chromatin remodelers to regulate gene expression and also function as miRNA sponges. In this review we attempt to summarize recent literature on how miRNAs and lncRNAs are differentially expressed during the course of M. tuberculosis infection, and how they influence the outcome of infection. We also discuss the potential use of non-coding RNAs as biomarkers of active and latent tuberculosis. Comprehensive understanding of the role of these non-coding RNAs is the first step towards developing RNA-based therapeutics and diagnostic tools for the treatment of TB.
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Affiliation(s)
| | - Joyoti Basu
- Department of Chemistry, Bose Institute, Kolkata, India
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16
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Gao SH, Chen CG, Zhuang CB, Zeng YL, Zeng ZZ, Wen PH, Yu YM, Ming L, Zhao JW. Integrating serum microRNAs and electronic health records improved the diagnosis of tuberculosis. J Clin Lab Anal 2021; 35:e23871. [PMID: 34106501 PMCID: PMC8373357 DOI: 10.1002/jcla.23871] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/29/2021] [Accepted: 05/25/2021] [Indexed: 12/14/2022] Open
Abstract
Background To verify the differential expression of miR‐30c and miR‐142‐3p between tuberculosis patients and healthy controls and to investigate the performance of microRNA (miRNA) and subsequently models for the diagnosis of tuberculosis (TB). Methods We followed up 460 subjects suspected of TB, and finally enrolled 132 patients, including 60 TB patients, 24 non‐TB disease controls (TB‐DCs), and 48 healthy controls (HCs). The differential expression of miR‐30c and miR‐142‐3p in serum samples of the TB patients, TB‐DCs, and HCs were identified by reverse transcription–quantitative real‐time PCR. Diagnostic models were developed by analyzing the characteristics of miRNA and electronic health records (EHRs). These models evaluated by the area under the curves (AUC) and calibration curves were presented as nomograms. Results There were differential expression of miR‐30c and miR‐142‐3p between TB patients and HCs (p < 0.05). Individual miRNA has a limited diagnostic value for TB. However, diagnostic performance has been both significantly improved when we integrated miR‐142‐3p and ordinary EHRs to develop two models for the diagnosis of tuberculosis. The AUC of the model for distinguishing tuberculosis patients from healthy controls has increased from 0.75 (95% CI: 0.66–0.84) to 0.96 (95% CI: 0.92–0.99) and the model for distinguishing tuberculosis patients from non‐TB disease controls has increased from 0.67 (95% CI: 0.55–0.79) to 0.94 (95% CI: 0.89–0.99). Conclusions Integrating serum miR‐142‐3p and EHRs is a good strategy for improving TB diagnosis.
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Affiliation(s)
- Shu-Hui Gao
- Department of Clinical Laboratory, Key Clinical Laboratory of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Chun-Guang Chen
- Department of Clinical Laboratory, Henan Provincial Infectious Disease Hospital, Zhengzhou, 450000, China
| | - Chun-Bo Zhuang
- Department of Clinical Laboratory, Key Clinical Laboratory of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Yu-Ling Zeng
- Department of Clinical Laboratory, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Zhen-Zhen Zeng
- Department of Nuclear Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Pei-Hao Wen
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Yong-Min Yu
- Department of Clinical Laboratory, Henan Provincial Infectious Disease Hospital, Zhengzhou, 450000, China
| | - Liang Ming
- Department of Clinical Laboratory, Key Clinical Laboratory of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Jun-Wei Zhao
- Department of Clinical Laboratory, Key Clinical Laboratory of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
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17
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Krishnan S, Queiroz ATL, Gupta A, Gupte N, Bisson GP, Kumwenda J, Naidoo K, Mohapi L, Mave V, Mngqibisa R, Lama JR, Hosseinipour MC, Andrade BB, Karakousis PC. Integrative Multi-Omics Reveals Serum Markers of Tuberculosis in Advanced HIV. Front Immunol 2021; 12:676980. [PMID: 34168648 PMCID: PMC8217878 DOI: 10.3389/fimmu.2021.676980] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/13/2021] [Indexed: 11/13/2022] Open
Abstract
Tuberculosis (TB) accounts for disproportionate morbidity and mortality among persons living with HIV (PLWH). Conventional methods of TB diagnosis, including smear microscopy and Xpert MTB/RIF, have lower sensitivity in PLWH. Novel high-throughput approaches, such as miRNAomics and metabolomics, may advance our ability to recognize subclinical and difficult-to-diagnose TB, especially in very advanced HIV. We conducted a case-control study leveraging REMEMBER, a multi-country, open-label randomized controlled trial comparing 4-drug empiric standard TB treatment with isoniazid preventive therapy in PLWH initiating antiretroviral therapy (ART) with CD4 cell counts <50 cells/μL. Twenty-three cases of incident TB were site-matched with 32 controls to identify microRNAs (miRNAs), metabolites, and cytokines/chemokines, associated with the development of newly diagnosed TB in PLWH. Differentially expressed miRNA analysis revealed 11 altered miRNAs with a fold change higher than 1.4 or lower than -1.4 in cases relative to controls (p<0.05). Our analysis revealed no differentially abundant metabolites between cases and controls. We found higher TNFα and IP-10/CXCL10 in cases (p=0.011, p=0.0005), and higher MDC/CCL22 in controls (p=0.0072). A decision-tree algorithm identified gamma-glutamylthreonine and hsa-miR-215-5p as the optimal variables to classify incident TB cases (AUC 0.965; 95% CI 0.925-1.000). hsa-miR-215-5p, which targets genes in the TGF-β signaling pathway, was downregulated in cases. Gamma-glutamylthreonine, a breakdown product of protein catabolism, was less abundant in cases. To our knowledge, this is one of the first uses of a multi-omics approach to identify incident TB in severely immunosuppressed PLWH.
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Affiliation(s)
- Sonya Krishnan
- Center for Clinical Global Health Education and Center for Tuberculosis Research, Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Artur T. L. Queiroz
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Salvador, Brazil
| | - Amita Gupta
- Center for Clinical Global Health Education and Center for Tuberculosis Research, Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Byramjee Jeejeebhoy Government Medical College-Johns Hopkins University Clinical Research Site, Pune, India
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Nikhil Gupte
- Center for Clinical Global Health Education and Center for Tuberculosis Research, Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Byramjee Jeejeebhoy Government Medical College-Johns Hopkins University Clinical Research Site, Pune, India
| | - Gregory P. Bisson
- Department of Medicine, Division of Infectious Diseases, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | | | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa, Nelson R Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Lerato Mohapi
- Soweto ACTG CRS, Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Vidya Mave
- Byramjee Jeejeebhoy Government Medical College-Johns Hopkins University Clinical Research Site, Pune, India
| | - Rosie Mngqibisa
- Durban International Clinical Research Site, Enhancing Care Foundation, Durban, South Africa
| | | | - Mina C. Hosseinipour
- University of North Carolina Project-Malawi, Lilongwe, Malawi
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, United States
| | - Bruno B. Andrade
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Salvador, Brazil
- Curso de Medicina, Faculdade de Tecnologia e Ciências (FTC), Salvador, Brazil
- Curso de Medicina, Escola Bahiana de Medicina e Saúde Pública (EBMSP), Salvador, Brazil
| | - Petros C. Karakousis
- Center for Clinical Global Health Education and Center for Tuberculosis Research, Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
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18
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Serum levels of miR-21-5p and miR-339-5p associate with occupational trichloroethylene hypersensitivity syndrome. J Occup Med Toxicol 2021; 16:19. [PMID: 34001196 PMCID: PMC8127200 DOI: 10.1186/s12995-021-00308-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 05/03/2021] [Indexed: 12/29/2022] Open
Abstract
Background Trichloroethylene (TCE) hypersensitivity syndrome (THS) is a dose-independent and potentially life-threatening disease. In this study, we sought to identify THS-related miRNAs and evaluate its potential clinical value. Methods Serum samples of five patients and five matched TCE contacts were used for screening differential miRNAs. Another 34 patients and 34 matched TCE contacts were used for verifying significantly differential miRNAs with SYBR™ Green PCR and MGB PCR. The diagnostic model based on these miRNAs was established via the support vector machine (SVM) algorithm. Correlation between differential miRNAs and liver function was analyzed via the Spearman correlation test. Results A total of 69 miRNAs was found to be differentially expressed. MiR-21-5p and miR-339-5p were verified to have significant higher expressions in patients. The sensitivity, specificity and accuracy of disease model were 100, 75 and 86%, respectively. The two miRNAs showed significant correlations with liver function. Conclusion These findings suggested that miRNAs profiles in serum of THS patients had changed significantly, and miR-21-5p and miR-339-5p were associated with THS. Supplementary Information The online version contains supplementary material available at 10.1186/s12995-021-00308-0.
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19
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Mehta P. MicroRNA research: The new dawn of Tuberculosis. Indian J Tuberc 2020; 68:321-329. [PMID: 34099196 DOI: 10.1016/j.ijtb.2020.11.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/20/2020] [Indexed: 11/17/2022]
Abstract
Tuberculosis (TB) is global, one of the most fatal communicable diseases and leading cause of worldwide mortality. One-third of the global population is latently affected by Mtb (Mycobacterium tuberculosis) due to its ability to circumvent the host's immune response for its own survival. MicroRNAs (miRNAs) are small, non-coding RNAs which function at the post-transcriptional level and are critical in fine-tuning immune responses regulating the repertoire of genes expressed in immune cells. Recent studies have established their crucial role against TB. Furthermore, the differential expression pattern of miRNAs has revealed the potential role of miRNAs as biomarkers which could be utilized to differentiate between healthy controls and active TB patients or between active and latent TB. The recent advancements made in the field of miRNA regulation of the host responses against TB, as well as the potential of miRNAs as biomarkers for TB diagnosis are discussed here in this review.
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Affiliation(s)
- Priyanka Mehta
- Immunobiology Laboratory, Department of Zoology, University of Delhi, Delhi, 110 007, India.
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20
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Tuberculosis-Associated MicroRNAs: From Pathogenesis to Disease Biomarkers. Cells 2020; 9:cells9102160. [PMID: 32987746 PMCID: PMC7598604 DOI: 10.3390/cells9102160] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 09/20/2020] [Accepted: 09/23/2020] [Indexed: 12/25/2022] Open
Abstract
Tuberculosis (TB) caused by Mycobacterium tuberculosis is one of the most lethal infectious diseases with estimates of approximately 1.4 million human deaths in 2018. M. tuberculosis has a well-established ability to circumvent the host immune system to ensure its intracellular survival and persistence in the host. Mechanisms include subversion of expression of key microRNAs (miRNAs) involved in the regulation of host innate and adaptive immune response against M. tuberculosis. Several studies have reported differential expression of miRNAs during active TB and latent tuberculosis infection (LTBI), suggesting their potential use as biomarkers of disease progression and response to anti-TB therapy. This review focused on the miRNAs involved in TB pathogenesis and on the mechanism through which miRNAs induced during TB modulate cell antimicrobial responses. An attentive study of the recent literature identifies a group of miRNAs, which are differentially expressed in active TB vs. LTBI or vs. treated TB and can be proposed as candidate biomarkers.
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21
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Alipoor SD, Adcock IM, Tabarsi P, Folkerts G, Mortaz E. MiRNAs in tuberculosis: Their decisive role in the fate of TB. Eur J Pharmacol 2020; 886:173529. [PMID: 32919937 DOI: 10.1016/j.ejphar.2020.173529] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/28/2020] [Accepted: 08/28/2020] [Indexed: 12/20/2022]
Abstract
Tuberculosis (TB) is one of the most lethal global infectious diseases. Despite the availability of much higher levels of technology in health and medicine, tuberculosis still remains a serious global health problem. Mycobacterium tuberculosis has the capacity for prolonged survival inside macrophages by exploiting host metabolic and energy pathways and perturbing autophagy and apoptosis of infected cells. The mechanism(s) underlying this process are not completely understood but evidence suggests that mycobacteria subvert the host miRNA network to enable mycobacterial survival. We present here a comprehensive review on the role of miRNAs in TB immune escape mechanisms and the potential for miRNA-based TB therapeutics. Further validation studies are required to (i) elucidate the precise effect of TB on host miRNAs, (ii) determine the inhibition of mycobacterial burden using miRNA-based therapies and (iii) identify novel miRNA biomarkers that may prove useful in TB diagnosis and treatment monitoring.
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Affiliation(s)
- Shamila D Alipoor
- Department of Molecular Medicine, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Ian M Adcock
- National Heart and Lung Institute, Imperial College London, London, United Kingdom; Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, The University of Newcastle, Newcastle, NSW, Australia
| | - Payam Tabarsi
- Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Gert Folkerts
- Division of Pharmacology, Faculty of Science, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands
| | - Esmaeil Mortaz
- Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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22
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Tribolet L, Kerr E, Cowled C, Bean AGD, Stewart CR, Dearnley M, Farr RJ. MicroRNA Biomarkers for Infectious Diseases: From Basic Research to Biosensing. Front Microbiol 2020; 11:1197. [PMID: 32582115 PMCID: PMC7286131 DOI: 10.3389/fmicb.2020.01197] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/12/2020] [Indexed: 12/19/2022] Open
Abstract
In the pursuit of improved diagnostic tests for infectious diseases, several classes of molecules have been scrutinized as prospective biomarkers. Small (18–22 nucleotide), non-coding RNA transcripts called microRNAs (miRNAs) have emerged as promising candidates with extensive diagnostic potential, due to their role in numerous diseases, previously established methods for quantitation and their stability within biofluids. Despite efforts to identify, characterize and apply miRNA signatures as diagnostic markers in a range of non-infectious diseases, their application in infectious disease has advanced relatively slowly. Here, we outline the benefits that miRNA biomarkers offer to the diagnosis, management, and treatment of infectious diseases. Investigation of these novel biomarkers could advance the use of personalized medicine in infectious disease treatment, which raises important considerations for validating their use as diagnostic or prognostic markers. Finally, we discuss new and emerging miRNA detection platforms, with a focus on rapid, point-of-care testing, to evaluate the benefits and obstacles of miRNA biomarkers for infectious disease.
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Affiliation(s)
- Leon Tribolet
- Health and Biosecurity, Australian Animal Health Laboratory, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Geelong, VIC, Australia
| | - Emily Kerr
- Institute for Frontier Materials, Deakin University, Geelong, VIC, Australia
| | - Christopher Cowled
- Health and Biosecurity, Australian Animal Health Laboratory, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Geelong, VIC, Australia
| | - Andrew G D Bean
- Health and Biosecurity, Australian Animal Health Laboratory, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Geelong, VIC, Australia
| | - Cameron R Stewart
- Health and Biosecurity, Australian Animal Health Laboratory, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Geelong, VIC, Australia
| | - Megan Dearnley
- Diagnostics, Surveillance and Response (DSR), Australian Animal Health Laboratory, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Geelong, VIC, Australia
| | - Ryan J Farr
- Diagnostics, Surveillance and Response (DSR), Australian Animal Health Laboratory, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Geelong, VIC, Australia
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23
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Unraveling the Role of MicroRNAs in Mycobacterium tuberculosis Infection and Disease: Advances and Pitfalls. Infect Immun 2020; 88:IAI.00649-19. [PMID: 31871103 DOI: 10.1128/iai.00649-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Tuberculosis (TB) is an infectious disease of extremely high epidemiological burden worldwide that is easily acquired through the inhalation of infected respiratory droplets. The complex pathogenesis of this infection spans from subjects never developing this disease despite intense exposure, to others in which immune containment fails catastrophically and severe or disseminated forms of disease ensue. In recent decades, microRNAs (miRNAs) have gained increasing attention due to their role as gene silencers and because of their altered expression in diverse human diseases, including some infections. Recent research regarding miRNAs and TB has revealed that the expression profile for particular miRNAs clearly changes upon Mycobacterium tuberculosis infection and also varies in the different stages of this disease. However, despite the growing number of studies-some of which have even proposed some miRNAs as potential biomarkers-methodological variations and key differences in relevant factors, such as sex and age, cell type analyzed, M. tuberculosis strain, and antimicrobial therapy status, strongly hinder the comparison of data. In this review, we summarize and discuss the literature and highlight the role of selected miRNAs that have specifically and more consistently been associated with M. tuberculosis infection, together with a discussion of the possible gene and immune regulation pathways involved.
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24
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Li ZB, Han YS, Wei LL, Shi LY, Yi WJ, Chen J, Huang H, Jiang TT, Li JC. Screening and identification of plasma lncRNAs uc.48+ and NR_105053 as potential novel biomarkers for cured pulmonary tuberculosis. Int J Infect Dis 2020; 92:141-150. [PMID: 31931167 DOI: 10.1016/j.ijid.2020.01.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/02/2020] [Accepted: 01/03/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) treatment takes a long time, and a gold standard test to define TB cure is lacking. This may lead to early discharge of TB patients, resulting in an increased risk of disease transmission and drug resistance. Plasma lncRNAs might act as potential biomarkers to evaluate TB cure in an efficient and precise manner. METHODS A lncRNA microarray assay was used to screen differentially expressed plasma lncRNAs in untreated TB and cured TB subjects. The expression levels of lncRNAs were verified by qPCR. Target genes of lncRNAs were predicted using a coding-non-coding gene co-expression network and mRNA-lncRNA-miRNA interaction network analysis. RESULTS The expression levels of lncRNAs uc.48+ (p < 0.001) and NR_105053 (p = 0.03) were found to differ significantly between the untreated TB group and the cured TB group. The predicted target genes of uc.48+ were EP300, BAI1 and NR_105053 were TLR9, MYD88, BAI1, respectively. A predictive model for cured TB was established by the combination of uc.48+ and NR_105053 expression, with a sensitivity of 90.00% and specificity of 86.36%, and an area under the curve (AUC) value of 0.945. CONCLUSIONS lncRNAs uc.48+ and NR_105053 may serve as potential biomarkers to distinguish between untreated TB patients and cured TB subjects. This study provides an experimental basis to evaluate the effect of TB treatment and may also provide new clues to the pathological mechanisms of TB.
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Affiliation(s)
- Zhi-Bin Li
- Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yu-Shuai Han
- Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Li-Liang Wei
- Department of Pneumology, Shaoxing University Affiliated Hospital, Shaoxing 312000, China
| | - Li-Ying Shi
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou, 310058, China
| | - Wen-Jing Yi
- Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Jing Chen
- Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Huai Huang
- Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Ting-Ting Jiang
- Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Ji-Cheng Li
- Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou, 310058, China; Medical Research Center, Yubei People's Hospital, Shaoguan 512026, China.
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Gan L, Jiang T, Yi W, Lu R, Xu F, Liu C, Li Z, Han Y, Hu Y, Chen J, Tu H, Huang H, Li J. Study on potential biomarkers of energy metabolism‐related to early‐stage Yin‐deficiency‐heat syndrome based on metabolomics and transcriptomics. Anat Rec (Hoboken) 2020; 303:2109-2120. [PMID: 31909898 DOI: 10.1002/ar.24355] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 12/10/2019] [Accepted: 12/10/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Lin Gan
- South China University of Technology School of Medicine Guangzhou China
- Department of Anatomy and Embryology Zhejiang University Hangzhou China
| | - Ting‐Ting Jiang
- South China University of Technology School of Medicine Guangzhou China
- Department of Anatomy and Embryology Zhejiang University Hangzhou China
| | - Wen‐Jing Yi
- Medical Research Center, Yuebei People's Hospital Shaoguan China
| | - Ren Lu
- Health Management Center, The People's Liberation Army No.117 Hospital Hangzhou China
| | - Fang‐Yan Xu
- Xiaoshan Hospital of Traditional Chinese Medicine Hangzhou China
| | - Chang‐Ming Liu
- Department of Anatomy and Embryology Zhejiang University Hangzhou China
| | - Zhi‐Bin Li
- Department of Anatomy and Embryology Zhejiang University Hangzhou China
| | - Yu‐Shuai Han
- Department of Anatomy and Embryology Zhejiang University Hangzhou China
| | - Yu‐Ting Hu
- Medical Research Center, Yuebei People's Hospital Shaoguan China
| | - Jing Chen
- Department of Anatomy and Embryology Zhejiang University Hangzhou China
| | - Hui‐Hui Tu
- Department of Anatomy and Embryology Zhejiang University Hangzhou China
| | - Huai Huang
- Medical Research Center, Yuebei People's Hospital Shaoguan China
| | - Ji‐Cheng Li
- Department of Anatomy and Embryology Zhejiang University Hangzhou China
- Medical Research Center, Yuebei People's Hospital Shaoguan China
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Yuan Q, Chen H, Yang Y, Fu Y, Yi Z. miR-18a promotes Mycobacterial survival in macrophages via inhibiting autophagy by down-regulation of ATM. J Cell Mol Med 2019; 24:2004-2012. [PMID: 31845528 PMCID: PMC6991191 DOI: 10.1111/jcmm.14899] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/24/2019] [Accepted: 11/19/2019] [Indexed: 02/06/2023] Open
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), is one of leading causes of global deaths. This study aimed to explore the role of miR-18a in RAW264.7 cells response to Mtb infection. Exosomes derived from Mtb-infected cells were isolated and further validated by size, transmission electron microscopy and Western blot. RT-PCR was utilized to measure miR-18a expression. Cell viability and ultrastructure were examined by CFU counting, CCK-8 and electron microscope, respectively. Potential target genes of miR-18a were predicted with bioinformatics and further confirmed using RT-PCR, Western blot and laser confocal microscope analysis, respectively. LC3, AMPK and mTOR were measured using Western blot. We found that miR-18a was induced both in Mtb-infected RAW264.7 cells and its derived exosomes compared with the controls. In addition, up-regulation of miR-18a promoted intracellular Mtb survival, attenuated cell viability and reduced LC3-II level, while its down-regulation had the opposite effect. miR-18a overexpression suppressed level of ATM, one possible target of miR-18a, while its underexpression enhanced ATM. We also found that inhibition of ATM induced LC3-II decrease in Mtb-infected cells and could reverse the increase of LC3-II caused by inhibition of miR-18a. Moreover, down-regulation of miR-18a increased p-AMPK level while reduction of ATM could reverse the change. Taken together, our results suggest that miR-18a is up-regulated in macrophages response to Mtb infection, and it promotes intracellular Mtb survival through repressing autophagic process by down-regulation of ATM pathway. This provides new thought for TB pathogenesis, diagnosis and treatment.
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Affiliation(s)
- Qiulu Yuan
- Key Laboratory of Clinical Laboratory Diagnostics in Universities of Shandong, Department of Laboratory Medicine, Weifang Medical University, Weifang, China
| | - Haotian Chen
- Key Laboratory of Clinical Laboratory Diagnostics in Universities of Shandong, Department of Laboratory Medicine, Weifang Medical University, Weifang, China
| | - Yuxin Yang
- Key Laboratory of Clinical Laboratory Diagnostics in Universities of Shandong, Department of Laboratory Medicine, Weifang Medical University, Weifang, China
| | - Yurong Fu
- Key Laboratory of Clinical Laboratory Diagnostics in Universities of Shandong, Department of Laboratory Medicine, Weifang Medical University, Weifang, China.,Department of Medical Microbiology, Clinical Medicine College, Weifang Medical University, Weifang, China
| | - Zhengjun Yi
- Key Laboratory of Clinical Laboratory Diagnostics in Universities of Shandong, Department of Laboratory Medicine, Weifang Medical University, Weifang, China
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Pedersen JL, Bokil NJ, Saunders BM. Developing new TB biomarkers, are miRNA the answer? Tuberculosis (Edinb) 2019; 118:101860. [PMID: 31472444 DOI: 10.1016/j.tube.2019.101860] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/19/2019] [Accepted: 08/20/2019] [Indexed: 12/14/2022]
Abstract
Efforts to reduce the global TB burden are hindered by the lack of simple, reliable non-sputum based diagnostics. To date studies investigating the biomarker potential of circulating host proteins and mRNA have not shown sufficient diagnostic utility. Recently, there has been increasing interest in circulating miRNA as a biomarker of TB disease. This review examined all published miRNA-TB biomarker studies to determine if a reproducible miRNA signature of TB disease could be elucidated. From 15 miRNA profiling studies, 894 miRNA differentially expressed between TB patients and healthy controls were identified in at least one study. Of these, 143 miRNA were validated by qPCR with 53 differentially expressed between TB patients and controls. Interestingly, only 8 of these miRNA were identified in 2 or more studies, and no consensus on a reproducible miRNA signature for identification of TB disease could be identified. TB disease is clearly associated with a wide breadth of differentially expressed miRNA. This review highlights our recent progress and the multiple factors, including environment, source of tissue, ethnicity and extent of TB disease that may influence miRNA expression. Coordinated efforts are required to validate identified targets in multiple populations to progress miRNA biomarker development.
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Affiliation(s)
- Jessica L Pedersen
- School of Life Sciences, Faculty of Science, University of Technology Sydney, 15 Broadway, Ultimo, Sydney, 2007, Australia.
| | - Nilesh J Bokil
- School of Life Sciences, Faculty of Science, University of Technology Sydney, 15 Broadway, Ultimo, Sydney, 2007, Australia.
| | - Bernadette M Saunders
- School of Life Sciences, Faculty of Science, University of Technology Sydney, 15 Broadway, Ultimo, Sydney, 2007, Australia.
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Tu H, Yang S, Jiang T, Wei L, Shi L, Liu C, Wang C, Huang H, Hu Y, Chen Z, Chen J, Li Z, Li J. Elevated pulmonary tuberculosis biomarker miR-423-5p plays critical role in the occurrence of active TB by inhibiting autophagosome-lysosome fusion. Emerg Microbes Infect 2019; 8:448-460. [PMID: 30898038 PMCID: PMC6455132 DOI: 10.1080/22221751.2019.1590129] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Rapid diagnosis of pulmonary tuberculosis is an effective measure to prevent the spread of tuberculosis. However, the grim fact is that the new, rapid, and safe methods for clinical diagnosis are lacking. Moreover, although auto-lysosome is critical in clearing Mycobacterium tuberculosis, the pathological significance of microRNAs, as biomarkers of tuberculosis, in autophagosome maturation is unclear. Here, these microRNAs were investigated by Solexa sequencing and qPCR validation, and a potential diagnostic model was established by logistic regression. Besides that, the mechanism of one of the microRNAs involved in the occurrence of tuberculosis was studied. The results showed that the expression of miR-423-5p, miR-17-5p, and miR-20b-5p were significantly increased in the serum of patients with tuberculosis. The combination of these three microRNAs established a model to diagnose tuberculosis with an accuracy of 78.18%, and an area under the curve value of 0.908. Bioinformatics analysis unveiled miR-423-5p as the most likely candidate in regulating autophagosome maturation. The up-regulation of miR-423-5p could inhibit autophagosome maturation through suppressing autophagosome–lysosome fusion in macrophages. Further investigations showed that VPS33A was the direct target of miR-423-5p, and the two CUGCCCCUC domains in VPS33A 3’-UTR were the direct regulatory sites for miR-423-5p. In addition, an inverse correlation between VPS33A and miR-423-5p was found in peripheral blood mononuclear cells of patients with tuberculosis. Since the inhibition of autolysosome formation plays a critical role in tuberculosis occurrence, our findings suggests that miR-423-5p could suppress autophagosome–lysosome fusion by post-transcriptional regulation of VPS33A, which might be important for the occurrence of active tuberculosis.
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Affiliation(s)
- Huihui Tu
- a Institute of Cell Biology , Zhejiang University School of Medicine , Hangzhou , People's Republic of China
| | - Su Yang
- a Institute of Cell Biology , Zhejiang University School of Medicine , Hangzhou , People's Republic of China
| | - Tingting Jiang
- a Institute of Cell Biology , Zhejiang University School of Medicine , Hangzhou , People's Republic of China.,b School of Medicine , South China University of Technology , Guangzhou , People's Republic of China
| | - Liliang Wei
- c Department of Pneumology , Shaoxing Municipal Hospital , Shaoxing , People's Republic of China
| | - Liying Shi
- d Department of Clinical Laboratory , Zhejiang Hospital , Hangzhou , People's Republic of China
| | - Changming Liu
- a Institute of Cell Biology , Zhejiang University School of Medicine , Hangzhou , People's Republic of China
| | - Chong Wang
- a Institute of Cell Biology , Zhejiang University School of Medicine , Hangzhou , People's Republic of China
| | - Huai Huang
- b School of Medicine , South China University of Technology , Guangzhou , People's Republic of China
| | - Yuting Hu
- b School of Medicine , South China University of Technology , Guangzhou , People's Republic of China
| | - Zhongliang Chen
- a Institute of Cell Biology , Zhejiang University School of Medicine , Hangzhou , People's Republic of China
| | - Jing Chen
- a Institute of Cell Biology , Zhejiang University School of Medicine , Hangzhou , People's Republic of China
| | - Zhongjie Li
- a Institute of Cell Biology , Zhejiang University School of Medicine , Hangzhou , People's Republic of China
| | - Jicheng Li
- a Institute of Cell Biology , Zhejiang University School of Medicine , Hangzhou , People's Republic of China
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Yi WJ, Han YS, Wei LL, Shi LY, Huang H, Jiang TT, Li ZB, Chen J, Hu YT, Tu HH, Li JC. l-Histidine, arachidonic acid, biliverdin, and l-cysteine-glutathione disulfide as potential biomarkers for cured pulmonary tuberculosis. Biomed Pharmacother 2019; 116:108980. [PMID: 31125821 DOI: 10.1016/j.biopha.2019.108980] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 04/15/2019] [Accepted: 05/08/2019] [Indexed: 11/25/2022] Open
Abstract
Lack of laboratory standards for cured tuberculosis (TB) can lead to early discharge of untreated TB patients from the hospital, resulting in increased risk of TB spread and of developing drug resistant Mycobacterium tuberculosis (Mtb). We used ultra-high performance liquid chromatography coupled with mass spectrometry (LC-MS) to detect heparin anticoagulant in plasma of untreated TB patients, two-month treated TB patients, cured TB subjects, and healthy controls. Screening of differentially expressed metabolites resulted in identification of four differentially expressed metabolites such as, l-Histidine, Arachidonic acid (AA), Biliverdin, and l-Cysteine-glutathione disulfide after 6 months of TB treatment. Among them, l-Cysteine-glutathione disulfide and AA could be identified after 2 months of TB treatment. We established a cured TB model with an area under the curve (AUC) of 0.909 (95% CI, 0.802-0.970), 86.2% sensitivity, and 85.2% specificity. The diagnostic model fitted from the four differential metabolites in combination (l-Histidine, AA, Biliverdin, and l-Cysteine-glutathione disulfide) can be used as potential biomarkers for cured TB. Our study provided laboratory standards for hospital discharge of TB patients, as well as experimental basis for evaluating the efficacy of anti-TB drugs.
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Affiliation(s)
- Wen-Jing Yi
- Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou, 310058, China.
| | - Yu-Shuai Han
- Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou, 310058, China.
| | - Li-Liang Wei
- Department of Pneumology, Shaoxing Municipal Hospital, Shaoxing, 312000, China.
| | - Li-Ying Shi
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou, 310058, China.
| | - Huai Huang
- School of Medicine, South China University of Technology, Guangzhou, 510000, China.
| | - Ting-Ting Jiang
- School of Medicine, South China University of Technology, Guangzhou, 510000, China.
| | - Zhi-Bin Li
- Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou, 310058, China.
| | - Jing Chen
- Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou, 310058, China.
| | - Yu-Ting Hu
- School of Medicine, South China University of Technology, Guangzhou, 510000, China.
| | - Hui-Hui Tu
- Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou, 310058, China.
| | - Ji-Cheng Li
- Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou, 310058, China.
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Bai H, Wu Q, Hu X, Wu T, Song J, Liu T, Meng Z, Lv M, Lu X, Chen X, Zhou Y, Ying B. Clinical significance of lnc-AC145676.2.1-6 and lnc-TGS1-1 and their variants in western Chinese tuberculosis patients. Int J Infect Dis 2019; 84:8-14. [PMID: 31028876 DOI: 10.1016/j.ijid.2019.04.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 04/15/2019] [Accepted: 04/18/2019] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVES Tuberculosis (TB) remains a global public health problem. Recent studies have implicated long non-coding RNAs and their variants as possibly playing important roles in TB. The aim of this study was to assess the clinical relevance of lnc-AC145676.2.1-6 and lnc-TGS1-1 and their variants in a western Chinese population. METHODS This case-control study included 467 TB patients and 473 healthy controls from West China Hospital. The expression levels of lnc-AC145676.2.1-6 and lnc-TGS1-1 were analyzed by reverse transcriptase quantitative real-time PCR. Single-nucleotide polymorphism genotyping was performed using a custom-designed 2 × 48-Plex SNPscan kit. RESULTS It was observed that lnc-AC145676.2.1-6 and lnc-TGS1-1 expression levels were both obviously down-regulated in TB patients. In addition, a lower expression level of lnc-TGS1-1 was associated with the presence of thrombocytopenia in TB patients during anti-TB treatment, and the homozygous CC genotype of rs4737420 correlated with a decreased risk of leukopenia, compared with individuals with the T allele (TT/CT genotype), in the dominant mode. CONCLUSIONS For the first time, potential TB-associated promoting effects were identified for the decreased expression levels of lnc-AC145676.2.1-6 and lnc-TGS-1, while lnc-TGS1-1 and its variant rs4737420 may be predictive indicators of anti-TB drug-induced adverse drug reactions. Larger validation studies on different populations are warranted to confirm these findings.
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Affiliation(s)
- Hao Bai
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Qian Wu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Xuejiao Hu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Tao Wu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Jiajia Song
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Tangyuheng Liu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Zirui Meng
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Mengyuan Lv
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Xiaojun Lu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Xuerong Chen
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Yanhong Zhou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, PR China.
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Liang J, Cui Y, Meng Y, Li X, Wang X, Liu W, Huang L, Du H. Integrated analysis of transcription factors and targets co-expression profiles reveals reduced correlation between transcription factors and target genes in cancer. Funct Integr Genomics 2018; 19:191-204. [PMID: 30251028 DOI: 10.1007/s10142-018-0636-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 09/03/2018] [Accepted: 09/13/2018] [Indexed: 12/11/2022]
Abstract
Transcription factors are recognized as the key regulators of gene expression. However, the changes in the correlation of transcription factors and their target genes between normal and tumor tissues are usually ignored. In this research, we used mRNA expression profile data from The Cancer Genome Atlas which included 5726 samples across 11 major human cancers to perform co-expression analysis by the Pearson correlation coefficients. Then, integrating 81,357 pairs of transcription factors and target genes from transcription factors databases to find out the changes in the co-expression correlation of these gene pairs from normal to tumor tissues. Based on the changes in the number of co-expressed TF-TG pairs and changes in the level of co-expression, we found the generally reduced correlation between transcription factors and their target genes in cancer. Additionally, we screened out universal and specific transcription factors-target genes pairs which may significant influence particular cancer. Then, we obtained 423 cancer cell line expression profiles from Broad Institute Cancer Cell Line Encyclopedia to verify our results. Some of these pairs like XRCC5-XRCC6 have been reported to involve in multiple cancers, while pairs like IRF1-PSMB9 without any previous articles related to tumor but involve in the biological processes of cancer, which are of great potential to be therapeutic targets. Our research may provide insights to better understand the tumor development mechanisms and find potential therapeutic targets.
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Affiliation(s)
- Jinsheng Liang
- School of Biology and Biological Engineering, South China University of Technology, 382 Zhonghuan Road East, Panyu District, Guangzhou Higher Education Mega Centre, Guangzhou, 510006, Guangdong, China
| | - Ying Cui
- School of Biology and Biological Engineering, South China University of Technology, 382 Zhonghuan Road East, Panyu District, Guangzhou Higher Education Mega Centre, Guangzhou, 510006, Guangdong, China
| | - Yuhuan Meng
- School of Biology and Biological Engineering, South China University of Technology, 382 Zhonghuan Road East, Panyu District, Guangzhou Higher Education Mega Centre, Guangzhou, 510006, Guangdong, China
| | - Xingsong Li
- School of Biology and Biological Engineering, South China University of Technology, 382 Zhonghuan Road East, Panyu District, Guangzhou Higher Education Mega Centre, Guangzhou, 510006, Guangdong, China
| | - Xueping Wang
- Department of Laboratory Medicine, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wanli Liu
- Department of Laboratory Medicine, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Lizhen Huang
- School of Biology and Biological Engineering, South China University of Technology, 382 Zhonghuan Road East, Panyu District, Guangzhou Higher Education Mega Centre, Guangzhou, 510006, Guangdong, China
| | - Hongli Du
- School of Biology and Biological Engineering, South China University of Technology, 382 Zhonghuan Road East, Panyu District, Guangzhou Higher Education Mega Centre, Guangzhou, 510006, Guangdong, China.
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Hermans-Beijnsberger S, van Bilsen M, Schroen B. Long non-coding RNAs in the failing heart and vasculature. Noncoding RNA Res 2018; 3:118-130. [PMID: 30175285 PMCID: PMC6114261 DOI: 10.1016/j.ncrna.2018.04.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 04/09/2018] [Accepted: 04/09/2018] [Indexed: 02/06/2023] Open
Abstract
Following completion of the human genome, it became evident that the majority of our DNA is transcribed into non-coding RNAs (ncRNAs) instead of protein-coding messenger RNA. Deciphering the function of these ncRNAs, including both small- and long ncRNAs (lncRNAs), is an emerging field of research. LncRNAs have been associated with many disorders and a number have been identified as key regulators in the development and progression of disease, including cardiovascular disease (CVD). CVD causes millions of deaths worldwide, annually. Risk factors include coronary artery disease, high blood pressure and ageing. In this review, we will focus on the roles of lncRNAs in the cellular and molecular processes that underlie the development of CVD: cardiomyocyte hypertrophy, fibrosis, inflammation, vascular disease and ageing. Finally, we discuss the biomarker and therapeutic potential of lncRNAs.
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Affiliation(s)
- Steffie Hermans-Beijnsberger
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, Universiteitssingel 50, 6200 MD, Maastricht, The Netherlands
| | - Marc van Bilsen
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, Universiteitssingel 50, 6200 MD, Maastricht, The Netherlands
- Department of Physiology, CARIM School for Cardiovascular Diseases, Maastricht University, Universiteitssingel 50, 6200 MD, Maastricht, The Netherlands
| | - Blanche Schroen
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, Universiteitssingel 50, 6200 MD, Maastricht, The Netherlands
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33
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Yang T, Ge B. miRNAs in immune responses to Mycobacterium tuberculosis infection. Cancer Lett 2018; 431:22-30. [PMID: 29803788 DOI: 10.1016/j.canlet.2018.05.028] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 05/16/2018] [Accepted: 05/17/2018] [Indexed: 12/21/2022]
Abstract
Tuberculosis (TB) is one of the most fatal infectious diseases, affecting one third of the world's population. The causative agent, Mycobacterium tuberculosis (Mtb), has a well-established ability to circumvent the host's immune system for its long-term intracellular survival. MicroRNAs (miRNAs) are crucial post-transcriptional regulators of immune response. They act by negatively regulating the expression levels of important genes in both innate and adaptive immunity. It has been established in recent studies that the host immune response against Mtb is regulated by many miRNAs, most of which are induced by Mtb infection. Moreover, differential expression of miRNA in tuberculosis (TB) patients may help distinguish between TB patients and healthy individuals or latent TB. In this review, we present the recent advancements on the miRNA regulation of the host responses against Mtb infection, as well as the potential of miRNAs to as biomarkers for TB diagnosis.
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Affiliation(s)
- Tianshu Yang
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China; Department of Microbiology and Immunology, Tongji University Medicine, Shanghai, China
| | - Baoxue Ge
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China; Department of Microbiology and Immunology, Tongji University Medicine, Shanghai, China.
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