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Gosetti di Sturmeck T, Malimpensa L, Ferrazzano G, Belvisi D, Leodori G, Lembo F, Brandi R, Pascale E, Cattaneo A, Salvetti M, Conte A, D’Onofrio M, Arisi I. Exploring miRNAs' Based Modeling Approach for Predicting PIRA in Multiple Sclerosis: A Comprehensive Analysis. Int J Mol Sci 2024; 25:6342. [PMID: 38928049 PMCID: PMC11203572 DOI: 10.3390/ijms25126342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 05/31/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
The current hypothesis on the pathophysiology of multiple sclerosis (MS) suggests the involvement of both inflammatory and neurodegenerative mechanisms. Disease Modifying Therapies (DMTs) effectively decrease relapse rates, thus reducing relapse-associated disability in people with MS. In some patients, disability progression, however, is not solely linked to new lesions and clinical relapses but can manifest independently. Progression Independent of Relapse Activity (PIRA) significantly contributes to long-term disability, stressing the urge to unveil biomarkers to forecast disease progression. Twenty-five adult patients with relapsing-remitting multiple sclerosis (RRMS) were enrolled in a cohort study, according to the latest McDonald criteria, and tested before and after high-efficacy Disease Modifying Therapies (DMTs) (6-24 months). Through Agilent microarrays, we analyzed miRNA profiles from peripheral blood mononuclear cells. Multivariate logistic and linear models with interactions were generated. Robustness was assessed by randomization tests in R. A subset of miRNAs, correlated with PIRA, and the Expanded Disability Status Scale (EDSS), was selected. To refine the patient stratification connected to the disease trajectory, we computed a robust logistic classification model derived from baseline miRNA expression to predict PIRA status (AUC = 0.971). We built an optimal multilinear model by selecting four other miRNA predictors to describe EDSS changes compared to baseline. Multivariate modeling offers a promising avenue to uncover potential biomarkers essential for accurate prediction of disability progression in early MS stages. These models can provide valuable insights into developing personalized and effective treatment strategies.
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Affiliation(s)
- Tommaso Gosetti di Sturmeck
- European Brain Research Institute (EBRI) Rita Levi-Montalcini, 00161 Rome, Italy; (T.G.d.S.); (R.B.); (A.C.)
| | - Leonardo Malimpensa
- IRCCS Istituto Neurologico Mediterraneo Neuromed, 86077 Pozzilli, Italy; (L.M.); (D.B.); (G.L.); (M.S.); (A.C.)
| | - Gina Ferrazzano
- Department of Human Neurosciences, Sapienza University of Rome, 00185 Rome, Italy; (G.F.); (F.L.)
| | - Daniele Belvisi
- IRCCS Istituto Neurologico Mediterraneo Neuromed, 86077 Pozzilli, Italy; (L.M.); (D.B.); (G.L.); (M.S.); (A.C.)
- Department of Human Neurosciences, Sapienza University of Rome, 00185 Rome, Italy; (G.F.); (F.L.)
| | - Giorgio Leodori
- IRCCS Istituto Neurologico Mediterraneo Neuromed, 86077 Pozzilli, Italy; (L.M.); (D.B.); (G.L.); (M.S.); (A.C.)
- Department of Human Neurosciences, Sapienza University of Rome, 00185 Rome, Italy; (G.F.); (F.L.)
| | - Flaminia Lembo
- Department of Human Neurosciences, Sapienza University of Rome, 00185 Rome, Italy; (G.F.); (F.L.)
| | - Rossella Brandi
- European Brain Research Institute (EBRI) Rita Levi-Montalcini, 00161 Rome, Italy; (T.G.d.S.); (R.B.); (A.C.)
| | - Esterina Pascale
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, 04100 Latina, Italy;
| | - Antonino Cattaneo
- European Brain Research Institute (EBRI) Rita Levi-Montalcini, 00161 Rome, Italy; (T.G.d.S.); (R.B.); (A.C.)
- Bio@SNS Laboratory of Biology, Scuola Normale Superiore (SNS), 56126 Pisa, Italy
| | - Marco Salvetti
- IRCCS Istituto Neurologico Mediterraneo Neuromed, 86077 Pozzilli, Italy; (L.M.); (D.B.); (G.L.); (M.S.); (A.C.)
- Centre for Experimental Neurological Therapies (CENTERS), Department of Neurosciences, Mental Health and Sensory Organs, Sapienza University of Rome, 00189 Rome, Italy
| | - Antonella Conte
- IRCCS Istituto Neurologico Mediterraneo Neuromed, 86077 Pozzilli, Italy; (L.M.); (D.B.); (G.L.); (M.S.); (A.C.)
- Department of Human Neurosciences, Sapienza University of Rome, 00185 Rome, Italy; (G.F.); (F.L.)
| | - Mara D’Onofrio
- European Brain Research Institute (EBRI) Rita Levi-Montalcini, 00161 Rome, Italy; (T.G.d.S.); (R.B.); (A.C.)
| | - Ivan Arisi
- European Brain Research Institute (EBRI) Rita Levi-Montalcini, 00161 Rome, Italy; (T.G.d.S.); (R.B.); (A.C.)
- Institute of Translational Pharmacology, National Research Council, 00133 Rome, Italy
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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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Sampath P, Moorthy M, Menon A, Madhav L, Janaki A, Dhanapal M, Natarajan AP, Hissar S, Ranganathan UD, Ramaswamy G, Bethunaickan R. Downregulation of monocyte miRNAs: implications for immune dysfunction and disease severity in drug-resistant tuberculosis. Front Immunol 2023; 14:1197805. [PMID: 37457712 PMCID: PMC10345223 DOI: 10.3389/fimmu.2023.1197805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/02/2023] [Indexed: 07/18/2023] Open
Abstract
Background Monocyte miRNAs govern both protective and pathological responses during tuberculosis (TB) through their differential expression and emerged as potent targets for biomarker discovery and host-directed therapeutics. Thus, this study examined the miRNA profile of sorted monocytes across the TB disease spectrum [drug-resistant TB (DR-TB), drug-sensitive TB (DS-TB), and latent TB] and in healthy individuals (HC) to understand the underlying pathophysiology and their regulatory mechanism. Methods We sorted total monocytes including three subsets (HLA-DR+CD14+, HLA-DR+CD14+CD16+, and HLA-DR+CD16+cells) from peripheral blood mononuclear cells (PBMCs) of healthy and TB-infected individuals through flow cytometry and subjected them to NanoString-based miRNA profiling. Results The outcome was the differential expression of 107 miRNAs particularly the downregulation of miRNAs in the active TB groups (both drug-resistant and drug-sensitive). The miRNA profile revealed differential expression signatures: i) decline of miR-548m in DR-TB alone, ii) decline of miR-486-3p in active TB but significant elevation only in LTB iii) elevation of miR-132-3p only in active TB (DR-TB and DS-TB) and iv) elevation of miR-150-5p in DR-TB alone. The directionality of functions mediated by monocyte miRNAs from Gene Set Enrichment Analysis (GSEA) facilitated two phenomenal findings: i) a bidirectional response between active disease (activation profile in DR-TB and DS-TB compared to LTB and HC) and latent infection (suppression profile in LTB vs HC) and ii) hyper immune activation in the DR-TB group compared to DS-TB. Conclusion Thus, monocyte miRNA signatures provide pathological clues for altered monocyte function, drug resistance, and disease severity. Further studies on monocyte miRNAs may shed light on the immune regulatory mechanism for tuberculosis.
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Affiliation(s)
- Pavithra Sampath
- Department of Immunology, Indian Council of Medical Research (ICMR)-National Institute for Research in Tuberculosis (NIRT), Chennai, India
| | | | - Athul Menon
- TheraCUES Innovations Pvt. Ltd, Bangalore, India
| | | | - Aishwarya Janaki
- Department of Immunology, Indian Council of Medical Research (ICMR)-National Institute for Research in Tuberculosis (NIRT), Chennai, India
| | - Madhavan Dhanapal
- Department of Immunology, Indian Council of Medical Research (ICMR)-National Institute for Research in Tuberculosis (NIRT), Chennai, India
| | | | - Syed Hissar
- Department of Clinical Research, ICMR-National Institute of Research in Tuberculosis (NIRT), Chennai, India
| | - Uma Devi Ranganathan
- Department of Immunology, Indian Council of Medical Research (ICMR)-National Institute for Research in Tuberculosis (NIRT), Chennai, India
| | | | - Ramalingam Bethunaickan
- Department of Immunology, Indian Council of Medical Research (ICMR)-National Institute for Research in Tuberculosis (NIRT), Chennai, India
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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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5
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Study on the Predictive Value of P53 Protein Expression in Brain Metastasis in NSCLC and the Mechanism of miR-424 Reversing Platinum Resistance in NSCLC. CONTRAST MEDIA & MOLECULAR IMAGING 2022; 2022:5273772. [PMID: 36043143 PMCID: PMC9377954 DOI: 10.1155/2022/5273772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/14/2022] [Accepted: 06/24/2022] [Indexed: 11/17/2022]
Abstract
In order to analyze the predictive value of P53 protein expression in brain metastases in NSCLC and the mechanism of miR-424 reversing platinum resistance in NSCLC, a retrospective analysis is conducted in this study. Eighty-two NSCLC patients who received relevant diagnosis and treatment in our hospital from September 2020 to September 2021 are chosen. The prognosis of the patients is observed, and the patients were divided into two groups according to the occurrence of BMS. The comparison of clinical baseline data and the expression of P53 protein and miR-424 after surgery are performed. Furthermore, the predictive value of the P53 protein gene on the occurrence of BMS in NSCLC is analyzed by the ROC curve, and the expression of miR-424 in serum of the patients before and after drug resistance is compared. The results demonstrate that the expression of P53 protein has a high predictive value for predicting the occurrence of BRAIN metastases in NSCLC patients. Also, the high expression of miR-424 suggests that it is closely related to the occurrence of platinum resistance in NSCLC patients.
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Kaushik A, Bandyopadhyay S, Porwal C, Srinivasan A, Rukmangadachar LA, Hariprasad G, Kola S, Kataria J, Singh UB. 2D-DIGE based urinary proteomics and functional enrichment studies to reveal novel Mycobacterium tuberculosis and human protein biomarker candidates for pulmonary tuberculosis. Biochem Biophys Res Commun 2022; 619:15-21. [PMID: 35728279 DOI: 10.1016/j.bbrc.2022.06.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/01/2022] [Accepted: 06/08/2022] [Indexed: 11/30/2022]
Abstract
In the absence of a sensitive and specific diagnostic modality capable of detecting all forms of tuberculosis (TB), proteomics may identify specific Mycobacterium tuberculosis (M.tb) proteins in urine, with a potential as biomarkers. To identify candidate biomarkers for TB, proteome profile of urine from pulmonary TB patients was compared with non-disease controls (NDC) and disease controls (DC, Streptococcus pneumonia infected patients) using a combination of two-dimensional difference gel electrophoresis (2D-DIGE) and liquid chromatography tandem mass spectrometry (LCMS/MS). Eleven differentially expressed host proteins and Eighteen high abundant M.tb proteins were identified. Protein-protein interactome (PPI) and functional enrichment analyses like Gene Ontologies, Reactome pathway etc. demonstrated that the human proteins mainly belong to extracellular space and show physiological pathways for immune response and hematological disorders. Whereas, M.tb proteins belong to the cell periphery, plasma membrane and cell wall, and demonstrated catalytic, nucleotide binding and ATPase activities along with other functional processes. The study findings provide valuable inputs about the biomarkers of TB and shed light on the probable disease consequences as an outcome of the bacterial pathogenicity.
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Affiliation(s)
- Amit Kaushik
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | | | - Chhavi Porwal
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Alagiri Srinivasan
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | | | - Gururao Hariprasad
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Srujana Kola
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Jitender Kataria
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Urvashi B Singh
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, 110029, India.
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Dong W, Wang G, Feng J, Li P, Wang R, Lu H, Lu W, Wang C, Wang X, Chen H, Xiang Y, Tan C. MiR-25 blunts autophagy and promotes the survival of Mycobacterium tuberculosis by regulating NPC1. iScience 2022; 25:104279. [PMID: 35586071 PMCID: PMC9108763 DOI: 10.1016/j.isci.2022.104279] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/28/2022] [Accepted: 04/19/2022] [Indexed: 02/08/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) evades host clearance by inhibiting autophagy. MicroRNA-25 (miR-25) expression was significantly up-regulated in the lung tissues of mice infected with Bacillus Calmette-Guerin (BCG) and macrophages infected with Mtb or BCG, especially in the early stages of infection. MiR-25 can significantly increase the survival of Mtb and BCG in macrophages. We validated that miR-25 targets the NPC1 protein located on the lysosomal membrane, resulting in damage to lysosomal function, thereby inhibiting autophagolysosome formation and promoting the survival of Mtb and BCG. Consistently, mice lacking miR-25 exhibited more resistant to BCG infection. In addition, we found that Rv1759c induces the expression of miR-25 through NFKB inhibitor zeta (NFKBIZ). This study demonstrates that the role of miR-25 during Mtb infection contributes to a better understanding of the pathogenesis of tuberculosis (TB). Mtb up-modulates miR-25 expression especially in the early stage of infection miR-25 targeting NPC1 impairs autophagic flux in macrophages Mice lacking miR-25 exhibits more resistant to BCG infection Rv1759c regulates miR-25 expression and Mtb survival via NFKBIZ
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Affiliation(s)
- Wenqi Dong
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China.,Hubei Hongshan Laboratory, Wuhan, Hubei, China
| | - Gaoyan Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China.,Hubei Hongshan Laboratory, Wuhan, Hubei, China
| | - Jiajia Feng
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China.,Hubei Hongshan Laboratory, Wuhan, Hubei, China
| | - Pei Li
- Department of Gastrointestinal Surgery, The Second Clinical Medical College of Jinan University, Shenzhen, Guangdong, China
| | - Rui Wang
- Department of Experimental Animal Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hao Lu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China.,Hubei Hongshan Laboratory, Wuhan, Hubei, China
| | - Wenjia Lu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China.,Hubei Hongshan Laboratory, Wuhan, Hubei, China
| | - Chenchen Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China.,Hubei Hongshan Laboratory, Wuhan, Hubei, China
| | - Xiangru Wang
- Hubei Hongshan Laboratory, Wuhan, Hubei, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, Hubei, China.,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture of the People's Republic of China, Wuhan, Hubei, China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China.,Hubei Hongshan Laboratory, Wuhan, Hubei, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, Hubei, China.,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture of the People's Republic of China, Wuhan, Hubei, China
| | - Yaozu Xiang
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Chen Tan
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China.,Hubei Hongshan Laboratory, Wuhan, Hubei, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, Hubei, China.,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture of the People's Republic of China, Wuhan, Hubei, China
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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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Saccon TD, Dhahbi JM, Schneider A, Nunez Lopez YO, Qasem A, Cavalcante MB, Sing LK, Naser SA, Masternak MM. Plasma miRNA Profile of Crohn's Disease and Rheumatoid Arthritis Patients. BIOLOGY 2022; 11:508. [PMID: 35453708 PMCID: PMC9033111 DOI: 10.3390/biology11040508] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
Crohn's disease (CD) and rheumatoid arthritis (RA) are immune mediated inflammatory diseases. Several studies indicate a role for microRNAs (miRNAs) in the pathogenesis of a variety of autoimmune diseases, including CD and RA. Our study's goal was to investigate circulating miRNAs in CD and RA patients to identify potential new biomarkers for early detection and personalized therapeutic approaches for autoimmune diseases. For this study, subjects with CD (n = 7), RA (n = 8) and healthy controls (n = 7) were recruited, and plasma was collected for miRNA sequencing. Comparison of the expression patterns of miRNAs between CD and healthy patients identified 99 differentially expressed miRNAs. Out of these miRNAs, 4 were down regulated, while 95 were up regulated. Comparison of miRNAs between RA and healthy patients identified 57 differentially expressed miRNAs. Out of those, 12 were down regulated, while 45 were up regulated. For all the miRNAs down regulated in CD and RA patients, 420 GO terms for biological processes were similarly regulated between both groups. Therefore, the identification of new plasma miRNAs allows the emergence of new biomarkers that can assist in the diagnosis and treatment of CD and RA.
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Affiliation(s)
- Tatiana D. Saccon
- Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas 96010-610, Brazil;
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32816, USA; (A.Q.); (M.B.C.); (S.A.N.)
| | - Joseph M. Dhahbi
- Department of Medical Education, School of Medicine, California University of Science & Medicine, San Bernardino, CA 92324, USA; (J.M.D.); (L.K.S.)
| | - Augusto Schneider
- Faculdade de Nutrição, Universidade Federal de Pelotas, Pelotas 96010-610, Brazil;
| | | | - Ahmad Qasem
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32816, USA; (A.Q.); (M.B.C.); (S.A.N.)
| | - Marcelo B. Cavalcante
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32816, USA; (A.Q.); (M.B.C.); (S.A.N.)
- Department of Obstetrics and Gynecology, Fortaleza University, Fortaleza 60811-905, Brazil
| | - Lauren K. Sing
- Department of Medical Education, School of Medicine, California University of Science & Medicine, San Bernardino, CA 92324, USA; (J.M.D.); (L.K.S.)
| | - Saleh A. Naser
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32816, USA; (A.Q.); (M.B.C.); (S.A.N.)
| | - Michal M. Masternak
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32816, USA; (A.Q.); (M.B.C.); (S.A.N.)
- Department of Head and Neck Surgery, Poznan University of Medical Sciences, 61-701 Poznan, Poland
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10
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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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11
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Zhao J, Gao S, Chen C, Li H, Wang S, Yu Y, Ming L. Screening and identification of differentially expressed long non-coding RNAs in multidrug-resistant tuberculosis. PeerJ 2022; 10:e12776. [PMID: 35111403 PMCID: PMC8772445 DOI: 10.7717/peerj.12776] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 12/21/2021] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Efforts to eradicate tuberculosis are largely threatened by drug-resistant tuberculosis, particularly, multidrug-resistant tuberculosis (MDR-TB). Screening and identification potential biomarkers for MDR-TB is crucial to diagnose early and reduce the incidence of MDR-TB. METHODS To screen the differentially expressed long non-coding RNAs in MDR-TB, the lncRNA and mRNA expression profiles in serum derived from healthy controls (HCs), individuals with MDR-TB and drug-sensitive tuberculosis (DS-TB) were analyzed by microarray assay and 10 lncRNAs were randomly selected for further validation by reverse transcription-quantitative real-time PCR(RT-qPCR). The biological functions of differentially expressed mRNAs as well as relationships between genes and signaling pathways were investigated using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG), respectively. RESULTS A total of 353 differentially expressed lncRNAs (312 upregulated) and 202 mRNAs (99 upregulated) were found in the MDR-TB group compared to HCs. And compared with the DS-TB group, 442 differentially expressed lncRNAs (115 upregulated) and 190 mRNAs (87 upregulated) were found in the MDR-TB group. The expression levels of lncRNA n335659 were found to differ significantly between each group by RT-qPCR. Compared with DS-TB group, the GO analysis showed that the differential mRNAs were mainly enriched in the processes associated with the detection of the chemical stimulus, the regulation of mRNA metabolic process and neutrophil activation in the MDR-TB group; the KEGG analysis indicated that the differential mRNAs between DS-TB and MDR-TB were mainly enriched in proteasome and Notch signaling pathway, which might reveal a fraction of the mechanism of MDR-TB. The discovery of the serum lncRNA n335659 might serve as a potential biomarker for MDR-TB and Notch signaling pathway provided a new clue for the investigation of the pathological mechanism of MDR-TB.
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Affiliation(s)
- Junwei Zhao
- Department of Clinical Laboratory, Key Clinical Laboratory of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - ShuHui Gao
- Department of Clinical Laboratory, Key Clinical Laboratory of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chunguang Chen
- Department of Clinical Laboratory, Henan Provincial Infectious Disease Hospital, Zhengzhou, China
| | - Hui Li
- Tuberculosis Reference Laboratory, Centers for Disease Control and Prevention of Henan Province, Zhengzhou, China
| | - Shaohua Wang
- Tuberculosis Reference Laboratory, Centers for Disease Control and Prevention of Henan Province, Zhengzhou, China
| | - Yongmin Yu
- Department of Clinical Laboratory, Henan Provincial Infectious Disease Hospital, Zhengzhou, China
| | - Liang Ming
- Department of Clinical Laboratory, Key Clinical Laboratory of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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12
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Carranza C, Herrera MT, Guzmán-Beltrán S, Salgado-Cantú MG, Salido-Guadarrama I, Santiago E, Chávez-Galán L, Gutiérrez-González LH, González Y. A Dual Marker for Monitoring MDR-TB Treatment: Host-Derived miRNAs and M. tuberculosis-Derived RNA Sequences in Serum. Front Immunol 2021; 12:760468. [PMID: 34804048 PMCID: PMC8600136 DOI: 10.3389/fimmu.2021.760468] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/18/2021] [Indexed: 12/18/2022] Open
Abstract
Background In the absence of a late marker of treatment failure or relapse in MDR-TB patients, biomarkers based on host-miRNAs coupled with M. tuberculosis-RNAs evaluated in extracellular vesicles (EVs) are an alternative follow-up for MDR-TB disease. Characterization of EVs cargo to identify differentially expressed miRNAs before and after treatment, and to identify M. tuberculosis-derived RNA in serum EVs from resistant TB patients. Methods EVs were isolated from serum of 26 drug-resistant TB (DR-TB) patients and 16 healthy subjects. Differential expression of miRNAs in pooled exosomes from both untreated and treated patients was assessed and individually validated at different time points during treatment. In addition, M. tuberculosis RNA was amplified in the same samples by qPCR. Results A multivariate analysis using miR-let-7e-5p, -197-3p and -223-3p were found to be a more sensitive discriminator between healthy individuals and those with TB for both DR-TB (AUC= 0.96, 95%, CI=0.907-1) and MDR-TB groups (AUC= 0.95, 95%, CI= 0.89-1). Upregulation of miR-let-7e-5p were observed at the time of M. tuberculosis negative culture T(3-5) for MDR-TB group or for long-term T(9-15) for MDR-TB group without diabetes (T2DM). A second pathogen-based marker based on 30kDa and 5KST sequences was detected in 33% of the MDR-TB patients after the intensive phase of treatment. The miR-let7e-5p is a candidate biomarker for long-term monitoring of treatment for the group of MDR-TB without T2DM. A dual marker of host-derived miR-let7e-5p and M. tuberculosis-derived RNA for monitoring-TB treatment based in serum EVs. Conclusion A dual marker consisting of host-derived miR-let7e-5p and M. tuberculosis-derived RNA, could be an indicator of treatment failure or relapse time after treatment was completed.
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Affiliation(s)
- Claudia Carranza
- Laboratorio de Inmunobiología de la Tuberculosis, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico, Mexico
| | - María Teresa Herrera
- Department of Microbiology, National Institute for Respiratory Diseases Ismael Cosío Villegas, Mexico, Mexico
| | - Silvia Guzmán-Beltrán
- Department of Microbiology, National Institute for Respiratory Diseases Ismael Cosío Villegas, Mexico, Mexico
| | | | - Ivan Salido-Guadarrama
- Department of Microbiology, National Institute for Respiratory Diseases Ismael Cosío Villegas, Mexico, Mexico
| | - Elizabeth Santiago
- Laboratorio de Biología Computacional, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico, Mexico
| | - Leslie Chávez-Galán
- Laboratory of Integrative Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico, Mexico
| | | | - Yolanda González
- Department of Microbiology, National Institute for Respiratory Diseases Ismael Cosío Villegas, Mexico, Mexico
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Liu S, Sun Y, Yang R, Ren W, Li C, Tang S. Expression profiling of TRIM gene family reveals potential diagnostic biomarkers for rifampicin-resistant tuberculosis. Microb Pathog 2021; 157:104916. [PMID: 34000303 DOI: 10.1016/j.micpath.2021.104916] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 03/28/2021] [Accepted: 03/29/2021] [Indexed: 11/19/2022]
Abstract
The epidemic of pulmonary tuberculosis (TB), especially rifampin-resistant tuberculosis (RR-TB) presents a major challenge for TB control today. However, there is a lack of reliable and specific biomarkers for the early diagnosis of RR-TB. We utilized reverse transcription-quantitative polymerase chain reaction (RT-qPCR) to profile the transcript levels of 72 tripartite motif (TRIM) genes from a discovery cohort of 10 drug-sensitive tuberculosis (DS-TB) patients, 10 RR-TB patients, and 10 healthy controls (HCs). A total of 35 differentially expressed genes (DEGs) were screened out, all of which were down-regulated. The bio functions and pathways of these DEGs were enriched in protein ubiquitination, regulation of the viral process, Interferon signaling, and innate immune response, etc. A protein-protein interaction network (PPI) was constructed and analyzed using STRING and Cytoscape. Twelve TRIM genes were identified as hub genes, and seven (TRIM1, 9, 21, 32, 33, 56, 66) of them were verified by RT-qPCR in a validation cohort of 95 subjects. Moreover, we established the RR-TB decision tree models based on the 7 biomarkers. The receiver operating characteristic (ROC) analyses showed that the models exhibited the areas under the curve (AUC) values of 0.878 and 0.868 in discriminating RR-TB from HCs and DS-TB, respectively. Our study proposes potential biomarkers for RR-TB diagnosis, and also provides a new experimental basis to understand the pathogenesis of RR-TB.
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Affiliation(s)
- Shengsheng Liu
- Department of Bacteriology and Immunology, Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China; Multidisciplinary Diagnosis and Treatment Centre for Tuberculosis, Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China; Department of Tuberculosis, Anhui Chest Hospital, Anhui, 230022, China
| | - Yong Sun
- Department of Clinical Laboratory, Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China
| | - Ruifang Yang
- Department of Bacteriology and Immunology, Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China
| | - Weicong Ren
- Department of Bacteriology and Immunology, Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China.
| | - Chuanyou Li
- Department of Bacteriology and Immunology, Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China.
| | - Shenjie Tang
- Multidisciplinary Diagnosis and Treatment Centre for Tuberculosis, Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China.
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14
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Singh AK, Ghosh M, Kumar V, Aggarwal S, Patil SA. Interplay between miRNAs and Mycobacterium tuberculosis: diagnostic and therapeutic implications. Drug Discov Today 2021; 26:1245-1255. [PMID: 33497829 DOI: 10.1016/j.drudis.2021.01.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 10/14/2020] [Accepted: 01/19/2021] [Indexed: 12/21/2022]
Abstract
Increasing evidence suggests that mycobacteria change the host miRNA profile to their advantage. The active participation of miRNAs in controlling immune responses in TB has raised the possibility of utilizing miRNA-based therapy itself or canonically with a standard drug regimen for shortening the duration of treatment. The development of delivery systems for optimal delivery of oligonucleotides, including small interfering (si)RNA/miRNAs-based therapeutics has shown potential as a new therapeutic intervention. However, studies related to the exploitation of miRNAs as both biomarkers and as therapeutics in TB are scarce; thus, more in vitro and in vivo studies are required to fully determine the role of miRNAs as potential diagnostic biomarkers and to improve the pharmacological profile of this class of therapeutics.
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Affiliation(s)
- Amit Kumar Singh
- Experimental Animal Facility, ICMR-National JALMA Institute For Leprosy & Other Mycobacterial Diseases, M. Miyazaki Marg, Tajganj, Agra, Uttar Pradesh, India.
| | - Mrinmoy Ghosh
- KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar-751024
| | - Vimal Kumar
- Experimental Animal Facility, ICMR-National JALMA Institute For Leprosy & Other Mycobacterial Diseases, M. Miyazaki Marg, Tajganj, Agra, Uttar Pradesh, India
| | - Sumit Aggarwal
- Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, Ansari Nagar, New Delhi, India
| | - Shripad A Patil
- Immunology Division, ICMR-National JALMA Institute For Leprosy & Other Mycobacterial Diseases, M. Miyazaki Marg, Tajganj, Agra, India
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15
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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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16
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Xie L, Chao X, Teng T, Li Q, Xie J. Identification of Potential Biomarkers and Related Transcription Factors in Peripheral Blood of Tuberculosis Patients. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17196993. [PMID: 32987825 PMCID: PMC7579196 DOI: 10.3390/ijerph17196993] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/13/2020] [Accepted: 09/22/2020] [Indexed: 12/16/2022]
Abstract
Tuberculosis (TB), one major threat to humans, can infect one third of the worldwide population, and cause more than one million deaths each year. This study aimed to identify the effective diagnosis and therapy biomarkers of TB. Hence, we analyzed two microarray datasets (GSE54992 and GSE62525) derived from the Gene Expression Omnibus (GEO) database to find the differentially expressed genes (DEGs) of peripheral blood mononuclear cell (PBMC) between TB patients and healthy specimens. Functional and pathway enrichment of the DEGs were analyzed by Metascape database. Protein-protein interaction (PPI) network among the DEGs were constructed by STRING databases and visualized in Cytoscape software. The related transcription factors regulatory network of the DEGs was also constructed. A total of 190 DEGs including 36 up-regulated genes and 154 down-regulated genes were obtained in TB samples. Gene functional enrichment analysis showed that these DEGs were enriched in T cell activation, chemotaxis, leukocyte activation involved in immune response, cytokine secretion, head development, etc. The top six hub genes (namely, LRRK2, FYN, GART, CCR7, CXCR5, and FASLG) and two significant modules were got from PPI network of DEGs. Vital transcriptional factors, such as FoxC1 and GATA2, were discovered with close interaction with these six hub DEGs. By systemic bioinformatic analysis, many DEGs associated with TB were screened, and these identified hub DEGs may be potential biomarkers for diagnosis and treatment of TB in the future.
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Affiliation(s)
- Longxiang Xie
- Cell Signal Transduction Laboratory, Bioinformatics Center, Department of Pathology, Institute of Biomedical Informatics, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China; (L.X.); (X.C.); (T.T.); (Q.L.)
| | - Xiaoyu Chao
- Cell Signal Transduction Laboratory, Bioinformatics Center, Department of Pathology, Institute of Biomedical Informatics, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China; (L.X.); (X.C.); (T.T.); (Q.L.)
| | - Tieshan Teng
- Cell Signal Transduction Laboratory, Bioinformatics Center, Department of Pathology, Institute of Biomedical Informatics, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China; (L.X.); (X.C.); (T.T.); (Q.L.)
| | - Qiming Li
- Cell Signal Transduction Laboratory, Bioinformatics Center, Department of Pathology, Institute of Biomedical Informatics, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China; (L.X.); (X.C.); (T.T.); (Q.L.)
| | - Jianping Xie
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Institute of Modern Biopharmaceuticals, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
- Correspondence: ; Tel.: +86-236-836-7108
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17
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Chen J, Han YS, Yi WJ, Huang H, Li ZB, Shi LY, Wei LL, Yu Y, Jiang TT, Li JC. Serum sCD14, PGLYRP2 and FGA as potential biomarkers for multidrug-resistant tuberculosis based on data-independent acquisition and targeted proteomics. J Cell Mol Med 2020; 24:12537-12549. [PMID: 32967043 PMCID: PMC7686995 DOI: 10.1111/jcmm.15796] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 07/23/2020] [Accepted: 07/30/2020] [Indexed: 12/13/2022] Open
Abstract
Multidrug‐resistant tuberculosis (MDR‐TB), defined as tuberculosis (TB) resistant to at least isoniazid and rifampicin, is a major concern of TB control worldwide. However, the diagnosis of MDR‐TB remains a huge challenge to its prevention and control. To identify new diagnostic methods for MDR‐TB, a mass spectrometry strategy of data‐independent acquisition and parallel reaction monitoring was used to detect and validate differential serum proteins. The bioinformatic analysis showed that the functions of differential serum proteins between the MDR‐TB group and the drug‐sensitive tuberculosis group were significantly correlated to the complement coagulation cascade, surface adhesion and extracellular matrix receptor interaction, suggesting a disorder of coagulation in TB. Here, we identified three potential candidate biomarkers such as sCD14, PGLYRP2 and FGA, and established a diagnostic model using these three candidate biomarkers with a sensitivity of 81.2%, a specificity of 90% and the area under the curve value of 0.934 in receiver operation characteristics curve to diagnose MDR‐TB. Our study has paved the way for a novel method to diagnose MDR‐TB and may contribute to elucidate the mechanisms underlying MDR‐TB.
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Affiliation(s)
- Jing Chen
- Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou, China
| | - Yu-Shuai Han
- Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou, China
| | - Wen-Jing Yi
- Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou, China
| | - Huai Huang
- Yuebei People's Hospital, Shaoguan, China
| | - Zhi-Bin Li
- Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou, China
| | - Li-Ying Shi
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou, China
| | - Li-Liang Wei
- Department of Pneumology, Shaoxing Municipal Hospital, Shaoxing, China
| | - Yi Yu
- Yuebei People's Hospital, Shaoguan, China
| | | | - Ji-Cheng Li
- Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou, China.,Yuebei People's Hospital, Shaoguan, China
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18
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Garay-Baquero DJ, White CH, Walker NF, Tebruegge M, Schiff HF, Ugarte-Gil C, Morris-Jones S, Marshall BG, Manousopoulou A, Adamson J, Vallejo AF, Bielecka MK, Wilkinson RJ, Tezera LB, Woelk CH, Garbis SD, Elkington P. Comprehensive plasma proteomic profiling reveals biomarkers for active tuberculosis. JCI Insight 2020; 5:137427. [PMID: 32780727 PMCID: PMC7526553 DOI: 10.1172/jci.insight.137427] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 07/31/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUNDTuberculosis (TB) kills more people than any other infection, and new diagnostic tests to identify active cases are required. We aimed to discover and verify novel markers for TB in nondepleted plasma.METHODSWe applied an optimized quantitative proteomics discovery methodology based on multidimensional and orthogonal liquid chromatographic separation combined with high-resolution mass spectrometry to study nondepleted plasma of 11 patients with active TB compared with 10 healthy controls. Prioritized candidates were verified in independent UK (n = 118) and South African cohorts (n = 203).RESULTSWe generated the most comprehensive TB plasma proteome to date, profiling 5022 proteins spanning 11 orders-of-magnitude concentration range with diverse biochemical and molecular properties. We analyzed the predominantly low-molecular weight subproteome, identifying 46 proteins with significantly increased and 90 with decreased abundance (peptide FDR ≤ 1%, q ≤ 0.05). Verification was performed for novel candidate biomarkers (CFHR5, ILF2) in 2 independent cohorts. Receiver operating characteristics analyses using a 5-protein panel (CFHR5, LRG1, CRP, LBP, and SAA1) exhibited discriminatory power in distinguishing TB from other respiratory diseases (AUC = 0.81).CONCLUSIONWe report the most comprehensive TB plasma proteome to date, identifying novel markers with verification in 2 independent cohorts, leading to a 5-protein biosignature with potential to improve TB diagnosis. With further development, these biomarkers have potential as a diagnostic triage test.FUNDINGColciencias, Medical Research Council, Innovate UK, NIHR, Academy of Medical Sciences, Program for Advanced Research Capacities for AIDS, Wellcome Centre for Infectious Diseases Research.
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Affiliation(s)
- Diana J Garay-Baquero
- School of Clinical and Experimental Sciences, Faculty of Medicine, and.,Institute for Life Sciences, University of Southampton, Southampton, United Kingdom.,Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, California, USA
| | - Cory H White
- School of Clinical and Experimental Sciences, Faculty of Medicine, and
| | - Naomi F Walker
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory 7925, South Africa.,Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom.,Department of Medicine, University of Cape Town, Observatory 7925, South Africa.,TB Centre and Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Marc Tebruegge
- Department of Paediatric Infectious Diseases & Immunology, Evelina London Children's Hospital, Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom.,Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom.,Department of Paediatrics, University of Melbourne, Parkville, Australia
| | - Hannah F Schiff
- School of Clinical and Experimental Sciences, Faculty of Medicine, and
| | - Cesar Ugarte-Gil
- TB Centre and Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, United Kingdom.,Instituto de Medicina Tropical Alexander von Humboldt, School of Medicine, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Stephen Morris-Jones
- Department of Microbiology, University College London Hospitals NHS Trust, London, United Kingdom.,Division of Infection and Immunity, University College London, London, United Kingdom
| | - Ben G Marshall
- School of Clinical and Experimental Sciences, Faculty of Medicine, and.,National Institute for Health Research (NIHR) Biomedical Research Centre, University Hospital NHS Foundation Trust, Southampton, Southampton, United Kingdom
| | | | - John Adamson
- Pharmacology Core, Africa Health Research Institute (AHRI), Durban, South Africa
| | - Andres F Vallejo
- School of Clinical and Experimental Sciences, Faculty of Medicine, and
| | | | - Robert J Wilkinson
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory 7925, South Africa.,Department of Medicine, University of Cape Town, Observatory 7925, South Africa.,The Francis Crick Institute, London, United Kingdom.,Department of Infectious Diseases, Faculty of Medicine, Imperial College, London, United Kingdom
| | - Liku B Tezera
- School of Clinical and Experimental Sciences, Faculty of Medicine, and.,Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | | | - Spiros D Garbis
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom.,Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, California, USA.,Cancer Sciences Division, Faculty of Medicine, University of Southampton, United Kingdom
| | - Paul Elkington
- School of Clinical and Experimental Sciences, Faculty of Medicine, and.,Institute for Life Sciences, University of Southampton, Southampton, United Kingdom.,National Institute for Health Research (NIHR) Biomedical Research Centre, University Hospital NHS Foundation Trust, Southampton, Southampton, United Kingdom
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19
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Shi WJ, Zhuang Y, Russell PH, Hobbs BD, Parker MM, Castaldi PJ, Rudra P, Vestal B, Hersh CP, Saba LM, Kechris K. Unsupervised discovery of phenotype-specific multi-omics networks. Bioinformatics 2020; 35:4336-4343. [PMID: 30957844 DOI: 10.1093/bioinformatics/btz226] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 02/01/2019] [Accepted: 04/05/2019] [Indexed: 12/15/2022] Open
Abstract
MOTIVATION Complex diseases often involve a wide spectrum of phenotypic traits. Better understanding of the biological mechanisms relevant to each trait promotes understanding of the etiology of the disease and the potential for targeted and effective treatment plans. There have been many efforts towards omics data integration and network reconstruction, but limited work has examined the incorporation of relevant (quantitative) phenotypic traits. RESULTS We propose a novel technique, sparse multiple canonical correlation network analysis (SmCCNet), for integrating multiple omics data types along with a quantitative phenotype of interest, and for constructing multi-omics networks that are specific to the phenotype. As a case study, we focus on miRNA-mRNA networks. Through simulations, we demonstrate that SmCCNet has better overall prediction performance compared to popular gene expression network construction and integration approaches under realistic settings. Applying SmCCNet to studies on chronic obstructive pulmonary disease (COPD) and breast cancer, we found enrichment of known relevant pathways (e.g. the Cadherin pathway for COPD and the interferon-gamma signaling pathway for breast cancer) as well as less known omics features that may be important to the diseases. Although those applications focus on miRNA-mRNA co-expression networks, SmCCNet is applicable to a variety of omics and other data types. It can also be easily generalized to incorporate multiple quantitative phenotype simultaneously. The versatility of SmCCNet suggests great potential of the approach in many areas. AVAILABILITY AND IMPLEMENTATION The SmCCNet algorithm is written in R, and is freely available on the web at https://cran.r-project.org/web/packages/SmCCNet/index.html. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- W Jenny Shi
- Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Yonghua Zhuang
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Pamela H Russell
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Brian D Hobbs
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Margaret M Parker
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Peter J Castaldi
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Pratyaydipta Rudra
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,Department of Statistics, Oklahoma State University, Stillwater, OK
| | - Brian Vestal
- Center for Genes, Environment & Health, National Jewish Health, Denver, CO, USA
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Laura M Saba
- Department of Pharmaceutical Sciences, University of Colorado, Aurora, CO, USA
| | - Katerina Kechris
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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20
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Huang H, Han YS, Chen J, Shi LY, Wei LL, Jiang TT, Yi WJ, Yu Y, Li ZB, Li JC. The novel potential biomarkers for multidrug-resistance tuberculosis using UPLC-Q-TOF-MS. Exp Biol Med (Maywood) 2020; 245:501-511. [PMID: 32046521 DOI: 10.1177/1535370220903464] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The lack of rapid and efficient diagnostics impedes largely the epidemic control of multidrug-resistant tuberculosis, and might misguide the therapeutic strategies as well. This study aimed to identify novel multidrug-resistant tuberculosis biomarkers to improve the early intervention, symptomatic treatment and control of the prevalence of multidrug-resistant tuberculosis. The serum small molecule metabolites in healthy controls, patients with drug-susceptible tuberculosis, and patients with multidrug-resistant tuberculosis were screened using ultra-high-performance liquid chromatography combined with quadrupole-time-of-flight mass spectrometry (UPLC-Q-TOF-MS). The differentially abundant metabolites were filtered out through multidimensional statistical analysis and bioinformatics analysis. Compared with drug-susceptible tuberculosis patients and healthy controls, the levels of 13 metabolites in multidrug-resistant tuberculosis patients altered. Among them, the most significant changes were found in N1-Methyl-2-pyridone-5-carboxamide (N1M2P5C), 1-Myristoyl-sn-glycerol-3-phosphocholine (MG3P), Caprylic acid (CA), and D-Xylulose (DX). And a multidrug-resistant tuberculosis/drug-susceptible tuberculosis differential diagnostic model was built based on these four metabolites, achieved the accuracy, sensitivity, and specificity of 0.928, 86.7%, and 86.7%, respectively. The enrichment analysis of metabolic pathways showed that the phospholipid remodeling of cell membranes was active in multidrug-resistant tuberculosis patients. In addition, in patients with tuberculosis, the metabolites of dipalmitoyl phosphatidylcholine (DPPC), a major component of pulmonary surfactant, were down-regulated. N1M2P5C, MG3P, CA, and DX may have the potential to serve as novel multidrug-resistant tuberculosis biomarkers. This research provides a preliminary experimental basis to further investigate potential multidrug-resistant tuberculosis biomarkers. Impact statement The MDR-TB incidence remains high, making the effective control of TB epidemic yet challenging. Rapid and accurate diagnosis is vitally important for improving the therapeutic efficacy and controlling the prevalence of drug resistance TB. Metabolomics has dramatic potential to distinguish MDR-TB and DS-TB. N1M2P5C, MG3P, CA, and DX that we identified in this study might have potential as novel MDR-TB biomarkers. The phospholipid remodeling of cell membranes was highly active in MDR-TB. The DPPC metabolites in TB were significantly down-regulated. This work aimed to investigate potential MDR-TB biomarkers to enhance the clinical diagnostic efficacy. The metabolic pathway distinctly altered in MDR-TB might provide novel targets to develop new anti-TB drugs.
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Affiliation(s)
- Huai Huang
- Medical Research Center, Yue Bei People's Hospital, Shaoguan 512025, China.,School of Medicine, South China University of Technology, Guangzhou, 510006, China
| | - Yu-Shuai Han
- Medical Research Center, Yue Bei People's Hospital, Shaoguan 512025, China.,Institute of Cell Biology, Zhejiang University, Hangzhou 310058, China
| | - Jing Chen
- Medical Research Center, Yue Bei People's Hospital, Shaoguan 512025, China.,Institute of Cell Biology, Zhejiang University, Hangzhou 310058, China
| | - Li-Ying Shi
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou 310013, China
| | - Li-Liang Wei
- Department of Pneumology, Shaoxing University Affiliated Hospital, Shaoxing 312099, China
| | - Ting-Ting Jiang
- Medical Research Center, Yue Bei People's Hospital, Shaoguan 512025, China.,Institute of Cell Biology, Zhejiang University, Hangzhou 310058, China
| | - Wen-Jing Yi
- Medical Research Center, Yue Bei People's Hospital, Shaoguan 512025, China.,Institute of Cell Biology, Zhejiang University, Hangzhou 310058, China
| | - Yi Yu
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Zhi-Bin Li
- Medical Research Center, Yue Bei People's Hospital, Shaoguan 512025, China.,Institute of Cell Biology, Zhejiang University, Hangzhou 310058, China
| | - Ji-Cheng Li
- Medical Research Center, Yue Bei People's Hospital, Shaoguan 512025, China.,Institute of Cell Biology, Zhejiang University, Hangzhou 310058, China
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21
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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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22
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Reprogramming of Small Noncoding RNA Populations in Peripheral Blood Reveals Host Biomarkers for Latent and Active Mycobacterium tuberculosis Infection. mBio 2019; 10:mBio.01037-19. [PMID: 31796535 PMCID: PMC6890987 DOI: 10.1128/mbio.01037-19] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Tuberculosis is the infectious disease with the worldwide largest disease burden and there remains a great need for better diagnostic biomarkers to detect latent and active M. tuberculosis infection. RNA molecules hold great promise in this regard, as their levels of expression may differ considerably between infected and uninfected subjects. We have measured expression changes in the four major classes of small noncoding RNAs in blood samples from patients with different stages of TB infection. We found that, in addition to miRNAs (which are known to be highly regulated in blood cells from TB patients), expression of piRNA and snoRNA is greatly altered in both latent and active TB, yielding promising biomarkers. Even though the functions of many sncRNA other than miRNA are still poorly understood, our results strongly suggest that at least piRNA and snoRNA populations may represent hitherto underappreciated players in the different stages of TB infection. In tuberculosis (TB), as in other infectious diseases, studies of small noncoding RNAs (sncRNA) in peripheral blood have focused on microRNAs (miRNAs) but have neglected the other major sncRNA classes in spite of their potential functions in host gene regulation. Using RNA sequencing of whole blood, we have therefore determined expression of miRNA, PIWI-interacting RNA (piRNA), small nucleolar RNA (snoRNA), and small nuclear RNA (snRNA) in patients with TB (n = 8), latent TB infection (LTBI; n = 21), and treated LTBI (LTBItt; n = 6) and in uninfected exposed controls (ExC; n = 14). As expected, sncRNA reprogramming was greater in TB than in LTBI, with the greatest changes seen in miRNA populations. However, substantial dynamics were also evident in piRNA and snoRNA populations. One miRNA and 2 piRNAs were identified as moderately accurate (area under the curve [AUC] = 0.70 to 0.74) biomarkers for LTBI, as were 1 miRNA, 1 piRNA, and 2 snoRNAs (AUC = 0.79 to 0.91) for accomplished LTBI treatment. Logistic regression identified the combination of 4 sncRNA (let-7a-5p, miR-589-5p, miR-196b-5p, and SNORD104) as a highly sensitive (100%) classifier to discriminate TB from all non-TB groups. Notably, it reclassified 8 presumed LTBI cases as TB cases, 5 of which turned out to have features of Mycobacterium tuberculosis infection on chest radiographs. SNORD104 expression decreased during M. tuberculosis infection of primary human peripheral blood mononuclear cells (PBMC) and M2-like (P = 0.03) but not M1-like (P = 0.31) macrophages, suggesting that its downregulation in peripheral blood in TB is biologically relevant. Taken together, the results demonstrate that snoRNA and piRNA should be considered in addition to miRNA as biomarkers and pathogenesis factors in the various stages of TB.
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23
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Pan L, Zhang X, Jia H, Huang M, Liu F, Wang J, Du B, Wei R, Sun Q, Xing A, Li Q, Zhang Z. Label-Free Quantitative Proteomics Identifies Novel Biomarkers for Distinguishing Tuberculosis Pleural Effusion from Malignant Pleural Effusion. Proteomics Clin Appl 2019; 14:e1900001. [PMID: 31715074 DOI: 10.1002/prca.201900001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 10/29/2019] [Indexed: 02/04/2023]
Abstract
PURPOSE To identify potential protein biomarkers for distinguishing tuberculosis plural effusion (TBPE) from malignant plural effusion (MPE). EXPERIMENTAL DESIGN Five independent samples from each group (TBPE and MPE) are enrolled for label-free quantitative proteomics analyses. The differentially expressed proteins are validated by western blot and ELISA. Logistic regression analysis is used to obtain the optimal diagnostic model. RESULTS In total, 14 proteins with significant difference are identified between TBPE and MPE. Seven differentially expressed proteins are validated using western blot, and the expression patterns of these seven proteins are similar with those in proteomics analysis. Statistically significant differences in four proteins (AGP1, ORM2, C9, and SERPING1) are noted between TBPE and MPE in the training set (n = 230). Logistic regression analysis shows the combination of AGP1-ORM2-C9 presents a sensitivity of 73.0% (92/126) and specificity of 89.4% (93/104) in discriminating TBPE from MPE. Additional validation is performed to evaluate the diagnostic model in an independent blind testing set (n = 80), and yielded a sensitivity of 74.4% (32/43) and specificity of 91.9% (34/37) in discriminating TBPE from MPE. CONCLUSION The study uncovers the proteomic profiles of TBPE and MPE, and provides new potential diagnostic biomarkers for distinguishing TBPE from MPE.
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Affiliation(s)
- Liping Pan
- Beijing Chest Hospital, Capital Medical University; Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, 101149, China
| | - Xia Zhang
- Beijing Chest Hospital, Capital Medical University; Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, 101149, China
| | - Hongyan Jia
- Beijing Chest Hospital, Capital Medical University; Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, 101149, China
| | - Mailing Huang
- Department of Tuberculosis, Beijing Chest Hospital Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, 101149, China
| | - Fei Liu
- Department of Tuberculosis, Beijing Chest Hospital Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, 101149, China
| | - Jinghui Wang
- Department of Medical Oncology, Beijing Chest Hospital Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, 101149, China
| | - Boping Du
- Beijing Chest Hospital, Capital Medical University; Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, 101149, China
| | - Rongrong Wei
- Beijing Chest Hospital, Capital Medical University; Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, 101149, China
| | - Qi Sun
- Beijing Chest Hospital, Capital Medical University; Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, 101149, China
| | - Aiying Xing
- Beijing Chest Hospital, Capital Medical University; Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, 101149, China
| | - Qi Li
- Department of Tuberculosis, Beijing Chest Hospital Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, 101149, China
| | - Zongde Zhang
- Beijing Chest Hospital, Capital Medical University; Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, 101149, China
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24
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Lim HS, Lee SI, Park S. Association between Tuberculosis Case and CD44Gene Polymorphism. KOREAN JOURNAL OF CLINICAL LABORATORY SCIENCE 2019. [DOI: 10.15324/kjcls.2019.51.3.323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Hee-Seon Lim
- Department of Biomedical Laboratory Science, College of Life and Health Sciences, Hoseo University, Asan, Korea
| | - Sang-In Lee
- Department of Biomedical Laboratory Science, College of Life and Health Sciences, Hoseo University, Asan, Korea
| | - Sangjung Park
- Department of Biomedical Laboratory Science, College of Life and Health Sciences, Hoseo University, Asan, Korea
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25
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Pan L, Liu F, Zhang J, Li J, Jia H, Huang M, Liu X, Chen W, Ding Z, Wang Y, Du B, Wei R, Sun Q, Xing A, Zhang Z. Genome-Wide miRNA Analysis Identifies Potential Biomarkers in Distinguishing Tuberculous and Viral Meningitis. Front Cell Infect Microbiol 2019; 9:323. [PMID: 31572691 PMCID: PMC6749153 DOI: 10.3389/fcimb.2019.00323] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 08/28/2019] [Indexed: 12/13/2022] Open
Abstract
Tuberculous meningitis (TBM) is the most common and severe form of central nervous system tuberculosis. Due to the non-specific clinical presentation and lack of efficient diagnosis methods, it is difficult to discriminate TBM from other frequent types of meningitis, especially viral meningitis (VM). In order to identify the potential biomarkers for discriminating TBM and VM and to reveal the different pathophysiological processes between TBM and VM, a genome-wide miRNA screening of PBMCs from TBM, VM, and healthy controls (HCs) using microarray assay was performed (12 samples). Twenty-eight differentially expressed miRNAs were identified between TBM and VM, and 11 differentially expressed miRNAs were identified between TBM and HCs. The 6 overlapping miRNAs detected in both TBM vs. VM and TBM vs. HCs were verified by qPCR analysis and showed a 100% consistent expression patterns with that in microarray test. Statistically significant differences of 4 miRNAs (miR-126-3p, miR-130a-3p, miR-151a-3p, and miR-199a-5p) were further confirmed in TBM compared with VM and HCs in independent PBMCs sample set (n = 96, P < 0.01). Three of which were also showed significantly different between TBM and VM in CSF samples (n = 70, P < 0.05). The receiver operating characteristic curve (ROC) analysis showed that the area under the ROC curve (AUC) of these 4 miRNAs in PBMCs were more than 0.70 in discriminating TBM from VM. Combination of these 4 miRNAs could achieve better discriminative capacity [AUC = 0.893 (0.788-0.957)], with a sensitivity of 90.6% (75.0-98.0%), and a specificity of 86.7% (69.3-96.2%). Additional validation was performed to evaluate the diagnostic panel in another independent sample set (n = 49), which yielded a sensitivity of 81.8% (9/11), and specificity of 90.0% (9/10) in distinguishing TBM and VM, and a sensitivity of 81.8% (9/11), and a specificity of 84.6% (11/13) in discriminating TBM from other non-TBM patients. This study uncovered the miRNA profiles of TBM and VM patients, which can facilitate better understanding of the pathogenesis involved in these two diseases and identified 4 novel miRNAs in distinguishing TBM and VM.
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Affiliation(s)
- Liping Pan
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Fei Liu
- Tuberculosis Department, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Jinli Zhang
- Neurology Department, Chinese People's Liberation Army 263 Hospital, Beijing, China
| | - Jing Li
- Neurology Department, Chinese People's Liberation Army 263 Hospital, Beijing, China
| | - Hongyan Jia
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Mailing Huang
- Tuberculosis Department, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Xuehua Liu
- Hyperbaric Oxygen Department, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Weibi Chen
- Neurology Department, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Zeyu Ding
- Neurology Department, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yajie Wang
- Laboratory Medical Center, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Boping Du
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Rongrong Wei
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Qi Sun
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Aiying Xing
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Zongde Zhang
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
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26
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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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27
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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: 34] [Impact Index Per Article: 6.8] [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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28
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Zhang Y, Zhang X, Zhao Z, Zheng Y, Xiao Z, Li F. Integrated bioinformatics analysis and validation revealed potential immune-regulatory miR-892b, miR-199b-5p and miR-582-5p as diagnostic biomarkers in active tuberculosis. Microb Pathog 2019; 134:103563. [PMID: 31175974 DOI: 10.1016/j.micpath.2019.103563] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 05/21/2019] [Accepted: 05/31/2019] [Indexed: 01/16/2023]
Abstract
Tuberculosis (TB) is one of the most prevalent pulmonary diseases caused by Mycobacterium tuberculosis (Mtb). MiRNAs (miRNAs) participate in TB progression by modulating the host-pathogen interaction. Bioinformatics advancements provide basis for exploring novel immunoregulatory miRNAs and their performance as diagnostic biomarkers. Gene and miRNA expression datasets, GSE29190 and GSE54992, were downloaded from Gene Expression Omnibus (GEO) database. Based on fold changes and statistical significance, a total of 7463 differentially expressed mRNAs (DE-mRNAs) and 38 differentially expressed miRNAs (DE-miRNAs) were screened. Function annotation and protein-protein interaction (PPI) network were constructed to reveal underlying mechanisms of TB pathogenesis. Functional annotation identified the MAPK signalling pathway and leukocyte migration as the top enriched processes. The PPI and MGIP networks indicated that chemokine ligands like CXCL1/CXCL2 and receptors, like CCR7 were important down-regulated genes, implying that a protective mechanism against overdue inflammation induced cell death. MiRNA-gene-immune processes (MGIP) network enriched 7 deregulated miRNAs, and their expression was further examined with quantitative real-time PCR (qRT-PCR), in PBMC samples of 20 active TB patients and 20 healthy donors. The diagnostic performance was evaluated with ROC curves. MiR-892b; miR-199b-5p and miR-582-5p were significantly deregulated in TB patients, compared with healthy participants. The best overall performance was from miR-892b, with an area under curve (AUC) of 0.77, 55% sensitivity and 90% specificity. AUC of miR-199b-5p and miR-582-5p were 0.71 and 0.70, respectively. MiR-892b, miR-199b-5p and miR-582-5p could be considered promising novel diagnostic biomarkers for active tuberculosis.
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Affiliation(s)
- Yunbin Zhang
- Department of Respirology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China; Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Xiaolin Zhang
- Department of Respirology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Zhangyan Zhao
- Department of Respirology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Yuling Zheng
- Department of Respirology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Zhen Xiao
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.
| | - Feng Li
- Department of Respirology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.
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29
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Lyu L, Zhang X, Li C, Yang T, Wang J, Pan L, Jia H, Li Z, Sun Q, Yue L, Chen F, Zhang Z. Small RNA Profiles of Serum Exosomes Derived From Individuals With Latent and Active Tuberculosis. Front Microbiol 2019; 10:1174. [PMID: 31191492 PMCID: PMC6546874 DOI: 10.3389/fmicb.2019.01174] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 05/08/2019] [Indexed: 12/17/2022] Open
Abstract
Tuberculosis (TB) has been the leading lethal infectious disease worldwide since 2014, and about one third of the world’s population has a latent TB infection (LTBI). This is largely attributed to the difficulties in diagnosis and treatment of TB and LTBI patients. Exosomes offer a new perspective on investigation of the process of TB infection. In this study, we performed small RNA sequencing to explore small RNA profiles of serum exosomes derived from LTBI and TB patients and healthy controls (HC). Our results revealed distinct miRNA profile of the exosomes in the three groups. We screened 250 differentially expressed miRNAs including 130 specifically expressed miRNAs. Some miRNAs were further validated to be specifically expressed in LTBI (hsa-let-7e-5p, hsa-let-7d-5p, hsa-miR-450a-5p, and hsa-miR-140-5p) and TB samples (hsa-miR-1246, hsa-miR-2110, hsa-miR-370-3P, hsa-miR-28-3p, and hsa-miR-193b-5p). Additionally, we demonstrated four expression panels in LTBI and TB groups, and six expression patterns among the three groups. These specifically expressed miRNAs and differentially expressed miRNAs in different panels and patterns provide potential biomarkers for detection/diagnosis of latent and active TB using exosomal miRNAs. Additionally, we also discovered plenty of small RNAs derived from genomic repetitive sequences, which might play roles in host immune responses along with Mtb infection progresses. Overall, our findings provide important reference and an improved understanding about miRNAs and repetitive region-derived small RNAs in exosomes during the Mtb infectious process, and facilitate the development of potential molecular targets for detection/diagnosis of latent and active tuberculosis.
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Affiliation(s)
- Lingna Lyu
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Xiuli Zhang
- CAS Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Cuidan Li
- CAS Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Tingting Yang
- CAS Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jinghui Wang
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Liping Pan
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Hongyan Jia
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Zihui Li
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Qi Sun
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Liya Yue
- CAS Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Fei Chen
- CAS Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zongde Zhang
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
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Bisht D, Sharma D, Sharma D, Singh R, Gupta VK. Recent insights intoMycobacterium tuberculosisthrough proteomics and implications for the clinic. Expert Rev Proteomics 2019; 16:443-456. [DOI: 10.1080/14789450.2019.1608185] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Deepa Bisht
- Department of Biochemistry, National JALMA Institute for Leprosy & Other Mycobacterial Diseases (ICMR), Agra, India
| | - Devesh Sharma
- Department of Biochemistry, National JALMA Institute for Leprosy & Other Mycobacterial Diseases (ICMR), Agra, India
| | - Divakar Sharma
- Medical Microbiology and Molecular Biology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Rananjay Singh
- Department of Biochemistry, National JALMA Institute for Leprosy & Other Mycobacterial Diseases (ICMR), Agra, India
| | - Vivek Kumar Gupta
- Department of Biochemistry, National JALMA Institute for Leprosy & Other Mycobacterial Diseases (ICMR), Agra, India
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31
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Host and MTB genome encoded miRNA markers for diagnosis of tuberculosis. Tuberculosis (Edinb) 2019; 116:37-43. [PMID: 31153517 DOI: 10.1016/j.tube.2019.04.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 02/26/2019] [Accepted: 04/16/2019] [Indexed: 02/08/2023]
Abstract
MicroRNAs (miRNAs) are a class of noncoding RNA molecules which are involved in various cellular and physiological processes. Previously, studies have identified several miRNAs that are potential diagnostic biomarkers for various infectious diseases including tuberculosis. We have performed small RNA sequencing using the Ion Torrent PGM platform in extra pulmonary tuberculosis (EPTB) subject's serum samples to identify circulating miRNAs during mycobacterium tuberculosis (MTB) infection. Our analysis identified 20 circulating miRNAs upregulated and 5 miRNAs downregulated during MTB infection in patient's serum. In addition, we have identified 6 MTB genome encoded miRNAs upregulated in EPTB patient's serum samples. Taqman based qRT-PCR analysis of host-genome encoded (hsa-miR-146a-5p and hsa-miR-125b-5p) and MTB genome encoded (MTB-miR5) miRNAs showed increased expression in a cohort of 52 healthy, pulmonary tuberculosis (PTB) and extra pulmonary tuberculosis (EPTB) patients serum samples. Our study identified for the first time a panel of host and MTB genome specific differentially expressed circulating miRNAs in serum samples of an Indian patient cohort with tuberculosis infection with a potential as a non-invasive diagnostic biomarker for tuberculosis infection.
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Significance of the Differential Peptidome in Multidrug-Resistant Tuberculosis. BIOMED RESEARCH INTERNATIONAL 2019; 2019:5653424. [PMID: 30792993 PMCID: PMC6354167 DOI: 10.1155/2019/5653424] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 12/21/2018] [Accepted: 01/03/2019] [Indexed: 12/23/2022]
Abstract
Most multidrug-resistant tuberculosis (MDR-TB) patients fail to receive a timely diagnosis and treatment. Therefore, we explored the differentially expressed peptides in MDR-TB compared with drug-susceptible tuberculosis (DS-TB) patients using LC-MS/MS and Ingenuity Pathway Analysis (IPA) to analyse the potential significance of these differentially expressed peptides. A total of 301 peptides were differentially expressed between MDR-TB and DS-TB groups. Of these, 24 and 16 peptides exhibited presented high (fold change ≥ 2.0, P < 0.05) and low (fold change ≤ −2.0, P < 0.05) levels in MDR-TB. Significant canonical pathways included the prothrombin activation system, coagulation system, and complement system. In the network of differentially expressed precursor proteins, lipopolysaccharide (LPS) regulates many precursor proteins, including four proteins correlated with organism survival. These four important differentially expressed proteins are prothrombin (F2), complement receptor type 2 (CR2), collagen alpha-2(V) chain (COL5A2), and inter-alpha-trypsin inhibitor heavy chain H4 (ITIH4). After addition of CR2 peptide, IL-6 mRNA expression in THP-1 cells decreased significantly in dose- and time-dependent manners. Cumulatively, our study proposes potential biomarkers for MDR-TB diagnosis and enables a better understanding of the pathogenesis of MDR-TB. The functions of differentially expressed peptides, especially CR2, in MDR-TB require further investigation.
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Moulder R, Bhosale SD, Goodlett DR, Lahesmaa R. Analysis of the plasma proteome using iTRAQ and TMT-based Isobaric labeling. MASS SPECTROMETRY REVIEWS 2018; 37:583-606. [PMID: 29120501 DOI: 10.1002/mas.21550] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 09/26/2017] [Indexed: 05/23/2023]
Abstract
Over the past decade, chemical labeling with isobaric tandem mass tags, such as isobaric tags for relative and absolute quantification reagents (iTRAQ) and tandem mass tag (TMT) reagents, has been employed in a wide range of different clinically orientated serum and plasma proteomics studies. In this review the scope of these works is presented with attention to the areas of research, methods employed and performance limitations. These applications have covered a wide range of diseases, disorders and infections, and have implemented a variety of different preparative and mass spectrometric approaches. In contrast to earlier works, which struggled to quantify more than a few hundred proteins, increasingly these studies have provided deeper insight into the plasma proteome extending the numbers of quantified proteins to over a thousand.
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Affiliation(s)
- Robert Moulder
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Santosh D Bhosale
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | | | - Riitta Lahesmaa
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
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Yan H, Xu R, Zhang X, Wang Q, Pang J, Zhang X, Chang X, Zhang Y. Identifying differentially expressed long non-coding RNAs in PBMCs in response to the infection of multidrug-resistant tuberculosis. Infect Drug Resist 2018; 11:945-959. [PMID: 30034244 PMCID: PMC6047615 DOI: 10.2147/idr.s154255] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Purpose The aim of this paper was to identify differentially expressed long non-coding RNAs (lncRNAs) in peripheral blood mononuclear cells (PBMCs) influenced by the infection of multidrug-resistant tuberculosis (MDR-TB). Materials and methods IncRNA and mRNA expression profiles in PBMCs derived from healthy controls (HCs) and individuals with MDR-TB and drug-sensitive tuberculosis (DS-TB) were analyzed and compared by microarray assay. Six lncRNAs were randomly selected for validation by using real-time quantitative polymerase chain reaction (RT-qPCR). The biological functions and signaling pathways affected by the differentially expressed mRNAs were investigated by using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway-based approaches. Results Compared with the HC group, 1,429 lncRNAs (983 mRNAs) and 2,040 lncRNAs (1,407 mRNAs) were identified to be deregulated in the MDR-TB group and in the DS-TB group, respectively, and 1,511 lncRNAs and 1,047 mRNAs were identified to be differentially expressed in both MDR-TB and DS-TB groups. Between the three groups, 22 lncRNAs and 38 mRNAs were found deregulated. Most deregulated lncRNAs were from intergenic regions (~55% of the total), natural antisense to protein-coding loci (~32% of the total), or intronic antisense to protein-coding loci (~5% of the total). Significantly enriched signaling pathways regulated by the deregulated mRNAs were mainly associated with natural killer cell-mediated cytotoxicity, antigen processing and presentation, graft-vs-host disease, the transforming growth factor-β signaling pathway, and the Hippo signaling pathway. Conclusion This study is the first to report differentially expressed lncRNAs in PBMCs in response to MDR-TB infection. It revealed that some lncRNAs might be associated with regulating host immune response to MDR-TB infection. Further elucidation of the potential of these deregulated lncRNAs in MDR-TB and its reactivation requires further study.
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Affiliation(s)
- Hong Yan
- Department of Laboratory Medicine, Nanjing Chest Hospital, Nanjing 210029, China
| | - Rufeng Xu
- Department of Biochemistry and Molecular Biology, Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, Jiangsu 210029, China,
| | - Xiangrong Zhang
- Nanjing Public Health Clinical Center, Nanjing, Jiangsu 211133, China
| | - Qian Wang
- Department of Laboratory Medicine, Nanjing Chest Hospital, Nanjing 210029, China
| | - Jing Pang
- Department of Biochemistry and Molecular Biology, Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, Jiangsu 210029, China,
| | - Xia Zhang
- Nanjing Public Health Clinical Center, Nanjing, Jiangsu 211133, China
| | - Xiaoai Chang
- Department of Biochemistry and Molecular Biology, Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, Jiangsu 210029, China,
| | - Yaqin Zhang
- Department of Biochemistry and Molecular Biology, Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, Jiangsu 210029, China,
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Huang D, Yuan W, Li H, Li S, Chen Z, Yang H. Identification of key pathways and biomarkers in sorafenib-resistant hepatocellular carcinoma using bioinformatics analysis. Exp Ther Med 2018; 16:1850-1858. [PMID: 30186410 PMCID: PMC6122189 DOI: 10.3892/etm.2018.6427] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 04/26/2018] [Indexed: 02/06/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common malignant types of cancer, with a high mortality rate. Sorafenib is the sole approved oral clinical therapy against advanced HCC. However, individual patients exhibit varying responses to sorafenib and the development of sorafenib resistance has been a new challenge for its clinical efficacy. The current study identified gene biomarkers and key pathways in sorafenib-resistant HCC using bioinformatics analysis. Gene dataset GSE73571 was obtained from the Gene Expression Omnibus (GEO) database, including four sorafenib-acquired resistant and three sorafenib-sensitive HCC phenotypes. Differentially expressed genes (DEGs) were identified using the web tool GEO2R. Functional and pathway enrichment of DEGs were analyzed using the Database for Annotation, Visualization and Integrated Discovery and the protein-protein interaction (PPI) network was constructed using the Search Tool for the Retrieval of Interacting Genes/Proteins and Cytoscape. A total of 1,319 DEGs were selected, which included 593 upregulated and 726 downregulated genes. Functional and pathway enrichment analysis revealed DEGs enriched in negative regulation of endopeptidase activity, cholesterol homeostasis, DNA replication and repair, coagulation cascades, insulin resistance, RNA transport, cell cycle and others. Eight hub genes, including kininogen 1, vascular cell adhesion molecule 1, apolipoprotein C3, alpha 2-HS glycoprotein, erb-b2 receptor tyrosine kinase 2, secreted protein acidic and cysteine rich, vitronectin and vimentin were identified from the PPI network. In conclusion, the present study identified DEGs and key genes in sorafenib-resistant HCC, which further the knowledge of potential mechanisms in the development of sorafenib resistance and may provide potential targets for early diagnosis and new treatments for sorafenib-resistant HCC.
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Affiliation(s)
- Danping Huang
- Guangdong Key Laboratory of Liver Disease Research, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510000, P.R. China
| | - Weiqu Yuan
- Acupuncture Department, The Fourth Clinical Medical College of Guangzhou University Chinese Medicine, Shenzhen, Guangdong 518000, P.R. China
| | - Hanmin Li
- Hepatopathy Institution, Affiliated Hospital Hubei University Chinese Medicine, Wuhan, Hubei 430061, P.R. China
| | - Shaodong Li
- Guangdong Key Laboratory of Liver Disease Research, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510000, P.R. China
| | - Zuanguang Chen
- Pharmaceutical Analysis Department, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, P.R. China
| | - Hongzhi Yang
- Guangdong Key Laboratory of Liver Disease Research, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510000, P.R. China
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36
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Barry SE, Ellis M, Yang Y, Guan G, Wang X, Britton WJ, Saunders BM. Identification of a plasma microRNA profile in untreated pulmonary tuberculosis patients that is modulated by anti-mycobacterial therapy. J Infect 2018; 77:341-348. [PMID: 29746939 DOI: 10.1016/j.jinf.2018.03.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 02/07/2018] [Accepted: 03/05/2018] [Indexed: 11/19/2022]
Abstract
OBJECTIVE microRNA expression profiles are of interest as a biomarker of tuberculosis (TB). How anti-TB therapy effects miRNA profiles is unknown and was examined. METHODS We identified 87 plasma miRNAs that were significantly modified in an exploratory group of 19 Chinese pulmonary TB (PTB) patients compared to 14 healthy controls. We selected 10 of these miRNAs for analysis in a cohort of 100 PTB patients prior to, and at one, two and six months during treatment. RESULTS Five miRNAs were differentially expressed in PTB patients compared to controls at diagnosis; miRs -29a and -99b were up-regulated, whilst miRs -21, -146a and -652 were down-regulated. A combination of 5 miRNA distinguished TB from healthy controls with a sensitivity of 94%, a specificity of 88%, and an AUC of 0.976. Within one month of treatment, significant changes in miRs -29a, -99b, -26a and 146a levels occurred in successfully treated patients, although not all miRNAs returned to baseline by treatment completion. CONCLUSION A 5-miRNA signature shows potential for development as a novel biomarker for TB disease with potential to predict response to treatment. The failure of all miRNA to return to baseline levels may reflect ongoing remodelling in the lung parenchyma that continues after completion of anti-TB therapy.
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Affiliation(s)
- Simone E Barry
- Centenary Institute, The University of Sydney, Locked Bag No 6, Newtown, NSW 2042, Australia
| | - Magda Ellis
- Centenary Institute, The University of Sydney, Locked Bag No 6, Newtown, NSW 2042, Australia
| | - YuRong Yang
- Ningxia Medical University, Yinchuan, Ningxia, PR China; QIMR Berghofer Medical Research Institute, QLD, Australia
| | - Guangyu Guan
- Ningxia Centre for Disease Control and Prevention, Yinchuan, Ningxia, PR China
| | - Xiaolin Wang
- Infectious Disease Hospital of Ningxia, Yinchuan, 7500004, PR China
| | - Warwick J Britton
- Centenary Institute, The University of Sydney, Locked Bag No 6, Newtown, NSW 2042, Australia; Discipline of Medicine, Sydney Medical School, The University of Sydney, Sydney, NSW 2006 Australia
| | - Bernadette M Saunders
- Centenary Institute, The University of Sydney, Locked Bag No 6, Newtown, NSW 2042, Australia; School of Life Science, University of Technology, PO Box 123, Broadway, NSW 2007, Australia.
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Muthu M, Deenadayalan A, Ramachandran D, Paul D, Gopal J, Chun S. A state-of-art review on the agility of quantitative proteomics in tuberculosis research. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2018.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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38
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Identification of potential urine proteins and microRNA biomarkers for the diagnosis of pulmonary tuberculosis patients. Emerg Microbes Infect 2018; 7:63. [PMID: 29636444 PMCID: PMC5893550 DOI: 10.1038/s41426-018-0066-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 02/23/2018] [Accepted: 03/02/2018] [Indexed: 12/31/2022]
Abstract
This study identified urinary biomarkers for tuberculosis (TB) diagnosis. The urine proteomic profiles of 45 pulmonary tuberculosis patients prior to anti-TB treatment and 45 healthy controls were analyzed and compared using two-dimensional electrophoresis with matrix-assisted laser desorption/ionization time of flight mass spectrometry. Nineteen differentially expressed proteins were identified preliminarily, and western blotting and qRT-PCR were performed to confirm these changes at the translational and transcriptional levels, respectively, using samples from 122 additional pulmonary tuberculosis patients and 73 additional healthy controls. Two proteins, mannose-binding lectin 2 and a 35-kDa fragment of inter-α-trypsin inhibitor H4, exhibited the highest differential expression. We constructed a protein-microRNA interaction network that primarily involved complement and inflammatory responses. Eleven microRNAs from microRNA-target protein interactions were screened and validated using qRT-PCR with some of the above samples, including 97 pulmonary tuberculosis patients and 48 healthy controls. Only miR-625-3p exhibited significant differential expression (p < 0.05). miR-625-3p was increased to a greater extent in samples of smear-positive than smear-negative patients. miR-625-3p was predicted to target mannose-binding lectin 2 protein. A binary logistic regression model based on miR-625-3p, mannose-binding lectin 2, and inter-α-trypsin inhibitor H4 was further established. This three-biomarker combination exhibited better performance for tuberculosis diagnosis than individual biomarkers or any two-biomarker combination and generated a diagnostic sensitivity of 85.87% and a specificity of 87.50%. These novel urine biomarkers may significantly improve tuberculosis diagnosis.
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Sabir N, Hussain T, Shah SZA, Peramo A, Zhao D, Zhou X. miRNAs in Tuberculosis: New Avenues for Diagnosis and Host-Directed Therapy. Front Microbiol 2018; 9:602. [PMID: 29651283 PMCID: PMC5885483 DOI: 10.3389/fmicb.2018.00602] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 03/15/2018] [Indexed: 12/30/2022] Open
Abstract
Tuberculosis (TB) is one of the most fatal infectious diseases and a leading cause of mortality, with 95% of these deaths occurring in developing countries. The causative agent, Mycobacterium tuberculosis (Mtb), has a well-established ability to circumvent the host's immune system for its intracellular survival. microRNAs (miRNAs) are small, non-coding RNAs having an important function at the post-transcriptional level and are involved in shaping immunity by regulating the repertoire of genes expressed in immune cells. It has been established in recent studies that the innate immune response against TB is significantly regulated by miRNAs. Moreover, differential expression of miRNA in Mtb infection can reflect the disease progression and may help distinguish between active and latent TB infection (LTBI). These findings encouraged the application of miRNAs as potential biomarkers. Similarly, active participation of miRNAs in modulation of autophagy and apoptosis responses against Mtb opens an exciting avenue for the exploitation of miRNAs as host directed therapy (HDT) against TB. Nanoparticles mediated delivery of miRNAs to treat various diseases has been reported and this technology has a great potential to be used in TB. In reality, this exploitation of miRNAs as biomarkers and in HDT is still in its infancy stage, and more studies using animal models mimicking human TB are advocated to assess the role of miRNAs as biomarkers and therapeutic targets. In this review, we attempt to summarize the recent advancements in the role of miRNAs in TB as immune modulator, miRNAs' capability to distinguish between active and latent TB and, finally, usage of miRNAs as therapeutic targets against TB.
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Affiliation(s)
| | | | | | | | | | - Xiangmei Zhou
- State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, China
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40
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Chen C, Yan T, Liu L, Wang J, Jin Q. Identification of a Novel Serum Biomarker for Tuberculosis Infection in Chinese HIV Patients by iTRAQ-Based Quantitative Proteomics. Front Microbiol 2018. [PMID: 29535695 PMCID: PMC5834467 DOI: 10.3389/fmicb.2018.00330] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Tuberculosis (TB) is a major comorbidity in HIV patients as well as a serious co-epidemic. Traditional detection methods are not effective or sensitive for the detection of Mycobacterium tuberculosis at the early stage. TB has become a major cause of lethal on HIV patients. We employed isobaric tags for relative and absolute quantitation (iTRAQ) technology to identify the different host responses in HIV-noTB and HIV-TB patients’ sera. Given the diversity of HIV subtypes, which results in a variety of host responses in different human populations, we focused on the Chinese patients. Of the 25 proteins identified, 7 were increased and 18 were decreased in HIV-TB co-infected patients. These proteins were found to be involved in host immune response processes. We identified a candidate protein, endoglin (ENG), which showed an 4.9 times increase by iTRAQ and 11.5 times increase by ELISA. ENG demonstrated the diagnostic efficacy and presented a novel molecular biomarker for TB in HIV-infected Chinese patients. This study provides new insight into the challenges in the diagnosis and effective management of patients with HIV-TB.
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Affiliation(s)
- Cong Chen
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tao Yan
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Liguo Liu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianmin Wang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qi Jin
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
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Li J, Wu L, Guo W, Chen J, Hu X, Wang M, Zhao Z, Ying B. Clinical relevance of LINC00152 and its variants in western Chinese tuberculosis patients. Oncotarget 2017; 8:115456-115468. [PMID: 29383173 PMCID: PMC5777785 DOI: 10.18632/oncotarget.23297] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 12/03/2017] [Indexed: 02/05/2023] Open
Abstract
Recent studies indicate that the long intergenic non-coding RNA LINC00152 plays crucial roles in various human diseases. Here, we investigated whether levels of LINC00152 or its genetic variants correlate with the clinical features of tuberculosis (TB) in western Chinese patients. We genotyped the single nucleotide polymorphism LINC00152 rs80292941 in 476 TB patients and 475 healthy subjects using a custom-by-design 48-Plex SNPscan Kit, and measured relative levels of LINC00152 using RT-qPCR. We observed that LINC00152 levels were lower in TB patients than controls. Moreover, rs80292941 TT genotype carriers had the lowest LINC00152 levels among TB patients, and rs80292941 AA genotype carriers are more likely to suffer from hepatotoxicity induced by antituberculosis therapy [OR = 3.97, 95% = 1.53-10.13, p = 0.002]. Our findings strongly suggest that LINC00152 may promote TB progression and highlight rs80292941 single nucleotide polymorphism as a novel predisposition marker for antituberculosis drug-induced hepatotoxicity.
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Affiliation(s)
- Jing Li
- Department of Clinical Laboratory, Central Hospital of Panzhihua City, Panzhihua, Sichuan 617067, P. R. China
| | - Lijuan Wu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China
| | - Weihua Guo
- Department of Clinical Laboratory, Central Hospital of Panzhihua City, Panzhihua, Sichuan 617067, P. R. China
| | - Juli Chen
- Department of Clinical Laboratory, Central Hospital of Panzhihua City, Panzhihua, Sichuan 617067, P. R. China
| | - Xuejiao Hu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China
| | - Minjin Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China
| | - Zhenzhen Zhao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China
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42
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Screening and identification of four serum miRNAs as novel potential biomarkers for cured pulmonary tuberculosis. Tuberculosis (Edinb) 2017. [PMID: 29523324 DOI: 10.1016/j.tube.2017.08.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Rapid and efficient methods for the determination of cured pulmonary tuberculosis (TB) are lacking. We screened serum miRNAs using the Solexa sequencing method among untreated TB patients, two-month treated TB patients, cured TB patients, and healthy controls. A total of 100 differentially expressed miRNAs were identified in cured TB patients, including 37 up-regulated (fold change >1.50, P < 0.05) and 63 down-regulated (fold change <0.60, P < 0.05) miRNAs. Gene ontology (GO) enrichment analysis revealed that most of the predicted genes were present in the nucleus with a strong protein binding function. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis strongly suggested alterations in the metabolic pathways. Following quantitative real time chain reaction (qRT-PCR), significantly reduced expression levels of miR-21-5p (0.30, P < 0.001), miR-92a-3p (0.63, P < 0.001), and miR-148b-3p (0.17, P < 0.001) were found in the cured TB patients compared with the untreated TB patients, while significantly increased expression levels of miR-21-5p (2.09, P = 0.001), miR-92a-3p (1.40, P = 0.005), and miR-148b-3p (4.80, P = 0.003) were found in the untreated TB patients compared with the healthy controls. And significantly increased level of miR-125a-5p was found between two-month treated TB patients and untreated TB patients (1.81, P = 0.004). We established a cured TB model with 83.96% accuracy by four miRNAs (miR-21-5p, miR-92a-3p, miR-148b-3p, and miR-125a-5p), and also established a diagnostic model with 70.09% accuracy. Our study provides experimental data for establishing objective indicators of cured TB, and also provides a new experimental basis to understand the pathogenesis and prognosis of TB.
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Zhang B, Chamba Y, Shang P, Wang Z, Ma J, Wang L, Zhang H. Comparative transcriptomic and proteomic analyses provide insights into the key genes involved in high-altitude adaptation in the Tibetan pig. Sci Rep 2017. [PMID: 28623314 PMCID: PMC5473931 DOI: 10.1038/s41598-017-03976-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Tibetan pigs that inhabit the Tibetan Plateau exhibit striking phenotypic and physiological differences from lowland pigs, and have adapted well to extreme conditions. However, the mechanisms involved in regulating gene expression at high altitude in these animals are not fully understood. In this study, we obtained transcriptomic and proteomic data from the heart tissues of Tibetan and Yorkshire pigs raised in the highlands (TH and YH) and lowlands (TL and YL) via RNA-seq and iTRAQ (isobaric tags for relative and absolute quantitation) analyses, respectively. Comparative analyses of TH vs. YH, TH vs.TL, TL vs. YL, and YH vs. YL yielded 299, 169, 242, and 368 differentially expressed genes (DEGs), and 473, 297, 394, and 297 differentially expressed proteins (DEPs), respectively. By functional annotation of these DEGs and DEPs, genes that were enriched in the HIF-1 signaling pathway (NPPA, ERK2, ENO3, and EGLN3), VEGF signaling pathway (ERK2, A2M, FGF1, CTGF, and DPP4), and hypoxia-related processes (CRYAB, EGLN3, TGFB2, DPP4, and ACE) were identified as important candidate genes for high-altitude adaptation in the Tibetan pig. This study enhances our understanding of the molecular mechanisms involved in hypoxic adaptation in pigs, and furthers our understanding of human hypoxic diseases.
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Affiliation(s)
- Bo Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd., Beijing, 100193, China
| | - Yangzom Chamba
- Tibet Agriculture and Animal Husbandry College, Linzhi, Tibet, 860000, China
| | - Peng Shang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd., Beijing, 100193, China.,Tibet Agriculture and Animal Husbandry College, Linzhi, Tibet, 860000, China
| | - Zhixiu Wang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd., Beijing, 100193, China
| | - Jun Ma
- National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd., Beijing, 100193, China
| | - Liyuang Wang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd., Beijing, 100193, China
| | - Hao Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd., Beijing, 100193, China.
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iTRAQ-Based Proteomics of Chronic Renal Failure Rats after FuShengong Decoction Treatment Reveals Haptoglobin and Alpha-1-Antitrypsin as Potential Biomarkers. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2017; 2017:1480514. [PMID: 28536642 PMCID: PMC5425835 DOI: 10.1155/2017/1480514] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Revised: 03/29/2017] [Accepted: 04/10/2017] [Indexed: 02/06/2023]
Abstract
Background. Chronic renal failure (CRF) has become a global health problem and bears a huge economic burden. FuShengong Decoction (FSGD) as traditional Chinese medicine has multiple pharmacological effects. Objectives. To understand the underlying molecular mechanism and signaling pathway involved in the FSGD treatment of CRF and screen differentially expressed proteins in rats with CRF treated with FSGD. Methods. Thirty-three male Sprague-Dawley rats were randomly divided into control group, CRF group, and FSGD group. Differentially expressed proteins were screened by iTRAQ coupled with nanoLC-MS/MS, and these identified proteins were later analyzed by GO, KEGG, and STRING. Additionally, haptoglobin (HP) and alpha-1-antitrypsin (AAT) were finally verified by ELISA, Western blot, and real time PCR. Results. A total of 417 proteins were identified. Nineteen differentially expressed proteins were identified in the FSGD group compared with the model group, of which 3 proteins were upregulated and 16 proteins were downregulated. Cluster analysis indicated that inflammatory response was associated with these proteins and complement and coagulation cascade pathways were predominantly involved. The validation methods further confirmed that the levels of HP and AAT were significantly increased. Conclusions. HP and AAT may be the important biomarkers in the pathogenesis of CRF and FSGD therapy.
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Jiang TT, Shi LY, Wei LL, Li X, Yang S, Wang C, Liu CM, Chen ZL, Tu HH, Li ZJ, Li JC. Serum amyloid A, protein Z, and C4b-binding protein β chain as new potential biomarkers for pulmonary tuberculosis. PLoS One 2017; 12:e0173304. [PMID: 28278182 PMCID: PMC5344400 DOI: 10.1371/journal.pone.0173304] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 02/17/2017] [Indexed: 11/24/2022] Open
Abstract
The aim of this study was to discover novel biomarkers for pulmonary tuberculosis (TB). Differentially expressed proteins in the serum of patients with TB were screened and identified by iTRAQ-two dimensional liquid chromatography tandem mass spectrometry analysis. A total of 79 abnormal proteins were discovered in patients with TB compared with healthy controls. Of these, significant differences were observed in 47 abnormally expressed proteins between patients with TB or pneumonia and chronic obstructive pulmonary disease (COPD). Patients with TB (n = 136) exhibited significantly higher levels of serum amyloid A (SAA), vitamin K-dependent protein Z (PROZ), and C4b-binding protein β chain (C4BPB) than those in healthy controls (n = 66) (P<0.0001 for each) albeit significantly lower levels compared with those in patients with pneumonia (n = 72) (P<0.0001 for each) or COPD (n = 72) (P<0.0001, P<0.0001, P = 0.0016, respectively). After 6 months of treatment, the levels of SAA and PROZ were significantly increased (P = 0.022, P<0.0001, respectively), whereas the level of C4BPB was significantly decreased (P = 0.0038) in treated TB cases (n = 72). Clinical analysis showed that there were significant differences in blood clotting and lipid indices in patients with TB compared with healthy controls, patients with pneumonia or COPD, and treated TB cases (P<0.05). Correlation analysis revealed significant correlations between PROZ and INR (rs = 0.414, P = 0.044), and between C4BPB and FIB (rs = 0.617, P = 0.0002) in patients with TB. Receiver operating characteristic curve analysis revealed that the area under the curve value of the diagnostic model combining SAA, PROZ, and C4BPB to discriminate the TB group from the healthy control, pneumonia, COPD, and cured TB groups was 0.972, 0.928, 0.957, and 0.969, respectively. Together, these results suggested that SAA, PROZ, and C4BPB may serve as new potential biomarkers for TB. Our study may thus provide experimental data for the differential diagnosis of TB.
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Affiliation(s)
- Ting-Ting Jiang
- South China University of Technology School of Medicine, Guangzhou, P.R. China
| | - Li-Ying Shi
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou, P.R. China
| | - Li-Liang Wei
- Department of Pneumology, Shaoxing Municipal Hospital, Shaoxing, P.R. China
| | - Xiang Li
- Key Laboratory of Gastroenteropathy, Zhejiang Province People’s Hospital, Hangzhou, China
| | - Su Yang
- Institute of Cell Biology, Zhejiang University, Hangzhou, P.R. China
| | - Chong Wang
- Institute of Cell Biology, Zhejiang University, Hangzhou, P.R. China
| | - Chang-Ming Liu
- Institute of Cell Biology, Zhejiang University, Hangzhou, P.R. China
| | - Zhong-Liang Chen
- Institute of Cell Biology, Zhejiang University, Hangzhou, P.R. China
| | - Hui-Hui Tu
- Institute of Cell Biology, Zhejiang University, Hangzhou, P.R. China
| | - Zhong-Jie Li
- Institute of Cell Biology, Zhejiang University, Hangzhou, P.R. China
| | - Ji-Cheng Li
- South China University of Technology School of Medicine, Guangzhou, P.R. China
- Institute of Cell Biology, Zhejiang University, Hangzhou, P.R. China
- * E-mail:
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