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Kameni C, Mezajou CF, Ngongang NN, Ngum JA, Simo USF, Tatang FJ, Nguengo SN, Nouthio APC, Pajiep MAW, Toumeni MH, Madjoumo EST, Tchinda MF, Ngangue RJEM, Koro Koro F, Wade A, Akami M, Ngono ARN, Tamgue O. p50-associated Cyclooxygenase-2 Extragenic RNA (PACER) and Long Non-coding RNA 13 (LNC13) as potential biomarkers for monitoring tuberculosis treatment. FRONTIERS IN TROPICAL DISEASES 2022. [DOI: 10.3389/fitd.2022.969347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Gaps in early and accurate diagnosis, effective drug control, and treatment monitoring are hindering the global eradication effort of tuberculosis. This infectious disease has become the deadliest worldwide before the outbreak of Covid-19. The search for new molecular biomarkers of tuberculosis will help to reverse this trend. Long non-coding RNAs (lncRNAs) have emerged as important regulators of the host immune response to infection, hence their link with the etiology and diagnosis of tuberculosis has attracted some attention from the research community. However, very little is known about their potential for the monitoring of tuberculosis treatment. This study aimed at assessing the potential of two lncRNAs: p50-associated Cyclooxygenase-2 Extragenic RNA (PACER) and Long Non-coding RNA 13 (LNC13) in the monitoring of tuberculosis treatment. This was a cross-sectional study carried out in Douala, Cameroon from December 2020 to August 2021. A quantitative real-time polymerase chain reaction followed by Cq analysis using the Livak method were performed to measure the relative expression levels of PACER and LNC13 in whole blood of healthy controls, patients with active pulmonary tuberculosis at the initiation of treatment, after two, five, and six months into treatment. Receiver Operating Characteristic curves analysis was used to assess the ability of targeted lncRNAs to discriminate among those groups. The study showed that the lncRNAs PACER and LNC13 were significantly upregulated in patients with active pulmonary tuberculosis at the initiation of treatment than in healthy controls. The expression levels of the two lncRNAs were significantly downregulated in patients during the treatment as compared to the active pulmonary tuberculosis patients. However, the expression levels of the lncRNAs PACER and LNC13 in whole blood of patients after six months of treatment were similar to those in healthy controls. Similarly, lncRNAs PACER and LNC13 showed very good performance in distinguishing between active tuberculosis patients and healthy controls as well as in differentiating between newly diagnosed active tuberculosis patients and those under treatment. Interestingly, those lncRNAs could not discriminate healthy controls from patients after six months of treatment. The lncRNAs PACER and LNC13 are therefore potential biomarkers for the monitoring of tuberculosis treatment.
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Huang Y, Li Y, Lin W, Fan S, Chen H, Xia J, Pi J, Xu JF. Promising Roles of Circular RNAs as Biomarkers and Targets for Potential Diagnosis and Therapy of Tuberculosis. Biomolecules 2022; 12:biom12091235. [PMID: 36139074 PMCID: PMC9496049 DOI: 10.3390/biom12091235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 09/01/2022] [Accepted: 09/02/2022] [Indexed: 12/02/2022] Open
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb) infection, remains one of the most threatening infectious diseases worldwide. A series of challenges still exist for TB prevention, diagnosis and treatment, which therefore require more attempts to clarify the pathological and immunological mechanisms in the development and progression of TB. Circular RNAs (circRNAs) are a large class of non-coding RNA, mostly expressed in eukaryotic cells, which are generated by the spliceosome through the back-splicing of linear RNAs. Accumulating studies have identified that circRNAs are widely involved in a variety of physiological and pathological processes, acting as the sponges or decoys for microRNAs and proteins, scaffold platforms for proteins, modulators for transcription and special templates for translation. Due to the stable and widely spread characteristics of circRNAs, they are expected to serve as promising prognostic/diagnostic biomarkers and therapeutic targets for diseases. In this review, we briefly describe the biogenesis, classification, detection technology and functions of circRNAs, and, in particular, outline the dynamic, and sometimes aberrant changes of circRNAs in TB. Moreover, we further summarize the recent progress of research linking circRNAs to TB-related pathogenetic processes, as well as the potential roles of circRNAs as diagnostic biomarkers and miRNAs sponges in the case of Mtb infection, which is expected to enhance our understanding of TB and provide some novel ideas about how to overcome the challenges associated TB in the future.
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Affiliation(s)
- Yifan Huang
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China
- Institute of Laboratory Medicine, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China
| | - Ying Li
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China
- Institute of Laboratory Medicine, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China
| | - Wensen Lin
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China
- Institute of Laboratory Medicine, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China
| | - Shuhao Fan
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China
- Institute of Laboratory Medicine, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China
| | - Haorong Chen
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China
- Institute of Laboratory Medicine, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China
| | - Jiaojiao Xia
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China
- Institute of Laboratory Medicine, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China
| | - Jiang Pi
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China
- Institute of Laboratory Medicine, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China
- Correspondence: (J.P.); (J.-F.X.)
| | - Jun-Fa Xu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China
- Institute of Laboratory Medicine, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China
- Correspondence: (J.P.); (J.-F.X.)
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Li X, Gao Y, Liu J, Xujian Q, Luo Q, Huang Z, Li J. Validation of Serotransferrin in the Serum as Candidate Biomarkers for the Diagnosis of Pulmonary Tuberculosis by Label-Free LC/MS. ACS OMEGA 2022; 7:24174-24183. [PMID: 35874208 PMCID: PMC9301696 DOI: 10.1021/acsomega.2c00837] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
This study aimed to identify secreted protein biomarkers in serum from the label-free LC/MS proteomics of neutrophils in pulmonary tuberculosis (TB) patients for the diagnosis biomarkers of TB label-free LC/MS. The proteomic profiles of neutrophils from 15 active TB patients and 15 healthy controls (HCs) were analyzed using label-free LC/MS. We identified 358 differentially expressed proteins preliminarily, including 279 up-regulated proteins and 79 down-regulated proteins. Thirty-eight differentially expressed secreted proteins involved in the progress of platelet degranulation between TB patients and HCs were focused. Of these, serotransferrin (TRF), alpha-2-macroglobulin (AMG), alpha-1-antitrypsin (AAT), alpha-1-acid glycoprotein 1 (AAG), alpha-1-acid glycoprotein 2 (AGP2), and alpha-1B-glycoprotein (A1BG) were selected for further verification in the serum of additional 134 TB patients and 138 HCs by nephelometry and ELISA in the training set. Statistically significant differences of TRF (P < 0.0001), AAT (P < 0.0001), AAG (P < 0.0001), AGP2 (P < 0.0001), and A1BG (P = 0.0003) were observed. The serum concentration of TRF was down-regulated in TB patients compared with healthy controls, which was coincident with the proteomics results. An additional validation of TRF was performed in an independent cohort of patients with active TB (n = 46), patients with lung cancer (n = 37), 20 HCs, and patients with pneumonia (n = 35) in the test set by nephelometry. The serum expression levels of TRF in the TB patients showed lower levels compared with those in patients with pneumonia (P = 0.0125), lung cancer (P = 0.0005), HCs (P < 0.0001), and the non-TB controls (P < 0.0001). Furthermore, the AUC value of TRF was 0.647 with 90.22% sensitivity and 42.86% specificity in discriminating the TB group from the pneumonia group, 0.702 with 93.48% sensitivity and 47.16% specificity in discriminating the TB group from the lung cancer group, 0.894 with 91.30% sensitivity and 71.62% specificity in discriminating the TB group from all HCs, and 0.792 with 91.30% sensitivity and 58.90% specificity in discriminating the TB group from the non-TB controls. This study obtained the proteomic profiles of neutrophils in the TB patients and HCs, which contribute to a better understanding of the pathogenesis molecules existing in the neutrophils of pulmonary tuberculosis and provide candidate biomarkers for the diagnosis of pulmonary tuberculosis.
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Affiliation(s)
- Xue Li
- Department
of Clinical Laboratory, The First Affiliated
Hospital of Nanchang University; Institute of Infection and Immunity,
Nanchang University, Nanchang, Jiangxi 330006, China
| | - Yujie Gao
- Department
of Clinical Laboratory, The First Affiliated
Hospital of Nanchang University; Institute of Infection and Immunity,
Nanchang University, Nanchang, Jiangxi 330006, China
| | - Jun Liu
- Department
of Clinical Laboratory, The First Affiliated
Hospital of Nanchang University; Institute of Infection and Immunity,
Nanchang University, Nanchang, Jiangxi 330006, China
| | - Qing Xujian
- Department
of Clinical Laboratory, The First Affiliated
Hospital of Nanchang University; Institute of Infection and Immunity,
Nanchang University, Nanchang, Jiangxi 330006, China
| | - Qing Luo
- Department
of Clinical Laboratory, The First Affiliated
Hospital of Nanchang University; Institute of Infection and Immunity,
Nanchang University, Nanchang, Jiangxi 330006, China
| | - Zikun Huang
- Department
of Clinical Laboratory, The First Affiliated
Hospital of Nanchang University; Institute of Infection and Immunity,
Nanchang University, Nanchang, Jiangxi 330006, China
| | - Junming Li
- Department
of Clinical Laboratory, The First Affiliated
Hospital of Nanchang University; Institute of Infection and Immunity,
Nanchang University, Nanchang, Jiangxi 330006, China
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Zhang X, Chen C, Xu Y. Long Non-coding RNAs in Tuberculosis: From Immunity to Biomarkers. Front Microbiol 2022; 13:883513. [PMID: 35633669 PMCID: PMC9130765 DOI: 10.3389/fmicb.2022.883513] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/24/2022] [Indexed: 12/05/2022] Open
Abstract
Tuberculosis (TB) caused by Mycobacterium tuberculosis (Mtb) is the leading lethal infectious disease with 1.3 million deaths in 2020. Despite significant advances have been made in detection techniques and therapeutic approaches for tuberculosis, no suitable diagnostic tools are available for early and precise screening. Many studies have reported that Long non-coding RNAs (lncRNAs) play a regulatory role in gene expression in the host immune response against Mtb. Dysregulation of lncRNAs expression patterns associated with immunoregulatory pathways arose in mycobacterial infection. Meanwhile, host-induced lncRNAs regulate antibacterial processes such as apoptosis and autophagy to limit bacterial proliferation. In this review, we try to summarize the latest reports on how dysregulated expressed lncRNAs influence host immune response in tuberculosis infection. We also discuss their potential clinical prospects for tuberculosis diagnosis and development as molecular biomarkers.
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Affiliation(s)
- Xianyi Zhang
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China.,The People's Hospital of Baoan Shenzhen, Southern Medical University, Shenzhen, China
| | - Chan Chen
- The People's Hospital of Baoan Shenzhen, Southern Medical University, Shenzhen, China
| | - Yuzhong Xu
- The People's Hospital of Baoan Shenzhen, Southern Medical University, Shenzhen, China
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5
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Lyu M, Zhou J, Jiao L, Wang Y, Zhou Y, Lai H, Xu W, Ying B. Deciphering a TB-related DNA methylation biomarker and constructing a TB diagnostic classifier. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 27:37-49. [PMID: 34938605 PMCID: PMC8645423 DOI: 10.1016/j.omtn.2021.11.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 11/16/2021] [Indexed: 02/09/2023]
Abstract
We systemically identified tuberculosis (TB)-related DNA methylation biomarkers and further constructed classifiers for TB diagnosis. TB-related DNA methylation datasets were searched through October 3, 2020. Limma and DMRcate were employed to identify differentially methylated probes (DMPs) and regions (DMRs). Machine learning methods were used to construct classifiers. The performance of the classifiers was evaluated in discovery datasets and a prospective independent cohort. Eighty-nine DMPs and 24 DMRs were identified based on 67 TB patients and 45 healthy controls from 4 datasets. Nine and three DMRs were selected by elastic net regression and logistic regression, respectively. Among the selected DMRs, two regions (chr3: 195635643-195636243 and chr6: 29691631-29692475) were differentially methylated in the independent cohort (p = 4.19 × 10-5 and 0.024, respectively). Among the ten classifiers, the 3-DMR logistic regression classifier exhibited the strongest performance. The sensitivity, specificity, and area under the curve were, respectively, 79.1%, 84.4%, and 0.888 in the discovery datasets and 64.5%, 90.3%, and 0.838 in the independent cohort. The differential diagnostic ability of this classifier was also assessed. Collectively, these data showed that DNA methylation might be a promising TB diagnostic biomarker. The 3-DMR logistic regression classifier is a potential clinical tool for TB diagnosis, and further validation is needed.
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Affiliation(s)
- Mengyuan Lyu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, No. 37, Guoxue Alley, Chengdu, Sichuan 610041, China.,West China School of Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jian Zhou
- West China School of Medicine, Sichuan University, Chengdu, Sichuan 610041, China.,Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Lin Jiao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, No. 37, Guoxue Alley, Chengdu, Sichuan 610041, China.,West China School of Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yili Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, No. 37, Guoxue Alley, Chengdu, Sichuan 610041, China.,West China School of Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yanbing Zhou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, No. 37, Guoxue Alley, Chengdu, Sichuan 610041, China.,West China School of Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Hongli Lai
- West China School of Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Wei Xu
- Department of Biostatistics, Princess Margaret Cancer Centre, University Health Network, 10-511, 610 University Avenue, Toronto, ON M5G 2M9 Canada.,Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7 Canada
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, No. 37, Guoxue Alley, Chengdu, Sichuan 610041, China.,West China School of Medicine, Sichuan University, Chengdu, Sichuan 610041, China
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6
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Tamgue O, Mezajou CF, Ngongang NN, Kameni C, Ngum JA, Simo USF, Tatang FJ, Akami M, Ngono AN. Non-Coding RNAs in the Etiology and Control of Major and Neglected Human Tropical Diseases. Front Immunol 2021; 12:703936. [PMID: 34737736 PMCID: PMC8560798 DOI: 10.3389/fimmu.2021.703936] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 09/09/2021] [Indexed: 12/19/2022] Open
Abstract
Non-coding RNAs (ncRNAs) including microRNAs (miRs) and long non-coding RNAs (lncRNAs) have emerged as key regulators of gene expression in immune cells development and function. Their expression is altered in different physiological and disease conditions, hence making them attractive targets for the understanding of disease etiology and the development of adjunctive control strategies, especially within the current context of mitigated success of control measures deployed to eradicate these diseases. In this review, we summarize our current understanding of the role of ncRNAs in the etiology and control of major human tropical diseases including tuberculosis, HIV/AIDS and malaria, as well as neglected tropical diseases including leishmaniasis, African trypanosomiasis and leprosy. We highlight that several ncRNAs are involved at different stages of development of these diseases, for example miR-26-5p, miR-132-3p, miR-155-5p, miR-29-3p, miR-21-5p, miR-27b-3p, miR-99b-5p, miR-125-5p, miR-146a-5p, miR-223-3p, miR-20b-5p, miR-142-3p, miR-27a-5p, miR-144-5p, miR-889-5p and miR-582-5p in tuberculosis; miR-873, MALAT1, HEAL, LINC01426, LINC00173, NEAT1, NRON, GAS5 and lincRNA-p21 in HIV/AIDS; miR-451a, miR-let-7b and miR-106b in malaria; miR-210, miR-30A-5P, miR-294, miR-721 and lncRNA 7SL RNA in leishmaniasis; and miR-21, miR-181a, miR-146a in leprosy. We further report that several ncRNAs were investigated as diseases biomarkers and a number of them showed good potential for disease diagnosis, including miR-769-5p, miR-320a, miR-22-3p, miR-423-5p, miR-17-5p, miR-20b-5p and lncRNA LOC152742 in tuberculosis; miR-146b-5p, miR-223, miR-150, miR-16, miR-191 and lncRNA NEAT1 in HIV/AIDS; miR-451 and miR-16 in malaria; miR-361-3p, miR-193b, miR-671, lncRNA 7SL in leishmaniasis; miR-101, miR-196b, miR-27b and miR-29c in leprosy. Furthermore, some ncRNAs have emerged as potential therapeutic targets, some of which include lncRNAs NEAT1, NEAT2 and lnr6RNA, 152742 in tuberculosis; MALAT1, HEAL, SAF, lincRNA-p21, NEAT1, GAS5, NRON, LINC00173 in HIV/AIDS; miRNA-146a in malaria. Finally, miR-135 and miR-126 were proposed as potential targets for the development of therapeutic vaccine against leishmaniasis. We also identify and discuss knowledge gaps that warrant for increased research work. These include investigation of the role of ncRNAs in the etiology of African trypanosomiasis and the assessment of the diagnostic potential of ncRNAs for malaria, and African trypanosomiasis. The potential targeting of ncRNAs for adjunctive therapy against tuberculosis, leishmaniasis, African trypanosomiasis and leprosy, as well as their targeting in vaccine development against tuberculosis, HIV/AIDS, malaria, African trypanosomiasis and leprosy are also new avenues to explore.
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Affiliation(s)
- Ousman Tamgue
- Department of Biochemistry, Faculty of Sciences, University of Douala, Douala, Cameroon
| | | | | | - Charleine Kameni
- Department of Biochemistry, Faculty of Sciences, University of Douala, Douala, Cameroon
| | - Jubilate Afuoti Ngum
- Department of Biochemistry, Faculty of Sciences, University of Douala, Douala, Cameroon
| | | | - Fabrice Junior Tatang
- Department of Biochemistry, Faculty of Sciences, University of Douala, Douala, Cameroon
| | - Mazarin Akami
- Department of Biochemistry, Faculty of Sciences, University of Douala, Douala, Cameroon
| | - Annie Ngane Ngono
- Department of Biochemistry, Faculty of Sciences, University of Douala, Douala, Cameroon
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7
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Meng Z, Wang M, Guo S, Zhou Y, Lyu M, Hu X, Bai H, Wu Q, Tao C, Ying B. Novel Long Non-coding RNA and LASSO Prediction Model to Better Identify Pulmonary Tuberculosis: A Case-Control Study in China. Front Mol Biosci 2021; 8:632185. [PMID: 34113649 PMCID: PMC8185277 DOI: 10.3389/fmolb.2021.632185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/25/2021] [Indexed: 02/05/2023] Open
Abstract
Introduction The insufficient understanding and misdiagnosis of clinically diagnosed pulmonary tuberculosis (PTB) without an aetiological evidence is a major problem in the diagnosis of tuberculosis (TB). This study aims to confirm the value of Long non-coding RNA (lncRNA) n344917 in the diagnosis of PTB and construct a rapid, accurate, and universal prediction model. Methods A total of 536 patients were prospectively and consecutively recruited, including clinically diagnosed PTB, PTB with an aetiological evidence and non-TB disease controls, who were admitted to West China hospital from Dec 2014 to Dec 2017. The expression levels of lncRNA n344917 of all patients were analyzed using reverse transcriptase quantitative real-time PCR. Then, the laboratory findings, electronic health record (EHR) information and expression levels of n344917 were used to construct a prediction model through the Least Absolute Shrinkage and Selection Operator algorithm and multivariate logistic regression. Results The factors of n344917, age, CT calcification, cough, TBIGRA, low-grade fever and weight loss were included in the prediction model. It had good discrimination (area under the curve = 0.88, cutoff = 0.657, sensitivity = 88.98%, specificity = 86.43%, positive predictive value = 85.61%, and negative predictive value = 89.63%), consistency and clinical availability. It also showed a good replicability in the validation cohort. Finally, it was encapsulated as an open-source and free web-based application for clinical use and is available online at https://ziruinptb.shinyapps.io/shiny/. Conclusion Combining the novel potential molecular biomarker n344917, laboratory and EHR variables, this web-based prediction model could serve as a user-friendly, accurate platform to improve the clinical diagnosis of PTB.
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Affiliation(s)
- Zirui Meng
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Minjin Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Shuo Guo
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Yanbing Zhou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Mengyuan Lyu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Xuejiao Hu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Hao Bai
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Qian Wu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Chuanmin Tao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
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8
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Lyu M, Cheng Y, Zhou J, Chong W, Wang Y, Xu W, Ying B. Systematic evaluation, verification and comparison of tuberculosis-related non-coding RNA diagnostic panels. J Cell Mol Med 2020; 25:184-202. [PMID: 33314695 PMCID: PMC7810967 DOI: 10.1111/jcmm.15903] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/23/2020] [Accepted: 09/01/2020] [Indexed: 02/06/2023] Open
Abstract
We systematically summarized tuberculosis (TB)‐related non‐coding RNA (ncRNA) diagnostic panels, validated and compared panel performance. We searched TB‐related ncRNA panels in PubMed, OVID and Web of Science up to 28 February 2020, and available datasets in GEO, SRA and EBI ArrayExpress up to 1 March 2020. We rebuilt models and synthesized the results of each model in validation sets by bivariate mixed models. Specificity at 90% sensitivity, area under curve (AUC) and inconsistence index (I2) were calculated. NcRNA biofunctions were analysed. Nineteen models based on 18 ncRNA panels (miRNA, lncRNA, circRNA and snoRNA panels) and 18 datasets were included. Limited available datasets only allowed to evaluate miRNA panels further. Cui 2017 and Latorre 2015 exhibited specificity >70% at 90% sensitivity and AUC >80% in all validation sets. Cui 2017 showed higher specificity at 90% sensitivity (92%) and AUC (95%) and lower heterogeneity (I2 = 0%) in ethological‐confirmation validation sets. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis indicated that most ncRNAs in panels involved in immune cell activation, oxidative stress, and Wnt and MAPK signalling pathway. Cui 2017 outperformed other models in both all available and aetiological‐confirmed validation sets, meeting the criteria of target product profile of WHO. This work provided a basis for clinical choice of TB‐related ncRNA diagnostic panels to a certain extent.
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Affiliation(s)
- Mengyuan Lyu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China.,West China School of Medicine, Sichuan University, Chengdu, China
| | - Yuhui Cheng
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China.,West China School of Medicine, Sichuan University, Chengdu, China
| | - Jian Zhou
- West China School of Medicine, Sichuan University, Chengdu, China.,Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Weelic Chong
- Sidney Kimmel School of Medicine, Thomas Jefferson University, Philadelphia, PA, USA
| | - Yili Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China.,West China School of Medicine, Sichuan University, Chengdu, China
| | - Wei Xu
- Department of Biostatistics, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China.,West China School of Medicine, Sichuan University, Chengdu, China
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