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Li S, Zhang Y, Ishfaq M, Liu R, Wei G, Zhang X. Curcumin alleviates Aflatoxin B1-triggered chicken liver necroptosis by targeting the LOC769044/miR-1679/STAT1 axis. Poult Sci 2024; 103:103883. [PMID: 38865767 PMCID: PMC11223116 DOI: 10.1016/j.psj.2024.103883] [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: 01/09/2024] [Revised: 05/05/2024] [Accepted: 05/17/2024] [Indexed: 06/14/2024] Open
Abstract
Aflatoxin B1 (AFB1) is an unavoidable environmental toxin. The accumulation of AFB1 and its metabolites in the liver poses a threat to both human and animal health. Curcumin exhibits anti-oxidative, anti-tumor, and anti-inflammatory properties. There is no report on the mechanism regarding how curcumin relived liver necroptosis in chickens induced by AFB1 based on the regulatory network of ceRNA. To explore this, we performed transmission electron microscopy and sequenced lncRNA and mRNA in chicken livers treated with AFB1 and/or curcumin for 28 d in vivo. We observed substantial alterations in the lncRNA and mRNA expression profiles within the chicken liver, indicating that curcumin can mitigate AFB1-induced necroptosis both in vivo and in vitro. Further analysis, including the establishment of an lncRNA-miRNA-mRNA network and the utilization of a dual luciferase reporter assay, revealed that LOC769044 acts as a competing endogenous RNA (ceRNA) for miR-1679. In addition, STAT1 was identified as a direct target of miR-1679. Modulating miR-1679 levels through overexpression, and silencing LOC769044 and STAT1, effectively reversed the necroptotic effects induced by AFB1, a reversal that was also observed with curcumin supplementation. In conclusion, our data demonstrate that curcumin alleviates AFB1-induced liver necroptosis through the LOC769044/miR-1679/STAT1 signaling axis. This study suggests that LOC769044 may serve as a novel therapeutic target for managing AFB1-mediated liver toxicity.
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Affiliation(s)
- Sihong Li
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development. Faculty of Basic Veterinary Science, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Xiangfang District, Harbin, China; Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, Zhejiang Province 311300, China
| | - Yixin Zhang
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development. Faculty of Basic Veterinary Science, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Xiangfang District, Harbin, China
| | - Muhammad Ishfaq
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ruimeng Liu
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development. Faculty of Basic Veterinary Science, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Xiangfang District, Harbin, China
| | - Gaoqiang Wei
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development. Faculty of Basic Veterinary Science, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Xiangfang District, Harbin, China
| | - Xiuying Zhang
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development. Faculty of Basic Veterinary Science, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Xiangfang District, Harbin, China.
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Shi L, Han X, Liu F, Long J, Jin Y, Chen S, Duan G, Yang H. Review on Long Non-Coding RNAs as Biomarkers and Potentially Therapeutic Targets for Bacterial Infections. Curr Issues Mol Biol 2024; 46:7558-7576. [PMID: 39057090 PMCID: PMC11276060 DOI: 10.3390/cimb46070449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/13/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
The confrontation between humans and bacteria is ongoing, with strategies for combating bacterial infections continually evolving. With the advancement of RNA sequencing technology, non-coding RNAs (ncRNAs) associated with bacterial infections have garnered significant attention. Recently, long ncRNAs (lncRNAs) have been identified as regulators of sterile inflammatory responses and cellular defense against live bacterial pathogens. They are involved in regulating host antimicrobial immunity in both the nucleus and cytoplasm. Increasing evidence indicates that lncRNAs are critical for the intricate interactions between host and pathogen during bacterial infections. This paper emphatically elaborates on the potential applications of lncRNAs in clinical hallmarks, cellular damage, immunity, virulence, and drug resistance in bacterial infections in greater detail. Additionally, we discuss the challenges and limitations of studying lncRNAs in the context of bacterial infections and highlight clear directions for this promising field.
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Affiliation(s)
| | | | | | | | | | | | | | - Haiyan Yang
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China; (L.S.); (X.H.); (F.L.); (J.L.); (Y.J.); (S.C.); (G.D.)
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Dong J, Song R, Shang X, Wang Y, Liu Q, Zhang Z, Jia H, Huang M, Zhu C, Sun Q, Du B, Xing A, Li Z, Zhang L, Pan L, Zhang Z. Identification of important modules and biomarkers in tuberculosis based on WGCNA. Front Microbiol 2024; 15:1354190. [PMID: 38389525 PMCID: PMC10882270 DOI: 10.3389/fmicb.2024.1354190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 01/23/2024] [Indexed: 02/24/2024] Open
Abstract
Background Tuberculosis (TB) is a significant public health concern, particularly in China. Long noncoding RNAs (lncRNAs) can provide abundant pathological information regarding etiology and could include candidate biomarkers for diagnosis of TB. However, data regarding lncRNA expression profiles and specific lncRNAs associated with TB are limited. Methods We performed ceRNA-microarray analysis to determine the expression profile of lncRNAs in peripheral blood mononuclear cells (PBMCs). Weighted gene co-expression network analysis (WGCNA) was then conducted to identify the critical module and genes associated with TB. Other bioinformatics analyses, including Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), and co-expression networks, were conducted to explore the function of the critical module. Finally, real-time quantitative polymerase chain reaction (qPCR) was used to validate the candidate biomarkers, and receiver operating characteristic analysis was used to assess the diagnostic performance of the candidate biomarkers. Results Based on 8 TB patients and 9 healthy controls (HCs), a total of 1,372 differentially expressed lncRNAs were identified, including 738 upregulated lncRNAs and 634 downregulated lncRNAs. Among all lncRNAs and mRNAs in the microarray, the top 25% lncRNAs (3729) and top 25% mRNAs (2824), which exhibited higher median expression values, were incorporated into the WGCNA. The analysis generated 16 co-expression modules, among which the blue module was highly correlated with TB. GO and KEGG analyses showed that the blue module was significantly enriched in infection and immunity. Subsequently, considering module membership values (>0.85), gene significance values (>0.90) and fold-change value (>2 or < 0.5) as selection criteria, the top 10 upregulated lncRNAs and top 10 downregulated lncRNAs in the blue module were considered as potential biomarkers. The candidates were then validated in an independent validation sample set (31 TB patients and 32 HCs). The expression levels of 8 candidates differed significantly between TB patients and HCs. The lncRNAs ABHD17B (area under the curve [AUC] = 1.000) and ENST00000607464.1 (AUC = 1.000) were the best lncRNAs in distinguishing TB patients from HCs. Conclusion This study characterized the lncRNA profiles of TB patients and identified a significant module associated with TB as well as novel potential biomarkers for TB diagnosis.
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Affiliation(s)
- Jing Dong
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Ruixue Song
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Xuetian Shang
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Yingchao Wang
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Qiuyue Liu
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
- Department of Intensive Care Unit, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Zhiguo Zhang
- Changping Tuberculosis Prevent and Control Institute of Beijing, Beijing, China
| | - Hongyan Jia
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Mailing Huang
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
- Department of Tuberculosis, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Chuanzhi Zhu
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Qi Sun
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Boping Du
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Aiying Xing
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Zihui Li
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Lanyue Zhang
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Liping Pan
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Zongde Zhang
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
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Li G, Feng Z, Song H, Wang Y, Zhu L, Li Y. Long non-coding RNA expression in PBMCs of patients with active pulmonary tuberculosis. Front Microbiol 2023; 14:1257267. [PMID: 38156018 PMCID: PMC10753990 DOI: 10.3389/fmicb.2023.1257267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 11/06/2023] [Indexed: 12/30/2023] Open
Abstract
Purpose Mycobacterium tuberculosis (Mtb) infection is the primary cause of the chronic infectious illness tuberculosis (TB). Long non-coding RNAs (lncRNAs) are functional RNA molecules that cannot be translated into proteins and play a crucial role in regulating the immune system's innate and adaptive responses. It has been demonstrated that the dysregulation of lncRNA expression is associated with various human diseases. However, the mechanism underlying the involvement of so many lncRNAs in the immune response to TB infection remains unclear. The objective of our current study was to identify a number of significantly differentially expressed lncRNAs in peripheral blood mononuclear cells (PBMCs) from TB patients and to select the most indicative lncRNAs as potential biomarkers for active pulmonary tuberculosis. Methods Microarray analysis was performed to determine the lncRNA and mRNA expression profiles in TB patients using a case-control model. The differentially expressed lncRNAs were subjected to gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis to investigate potential roles and pathways associated with the pathogenesis of TB infection, and to screen lncRNAs specifically linked to TB infection. Using real-time fluorescence quantitative PCR (QRT-PCR), specific lncRNAs were identified in TB patients and latent infections. Results Our findings revealed that various signaling pathways were differentially expressed in TB-infected individuals, suggesting a potential role for lncRNAs in the immunological responses driven by TB infection. This study provides crucial guidelines for future functional research. Upregulated lncRNAs were mainly enriched in Neutrophil extracellular trap formation and Chemokine signaling pathways, while downregulated lncRNAs were enriched in Neuroactive ligand-receptor interaction and Cushing syndrome in TB PBMCs. Furthermore, we found that lnc-XPNPEP1-5, lnc-CASKIN2-2, lnc-HSPA13-6, lnc-CLIC5-1, and LINC02502 were significantly downregulated in TB-infected patients, while LINC00528, lnc-SLC45A4-3, and LINC00926 were significantly upregulated in TB patients and latent infections. These eight lncRNAs, identified as novel biological marker candidates for diagnosing TB infection, were validated by real-time fluorescence quantitative PCR (QRT-PCR). Conclusion The abnormally expressed lncRNAs identified in this research may provide crucial information for understanding the pathophysiological characteristics of TB patients and the dysfunction of PBMCs. Our findings reveal potential targets for early TB diagnosis and therapy, as well as offer new insights into the mechanisms underlying TB infection.
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Affiliation(s)
- Guoli Li
- Department of Chronic Communicable Disease, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Zhelong Feng
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Honghuan Song
- Department of Chronic Communicable Disease, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Yajing Wang
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Limei Zhu
- Department of Chronic Communicable Disease, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Yan Li
- Integrated Service and Management Office, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
- Department of Chronic Communicable Disease, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
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Xia J, Liu Y, Ma Y, Yang F, Ruan Y, Xu JF, Pi J. Advances of Long Non-Coding RNAs as Potential Biomarkers for Tuberculosis: New Hope for Diagnosis? Pharmaceutics 2023; 15:2096. [PMID: 37631310 PMCID: PMC10458399 DOI: 10.3390/pharmaceutics15082096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
Tuberculosis (TB), one of the top ten causes of death globally induced by the infection of Mycobacterium tuberculosis (Mtb), remains a grave public health issue worldwide. With almost one-third of the world's population getting infected by Mtb, between 5% and 10% of these infected individuals are predicted to develop active TB disease, which would not only result in severe tissue damage and necrosis, but also pose serious threats to human life. However, the exact molecular mechanisms underlying the pathogenesis and immunology of TB remain unclear, which significantly restricts the effective control of TB epidemics. Despite significant advances in current detection technologies and treatments for TB, there are still no appropriate solutions that are suitable for simultaneous, early, rapid, and accurate screening of TB. Various cellular events can perturb the development and progression of TB, which are always associated with several specific molecular signaling events controlled by dysregulated gene expression patterns. Long non-coding RNAs (lncRNAs), a kind of non-coding RNA (ncRNA) with a transcript of more than 200 nucleotides in length in eukaryotic cells, have been found to regulate the expression of protein-coding genes that are involved in some critical signaling events, such as inflammatory, pathological, and immunological responses. Increasing evidence has claimed that lncRNAs might directly influence the susceptibility to TB, as well as the development and progression of TB. Therefore, lncRNAs have been widely expected to serve as promising molecular biomarkers and therapeutic targets for TB. In this review, we summarized the functions of lncRNAs and their regulatory roles in the development and progression of TB. More importantly, we widely discussed the potential of lncRNAs to act as TB biomarkers, which would offer new possibilities in novel diagnostic strategy exploration and benefit the control of the TB epidemic.
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Affiliation(s)
- Jiaojiao Xia
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China; (J.X.); (Y.L.); (Y.M.); (F.Y.); (Y.R.)
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Kunming Medical University, Kunming 650500, China
| | - Yilin Liu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China; (J.X.); (Y.L.); (Y.M.); (F.Y.); (Y.R.)
- Institute of Laboratory Medicine, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China
| | - Yuhe Ma
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China; (J.X.); (Y.L.); (Y.M.); (F.Y.); (Y.R.)
- Institute of Laboratory Medicine, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China
| | - Fen Yang
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China; (J.X.); (Y.L.); (Y.M.); (F.Y.); (Y.R.)
- Institute of Laboratory Medicine, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China
| | - Yongdui Ruan
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China; (J.X.); (Y.L.); (Y.M.); (F.Y.); (Y.R.)
| | - Jun-Fa Xu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China; (J.X.); (Y.L.); (Y.M.); (F.Y.); (Y.R.)
- The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang 524023, China
| | - Jiang Pi
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China; (J.X.); (Y.L.); (Y.M.); (F.Y.); (Y.R.)
- Institute of Laboratory Medicine, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China
- The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang 524023, China
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Chen B, Xu X, Wu W, Zheng K, Yu Y. LINC00659 Inhibits Hepatocellular Carcinoma Malignant Progression by Blocking Aerobic Glycolysis through FUS Recruitment and SLC10A1 Modulation. Anal Cell Pathol (Amst) 2023; 2023:5852963. [PMID: 37234237 PMCID: PMC10208759 DOI: 10.1155/2023/5852963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 04/04/2023] [Accepted: 04/29/2023] [Indexed: 05/27/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a malignant type of liver cancer that poses severe threat to human health worldwide. Aerobic glycolysis is a hallmark of HCC and facilitates its progression. Solute carrier family 10 member 1 (SLC10A1) and long intergenic non-protein coding RNA 659 (LINC00659) were detected to be downregulated in HCC cells, yet their potential functions underlying HCC progression remained unidentified. In the current work, colony formation and transwell assays were used to detect HCC cells (HepG2 and HuH-7) proliferation and migration in vitro study. The quantitative real-time polymerase chain reaction (qRT-PCR) and western blot assays were used for gene/protein expression determination. Seahorse assay was performed for aerobic glycolysis assessment. RNA immunoprecipitation (RIP) and RNA pull-down assays were conducted for detection of the molecular interaction between LINC00659 and SLC10A1. The results showed that overexpressed SLC10A1 significantly suppressed the proliferation, migration, and aerobic glycolysis in HCC cells. Mechanical experiments further demonstrated that LINC00659 positively regulated SLC10A1 expression in HCC cells by recruiting fused protein in sarcoma (FUS). Our work elucidated that LINC00659 inhibited HCC progression and aerobic glycolysis via the FUS/SLC10A1 axis, revealing a novel lncRNA-RNA-binding protein-mRNA network in HCC, which might provide potential therapeutic targets for HCC.
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Affiliation(s)
- Bin Chen
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Hangzhou Normal University, Zhejiang, Hangzhou 310011, China
| | - Xin Xu
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Hangzhou Normal University, Zhejiang, Hangzhou 310011, China
| | - Wei Wu
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Hangzhou Normal University, Zhejiang, Hangzhou 310011, China
| | - Ke Zheng
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Hangzhou Normal University, Zhejiang, Hangzhou 310011, China
| | - Yijun Yu
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Hangzhou Normal University, Zhejiang, Hangzhou 310011, China
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Sengupta S, Pattanaik KP, Mishra S, Sonawane A. Epigenetic orchestration of host immune defences by Mycobacterium tuberculosis. Microbiol Res 2023; 273:127400. [PMID: 37196490 DOI: 10.1016/j.micres.2023.127400] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 04/09/2023] [Accepted: 05/02/2023] [Indexed: 05/19/2023]
Abstract
Being among the top 10 causes of adult deaths, tuberculosis (TB) disease is considered a major global public health concern to address. The human tuberculosis pathogen, Mycobacterium tuberculosis (Mtb), is an extremely competent and well-versed pathogen that promotes pathogenesis by evading the host immune systems through numerous tactics. Investigations revealed that Mtb could evade the host defense mechanisms by reconfiguring the host gene transcription and causing epigenetic changes. Although results indicate the link between epigenetics and disease manifestation in other bacterial infections, little is known regarding the kinetics of the epigenetic alterations in mycobacterial infection. This literature review discusses the studies in Mtb-induced epigenetic alterations inside the host and its contribution in the host immune evasion strategies. It also discusses how the Mtb-induced alterations could be used as 'epibiomarkers' to diagnose TB. Additionally, this review also discusses therapeutic interventions to be enhanced through remodification by 'epidrugs'.
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Affiliation(s)
- Srabasti Sengupta
- School of Biotechnology, Campus-11, KIIT Deemed to be University, Patia, Bhubaneswar 751024, India
| | - Kali Prasad Pattanaik
- School of Biotechnology, Campus-11, KIIT Deemed to be University, Patia, Bhubaneswar 751024, India
| | - Snehasish Mishra
- School of Biotechnology, Campus-11, KIIT Deemed to be University, Patia, Bhubaneswar 751024, India
| | - Avinash Sonawane
- Discipline of Biosciences and Biomedical Engineering, Indian Institutes of Technology Indore, Khandwa Road, Simrol, Indore 453552, India.
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Song J, Sun J, Wang Y, Ding Y, Zhang S, Ma X, Chang F, Fan B, Liu H, Bao C, Meng W. CeRNA network identified hsa-miR-17-5p, hsa-miR-106a-5p and hsa-miR-2355-5p as potential diagnostic biomarkers for tuberculosis. Medicine (Baltimore) 2023; 102:e33117. [PMID: 36930090 PMCID: PMC10019109 DOI: 10.1097/md.0000000000033117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/08/2023] [Indexed: 03/18/2023] Open
Abstract
This study aims to analyze the regulatory non-coding RNAs in the pathological process of tuberculosis (TB), and identify novel diagnostic biomarkers. A longitudinal study was conducted in 5 newly diagnosed pulmonary tuberculosis patients, peripheral blood samples were collected before and after anti-TB treatment for 6 months, separately. After whole transcriptome sequencing, the differentially expressed RNAs (DE RNAs) were filtrated with |log2 (fold change) | > log2(1.5) and P value < .05 as screening criteria. Then functional annotation was actualized by gene ontology enrichment analysis, and enrichment pathway analysis was conducted by Kyoto Encyclopedia of Genes and Genomes database. And finally, the competitive endogenous RNA (ceRNA) regulatory network was established according to the interaction of ceRNA pairs and miRNA-mRNA pairs. Five young women were recruited and completed this study. Based on the differential expression analysis, a total of 1469 mRNAs, 996 long non-coding RNAs, 468 circular RNAs, and 86 miRNAs were filtrated as DE RNAs. Functional annotation demonstrated that those DE-mRNAs were strongly involved in the cellular process (n = 624), metabolic process (n = 513), single-organism process (n = 505), cell (n = 651), cell part (n = 650), organelle (n = 569), and binding (n = 629). Enrichment pathway analysis revealed that the differentially expressed genes were mainly enriched in HTLV-l infection, T cell receptor signaling pathway, glycosaminoglycan biosynthesis-heparan sulfate/heparin, and Hippo signaling pathway. CeRNA networks revealed that hsa-miR-17-5p, hsa-miR-106a-5p and hsa-miR-2355-5p might be regarded as potential diagnostic biomarkers for TB. Immunomodulation-related genes are differentially expressed in TB patients, and hsa-miR-106a-5p, hsa-miR-17-5p, hsa-miR-2355-5p might serve as potential diagnostic biomarkers.
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Affiliation(s)
- Jie Song
- School of Public Health, Xinxiang Medical University, Xinxiang, China
| | - Jiaguan Sun
- School of Public Health, Xinxiang Medical University, Xinxiang, China
| | - Yuqing Wang
- The 4th People’s Hospital of Qinghai Province, Xining, China
| | - Yuehe Ding
- The 4th People’s Hospital of Qinghai Province, Xining, China
| | - Shengrong Zhang
- The 4th People’s Hospital of Qinghai Province, Xining, China
| | - Xiuzhen Ma
- The 4th People’s Hospital of Qinghai Province, Xining, China
| | - Fengxia Chang
- The 4th People’s Hospital of Qinghai Province, Xining, China
| | - Bingdong Fan
- The 4th People’s Hospital of Qinghai Province, Xining, China
| | - Hongjuan Liu
- The 4th People’s Hospital of Qinghai Province, Xining, China
| | - Chenglan Bao
- The 4th People’s Hospital of Qinghai Province, Xining, China
| | - Weimin Meng
- The 4th People’s Hospital of Qinghai Province, Xining, China
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Epigenetic-Mediated Antimicrobial Resistance: Host versus Pathogen Epigenetic Alterations. Antibiotics (Basel) 2022; 11:antibiotics11060809. [PMID: 35740215 PMCID: PMC9220109 DOI: 10.3390/antibiotics11060809] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/07/2022] [Accepted: 06/13/2022] [Indexed: 02/04/2023] Open
Abstract
Since the discovery of antibiotics, humans have been benefiting from them by decreasing the morbidity and mortality associated with bacterial infections. However, in the past few decades, misuse of antibiotics has led to the emergence of bacterial infections resistant to multiple drugs, a significant health concern. Bacteria exposed to inappropriate levels of antibiotics lead to several genetic changes, enabling them to survive in the host and become more resistant. Despite the understanding and targeting of genetic-based biochemical changes in the bacteria, the increasing levels of antibiotic resistance are not under control. Many reports hint at the role of epigenetic modifications in the bacterial genome and host epigenetic reprogramming due to interaction with resistant pathogens. Epigenetic changes, such as the DNA-methylation-based regulation of bacterial mutation rates or bacteria-induced histone modification in human epithelial cells, facilitate its long-term survival. In this review article, epigenetic changes leading to the development of antibiotic resistance in clinically relevant bacteria are discussed. Additionally, recent lines of evidence focusing on human host epigenetic changes due to the human–pathogen interactions are presented. As genetic mechanisms cannot explain the transient nature of antimicrobial resistance, we believe that epigenetics may provide new frontiers in antimicrobial discovery.
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Liu J, Huang J, Cheng X, Liao Z, Gao X. miR-556-3p/Disabled Homolog 2-Interacting Protein (dab2ip) Promotes Cancer Progression by Down-Regulating Bcl-2-Like Protein 11 (BIM) Expression in Colorectal Cancer. J BIOMATER TISS ENG 2022. [DOI: 10.1166/jbt.2022.3035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Colorectal cancer (CRC) is a major threat affecting human health. Studies have shown that miR-556-3p can regulate dab2ip and promote tumor deterioration, and up-regulation of BIM inhibits CRC cell progression. However, the interaction between miR-556-3p/dab2ip and BIM in CRC is unknown.
We examined miR-556-3p expression in CRC tissues and cells by RT-qPCR. The impact of miR-556-3p/dab2ip and BIM on CRC cell behaviors were assessed by western blot, transwell and MTT assay. miR-556-3p was highly expressed in CRC and its overexpression increased CRC cell proliferation and migration
as well as up-regulated dab2ip and Ki-67 expression. Besides, miR-556-3p could target the BIM and overexpressed miR-556-3p decreased BIM expression. However, silencing of BIM abrogated the impact of overexpressed miR-556-3p on CRC cell proliferation and migration. In conclusion, miR-556-3p/dab2ip
promotes cell growth by down-regulating the expression of BIM, thereby promoting the progression of CRC.
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Affiliation(s)
- Jiaqi Liu
- Department of General Surgery, Beihai People’s Hospital, Beihai City, Guangxi Zhuang Autonomous Region, 536000, China
| | - Jingping Huang
- Department of Nutrition, Beihai People’s Hospital, Beihai City, Guangxi Zhuang Autonomous Region, 536000, China
| | - Xueyuan Cheng
- Department of General Surgery, Beihai People’s Hospital, Beihai City, Guangxi Zhuang Autonomous Region, 536000, China
| | - Zuowei Liao
- Department of General Surgery, Beihai People’s Hospital, Beihai City, Guangxi Zhuang Autonomous Region, 536000, China
| | - Xueyuan Gao
- Department of General Surgery, Beihai People’s Hospital, Beihai City, Guangxi Zhuang Autonomous Region, 536000, China
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11
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Downregulation of HULC Induces Ferroptosis in Hepatocellular Carcinoma via Targeting of the miR-3200-5p/ATF4 Axis. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:9613095. [PMID: 35615577 PMCID: PMC9126659 DOI: 10.1155/2022/9613095] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/12/2022] [Accepted: 04/30/2022] [Indexed: 12/20/2022]
Abstract
Hepatocellular carcinoma is a malignant tumor that poses a serious threat to human health. Ferroptosis, which represents an identified type of regulated iron-dependent cell death, may play an important role in hepatocellular carcinoma. However, it is unclear as to whether ferroptosis is involved with the mechanisms of lncRNA HULC in liver cancer cells. Here, we show that knockdown of HULC increases ferroptosis and oxidative stress in liver cancer cells. We also found changes in some related miRNAs in cells treated with HULC siRNA. Differential miRNA expression levels were determined with the use of high-throughput sequencing and prediction target genes identified using bioinformatics analysis. HULC was found to function as a ceRNA of miR-3200-5p, and miR-3200-5p regulates ferroptosis by targeting ATF4, resulting in the inhibition of proliferation and metastasis within HCC cells. In summary, these findings illuminate some of the molecular mechanisms through which downregulation of HULC induces liver cancer cell ferroptosis by targeting the miR-3200-5p/ATF4 axis to modulate the development of hepatocellular carcinoma.
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12
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Luo F, Wen Y, Zhao L, Su S, Lei W, Chen L, Chen C, Huang Q, Li Z. LncRNA ZEB1-AS1/miR-1224-5p / MAP4K4 axis regulates mitochondria-mediated HeLa cell apoptosis in persistent Chlamydia trachomatis infection. Virulence 2022; 13:444-457. [PMID: 35266440 PMCID: PMC8920228 DOI: 10.1080/21505594.2022.2044666] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Persistent infection of Chlamydia trachomatis is thought to be responsible for the debilitating sequelae of blinding trachoma and infertility. Inhibition of host cell apoptosis is a persistent C. trachomatis infection mechanism. ZEB1-AS1 is a long non-coding RNA (lncRNA), which was up-regulated in persistent C. trachomatis infection in our previous work. In this study, we investigated the role of ZEB1-AS1 in persistent infection and the potential mechanisms. The results showed that ZEB1-AS1 was involved in the regulation of apoptosis, and targeted silencing of ZEB1-AS1 could increase the apoptosis rate of persistently infected cells. Mechanically, interference ZEB1-AS1 caused an apparent down-regulation of the Bcl-2/Bax ratio and the repression of the mitochondrial membrane potential with the remarkable release of cytochrome c, resulting in the significant elevation level of caspase-3 activation. Meanwhile, the luciferase reporter assay confirmed that ZEB1-AS1 acted as a sponge for miR-1224-5p to target MAP4K4. The regulatory effect of miR-1224-5p/MAP4K4 on persistent infection-induced antiapoptosis was regulated by ZEB1-AS1. In addition, ZEB1-AS1 inhibited the apoptosis of Chlamydia-infected cells by activating the MAPK/ERK pathway. In conclusion, we found a new molecular mechanism that the ZEB1-AS1/miR-1224-5p/MAP4K4 axis contributes to apoptosis resistance in persistent C. trachomatis infection. This work may help understand the pathogenic mechanisms of persistent C. trachomatis infection and reveal a potential therapeutic strategy for its treatment.
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Affiliation(s)
- Fangzhen Luo
- Institute of Pathogenic Biology, Hengyang Medical School, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, University of South China, Hengyang, P. R. China.,College of Medical Technology, Hunan Polytechnic of Environment and Biology, Hengyang, P. R. China
| | - Yating Wen
- Institute of Pathogenic Biology, Hengyang Medical School, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, University of South China, Hengyang, P. R. China
| | - Lanhua Zhao
- Institute of Pathogenic Biology, Hengyang Medical School, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, University of South China, Hengyang, P. R. China
| | - Shengmei Su
- Institute of Pathogenic Biology, Hengyang Medical School, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, University of South China, Hengyang, P. R. China
| | - Wenbo Lei
- Institute of Pathogenic Biology, Hengyang Medical School, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, University of South China, Hengyang, P. R. China
| | - Lili Chen
- Institute of Pathogenic Biology, Hengyang Medical School, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, University of South China, Hengyang, P. R. China
| | - Chaoqun Chen
- Institute of Pathogenic Biology, Hengyang Medical School, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, University of South China, Hengyang, P. R. China
| | - Qiulin Huang
- The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, P. R. China
| | - Zhongyu Li
- Institute of Pathogenic Biology, Hengyang Medical School, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, University of South China, Hengyang, P. R. China
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13
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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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14
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Luo F, Wen Y, Zhao L, Su S, Zhao Y, Lei W, Li Z. Chlamydia trachomatis induces lncRNA MIAT upregulation to regulate mitochondria-mediated host cell apoptosis and chlamydial development. J Cell Mol Med 2021; 26:163-177. [PMID: 34859581 PMCID: PMC8742237 DOI: 10.1111/jcmm.17069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 10/27/2021] [Accepted: 11/11/2021] [Indexed: 01/12/2023] Open
Abstract
Chlamydia trachomatis persistent infection is the leading cause of male prostatitis and female genital tract diseases. Inhibition of host cell apoptosis is the key to maintaining Chlamydia survival in vivo, and long noncoding RNAs (lncRNAs) play important roles in its developmental cycle and pathogenesis. However, it is not clear how lncRNAs regulate persistent Chlamydia infection. Here, using a microarray method, we identified 1718 lncRNAs and 1741 mRNAs differentially expressed in IFN-γ-induced persistent C. trachomatis infection. Subsequently, 10 upregulated and 5 downregulated differentially expressed lncRNAs were verified by qRT-PCR to confirm the reliability of the chip data. The GO and KEGG analyses revealed that differentially regulated transcripts were predominantly involved in various signalling pathways related to host immunity and apoptosis response. Targeted silencing of three lncRNAs (MIAT, ZEB1-AS1 and IRF1) resulted in increased apoptosis rates. Furthermore, interference with lncRNA MIAT caused not only an obvious downregulation of the Bcl-2/Bax ratio but also a marked release of cytochrome c, resulting in a significantly elevated level of caspase-3 activation. Meanwhile, MIAT was involved in the regulation of chlamydial development during the persistent infection. Collectively, these observations shed light on the enormous complex lncRNA regulatory networks involved in mitochondria-mediated host cell apoptosis and the growth and development of C. trachomatis.
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Affiliation(s)
- Fangzhen Luo
- Institute of Pathogenic Biology, Hengyang Medical College, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, University of South China, Hengyang, China.,Hunan Polytechnic of Environment and Biology, Hengyang, China
| | - Yating Wen
- Institute of Pathogenic Biology, Hengyang Medical College, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, University of South China, Hengyang, China
| | - Lanhua Zhao
- Institute of Pathogenic Biology, Hengyang Medical College, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, University of South China, Hengyang, China
| | - Shengmei Su
- Institute of Pathogenic Biology, Hengyang Medical College, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, University of South China, Hengyang, China
| | - Yuqi Zhao
- Institute of Pathogenic Biology, Hengyang Medical College, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, University of South China, Hengyang, China
| | - Wenbo Lei
- Institute of Pathogenic Biology, Hengyang Medical College, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, University of South China, Hengyang, China
| | - Zhongyu Li
- Institute of Pathogenic Biology, Hengyang Medical College, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, University of South China, Hengyang, China
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15
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Arumugam P, Singla M, Lodha R, Rao V. Identification and characterization of novel infection associated transcripts in macrophages. RNA Biol 2021; 18:604-611. [PMID: 34747322 DOI: 10.1080/15476286.2021.1989217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
By analysis of lncRNA expression profiles of macrophages in response to Mycobacterium tuberculosis (Mtb) infection, we identified novel highly expressed transcripts, unique in encompassing a protein coding transcript- Cytidine Monophosphate Kinase 2 (CMPK2) and a previously identified lncRNA- Negative Regulator of Interferon Response (NRIR). While these transcripts (TILT1, 2,3 - TLR4 and Infection induced Long Transcript) are induced by virulent Mtb as well as lipopolysaccharide (LPS) early, lack of/delayed expression in non-viable Mtb/BCG infected cells, respectively, suggest an important role in macrophage responses. The elevated expression by 3 hr in response to fast growing bacteria further emphasizes the importance of these RNAs in the macrophage infection response. Overall, we provide evidence for the presence of multiple transcripts that form a part of the early infection response programme of macrophages.Abbreviations: IFN: Interferon; NRIR: negative regulator of interferon response; CMPK2: cytidine/ uridine monophosphate kinase; LPS: lipopolysaccharide; LAM: Lipoarabinomannan; PIMs: Phosphatidylinositol Mannosides; TILT1, 2,3: TLR4 and Infection induced Long Transcript; TLR4: Toll-like receptor 4; Mtb: Mycobacterium tuberculosis; BCG: Mycobacterium bovis BCG; MDMs: human monocyte derived macrophages.
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Affiliation(s)
- Prabhakar Arumugam
- Department of Cardio- Respiratory Disease Biology, CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi-110025, India.,Department of Biological Sciences, Academy of Scientific and Innovative Research, CSIR- HRDC campus, Sector 19, Kamla Nehru Nagar, Ghaziabad- 201002, India
| | - Mohit Singla
- Department of Pediatrics, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Rakesh Lodha
- Department of Pediatrics, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Vivek Rao
- Department of Cardio- Respiratory Disease Biology, CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi-110025, India.,Department of Biological Sciences, Academy of Scientific and Innovative Research, CSIR- HRDC campus, Sector 19, Kamla Nehru Nagar, Ghaziabad- 201002, India
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16
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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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17
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Kundu M, Basu J. The Role of microRNAs and Long Non-Coding RNAs in the Regulation of the Immune Response to Mycobacterium tuberculosis Infection. Front Immunol 2021; 12:687962. [PMID: 34248974 PMCID: PMC8264550 DOI: 10.3389/fimmu.2021.687962] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/09/2021] [Indexed: 12/16/2022] Open
Abstract
Non-coding RNAs have emerged as critical regulators of the immune response to infection. MicroRNAs (miRNAs) are small non-coding RNAs which regulate host defense mechanisms against viruses, bacteria and fungi. They are involved in the delicate interplay between Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), and its host, which dictates the course of infection. Differential expression of miRNAs upon infection with M. tuberculosis, regulates host signaling pathways linked to inflammation, autophagy, apoptosis and polarization of macrophages. Experimental evidence suggests that virulent M. tuberculosis often utilize host miRNAs to promote pathogenicity by restricting host-mediated antibacterial signaling pathways. At the same time, host- induced miRNAs augment antibacterial processes such as autophagy, to limit bacterial proliferation. Targeting miRNAs is an emerging option for host-directed therapies. Recent studies have explored the role of long non-coding RNA (lncRNAs) in the regulation of the host response to mycobacterial infection. Among other functions, lncRNAs interact with chromatin remodelers to regulate gene expression and also function as miRNA sponges. In this review we attempt to summarize recent literature on how miRNAs and lncRNAs are differentially expressed during the course of M. tuberculosis infection, and how they influence the outcome of infection. We also discuss the potential use of non-coding RNAs as biomarkers of active and latent tuberculosis. Comprehensive understanding of the role of these non-coding RNAs is the first step towards developing RNA-based therapeutics and diagnostic tools for the treatment of TB.
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Affiliation(s)
| | - Joyoti Basu
- Department of Chemistry, Bose Institute, Kolkata, India
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18
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Wei L, Liu K, Jia Q, Zhang H, Bie Q, Zhang B. The Roles of Host Noncoding RNAs in Mycobacterium tuberculosis Infection. Front Immunol 2021; 12:664787. [PMID: 34093557 PMCID: PMC8170620 DOI: 10.3389/fimmu.2021.664787] [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: 02/06/2021] [Accepted: 04/23/2021] [Indexed: 12/21/2022] Open
Abstract
Tuberculosis remains a major health problem. Mycobacterium tuberculosis, the causative agent of tuberculosis, can replicate and persist in host cells. Noncoding RNAs (ncRNAs) widely participate in various biological processes, including Mycobacterium tuberculosis infection, and play critical roles in gene regulation. In this review, we summarize the latest reports on ncRNAs (microRNAs, piRNAs, circRNAs and lncRNAs) that regulate the host response against Mycobacterium tuberculosis infection. In the context of host-Mycobacterium tuberculosis interactions, a broad and in-depth understanding of host ncRNA regulatory mechanisms may lead to potential clinical prospects for tuberculosis diagnosis and the development of new anti-tuberculosis therapies.
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Affiliation(s)
- Li Wei
- Department of Laboratory Medicine, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, China
| | - Kai Liu
- Nursing Department, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, China
| | - Qingzhi Jia
- Department of Laboratory Medicine, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, China
| | - Hui Zhang
- Institute of Immunology and Molecular Medicine, Jining Medical University, Jining, China
| | - Qingli Bie
- Department of Laboratory Medicine, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, China
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Jining, China
| | - Bin Zhang
- Department of Laboratory Medicine, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, China
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Jining, China
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19
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Fang Y, Zhao J, Wang X, Wang X, Wang L, Liu L, Liu J, Gao M, Yuan C. Identification of differentially expressed lncRNAs as potential plasma biomarkers for active tuberculosis. Tuberculosis (Edinb) 2021; 128:102065. [PMID: 33690081 DOI: 10.1016/j.tube.2021.102065] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 12/20/2022]
Abstract
BACKGROUND Tuberculosis, one of the deadliest infectious diseases worldwide, is difficult to diagnose. As long noncoding RNAs (lncRNAs) were demonstrated to be promising biomarkers, we aimed to identify lncRNAs in plasma as potential biomarkers for tuberculosis. METHODS We analyzed a GEO dataset (GSE94907) to identify the differential lncRNAs in serum exosomes between active tuberculosis (ATB) patients and healthy controls. To search for promising candidates that can be used for tuberculosis diagnosis, we excluded low-abundance lncRNAs using a cutoff value of FPKM >5. Four lncRNAs were selected for validation using real-time quantitative PCR in 69 ATB patients and 69 healthy individuals. A receiver operating characteristic (ROC) curve was constructed to evaluate the diagnostic value of these lncRNAs for ATB. RESULTS Integrated analysis of the GEO dataset and NONCODE database identified nine dysregulated lncRNAs in ATB patient serum exosomes. Compared with the heathy controls, NONHSAT101518.2, NONHSAT067134.2, NONHSAT148822.1 and NONHSAT078957.2 were significantly downregulated in ATB patient plasma. ROC curve analysis suggests that these four lncRNAs can discriminate ATB from healthy individuals with high specificity and sensitivity. CONCLUSION We identified four differentially expressed lncRNAs in ATB patient plasma that can be used as potential diagnostic biomarkers of ATB.
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Affiliation(s)
- Yalun Fang
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, 250033, Jinan, Shandong, People's Republic of China; Department of Clinical Laboratory, Qilu Hospital of Shandong University (Qingdao), 266000, Qingdao, Shandong, People's Republic of China.
| | - Jingjie Zhao
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, 250033, Jinan, Shandong, People's Republic of China.
| | - Xiaoyan Wang
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250021, Jinan, Shandong, People's Republic of China.
| | - Xinfeng Wang
- Department of Lab Medicine, Shandong Provincial Chest Hospital, 250013, Jinan, Shandong, People's Republic of China.
| | - Li Wang
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, 250033, Jinan, Shandong, People's Republic of China.
| | - Ling Liu
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, 250033, Jinan, Shandong, People's Republic of China.
| | - Junli Liu
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, 250033, Jinan, Shandong, People's Republic of China.
| | - Meng Gao
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, 250033, Jinan, Shandong, People's Republic of China.
| | - Chao Yuan
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, 250033, Jinan, Shandong, People's Republic of China.
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20
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Li S, Liu R, Wei G, Guo G, Yu H, Zhang Y, Ishfaq M, Fazilani SA, Zhang X. Curcumin protects against Aflatoxin B1-induced liver injury in broilers via the modulation of long non-coding RNA expression. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 208:111725. [PMID: 33396056 DOI: 10.1016/j.ecoenv.2020.111725] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 10/13/2020] [Accepted: 11/23/2020] [Indexed: 06/12/2023]
Abstract
Aflatoxin B1 (AFB1) is a potent hepatotoxic and carcinogenic agent. Curcumin possesses potential anti-inflammatory, anti-oxidative and hepatoprotective effects. However, the role of LncRNAs in the protective mechanisms of curcumin against AFB1-induced liver damage is still elusive. Experimental broilers were randomly divided into 1) control group, 2) AFB1 group (1 mg/kg feed), 3) cur + AFB1 group (1 mg/kg AFB1 plus 300 mg/kg curcumin diet) and 4) curcumin group (300 mg/kg curcumin diet). Liver transcriptome analyses and qPCR were performed to identify shifts in genes expression. In addition, histopathological assessment and oxidant status were determined. Dietary AFB1 caused hepatic morphological injury, significantly increased the production of ROS, decreased liver antioxidant enzymes activities and induced inflammation and apoptosis. However, dietary curcumin partially attenuated the abnormal morphological changes, oxidative stress, and apoptosis in liver tissues. Transcriptional profiling results showed that 34 LncRNAs and 717 mRNAs were differentially expressed with AFB1 and curcumin co-treatment in livers of broilers. Analysis of the LncRNA-mRNA network, GO and KEGG enrichment data suggested that oxidative stress, inflammation and apoptosis pathway were crucial in curcumin's alleviating AFB1-induced liver damage. In conclusion, curcumin prevented AFB1-induced oxidative stress, inflammation and apoptosis through LncRNAs. These results provide new insights for unveiling the protective mechanisms of curcumin against AFB1-induced liver damage.
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Affiliation(s)
- Sihong Li
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development. Faculty of Basic Veterinary Science, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Harbin, PR China
| | - Ruimeng Liu
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development. Faculty of Basic Veterinary Science, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Harbin, PR China
| | - Gaoqiang Wei
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development. Faculty of Basic Veterinary Science, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Harbin, PR China
| | - Guifang Guo
- The Department of Chemical Drug Review, China Institute of Veterinary Drugs Control, Beijing 100081, PR China
| | - Hongxiao Yu
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development. Faculty of Basic Veterinary Science, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Harbin, PR China
| | - Yixin Zhang
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development. Faculty of Basic Veterinary Science, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Harbin, PR China
| | - Muhammad Ishfaq
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development. Faculty of Basic Veterinary Science, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Harbin, PR China
| | - Saqib Ali Fazilani
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development. Faculty of Basic Veterinary Science, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Harbin, PR China; Department of Veterinary Pharmacology and Toxicology, Faculty of Bio-Sciences, Shaheed Benazir Bhutto University of Veterinary and Animal Sciences, Shaheed Benazir Abad, Sakrand 67210, Pakistan
| | - Xiuying Zhang
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development. Faculty of Basic Veterinary Science, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Harbin, PR China.
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21
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Long Noncoding RNA and Predictive Model To Improve Diagnosis of Clinically Diagnosed Pulmonary Tuberculosis. J Clin Microbiol 2020; 58:JCM.01973-19. [PMID: 32295893 PMCID: PMC7315016 DOI: 10.1128/jcm.01973-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 04/02/2020] [Indexed: 02/07/2023] Open
Abstract
Clinically diagnosed pulmonary tuberculosis (PTB) patients lack microbiological evidence of Mycobacterium tuberculosis, and misdiagnosis or delayed diagnosis often occurs as a consequence. We investigated the potential of long noncoding RNAs (lncRNAs) and corresponding predictive models to diagnose these patients. We enrolled 1,764 subjects, including clinically diagnosed PTB patients, microbiologically confirmed PTB cases, non-TB disease controls, and healthy controls, in three cohorts (screening, selection, and validation). Clinically diagnosed pulmonary tuberculosis (PTB) patients lack microbiological evidence of Mycobacterium tuberculosis, and misdiagnosis or delayed diagnosis often occurs as a consequence. We investigated the potential of long noncoding RNAs (lncRNAs) and corresponding predictive models to diagnose these patients. We enrolled 1,764 subjects, including clinically diagnosed PTB patients, microbiologically confirmed PTB cases, non-TB disease controls, and healthy controls, in three cohorts (screening, selection, and validation). Candidate lncRNAs differentially expressed in blood samples of the PTB and healthy control groups were identified by microarray and reverse transcription-quantitative PCR (qRT-PCR) in the screening cohort. Logistic regression models were developed using lncRNAs and/or electronic health records (EHRs) from clinically diagnosed PTB patients and non-TB disease controls in the selection cohort. These models were evaluated by area under the concentration-time curve (AUC) and decision curve analyses, and the optimal model was presented as a Web-based nomogram, which was evaluated in the validation cohort. Three differentially expressed lncRNAs (ENST00000497872, n333737, and n335265) were identified. The optimal model (i.e., nomogram) incorporated these three lncRNAs and six EHRs (age, hemoglobin, weight loss, low-grade fever, calcification detected by computed tomography [CT calcification], and interferon gamma release assay for tuberculosis [TB-IGRA]). The nomogram showed an AUC of 0.89, a sensitivity of 0.86, and a specificity of 0.82 in differentiating clinically diagnosed PTB cases from non-TB disease controls of the validation cohort, which demonstrated better discrimination and clinical net benefit than the EHR model. The nomogram also had a discriminative power (AUC, 0.90; sensitivity, 0.85; specificity, 0.81) in identifying microbiologically confirmed PTB patients. lncRNAs and the user-friendly nomogram could facilitate the early identification of PTB cases among suspected patients with negative M. tuberculosis microbiological evidence.
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Crimi E, Benincasa G, Cirri S, Mutesi R, Faenza M, Napoli C. Clinical epigenetics and multidrug-resistant bacterial infections: host remodelling in critical illness. Epigenetics 2020; 15:1021-1034. [PMID: 32290755 DOI: 10.1080/15592294.2020.1748918] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The inappropriate use of antibiotics in man is driving to insurgence of pathogenic bacteria resistant to multiple drugs (MDR) representing a challenge in critical illness. The interaction of MDR bacteria with host cells can guide molecular perturbations of host transcriptional programmes involving epigenetic-sensitive mechanisms, mainly DNA methylation, histone modifications, and non-coding RNAs leading to pathogen survival. Clinical evidence of epigenetic manipulation from MDR bacteria mainly arises from Mycobacterium tuberculosis as well as Helicobacter pylori, Escherichia coli, Listeria monocytogenes, Pseudomonas aeruginosa, and Legionella pneumophila infection suggesting possible biomarkers of disease. For example, DNA hypermethylation of E-cadherin (CDH1), upstream transcription factor 1/2 (USF1/2), WW domain containing oxidoreductase (WWOX), and mutL homolog 1 (MLH1) genes in gastric mucosa is correlated with malignancy suggesting useful biomarkers of early disease state. Moreover, upregulated circulating miR-361-5p, miR-889, miR-576-3p may be useful biomarkers to discriminate tuberculosis patients. Moreover, Listeria monocytogenes can indirectly induce H3 hyperacetylation leading to inflammation in human endothelial cells whereas Pseudomonas aeruginosa excretes QS 2-AA to directly induce H3 deacetylation leading to bacterial persistence in human monocytes. Remarkably, epigenetic-sensitive drugs may aid to counteract MDR in clinical setting. Trichostatin A, a histone deacetyltransferase inhibitor (HDACi), leads to AMP β-defensin 2 (HBD2) gene up-regulation in human epithelial cells suggesting a useful 'epi-therapy' for Escherichia coli-induced intestinal diseases. We update on the most current clinical studies focusing on epigenetic changes involved in bacterial-host interactions and their putative role as biomarkers or drug targets to improve precision medicine and personalized therapy in critical illness and transplantation setting.
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Affiliation(s)
- Ettore Crimi
- College of Medicine, University of Central Florida , Orlando, FL, USA.,Department of Anesthesiology and Critical Care Medicine, Ocala Health , Ocala, FL, USA
| | - Giuditta Benincasa
- Clinical Department of Internal Medicine and Specialistics, Department of Advanced Clinical and Surgical Sciences, University of Campania "Luigi Vanvitelli" , Naples, Italy
| | - Silvia Cirri
- Division of Anesthesiology and Intensive Care, Cardiothoracic Department, Istituto Clinico Sant'Ambrogio, Gruppo Ospedaliero San Donato , Milan, Italy
| | - Rebecca Mutesi
- College of Medicine, University of Central Florida , Orlando, FL, USA
| | - Mario Faenza
- Multidisciplinary Department of Medical and Dental Specialties, Plastic Surgery Unit, University of Campania "Luigi Vanvitelli" , Naples, Italy
| | - Claudio Napoli
- Clinical Department of Internal Medicine and Specialistics, Department of Advanced Clinical and Surgical Sciences, University of Campania "Luigi Vanvitelli" , Naples, Italy.,IRCCS Foundation SDN , Naples, Italy
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23
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Long non-coding RNA molecules in tuberculosis. Int J Biol Macromol 2020; 156:340-346. [PMID: 32283111 DOI: 10.1016/j.ijbiomac.2020.04.030] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/03/2020] [Accepted: 04/04/2020] [Indexed: 02/06/2023]
Abstract
Tuberculosis (TB), a chronic disease caused by Mycobacterium tuberculosis, is one of the deadliest infectious diseases in the world. Despite significant advances in detection techniques and therapeutic approaches for tuberculosis, there is still no suitable solution for early screening and reducing the number of individuals affected and their effective treatment. Various cellular events can disrupt the development of TB. The basis of these events is dysregulating of genes expression patterns related with specific molecules. Long non-coding RNAs (lncRNAs) are molecules discovered to regulate the expression of protein-coding genes and participate in gene silencing, cell cycle regulation and cellular differentiation processes. Dysregulation of lncRNAs has been found to be associated with many diseases, including cancers and infectious diseases. Thus, the recognition of lncRNAs as novel molecular biomarkers and therapeutic targets for tuberculosis is promising. In the present review, we try to summarize the current findings of lncRNA expression patterns and its role in tuberculosis infection process.
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24
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Liu G, Xia R, Wang Q, Wang Z, Ying B, Yan H. Significance of LncRNA CASC8 genetic polymorphisms on the tuberculosis susceptibility in Chinese population. J Clin Lab Anal 2020; 34:e23234. [PMID: 32034808 PMCID: PMC7307370 DOI: 10.1002/jcla.23234] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 12/29/2019] [Accepted: 01/21/2020] [Indexed: 02/05/2023] Open
Abstract
Background Tuberculosis remains an important disease threatening the security of public health, and no effective targets have been found for the immunological diagnosis or therapy of tuberculosis. The aim of this study was to explore the associations between lncRNA CASC8 genetic polymorphism and tuberculosis risk. Method A total of 900 tuberculosis patients and 1534 healthy individuals in the Western Chinese Han population were recruited for our study. Candidate SNPs of CASC8 were initially filtered by importing the 1000 genomes database into Haploview, and subsequently genotyped using modified multiplex ligation detection reactions. Results The lncRNA CASC8 genetic variant rs7836840 was associated with an increased tuberculosis risk with a P‐value of .034, but .134 after Bonferroni correction. Using subtype analysis, the C allele in rs7836840 showed a significant association with tuberculosis susceptibility (OR = 1.196, 95% CI = 1.05‐1.362, P = .02739 after Bonferroni correction). Patients carrying genotype AG and GG of rs7825118 and rs9297758 exhibited lower Hb concentrations (P = .006) and neutrophil counts (P = .015), respectively, while genotype AG and AA in rs6981424 demonstrated higher levels of ALT (P = .005) and AST (P = .033) in a dominant model, which were consistent with a tendency toward increased TB risk. Conclusions This study was the first to explore the association between lncRNA CASC8 polymorphisms and TB infection risk and clinical manifestations. Our results provide evidence that CASC8 may act as a biomarker for the progression of clinical tuberculosis.
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Affiliation(s)
- Guoye Liu
- Department of Laboratory medicine, Affiliated Brain Hospital of Nanjing Medical University (Chest Branch), Nanjing, China
| | - Rui Xia
- Department of Laboratory medicine, Affiliated Brain Hospital of Nanjing Medical University (Chest Branch), Nanjing, China
| | - Qian Wang
- Department of Laboratory medicine, Affiliated Brain Hospital of Nanjing Medical University (Chest Branch), Nanjing, China
| | - Zhiqiang Wang
- Department of Laboratory medicine, Affiliated Brain Hospital of Nanjing Medical University (Chest Branch), Nanjing, China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Hong Yan
- Department of Laboratory medicine, Affiliated Brain Hospital of Nanjing Medical University (Chest Branch), Nanjing, China
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25
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Zhang X, Liang Z, Zhang Y, Dai K, Zhu M, Wang J, Hu X. Comprehensive analysis of long non-coding RNAs expression pattern in the pathogenesis of pulmonary tuberculosis. Genomics 2019; 112:1970-1977. [PMID: 31756428 DOI: 10.1016/j.ygeno.2019.11.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 10/17/2019] [Accepted: 11/16/2019] [Indexed: 12/19/2022]
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) play crucial roles in the progression and pathogenesis of cancer. Right now, less is known about the association between the expression of lncRNAs and the pathogenesis of pulmonary tuberculosis (PTB). METHODS In present study, the expression profiles of lncRNAs were investigated by transcriptome sequencing from PTB patients vs. healthy individuals. RESULTS A total of 449 differentially expressed (DE) (fold change ≥2, false discovery rate ≤ 0.05) lncRNAs were screened out from the PTB patients. Lnc-HNRNPU-1:7 and lnc-FAM76B-4:1 was found the most upregulated lncRNAs and downregulated lncRNAs in PTB patients, respectively. GO annotation and KEGG analysis were used to explore the potential roles of these DE lncRNAs. The JAK/STAT and TGF-β signaling pathways related to PTB pathogenesis were enriched in PTB patients. The co-expressed of a few lncRNAs and mRNAs on chromosome were shown by cis-regulatory gene analysis. Trans analysis indicated that STAT1, STAT2 and TAF7 transcription factors regulated the expression of lncRNA and mRNA. The constructed lncRNA ceRNA network suggested that lncRNAs regulating mRNAs expression may mediate by sponged miRNAs. CONCLUSION We comprehensively analyzed the expression profiles of lncRNAs in PTB patients, thus providing new clues for exploring the regulatory mechanisms of dysregulated lncRNAs in the pathogenesis of PTB.
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Affiliation(s)
- Xing Zhang
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, China
| | - Zi Liang
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, China
| | - Yunshan Zhang
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, China
| | - Kun Dai
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, China
| | - Min Zhu
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, China
| | - Ji Wang
- Department of Oncology, The Second Affiliated Hospital of Soochow University, Suzhou 215004, China.
| | - Xiaolong Hu
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, China.
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Lin Y, Zhang Y, Yu H, Tian R, Wang G, Li F. Identification of unique key genes and miRNAs in latent tuberculosis infection by network analysis. Mol Immunol 2019; 112:103-114. [PMID: 31082644 DOI: 10.1016/j.molimm.2019.04.032] [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: 11/29/2018] [Revised: 04/17/2019] [Accepted: 04/30/2019] [Indexed: 02/04/2023]
Abstract
Tuberculosis (TB) is a chronic infectious disease caused by Mycobacterium tuberculosis (M.tb). New cases are now mainly caused by the progression of latent tuberculosis infection (LTBI). Thus, methods to diagnose and treat LTBI are urgently needed to prevent the development of active TB in infected individuals and the subsequent spread of the disease. In this study, a systems biology approach was utilized to obtain numerous microarray data sets for mRNAs and microRNAs (miRNAs) expressed in the peripheral blood mononuclear cells (PBMCs) of TB patients and individuals with LTBI. Within these data sets, we identified the differentially expressed mRNAs and miRNAs and further investigated which differentially expressed genes and miRNAs were uniquely expressed during LTBI. The Database for Annotation, Visualization and Integrated Discovery (DAVID) was employed to analyze the functional annotations and pathway classifications of the identified genes. To further understand the unique miRNA-gene regulatory network of LTBI, we constructed a protein-protein interaction (PPI) network for the targeted genes. The PPI network included 39 genes that were differentially and uniquely expressed in PBMCs of individuals with LTBI, and KEGG pathway enrichment analysis showed that these genes were predominantly involved in the PI3K-Akt signaling pathway, which plays an important role in chronic inflammation. DIANA TOOLs-mirPath analysis revealed that the identified miRNAs in the miRNA-gene regulatory network for LTBI were mainly associated with the Hippo signaling pathway, which functions in the development of inflammation. Quantitative real-time PCR verified the up expression of hsa-miR-212-3p and its predicted target gene -MAPK1 which had low expression and was a major component of the PPI network, and MAPK1 expression was correlated with the clinicopathological characteristics of LTBI by receiver operating characteristic (ROC) curve analysis. Therefore, MAPK1 has potential to be a new investigable marker during LTBI, which merits our further study and solution. The unique aberrant miRNA-gene regulatory network and the related PPI network identified in this study provide insight into the molecular mechanisms of the immune response to LTBI, and thus, may aid in the development of a novel treatment strategy.
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Affiliation(s)
- Yan Lin
- Department of Pathogenobiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medicine, Jilin University, Changchun, Jilin, 130021, China
| | - Yuwei Zhang
- Department of Pathogenobiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medicine, Jilin University, Changchun, Jilin, 130021, China
| | - Huiyuan Yu
- School of Public Health, Jilin University, Changchun, Jilin, 130021, China
| | - Ruonan Tian
- Department of Pathogenobiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medicine, Jilin University, Changchun, Jilin, 130021, China
| | - Guoqing Wang
- Department of Pathogenobiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medicine, Jilin University, Changchun, Jilin, 130021, China; The Key Laboratory for Bionics Engineering, Ministry of Education, China, Jilin University, Changchun, Jilin, 130021, China
| | - Fan Li
- Department of Pathogenobiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medicine, Jilin University, Changchun, Jilin, 130021, China; The Key Laboratory for Bionics Engineering, Ministry of Education, China, Jilin University, Changchun, Jilin, 130021, China; Engineering Research Center for Medical Biomaterials of Jilin Province, Jilin University, Changchun, Jilin, 130021, China; Key Laboratory for Biomedical Materials of Jilin Province, Jilin University, Changchun, Jilin, 130021, China; State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Xinjiang, China.
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