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Chen S, Lei Z, Sun T. The critical role of miRNA in bacterial zoonosis. Int Immunopharmacol 2024; 143:113267. [PMID: 39374566 DOI: 10.1016/j.intimp.2024.113267] [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: 05/06/2024] [Revised: 08/21/2024] [Accepted: 09/24/2024] [Indexed: 10/09/2024]
Abstract
The public's health and the financial sustainability of international societies remain threatened by bacterial zoonoses, with limited reliable diagnostic and therapeutic options available for bacterial diseases. Bacterial infections influence mammalian miRNA expression in host-pathogen interactions. In order to counteract bacterial infections, miRNAs participate in gene-specific expression and play important regulatory roles that rely on translational inhibition and target gene degradation by binding to the 3' non-coding region of target genes. Intriguingly, according to current studies, that exogenous miRNAs derived from plants could potentially serve as effective medicinal components sourced from traditional Chinese medicine plants. These exogenous miRNAs exhibit stable functionality in mammals and mimic the regulatory roles of endogenous miRNAs, illuminating the molecular processes behind the therapeutic effects of plants. This review details the immune defense mechanisms of inflammation, apoptosis, autophagy and cell cycle disturbance caused by some typical bacterial infections, summarizes the role of some mammalian miRNAs in regulating these mechanisms, and introduces the cGAS-STING signaling pathway in detail. Evidence suggests that this newly discovered immune defense mechanism in mammalian cells can also be affected by miRNAs. Meanwhile, some examples of transboundary regulation of mammalian mRNA and even bacterial diseases by exogenous miRNAs from plants are also summarized. This viewpoint provides fresh understanding of microbial tactics and host mechanisms in the management of bacterial illnesses.
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Affiliation(s)
- Si Chen
- School of Chemistry, Chemical Engineering and Life Science, Hubei Key Laboratory of Nanomedicine for Neurodegenerative Disease, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China
| | - Zhixin Lei
- School of Chemistry, Chemical Engineering and Life Science, Hubei Key Laboratory of Nanomedicine for Neurodegenerative Disease, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China.
| | - Taolei Sun
- School of Chemistry, Chemical Engineering and Life Science, Hubei Key Laboratory of Nanomedicine for Neurodegenerative Disease, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China.
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Muwanga VM, Mendelsohn SC, Leukes V, Stanley K, Mbandi SK, Erasmus M, Flinn M, Fisher TL, Raphela R, Bilek N, Malherbe ST, Tromp G, Van Der Spuy G, Walzl G, Chegou NN, Scriba TJ. Blood transcriptomic signatures for symptomatic tuberculosis in an African multicohort study. Eur Respir J 2024; 64:2400153. [PMID: 38964778 PMCID: PMC11325265 DOI: 10.1183/13993003.00153-2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 06/12/2024] [Indexed: 07/06/2024]
Abstract
BACKGROUND Multiple host blood transcriptional signatures have been developed as non-sputum triage tests for tuberculosis (TB). We aimed to compare the diagnostic performance of 20 blood transcriptomic TB signatures for differentiating between symptomatic patients who have TB versus other respiratory diseases (ORD). METHODS As part of a nested case-control study, individuals presenting with respiratory symptoms at primary healthcare clinics in Ethiopia, Malawi, Namibia, Uganda, South Africa and The Gambia were enrolled. TB was diagnosed based on clinical, microbiological and radiological findings. Transcriptomic signatures were measured in whole blood using microfluidic real-time quantitative PCR. Diagnostic performance was benchmarked against the World Health Organization Target Product Profile (TPP) for a non-sputum TB triage test. RESULTS Among 579 participants, 158 had definite, microbiologically confirmed TB, 32 had probable TB, while 389 participants had ORD. Nine signatures differentiated between ORD and TB with equivalent performance (Satproedprai7: area under the curve 0.83 (95% CI 0.79-0.87); Jacobsen3: 0.83 (95% CI 0.79-0.86); Suliman2: 0.82 (95% CI 0.78-0.86); Roe1: 0.82 (95% CI 0.78-0.86); Kaforou22: 0.82 (95% CI 0.78-0.86); Sambarey10: 0.81 (95% CI 0.77-0.85); Duffy9: 0.81 (95% CI 0.76-0.86); Gliddon3: 0.8 (95% CI 0.75-0.85); Suliman4 0.79 (95% CI 0.75-0.84)). Benchmarked against a 90% sensitivity, these signatures achieved specificities between 44% (95% CI 38-49%) and 54% (95% CI 49-59%), not meeting the TPP criteria. Signature scores significantly varied by HIV status and country. In country-specific analyses, several signatures, such as Satproedprai7 and Penn-Nicholson6, met the minimal TPP criteria for a triage test in Ethiopia, Malawi and South Africa. CONCLUSION No signatures met the TPP criteria in a pooled analysis of all countries, but several signatures met the minimum criteria for a non-sputum TB triage test in some countries.
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Affiliation(s)
- Vanessa Mwebaza Muwanga
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Simon C Mendelsohn
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Vinzeigh Leukes
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Immunology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Kim Stanley
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Immunology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Stanley Kimbung Mbandi
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Mzwandile Erasmus
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Marika Flinn
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Immunology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Tarryn-Lee Fisher
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Immunology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Rodney Raphela
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Nicole Bilek
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Stephanus T Malherbe
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Immunology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Gerard Tromp
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Immunology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Gian Van Der Spuy
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Gerhard Walzl
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Immunology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Novel N Chegou
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Immunology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
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3
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Ran F, Wang Y, Zhang G, Guo H, Li J, Zhang X, Wu Z, Bi L. Whole-transcriptome sequencing of phagocytes reveals a ceRNA network contributing to natural resistance to tuberculosis infection. Microb Pathog 2024; 192:106681. [PMID: 38754565 DOI: 10.1016/j.micpath.2024.106681] [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: 10/03/2023] [Revised: 03/14/2024] [Accepted: 05/06/2024] [Indexed: 05/18/2024]
Abstract
Tuberculosis (TB) is a major fatal infectious disease globally, exhibiting high morbidity rates and impacting public health and other socio-economic factors. However, some individuals are resistant to TB infection and are referred to as "Resisters". Resisters remain uninfected even after exposure to high load of Mycobacterium tuberculosis (Mtb). To delineate this further, this study aimed to investigate the factors and mechanisms influencing the Mtb resistance phenotype. We assayed the phagocytic capacity of peripheral blood mononuclear cells (PBMCs) collected from Resisters, patients with latent TB infection (LTBI), and patients with active TB (ATB), following infection with fluorescent Mycobacterium bovis Bacillus Calmette-Guérin (BCG). Phagocytosis was stronger in PBMCs from ATB patients, and comparable in LTBI patients and Resisters. Subsequently, phagocytes were isolated and subjected to whole transcriptome sequencing and small RNA sequencing to analyze transcriptional expression profiles and identify potential targets associated with the resistance phenotype. The results revealed that a total of 277 mRNAs, 589 long non-coding RNAs, 523 circular RNAs, and 35 microRNAs were differentially expressed in Resisters and LTBI patients. Further, the endogenous competitive RNA (ceRNA) network was constructed from differentially expressed genes after screening. Bioinformatics, statistical analysis, and quantitative real-time polymerase chain reaction were used for the identification and validation of potential crucial targets in the ceRNA network. As a result, we obtained a ceRNA network that contributes to the resistance phenotype. TCONS_00034796-F3, ENST00000629441-DDX43, hsa-ATAD3A_0003-CYP17A1, and XR_932996.2-CERS1 may be crucial association pairs for resistance to TB infection. Overall, this study demonstrated that the phagocytic capacity of PBMCs was not a determinant of the resistance phenotype and that some non-coding RNAs could be involved in the natural resistance to TB infection through a ceRNA mechanism.
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Affiliation(s)
- Fanlei Ran
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Guangzhou National Laboratory, Guangzhou, 510005, China
| | - Yaguo Wang
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China; TB Healthcare Co., Ltd., Foshan, 528300, China
| | - Guoqin Zhang
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haiyan Guo
- Department of Geriatrics, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, China; Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Jinlong Li
- TB Healthcare Co., Ltd., Foshan, 528300, China
| | - Xilin Zhang
- Foshan Fourth People's Hospital, Foshan, 528000, China.
| | - Zhilong Wu
- Foshan Fourth People's Hospital, Foshan, 528000, China.
| | - Lijun Bi
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Guangzhou National Laboratory, Guangzhou, 510005, China.
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Jiang M, Hong X, Gao Y, Kho AT, Tantisira KG, Li J. piRNA associates with immune diseases. Cell Commun Signal 2024; 22:347. [PMID: 38943141 PMCID: PMC11214247 DOI: 10.1186/s12964-024-01724-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 06/23/2024] [Indexed: 07/01/2024] Open
Abstract
PIWI-interacting RNA (piRNA) is the most abundant small non-coding RNA in animal cells, typically 26-31 nucleotides in length and it binds with PIWI proteins, a subfamily of Argonaute proteins. Initially discovered in germ cells, piRNA is well known for its role in silencing transposons and maintaining genome integrity. However, piRNA is also present in somatic cells as well as in extracellular vesicles and exosomes. While piRNA has been extensively studied in various diseases, particular cancer, its function in immune diseases remains unclear. In this review, we summarize current research on piRNA in immune diseases. We first introduce the basic characteristics, biogenesis and functions of piRNA. Then, we review the association of piRNA with different types of immune diseases, including autoimmune diseases, immunodeficiency diseases, infectious diseases, and other immune-related diseases. piRNA is considered a promising biomarker for diseases, highlighting the need for further research into its potential mechanisms in disease pathogenesis.
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Affiliation(s)
- Mingye Jiang
- Clinical Big Data Research Center, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, China
| | - Xiaoning Hong
- Clinical Big Data Research Center, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, China
| | - Yunfei Gao
- Department of Otolaryngology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Alvin T Kho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
| | - Kelan G Tantisira
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatrics, Division of Respiratory Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jiang Li
- Clinical Big Data Research Center, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, China.
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Shenzhen Key Laboratory of Chinese Medicine Active Substance Screening and Translational Research, Guangdong, Shenzhen, China.
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Saleh RO, Jasim SA, Kadhum WR, Hjazi A, Faraz A, Abid MK, Yumashev A, Alawadi A, Aiad IAZ, Alsalamy A. Exploring the detailed role of interleukins in cancer: A comprehensive review of literature. Pathol Res Pract 2024; 257:155284. [PMID: 38663179 DOI: 10.1016/j.prp.2024.155284] [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: 02/06/2024] [Revised: 03/25/2024] [Accepted: 03/30/2024] [Indexed: 05/12/2024]
Abstract
The cancer cells that are not normal can grow into tumors, invade surrounding tissues, and travel to other parts of the body via the lymphatic or circulatory systems. Interleukins, a vital class of signaling proteins, facilitate cell-to-cell contact within the immune system. A type of non-coding RNA known as lncRNAs mediates its actions by regulating miRNA-mRNA roles (Interleukins). Because of their dual function in controlling the growth of tumors and altering the immune system's response to cancer cells, interleukins have been extensively studied concerning cancer. Understanding the complex relationships between interleukins, the immune system, the tumor microenvironment, and the components of interleukin signaling pathways that impact the miRNA-mRNA axis, including lncRNAs, has advanced significantly in cancer research. Due to the significant and all-encompassing influence of interleukins on the immune system and the development and advancement of cancers, lncRNAs play a crucial role in cancer research by modulating interleukins. Their diverse effects on immune system regulation, tumor growth encouragement, and tumor inhibition make them appealing candidates for potential cancer treatments and diagnostics. A deeper understanding of the relationship between the biology of interleukin and lncRNAs will likely result in more effective immunotherapy strategies and individualized cancer treatments.
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Affiliation(s)
- Raed Obaid Saleh
- Department of Medical Laboratory Techniques, Al-Maarif University College, Al-Anbar, Iraq
| | - Saade Abdalkareem Jasim
- Pharmacy Department, Al-Huda University College, Anbar, Iraq; Biotechnology Department, College of Applied Science, Fallujah University, Anbar, Iraq.
| | - Wesam R Kadhum
- Department of Pharmacy, Kut University College, Kut, Wasit 52001, Iraq; Advanced Research Center, Kut University College, Kut, Wasit 52001, Iraq
| | - Ahmed Hjazi
- Department of Medical Laboratory, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Ali Faraz
- Department of Basic Medical Sciences, College of Medicine, Majmaah University, Majmaah 11952, Saudi Arabia.
| | - Mohammed Kadhem Abid
- Department of Anesthesia, College of Health & Medical Technology, Al-Ayen University, Thi-Qar, Iraq
| | - Alexey Yumashev
- Department of Prosthetic Dentistry, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Ahmed Alawadi
- College of Technical Engineering, the Islamic University, Najaf, Iraq; College of Technical Engineering, the Islamic University of Al Diwaniyah, Iraq; College of Technical Engineering, the Islamic University of Babylon, Iraq
| | - Ibrahim Ahmed Zaki Aiad
- Department of Pediatrics, General Medicine Practice Program, Batterjee Medical College, Jeddah 21442, Saudi Arabia
| | - Ali Alsalamy
- College of Technical Engineering, Imam Ja'afar Al-Sadiq University, Al-Muthanna 66002, Iraq
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6
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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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Triantaphyllopoulos KA. Long Non-Coding RNAs and Their "Discrete" Contribution to IBD and Johne's Disease-What Stands out in the Current Picture? A Comprehensive Review. Int J Mol Sci 2023; 24:13566. [PMID: 37686376 PMCID: PMC10487966 DOI: 10.3390/ijms241713566] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/23/2023] [Accepted: 08/27/2023] [Indexed: 09/10/2023] Open
Abstract
Non-coding RNAs (ncRNA) have paved the way to new perspectives on the regulation of gene expression, not only in biology and medicine, but also in associated fields and technologies, ensuring advances in diagnostic means and therapeutic modalities. Critical in this multistep approach are the associations of long non-coding RNA (lncRNA) with diseases and their causal genes in their networks of interactions, gene enrichment and expression analysis, associated pathways, the monitoring of the involved genes and their functional roles during disease progression from one stage to another. Studies have shown that Johne's Disease (JD), caused by Mycobacterium avium subspecies partuberculosis (MAP), shares common lncRNAs, clinical findings, and other molecular entities with Crohn's Disease (CD). This has been a subject of vigorous investigation owing to the zoonotic nature of this condition, although results are still inconclusive. In this review, on one hand, the current knowledge of lncRNAs in cells is presented, focusing on the pathogenesis of gastrointestinal-related pathologies and MAP-related infections and, on the other hand, we attempt to dissect the associated genes and pathways involved. Furthermore, the recently characterized and novel lncRNAs share common pathologies with IBD and JD, including the expression, molecular networks, and dataset analysis results. These are also presented in an attempt to identify potential biomarkers pertinent to cattle and human disease phenotypes.
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Affiliation(s)
- Kostas A Triantaphyllopoulos
- Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos St., 11855 Athens, Greece
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Chen L, Hua J, Dai X, He X. Assessment of ferroptosis-associated gene signatures as potential biomarkers for differentiating latent from active tuberculosis in children. Microb Genom 2023; 9. [PMID: 37163321 DOI: 10.1099/mgen.0.000997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
Ferroptotic cell death is a regulated process that is governed by iron-dependent membrane lipid peroxide accumulation that plays a pathogenic role in several disease-related settings. The use of ferroptosis-related genes (FRGs) to distinguish active tuberculosis (ATB) from latent tuberculosis infection (LTBI) among children, however, remains to be analysed. Tuberculosis-related gene expression data and FRG lists were obtained, respectively, from Gene Expression Omnibus (GEO) and FerrDb. Differentially expressed FRGs (DE-FRGs) detected when comparing samples from paediatric ATB and LTBI patients were explored using appropriate bioinformatics techniques, after which enrichment analyses were performed for these genes and hub genes were identified, with these genes then being used to explore potential drug interactions and construct competing endogenous RNA (ceRNA) networks. The GSE39939 dataset yielded 124 DE-FRGs that were primarily related to responses to oxidative, chemical and extracellular stimulus-associated stress. In total, the LASSO and SVM-RFE algorithms enabled the identification of nine hub genes (MAPK14, EGLN2, IDO1, USP11, SCD, CBS, PARP8, PARP16, CDC25A) that exhibited good diagnostic utility. Functional enrichment analyses of these genes suggested that they may govern ATB transition from LTBI through the control of many pathways, including the immune response, DNA repair, transcription, RNA degradation, and glycan and energy metabolism pathways. The CIBERSORT algorithm suggested that these genes were positively correlated with inflammatory and myeloid cell activity while being negatively correlated with the activity of lymphocytes. A total of 50 candidate drugs targeting 6 hub DE-FRGs were also identified, and a ceRNA network was used to explore the complex interplay among these hub genes. The nine hub FRGs defined in this study may serve as valuable biomarkers differentiating between ATB and LTBI in young patients.
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Affiliation(s)
- Liang Chen
- Department of Infectious Diseases, Nanjing Lishui People's Hospital, Zhongda Hospital Lishui Branch, Southeast University, Nanjing, PR China
| | - Jie Hua
- Department of Gastroenterology, Liyang People's Hospital, Liyang Branch Hospital of Jiangsu Province Hospital, Nanjing, PR China
| | - Xiaoting Dai
- Department of Infectious Diseases, Nanjing Lishui People's Hospital, Zhongda Hospital Lishui Branch, Southeast University, Nanjing, PR China
| | - Xiaopu He
- Department of Geriatric Gastroenterology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, PR China
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Sun H, Yang Y, Ma Y, Li N, Tan J, Sun C, Li H. Analysis of circRNA expression in chicken HD11 cells in response to avian pathogenic E.coli. Front Vet Sci 2022; 9:1005899. [PMID: 36187840 PMCID: PMC9521048 DOI: 10.3389/fvets.2022.1005899] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 08/24/2022] [Indexed: 11/20/2022] Open
Abstract
Avian pathogenic E. coli (APEC), one of the widespread zoonotic-pathogen, can cause a series of diseases collectively known as colibacillosis. This disease can cause thousands of million dollars economic loss each year in poultry industry and threaten to human health via meat or egg contamination. However, the detailed molecular mechanism underlying APEC infection is still not fully understood. Circular RNAs, a new type of endogenous noncoding RNA, have been demonstrated to involve in various biological processes. However, it is still not clear whether the circRNAs participate in host response against APEC infection. Herein, we utilized the high-throughput sequence technology to identify the circRNA expression profiles in APEC infected HD11 cells. A total of 49 differentially expressed (DE) circRNAs were detected in the comparison of APEC infected HD11 cells vs. wild type HD11 cells, which were involved in MAPK signaling pathway, Endocytosis, Focal adhesion, mTOR signaling pathway, and VEGF signaling pathway. Specifically, the source genes (BRAF, PPP3CB, BCL2L13, RAB11A, and TSC2) and their corresponding DE circRNAs may play a significant role in APEC infection. Moreover, based on ceRNA regulation, we constructed the circRNA-miRNA network and identified a couple of important regulatory relationship pairs related to APEC infection, including circRAB11A-gga-miR-125b-3p, circRAB11A-gga-miR-1696, and circTSC2-gga-miR-1649-5p. Results indicate that the aforementioned specific circRNAs and circRNA-miRNA network might have important role in regulating host immune response against APEC infection. This study is the first time to investigate the circRNAs expression profile and the biological function of the source genes of the identified DE circRNAs after APEC infection of chicken HD11 cells. These results would contribute to a better understanding of the molecular mechanisms in host response against APEC infection.
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Affiliation(s)
- Hongyan Sun
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou, China
- *Correspondence: Hongyan Sun
| | - Yexin Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yuyi Ma
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Nayin Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jishuang Tan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Changhua Sun
- School of Biological and Chemical Engineering, Yangzhou Polytechnic College, Yangzhou University, Yangzhou, China
| | - Huan Li
- School of Biological and Chemical Engineering, Yangzhou Polytechnic College, Yangzhou University, Yangzhou, China
- Huan Li
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Ning H, Kang J, Lu Y, Liang X, Zhou J, Ren R, Zhou S, Zhao Y, Xie Y, Bai L, Zhang L, Kang Y, Gao X, Xu M, Ma Y, Zhang F, Bai Y. Cyclic di-AMP as endogenous adjuvant enhanced BCG-induced trained immunity and protection against Mycobacterium tuberculosis in mice. Front Immunol 2022; 13:943667. [PMID: 36081510 PMCID: PMC9445367 DOI: 10.3389/fimmu.2022.943667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 07/13/2022] [Indexed: 11/13/2022] Open
Abstract
Bacillus Calmette-Guérin (BCG) is a licensed prophylactic vaccine against tuberculosis (TB). Current TB vaccine efforts focus on improving BCG effects through recombination or genetic attenuation and/or boost with different vaccines. Recent years, it was revealed that BCG could elicit non-specific heterogeneous protection against other pathogens such as viruses through a process termed trained immunity. Previously, we constructed a recombinant BCG (rBCG-DisA) with elevated c-di-AMP as endogenous adjuvant by overexpressing di-adenylate cyclase of Mycobacterium tuberculosis DisA, and found that rBCG-DisA induced enhanced immune responses by subcutaneous route in mice after M. tuberculosis infection. In this study, splenocytes from rBCG-DisA immunized mice by intravenous route (i.v) elicited greater proinflammatory cytokine responses to homologous and heterologous re-stimulations than BCG. After M. tuberculosis infection, rBCG-DisA immunized mice showed hallmark responses of trained immunity including potent proinflammatory cytokine responses, enhanced epigenetic changes, altered lncRNA expressions and metabolic rewiring in bone marrow cells and other tissues. Moreover, rBCG-DisA immunization induced higher levels of antibodies and T cells responses in the lung and spleen of mice after M. tuberculosis infection. It was found that rBCG-DisA resided longer than BCG in the lung of M. tuberculosis infected mice implying prolonged duration of vaccine efficacy. Then, we found that rBCG-DisA boosting could prolong survival of BCG-primed mice over 90 weeks against M. tuberculosis infection. Our findings provided in vivo experimental evidence that rBCG-DisA with c-di-AMP as endogenous adjuvant induced enhanced trained immunity and adaptive immunity. What’s more, rBCG-DisA showed promising potential in prime-boost strategy against M. tuberculosis infection in adults.
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Affiliation(s)
- Huanhuan Ning
- Department of Microbiology and Pathogen Biology, School of Preclinical Medicine, Air Force Medical University, Xi’an, China
| | - Jian Kang
- Department of Microbiology and Pathogen Biology, School of Preclinical Medicine, Air Force Medical University, Xi’an, China
| | - Yanzhi Lu
- Department of Microbiology and Pathogen Biology, School of Preclinical Medicine, Air Force Medical University, Xi’an, China
| | - Xuan Liang
- Department of Microbiology and Pathogen Biology, School of Preclinical Medicine, Air Force Medical University, Xi’an, China
- College of Life Sciences, Northwest University, Xi’an, China
| | - Jie Zhou
- Department of Endocrinology, Xijing Hospital, Air Force Medical University, Xi’an, China
| | - Rui Ren
- Department of Microbiology and Pathogen Biology, School of Preclinical Medicine, Air Force Medical University, Xi’an, China
| | - Shan Zhou
- Department of Clinical Laboratory, Xijing Hospital, Air Force Medical University, Xi’an, China
| | - Yong Zhao
- Laboratory Animal Center, Air Force Medical University, Xi’an, China
| | - Yanling Xie
- Department of Microbiology and Pathogen Biology, School of Preclinical Medicine, Air Force Medical University, Xi’an, China
- School of Life Sciences, Yan’an University, Yan’an, China
| | - Lu Bai
- Department of Microbiology and Pathogen Biology, School of Preclinical Medicine, Air Force Medical University, Xi’an, China
- School of Life Sciences, Yan’an University, Yan’an, China
| | - Linna Zhang
- Department of Physiology, Basic Medical School, Ningxia Medical University, Yinchuan, China
| | - Yali Kang
- Department of Microbiology and Pathogen Biology, School of Preclinical Medicine, Air Force Medical University, Xi’an, China
- Department of Physiology, Basic Medical School, Ningxia Medical University, Yinchuan, China
| | - Xiaojing Gao
- Department of Microbiology and Pathogen Biology, School of Preclinical Medicine, Air Force Medical University, Xi’an, China
- Department of Physiology, Basic Medical School, Ningxia Medical University, Yinchuan, China
| | - Mingze Xu
- Department of Microbiology and Pathogen Biology, School of Preclinical Medicine, Air Force Medical University, Xi’an, China
| | - Yanling Ma
- College of Life Sciences, Northwest University, Xi’an, China
| | - Fanglin Zhang
- Department of Microbiology and Pathogen Biology, School of Preclinical Medicine, Air Force Medical University, Xi’an, China
- *Correspondence: Yinlan Bai, ; Fanglin Zhang,
| | - Yinlan Bai
- Department of Microbiology and Pathogen Biology, School of Preclinical Medicine, Air Force Medical University, Xi’an, China
- *Correspondence: Yinlan Bai, ; Fanglin Zhang,
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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: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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12
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Protective Effect of Rifampicin Loaded by HPMA-PLA Nanopolymer on Macrophages Infected with Mycobacterium Tuberculosis. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:5784283. [PMID: 35027942 PMCID: PMC8752210 DOI: 10.1155/2022/5784283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 11/30/2021] [Accepted: 12/07/2021] [Indexed: 12/02/2022]
Abstract
Purpose This research was designed to investigate the protective effect of rifampicin (RIF) loaded by N-(2-hydroxypropyl) methylacrylamide- (HPMA-) polylactic acid (PLA) nanopolymer on macrophages infected with Mycobacterium tuberculosis (MTB). Methods We first induced H37Rv to infect macrophages to build a cell model. Then, the HPMA-PLA nanopolymer loaded with RIF was prepared to treat MTB-infected macrophages. The macrophage activity was tested by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, the nitric oxide (NO) in cells was measured through Griess reagent, and the bacterial activity of MTB was observed via the colony-forming unit (CFU) assay. The inflammation-related factors in cells were detected via the enzyme-linked immunosorbent assay (ELISA), the apoptosis of macrophages was examined via flow cytometry, and the expression of apoptosis-related proteins was determined by western blot (WB). Results HPMA-PLA had no obvious toxicity to macrophages. The expression of NO and inflammatory factors in macrophages infected with MTB increased significantly, but the apoptosis rate was not significantly different from that of uninfected cells. However, after treatment with HPMA-PLA-RIF or free RIF, the inflammatory reaction of infected cells was inhibited, the expression of NO was decreased, the apoptosis rate was increased, and the bacterial activity in cells was decreased, with statistically significant differences; moreover, HPMA-PLA-RIF was more effective than free RIF. Conclusions HPMA-PLA-RIF has a high protective effect on macrophages infected with MTB, with high safety. Its protective mechanism is at least partly through inhibiting the production of NO and inflammatory response, which can inhibit bacterial activity and induce cell apoptosis.
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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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MicroRNA-155 Modulates Macrophages' Response to Non-Tuberculous Mycobacteria through COX-2/PGE2 Signaling. Pathogens 2021; 10:pathogens10080920. [PMID: 34451384 PMCID: PMC8398909 DOI: 10.3390/pathogens10080920] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 07/01/2021] [Accepted: 07/17/2021] [Indexed: 12/19/2022] Open
Abstract
Non-tuberculous mycobacteria (NTM) have been recognized as a causative agent of various human diseases, including severe infections in immunocompromised patients, such as people living with HIV. The most common species identified is the Mycobacterium avium-intracellulare complex (MAI/MAC), accounting for a majority of infections. Despite abundant information detailing the clinical significance of NTM, little is known about host–pathogen interactions in NTM infection. MicroRNAs (miRs) serve as important post-transcriptional regulators of gene expression. Using a microarray profile, we found that the expression of miR-155 and cyclo-oxygenase 2 (COX-2) is significantly increased in bone-marrow-derived macrophages from mice and human monocyte-derived macrophages from healthy volunteers that are infected with NTM. Antagomir against miR-155 effectively suppressed expression of COX-2 and reduced Prostaglandin E2(PGE2) secretion, suggesting that COX-2/PGE2 expression is dependent on miR-155. Mechanistically, we found that inhibition of NF-κB activity significantly reduced miR-155/COX-2 expression in infected macrophages. Most importantly, blockade of COX-2, E-prostanoid receptors (EP2 and EP4) enhanced killing of MAI in macrophages. These findings provide novel mechanistic insights into the role of miR-155/COX-2/PGE2 signalling and suggest that induction of these pathways enhances survival of mycobacteria in macrophages. Defining host–pathogen interactions can lead to novel immunomodulatory therapies for NTM infections which are difficult to treat.
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