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Rai A, Bhagchandani T, Tandon R. Transcriptional landscape of long non-coding RNAs (lncRNAs) and its implication in viral diseases. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195023. [PMID: 38513793 DOI: 10.1016/j.bbagrm.2024.195023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 02/26/2024] [Accepted: 03/13/2024] [Indexed: 03/23/2024]
Abstract
Long non-coding RNAs (lncRNAs) are RNA transcripts of size >200 bp that do not translate into proteins. Emerging data revealed that viral infection results in systemic changes in the host at transcriptional level. These include alterations in the lncRNA expression levels and triggering of antiviral immune response involving several effector molecules and diverse signalling pathways. Thus, lncRNAs have emerged as an essential mediatory element at distinct phases of the virus infection cycle. The complete eradication of the viral disease requires more precise and novel approach, thus manipulation of the lncRNAs could be one of them. This review shed light upon the existing knowledge of lncRNAs wherein the implication of differentially expressed lncRNAs in blood-borne, air-borne, and vector-borne viral diseases and its promising therapeutic applications under clinical settings has been discussed. It further enhances our understanding of the complex interplay at host-pathogen interface with respect to lncRNA expression and function.
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Affiliation(s)
- Ankita Rai
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Tannu Bhagchandani
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Ravi Tandon
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.
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2
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Bermudez-Santana CI, Gallego-Gómez JC. Toward a Categorization of Virus-ncRNA Interactions in the World of RNA to Disentangle the Tiny Secrets of Dengue Virus. Viruses 2024; 16:804. [PMID: 38793685 PMCID: PMC11125801 DOI: 10.3390/v16050804] [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: 04/03/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
In recent years, the function of noncoding RNAs (ncRNAs) as regulatory molecules of cell physiology has begun to be better understood. Advances in viral molecular biology have shown that host ncRNAs, cellular factors, and virus-derived ncRNAs and their interplay are strongly disturbed during viral infections. Nevertheless, the folding of RNA virus genomes has also been identified as a critical factor in regulating canonical and non-canonical functions. Due to the influence of host ncRNAs and the structure of RNA viral genomes, complex molecular and cellular processes in infections are modulated. We propose three main categories to organize the current information about RNA-RNA interactions in some well-known human viruses. The first category shows examples of host ncRNAs associated with the immune response triggered in viral infections. Even though miRNAs introduce a standpoint, they are briefly presented to keep researchers moving forward in uncovering other RNAs. The second category outlines interactions between virus-host ncRNAs, while the third describes how the structure of the RNA viral genome serves as a scaffold for processing virus-derived RNAs. Our grouping may provide a comprehensive framework to classify ncRNA-host-cell interactions for emerging viruses and diseases. In this sense, we introduced them to organize DENV-host-cell interactions.
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Affiliation(s)
- Clara Isabel Bermudez-Santana
- Computational and theoretical RNomics Group, Center of Excellence in Scientific Computing, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Juan Carlos Gallego-Gómez
- Grupo de Medicina de Traslación, Facultad de Medicina, Universidad de Antioquia, Medellín 050010, Colombia;
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Kuzmina A, Sadhu L, Hasanuzzaman M, Fujinaga K, Schwartz JC, Fackler OT, Taube R. Direct and indirect effects of CYTOR lncRNA regulate HIV gene expression. PLoS Pathog 2024; 20:e1012172. [PMID: 38662769 PMCID: PMC11075828 DOI: 10.1371/journal.ppat.1012172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 05/07/2024] [Accepted: 04/05/2024] [Indexed: 05/08/2024] Open
Abstract
The implementation of antiretroviral therapy (ART) has effectively restricted the transmission of Human Immunodeficiency Virus (HIV) and improved overall clinical outcomes. However, a complete cure for HIV remains out of reach, as the virus persists in a stable pool of infected cell reservoir that is resistant to therapy and thus a main barrier towards complete elimination of viral infection. While the mechanisms by which host proteins govern viral gene expression and latency are well-studied, the emerging regulatory functions of non-coding RNAs (ncRNA) in the context of T cell activation, HIV gene expression and viral latency have not yet been thoroughly explored. Here, we report the identification of the Cytoskeleton Regulator (CYTOR) long non-coding RNA (lncRNA) as an activator of HIV gene expression that is upregulated following T cell stimulation. Functional studies show that CYTOR suppresses viral latency by directly binding to the HIV promoter and associating with the cellular positive transcription elongation factor (P-TEFb) to activate viral gene expression. CYTOR also plays a global role in regulating cellular gene expression, including those involved in controlling actin dynamics. Depletion of CYTOR expression reduces cytoplasmic actin polymerization in response to T cell activation. In addition, treating HIV-infected cells with pharmacological inhibitors of actin polymerization reduces HIV gene expression. We conclude that both direct and indirect effects of CYTOR regulate HIV gene expression.
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Affiliation(s)
- Alona Kuzmina
- The Shraga Segal Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel
| | - Lopamudra Sadhu
- Department of Infectious Diseases, Heidelberg University, Medical Faculty Heidelberg, Integrative Virology, Center for Integrative Infectious Disease Research (CIID), Heidelberg, Germany
| | - Md Hasanuzzaman
- Department of Infectious Diseases, Heidelberg University, Medical Faculty Heidelberg, Integrative Virology, Center for Integrative Infectious Disease Research (CIID), Heidelberg, Germany
| | - Koh Fujinaga
- Department of Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Jacob C. Schwartz
- Department of Pharmacology, University of Arizona College of Medicine, Tucson, Arizona, United States of America
| | - Oliver T. Fackler
- Department of Infectious Diseases, Heidelberg University, Medical Faculty Heidelberg, Integrative Virology, Center for Integrative Infectious Disease Research (CIID), Heidelberg, Germany
- German Center for Infection Research, DZIF, Partner Site Heidelberg, Heidelberg. Germany
| | - Ran Taube
- The Shraga Segal Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel
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Ding D, Zhao H, Liu Y, Li S, Wei J, Yang Y, Wang S, Xing G, Hou S, Wang X, Zhang Y. Whole-transcriptome sequencing revealed the role of noncoding RNAs in susceptibility and resistance of Pekin ducks to DHAV-3. Poult Sci 2024; 103:103416. [PMID: 38301494 PMCID: PMC10846394 DOI: 10.1016/j.psj.2023.103416] [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: 10/21/2023] [Revised: 12/26/2023] [Accepted: 12/27/2023] [Indexed: 02/03/2024] Open
Abstract
As the most prevalent pathogen of duck viral hepatitis (DVH), duck hepatitis A virus genotype 3 (DHAV-3) has caused huge economic losses to the duck industry in China. Herein, we obtained whole-transcriptome sequencing data of susceptible (S) and resistant (R) Pekin duckling samples at 0 h, 12 h, and 24 h after DHAV-3 infection. We found that DHAV-3 infection induces 5,396 differentially expressed genes (DEGs), 85 differentially expressed miRNAs (DEMs), and 727 differentially expressed lncRNAs (DELs) at 24 hpi in S vs. R ducks, those upregulated genes were enriched in inflammation and cell communications pathways and downregulated genes were related to metabolic processes. Upregulated genes showed high connectivity with the miR-33, miR-193, and miR-11591, and downregulated genes were mainly regulated by miR-2954, miR-125, and miR-146b. With the construction of lncRNA-miRNA-mRNA axis, we further identified a few aberrantly expressed lncRNAs (e.g., MSTRG.36194.1, MSTRG.50601.1, MSTRG.34328.7, and MSTRG.29445.1) that regulate expression of hub genes (e.g., THBD, CLIC2, IL8, ACOX2, GPHN, SMLR1, and HAO1) by sponging those highly connected miRNAs. Altogether, our findings defined a dual role of ncRNAs in immune and metabolic regulation during DHAV-3 infection, suggesting potential new targets for treating DHAV-3 infected ducks.
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Affiliation(s)
- Dingbang Ding
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Haonan Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Ying Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Shaofei Li
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jie Wei
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yuze Yang
- Beijing General Station of Animal Husbandry, Beijing 100101, China
| | - Shuaiqin Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Guangnan Xing
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Shuisheng Hou
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xia Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Yunsheng Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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5
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Zhang D, Zhang M, Zhang L, Wang W, Hua S, Zhou C, Sun X. Long non-coding RNAs and immune cells: Unveiling the role in viral infections. Biomed Pharmacother 2024; 170:115978. [PMID: 38056234 DOI: 10.1016/j.biopha.2023.115978] [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: 10/01/2023] [Revised: 11/26/2023] [Accepted: 11/29/2023] [Indexed: 12/08/2023] Open
Abstract
Viral infections present significant challenges to human health, underscoring the importance of understanding the immune response for effective therapeutic strategies. Immune cell activation leads to dynamic changes in gene expression. Numerous studies have demonstrated the crucial role of long noncoding RNAs (lncRNAs) in immune activation and disease processes, including viral infections. This review provides a comprehensive overview of lncRNAs expressed in immune cells, including CD8 T cells, CD4 T cells, B cells, monocytes, macrophages, dendritic cells, and granulocytes, during both acute and chronic viral infections. LncRNA-mediated gene regulation encompasses various mechanisms, including the modulation of viral replication, the establishment of latency, activation of interferon pathways and other critical signaling pathways, regulation of immune exhaustion and aging, and control of cytokine and chemokine production, as well as the modulation of interferon-stimulated genes. By highlighting specific lncRNAs in different immune cell types, this review enhances our understanding of immune responses to viral infections from a lncRNA perspective and suggests potential avenues for exploring lncRNAs as therapeutic targets against viral diseases.
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Affiliation(s)
- Dan Zhang
- Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
| | - Mengna Zhang
- Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
| | - Liqin Zhang
- Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
| | - Weijuan Wang
- Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
| | - Stéphane Hua
- Laboratory of Cellular Immunology and Biotechnology, Molecular Engineering for Health Unit CEA Saclay, 91191 Gif-sur-Yvette cedex, France
| | - Chan Zhou
- Department of Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Xiaoming Sun
- Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China.
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Suzuki T, Sakai S, Ota K, Yoshida M, Uchida C, Niida H, Suda T, Kitagawa M, Ohhata T. Expression of Tumor Suppressor FHIT Is Regulated by the LINC00173-SNAIL Axis in Human Lung Adenocarcinoma. Int J Mol Sci 2023; 24:17011. [PMID: 38069335 PMCID: PMC10707390 DOI: 10.3390/ijms242317011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) play a critical role in a variety of human diseases such as cancer. Here, to elucidate a novel function of a lncRNA called LINC00173, we investigated its binding partner, target gene, and its regulatory mechanism in lung adenocarcinoma, including the A549 cell line and patients. In the A549 cell line, RNA immunoprecipitation (RIP) assays revealed that LINC00173 efficiently binds to SNAIL. RNA-seq and RT-qPCR analyses revealed that the expression of FHIT was decreased upon LINC00173 depletion, indicating that FHIT is a target gene of LINC00173. Overexpression of SNAIL suppressed and depletion of SNAIL increased the expression of FHIT, indicating that SNAIL negatively regulates FHIT. The downregulation of FHIT expression upon LINC00173 depletion was restored by additional SNAIL depletion, revealing a LINC00173-SNAIL-FHIT axis for FHIT regulation. Data from 501 patients with lung adenocarcinoma also support the existence of a LINC00173-SNAIL-FHIT axis, as FHIT expression correlated positively with LINC00173 (p = 1.75 × 10-6) and negatively with SNAIL (p = 7.00 × 10-5). Taken together, we propose that LINC00173 positively regulates FHIT gene expression by binding to SNAIL and inhibiting its function in human lung adenocarcinoma. Thus, this study sheds light on the LINC00173-SNAIL-FHIT axis, which may be a key mechanism for carcinogenesis and progression in human lung adenocarcinoma.
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Grants
- 19H03501 Ministry of Education, Culture, Sports, Science and Technology of Japan
- 22H02901 Ministry of Education, Culture, Sports, Science and Technology of Japan
- 20K07569 Ministry of Education, Culture, Sports, Science and Technology of Japan
- NA Project Mirai Cancer Research Grants, the Princes Takamatsu Cancer Research Foundation
- NA The Smoking Research Foundation
- NA Hamamatsu University School of Medicine Grant-in-Aid
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Affiliation(s)
- Takahito Suzuki
- Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Satoshi Sakai
- Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Kosuke Ota
- Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Mika Yoshida
- Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Chiharu Uchida
- Advanced Research Facilities & Services, Preeminent Medical Photonics Education & Research Center, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Hiroyuki Niida
- Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Takafumi Suda
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Masatoshi Kitagawa
- Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Tatsuya Ohhata
- Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
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7
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Nelson TM, Ghosh S, Postler TS. L-RAPiT: A Cloud-Based Computing Pipeline for the Analysis of Long-Read RNA Sequencing Data. Int J Mol Sci 2022; 23:ijms232415851. [PMID: 36555493 PMCID: PMC9781625 DOI: 10.3390/ijms232415851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/07/2022] [Accepted: 12/11/2022] [Indexed: 12/15/2022] Open
Abstract
Long-read sequencing (LRS) has been adopted to meet a wide variety of research needs, ranging from the construction of novel transcriptome annotations to the rapid identification of emerging virus variants. Amongst other advantages, LRS preserves more information about RNA at the transcript level than conventional high-throughput sequencing, including far more accurate and quantitative records of splicing patterns. New studies with LRS datasets are being published at an exponential rate, generating a vast reservoir of information that can be leveraged to address a host of different research questions. However, mining such publicly available data in a tailored fashion is currently not easy, as the available software tools typically require familiarity with the command-line interface, which constitutes a significant obstacle to many researchers. Additionally, different research groups utilize different software packages to perform LRS analysis, which often prevents a direct comparison of published results across different studies. To address these challenges, we have developed the Long-Read Analysis Pipeline for Transcriptomics (L-RAPiT), a user-friendly, free pipeline requiring no dedicated computational resources or bioinformatics expertise. L-RAPiT can be implemented directly through Google Colaboratory, a system based on the open-source Jupyter notebook environment, and allows for the direct analysis of transcriptomic reads from Oxford Nanopore and PacBio LRS machines. This new pipeline enables the rapid, convenient, and standardized analysis of publicly available or newly generated LRS datasets.
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8
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Long Intergenic Non-Protein Coding RNA 173 in Human Cancers. Cancers (Basel) 2022; 14:cancers14235923. [PMID: 36497407 PMCID: PMC9737410 DOI: 10.3390/cancers14235923] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022] Open
Abstract
Long non-coding RNAs belong to non-coding RNAs (ncRNAs) with a length of more than 200 nucleotides and limited protein-coding ability. Growing research has clarified that dysregulated lncRNAs are correlated with the development of various complex diseases, including cancer. LINC00173 has drawn researchers' attention as one of the recently discovered lncRNAs. Aberrant expression of LINC00173 affects the initiation and progression of human cancers. In the present review, we summarize the recent considerable research on LINC00173 in 11 human cancers. Through the summary of the abnormal expression of LINC00173 and its potential molecular regulation mechanism in cancers, this article indicates that LINC00173 may serve as a potential diagnostic biomarker and a target for drug therapy, thus providing novel clues for future related research.
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Chu M, Chen Y, Qin G, Lu R, Yu Y, Xu Z, Ge Q, Cheng Z, Li M, Cao L, Liang Y, Zou M, Zhuang X. Identification of novel lncRNAs associated with sensitivity of HIV antiretroviral therapy: a two-stage matched case-control study. J Infect Public Health 2022; 15:1446-1454. [DOI: 10.1016/j.jiph.2022.10.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 09/19/2022] [Accepted: 10/30/2022] [Indexed: 11/06/2022] Open
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Liu X, Xu M, Li P, Zhang W, Zeng LH, Yang Y, Yang G. Roles of lncRNAs in the transcription regulation of HIV-1. Biomed J 2022; 45:580-593. [PMID: 35364293 PMCID: PMC9486250 DOI: 10.1016/j.bj.2022.03.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 03/10/2022] [Accepted: 03/21/2022] [Indexed: 12/13/2022] Open
Abstract
Long noncoding RNAs (LncRNAs) is a class of RNA molecules that are more than 200bp but cannot be translated into proteins. More and more studies have proved that lncRNA plays a crucial role in various biological functions and disease processes, including virus infection. It's worth noting that studies have also shown that lncRNAs play an essential role in the pathogenesis of human immunodeficiency virus 1 (HIV-1), one of the lethal virus that can destroy immune system. Although lncRNA-mediated gene regulation involves a variety of mechanisms, such as transcription regulation, translation regulation, protein modification, and the formation of RNA-protein complexes, in this review, we primarily focus on the role of lncRNAs in HIV-1 transcription regulation, which is one of the most important mechanisms that control the activation and development of HIV-1. This review also briefly summarizes the latest research progress of lncRNAs related to HIV-1 infection and its potential application in HIV-1 therapy. Although there are antiretroviral drugs that interfere with the function of HIV-1 virus-encoded proteins, this treatment for the HIV-1 virus is limited by its ability to produce drug resistance. Hence, a further understanding of HIV-1 transcription regulation by lncRNAs might help develop non-traditional antiviral therapy strategies.
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Affiliation(s)
- Xingzhu Liu
- Institute of Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China
| | - Mengjiao Xu
- Institute of Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China
| | - Ping Li
- Institute of Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China
| | - Wenyuan Zhang
- Institute of Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China
| | - Ling-Hui Zeng
- Department of Clinical Medicine, School of Medicine, Zhejiang University City College, Hangzhou, 310015, China.
| | - Yadong Yang
- Institute of Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China
| | - Geng Yang
- Department of Clinical Medicine, School of Medicine, Zhejiang University City College, Hangzhou, 310015, China.
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Functional Implications of Intergenic GWAS SNPs in Immune-Related LncRNAs. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1363:147-160. [DOI: 10.1007/978-3-030-92034-0_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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12
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Ghafouri-Fard S, Mahmud Hussen B, Abak A, Taheri M, Abdulmajid Ayatollahi S. Emerging role of non-coding RNAs in the course of HIV infection. Int Immunopharmacol 2021; 103:108460. [PMID: 34942460 DOI: 10.1016/j.intimp.2021.108460] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/27/2021] [Accepted: 12/10/2021] [Indexed: 11/05/2022]
Abstract
Recent studies have shown that non-coding region of the human genome can exert important regulatory roles on critical biological functions, including response to viral infections, among them is human immunodeficiency virus (HIV). HIV/AIDS is characterized by a gradual diminution of CD4 + T cells resulting in progressive deterioration of host immune responses and eventually high vulnerability to opportunistic infections and cancer. T cells functions have been shown to be delicately regulated by an active functional network of non-coding RNAs. Several lncRNAs such as MALAT1, NEAT1, GAS5, LOC102549805, NKILA, BACE1-AS, LINC00313, RP11-539L10.2, PVT1, LINC00173, NRON and AK130181 have been found to affect response of immune system to HIV or its pathological consequences. Moreover, numerous miRNAs such as hsa-miR-191-5p, miR-155, miR-103, miR-107, miR-150, miR-144, miR-125b, miR-146a, miR-146b-5p and miR-15a are involved in this process. In the current manuscript, we explain the role of lncRNAs and miRNAs in the regulation of response to HIV infection, apoptosis and activity of T cells, reactivation or latency of this virus and even pathological manifestations such as Tat-mediated induction of astrocytic amyloidosis.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Kurdistan Region, Iraq
| | - Atefe Abak
- Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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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: 9] [Impact Index Per Article: 3.0] [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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14
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Yang Q, Kong S, Zheng M, Hong Y, Sun J, Ming X, Gu Y, Shen X, Ju S. Long intergenic noncoding RNA LINC00173 as a potential serum biomarker for diagnosis of non-small-cell lung cancer. Cancer Biomark 2021; 29:441-451. [PMID: 32623390 DOI: 10.3233/cbm-201616] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
BACKGROUND Long intergenic non-coding RNA (lincRNA) belongs to a special type of RNA that is unable to encode proteins but has been proved to play a role in gene regulation and differentially expressed in various malignant tumors. OBJECTIVE In this study, we aimed to identify whether lincRNA LINC00173 was differentially expressed in non-small-cell lung cancer (NSCLC) and whether it could serve as a potential diagnostic biomarker. METHODS The quantification real-time quantitative polymerase chain reaction (qRT-PCR) was used to detect the expression of LINC00173 in serum and cultured cells. For large sample analysis, the lncRNA expression matrix in TCGA database were generated via R software. To evaluate the diagnostic performance of serum LINC00173, the receiver operating characteristic (ROC) curve was used. RESULTS The qRT-PCR analysis showed that the serum LINC00173 expression level in 108 NSCLC patients was higher than that in 91 healthy donors and 55 patients with benign pulmonary disease (BPD). And the area under the curve (AUC) of serum LINC00173 was 0.809 for the diagnosis of NSCLC (95% CI: 0.750-0.868, p< 0.001), 0.670 for BPD (95% CI: 0.584-0.756, P< 0.001), and 0.730 for small-cell lung cancer (SCLC, 95% CI: 0.636-0.825, P< 0.001). Besides, we established a diagnostic model of combined detection of LINC00173, CEA and Cyfra21-1, and found that combined detection of these indicators significantly improved the diagnostic efficiency. Analysis of the Clinicopathological parameters showed that high LINC00173 expression was correlated with histological typing of tumor, tumor metastasis and serum Cyfra21-1 levels. In addition, serum LINC00173 expression decreased in patients who received chemotherapy and rebound in recurrent NSCLC patients. CONCLUSION Serum LINC00173 may prove to be a potential non-invasive auxiliary diagnostic biomarker for NSCLC patients.
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Affiliation(s)
- Qian Yang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China.,Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Shan Kong
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China.,Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Ming Zheng
- School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Yuelan Hong
- School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Jing Sun
- School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Xiaotian Ming
- School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Yingqiu Gu
- School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Xianjuan Shen
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Shaoqing Ju
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China.,School of Public Health, Nantong University, Nantong, Jiangsu, China
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15
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Non-Coding RNAs and Reactive Oxygen Species–Symmetric Players of the Pathogenesis Associated with Bacterial and Viral Infections. Symmetry (Basel) 2021. [DOI: 10.3390/sym13071307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Infections can be triggered by a wide range of pathogens. However, there are few strains of bacteria that cause illness, but some are quite life-threatening. Likewise, viral infections are responsible for many human diseases, usually characterized by high contagiousness. Hence, as bacterial and viral infections can both cause similar symptoms, it can be difficult to determine the exact cause of a specific infection, and this limitation is critical. However, recent scientific advances have geared us up with the proper tools required for better diagnoses. Recent discoveries have confirmed the involvement of non-coding RNAs (ncRNAs) in regulating the pathogenesis of certain bacterial or viral infections. Moreover, the presence of reactive oxygen species (ROS) is also known as a common infection trait that can be used to achieve a more complete description of such pathogen-driven conditions. Thus, this opens further research opportunities, allowing scientists to explore infection-associated genetic patterns and develop better diagnosis and treatment methods. Therefore, the aim of this review is to summarize the current knowledge of the implication of ncRNAs and ROS in bacterial and viral infections, with great emphasis on their symmetry but, also, on their main differences.
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16
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Li Q, Li X, Yang X, Zhang B, Gu Y, Gu G, Xiong J, Li Y, Qian Z. Long Intergenic Nonprotein Coding RNA 173 Inhibits Tumor Growth and Promotes Apoptosis by Repressing Sphingosine Kinase 1 Protein Expression in Pancreatic Cancer. DNA Cell Biol 2021; 40:757-775. [PMID: 33978457 DOI: 10.1089/dna.2020.6103] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Pancreatic cancer is a common malignant tumor worldwide. Extensive studies have been conducted on the functional role of long noncoding RNAs in pancreatic cancer. In this study, long intergenic nonprotein coding RNA 173 (LINC00173) was highly expressed in pancreatic cancer tissues. In vitro functional experiments showed that LINC00173 overexpression inhibited the proliferation and invasion of pancreatic cancer cells and promoted cell apoptosis in MIA PaCa-2 and PANC-1 cells. RNA sequencing analysis and Western blot assays demonstrated that LINC00173 reduced the expression of sphingosine kinase 1 (SPHK1) and then inhibited the protein expression of activated phospho-protein kinase B (AKT) and NF-κB. In vivo functional assays also revealed that LINC00173 inhibited the growth of pancreatic cancer xenografts, repressed cell proliferation, promoted cell apoptosis, and inhibited SPHK1 expression. The combined results of this study indicate that LINC00173 inhibits pancreatic cancer progression by repressing SPHK1 expression. Improving LINC00173 may represent a therapeutic strategy for pancreatic cancer in the future.
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Affiliation(s)
- Qian Li
- Pancreas Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Department of Plastic & Cosmetic Surgery, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Xingxing Li
- Pancreas Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaojun Yang
- Pancreas Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Bin Zhang
- Pancreas Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yuqing Gu
- Pancreas Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Guangliang Gu
- Pancreas Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jiageng Xiong
- Pancreas Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yanan Li
- Pancreas Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zhuyin Qian
- Pancreas Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Ma L, Zhang H, Zhang Y, Li H, An M, Zhao B, Ding H, Xu J, Shang H, Han X. Integrated analysis of lncRNA, miRNA and mRNA profiles reveals potential lncRNA functions during early HIV infection. J Transl Med 2021; 19:135. [PMID: 33794921 PMCID: PMC8015739 DOI: 10.1186/s12967-021-02802-9] [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: 12/17/2020] [Accepted: 03/19/2021] [Indexed: 02/06/2023] Open
Abstract
Background Long noncoding RNAs (lncRNAs) can regulate gene expression in a cis-regulatory fashion or as “microRNA sponges”. However, the expression and functions of lncRNAs during early human immunodeficiency virus (HIV) infection (EHI) remain unclear. Methods 3 HAART-naive EHI patients and 3 healthy controls (HCs) were recruited in this study to perform RNA sequencing and microRNA (miRNA) sequencing. The expression profiles of lncRNAs, mRNAs and miRNAs were obtained, and the potential roles of lncRNAs were analysed based on discovering lncRNA cis-regulatory target mRNAs and constructing lncRNA–miRNA–mRNA competing endogenous RNA (ceRNA) networks. Then, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed on 175 lncRNA-associated differentially expressed (DE) mRNAs to investigate the potential functions of DE lncRNAs in ceRNA networks. Results A total of 242 lncRNAs, 1240 mRNAs and 21 mature known miRNAs were determined as differentially expressed genes in HAART-naive EHI patients compared to HCs. Among DE lncRNAs, 44 lncRNAs were predicted to overlap with 41 target mRNAs, and 107 lncRNAs might regulate their nearby DE mRNAs. Two DE lncRNAs might regulate their cis-regulatory target mRNAs BTLA and ZAP70, respectively, which were associated with immune activation. In addition, the ceRNA networks comprised 160 DE lncRNAs, 21 DE miRNAs and 175 DE mRNAs. Seventeen DE lncRNAs were predicted to regulate HIF1A and TCF7L2, which are involved in the process of HIV-1 replication. Twenty DE lncRNAs might share miRNA response elements (MREs) with FOS, FOSB and JUN, which are associated with both immune activation and HIV-1 replication. Conclusions This study revealed that lncRNAs might play a critical role in HIV-1 replication and immune activation during EHI. These novel findings are helpful for understanding of the pathogenesis of HIV infection and provide new insights into antiviral therapy. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-02802-9.
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Affiliation(s)
- Lianwei Ma
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, No 155, Nanjing North Street, Heping District, Shenyang, 110001, Liaoning, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, 110001, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003, China
| | - Hui Zhang
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, No 155, Nanjing North Street, Heping District, Shenyang, 110001, Liaoning, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, 110001, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003, China
| | - Yue Zhang
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, No 155, Nanjing North Street, Heping District, Shenyang, 110001, Liaoning, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, 110001, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003, China
| | - Hailong Li
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, No 155, Nanjing North Street, Heping District, Shenyang, 110001, Liaoning, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, 110001, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003, China
| | - Minghui An
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, No 155, Nanjing North Street, Heping District, Shenyang, 110001, Liaoning, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, 110001, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003, China
| | - Bin Zhao
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, No 155, Nanjing North Street, Heping District, Shenyang, 110001, Liaoning, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, 110001, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003, China
| | - Haibo Ding
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, No 155, Nanjing North Street, Heping District, Shenyang, 110001, Liaoning, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, 110001, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003, China
| | - Junjie Xu
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, No 155, Nanjing North Street, Heping District, Shenyang, 110001, Liaoning, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, 110001, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003, China
| | - Hong Shang
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, No 155, Nanjing North Street, Heping District, Shenyang, 110001, Liaoning, China. .,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001, China. .,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, 110001, China. .,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003, China.
| | - Xiaoxu Han
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, No 155, Nanjing North Street, Heping District, Shenyang, 110001, Liaoning, China. .,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001, China. .,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, 110001, China. .,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003, China.
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18
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Li Q, Chen X, Chen L, Yan H, Li J. LINC00173 promotes the apoptosis of hypertrophic scar fibroblasts through increasing β-catenin expression. Mol Cell Biochem 2020; 476:1005-1014. [PMID: 33141309 DOI: 10.1007/s11010-020-03966-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 10/27/2020] [Indexed: 10/23/2022]
Abstract
Previous studies have demonstrated the involvement of long intergenic nonprotein coding RNA 173 (LINC00173) in several pathological disorders. However, the function of LINC00173 in the hypertrophic scar is not well understood. This study confirmed that the two transcript variants of TSV1 and TSV2 were both upregulated in hypertrophic scar fibroblasts. The overexpression of TSV1 or TSV2 promoted the apoptosis of fibroblasts, whereas the overexpression of TSV2 inhibited the proliferation of fibroblasts. RNA-sequencing (RNA-seq), Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis, and gene set enrichment analysis (GSEA) showed that phosphatidylinositol 3-kinase (PI3K)/Akt and Mitogen-activated protein kinases (MAPK) signaling might be involved in the role of LINC00173 in hypertrophic scar pathogenesis. Furthermore, the protein expression of β-catenin was upregulated in the TSV1 or TSV2 overexpression group. Overall, the study demonstrated that LINC00173 promoted the apoptosis of fibroblasts through increasing β-catenin expression, suggesting that LINC00173 might be a new target for hypertrophic scar treatment.
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Affiliation(s)
- Qian Li
- Department of Plastic & Cosmetic Surgery, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), 123rd Tianfei Street, Mochou Road, Nanjing, 210004, China
| | - Xin Chen
- Department of Caridology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Ling Chen
- Department of Plastic & Cosmetic Surgery, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), 123rd Tianfei Street, Mochou Road, Nanjing, 210004, China
| | - Hui Yan
- Department of Plastic & Cosmetic Surgery, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), 123rd Tianfei Street, Mochou Road, Nanjing, 210004, China
| | - Jun Li
- Department of Plastic & Cosmetic Surgery, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), 123rd Tianfei Street, Mochou Road, Nanjing, 210004, China.
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19
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French AJ, Natesampillai S, Krogman A, Correia C, Peterson KL, Alto A, Chandrasekar AP, Misra A, Li Y, Kaufmann SH, Badley AD, Cummins NW. Reactivating latent HIV with PKC agonists induces resistance to apoptosis and is associated with phosphorylation and activation of BCL2. PLoS Pathog 2020; 16:e1008906. [PMID: 33075109 PMCID: PMC7595626 DOI: 10.1371/journal.ppat.1008906] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 10/29/2020] [Accepted: 08/20/2020] [Indexed: 02/07/2023] Open
Abstract
Eradication of HIV-1 by the "kick and kill" strategy requires reactivation of latent virus to cause death of infected cells by either HIV-induced or immune-mediated apoptosis. To date this strategy has been unsuccessful, possibly due to insufficient cell death in reactivated cells to effectively reduce HIV-1 reservoir size. As a possible cause for this cell death resistance, we examined whether leading latency reversal agents (LRAs) affected apoptosis sensitivity of CD4 T cells. Multiple LRAs of different classes inhibited apoptosis in CD4 T cells. Protein kinase C (PKC) agonists bryostatin-1 and prostratin induced phosphorylation and enhanced neutralizing capability of the anti-apoptotic protein BCL2 in a PKC-dependent manner, leading to resistance to apoptosis induced by both intrinsic and extrinsic death stimuli. Furthermore, HIV-1 producing CD4 T cells expressed more BCL2 than uninfected cells, both in vivo and after ex vivo reactivation. Therefore, activation of BCL2 likely contributes to HIV-1 persistence after latency reversal with PKC agonists. The effects of LRAs on apoptosis sensitivity should be considered in designing HIV cure strategies predicated upon the "kick and kill" paradigm.
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Affiliation(s)
- Andrea J. French
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Sekar Natesampillai
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Ashton Krogman
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Cristina Correia
- Division of Oncology Research, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Kevin L. Peterson
- Division of Oncology Research, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Alecia Alto
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Aswath P. Chandrasekar
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Anisha Misra
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Ying Li
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Scott H. Kaufmann
- Division of Oncology Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Andrew D. Badley
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, United States of America
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Nathan W. Cummins
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, United States of America
- * E-mail:
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20
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LncRNA Neat1 positively regulates MAPK signaling and is involved in the pathogenesis of Sjögren's syndrome. Int Immunopharmacol 2020; 88:106992. [PMID: 33182021 DOI: 10.1016/j.intimp.2020.106992] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 09/07/2020] [Accepted: 09/07/2020] [Indexed: 12/15/2022]
Abstract
OBJECTIVE Primary Sjögren's syndrome (pSS) is a systemic autoimmune disease characterized by lymphocytic infiltration of the exocrine glands. Recent, studies have shown that the long noncoding RNA (lncRNA) NEAT1 plays a crucial role in regulating the immune response. However, studies on the lncRNA NEAT1 in pSS are limited. Exploring the role of the lncRNA NEAT1 in the pathogenesis of pSS was the purpose of this study. METHODS The expression of NEAT1 in peripheral blood mononuclear cells (PBMCs) of patients with pSS and healthy controls (HCs) was analyzed by real-time polymerase chain reaction (RT-PCR). Antisense oligonucleotides (ASOs) and siRNA or immune stimulation with PMA/ionomycin were used to perform loss-and-gain-of-function experiments. RT-PCR, enzyme-linked immunosorbent assay (ELISA), and Western blot were performed to detect the RNA and protein levels of specific genes induced by PMA/ionomycin stimulation. Microarray analysis was used to generate an overview of the genes that might be regulated by NEAT1. RESULTS Compared with that in HC patient cells, the expression of NEAT1 in pSS patients was mainly increased in peripheral T cells, including CD4+ and CD8+ T cells. Additionally, the expression of NEAT1 in CD4+ T cells of patients with pSS was positively correlated with the course of disease. NEAT1 expression in Jurkat cells was induced by PMA/ionomycin stimulation upon activation of the TCR-p38 pathway. Upregulation of NEAT1 expression also increased the expression of CXCL8 and TNF-α. Knocking down NEAT1 expression with an ASO suppressed the expression of CXCL8 and TNF-α in PMA/ionomycin-stimulated Jurkat cells. Then, we found that NEAT1 regulated the activation of MAPK pathway to regulate NEAT1-induced factors, selectively activating the expression of p-p38 and p-ERK1/2. Furthermore, we also detected the expression profile of Jurkat cells stimulated by PMA/ionomycin when NEAT1 was silenced or not, in order to produce an overview of NEAT1-regulated genes. CONCLUSION These results provide a new understanding of the mechanisms of pSS and reveal that NEAT1 is a positive regulator of pSS, which is of substantial significance to its pathogenesis. Thus, NEAT1 provides a potential therapeutic target for pSS.
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Zhang J, Zhou M, Zhao X, Wang G, Li J. Long noncoding RNA LINC00173 is downregulated in cervical cancer and inhibits cell proliferation and invasion by modulating the miR-182-5p/FBXW7 axis. Pathol Res Pract 2020; 216:152994. [PMID: 32402537 DOI: 10.1016/j.prp.2020.152994] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 04/01/2020] [Accepted: 04/22/2020] [Indexed: 12/24/2022]
Abstract
Accumulating evidence has supported the concept that long noncoding RNAs (lncRNAs) participate in the initiation and progression of human cervical cancer (CC). The long intergenic nonprotein-coding RNA 173 (LINC00173) is a recently identified cancer-associated factor. However, the expression and biological role of LINC00173 in CC are poorly understood. Here, for the first time, we found that the expression of LINC00173 was decreased in CC tissues compared with that in nontumor tissues. Data from The Cancer Genome Atlas (TCGA) further revealed that the downregulated expression of LINC00173 in CC tissues was correlated with poor survival. Functionally, LINC00173 overexpression suppressed HeLa cell proliferation via induction of G0/G1 phase arrest. Ectopic expression of LINC00173 also repressed the invasiveness of HeLa cells. Conversely, LINC00173 depletion resulted in the enhanced proliferation and invasiveness of C33A cells. Mechanistically, LINC00173 functioned as a molecular sponge for miR-182-5p and inversely regulated the miR-182-5p level in CC cells. F-box and WD repeat domain-containing 7 (FBXW7) was identified as the target of miR-182-5p. LINC00173 overexpression enhanced the FBXW7 level via regulation of miR-182-5p in HeLa Cells. More importantly, the inhibitory effects of LINC00173 on HeLa cell proliferation and invasiveness were reversed by FBXW7 silencing. Taken together, the results indicate that the LINC00173/miR-182-5p/FBXW7 axis is critical for CC progression, which might offer new insights into effective therapy for CC.
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Affiliation(s)
- Jing Zhang
- Department of Gynecologic Oncology, Shaanxi Provincial Tumor Hospital, Affiliated Hospital of Medical College of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Min Zhou
- Department of Gynecologic Oncology, Shaanxi Provincial Tumor Hospital, Affiliated Hospital of Medical College of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Xixia Zhao
- Department of Gynecologic Oncology, Shaanxi Provincial Tumor Hospital, Affiliated Hospital of Medical College of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Guoqing Wang
- Department of Gynecologic Oncology, Shaanxi Provincial Tumor Hospital, Affiliated Hospital of Medical College of Xi'an Jiaotong University, Xi'an, 710061, China.
| | - Jieqiong Li
- Department of Nursing, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China.
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Ray RM, Morris KV. Long Non-coding RNAs Mechanisms of Action in HIV-1 Modulation and the Identification of Novel Therapeutic Targets. Noncoding RNA 2020; 6:ncrna6010012. [PMID: 32183241 PMCID: PMC7151623 DOI: 10.3390/ncrna6010012] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 03/01/2020] [Accepted: 03/10/2020] [Indexed: 12/17/2022] Open
Abstract
This review aims to highlight the role of long non-coding RNAs in mediating human immunodeficiency virus (HIV-1) viral replication, latency, disease susceptibility and progression. In particular, we focus on identifying possible lncRNA targets and their purported mechanisms of action for future drug design or gene therapeutics.
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Kazimierczyk M, Kasprowicz MK, Kasprzyk ME, Wrzesinski J. Human Long Noncoding RNA Interactome: Detection, Characterization and Function. Int J Mol Sci 2020; 21:E1027. [PMID: 32033158 PMCID: PMC7037361 DOI: 10.3390/ijms21031027] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 01/31/2020] [Accepted: 02/02/2020] [Indexed: 01/17/2023] Open
Abstract
The application of a new generation of sequencing techniques has revealed that most of the genome has already been transcribed. However, only a small part of the genome codes proteins. The rest of the genome "dark matter" belongs to divergent groups of non-coding RNA (ncRNA), that is not translated into proteins. There are two groups of ncRNAs, which include small and long non-coding RNAs (sncRNA and lncRNA respectively). Over the last decade, there has been an increased interest in lncRNAs and their interaction with cellular components. In this review, we presented the newest information about the human lncRNA interactome. The term lncRNA interactome refers to cellular biomolecules, such as nucleic acids, proteins, and peptides that interact with lncRNA. The lncRNA interactome was characterized in the last decade, however, understanding what role the biomolecules associated with lncRNA play and the nature of these interactions will allow us to better understand lncRNA's biological functions in the cell. We also describe a set of methods currently used for the detection of lncRNA interactome components and the analysis of their interactions. We think that such a holistic and integrated analysis of the lncRNA interactome will help to better understand its potential role in the development of organisms and cancers.
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Affiliation(s)
| | | | | | - Jan Wrzesinski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland (M.K.K.); (M.E.K.)
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Shen L, Wu C, Zhang J, Xu H, Liu X, Wu X, Wang T, Mao L. Roles and potential applications of lncRNAs in HIV infection. Int J Infect Dis 2020; 92:97-104. [PMID: 31945493 DOI: 10.1016/j.ijid.2020.01.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 12/28/2019] [Accepted: 01/08/2020] [Indexed: 12/11/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are defined as a class of RNA molecules with a length of more than 200 nucleotides that are not translated into protein, and are known to participate in a variety of biological processes. They have recently been implicated as having roles in viral infections, and several research groups have identified that complex interactions exist between lncRNAs and the progression of human immunodeficiency virus (HIV) infection. lncRNAs derived from both the human host and HIV itself are emerging as key regulators of various cellular functions, playing crucial roles in virus-host interactions and viral pathogenesis. This review provides a brief discussion of the roles and associated mechanisms of lncRNAs in HIV infection. Moreover, due to the continued lack of effective HIV vaccines or treatments, we provide an insight into the complex interplay between lncRNAs and HIV and suggest innovative therapeutic strategies for HIV/acquired immunodeficiency syndrome (AIDS). The available data on lncRNAs that have been associated with HIV infection and their potential applications for the treatment of HIV are summarized for the first time, providing a new perspective for the future development of therapeutic strategies.
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Affiliation(s)
- Li Shen
- Zhenjiang Center for Disease Control and Prevention, Jiangsu, China
| | - Cuisong Wu
- Zhenjiang Third People's Hospital, Jiangsu, China
| | - Jun Zhang
- Zhenjiang Center for Disease Control and Prevention, Jiangsu, China
| | - Hong Xu
- Zhenjiang Center for Disease Control and Prevention, Jiangsu, China
| | - Xiaoxia Liu
- Zhenjiang Center for Disease Control and Prevention, Jiangsu, China
| | - Xiao Wu
- Zhenjiang Center for Disease Control and Prevention, Jiangsu, China
| | - Ting Wang
- Zhenjiang Center for Disease Control and Prevention, Jiangsu, China
| | - Lingxiang Mao
- The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China.
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25
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Involvement and Roles of Long Noncoding RNAs in the Molecular Mechanisms of Emerging and Reemerging Viral Infections. EMERGING AND REEMERGING VIRAL PATHOGENS 2020. [PMCID: PMC7150007 DOI: 10.1016/b978-0-12-814966-9.00006-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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26
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West KA, Lagos D. Long Non-Coding RNA Function in CD4 + T Cells: What We Know and What Next? Noncoding RNA 2019; 5:ncrna5030043. [PMID: 31336952 PMCID: PMC6789709 DOI: 10.3390/ncrna5030043] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/03/2019] [Accepted: 07/12/2019] [Indexed: 02/06/2023] Open
Abstract
The non-coding genome has previously been regarded as "junk" DNA; however, emerging evidence suggests that the non-coding genome accounts for some of the greater biological complexity observed in mammals. Research into long non-coding RNAs (lncRNAs) has gathered speed in recent years, and a growing body of evidence has implicated lncRNAs in a vast range of cellular functions including gene regulation, chromosome organisation and splicing. T helper cells offer an ideal platform for the study of lncRNAs given they function as part of a complex cellular network and undergo remarkable and finely regulated gene expression changes upon antigenic stimulation. Using various knock down and RNA interaction studies several lncRNAs have been shown to be crucial for T helper cell differentiation, activation and function. Given that RNA targeting therapeutics are rapidly gaining attention, further understanding the mechanistic role of lncRNAs in a T helper context is an exciting area of research, as it may unearth a wide range of new candidate targets for treatment of CD4+ mediated pathologies.
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Affiliation(s)
- Katie A West
- York Biomedical Research Institute, University of York, Wentworth Way, York YO10 5DD, UK
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
- Hull York Medical School, University of York, Wentworth Way, York YO10 5DD, UK
| | - Dimitris Lagos
- York Biomedical Research Institute, University of York, Wentworth Way, York YO10 5DD, UK.
- Hull York Medical School, University of York, Wentworth Way, York YO10 5DD, UK.
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27
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Noncoding RNAs in Retrovirus Replication. RETROVIRUS-CELL INTERACTIONS 2018. [PMCID: PMC7173536 DOI: 10.1016/b978-0-12-811185-7.00012-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Although a limited percentage of the genome produces proteins, approximately 90% is transcribed, indicating important roles for noncoding RNA (ncRNA). It is now known that these ncRNAs have a multitude of cellular functions ranging from the regulation of gene expression to roles as structural elements in ribonucleoprotein complexes. ncRNA is also represented at nearly every step of viral life cycles. This chapter will focus on ncRNAs of both host and viral origin and their roles in retroviral life cycles. Cellular ncRNA represents a significant portion of material packaged into retroviral virions and includes transfer RNAs, 7SL RNA, U RNA, and vault RNA. Initially thought to be random packaging events, these host RNAs are now proposed to contribute to viral assembly and infectivity. Within the cell, long ncRNA and endogenous retroviruses have been found to regulate aspects of the retroviral life cycle in diverse ways. Additionally, the HIV-1 transactivating response element RNA is thought to impact viral infection beyond the well-characterized role as a transcription activator. RNA interference, thought to be an early version of the innate immune response to viral infection, can still be observed in plants and invertebrates today. The ability of retroviral infection to manipulate the host RNAi pathway is described here. Finally, RNA-based therapies, including gene editing approaches, are being explored as antiretroviral treatments and are discussed.
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