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Beliakova-Bethell N. Targeting noncoding RNAs to reactivate or eliminate latent HIV reservoirs. Curr Opin HIV AIDS 2024; 19:47-55. [PMID: 38169367 PMCID: PMC10872953 DOI: 10.1097/coh.0000000000000838] [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] [Indexed: 01/05/2024]
Abstract
PURPOSE OF REVIEW Expression of noncoding RNAs (ncRNAs) is more tissue and cell type-specific than expression of protein-coding genes. Understanding the mechanisms of action of ncRNAs and their roles in HIV replication and latency may inform targets for the latent HIV reservoir reactivation or elimination with high specificity to CD4 + T cells latently infected with HIV. RECENT FINDINGS While the number of studies in the field of ncRNAs and HIV is limited, evidence points to complex interactions between different ncRNAs, protein-coding RNAs, and proteins. Latency-reversing agents modulate the expression of ncRNAs, with some effects being inhibitory for HIV reactivation. An important limitation of basic research on the ncRNA mechanisms of action is the reliance on cell lines. Because of cell type specificity, it is uncertain whether the ncRNAs function similarly in primary cells. SUMMARY Comprehensive functional screens to uncover all ncRNAs that regulate HIV expression and the detailed exploration of their mechanisms of action in relevant cell types are needed to identify promising targets for HIV reservoir clearance. Classes of ncRNAs as a whole rather than individual ncRNAs might represent an attractive target for reservoir elimination. Compound screens for latency reversal should factor in the complexity of their effects on ncRNAs.
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Affiliation(s)
- Nadejda Beliakova-Bethell
- Department of Medicine, University of California at San Diego, CA, USA
- VA San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, CA, USA
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Vaidyanathan A, Taylor HE, Hope TJ, D'Aquila RT, Bartom ET, Hultquist JF, Peter ME. Analysis of the Contribution of 6-mer Seed Toxicity to HIV-1-Induced Cytopathicity. J Virol 2023; 97:e0065223. [PMID: 37310263 PMCID: PMC10373551 DOI: 10.1128/jvi.00652-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 05/16/2023] [Indexed: 06/14/2023] Open
Abstract
HIV-1 (HIV) infects CD4+ T cells, the gradual depletion of which can lead to AIDS in the absence of antiretroviral therapy (ART). Some cells, however, survive HIV infection and persist as part of the latently infected reservoir that causes recurrent viremia after ART cessation. Improved understanding of the mechanisms of HIV-mediated cell death could lead to a way to clear the latent reservoir. Death induced by survival gene elimination (DISE), an RNA interference (RNAi)-based mechanism, kills cells through short RNAs (sRNAs) with toxic 6-mer seeds (positions 2 to 7 of sRNA). These toxic seeds target the 3' untranslated region (UTR) of mRNAs, decreasing the expression of hundreds of genes critical for cell survival. In most cells under normal conditions, highly expressed cell-encoded nontoxic microRNAs (miRNAs) block access of toxic sRNAs to the RNA-induced silencing complex (RISC) that mediates RNAi, promoting cell survival. HIV has been shown to inhibit the biogenesis of host miRNAs in multiple ways. We now report that HIV infection of cells deficient in miRNA expression or function results in enhanced RISC loading of an HIV-encoded miRNA HIV-miR-TAR-3p, which can kill cells by DISE through a noncanonical (positions 3 to 8) 6-mer seed. In addition, cellular RISC-bound sRNAs shift to lower seed viability. This also occurs after latent HIV provirus reactivation in J-Lat cells, suggesting independence of permissiveness of cells to viral infection. More precise targeting of the balance between protective and cytotoxic sRNAs could provide new avenues to explore novel cell death mechanisms that could be used to kill latent HIV. IMPORTANCE Several mechanisms by which initial HIV infection is cytotoxic to infected cells have been reported and involve various forms of cell death. Characterizing the mechanisms underlying the long-term survival of certain T cells that become persistent provirus reservoirs is critical to developing a cure. We recently discovered death induced by survival gene elimination (DISE), an RNAi-based mechanism of cell death whereby toxic short RNAs (sRNAs) containing 6-mer seed sequences (exerting 6-mer seed toxicity) targeting essential survival genes are loaded into RNA-induced silencing complex (RISC) complexes, resulting in inescapable cell death. We now report that HIV infection in cells with low miRNA expression causes a shift of mostly cellular RISC-bound sRNAs to more toxic seeds. This could prime cells to DISE and is further enhanced by the viral microRNA (miRNA) HIV-miR-TAR-3p, which carries a toxic noncanonical 6-mer seed. Our data provide multiple new avenues to explore novel cell death mechanisms that could be used to kill latent HIV.
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Affiliation(s)
- Aparajitha Vaidyanathan
- Department of Medicine, Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Harry E. Taylor
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Department of Preventive Medicine, Division of Biostatistics, Northwestern University, Chicago, Illinois, USA
| | - Thomas J. Hope
- Department of Cell & Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Richard T. D'Aquila
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Elizabeth T. Bartom
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Department of Preventive Medicine, Division of Biostatistics, Northwestern University, Chicago, Illinois, USA
| | - Judd F. Hultquist
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Marcus E. Peter
- Department of Medicine, Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
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3
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Ramirez PW, Pantoja C, Beliakova-Bethell N. An Evaluation on the Role of Non-Coding RNA in HIV Transcription and Latency: A Review. HIV AIDS (Auckl) 2023; 15:115-134. [PMID: 36942082 PMCID: PMC10024501 DOI: 10.2147/hiv.s383347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/24/2023] [Indexed: 03/16/2023] Open
Abstract
The existence of latent cellular reservoirs is recognized as the major barrier to an HIV cure. Reactivating and eliminating "shock and kill" or permanently silencing "block and lock" the latent HIV reservoir, as well as gene editing, remain promising approaches, but so far have proven to be only partially successful. Moreover, using latency reversing agents or "block and lock" drugs pose additional considerations, including the ability to cause cellular toxicity, a potential lack of specificity for HIV, or low potency when each agent is used alone. RNA molecules, such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are becoming increasingly recognized as important regulators of gene expression. RNA-based approaches for combatting HIV latency represent a promising strategy since both miRNAs and lncRNAs are more cell-type and tissue specific than protein coding genes. Thus, a higher specificity of targeting the latent HIV reservoir with less overall cellular toxicity can likely be achieved. In this review, we summarize current knowledge about HIV gene expression regulation by miRNAs and lncRNAs encoded in the human genome, as well as regulatory molecules encoded in the HIV genome. We discuss both the transcriptional and post-transcriptional regulation of HIV gene expression to align with the current definition of latency, and describe RNA molecules that either promote HIV latency or have anti-latency properties. Finally, we provide perspectives on using each class of RNAs as potential targets for combatting HIV latency, and describe the complexity of the interactions between different RNA molecules, their protein targets, and HIV.
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Affiliation(s)
- Peter W Ramirez
- Department of Biological Sciences, California State University, Long Beach, CA, USA
| | - Christina Pantoja
- Department of Biological Sciences, California State University, Long Beach, CA, USA
| | - Nadejda Beliakova-Bethell
- VA San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, CA, USA
- Department of Medicine, University of California, San Diego, CA, USA
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4
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Periwal N, Bhardwaj U, Sarma S, Arora P, Sood V. In silico analysis of SARS-CoV-2 genomes: Insights from SARS encoded non-coding RNAs. Front Cell Infect Microbiol 2022; 12:966870. [PMID: 36519126 PMCID: PMC9742375 DOI: 10.3389/fcimb.2022.966870] [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: 06/11/2022] [Accepted: 10/05/2022] [Indexed: 11/29/2022] Open
Abstract
The recent pandemic caused by Severe Acute Respiratory Syndrome Coronavirus-2 has resulted in enormous deaths around the world. Clues from genomic sequences of parent and their mutants can be obtained to understand the evolving pathogenesis of this virus. Apart from the viral proteins, virus-encoded microRNAs (miRNAs) have been shown to play a vital role in regulating viral pathogenesis. Thus we sought to investigate the miRNAs encoded by SARS-CoV-2, its mutants, and the host. Here, we present the results obtained using a dual approach i.e (i) identifying host-encoded miRNAs that might regulate viral pathogenesis and (ii) identifying viral-encoded miRNAs that might regulate host cell signaling pathways and aid in viral pathogenesis. Analysis utilizing the first approach resulted in the identification of ten host-encoded miRNAs that could target the SARS, SARS-CoV-2, and its mutants. Interestingly our analysis revealed that there is a significantly higher number of host miRNAs that could target the SARS-CoV-2 genome as compared to the SARS reference genome. Results from the second approach resulted in the identification of a set of virus-encoded miRNAs which might regulate host signaling pathways. Our analysis further identified a similar "GA" rich motif in the SARS-CoV-2 and its mutant genomes that was shown to play a vital role in lung pathogenesis during severe SARS infections. In summary, we have identified human and virus-encoded miRNAs that might regulate the pathogenesis of SARS coronaviruses and describe similar non-coding RNA sequences in SARS-CoV-2 that were shown to regulate SARS-induced lung pathology in mice.
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Affiliation(s)
- Neha Periwal
- Department of Biochemistry, Jamia Hamdard, New Delhi, India
| | | | - Sankritya Sarma
- Department of Zoology, Hansraj College, University of Delhi, Delhi, India
| | - Pooja Arora
- Department of Zoology, Hansraj College, University of Delhi, Delhi, India
| | - Vikas Sood
- Department of Biochemistry, Jamia Hamdard, New Delhi, India,*Correspondence: Vikas Sood,
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Joshi N, Chandane Tak M, Mukherjee A. The involvement of microRNAs in HCV and HIV infection. Ther Adv Vaccines Immunother 2022; 10:25151355221106104. [PMID: 35832725 PMCID: PMC9272158 DOI: 10.1177/25151355221106104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 05/24/2022] [Indexed: 11/17/2022] Open
Abstract
Approximately 2.3 million people are suffering from human immunodeficiency virus (HIV)/hepatitis C virus (HCV) co-infection worldwide. Faster disease progression and increased mortality rates during the HIV/HCV co-infection have become global health concerns. Effective therapeutics against co-infection and complete infection eradication has become a mandatory requirement. The study of small non-coding RNAs in cellular processes and viral infection has so far been beneficial in various terms. Currently, microRNAs are an influential candidate for disease diagnosis and treatment. Dysregulation in miRNA expression can lead to unfavorable outcomes; hence, this exact inevitable nature has made various studies a focal point. A considerable improvement in comprehending HIV and HCV mono-infection pathogenesis is seen using miRNAs. The prominent reason behind HIV/HCV co-infection is seen to be their standard route of transmission, while some pieces of evidence also suspect viral interplay between having a role in increased viral infection. This review highlights the involvement of microRNAs in HIV/HCV co-infection, along with their contribution in HIV mono- and HCV mono-infection. We also discuss miRNAs that carry the potentiality of becoming a biomarker for viral infection and early disease progression.
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Affiliation(s)
- Nicky Joshi
- Division of Virology, ICMR-National AIDS Research Institute, Pune, India
| | | | - Anupam Mukherjee
- Scientist D & RAMANUJAN Fellow, Division of Virology, ICMR-National AIDS Research Institute, Plot No. 73, 'G' Block, MIDC, Bhosari, Pune 411026, Maharashtra, India
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6
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Moranguinho I, Valente ST. Block-And-Lock: New Horizons for a Cure for HIV-1. Viruses 2020; 12:v12121443. [PMID: 33334019 PMCID: PMC7765451 DOI: 10.3390/v12121443] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/01/2020] [Accepted: 12/08/2020] [Indexed: 12/12/2022] Open
Abstract
HIV-1/AIDS remains a global public health problem. The world health organization (WHO) reported at the end of 2019 that 38 million people were living with HIV-1 worldwide, of which only 67% were accessing antiretroviral therapy (ART). Despite great success in the clinical management of HIV-1 infection, ART does not eliminate the virus from the host genome. Instead, HIV-1 remains latent as a viral reservoir in any tissue containing resting memory CD4+ T cells. The elimination of these residual proviruses that can reseed full-blown infection upon treatment interruption remains the major barrier towards curing HIV-1. Novel approaches have recently been developed to excise or disrupt the virus from the host cells (e.g., gene editing with the CRISPR-Cas system) to permanently shut off transcription of the virus (block-and-lock and RNA interference strategies), or to reactivate the virus from cell reservoirs so that it can be eliminated by the immune system or cytopathic effects (shock-and-kill strategy). Here, we will review each of these approaches, with the major focus placed on the block-and-lock strategy.
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7
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Zhan S, Wang Y, Chen X. RNA virus-encoded microRNAs: biogenesis, functions and perspectives on application. ACTA ACUST UNITED AC 2020; 2:15. [PMID: 33209991 PMCID: PMC7548135 DOI: 10.1186/s41544-020-00056-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 09/22/2020] [Indexed: 12/12/2022]
Abstract
MicroRNAs (miRNAs) are small, noncoding RNAs that regulate gene expression at the posttranscriptional level and play a crucial role in development and many diseases. The discovery of miRNAs has greatly expanded our understanding of the intricate scenario of genome-wide regulation. Over the last two decades, hundreds of virus-encoded miRNAs have been identified, most of which are from DNA viruses. Although the number of reported RNA virus-derived miRNAs is increasing, current knowledge of their roles in physiological and pathological processes has remained lacking. In this review, we discuss the biogenesis and biological functions of RNA virus- encoded miRNAs and their proposed roles in virus-host interactions and further underscore their potential value in the diagnosis and treatment of viral diseases.
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Affiliation(s)
- Shoubin Zhan
- Nanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, State Key Laboratory of Pharmaceutical Biotechnology and Department of Physiology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023 China
| | - Yanbo Wang
- Nanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, State Key Laboratory of Pharmaceutical Biotechnology and Department of Physiology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023 China
| | - Xi Chen
- Nanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, State Key Laboratory of Pharmaceutical Biotechnology and Department of Physiology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023 China
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8
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Komori C, Takahashi T, Nakano Y, Ui-Tei K. TRBP-Dicer interaction may enhance HIV-1 TAR RNA translation via TAR RNA processing, repressing host-cell apoptosis. Biol Open 2020; 9:bio050435. [PMID: 32051109 PMCID: PMC7055394 DOI: 10.1242/bio.050435] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 02/03/2020] [Indexed: 12/24/2022] Open
Abstract
The transactivating response (TAR) RNA-binding protein (TRBP) has been identified as a double-stranded RNA (dsRNA)-binding protein, which associates with a stem-loop region known as the TAR element in human immunodeficiency virus-1 (HIV-1). However, TRBP is also known to be an enhancer of RNA silencing, interacting with Dicer, an enzyme that belongs to the RNase III family. Dicer cleaves long dsRNA into small dsRNA fragments called small interfering RNA or microRNA (miRNA) to mediate RNA silencing. During HIV-1 infection, TAR RNA-mediated translation is suppressed by the secondary structure of 5'UTR TAR RNA. However, TRBP binding to TAR RNA relieves its inhibitory action of translation and Dicer processes HIV-1 TAR RNA to generate TAR miRNA. However, whether the interaction between TRBP and Dicer is necessary for TAR RNA translation or TAR miRNA processing remains unclear. In this study, we constructed TRBP mutants that were unable to interact with Dicer by introducing mutations into amino acid residues necessary for the interaction. Furthermore, we established cell lines expressing such TRBP mutants. Then, we revealed that the TRBP-Dicer interaction is essential for both the TAR-containing RNA translation and the TAR miRNA processing in HIV-1.
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Affiliation(s)
- Chiaki Komori
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Tokyo 113-0033, Japan
| | - Tomoko Takahashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Tokyo 113-0033, Japan
| | - Yuko Nakano
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Tokyo 113-0033, Japan
| | - Kumiko Ui-Tei
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Tokyo 113-0033, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwano-ha, Chiba 277-8561, Japan
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9
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Olson A, Basukala B, Wong WW, Henderson AJ. Targeting HIV-1 proviral transcription. Curr Opin Virol 2019; 38:89-96. [PMID: 31473372 DOI: 10.1016/j.coviro.2019.07.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 07/29/2019] [Accepted: 07/30/2019] [Indexed: 12/13/2022]
Abstract
Despite the success of antiretroviral therapies, there is no cure for HIV-1 infection due to the establishment of a long-lived latent reservoir that fuels viral rebound upon treatment interruption. 'Shock-and-kill' strategies to diminish the latent reservoir have had modest impact on the reservoir leading to considerations of alternative approaches to target HIV-1 proviruses. This review explores approaches to target HIV-1 transcription as a way to block the provirus expression.
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Affiliation(s)
- Alex Olson
- Department of Medicine, Section of Infectious Diseases, Boston University School of Medicine, United States
| | - Binita Basukala
- Cell & Molecular Biology, Biology, Boston University, United States
| | - Wilson W Wong
- Biomedical Engineering, Boston University, United States
| | - Andrew J Henderson
- Department of Medicine, Section of Infectious Diseases, Boston University School of Medicine, United States.
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10
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CRISPR/Cas9-mediated deletion of miR-146a enhances antiviral response in HIV-1 infected cells. Genes Immun 2018; 20:327-337. [PMID: 29961753 DOI: 10.1038/s41435-018-0036-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 04/16/2018] [Accepted: 04/17/2018] [Indexed: 02/07/2023]
Abstract
The human immunodeficiency virus type 1 (HIV-1) causes persistent infection in human and induces miR-146a expression in infected cells. miR-146a represses the innate immune response by inhibiting the expression of TRAF6 and IRAK1 genes, thus negatively controls the NF-κB-related cytokines and interferon stimulated genes. Here we reported that lentiviral CRISPR/Cas9 system was highly efficient in introducing mutations in the precursor miR-146a genomic sequences, resulting in a loss of miR-146a expression and function. miR-146a ablation led to increasing cytokines production in LPS-stimulated A549 cells. Moreover, miR-146a knockout in HIV-1 infected MT2 cells markedly increased the expression of cytokines and HIV-1 restriction factors and reversed T cell exhaustion markers expression, thus influencing HIV-1 replication. Our study indicates that lentiviral CRISPR/Cas9-mediated gene editing is an effective approach to abrogate miR-146a expression, which consequently inhibits HIV-1 replication as well as proviral reactivation by enhancing the expression of cytokines and HIV-1 restriction factors.
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11
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Huang Q, Chen L, Luo M, Lv H, Luo D, Li T, Huang S, Xie L, Teng Y, Liu Z, Luo F, Xiong H, Zeng Y, Hou W, Feng Y. HIV-1-Induced miR-146a Attenuates Monocyte Migration by Targeting CCL5 in Human Primary Macrophages. AIDS Res Hum Retroviruses 2018; 34:580-589. [PMID: 29717615 DOI: 10.1089/aid.2017.0217] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) are widely involved in immune regulation during virus infection. Several studies showed that the expression of miR-146a was increased in human immunodeficiency virus type I (HIV-1)-infected cells, but the definitive function of miR-146a in HIV-1 infection remains obscure. The production of chemokine (C-C motif) ligand 5 (CCL5) in macrophages has been reported to play an important role in HIV/AIDS-associated pathogenesis. In this study, we examined the effects of miR-146a on CCL5 regulation in HIV-1-infected macrophages. Gain and loss of function studies showed that CCL5 might be one of the miR-146a targets, as miR-146a mimic reduced, while miR-146a inhibitor increased CCL5 production in HIV-1-infected macrophages. In addition, we demonstrated that miR-146a reduced CCL5-induced monocyte migration. Our study provided evidence that miR-146a targets CCL5 3' untranslated regions, downregulates its release from macrophages, and affects monocyte migration consequently. These findings drew a novel layer of posttranscriptional control of the chemokine CCL5 by miR-146a during HIV infection, which might contribute to HIV pathogenesis.
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Affiliation(s)
- Qiuling Huang
- State Key Laboratory of Virology/Institute of Medical Virology/Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Lang Chen
- State Key Laboratory of Virology/Institute of Medical Virology/Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Mingqi Luo
- Zhongnan Hospital of Wuhan University, Wuhan, People's Republic of China
| | - Hanlin Lv
- Renmin Hospital of Wuhan University, Wuhan, People's Republic of China
| | - Da Luo
- Renmin Hospital of Wuhan University, Wuhan, People's Republic of China
| | - Tian Li
- State Key Laboratory of Virology/Institute of Medical Virology/Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Szuyuan Huang
- State Key Laboratory of Virology/Institute of Medical Virology/Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Linlin Xie
- State Key Laboratory of Virology/Institute of Medical Virology/Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Yan Teng
- State Key Laboratory of Virology/Institute of Medical Virology/Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Zhiyu Liu
- State Key Laboratory of Virology/Institute of Medical Virology/Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Fan Luo
- State Key Laboratory of Virology/Institute of Medical Virology/Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Hairong Xiong
- State Key Laboratory of Virology/Institute of Medical Virology/Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Yan Zeng
- Department of Zoology, College of Life Sciences, Nanjing Agriculture University, Nanjing, People's Republic of China
| | - Wei Hou
- State Key Laboratory of Virology/Institute of Medical Virology/Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Yong Feng
- State Key Laboratory of Virology/Institute of Medical Virology/Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, People's Republic of China
- Zhongnan Hospital of Wuhan University, Wuhan, People's Republic of China
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12
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The Role of miRNAs in Virus-Mediated Oncogenesis. Int J Mol Sci 2018; 19:ijms19041217. [PMID: 29673190 PMCID: PMC5979478 DOI: 10.3390/ijms19041217] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/12/2018] [Accepted: 04/13/2018] [Indexed: 12/16/2022] Open
Abstract
To date, viruses are reported to be responsible for more than 15% of all tumors worldwide. The oncogenesis could be influenced directly by the activity of viral oncoproteins or by the chronic infection or inflammation. The group of human oncoviruses includes Epstein–Barr virus (EBV), human papillomavirus (HPV), hepatitis B virus (HBV), hepatitis C virus (HCV), human herpesvirus 8 (HHV-8) or polyomaviruses, and transregulating retroviruses such as HIV or HTLV-1. Most of these viruses express short noncoding RNAs called miRNAs to regulate their own gene expression or to influence host gene expression and thus contribute to the carcinogenic processes. In this review, we will focus on oncogenic viruses and summarize the role of both types of miRNAs, viral as well as host’s, in the oncogenesis.
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13
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Eilebrecht S, Benecke BJ, Benecke AG. Latent HIV-1 TAR Regulates 7SK-responsive P-TEFb Target Genes and Targets Cellular Immune Responses in the Absence of Tat. GENOMICS PROTEOMICS & BIOINFORMATICS 2017; 15:313-323. [PMID: 29037489 PMCID: PMC5673678 DOI: 10.1016/j.gpb.2017.05.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 05/10/2017] [Accepted: 05/24/2017] [Indexed: 01/04/2023]
Abstract
The transactivating response element (TAR) structure of the nascent HIV-1 transcript is critically involved in the recruitment of inactive positive transcription elongation factor b (P-TEFb) to the promoter proximal paused RNA polymerase II. The viral transactivator Tat is responsible for subsequent P-TEFb activation in order to start efficient viral transcription elongation. In the absence of the viral transactivator of transcription (Tat), e.g., during latency or in early stages of HIV transcription, TAR mediates an interaction of P-TEFb with its inhibitor hexamethylene bis-acetamide-inducible protein 1 (HEXIM1), keeping P-TEFb in its inactive form. In this study, we address the function of HIV-1 TAR in the absence of Tat by analyzing consequences of HIV-1 TAR overexpression on host cellular gene expression. An RNA chimera consisting of Epstein-Barr virus-expressed RNA 2 (EBER2) and HIV-1 TAR was developed to assure robust overexpression of TAR in HEK293 cells. The overexpression results in differential expression of more than 800 human genes. A significant proportion of these genes is involved in the suppression of cellular immune responses, including a significant set of 7SK-responsive P-TEFb target genes. Our findings identify a novel role for HIV-1 TAR in the absence of Tat, involving the interference with host cellular immune responses by targeting 7SK RNA-mediated gene expression and P-TEFb inactivation.
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Affiliation(s)
- Sebastian Eilebrecht
- CNRS UMR8246, Université Pierre et Marie Curie, Paris 75005, France; ACSIOMA GmbH, Technologiezentrum Ruhr, Bochum 44799, Germany.
| | | | - Arndt G Benecke
- CNRS UMR8246, Université Pierre et Marie Curie, Paris 75005, France; Center for Innate Immunity and Immune Disease, University of Washington School of Medicine, Seattle, WA 98195, USA.
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Sharma N, Singh SK. Implications of non-coding RNAs in viral infections. Rev Med Virol 2016; 26:356-68. [PMID: 27401792 DOI: 10.1002/rmv.1893] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 05/30/2016] [Accepted: 05/31/2016] [Indexed: 02/06/2023]
Abstract
The advances in RNA sequencing have unveiled various non-coding RNAs (ncRNAs), which modulate the gene expression. ncRNAs do not get translated into proteins. These include transfer RNAs, ribosomal RNAs, microRNA (miRNA), short interfering RNA, long non-coding RNA, piwi-interacting RNA and small nuclear RNA. ncRNAs regulate gene expression at various levels and control cellular machinery. miRNAs have been reported in plants, animals, several invertebrates and viruses. The miRNAs regulate the gene expression post-transcriptionally. Viral infection strongly influences the abundance and the distribution of miRNAs and other ncRNAs within the host cells. Viruses may encode their own miRNA, which help in the viral life cycle and other aspects of pathogenesis. Viruses are known to successfully modulate the expression pattern of ncRNAs. The ncRNA-based strategies adopted by viruses for their survival present a complex picture of host-virus interactions. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Nikhil Sharma
- Laboratory of Neurovirology and Inflammation Biology, CSIR-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
| | - Sunit K Singh
- Laboratory of Human Molecular Virology and Immunology, Molecular Biology Unit, Faculty of Medicine, Institute of Medical Sciences (IMS), Banaras Hindu University (BHU), Varanasi, India.
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