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Kroeze S, Kootstra NA, van Nuenen AC, Rossouw TM, Kityo CM, Siwale M, Akanmu S, Mandaliya K, de Jager M, Ondoa P, Wit FW, Reiss P, Rinke de Wit TF, Hamers RL. Specific plasma microRNAs are associated with CD4 + T-cell recovery during suppressive antiretroviral therapy for HIV-1. AIDS 2024; 38:791-801. [PMID: 38300257 PMCID: PMC10994156 DOI: 10.1097/qad.0000000000003853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 12/12/2023] [Accepted: 12/19/2023] [Indexed: 02/02/2024]
Abstract
OBJECTIVE This study investigated the association of plasma microRNAs before and during antiretroviral therapy (ART) with poor CD4 + T-cell recovery during the first year of ART. DESIGN MicroRNAs were retrospectively measured in stored plasma samples from people with HIV (PWH) in sub-Saharan Africa who were enrolled in a longitudinal multicountry cohort and who had plasma viral-load less than 50 copies/ml after 12 months of ART. METHODS First, the levels of 179 microRNAs were screened in a subset of participants from the lowest and highest tertiles of CD4 + T-cell recovery (ΔCD4) ( N = 12 each). Next, 11 discordant microRNAs, were validated in 113 participants (lowest tertile ΔCD4: n = 61, highest tertile ΔCD4: n = 52). For discordant microRNAs in the validation, a pathway analysis was conducted. Lastly, we compared microRNA levels of PWH to HIV-negative controls. RESULTS Poor CD4 + T-cell recovery was associated with higher levels of hsa-miR-199a-3p and hsa-miR-200c-3p before ART, and of hsa-miR-17-5p and hsa-miR-501-3p during ART. Signaling by VEGF and MET, and RNA polymerase II transcription pathways were identified as possible targets of hsa-miR-199a-3p, hsa-200c-3p, and hsa-miR-17-5p. Compared with HIV-negative controls, we observed lower hsa-miR-326, hsa-miR-497-5p, and hsa-miR-501-3p levels before and during ART in all PWH, and higher hsa-miR-199a-3p and hsa-miR-200c-3p levels before ART in all PWH, and during ART in PWH with poor CD4 + T-cell recovery only. CONCLUSION These findings add to the understanding of pathways involved in persistent HIV-induced immune dysregulation during suppressive ART.
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Affiliation(s)
- Stefanie Kroeze
- Amsterdam Institute for Global Health and Development
- Amsterdam UMC location University of Amsterdam, Department of Global Health
- Amsterdam UMC location University of Amsterdam, Laboratory for Experimental Immunology, Meibergdreef 9
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Neeltje A. Kootstra
- Amsterdam Institute for Global Health and Development
- Amsterdam UMC location University of Amsterdam, Department of Global Health
- Amsterdam UMC location University of Amsterdam, Laboratory for Experimental Immunology, Meibergdreef 9
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Ad C. van Nuenen
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Theresa M. Rossouw
- Department of Immunology, University of Pretoria, Pretoria, South Africa
| | | | | | - Sulaimon Akanmu
- Department of Haematology and Blood Transfusion, College of Medicine of the University of Lagos and the Lagos University Teaching Hospital, Lagos, Nigeria
| | | | | | - Pascale Ondoa
- Amsterdam Institute for Global Health and Development
- Amsterdam UMC location University of Amsterdam, Department of Global Health
- African Society for Laboratory Medicine, Addis Ababa, Ethiopia
| | - Ferdinand W. Wit
- Amsterdam Institute for Global Health and Development
- Amsterdam UMC location University of Amsterdam, Department of Global Health
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
- Stichting HIV Monitoring
- Amsterdam UMC location University of Amsterdam, Internal Medicine, Division of Infectious Diseases, Meibergdreef 9, Amsterdam, The Netherlands
| | - Peter Reiss
- Amsterdam Institute for Global Health and Development
- Amsterdam UMC location University of Amsterdam, Department of Global Health
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
- Amsterdam UMC location University of Amsterdam, Internal Medicine, Division of Infectious Diseases, Meibergdreef 9, Amsterdam, The Netherlands
| | - Tobias F. Rinke de Wit
- Amsterdam Institute for Global Health and Development
- Amsterdam UMC location University of Amsterdam, Department of Global Health
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Raph L. Hamers
- Amsterdam Institute for Global Health and Development
- Amsterdam UMC location University of Amsterdam, Department of Global Health
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
- Amsterdam UMC location University of Amsterdam, Internal Medicine, Division of Infectious Diseases, Meibergdreef 9, Amsterdam, The Netherlands
- Oxford University Clinical Research Unit Indonesia, Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
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2
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Morando N, Rosenzvit MC, Pando MA, Allmer J. The Role of MicroRNAs in HIV Infection. Genes (Basel) 2024; 15:574. [PMID: 38790203 PMCID: PMC11120859 DOI: 10.3390/genes15050574] [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: 03/10/2024] [Revised: 04/17/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024] Open
Abstract
MicroRNAs (miRNAs), a class of small, non-coding RNAs, play a pivotal role in regulating gene expression at the post-transcriptional level. These regulatory molecules are integral to many biological processes and have been implicated in the pathogenesis of various diseases, including Human Immunodeficiency Virus (HIV) infection. This review aims to cover the current understanding of the multifaceted roles miRNAs assume in the context of HIV infection and pathogenesis. The discourse is structured around three primary focal points: (i) elucidation of the mechanisms through which miRNAs regulate HIV replication, encompassing both direct targeting of viral transcripts and indirect modulation of host factors critical for viral replication; (ii) examination of the modulation of miRNA expression by HIV, mediated through either viral proteins or the activation of cellular pathways consequent to viral infection; and (iii) assessment of the impact of miRNAs on the immune response and the progression of disease in HIV-infected individuals. Further, this review delves into the potential utility of miRNAs as biomarkers and therapeutic agents in HIV infection, underscoring the challenges and prospects inherent to this line of inquiry. The synthesis of current evidence positions miRNAs as significant modulators of the host-virus interplay, offering promising avenues for enhancing the diagnosis, treatment, and prevention of HIV infection.
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Affiliation(s)
- Nicolas Morando
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)-Universidad de Buenos Aires, Buenos Aires 1121, Argentina; (N.M.); (M.A.P.)
| | - Mara Cecilia Rosenzvit
- Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires 1121, Argentina;
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Universidad de Buenos Aires, Buenos Aires 1121, Argentina
| | - Maria A. Pando
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)-Universidad de Buenos Aires, Buenos Aires 1121, Argentina; (N.M.); (M.A.P.)
| | - Jens Allmer
- Medical Informatics and Bioinformatics, Institute for Measurement Engineering and Sensor Technology, Hochschule Ruhr West, University of Applied Sciences, 45479 Mülheim an der Ruhr, Germany
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3
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Alpuche-Lazcano SP, Scarborough RJ, Gatignol A. MicroRNAs and long non-coding RNAs during transcriptional regulation and latency of HIV and HTLV. Retrovirology 2024; 21:5. [PMID: 38424561 PMCID: PMC10905857 DOI: 10.1186/s12977-024-00637-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 02/21/2024] [Indexed: 03/02/2024] Open
Abstract
Human immunodeficiency virus (HIV) and human T cell leukemia virus (HTLV) have replicative and latent stages of infection. The status of the viruses is dependent on the cells that harbour them and on different events that change the transcriptional and post-transcriptional events. Non-coding (nc)RNAs are key factors in the regulation of retrovirus replication cycles. Notably, micro (mi)RNAs and long non-coding (lnc)RNAs are important regulators that can induce switches between active transcription-replication and latency of retroviruses and have important impacts on their pathogenesis. Here, we review the functions of miRNAs and lncRNAs in the context of HIV and HTLV. We describe how specific miRNAs and lncRNAs are involved in the regulation of the viruses' transcription, post-transcriptional regulation and latency. We further discuss treatment strategies using ncRNAs for HIV and HTLV long remission, reactivation or possible cure.
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Affiliation(s)
- Sergio P Alpuche-Lazcano
- Virus-Cell Interactions Laboratory, Lady Davis Institute for Medical Research, 3999, Côte Ste Catherine St., Montréal, QC, H3T 1E2, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC, H4A 3J1, Canada
- National Research Council Canada, Montréal, QC, H4P 2R2, Canada
| | - Robert J Scarborough
- Virus-Cell Interactions Laboratory, Lady Davis Institute for Medical Research, 3999, Côte Ste Catherine St., Montréal, QC, H3T 1E2, Canada
- Department of Microbiology and Immunology, McGill University, Montréal, QC, H3A 2B4, Canada
| | - Anne Gatignol
- Virus-Cell Interactions Laboratory, Lady Davis Institute for Medical Research, 3999, Côte Ste Catherine St., Montréal, QC, H3T 1E2, Canada.
- Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC, H4A 3J1, Canada.
- Department of Medicine, Division of Infectious Diseases, McGill University, Montréal, QC, H4A 3J1, Canada.
- Department of Microbiology and Immunology, McGill University, Montréal, QC, H3A 2B4, Canada.
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4
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Madhuravasal Krishnan J, Kong L, Karns R, Medvedovic M, Sherman KE, Blackard JT. The Synthetic Opioid Fentanyl Increases HIV Replication and Chemokine Co-Receptor Expression in Lymphocyte Cell Lines. Viruses 2023; 15:1027. [PMID: 37113007 PMCID: PMC10145664 DOI: 10.3390/v15041027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/11/2023] [Accepted: 04/15/2023] [Indexed: 04/29/2023] Open
Abstract
BACKGROUND In the United States, the illicit use of synthetic opioids such as fentanyl has led to a serious public health crisis. Synthetic opioids are known to enhance viral replication and to suppress immunologic responses, but their effects on HIV pathogenesis remain unclear. Thus, we examined the impact of fentanyl on HIV-susceptible and HIV-infected cell types. METHODS TZM-bl and HIV-infected lymphocyte cells were incubated with fentanyl at varying concentrations. Expression levels of the CXCR4 and CCR5 chemokine receptors and HIV p24 antigen were quantified with ELISA. HIV proviral DNA was quantified using SYBR RT-PCR. Cell viability was detected with the MTT assay. RNAseq was performed to characterize cellular gene regulation in the presence of fentanyl. RESULTS Fentanyl enhanced expression of both chemokine receptor levels in a dose-dependent manner in HIV-susceptible and infected cell lines. Similarly, fentanyl induced viral expression in HIV-exposed TZM-bl cells and in HIV-infected lymphocyte cell lines. Multiple genes associated with apoptosis, antiviral/interferon response, chemokine signaling, and NFκB signaling were differentially regulated. CONCLUSIONS Synthetic opioid fentanyl impacts HIV replication and chemokine co-receptor expression. Increased virus levels suggest that opioid use may increase the likelihood of transmission and accelerate disease progression.
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Affiliation(s)
- Janani Madhuravasal Krishnan
- Division of Digestive Diseases, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; (J.M.K.)
| | - Ling Kong
- Division of Digestive Diseases, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; (J.M.K.)
| | - Rebekah Karns
- Digestive Health Center, Cincinnati Children’s Hospital, Cincinnati, OH 45229, USA
| | - Mario Medvedovic
- Department of Environmental & Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Kenneth E. Sherman
- Division of Digestive Diseases, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; (J.M.K.)
- Center for Addiction Research, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Jason T. Blackard
- Division of Digestive Diseases, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; (J.M.K.)
- Center for Addiction Research, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
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5
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Crespo R, Rao S, Mahmoudi T. HibeRNAtion: HIV-1 RNA Metabolism and Viral Latency. Front Cell Infect Microbiol 2022; 12:855092. [PMID: 35774399 PMCID: PMC9237370 DOI: 10.3389/fcimb.2022.855092] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 05/10/2022] [Indexed: 01/12/2023] Open
Abstract
HIV-1 infection remains non-curative due to the latent reservoir, primarily a small pool of resting memory CD4+ T cells bearing replication-competent provirus. Pharmacological reversal of HIV-1 latency followed by intrinsic or extrinsic cell killing has been proposed as a promising strategy to target and eliminate HIV-1 viral reservoirs. Latency reversing agents have been extensively studied for their role in reactivating HIV-1 transcription in vivo, although no permanent reduction of the viral reservoir has been observed thus far. This is partly due to the complex nature of latency, which involves strict intrinsic regulation at multiple levels at transcription and RNA processing. Still, the molecular mechanisms that control HIV-1 latency establishment and maintenance have been almost exclusively studied in the context of chromatin remodeling, transcription initiation and elongation and most known LRAs target LTR-driven transcription by manipulating these. RNA metabolism is a largely understudies but critical mechanistic step in HIV-1 gene expression and latency. In this review we provide an update on current knowledge on the role of RNA processing mechanisms in viral gene expression and latency and speculate on the possible manipulation of these pathways as a therapeutic target for future cure studies.
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Affiliation(s)
- Raquel Crespo
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Shringar Rao
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Tokameh Mahmoudi
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Pathology, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Urology, Erasmus University Medical Center, Rotterdam, Netherlands
- *Correspondence: Tokameh Mahmoudi,
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6
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Chinniah R, Adimulam T, Nandlal L, Arumugam T, Ramsuran V. The Effect of miRNA Gene Regulation on HIV Disease. Front Genet 2022; 13:862642. [PMID: 35601502 PMCID: PMC9117004 DOI: 10.3389/fgene.2022.862642] [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: 01/26/2022] [Accepted: 04/13/2022] [Indexed: 12/24/2022] Open
Abstract
Over many years, research on HIV/AIDS has advanced with the introduction of HAART. Despite these advancements, significant gaps remain with respect to aspects in HIV life cycle, with specific attention to virus-host interactions. Investigating virus-host interactions may lead to the implementation of novel therapeutic strategies against HIV/AIDS. Notably, host gene silencing can be facilitated by cellular small non-coding RNAs such as microRNAs paving the way for epigenetic anti-viral therapies. Numerous studies have elucidated the importance of microRNAs in HIV pathogenesis. Some microRNAs can either promote viral infection, while others can be detrimental to viral replication. This is accomplished by targeting the HIV-proviral genome or by regulating host genes required for viral replication and immune responses. In this review, we report on 1) the direct association of microRNAs with HIV infection; 2) the indirect association of known human genetic factors with HIV infection; 3) the regulation of human genes by microRNAs in other diseases that can be explored experimentally to determine their effect on HIV-1 infection; and 4) therapeutic interactions of microRNA against HIV infection.
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Affiliation(s)
- Romona Chinniah
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Theolan Adimulam
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Louansha Nandlal
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Thilona Arumugam
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Veron Ramsuran
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
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7
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Lei L, Cheng A, Wang M, Jia R. The Influence of Host miRNA Binding to RNA Within RNA Viruses on Virus Multiplication. Front Cell Infect Microbiol 2022; 12:802149. [PMID: 35531344 PMCID: PMC9069554 DOI: 10.3389/fcimb.2022.802149] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
microRNAs (miRNAs), non-coding RNAs about 22 nt long, regulate the post-transcription expression of genes to influence many cellular processes. The expression of host miRNAs is affected by virus invasion, which also affects virus replication. Increasing evidence has demonstrated that miRNA influences RNA virus multiplication by binding directly to the RNA virus genome. Here, the knowledge relating to miRNAs’ relationships between host miRNAs and RNA viruses are discussed.
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Affiliation(s)
- Lin Lei
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Anchun Cheng
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Mingshu Wang
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Renyong Jia
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Renyong Jia,
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8
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Zucko D, Hayir A, Grinde K, Boris-Lawrie K. Circular RNA Profiles in Viremia and ART Suppression Predict Competing circRNA–miRNA–mRNA Networks Exclusive to HIV-1 Viremic Patients. Viruses 2022; 14:v14040683. [PMID: 35458413 PMCID: PMC9027527 DOI: 10.3390/v14040683] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/17/2022] [Accepted: 03/19/2022] [Indexed: 02/01/2023] Open
Abstract
Since the onset of the HIV-1/AIDS epidemic in 1981, 75 million people have been infected with the virus, and the disease remains a public health crisis worldwide. Circular RNAs (circRNAs) are derived from excised exons and introns during backsplicing, a form of alternative splicing. The relevance of unconventional, non-capped, and non-poly(A) transcripts to transcriptomics studies remains to be routinely investigated. Knowledge gaps to be filled are the interface between host-encoded circRNAs and viral replication in chronically progressed patients and upon treatment with antiviral drugs. We implemented a bioinformatic pipeline and repurpose publicly archived RNA sequence reads from the blood of 19 HIV-1-positive patients that previously compared transcriptomes during viremia and viremia suppression by antiretroviral therapy (ART). The in silico analysis identified viremic patients’ circRNA that became undetectable after ART. The circRNAs originated from a subset of host genes enriched in the HDAC biological pathway. These circRNAs and parental mRNAs held in common a small collection of miRNA response elements (MREs), some of which were present in HIV-1 mRNAs. The function of the MRE-containing target mRNA enriched the RNA polymerase II GO pathway. To visualize the interplay between individual circRNA–miRNA–target mRNA, important for HIV-1 and potentially other diseases, an Interactive Circos tool was developed to efficiently parse the intricately competing endogenous network of circRNA–miRNA–mRNA interactions originating from seven circRNA singled out in viremic versus non-viremic patients. The combined downregulation of the identified circRNAs warrants investigation as a novel antiviral targeting strategy.
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Affiliation(s)
- Dora Zucko
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA; (D.Z.); (A.H.)
| | - Abdullgadir Hayir
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA; (D.Z.); (A.H.)
- Department of Mathematics, Statistics and Computer Science, Macalester College, Saint Paul, MN 55105, USA;
| | - Kelsey Grinde
- Department of Mathematics, Statistics and Computer Science, Macalester College, Saint Paul, MN 55105, USA;
| | - Kathleen Boris-Lawrie
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA; (D.Z.); (A.H.)
- Correspondence:
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9
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Gibson MS, Noronha-Estima C, Gama-Carvalho M. Therapeutic Metabolic Reprograming Using microRNAs: From Cancer to HIV Infection. Genes (Basel) 2022; 13:273. [PMID: 35205318 PMCID: PMC8872267 DOI: 10.3390/genes13020273] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/27/2022] [Accepted: 01/27/2022] [Indexed: 02/04/2023] Open
Abstract
MicroRNAs (miRNAs) are crucial regulators of cellular processes, including metabolism. Attempts to use miRNAs as therapeutic agents are being explored in several areas, including the control of cancer progression. Recent evidence suggests fine tuning miRNA activity to reprogram tumor cell metabolism has enormous potential as an alternative treatment option. Indeed, cancer growth is known to be linked to profound metabolic changes. Likewise, the emerging field of immunometabolism is leading to a refined understanding of how immune cell proliferation and function is governed by glucose homeostasis. Different immune cell types are now known to have unique metabolic signatures that switch in response to a changing environment. T-cell subsets exhibit distinct metabolic profiles which underlie their alternative differentiation and phenotypic functions. Recent evidence shows that the susceptibility of CD4+ T-cells to HIV infection is intimately linked to their metabolic activity, with many of the metabolic features of HIV-1-infected cells resembling those found in tumor cells. In this review, we discuss the use of miRNA modulation to achieve metabolic reprogramming for cancer therapy and explore the idea that the same approach may serve as an effective mechanism to restrict HIV replication and eliminate infected cells.
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Affiliation(s)
| | | | - Margarida Gama-Carvalho
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal; (M.S.G.); (C.N.-E.)
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10
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Zhu L, Qiu C, Dai L, Zhang L, Feng M, Yang Y, Qiu C, Zhang A, Huang J, Wang Y, Wan Y, Zhao C, Wu H, Lyu J, Zhang X, Xu J. Hsa-miR-31 Governs T-Cell Homeostasis in HIV Protection via IFN-γ-Stat1-T-Bet Axis. Front Immunol 2021; 12:771279. [PMID: 34804062 PMCID: PMC8602903 DOI: 10.3389/fimmu.2021.771279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 10/21/2021] [Indexed: 11/20/2022] Open
Abstract
It remains poorly defined whether any human miRNAs play protective roles during HIV infection. Here, focusing on a unique cohort of HIV-infected former blood donors, we identified miR-31 (hsa-miR-31) by comparative miRNA profiling as the only miRNA inversely correlating with disease progression. We further validated this association in two prospective cohort studies. Despite conservation during evolution, hsa-miR-31, unlike its mouse counterpart (mmu-miR-31), was downregulated in human T cell upon activation. Our ex vivo studies showed that inhibiting miR-31 in naïve CD4+ T cells promoted a transcriptional profile with activation signature. Consistent with this skewing effect, miR-31 inhibition led to remarkably increased susceptibility to HIV infection. The suppressive nature of miR-31 in CD4+ T cell activation was pinpointed to its ability to decrease T-bet, the key molecule governing IFN-γ production and activation of CD4+ T cells, by directly targeting the upstream STAT1 transcriptional factor for downregulation, thus blunting Th1 response. Our results implicated miR-31 as a useful biomarker for tracking HIV disease progression and, by demonstrating its importance in tuning the activation of CD4+ T cells, suggested that miR-31 may play critical roles in other physiological contexts where the CD4+ T cell homeostasis needs to be deliberately controlled.
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Affiliation(s)
- Lingyan Zhu
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Chao Qiu
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Lili Dai
- Beijing You'an Hospital, Capital Medical University, Beijing, China
| | - Linxia Zhang
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Meiqi Feng
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yu Yang
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Chenli Qiu
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Anli Zhang
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jun Huang
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Ying Wang
- Department of AIDS/STD, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Ying Wan
- Biomedical Analysis Center, Army Medical University, Chongqing, China
| | - Chen Zhao
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Hao Wu
- Beijing You'an Hospital, Capital Medical University, Beijing, China
| | - Jianxin Lyu
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Xiaoyan Zhang
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jianqing Xu
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
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11
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Tamgue O, Mezajou CF, Ngongang NN, Kameni C, Ngum JA, Simo USF, Tatang FJ, Akami M, Ngono AN. Non-Coding RNAs in the Etiology and Control of Major and Neglected Human Tropical Diseases. Front Immunol 2021; 12:703936. [PMID: 34737736 PMCID: PMC8560798 DOI: 10.3389/fimmu.2021.703936] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 09/09/2021] [Indexed: 12/19/2022] Open
Abstract
Non-coding RNAs (ncRNAs) including microRNAs (miRs) and long non-coding RNAs (lncRNAs) have emerged as key regulators of gene expression in immune cells development and function. Their expression is altered in different physiological and disease conditions, hence making them attractive targets for the understanding of disease etiology and the development of adjunctive control strategies, especially within the current context of mitigated success of control measures deployed to eradicate these diseases. In this review, we summarize our current understanding of the role of ncRNAs in the etiology and control of major human tropical diseases including tuberculosis, HIV/AIDS and malaria, as well as neglected tropical diseases including leishmaniasis, African trypanosomiasis and leprosy. We highlight that several ncRNAs are involved at different stages of development of these diseases, for example miR-26-5p, miR-132-3p, miR-155-5p, miR-29-3p, miR-21-5p, miR-27b-3p, miR-99b-5p, miR-125-5p, miR-146a-5p, miR-223-3p, miR-20b-5p, miR-142-3p, miR-27a-5p, miR-144-5p, miR-889-5p and miR-582-5p in tuberculosis; miR-873, MALAT1, HEAL, LINC01426, LINC00173, NEAT1, NRON, GAS5 and lincRNA-p21 in HIV/AIDS; miR-451a, miR-let-7b and miR-106b in malaria; miR-210, miR-30A-5P, miR-294, miR-721 and lncRNA 7SL RNA in leishmaniasis; and miR-21, miR-181a, miR-146a in leprosy. We further report that several ncRNAs were investigated as diseases biomarkers and a number of them showed good potential for disease diagnosis, including miR-769-5p, miR-320a, miR-22-3p, miR-423-5p, miR-17-5p, miR-20b-5p and lncRNA LOC152742 in tuberculosis; miR-146b-5p, miR-223, miR-150, miR-16, miR-191 and lncRNA NEAT1 in HIV/AIDS; miR-451 and miR-16 in malaria; miR-361-3p, miR-193b, miR-671, lncRNA 7SL in leishmaniasis; miR-101, miR-196b, miR-27b and miR-29c in leprosy. Furthermore, some ncRNAs have emerged as potential therapeutic targets, some of which include lncRNAs NEAT1, NEAT2 and lnr6RNA, 152742 in tuberculosis; MALAT1, HEAL, SAF, lincRNA-p21, NEAT1, GAS5, NRON, LINC00173 in HIV/AIDS; miRNA-146a in malaria. Finally, miR-135 and miR-126 were proposed as potential targets for the development of therapeutic vaccine against leishmaniasis. We also identify and discuss knowledge gaps that warrant for increased research work. These include investigation of the role of ncRNAs in the etiology of African trypanosomiasis and the assessment of the diagnostic potential of ncRNAs for malaria, and African trypanosomiasis. The potential targeting of ncRNAs for adjunctive therapy against tuberculosis, leishmaniasis, African trypanosomiasis and leprosy, as well as their targeting in vaccine development against tuberculosis, HIV/AIDS, malaria, African trypanosomiasis and leprosy are also new avenues to explore.
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Affiliation(s)
- Ousman Tamgue
- Department of Biochemistry, Faculty of Sciences, University of Douala, Douala, Cameroon
| | | | | | - Charleine Kameni
- Department of Biochemistry, Faculty of Sciences, University of Douala, Douala, Cameroon
| | - Jubilate Afuoti Ngum
- Department of Biochemistry, Faculty of Sciences, University of Douala, Douala, Cameroon
| | | | - Fabrice Junior Tatang
- Department of Biochemistry, Faculty of Sciences, University of Douala, Douala, Cameroon
| | - Mazarin Akami
- Department of Biochemistry, Faculty of Sciences, University of Douala, Douala, Cameroon
| | - Annie Ngane Ngono
- Department of Biochemistry, Faculty of Sciences, University of Douala, Douala, Cameroon
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12
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Royo-Rubio E, Rodríguez-Izquierdo I, Moreno-Domene M, Lozano-Cruz T, de la Mata FJ, Gómez R, Muñoz-Fernández MA, Jiménez JL. Promising PEGylated cationic dendrimers for delivery of miRNAs as a possible therapy against HIV-1 infection. J Nanobiotechnology 2021; 19:158. [PMID: 34049570 PMCID: PMC8161934 DOI: 10.1186/s12951-021-00899-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 05/18/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The appearance of resistance against new treatments and the fact that HIV-1 can infect various cell types and develop reservoirs and sanctuaries makes it necessary to develop new therapeutic approaches to overcome those failures. RESULTS Studies of cytotoxicity, genotoxicity, complexes formation, stability, resistance, release and particle size distribution confirmed that G2-SN15-PEG, G3-SN31-PEG, G2-SN15-PEG-FITC and G3-SN31-PEG-FITC dendrimers can form complexes with miRNAs being biocompatible, stable and conferring protection to these nucleic acids. Confocal microscopy and flow cytometry showed effective delivery of these four dendrimers into the target cells, confirming their applicability as delivery systems. Dendriplexes formed with the dendrimers and miRNAs significantly inhibited HIV-1 infection in PBMCs. CONCLUSIONS These dendrimers are efficient delivery systems for miRNAs and they specifically and significantly improved the anti-R5-HIV-1 activity of these RNA molecules.
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Affiliation(s)
- E Royo-Rubio
- Laboratorio InmunoBiología Molecular, Hospital General Universitario Gregorio Marañón (HGUGM), Instituto Investigación Sanitaria Gregorio Marañón (IiSGM), Spanish HIV HGM BioBanco, Madrid, Spain
- Plataforma de Laboratorio (Inmunología), HGUGM, IiSGM, Spanish HIV HGM BioBank, Madrid, Spain
| | - I Rodríguez-Izquierdo
- Laboratorio InmunoBiología Molecular, Hospital General Universitario Gregorio Marañón (HGUGM), Instituto Investigación Sanitaria Gregorio Marañón (IiSGM), Spanish HIV HGM BioBanco, Madrid, Spain
- Plataforma de Laboratorio (Inmunología), HGUGM, IiSGM, Spanish HIV HGM BioBank, Madrid, Spain
| | - M Moreno-Domene
- Laboratorio Dosimetría Biológica, HGUGM, IiSGM, Madrid, Spain
| | - T Lozano-Cruz
- Departmento Química Orgánica Y Química Inorgánica E Instituto de Investigación Química "Andrés M. del Río″ (IQAR), Universidad de Alcalá (IRYCIS), Campus Universitario, 28871, Madrid, Spain
- Networking Research Center On Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN, Madrid, Spain
| | - F J de la Mata
- Departmento Química Orgánica Y Química Inorgánica E Instituto de Investigación Química "Andrés M. del Río″ (IQAR), Universidad de Alcalá (IRYCIS), Campus Universitario, 28871, Madrid, Spain
- Networking Research Center On Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN, Madrid, Spain
| | - R Gómez
- Departmento Química Orgánica Y Química Inorgánica E Instituto de Investigación Química "Andrés M. del Río″ (IQAR), Universidad de Alcalá (IRYCIS), Campus Universitario, 28871, Madrid, Spain
- Networking Research Center On Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN, Madrid, Spain
| | - M A Muñoz-Fernández
- Laboratorio InmunoBiología Molecular, Hospital General Universitario Gregorio Marañón (HGUGM), Instituto Investigación Sanitaria Gregorio Marañón (IiSGM), Spanish HIV HGM BioBanco, Madrid, Spain.
| | - J L Jiménez
- Plataforma de Laboratorio (Inmunología), HGUGM, IiSGM, Spanish HIV HGM BioBank, Madrid, Spain.
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13
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Diurnal Variation of Plasma Extracellular Vesicle Is Disrupted in People Living with HIV. Pathogens 2021; 10:pathogens10050518. [PMID: 33923310 PMCID: PMC8145918 DOI: 10.3390/pathogens10050518] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/10/2021] [Accepted: 04/19/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Several types of extracellular vesicles (EVs) secreted by various immune and non-immune cells are present in the human plasma. We previously demonstrated that EV abundance and microRNA content change in pathological conditions, such as HIV infection. Here, we investigated daily variations of large and small EVs, in terms of abundance and microRNA contents in people living with HIV (PLWH) receiving antiretroviral therapy (HIV+ART) and uninfected controls (HIV-). METHODS Venous blood samples from n = 10 HIV+ART and n = 10 HIV- participants were collected at 10:00 and 22:00 the same day. Large and small plasma EVs were purified, counted, and the mature miRNAs miR-29a, miR-29b, miR-92, miR-155, and miR-223 copies were measured by RT-PCR. RESULTS Large EVs were significantly bigger in the plasma collected at 10:00 versus 22:00 in both groups. There was a significant day-night increase in the quantity of 5 miRNAs in HIV- large EVs. In HIV+ART, only miR-155 daily variation has been observed in large EVs. Finally, EV-miRNA content permits to distinguish HIV- to HIV+ART in multivariate analysis. CONCLUSION These results point that plasma EV amount and microRNA contents are under daily variation in HIV- people. This new dynamic measure is disrupted in PLWH despite viral-suppressive ART. This study highlights a significant difference concerning EV abundance and their content measured at 22:00 between both groups. Therefore, the time of blood collection must be considered in the future for the EV as biomarkers.
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14
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Bazié WW, Boucher J, Vitry J, Goyer B, Routy JP, Tremblay C, Trottier S, Jenabian MA, Provost P, Alary M, Gilbert C. Plasma Extracellular Vesicle Subtypes May be Useful as Potential Biomarkers of Immune Activation in People With HIV. Pathog Immun 2021; 6:1-28. [PMID: 33987483 PMCID: PMC8109236 DOI: 10.20411/pai.v6i1.384] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 11/02/2020] [Indexed: 12/15/2022] Open
Abstract
Background Extracellular vesicles (EVs) are intercellular messengers with epigenetic potential since they can shuttle microRNA (miRNA). EVs and miRNA play a role in human immunodeficiency virus (HIV) infection immunopathogenesis. Chronic immune activation and systemic inflammation during HIV infection despite effective antiretroviral therapy (ART) are associated with non-acquired immunodeficiency syndrome (AIDS) comorbidities in people living with HIV (PLWH). Analysis of plasma EVs and their miRNA content may be useful as immune activation or inflammatory biomarkers in PLWH receiving ART. In this study, we hypothesized that the number, size, and miRNA of large and small EVs could reflect immune activation associated with an elevated CD8 T-cell count or a low CD4/CD8 ratio in PLWH. Methods Plasma EVs subtype purified from PLWH and uninfected controls were sized using dynamic light scattering and quantified using flow cytometry and acetylcholine esterase (AChE) activity. Expression of mature miRNAs miR-92, miR-155, miR-223 was measured by quantitative reverse-transcriptase polymerase chain reaction in EVs and leucocytes. Results HIV infection induces increased production of small EVs in plasma. EV subtypes were differentially enriched in miR-92, miR-155, and miR-223. Positive correlations between CD8 T-cell count and large EVs abundance and small EVs AChE activity were observed. CD4/CD8 ratio was negatively correlated with small EV AChE activity, and miRNA-155 level per small EV was negatively correlated with CD8 T-cell count. Conclusions These findings suggest that quantifying large or small EVs and profiling miRNA content per EV might provide new functional biomarkers of immune activation and inflammation.
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Affiliation(s)
- Wilfried Wenceslas Bazié
- Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada.,Département de microbiologie-infectiologie et d'immunologie, Faculté de médecine, Université Laval, Québec, QC, Canada.,Programme de recherche sur les maladies infectieuses, Centre Muraz, Institut National de Santé Publique, Bobo-Dioulasso, Burkina Faso
| | - Julien Boucher
- Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada.,Département de microbiologie-infectiologie et d'immunologie, Faculté de médecine, Université Laval, Québec, QC, Canada
| | - Julien Vitry
- Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada.,Département de microbiologie-infectiologie et d'immunologie, Faculté de médecine, Université Laval, Québec, QC, Canada
| | - Benjamin Goyer
- Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada
| | - Jean Pierre Routy
- Chronic Viral Illness Service and Division of Hematology, McGill University Health Centre, Montreal, QC, Canada.,Infectious Diseases and Immunity in Global Health Program, Research Institute, McGill University Health Centre, Montréal, QC, Canada
| | - Cécile Tremblay
- Centre de recherche du Centre Hospitalier de l'Université de Montréal, Montréal, QC, Canada.,Département de microbiologie, infectiologie et immunologie, Faculté de médecine, Université de Montréal, Montréal, QC, Canada
| | - Sylvie Trottier
- Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada.,Département de microbiologie-infectiologie et d'immunologie, Faculté de médecine, Université Laval, Québec, QC, Canada
| | - Mohammad-Ali Jenabian
- Département des sciences biologiques, Université de Québec à Montréal (UQAM), Montréal, QC, Canada
| | - Patrick Provost
- Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada.,Département de microbiologie-infectiologie et d'immunologie, Faculté de médecine, Université Laval, Québec, QC, Canada
| | - Michel Alary
- Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada.,Département de médecine sociale et préventive, Faculté de médecine, Université de Laval, Québec, C, Canada.,Institut national de santé publique du Québec, Québec, QC, Canada
| | - Caroline Gilbert
- Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada.,Département de microbiologie-infectiologie et d'immunologie, Faculté de médecine, Université Laval, Québec, QC, Canada
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15
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Imrat, Labala RK, Velhal S, Bhagat S, Patel V, Jeyaram K. Small double-stranded RNA with anti-HIV activity abundantly produced by Bacillus subtilis MTCC5480 isolated from fermented soybean. Int J Biol Macromol 2020; 161:828-835. [PMID: 32553954 DOI: 10.1016/j.ijbiomac.2020.06.112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/10/2020] [Accepted: 06/11/2020] [Indexed: 12/27/2022]
Abstract
Anti-viral RNA therapy is on high demand nowadays due to the emergence of several new viral infections. The small non-coding regulatory RNAs (dsRNA) from the microbial sources are not yet explored for anti-viral activity. In this study, we assessed the anti-HIV activity of the small dsRNA produced by 12 different microbial species isolated from naturally fermented foods of North-East India. For this, we selectively extracted the dsRNA from the microbial culture, confirmed its double-stranded nature by immunoblotting, and deep sequenced the cDNA library using Illumina platform. Further, we used conventional algorithms to predict the potential targets of the dsRNA sequences within the 3'-UTR region of HIV-1. A small dsRNA fragment with 34 bases in size with a sequence of 3'-UUGGUACACGAGAUGGUUCGACUCGAUGAAGGGC-5' produced abundantly (9.17% of the total dsRNA fraction) by Bacillus subtilis MTCC5480 showed a much higher base complementarity values than previously reported miRNAs analysed against HIV-1. We separated the dsRNA fraction and validated the anti-HIV activity against human peripheral blood mononuclear cells (PBMC) infected with JRCSF strain of HIV-1 virus and the EC50 value ranges from 0.2-0.3 μM. This small dsRNA abundantly produced by B. subtilis could be studied further for its application as an anti-viral therapeutic agent.
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Affiliation(s)
- Imrat
- Microbial Resources Division, Institute of Bioresources and Sustainable Development (IBSD), Takyelpat Institutional Area, Imphal 795001, Manipur, India; Department of Biotechnology, Gauhati University, Guwahati 781014, Assam, India
| | - Rajendra Kumar Labala
- Distributed Information Sub-Centre (DISC), Institute of Bioresources and Sustainable Development (IBSD), Takyelpat Institutional Area, Imphal 795001, Manipur, India
| | - Shilpa Velhal
- Department of Biochemistry and Virology, National Institute for Research in Reproductive Health (ICMR), Mumbai 400012, India
| | - Sharad Bhagat
- Department of Biochemistry and Virology, National Institute for Research in Reproductive Health (ICMR), Mumbai 400012, India
| | - Vainav Patel
- Department of Biochemistry and Virology, National Institute for Research in Reproductive Health (ICMR), Mumbai 400012, India
| | - Kumaraswamy Jeyaram
- Microbial Resources Division, Institute of Bioresources and Sustainable Development (IBSD), Takyelpat Institutional Area, Imphal 795001, Manipur, India; Institute of Bioresources and Sustainable Development (IBSD), Mizoram Center, Nursery Veng, Khatla, Aizawl 796005, Mizoram, India.
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16
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Ayala-Suárez R, Díez-Fuertes F, Calonge E, De La Torre Tarazona HE, Gracia-Ruíz de Alda M, Capa L, Alcamí J. Insight in miRNome of Long-Term Non-Progressors and Elite Controllers Exposes Potential RNAi Role in Restraining HIV-1 Infection. J Clin Med 2020; 9:jcm9082452. [PMID: 32751854 PMCID: PMC7464121 DOI: 10.3390/jcm9082452] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/17/2020] [Accepted: 07/29/2020] [Indexed: 12/14/2022] Open
Abstract
Long-term non-progressors (LTNP) and elite controllers (EC) represent spontaneous natural models of efficient HIV-1 response in the absence of treatment. The main purposes of this work are to describe the miRNome of HIV-1 infected patients with different extreme phenotypes and identify potentially altered pathways regulated by differentially expressed (DE) miRNAs. The miRNomes from peripheral blood mononuclear cells (PBMCs) of dual phenotype EC-LTNP or LTNP with detectable viremia and HIV-infected patients with typical progression before and after treatment, were obtained through miRNA-Seq and compared among them. The administration of treatment produces 18 DE miRNAs in typical progressors. LTNP condition shows 14 DE miRNA when compared to typical progressors, allowing LTNP phenotype differentiation. A set of four miRNAs: miR-144-3p, miR-18a-5p, miR-451a, and miR-324 is strongly downregulated in LTNP and related to protein regulation as AKT, mTOR, ERK or IKK, involved in immune response pathways. Deregulation of 28 miRNA is observed between EC-LTNP and viremic-LTNP, including previously described anti-HIV miRNAs: miR-29a, associated with LTNP phenotype, and miR-155, targeting different pre-integration complexes such as ADAM10 and TNPO3. A holistic perspective of the changes observed in the miRNome of patients with different phenotypes of HIV-control and non-progression is provided.
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Affiliation(s)
- Rubén Ayala-Suárez
- AIDS Immunopathology Unit, National Center for Microbiology, Institute of Health Carlos III, Majadahonda, 28220 Madrid, Spain; (R.A.-S.); (E.C.); (H.E.D.L.T.T.); (L.C.)
| | - Francisco Díez-Fuertes
- AIDS Immunopathology Unit, National Center for Microbiology, Institute of Health Carlos III, Majadahonda, 28220 Madrid, Spain; (R.A.-S.); (E.C.); (H.E.D.L.T.T.); (L.C.)
- HIV Unit, Hospital Clínic de Barcelona, 08036 Barcelona, Spain
- Correspondence: (F.D.-F.); (J.A.); Tel.: +34-91-822-3234 (F.D.-F.); +34-91-822-3943 (J.A.)
| | - Esther Calonge
- AIDS Immunopathology Unit, National Center for Microbiology, Institute of Health Carlos III, Majadahonda, 28220 Madrid, Spain; (R.A.-S.); (E.C.); (H.E.D.L.T.T.); (L.C.)
| | - Humberto Erick De La Torre Tarazona
- AIDS Immunopathology Unit, National Center for Microbiology, Institute of Health Carlos III, Majadahonda, 28220 Madrid, Spain; (R.A.-S.); (E.C.); (H.E.D.L.T.T.); (L.C.)
| | - María Gracia-Ruíz de Alda
- Sección de Enfermedades Infecciosas, Medicina Interna, Complejo Hospitalario de Navarra, 31008 Pamplona, Spain;
| | - Laura Capa
- AIDS Immunopathology Unit, National Center for Microbiology, Institute of Health Carlos III, Majadahonda, 28220 Madrid, Spain; (R.A.-S.); (E.C.); (H.E.D.L.T.T.); (L.C.)
| | - José Alcamí
- AIDS Immunopathology Unit, National Center for Microbiology, Institute of Health Carlos III, Majadahonda, 28220 Madrid, Spain; (R.A.-S.); (E.C.); (H.E.D.L.T.T.); (L.C.)
- HIV Unit, Hospital Clínic de Barcelona, 08036 Barcelona, Spain
- Correspondence: (F.D.-F.); (J.A.); Tel.: +34-91-822-3234 (F.D.-F.); +34-91-822-3943 (J.A.)
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17
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Nahand JS, Bokharaei-Salim F, Karimzadeh M, Moghoofei M, Karampoor S, Mirzaei HR, Tbibzadeh A, Jafari A, Ghaderi A, Asemi Z, Mirzaei H, Hamblin MR. MicroRNAs and exosomes: key players in HIV pathogenesis. HIV Med 2020; 21:246-278. [PMID: 31756034 PMCID: PMC7069804 DOI: 10.1111/hiv.12822] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2019] [Indexed: 12/29/2022]
Abstract
OBJECTIVES HIV infection is well known to cause impairment of the human immune system, and until recently was a leading cause of death. It has been shown that T lymphocytes are the main targets of HIV. The virus inactivates T lymphocytes by interfering with a wide range of cellular and molecular targets, leading to suppression of the immune system. The objective of this review is to investigate to what extent microRNAs (miRNAs) are involved in HIV pathogenesis. METHODS The scientific literature (Pubmed and Google scholar) for the period 1988-2019 was searched. RESULTS Mounting evidence has revealed that miRNAs are involved in viral replication and immune response, whether by direct targeting of viral transcripts or through indirect modulation of virus-related host pathways. In addition, exosomes have been found to act as nanoscale carriers involved in HIV pathogenesis. These nanovehicles target their cargos (i.e. DNA, RNA, viral proteins and miRNAs) leading to alteration of the behaviour of recipient cells. CONCLUSIONS miRNAs and exosomes are important players in HIV pathogenesis. Additionally, there are potential diagnostic applications of miRNAs as biomarkers in HIV infection.
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Affiliation(s)
- Javid Sadri Nahand
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Farah Bokharaei-Salim
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Karimzadeh
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohsen Moghoofei
- Department of Microbiology, Faculty of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sajad Karampoor
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hamid Reza Mirzaei
- Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Tbibzadeh
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Amir Jafari
- Department of Medical Nanotechnology, Faculty of Advanced Technology in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Amir Ghaderi
- Department of Addiction Studies, School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Zatollah Asemi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, I.R. Iran
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, I.R. Iran
| | - Michael R. Hamblin
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, 40 Blossom Street, Boston, MA, 02114, USA
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18
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Fenizia C, Saulle I, Clerici M, Biasin M. Genetic and epigenetic regulation of natural resistance to HIV-1 infection: new approaches to unveil the HESN secret. Expert Rev Clin Immunol 2020; 16:429-445. [PMID: 32085689 DOI: 10.1080/1744666x.2020.1732820] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Introduction: Since the identification of HIV, several studies reported the unusual case of small groups of subjects showing natural resistance to HIV infection. These subjects are referred to as HIV-1-exposed seronegative (HESN) individuals and include people located in different areas, with diverse ethnic backgrounds and routes of exposure. The mechanism/s responsible for protection from infection in HESN individuals are basically indefinite and most likely are multifactorial.Areas covered: Host factors, including genetic background as well as natural and acquired immunity, have all been associated with this phenomenon. Recently, epigenetic factors have been investigated as possible determinants of reduced susceptibility to HIV infection. With the advent of the OMICS era, the availability of techniques such as GWAS, RNAseq, and exome-sequencing in both bulk cell populations and single cells will likely lead to great strides in the understanding of the HESN mystery.Expert opinion: The employment of increasingly sophisticated techniques is allowing the gathering of enormous amounts of data. The integration of such information will provide important hints that could lead to the identification of viral and host correlates of protection against HIV infection, allowing the development of more effective preventative and therapeutic regimens.
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Affiliation(s)
- Claudio Fenizia
- Department of Physiopathology and Transplantation, University of Milan, Milan, Italy
| | - Irma Saulle
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Milan, Italy
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, Milan, Italy.,Don C. Gnocchi Foundation ONLUS, IRCCS, Milan, Italy
| | - Mara Biasin
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Milan, Italy
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19
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Li CW, Chen BS. Investigating HIV-Human Interaction Networks to Unravel Pathogenic Mechanism for Drug Discovery: A Systems Biology Approach. Curr HIV Res 2019; 16:77-95. [PMID: 29468972 DOI: 10.2174/1570162x16666180219155324] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 01/18/2018] [Accepted: 02/14/2018] [Indexed: 02/08/2023]
Abstract
BACKGROUND Two big issues in the study of pathogens are determining how pathogens infect hosts and how the host defends itself against infection. Therefore, investigating host-pathogen interactions is important for understanding pathogenicity and host defensive mechanisms and treating infections. METHODS In this study, we used omics data, including time-course data from high-throughput sequencing, real-time polymerase chain reaction, and human microRNA (miRNA) and protein-protein interaction to construct an interspecies protein-protein and miRNA interaction (PPMI) network of human CD4+ T cells during HIV-1 infection through system modeling and identification. RESULTS By applying a functional annotation tool to the identified PPMI network at each stage of HIV infection, we found that repressions of three miRNAs, miR-140-5p, miR-320a, and miR-941, are involved in the development of autoimmune disorders, tumor proliferation, and the pathogenesis of T cells at the reverse transcription stage. Repressions of miR-331-3p and miR-320a are involved in HIV-1 replication, replicative spread, anti-apoptosis, cell proliferation, and dysregulation of cell cycle control at the integration/replication stage. Repression of miR-341-5p is involved in carcinogenesis at the late stage of HIV-1 infection. CONCLUSION By investigating the common core proteins and changes in specific proteins in the PPMI network between the stages of HIV-1 infection, we obtained pathogenic insights into the functional core modules and identified potential drug combinations for treating patients with HIV-1 infection, including thalidomide, oxaprozin, and metformin, at the reverse transcription stage; quercetin, nifedipine, and fenbendazole, at the integration/replication stage; and staurosporine, quercetin, prednisolone, and flufenamic acid, at the late stage.
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Affiliation(s)
- Cheng-Wei Li
- Laboratory of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Bor-Sen Chen
- Laboratory of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, Taiwan
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20
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Yan Y, Acevedo M, Mignacca L, Desjardins P, Scott N, Imane R, Quenneville J, Robitaille J, Feghaly A, Gagnon E, Ferbeyre G, Major F. The sequence features that define efficient and specific hAGO2-dependent miRNA silencing guides. Nucleic Acids Res 2018; 46:8181-8196. [PMID: 30239883 PMCID: PMC6144789 DOI: 10.1093/nar/gky546] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 05/10/2018] [Accepted: 06/05/2018] [Indexed: 01/18/2023] Open
Abstract
MicroRNAs (miRNAs) are ribonucleic acids (RNAs) of ∼21 nucleotides that interfere with the translation of messenger RNAs (mRNAs) and play significant roles in development and diseases. In bilaterian animals, the specificity of miRNA targeting is determined by sequence complementarity involving the seed. However, the role of the remaining nucleotides (non-seed) is only vaguely defined, impacting negatively on our ability to efficiently use miRNAs exogenously to control gene expression. Here, using reporter assays, we deciphered the role of the base pairs formed between the non-seed region and target mRNA. We used molecular modeling to reveal that this mechanism corresponds to the formation of base pairs mediated by ordered motions of the miRNA-induced silencing complex. Subsequently, we developed an algorithm based on this distinctive recognition to predict from sequence the levels of mRNA downregulation with high accuracy (r2 > 0.5, P-value < 10-12). Overall, our discovery improves the design of miRNA-guide sequences used to simultaneously downregulate the expression of multiple predetermined target genes.
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Affiliation(s)
- Yifei Yan
- Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada
- Institut de recherche en immunologie et en cancérologie (IRIC), Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Mariana Acevedo
- Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Lian Mignacca
- Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Philippe Desjardins
- Institut de recherche en immunologie et en cancérologie (IRIC), Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Nicolas Scott
- Institut de recherche en immunologie et en cancérologie (IRIC), Université de Montréal, Montréal, Québec H3C 3J7, Canada
- Département d’informatique et de recherche opérationnelle, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Roqaya Imane
- Institut de recherche en immunologie et en cancérologie (IRIC), Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Jordan Quenneville
- Institut de recherche en immunologie et en cancérologie (IRIC), Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Julie Robitaille
- Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada
- Institut de recherche en immunologie et en cancérologie (IRIC), Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Albert Feghaly
- Institut de recherche en immunologie et en cancérologie (IRIC), Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Etienne Gagnon
- Institut de recherche en immunologie et en cancérologie (IRIC), Université de Montréal, Montréal, Québec H3C 3J7, Canada
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Gerardo Ferbeyre
- Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - François Major
- Institut de recherche en immunologie et en cancérologie (IRIC), Université de Montréal, Montréal, Québec H3C 3J7, Canada
- Département d’informatique et de recherche opérationnelle, Université de Montréal, Montréal, Québec H3C 3J7, Canada
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Jadideslam G, Ansarin K, Sakhinia E, Alipour S, Pouremamali F, Khabbazi A. The MicroRNA-326: Autoimmune diseases, diagnostic biomarker, and therapeutic target. J Cell Physiol 2018; 233:9209-9222. [PMID: 30078204 DOI: 10.1002/jcp.26949] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 06/13/2018] [Indexed: 12/21/2022]
Abstract
MicroRNAs (miRNAs) are uniquely regulated in healthy, inflamed, activated, cancerous, or other cells and tissues of a pathological state. Many studies confirm that immune dysregulation and autoimmune diseases with inflammation are correlated with various miRNA expression changes in targeted tissues and cells in innate or adaptive immunity. In this review, we will explain the history and classification of epigenetic changes. Next, we will describe the role of miRNAs changes, especially mir-326 in autoimmunity, autoinflammatory, and other pathological conditions. A systematic search of MEDLINE, Embase, and Cochrane Library was presented for all related studies from 1899 to 2017 with restrictions in the English language. In recent years, researchers have concentrated on mostly those roles of miRNA that are correlated with the inflammatory and anti-inflammatory process. Latest studies have proposed a fundamental pathogenic role in cancers and autoinflammatory diseases. Studies have described the role of microRNAs in autoimmunity and autoinflammatory diseases, cancers, and so on. The miRNA-326 expression plays a significant role in autoimmune and other types of diseases.
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Affiliation(s)
- Golamreza Jadideslam
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.,Connective Tissue Diseases Research Center, Tabriz University of Medical Science, Iran.,Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Iran
| | - Khalil Ansarin
- Tuberculosis and Lung Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ebrahim Sakhinia
- Connective Tissue Diseases Research Center, Tabriz University of Medical Science, Iran.,Department of Medical Genetics, Faculty of Medicine and Tabriz Genetic Analysis Centre (TGAC), Tabriz University of Medical Sciences, Tabriz, Iran
| | - Shahriar Alipour
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.,Connective Tissue Diseases Research Center, Tabriz University of Medical Science, Iran
| | - Farhad Pouremamali
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Alireza Khabbazi
- Connective Tissue Diseases Research Center, Tabriz University of Medical Science, Iran
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22
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Lnc-ISG20 Inhibits Influenza A Virus Replication by Enhancing ISG20 Expression. J Virol 2018; 92:JVI.00539-18. [PMID: 29899085 DOI: 10.1128/jvi.00539-18] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 05/31/2018] [Indexed: 02/06/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are involved in many aspects of cellular processes, including the antiviral immune response. To identify influenza A virus (IAV)-related lncRNAs, we performed RNA deep sequencing to compare the profiles of lncRNAs in A549 and HEK293T cells with or without IAV infection. We identified an IAV-upregulated lncRNA named lnc-ISG20 because it shares most of its sequence with ISG20. We found that lnc-ISG20 is an interferon-stimulated gene similar to ISG20. Overexpression of lnc-ISG20 inhibited IAV replication, while lnc-ISG20 knockdown favored viral replication, suggesting that lnc-ISG20 is inhibitory to IAV replication. Further study indicated that overexpression of lnc-ISG20 enhances ISG20 protein levels, while knockdown of lnc-ISG20 reduces ISG20 protein levels in A549 cells induced with poly(I·C) and Sendai virus. We demonstrated that lnc-ISG20 inhibits IAV replication in an ISG20-dependent manner. As lnc-ISG20 did not affect the mRNA level of ISG20, we postulated that lnc-ISG20 may function as endogenous RNA competing with ISG20 to enhance its translation. Indeed, we identified that microRNA 326 (miR-326) is a mutual microRNA for both ISG20 and lnc-ISG20 that targets the 3' untranslated region of ISG20 mRNA to inhibit its translation. We confirmed that lnc-ISG20 can bind miR-326, which in turn decreased the amount of miR-326 bound to ISG20 mRNA. In conclusion, we identified that the IAV-upregulated lnc-ISG20 is a novel interferon-stimulated gene that elicits its inhibitory effect on IAV replication by enhancing ISG20 expression. We demonstrated that lnc-ISG20 functions as a competitive endogenous RNA to bind miR-326 to reduce its inhibition of ISG20 translation. Our results revealed the mechanism by which lnc-ISG20 inhibits IAV replication.IMPORTANCE The replication of influenza A virus is regulated by host factors. However, the mechanisms by which lncRNAs regulate IAV infection are not well understood. We identified that lnc-ISG20 is upregulated during IAV infection and is also an interferon-stimulated gene. We demonstrated that lnc-ISG20 can enhance ISG20 expression, which in turn inhibits IAV replication. Our studies indicate that lnc-ISG20 functions as a competing endogenous RNA that binds miR-326 and reduces its inhibitory effect on ISG20. Taken together, our findings reveal the mechanistic details of lnc-ISG20 negatively regulating IAV replication. These findings indicate that lnc-ISG20 plays an important role during the host antiviral immune response.
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Are microRNAs Important Players in HIV-1 Infection? An Update. Viruses 2018; 10:v10030110. [PMID: 29510515 PMCID: PMC5869503 DOI: 10.3390/v10030110] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Revised: 02/21/2018] [Accepted: 02/25/2018] [Indexed: 12/15/2022] Open
Abstract
HIV-1 has already claimed over 35 million human lives globally. No curative treatments are currently available, and the only treatment option for over 36 million people currently living with HIV/AIDS are antiretroviral drugs that disrupt the function of virus-encoded proteins. However, such virus-targeted therapeutic strategies are constrained by the ability of the virus to develop drug-resistance. Despite major advances in HIV/AIDS research over the years, substantial knowledge gaps exist in many aspects of HIV-1 replication, especially its interaction with the host. Hence, understanding the mechanistic details of virus–host interactions may lead to novel therapeutic strategies for the prevention and/or management of HIV/AIDS. Notably, unprecedented progress in deciphering host gene silencing processes mediated by several classes of cellular small non-coding RNAs (sncRNA) presents a promising and timely opportunity for developing non-traditional antiviral therapeutic strategies. Cellular microRNAs (miRNA) belong to one such important class of sncRNAs that regulate protein synthesis. Evidence is mounting that cellular miRNAs play important roles in viral replication, either usurped by the virus to promote its replication or employed by the host to control viral infection by directly targeting the viral genome or by targeting cellular proteins required for productive virus replication. In this review, we summarize the findings to date on the role of miRNAs in HIV-1 biology.
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24
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Zhang X, Ma X, Jing S, Zhang H, Zhang Y. Non-coding RNAs and retroviruses. Retrovirology 2018; 15:20. [PMID: 29426337 PMCID: PMC5807749 DOI: 10.1186/s12977-018-0403-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 01/31/2018] [Indexed: 02/06/2023] Open
Abstract
Retroviruses can cause severe diseases such as cancer and acquired immunodeficiency syndrome. A unique feature in the life cycle of retroviruses is that their RNA genome is reverse transcribed into double-stranded DNA, which then integrates into the host genome to exploit the host machinery for their benefits. The metazoan genome encodes numerous non-coding RNAs (ncRNA), which act as key regulators in essential cellular processes such as antiviral response. The development of next-generation sequencing technology has greatly accelerated the detection of ncRNAs from viruses and their hosts. ncRNAs have been shown to play important roles in the retroviral life cycle and virus–host interactions. Here, we review recent advances in ncRNA studies with special focus on those have changed our understanding of retroviruses or provided novel strategies to treat retrovirus-related diseases. Many ncRNAs such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are involved in the late phase of the retroviral life cycle. However, their roles in the early phase of viral replication merit further investigations.
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Affiliation(s)
- Xu Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China.,Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Xiancai Ma
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China.,Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Shuliang Jing
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China.,Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Hui Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China. .,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China. .,Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China.
| | - Yijun Zhang
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, 06520, USA.
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Multiple Inhibitory Factors Act in the Late Phase of HIV-1 Replication: a Systematic Review of the Literature. Microbiol Mol Biol Rev 2018; 82:82/1/e00051-17. [PMID: 29321222 DOI: 10.1128/mmbr.00051-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The use of lentiviral vectors for therapeutic purposes has shown promising results in clinical trials. The ability to produce a clinical-grade vector at high yields remains a critical issue. One possible obstacle could be cellular factors known to inhibit human immunodeficiency virus (HIV). To date, five HIV restriction factors have been identified, although it is likely that more factors are involved in the complex HIV-cell interaction. Inhibitory factors that have an adverse effect but do not abolish virus production are much less well described. Therefore, a gap exists in the knowledge of inhibitory factors acting late in the HIV life cycle (from transcription to infection of a new cell), which are relevant to the lentiviral vector production process. The objective was to review the HIV literature to identify cellular factors previously implicated as inhibitors of the late stages of lentivirus production. A search for publications was conducted on MEDLINE via the PubMed interface, using the keyword sequence "HIV restriction factor" or "HIV restriction" or "inhibit HIV" or "repress HIV" or "restrict HIV" or "suppress HIV" or "block HIV," with a publication date up to 31 December 2016. Cited papers from the identified records were investigated, and additional database searches were performed. A total of 260 candidate inhibitory factors were identified. These factors have been identified in the literature as having a negative impact on HIV replication. This study identified hundreds of candidate inhibitory factors for which the impact of modulating their expression in lentiviral vector production could be beneficial.
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26
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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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27
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Qiu GH, Yang X, Zheng X, Huang C. The eukaryotic genome is structurally and functionally more like a social insect colony than a book. Epigenomics 2017; 9:1469-1483. [PMID: 28972397 DOI: 10.2217/epi-2017-0059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Traditionally, the genome has been described as the 'book of life'. However, the metaphor of a book may not reflect the dynamic nature of the structure and function of the genome. In the eukaryotic genome, the number of centrally located protein-coding sequences is relatively constant across species, but the amount of noncoding DNA increases considerably with the increase of organismal evolutional complexity. Therefore, it has been hypothesized that the abundant peripheral noncoding DNA protects the genome and the central protein-coding sequences in the eukaryotic genome. Upon comparison with the habitation, sociality and defense mechanisms of a social insect colony, it is found that the genome is similar to a social insect colony in various aspects. A social insect colony may thus be a better metaphor than a book to describe the spatial organization and physical functions of the genome. The potential implications of the metaphor are also discussed.
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Affiliation(s)
- Guo-Hua Qiu
- Fujian Provincial Key Laboratory for the Prevention & Control of Animal Infectious Diseases & Biotechnology, College of Life Sciences, Longyan University, Longyan 364012, Fujian, PR China
| | - Xiaoyan Yang
- Fujian Provincial Key Laboratory for the Prevention & Control of Animal Infectious Diseases & Biotechnology, College of Life Sciences, Longyan University, Longyan 364012, Fujian, PR China
| | - Xintian Zheng
- Fujian Provincial Key Laboratory for the Prevention & Control of Animal Infectious Diseases & Biotechnology, College of Life Sciences, Longyan University, Longyan 364012, Fujian, PR China
| | - Cuiqin Huang
- Fujian Provincial Key Laboratory for the Prevention & Control of Animal Infectious Diseases & Biotechnology, College of Life Sciences, Longyan University, Longyan 364012, Fujian, PR China
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29
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Frattari G, Aagaard L, Denton PW. The role of miR-29a in HIV-1 replication and latency. J Virus Erad 2017; 3:185-191. [PMID: 29057080 PMCID: PMC5632543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The development of an effective HIV-1 eradication strategy relies upon a clear understanding of the cellular mechanisms involved in HIV-1 latency. Among such cellular processes, microRNA activities affect HIV-1 production by regulating viral transcripts as well as host cell HIV-1 dependency factors. miR-29a stands apart from other relevant microRNAs as a potential therapeutic target in HIV-1 eradication. In vitro experiments have shown that miR-29a binds to a sequence in the 3'UTR of viral transcripts and inhibits their expression. In vivo data revealed the existence of a cytokine-microRNA (i.e. IL-21/miR-29a) pathway that significantly impacts HIV-1 replication. Here we present and discuss evidence supporting the role of miR-29a in HIV-1 replication and latency. We also discuss potential clinical applications of miR-29a inhibitors and enhancers in HIV-1 eradication strategies.
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Affiliation(s)
- Giacomo Frattari
- Department of Infectious Diseases,
Aarhus University Hospital Skejby,
Aarhus,
Denmark,Corresponding author: Giacomo Frattari,
Department of Infectious Diseases (Q),
Aarhus University Hospital,
Skejby, Palle Juul-Jensens Boulevard 99,
8200Aarhus N,
Denmark
| | - Lars Aagaard
- Department of Biomedicine,
Aarhus University,
Aarhus,
Denmark
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30
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Identification of a Specific miRNA Profile in HIV-Exposed Seronegative Individuals. J Acquir Immune Defic Syndr 2017; 73:11-9. [PMID: 27171739 DOI: 10.1097/qai.0000000000001070] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
OBJECTIVE MicroRNAs (miRNAs) are small noncoding RNAs involved in the posttranscriptional regulation of gene expression that play important roles in viral infections. Alterations of specific miRNAs are described in HIV infection, suggesting a role for miRNAs in pathogenesis of this disease. We verified whether a particular miRNA signature could be identified in natural resistance to HIV-1. METHODS Expression level of 84 miRNAs was analyzed by RT-qPCR in plasma and unstimulated peripheral blood mononuclear cell (PBMC) of 30 seronegative individuals repeatedly exposed to HIV-1 (HESN), 30 HIV seropositive subjects (HIV+), and 30 healthy controls (HC). Results were confirmed by individual RT-qPCR in in vitro HIV-1-infected PBMC and in their cell culture medium. Dicer and Drosha expression was analyzed in basal PBMC. RESULTS Whereas Dicer and Drosha expression was comparable in HESN, HIV+ and HC, several miRNAs were upregulated both in HESN and HIV+ compared with HC. Furthermore, miRNA-29a and miR-223 were upregulated in both unstimulated PBMC and plasma of HESN alone; their expression was reduced upon in vitro HIV-1 infection of HESN PBMC indicating that, upon infection, they are secreted in the extracellular milieu. These results were confirmed by individual qPCR. CONCLUSIONS Our studies demonstrate that HIV-1 exposure modifies miRNAs expression even in the absence of productive infection. Because those miRNAs that are specifically increased only in HESN have been known to reduce HIV-1 replication, their modulation could represent an important mechanism in resistance to HIV-1 infection.
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31
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Mamik MK, Hui E, Branton WG, McKenzie BA, Chisholm J, Cohen EA, Power C. HIV-1 Viral Protein R Activates NLRP3 Inflammasome in Microglia: implications for HIV-1 Associated Neuroinflammation. J Neuroimmune Pharmacol 2016; 12:233-248. [PMID: 27726055 DOI: 10.1007/s11481-016-9708-3] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 09/09/2016] [Indexed: 02/07/2023]
Abstract
Human Immunodeficiency virus (HIV) enters the brain soon after seroconversion and induces chronic neuroinflammation by infecting and activating brain macrophages. Inflammasomes are cytosolic protein complexes that mediate caspase-1 activation and ensuing cleavage and release of IL-1β and -18 by macrophages. Our group recently showed that HIV-1 infection of human microglia induced inflammasome activation in NLRP3-dependent manner. The HIV-1 viral protein R (Vpr) is an accessory protein that is released from HIV-infected cells, although its effects on neuroinflammation are undefined. Infection of human microglia with Vpr-deficient HIV-1 resulted in reduced caspase-1 activation and IL-1β production, compared to cells infected with a Vpr-encoding HIV-1 virus. Vpr was detected at low nanomolar concentrations in cerebrospinal fluid from HIV-infected patients and in supernatants from HIV-infected primary human microglia. Exposure of human macrophages to Vpr caused caspase-1 cleavage and IL-1β release with reduced cell viability, which was dependent on NLRP3 expression. Increased NLRP3, caspase-1, and IL-1β expression was evident in HIV-1 Vpr transgenic mice compared to wild-type littermates, following systemic immune stimulation. Treatment with the caspase-1 inhibitor, VX-765, suppressed NLRP3 expression with reduced IL-1β expression and associated neuroinflammation. Neurobehavioral deficits showed improvement in Vpr transgenic animals treated with VX-765. Thus, Vpr-induced NLRP3 inflammasome activation, which contributed to neuroinflammation and was abrogated by caspase-1 inhibition. This study provides a new therapeutic perspective for HIV-associated neuropsychiatric disease.
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Affiliation(s)
- Manmeet K Mamik
- Department of Medicine, University of Alberta, T6G 2S2, Edmonton, AB, Canada
| | - Elizabeth Hui
- Department of Medicine, University of Alberta, T6G 2S2, Edmonton, AB, Canada
| | - William G Branton
- Department of Medicine, University of Alberta, T6G 2S2, Edmonton, AB, Canada
| | - Brienne A McKenzie
- Department of Medicine, University of Alberta, T6G 2S2, Edmonton, AB, Canada
| | - Jesse Chisholm
- Department of Medicine, University of Alberta, T6G 2S2, Edmonton, AB, Canada
| | - Eric A Cohen
- Institut de recherches cliniques de Montréal (IRCM) and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC, Canada
| | - Christopher Power
- Department of Medicine, University of Alberta, T6G 2S2, Edmonton, AB, Canada.
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Anti-HIV microRNA expression in a novel Indian cohort. Sci Rep 2016; 6:28279. [PMID: 27320691 PMCID: PMC4913240 DOI: 10.1038/srep28279] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 05/31/2016] [Indexed: 12/31/2022] Open
Abstract
HIV-1 replication inside host cells is known to be regulated by various host factors. Host miRNAs, by virtue of its normal functioning, also regulate HIV-1 RNA expression by either directly targeting virus mRNAs or indirectly by regulating host proteins that HIV-1 uses for own replication. Therefore, it is highly possible that with differential miRNA expression, rate of disease progression will vary in HIV-1 infected individuals. In this study we have compared expression of a panel of 13 reported anti-HIV miRNAs in human PBMCs from long term non progressors (LTNPs), regular progressors and rapid progressors. We found that LTNPs have substantial lower expression of miR-382-5p that positively correlates with viral loads. Combinatorial regulation is highly probable in dictating differential disease progression as average expression of miR-382-5p and miR-155-5p can substantially distinguish LTNP individuals from regular progressors.
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Poltronieri P, Sun B, Mallardo M. RNA Viruses: RNA Roles in Pathogenesis, Coreplication and Viral Load. Curr Genomics 2016; 16:327-35. [PMID: 27047253 PMCID: PMC4763971 DOI: 10.2174/1389202916666150707160613] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Revised: 04/10/2015] [Accepted: 04/14/2015] [Indexed: 01/30/2023] Open
Abstract
The review intends to present and recapitulate the current knowledge on the roles and importance of regulatory RNAs, such as microRNAs and small interfering RNAs, RNA binding proteins and enzymes processing RNAs or activated by RNAs, in cells infected by RNA viruses. The review focuses on how non-coding RNAs are involved in RNA virus replication, pathogenesis and host response, especially in retroviruses HIV, with examples of the mechanisms of action, transcriptional regulation, and promotion of increased stability of their targets or their degradation.
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Affiliation(s)
- Palmiro Poltronieri
- CNR-ISPA, Institute of Sciences of Food Productions, National Research Council of Italy, Lecce, Italy
| | - Binlian Sun
- Research Group of HIV Molecular Epidemiology and Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, PR China
| | - Massimo Mallardo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II°, Napoli, Italy
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Piedade D, Azevedo-Pereira JM. MicroRNAs, HIV and HCV: a complex relation towards pathology. Rev Med Virol 2016; 26:197-215. [PMID: 27059433 DOI: 10.1002/rmv.1881] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 03/11/2016] [Accepted: 03/15/2016] [Indexed: 12/13/2022]
Abstract
MicroRNAs are small non-coding RNAs that modulate protein production by post-transcriptional gene regulation. They impose gene expression control by interfering with mRNA translation and stability in cell cytoplasm through a mechanism involving specific binding to mRNA based on base pair complementarity. Because of their intracellular replication cycle it is no surprise that viruses evolved in a way that allows them to use microRNAs to infect, replicate and persist in host cells. Several ways of interference between virus and host-cell microRNA machinery have been described. Most of the time, viruses drastically alter host-cell microRNA expression or synthesize their own microRNA to facilitate infection and pathogenesis. HIV and HCV are two prominent examples of this complex interplay revealing how fine-tuning of microRNA expression is crucial for controlling key host pathways that allow viral infection and replication, immune escape and persistence. In this review we delve into the mechanisms underlying cellular and viral-encoded microRNA functions in the context of HIV and HCV infections. We focus on which microRNAs are differently expressed and deregulated upon viral infection and how these alterations dictate the fate of virus and cell. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Diogo Piedade
- Host-Pathogen Interaction Unit, iMed.ULisboa, Faculdade de Farmácia, Universidade de Lisboa, Portugal
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Abstract
The discovery of long non-coding RNAs (lncRNAs) and the elucidation of the mechanisms by which they affect different disease states are providing researchers with a better understanding of a wide array of disease pathways. Moreover, lncRNAs are presenting themselves as both unique diagnostic biomarkers as well as novel targets against which to develop new therapeutics. Here we will explore the intricate network of non-coding RNAs associated with infection by the human immunodeficiency virus (HIV). Non-coding RNAs derived from both the human host as well as those from HIV itself are emerging as important regulatory elements. We discuss here the various mechanisms through which both small and long non-coding RNAs impact viral replication, pathogenesis and disease progression. Given the lack of an effective vaccine or cure for HIV and the scale of the current pandemic, a deeper understanding of the complex interplay between non-coding RNAs and HIV will support the development of innovative strategies for the treatment of HIV/acquired immunodeficiency disease (AIDS).
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Affiliation(s)
- Daniel C Lazar
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA.
| | - Kevin V Morris
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA; School of Biotechnology and Biomedical Sciences, University of New South Wales, Kensington, NSW, Australia.
| | - Sheena M Saayman
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA.
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36
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Lin L, Cai Q, Zhang X, Zhang H, Zhong Y, Xu C, Li Y. Two less common human microRNAs miR-875 and miR-3144 target a conserved site of E6 oncogene in most high-risk human papillomavirus subtypes. Protein Cell 2015; 6:575-588. [PMID: 25913515 PMCID: PMC4506288 DOI: 10.1007/s13238-015-0142-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 01/28/2015] [Indexed: 01/08/2023] Open
Abstract
Human papillomaviruses (HPVs) including high-risk (HR) and low-risk (LR) subtypes have distinguishable variation on both genotypes and phenotypes. The co-infection of multiple HR-HPVs, headed by HPV16, is common in cervical cancer in female. Recently accumulating reports have focused on the interaction between virus and host, particularly the role of human microRNAs (miRNAs) in anti-viral defense by targeting viral genome. Here, we found a well-conserved target site of miRNAs in the genomes of most HR-HPVs, not LR-HPVs, by scanning all potential target sites of human miRNAs on 24 HPVs of unambiguous subtypes of risk. The site is targeted by two less common human miRNAs, miR-875 and miR-3144, and is located in E6 oncogene open reading frame (ORF) and overlap with the first alternative splice exon of viral early transcripts. In validation tests, miR-875 and miR-3144 were identified to suppress the target reporter activity markedly and inhibit the expression of both synthetically exogenous E6 and endogenous E6 oncogene. High level of two miRNAs can inhibit cell growth and promote apoptosis in HPV16-positive cervical cancer cells. This study provides a promising common target of miRNAs for most HR-HPVs and highlights the effects of two low expressed human miRNAs on tumour suppression.
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Affiliation(s)
- Lin Lin
- Department of Gynecology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200011 China
| | - Qingqing Cai
- Department of Gynecology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200011 China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, 200011 China
| | - Xiaoyan Zhang
- School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China
| | - Hongwei Zhang
- Department of Gynecology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200011 China
| | - Yang Zhong
- Shanghai Center for Bioinformation Technology, Shanghai, 200235 China.,School of Life Sciences, Fudan University, Shanghai, 200433 China
| | - Congjian Xu
- Department of Gynecology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200011 China.,Department of Obstetrics and Gynecology of Shanghai Medical School, Fudan University, Shanghai, 200032 China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, 200011 China.,Institute of Biomedical Sciences, Fudan University, Shanghai, 200032 China
| | - Yanyun Li
- Department of Gynecology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200011 China
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Barichievy S, Naidoo J, Mhlanga MM. Non-coding RNAs and HIV: viral manipulation of host dark matter to shape the cellular environment. Front Genet 2015; 6:108. [PMID: 25859257 PMCID: PMC4374539 DOI: 10.3389/fgene.2015.00108] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 03/02/2015] [Indexed: 11/13/2022] Open
Abstract
On October 28th 1943 Winston Churchill said “we shape our buildings, and afterward our buildings shape us” (Humes, 1994). Churchill was pondering how and when to rebuild the British House of Commons, which had been destroyed by enemy bombs on May 10th 1941. The old House had been small and insufficient to hold all its members, but was restored to its original form in 1950 in order to recapture the “convenience and dignity” that the building had shaped into its parliamentary members. The circular loop whereby buildings or dwellings are shaped and go on to shape those that reside in them is also true of pathogens and their hosts. As obligate parasites, pathogens need to alter their cellular host environments to ensure survival. Typically pathogens modify cellular transcription profiles and in doing so, the pathogen in turn is affected, thereby closing the loop. As key orchestrators of gene expression, non-coding RNAs provide a vast and extremely precise set of tools for pathogens to target in order to shape the cellular environment. This review will focus on host non-coding RNAs that are manipulated by the infamous intracellular pathogen, the human immunodeficiency virus (HIV). We will briefly describe both short and long host non-coding RNAs and discuss how HIV gains control of these factors to ensure widespread dissemination throughout the host as well as the establishment of lifelong, chronic infection.
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Affiliation(s)
- Samantha Barichievy
- Gene Expression and Biophysics Group, Synthetic Biology Emerging Research Area, Council for Scientific and Industrial Research, Pretoria South Africa ; Discovery Sciences, Research & Development, AstraZeneca, Mölndal Sweden
| | - Jerolen Naidoo
- Gene Expression and Biophysics Group, Synthetic Biology Emerging Research Area, Council for Scientific and Industrial Research, Pretoria South Africa
| | - Musa M Mhlanga
- Gene Expression and Biophysics Group, Synthetic Biology Emerging Research Area, Council for Scientific and Industrial Research, Pretoria South Africa ; Gene Expression and Biophysics Unit, Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisbon Portugal
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Du X, Wang H, Xu F, Huang Y, Liu Z, Liu T. Enterovirus 71 induces apoptosis of SH‑SY5Y human neuroblastoma cells through stimulation of endogenous microRNA let-7b expression. Mol Med Rep 2015; 12:953-9. [PMID: 25779425 PMCID: PMC4438926 DOI: 10.3892/mmr.2015.3482] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 07/21/2014] [Indexed: 11/05/2022] Open
Abstract
Enterovirus 71 (EV71) is a pathogenic microorganism that causes hand, foot and mouth disease. However, the epigenetic mechanisms behind how EV71 regulates host cell proliferation and apoptosis are unclear. In the present study, the ability of EV71 to induce apoptosis was analyzed in the SH-SY5Y human neuroblastoma cell line and the effect of this virus on the mRNA expression levels of various apoptotic markers, miRNA let-7b and cyclin D1 (CCND1), was also investigated. The results demonstrated that EV71 induced SH-SY5Y cell apoptosis. An MTT assay revealed a significant inhibitory effect of EV71 on cell proliferation between 12-72 h post injection, compared with the control group. Furthermore, quantitative polymerase chain reaction and western blot analyses demonstrated that expression level of the apoptosis inhibitor Bcl-2 was markedly reduced, but the expression levels of the apoptosis-promoting factors Bax, caspase-7, caspase‑3 and active caspase-3 were markedly higher in the SH-SY5Y cells 12-48 h after EV71 infection, compared with the non-infected cells. In addition, flow cytometric assays revealed that EV71 arrested the cell cycle of host SH-SY5Y cells. Northern blot analysis revealed a marked miRNA let-7b hybridization signal in the EV71 virus-infected group compared with the non-infected group. Furthermore, western blotting confirmed that the CCND1 protein expression levels were significantly reduced in EV71-infected SH-SY5Y cells. EV71-inhibited SH-SY5Y proliferation was abrogated using let-7b specific 2'-O-Methyl-RNA, which inhibited endogenous miRNA let-7b expression. Thus, EV71 regulated the host SH‑SY5Y cell cycle and cell proliferation via stimulating endo-genous miRNA let-7b and directly targeting CCND1, therefore EV71 is a potential candidate for antiviral therapy.
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Affiliation(s)
- Xiling Du
- School of Life Science and Technology, Tongji University, Shanghai 200092, P.R. China
| | - Haipeng Wang
- School of Life Science and Technology, Tongji University, Shanghai 200092, P.R. China
| | - Fuhui Xu
- School of Life Science and Technology, Tongji University, Shanghai 200092, P.R. China
| | - Yongyi Huang
- School of Life Science and Technology, Tongji University, Shanghai 200092, P.R. China
| | - Zhixue Liu
- School of Life Science and Technology, Tongji University, Shanghai 200092, P.R. China
| | - Te Liu
- School of Life Science and Technology, Tongji University, Shanghai 200092, P.R. China
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HIV Latency and the noncoding RNA therapeutic landscape. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 848:169-89. [PMID: 25757621 DOI: 10.1007/978-1-4939-2432-5_9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The Human Immunodeficiency Virus (HIV) belongs to the subfamily of lentiviruses that are characterized by long incubation periods and chronic, persistent infection. The virus integrates into the genome of infected CD4+ cells and, in a subpopulation of cells, adopts a transcriptionally silent state, a process referred to a viral latency. This property makes it exceedingly difficult to therapeutically target the virus and eradicate infection. If left untreated, the inexorable demise of the infected individual's immune system ensues, a causal result of Acquired Immunodeficiency Syndrome (AIDS). Latently infected cells provide a reservoir that maintains viral infection indefinitely. In this chapter we explore the role of noncoding RNAs in HIV infection and in the establishment and maintenance of viral latency. Both short and long noncoding RNAs are endogenous modulators of epigenetic regulation in human cells and play an active role in gene expression. Lastly, we explore therapeutic modalities based on expressed RNAs that are capable of countering infection, transcriptionally regulating the virus, and suppressing or activating the latent state.
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Abdel-Mohsen M, Deng X, Danesh A, Liegler T, Jacobs ES, Rauch A, Ledergerber B, Norris PJ, Günthard HF, Wong JK, Pillai SK. Role of microRNA modulation in the interferon-α/ribavirin suppression of HIV-1 in vivo. PLoS One 2014; 9:e109220. [PMID: 25275557 PMCID: PMC4183579 DOI: 10.1371/journal.pone.0109220] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 08/29/2014] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Interferon-α (IFN-α) treatment suppresses HIV-1 viremia and reduces the size of the HIV-1 latent reservoir. Therefore, investigation of the molecular and immunologic effects of IFN-α may provide insights that contribute to the development of novel prophylactic, therapeutic and curative strategies for HIV-1 infection. In this study, we hypothesized that microRNAs (miRNAs) contribute to the IFN-α-mediated suppression of HIV-1. To inform the development of novel miRNA-based antiretroviral strategies, we investigated the effects of exogenous IFN-α treatment on global miRNA expression profile, HIV-1 viremia, and potential regulatory networks between miRNAs and cell-intrinsic anti-HIV-1 host factors in vivo. METHODS Global miRNA expression was examined in longitudinal PBMC samples obtained from seven HIV/HCV-coinfected, antiretroviral therapy-naïve individuals before, during, and after pegylated interferon-α/ribavirin therapy (IFN-α/RBV). We implemented novel hybrid computational-empirical approaches to characterize regulatory networks between miRNAs and anti-HIV-1 host restriction factors. RESULTS miR-422a was the only miRNA significantly modulated by IFN-α/RBV in vivo (p<0.0001, paired t test; FDR<0.037). Our interactome mapping revealed extensive regulatory involvement of miR-422a in p53-dependent apoptotic and pyroptotic pathways. Based on sequence homology and inverse expression relationships, 29 unique miRNAs may regulate anti-HIV-1 restriction factor expression in vivo. CONCLUSIONS The specific reduction of miR-422a is associated with exogenous IFN-α treatment, and likely contributes to the IFN-α suppression of HIV-1 through the enhancement of anti-HIV-1 restriction factor expression and regulation of genes involved in programmed cell death. Moreover, our regulatory network analysis presents additional candidate miRNAs that may be targeted to enhance anti-HIV-1 restriction factor expression in vivo.
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Affiliation(s)
- Mohamed Abdel-Mohsen
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
- Blood Systems Research Institute, San Francisco, California, United States of America
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, California, United States of America
| | - Ali Danesh
- Blood Systems Research Institute, San Francisco, California, United States of America
| | - Teri Liegler
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Evan S. Jacobs
- Blood Systems Research Institute, San Francisco, California, United States of America
| | - Andri Rauch
- Department of Infectious Diseases, Bern University Hospital and University of Bern, Bern, Switzerland
| | - Bruno Ledergerber
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Philip J. Norris
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
- Blood Systems Research Institute, San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Huldrych F. Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Joseph K. Wong
- Department of Medicine, San Francisco Veterans Affairs Medical Center, San Francisco, California, United States of America
| | - Satish K. Pillai
- Blood Systems Research Institute, San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America
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Bouwman RD, Palser A, Parry CM, Coulter E, Rasaiyaah J, Kellam P, Jenner RG. Human immunodeficiency virus Tat associates with a specific set of cellular RNAs. Retrovirology 2014; 11:53. [PMID: 24990269 PMCID: PMC4086691 DOI: 10.1186/1742-4690-11-53] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 06/18/2014] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Human Immunodeficiency Virus 1 (HIV-1) exhibits a wide range of interactions with the host cell but whether viral proteins interact with cellular RNA is not clear. A candidate interacting factor is the trans-activator of transcription (Tat) protein. Tat is required for expression of virus genes but activates transcription through an unusual mechanism; binding to an RNA stem-loop, the transactivation response element (TAR), with the host elongation factor P-TEFb. HIV-1 Tat has also been shown to alter the expression of host genes during infection, contributing to viral pathogenesis but, whether Tat also interacts with cellular RNAs is unknown. RESULTS Using RNA immunoprecipitation coupled with microarray analysis, we have discovered that HIV-1 Tat is associated with a specific set of human mRNAs in T cells. mRNAs bound by Tat share a stem-loop structural element and encode proteins with common biological roles. In contrast, we do not find evidence that Tat associates with microRNAs or the RNA-induced silencing complex (RISC). The interaction of Tat with cellular RNA requires an intact RNA binding domain and Tat RNA binding is linked to an increase in RNA abundance in cell lines and during infection of primary CD4+ T cells by HIV. CONCLUSIONS We conclude that Tat interacts with a specific set of human mRNAs in T cells, many of which show changes in abundance in response to Tat and HIV infection. This work uncovers a previously unrecognised interaction between HIV and its host that may contribute to viral alteration of the host cellular environment.
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Affiliation(s)
| | | | | | | | | | | | - Richard G Jenner
- MRC Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, London WC1E 6BT, UK.
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Swaminathan S, Murray DD, Kelleher AD. miRNAs and HIV: unforeseen determinants of host-pathogen interaction. Immunol Rev 2014; 254:265-80. [PMID: 23772625 DOI: 10.1111/imr.12077] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Our understanding of the complexity of gene regulation has significantly improved in the last decade as the role of small non-coding RNAs, called microRNAs (miRNAs), has been appreciated. These 19-22 nucleotide RNA molecules are critical regulators of mRNA translation and turnover. The miRNAs bind via a protein complex to the 3' untranslated region (3' UTR) of mRNA, ultimately leading to mRNA translational inhibition, degradation, or repression. Although many mechanisms by which human immunodeficiency virus-1 (HIV-1) infection eventually induces catastrophic immune destruction have been elucidated, the important role that miRNAs play in HIV-1 pathogenesis is only now emerging. Accumulating evidence demonstrates that changes to endogenous miRNA levels following infection is important: in maintaining HIV-1 latency in resting CD4(+) T cells, potentially affect immune function via changes to cytokines such as interleukin-2 (IL-2) and IL-10 and may predict disease progression. We review the roles that both viral and host miRNAs play in different cell types and disease conditions that are important in HIV-1 infection and discuss how miRNAs affect key immunomodulatory molecules contributing to immune dysfunction. Further, we discuss whether miRNAs may be used as novel biomarkers in serum and the potential to modulate miRNA levels as a unique approach to combating this pathogen.
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Affiliation(s)
- Sanjay Swaminathan
- Laboratory of Human Retrovirology, Applied and Developmental Research Directorate (ADD), Science Application International Corporation (SAIC)-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
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Biasin M, De Luca M, Gnudi F, Clerici M. The genetic basis of resistance to HIV infection and disease progression. Expert Rev Clin Immunol 2013; 9:319-34. [PMID: 23557268 DOI: 10.1586/eci.13.16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Susceptibility to HIV infection and the modulation of disease progression are strictly dependent on inter-individual variability, much of which is secondary to host genetic heterogeneity. The study of host factors that control these phenomena relies not only on candidate gene approaches but also on unbiased genome-wide genetic and functional analyses. Additional new insights stem from the study of mechanisms that control the expression of host and viral genes, such as miRNA. The genetic host factors that have been suggested to be associated either with resistance to HIV-1 infection or with absent/delayed progression to AIDS are nevertheless unable to fully justify the phenomenon of differential susceptibility to HIV. Multidisciplinary approaches are needed to further analyze individuals who deviate from the expected response to HIV exposure/infection. Results of these analyses will facilitate the identification of novel targets that could be exploited in the setting up of innovative therapeutic or vaccine approaches.
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Affiliation(s)
- Mara Biasin
- Department of Biomedical and Clinical Sciences, University of Milan, Via GB Grassi 74, 20157 Milan, Italy.
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Zhang H, Li Z, Li Y, Liu Y, Liu J, Li X, Shen T, Duan Y, Hu M, Xu D. A computational method for predicting regulation of human microRNAs on the influenza virus genome. BMC SYSTEMS BIOLOGY 2013; 7 Suppl 2:S3. [PMID: 24565017 PMCID: PMC3851852 DOI: 10.1186/1752-0509-7-s2-s3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Background While it has been suggested that host microRNAs (miRNAs) may downregulate viral gene expression as an antiviral defense mechanism, such a mechanism has not been explored in the influenza virus for human flu studies. As it is difficult to conduct related experiments on humans, computational studies can provide some insight. Although many computational tools have been designed for miRNA target prediction, there is a need for cross-species prediction, especially for predicting viral targets of human miRNAs. However, finding putative human miRNAs targeting influenza virus genome is still challenging. Results We developed machine-learning features and conducted comprehensive data training for predicting interactions between H1N1 genome segments and host miRNA. We defined our seed region as the first ten nucleotides from the 5' end of the miRNA to the 3' end of the miRNA and integrated various features including the number of consecutive matching bases in the seed region of 10 bases, a triplet feature in seed regions, thermodynamic energy, penalty of bulges and wobbles at binding sites, and the secondary structure of viral RNA for the prediction. Conclusions Compared to general predictive models, our model fully takes into account the conservation patterns and features of viral RNA secondary structures, and greatly improves the prediction accuracy. Our model identified some key miRNAs including hsa-miR-489, hsa-miR-325, hsa-miR-876-3p and hsa-miR-2117, which target HA, PB2, MP and NS of H1N1, respectively. Our study provided an interesting hypothesis concerning the miRNA-based antiviral defense mechanism against influenza virus in human, i.e., the binding between human miRNA and viral RNAs may not result in gene silencing but rather may block the viral RNA replication.
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Sisk JM, Witwer KW, Tarwater PM, Clements JE. SIV replication is directly downregulated by four antiviral miRNAs. Retrovirology 2013; 10:95. [PMID: 23988154 PMCID: PMC3766675 DOI: 10.1186/1742-4690-10-95] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 08/21/2013] [Indexed: 12/30/2022] Open
Abstract
Background Host cell microRNAs (miRNAs) have been shown to regulate the expression of both cellular and viral RNAs, in particular impacting both Hepatitis C Virus (HCV) and Human Immunodeficiency Virus (HIV). To investigate the role of miRNAs in regulating replication of the simian immunodeficiency virus (SIV) in macrophage lineage cells, we used primary macrophages to study targeting of SIV RNA by miRNAs. We examined whether specific host miRNAs directly target SIV RNA early in infection and might be induced via type I interferon pathways. Results miRNA target prediction programs identified miRNA binding sites within SIV RNA. Predicted binding sites for miRs-29a, -29b, -9 and -146a were identified in the SIV Nef/U3 and R regions, and all four miRNAs decreased virus production and viral RNA expression in primary macrophages. To determine whether levels of these miRNAs were affected by SIV infection, IFNβ or TNFα treatments, miRNA RT-qPCR assays measured miRNA levels after infection or treatment of macrophages. SIV RNA levels as well as virus production was downregulated by direct targeting of the SIV Nef/U3 and R regions by four miRNAs. miRs-29a, -29b, -9 and -146a were induced in primary macrophages after SIV infection. Each of these miRNAs was regulated by innate immune signaling through TNFα and/or the type I IFN, IFNβ. Conclusions The effects on miRNAs caused by HIV/SIV infection are illustrated by changes in their cellular expression throughout the course of disease, and in different patient populations. Our data demonstrate that levels of primary transcripts and mature miRs-29a, -29b, -9 and -146a are modulated by SIV infection. We show that the SIV 3′ UTR contains functional miRNA response elements (MREs) for all four miRNAs. Notably, these miRNAs regulate virus production and viral RNA levels in macrophages, the primary cells infected in the CNS that drive inflammation leading to HIV-associated neurocognitive disorders. This report may aid in identification miRNAs that target viral RNAs and HIV/SIV specifically, as well as in identification of miRNAs that may be targets of new therapies to treat HIV.
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Affiliation(s)
- Jeanne M Sisk
- Department of Molecular and Comparative Pathobiology, Edward D, Miller Research Building, The Johns Hopkins University School of Medicine, 733 N Broadway, Baltimore, MD 21205, USA.
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46
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Gupta P, Saksena NK. miRNAs: small molecules with a big impact on HIV infection and pathogenesis. Future Virol 2013. [DOI: 10.2217/fvl.13.59] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
miRNAs belong to a class of small noncoding RNAs that regulate gene expression at the post-transcriptional level. These are approximately 22-nt long sequences and control expression of 30–60% of all human genes, which has considerable significance in HIV infection, especially the way in which host–virus interaction occurs in vivo. Over the course of human evolution, viruses too have evolved, but there is still controversy surrounding the presence of miRNAs encoded by HIV. Considering the wide involvement of miRNAs in host gene regulation during infection and their association with HIV, this review provides insights into miRNAs encoded by the host and their role in host–virus interactions in addition to controlling host gene expression.
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Affiliation(s)
- Priyanka Gupta
- Retroviral Genetics Division, Centre for Virus Research, Westmead Millennium Institute, Westmead Hospital, University of Sydney, Westmead, NSW 2145, Sydney, Australia
| | - Nitin K Saksena
- Retroviral Genetics Division, Centre for Virus Research, Westmead Millennium Institute, Westmead Hospital, University of Sydney, Westmead, NSW 2145, Sydney, Australia.
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Vlachakis D, Tsiliki G, Pavlopoulou A, Roubelakis MG, Tsaniras SC, Kossida S. Antiviral Stratagems Against HIV-1 Using RNA Interference (RNAi) Technology. Evol Bioinform Online 2013; 9:203-13. [PMID: 23761954 PMCID: PMC3662398 DOI: 10.4137/ebo.s11412] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The versatility of human immunodeficiency virus (HIV)-1 and its evolutionary potential to elude antiretroviral agents by mutating may be its most invincible weapon. Viruses, including HIV, in order to adapt and survive in their environment evolve at extremely fast rates. Given that conventional approaches which have been applied against HIV have failed, novel and more promising approaches must be employed. Recent studies advocate RNA interference (RNAi) as a promising therapeutic tool against HIV. In this regard, targeting multiple HIV sites in the context of a combinatorial RNAi-based approach may efficiently stop viral propagation at an early stage. Moreover, large high-throughput RNAi screens are widely used in the fields of drug development and reverse genetics. Computer-based algorithms, bioinformatics, and biostatistical approaches have been employed in traditional medicinal chemistry discovery protocols for low molecular weight compounds. However, the diversity and complexity of RNAi screens cannot be efficiently addressed by these outdated approaches. Herein, a series of novel workflows for both wet- and dry-lab strategies are presented in an effort to provide an updated review of state-of-the-art RNAi technologies, which may enable adequate progress in the fight against the HIV-1 virus.
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Affiliation(s)
- Dimitrios Vlachakis
- Bioinformatics and Medical Informatics Team, Biomedical Research Foundation, Academy of Athens, Athens, Greece
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48
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Abstract
In this review, we focus on the roles of long noncoding RNAs (lncRNAs), including cellular and viral lncRNAs, in virus replication in infected cells. We survey the interactions and functions of several cellular lncRNAs such as XIST, HOTAIR, NEAT1, BIC, and several virus-encoded lncRNAs.
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Affiliation(s)
- Quan Zhang
- Molecular Virology Section, Laboratory of Molecular Microbiology, National Institutes of Allergy and Infectious Diseases, the National Institutes of Health, Bethesda, Maryland 20892-0460, USA
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Zhang Q, Chen CY, Yedavalli VSRK, Jeang KT. NEAT1 long noncoding RNA and paraspeckle bodies modulate HIV-1 posttranscriptional expression. mBio 2013. [PMID: 23362321 DOI: 10.1128/mbio.00596-12.editor] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
Most of the human genome is transcribed into protein-noncoding RNAs (ncRNAs), including small ncRNAs and long ncRNAs (lncRNAs). Over the past decade, rapidly emerging evidence has increasingly supported the view that lncRNAs serve key regulatory and functional roles in mammal cells. HIV-1 replication relies on various cell functions. To date, while the involvement of host protein factors and microRNAs (miRNAs) in the HIV-1 life cycle has been extensively studied, the relationship between lncRNAs and HIV-1 remains uncharacterized. Here, we have profiled 83 disease-related lncRNAs in HIV-1-infected T cells. We found NEAT1 to be one of several lncRNAs whose expression is changed by HIV-1 infection, and we have characterized its role in HIV-1 replication. We In the abstract, added definition of INS OK, or should "cis-acting" be added?report here that the knockdown of NEAT1 enhances virus production through increased nucleus-to-cytoplasm export of Rev-dependent instability element (INS)-containing HIV-1 mRNAs. IMPORTANCE Long protein-noncoding RNAs (lncRNAs) play roles in regulating gene expression and modulating protein activities. There is emerging evidence that lncRNAs are involved in the replication of viruses. To our knowledge, this report is the first to characterize a role contributed by an lncRNA, NEAT1, to HIV-1 replication. NEAT1 is essential for the integrity of the nuclear paraspeckle substructure. Based on our findings from NEAT1 knockdown, we have identified the nuclear paraspeckle body as another important subcellular organelle for HIV-1 replication.
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Affiliation(s)
- Quan Zhang
- Molecular Virology Section, Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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50
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NEAT1 long noncoding RNA and paraspeckle bodies modulate HIV-1 posttranscriptional expression. mBio 2013; 4:e00596-12. [PMID: 23362321 PMCID: PMC3560530 DOI: 10.1128/mbio.00596-12] [Citation(s) in RCA: 293] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Most of the human genome is transcribed into protein-noncoding RNAs (ncRNAs), including small ncRNAs and long ncRNAs (lncRNAs). Over the past decade, rapidly emerging evidence has increasingly supported the view that lncRNAs serve key regulatory and functional roles in mammal cells. HIV-1 replication relies on various cell functions. To date, while the involvement of host protein factors and microRNAs (miRNAs) in the HIV-1 life cycle has been extensively studied, the relationship between lncRNAs and HIV-1 remains uncharacterized. Here, we have profiled 83 disease-related lncRNAs in HIV-1-infected T cells. We found NEAT1 to be one of several lncRNAs whose expression is changed by HIV-1 infection, and we have characterized its role in HIV-1 replication. We In the abstract, added definition of INS OK, or should "cis-acting" be added?report here that the knockdown of NEAT1 enhances virus production through increased nucleus-to-cytoplasm export of Rev-dependent instability element (INS)-containing HIV-1 mRNAs. IMPORTANCE Long protein-noncoding RNAs (lncRNAs) play roles in regulating gene expression and modulating protein activities. There is emerging evidence that lncRNAs are involved in the replication of viruses. To our knowledge, this report is the first to characterize a role contributed by an lncRNA, NEAT1, to HIV-1 replication. NEAT1 is essential for the integrity of the nuclear paraspeckle substructure. Based on our findings from NEAT1 knockdown, we have identified the nuclear paraspeckle body as another important subcellular organelle for HIV-1 replication.
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