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Kesheh MM, Bayat M, Kobravi S, Lotfalizadeh MH, Heydari A, Memar MY, Baghi HB, Kermanshahi AZ, Ravaei F, Taghavi SP, Zarepour F, Nahand JS, Hashemian SMR, Mirzaei H. MicroRNAs and human viral diseases: A focus on the role of microRNA-29. Biochim Biophys Acta Mol Basis Dis 2024; 1871:167500. [PMID: 39260679 DOI: 10.1016/j.bbadis.2024.167500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 06/01/2024] [Accepted: 08/01/2024] [Indexed: 09/13/2024]
Abstract
The viral replication can impress through cellular miRNAs. Indeed, either the antiviral responses or the viral infection changes through cellular miRNAs resulting in affecting many regulatory signaling pathways. One of the microRNA families that is effective in human cancers, diseases, and viral infections is the miR-29 family. Members of miR-29 family are effective in different viral infections as their roles have appeared in regulation of immunity pathways either in innate immunity including interferon and inflammatory pathways or in adaptive immunity including activation of T-cells and antibodies production. Although miR-29a affects viral replication by suppressing antiviral responses, it can inhibit the expression of viral mRNAs via binding to their 3'UTR. In the present work, we discuss the evidence related to miR-29a and viral infection through host immunity regulation. We also review roles of other miR-29 family members by focusing on their role as biomarkers for diagnosing and targets for viral diseases management.
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Affiliation(s)
- Mina Mobini Kesheh
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mobina Bayat
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sepehr Kobravi
- Department of Oral and Maxillofacial Surgery, Faculty of Dentistry, Tehran Azad University, Tehran, Iran
| | | | - Azhdar Heydari
- Physiology Research Center, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran; Department of Physiology, School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Mohammad Yousef Memar
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Bannazadeh Baghi
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Atefeh Zamani Kermanshahi
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Fatemeh Ravaei
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran; Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Seyed Pouya Taghavi
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran; Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Fatemeh Zarepour
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran; Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Javid Sadri Nahand
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Seyed Mohammad Reza Hashemian
- Chronic Respiratory Diseases Research Center (CRDRC), National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Islamic Republic of Iran
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran.
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2
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Vasconcelos Komninakis S, Domingues W, Saeed Sanabani S, Angelo Folgosi V, Neves Barbosa I, Casseb J. CRISPR/CAS as a Powerful Tool for Human Immunodeficiency Virus Cure: A Review. AIDS Res Hum Retroviruses 2024; 40:363-375. [PMID: 38164106 DOI: 10.1089/aid.2022.0148] [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] [Indexed: 01/03/2024] Open
Abstract
Despite care and the availability of effective antiretroviral treatment, some human immunodeficiency virus (HIV)-infected individuals suffer from neurocognitive disorders associated with HIV (HAND) that significantly affect their quality of life. The different types of HAND can be divided into asymptomatic neurocognitive impairment, mild neurocognitive disorder, and the most severe form known as HIV-associated dementia. Little is known about the mechanisms of HAND, but it is thought to be related to infection of astrocytes, microglial cells, and macrophages in the human brain. The formation of a viral reservoir that lies dormant as a provirus in resting CD4+ T lymphocytes and in refuge tissues such as the brain contributes significantly to HIV eradication. In recent years, a new set of tools have emerged: the gene editing based on the clustered regularly interspaced palindromic repeats (CRISPR)/Cas9 system, which can alter genome segments by insertion, deletion, and replacement and has great therapeutic potential. This technology has been used in research to treat HIV and appears to offer hope for a possible cure for HIV infection and perhaps prevention of HAND. This approach has the potential to directly impact the quality of life of HIV-infected individuals, which is a very important topic to be known and discussed.
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Affiliation(s)
- Shirley Vasconcelos Komninakis
- Laboratory of Medical Investigation (LIM56) of the School of Medicine/Institute de Tropical Medicine, Department of Dermatology, São Paulo University, São Paulo, São Paulo, Brazil
| | - Wilson Domingues
- Laboratory of Medical Investigation (LIM56) of the School of Medicine/Institute de Tropical Medicine, Department of Dermatology, São Paulo University, São Paulo, São Paulo, Brazil
| | - Sabri Saeed Sanabani
- Laboratory of Medical Investigation (LIM56) of the School of Medicine/Institute de Tropical Medicine, Department of Dermatology, São Paulo University, São Paulo, São Paulo, Brazil
| | - Victor Angelo Folgosi
- Laboratory of Medical Investigation (LIM56) of the School of Medicine/Institute de Tropical Medicine, Department of Dermatology, São Paulo University, São Paulo, São Paulo, Brazil
| | - Igor Neves Barbosa
- Institute of Genetic Biology at the Biological Institute of São Paulo University, São Paulo, São Paulo, Brazil
| | - Jorge Casseb
- Laboratory of Medical Investigation (LIM56) of the School of Medicine/Institute de Tropical Medicine, Department of Dermatology, São Paulo University, São Paulo, São Paulo, Brazil
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Huang Y, Abdelgawad A, Turchinovich A, Queen S, Abreu CM, Zhu X, Batish M, Zheng L, Witwer KW. RNA Landscapes of Brain and Brain-Derived Extracellular Vesicles in Simian Immunodeficiency Virus Infection and Central Nervous System Pathology. J Infect Dis 2024; 229:1295-1305. [PMID: 38079216 PMCID: PMC11095537 DOI: 10.1093/infdis/jiad563] [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: 07/24/2023] [Revised: 11/20/2023] [Accepted: 12/07/2023] [Indexed: 12/26/2023] Open
Abstract
BACKGROUND Brain tissue-derived extracellular vesicles (bdEVs) act locally in the central nervous system (CNS) and may indicate molecular mechanisms in human immunodeficiency virus (HIV) CNS pathology. Using brain homogenate (BH) and bdEVs from a simian immunodeficiency virus (SIV) model of HIV disease, we identified RNA networks in SIV infection and neuroinflammation. METHODS Postmortem occipital cortex samples were obtained from uninfected controls and SIV-infected subjects (acute and chronic phases with or without CNS pathology [SIV encephalitis]). bdEVs were separated and characterized per international consensus guidelines. RNAs from bdEVs and BH were sequenced and quantitative polymerase chain reaction (qPCR)-amplified to detect levels of small RNAs (sRNAs, including microRNAs [miRNAs]) and longer RNAs including messenger RNAs (mRNAs) and circular RNAs (circRNAs). RESULTS Dysregulated RNAs in BH and bdEVs were identified in acute and chronic infection with pathology groups, including mRNAs, miRNAs, and circRNAs. Most dysregulated mRNAs in bdEVs reflected dysregulation in source BH. These mRNAs are disproportionately involved in inflammation and immune responses. Based on target prediction, several circRNAs that were differentially abundant in source tissue might be responsible for specific differences in sRNA levels in bdEVs during SIV infection. CONCLUSIONS RNA profiling of bdEVs and source tissues reveals potential regulatory networks in SIV infection and SIV-related CNS pathology.
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Affiliation(s)
- Yiyao Huang
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Ahmed Abdelgawad
- Department of Medical and Molecular Sciences, University of Delaware, Newark, Delaware, USA
| | - Andrey Turchinovich
- Division of Cancer Genome Research, German Cancer Research Center, Heidelberg, Germany
- Heidelberg Biolabs, GmbH, Heidelberg, Germany
| | - Suzanne Queen
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Celina Monteiro Abreu
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Xianming Zhu
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Mona Batish
- Department of Medical and Molecular Sciences, University of Delaware, Newark, Delaware, USA
| | - Lei Zheng
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Kenneth W Witwer
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Di Carlo D, Falasca F, Mazzuti L, Guerrizio G, Migliara G, Santori M, Lazzaro A, Mezzaroma I, D'Ettorre G, Fimiani C, Iaiani G, Antonelli G, Turriziani O. MicroRNA Expression Levels in Peripheral Blood Mononuclear Cells from Human Immunodeficiency Virus Type 1 Positive Individuals and Relationship with Different Levels of Viral Suppression. AIDS Res Hum Retroviruses 2024; 40:321-329. [PMID: 37523231 DOI: 10.1089/aid.2022.0165] [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] [Indexed: 08/01/2023] Open
Abstract
The persistence of low human immunodeficiency virus type 1 (HIV-1) replication in individuals undergoing antiretroviral therapy (ART) still threatens their health. Previous findings have shown that microRNAs (miRNAs) could interfere with several steps of the viral life cycle. Herein, we set out to investigate the expression of miR-150, miR-223, miR-382, miR-324-5p, miR-33a-5p, miR-34a, and miR-132 in the whole peripheral blood mononuclear cell (PBMC) population from people living with HIV-1 showing different levels of viral suppression. Levels of PBMC-associated miRNAs were analyzed in 30 individuals with undetectable viremia (target not detected) and 30 individuals with detectable low-level viremia (1-200 copies/mL). In addition, 30 samples from treatment-naive (NAIVE) individuals were investigated. Results were compared to a control group of 28 HIV-negative donors. All miRNAs analyzed were strongly downregulated in the NAIVE population, either compared to the treated group or to controls. Stratification of ART-treated donors according to the therapeutic regimen showed the downregulation of miR-33a-5p in subjects treated with non-nucleoside reverse transcriptase inhibitors compared with those treated with protease inhibitors. Collectively, the present study shows that uncontrolled viral replication leads to profound miRNA deregulation while treated individuals, irrespective of the degree of viral suppression, and even the types of antiviral drugs seem to be specifically associated with miRNA expression profiles. These evidences suggest that virological suppression could be favored by miRNA modulation.
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Affiliation(s)
- Daniele Di Carlo
- Department of Molecular Medicine, Sapienza University of Rome, Policlinico Umberto I, Rome, Italy
- Pasteur Laboratories, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy
| | - Francesca Falasca
- Department of Molecular Medicine, Sapienza University of Rome, Policlinico Umberto I, Rome, Italy
- Transfusion Medicine Unit, "F. Veneziale" Hospital, Isernia, Italy
| | - Laura Mazzuti
- Department of Molecular Medicine, Sapienza University of Rome, Policlinico Umberto I, Rome, Italy
- Department of Clinical and Molecular Medicine, Sapienza University, Sant'Andrea Hospital, Rome, Italy
| | - Giuliana Guerrizio
- Department of Molecular Medicine, Sapienza University of Rome, Policlinico Umberto I, Rome, Italy
| | - Giuseppe Migliara
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Policlinico Umberto I, Rome, Italy
| | - Marta Santori
- Department Internal Medicine, Endocrine-Metabolic Sciences and Infectious Diseases, Policlinico Umberto I, Rome, Italy
| | - Alessandro Lazzaro
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Policlinico Umberto I, Rome, Italy
| | - Ivano Mezzaroma
- Department of Translational and Precision Medicine, Sapienza University of Rome, Policlinico Umberto I, Rome, Italy
| | - Gabriella D'Ettorre
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Policlinico Umberto I, Rome, Italy
| | - Caterina Fimiani
- Department Internal Medicine, Endocrine-Metabolic Sciences and Infectious Diseases, Policlinico Umberto I, Rome, Italy
| | - Giancarlo Iaiani
- Department Internal Medicine, Endocrine-Metabolic Sciences and Infectious Diseases, Policlinico Umberto I, Rome, Italy
| | - Guido Antonelli
- Department of Molecular Medicine, Sapienza University of Rome, Policlinico Umberto I, Rome, Italy
| | - Ombretta Turriziani
- Department of Molecular Medicine, Sapienza University of Rome, Policlinico Umberto I, Rome, Italy
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Kobayashi-Ishihara M, Tsunetsugu-Yokota Y. Post-Transcriptional HIV-1 Latency: A Promising Target for Therapy? Viruses 2024; 16:666. [PMID: 38793548 PMCID: PMC11125802 DOI: 10.3390/v16050666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/26/2024] Open
Abstract
Human Immunodeficiency Virus type 1 (HIV-1) latency represents a significant hurdle in finding a cure for HIV-1 infections, despite tireless research efforts. This challenge is partly attributed to the intricate nature of HIV-1 latency, wherein various host and viral factors participate in multiple physiological processes. While substantial progress has been made in discovering therapeutic targets for HIV-1 transcription, targets for the post-transcriptional regulation of HIV-1 infections have received less attention. However, cumulative evidence now suggests the pivotal contribution of post-transcriptional regulation to the viral latency in both in vitro models and infected individuals. In this review, we explore recent insights on post-transcriptional latency in HIV-1 and discuss the potential of its therapeutic targets, illustrating some host factors that restrict HIV-1 at the post-transcriptional level.
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Affiliation(s)
- Mie Kobayashi-Ishihara
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
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6
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Tang Z, Lu Y, Dong JL, Wu W, Li J. The extracellular vesicles in HIV infection and progression: mechanisms, and theranostic implications. Front Bioeng Biotechnol 2024; 12:1376455. [PMID: 38655385 PMCID: PMC11035885 DOI: 10.3389/fbioe.2024.1376455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 03/11/2024] [Indexed: 04/26/2024] Open
Abstract
Extracellular vesicles (EVs), these minute yet mighty cellular messengers are redefining our understanding of a spectrum of diseases, from cancer to cardiovascular ailments, neurodegenerative disorders, and even infectious diseases like HIV. Central to cellular communication, EVs emerge as both potent facilitators and insightful biomarkers in immune response and the trajectory of disease progression. This review ventures deep into the realm of EVs in HIV-unraveling their pivotal roles in diagnosis, disease mechanism unravelling, and therapeutic innovation. With a focus on HIV, we will highlights the transformative potential of EVs in both diagnosing and treating this formidable virus. Unveiling the intricate dance between EVs and HIV, the review aims to shed light on novel therapeutic strategies that could significantly benefit HIV therapy, potentially even leading to the eradication of HIV.
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Affiliation(s)
- Zhen Tang
- AIDS Prevention and Control Center of Yichang Third People’s Hospital, Third People’s Hospital Affiliated to Sanxia University, Yichang, Hubei, China
| | - Yao Lu
- Yichang Changyang County People’s Hospital, Yichang, Hubei, China
| | - Jiu-Long Dong
- AIDS Prevention and Control Center of Yichang Third People’s Hospital, Third People’s Hospital Affiliated to Sanxia University, Yichang, Hubei, China
| | - Wen Wu
- AIDS Prevention and Control Center of Yichang Third People’s Hospital, Third People’s Hospital Affiliated to Sanxia University, Yichang, Hubei, China
| | - Jian Li
- AIDS Prevention and Control Center of Yichang Third People’s Hospital, Third People’s Hospital Affiliated to Sanxia University, Yichang, Hubei, China
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Beliakova-Bethell N. Targeting noncoding RNAs to reactivate or eliminate latent HIV reservoirs. Curr Opin HIV AIDS 2024; 19:47-55. [PMID: 38169367 PMCID: PMC10872953 DOI: 10.1097/coh.0000000000000838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
PURPOSE OF REVIEW Expression of noncoding RNAs (ncRNAs) is more tissue and cell type-specific than expression of protein-coding genes. Understanding the mechanisms of action of ncRNAs and their roles in HIV replication and latency may inform targets for the latent HIV reservoir reactivation or elimination with high specificity to CD4 + T cells latently infected with HIV. RECENT FINDINGS While the number of studies in the field of ncRNAs and HIV is limited, evidence points to complex interactions between different ncRNAs, protein-coding RNAs, and proteins. Latency-reversing agents modulate the expression of ncRNAs, with some effects being inhibitory for HIV reactivation. An important limitation of basic research on the ncRNA mechanisms of action is the reliance on cell lines. Because of cell type specificity, it is uncertain whether the ncRNAs function similarly in primary cells. SUMMARY Comprehensive functional screens to uncover all ncRNAs that regulate HIV expression and the detailed exploration of their mechanisms of action in relevant cell types are needed to identify promising targets for HIV reservoir clearance. Classes of ncRNAs as a whole rather than individual ncRNAs might represent an attractive target for reservoir elimination. Compound screens for latency reversal should factor in the complexity of their effects on ncRNAs.
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Affiliation(s)
- Nadejda Beliakova-Bethell
- Department of Medicine, University of California at San Diego, CA, USA
- VA San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, CA, USA
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8
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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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Mahmoudi MK, Letafati A, Soltani BM, Jazayeri SM, Ghaziasadi A. A negative correlation between hsa-miR29a-3p level and HIV-1 viral load in human serum; potentiate criteria for patients screening. Microb Pathog 2023; 184:106376. [PMID: 37777141 DOI: 10.1016/j.micpath.2023.106376] [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: 07/31/2023] [Revised: 09/06/2023] [Accepted: 09/28/2023] [Indexed: 10/02/2023]
Abstract
Human Immunodeficiency Virus type-1 (HIV-1) causes persistent and life-threatening infection, leading to progressive disease. MicroRNAs (miRNAs) are regulators of gene expression which can be found in circulating human blood samples. hsa-miR-29a-3p has been identified as a potential regulator of the Negative Regulatory Factor (Nef) gene from the HIV-1 viral genome. In this study, we aimed to compare the serum levels of hsa-miR-29a-3p with HIV-1 viral load in a substantial number of infected individuals. We collected serum samples from a total of 48 participants, including 36 untreated HIV-positive patients, and 12 HIV-negative individuals as a control group, matched for age and sex. The HIV-1 viral load in both the case and control groups was confirmed using qRT-PCR. Subsequent qRT-PCR analysis of circulating hsa-miR-29a-3p levels revealed lower miRNA expression in the groups with higher viral loads. A negative correlation (r = -0.58) was calculated between hsa-miR-29a-3p levels and HIV-1 viral load. These findings suggest that the expression level of hsa-miR-29a-3p may serve as an indicator of HIV-1 viral load in human serum samples. Additionally, this miR may hold promise as a potential tool for enhancing HIV-1 treatment strategies.
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Affiliation(s)
| | - Arash Letafati
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Iran
| | - Bahram Mohammad Soltani
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Seyed Mohammad Jazayeri
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Iran; Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Azam Ghaziasadi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Iran; Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran.
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Ramirez PW, Pantoja C, Beliakova-Bethell N. An Evaluation on the Role of Non-Coding RNA in HIV Transcription and Latency: A Review. HIV AIDS (Auckl) 2023; 15:115-134. [PMID: 36942082 PMCID: PMC10024501 DOI: 10.2147/hiv.s383347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/24/2023] [Indexed: 03/16/2023] Open
Abstract
The existence of latent cellular reservoirs is recognized as the major barrier to an HIV cure. Reactivating and eliminating "shock and kill" or permanently silencing "block and lock" the latent HIV reservoir, as well as gene editing, remain promising approaches, but so far have proven to be only partially successful. Moreover, using latency reversing agents or "block and lock" drugs pose additional considerations, including the ability to cause cellular toxicity, a potential lack of specificity for HIV, or low potency when each agent is used alone. RNA molecules, such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are becoming increasingly recognized as important regulators of gene expression. RNA-based approaches for combatting HIV latency represent a promising strategy since both miRNAs and lncRNAs are more cell-type and tissue specific than protein coding genes. Thus, a higher specificity of targeting the latent HIV reservoir with less overall cellular toxicity can likely be achieved. In this review, we summarize current knowledge about HIV gene expression regulation by miRNAs and lncRNAs encoded in the human genome, as well as regulatory molecules encoded in the HIV genome. We discuss both the transcriptional and post-transcriptional regulation of HIV gene expression to align with the current definition of latency, and describe RNA molecules that either promote HIV latency or have anti-latency properties. Finally, we provide perspectives on using each class of RNAs as potential targets for combatting HIV latency, and describe the complexity of the interactions between different RNA molecules, their protein targets, and HIV.
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Affiliation(s)
- Peter W Ramirez
- Department of Biological Sciences, California State University, Long Beach, CA, USA
| | - Christina Pantoja
- Department of Biological Sciences, California State University, Long Beach, CA, USA
| | - Nadejda Beliakova-Bethell
- VA San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, CA, USA
- Department of Medicine, University of California, San Diego, CA, USA
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11
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Kim IS, Lee SG, Shin SG, Jeong H, Sohn KM, Park KS, Silwal P, Cheon S, Kim J, Kym S, Kim YS, Jo EK, Park C. Dysregulated thrombospondin 1 and miRNA-29a-3p in severe COVID-19. Sci Rep 2022; 12:21227. [PMID: 36481664 PMCID: PMC9732043 DOI: 10.1038/s41598-022-23533-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 10/31/2022] [Indexed: 12/13/2022] Open
Abstract
Although nearly a fifth of symptomatic COVID-19 patients suffers from severe pulmonary inflammation, the mechanism of developing severe illness is not yet fully understood. To identify significantly altered genes in severe COVID-19, we generated messenger RNA and micro-RNA profiling data of peripheral blood mononuclear cells (PBMCs) from five COVID-19 patients (2 severe and 3 mild patients) and three healthy controls (HC). For further evaluation, two publicly available RNA-Seq datasets (GSE157103 and GSE152418) and one single-cell RNA-Seq dataset (GSE174072) were employed. Based on RNA-Seq datasets, thrombospondin 1 (THBS1) and interleukin-17 receptor A (IL17RA) were significantly upregulated in severe COVID-19 patients' blood. From single-cell RNA-sequencing data, IL17RA level is increased in monocytes and neutrophils, whereas THBS1 level is mainly increased in the platelets. Moreover, we identified three differentially expressed microRNAs in severe COVID-19 using micro-RNA sequencings. Intriguingly, hsa-miR-29a-3p significantly downregulated in severe COVID-19 was predicted to bind the 3'-untranslated regions of both IL17RA and THBS1 mRNAs. Further validation analysis of our cohort (8 HC, 7 severe and 8 mild patients) showed that THBS1, but not IL17RA, was significantly upregulated, whereas hsa-miR-29a-3p was downregulated, in PBMCs from severe patients. These findings strongly suggest that dysregulated expression of THBS1, IL17RA, and hsa-miR-29a-3p involves severe COVID-19.
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Affiliation(s)
- In Soo Kim
- grid.254230.20000 0001 0722 6377Department of Medical Science, Chungnam National University School of Medicine, Daejeon, Korea ,grid.254230.20000 0001 0722 6377Department of Microbiology, Chungnam National University School of Medicine, Daejeon, Korea ,grid.254230.20000 0001 0722 6377Infection Control Convergence Research Center, Chungnam National University School of Medicine, Daejeon, Korea
| | - Sung-Gwon Lee
- grid.14005.300000 0001 0356 9399School of Biological Sciences and Technology, Chonnam National University, Gwangju, Korea
| | - Seul Gi Shin
- grid.254230.20000 0001 0722 6377Department of Microbiology, Chungnam National University School of Medicine, Daejeon, Korea ,grid.254230.20000 0001 0722 6377Infection Control Convergence Research Center, Chungnam National University School of Medicine, Daejeon, Korea
| | - Hyeongseok Jeong
- grid.254230.20000 0001 0722 6377Division of Infectious Diseases, Department of Internal Medicine, Chungnam National University School of Medicine, Daejeon, Korea
| | - Kyung Mok Sohn
- grid.254230.20000 0001 0722 6377Division of Infectious Diseases, Department of Internal Medicine, Chungnam National University School of Medicine, Daejeon, Korea
| | - Ki-Sun Park
- grid.418980.c0000 0000 8749 5149KM Science Research Division, Korea Institute of Oriental Medicine, Daejeon, Korea
| | - Prashanta Silwal
- grid.254230.20000 0001 0722 6377Department of Microbiology, Chungnam National University School of Medicine, Daejeon, Korea ,grid.254230.20000 0001 0722 6377Infection Control Convergence Research Center, Chungnam National University School of Medicine, Daejeon, Korea
| | - Shinhye Cheon
- grid.254230.20000 0001 0722 6377Division of Infectious Diseases, Department of Internal Medicine, Chungnam National University School of Medicine, Daejeon, Korea
| | - Jungok Kim
- grid.254230.20000 0001 0722 6377Division of Infectious Diseases, Department of Internal Medicine, Chungnam National University School of Medicine, Daejeon, Korea
| | - Sungmin Kym
- grid.254230.20000 0001 0722 6377Division of Infectious Diseases, Department of Internal Medicine, Chungnam National University School of Medicine, Daejeon, Korea
| | - Yeon-Sook Kim
- grid.254230.20000 0001 0722 6377Division of Infectious Diseases, Department of Internal Medicine, Chungnam National University School of Medicine, Daejeon, Korea
| | - Eun-Kyeong Jo
- grid.254230.20000 0001 0722 6377Department of Medical Science, Chungnam National University School of Medicine, Daejeon, Korea ,grid.254230.20000 0001 0722 6377Department of Microbiology, Chungnam National University School of Medicine, Daejeon, Korea ,grid.254230.20000 0001 0722 6377Infection Control Convergence Research Center, Chungnam National University School of Medicine, Daejeon, Korea
| | - Chungoo Park
- grid.14005.300000 0001 0356 9399School of Biological Sciences and Technology, Chonnam National University, Gwangju, Korea
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12
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Bazié WW, Boucher J, Goyer B, Traoré IT, Kania D, Somé DY, Alary M, Gilbert C. Plasma vesicular miR-155 as a biomarker of immune activation in antiretroviral treated people living with HIV. Front Immunol 2022; 13:916599. [PMID: 36105810 PMCID: PMC9464867 DOI: 10.3389/fimmu.2022.916599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 08/03/2022] [Indexed: 11/13/2022] Open
Abstract
People living with HIV (PLWH), despite suppression of viral replication with antiretroviral therapy (ART), have high morbidity and mortality due to immune activation and chronic inflammation. Discovering new biomarkers of immune activation status under ART will be pertinent to improve PLWH quality of life when the majority will be treated. We stipulate that plasma large and small extracellular vesicle (EVs) and their microRNA content could be easily measured biomarkers to monitor immune activation in PLWH. Venous blood samples from n = 128 ART-treated PLWH with suppressed viral load (≤ 20 copies/mL) and n = 60 HIV-uninfected participants were collected at five testing or treatment centers of PLWH in Burkina Faso. Large and small plasma EVs were purified, counted, and the mature miRNAs miR-29a, miR-146a, and miR-155 were quantified by RT-qPCR. Diagnostic performances of large and small EVs miRNAs level were evaluated by receiver operating characteristic (ROC) curve analysis and principal component analysis (PCA). Among the EVs microRNA measured, only large EVs miR-155 copies distinguished PLWH with immune activation, with AUC of 0.75 for CD4/CD8 < 1 (95% CI: 0.58–0.91, P = 0.0212), and 0.77 for CD8 T cells ≥ 500/µL (95% CI: 0.63–0.92, P = 0.0096). In addition, PCA results suggest that large EVs miR-155 copies may be a biomarker of immune activation. Since miR-155 may influence immune cell function, its enrichment in large EV subpopulations could be a functional biomarker of immune activation in PLWH on ART. This measure could help to monitor and diagnose the immune activation with more accuracy.
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Affiliation(s)
- Wilfried Wenceslas Bazié
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada
- Programme de Recherche sur les Maladies Infectieuses, Centre Muraz, Institut National de Santé Publique, Bobo-Dioulasso, Burkina Faso
- *Correspondence: Caroline Gilbert, ; Wilfried Wenceslas Bazié,
| | - Julien Boucher
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada
| | - Benjamin Goyer
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada
| | - Isidore Tiandiogo Traoré
- Programme de Recherche sur les Maladies Infectieuses, Centre Muraz, Institut National de Santé Publique, Bobo-Dioulasso, Burkina Faso
- Institut Supérieur des Sciences de la Santé, Université Nazi Boni, Bobo-Dioulasso, Burkina Faso
| | - Dramane Kania
- Programme de Recherche sur les Maladies Infectieuses, Centre Muraz, Institut National de Santé Publique, Bobo-Dioulasso, Burkina Faso
| | - Diane Yirgnur Somé
- Programme de Recherche sur les Maladies Infectieuses, Centre Muraz, Institut National de Santé Publique, Bobo-Dioulasso, Burkina Faso
| | - Michel Alary
- Axe de Recherche Santé des Populations et Pratiques Optimales en Santé, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada
- Département de Médecine Sociale et Préventive, Faculté de Médecine, Université Laval, Québec, QC, Canada
- Institut National de Santé Publique du Québec, Québec, QC, Canada
| | - Caroline Gilbert
- Axe de Recherche Maladies Infectieuses et Immunitaires, 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
- *Correspondence: Caroline Gilbert, ; Wilfried Wenceslas Bazié,
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13
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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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14
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Kim YJ, Yeon Y, Lee WJ, Shin YU, Cho H, Lim HW, Kang MH. Analysis of MicroRNA Expression in Tears of Patients with Herpes Epithelial Keratitis: A Preliminary Study. Invest Ophthalmol Vis Sci 2022; 63:21. [PMID: 35475887 PMCID: PMC9055549 DOI: 10.1167/iovs.63.4.21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Purpose Herpes epithelial keratitis (HEK) is the most common form of herpes simplex virus (HSV) eye involvement, and understanding the molecular mechanisms underlying HEK is important. We investigated the expression of microRNAs (miRNAs) in the tears of patients with HEK. Methods Tear samples from eight patients with HEK and seven age-matched controls were evaluated. Clinical ophthalmologic evaluation was performed, and an anterior segment photograph was obtained after fluorescence staining. Dendritic or geographic ulcer areas were measured using ImageJ software. The expression of 43 different miRNAs in tears was measured using real-time polymerase chain reaction and compared between patients with HEK and controls. Differences in miRNA expression between the dendritic and geographic ulcer groups and correlations involving miRNA expression and ulcer area were evaluated. Results Of the 43 miRNAs, 23 were upregulated in patients with HEK compared to normal controls. MiR-15b-5p, miR-16-5p, miR-20b-5p, miR-21-5p, miR-23b-3p, miR-25-3p, miR-29a-3p, miR-30a-3p, miR-30d-5p, miR-92a-3p, miR-124-3p, miR-127-3p, miR-132-3p, miR-142-3p, miR-145-5p, miR-146a-5p, miR-146b-5p, miR-155-5p, miR-182-5p, miR-183-5p, miR-221-3p, miR-223-3p, and miR-338-5p were significantly upregulated in patients with HEK. MiR-29a-3p exhibited significant differences between the dendritic and geographic ulcer groups. All 23 miRNAs with significant differences between patients with HEK and the control group were not significantly correlated with ulcer area. Conclusions Twenty-three miRNAs were significantly upregulated in the tears of patients with HEK, and the expression of miRNAs may play important roles in herpes infection in relation to host immunity.
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Affiliation(s)
- Yu Jeong Kim
- Department of Ophthalmology, Hanyang University Hospital, Hanyang University College of Medicine, Seoul, Republic of Korea
| | - Yeji Yeon
- Department of Ophthalmology, Hanyang University Hospital, Hanyang University College of Medicine, Seoul, Republic of Korea
| | - Won June Lee
- Department of Ophthalmology, Hanyang University Hospital, Hanyang University College of Medicine, Seoul, Republic of Korea
| | - Yong Un Shin
- Department of Ophthalmology, Hanyang University Hospital, Hanyang University College of Medicine, Seoul, Republic of Korea
| | - Heeyoon Cho
- Department of Ophthalmology, Hanyang University Hospital, Hanyang University College of Medicine, Seoul, Republic of Korea
| | - Han Woong Lim
- Department of Ophthalmology, Hanyang University Hospital, Hanyang University College of Medicine, Seoul, Republic of Korea
| | - Min Ho Kang
- Department of Ophthalmology, Hanyang University Hospital, Hanyang University College of Medicine, Seoul, Republic of Korea
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15
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Bazié WW, Boucher J, Traoré IT, Kania D, Somé DY, Alary M, Gilbert C. Vesicular MicroRNA as Potential Biomarkers of Viral Rebound. Cells 2022; 11:cells11050859. [PMID: 35269481 PMCID: PMC8909274 DOI: 10.3390/cells11050859] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/24/2022] [Accepted: 02/24/2022] [Indexed: 02/04/2023] Open
Abstract
Changes in the cellular microRNA (miRNA) expression profile in response to HIV infection, replication or latency have been reported. Nevertheless, little is known concerning the abundance of miRNA in extracellular vesicles (EVs). In the search for a reliable predictor of viral rebound, we quantified the amount of miR-29a, miR-146a, and miR-155 in two types of plasma extracellular vesicles. Venous blood was collected from 235 ART-treated and ART-naive persons living with HIV (85 with ongoing viral replication, ≥20 copies/mL) and 60 HIV-negative participants at five HIV testing or treatment centers in Burkina Faso. Large and small plasma EVs were purified and counted, and mature miRNA miR-29a, miR-146a, and miR-155 were measured by RT-qPCR. Diagnostic performance of miRNA levels in large and small EVs was evaluated by a receiver operating characteristic curve analysis. The median duration of HIV infection was 36 months (IQR 14-117). The median duration of ART was 34 months (IQR 13-85). The virus was undetectable in 63.8% of these persons. In the others, viral load ranged from 108 to 33,978 copies/mL (median = 30,032). Large EVs were more abundant in viremic participants than aviremic. All three miRNAs were significantly more abundant in small EVs in persons with detectable HIV RNA, and their expression levels in copies per vesicle were a more reliable indicator of viral replication in ART-treated patients with low viremia (20-1000 copies/mL). HIV replication increased the production of large EVs more than small EVs. Combined with viral load measurement, quantifying EV-associated miRNA abundance relative to the number of vesicles provides a more reliable marker of the viral status. The expression level as copies per small vesicle could predict the viral rebound in ART-treated patients with undetectable viral loads.
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Affiliation(s)
- Wilfried Wenceslas Bazié
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Quebec City, QC G1V 4G2, Canada;
- Programme de Recherche sur les Maladies Infectieuses, Centre Muraz, Institut National de Santé Publique, Bobo-Dioulasso 01 BP 390, Burkina Faso; (I.T.T.); (D.K.); (D.Y.S.)
- Correspondence: (W.W.B.); (C.G.); Tel.: +1-(418)-525-4444 (ext. 44104) (W.W.B.); +1-(418)-525-4444 (ext. 46107) (C.G.); Fax: +1-(418)-654-2765 (C.G.)
| | - Julien Boucher
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Quebec City, QC G1V 4G2, Canada;
| | - Isidore Tiandiogo Traoré
- Programme de Recherche sur les Maladies Infectieuses, Centre Muraz, Institut National de Santé Publique, Bobo-Dioulasso 01 BP 390, Burkina Faso; (I.T.T.); (D.K.); (D.Y.S.)
- Département de Santé Publique, Institut Supérieur des Sciences de la Santé, Université Nazi Boni, Bobo-Dioulasso 01 BP 1091, Burkina Faso
| | - Dramane Kania
- Programme de Recherche sur les Maladies Infectieuses, Centre Muraz, Institut National de Santé Publique, Bobo-Dioulasso 01 BP 390, Burkina Faso; (I.T.T.); (D.K.); (D.Y.S.)
| | - Diane Yirgnur Somé
- Programme de Recherche sur les Maladies Infectieuses, Centre Muraz, Institut National de Santé Publique, Bobo-Dioulasso 01 BP 390, Burkina Faso; (I.T.T.); (D.K.); (D.Y.S.)
| | - Michel Alary
- Axe de Recherche Santé des Populations et Pratiques Optimales en Santé, Centre de Recherche du CHU de Québec-Université Laval, Quebec City, QC G1S 4L8, Canada;
- Département de Médecine Sociale et Préventive, Faculté de Médecine, Université Laval, Quebec City, QC G1V 0A6, Canada
- Institut National de Santé Publique du Québec, Quebec City, QC G1V 5B3, Canada
| | - Caroline Gilbert
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Quebec City, QC G1V 4G2, Canada;
- Département de Microbiologie-Infectiologie et d’Immunologie, Faculté de Médecine, Université Laval, Quebec City, QC G1V 0A6, Canada
- Correspondence: (W.W.B.); (C.G.); Tel.: +1-(418)-525-4444 (ext. 44104) (W.W.B.); +1-(418)-525-4444 (ext. 46107) (C.G.); Fax: +1-(418)-654-2765 (C.G.)
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16
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Abstract
As already discussed for T cell lines, also myeloid cell lines as served as the earliest models of chronic HIV infection. They were particularly relevant in the late 1980s and early 1990s when most experimental in vitro infections were based on laboratory-adapted "T-cell tropic" strains of HIV-1, such as LAI/IIIB or others, that later were found to rely upon CXCR4 as coreceptor for viral entry in addition to CD4 as primary receptor. Although primary macrophages do express CXCR4 together with CD4, virus replication is much less efficient than that observed with CCR5-using "macrophage-tropic" strains, as discussed separately in this book. Although different myeloid cell lines have been used to generate models of chronic HIV-1 infection that could be used to investigate features of proviral reactivation, as reviewed in (Cassol et al. J Leukoc Biol 80:1018-1030, 2006), two cell lines in particular have been broadly used and will be here discussed: the U937-derived U1 and HL-60-derived OM-10.1.
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Affiliation(s)
- Guido Poli
- Human Immuno-Virology (H.I.V.) Unit, San Raffaele Scientific Institute and School of Medicine, Vita-Salute San Raffaele University, Milano, Italy.
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17
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Consuegra I, Gasco S, Serramía MJ, Jiménez JL, Mellado MJ, Muñoz-Fernández MÁ. Establishment of a miRNA profile in paediatric HIV-1 patients and its potential as a biomarker for effectiveness of the combined antiretroviral therapy. Sci Rep 2021; 11:23477. [PMID: 34873266 PMCID: PMC8648729 DOI: 10.1038/s41598-021-03020-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 11/12/2021] [Indexed: 11/18/2022] Open
Abstract
miRNAs have been extensively studied in pathological conditions, including viral infections, such as those provoked by HIV-1. Several cellular and circulating miRNAs are altered during HIV-1 infection, with either beneficial effects on host defenses or enhanced virus infectivity. Blood samples were collected in sterile EDTA tubes and plasma was separated and stored, as were PBMCs. RNA was isolated and reverse-transcribed. Finally, the miRNA gene expression profile was assessed using TaqMan Array Human microRNA Card A v2.0. A comprehensive statistical analysis was performed on the results obtained. This is the first study on miRNAs in HIV-1 paediatric patients, and a miRNA profile differentiating patients starting combination antiretroviral therapy (cART) at different times after HIV-1 diagnosis was established. Thirty-four miRNAs were observed to have different expression levels between the control group and the cART group. The data indicates the need to start cART as soon as possible after the establishment of HIV-1 infection to assure the best outcome possible. Finally, the selected 34 miRNAs may be used as biomarkers for prognosis and assessing therapy effectiveness. However, more research must be conducted to establish adequate quantitative correlations.
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Affiliation(s)
- Irene Consuegra
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain.,Spanish HIV HGM BioBank, Madrid, Spain
| | - Samanta Gasco
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - María Jesús Serramía
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain.,Laboratorio InmunoBiología Molecular, Head Immunology Section, (Hospital General Universitario Gregorio Marañón), C/Dr. Esquerdo 46, 28007, Madrid, Spain
| | - José Luis Jiménez
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain.,Spanish HIV HGM BioBank, Madrid, Spain.,Plataforma-Laboratorio (IiSGM), Madrid, Spain
| | - Maria Jose Mellado
- General Pediatrics, Infectious and Tropical Diseases Department Hospital, Universitario La Paz, Madrid, Spain.,IdiPAZ, Madrid, Spain.,Translational Research Network in Pediatric Infectious Diseases (RITIP), Madrid, Spain
| | - María Ángeles Muñoz-Fernández
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain. .,Spanish HIV HGM BioBank, Madrid, Spain. .,Laboratorio InmunoBiología Molecular, Head Immunology Section, (Hospital General Universitario Gregorio Marañón), C/Dr. Esquerdo 46, 28007, Madrid, Spain. .,Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain.
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18
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Shen F, Liu Y, Wang L, Chai X, Yang J, Feng Q, Li X. Identification of HIV-1-specific cascaded microRNA-mRNA regulatory relationships by parallel mRNA and microRNA expression profiling with AIDS patients after antiviral treatment. Medicine (Baltimore) 2021; 100:e27428. [PMID: 34871208 PMCID: PMC8568437 DOI: 10.1097/md.0000000000027428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 09/17/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The pathogenesis of human immunodeficiency virus 1 (HIV-1) infection is so complex that have not been clearly defined, despite intensive efforts have been made by many researchers. MicroRNA (miRNA) as regulation factor in various human diseases may influence the course of HIV-1 infection by targeting mRNAs. Thus, studies combining transcription of posttranscriptional miRNA regulation are required. METHODS With the purpose of identifying cascaded miRNA-mRNA regulatory relationships related to HIV infection in gene level, the parallel miRNA, and mRNA expression profiles were analyzed to select differential expressed miRNAs and mRNAs. Then, miRNA-mRNA interactions were predicted using 3 data sources and Pearson correlation coefficient was calculated based on the gene expression level for accuracy improvement. Furthermore, the calculation of the regulatory impact factors was conducted to reveal crucial regulators in HIV-1 infection. To give further insight into these transcription factor (TF) regulators, the differentially co-expression analysis was conducted to identify differentially co-expressed links and differential co-expressed genes and the co-expression gene modules were identified using a threshold-based hierarchical clustering method, then modules were combined into a miRNA-TF-mRNA network. RESULTS A total of 69,126 differentially co-expressed links and 626 differential co-expressed genes were identified. Functional enrichment analysis indicated that these co-expressed genes were significantly involved in immune response and apoptosis. Moreover, according to regulatory impact factors, 5 most influential TFs and miRNA in HIV-1 infection were identified and miRNA-TF-mRNA regulatory networks were built during the computing process. CONCLUSIONS In our study, a set of integrated methods was generated to identify important regulators and miRNA-TF-mRNA interactions. Parallel profiling analysis of the miRNAs and mRNAs expression of HIV/acquired immunodeficiency syndrome (AIDS) patients after antiretroviral therapy indicated that some regulators have wide impact on gene regulation and that these regulatory elements may bear significant implications on the underlying molecular mechanism and pathogenesis of AIDS occurrence.
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Affiliation(s)
- Fangyuan Shen
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yefang Liu
- College of Basic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- No. 3 Affiliated Hospital of Chengdu University of TCM (West District), Chengdu Pidu District Hospital of TCM, China
| | - Lanchun Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xiaoqiang Chai
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jian Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Quansheng Feng
- College of Basic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xiao Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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19
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Leo CG, Mincarone P, Tumolo MR, Panico A, Guido M, Zizza A, Guarino R, De Santis G, Sedile R, Sabina S. MiRNA expression profiling in HIV pathogenesis, disease progression and response to treatment: a systematic review. Epigenomics 2021; 13:1653-1671. [PMID: 34693727 DOI: 10.2217/epi-2021-0237] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Aim: A systematic review was conducted to identify the association of miRNA expression with HIV pathogenesis, progression and treatment. Methods: A search of articles was conducted in MEDLINE®, Cochrane Central Register of Controlled Trials and Global Health. Results: 35 articles were included. Due to the heterogeneity of HIV phenotypes, a harmonization based on key progression parameters was proposed. The hsa-miR-29 family, hsa-miR-146b-5p and hsa-miR-150-5p, are the most frequently differentially expressed in HIV. Direct comparison of studies was not possible due to heterogeneity in biological samples and miRNA analysis techniques. Conclusion: This is the first attempt to systematically identify miRNA's different expression in well-defined patient phenotypes and could represent a helpful way to increase general knowledge in this field.
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Affiliation(s)
- Carlo Giacomo Leo
- Institute of Clinical Physiology National Research Council, Branch of Lecce, 73100, Italy
| | - Pierpaolo Mincarone
- Institute for Research on Population & Social Policies National Research Council, Research Unit of Brindisi, 72100, Italy
| | - Maria Rosaria Tumolo
- Institute for Research on Population & Social Policies National Research Council, Research Unit of Brindisi, 72100, Italy
| | - Alessandra Panico
- University of Salento, Department of Biological & Environmental Sciences & Technologies, Lecce, 73039, Italy
| | - Marcello Guido
- University of Salento, Department of Biological & Environmental Sciences & Technologies, Lecce, 73039, Italy
| | - Antonella Zizza
- Institute of Clinical Physiology National Research Council, Branch of Lecce, 73100, Italy
| | - Roberto Guarino
- Institute of Clinical Physiology National Research Council, Branch of Lecce, 73100, Italy
| | - Giuseppe De Santis
- Department of Neurology, Card. G. Panico Hospital, Tricase, 73039, Italy
| | - Raffaella Sedile
- Institute of Clinical Physiology National Research Council, Branch of Lecce, 73100, Italy
| | - Saverio Sabina
- Institute of Clinical Physiology National Research Council, Branch of Lecce, 73100, Italy
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20
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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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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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22
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Cortés-Rubio CN, Salgado-Montes de Oca G, Prado-Galbarro FJ, Matías-Florentino M, Murakami-Ogasawara A, Kuri-Cervantes L, Carranco-Arenas AP, Ormsby CE, Cortés-Rubio IK, Reyes-Terán G, Ávila-Ríos S. Longitudinal variation in human immunodeficiency virus long terminal repeat methylation in individuals on suppressive antiretroviral therapy. Clin Epigenetics 2019; 11:134. [PMID: 31519219 PMCID: PMC6743183 DOI: 10.1186/s13148-019-0735-9] [Citation(s) in RCA: 10] [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: 05/14/2019] [Accepted: 08/30/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Persistence of latent, replication-competent provirus in CD4+ T cells of human immunodeficiency virus (HIV)-infected individuals on antiretroviral treatment (ART) is the main obstacle for virus eradication. Methylation of the proviral 5' long terminal repeat (LTR) promoter region has been proposed as a possible mechanism contributing to HIV latency; however, conflicting observations exist regarding its relevance. We assessed 5'-LTR methylation profiles in total CD4+ T cells from blood of 12 participants on short-term ART (30 months) followed up for 2 years, and a cross-sectional group of participants with long-term ART (6-15 years), using next generation sequencing. We then looked for associations between specific 5'-LTR methylation patterns and baseline and follow-up clinical characteristics. RESULTS 5'-LTR methylation was observed in all participants and behaved dynamically. The number of 5'-LTR variants found per sample ranged from 1 to 13, with median sequencing depth of 16270× (IQR 4107×-46760×). An overall significant 5'-LTR methylation increase was observed at month 42 compared to month 30 (median CpG Methylation Index: 74.7% vs. 0%, p = 0.025). This methylation increase was evident in a subset of participants (methylation increase group), while the rest maintained fairly high and constant methylation (constant methylation group). Persons in the methylation increase group were younger, had higher CD4+ T cell gain, larger CD8% decrease, and larger CD4/CD8 ratio change after 48 months on ART (all p < 0.001). Using principal component analysis, the constant methylation and methylation increase groups showed low evidence of separation along time (factor 2: p = 0.04). Variance was largely explained (21%) by age, CD4+/CD8+ T cell change, and CD4+ T cell subpopulation proportions. Persons with long-term ART showed overall high methylation (median CpG Methylation Index: 78%; IQR 71-87%). No differences were observed in residual plasma viral load or proviral load comparing individuals on short-term (both at 30 or 42 months) and long-term ART. CONCLUSIONS Our study shows evidence that HIV 5'-LTR methylation in total CD4+ T cells is dynamic along time and that it can follow different temporal patterns that are associated with a combination of baseline and follow-up clinical characteristics. These observations may account for differences observed between previous contrasting studies.
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Affiliation(s)
- César N. Cortés-Rubio
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Tlalpan 4502, 14080 Mexico City, Mexico
| | - Gonzalo Salgado-Montes de Oca
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Tlalpan 4502, 14080 Mexico City, Mexico
| | | | - Margarita Matías-Florentino
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Tlalpan 4502, 14080 Mexico City, Mexico
| | - Akio Murakami-Ogasawara
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Tlalpan 4502, 14080 Mexico City, Mexico
| | - Leticia Kuri-Cervantes
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Ana P. Carranco-Arenas
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Tlalpan 4502, 14080 Mexico City, Mexico
| | - Christopher E. Ormsby
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Tlalpan 4502, 14080 Mexico City, Mexico
| | | | - Gustavo Reyes-Terán
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Tlalpan 4502, 14080 Mexico City, Mexico
| | - Santiago Ávila-Ríos
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Tlalpan 4502, 14080 Mexico City, Mexico
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Xiao Q, Guo D, Chen S. Application of CRISPR/Cas9-Based Gene Editing in HIV-1/AIDS Therapy. Front Cell Infect Microbiol 2019; 9:69. [PMID: 30968001 PMCID: PMC6439341 DOI: 10.3389/fcimb.2019.00069] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 03/04/2019] [Indexed: 01/09/2023] Open
Abstract
Despite the fact that great efforts have been made in the prevention and therapy of HIV-1 infection, HIV-1/AIDS remains a major threat to global human health. Highly active antiretroviral therapy (HAART) can suppress virus replication, but it cannot eradicate latent viral reservoirs in HIV-1/AIDS patients. Recently, the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated nuclease 9 (Cas9) system has been engineered as an effective gene-editing technology with the potential to treat HIV-1/AIDS. It can be used to target cellular co-factors or HIV-1 genome to reduce HIV-1 infection and clear the provirus, as well as to induce transcriptional activation of latent virus in latent viral reservoirs for elimination. This versatile gene editing technology has been successfully applied to HIV-1/AIDS prevention and reduction in human cells and animal models. Here, we update the rapid progress of CRISPR/Cas9-based HIV-1/AIDS therapy research in recent years and discuss the limitations and future perspectives of its application.
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Affiliation(s)
- Qiaoqiao Xiao
- School of Basic Medical Sciences, Institute of Medical Virology, Wuhan University, Wuhan, China.,Laboratory of Medical Virology, School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Deyin Guo
- Laboratory of Medical Virology, School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Shuliang Chen
- School of Basic Medical Sciences, Institute of Medical Virology, Wuhan University, Wuhan, China.,Department of Veterinary Biosciences, Center for Retrovirus Research, Ohio State University, Columbus, OH, United States
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Moghoofei M, Bokharaei-Salim F, Esghaei M, Keyvani H, Honardoost M, Mostafaei S, Ghasemi A, Tavakoli A, Javanmard D, Babaei F, Garshasbi S, Monavari SH. microRNAs 29, 150, 155, 223 level and their relation to viral and immunological markers in HIV-1 infected naive patients. Future Virol 2018. [DOI: 10.2217/fvl-2018-0055] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Aim: The aim of this study was to assess the relationship between microRNAs and viral and immunological markers in HIV-1 infection. Materials & methods: The expression level of miRNAs was evaluated in 60 HIV-1 patients and 20 healthy controls using real-time PCR assays. Results: The results showed that among all miRNAs, miR-29 and miR-150 were significantly downregulated in HIV-1 patients compared with healthy controls, while miR-155 and miR-223 were significantly upregulated compared with healthy controls (p < 0.001 for all comparisons). Conclusion: The mentioned miRNAs seem to influence the clinical progression of HIV-1 infection in naive patients. Moreover, determining the profiles of miRNAs involved in the pathogenesis of HIV infection and manipulating these miRNAs could lead to opening a new gate to HIV-1 infection control.
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Affiliation(s)
- Mohsen Moghoofei
- 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
- HIV Laboratory of National Center, Vice Chancellor for Health, Iran University of Medical Sciences, Tehran, Iran
| | - Maryam Esghaei
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hossein Keyvani
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Maryam Honardoost
- Endocrine Research Center, Institute of Endocrinology & Metabolism, Iran University of Medical Sciences, Tehran, Iran
| | - Shayan Mostafaei
- Department of Community Medicine, Faculty of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Amir Ghasemi
- Department of Materials Science & Engineering, Sharif University of Technology, Tehran, Iran
| | - Ahmad Tavakoli
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Davod Javanmard
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Farhad Babaei
- Department of Microbiology, Faculty of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Saba Garshasbi
- HIV Laboratory of National Center, Vice Chancellor for Health, Iran University of Medical Sciences, Tehran, Iran
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Changes in the cellular microRNA profile by the intracellular expression of HIV-1 Tat regulator: A potential mechanism for resistance to apoptosis and impaired proliferation in HIV-1 infected CD4+ T cells. PLoS One 2017; 12:e0185677. [PMID: 28968466 PMCID: PMC5624617 DOI: 10.1371/journal.pone.0185677] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 08/28/2017] [Indexed: 12/13/2022] Open
Abstract
HIV-1 induces changes in the miRNA expression profile of infected CD4+ T cells that could improve viral replication. HIV-1 regulator Tat modifies the cellular gene expression and has been appointed as an RNA silencing suppressor. Tat is a 101-residue protein codified by two exons that regulates the elongation of viral transcripts. The first exon of Tat (amino acids 1–72) forms the transcriptionally active protein Tat72, but the presence of the second exon (amino acids 73–101) results in a more competent regulatory protein (Tat101) with additional functions. Intracellular, full-length Tat101 induces functional and morphological changes in CD4+ T cells that contribute to HIV-1 pathogenesis such as delay in T-cell proliferation and protection against FasL-mediated apoptosis. But the precise mechanism by which Tat produces these changes remains unknown. We analyzed how the stable expression of intracellular Tat101 and Tat72 modified the miRNA expression profile in Jurkat cells and if this correlated with changes in apoptotic pathways and cell cycle observed in Tat-expressing cells. Specifically, the enhanced expression of hsa-miR-21 and hsa-miR-222 in Jurkat-Tat101 cells was associated with the reduced expression of target mRNAs encoding proteins related to apoptosis and cell cycle such as PTEN, PDCD4 and CDKN1B. We developed Jurkat cells with stable expression of hsa-miR-21 or hsa-miR-222 and observed a similar pattern to Jurkat-Tat101 in resistance to FasL-mediated apoptosis, cell cycle arrest in G2/M and altered cell morphology. Consequently, upregulation of hsa-miR-21 and hsa-miR-222 by Tat may contribute to protect against apoptosis and to anergy observed in HIV-infected CD4+ T cells.
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27
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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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Abstract
OBJECTIVE Chronic HIV-1 infection leads to widespread inflammation and immune dysregulation. The gastrointestinal mucosa, a primary site for HIV-1 replication, is thought to play a significant role in this response. MicroRNAs (miRs) are small noncoding RNAs that regulate gene expression, including immune activation and inflammation. Here we investigate miR expression and function in the colonic mucosa during HIV-1 infection. DESIGN AND METHODS Using miR profiling, we examined miR expression in the colonic mucosa of HIV-infected patients. These miRs were further parsed to identify those that most likely function in HIV-related inflammation. Using bioinformatics tools, we identified potential target genes which were confirmed using in-vitro functional testing. RESULTS We identified 12 miRs that were differentially expressed in the colonic mucosa of HIV-infected patients with high versus undetectable plasma viral concentrations. Of these, both miR-26a and miR-29a were downregulated in untreated HIV-1 infection, yet not in the colonic mucosa from inflammatory bowel disease. This downregulation occurs within the first hours after infection. These miRs were further shown to directly target IL-6 and STAT3, respectively, with similar changes confirmed in an ex-vivo explant infection model. CONCLUSION miR-26a and miR-29a levels are decreased in the colonic mucosa during chronic HIV-1 infection, and this change may be initiated during acute infection. Both miRs de-repress the IL-6/STAT3 signaling pathway, which could contribute to increased inflammation during infection. These miRs may represent novel therapeutic targets for HIV-1-associated inflammation in the colonic mucosa.
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Huang Z, Nair M. A CRISPR/Cas9 guidance RNA screen platform for HIV provirus disruption and HIV/AIDS gene therapy in astrocytes. Sci Rep 2017; 7:5955. [PMID: 28729655 PMCID: PMC5519727 DOI: 10.1038/s41598-017-06269-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 06/08/2017] [Indexed: 12/13/2022] Open
Abstract
HIV/AIDS remains a major health threat despite significant advances in the prevention and treatment of HIV infection. The major reason is the inability of existing treatments to eradicate the multiple HIV reservoirs in the human body, including astrocytes in the human brain. CRISPR/Cas9 system is an emerging gene-editing technique with the potential to eliminate or disrupt HIV provirus in HIV reservoir cells, which may lead to a complete cure of HIV/AIDS. The key components of CRISPR/Cas9 are guide RNAs (gRNAs) which determine specific sequence targeting of DNAs. This study established a novel, simple and quick screening method to identify gRNA candidates for targeting HIV provirus in astrocytes. Briefly, stable astrocytes clones with an integrated fluorescent HIV reporter and Cas9 expression gene were generated. Various gRNAs were screened for their efficiencies against HIV provirus in these cells. Moreover, these gRNAs and Cas9 protein were successfully tested on HIV latent astrocytes without Cas9 expression to mimic clinical conditions. HIV provirus gene-editing were confirmed by cell genomic DNA PCR and fluorescent marker expression analysis. In the future, the established transgenic cells can be used for other gene-editing studies and is well-suited for high-throughput screen application.
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Affiliation(s)
- Zaohua Huang
- Department of Immunology, Institute of NeuroImmune Pharmacology, Centre for Personalized Nanomedicine, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, 33199, USA
| | - Madahavan Nair
- Department of Immunology, Institute of NeuroImmune Pharmacology, Centre for Personalized Nanomedicine, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, 33199, USA.
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MicroRNA-210, MicroRNA-331, and MicroRNA-7 Are Differentially Regulated in Treated HIV-1-Infected Individuals and Are Associated With Markers of Systemic Inflammation. J Acquir Immune Defic Syndr 2017; 74:e104-e113. [PMID: 27749601 DOI: 10.1097/qai.0000000000001191] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
OBJECTIVE Inflammation may contribute to an increased risk of cardiovascular disease (CVD) in HIV-1 infection. MicroRNAs (miRNAs) are involved in the regulation of inflammation. In treated HIV-1-infected individuals, we aimed to identify differentially expressed miRNAs with known roles in inflammation and CVD risk and to investigate associations between these and systemic inflammation. METHODS In a screening cohort including 14 HIV-1-infected individuals and 9 uninfected controls, microarray profiling was performed using peripheral blood mononuclear cells (PBMCs). Differentially regulated miRNAs previously related to inflammation and CVD were validated using real-time quantitative reverse-transcription polymerase chain reaction in 26 HIV-1-infected individuals and 20 uninfected controls. Validated miRNAs were measured in PBMCs, CD4 and CD8 T cells. Interleukin-6, tumor necrosis factor-alpha, high-sensitivity C-reactive protein, lipopolysaccharide (LPS), cytomegalovirus immunoglobulin G, lipids, and fasting glucose were measured, and associations with validated miRNAs were assessed with multiple linear regression analysis. RESULTS Upregulation of miR-210, miR-7, and miR-331 was found in PBMCs from HIV-1-infected individuals when compared with those from uninfected controls (P < 0.005). In contrast, miR-210 and miR-331 were downregulated in CD8 T cells. In multivariate analysis, miR-210 in CD8 T cells was negatively associated with LPS (P = 0.023) and triglycerides (P = 0.003) but positively associated with tumor necrosis factor-alpha (P = 0.004). MiR-7 in PBMC was positively associated with interleukin-6 (P = 0.025) and fasting glucose (P = 0.005), whereas miR-331 was negatively associated with LPS (P = 0.006). In PBMCs from HIV-1-infected individuals with low cytomegalovirus immunoglobulin G, miR-7, miR-29a, miR-221, and miR-222 were downregulated. CONCLUSION In 2 independent cohorts, miR-210, miR-7, and miR-331 were differentially regulated in treated HIV-1-infected individuals and associated with markers of systemic inflammation.
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Current application of CRISPR/Cas9 gene-editing technique to eradication of HIV/AIDS. Gene Ther 2017; 24:377-384. [PMID: 28471431 DOI: 10.1038/gt.2017.35] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 01/25/2017] [Accepted: 02/01/2017] [Indexed: 12/14/2022]
Abstract
Human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome (AIDS) remains a major health hazard despite significant advances in prevention and treatment of HIV infection. The major reason for the persistence of HIV/AIDS is the inability of existing treatments to clear or eradicate the multiple HIV reservoirs that exist in the human body. To suppress the virus replication and rebound, HIV/AIDS patients must take life-long antiviral medications. The clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated nuclease 9 (Cas9) system is an emerging gene-editing technique with the potential to eliminate or disrupt HIV-integrated genomes or HIV-infected cells from multiple HIV reservoirs, which could result in the complete cure of HIV/AIDS. Encouraging progress has already been reported for the application of the CRISPR/Cas9 technique to HIV/AIDS treatment and prevention, both in vitro in human patient cells and in vivo in animal model experiments. In this review, we will summarize the most recent progress in the application of the CRISPR/Cas9 gene-editing technique to HIV/AIDS therapy and elimination. Future directions and trends of such applications are also discussed.
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Peng F, He J, Loo JFC, Kong SK, Li B, Gu D. Identification of serum MicroRNAs as diagnostic biomarkers for influenza H7N9 infection. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.virep.2016.11.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Advay S, Ahmadi A, Abdi M, Arabzadeh AM. Study of miR-29a-5p Expression in HIV Positive and HIV/HCV Co-Infected Patients in Sanandaj-Iran. HEPATITIS MONTHLY 2016; 17. [DOI: 10.5812/hepatmon.41594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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Rosca A, Anton G, Botezatu A, Temereanca A, Ene L, Achim C, Ruta S. miR-29a associates with viro-immunological markers of HIV infection in treatment experienced patients. J Med Virol 2016; 88:2132-2137. [PMID: 27232693 DOI: 10.1002/jmv.24586] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2016] [Indexed: 01/05/2023]
Abstract
MicroRNAs (miRNAs) are small, non-coding RNA species essential for the post-translational regulation of gene expression. Several miRNA have been proposed to contribute to Human immunodeficiency virus-1 (HIV-1) infection establishment, progression and latency. Among them, miR-29a seems to be of particular interest. The aim of this study was to investigate the association between miR-29a expression and immunologic and virologic markers of HIV infection progression in long-term antiretroviral-treated individuals. In a homogenous group of 165 young adults, with chronic HIV infection, parenterally acquired during childhood, the expression level of miR-29a was found to be inversely correlated with HIV viral load and the degree of immunosuppression, expressed by both CD4 cell count and the CD4/CD8 ratio. There was a significant difference in miR-29a expression according to the patient's response to treatment, with the lowest levels expressed by patients with treatment failure, defined as detectable viremia and CD4 < 350 cells/mm3 . No significant correlation was found between miRNA level and the nadir CD4 count or zenith HIV viral load. This study establishes the association between miR-29a expression and markers of HIV infection in long-term survivors, treatment-experienced patients, suggesting its potential use as an indicator for the on-treatment disease evolution. J. Med. Virol. 88:2132-2137, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Adelina Rosca
- Virology Chair, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania.,Stefan S. Nicolau Virology Institute, Bucharest, Romania
| | - Gabriela Anton
- Stefan S. Nicolau Virology Institute, Bucharest, Romania
| | - Anca Botezatu
- Stefan S. Nicolau Virology Institute, Bucharest, Romania
| | - Aura Temereanca
- Virology Chair, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania.,Stefan S. Nicolau Virology Institute, Bucharest, Romania
| | - Luminita Ene
- Victor Babes Hospital for Infectious and Tropical Diseases, Bucharest, Romania
| | | | - Simona Ruta
- Virology Chair, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania. .,Stefan S. Nicolau Virology Institute, Bucharest, Romania.
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The Regulatory Roles of MicroRNAs in Bone Remodeling and Perspectives as Biomarkers in Osteoporosis. BIOMED RESEARCH INTERNATIONAL 2016; 2016:1652417. [PMID: 27073801 PMCID: PMC4814634 DOI: 10.1155/2016/1652417] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 02/26/2016] [Accepted: 02/29/2016] [Indexed: 02/05/2023]
Abstract
MicroRNAs are involved in many cellular and molecular activities and played important roles in many biological and pathological processes, such as tissue formation, cancer development, diabetes, neurodegenerative diseases, and cardiovascular diseases. Recently, it has been reported that microRNAs can modulate the differentiation and activities of osteoblasts and osteoclasts, the key cells that are involved in bone remodeling process. Meanwhile, the results from our and other research groups showed that the expression profiles of microRNAs in the serum and bone tissues are significantly different in postmenopausal women with or without fractures compared to the control. Therefore, it can be postulated that microRNAs might play important roles in bone remodeling and that they are very likely to be involved in the pathological process of postmenopausal osteoporosis. In this review, we will present the updated research on the regulatory roles of microRNAs in osteoblasts and osteoclasts and the expression profiles of microRNAs in osteoporosis and osteoporotic fracture patients. The perspective of serum microRNAs as novel biomarkers in bone loss disorders such as osteoporosis has also been discussed.
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Recent advances in the identification of Tat-mediated transactivation inhibitors: progressing toward a functional cure of HIV. Future Med Chem 2016; 8:421-42. [PMID: 26933891 DOI: 10.4155/fmc.16.3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The current anti-HIV combination therapy does not eradicate the virus that persists mainly in quiescent infected CD4(+) T cells as a latent integrated provirus that resumes after therapy interruption. The Tat-mediated transactivation (TMT) is a critical step in the HIV replication cycle that could give the opportunity to reduce the size of latent reservoirs. More than two decades of research led to the identification of various TMT inhibitors. While none of them met the criteria to reach the market, the search for a suitable TMT inhibitor is still actively pursued. Really promising compounds, including one in a Phase III clinical trial, have been recently identified, thus warranting an update.
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Louten J, Beach M, Palermino K, Weeks M, Holenstein G. MicroRNAs Expressed during Viral Infection: Biomarker Potential and Therapeutic Considerations. Biomark Insights 2016; 10:25-52. [PMID: 26819546 PMCID: PMC4718089 DOI: 10.4137/bmi.s29512] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 10/22/2015] [Accepted: 10/24/2015] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) are short sequences of noncoding single-stranded RNAs that exhibit inhibitory effects on complementary target mRNAs. Recently, it has been discovered that certain viruses express their own miRNAs, while other viruses activate the transcription of cellular miRNAs for their own benefit. This review summarizes the viral and/or cellular miRNAs that are transcribed during infection, with a focus on the biomarker and therapeutic potential of miRNAs (or their antagomirs). Several human viruses of clinical importance are discussed, namely, herpesviruses, polyomaviruses, hepatitis B virus, hepatitis C virus, human papillomavirus, and human immunodeficiency virus.
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Affiliation(s)
- Jennifer Louten
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, GA, USA
| | - Michael Beach
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, GA, USA
| | - Kristina Palermino
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, GA, USA
| | - Maria Weeks
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, GA, USA
| | - Gabrielle Holenstein
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, GA, USA
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Peng F, He J, Loo JFC, Yao J, Shi L, Liu C, Zhao C, Xie W, Shao Y, Kong SK, Gu D. Identification of microRNAs in Throat Swab as the Biomarkers for Diagnosis of Influenza. Int J Med Sci 2016; 13:77-84. [PMID: 26917988 PMCID: PMC4747873 DOI: 10.7150/ijms.13301] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 12/15/2015] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Influenza is a serious worldwide disease that captures global attention in the past few years after outbreaks. The recent discoveries of microRNA (miRNA) and its unique expression profile in influenza patients have offered a new method for early influenza diagnosis. The aim of this study was to examine the utility of miRNAs for the diagnosis of influenza. METHODS Thirteen selected miRNAs were investigated with the hosts' throat swabs (25 H1N1, 20 H3N2, 20 influenza B and 21 healthy controls) by real-time quantitative polymerase chain reaction (RT-qPCR) using U6 snRNA as endogenous control for normalization, and receiver operating characteristic (ROC) curve/Area under curve (AUC) for analysis. RESULTS miR-29a-3p, miR-30c-5p, miR-34c-3p and miR-181a-5p are useful biomarkers for influenza A detection; and miR-30c-5p, miR-34b-5p, miR-205-5p and miR-449b-5p for influenza B detection. Also, use of both miR-30c-5p and miR-34c-3p (AUC=0.879); and miR-30c-5p and miR-449b-5p (AUC=0.901) are better than using one miRNA to confirm influenza A and influenza B infection, respectively. CONCLUSIONS Given its simplicity, non-invasiveness and specificity, we found that the throat swab-derived miRNAs miR-29a-3p, miR-30c-5p, miR-34b-5p, miR-34c-3p, miR-181a-5p, miR-205-5p and miR-449b-5p are a useful tool for influenza diagnosis on influenza A and B.
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Affiliation(s)
- Fang Peng
- 1. Department of Health Inspection and Quarantine, School of Public Health, Sun Yat-sen University, Guangzhou, China; 2. Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen, China
| | - Jianan He
- 2. Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen, China
| | - Jacky Fong Chuen Loo
- 3. Biochemistry Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Jingyu Yao
- 4. Guangdong Medical University, Zhanjiang, China
| | - Lei Shi
- 2. Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen, China
| | - Chunxiao Liu
- 2. Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen, China
| | - Chunzhong Zhao
- 2. Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen, China
| | - Weidong Xie
- 5. Shenzhen Key Lab of Health Science and Technology, Division of Life Sciences & Health, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
| | - Yonghong Shao
- 6. College of Optoelectronics Engineering, Key Laboratory of Optoelectronic Devices and Systems, Ministry of Education and Guangdong Province, Shenzhen Key Laboratory of Sensor Technology, Shenzhen University, Shenzhen, China
| | - Siu Kai Kong
- 3. Biochemistry Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Dayong Gu
- 1. Department of Health Inspection and Quarantine, School of Public Health, Sun Yat-sen University, Guangzhou, China; 2. Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen, China
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Wang P, Qu X, Zhou X, Shen Y, Ji H, Fu Z, Deng J, Lu P, Yu W, Lu H, Zhu H. Two cellular microRNAs, miR-196b and miR-1290, contribute to HIV-1 latency. Virology 2015; 486:228-38. [PMID: 26469550 DOI: 10.1016/j.virol.2015.09.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 09/19/2015] [Accepted: 09/24/2015] [Indexed: 12/15/2022]
Abstract
Understanding the mechanism of HIV-1 latency is crucial to the viral reservoir eradication. Human cellular miRNAs can modulate HIV-1 expression by targeting of viral RNAs or host gene transcripts. To identify miRNAs modulating HIV-1 latency, we determined the miRNA expression profiles of HIV-1 latently infected and productively infected cells by microarray and qRT-PCR. Among the differentially expressed miRNAs, miR-196b and miR-1290 targeted the 3' untranslated region of HIV-1 and affected its expression. Ectopic expression of these two miRNAs efficiently suppressed HIV-1 production and infectivity. Specific inhibitors of these miRNAs substantially counteracted their effects on HIV-1, as measured either as viral production and infectivity in HEK-293T cells or as HIV-1 RNA expression or viral production in cells isolated from HIV-1-infected individuals. Our study emphasizes the role of cellular miRNAs in HIV-1 latency regulation, and it suggests that inhibitors of miR-196b and miR-1290 could be used to activate latent HIV-1.
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Affiliation(s)
- Pengfei Wang
- State Key Laboratory of Genetic Engineering, and Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, School of Life Sciences, Fudan University, Shanghai, China
| | - Xiying Qu
- State Key Laboratory of Genetic Engineering, and Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, School of Life Sciences, Fudan University, Shanghai, China
| | - Xin Zhou
- State Key Laboratory of Genetic Engineering, and Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, School of Life Sciences, Fudan University, Shanghai, China
| | - Yinzhong Shen
- Department of Infectious Diseases, and Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Haiyan Ji
- State Key Laboratory of Genetic Engineering, and Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, School of Life Sciences, Fudan University, Shanghai, China
| | - Zheng Fu
- State Key Laboratory of Genetic Engineering, and Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, School of Life Sciences, Fudan University, Shanghai, China
| | - Junxiao Deng
- State Key Laboratory of Genetic Engineering, and Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, School of Life Sciences, Fudan University, Shanghai, China
| | - Panpan Lu
- State Key Laboratory of Genetic Engineering, and Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, School of Life Sciences, Fudan University, Shanghai, China
| | - Wenbo Yu
- State Key Laboratory of Genetic Engineering, and Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, School of Life Sciences, Fudan University, Shanghai, China
| | - Hongzhou Lu
- Department of Infectious Diseases, and Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Huanzhang Zhu
- State Key Laboratory of Genetic Engineering, and Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, School of Life Sciences, Fudan University, Shanghai, China.
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Kumar A, Darcis G, Van Lint C, Herbein G. Epigenetic control of HIV-1 post integration latency: implications for therapy. Clin Epigenetics 2015; 7:103. [PMID: 26405463 PMCID: PMC4581042 DOI: 10.1186/s13148-015-0137-6] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 09/17/2015] [Indexed: 12/31/2022] Open
Abstract
With the development of effective combined anti-retroviral therapy (cART), there is significant reduction in deaths associated with human immunodeficiency virus type 1 (HIV-1) infection. However, the complete cure of HIV-1 infection is difficult to achieve without the elimination of latent reservoirs which exist in the infected individuals even under cART regimen. These latent reservoirs established during early infection have long life span, include resting CD4+ T cells, macrophages, central nervous system (CNS) resident macrophage/microglia, and gut-associated lymphoid tissue/macrophages, and can actively produce virus upon interruption of the cART. Several epigenetic and non-epigenetic mechanisms have been implicated in the regulation of viral latency. Epigenetic mechanisms such as histone post translational modifications (e.g., acetylation and methylation) and DNA methylation of the proviral DNA and microRNAs are involved in the establishment of HIV-1 latency. The better understanding of epigenetic mechanisms modulating HIV-1 latency could give clues for the complete eradication of these latent reservoirs. Several latency-reversing agents (LRA) have been found effective in reactivating HIV-1 reservoirs in vitro, ex vivo, and in vivo. Some of these agents target epigenetic modifications to elicit viral expression in order to kill latently infected cells through viral cytopathic effect or host immune response. These therapeutic approaches aimed at achieving a sterilizing cure (elimination of HIV-1 from the human body). In the present review, we will discuss our current understanding of HIV-1 epigenomics and how this information can be moved from the laboratory bench to the patient’s bedside.
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Affiliation(s)
- Amit Kumar
- Department of Virology, Pathogens & Inflammation Laboratory, University of Franche-Comté and COMUE Bourgogne Franche-Comté University, UPRES EA4266, SFR FED 4234, CHRU Besançon, Hôpital Saint-Jacques, 2 place Saint-Jacques, F-25030 Besançon cedex, France
| | - Gilles Darcis
- Service of Molecular Virology, Institute of Molecular Biology and Medicine, Université Libre de Bruxelles (ULB), 12 Rue des Profs Jeener et Brachet, 6041 Gosselies, Belgium
| | - Carine Van Lint
- Service of Molecular Virology, Institute of Molecular Biology and Medicine, Université Libre de Bruxelles (ULB), 12 Rue des Profs Jeener et Brachet, 6041 Gosselies, Belgium
| | - Georges Herbein
- Department of Virology, Pathogens & Inflammation Laboratory, University of Franche-Comté and COMUE Bourgogne Franche-Comté University, UPRES EA4266, SFR FED 4234, CHRU Besançon, Hôpital Saint-Jacques, 2 place Saint-Jacques, F-25030 Besançon cedex, France
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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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Masotti A, Donninelli G, Da Sacco L, Varano B, Del Cornò M, Gessani S. HIV-1 gp120 influences the expression of microRNAs in human monocyte-derived dendritic cells via STAT3 activation. BMC Genomics 2015; 16:480. [PMID: 26116514 PMCID: PMC4483217 DOI: 10.1186/s12864-015-1673-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 05/29/2015] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND MicroRNAs (miRs) are an abundant class of small non-coding RNAs (~22 nt) that reprogram gene expression by targeting mRNA degradation and translational disruption. An emerging concept implicates miR coupling with transcription factors in myeloid cell development and function, thus contributing to host defense and inflammation. The important role that these molecules play in the pathogenesis of HIV-1 is only now emerging. RESULTS We provide evidence that exposure of monocyte-derived dendritic cells (MDDCs) to recombinant HIV-1 R5 gp120, but not to CCR5 natural ligand CCL4, influences the expression of a panel of miRs (i.e., miR-21, miR-155 and miR-181b) regulated by STAT3 and potentially targeting genes belonging to the STAT3 signaling pathway. The blockage of gp120-induced STAT3 activation impairs gp120 capacity to modulate the expression level of above mentioned miRs. Predictive analysis of miR putative targets emphasizes that these miRs share common target genes. Furthermore, gene ontology and pathway enrichment analysis outline that these genes mainly belong to biological processes related to regulation of transcription, in a complex network of interactions involving pathways relevant to HIV-DC interaction. CONCLUSIONS Overall, these results point to gp120-triggered modulation of miR expression via STAT3 activation as a novel molecular mechanism exploited by HIV-1 to affect DC biology and thus modulate the immune response through complex regulatory loops involving, at the same time, miRs and transcription factors.
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Affiliation(s)
- Andrea Masotti
- Bambino Gesù Children's Hospital-IRCCS, Viale di San Paolo 15, 00146, Rome, Italy.
| | - Gloria Donninelli
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy.
| | - Letizia Da Sacco
- Bambino Gesù Children's Hospital-IRCCS, Viale di San Paolo 15, 00146, Rome, Italy.
| | - Barbara Varano
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy.
| | - Manuela Del Cornò
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy.
| | - Sandra Gessani
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy.
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