1
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Gibaut QM, Li C, Cheng A, Moranguinho I, Mori LP, Valente ST. FUBP3 enhances HIV-1 transcriptional activity and regulates immune response pathways in T cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2025; 36:102525. [PMID: 40248217 PMCID: PMC12005928 DOI: 10.1016/j.omtn.2025.102525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2024] [Accepted: 03/21/2025] [Indexed: 04/19/2025]
Abstract
Far-upstream element-binding protein 3 (FUBP3) was identified at actively transcribing HIV promoters through chromatin affinity purification and mass spectrometry. Known for regulating cellular processes such as transcription and translation by binding to DNAs and RNAs, FUBP3's role in HIV transcriptional regulation was previously unrecognized. This study reveals that FUBP3 enhances HIV-1 transcriptional activation by interacting with Tat and trans-activation response (TAR)-RNA, critical for boosting viral transcription through recruitment of activating factors that promote RNA polymerase II (RNAPII) elongation. Transcriptomic analysis, chromatin immunoprecipitation, and biochemical assays demonstrated that FUBP3 associates with and stabilizes TAR-RNA, in a Tat-dependent manner, and enhances Tat steady-state levels via interaction with Tat's basic domain. Suppressing FUBP3 decreased HIV-1 transcription and altered expression of host genes linked to T cell activation and inflammation, underscoring its broad regulatory impact. Additionally, FUBP3 was enriched at active promoters, confirming its role in transcriptional regulation at specific genomic locations. These findings highlight FUBP3's critical role in the HIV-1 life cycle and suggest its potential as a therapeutic target in HIV-1 infection. Additionally, this study expands our understanding of FUBP3's functions in oncogenic and inflammatory pathways.
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Affiliation(s)
- Quentin M.R. Gibaut
- The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, FL 33458, USA
- Department of Immunology and Microbiology, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458, USA
| | - Chuan Li
- Department of Immunology and Microbiology, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458, USA
| | - Anqi Cheng
- The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, FL 33458, USA
- Department of Immunology and Microbiology, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458, USA
| | - Ines Moranguinho
- Department of Immunology and Microbiology, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458, USA
| | - Luisa P. Mori
- The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, FL 33458, USA
- Department of Immunology and Microbiology, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458, USA
| | - Susana T. Valente
- The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, FL 33458, USA
- Department of Immunology and Microbiology, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458, USA
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2
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Schlösser V, Lightfoot HL, Leemann C, Bejoy AM, Tiwari S, Schloßhauer JL, Vongrad V, Brunschweiger A, Hall J, Metzner KJ, Imig J. Anti-HIV-1 Effect of the Fluoroquinolone Enoxacin and Modulation of Pro-Viral hsa-miR-132 Processing in CEM-SS Cells. Noncoding RNA 2025; 11:8. [PMID: 39846686 PMCID: PMC11755467 DOI: 10.3390/ncrna11010008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2024] [Revised: 01/06/2025] [Accepted: 01/13/2025] [Indexed: 01/24/2025] Open
Abstract
BACKGROUND Despite tremendous advances in antiretroviral therapy (ART) against HIV-1 infections, no cure or vaccination is available. Therefore, discovering novel therapeutic strategies remains an urgent need. In that sense, miRNAs and miRNA therapeutics have moved intensively into the focus of recent HIV-1-related investigations. A strong reciprocal interdependence has been demonstrated between HIV-1 infection and changes of the intrinsic cellular miRNA milieu. This interrelationship may direct potential alterations of the host cells' environment beneficial for the virus or its suppression of replication. Whether this tightly balanced and controlled battle can be exploited therapeutically remains to be further addressed. In this context, the fluoroquinolone antibiotic Enoxacin has been demonstrated as a potent modulator of miRNA processing. Here, we test the hypothesis that this applies also to selected HIV-1-related miRNAs. METHODS We studied the effect of Enoxacin on HIV-1 replication coupled with miRNA qRT-PCR analysis of HIV-1-related miRNAs in CEM-SS and MT-4 T-cells. The effects of miRNA mimic transfections combined with Enoxacin treatment on HIV-1 replication were assessed. Finally, we employed an in vitro DICER1 cleavage assay to study the effects of Enoxacin on a pro-HIV-1 miRNA hsa-miR-132 processing. RESULTS We established that Enoxacin, but not the structurally similar compound nalidixic acid, exhibits strong anti-HIV-1 effects in the T-cell line CEM-SS, but not MT-4. We provide experimental data that this effect of Enoxacin is partly attributed to the specific downregulation of mature hsa-miR-132-3p, but not other tested pro- or anti-HIV-1 miRNAs, which is likely due to affecting DICER1 processing. CONCLUSIONS Our findings show an anti-retroviral activity of Enoxacin at least in part by downregulation of hsa-miR-132-3p, which may be relevant for future antiviral therapeutic applications by modulation of the RNA interference pathway.
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Affiliation(s)
- Verena Schlösser
- Institute of Pharmaceutical Sciences, ETH Zurich, 8093 Zurich, Switzerland
| | | | - Christine Leemann
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Aathma Merin Bejoy
- Max Planck Institute of Molecular Physiology, Chemical Genomics Centre, 44227 Dortmund, Germany
| | - Shashank Tiwari
- Max Planck Institute of Molecular Physiology, Chemical Genomics Centre, 44227 Dortmund, Germany
| | - Jeffrey L. Schloßhauer
- Max Planck Institute of Molecular Physiology, Chemical Genomics Centre, 44227 Dortmund, Germany
| | - Valentina Vongrad
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Andreas Brunschweiger
- Institute of Pharmaceutical Sciences, ETH Zurich, 8093 Zurich, Switzerland
- Department of Pharmaceutical and Medicinal Chemistry, University Würzburg, 97074 Würzburg, Germany
| | - Jonathan Hall
- Institute of Pharmaceutical Sciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Karin J. Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Jochen Imig
- Institute of Pharmaceutical Sciences, ETH Zurich, 8093 Zurich, Switzerland
- Max Planck Institute of Molecular Physiology, Chemical Genomics Centre, 44227 Dortmund, Germany
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3
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Tough RH, McLaren PJ. Functionally-informed fine-mapping identifies genetic variants linking increased CHD1L expression and HIV restriction in monocytes. Sci Rep 2025; 15:2325. [PMID: 39825011 PMCID: PMC11748618 DOI: 10.1038/s41598-024-84817-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: 06/13/2024] [Accepted: 12/27/2024] [Indexed: 01/20/2025] Open
Abstract
Human Immunodeficiency Virus Type 1 (HIV) set-point viral load is a strong predictor of disease progression and transmission risk. A recent genome-wide association study in individuals of African ancestries identified a region on chromosome 1 significantly associated with decreased HIV set-point viral load. Knockout of the closest gene, CHD1L, enhanced HIV replication in vitro in myeloid cells. However, it remains unclear if HIV spVL associated variants are associated with CHD1L gene expression changes. Here we apply a heuristic fine-mapping approach to prioritize combinations of variants that explain the majority of set-point viral load variance and identify variants likely driving the association. We assess the combined impact of these variants on CHD1L regulation using publicly available sequencing studies, and test the relationship between CHD1L expression and set-point viral load using imputed CHD1L expression from monocytes. Taken together, this work characterizes genetically regulated CHD1L expression and further expands our knowledge of CHD1L-mediated HIV restriction in monocytes.
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Affiliation(s)
- Riley H Tough
- Sexually Transmitted and Bloodborne Infections Surveillance and Molecular Epidemiology, Sexually Transmitted and Bloodborne Infections Division at the JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, MB, R3E 3L5, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada
| | - Paul J McLaren
- Sexually Transmitted and Bloodborne Infections Surveillance and Molecular Epidemiology, Sexually Transmitted and Bloodborne Infections Division at the JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, MB, R3E 3L5, Canada.
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada.
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4
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Chen X, Chen R, Wen L, Qin T, Liao Y, Tao X, Yuan Z, Wei W, Li J, Huang Y, Wei W, Liu J, Su J, Ye L, Liang H, Jiang J. Long Noncoding RNA LINC02453 Inhibits HIV-1 Replication by Binding With SEC13 to Regulate the Viral Productive Cycle. J Med Virol 2024; 96:e70116. [PMID: 39704187 DOI: 10.1002/jmv.70116] [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: 04/27/2024] [Revised: 10/31/2024] [Accepted: 11/26/2024] [Indexed: 12/21/2024]
Abstract
Emerging evidence underscores the pivotal role of long noncoding RNAs (lncRNAs) as crucial regulators within the HIV life cycle. However, the precise functions and detailed mechanisms by which lncRNAs operate in HIV-1 highly exposed but persistently seronegative (HESN) individuals remain currently unknown. Through RNA sequencing analysis of the HESN individual and the matched control, we identified potential lncRNAs. Then, we conducted validation experiments at the population level, while cellular models of HIV-1 infection were constructed for functional experimental investigations in vitro. Subcellular localization of the identified lncRNA was determined, followed by an exploration of the specific regulatory mechanism underlying HIV resistance through some experiments, such as RNA pull-down, western blot and Hirt assays. LncRNA LINC02453 is highly expressed in HESN. Moreover, LINC02453 is identified as a novel lncRNA associated with heightened resistance to HIV-1. LINC02453 is predominantly localized in the nucleus and binds to SEC13, a component of the nuclear pore complex, leading to the inhibition of HIV-1 replication by regulating key processes such as late reverse transcription, nuclear import, and DNA integration. Our findings suggest that LINC02453 may serve as a prospective target for the development of innovative anti-HIV therapeutics.
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Affiliation(s)
- Xiu Chen
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Engineering Center for Organoids and Organ-on-Chips of Highly Pathogenic Microbial Infections & Biosafety III Laboratory, Life Science Institute, Guangxi Medical University, Nanning, Guangxi, China
| | - Rongfeng Chen
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Engineering Center for Organoids and Organ-on-Chips of Highly Pathogenic Microbial Infections & Biosafety III Laboratory, Life Science Institute, Guangxi Medical University, Nanning, Guangxi, China
| | - Liufang Wen
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Engineering Center for Organoids and Organ-on-Chips of Highly Pathogenic Microbial Infections & Biosafety III Laboratory, Life Science Institute, Guangxi Medical University, Nanning, Guangxi, China
| | - Tongxue Qin
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Engineering Center for Organoids and Organ-on-Chips of Highly Pathogenic Microbial Infections & Biosafety III Laboratory, Life Science Institute, Guangxi Medical University, Nanning, Guangxi, China
| | - Yinlu Liao
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Engineering Center for Organoids and Organ-on-Chips of Highly Pathogenic Microbial Infections & Biosafety III Laboratory, Life Science Institute, Guangxi Medical University, Nanning, Guangxi, China
| | - Xing Tao
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Engineering Center for Organoids and Organ-on-Chips of Highly Pathogenic Microbial Infections & Biosafety III Laboratory, Life Science Institute, Guangxi Medical University, Nanning, Guangxi, China
| | - Zongxiang Yuan
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Engineering Center for Organoids and Organ-on-Chips of Highly Pathogenic Microbial Infections & Biosafety III Laboratory, Life Science Institute, Guangxi Medical University, Nanning, Guangxi, China
| | - Wudi Wei
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Engineering Center for Organoids and Organ-on-Chips of Highly Pathogenic Microbial Infections & Biosafety III Laboratory, Life Science Institute, Guangxi Medical University, Nanning, Guangxi, China
| | - Jinmiao Li
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Engineering Center for Organoids and Organ-on-Chips of Highly Pathogenic Microbial Infections & Biosafety III Laboratory, Life Science Institute, Guangxi Medical University, Nanning, Guangxi, China
| | - Youjin Huang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Engineering Center for Organoids and Organ-on-Chips of Highly Pathogenic Microbial Infections & Biosafety III Laboratory, Life Science Institute, Guangxi Medical University, Nanning, Guangxi, China
| | - Wenfei Wei
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Engineering Center for Organoids and Organ-on-Chips of Highly Pathogenic Microbial Infections & Biosafety III Laboratory, Life Science Institute, Guangxi Medical University, Nanning, Guangxi, China
| | - Jie Liu
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Engineering Center for Organoids and Organ-on-Chips of Highly Pathogenic Microbial Infections & Biosafety III Laboratory, Life Science Institute, Guangxi Medical University, Nanning, Guangxi, China
| | - Jinming Su
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Engineering Center for Organoids and Organ-on-Chips of Highly Pathogenic Microbial Infections & Biosafety III Laboratory, Life Science Institute, Guangxi Medical University, Nanning, Guangxi, China
| | - Li Ye
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Engineering Center for Organoids and Organ-on-Chips of Highly Pathogenic Microbial Infections & Biosafety III Laboratory, Life Science Institute, Guangxi Medical University, Nanning, Guangxi, China
| | - Hao Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Engineering Center for Organoids and Organ-on-Chips of Highly Pathogenic Microbial Infections & Biosafety III Laboratory, Life Science Institute, Guangxi Medical University, Nanning, Guangxi, China
| | - Junjun Jiang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Engineering Center for Organoids and Organ-on-Chips of Highly Pathogenic Microbial Infections & Biosafety III Laboratory, Life Science Institute, Guangxi Medical University, Nanning, Guangxi, China
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5
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Schynkel T, Snippenberg WV, Verniers K, Jang GM, Krogan NJ, Mestdagh P, Vandekerckhove L, Trypsteen W. Interactome of the HIV-1 proteome and human host RNA. EMBO Rep 2024; 25:4078-4090. [PMID: 39122863 PMCID: PMC11387401 DOI: 10.1038/s44319-024-00222-6] [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: 11/09/2023] [Revised: 07/18/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024] Open
Abstract
The human immunodeficiency virus (HIV-1) is highly dependent on a variety of host factors. Beside proteins, host RNA molecules are reported to aid HIV-1 replication and latency maintenance. Here, we implement multiple workflows of native RNA immunoprecipitation and sequencing (nRIPseq) to determine direct host RNA interaction partners of all 18 HIV-1 (poly)proteins. We identify 1,727 HIV-1 protein - human RNA interactions in the Jurkat cell line and 1,558 interactions in SupT1 cells for a subset of proteins, and discover distinct cellular pathways that seem to be used or controlled by HIV-1 on the RNA level: Tat binds mRNAs of proteins involved in the super elongation complex (AFF1-4, Cyclin-T1). Correlation of the interaction scores (based on binding abundancy) allows identifying the highest confidence interactions, for which we perform a small-scale knockdown screen that leads to the identification of three HIV-1 protein binding RNA interactors involved in HIV-1 replication (AFF2, H4C9 and RPLP0).
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Affiliation(s)
- Tinus Schynkel
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University and Ghent University Hospital, Ghent, 9000, Belgium
| | - Willem van Snippenberg
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University and Ghent University Hospital, Ghent, 9000, Belgium
- OncoRNALab, Center for Medical Genetics (CMGG), Ghent University, Ghent, 9000, Belgium
| | - Kimberly Verniers
- OncoRNALab, Center for Medical Genetics (CMGG), Ghent University, Ghent, 9000, Belgium
| | - Gwendolyn M Jang
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
| | - Pieter Mestdagh
- OncoRNALab, Center for Medical Genetics (CMGG), Ghent University, Ghent, 9000, Belgium
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University and Ghent University Hospital, Ghent, 9000, Belgium.
| | - Wim Trypsteen
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University and Ghent University Hospital, Ghent, 9000, Belgium.
- OncoRNALab, Center for Medical Genetics (CMGG), Ghent University, Ghent, 9000, Belgium.
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6
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Kmiec D, Kirchhoff F. Antiviral factors and their counteraction by HIV-1: many uncovered and more to be discovered. J Mol Cell Biol 2024; 16:mjae005. [PMID: 38318650 PMCID: PMC11334937 DOI: 10.1093/jmcb/mjae005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/13/2023] [Accepted: 02/04/2024] [Indexed: 02/07/2024] Open
Abstract
Extensive studies on HIV-1 have led to the discovery of a variety of structurally and functionally diverse innate defense factors that target various steps of the retroviral replication cycle. Some of them, such as APOBEC3, tetherin, and SERINC5, are well established. Their importance is evident from the fact that HIV-1 uses its accessory proteins Vif, Vpu, and Nef to counteract them. However, the list of antiviral factors is constantly increasing, and accumulating evidence suggests that innate defense mechanisms, which restrict HIV-1 and/or are counteracted by viral proteins, remain to be discovered. These antiviral factors are relevant to diseases other than HIV/AIDS, since they are commonly active against various viral pathogens. In this review, we provide an overview of recently reported antiretroviral factors and viral countermeasures, present the evidence suggesting that more innate defense mechanisms remain to be discovered, and discuss why this is a challenging but rewarding task.
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Affiliation(s)
- Dorota Kmiec
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
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7
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Chua SCJH, Cui J, Sachaphibulkij K, Tan ISL, Tan HQ, Lim HM, Engelberg D, Lim LHK. The ER-Golgi transport of influenza virus through NS1-Sec13 association during virus replication. Microbiol Spectr 2024; 12:e0260923. [PMID: 38038453 PMCID: PMC10782970 DOI: 10.1128/spectrum.02609-23] [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: 06/26/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023] Open
Abstract
IMPORTANCE Influenza A virus is a respiratory virus that can cause complications such as acute bronchitis and secondary bacterial pneumonia. Drug therapies and vaccines are available against influenza, albeit limited by drug resistance and the non-universal vaccine administration. Hence there is a need for host-targeted therapies against influenza to provide an effective alternative therapeutic target. Sec13 was identified as a novel host interactor of influenza. Endoplasmic reticulum-to-Golgi transport is an important pathway of influenza virus replication and viral export. Specifically, Sec13 has a functional role in influenza replication and virulence.
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Affiliation(s)
- Sonja C. J. H. Chua
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Immunology Program, Life Sciences Institute, National University of Singapore, Singapore, Singapore
- NUSMED Immunology Translational Research Programme, National University of Singapore, Singapore, Singapore
- CREATE-NUS-HUJ Molecular Mechanisms of Inflammatory Diseases Programme, National University of Singapore, Singapore, Singapore
- Department of Biological Chemistry, The Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jianzhou Cui
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Immunology Program, Life Sciences Institute, National University of Singapore, Singapore, Singapore
- NUSMED Immunology Translational Research Programme, National University of Singapore, Singapore, Singapore
| | - Karishma Sachaphibulkij
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Immunology Program, Life Sciences Institute, National University of Singapore, Singapore, Singapore
- NUSMED Immunology Translational Research Programme, National University of Singapore, Singapore, Singapore
| | - Isabelle Siang Ling Tan
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Immunology Program, Life Sciences Institute, National University of Singapore, Singapore, Singapore
- NUSMED Immunology Translational Research Programme, National University of Singapore, Singapore, Singapore
| | - Hui Qing Tan
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Immunology Program, Life Sciences Institute, National University of Singapore, Singapore, Singapore
- NUSMED Immunology Translational Research Programme, National University of Singapore, Singapore, Singapore
| | - Hong Meng Lim
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Immunology Program, Life Sciences Institute, National University of Singapore, Singapore, Singapore
- NUSMED Immunology Translational Research Programme, National University of Singapore, Singapore, Singapore
| | - David Engelberg
- CREATE-NUS-HUJ Molecular Mechanisms of Inflammatory Diseases Programme, National University of Singapore, Singapore, Singapore
- Department of Biological Chemistry, The Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Lina H. K. Lim
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Immunology Program, Life Sciences Institute, National University of Singapore, Singapore, Singapore
- NUSMED Immunology Translational Research Programme, National University of Singapore, Singapore, Singapore
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8
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Sertznig H, Roesmann F, Wilhelm A, Heininger D, Bleekmann B, Elsner C, Santiago M, Schuhenn J, Karakoese Z, Benatzy Y, Snodgrass R, Esser S, Sutter K, Dittmer U, Widera M. SRSF1 acts as an IFN-I-regulated cellular dependency factor decisively affecting HIV-1 post-integration steps. Front Immunol 2022; 13:935800. [PMID: 36458014 PMCID: PMC9706209 DOI: 10.3389/fimmu.2022.935800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 10/19/2022] [Indexed: 08/24/2023] Open
Abstract
Efficient HIV-1 replication depends on balanced levels of host cell components including cellular splicing factors as the family of serine/arginine-rich splicing factors (SRSF, 1-10). Type I interferons (IFN-I) play a crucial role in the innate immunity against HIV-1 by inducing the expression of IFN-stimulated genes (ISGs) including potent host restriction factors. The less well known IFN-repressed genes (IRepGs) might additionally affect viral replication by downregulating host dependency factors that are essential for the viral life cycle; however, so far, the knowledge about IRepGs involved in HIV-1 infection is very limited. In this work, we could demonstrate that HIV-1 infection and the associated ISG induction correlated with low SRSF1 levels in intestinal lamina propria mononuclear cells (LPMCs) and peripheral blood mononuclear cells (PBMCs) during acute and chronic HIV-1 infection. In HIV-1-susceptible cell lines as well as primary monocyte-derived macrophages (MDMs), expression levels of SRSF1 were transiently repressed upon treatment with specific IFNα subtypes in vitro. Mechanically, 4sU labeling of newly transcribed mRNAs revealed that IFN-mediated SRSF1 repression is regulated on early RNA level. SRSF1 knockdown led to an increase in total viral RNA levels, but the relative proportion of the HIV-1 viral infectivity factor (Vif) coding transcripts, which is essential to counteract APOBEC3G-mediated host restriction, was significantly reduced. In the presence of high APOBEC3G levels, however, increased LTR activity upon SRSF1 knockdown facilitated the overall replication, despite decreased vif mRNA levels. In contrast, SRSF1 overexpression significantly impaired HIV-1 post-integration steps including LTR transcription, alternative splice site usage, and virus particle production. Since balanced SRSF1 levels are crucial for efficient viral replication, our data highlight the so far undescribed role of SRSF1 acting as an IFN-modulated cellular dependency factor decisively regulating HIV-1 post-integration steps.
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Affiliation(s)
- Helene Sertznig
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Fabian Roesmann
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - Alexander Wilhelm
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - Delia Heininger
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - Barbara Bleekmann
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Carina Elsner
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Mario Santiago
- Department of Medicine, University of Colorado Denver, Aurora, CO, United States
| | - Jonas Schuhenn
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Zehra Karakoese
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Yvonne Benatzy
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt am Main, Frankfurt, Germany
| | - Ryan Snodgrass
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt am Main, Frankfurt, Germany
| | - Stefan Esser
- Clinic of Dermatology, University Hospital, University of Duisburg-Essen, Essen, Germany
| | - Kathrin Sutter
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Ulf Dittmer
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Marek Widera
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
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9
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Cisneros WJ, Cornish D, Hultquist JF. Application of CRISPR-Cas9 Gene Editing for HIV Host Factor Discovery and Validation. Pathogens 2022; 11:891. [PMID: 36015010 PMCID: PMC9415735 DOI: 10.3390/pathogens11080891] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/30/2022] [Accepted: 08/03/2022] [Indexed: 12/04/2022] Open
Abstract
Human Immunodeficiency Virus (HIV) interacts with a wide array of host factors at each stage of its lifecycle to facilitate replication and circumvent the immune response. Identification and characterization of these host factors is critical for elucidating the mechanism of viral replication and for developing next-generation HIV-1 therapeutic and curative strategies. Recent advances in CRISPR-Cas9-based genome engineering approaches have provided researchers with an assortment of new, valuable tools for host factor discovery and interrogation. Genome-wide screening in a variety of in vitro cell models has helped define the critical host factors that play a role in various cellular and biological contexts. Targeted manipulation of specific host factors by CRISPR-Cas9-mediated gene knock-out, overexpression, and/or directed repair have furthermore allowed for target validation in primary cell models and mechanistic inquiry through hypothesis-based testing. In this review, we summarize several CRISPR-based screening strategies for the identification of HIV-1 host factors and highlight how CRISPR-Cas9 approaches have been used to elucidate the molecular mechanisms of viral replication and host response. Finally, we examine promising new technologies in the CRISPR field and how these may be applied to address critical questions in HIV-1 biology going forward.
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Affiliation(s)
- William J. Cisneros
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Daphne Cornish
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Judd F. Hultquist
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
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10
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Abstract
To identify novel host factors as putative targets to reverse HIV-1 latency, we performed an insertional mutagenesis genetic screen in a latent HIV-1 infected pseudohaploid KBM7 cell line (Hap-Lat). Following mutagenesis, insertions were mapped to the genome, and bioinformatic analysis resulted in the identification of 69 candidate host genes involved in maintaining HIV-1 latency. A select set of candidate genes was functionally validated using short hairpin RNA (shRNA)-mediated depletion in latent HIV-1 infected J-Lat A2 and 11.1 T cell lines. We confirmed ADK, CHD9, CMSS1, EVI2B, EXOSC8, FAM19A, GRIK5, IRF2BP2, NF1, and USP15 as novel host factors involved in the maintenance of HIV-1 latency. Chromatin immunoprecipitation assays indicated that CHD9, a chromodomain helicase DNA-binding protein, maintains HIV-1 latency via direct association with the HIV-1 5′ long terminal repeat (LTR), and its depletion results in increased histone acetylation at the HIV-1 promoter, concomitant with HIV-1 latency reversal. FDA-approved inhibitors 5-iodotubercidin, trametinib, and topiramate, targeting ADK, NF1, and GRIK5, respectively, were characterized for their latency reversal potential. While 5-iodotubercidin exhibited significant cytotoxicity in both J-Lat and primary CD4+ T cells, trametinib reversed latency in J-Lat cells but not in latent HIV-1 infected primary CD4+ T cells. Importantly, topiramate reversed latency in cell line models, in latently infected primary CD4+ T cells, and crucially in CD4+ T cells from three people living with HIV-1 (PLWH) under suppressive antiretroviral therapy, without inducing T cell activation or significant toxicity. Thus, using an adaptation of a haploid forward genetic screen, we identified novel and druggable host factors contributing to HIV-1 latency.
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11
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D'Amico D, Valdebenito S, Eugenin EA. The role of Pannexin-1 channels and extracellular ATP in the pathogenesis of the human immunodeficiency virus. Purinergic Signal 2021; 17:563-576. [PMID: 34542793 DOI: 10.1007/s11302-021-09817-3] [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: 06/03/2021] [Accepted: 08/03/2021] [Indexed: 10/20/2022] Open
Abstract
Only recently, the role of large ionic channels such as Pannexin-1 channels and Connexin hemichannels has been implicated in several physiological and pathological conditions, including HIV infection and associated comorbidities. These channels are in a closed stage in healthy conditions, but in pathological conditions including HIV, Pannexin-1 channels and Connexin hemichannels become open. Our data demonstrate that acute and chronic HIV infection induces channel opening (Pannexin and Connexin channels), ATP release into the extracellular space, and subsequent activation of purinergic receptors in immune and non-immune cells. We demonstrated that Pannexin and Connexin channels contribute to HIV infection and replication, the long-term survival of viral reservoirs, and comorbidities such as NeuroHIV. Here, we discuss the available data to support the participation of these channels in the HIV life cycle and the potential therapeutic approach to prevent HIV-associated comorbidities.
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Affiliation(s)
- Daniela D'Amico
- Department of Neuroscience , Cell Biology, and Anatomy, University of Texas Medical Branch (UTMB), Research Building 17, 105 11th Street, Galveston, TX, 77555, USA
| | - Silvana Valdebenito
- Department of Neuroscience , Cell Biology, and Anatomy, University of Texas Medical Branch (UTMB), Research Building 17, 105 11th Street, Galveston, TX, 77555, USA
| | - Eliseo A Eugenin
- Department of Neuroscience , Cell Biology, and Anatomy, University of Texas Medical Branch (UTMB), Research Building 17, 105 11th Street, Galveston, TX, 77555, USA.
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12
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Katz S, Song J, Webb KP, Lounsbury NW, Bryant CE, Fraser IDC. SIGNAL: A web-based iterative analysis platform integrating pathway and network approaches optimizes hit selection from genome-scale assays. Cell Syst 2021; 12:338-352.e5. [PMID: 33894945 DOI: 10.1016/j.cels.2021.03.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 11/25/2020] [Accepted: 03/03/2021] [Indexed: 01/13/2023]
Abstract
Hit selection from high-throughput assays remains a critical bottleneck in realizing the potential of omic-scale studies in biology. Widely used methods such as setting of cutoffs, prioritizing pathway enrichments, or incorporating predicted network interactions offer divergent solutions yet are associated with critical analytical trade-offs. The specific limitations of these individual approaches and the lack of a systematic way by which to integrate their rankings have contributed to limited overlap in the reported results from comparable genome-wide studies and costly inefficiencies in secondary validation efforts. Using comparative analysis of parallel independent studies as a benchmark, we characterize the specific complementary contributions of each approach and demonstrate an optimal framework to integrate these methods. We describe selection by iterative pathway group and network analysis looping (SIGNAL), an integrated, iterative approach that uses both pathway and network methods to optimize gene prioritization. SIGNAL is accessible as a rapid user-friendly web-based application (https://signal.niaid.nih.gov). A record of this paper's transparent peer review is included in the Supplemental information.
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Affiliation(s)
- Samuel Katz
- NIAID, National Institutes of Health, Laboratory of Immune System Biology, Bethesda, MD 20892, USA; University of Cambridge, Department of Veterinary Medicine, Cambridge, UK
| | - Jian Song
- NIAID, National Institutes of Health, Laboratory of Immune System Biology, Bethesda, MD 20892, USA
| | - Kyle P Webb
- NIAID, National Institutes of Health, Laboratory of Immune System Biology, Bethesda, MD 20892, USA
| | - Nicolas W Lounsbury
- NIAID, National Institutes of Health, Laboratory of Immune System Biology, Bethesda, MD 20892, USA
| | - Clare E Bryant
- University of Cambridge, Department of Veterinary Medicine, Cambridge, UK
| | - Iain D C Fraser
- NIAID, National Institutes of Health, Laboratory of Immune System Biology, Bethesda, MD 20892, USA.
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13
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Chand K, Iyer K, Mitra D. Comparative analysis of differential gene expression of HSP40 and HSP70 family isoforms during heat stress and HIV-1 infection in T-cells. Cell Stress Chaperones 2021; 26:403-416. [PMID: 33405054 PMCID: PMC7925753 DOI: 10.1007/s12192-020-01185-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 11/25/2020] [Accepted: 12/01/2020] [Indexed: 12/17/2022] Open
Abstract
Heat shock proteins (HSPs) are a family of cellular proteins involved in a variety of biological functions including chaperone activity. HSPs are classified based on their molecular weight and each family has several isoforms in eukaryotes. HSP40 is the most diverse family acting as a co-chaperone for the highly conserved HSP70 family. Some of the isoforms are reported to be induced during heat stress. Few studies have also highlighted the diverse role of some isoforms in different stress conditions including viral infections. But till date, no study has comprehensively examined the expression profile of different HSP40 and 70 isoforms in either heat stress or HIV-1 infection, a virus that is responsible for the pandemic of AIDS. In the present study, we have compared the mRNA expression profile of HSP40 and HSP70 isoforms during heat stress and HIV-1 infection in a T-cell line and also validated the HIV-1 stress results in peripheral blood mononuclear cells. In case of HSP70, we observed that three isoforms (HSPA1A, HSPA1B, and HSPA6) are highly upregulated during heat stress, but these isoforms were found to be downregulated during the peak of HIV-1 infection. While in case of HSP40, we found that only DNAJA4, DNAJB1, and DNAJB4 showed significant upregulation during heat stress, whereas in HIV-1 infection, majority of the isoforms were induced significantly. Stress-dependent differential expression observed here indicates that different HSP40 and HSP70 isoforms may have specific roles during HIV-1 infection and thus could be important for future studies.
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Affiliation(s)
- Kailash Chand
- National Centre for Cell Science, SP Pune University Campus, Ganeshkhind, Pune, Maharashtra, 411007, India
| | - Kruthika Iyer
- National Centre for Cell Science, SP Pune University Campus, Ganeshkhind, Pune, Maharashtra, 411007, India
| | - Debashis Mitra
- National Centre for Cell Science, SP Pune University Campus, Ganeshkhind, Pune, Maharashtra, 411007, India.
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14
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Song G, Lee EM, Pan J, Xu M, Rho HS, Cheng Y, Whitt N, Yang S, Kouznetsova J, Klumpp-Thomas C, Michael SG, Moore C, Yoon KJ, Christian KM, Simeonov A, Huang W, Xia M, Huang R, Lal-Nag M, Tang H, Zheng W, Qian J, Song H, Ming GL, Zhu H. An Integrated Systems Biology Approach Identifies the Proteasome as A Critical Host Machinery for ZIKV and DENV Replication. GENOMICS, PROTEOMICS & BIOINFORMATICS 2021; 19:108-122. [PMID: 33610792 PMCID: PMC8498969 DOI: 10.1016/j.gpb.2020.06.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 04/04/2020] [Accepted: 08/06/2020] [Indexed: 01/22/2023]
Abstract
The Zika virus (ZIKV) and dengue virus (DENV) flaviviruses exhibit similar replicative processes but have distinct clinical outcomes. A systematic understanding of virus-host protein-protein interaction networks can reveal cellular pathways critical to viral replication and disease pathogenesis. Here we employed three independent systems biology approaches toward this goal. First, protein array analysis of direct interactions between individual ZIKV/DENV viral proteins and 20,240 human proteins revealed multiple conserved cellular pathways and protein complexes, including proteasome complexes. Second, an RNAi screen of 10,415 druggable genes identified the host proteins required for ZIKV infection and uncovered that proteasome proteins were crucial in this process. Third, high-throughput screening of 6016 bioactive compounds for ZIKV inhibition yielded 134 effective compounds, including six proteasome inhibitors that suppress both ZIKV and DENV replication. Integrative analyses of these orthogonal datasets pinpoint proteasomes as critical host machinery for ZIKV/DENV replication. Our study provides multi-omics datasets for further studies of flavivirus-host interactions, disease pathogenesis, and new drug targets.
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Affiliation(s)
- Guang Song
- Department of Pharmacology & Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Emily M. Lee
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Jianbo Pan
- Department of Ophthalmology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Miao Xu
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA,Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Hee-Sool Rho
- Department of Pharmacology & Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Yichen Cheng
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Nadia Whitt
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shu Yang
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jennifer Kouznetsova
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Carleen Klumpp-Thomas
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Samuel G. Michael
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cedric Moore
- Department of Pharmacology & Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Ki-Jun Yoon
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA,Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kimberly M. Christian
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wenwei Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Menghang Xia
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ruili Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Madhu Lal-Nag
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA,Corresponding authors.
| | - Hengli Tang
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA,Corresponding authors.
| | - Wei Zheng
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA,Corresponding authors.
| | - Jiang Qian
- Department of Ophthalmology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA,Corresponding authors.
| | - Hongjun Song
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA,Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Department of Cell and Developmental Biology, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Institute for Regenerative Medicine, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,The Epigenetics Institute, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Corresponding authors.
| | - Guo-li Ming
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA,Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Department of Cell and Developmental Biology, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Institute for Regenerative Medicine, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Corresponding authors.
| | - Heng Zhu
- Department of Pharmacology & Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA,Corresponding authors.
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15
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Moron-Lopez S, Telwatte S, Sarabia I, Battivelli E, Montano M, Macedo AB, Aran D, Butte AJ, Jones RB, Bosque A, Verdin E, Greene WC, Wong JK, Yukl SA. Human splice factors contribute to latent HIV infection in primary cell models and blood CD4+ T cells from ART-treated individuals. PLoS Pathog 2020; 16:e1009060. [PMID: 33253324 PMCID: PMC7728277 DOI: 10.1371/journal.ppat.1009060] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 12/10/2020] [Accepted: 10/09/2020] [Indexed: 01/04/2023] Open
Abstract
It is unclear what mechanisms govern latent HIV infection in vivo or in primary cell models. To investigate these questions, we compared the HIV and cellular transcription profile in three primary cell models and peripheral CD4+ T cells from HIV-infected ART-suppressed individuals using RT-ddPCR and RNA-seq. All primary cell models recapitulated the block to HIV multiple splicing seen in cells from ART-suppressed individuals, suggesting that this may be a key feature of HIV latency in primary CD4+ T cells. Blocks to HIV transcriptional initiation and elongation were observed more variably among models. A common set of 234 cellular genes, including members of the minor spliceosome pathway, was differentially expressed between unstimulated and activated cells from primary cell models and ART-suppressed individuals, suggesting these genes may play a role in the blocks to HIV transcription and splicing underlying latent infection. These genes may represent new targets for therapies designed to reactivate or silence latently-infected cells.
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Affiliation(s)
- Sara Moron-Lopez
- University of California San Francisco, San Francisco, California, United States of America
- San Francisco VA Medical Center, San Francisco, California, United States of America
| | - Sushama Telwatte
- University of California San Francisco, San Francisco, California, United States of America
- San Francisco VA Medical Center, San Francisco, California, United States of America
| | - Indra Sarabia
- George Washington University, Washington DC, United States of America
| | | | - Mauricio Montano
- Gladstone Institutes, San Francisco, California, United States of America
| | - Amanda B. Macedo
- George Washington University, Washington DC, United States of America
| | - Dvir Aran
- University of California San Francisco, San Francisco, California, United States of America
| | - Atul J. Butte
- University of California San Francisco, San Francisco, California, United States of America
| | - R. Brad Jones
- Infectious Diseases Division, Weill Cornell Medicine, New York City, New York, United States of America
| | - Alberto Bosque
- George Washington University, Washington DC, United States of America
| | - Eric Verdin
- Buck Institute, Novato, California, United States of America
| | - Warner C. Greene
- University of California San Francisco, San Francisco, California, United States of America
- Gladstone Institutes, San Francisco, California, United States of America
| | - Joseph K. Wong
- University of California San Francisco, San Francisco, California, United States of America
- San Francisco VA Medical Center, San Francisco, California, United States of America
| | - Steven A. Yukl
- University of California San Francisco, San Francisco, California, United States of America
- San Francisco VA Medical Center, San Francisco, California, United States of America
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16
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Kong W, Biswas A, Zhou D, Fiches G, Fujinaga K, Santoso N, Zhu J. Nucleolar protein NOP2/NSUN1 suppresses HIV-1 transcription and promotes viral latency by competing with Tat for TAR binding and methylation. PLoS Pathog 2020; 16:e1008430. [PMID: 32176734 PMCID: PMC7098636 DOI: 10.1371/journal.ppat.1008430] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 03/26/2020] [Accepted: 02/24/2020] [Indexed: 01/11/2023] Open
Abstract
Recent efforts have been paid to identify previously unrecognized HIV-1 latency-promoting genes (LPGs) that can potentially be targeted for eradication of HIV-1 latent reservoirs. From our earlier orthologous RNAi screens of host factors regulating HIV-1 replication, we identified that the nucleolar protein NOP2/NSUN1, a m5C RNA methyltransferase (MTase), is an HIV-1 restriction factor. Loss- and gain-of-function analyses confirmed that NOP2 restricts HIV-1 replication. Depletion of NOP2 promotes the reactivation of latently infected HIV-1 proviruses in multiple cell lines as well as primary CD4+ T cells, alone or in combination with latency-reversing agents (LRAs). Mechanistically, NOP2 associates with HIV-1 5' LTR, interacts with HIV-1 TAR RNA by competing with HIV-1 Tat protein, as well as contributes to TAR m5C methylation. RNA MTase catalytic domain (MTD) of NOP2 mediates its competition with Tat and binding with TAR. Overall, these findings verified that NOP2 suppresses HIV-1 transcription and promotes viral latency.
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Affiliation(s)
- Weili Kong
- Department of Pathology, Ohio State University College of Medicine, Columbus, Ohio, United States of America
- Gladstone Institute of Virology and Immunology, University of California, San Francisco, California, United States of America
| | - Ayan Biswas
- Department of Pathology, Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Dawei Zhou
- Department of Pathology, Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Guillaume Fiches
- Department of Pathology, Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Koh Fujinaga
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Netty Santoso
- Department of Pathology, Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Jian Zhu
- Department of Pathology, Ohio State University College of Medicine, Columbus, Ohio, United States of America
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17
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A Role for the VPS Retromer in Brucella Intracellular Replication Revealed by Genomewide siRNA Screening. mSphere 2019; 4:4/3/e00380-19. [PMID: 31243080 PMCID: PMC6595151 DOI: 10.1128/msphere.00380-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Brucella, the agent causing brucellosis, is a major zoonotic pathogen with worldwide distribution. Brucella resides and replicates inside infected host cells in membrane-bound compartments called Brucella-containing vacuoles (BCVs). Following uptake, Brucella resides in endosomal BCVs (eBCVs) that gradually mature from early to late endosomal features. Through a poorly understood process that is key to the intracellular lifestyle of Brucella, the eBCV escapes fusion with lysosomes by transitioning to the replicative BCV (rBCV), a replicative niche directly connected to the endoplasmic reticulum (ER). Despite the notion that this complex intracellular lifestyle must depend on a multitude of host factors, a holistic view on which of these components control Brucella cell entry, trafficking, and replication is still missing. Here we used a systematic cell-based small interfering RNA (siRNA) knockdown screen in HeLa cells infected with Brucella abortus and identified 425 components of the human infectome for Brucella infection. These include multiple components of pathways involved in central processes such as the cell cycle, actin cytoskeleton dynamics, or vesicular trafficking. Using assays for pathogen entry, knockdown complementation, and colocalization at single-cell resolution, we identified the requirement of the VPS retromer for Brucella to escape the lysosomal degradative pathway and to establish its intracellular replicative niche. We thus validated the VPS retromer as a novel host factor critical for Brucella intracellular trafficking. Further, our genomewide data shed light on the interplay between central host processes and the biogenesis of the Brucella replicative niche.IMPORTANCE With >300,000 new cases of human brucellosis annually, Brucella is regarded as one of the most important zoonotic bacterial pathogens worldwide. The agent causing brucellosis resides inside host cells within vacuoles termed Brucella-containing vacuoles (BCVs). Although a few host components required to escape the degradative lysosomal pathway and to establish the ER-derived replicative BCV (rBCV) have already been identified, the global understanding of this highly coordinated process is still partial, and many factors remain unknown. To gain deeper insight into these fundamental questions, we performed a genomewide RNA interference (RNAi) screen aiming at discovering novel host factors involved in the Brucella intracellular cycle. We identified 425 host proteins that contribute to Brucella cellular entry, intracellular trafficking, and replication. Together, this study sheds light on previously unknown host pathways required for the Brucella infection cycle and highlights the VPS retromer components as critical factors for the establishment of the Brucella intracellular replicative niche.
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18
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Tough RH, McLaren PJ. Interaction of the Host and Viral Genome and Their Influence on HIV Disease. Front Genet 2019; 9:720. [PMID: 30728828 PMCID: PMC6351501 DOI: 10.3389/fgene.2018.00720] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 12/21/2018] [Indexed: 01/23/2023] Open
Abstract
The course of Human Immunodeficiency Virus type 1 (HIV) infection is a dynamic interplay in which both host and viral genetic variation, among other factors, influence disease susceptibility and rate of progression. HIV set-point viral load (spVL), a key indicator of HIV disease progression, has an estimated 30% of variance attributable to common heritable effects and roughly 70% attributable to environmental factors and/or additional non-genetic factors. Genome-wide genotyping and sequencing studies have allowed for large-scale association testing studying host and viral genetic variants associated with infection and disease progression. Host genomics of HIV infection has been studied predominantly in Caucasian populations consistently identifying human leukocyte antigen (HLA) genes and C-C motif chemokine receptor 5 as key factors of HIV susceptibility and progression. However, these studies don’t fully assess all classes of genetic variation (e.g., very rare polymorphisms, copy number variants etc.) and do not inform on non-European ancestry groups. Additionally, viral sequence variability has been demonstrated to influence disease progression independently of host genetic variation. Viral sequence variation can be attributed to the rapid evolution of the virus within the host due to the selective pressure of the host immune response. As the host immune system responds to the virus, e.g., through recognition of HIV antigens, the virus is able to mitigate this response by evolving HLA-specific escape mutations. Diversity of viral genotypes has also been correlated with moderate to strong effects on CD4+ T cell decline and some studies showing weak to no correlation with spVL. There is evidence to support these viral genetic factors being heritable between individuals and the evolution of these factors having important consequences in the genetic epidemiology of HIV infection on a population level. This review will discuss the host-pathogen interaction of HIV infection, explore the importance of host and viral genetics for a better understanding of pathogenesis and identify opportunities for additional genetic studies.
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Affiliation(s)
- Riley H Tough
- JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB, Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Paul J McLaren
- JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB, Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
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19
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Golumbeanu M, Desfarges S, Hernandez C, Quadroni M, Rato S, Mohammadi P, Telenti A, Beerenwinkel N, Ciuffi A. Proteo-Transcriptomic Dynamics of Cellular Response to HIV-1 Infection. Sci Rep 2019; 9:213. [PMID: 30659199 PMCID: PMC6338737 DOI: 10.1038/s41598-018-36135-3] [Citation(s) in RCA: 14] [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: 09/04/2018] [Accepted: 11/14/2018] [Indexed: 01/19/2023] Open
Abstract
Throughout the HIV-1 replication cycle, complex host-pathogen interactions take place in the infected cell, leading to the production of new virions. The virus modulates the host cellular machinery in order to support its life cycle, while counteracting intracellular defense mechanisms. We investigated the dynamic host response to HIV-1 infection by systematically measuring transcriptomic, proteomic, and phosphoproteomic expression changes in infected and uninfected SupT1 CD4+ T cells at five time points of the viral replication process. By means of a Gaussian mixed-effects model implemented in the new R/Bioconductor package TMixClust, we clustered host genes based on their temporal expression patterns. We identified a proteo-transcriptomic gene expression signature of 388 host genes specific for HIV-1 replication. Comprehensive functional analyses of these genes confirmed the previously described roles of some of the genes and revealed novel key virus-host interactions affecting multiple molecular processes within the host cell, including signal transduction, metabolism, cell cycle, and immune system. The results of our analysis are accessible through a freely available, dedicated and user-friendly R/Shiny application, called PEACHi2.0. This resource constitutes a catalogue of dynamic host responses to HIV-1 infection that provides a basis for a more comprehensive understanding of virus-host interactions.
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Affiliation(s)
- Monica Golumbeanu
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Sébastien Desfarges
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- InvivoGen, Toulouse, France
| | - Céline Hernandez
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
- Computational Systems Biology Team, Institut de Biologie de I'Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, ENS, PSL Université, Paris, France
| | - Manfredo Quadroni
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Sylvie Rato
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Pejman Mohammadi
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, (CA), USA
| | - Amalio Telenti
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, (CA), USA.
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland.
| | - Angela Ciuffi
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.
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20
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Strang BL, Asquith CRM, Moshrif HF, Ho CMK, Zuercher WJ, Al-Ali H. Identification of lead anti-human cytomegalovirus compounds targeting MAP4K4 via machine learning analysis of kinase inhibitor screening data. PLoS One 2018; 13:e0201321. [PMID: 30048526 PMCID: PMC6062112 DOI: 10.1371/journal.pone.0201321] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 07/12/2018] [Indexed: 01/29/2023] Open
Abstract
Chemogenomic approaches involving highly annotated compound sets and cell based high throughput screening are emerging as a means to identify novel drug targets. We have previously screened a collection of highly characterized kinase inhibitors (Khan et al., Journal of General Virology, 2016) to identify compounds that increase or decrease expression of a human cytomegalovirus (HCMV) protein in infected cells. To identify potential novel anti-HCMV drug targets we used a machine learning approach to relate our phenotypic data from the aforementioned screen to kinase inhibition profiling of compounds used in this screen. Several of the potential targets had no previously reported role in HCMV replication. We focused on one potential anti-HCMV target, MAPK4K, and identified lead compounds inhibiting MAP4K4 that have anti-HCMV activity with little cellular cytotoxicity. We found that treatment of HCMV infected cells with inhibitors of MAP4K4, or an siRNA that inhibited MAP4K4 production, reduced HCMV replication and impaired detection of IE2-60, a viral protein necessary for efficient HCMV replication. Our findings demonstrate the potential of this machine learning approach to identify novel anti-viral drug targets, which can inform the discovery of novel anti-viral lead compounds.
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Affiliation(s)
- Blair L. Strang
- Institute for Infection & Immunity, St George’s, University of London, London, United Kingdom
| | - Christopher R. M. Asquith
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Hanan F. Moshrif
- Institute for Infection & Immunity, St George’s, University of London, London, United Kingdom
| | - Catherine M-K Ho
- Institute for Infection & Immunity, St George’s, University of London, London, United Kingdom
| | - William J. Zuercher
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Hassan Al-Ali
- Miami Project to Cure Paralysis, University of Miami, Miami, Florida, United States of America
- Department of Neurological Surgery, University of Miami, Miami, Florida, United States of America
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida, United States of America
- Katz Drug Discovery Center, University of Miami, Miami, Florida, United States of America
- Department of Medicine, University of Miami, Miami, Florida, United States of America
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21
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Chen T, Wang D, Xie T, Xu LG. Sec13 is a positive regulator of VISA-mediated antiviral signaling. Virus Genes 2018; 54:514-526. [PMID: 29948782 DOI: 10.1007/s11262-018-1581-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 06/04/2018] [Indexed: 12/21/2022]
Abstract
Viral infection triggers the innate antiviral immune response that rapidly produces type I interferons in most cell types to combat viruses invading. Upon viral infection, the cytoplasmic RNA sensors RIG-I/MDA5 recognize viral RNA, and then RIG-I/MDA5 is transported to mitochondria interacting with VISA through the CARD domain. From there, VISA recruits downstream antiviral signaling pathways molecules, such as TRAFs and TBK1. Eventually, IRF3 is phosphorylated and type I IFNs are induced to fight as the first line of defense against viruses. However, it remains unclear how VISA acts as a scaffold to assemble the signalosome in RIG-I-mediated antiviral signaling. Here, we demonstrated Sec13 as a novel component that was involved in VISA-mediated antiviral signaling pathway. The co-immunoprecipitation assays showed that Sec13 specifically interacts with VISA. Overexpression of Sec13 increases VISA's aggregation and ubiquitination and significantly enhances the phosphorylation and dimerization of IRF3, facilitating the IFN-β production. Conversely, the knockdown of Sec13 attenuates Sendai virus-induced and VISA-mediated IRF3 activation and the production of IFNβ, thus weakens antiviral immune activity.
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Affiliation(s)
- Tian Chen
- Key Laboratory of Functional Small Organic Molecule, Ministry of Education and College of Life Science, Jiangxi Normal University, 99 Ziyang Road, Nanchang, 330022, Jiangxi, China
| | - Dandan Wang
- Key Laboratory of Functional Small Organic Molecule, Ministry of Education and College of Life Science, Jiangxi Normal University, 99 Ziyang Road, Nanchang, 330022, Jiangxi, China
| | - Tao Xie
- Key Laboratory of Functional Small Organic Molecule, Ministry of Education and College of Life Science, Jiangxi Normal University, 99 Ziyang Road, Nanchang, 330022, Jiangxi, China
| | - Liang-Guo Xu
- Key Laboratory of Functional Small Organic Molecule, Ministry of Education and College of Life Science, Jiangxi Normal University, 99 Ziyang Road, Nanchang, 330022, Jiangxi, China.
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22
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Sertznig H, Hillebrand F, Erkelenz S, Schaal H, Widera M. Behind the scenes of HIV-1 replication: Alternative splicing as the dependency factor on the quiet. Virology 2018; 516:176-188. [PMID: 29407375 DOI: 10.1016/j.virol.2018.01.011] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/10/2018] [Accepted: 01/11/2018] [Indexed: 01/31/2023]
Abstract
Alternative splicing plays a key role in the HIV-1 life cycle and is essential to maintain an equilibrium of mRNAs that encode viral proteins and polyprotein-isoforms. In particular, since all early HIV-1 proteins are expressed from spliced intronless and late enzymatic and structural proteins from intron containing, i.e. splicing repressed viral mRNAs, cellular splicing factors and splicing regulatory proteins are crucial for the replication capacity. In this review, we will describe the complex network of cis-acting splicing regulatory elements (SREs), which are mainly localized in the neighbourhoods of all HIV-1 splice sites and warrant the proper ratio of individual transcript isoforms. Since SREs represent binding sites for trans-acting cellular splicing factors interacting with the cellular spliceosomal apparatus we will review the current knowledge of interactions between viral RNA and cellular proteins as well as their impact on viral replication. Finally, we will discuss potential therapeutic approaches targeting HIV-1 alternative splicing.
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Affiliation(s)
- Helene Sertznig
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Frank Hillebrand
- Institute of Virology, Heinrich Heine University, University Hospital, Düsseldorf, Germany
| | - Steffen Erkelenz
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Germany
| | - Heiner Schaal
- Institute of Virology, Heinrich Heine University, University Hospital, Düsseldorf, Germany
| | - Marek Widera
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.
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23
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CRISPR genetic screens to discover host–virus interactions. Curr Opin Virol 2018; 29:87-100. [DOI: 10.1016/j.coviro.2018.03.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Revised: 03/17/2018] [Accepted: 03/26/2018] [Indexed: 12/26/2022]
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24
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McLaren PJ, Pulit SL, Gurdasani D, Bartha I, Shea PR, Pomilla C, Gupta N, Gkrania-Klotsas E, Young EH, Bannert N, Del Amo J, Gill MJ, Gilmour J, Kellam P, Kelleher AD, Sönnerborg A, Wolinsky SM, Zangerle R, Post FA, Fisher M, Haas DW, Walker BD, Porter K, Goldstein DB, Sandhu MS, de Bakker PIW, Fellay J. Evaluating the Impact of Functional Genetic Variation on HIV-1 Control. J Infect Dis 2017; 216:1063-1069. [PMID: 28968755 PMCID: PMC5853944 DOI: 10.1093/infdis/jix470] [Citation(s) in RCA: 20] [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: 05/02/2017] [Accepted: 09/06/2017] [Indexed: 12/21/2022] Open
Abstract
Background Previous genetic association studies of human immunodeficiency virus-1 (HIV-1) progression have focused on common human genetic variation ascertained through genome-wide genotyping. Methods We sought to systematically assess the full spectrum of functional variation in protein coding gene regions on HIV-1 progression through exome sequencing of 1327 individuals. Genetic variants were tested individually and in aggregate across genes and gene sets for an influence on HIV-1 viral load. Results Multiple single variants within the major histocompatibility complex (MHC) region were observed to be strongly associated with HIV-1 outcome, consistent with the known impact of classical HLA alleles. However, no single variant or gene located outside of the MHC region was significantly associated with HIV progression. Set-based association testing focusing on genes identified as being essential for HIV replication in genome-wide small interfering RNA (siRNA) and clustered regularly interspaced short palindromic repeats (CRISPR) studies did not reveal any novel associations. Conclusions These results suggest that exonic variants with large effect sizes are unlikely to have a major contribution to host control of HIV infection.
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Affiliation(s)
- Paul J McLaren
- JC Wilt Infectious Diseases Research Centre, National HIV and Retrovirology Laboratory, Public Health Agency of Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Sara L Pulit
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, The Netherlands
| | - Deepti Gurdasani
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Department of Medicine, University of Cambridge, United Kingdom
| | - Istvan Bartha
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Switzerland
| | - Patrick R Shea
- Institute for Genomic Medicine, Columbia University, New York
| | - Cristina Pomilla
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Department of Medicine, University of Cambridge, United Kingdom
| | - Namrata Gupta
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, USA
| | | | - Elizabeth H Young
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Department of Medicine, University of Cambridge, United Kingdom
| | - Norbert Bannert
- Division of HIV and Other Retroviruses, Robert Koch Institute, Berlin, Germany
| | - Julia Del Amo
- Centro Nacional de Epidemiología, Instituto de Salud Carlos III, Madrid, Spain
| | - M John Gill
- Department of Medicine, University of Calgary, Canada
| | - Jill Gilmour
- Human Immunology Laboratory, International AIDS Vaccine Initiative, Imperial College, London, United Kingdom
| | - Paul Kellam
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Research Department of Infection, Division of Infection and Immunity, University College London, United Kingdom
| | - Anthony D Kelleher
- The Kirby Institute for Infection and Immunity in Society, University of New South Wales, Sydney, Australia
| | - Anders Sönnerborg
- Unit of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Steven M Wolinsky
- Division of Infectious Diseases, The Feinberg School of Medicine, Northwestern University, Chicago
| | - Robert Zangerle
- Department of Dermatology and Venereology, Medical University Innsbruck, Austria
| | | | - Martin Fisher
- Royal Sussex County Hospital, Brighton, United Kingdom
| | - David W Haas
- Department of Medicine, Vanderbilt University School of Medicine, Nashville
| | - Bruce D Walker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Boston
- Howard Hughes Medical Institute, Chevy Chase
| | | | | | - Manjinder S Sandhu
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Department of Medicine, University of Cambridge, United Kingdom
| | - Paul I W de Bakker
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, The Netherlands
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, The Netherlands
| | - Jacques Fellay
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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25
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Québatte M, Dehio C. Systems-level interference strategies to decipher host factors involved in bacterial pathogen interaction: from RNAi to CRISPRi. Curr Opin Microbiol 2017; 39:34-41. [DOI: 10.1016/j.mib.2017.08.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 08/02/2017] [Accepted: 08/02/2017] [Indexed: 12/16/2022]
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26
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Hayashi T, Jean M, Huang H, Simpson S, Santoso NG, Zhu J. Screening of an FDA-approved compound library identifies levosimendan as a novel anti-HIV-1 agent that inhibits viral transcription. Antiviral Res 2017; 146:76-85. [PMID: 28842263 DOI: 10.1016/j.antiviral.2017.08.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/18/2017] [Accepted: 08/21/2017] [Indexed: 01/06/2023]
Abstract
Combination antiretroviral therapy (cART) has been proven to efficiently inhibit ongoing replication of human immunodeficiency virus type 1 (HIV-1), and significantly improve the health outcome in patients of acquired immune deficiency syndrome (AIDS). However, cART is unable to cure HIV-1/AIDS. Even in presence of cART there exists a residual viremia, contributed from the viral reservoirs of latently infected HIV-1 proviruses; this constitutes a major hurdle. Currently, there are multiple strategies aimed at eliminating or permanently silence these HIV-1 latent reservoirs being intensely explored. One such strategy, a recently emerged "block and lock" approach is appealing. For this approach, so-called HIV-1 latency-promoting agents (LPAs) are used to reinforce viral latency and to prevent the low-level or sporadic transcription of integrated HIV-1 proviruses. Although several LPAs have been reported, there is still a question of their suitability to be further developed as a safe and valid therapeutic agent for the clinical use. In this study, we aimed to identify new potential LPAs through the screening an FDA-approved compound library. A new and promising anti-HIV-1 inhibitor, levosimendan, was identified from these screens. Levosimendan is currently used to treat heart failure in clinics, but it demonstrates strong inhibition of TNFα-induced HIV-1 reactivation in multiple cell lines of HIV-1 latency through affecting the HIV-1 Tat-LTR transcriptional axis. Furthermore, we confirmed that in primary CD4+ T cells levosimendan inhibits both the acute HIV-1 replication and the reactivation of latent HIV-1 proviruses. As a summary, our studies successfully identify levosimendan as a novel and promising anti-HIV-1 inhibitor, which should be immediately investigated in vivo given that it is already an FDA-approved drug.
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Affiliation(s)
- Tsuyoshi Hayashi
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Maxime Jean
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Huachao Huang
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Sydney Simpson
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Netty G Santoso
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Jian Zhu
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642, USA; Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA.
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27
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Naranbhai V, Carrington M. Host genetic variation and HIV disease: from mapping to mechanism. Immunogenetics 2017; 69:489-498. [PMID: 28695282 PMCID: PMC5537324 DOI: 10.1007/s00251-017-1000-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 05/07/2017] [Indexed: 12/12/2022]
Abstract
This review aims to provide a summary of current knowledge of host genetic effects on human immunodeficiency virus (HIV) disease. Mapping of simple single nucleotide polymorphisms (SNP) has been largely successful in HIV, but more complex genetic associations involving haplotypic or epigenetic variation, for example, remain elusive. Mechanistic insights explaining SNP associations are incomplete, but continue to be forthcoming. The number of robust immunogenetic correlates of HIV is modest and their discovery mostly predates the genome-wide era. Nevertheless, genome-wide evaluations have nicely validated the impact of HLA and CCR5 variants on HIV disease, and importantly, made clear the many false positive associations that were previously suggested by studies using the candidate gene approach. We describe how multiple HIV outcome measures such as acquisition, viral control, and immune decline have been studied in adults and in children, but that collectively these identify only the two replicable loci responsible for modifying HIV disease, CCR5, and HLA. Recent heritability estimates in this disease corroborate the modest impact of genetic determinants and their oligogenic nature. While the mechanism of protection afforded by genetic variants that diminish CCR5 expression is clear, new aspects of HLA class I-mediated protection continue to be uncovered. We describe how these genetic findings have enhanced insights into immunobiology, been clinically translated into CCR5 antagonists, allowed prioritization of antigens for vaccination efforts, and identified targets for genome-editing interventions. Finally, we describe how studies of genetically complex parts of the genome using new tools may begin revealing additional correlates.
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Affiliation(s)
- Vivek Naranbhai
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA.
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa.
| | - Mary Carrington
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
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28
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Abstract
A CRISPR screen conducted in a CD4+ T cell leukemia line has identified host factors required for HIV infection but dispensable for cellular survival. The results highlight sulfation on the HIV co-receptor CCR5 and cellular aggregation as potential targets for therapeutic intervention.
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29
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Taye B, Vaz C, Tanavde V, Kuznetsov VA, Eisenhaber F, Sugrue RJ, Maurer-Stroh S. Benchmarking selected computational gene network growing tools in context of virus-host interactions. Sci Rep 2017; 7:5805. [PMID: 28724991 PMCID: PMC5517527 DOI: 10.1038/s41598-017-06020-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 06/07/2017] [Indexed: 01/04/2023] Open
Abstract
Several available online tools provide network growing functions where an algorithm utilizing different data sources suggests additional genes/proteins that should connect an input gene set into functionally meaningful networks. Using the well-studied system of influenza host interactions, we compare the network growing function of two free tools GeneMANIA and STRING and the commercial IPA for their performance of recovering known influenza A virus host factors previously identified from siRNA screens. The result showed that given small (~30 genes) or medium (~150 genes) input sets all three network growing tools detect significantly more known host factors than random human genes with STRING overall performing strongest. Extending the networks with all the three tools significantly improved the detection of GO biological processes of known host factors compared to not growing networks. Interestingly, the rate of identification of true host factors using computational network growing is equal or better to doing another experimental siRNA screening study which could also be true and applied to other biological pathways/processes.
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Affiliation(s)
- Biruhalem Taye
- Bioinformatics Institute, A*STAR, 30 Biopolis Street #07-01 Matrix, Singapore, 138671, Singapore. .,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore. .,Aklilu Lemma Institute of Pathobiology, Addis Ababa University, P.O.BOX 1176, Addis Ababa, Ethiopia.
| | - Candida Vaz
- Bioinformatics Institute, A*STAR, 30 Biopolis Street #07-01 Matrix, Singapore, 138671, Singapore
| | - Vivek Tanavde
- Bioinformatics Institute, A*STAR, 30 Biopolis Street #07-01 Matrix, Singapore, 138671, Singapore.,Institute of Medical Biology, A*STAR, 8A Biomedical Grove, #06-06 Immunos, Singapore, 138648, Singapore
| | - Vladimir A Kuznetsov
- Bioinformatics Institute, A*STAR, 30 Biopolis Street #07-01 Matrix, Singapore, 138671, Singapore.,School of Computer Engineering, Nanyang Technological University, 50 Nanyang Drive, Singapore, 637553, Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute, A*STAR, 30 Biopolis Street #07-01 Matrix, Singapore, 138671, Singapore.,Department of Biological Sciences, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore.,School of Computer Engineering, Nanyang Technological University, 50 Nanyang Drive, Singapore, 637553, Singapore
| | - Richard J Sugrue
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute, A*STAR, 30 Biopolis Street #07-01 Matrix, Singapore, 138671, Singapore.,Department of Biological Sciences, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore.,National Public Health Laboratory, Ministry of Health, 3 Biopolis Drive, Synapse #05-14/16, Singapore, 138623, Singapore
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30
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Identification of HIV-1 Tat-Associated Proteins Contributing to HIV-1 Transcription and Latency. Viruses 2017; 9:v9040067. [PMID: 28368303 PMCID: PMC5408673 DOI: 10.3390/v9040067] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 03/19/2017] [Accepted: 03/24/2017] [Indexed: 12/31/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) Tat is a virus-encoded trans-activator that plays a central role in viral transcription. We used our recently developed parallel analysis of in vitro translated open reading frames (ORFs) (PLATO) approach to identify host proteins that associate with HIV-1 Tat. From this proteomic assay, we identify 89 Tat-associated proteins (TAPs). We combine our results with other datasets of Tat or long terminal repeat (LTR)-associated proteins. For some of these proteins (NAT10, TINP1, XRCC5, SIN3A), we confirm their strong association with Tat. These TAPs also suppress Tat-mediated HIV-1 transcription. Removing suppression of HIV-1 transcription benefits the reversal of post-integrated, latent HIV-1 proviruses. We demonstrate that these transcriptionally suppressing TAPs contribute to HIV-1 latency in Jurkat latency (J-LAT) cells. Therefore, our proteomic analysis highlights the previously unappreciated TAPs that play a role in maintaining HIV-1 latency and can be further studied as potential pharmacological targets for the “shock and kill” HIV-1 cure strategy.
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31
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Schott K, König R. Picking the Survivor! CRISPR Reveals HIV Dependency Factors. Trends Microbiol 2017; 25:243-245. [PMID: 28233621 DOI: 10.1016/j.tim.2017.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 02/07/2017] [Indexed: 01/11/2023]
Abstract
A new study employs genome-wide loss-of-function CRISPR/Cas9 screening to identify three novel factors for HIV-1 entry. The factors represent promising targets for therapeutics as they are essential for HIV-1 infection, but dispensable for cell survival. The involved pathways were validated in primary CD4+ T cells, target cells for HIV-1.
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Affiliation(s)
- Kerstin Schott
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Renate König
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, 63225 Langen, Germany; Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA; German Center for Infection Research (DZIF), 63225 Langen, Germany.
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32
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Rupp JC, Locatelli M, Grieser A, Ramos A, Campbell PJ, Yi H, Steel J, Burkhead JL, Bortz E. Host Cell Copper Transporters CTR1 and ATP7A are important for Influenza A virus replication. Virol J 2017; 14:11. [PMID: 28115001 PMCID: PMC5259989 DOI: 10.1186/s12985-016-0671-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 12/13/2016] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The essential role of copper in eukaryotic cellular physiology is known, but has not been recognized as important in the context of influenza A virus infection. In this study, we investigated the effect of cellular copper on influenza A virus replication. METHODS Influenza A/WSN/33 (H1N1) virus growth and macromolecule syntheses were assessed in cultured human lung cells (A549) where the copper concentration of the growth medium was modified, or expression of host genes involved in copper homeostasis was targeted by RNA interference. RESULTS Exogenously increasing copper concentration, or chelating copper, resulted in moderate defects in viral growth. Nucleoprotein (NP) localization, neuraminidase activity assays and transmission electron microscopy did not reveal significant defects in virion assembly, morphology or release under these conditions. However, RNAi knockdown of the high-affinity copper importer CTR1 resulted in significant viral growth defects (7.3-fold reduced titer at 24 hours post-infection, p = 0.04). Knockdown of CTR1 or the trans-Golgi copper transporter ATP7A significantly reduced polymerase activity in a minigenome assay. Both copper transporters were required for authentic viral RNA synthesis and NP and matrix (M1) protein accumulation in the infected cell. CONCLUSIONS These results demonstrate that intracellular copper regulates the influenza virus life cycle, with potentially distinct mechanisms in specific cellular compartments. These observations provide a new avenue for drug development and studies of influenza virus pathogenesis.
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Affiliation(s)
- Jonathan C. Rupp
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK USA
| | - Manon Locatelli
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK USA
- Present address: Institute Albert Bonniot – INSERM U1209, Université Grenoble Alpes, Grenoble, France
| | - Alexis Grieser
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK USA
| | - Andrea Ramos
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK USA
| | - Patricia J. Campbell
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia USA
| | - Hong Yi
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia USA
| | - John Steel
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia USA
| | - Jason L. Burkhead
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK USA
| | - Eric Bortz
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK USA
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33
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Park RJ, Wang T, Koundakjian D, Hultquist JF, Lamothe-Molina P, Monel B, Schumann K, Yu H, Krupzcak KM, Garcia-Beltran W, Piechocka-Trocha A, Krogan NJ, Marson A, Sabatini DM, Lander ES, Hacohen N, Walker BD. A genome-wide CRISPR screen identifies a restricted set of HIV host dependency factors. Nat Genet 2016; 49:193-203. [PMID: 27992415 DOI: 10.1038/ng.3741] [Citation(s) in RCA: 244] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 11/15/2016] [Indexed: 12/14/2022]
Abstract
Host proteins are essential for HIV entry and replication and can be important nonviral therapeutic targets. Large-scale RNA interference (RNAi)-based screens have identified nearly a thousand candidate host factors, but there is little agreement among studies and few factors have been validated. Here we demonstrate that a genome-wide CRISPR-based screen identifies host factors in a physiologically relevant cell system. We identify five factors, including the HIV co-receptors CD4 and CCR5, that are required for HIV infection yet are dispensable for cellular proliferation and viability. Tyrosylprotein sulfotransferase 2 (TPST2) and solute carrier family 35 member B2 (SLC35B2) function in a common pathway to sulfate CCR5 on extracellular tyrosine residues, facilitating CCR5 recognition by the HIV envelope. Activated leukocyte cell adhesion molecule (ALCAM) mediates cell aggregation, which is required for cell-to-cell HIV transmission. We validated these pathways in primary human CD4+ T cells through Cas9-mediated knockout and antibody blockade. Our findings indicate that HIV infection and replication rely on a limited set of host-dispensable genes and suggest that these pathways can be studied for therapeutic intervention.
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Affiliation(s)
- Ryan J Park
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard University, Cambridge, Massachusetts, USA.,Harvard-MIT Health Sciences and Technology, Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute of MIT and Harvard University, Cambridge, Massachusetts, USA
| | - Tim Wang
- Broad Institute of MIT and Harvard University, Cambridge, Massachusetts, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA.,David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, Massachusetts, USA
| | - Dylan Koundakjian
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard University, Cambridge, Massachusetts, USA
| | - Judd F Hultquist
- Department of Cellular and Molecular Pharmacology, California Institute for Quantitative Biosciences, QB3, University of California at San Francisco (UCSF), San Francisco, California, USA.,Gladstone Institute of Virology and Immunology, J. David Gladstone Institutes, San Francisco, California, USA
| | - Pedro Lamothe-Molina
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard University, Cambridge, Massachusetts, USA.,Biological Sciences in Public Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Blandine Monel
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard University, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Kathrin Schumann
- Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, California, USA
| | - Haiyan Yu
- Broad Institute of MIT and Harvard University, Cambridge, Massachusetts, USA
| | - Kevin M Krupzcak
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
| | - Wilfredo Garcia-Beltran
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard University, Cambridge, Massachusetts, USA.,Harvard-MIT Health Sciences and Technology, Harvard Medical School, Boston, Massachusetts, USA
| | - Alicja Piechocka-Trocha
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard University, Cambridge, Massachusetts, USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, California Institute for Quantitative Biosciences, QB3, University of California at San Francisco (UCSF), San Francisco, California, USA.,Gladstone Institute of Virology and Immunology, J. David Gladstone Institutes, San Francisco, California, USA
| | - Alexander Marson
- Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, California, USA.,Diabetes Center, University of California at San Francisco, San Francisco, California, USA.,Department of Medicine, University of California at San Francisco, San Francisco, California, USA.,Innovative Genomics Initiative (IGI), University of California, Berkeley, Berkeley, California, USA.,UCSF Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, California, USA
| | - David M Sabatini
- Broad Institute of MIT and Harvard University, Cambridge, Massachusetts, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA.,David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Eric S Lander
- Broad Institute of MIT and Harvard University, Cambridge, Massachusetts, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard University, Cambridge, Massachusetts, USA.,Massachusetts General Hospital Cancer Center, Boston, Massachusetts, USA
| | - Bruce D Walker
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard University, Cambridge, Massachusetts, USA.,Broad Institute of MIT and Harvard University, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Institute of Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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34
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Chen M, Xia D, Min C, Zhao X, Chen Y, Liu L, Li X. Neonatal repetitive pain in rats leads to impaired spatial learning and dysregulated hypothalamic-pituitary-adrenal axis function in later life. Sci Rep 2016; 6:39159. [PMID: 27966656 PMCID: PMC5155224 DOI: 10.1038/srep39159] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 11/18/2016] [Indexed: 01/09/2023] Open
Abstract
Preterm birth is a major health issue. As part of their life-saving care, most preterm infants require hospitalization and are inevitably exposed to repetitive skin-breaking procedures. The long-term effects of neonatal repetitive pain on cognitive and emotional behaviors involving hypothalamic-pituitary-adrenal (HPA) axis function in young and adult rats are unknown. From P8 to P85, mechanical hypersensitivity of the bilateral hindpaws was observed in the Needle group (P < 0.001). Compared with the Tactile group, the Needle group took longer to find the platform on P30 than on P29 (P = 0.03), with a decreased number of original platform site crossings during the probe trial of the Morris water maze test (P = 0.026). Moreover, the Needle group spent more time and took longer distances in the central area than the Tactile group in the Open-field test, both in prepubertal and adult rats (P < 0.05). The HPA axis function in the Needle group differed from the Tactile group (P < 0.05), with decreased stress responsiveness in prepuberty and puberty (P < 0.05) and increased stress responsiveness in adulthood (P < 0.05). This study indicates that repetitive pain that occurs during a critical period may cause severe consequences, with behavioral and neuroendocrine disturbances developing through prepuberty to adult life.
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Affiliation(s)
- Mengying Chen
- Department of Child Health Care, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Dongqing Xia
- Department of Child Health Care, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Cuiting Min
- Department of Child Health Care, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaoke Zhao
- Department of Rehabilitation, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Yinhua Chen
- Department of Child Health Care, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Li Liu
- Department of Applied Physics and Electronics, Umeå University, Umeå, Sweden
| | - Xiaonan Li
- Department of Child Health Care, Children's Hospital of Nanjing Medical University, Nanjing, China
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35
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High-Throughput Small Interfering RNA Screening Identifies Phosphatidylinositol 3-Kinase Class II Alpha as Important for Production of Human Cytomegalovirus Virions. J Virol 2016; 90:8360-71. [PMID: 27412598 DOI: 10.1128/jvi.01134-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 07/05/2016] [Indexed: 12/23/2022] Open
Abstract
UNLABELLED High-throughput small interfering RNA (siRNA) screening is a useful methodology to identify cellular factors required for virus replication. Here we utilized a high-throughput siRNA screen based on detection of a viral antigen by microscopy to interrogate cellular protein kinases and phosphatases for their importance during human cytomegalovirus (HCMV) replication and identified the class II phosphatidylinositol 3-kinase class II alpha (PI3K-C2A) as being involved in HCMV replication. Confirming this observation, infected cells treated with either pooled or individual siRNAs targeting PI3K-C2A mRNA produced approximately 10-fold less infectious virus than the controls. Western blotting and quantitative PCR analysis of infected cells treated with siRNAs indicated that depletion of PI3K-C2A slightly reduced the accumulation of late but not immediate early or early viral antigens and had no appreciable effect on viral DNA synthesis. Analysis of siRNA-treated cells by electron microscopy and Western blotting indicated that PI3K-C2A was not required for the production of viral capsids but did lead to increased numbers of enveloped capsids in the cytoplasm that had undergone secondary envelopment and a reduction in the amount of viral particles exiting the cell. Therefore, PI3K-C2A is a factor important for HCMV replication and has a role in the production of HCMV virions. IMPORTANCE There is limited information about the cellular factors required for human cytomegalovirus (HCMV) replication. Therefore, to identify proteins involved in HCMV replication, we developed a methodology to conduct a high-throughput siRNA screen of HCMV-infected cells. From our screening data, we focused our studies on the top hit from our screen, the lipid kinase phosphatidylinositol 3-kinase class II alpha (PI3K-C2A), as its role in HCMV replication was unknown. Interestingly, we found that PI3K-C2A is important for the production of HCMV virions and is involved in virion production after secondary envelopment of viral capsids, the encapsidation of HCMV capsids by a lipid bilayer that occurs before virions exit the cell.
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36
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Savidis G, McDougall WM, Meraner P, Perreira JM, Portmann JM, Trincucci G, John SP, Aker AM, Renzette N, Robbins DR, Guo Z, Green S, Kowalik TF, Brass AL. Identification of Zika Virus and Dengue Virus Dependency Factors using Functional Genomics. Cell Rep 2016; 16:232-246. [PMID: 27342126 DOI: 10.1016/j.celrep.2016.06.028] [Citation(s) in RCA: 286] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 06/02/2016] [Accepted: 06/10/2016] [Indexed: 01/10/2023] Open
Abstract
The flaviviruses dengue virus (DENV) and Zika virus (ZIKV) are severe health threats with rapidly expanding ranges. To identify the host cell dependencies of DENV and ZIKV, we completed orthologous functional genomic screens using RNAi and CRISPR/Cas9 approaches. The screens recovered the ZIKV entry factor AXL as well as multiple host factors involved in endocytosis (RAB5C and RABGEF), heparin sulfation (NDST1 and EXT1), and transmembrane protein processing and maturation, including the endoplasmic reticulum membrane complex (EMC). We find that both flaviviruses require the EMC for their early stages of infection. Together, these studies generate a high-confidence, systems-wide view of human-flavivirus interactions and provide insights into the role of the EMC in flavivirus replication.
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Affiliation(s)
- George Savidis
- Department of Microbiology and Physiological Systems (MaPS), University of Massachusetts Medical, School, Worcester, MA 01655, USA
| | - William M McDougall
- Department of Microbiology and Physiological Systems (MaPS), University of Massachusetts Medical, School, Worcester, MA 01655, USA
| | - Paul Meraner
- Department of Microbiology and Physiological Systems (MaPS), University of Massachusetts Medical, School, Worcester, MA 01655, USA
| | - Jill M Perreira
- Department of Microbiology and Physiological Systems (MaPS), University of Massachusetts Medical, School, Worcester, MA 01655, USA
| | - Jocelyn M Portmann
- Department of Microbiology and Physiological Systems (MaPS), University of Massachusetts Medical, School, Worcester, MA 01655, USA
| | - Gaia Trincucci
- Department of Microbiology and Physiological Systems (MaPS), University of Massachusetts Medical, School, Worcester, MA 01655, USA
| | - Sinu P John
- Signaling Systems Unit, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Aaron M Aker
- Department of Microbiology and Physiological Systems (MaPS), University of Massachusetts Medical, School, Worcester, MA 01655, USA
| | - Nicholas Renzette
- Department of Microbiology and Physiological Systems (MaPS), University of Massachusetts Medical, School, Worcester, MA 01655, USA
| | - Douglas R Robbins
- Department of Microbiology and Physiological Systems (MaPS), University of Massachusetts Medical, School, Worcester, MA 01655, USA
| | - Zhiru Guo
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Sharone Green
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Timothy F Kowalik
- Department of Microbiology and Physiological Systems (MaPS), University of Massachusetts Medical, School, Worcester, MA 01655, USA
| | - Abraham L Brass
- Department of Microbiology and Physiological Systems (MaPS), University of Massachusetts Medical, School, Worcester, MA 01655, USA; Division of Gastroenterology, Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA.
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37
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Lopez AP, Kugelman JR, Garcia-Rivera J, Urias E, Salinas SA, Fernandez-Zapico ME, Llano M. The Structure-Specific Recognition Protein 1 Associates with Lens Epithelium-Derived Growth Factor Proteins and Modulates HIV-1 Replication. J Mol Biol 2016; 428:2814-31. [PMID: 27216501 DOI: 10.1016/j.jmb.2016.05.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 04/21/2016] [Accepted: 05/16/2016] [Indexed: 10/21/2022]
Abstract
The lens epithelium-derived growth factor p75 (LEDGF/p75) is a chromatin-bound protein essential for efficient lentiviral integration. Genome-wide studies have located LEDGF/p75 inside actively transcribed genes where it mediates lentiviral integration. Although its role in HIV-1 integration is clearly established, the role of LEDGF/p75-associated proteins in HIV-1 infection remains unexplored. Using protein-protein interaction assays, we demonstrated that LEDGF/p75 complexes with a chromatin-remodeling complex facilitates chromatin transcription (FACT), a heterodimer of the structure-specific recognition protein 1 (SSRP1) and the human homolog of suppressor of Ty 16 (hSpt16). Detailed analysis of the interaction of LEDGF/p75 with the FACT complex indicates that LEDGF/p75 interacts with SSRP1 in an hSpt16-independent manner that requires the PWWP domain of LEDGF proteins and the HMG domain of SSRP1. Functional characterizations demonstrate a LEDGF/p75-independent role of SSRP1 in the regulation of HIV-1 replication. shRNA-mediated partial knockdown of SSRP1 reduces HIV-1 infection, but not Murine Leukemia Virus, in human CD4(+) T cells. Similarly, SSRP1 knockdown affects infection by HIV-1-derived viruses that express genes from the viral LTR but not from an internal immediate-early CMV promoter, suggesting a role of SSRP1 in LTR-driven gene expression but not in viral DNA integration. Together, our data demonstrate for the first time the association of LEDGF proteins with the FACT complex and give further support to a role of SSRP1 in HIV-1 infection.
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Affiliation(s)
- Angelica P Lopez
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968, USA
| | - Jeffrey R Kugelman
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968, USA
| | - Jose Garcia-Rivera
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968, USA
| | - Eduardo Urias
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968, USA
| | - Sandra A Salinas
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968, USA
| | | | - Manuel Llano
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968, USA.
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38
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Making Bunyaviruses Talk: Interrogation Tactics to Identify Host Factors Required for Infection. Viruses 2016; 8:v8050130. [PMID: 27187446 PMCID: PMC4885085 DOI: 10.3390/v8050130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 05/03/2016] [Accepted: 05/06/2016] [Indexed: 12/26/2022] Open
Abstract
The identification of host cellular genes that act as either proviral or antiviral factors has been aided by the development of an increasingly large number of high-throughput screening approaches. Here, we review recent advances in which these new technologies have been used to interrogate host genes for the ability to impact bunyavirus infection, both in terms of technical advances as well as a summary of biological insights gained from these studies.
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39
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Functional Genomic Strategies for Elucidating Human-Virus Interactions: Will CRISPR Knockout RNAi and Haploid Cells? Adv Virus Res 2016; 94:1-51. [PMID: 26997589 PMCID: PMC7112329 DOI: 10.1016/bs.aivir.2015.11.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Over the last several years a wealth of transformative human–virus interaction discoveries have been produced using loss-of-function functional genomics. These insights have greatly expanded our understanding of how human pathogenic viruses exploit our cells to replicate. Two technologies have been at the forefront of this genetic revolution, RNA interference (RNAi) and random retroviral insertional mutagenesis using haploid cell lines (haploid cell screening), with the former technology largely predominating. Now the cutting edge gene editing of the CRISPR/Cas9 system has also been harnessed for large-scale functional genomics and is poised to possibly displace these earlier methods. Here we compare and contrast these three screening approaches for elucidating host–virus interactions, outline their key strengths and weaknesses including a comparison of an arrayed multiple orthologous RNAi reagent screen to a pooled CRISPR/Cas9 human rhinovirus 14–human cell interaction screen, and recount some notable insights made possible by each. We conclude with a brief perspective on what might lie ahead for the fast evolving field of human–virus functional genomics.
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40
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An interactive web-based application for Comprehensive Analysis of RNAi-screen Data. Nat Commun 2016; 7:10578. [PMID: 26902267 PMCID: PMC5477503 DOI: 10.1038/ncomms10578] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 12/30/2015] [Indexed: 01/13/2023] Open
Abstract
RNAi screens are widely used in functional genomics. Although the screen data can be susceptible to a number of experimental biases, many of these can be corrected by computational analysis. For this purpose, here we have developed a web-based platform for integrated analysis and visualization of RNAi screen data named CARD (for Comprehensive Analysis of RNAi Data; available at https://card.niaid.nih.gov). CARD allows the user to seamlessly carry out sequential steps in a rigorous data analysis workflow, including normalization, off-target analysis, integration of gene expression data, optimal thresholds for hit selection and network/pathway analysis. To evaluate the utility of CARD, we describe analysis of three genome-scale siRNA screens and demonstrate: (i) a significant increase both in selection of subsequently validated hits and in rejection of false positives, (ii) an increased overlap of hits from independent screens of the same biology and (iii) insight to microRNA (miRNA) activity based on siRNA seed enrichment. Analysis of RNAi screens is a multi-step process requiring the sequential use of several unrelated resources. Here the authors generate an online resource integrating RNAi analytic tools and filters into a seamless workflow, which improves the specificity, selectivity and reproducibility of the results.
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41
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Creating Knockouts of Conserved Oligomeric Golgi Complex Subunits Using CRISPR-Mediated Gene Editing Paired with a Selection Strategy Based on Glycosylation Defects Associated with Impaired COG Complex Function. Methods Mol Biol 2016; 1496:145-61. [PMID: 27632008 DOI: 10.1007/978-1-4939-6463-5_12] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The conserved oligomeric Golgi (COG) complex is a key evolutionally conserved multisubunit protein machinery that regulates tethering and fusion of intra-Golgi transport vesicles. The Golgi apparatus specifically promotes sorting and complex glycosylation of glycoconjugates. Without proper glycosylation and processing, proteins and lipids will be mislocalized and/or have impaired function. The Golgi glycosylation machinery is kept in homeostasis by a careful balance of anterograde and retrograde trafficking to ensure proper localization of the glycosylation enzymes and their substrates. This balance, like other steps of membrane trafficking, is maintained by vesicle trafficking machinery that includes COPI vesicular coat proteins, SNAREs, Rabs, and both coiled-coil and multi-subunit vesicular tethers. The COG complex interacts with other membrane trafficking components and is essential for proper localization of Golgi glycosylation machinery. Here we describe using CRISPR-mediated gene editing coupled with a phenotype-based selection strategy directly linked to the COG complex's role in glycosylation homeostasis to obtain COG complex subunit knockouts (KOs). This has resulted in clonal KOs for each COG subunit in HEK293T cells and gives the ability to further probe the role of the COG complex in Golgi homeostasis.
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42
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Direct Visualization of HIV-1 Replication Intermediates Shows that Capsid and CPSF6 Modulate HIV-1 Intra-nuclear Invasion and Integration. Cell Rep 2015; 13:1717-31. [PMID: 26586435 DOI: 10.1016/j.celrep.2015.10.036] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 08/31/2015] [Accepted: 10/11/2015] [Indexed: 11/23/2022] Open
Abstract
Direct visualization of HIV-1 replication would improve our understanding of the viral life cycle. We adapted established technology and reagents to develop an imaging approach, ViewHIV, which allows evaluation of early HIV-1 replication intermediates, from reverse transcription to integration. These methods permit the simultaneous evaluation of both the capsid protein (CA) and viral DNA genome (vDNA) components of HIV-1 in both the cytosol and nuclei of single cells. ViewHIV is relatively rapid, uses readily available reagents in combination with standard confocal microscopy, and can be done with virtually any HIV-1 strain and permissive cell lines or primary cells. Using ViewHIV, we find that CA enters the nucleus and associates with vDNA in both transformed and primary cells. We also find that CA's interaction with the host polyadenylation factor, CPSF6, enhances nuclear entry and potentiates HIV-1's depth of nuclear invasion, potentially aiding the virus's integration into gene-dense regions.
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43
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Nishitsuji H, Ujino S, Shimizu Y, Harada K, Zhang J, Sugiyama M, Mizokami M, Shimotohno K. Novel reporter system to monitor early stages of the hepatitis B virus life cycle. Cancer Sci 2015; 106:1616-24. [PMID: 26310603 PMCID: PMC4714683 DOI: 10.1111/cas.12799] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 08/19/2015] [Accepted: 08/24/2015] [Indexed: 01/01/2023] Open
Abstract
A recombinant hepatitis B virus (HBV) expressing NanoLuc (NL) (HBV/NL) was produced by cotransfecting a plasmid containing a 1.2‐fold HBV genome carrying the NL gene with a plasmid bearing a packaging‐defective 1.2‐fold HBV genome into a human hepatoma cell line, HepG2. We found that NL activity in HBV/NL‐infected primary hepatocytes or sodium taurocholate cotransporting polypeptide‐transduced human hepatocyte‐derived cell lines increased linearly for several days after infection and was concordant with HBV RNA levels in the cells. Treatment of the virus‐infected cells with HBV inhibitors reduced NL activity in a dose‐dependent manner. Detection of HBV/NL infection, monitored by NL activity, was highly sensitive and less expensive than detection using the conventional method to evaluate HBV infection. In addition, because we also studied host factors, this system is applicable not only for studying the HBV life cycle, but also for exploring agent(s) that regulate HBV proliferation.
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Affiliation(s)
- Hironori Nishitsuji
- Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa, Japan
| | - Saneyuki Ujino
- Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa, Japan
| | - Yuko Shimizu
- Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa, Japan
| | - Keisuke Harada
- Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa, Japan.,Central Pharmaceutical Research Institute, Japan Tobacco Inc., Osaka, Japan
| | - Jing Zhang
- Research and Development Center, FUSO Pharmaceutical Industries, Ltd, Osaka, Japan
| | - Masaya Sugiyama
- Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa, Japan
| | - Masashi Mizokami
- Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa, Japan
| | - Kunitada Shimotohno
- Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa, Japan
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Huang H, Santoso N, Power D, Simpson S, Dieringer M, Miao H, Gurova K, Giam CZ, Elledge SJ, Zhu J. FACT Proteins, SUPT16H and SSRP1, Are Transcriptional Suppressors of HIV-1 and HTLV-1 That Facilitate Viral Latency. J Biol Chem 2015; 290:27297-27310. [PMID: 26378236 DOI: 10.1074/jbc.m115.652339] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Indexed: 11/06/2022] Open
Abstract
Our functional genomic RNAi screens have identified the protein components of the FACT (facilitates chromatin transcription) complex, SUPT16H and SSRP1, as top host factors that negatively regulate HIV-1 replication. FACT interacts specifically with histones H2A/H2B to affect assembly and disassembly of nucleosomes, as well as transcription elongation. We further investigated the suppressive role of FACT proteins in HIV-1 transcription. First, depletion of SUPT16H or SSRP1 protein enhances Tat-mediated HIV-1 LTR (long terminal repeat) promoter activity. Second, HIV-1 Tat interacts with SUPT16H but not SSRP1 protein. However, both SUPT16H and SSRP1 are recruited to LTR promoter. Third, the presence of SUPT16H interferes with the association of Cyclin T1 (CCNT1), a subunit of P-TEFb, with the Tat-LTR axis. Removing inhibitory mechanisms to permit HIV-1 transcription is an initial and key regulatory step to reverse post-integrated latent HIV-1 proviruses for purging of reservoir cells. We therefore evaluated the role of FACT proteins in HIV-1 latency and reactivation. Depletion of SUPT16H or SSRP1 protein affects both HIV-1 transcriptional initiation and elongation and spontaneously reverses latent HIV-1 in U1/HIV and J-LAT cells. Similar effects were observed with a primary CD4+ T cell model of HIV-1 latency. FACT proteins also interfere with HTLV-1 Tax-LTR-mediated transcription and viral latency, indicating that they may act as general transcriptional suppressors for retroviruses. We conclude that FACT proteins SUPT16H and SSRP1 play a key role in suppressing HIV-1 transcription and promoting viral latency, which may serve as promising gene targets for developing novel HIV-1 latency-reversing agents.
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Affiliation(s)
- Huachao Huang
- Departments of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642
| | - Netty Santoso
- Departments of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642
| | - Derek Power
- Departments of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642
| | - Sydney Simpson
- the School of Arts and Sciences, University of Rochester, Rochester, New York 14627
| | - Michael Dieringer
- the School of Arts and Sciences, University of Rochester, Rochester, New York 14627
| | - Hongyu Miao
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, New York 14642
| | - Katerina Gurova
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, New York 14263
| | - Chou-Zen Giam
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814
| | - Stephen J Elledge
- the Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Boston, Massachusetts 02115; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
| | - Jian Zhu
- Departments of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642; Departments of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642.
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45
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Abstract
Deciphering the many interactions that occur between a virus and host cell over the course of infection is paramount to understanding mechanisms of pathogenesis and to the future development of antiviral therapies. Over the past decade, researchers have started to understand these complicated relationships through the development of methodologies, including advances in RNA interference, proteomics, and the development of genetic tools such as haploid cell lines, allowing high-throughput screening to identify critical contact points between virus and host. These advances have produced a wealth of data regarding host factors hijacked by viruses to promote infection, as well as antiviral factors responsible for subverting viral infection. This review highlights findings from virus-host screens and discusses our thoughts on the direction of screening strategies moving forward.
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Affiliation(s)
- Holly Ramage
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104; ,
| | - Sara Cherry
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104; ,
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McLaren PJ, Carrington M. The impact of host genetic variation on infection with HIV-1. Nat Immunol 2015; 16:577-83. [PMID: 25988890 PMCID: PMC6296468 DOI: 10.1038/ni.3147] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 03/12/2015] [Indexed: 12/16/2022]
Abstract
The outcome after infection with the human immunodeficiency virus type 1 (HIV-1) is a complex phenotype determined by interactions among the pathogen, the human host and the surrounding environment. An impact of host genetic variation on HIV-1 susceptibility was identified early in the pandemic, with a major role attributed to the genes encoding class I human leukocyte antigens (HLA) and the chemokine receptor CCR5. Studies using genome-wide data sets have underscored the strength of these associations relative to variants located throughout the rest of the genome. However, the extent to which additional polymorphisms influence HIV-1 disease progression, and how much of the variability in outcome can be attributed to host genetics, remain largely unclear. Here we discuss findings concerning the functional impact of associated variants, outline methods for quantifying the host genetic component and examine how available genome-wide data sets may be leveraged to discover gene variants that affect the outcome of HIV-1 infection.
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Affiliation(s)
- Paul J McLaren
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Mary Carrington
- 1] Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA. [2] The Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
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IFI44 suppresses HIV-1 LTR promoter activity and facilitates its latency. Virology 2015; 481:142-50. [PMID: 25776761 DOI: 10.1016/j.virol.2015.02.046] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 12/08/2014] [Accepted: 02/07/2015] [Indexed: 01/23/2023]
Abstract
IFI44 is an interferon-alfa inducible protein, and is associated with infection of several viruses. However, IFI44 elicits minimal antiviral effects on these viruses, and its exact role is still unknown. Here we show that IFI44 inhibits HIV-1 replication in vitro. Through depletion of endogenous IFI44 or overexpression of IFI44 we confirm that IFI44 suppresses HIV-1 LTR promoter activity and affects viral transcription. Furthermore, we find that IFI44 localizes to nuclei and binds to the HIV-1 LTR promoter in HIV-1 infected cells. Removing suppression of HIV-1 transcription benefits reactivation of HIV-1 proviruses for purging latent reservoirs. We demonstrate that depletion of endogenous IFI44 in J-LAT cells induces reactivation of latent HIV-1. Based on these results, we propose a model in which IFI44 is recruited to the HIV-1 LTR, which may suppress viral transcription and prevent reactivation of latent HIV-1. Our study suggests a previously unrecognized anti-HIV phenomenon for interferon-stimulated proteins.
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48
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Abstract
Despite effective treatment, HIV is not completely eliminated from the infected organism because of the existence of viral reservoirs. A major reservoir consists of infected resting CD4+ T cells, mostly of memory type, that persist over time due to the stable proviral insertion and a long cellular lifespan. Resting cells do not produce viral particles and are protected from viral-induced cytotoxicity or immune killing. However, these latently infected cells can be reactivated by stochastic events or by external stimuli. The present review focuses on novel genome-wide technologies applied to the study of integration, transcriptome, and proteome characteristics and their recent contribution to the understanding of HIV latency.
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Affiliation(s)
- Angela Ciuffi
- Institute of Microbiology, University Hospital of Lausanne (CHUV), University of Lausanne, Bugnon 48, 1011, Lausanne, Switzerland,
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