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Janevska M, Cammaert T, Naessens E, Verhasselt B. A cGAS-mediated type I interferon response in human CD4+ T cells depends on productive infection and is conserved over HIV types and strains. J Virol 2024:e0087724. [PMID: 39269176 DOI: 10.1128/jvi.00877-24] [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: 06/04/2024] [Accepted: 08/11/2024] [Indexed: 09/15/2024] Open
Abstract
Human immunodeficiency virus (HIV) type 2 is known to be less pathogenic than HIV-1, possibly due to more effective immune control mechanisms. The mechanism of innate sensing of HIV-2 by T cells is at present unclear. In this study, we show that several primary isolates of HIV-2 (CBL20 and CI85) and HIV-1 (A8 and D2), similar to the molecular clone HIV-1 NL4.3-GFP-I, induce a significant type I interferon response in its main target, activated CD4+ T cells. However, they are unable to do so after shRNA-mediated knock-down of cGAS. In addition, both HIV-1- and HIV-2-induced type I interferon response in CD4+ T cells was dependent on productive infection and integration, as the presence of RT or integrase inhibitor dramatically suppressed the sensing. Our findings collectively showed that the cGAS-dependent type I interferon response of CD4+ T cells to HIV infection is conserved over HIV types and critically depends on productive infection.IMPORTANCEBy unveiling the role of cGAS in sensing Human immunodeficiency virus types 1 and 2 (HIV-1 and HIV-2) across CD4+ T cells and highlighting its broader relevance that might be mirrored in other cell types, our research provides insights into the uniform mechanism of innate immune activation by different HIV isolates. By demonstrating the necessity of productive infection, we highlight the robust and specific nature of the observed cGAS-mediated innate response, dispelling concerns about contaminating plasmids triggering an immune response. Our preliminary data suggest that the lower pathogenicity of HIV-2 may not be directly correlated to superior innate immune control mediated by cGAS.
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Affiliation(s)
- Marija Janevska
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Timothy Cammaert
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Evelien Naessens
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Ghent University Hospital, Ghent, Belgium
| | - Bruno Verhasselt
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Ghent University Hospital, Ghent, Belgium
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2
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Pascoal C, Francisco R, Mexia P, Pereira BL, Granjo P, Coelho H, Barbosa M, dos Reis Ferreira V, Videira PA. Revisiting the immunopathology of congenital disorders of glycosylation: an updated review. Front Immunol 2024; 15:1350101. [PMID: 38550576 PMCID: PMC10972870 DOI: 10.3389/fimmu.2024.1350101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 02/26/2024] [Indexed: 04/02/2024] Open
Abstract
Glycosylation is a critical post-translational modification that plays a pivotal role in several biological processes, such as the immune response. Alterations in glycosylation can modulate the course of various pathologies, such as the case of congenital disorders of glycosylation (CDG), a group of more than 160 rare and complex genetic diseases. Although the link between glycosylation and immune dysfunction has already been recognized, the immune involvement in most CDG remains largely unexplored and poorly understood. In this study, we provide an update on the immune dysfunction and clinical manifestations of the 12 CDG with major immune involvement, organized into 6 categories of inborn errors of immunity according to the International Union of Immunological Societies (IUIS). The immune involvement in phosphomannomutase 2 (PMM2)-CDG - the most frequent CDG - was comprehensively reviewed, highlighting a higher prevalence of immune issues during infancy and childhood and in R141H-bearing genotypes. Finally, using PMM2-CDG as a model, we point to links between abnormal glycosylation patterns in host cells and possibly favored interactions with microorganisms that may explain the higher susceptibility to infection. Further characterizing immunopathology and unusual host-pathogen adhesion in CDG can not only improve immunological standards of care but also pave the way for innovative preventive measures and targeted glycan-based therapies that may improve quality of life for people living with CDG.
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Affiliation(s)
- Carlota Pascoal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO– Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- CDG & Allies-Professionals and Patient Associations International Network, Caparica, Portugal
| | - Rita Francisco
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO– Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- CDG & Allies-Professionals and Patient Associations International Network, Caparica, Portugal
| | - Patrícia Mexia
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO– Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- CDG & Allies-Professionals and Patient Associations International Network, Caparica, Portugal
| | - Beatriz Luís Pereira
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO– Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- CDG & Allies-Professionals and Patient Associations International Network, Caparica, Portugal
| | - Pedro Granjo
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO– Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- CDG & Allies-Professionals and Patient Associations International Network, Caparica, Portugal
| | - Helena Coelho
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Mariana Barbosa
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO– Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- CDG & Allies-Professionals and Patient Associations International Network, Caparica, Portugal
| | - Vanessa dos Reis Ferreira
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO– Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- CDG & Allies-Professionals and Patient Associations International Network, Caparica, Portugal
| | - Paula Alexandra Videira
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO– Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- CDG & Allies-Professionals and Patient Associations International Network, Caparica, Portugal
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3
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Li Y, Lefebvre F, Nakku-Joloba E, Ronald A, Gray G, de Bruyn G, Kiarie J, Celum C, Cameron MJ, Lingappa JR, Mackelprang RD. Upregulation of PTPRC and Interferon Response Pathways in HIV-1 Seroconverters Prior to Infection. J Infect Dis 2023; 227:714-719. [PMID: 36637125 PMCID: PMC9978315 DOI: 10.1093/infdis/jiac498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 12/16/2022] [Accepted: 12/27/2022] [Indexed: 01/14/2023] Open
Abstract
Human immunodeficiency virus 1 (HIV-1) exposed seronegative (HESN) individuals may have unique characteristics that alter susceptibility to HIV-1 infection. However, identifying truly exposed HESN is challenging. We utilized stored data and biospecimens from HIV-1 serodifferent couple cohorts, in which couples' HIV-1 exposures were quantified based on unprotected sex frequency and viral load of the partner with HIV-1. We compared peripheral blood gene expression between 15 HESN and 18 seroconverters prior to infection. We found PTPRC (encoding CD45 antigen) and interferon-response pathways had significantly higher expression among individuals who went on to become seropositive and thus may be a signature for increased acquisition risk.
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Affiliation(s)
- Yunqi Li
- Institute for Public Health Genetics, University of Washington, Seattle, Washington, USA
| | - Francois Lefebvre
- Canadian Centre for Computational Genomics-Montréal Node, Montreal, Quebec, Canada
| | | | - Allan Ronald
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Glenda Gray
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Guy de Bruyn
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - James Kiarie
- Department of Obstetrics and Gynecology, University of Nairobi, Nairobi, Kenya
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Connie Celum
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Mark J Cameron
- Department of Population and Quantitative Health Science, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jairam R Lingappa
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Romel D Mackelprang
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington, USA
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4
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Wu VH, Nordin JML, Nguyen S, Joy J, Mampe F, Del Rio Estrada PM, Torres-Ruiz F, González-Navarro M, Luna-Villalobos YA, Ávila-Ríos S, Reyes-Terán G, Tebas P, Montaner LJ, Bar KJ, Vella LA, Betts MR. Profound phenotypic and epigenetic heterogeneity of the HIV-1-infected CD4 + T cell reservoir. Nat Immunol 2023; 24:359-370. [PMID: 36536105 PMCID: PMC9892009 DOI: 10.1038/s41590-022-01371-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 10/24/2022] [Indexed: 12/24/2022]
Abstract
Understanding the complexity of the long-lived HIV reservoir during antiretroviral therapy (ART) remains a considerable impediment in research towards a cure for HIV. To address this, we developed a single-cell strategy to precisely define the unperturbed peripheral blood HIV-infected memory CD4+ T cell reservoir from ART-treated people living with HIV (ART-PLWH) via the presence of integrated accessible proviral DNA in concert with epigenetic and cell surface protein profiling. We identified profound reservoir heterogeneity within and between ART-PLWH, characterized by new and known surface markers within total and individual memory CD4+ T cell subsets. We further uncovered new epigenetic profiles and transcription factor motifs enriched in HIV-infected cells that suggest infected cells with accessible provirus, irrespective of reservoir distribution, are poised for reactivation during ART treatment. Together, our findings reveal the extensive inter- and intrapersonal cellular heterogeneity of the HIV reservoir, and establish an initial multiomic atlas to develop targeted reservoir elimination strategies.
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Grants
- K08 AI136660 NIAID NIH HHS
- T32 AI007632 NIAID NIH HHS
- R21 AI172629 NIAID NIH HHS
- UM1 AI164570 NIAID NIH HHS
- P30 AI045008 NIAID NIH HHS
- R01 AI031338 NIAID NIH HHS
- U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)
- Support for this study was provided by the following NIH grants: U19-A1-149680-02 (MRB), P01-AI31338 (MRB, KJB), K08-AI136660 (LAV), T32-AI007632 (VW), P30-AI045008 (Penn Center for AIDS Research) (MRB, LAV, KJB, PT, LJM), UM-1AI164570 (BEAT-HIV Collaboratory) which is co-supported by the National Institute of Allergies and Infectious Diseases (NIAID), the National Institute of Mental Health (NIMH), the National Institute of Neurological Disorders and Stroke (NINDS), the National Institute on Drug Abuse (NIDA), and the Robert I. Jacobs Fund of The Philadelphia Foundation (MRB, KJB, PT, LJM). LJM is also supported by the Herbert Kean, M.D., Family Professorship. CIENI-INER is supported by the Mexican Government (Programa Presupuestal P016; Anexo 13 del Decreto del Presupuesto de Egresos de la Federación).
- CIENI-INER is supported by the Mexican Government (Programa Presupuestal P016; Anexo 13 del Decreto del Presupuesto de Egresos de la Federación).
- LJM is also supported by the Herbert Kean, M.D., Family Professorship.
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Affiliation(s)
- Vincent H Wu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for AIDS Research, University of Pennsylvania, Philadelphia, PA, USA
| | - Jayme M L Nordin
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for AIDS Research, University of Pennsylvania, Philadelphia, PA, USA
| | - Son Nguyen
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Medical Engineering and Science, Department of Chemistry, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jaimy Joy
- Center for AIDS Research, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Felicity Mampe
- Center for AIDS Research, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Perla M Del Rio Estrada
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Fernanda Torres-Ruiz
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Mauricio González-Navarro
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Yara Andrea Luna-Villalobos
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Santiago Ávila-Ríos
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Gustavo Reyes-Terán
- Institutos Nacionales de Salud y Hospitales de Alta Especialidad, Secretaría de Salud de México, Mexico City, Mexico
| | - Pablo Tebas
- Center for AIDS Research, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Luis J Montaner
- Center for AIDS Research, University of Pennsylvania, Philadelphia, PA, USA
- The Wistar Institute, Philadelphia, PA, USA
| | - Katharine J Bar
- Center for AIDS Research, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Laura A Vella
- Center for AIDS Research, University of Pennsylvania, Philadelphia, PA, USA.
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Michael R Betts
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Center for AIDS Research, University of Pennsylvania, Philadelphia, PA, USA.
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5
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Iyer K, Chand K, Mitra A, Trivedi J, Mitra D. Diversity in heat shock protein families: functional implications in virus infection with a comprehensive insight of their role in the HIV-1 life cycle. Cell Stress Chaperones 2021; 26:743-768. [PMID: 34318439 PMCID: PMC8315497 DOI: 10.1007/s12192-021-01223-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 02/07/2023] Open
Abstract
Heat shock proteins (HSPs) are a group of cellular proteins that are induced during stress conditions such as heat stress, cold shock, UV irradiation and even pathogenic insult. They are classified into families based on molecular size like HSP27, 40, 70 and 90 etc, and many of them act as cellular chaperones that regulate protein folding and determine the fate of mis-folded or unfolded proteins. Studies have also shown multiple other functions of these proteins such as in cell signalling, transcription and immune response. Deregulation of these proteins leads to devastating consequences, such as cancer, Alzheimer's disease and other life threatening diseases suggesting their potential importance in life processes. HSPs exist in multiple isoforms, and their biochemical and functional characterization still remains a subject of active investigation. In case of viral infections, several HSP isoforms have been documented to play important roles with few showing pro-viral activity whereas others seem to have an anti-viral role. Earlier studies have demonstrated that HSP40 plays a pro-viral role whereas HSP70 inhibits HIV-1 replication; however, clear isoform-specific functional roles remain to be established. A detailed functional characterization of all the HSP isoforms will uncover their role in cellular homeostasis and also may highlight some of them as potential targets for therapeutic strategies against various viral infections. In this review, we have tried to comprehend the details about cellular HSPs and their isoforms, their role in cellular physiology and their isoform-specific functions in case of virus infection with a specific focus on HIV-1 biology.
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Affiliation(s)
- Kruthika Iyer
- Laboratory for HIV Research, National Centre for Cell Science, SP Pune University, Ganeshkhind, Pune, 411007, India
| | - Kailash Chand
- Laboratory for HIV Research, National Centre for Cell Science, SP Pune University, Ganeshkhind, Pune, 411007, India
| | - Alapani Mitra
- Laboratory for HIV Research, National Centre for Cell Science, SP Pune University, Ganeshkhind, Pune, 411007, India
| | - Jay Trivedi
- Laboratory for HIV Research, National Centre for Cell Science, SP Pune University, Ganeshkhind, Pune, 411007, India
| | - Debashis Mitra
- Laboratory for HIV Research, National Centre for Cell Science, SP Pune University, Ganeshkhind, Pune, 411007, India.
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6
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Che M, Gong W, Zhao Y, Liu M. Long noncoding RNA HCG18 inhibits the differentiation of human bone marrow-derived mesenchymal stem cells in osteoporosis by targeting miR-30a-5p/NOTCH1 axis. Mol Med 2020; 26:106. [PMID: 33176682 PMCID: PMC7656763 DOI: 10.1186/s10020-020-00219-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 09/14/2020] [Indexed: 12/15/2022] Open
Abstract
Background Recent studies have demonstrated that long non-coding RNAs (LncRNAs) can influence bone cell differentiation and formation. However, it is unclear whether lncRNA HCG18 is involved in osteoporosis (OP). This study was conducted to investigate the regulation of HCG18 in osteogenic differentiation of bone marrow mesenchymal stem cells (BMSCs). Methods BMSCs were isolated and cultured from mouse pathological models and osteoporosis patients. RT-qPCR was performed to detect the expression of HCG18 and miR-30a-5p in BMSCs. The interaction between HCG18 and miR-30a-5p was analyzed by dual luciferase assay and RNA pulldown assay. The interaction between miR-30a-5p and NOTCH1 3′-UTR was analyzed by dual luciferase assay. RT-qPCR and Western blotting were used to detect the expression of osteogenic genes Runx2, OCN and OPN. Hindlimb-unloaded (HU) mice model was established, and HCG18 was knocked down on bone-formation surfaces by using lentivirus mediated shRNA transfection. Results The expression of HCG18 was increased in BMSCs of OP patients, while the expression of miR-30a-5p was decreased. The expression of HCG18 and miR-30a-5p was negatively correlated in BMSCs. During the differentiation from BMSCs to osteoblasts, the expression of HCG18 was significantly downregulated, and the expression of miR-30a-5p was significantly upregulated. Overexpression of HCG18 was able to reverse the osteogenic-induced upregulation of miR-30a-5p expression, and knockdown of HCG18 further promoted the expression of miR-30a-5p. In addition, miR-30a-5p partially abolished the effect of HCG18 on osteogenic differentiation of BMSCs. NOTCH1 was a target protein of miR-30a-5p, and upregulation of NOTCH1 reversed the effect of miR-30a-5p on osteogenic differentiation of BMSCs. Furthermore, this study found that lentivirus mediated HCG18 knockdown on the bone-formation surfaces of hindlimb-unloaded (HU) mice partially alleviated unloading-induced bone loss Conclusions HCG18 inhibited osteogenic differentiation of BMSCs induced by OP via the miR-30a-5p/NOTCH1 axis. HCG18 can be identified as a regulator of osteogenic differentiation of BMSCs.
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Affiliation(s)
- Mingxue Che
- Department of Spine Surgery, The First Hospital of Jilin University, No.1 Xinmin Street, Changchun, 130021, Jilin Province, China
| | - Weiquan Gong
- Department of Spine Surgery, The First Hospital of Jilin University, No.1 Xinmin Street, Changchun, 130021, Jilin Province, China
| | - Yao Zhao
- Department of Joint Surgery, The First Hospital of Jilin University, No.1 Xinmin Street, Changchun, 130021, Jilin Province, China
| | - Mingxi Liu
- Department of Orthopedic Traumatology, The First Hospital of Jilin University, No.1 Xinmin Street, Changchun, 130021, Jilin Province, China.
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7
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Ali A, Furler RL, Pedroza-Martins L, Colantonio AD, Anisman-Posner D, Bryson Y, Yang OO, Uittenbogaart CH. A Novel HIV-1 Nef Mutation in a Primary Pediatric Isolate Impairs MHC-Class I Downregulation and Cytopathicity. AIDS Res Hum Retroviruses 2020; 36:122-130. [PMID: 31571497 DOI: 10.1089/aid.2019.0160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
HIV-1-induced cytopathicity of thymocytes is a major cause of reduced peripheral T cells and rapid disease progression observed in HIV-1-infected infants. Understanding the virulence factors responsible for thymocyte depletion has paramount importance in addressing the pathogenesis of disease progression in children. In this study, thymocyte depletion was analyzed following infection with two primary CXCR4-tropic HIV-1 pediatric isolates (PI), PI-2 and PI-2.1, which were serially derived from an in utero-infected infant. Although highly similar to each other, PI-2 showed markedly decreased thymocyte depletion in vitro compared with PI-2.1. Further analysis showed a novel deletion in the Nef protein (NefΔK7S) of PI-2, which was absent in PI-2.1. This deletion inhibited Nef-mediated major histocompatibility complex class I (MHC-I) downregulation in infected thymocytes in vitro and in vivo; in contrast, the mutated Nef continued to downregulate CD4 surface expression in vitro. These results suggest that HIV-1 Nef contributes to thymic damage in infants through selective functions.
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Affiliation(s)
- Ayub Ali
- UCLA AIDS Institute, University of California, Los Angeles, Los Angeles, California
- Division of Infectious Diseases, Department of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Robert L. Furler
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Livia Pedroza-Martins
- ANRS, French National Agency for Research on AIDS and Viral Hepatitis, Paris, France
| | - Arnaud D. Colantonio
- UCLA AIDS Institute, University of California, Los Angeles, Los Angeles, California
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, California
| | - Deborah Anisman-Posner
- UCLA AIDS Institute, University of California, Los Angeles, Los Angeles, California
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, California
| | - Yvonne Bryson
- UCLA AIDS Institute, University of California, Los Angeles, Los Angeles, California
- Department of Pediatrics, University of California, Los Angeles, Los Angeles, California
| | - Otto O. Yang
- UCLA AIDS Institute, University of California, Los Angeles, Los Angeles, California
- Division of Infectious Diseases, Department of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Christel H. Uittenbogaart
- UCLA AIDS Institute, University of California, Los Angeles, Los Angeles, California
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, California
- Department of Pediatrics, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California
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8
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Pascoal C, Francisco R, Ferro T, Dos Reis Ferreira V, Jaeken J, Videira PA. CDG and immune response: From bedside to bench and back. J Inherit Metab Dis 2020; 43:90-124. [PMID: 31095764 DOI: 10.1002/jimd.12126] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 05/13/2019] [Accepted: 05/15/2019] [Indexed: 12/20/2022]
Abstract
Glycosylation is an essential biological process that adds structural and functional diversity to cells and molecules, participating in physiological processes such as immunity. The immune response is driven and modulated by protein-attached glycans that mediate cell-cell interactions, pathogen recognition and cell activation. Therefore, abnormal glycosylation can be associated with deranged immune responses. Within human diseases presenting immunological defects are congenital disorders of glycosylation (CDG), a family of around 130 rare and complex genetic diseases. In this review, we have identified 23 CDG with immunological involvement, characterized by an increased propensity to-often life-threatening-infection. Inflammatory and autoimmune complications were found in 7 CDG types. CDG natural history(ies) and the mechanisms behind the immunological anomalies are still poorly understood. However, in some cases, alterations in pathogen recognition and intracellular signaling (eg, TGF-β1, NFAT, and NF-κB) have been suggested. Targeted therapies to restore immune defects are only available for PGM3-CDG and SLC35C1-CDG. Fostering research on glycoimmunology may elucidate the involved pathophysiological mechanisms and open new therapeutic avenues, thus improving CDG patients' quality of life.
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Affiliation(s)
- Carlota Pascoal
- Portuguese Association for CDG, Lisbon, Portugal
- CDG & Allies - Professionals and Patient Associations International Network (CDG & Allies - PPAIN), Caparica, Portugal
- UCIBIO, Departamento Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Rita Francisco
- Portuguese Association for CDG, Lisbon, Portugal
- CDG & Allies - Professionals and Patient Associations International Network (CDG & Allies - PPAIN), Caparica, Portugal
- UCIBIO, Departamento Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Tiago Ferro
- CDG & Allies - Professionals and Patient Associations International Network (CDG & Allies - PPAIN), Caparica, Portugal
- UCIBIO, Departamento Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Vanessa Dos Reis Ferreira
- Portuguese Association for CDG, Lisbon, Portugal
- CDG & Allies - Professionals and Patient Associations International Network (CDG & Allies - PPAIN), Caparica, Portugal
| | - Jaak Jaeken
- CDG & Allies - Professionals and Patient Associations International Network (CDG & Allies - PPAIN), Caparica, Portugal
- Center for Metabolic Diseases, Department of Development and Regeneration, UZ and KU Leuven, Leuven, Belgium
| | - Paula A Videira
- Portuguese Association for CDG, Lisbon, Portugal
- CDG & Allies - Professionals and Patient Associations International Network (CDG & Allies - PPAIN), Caparica, Portugal
- UCIBIO, Departamento Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
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9
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Sun Q, Zhou WX, Fan J. Adaptive Huber Regression. J Am Stat Assoc 2019; 115:254-265. [PMID: 33139964 PMCID: PMC7603940 DOI: 10.1080/01621459.2018.1543124] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 10/13/2018] [Accepted: 10/24/2018] [Indexed: 10/27/2022]
Abstract
Big data can easily be contaminated by outliers or contain variables with heavy-tailed distributions, which makes many conventional methods inadequate. To address this challenge, we propose the adaptive Huber regression for robust estimation and inference. The key observation is that the robustification parameter should adapt to the sample size, dimension and moments for optimal tradeoff between bias and robustness. Our theoretical framework deals with heavy-tailed distributions with bounded (1 + δ)-th moment for any δ > 0. We establish a sharp phase transition for robust estimation of regression parameters in both low and high dimensions: when δ ≥ 1, the estimator admits a sub-Gaussian-type deviation bound without sub-Gaussian assumptions on the data, while only a slower rate is available in the regime 0 < δ < 1 and the transition is smooth and optimal. In addition, we extend the methodology to allow both heavy-tailed predictors and observation noise. Simulation studies lend further support to the theory. In a genetic study of cancer cell lines that exhibit heavy-tailedness, the proposed methods are shown to be more robust and predictive.
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Affiliation(s)
- Qiang Sun
- Department of Statistical Sciences, University of Toronto, Toronto, ON M5S 3G3, Canada
| | - Wen-Xin Zhou
- Department of Mathematics, University of California, San Diego, La Jolla, CA 92093
| | - Jianqing Fan
- Honorary Professor, School of Data Science, Fudan University, Shanghai, China and Frederick L. Moore '18 Professor of Finance, Department of Operations Research and Financial Engineering, Princeton University, NJ 08544
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10
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Transduction with Lentiviral Vectors Altered the Expression Profile of Host MicroRNAs. J Virol 2018; 92:JVI.00503-18. [PMID: 29997205 DOI: 10.1128/jvi.00503-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 06/22/2018] [Indexed: 01/07/2023] Open
Abstract
RNA interference (RNAi) is widely used in gene knockdown analysis and as a tool to screen host genes involved in viral infection. Owing to the limitations of transducing cells with synthetic small interfering RNAs (siRNAs), lentiviral short hairpin RNA (shRNA) vectors are more widely used. However, we found that stable transduction with lentiviral shRNA vectors inhibited hepatitis C virus (HCV) propagation in human hepatoma cells. We found by microRNA (miRNA) microarray analysis that this inhibition was induced by the alteration of host miRNA expression. In addition to one miRNA (miR-196b-5p) previously reported to be involved in HCV infection, other miRNAs (miR-216a-5p, -216b-5p, 217, and -30b-5p) were found to influence HCV infection in this study. Further studies suggested that this effect was independent of the transcription of shRNAs. The lentiviral vector itself and the integration site of the lentiviral vector might determine the change in miRNA expression. Moreover, the upregulation of JUN contributed to the dysregulation of miR-216a-5p, -216b-5p, and -217 in stably transduced cells. Although the changes in miRNA expression were beneficial for inhibiting HCV infection in our study, this off-target effect should be considered when transduction with lentiviral vectors is performed for other purposes, especially in therapy.IMPORTANCE We found that stable transduction with lentiviral shRNA was able to nonspecifically inhibit HCV infection by the dysregulation of host miRNAs. Previous studies showed that the overexpression of shRNAs oversaturated the host miRNA pathways to inhibit HCV infection. In contrast, the miRNA machinery was not affected in our study. Knockout studies suggested that the nonspecific effect was independent of the transcription of shRNAs. The lentiviral vector itself and the integration sites in the host genome determined the changes in miRNAs. Stable transduction with lentiviral vectors was able to increase the expression of JUN, which in turn upregulated miR-216a-5p, miR-216b-5p, and miR-217. miR-216a-5p and miR-216b-5p might inhibit HCV by suppressing the host autophagic machinery. Our study suggested a novel nonspecific effect of lentiviral vectors, and this side effect should be considered when transduction with lentiviral vectors is performed for other purposes, especially in therapy.
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11
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Khwaja SS, Cai C, Badiyan SN, Wang X, Huang J. The immune-related microRNA miR-146b is upregulated in glioblastoma recurrence. Oncotarget 2018; 9:29036-29046. [PMID: 30018734 PMCID: PMC6044384 DOI: 10.18632/oncotarget.25528] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 05/16/2018] [Indexed: 12/18/2022] Open
Abstract
Background Glioblastoma (GBM) has a high rate of local recurrence despite chemoradiotherapy (CRT). Genome-wide expression profiling was performed on patient tumors before and after chemoradiotherapy to identify genes and gene pathways associated with recurrence. Results Median time to recurrence was 8.9 months with median time to second surgery of 9.6 months. The microRNA (miRNA) analysis identified 9 oncologic and immune-related miRNAs to be differentially expressed, including the hypoxia-related miR-210 and the immune-modulatory miR-146b. More than 1200 differentially-expressed genes were identified with RNA-sequencing (RNA-seq). Gene set enrichment analysis (GSEA) identified p53 signaling, Notch, Wnt, VEGF, and MEK gene sets enriched in recurrent GBM. Consistent with the miRNA profiling data, the miR-146b target gene set from GSEA analysis was also associated with recurrence. Methods Fourteen patients with GBM recurrence after CRT who had available tumor tissue from the initial diagnosis as well as recurrence were selected. Total RNA was isolated from formalin-fixed paraffin-embedded (FFPE) tumor specimens. Genome-wide expression profiling using RT-PCR for miRNA analysis and RNA-seq for messenger RNA (mRNA) analysis were conducted to identify differentially-expressed genes. GSEA was performed on the differential expression data. Conclusions Genome-wide expression profiling identifies multiple oncologic and immune-related gene sets associated with GBM recurrence. In particular, immune-related miR-146b is upregulated in recurrence and deserves further investigation.
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Affiliation(s)
- Shariq S Khwaja
- Department of Neurosurgery, UTHealth McGovern School of Medicine, Mischer Neuroscience Associates, Houston, TX, USA
| | - Chunyu Cai
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Shahed N Badiyan
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Xiaowei Wang
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Jiayi Huang
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
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12
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Frączek T, Kamiński R, Krakowiak A, Naessens E, Verhasselt B, Paneth P. Diaryl ethers with carboxymethoxyphenacyl motif as potent HIV-1 reverse transcriptase inhibitors with improved solubility. J Enzyme Inhib Med Chem 2017; 33:9-16. [PMID: 29098886 PMCID: PMC6009982 DOI: 10.1080/14756366.2017.1387542] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In search of new non-nucleoside reverse transcriptase inhibitors (NNRTIs) with improved solubility, two series of novel diaryl ethers with phenacyl moiety were designed and evaluated for their HIV-1 reverse transcriptase inhibition potentials. All compounds exhibited good to excellent results with IC50 at low micromolar to submicromolar concentrations. Two most active compounds (7e and 7 g) exhibit inhibitory potency comparable or even better than that of nevirapine and rilpivirine. Furthermore, SupT1 and CD4+ cell infectivity assays for the most promising (7e) have confirmed its strong antiviral potential while docking studies indicate a novel binding interactions responsible for high activity.
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Affiliation(s)
- Tomasz Frączek
- a Institute of Applied Radiation Chemistry , Lodz University of Technology , Lodz , Poland
| | - Rafał Kamiński
- a Institute of Applied Radiation Chemistry , Lodz University of Technology , Lodz , Poland
| | - Agnieszka Krakowiak
- a Institute of Applied Radiation Chemistry , Lodz University of Technology , Lodz , Poland.,b Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies , Polish Academy of Sciences , Lodz , Poland
| | - Evelien Naessens
- c Department of Clinical Chemistry, Microbiology and Immunology , Ghent University, Ghent University Hospital , Ghent , Belgium
| | - Bruno Verhasselt
- c Department of Clinical Chemistry, Microbiology and Immunology , Ghent University, Ghent University Hospital , Ghent , Belgium
| | - Piotr Paneth
- a Institute of Applied Radiation Chemistry , Lodz University of Technology , Lodz , Poland
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13
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Baeyens A, Naessens E, Van Nuffel A, Weening KE, Reilly AM, Claeys E, Trypsteen W, Vandekerckhove L, Eyckerman S, Gevaert K, Verhasselt B. HIV-1 Vpr N-terminal tagging affects alternative splicing of the viral genome. Sci Rep 2016; 6:34573. [PMID: 27721439 PMCID: PMC5056386 DOI: 10.1038/srep34573] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 09/12/2016] [Indexed: 01/11/2023] Open
Abstract
To facilitate studies on Vpr function in replicating HIV-1, we aimed to tag the protein in an infectious virus. First we showed that N-, but not C-terminal HA/FLAG tagging of Vpr protein preserves Vpr cytopathicity. Cloning the tags into proviral DNA however ablated viral production and replication. By construction of additional viral variants we could show this defect was not protein- but RNA-dependent and sequence specific, and characterized by oversplicing of the genomic RNA. Simulation of genomic RNA folding suggested that introduction of the tag sequence induced an alternative folding structure in a region enriched in splice sites and splicing regulatory sequences. In silico predictions identified the HA/His6-Vpr tagging in HIV-1 to affect mRNA folding less than HA/FLAG-Vpr tagging. In vitro infectivity and mRNA splice pattern improved but did not reach wild-type values. Thus, sequence-specific insertions may interfere with mRNA splicing, possibly due to altered RNA folding. Our results point to the complexity of viral RNA genome sequence interactions. This should be taken into consideration when designing viral manipulation strategies, for both research as for biological interventions.
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Affiliation(s)
- Ann Baeyens
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University, Ghent, Belgium
| | - Evelien Naessens
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University, Ghent, Belgium
| | - Anouk Van Nuffel
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University, Ghent, Belgium
| | - Karin E Weening
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University, Ghent, Belgium
| | - Anne-Marie Reilly
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University, Ghent, Belgium
| | - Eva Claeys
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University, Ghent, Belgium
| | - Wim Trypsteen
- HIV Translational Research Unit, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Linos Vandekerckhove
- HIV Translational Research Unit, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Sven Eyckerman
- VIB Medical Biotechnology Center, B-9000 Ghent, Belgium.,Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Kris Gevaert
- VIB Medical Biotechnology Center, B-9000 Ghent, Belgium.,Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Bruno Verhasselt
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University, Ghent, Belgium
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14
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Zhang X, Justice AC, Hu Y, Wang Z, Zhao H, Wang G, Johnson EO, Emu B, Sutton RE, Krystal JH, Xu K. Epigenome-wide differential DNA methylation between HIV-infected and uninfected individuals. Epigenetics 2016; 11:750-760. [PMID: 27672717 PMCID: PMC5094631 DOI: 10.1080/15592294.2016.1221569] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Epigenetic control of human immunodeficiency virus-1 (HIV-1) genes is critical for viral integration and latency. However, epigenetic changes in the HIV-1-infected host genome have not been well characterized. Here, we report the first large-scale epigenome-wide association study of DNA methylation for HIV-1 infection. We recruited HIV-infected (n = 261) and uninfected (n = 117) patients from the Veteran Aging Cohort Study (VACS) and all samples were profiled for 485,521 CpG sites in DNA extracted from the blood. After adjusting for cell type and clinical confounders, we identified 20 epigenome-wide significant CpGs for HIV-1 infection. Importantly, 2 CpGs in the promoter of the NLR family, CARD domain containing gene 5 (NLRC5), a key regulator of major histocompatibility complex class I gene expression, showed significantly lower methylation in HIV-infected subjects than in uninfected subjects (cg07839457: t = −6.03, Pnominal = 4.96 × 10−9; cg16411857: t = −7.63, Pnominal = 3.07 × 10−13). Hypomethylation of these 2 CpGs was replicated in an independent sample (GSE67705: cg07839457: t = −4.44, Pnominal = 1.61 × 10−5; cg16411857: t = −5.90; P = 1.99 × 10−8). Methylation of these 2 CpGs in NLRC5 was negatively correlated with viral load in the 2 HIV-infected samples (cg07839457: P = 1.8 × 10−4; cg16411857: P = 0.03 in the VACS; and cg07839457: P = 0.04; cg164111857: P = 0.01 in GSE53840). Our findings demonstrate that differential DNA methylation is associated with HIV infection and suggest the involvement of a novel host gene, NLRC5, in HIV pathogenesis.
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Affiliation(s)
- Xinyu Zhang
- a Department of Psychiatry , Yale School of Medicine , New Haven , CT , USA.,b Connecticut Veteran Health System , West Haven , CT , USA
| | - Amy C Justice
- c Yale University School of Medicine, New Haven Veterans Affairs Connecticut Healthcare System , West Haven , CT , USA
| | - Ying Hu
- d Center for Biomedical Informatics & Information Technology, National Cancer Institute , Bethesda , MD , USA
| | - Zuoheng Wang
- e Department of Internal Medicine , Division of Infectious Disease, Yale University School of Medicine , New Haven , CT , USA
| | - Hongyu Zhao
- f Department of Biostatistics , Yale School of Public Health , New Haven , CT , USA
| | - Guilin Wang
- g Yale Center of Genomic Analysis, West Campus , Orange , CT , USA
| | - Eric O Johnson
- h Fellow Program and Behavioral Health and Criminal Justice Division, RTI International , Research Triangle Park, NC , USA
| | - Brinda Emu
- e Department of Internal Medicine , Division of Infectious Disease, Yale University School of Medicine , New Haven , CT , USA
| | - Richard E Sutton
- e Department of Internal Medicine , Division of Infectious Disease, Yale University School of Medicine , New Haven , CT , USA
| | - John H Krystal
- a Department of Psychiatry , Yale School of Medicine , New Haven , CT , USA.,b Connecticut Veteran Health System , West Haven , CT , USA
| | - Ke Xu
- a Department of Psychiatry , Yale School of Medicine , New Haven , CT , USA.,b Connecticut Veteran Health System , West Haven , CT , USA
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15
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Pereira EA, daSilva LLP. HIV-1 Nef: Taking Control of Protein Trafficking. Traffic 2016; 17:976-96. [PMID: 27161574 DOI: 10.1111/tra.12412] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 05/05/2016] [Accepted: 05/05/2016] [Indexed: 12/25/2022]
Abstract
The Nef protein of the human immunodeficiency virus is a crucial determinant of viral pathogenesis and disease progression. Nef is abundantly expressed early in infection and is thought to optimize the cellular environment for viral replication. Nef controls expression levels of various cell surface molecules that play important roles in immunity and virus life cycle, by directly interfering with the itinerary of these proteins within the endocytic and late secretory pathways. To exert these functions, Nef physically interacts with host proteins that regulate protein trafficking. In recent years, considerable progress was made in identifying host-cell-interacting partners for Nef, and the molecular machinery used by Nef to interfere with protein trafficking has started to be unraveled. Here, we briefly review the knowledge gained and discuss new findings regarding the mechanisms by which Nef modifies the intracellular trafficking pathways to prevent antigen presentation, facilitate viral particle release and enhance the infectivity of HIV-1 virions.
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Affiliation(s)
- Estela A Pereira
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Luis L P daSilva
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
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16
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Strobel B, Miller FD, Rist W, Lamla T. Comparative Analysis of Cesium Chloride- and Iodixanol-Based Purification of Recombinant Adeno-Associated Viral Vectors for Preclinical Applications. Hum Gene Ther Methods 2016. [PMID: 26222983 PMCID: PMC4554548 DOI: 10.1089/hgtb.2015.051] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Cesium chloride (CsCl)- and iodixanol-based density gradients represent the core step in most protocols for serotype-independent adeno-associated virus (AAV) purification established to date. However, despite controversial reports about the purity and bioactivity of AAV vectors derived from each of these protocols, systematic comparisons of state-of-the-art variants of these methods are sparse. To define exact conditions for such a comparison, we first fractionated both gradients to analyze the distribution of intact, bioactive AAVs and contaminants, respectively. Moreover, we tested four different polishing methods (ultrafiltration, size-exclusion chromatography, hollow-fiber tangential flow filtration, and polyethylene glycol precipitation) implemented after the iodixanol gradient for their ability to deplete iodixanol and protein contaminations. Last, we conducted a side-by-side comparison of the CsCl and iodixanol/ultrafiltration protocol. Our results demonstrate that iodixanol-purified AAV preparations show higher vector purity but harbor more (∼20%) empty particles as compared with CsCl-purified vectors (<1%). Using mass spectrometry, we analyzed prominent protein impurities in the AAV vector product, thereby identifying known and new, possibly AAV-interacting proteins as major contaminants. Thus, our study not only provides a helpful guide for the many laboratories entering the AAV field, but also builds a basis for further investigation of cellular processes involved in AAV vector assembly and trafficking.
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Affiliation(s)
- Benjamin Strobel
- 1 Target Discovery Research, Boehringer Ingelheim Pharma GmbH & Co. KG , Biberach an der Riss, Germany
| | - Felix D Miller
- 1 Target Discovery Research, Boehringer Ingelheim Pharma GmbH & Co. KG , Biberach an der Riss, Germany
| | - Wolfgang Rist
- 2 Drug Discovery Support, Boehringer Ingelheim Pharma GmbH & Co. KG , Biberach an der Riss, Germany
| | - Thorsten Lamla
- 1 Target Discovery Research, Boehringer Ingelheim Pharma GmbH & Co. KG , Biberach an der Riss, Germany
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17
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Schroyen M, Eisley C, Koltes JE, Fritz-Waters E, Choi I, Plastow GS, Guan L, Stothard P, Bao H, Kommadath A, Reecy JM, Lunney JK, Rowland RRR, Dekkers JCM, Tuggle CK. Bioinformatic analyses in early host response to Porcine Reproductive and Respiratory Syndrome virus (PRRSV) reveals pathway differences between pigs with alternate genotypes for a major host response QTL. BMC Genomics 2016; 17:196. [PMID: 26951612 PMCID: PMC4782518 DOI: 10.1186/s12864-016-2547-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 02/26/2016] [Indexed: 01/01/2023] Open
Abstract
Background A region on Sus scrofa chromosome 4 (SSC4) surrounding single nucleotide polymorphism (SNP) marker WUR10000125 (WUR) has been reported to be strongly associated with both weight gain and serum viremia in pigs after infection with PRRS virus (PRRSV). A proposed causal mutation in the guanylate binding protein 5 gene (GBP5) is predicted to truncate the encoded protein. To investigate transcriptional differences between WUR genotypes in early host response to PRRSV infection, an RNA-seq experiment was performed on globin depleted whole blood RNA collected on 0, 4, 7, 10 and 14 days post-infection (dpi) from eight littermate pairs with one AB (favorable) and one AA (unfavorable) WUR genotype animal per litter. Results Gene Ontology (GO) enrichment analysis of transcripts that were differentially expressed (DE) between dpi across both genotypes revealed an inflammatory response for all dpi when compared to day 0. However, at the early time points of 4 and 7dpi, several GO terms had higher enrichment scores compared to later dpi, including inflammatory response (p < 10-7), specifically regulation of NFkappaB (p < 0.01), cytokine, and chemokine activity (p < 0.01). At 10 and 14dpi, GO term enrichment indicated a switch to DNA damage response, cell cycle checkpoints, and DNA replication. Few transcripts were DE between WUR genotypes on individual dpi or averaged over all dpi, and little enrichment of any GO term was found. However, there were differences in expression patterns over time between AA and AB animals, which was confirmed by genotype-specific expression patterns of several modules that were identified in weighted gene co-expression network analyses (WGCNA). Minor differences between AA and AB animals were observed in immune response and DNA damage response (p = 0.64 and p = 0.11, respectively), but a significant effect between genotypes pointed to a difference in ion transport/homeostasis and the participation of G-coupled protein receptors (p = 8e-4), which was reinforced by results from regulatory and phenotypic impact factor analyses between genotypes. Conclusion We propose these pathway differences between WUR genotypes are the result of the inability of the truncated GBP5 of the AA genotyped pigs to inhibit viral entry and replication as quickly as the intact GBP5 protein of the AB genotyped pigs. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2547-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Martine Schroyen
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA, 50011, USA.
| | - Christopher Eisley
- Department of Statistics, Iowa State University, 1121 Snedecor Hall, Ames, IA, 50011, USA.
| | - James E Koltes
- Department of Animal Science, University of Arkansas, AFLS B106D, Fayetteville, AR, 72701, USA.
| | - Eric Fritz-Waters
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA, 50011, USA.
| | - Igseo Choi
- USDA-ARS, BARC, APDL, Bldg.1040, Beltsville, MD, 20705, USA.
| | - Graham S Plastow
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
| | - Leluo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
| | - Hua Bao
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
| | - Arun Kommadath
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
| | - James M Reecy
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA, 50011, USA.
| | - Joan K Lunney
- USDA-ARS, BARC, APDL, Bldg.1040, Beltsville, MD, 20705, USA.
| | - Robert R R Rowland
- College of Veterinary Medicine, Kansas State University, K-231 Mosier Hall, Manhattan, KS, 66506, USA.
| | - Jack C M Dekkers
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA, 50011, USA.
| | - Christopher K Tuggle
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA, 50011, USA.
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18
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Landi A, Timermans CG, Naessens E, Vanderstraeten H, Stove V, Verhasselt B. The human immunodeficiency virus (HIV) Rev-binding protein (HRB) is a co-factor for HIV-1 Nef-mediated CD4 downregulation. J Gen Virol 2015; 97:778-785. [PMID: 26701340 DOI: 10.1099/jgv.0.000382] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1)-mediated CD4 downregulation is an important determinant of viral replication in vivo. Research on cellular co-factors involved in this process could lead to the identification of potential therapeutic targets. We found that CD4 surface levels were significantly higher in HIV-1-infected cells knocked-down for the HIV Rev-binding protein (HRB) compared with control cells. HRB knock-down affected CD4 downregulation induced by Nef but not by HIV-1 Vpu. Interestingly, the knock-down of the related protein HRBL (HRB-like), but not of the HRB interaction partner EPS15 (epidermal growth factor receptor pathway substrate 15), increased CD4 levels in Vpu-expressing cells significantly. Both of these proteins are known to be involved in HIV-1-mediated CD4 downregulation as co-factors of HIV-1 Nef. These results identify HRB as a previously unknown co-factor for HIV-1 Nef-mediated CD4 downregulation and highlight differences with the related protein HRBL, which affects the CD4 downregulation in a dual role as co-factor of both HIV-1 Nef and Vpu.
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Affiliation(s)
- Alessia Landi
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University, Ghent, Belgium
| | | | - Evelien Naessens
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University, Ghent, Belgium
| | - Hanne Vanderstraeten
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University, Ghent, Belgium
| | - Veronique Stove
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University, Ghent, Belgium
| | - Bruno Verhasselt
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University, Ghent, Belgium
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19
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Chaudhary P, Khan SZ, Rawat P, Augustine T, Raynes DA, Guerriero V, Mitra D. HSP70 binding protein 1 (HspBP1) suppresses HIV-1 replication by inhibiting NF-κB mediated activation of viral gene expression. Nucleic Acids Res 2015; 44:1613-29. [PMID: 26538602 PMCID: PMC4770212 DOI: 10.1093/nar/gkv1151] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 10/19/2015] [Indexed: 12/21/2022] Open
Abstract
HIV-1 efficiently hijacks host cellular machinery and exploits a plethora of host–viral interactions for its successful survival. Identifying host factors that affect susceptibility or resistance to HIV-1 may offer a promising therapeutic strategy against HIV-1. Previously, we have reported that heat shock proteins, HSP40 and HSP70 reciprocally regulate HIV-1 gene-expression and replication. In the present study, we have identified HSP70 binding protein 1 (HspBP1) as a host-intrinsic inhibitor of HIV-1. HspBP1 level was found to be significantly down modulated during HIV-1 infection and virus production inversely co-related with HspBP1 expression. Our results further demonstrate that HspBP1 inhibits HIV-1 long terminal repeat (LTR) promoter activity. Gel shift and chromatin immunoprecipitation assays revealed that HspBP1 was recruited on HIV-1 LTR at NF-κB enhancer region (κB sites). The binding of HspBP1 to κB sites obliterates the binding of NF-κB hetero-dimer (p50/p65) to the same region, leading to repression in NF-κB mediated activation of LTR-driven gene-expression. HspBP1 also plays an inhibitory role in the reactivation of latently infected cells, corroborating its repressive effect on NF-κB pathway. Thus, our results clearly show that HspBP1 acts as an endogenous negative regulator of HIV-1 gene-expression and replication by suppressing NF-κB-mediated activation of viral transcription.
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Affiliation(s)
| | | | - Pratima Rawat
- National Centre for Cell Science, Pune, Maharashtra 411007, India
| | - Tracy Augustine
- National Centre for Cell Science, Pune, Maharashtra 411007, India
| | - Deborah A Raynes
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Vince Guerriero
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Debashis Mitra
- National Centre for Cell Science, Pune, Maharashtra 411007, India
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AP-2 Is the Crucial Clathrin Adaptor Protein for CD4 Downmodulation by HIV-1 Nef in Infected Primary CD4+ T Cells. J Virol 2015; 89:12518-24. [PMID: 26423947 DOI: 10.1128/jvi.01838-15] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 09/22/2015] [Indexed: 01/28/2023] Open
Abstract
HIV-1 Nef-mediated CD4 downmodulation involves various host factors. We investigated the importance of AP-1, AP-2, AP-3, V1H-ATPase, β-COP, and ACOT8 for CD4 downmodulation in HIV-1-infected short hairpin RNA (shRNA)-expressing CD4(+) T cells and characterized direct interaction with Nef by Förster resonance energy transfer (FRET). Binding of lentiviral Nefs to CD4 and AP-2 was conserved, and only AP-2 knockdown impaired Nef-mediated CD4 downmodulation from primary T cells. Altogether, among the factors tested, AP-2 is the most important player for Nef-mediated CD4 downmodulation.
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Vpx-Independent Lentiviral Transduction and shRNA-Mediated Protein Knock-Down in Monocyte-Derived Dendritic Cells. PLoS One 2015. [PMID: 26208151 PMCID: PMC4514788 DOI: 10.1371/journal.pone.0133651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The function of dendritic cells (DCs) in the immune system is based on their ability to sense and present foreign antigens. Powerful tools to research DC function and to apply in cell-based immunotherapy are either silencing or overexpression of genes achieved by lentiviral transduction. To date, efficient lentiviral transduction of DCs or their monocyte derived counterparts (MDDCs) required high multiplicity of infection (MOI) or the exposure to the HIV-2/SIV protein Vpx to degrade viral restriction factor SAM domain and HD domain-containing protein 1 (SAMHD1). Here we present a Vpx-independent method for efficient (>95%) transduction of MDDCs at lower MOI. The protocol can be used both for ectopic gene expression and knock-down. Introducing shRNA targeting viral entry receptor CD4 and restriction factor SAMHD1 into MDDCs resulted in down-regulation of targeted proteins and, consequently, expected impact on HIV infection. This protocol for MDDCs transduction is robust and free of the potential risk arising from the use of Vpx which creates a virus infection-prone environment, potentially dangerous in clinical setting.
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