1
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Nkuwi E, Judicate GP, Tan TS, Barabona G, Toyoda M, Sunguya B, Kamori D, Ueno T. Relative resistance of patient-derived envelope sequences to SERINC5-mediated restriction of HIV-1 infectivity. J Virol 2023; 97:e0082323. [PMID: 37768085 PMCID: PMC10617508 DOI: 10.1128/jvi.00823-23] [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: 06/13/2023] [Accepted: 08/13/2023] [Indexed: 09/29/2023] Open
Abstract
IMPORTANCE Pathogenesis of HIV-1 is enhanced through several viral-encoded proteins that counteract a range of host restriction molecules. HIV-1 Nef counteracts the cell membrane protein SERINC5 by downregulating it from the cell surface, thereby enhancing virion infectivity. Some subtype B reference Envelope sequences have shown the ability to bypass SERINC5 infectivity restriction independent of Nef. However, it is not clear if and to what extent circulating HIV-1 strains can exhibit resistance to SERINC5 restriction. Using a panel of Envelope sequences isolated from 50 Tanzanians infected with non-B HIV-1 subtypes, we show that the lentiviral reporters pseudotyped with patient-derived Envelopes have reduced sensitivity to SERINC5 and that this sensitivity differed among viral subtypes. Moreover, we found that SERINC5 sensitivity within patient-derived Envelopes can be modulated by separate regions, highlighting the complexity of viral/host interactions.
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Affiliation(s)
- Emmanuel Nkuwi
- Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection Kumamoto University, Kumamoto, Japan
- Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
- Department of Microbiology and Parasitology, The University of Dodoma, Dodoma, Tanzania
| | - George P. Judicate
- Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection Kumamoto University, Kumamoto, Japan
| | - Toong Seng Tan
- Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection Kumamoto University, Kumamoto, Japan
| | - Godfrey Barabona
- Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection Kumamoto University, Kumamoto, Japan
| | - Mako Toyoda
- Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection Kumamoto University, Kumamoto, Japan
| | - Bruno Sunguya
- Collaboration Unit for Infection, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
- Department of Community Health, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Doreen Kamori
- Collaboration Unit for Infection, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Takamasa Ueno
- Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection Kumamoto University, Kumamoto, Japan
- Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
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2
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Jones BR, Joy JB. Inferring Human Immunodeficiency Virus 1 Proviral Integration Dates With Bayesian Inference. Mol Biol Evol 2023; 40:msad156. [PMID: 37421655 PMCID: PMC10411489 DOI: 10.1093/molbev/msad156] [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: 11/18/2022] [Revised: 06/23/2023] [Accepted: 07/06/2023] [Indexed: 07/10/2023] Open
Abstract
Human immunodeficiency virus 1 (HIV) proviruses archived in the persistent reservoir currently pose the greatest obstacle to HIV cure due to their evasion of combined antiretroviral therapy and ability to reseed HIV infection. Understanding the dynamics of the HIV persistent reservoir is imperative for discovering a durable HIV cure. Here, we explore Bayesian methods using the software BEAST2 to estimate HIV proviral integration dates. We started with within-host longitudinal HIV sequences collected prior to therapy, along with sequences collected from the persistent reservoir during suppressive therapy. We built a BEAST2 model to estimate integration dates of proviral sequences collected during suppressive therapy, implementing a tip date random walker to adjust the sequence tip dates and a latency-specific prior to inform the dates. To validate our method, we implemented it on both simulated and empirical data sets. Consistent with previous studies, we found that proviral integration dates were spread throughout active infection. Path sampling to select an alternative prior for date estimation in place of the latency-specific prior produced unrealistic results in one empirical data set, whereas on another data set, the latency-specific prior was selected as best fitting. Our Bayesian method outperforms current date estimation techniques with a root mean squared error of 0.89 years on simulated data relative to 1.23-1.89 years with previously developed methods. Bayesian methods offer an adaptable framework for inferring proviral integration dates.
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Affiliation(s)
- Bradley R Jones
- Molecular Epidemiology and Evolutionary Genetics, B.C. Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Bioinformatics Program, University of British Columbia, Vancouver, Canada
| | - Jeffrey B Joy
- Molecular Epidemiology and Evolutionary Genetics, B.C. Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Bioinformatics Program, University of British Columbia, Vancouver, Canada
- Deparment of Medicine, University of British Columbia, Vancouver, Canada
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3
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Mohammadi A, Etemad B, Zhang X, Li Y, Bedwell GJ, Sharaf R, Kittilson A, Melberg M, Wong C, Fajnzylber J, Worrall DP, Rosenthal A, Jordan H, Jilg N, Kaseke C, Giguel F, Lian X, Deo R, Gillespie E, Chishti R, Abrha S, Adams T, Siagian A, Anderson PL, Deeks SG, Lederman MM, Yawetz S, Kuritzkes DR, Lichterfeld MD, Tsibris A, Carrington M, Brumme ZL, Castillo-Mancilla JR, Engelman AN, Gaiha GD, Li JZ. Viral and Host Mediators of Non-Suppressible HIV-1 Viremia. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.30.23287124. [PMID: 37034605 PMCID: PMC10081408 DOI: 10.1101/2023.03.30.23287124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Non-suppressible HIV-1 viremia (NSV) can occur in persons with HIV despite adherence to combination antiretroviral therapy (ART) and in the absence of significant drug resistance. Here, we show that plasma NSV sequences are comprised primarily of large clones without evidence of viral evolution over time. We defined proviruses that contribute to plasma viremia as "producer", and those that did not as "non-producer". Compared to ART-suppressed individuals, NSV participants had a significantly larger producer reservoir. Producer proviruses were enriched in chromosome 19 and in proximity to the activating H3K36me3 epigenetic mark. CD4+ cells from NSV participants demonstrated upregulation of anti-apoptotic genes and downregulation of pro-apoptotic and type I/II interferon-related pathways. Furthermore, NSV participants showed no elevation in HIV-specific CD8+ cell responses and producer proviruses were enriched for HLA escape mutations. We identified critical host and viral mediators of NSV that represent potential targets to disrupt HIV persistence and promote viral silencing.
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Affiliation(s)
- Abbas Mohammadi
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Behzad Etemad
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Xin Zhang
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Yijia Li
- University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Radwa Sharaf
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Autumn Kittilson
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Meghan Melberg
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Colline Wong
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Jesse Fajnzylber
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Alex Rosenthal
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Hannah Jordan
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Nikolaus Jilg
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Clarety Kaseke
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Francoise Giguel
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Xiaodong Lian
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Rinki Deo
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Rida Chishti
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Sara Abrha
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Taylor Adams
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Abigail Siagian
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Peter L. Anderson
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Steven G. Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, CA, USA
| | - Michael M. Lederman
- Center for AIDS Research, Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University/University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Sigal Yawetz
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Mathias D. Lichterfeld
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Athe Tsibris
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Mary Carrington
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Jose R. Castillo-Mancilla
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Alan N. Engelman
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Gaurav D. Gaiha
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jonathan Z. Li
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
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4
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Alves E, Al-Kaabi M, Keane NM, Leary S, Almeida CAM, Deshpande P, Currenti J, Chopra A, Smith R, Castley A, Mallal S, Kalams SA, Gaudieri S, John M. Adaptation to HLA-associated immune pressure over the course of HIV infection and in circulating HIV-1 strains. PLoS Pathog 2022; 18:e1010965. [PMID: 36525463 PMCID: PMC9803285 DOI: 10.1371/journal.ppat.1010965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 12/30/2022] [Accepted: 11/01/2022] [Indexed: 12/23/2022] Open
Abstract
Adaptation to human leukocyte antigen (HLA)-associated immune pressure represents a major driver of human immunodeficiency virus (HIV) evolution at both the individual and population level. To date, there has been limited exploration of the impact of the initial cellular immune response in driving viral adaptation, the dynamics of these changes during infection and their effect on circulating transmitting viruses at the population level. Capturing detailed virological and immunological data from acute and early HIV infection is challenging as this commonly precedes the diagnosis of HIV infection, potentially by many years. In addition, rapid initiation of antiretroviral treatment following a diagnosis is the standard of care, and central to global efforts towards HIV elimination. Yet, acute untreated infection is the critical period in which the diversity of proviral reservoirs is first established within individuals, and associated with greater risk of onward transmissions in a population. Characterizing the viral adaptations evident in the earliest phases of infection, coinciding with the initial cellular immune responses is therefore relevant to understanding which changes are of greatest impact to HIV evolution at the population level. In this study, we utilized three separate cohorts to examine the initial CD8+ T cell immune response to HIV (cross-sectional acute infection cohort), track HIV evolution in response to CD8+ T cell-mediated immunity over time (longitudinal chronic infection cohort) and translate the impact of HLA-driven HIV evolution to the population level (cross-sectional HIV sequence data spanning 30 years). Using next generation viral sequencing and enzyme-linked immunospot interferon-gamma recall responses to peptides representing HLA class I-specific HIV T cell targets, we observed that CD8+ T cell responses can select viral adaptations prior to full antibody seroconversion. Using the longitudinal cohort, we uncover that viral adaptations have the propensity to be retained over time in a non-selective immune environment, which reflects the increasing proportion of pre-adapted HIV strains within the Western Australian population over an approximate 30-year period.
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Affiliation(s)
- Eric Alves
- School of Human Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Marwah Al-Kaabi
- School of Human Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Niamh M. Keane
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
| | - Shay Leary
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
| | - Coral-Ann M. Almeida
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
| | - Pooja Deshpande
- School of Human Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
| | - Jennifer Currenti
- School of Human Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Abha Chopra
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
| | - Rita Smith
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Alison Castley
- Department of Clinical Immunology, Royal Perth Hospital, Perth, Western Australia, Australia
| | - Simon Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Spyros A. Kalams
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Silvana Gaudieri
- School of Human Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Mina John
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
- Department of Clinical Immunology, Royal Perth Hospital, Perth, Western Australia, Australia
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5
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Molnar S, Wieczorek L, Zemil M, Schulte B, Martinez E, Gift S, Tang L, Streeck H, Gramzinski RA, Michael NL, Joyce G, Polonis VR. Novel monoclonal antibodies to the SERINC5 HIV-1 restriction factor detect endogenous andvirion-associated SERINC5. MAbs 2021; 12:1802187. [PMID: 32835602 PMCID: PMC7531522 DOI: 10.1080/19420862.2020.1802187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
SERINC5 is a multi-pass transmembrane protein that is thought to play a role in serine incorporation during cellular membrane biosynthesis. This protein has also been identified as a human immunodeficiency virus Type 1 (HIV-1) restriction factor. The paucity of monoclonal antibodies (mAbs) against SERINC5 has posed a challenge for the study of the endogenous protein. Here we report the development of novel anti-SERINC5 mAbs that target three distinct loops on the protein. We demonstrate that these SERINC5 mAbs can be used to detect endogenously expressed SERINC5 protein in various cell lines using Western blot, whole-cell ELISA, flow cytometry, and immunocytochemistry. We further show that some of these antibodies can detect SERINC5 that is present in HIV-1 viral stocks. These antibodies will aid in the characterization of the functions and mechanisms of action of SERINC5 in different cell types.
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Affiliation(s)
- Sebastian Molnar
- Military HIV Research Program, Walter Reed Army Institute of Research , Silver Spring, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine , Bethesda, MD, USA
| | - Lindsay Wieczorek
- Military HIV Research Program, Walter Reed Army Institute of Research , Silver Spring, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine , Bethesda, MD, USA
| | - Michelle Zemil
- Military HIV Research Program, Walter Reed Army Institute of Research , Silver Spring, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine , Bethesda, MD, USA
| | - Bianca Schulte
- Institute for Virology, University Hospital Bonn , Bonn, Germany
| | - Elizabeth Martinez
- Military HIV Research Program, Walter Reed Army Institute of Research , Silver Spring, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine , Bethesda, MD, USA
| | - Syna Gift
- Military HIV Research Program, Walter Reed Army Institute of Research , Silver Spring, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine , Bethesda, MD, USA
| | - Lan Tang
- Biologics Department, GenScript , Piscataway, NJ, USA
| | - Hendrik Streeck
- Institute for Virology, University Hospital Bonn , Bonn, Germany
| | - Robert A Gramzinski
- Military HIV Research Program, Walter Reed Army Institute of Research , Silver Spring, MD, USA
| | - Nelson L Michael
- Military HIV Research Program, Walter Reed Army Institute of Research , Silver Spring, MD, USA
| | - Gordon Joyce
- Military HIV Research Program, Walter Reed Army Institute of Research , Silver Spring, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine , Bethesda, MD, USA
| | - Victoria R Polonis
- Military HIV Research Program, Walter Reed Army Institute of Research , Silver Spring, MD, USA
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6
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Pelizzola M, Behr M, Li H, Munk A, Futschik A. Multiple haplotype reconstruction from allele frequency data. NATURE COMPUTATIONAL SCIENCE 2021; 1:262-271. [PMID: 38217170 DOI: 10.1038/s43588-021-00056-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 03/12/2021] [Indexed: 01/15/2024]
Abstract
Because haplotype information is of widespread interest in biomedical applications, effort has been put into their reconstruction. Here, we propose an efficient method, called haploSep, that is able to accurately infer major haplotypes and their frequencies just from multiple samples of allele frequency data. Even the accuracy of experimentally obtained allele frequencies can be improved by re-estimating them from our reconstructed haplotypes. From a methodological point of view, we model our problem as a multivariate regression problem where both the design matrix and the coefficient matrix are unknown. Compared to other methods, haploSep is very fast, with linear computational complexity in the haplotype length. We illustrate our method on simulated and real data focusing on experimental evolution and microbial data.
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Affiliation(s)
- Marta Pelizzola
- Vetmeduni Vienna, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Merle Behr
- University of California, Berkeley, CA, USA
| | - Housen Li
- University of Göttingen, Göttingen, Germany
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Göttingen, Göttingen, Germany
| | - Axel Munk
- University of Göttingen, Göttingen, Germany
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Göttingen, Göttingen, Germany
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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7
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Kruize Z, van Nuenen AC, van Wijk SW, Girigorie AF, van Dort KA, Booiman T, Kootstra NA. Nef Obtained from Individuals with HIV-1 Vary in Their Ability to Antagonize SERINC3- and SERINC5-Mediated HIV-1 Restriction. Viruses 2021; 13:v13030423. [PMID: 33800773 PMCID: PMC8000780 DOI: 10.3390/v13030423] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/25/2021] [Accepted: 03/02/2021] [Indexed: 12/14/2022] Open
Abstract
Nef is a multifunctional viral protein that has the ability to downregulate cell surface molecules, including CD4 and major histocompatibility complex class I (MHC-I) and, as recently shown, also members of the serine incorporator family (SERINC). Here, we analyzed the impact of naturally occurring mutations in HIV-1 Nef on its ability to counteract SERINC restriction and the clinical course of infection. HIV-1 Nef sequences were obtained from 123 participants of the Amsterdam Cohort Studies and showed multiple amino acid variations and mutations. Most of the primary Nef proteins showed increased activity to counteract SERINC3 and SERINC5 as compared to NL4-3 Nef. Several mutations in Nef were associated with either an increased or decreased infectivity of Bal26-pseudotyped HIV-1 produced in the presence of SERINC3 or SERINC5. The 8R, 157N and R178G Nef mutations were shown to have an effect on disease progression. Survival analysis showed an accelerated disease progression of individuals infected with HIV-1 carrying arginine or asparagine at position 8 or 157 in Nef, respectively, or the R178G Nef mutation. Here, we observed that naturally occurring mutations in Nef affect the ability of Nef to counteract SERINC3- and SERINC5-mediated inhibition of viral infectivity. The majority of these Nef mutations had no significant effect on HIV-1 pathogenesis and only the 8R, 157N and R178G mutations were associated with disease course.
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8
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Impaired ability of Nef to counteract SERINC5 is associated with reduced plasma viremia in HIV-infected individuals. Sci Rep 2020; 10:19416. [PMID: 33173092 PMCID: PMC7656250 DOI: 10.1038/s41598-020-76375-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 10/28/2020] [Indexed: 01/23/2023] Open
Abstract
HIV-1 Nef plays an essential role in enhancing virion infectivity by antagonizing the host restriction molecule SERINC5. Because Nef is highly polymorphic due to the selective forces of host cellular immunity, we hypothesized that certain immune-escape polymorphisms may impair Nef’s ability to antagonize SERINC5 and thereby influence viral fitness in vivo. To test this hypothesis, we identified 58 Nef polymorphisms that were overrepresented in HIV-infected patients in Japan sharing the same HLA genotypes. The number of immune-associated Nef polymorphisms was inversely correlated with the plasma viral load. By breaking down the specific HLA allele-associated mutations, we found that a number of the HLA-B*51:01-associated Y120F and Q125H mutations were most significantly associated with a reduced plasma viral load. A series of biochemical experiments showed that the double mutations Y120F/Q125H, but not either single mutation, impaired Nef’s ability to antagonize SERINC5 and was associated with decreasing virion infectivity and viral replication in primary lymphocytes. In contrast, other Nef functions such as CD4, CCR5, CXCR4 and HLA class I downregulation and CD74 upregulation remained unchanged. Taken together, our results suggest that the differential ability of Nef to counteract SERINC5 by naturally occurring immune-associated mutations was associated with the plasma viral load in vivo.
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9
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Differential Pressures of SERINC5 and IFITM3 on HIV-1 Envelope Glycoprotein over the Course of HIV-1 Infection. J Virol 2020; 94:JVI.00514-20. [PMID: 32493821 DOI: 10.1128/jvi.00514-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 05/25/2020] [Indexed: 12/23/2022] Open
Abstract
Infection of human immunodeficiency virus type 1 (HIV-1) is subject to restriction by cellular factors. Serine incorporator 5 (SERINC5) and interferon-inducible transmembrane 3 (IFITM3) proteins represent two of these restriction factors, which inhibit HIV-1 entry into target cells. Both proteins impede fusion of the viral membrane with the cellular membrane and the formation of a viral fusion pore, and both are countered by the HIV-1 envelope glycoprotein (Env). Given the immense and lasting pressure which Env endures from host adaptive immune responses, it is important to understand whether and how HIV-1 Env is able to maintain the resistance to SERINC5 and IFITM3 throughout the course of infection. We have thus examined a panel of HIV-1 Env clones that were isolated at different stages of viral infection-transmission, acute, and chronic. While HIV-1 Env clones from the transmission stage are resistant to both SERINC5 and IFITM3, as infection progresses into the acute and chronic stages, the resistance to IFITM3 but not to SERINC5 is gradually lost. We further discovered a significant correlation between the resistance of HIV-1 Env to soluble CD4 inhibition and the resistance to SERINC5 but not to IFITM3. Interestingly, the miniprotein CD4 mimetic M48U1 sensitizes HIV-1 Env to the inhibition by SERINC5 but not IFITM3. Together, these data indicate that SERINC5 and IFITM3 exert differential inhibitory pressures on HIV-1 Env over different stages of HIV-1 infection and that HIV-1 Env uses varied strategies to resist these two restriction factors.IMPORTANCE HIV-1 Env protein is exposed to the inhibition not only by humoral response, but also by host restriction factors, including serine incorporator 5 (SERINC5) and interferon-inducible transmembrane 3 (IFITM3). This study investigates how HIV-1 envelope glycoprotein (Env) manages to overcome the pressures from all these different host inhibition mechanisms over the long course of viral infection. HIV-1 Env preserves the resistance to SERINC5 but becomes sensitive to IFITM3 when infection progresses into the chronic stage. Our study also supports the possibility of using CD4 mimetic compounds to sensitize HIV-1 Env to the inhibition by SERINC5 as a potential therapeutic strategy.
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