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Cobos Jiménez V, Geretz A, Tokarev A, Ehrenberg PK, Deletsu S, Machmach K, Mudvari P, Howard JN, Zelkoski A, Paquin-Proulx D, Del Prete GQ, Subra C, Boritz EA, Bosque A, Thomas R, Bolton DL. AP-1/c-Fos supports SIV and HIV-1 latency in CD4 T cells infected in vivo. iScience 2023; 26:108015. [PMID: 37860759 PMCID: PMC10582365 DOI: 10.1016/j.isci.2023.108015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/24/2023] [Accepted: 09/18/2023] [Indexed: 10/21/2023] Open
Abstract
Persistent HIV-1 reservoirs of infected CD4 T cells are a major barrier to HIV-1 cure, although the mechanisms by which they are established and maintained in vivo remain poorly characterized. To elucidate host cell gene expression patterns that govern virus gene expression, we analyzed viral RNA+ (vRNA) CD4 T cells of untreated simian immunodeficiency virus (SIV)-infected macaques by single-cell RNA sequencing. A subset of vRNA+ cells distinguished by spliced and high total vRNA (7-10% of reads) expressed diminished FOS, a component of the Activator protein 1 (AP-1) transcription factor, relative to vRNA-low and -negative cells. Conversely, FOS and JUN, another AP-1 component, were upregulated in HIV DNA+ infected cells compared to uninfected cells from people with HIV-1 on suppressive therapy. Inhibiting c-Fos in latently infected primary cells augmented reactivatable HIV-1 infection. These findings implicate AP-1 in latency establishment and maintenance and as a potential therapeutic target to limit HIV-1 reservoirs.
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Affiliation(s)
- Viviana Cobos Jiménez
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Aviva Geretz
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Andrey Tokarev
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Philip K. Ehrenberg
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | - Kawthar Machmach
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Prakriti Mudvari
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Amanda Zelkoski
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Dominic Paquin-Proulx
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Gregory Q. Del Prete
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Caroline Subra
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Eli A. Boritz
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Rasmi Thomas
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Diane L. Bolton
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
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2
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Schuetz A, Corley MJ, Sacdalan C, Phuang-Ngern Y, Nakpor T, Wansom T, Ehrenberg PK, Sriplienchan S, Thomas R, Ratnaratorn N, Sukhumvittaya S, Tragonlugsana N, Slike BM, Akapirat S, Pinyakorn S, Rerknimitr R, Pang AP, Kroon E, Teeratakulpisan N, Krebs SJ, Phanuphak N, Ndhlovu LC, Vasan S. Distinct mucosal and systemic immunological characteristics in transgender women potentially relating to HIV acquisition. JCI Insight 2023; 8:e169272. [PMID: 37432754 PMCID: PMC10543719 DOI: 10.1172/jci.insight.169272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 07/06/2023] [Indexed: 07/12/2023] Open
Abstract
Transgender women (TGW) are disproportionally affected by HIV infection, with a global estimated prevalence of 19.9%, often attributed to behavioral risk factors, with less known about biological factors. We evaluated potential biological risk factors for HIV acquisition in TGW at the sites of viral entry by assessing immune parameters of the neovaginal surface and gut mucosa. The neovagina in TGW, compared with the vagina in cisgender women (CW), shows distinct cell composition and may pose a more inflammatory environment, evidenced by increased CD4+ T cell activation and higher levels of soluble markers of inflammation (C-reactive protein, soluble CD30). Increased inflammation may be driven by microbiome composition, as shown by a greater abundance of Prevotella and a higher Shannon Diversity Index. In addition, we have observed higher frequency of CD4+CCR5+ target cells and decreased DNA methylation of the CCR5 gene in the gut mucosa of TGW compared with CW and men who have sex with men, which was inversely correlated with testosterone levels. The rectal microbiome composition in TGW appears to favor a proinflammatory milieu as well as mucosal barrier disruption. Thus, it is possible that increased inflammation and higher frequencies of CCR5-expressing target cells at sites of mucosal viral entry may contribute to increased risk of HIV acquisition in TGW, with further validation in larger studies warranted.
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Affiliation(s)
- Alexandra Schuetz
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
| | - Michael J. Corley
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | | | | | | | - Tanyaporn Wansom
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
| | - Philip K. Ehrenberg
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | | | - Rasmi Thomas
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | | | | | | | - Bonnie M. Slike
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
| | - Siriwat Akapirat
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Suteeraporn Pinyakorn
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
| | - Rungsun Rerknimitr
- Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Alina P.S. Pang
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Eugène Kroon
- Institute of HIV Research and Innovation, Bangkok, Thailand
| | | | - Shelly J. Krebs
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
| | | | - Lishomwa C. Ndhlovu
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Sandhya Vasan
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
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3
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Geretz A, Ehrenberg PK, Clifford RJ, Laliberté A, Prelli Bozzo C, Eiser D, Kundu G, Yum LK, Apps R, Creegan M, Gunady M, Shangguan S, Sanders-Buell E, Sacdalan C, Phanuphak N, Tovanabutra S, Russell RM, Bibollet-Ruche F, Robb ML, Michael NL, Ake JA, Vasan S, Hsu DC, Hahn BH, Kirchhoff F, Thomas R. Single-cell transcriptomics identifies prothymosin α restriction of HIV-1 in vivo. Sci Transl Med 2023; 15:eadg0873. [PMID: 37531416 DOI: 10.1126/scitranslmed.adg0873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 06/21/2023] [Indexed: 08/04/2023]
Abstract
Host restriction factors play key roles in innate antiviral defense, but it remains poorly understood which of them restricts HIV-1 in vivo. Here, we used single-cell transcriptomic analysis to identify host factors associated with HIV-1 control during acute infection by correlating host gene expression with viral RNA abundance within individual cells. Wide sequencing of cells from one participant with the highest plasma viral load revealed that intracellular viral RNA transcription correlates inversely with expression of the gene PTMA, which encodes prothymosin α. This association was genome-wide significant (Padjusted < 0.05) and was validated in 28 additional participants from Thailand and the Americas with HIV-1 CRF01_AE and subtype B infections, respectively. Overexpression of prothymosin α in vitro confirmed that this cellular factor inhibits HIV-1 transcription and infectious virus production. Our results identify prothymosin α as a host factor that restricts HIV-1 infection in vivo, which has implications for viral transmission and cure strategies.
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Affiliation(s)
- Aviva Geretz
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Philip K Ehrenberg
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Robert J Clifford
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Alexandre Laliberté
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | | | - Daina Eiser
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Gautam Kundu
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Lauren K Yum
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Richard Apps
- NIH Center for Human Immunology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew Creegan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Mohamed Gunady
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Shida Shangguan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Eric Sanders-Buell
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Carlo Sacdalan
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok 10330, Thailand
| | - Nittaya Phanuphak
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok 10330, Thailand
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Ronnie M Russell
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Frederic Bibollet-Ruche
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Merlin L Robb
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Nelson L Michael
- Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Julie A Ake
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Sandhya Vasan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Denise C Hsu
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | - Rasmi Thomas
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
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4
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Shangguan S, Ehrenberg PK, Geretz A, Butler L, Pinyakorn S, Sriplienchan S, Sacdalan C, Chomchey N, Phanuphak N, Tovanabutra S, Vasan S, Hsu D, Thomas R. HLA-B*57 and B*58 Associate with Predictors of Reservoir Size in an Acutely Treated HIV Cohort. AIDS Res Hum Retroviruses 2023; 39:114-118. [PMID: 36465028 PMCID: PMC9986004 DOI: 10.1089/aid.2022.0082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Much has been learnt about the role of human leukocyte antigen (HLA) alleles during natural infection of HIV-1, but far less is known about their role in people living with HIV (PLWH) on suppressive antiretroviral therapy (ART). In this study we used variable selection to identify predictors of HIV reservoir size, as measured by total HIV DNA in 192 participants in an acute HIV infection (AHI) cohort. Baseline clinical data including pre-ART CD4 T cell counts and plasma viral load (VL) were available from all participants along with longitudinal measurements after ART initiation during AHI. Time to VL suppression, time to CD4 reconstitution, and pre-ART viremia were the strongest predictors of undetectable total HIV DNA at 24 weeks after ART initiation. We next performed HLA typing in 526 participants from the same cohort and investigated associations with the three predictors of reservoir size. HLA-B*57 and B*58 both associated significantly with time to VL suppression, which was one of the predictors of the size of the HIV reservoir. These findings are significant in PLWH and have to be considered in the context of therapeutic intervention when conducting analytic treatment interruption studies as participants with these alleles could impact clinical findings given the small sizes of these studies.
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Affiliation(s)
- Shida Shangguan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Philip K Ehrenberg
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Aviva Geretz
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Lauryn Butler
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Suteeraporn Pinyakorn
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | | | - Carlo Sacdalan
- SEARCH, Institute of HIV Research and Innovation, Bangkok, Thailand
| | - Nitiya Chomchey
- SEARCH, Institute of HIV Research and Innovation, Bangkok, Thailand
| | | | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Sandhya Vasan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Denise Hsu
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Rasmi Thomas
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
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5
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Li SS, Hickey A, Shangguan S, Ehrenberg PK, Geretz A, Butler L, Kundu G, Apps R, Creegan M, Clifford RJ, Pinyakorn S, Eller LA, Luechai P, Gilbert PB, Holtz TH, Chitwarakorn A, Sacdalan C, Kroon E, Phanuphak N, de Souza M, Ananworanich J, O'Connell RJ, Robb ML, Michael NL, Vasan S, Thomas R. HLA-B∗46 associates with rapid HIV disease progression in Asian cohorts and prominent differences in NK cell phenotype. Cell Host Microbe 2022; 30:1173-1185.e8. [PMID: 35841889 DOI: 10.1016/j.chom.2022.06.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/17/2022] [Accepted: 06/09/2022] [Indexed: 12/12/2022]
Abstract
Human leukocyte antigen (HLA) alleles have been linked to HIV disease progression and attributed to differences in cytotoxic T lymphocyte (CTL) epitope representation. These findings are largely based on treatment-naive individuals of European and African ancestry. We assessed HLA associations with HIV-1 outcomes in 1,318 individuals from Thailand and found HLA-B∗46:01 (B∗46) associated with accelerated disease in three independent cohorts. B∗46 had no detectable effect on HIV-specific T cell responses, but this allele is unusual in containing an HLA-C epitope that binds inhibitory receptors on natural killer (NK) cells. Unbiased transcriptomic screens showed increased NK cell activation in people with HIV, without B∗46, and simultaneous single-cell profiling of surface proteins and transcriptomes revealed a NK cell subset primed for increased responses in the absence of B∗46. These findings support a role for NK cells in HIV pathogenesis, revealed by the unique properties of the B∗46 allele common only in Asia.
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Affiliation(s)
- Shuying S Li
- Fred Hutchinson Cancer Center, Vaccine and Infectious Disease Division, Seattle, WA 98104, USA
| | - Andrew Hickey
- Division of HIV Prevention, U.S. Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; Thailand Ministry of Public Health, U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi 11000, Thailand
| | - Shida Shangguan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Philip K Ehrenberg
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Aviva Geretz
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Lauryn Butler
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Gautam Kundu
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Richard Apps
- Center for Human Immunology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew Creegan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Robert J Clifford
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Suteeraporn Pinyakorn
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Leigh Anne Eller
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Pikunchai Luechai
- Division of HIV Prevention, U.S. Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; Thailand Ministry of Public Health, U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi 11000, Thailand
| | - Peter B Gilbert
- Fred Hutchinson Cancer Center, Vaccine and Infectious Disease Division, Seattle, WA 98104, USA
| | - Timothy H Holtz
- Division of HIV Prevention, U.S. Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; Thailand Ministry of Public Health, U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi 11000, Thailand; Office of AIDS Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anupong Chitwarakorn
- Department of Disease Control, Thailand Ministry of Public Health, Nonthaburi 11000, Thailand
| | - Carlo Sacdalan
- Institute of HIV Research and Innovation, Bangkok 10330, Thailand
| | - Eugène Kroon
- Institute of HIV Research and Innovation, Bangkok 10330, Thailand
| | | | - Mark de Souza
- Institute of HIV Research and Innovation, Bangkok 10330, Thailand
| | - Jintanat Ananworanich
- Department of Global Health, Amsterdam Medical Center, University of Amsterdam, 1105 BP Amsterdam, the Netherlands
| | | | - Merlin L Robb
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Nelson L Michael
- Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Sandhya Vasan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Rasmi Thomas
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA.
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6
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Shangguan S, Ehrenberg PK, Geretz A, Yum L, Kundu G, May K, Fourati S, Nganou-Makamdop K, Williams LD, Sawant S, Lewitus E, Pitisuttithum P, Nitayaphan S, Chariyalertsak S, Rerks-Ngarm S, Rolland M, Douek DC, Gilbert P, Tomaras GD, Michael NL, Vasan S, Thomas R. Monocyte-derived transcriptome signature indicates antibody-dependent cellular phagocytosis as a potential mechanism of vaccine-induced protection against HIV-1. eLife 2021; 10:69577. [PMID: 34533134 PMCID: PMC8514236 DOI: 10.7554/elife.69577] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 09/16/2021] [Indexed: 12/12/2022] Open
Abstract
A gene signature was previously found to be correlated with mosaic adenovirus 26 vaccine protection in simian immunodeficiency virus and simian-human immunodeficiency virus challenge models in non-human primates. In this report, we investigated the presence of this signature as a correlate of reduced risk in human clinical trials and potential mechanisms of protection. The absence of this gene signature in the DNA/rAd5 human vaccine trial, which did not show efficacy, strengthens our hypothesis that this signature is only enriched in studies that demonstrated protection. This gene signature was enriched in the partially effective RV144 human trial that administered the ALVAC/protein vaccine, and we find that the signature associates with both decreased risk of HIV-1 acquisition and increased vaccine efficacy (VE). Total RNA-seq in a clinical trial that used the same vaccine regimen as the RV144 HIV vaccine implicated antibody-dependent cellular phagocytosis (ADCP) as a potential mechanism of vaccine protection. CITE-seq profiling of 53 surface markers and transcriptomes of 53,777 single cells from the same trial showed that genes in this signature were primarily expressed in cells belonging to the myeloid lineage, including monocytes, which are major effector cells for ADCP. The consistent association of this transcriptome signature with VE represents a tool both to identify potential mechanisms, as with ADCP here, and to screen novel approaches to accelerate the development of new vaccine candidates.
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Affiliation(s)
- Shida Shangguan
- US Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, United States
| | - Philip K Ehrenberg
- US Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, United States
| | - Aviva Geretz
- US Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, United States
| | - Lauren Yum
- US Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, United States
| | - Gautam Kundu
- US Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, United States
| | - Kelly May
- US Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, United States
| | - Slim Fourati
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, United States
| | | | - LaTonya D Williams
- Departments of Surgery, Immunology and Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, United States
| | - Sheetal Sawant
- Departments of Surgery, Immunology and Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, United States
| | - Eric Lewitus
- US Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, United States
| | - Punnee Pitisuttithum
- Vaccine Trial Centre, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | | | - Suwat Chariyalertsak
- Research Institute for Health Sciences and Faculty of Public Health, Chiang Mai University, Chiang Mai, Thailand
| | | | - Morgane Rolland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, United States
| | | | - Peter Gilbert
- Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Georgia D Tomaras
- Departments of Surgery, Immunology and Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, United States
| | - Nelson L Michael
- US Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, United States
| | - Sandhya Vasan
- US Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, United States
| | - Rasmi Thomas
- US Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, United States
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7
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Townsley SM, Donofrio GC, Jian N, Leggat DJ, Dussupt V, Mendez-Rivera L, Eller LA, Cofer L, Choe M, Ehrenberg PK, Geretz A, Gift S, Grande R, Lee A, Peterson C, Piechowiak MB, Slike BM, Tran U, Joyce MG, Georgiev IS, Rolland M, Thomas R, Tovanabutra S, Doria-Rose NA, Polonis VR, Mascola JR, McDermott AB, Michael NL, Robb ML, Krebs SJ. B cell engagement with HIV-1 founder virus envelope predicts development of broadly neutralizing antibodies. Cell Host Microbe 2021; 29:564-578.e9. [PMID: 33662277 DOI: 10.1016/j.chom.2021.01.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/08/2020] [Accepted: 01/27/2021] [Indexed: 12/22/2022]
Abstract
Determining which immunological mechanisms contribute to the development of broad neutralizing antibodies (bNAbs) during HIV-1 infection is a major goal to inform vaccine design. Using samples from a longitudinal HIV-1 acute infection cohort, we found key B cell determinants within the first 14-43 days of viremia that predict the development of bNAbs years later. Individuals who develop neutralization breadth had significantly higher B cell engagement with the autologous founder HIV envelope (Env) within 1 month of initial viremia. A higher frequency of founder-Env-specific naive B cells was associated with increased B cell activation and differentiation and predictive of bNAb development. These data demonstrate that the initial B cell interaction with the founder HIV Env is important for the development of broadly neutralizing antibodies and provide evidence that events within HIV acute infection lead to downstream functional outcomes.
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Affiliation(s)
- Samantha M Townsley
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Gina C Donofrio
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Ningbo Jian
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - David J Leggat
- Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Vincent Dussupt
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Letzibeth Mendez-Rivera
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Leigh Anne Eller
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Lauryn Cofer
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Misook Choe
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA; Emerging Infectious Diseases Branch, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Philip K Ehrenberg
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Aviva Geretz
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Syna Gift
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Rebecca Grande
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Anna Lee
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Caroline Peterson
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA; Emerging Infectious Diseases Branch, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Mary Bryson Piechowiak
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Bonnie M Slike
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Ursula Tran
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - M Gordon Joyce
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA; Emerging Infectious Diseases Branch, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Ivelin S Georgiev
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37212, USA
| | - Morgane Rolland
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Rasmi Thomas
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | | | - Victoria R Polonis
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - John R Mascola
- Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | | | - Nelson L Michael
- Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Merlin L Robb
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Shelly J Krebs
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA.
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8
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Ehrenberg PK, Shangguan S, Issac B, Alter G, Geretz A, Izumi T, Bryant C, Eller MA, Wegmann F, Apps R, Creegan M, Bolton DL, Sekaly RP, Robb ML, Gramzinski RA, Pau MG, Schuitemaker H, Barouch DH, Michael NL, Thomas R. A vaccine-induced gene expression signature correlates with protection against SIV and HIV in multiple trials. Sci Transl Med 2020; 11:11/507/eaaw4236. [PMID: 31462510 DOI: 10.1126/scitranslmed.aaw4236] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/25/2019] [Accepted: 07/31/2019] [Indexed: 12/11/2022]
Abstract
Current HIV vaccines are only partially efficacious, presenting an opportunity to identify correlates of protection and, thereby, potential insight into mechanisms that prevent HIV acquisition. Two independent preclinical challenge studies in nonhuman primates (NHPs) previously showed partial efficacy of a mosaic adenovirus 26 (Ad26)-based HIV-1 vaccine candidate. To investigate the basis of this protection, we performed whole transcriptomics profiling by RNA sequencing (RNA-seq) in sorted lymphocytes from peripheral blood samples taken during these studies at different time points after vaccination but before challenge. We observed a transcriptional signature in B cells that associated with protection from acquisition of simian immunodeficiency virus (SIV) or the simian-human immunodeficiency virus (SHIV) in both studies. Strong antibody responses were elicited, and genes from the signature for which expression was enriched specifically associated with higher magnitude of functional antibody responses. The same gene expression signature also associated with protection in RV144 in the only human HIV vaccine trial to date that has shown efficacy and in two additional NHP studies that evaluated similar canarypox-based vaccine regimens. A composite gene expression score derived from the gene signature was one of the top-ranked correlates of protection in the NHP vaccine studies. This study aims to bridge preclinical and clinical data with the identification of a gene signature in B cells that is associated with protection from SIV and HIV infection by providing a new approach for evaluating future vaccine candidates.
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Affiliation(s)
- Philip K Ehrenberg
- U.S. Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Shida Shangguan
- U.S. Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Biju Issac
- U.S. Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Aviva Geretz
- U.S. Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Taisuke Izumi
- U.S. Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | | | - Michael A Eller
- U.S. Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Frank Wegmann
- Janssen Vaccines and Prevention B.V., 2329 Leiden, Netherlands
| | - Richard Apps
- Center for Human Immunology, National Institutes of Health, Bethesda, MD 20814, USA
| | - Matthew Creegan
- U.S. Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Diane L Bolton
- U.S. Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | | | - Merlin L Robb
- U.S. Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Robert A Gramzinski
- U.S. Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Maria G Pau
- Janssen Vaccines and Prevention B.V., 2329 Leiden, Netherlands
| | | | - Dan H Barouch
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA.,Center for Virology and Vaccine Research, BIDMC, Harvard Medical School, Boston, MA 02115, USA
| | - Nelson L Michael
- U.S. Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Rasmi Thomas
- U.S. Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA. .,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
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9
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Geretz A, Cofer L, Ehrenberg PK, Currier JR, Yoon IK, Alera MTP, Jarman R, Rothman AL, Thomas R. Next-generation sequencing of 11 HLA loci in a large dengue vaccine cohort from the Philippines. Hum Immunol 2020; 81:437-444. [PMID: 32654962 DOI: 10.1016/j.humimm.2020.06.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 05/27/2020] [Accepted: 06/17/2020] [Indexed: 01/25/2023]
Abstract
HLA genotyping by next-generation sequencing (NGS) has evolved with significant advancements in the last decade. Here we describe full-length HLA genotyping of 11 loci in 612 individuals comprising a dengue vaccine cohort from Cebu province in the Philippines. The multi-locus individual tagging NGS (MIT-NGS) method that we developed initially for genotyping 4-6 loci in one MiSeq run was expanded to 11 loci including HLA-A, B, C, DPA1, DPB1, DQA1, DQB1, DRB1, and DRB3/4/5. This change did not affect the overall coverage or depth of the sequencing reads. HLA alleles with frequencies greater than 10% were A*11:01:01, A*24:02:01, A*24:07:01, A*34:01:01, B*38:02:01, B*15:35, B*35:05:01, C*07:02:01, C*04:01:01, DPA1*02:02:02, DPB1*05:01:01, DPB1*01:01:01, DQA1*01:02:01, DQA1*06:01:01, DQB1*05:02:01, DQB1*03:01:01, DRB1*15:02:01, DRB1*12:02:01, DRB3*03:01:03, DRB4*01:03:01, and DRB5*01:01:01. Improvements in sequencing library preparation provide uniform and even coverage across all exons and introns. This has led to a marked reduction in allele imbalance and dropout. Furthermore, including more loci, such as DRB3/4/5, decreases cross-mapping and incorrect allele assignment at the DRB1 locus. The increased number of loci sequenced for each sample does not reduce the number of samples that can be multiplexed on a single MiSeq run and is therefore more cost-efficient. We believe that such improvements will help HLA genotyping by NGS to gain momentum over other conventional methods by increasing confidence in the calls.
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Affiliation(s)
- Aviva Geretz
- U.S. 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
| | - Lauryn Cofer
- U.S. 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
| | - Philip K Ehrenberg
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Jeffrey R Currier
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - In-Kyu Yoon
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Maria T P Alera
- Philippines-AFRIMS Virology Research Unit, Cebu City, Philippines
| | - Richard Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Alan L Rothman
- Institute for Immunology and Informatics and Department of Cell and Molecular Biology, University of Rhode Island, Providence, RI, USA
| | - Rasmi Thomas
- U.S. 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.
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10
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Ananworanich J, Geretz A, Colby D, Sarnecki M, Ehrenberg PK, Tomaka F, Phanuphak N, Robb M, Michael NL, Thomas R. P067 HLA-B*57 Carriage in a post-treatment viral load controller from an hiv-1 therapeutic vaccine clinical trial. Hum Immunol 2019. [DOI: 10.1016/j.humimm.2019.07.120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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11
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Geretz A, Ehrenberg PK, Bouckenooghe A, Fernández Viña MA, Michael NL, Chansinghakule D, Limkittikul K, Thomas R. Full-length next-generation sequencing of HLA class I and II genes in a cohort from Thailand. Hum Immunol 2018; 79:773-780. [PMID: 30243890 DOI: 10.1016/j.humimm.2018.09.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 08/17/2018] [Accepted: 09/18/2018] [Indexed: 01/02/2023]
Abstract
The human leukocyte antigen (HLA) genes are highly variable and are known to play an important role in disease outcomes, including infectious diseases. Prior knowledge of HLA polymorphisms in a population usually forms the basis for an effective case-control study design. As a prelude to future disease association analyses, we report HLA class I and II diversity in 334 unrelated donors from a Dengue vaccine efficacy trial conducted in Thailand. Long-range PCR amplification of six HLA loci was performed on DNA extracted from saliva samples. HLA-A, -B, -C, -DPB1, -DQB1 and -DRB1 were genotyped using a next-generation sequencing method presented at the 17th International HLA and Immunogenetics Workshop. In total, we identified 201 HLA alleles, including 35 HLA-A, 57 HLA-B, 28 HLA-C, 24 HLA-DPB1, 21 HLA-DQB1 and 36 HLA-DRB1 alleles. Very common HLA alleles with frequencies greater than 10 percent were A∗11:01:01, A∗33:03:01, A∗24:02:01, B∗46:01:01, C∗07:02:01, C∗01:02:01, C∗08:01:01, DPB1∗05:01:01, DPB1∗13:01:01, DPB1∗04:01:01, DPB1∗02:01:02, DQB1∗03:01:01, DQB1∗05:02:01, DQB1∗03:03:02, DRB1∗12:02:01, DRB1∗09:01:02, and DRB1∗15:02:01. A novel HLA allele, B∗15:450, had a non-synonymous substitution and occurred in more than one donor. Population-based full-length NGS HLA typing is more conclusive and provides a sound foundation for exploring disease association in a given population.
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Affiliation(s)
- Aviva Geretz
- U.S. 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
| | - Philip K Ehrenberg
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | | | - Nelson L Michael
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | - Kriengsak Limkittikul
- Department of Tropical Pediatrics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Rasmi Thomas
- U.S. 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.
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12
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Ehrenberg PK, Geretz A, Thomas R. High-Throughput Contiguous Full-Length Next-Generation Sequencing of HLA Class I and II Genes from 96 Donors in a Single MiSeq Run. Methods Mol Biol 2018; 1802:89-100. [PMID: 29858803 DOI: 10.1007/978-1-4939-8546-3_6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The human leukocyte antigen (HLA) genes regulate and drive the immune system, and are among the most polymorphic loci in the human genome. HLA diversity is known to play an important role in transplantation and disease association studies. There are multiple approaches to DNA-based HLA genotyping and recent advances in next-generation sequencing (NGS) technologies have facilitated the development of whole gene sequencing methods. We describe an accurate, efficient, scalable, and cost-effective approach to contiguously amplify and sequence full-length genes of six HLA class I and II loci from 96 individuals on a single Illumina MiSeq run.
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Affiliation(s)
- Philip K Ehrenberg
- U.S. Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Aviva Geretz
- U.S. Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine (HJF), Bethesda, MD, USA
| | - Rasmi Thomas
- U.S. Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, MD, USA.
- Henry M. Jackson Foundation for the Advancement of Military Medicine (HJF), Bethesda, MD, USA.
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13
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Prentice HA, Tomaras GD, Geraghty DE, Apps R, Fong Y, Ehrenberg PK, Rolland M, Kijak GH, Krebs SJ, Nelson W, DeCamp A, Shen X, Yates NL, Zolla-Pazner S, Nitayaphan S, Rerks-Ngarm S, Kaewkungwal J, Pitisuttithum P, Ferrari G, McElrath MJ, Montefiori DC, Bailer RT, Koup RA, O'Connell RJ, Robb ML, Michael NL, Gilbert PB, Kim JH, Thomas R. HLA class II genes modulate vaccine-induced antibody responses to affect HIV-1 acquisition. Sci Transl Med 2016; 7:296ra112. [PMID: 26180102 DOI: 10.1126/scitranslmed.aab4005] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In the RV144 vaccine trial, two antibody responses were found to correlate with HIV-1 acquisition. Because human leukocyte antigen (HLA) class II-restricted CD4(+) T cells are involved in antibody production, we tested whether HLA class II genotypes affected HIV-1-specific antibody levels and HIV-1 acquisition in 760 individuals. Indeed, antibody responses correlated with acquisition only in the presence of single host HLA alleles. Envelope (Env)-specific immunoglobulin A (IgA) antibodies were associated with increased risk of acquisition specifically in individuals with DQB1*06. IgG antibody responses to Env amino acid positions 120 to 204 were higher and were associated with decreased risk of acquisition and increased vaccine efficacy only in the presence of DPB1*13. Screening IgG responses to overlapping peptides spanning Env 120-204 and viral sequence analysis of infected individuals defined differences in vaccine response that were associated with the presence of DPB1*13 and could be responsible for the protection observed. Overall, the underlying genetic findings indicate that HLA class II modulated the quantity, quality, and efficacy of antibody responses in the RV144 trial.
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Affiliation(s)
- Heather A Prentice
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA. Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20818, USA
| | - Georgia D Tomaras
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Daniel E Geraghty
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Richard Apps
- Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Youyi Fong
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Philip K Ehrenberg
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Morgane Rolland
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA. Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20818, USA
| | - Gustavo H Kijak
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA. Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20818, USA
| | - Shelly J Krebs
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA. Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20818, USA
| | - Wyatt Nelson
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Allan DeCamp
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Xiaoying Shen
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Nicole L Yates
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Susan Zolla-Pazner
- Veterans Affairs New York Harbor Healthcare System and the Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Sorachai Nitayaphan
- Department of Retrovirology, U.S. Army Medical Component, Armed Forces Research Institute Medical Sciences, Bangkok 10400, Thailand
| | - Supachai Rerks-Ngarm
- Department of Disease Control, Ministry of Public Health, Nonthaburi 11000, Thailand
| | - Jaranit Kaewkungwal
- Center of Excellence for Biomedical and Public Health Informatics (BIOPHICS), Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Punnee Pitisuttithum
- Vaccine Trial Centre, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Guido Ferrari
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - David C Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Robert T Bailer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Richard A Koup
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert J O'Connell
- Department of Retrovirology, U.S. Army Medical Component, Armed Forces Research Institute Medical Sciences, Bangkok 10400, Thailand
| | - Merlin L Robb
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA. Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20818, USA
| | - Nelson L Michael
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Peter B Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jerome H Kim
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Rasmi Thomas
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA. Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20818, USA.
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14
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Jobe O, Trinh HV, Kim J, Alsalmi W, Tovanabutra S, Ehrenberg PK, Peachman KK, Gao G, Thomas R, Kim JH, Michael NL, Alving CR, Rao VB, Rao M. Effect of cytokines on Siglec-1 and HIV-1 entry in monocyte-derived macrophages: the importance of HIV-1 envelope V1V2 region. J Leukoc Biol 2015; 99:1089-106. [PMID: 26667473 PMCID: PMC4952014 DOI: 10.1189/jlb.2a0815-361r] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 11/17/2015] [Indexed: 02/02/2023] Open
Abstract
M-CSF increased Siglec-1 expression on macrophages, rendering them more permissive to HIV-1 infection due to interaction with V1V2 region of gp120 and associated sialic acids. Monocytes and monocyte–derived macrophages express relatively low levels of CD4. Despite this, macrophages can be effectively infected with human immunodeficiency virus type 1. Macrophages have a critical role in human immunodeficiency virus type 1 transmission; however, the mechanism or mechanisms of virus infection are poorly understood. We report that growth factors, such as granulocyte macrophage colony-stimulating factor and macrophage colony-stimulating factor affect the phenotypic profile and permissiveness of macrophages to human immunodeficiency virus type 1. Human immunodeficiency virus type 1 infection of monocyte–derived macrophages derived from granulocyte macrophage and macrophage colony-stimulating factors was predominantly facilitated by the sialic acid-binding immunoglobulin-like lectin-1. The number of sialic acid-binding immunoglobulin-like lectin receptors on macrophage colony-stimulating factor–derived monocyte–derived macrophages was significantly greater than on granulocyte macrophage colony-stimulating factor–derived monocyte–derived macrophages, and correspondingly, human immunodeficiency virus type 1 infection was greater in the macrophage colony-stimulating factor–derived monocyte–derived macrophages. Single-genome analysis and quantitative reverse transcriptase-polymerase chain reaction revealed that the differences in infectivity was not due to differences in viral fitness or in viral variants with differential infectivity but was due to reduced viral entry into the granulocyte macrophage colony-stimulating factor–derived monocyte–derived macrophages. Anti-sialic acid-binding immunoglobulin-like lectin, trimeric glycoprotein 145, and scaffolded V1V2 proteins were bound to sialic acid-binding immunoglobulin-like lectin and significantly reduced human immunodeficiency virus type 1 entry and infection. Furthermore, sialic acid residues present in the V1V2 region of the envelope protein mediated human immunodeficiency virus type 1 interaction with sialic acid-binding immunoglobulin-like lectin and entry into macrophage colony-stimulating factor–derived monocyte–derived macrophages. Removal of sialic acid residues or glycans from scaffolded V1V2 protein decreased human immunodeficiency virus type 1 infectivity. These results highlight the importance of sialic acids on the V1V2 region in binding to sialic acid-binding immunoglobulin-like lectin and suggest that the unusually long surface-exposed sialic acid-binding immunoglobulin-like lectin might aid in the capture and entry of human immunodeficiency virus type 1 into monocyte–derived macrophages.
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Affiliation(s)
- Ousman Jobe
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Silver Spring, Maryland, USA; Laboratory of Adjuvant and Antigen Research, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Hung V Trinh
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Silver Spring, Maryland, USA; Laboratory of Adjuvant and Antigen Research, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Jiae Kim
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Silver Spring, Maryland, USA; Laboratory of Adjuvant and Antigen Research, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Wadad Alsalmi
- Department of Biology, The Catholic University of America, Washington, DC, USA
| | - Sodsai Tovanabutra
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Silver Spring, Maryland, USA; Laboratory of Molecular Virology and Pathogenesis, Viral Sequencing Core, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA; and
| | - Philip K Ehrenberg
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Silver Spring, Maryland, USA; Host Genetics Section, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA; and
| | - Kristina K Peachman
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Silver Spring, Maryland, USA; Laboratory of Adjuvant and Antigen Research, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Guofen Gao
- Department of Biology, The Catholic University of America, Washington, DC, USA
| | - Rasmi Thomas
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Silver Spring, Maryland, USA; Host Genetics Section, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA; and
| | - Jerome H Kim
- Laboratory of Molecular Virology and Pathogenesis, Viral Sequencing Core, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA; and
| | - Nelson L Michael
- Laboratory of Molecular Virology and Pathogenesis, Viral Sequencing Core, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA; and
| | - Carl R Alving
- Laboratory of Adjuvant and Antigen Research, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Venigalla B Rao
- Department of Biology, The Catholic University of America, Washington, DC, USA
| | - Mangala Rao
- Laboratory of Adjuvant and Antigen Research, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA;
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15
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Baldwin KM, Ehrenberg PK, Geretz A, Prentice HA, Nitayaphan S, Rerks-Ngarm S, Kaewkungwal J, Pitisuttithum P, O'Connell RJ, Kim JH, Thomas R. HLA class II diversity in HIV-1 uninfected individuals from the placebo arm of the RV144 Thai vaccine efficacy trial. ACTA ACUST UNITED AC 2015; 85:117-26. [PMID: 25626602 DOI: 10.1111/tan.12507] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 11/11/2014] [Accepted: 12/13/2014] [Indexed: 11/29/2022]
Abstract
The RV144 HIV vaccine trial in Thailand elicited antibody responses to the envelope of HIV-1, which correlated significantly with the risk of HIV-1 acquisition. Human leukocyte antigen (HLA) class II molecules are essential in antigen presentation to CD4 T cells for activation of B cells to produce antibodies. We genotyped the classical HLA-DRB1, DQB1, and DPB1 genes in 450 individuals from the placebo arm of the RV144 study to determine the background allele and haplotype frequencies of these genes in this cohort. High-resolution 4 and 6-digit class II HLA typing data was generated using sequencing-based methods. The observed diversity for the HLA loci was 33 HLA-DRB1, 15 HLA-DQB1, and 26 HLA-DPB1 alleles. Common alleles with frequencies greater than 10% were DRB1*07:01, DRB1*09:01, DRB1*12:02, DRB1*15:02, DQB1*02:01/02, DQB1*03:01, DQB1*03:03, DQB1*05:01, DQB1*05:02, DPB1*04:01:01, DPB1*05:01:01, and DPB1*13:01:01. We identified 28 rare alleles with frequencies of less than 1% in the Thai individuals. Ambiguity for HLA-DPB1*28:01 in exon 2 was resolved to DPB1*296:01 by next-generation sequencing of all exons. Multi-locus haplotypes including HLA class I and II loci were reported in this study. This is the first comprehensive report of allele and haplotype frequencies of all three HLA class II genes from a Thai population. A high-resolution genotyping method such as next-generation sequencing avoids missing rare alleles and resolves ambiguous calls. The HLA class II genotyping data generated in this study will be beneficial not only for future disease association/vaccine efficacy studies related to the RV144 study, but also for similar studies in other diseases in the Thai population, as well as population genetics and transplantation studies.
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Affiliation(s)
- K M Baldwin
- U.S. 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
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16
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Ehrenberg PK, Geretz A, Baldwin KM, Apps R, Polonis VR, Robb ML, Kim JH, Michael NL, Thomas R. High-throughput multiplex HLA genotyping by next-generation sequencing using multi-locus individual tagging. BMC Genomics 2014; 15:864. [PMID: 25283548 PMCID: PMC4196003 DOI: 10.1186/1471-2164-15-864] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 09/23/2014] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Unambiguous human leukocyte antigen (HLA) typing is important in transplant matching and disease association studies. High-resolution HLA typing that is not restricted to the peptide-binding region can decrease HLA allele ambiguities. Cost and technology constraints have hampered high-throughput and efficient high resolution unambiguous HLA typing. We have developed a method for HLA genotyping that preserves the very high-resolution that can be obtained by next-generation sequencing (NGS) but also achieves substantially increased efficiency. Unambiguous HLA-A, B, C and DRB1 genotypes can be determined for 96 individuals in a single run of the Illumina MiSeq. RESULTS Long-range amplification of full-length HLA genes from four loci was performed in separate polymerase chain reactions (PCR) using primers and PCR conditions that were optimized to reduce co-amplification of other HLA loci. Amplicons from the four HLA loci of each individual were then pooled and subjected to enzymatic library generation. All four loci of an individual were then tagged with one unique index combination. This multi-locus individual tagging (MIT) method combined with NGS enabled the four loci of 96 individuals to be analyzed in a single 500 cycle sequencing paired-end run of the Illumina-MiSeq. The MIT-NGS method generated sequence reads from the four loci were then discriminated using commercially available NGS HLA typing software. Comparison of the MIT-NGS with Sanger sequence-based HLA typing methods showed that all the ambiguities and discordances between the two methods were due to the accuracy of the MIT-NGS method. CONCLUSIONS The MIT-NGS method enabled accurate, robust and cost effective simultaneous analyses of four HLA loci per sample and produced 6 or 8-digit high-resolution unambiguous phased HLA typing data from 96 individuals in a single NGS run.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Rasmi Thomas
- U, S, Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD, USA.
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17
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Prentice HA, Ehrenberg PK, Baldwin KM, Geretz A, Andrews C, Nitayaphan S, Rerks-Ngarm S, Kaewkungwal J, Pitisuttithum P, O'Connell RJ, Robb ML, Kim JH, Michael NL, Thomas R. HLA class I, KIR, and genome-wide SNP diversity in the RV144 Thai phase 3 HIV vaccine clinical trial. Immunogenetics 2014; 66:299-310. [PMID: 24682434 DOI: 10.1007/s00251-014-0765-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Accepted: 02/23/2014] [Indexed: 11/25/2022]
Abstract
RV144 is the first phase 3 HIV vaccine clinical trial to demonstrate efficacy. This study consisted of more than 8,000 individuals in each arm of the trial, representing the four major regions of Thailand. Human leukocyte antigen (HLA) class I and killer cell immunoglobulin-like receptor (KIR) genes, as well as 96 genome-wide ancestry informative markers (AIMs) were genotyped in 450 placebo HIV-1-uninfected individuals to identify the immunogenetic diversity and population structure of this cohort. High-resolution genotyping identified the common HLA alleles as A*02:03, A*02:07, A*11:01, A*24:02, A*24:07, A*33:03, B*13:01, B*15:02, B*18:01, B*40:01, B*44:03, B*46:01, B*58:01, C*01:02, C*03:02, C*03:04, C*07:01, C*07:02, C*07:04, and C*08:01. The most frequent three-loci haplotype was B*46:01-C*01:02-A*02:07. Framework genes KIR2DL4, 3DL2, and 3DL3 were present in all samples, and KIR2DL1, 2DL3, 3DL1, 2DS4, and 2DP1 occurred at frequencies greater than 90 %. The combined HLA and KIR profile suggests admixture with neighboring Asian populations. Principal component and correspondence analyses comparing the RV144 samples to the phase 3 International HapMap Project (HapMap3) populations using AIMs corroborated these findings. Structure analyses identified a distinct profile in the Thai population that did not match the Asian or other HapMap3 samples. This shows genetic variability unique to Thais in RV144, making it essential to take into account population stratification while performing genetic association studies. The overall analyses from all three genetic markers indicate that the RV144 samples are representative of the Thai population. This will inform subsequent host genetic analyses in the RV144 cohort and provide insight for future genetic association studies in the Thai population.
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Affiliation(s)
- Heather A Prentice
- U.S. Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, MD, USA
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18
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Ehrenberg PK, Michael NL. PCR amplification, cloning, and construction of HIV-1 infectious molecular clones from virtually full-length HIV-1 genomes. Methods Mol Biol 2005; 304:387-98. [PMID: 16061991 DOI: 10.1385/1-59259-907-9:387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The development of mixtures of highly processive and high-fidelity thermostable DNA polymerases has enabled the routine recovery of DNA sequences in excess of 25 kb generated by polymerase chain reaction. This powerful tool has been instrumental in the ability to recover virtually full-length HIV-1 proviral DNA as a single, contiguous fragment. Such fragments allow for the clean interpretation of the genomic organization of HIV-1 provirus, as they are not confounded by molecular mosaicism that accrues to overlapping subgenomic amplification strategies. We detail here a robust procedure to produce virtually full-length, single contiguous 9.2-kb HIV-1 amplimers whose full-length infectious potential is reconstituted upon cloning into long terminal repeat-replacement vectors. Large numbers of HIV-1 proviral clones can now be quickly generated and screened to identify the fraction of the viral quasispecies with the highest capacity for viral replication. The methods used to construct long terminal repeat-replacement vectors, amplify HIV-1 provirus, reconstitute full-length provirus, and recover viral stocks will be illustrated using a circulating recombinant form 1 (CRF01_AE, formerly known as subtype E) primary isolate.
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Affiliation(s)
- Philip K Ehrenberg
- Division of Retrovirology, Henry Jackson Foundation, Department of Molecular Diagnostics and Pathogenesis, Walter Reed Army Institute of Research, Rockville, MD, USA
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19
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Brachtel EF, Mascola JR, Wear DJ, Ehrenberg PK, Dayhoff DE, Sanders-Buell E, Michael NL, Frankel SS. Demonstration of de novo HIV type 1 production by detection of multiply spliced and unspliced HIV type 1 RNA in paraffin-embedded tonsils. AIDS Res Hum Retroviruses 2002; 18:785-90. [PMID: 12167270 DOI: 10.1089/08892220260139521] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
HIV-1 infection of tonsils takes place when virus spreads systemically, and may occur when tonsillar tissue serves as the initial portal of HIV-1 entry. The HIV replication cycle includes the production of regulatory and accessory gene mRNAs, produced by splicing of genomic mRNA, that are hallmarks of de novo virus production. We sought to demonstrate, for the first time, the presence of multiply spliced viral RNA transcripts in archival tissue as a marker for active virus replication. Further, amplified cDNA sequences from unspliced pol gene mRNA were used to define the genetic subtype of HIV-1 within these tissues. RNA was extracted from surgical pathological, formalin-fixed, paraffin-embedded specimens, and RT-PCR was performed with primers for unspliced and multiply spliced HIV-1 transcripts. Amplification products were analyzed by agarose gel electrophoresis and their specificity was confirmed by sequencing and Southern blot hybridization. Unspliced HIV-1 pol transcripts yielded cDNA amplicons of 184 base pairs (bp) that were cloned and sequenced. Phylogenetic analysis revealed these sequences to be of HIV-1 subtype B. Multiply spliced transcripts specific for the tat/rev (173 bp), tat (268 bp), and tat/rev/nef (146 bp) regulatory gene mRNAs could be demonstrated in all cases. These results support the demonstration of active replication of HIV-1 in archival tonsillar tissues previously shown by p24 antigen staining. They also show the feasibility of performing molecular epidemiologic studies on HIV-1 cDNA sequences from archived pathologic specimens.
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Affiliation(s)
- Elena F Brachtel
- Department of Infectious and Parasitic Disease Pathology, Armed Forces Institute of Pathology (AFIP), Washington, DC 20306, USA
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20
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Vijh S, Dayhoff DE, Wang CE, Imam Z, Ehrenberg PK, Michael NL. Transcription regulation of human chemokine receptor CCR3: evidence for a rare TATA-less promoter structure conserved between drosophila and humans. Genomics 2002; 80:86-95. [PMID: 12079287 DOI: 10.1006/geno.2002.6801] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The chemokine receptor CCR3 has a critical function in the pathogenesis of eosinophilic diseases and is an entry co-receptor for HIV-1. We describe here the genomic organization and general transcriptional control mechanism for the human gene CCR3. We identified six cDNA transcripts formed by alternative splicing of eight exons and seven introns. CCR3 contains a 37-bp core promoter domain (-3 to +34 relative to the transcription start point) lacking a TATA box but inclusive of an initiator sequence, a G at +24, and a downstream promoter element (DPE) at +28 to +33 common for Drosophila melanogaster but heretofore described for only two other human genes. Mutation of these elements significantly attenuates CCR3 transcription, as predicted by a model of RNA pol II engagement with DPE-containing Drosophila promoters. These results provide evidence for the functional conservation of a DPE-dependent, general transcription control mechanism between Drosophila and human genes.
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Affiliation(s)
- Sujata Vijh
- United States Military HIV Research Program, Walter Reed Army Institute of Research, 1600 East Gude Drive, Rockville, Maryland, 20850, USA
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21
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Salminen MO, Ehrenberg PK, Mascola JR, Dayhoff DE, Merling R, Blake B, Louder M, Hegerich S, Polonis VR, Birx DL, Robb ML, McCutchan FE, Michael NL. Construction and biological characterization of infectious molecular clones of HIV-1 subtypes B and E (CRF01_AE) generated by the polymerase chain reaction. Virology 2000; 278:103-10. [PMID: 11112486 DOI: 10.1006/viro.2000.0640] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We previously described the use of extended polymerase chain reaction (PCR) to amplify contiguous 9.2-kilobase (kb) single-long terminal repeat (LTR) proviral sequences from HIV-1 genetic subtypes A through G. We now extend these findings by describing a novel vector system to recover infectious molecular clones from long PCR amplicons. Directional ligation of 9.2-kb proviral amplicons into a recovery vector reconstitutes missing LTR sequences, providing candidate molecular clones for infectivity screening. We show that a previously characterized infectious molecular clone of HIV-1 retains its biological properties upon recovery with this strategy. Three additional infectious molecular clones generated, from primary isolates of subtype B (HIV-1(WR27)) and circulating recombinant form 01_AE (subtype E) (HIV-1(CM235)) by subtype-specific LTR reconstitution, displayed biological properties reflecting their cognate parental isolates. This represents the first report of infectious molecular clones from circulating recombinant form 01_AE (subtype E).
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Affiliation(s)
- M O Salminen
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville, Maryland 20850, USA
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22
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Frankel SS, Steinman RM, Michael NL, Kim SR, Bhardwaj N, Pope M, Louder MK, Ehrenberg PK, Parren PW, Burton DR, Katinger H, VanCott TC, Robb ML, Birx DL, Mascola JR. Neutralizing monoclonal antibodies block human immunodeficiency virus type 1 infection of dendritic cells and transmission to T cells. J Virol 1998; 72:9788-94. [PMID: 9811714 PMCID: PMC110490 DOI: 10.1128/jvi.72.12.9788-9794.1998] [Citation(s) in RCA: 76] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/1998] [Accepted: 08/20/1998] [Indexed: 11/20/2022] Open
Abstract
Prevention of the initial infection of mucosal dendritic cells (DC) and interruption of the subsequent transmission of HIV-1 from DC to T cells are likely to be important attributes of an effective human immunodeficiency virus type 1 (HIV-1) vaccine. While anti-HIV-1 neutralizing antibodies have been difficult to elicit by immunization, there are several human monoclonal antibodies (MAbs) that effectively neutralize virus infection of activated T cells. We investigated the ability of three well-characterized neutralizing MAbs (IgG1b12, 2F5, and 2G12) to block HIV-1 infection of human DC. DC were generated from CD14(+) blood cells or obtained from cadaveric human skin. The MAbs prevented viral entry into purified DC and the ensuing productive infection in DC/T-cell cultures. When DC were first pulsed with HIV-1, MAbs blocked the subsequent transmission to unstimulated CD3(+) T cells. Thus, neutralizing antibodies can block HIV-1 infection of DC and the cell-to-cell transmission of virus from infected DC to T cells. These data suggest that neutralizing antibodies could interrupt the initial events associated with mucosal transmission and regional spread of HIV-1.
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Affiliation(s)
- S S Frankel
- Division of Retrovirology, Walter Reed Army Institute of Research and Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville, Maryland, USA.
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23
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Wegner SA, Ehrenberg PK, Chang G, Dayhoff DE, Sleeker AL, Michael NL. Genomic organization and functional characterization of the chemokine receptor CXCR4, a major entry co-receptor for human immunodeficiency virus type 1. J Biol Chem 1998; 273:4754-60. [PMID: 9468539 DOI: 10.1074/jbc.273.8.4754] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
CXCR4 is both a chemokine receptor and entry co-receptor for T-cell line-adapted human immunodeficiency virus type 1. The genomic organization and promoter function for the entire transcription unit of CXCR4 were determined. The gene contains 2 exons of 103 and 1563 base pairs (bp) interrupted by a 2132-bp intron precisely between codons 5 and 6 of the coding sequences. A transcription start site was identified 88 bp upstream of the initiation codon, and a polyadenylate addition site was identified 22 bp 3' to a polyadenylation signal. Transient expression assays defined a minimal promoter at positions -114 to +43 relative to the transcription start site. This region contains a TATA box, a nuclear respiratory factor-1 (NRF-1) site, and two GC boxes. Specific factor binding to the NRF-1 site and GC boxes were demonstrated by gel mobility shifts and DNase I footprinting. Site-directed mutagenesis showed that the NRF-1 site is crucial for promoter activity providing the first evidence for the regulation of a signal transduction gene by NRF-1. Sequences between -691 and -191 repress CXCR4 promoter activity. Further study of these regulatory elements will be important to understanding how CXCR4 functions as both a chemokine receptor and human immunodeficiency virus type 1 entry co-receptor.
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Affiliation(s)
- S A Wegner
- Division of Retrovirology, Walter Reed Army Institute of Research, Rockville, Maryland 20850, USA
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24
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Salminen MO, Koch C, Sanders-Buell E, Ehrenberg PK, Michael NL, Carr JK, Burke DS, McCutchan FE. Recovery of virtually full-length HIV-1 provirus of diverse subtypes from primary virus cultures using the polymerase chain reaction. Virology 1995; 213:80-6. [PMID: 7483282 DOI: 10.1006/viro.1995.1548] [Citation(s) in RCA: 147] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
In the course of the global pandemic, the human immunodeficiency virus type-1 (HIV-1) has established at least eight distinct genotypes in the main (M), or prevalent, group of isolates, a variety of rare outlier forms, and intergenotypic recombinants of group M viruses. This genotypic diversity has been documented, for the most part, by sequencing of subgenomic segments of the provirus. Using DNA from virus cultures on peripheral blood mononuclear cells (PBMC) and recent improvements of the PCR technique, we have amplified virtually full-length HIV-1 genomes from genetic subtypes A through G of group M viruses and molecularly cloned several of them. Resequencing of the complete genome of a prototype strain after long PCR amplification and cloning has established a PCR error rate of 0.14%. We also report the first complete PCR-derived sequence of a U.S. clinical isolate of genotype B expanded only in primary PBMC; this provirus harbors a uniquely truncated V3 loop.
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Affiliation(s)
- M O Salminen
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville, Maryland 20850, USA
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25
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Michael NL, Chang G, d'Arcy LA, Ehrenberg PK, Mariani R, Busch MP, Birx DL, Schwartz DH. Defective accessory genes in a human immunodeficiency virus type 1-infected long-term survivor lacking recoverable virus. J Virol 1995; 69:4228-36. [PMID: 7769682 PMCID: PMC189160 DOI: 10.1128/jvi.69.7.4228-4236.1995] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
We have been studying a patient who acquired human immunodeficiency virus (HIV) infection via a blood transfusion 13 years ago. She has remained asymptomatic since that time. The blood donor and two other recipients have all died of AIDS. Although this patient has shown persistently strong seroreactivity to HIV type 1 (HIV-1) antigens by Western blot (immunoblot), she has been continually HIV culture negative in results from multiple laboratories over the last 6 years and has a very low viral burden. Her CD4+ T-cell count has fluctuated around a mean of 399 cells per microliters, with little change in lymphocyte subset percentages. Strong cellular immune responses to HIV-1 epitopes by this patient have been demonstrated. We now report the results of an intensive molecular genetic analysis of the HIV-1 proviral quasispecies from this patient sampled over 5 years. Long terminal repeat region sequences supported the argument for normal basal and Tat-mediated promoter activities. Sequential sequencing of the nef gene revealed a low frequency (8.3%) of defective genes and a striking lack of sequence evolution. Functional analysis of predominant nef genes by both a cell surface CD4 downregulation and a viral infectivity complementation assay showed wild-type function. In contrast, sequential analysis of an amplicon containing the vif, vpr, vpu, tat1, and rev1 genes revealed the presence of inactivating mutations in 64% of the clones. These data suggest that this patient, initially infected with a virulent swarm of HIV-1, is presently infected with a more-attenuated viral quasispecies as a result of effective host immunity.
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Affiliation(s)
- N L Michael
- Division of Retrovirology, Walter Reed Army Institute of Research, Rockville, MD 20850, USA
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26
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Michael NL, D'Arcy L, Ehrenberg PK, Redfield RR. Naturally occurring genotypes of the human immunodeficiency virus type 1 long terminal repeat display a wide range of basal and Tat-induced transcriptional activities. J Virol 1994; 68:3163-74. [PMID: 7908701 PMCID: PMC236807 DOI: 10.1128/jvi.68.5.3163-3174.1994] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The primary body of information on the structure of human immunodeficiency virus type 1 (HIV-1) long terminal repeat (LTR)/gag leader genotypes has been determined from the analysis of cocultivated isolates. Functional studies of this regulatory portion of the provirus have been derived from the study of in vitro-generated mutations of laboratory-adapted molecular clones of HIV-1. We have performed a longitudinal analysis of molecular clones from the LTR/gag leader region amplified directly from the peripheral blood of four patients over three years. We have found a remarkable number of point mutations and length polymorphisms in cis- and trans-acting regulatory elements within this cohort. Most of the length polymorphisms were associated with duplications of Sp1 and TCF-1 alpha sequences. These mutations were associated with a wide range of transcriptional activities for these genotypes in a reporter gene assay. Mutations in conserved Sp1 sequences correlated with a diminished capacity of such genotypes to bind purified Sp1 protein. Although no generalized trend in transcriptional activity was seen, a single patient accumulated mutations in NF-kappa B, Sp1, and TAR elements over this period. The analysis of naturally occurring mutations of LTR genotypes provides a means to study the molecular genetic consequences of virus-host interactions and to assess the functional impact of HIV therapeutics.
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MESH Headings
- Base Sequence
- Cloning, Molecular
- DNA-Binding Proteins/metabolism
- Gene Products, tat/pharmacology
- Genes, Reporter
- Genes, gag/genetics
- Genotype
- HIV Infections/blood
- HIV Long Terminal Repeat/genetics
- HIV-1/genetics
- Humans
- Leukocytes, Mononuclear/microbiology
- Lymphoid Enhancer-Binding Factor 1
- Molecular Sequence Data
- Point Mutation
- Polymorphism, Restriction Fragment Length
- Protein Binding
- Regulatory Sequences, Nucleic Acid/genetics
- Sequence Homology, Nucleic Acid
- Sp1 Transcription Factor/metabolism
- T Cell Transcription Factor 1
- Transcription Factors/metabolism
- Transcription, Genetic/drug effects
- tat Gene Products, Human Immunodeficiency Virus
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Affiliation(s)
- N L Michael
- Division of Retrovirology, Walter Reed Army Institute of Research, Rockville, Maryland
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Michael NL, Vahey MT, d'Arcy L, Ehrenberg PK, Mosca JD, Rappaport J, Redfield RR. Negative-strand RNA transcripts are produced in human immunodeficiency virus type 1-infected cells and patients by a novel promoter downregulated by Tat. J Virol 1994; 68:979-87. [PMID: 8289399 PMCID: PMC236536 DOI: 10.1128/jvi.68.2.979-987.1994] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Current understanding of human immunodeficiency virus type 1 (HIV-1) transcription is based on unidirectional expression of transcripts with positive-strand polarity from the 5' long terminal repeat. We now report HIV-1 transcripts with negative-strand polarity obtained from acutely and chronically infected cell lines by use of a template orientation-specific reverse transcriptase-PCR assay. These findings were confirmed in natural infection by analysis of RNA derived from peripheral blood mononuclear cell samples from 15 HIV-1-infected patients. A cDNA derived from a 2.3-kb polyadenylated HIV-1 RNA with negative-strand polarity which encodes a highly conserved 189-amino-acid open reading frame antiparallel to the envelope gene was isolated from acutely infected A3.01 cells. Through use of reporter gene constructions, we further found that a novel negative-strand promoter functions within the negative response element of the 3' long terminal repeat, which is downregulated by coexpression of Tat. Site-directed mutagenesis experiments demonstrated that NF-kappa B I and USF sites are crucial for negative-strand promoter activity. These data extend the coding capacity of HIV-1 and suggest a role for antisense regulation of the viral life cycle.
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Affiliation(s)
- N L Michael
- Department of Retroviral Research, Walter Reed Army Institute of Research, Rockville, Maryland
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Michael NL, Chang G, Ehrenberg PK, Vahey MT, Redfield RR. HIV-1 proviral genotypes from the peripheral blood mononuclear cells of an infected patient are differentially represented in expressed sequences. J Acquir Immune Defic Syndr (1988) 1993; 6:1073-85. [PMID: 8105071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The RNA genome of the human immunodeficiency virus type 1 (HIV-1) is established as proviral DNA in infected cells. Only some of these cells may actively produce the array of viral RNAs that support progeny virion production. In vivo expression of a subset of proviral genotypes could influence the experimental characterization of the viral quasispecies. We have explored the relationship between DNA and cDNA genotypes of the envelope gene by the molecular cloning and nucleotide sequencing of these templates from noncultivated peripheral blood mononuclear cells from an HIV-1-infected patient. Eleven proviral DNA and nine cDNA clones representing the V1-V3 region of gp120 were recovered and sequenced. The proviral group was more heterogeneous than the cDNA group by nucleotide sequence changes and V1 length polymorphisms. Deduced amino acid sequences from this data set showed that the two groups were distinct in primary structure, in the position of N-linked glycosylation sites, and in the net charge of the V3 loop. The V1-V2 region discriminated between the groups more strongly than the V3 region. The differential representation of HIV-1 envelope genotypes in the cDNA versus the proviral compartment may have important implications for the pathogenesis of disease and for the design of antiviral therapeutics.
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Affiliation(s)
- N L Michael
- Department of Retroviral Research, Walter Reed Army Institute of Research, Rockville, MD 20850
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