1
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Uslu K, Ozcelik F, Zararsiz G, Eldem V, Cephe A, Sahin IO, Yuksel RC, Sipahioglu H, Ozer Simsek Z, Baspinar O, Akalin H, Simsek Y, Gundogan K, Tutar N, Karayol Akin A, Ozkul Y, Yildiz O, Dundar M. Deciphering the host genetic factors conferring susceptibility to severe COVID-19 using exome sequencing. Genes Immun 2024; 25:14-42. [PMID: 38123822 DOI: 10.1038/s41435-023-00232-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 12/23/2023]
Abstract
The COVID-19 pandemic remains a significant public health concern despite the new vaccines and therapeutics. The clinical course of acute SARS-CoV-2 infection is highly variable and influenced by several factors related to the virus and the host. Numerous genetic studies, including candidate gene, exome, and genome sequencing studies, genome-wide association studies, and other omics efforts, have proposed various Mendelian and non-Mendelian associations with COVID-19 course. In this study, we conducted whole-exome sequencing on 90 unvaccinated patients from Turkey with no known comorbidities associated with severe COVID-19. Of these patients, 30 had severe, 30 had moderate, and 30 had mild/asymptomatic disease. We identified rare variants in genes associated with SARS-CoV-2 susceptibility and pathogenesis, with an emphasis on genes related to the regulation of inflammation, and discussed these in the context of the clinical course of the patients. In addition, we compared the frequencies of common variants between each group. Even though no variant remained statistically significant after correction for multiple testing, we observed that certain previously associated genes and variants showed significant associations before correction. Our study contributes to the existing literature regarding the genetic susceptibility to SARS-CoV-2. Future studies would be beneficial characterizing the host genetic properties in different populations.
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Affiliation(s)
- Kubra Uslu
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Firat Ozcelik
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Gokmen Zararsiz
- Department of Biostatistics, Faculty of Medicine, Erciyes University, Kayseri, Turkey
- Drug Application and Research Center (ERFARMA), Erciyes University, Kayseri, Turkey
| | - Vahap Eldem
- Department of Biology, Faculty of Science, Istanbul University, Istanbul, Turkey
| | - Ahu Cephe
- Institutional Data Management and Analytics Units, Erciyes University Rectorate, Kayseri, Turkey
| | - Izem Olcay Sahin
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Recep Civan Yuksel
- Division of Intensive Care Medicine, Department of Internal Medicine, Kayseri City Education and Research Hospital, Kayseri, Turkey
| | - Hilal Sipahioglu
- Division of Intensive Care Medicine, Department of Internal Medicine, Kayseri City Education and Research Hospital, Kayseri, Turkey
| | - Zuhal Ozer Simsek
- Division of Intensive Care Medicine, Department of Internal Medicine, Kayseri City Education and Research Hospital, Kayseri, Turkey
| | - Osman Baspinar
- Department of Internal Medicine, Kayseri City Education and Research Hospital, Kayseri, Turkey
| | - Hilal Akalin
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Yasin Simsek
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Kayseri City Education and Research Hospital, Kayseri, Turkey
| | - Kursat Gundogan
- Division of Intensive Care Medicine, Department of Internal Medicine, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Nuri Tutar
- Department of Chest Diseases, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Aynur Karayol Akin
- Department of Anesthesiology and Reanimation, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Yusuf Ozkul
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Orhan Yildiz
- Department of Infectious Diseases, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Munis Dundar
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, Turkey.
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2
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Luo Y, Kanai M, Choi W, Li X, Sakaue S, Yamamoto K, Ogawa K, Gutierrez-Arcelus M, Gregersen PK, Stuart PE, Elder JT, Forer L, Schönherr S, Fuchsberger C, Smith AV, Fellay J, Carrington M, Haas DW, Guo X, Palmer ND, Chen YDI, Rotter JI, Taylor KD, Rich SS, Correa A, Wilson JG, Kathiresan S, Cho MH, Metspalu A, Esko T, Okada Y, Han B, McLaren PJ, Raychaudhuri S. A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response. Nat Genet 2021; 53:1504-1516. [PMID: 34611364 PMCID: PMC8959399 DOI: 10.1038/s41588-021-00935-7] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 08/02/2021] [Indexed: 02/08/2023]
Abstract
Fine-mapping to plausible causal variation may be more effective in multi-ancestry cohorts, particularly in the MHC, which has population-specific structure. To enable such studies, we constructed a large (n = 21,546) HLA reference panel spanning five global populations based on whole-genome sequences. Despite population-specific long-range haplotypes, we demonstrated accurate imputation at G-group resolution (94.2%, 93.7%, 97.8% and 93.7% in admixed African (AA), East Asian (EAS), European (EUR) and Latino (LAT) populations). Applying HLA imputation to genome-wide association study data for HIV-1 viral load in three populations (EUR, AA and LAT), we obviated effects of previously reported associations from population-specific HIV studies and discovered a novel association at position 156 in HLA-B. We pinpointed the MHC association to three amino acid positions (97, 67 and 156) marking three consecutive pockets (C, B and D) within the HLA-B peptide-binding groove, explaining 12.9% of trait variance.
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Affiliation(s)
- Yang Luo
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Division of Rheumatology, Immunology, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Masahiro Kanai
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Wanson Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Xinyi Li
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Saori Sakaue
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Immunology, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kenichi Yamamoto
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Pediatrics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Kotaro Ogawa
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Neurology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Maria Gutierrez-Arcelus
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Immunology, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Peter K Gregersen
- The Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research,North Short LIJ Health System, Manhasset, NY, USA
| | - Philip E Stuart
- Department of Dermatology, University of Michigan, Ann Arbor, MI, USA
| | - James T Elder
- Department of Dermatology, University of Michigan, Ann Arbor, MI, USA
- Ann Arbor Veterans Affairs Hospital, Ann Arbor, MI, USA
| | - Lukas Forer
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Sebastian Schönherr
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Christian Fuchsberger
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Institute for Biomedicine, Eurac Research, Bolzano, Italy
| | - Albert V Smith
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Jacques Fellay
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
| | - David W Haas
- Vanderbilt University Medical Center, Nashville, TN, USA
- Meharry Medical College, Nashville, TN, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Adolfo Correa
- Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - James G Wilson
- Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, USA
| | - Sekar Kathiresan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cardiology Division of the Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Andres Metspalu
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Tonu Esko
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Buhm Han
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, South Korea
| | - Paul J McLaren
- J.C. Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Division of Rheumatology, Immunology, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Centre for Genetics and Genomics Versus Arthritis, University of Manchester, Manchester, UK.
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3
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Yildirim Z, Sahin OS, Yazar S, Bozok Cetintas V. Genetic and epigenetic factors associated with increased severity of Covid-19. Cell Biol Int 2021; 45:1158-1174. [PMID: 33590936 PMCID: PMC8014716 DOI: 10.1002/cbin.11572] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 02/14/2021] [Indexed: 01/07/2023]
Abstract
Since December 2019, a new form of severe acute respiratory syndrome (SARS) from a novel strain of coronavirus (SARS coronavirus 2 [SARS-CoV-2]) has been spreading worldwide. The disease caused by SARS-CoV-2 was named Covid-19 and declared as a pandemic by the World Health Organization in March 2020. Clinical symptoms of Covid-19 range from common cold to more severe disease defined as pneumonia, hypoxia, and severe respiratory distress. In the next stage, disease can become more critical with respiratory failure, sepsis, septic shock, and/or multiorgan failure. Outcomes of Covid-19 indicate large gaps between the male-female and the young-elder groups. Several theories have been proposed to explain variations, such as gender, age, comorbidity, and genetic factors. It is likely that mixture of genetic and nongenetic factors interplays between virus and host genetics and determines the severity of disease outcome. In this review, we aimed to summarize current literature in terms of potential host genetic and epigenetic factors that associated with increased severity of Covid-19. Several studies indicated that the genetic variants of the SARS-CoV-2 entry mechanism-related (angiotensin-converting enzymes, transmembrane serine protease-2, furin) and host innate immune response-related genes (interferons [IFNs], interleukins, toll-like receptors), and human leukocyte antigen, ABO, 3p21.31, and 9q34.2 loci are critical host determinants related to Covid-19 severity. Epigenetic mechanisms also affect Covid-19 outcomes by regulating IFN signaling, angiotensin-converting enzyme-2, and immunity-related genes that particularly escape from X chromosome inactivation. Enhanced understanding of host genetic and epigenetic factors and viral interactions of SARS-CoV-2 is critical for improved prognostic tools and innovative therapeutics.
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Affiliation(s)
- Zafer Yildirim
- Department of Medical Biology, Faculty of MedicineEge UniversityIzmirTurkey
| | - Oyku Semahat Sahin
- Department of Medical Biology, Faculty of MedicineEge UniversityIzmirTurkey
| | - Seyhan Yazar
- Garvan‐Weizmann Centre for Cellular GenomicsGarvan Institute of Medical ResearchSydneyNew South WalesAustralia
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4
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Kovacs AAZ, Kono N, Wang CH, Wang D, Frederick T, Operskalski E, Tien PC, French AL, Minkoff H, Kassaye S, T. Golub E, Aouizerat BE, Kuniholm MH, Millstein J. Association of HLA Genotype With T-Cell Activation in Human Immunodeficiency Virus (HIV) and HIV/Hepatitis C Virus-Coinfected Women. J Infect Dis 2020; 221:1156-1166. [PMID: 31802115 PMCID: PMC7325713 DOI: 10.1093/infdis/jiz589] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 11/06/2019] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Global immune activation and HLA alleles are each associated with the pathogenesis of human immunodeficiency virus (HIV) and hepatitis C virus . METHODS We evaluated the relationship between 44 HLA class I and 28 class II alleles and percentages of activated CD8 (CD8+CD38+DR+) and CD4 (CD4+CD38+DR+) T cells in 586 women who were naive to highly active antiretroviral therapy. We used linear generalized estimating equation regression models, adjusting for race/ethnicity, age, HIV load, and hepatitis C virus infection and controlling for multiplicity using a false discovery rate threshold of 0.10. RESULTS Ten HLA alleles were associated with CD8 and/or CD4 T-cell activation. Lower percentages of activated CD8 and/or CD4 T cells were associated with protective alleles B*57:03 (CD8 T cells, -6.6% [P = .002]; CD4 T cells, -2.7% [P = .007]), C*18:01 (CD8 T cells, -6.6%; P < .0008) and DRB1*13:01 (CD4 T cells, -2.7%; P < .0004), and higher percentages were found with B*18:01 (CD8 T cells, 6.2%; P < .0003), a detrimental allele. Other alleles/allele groups associated with activation included C*12:03, group DQA1*01:00, DQB1*03:01, DQB1*03:02, DQB1*06:02, and DQB1*06:03. CONCLUSION These findings suggest that a person's HLA type may play a role in modulating T-cell activation independent of viral load and sheds light on the relationship between HLA, T-cell activation, immune control, and HIV pathogenesis.
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Affiliation(s)
- Andrea A Z Kovacs
- Department of Pediatrics, Maternal, Child and Adolescent Center for Infectious Diseases and Virology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Naoko Kono
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Chia-Hao Wang
- Department of Pediatrics, Maternal, Child and Adolescent Center for Infectious Diseases and Virology, Keck School of Medicine, University of Southern California, Los Angeles, California
- City of Hope National Medical Center, Duarte, California
| | - Daidong Wang
- Department of Pediatrics, Maternal, Child and Adolescent Center for Infectious Diseases and Virology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Toni Frederick
- Department of Pediatrics, Maternal, Child and Adolescent Center for Infectious Diseases and Virology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Eva Operskalski
- Department of Pediatrics, Maternal, Child and Adolescent Center for Infectious Diseases and Virology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Phyllis C Tien
- Department of Medicine, University of California, San Francisco and Department of Veterans Affairs, San Francisco, California
| | - Audrey L French
- Department of Medicine, Stroger Hospital of Cook County/CORE Center, Rush Medical School, Chicago, Illinois
| | - Howard Minkoff
- Departments of Obstetrics and Gynecology Maimonides Medical Center and SUNY Downstate, Brooklyn, New York
| | - Seble Kassaye
- Department of Medicine, Georgetown University School of Medicine, Washington, DC
| | - Elizabeth T. Golub
- Johns Hopkins Bloomberg School of Public Health, Department of Epidemiology, Baltimore, Maryland
| | - Bradley E Aouizerat
- Bluestone Center for Clinical Research, New York University, New York, New York
- Department of Oral and Maxillofacial Surgery, New York University, New York, New York
| | - Mark H Kuniholm
- Department of Epidemiology and Biostatistics, University at Albany, State University of New York, Rensselaer, New York
| | - Joshua Millstein
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
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5
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Gray GE, Huang Y, Grunenberg N, Laher F, Roux S, Andersen-Nissen E, De Rosa SC, Flach B, Randhawa AK, Jensen R, Swann EM, Bekker LG, Innes C, Lazarus E, Morris L, Mkhize NN, Ferrari G, Montefiori DC, Shen X, Sawant S, Yates N, Hural J, Isaacs A, Phogat S, DiazGranados CA, Lee C, Sinangil F, Michael NL, Robb ML, Kublin JG, Gilbert PB, McElrath MJ, Tomaras GD, Corey L. Immune correlates of the Thai RV144 HIV vaccine regimen in South Africa. Sci Transl Med 2019; 11:eaax1880. [PMID: 31534016 PMCID: PMC7199879 DOI: 10.1126/scitranslmed.aax1880] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 08/13/2019] [Indexed: 12/14/2022]
Abstract
One of the most successful HIV vaccines to date, the RV144 vaccine tested in Thailand, demonstrated correlates of protection including cross-clade V1V2 immunoglobulin G (IgG) breadth, Env-specific CD4+ T cell polyfunctionality, and antibody-dependent cellular cytotoxicity (ADCC) in vaccinees with low IgA binding. The HIV Vaccine Trials Network (HVTN) 097 trial evaluated this vaccine regimen in South Africa, where clade C HIV-1 predominates. We compared cellular and humoral responses at peak and durability immunogenicity time points in HVTN 097 and RV144 vaccinee samples, and evaluated vaccine-matched and cross-clade immune responses. At peak immunogenicity, HVTN 097 vaccinees exhibited significantly higher cellular and humoral immune responses than RV144 vaccinees. CD4+ T cell responses were more frequent in HVTN 097 irrespective of age and sex, and CD4+ T cell Env-specific functionality scores were higher in HVTN 097. Env-specific CD40L+ CD4+ T cells were more common in HVTN 097, with individuals having this pattern of expression demonstrating higher median antibody responses to HIV-1 Env. IgG and IgG3 binding antibody rates and response magnitude to gp120 vaccine- and V1V2 vaccine-matched antigens were higher or comparable in HVTN 097 than in RV144 ADCC, and ADCP functional antibody responses were elicited in HVTN 097. Env-specific IgG and CD4+ Env responses declined significantly over time in both trials. Overall, cross-clade immune responses associated with protection were better than expected in South Africa, suggesting wider applicability of this regimen.
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Affiliation(s)
- Glenda E Gray
- Perinatal HIV Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 1864, South Africa.
- South African Medical Research Council, Cape Town 7505, South Africa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Ying Huang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Nicole Grunenberg
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Fatima Laher
- Perinatal HIV Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 1864, South Africa
| | - Surita Roux
- The Desmond Tutu HIV Centre, University of Cape Town, Cape Town 8001, South Africa
| | - Erica Andersen-Nissen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Cape Town HVTN Immunology Laboratory, Hutchinson Centre Research Institute of South Africa, Cape Town 8001, South Africa
| | - Stephen C De Rosa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Britta Flach
- Cape Town HVTN Immunology Laboratory, Hutchinson Centre Research Institute of South Africa, Cape Town 8001, South Africa
| | - April K Randhawa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Ryan Jensen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Edith M Swann
- Vaccine Research Program, Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20852, USA
| | - Linda-Gail Bekker
- The Desmond Tutu HIV Centre, University of Cape Town, Cape Town 8001, South Africa
| | - Craig Innes
- The Aurum Institute, Klerksdorp 2570, South Africa
| | - Erica Lazarus
- Perinatal HIV Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 1864, South Africa
| | - Lynn Morris
- National Institute for Communicable Diseases, National Health Laboratory Service, Sandringham, Johannesburg 2192, South Africa
| | - Nonhlanhla N Mkhize
- National Institute for Communicable Diseases, National Health Laboratory Service, Sandringham, Johannesburg 2192, South Africa
| | - Guido Ferrari
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - David C Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xiaoying Shen
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Sheetal Sawant
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Nicole Yates
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - John Hural
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Abby Isaacs
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | | | - Carter Lee
- Global Solutions for Infectious Diseases, South San Francisco, CA 94080, USA
| | - Faruk Sinangil
- Global Solutions for Infectious Diseases, South San Francisco, CA 94080, USA
| | - Nelson L Michael
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Merlin L Robb
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - James G Kublin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Peter B Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Georgia D Tomaras
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Lawrence Corey
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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6
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Zaunders J, Dyer WB, Churchill M, Munier CML, Cunningham PH, Suzuki K, McBride K, Hey-Nguyen W, Koelsch K, Wang B, Hiener B, Palmer S, Gorry PR, Bailey M, Xu Y, Danta M, Seddiki N, Cooper DA, Saksena NK, Sullivan JS, Riminton S, Learmont J, Kelleher AD. Possible clearance of transfusion-acquired nef/LTR-deleted attenuated HIV-1 infection by an elite controller with CCR5 Δ32 heterozygous and HLA-B57 genotype. J Virus Erad 2019. [DOI: 10.1016/s2055-6640(20)30056-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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7
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López-Galíndez C. HIV long-term non-progressors elite controllers: an interplay between host, immune and viral factors. Future Virol 2019. [DOI: 10.2217/fvl-2018-0207] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
There is a rare group of HIV-1-infected individuals who show permanent control of clinical progression for over 10 years, maintain CD4+ cells >500 μl and have undetectable viral loads; they are designated long-term non-progressors elite controllers (LTNPs ECs). Multiple studies have demonstrated the necessary contribution of at least two of host, immune and viral factors to the LTNP phenotype. This group of individuals is not homogenous because of the different involvement of these factors. We will review the role of each of these and their combinations to the LTNP EC phenotype. LTNP EC individuals offer an opportunity for the investigation into the mechanisms for the spontaneous control of HIV infection.
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Affiliation(s)
- Cecilio López-Galíndez
- Unidad de Virología Molecular, Laboratorio de Referencia e Investigación en Retrovirus, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid 28220, Spain
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8
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Zaunders J, Dyer WB, Churchill M, Munier CML, Cunningham PH, Suzuki K, McBride K, Hey-Nguyen W, Koelsch K, Wang B, Hiener B, Palmer S, Gorry PR, Bailey M, Xu Y, Danta M, Seddiki N, Cooper DA, Saksena NK, Sullivan JS, Riminton S, Learmont J, Kelleher AD. Possible clearance of transfusion-acquired nef/LTR-deleted attenuated HIV-1 infection by an elite controller with CCR5 Δ32 heterozygous and HLA-B57 genotype. J Virus Erad 2019; 5:73-83. [PMID: 31191910 PMCID: PMC6543488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Subject C135 is one of the members of the Sydney Blood Bank Cohort, infected in 1981 through transfusion with attenuated nef/3' long terminal repeat (LTR)-deleted HIV-1, and has maintained undetectable plasma viral load and steady CD4 cell count, in the absence of therapy. Uniquely, C135 combines five factors separately associated with control of viraemia: nef/LTR-deleted HIV-1, HLA-B57, HLA-DR13, heterozygous CCR5 Δ32 genotype and vigorous p24-stimulated peripheral blood mononuclear cell (PBMC) proliferation. Therefore, we studied in detail viral burden and immunological responses in this individual. METHODS PBMC and gut and lymph node biopsy samples were analysed for proviral HIV-1 DNA by real-time and nested PCRs, and nef/LTR alleles by nested PCR. HIV-specific antibodies were studied by Western blotting, and CD4+ and CD8+ T lymphocyte responses were measured by proliferation and cytokine production in vitro. RESULTS PBMC samples from 1996, but not since, showed amplification of nef alleles with gross deletions. Infectious HIV-1 was never recovered. Proviral HIV-1 DNA was not detected in recent PBMC or gut or lymph node biopsy samples. C135 has a consistently weak antibody response and a substantial CD4+ T cell proliferative response to a previously described HLA-DR13-restricted epitope of HIV-1 p24 in vitro, which augmented a CD8+ T cell response to an immunodominant HLA-B57-restricted epitope of p24, while his T cells show reduced levels of CCR5. CONCLUSIONS Subject C135's early PCR and weak antibody results are consistent with limited infection with a poorly replicating nef/LTR-deleted strain of HIV-1. With his HLA-B57-restricted gag-specific CD8 and helper HLA-DR13-restricted CD4 T cell proliferative responses, C135 appears to have cleared his HIV-1 infection 37 years after transfusion.
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Affiliation(s)
- John Zaunders
- Centre for Applied Medical Research,
St Vincent's Hospital,
Sydney,
NSW,
Australia,Kirby Institute,
University of New South Wales,
Sydney,
NSW,
Australia,Corresponding author: John Zaunders
Centre for Applied Medical Research,
St Vincent's Hospital,
Level 9 Lowy Packer Building, 405 Liverpool St,
Darlinghurst,
NSW2010,
Australia
| | - Wayne B Dyer
- Australian Red Cross Blood Service,
Sydney,
NSW,
Australia,Faculty of Medicine and Health,
University of Sydney,
NSW,
Australia
| | - Melissa Churchill
- School of Health and Biomedical Sciences, College of Science, Engineering and Health,
RMIT University,
Bundoora,
VIC,
Australia
| | - C Mee Ling Munier
- Kirby Institute,
University of New South Wales,
Sydney,
NSW,
Australia
| | - Philip H Cunningham
- Centre for Applied Medical Research,
St Vincent's Hospital,
Sydney,
NSW,
Australia
| | - Kazuo Suzuki
- Centre for Applied Medical Research,
St Vincent's Hospital,
Sydney,
NSW,
Australia
| | - Kristin McBride
- Kirby Institute,
University of New South Wales,
Sydney,
NSW,
Australia
| | - Will Hey-Nguyen
- Kirby Institute,
University of New South Wales,
Sydney,
NSW,
Australia
| | - Kersten Koelsch
- Kirby Institute,
University of New South Wales,
Sydney,
NSW,
Australia
| | - Bin Wang
- Ingham Institute,
Liverpool,
NSW,
Australia
| | - Bonnie Hiener
- Centre for Virus Research, Westmead Institute for Medical Research,
University of Sydney,
Sydney,
NSW,
Australia
| | - Sarah Palmer
- Centre for Virus Research, Westmead Institute for Medical Research,
University of Sydney,
Sydney,
NSW,
Australia
| | - Paul R Gorry
- School of Health and Biomedical Sciences, College of Science, Engineering and Health,
RMIT University,
Bundoora,
VIC,
Australia
| | - Michelle Bailey
- Kirby Institute,
University of New South Wales,
Sydney,
NSW,
Australia
| | - Yin Xu
- Kirby Institute,
University of New South Wales,
Sydney,
NSW,
Australia
| | - Mark Danta
- Department of Gastroenterology and Hepatology,
St Vincent's Hospital,
Sydney,
NSW,
Australia
| | - Nabila Seddiki
- Vaccine Research Institute, Faculté de Médecine,
Université Paris Est Créteil,
Créteil,
France
| | - David A Cooper
- Centre for Applied Medical Research,
St Vincent's Hospital,
Sydney,
NSW,
Australia,Kirby Institute,
University of New South Wales,
Sydney,
NSW,
Australia
| | - Nitin K Saksena
- IGO Neurodegenerative Disease Section,
Sydney,
NSW,
Australia,China National Gene Bank,
Beijing Institute of Genomics,
Shenzhen,
China
| | - John S Sullivan
- Australian Red Cross Blood Service,
Sydney,
NSW,
Australia,Central Clinical School,
University of Sydney,
NSW,
Australia
| | - Sean Riminton
- Department of Clinical Immunology,
Concord Repatriation General Hospital,
Sydney,
NSW,
Australia
| | - Jenny Learmont
- Australian Red Cross Blood Service,
Sydney,
NSW,
Australia
| | - Anthony D Kelleher
- Centre for Applied Medical Research,
St Vincent's Hospital,
Sydney,
NSW,
Australia,Kirby Institute,
University of New South Wales,
Sydney,
NSW,
Australia
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9
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Naranbhai V, Carrington M. Host genetic variation and HIV disease: from mapping to mechanism. Immunogenetics 2017; 69:489-498. [PMID: 28695282 PMCID: PMC5537324 DOI: 10.1007/s00251-017-1000-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 05/07/2017] [Indexed: 12/12/2022]
Abstract
This review aims to provide a summary of current knowledge of host genetic effects on human immunodeficiency virus (HIV) disease. Mapping of simple single nucleotide polymorphisms (SNP) has been largely successful in HIV, but more complex genetic associations involving haplotypic or epigenetic variation, for example, remain elusive. Mechanistic insights explaining SNP associations are incomplete, but continue to be forthcoming. The number of robust immunogenetic correlates of HIV is modest and their discovery mostly predates the genome-wide era. Nevertheless, genome-wide evaluations have nicely validated the impact of HLA and CCR5 variants on HIV disease, and importantly, made clear the many false positive associations that were previously suggested by studies using the candidate gene approach. We describe how multiple HIV outcome measures such as acquisition, viral control, and immune decline have been studied in adults and in children, but that collectively these identify only the two replicable loci responsible for modifying HIV disease, CCR5, and HLA. Recent heritability estimates in this disease corroborate the modest impact of genetic determinants and their oligogenic nature. While the mechanism of protection afforded by genetic variants that diminish CCR5 expression is clear, new aspects of HLA class I-mediated protection continue to be uncovered. We describe how these genetic findings have enhanced insights into immunobiology, been clinically translated into CCR5 antagonists, allowed prioritization of antigens for vaccination efforts, and identified targets for genome-editing interventions. Finally, we describe how studies of genetically complex parts of the genome using new tools may begin revealing additional correlates.
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Affiliation(s)
- Vivek Naranbhai
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA.
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa.
| | - Mary Carrington
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
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10
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Crux NB, Elahi S. Human Leukocyte Antigen (HLA) and Immune Regulation: How Do Classical and Non-Classical HLA Alleles Modulate Immune Response to Human Immunodeficiency Virus and Hepatitis C Virus Infections? Front Immunol 2017; 8:832. [PMID: 28769934 PMCID: PMC5513977 DOI: 10.3389/fimmu.2017.00832] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 06/30/2017] [Indexed: 12/13/2022] Open
Abstract
The genetic factors associated with susceptibility or resistance to viral infections are likely to involve a sophisticated array of immune response. These genetic elements may modulate other biological factors that account for significant influence on the gene expression and/or protein function in the host. Among them, the role of the major histocompatibility complex in viral pathogenesis in particular human immunodeficiency virus (HIV) and hepatitis C virus (HCV), is very well documented. We, recently, added a novel insight into the field by identifying the molecular mechanism associated with the protective role of human leukocyte antigen (HLA)-B27/B57 CD8+ T cells in the context of HIV-1 infection and why these alleles act as a double-edged sword protecting against viral infections but predisposing the host to autoimmune diseases. The focus of this review will be reexamining the role of classical and non-classical HLA alleles, including class Ia (HLA-A, -B, -C), class Ib (HLA-E, -F, -G, -H), and class II (HLA-DR, -DQ, -DM, and -DP) in immune regulation and viral pathogenesis (e.g., HIV and HCV). To our knowledge, this is the very first review of its kind to comprehensively analyze the role of these molecules in immune regulation associated with chronic viral infections.
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Affiliation(s)
- Nicole B Crux
- Faculty of Medicine and Dentistry, Department of Dentistry, University of Alberta, Edmonton, AB, Canada.,Faculty of Medicine and Dentistry, Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada
| | - Shokrollah Elahi
- Faculty of Medicine and Dentistry, Department of Dentistry, University of Alberta, Edmonton, AB, Canada.,Faculty of Medicine and Dentistry, Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada
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11
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Oriol-Tordera B, Llano A, Ganoza C, Cate S, Hildebrand W, Sanchez J, Calle ML, Brander C, Olvera A. Impact of HLA-DRB1 allele polymorphisms on control of HIV infection in a Peruvian MSM cohort. HLA 2017; 90:234-237. [PMID: 28677168 DOI: 10.1111/tan.13085] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 04/06/2017] [Accepted: 06/15/2017] [Indexed: 11/27/2022]
Abstract
Associations between HLA class II polymorphisms and HIV control were assessed in a Peruvian MSM cohort. Among 233 treatment naïve HIV+ individuals, DRB1*13:02 was linked to elevated viral loads (P = .044) while DRB1*12:01 showed significantly lower viral set points (P = .015) and restricted a dominant T cell response to HIV Gag p24 (P = .038). The present work contributes to a better knowledge of the Peruvian immunogenetics and supports the important role of HLA class II restricted T cells in HIV control.
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Affiliation(s)
- B Oriol-Tordera
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Barcelona, Spain
| | - A Llano
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Barcelona, Spain
| | - C Ganoza
- Asociación Civil IMPACTA Salud y Educacion, Lima, Peru
| | - S Cate
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma, Oklahoma
| | - W Hildebrand
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma, Oklahoma
| | - J Sanchez
- Asociación Civil IMPACTA Salud y Educacion, Lima, Peru.,Centro de Investigaciones Tecnológicas, Biomédicas y Medioambientales, Lima, Peru.,Department of Global Health, University of Washington, Seattle, Washington
| | - M L Calle
- Faculty of Medicine, University of Vic-Central University of Catalonia, Barcelona, Spain
| | - C Brander
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Barcelona, Spain.,Faculty of Medicine, University of Vic-Central University of Catalonia, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - A Olvera
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Barcelona, Spain
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12
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Vesa J, Chaillon A, Wagner GA, Anderson CM, Richman DD, Smith DM, Little SJ. Increased HIV-1 superinfection risk in carriers of specific human leukocyte antigen alleles. AIDS 2017; 31:1149-1158. [PMID: 28244954 PMCID: PMC5559224 DOI: 10.1097/qad.0000000000001445] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
OBJECTIVE The aim of this study was to characterize the demographic, behavioural, clinical and immunogenetic determinants of HIV-1 superinfection in a high-risk cohort of MSM. DESIGN A retrospective cohort study of prospectively followed MSM. METHODS Ninety-eight MSM with acute or early HIV-1 monoinfection were followed for a median of 15.6 months. Demographic and human leukocyte antigen (HLA) genotype data were collected at enrolment. Sexual behaviour, clinical and the infection status (monoinfection or superinfection) data were recorded at each visit (at enrolment and thereafter at a median of 4.2-month intervals). HIV-1 superinfection risk was determined by Cox regression and Kaplan-Meier survival analysis. RESULTS Ten individuals (10.2%) had superinfection during follow-up. Cox regression did not show significantly increased superinfection risk for individuals with an increased amount of condomless anal intercourse, lower CD4 T-cell count or higher viral load, but higher number of sexual contacts demonstrated a trend towards significance [hazard ratio, 4.74; 95% confidence interval (95% CI), 0.87-25.97; P = 0.073]. HLA-A*29 (hazard ratio, 4.10; 95% CI, 0.88-14.76; P = 0.069), HLA-B*35 (hazard ratio, 4.64; 95% CI, 1.33-18.17; P = 0.017), HLA-C*04 (hazard ratio, 5.30; 95% CI, 1.51-20.77; P = 0.010), HLA-C*16 (hazard ratio, 4.05; 95% CI, 0.87-14.62; P = 0.071), HLA-DRB1*07 (hazard ratio, 3.29; 95% CI, 0.94-12.90; P = 0.062) and HLA-DRB1*08 (hazard ratio, 15.37; 95% CI, 2.11-79.80; P = 0.011) were associated with an increased risk of superinfection at α = 0.10, whereas HLA-DRB1*11 was associated with decreased superinfection risk (hazard ratio, 0.13; 95% CI, 0.00-1.03; P = 0.054). CONCLUSION HLA genes may, in part, elucidate the genetic basis of differential superinfection risk, and provide important information for the development of efficient prevention and treatment strategies of HIV-1 superinfection.
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Affiliation(s)
- Jouni Vesa
- University of California San Diego, La Jolla
| | | | | | | | - Douglas D. Richman
- University of California San Diego, La Jolla
- Veterans Affairs San Diego Healthcare System, San Diego, California, USA
| | - Davey M. Smith
- University of California San Diego, La Jolla
- Veterans Affairs San Diego Healthcare System, San Diego, California, USA
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13
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Laher F, Ranasinghe S, Porichis F, Mewalal N, Pretorius K, Ismail N, Buus S, Stryhn A, Carrington M, Walker BD, Ndung'u T, Ndhlovu ZM. HIV Controllers Exhibit Enhanced Frequencies of Major Histocompatibility Complex Class II Tetramer + Gag-Specific CD4 + T Cells in Chronic Clade C HIV-1 Infection. J Virol 2017; 91:e02477-16. [PMID: 28077659 PMCID: PMC5355603 DOI: 10.1128/jvi.02477-16] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 01/09/2017] [Indexed: 11/20/2022] Open
Abstract
Immune control of viral infections is heavily dependent on helper CD4+ T cell function. However, the understanding of the contribution of HIV-specific CD4+ T cell responses to immune protection against HIV-1, particularly in clade C infection, remains incomplete. Recently, major histocompatibility complex (MHC) class II tetramers have emerged as a powerful tool for interrogating antigen-specific CD4+ T cells without relying on effector functions. Here, we defined the MHC class II alleles for immunodominant Gag CD4+ T cell epitopes in clade C virus infection, constructed MHC class II tetramers, and then used these to define the magnitude, function, and relation to the viral load of HIV-specific CD4+ T cell responses in a cohort of untreated HIV clade C-infected persons. We observed significantly higher frequencies of MHC class II tetramer-positive CD4+ T cells in HIV controllers than progressors (P = 0.0001), and these expanded Gag-specific CD4+ T cells in HIV controllers showed higher levels of expression of the cytolytic proteins granzymes A and B. Importantly, targeting of the immunodominant Gag41 peptide in the context of HLA class II DRB1*1101 was associated with HIV control (r = -0.5, P = 0.02). These data identify an association between HIV-specific CD4+ T cell targeting of immunodominant Gag epitopes and immune control, particularly the contribution of a single class II MHC-peptide complex to the immune response against HIV-1 infection. Furthermore, these results highlight the advantage of the use of class II tetramers in evaluating HIV-specific CD4+ T cell responses in natural infections.IMPORTANCE Increasing evidence suggests that virus-specific CD4+ T cells contribute to the immune-mediated control of clade B HIV-1 infection, yet there remains a relative paucity of data regarding the role of HIV-specific CD4+ T cells in shaping adaptive immune responses in individuals infected with clade C, which is responsible for the majority of HIV infections worldwide. Understanding the contribution of HIV-specific CD4+ T cell responses in clade C infection is particularly important for developing vaccines that would be efficacious in sub-Saharan Africa, where clade C infection is dominant. Here, we employed MHC class II tetramers designed to immunodominant Gag epitopes and used them to characterize CD4+ T cell responses in HIV-1 clade C infection. Our results demonstrate an association between the frequency of HIV-specific CD4+ T cell responses targeting an immunodominant DRB1*11-Gag41 complex and HIV control, highlighting the important contribution of a single class II MHC-peptide complex to the immune response against HIV-1 infections.
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Affiliation(s)
- Faatima Laher
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Srinika Ranasinghe
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California, USA
| | - Filippos Porichis
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California, USA
| | - Nikoshia Mewalal
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Karyn Pretorius
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Nasreen Ismail
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Søren Buus
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen N, Denmark
| | - Anette Stryhn
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen N, Denmark
| | - Mary Carrington
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts, USA
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Bruce D Walker
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts, USA
- KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Max Planck Institute for Infection Biology, Berlin, Germany
| | - Zaza M Ndhlovu
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts, USA
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14
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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] [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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15
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Assone T, Paiva A, Fonseca LAM, Casseb J. Genetic Markers of the Host in Persons Living with HTLV-1, HIV and HCV Infections. Viruses 2016; 8:v8020038. [PMID: 26848682 PMCID: PMC4776193 DOI: 10.3390/v8020038] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 01/11/2016] [Accepted: 01/15/2016] [Indexed: 12/21/2022] Open
Abstract
Human T-cell leukemia virus type 1 (HTLV-1), hepatitis C virus (HCV) and human immunodeficiency virus type 1 (HIV-1) are prevalent worldwide, and share similar means of transmission. These infections may influence each other in evolution and outcome, including cancer or immunodeficiency. Many studies have reported the influence of genetic markers on the host immune response against different persistent viral infections, such as HTLV-1 infection, pointing to the importance of the individual genetic background on their outcomes. However, despite recent advances on the knowledge of the pathogenesis of HTLV-1 infection, gaps in the understanding of the role of the individual genetic background on the progress to disease clinically manifested still remain. In this scenario, much less is known regarding the influence of genetic factors in the context of dual or triple infections or their influence on the underlying mechanisms that lead to outcomes that differ from those observed in monoinfection. This review describes the main factors involved in the virus–host balance, especially for some particular human leukocyte antigen (HLA) haplotypes, and other important genetic markers in the development of HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) and other persistent viruses, such as HIV and HCV.
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Affiliation(s)
- Tatiane Assone
- Laboratory of Dermatology and Immune deficiencies, Department of Dermatology, University of São Paulo Medical School, LIM56, Av. Dr. Eneas de Carvalho Aguiar 500, 3rd Floor, Building II, São Paulo, SP, Brazil.
- Institute of Tropical Medicine of São Paulo, São Paulo, Brazil.
| | - Arthur Paiva
- Institute of Tropical Medicine of São Paulo, São Paulo, Brazil.
| | - Luiz Augusto M Fonseca
- Department of Preventive Medicine, University of São Paulo Medical School, São Paulo, Brazil.
| | - Jorge Casseb
- Laboratory of Dermatology and Immune deficiencies, Department of Dermatology, University of São Paulo Medical School, LIM56, Av. Dr. Eneas de Carvalho Aguiar 500, 3rd Floor, Building II, São Paulo, SP, Brazil.
- Institute of Tropical Medicine of São Paulo, São Paulo, Brazil.
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16
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Rosa DS, Ribeiro SP, Fonseca SG, Almeida RR, Santana VC, Apostólico JDS, Kalil J, Cunha-Neto E. Multiple Approaches for Increasing the Immunogenicity of an Epitope-Based Anti-HIV Vaccine. AIDS Res Hum Retroviruses 2015; 31:1077-88. [PMID: 26149745 DOI: 10.1089/aid.2015.0101] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The development of a highly effective vaccine against the human immunodeficiency virus (HIV) will likely be based on rational vaccine design, since traditional vaccine approaches have failed so far. In recent years, an understanding of what type of immune response is protective against infection and/or disease facilitated vaccine design. T cell-based vaccines against HIV have the goal of limiting both transmission and disease progression by inducing broad and functionally relevant T cell responses. In this context, CD4(+) T cells play a direct cytotoxic role and are also important for the generation and maintenance of functional CD8(+) T and B cell responses. The use of MHC-binding algorithms has allowed the identification of novel CD4(+) T cell epitopes that could be used in vaccine design, the so-called epitope-driven vaccine design. Epitope-based vaccines have the ability to focus the immune response on highly antigenic, conserved epitopes that are fully recognized by the target population. We have recently mapped a set of conserved multiple HLA-DR-binding HIV-1 CD4 epitopes and observed interferon (IFN)-γ-producing CD4(+) T cells when we tested these peptides in peripheral blood mononuclear cells (PBMCs) from HIV-infected individuals. We then designed multiepitopic DNA vaccines that induced broad and polyfunctional T cell responses in immunized mice. In this review we will focus on alternative strategies to increase the immunogenicity of an epitope-based vaccine against HIV infection.
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Affiliation(s)
- Daniela Santoro Rosa
- Departament of Microbiology, Immunology and Parasitology, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
- Institute for Investigation in Immunology-INCT, São Paulo, Brazil
| | - Susan Pereira Ribeiro
- Institute for Investigation in Immunology-INCT, São Paulo, Brazil
- Laboratory of Clinical Immunology and Allergy-LIM60, University of São Paulo School of Medicine, São Paulo, Brazil
| | | | - Rafael Ribeiro Almeida
- Laboratory of Clinical Immunology and Allergy-LIM60, University of São Paulo School of Medicine, São Paulo, Brazil
- Institute for Tropical Pathology and Public Health, Federal University of Goiás, Goiás, Brazil
| | - Vinicius Canato Santana
- Laboratory of Clinical Immunology and Allergy-LIM60, University of São Paulo School of Medicine, São Paulo, Brazil
- Institute for Tropical Pathology and Public Health, Federal University of Goiás, Goiás, Brazil
| | - Juliana de Souza Apostólico
- Departament of Microbiology, Immunology and Parasitology, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
- Institute for Investigation in Immunology-INCT, São Paulo, Brazil
| | - Jorge Kalil
- Institute for Investigation in Immunology-INCT, São Paulo, Brazil
- Heart Institute (InCor), University of São Paulo School of Medicine, São Paulo, Brazil
| | - Edecio Cunha-Neto
- Institute for Investigation in Immunology-INCT, São Paulo, Brazil
- Laboratory of Clinical Immunology and Allergy-LIM60, University of São Paulo School of Medicine, São Paulo, Brazil
- Heart Institute (InCor), University of São Paulo School of Medicine, São Paulo, Brazil
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17
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Abstract
Chronic viral infections represent a unique challenge to the infected host. Persistently replicating viruses outcompete or subvert the initial antiviral response, allowing the establishment of chronic infections that result in continuous stimulation of both the innate and adaptive immune compartments. This causes a profound reprogramming of the host immune system, including attenuation and persistent low levels of type I interferons, progressive loss (or exhaustion) of CD8(+) T cell functions, and specialization of CD4(+) T cells to produce interleukin-21 and promote antibody-mediated immunity and immune regulation. Epigenetic, transcriptional, posttranscriptional, and metabolic changes underlie this adaptation or recalibration of immune cells to the emerging new environment in order to strike an often imperfect balance between the host and the infectious pathogen. In this review we discuss the common immunological hallmarks observed across a range of different persistently replicating viruses and host species, the underlying molecular mechanisms, and the biological and clinical implications.
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Affiliation(s)
- Elina I Zuniga
- Molecular Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093;
| | - Monica Macal
- Molecular Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093;
| | - Gavin M Lewis
- Molecular Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093;
| | - James A Harker
- Section of Inflammation, Repair and Development, National Heart and Lung Institute, Imperial College London, London SW7 2AZ, United Kingdom
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18
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Seki S, Matano T. Development of a Sendai virus vector-based AIDS vaccine inducing T cell responses. Expert Rev Vaccines 2015; 15:119-27. [PMID: 26512881 DOI: 10.1586/14760584.2016.1105747] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Virus-specific CD8(+) T-cell responses play a major role in the control of HIV replication, and induction of HIV-specific T-cell responses is an important strategy for AIDS vaccine development. Optimization of the delivery system and immunogen would be the key for the development of an effective T cell-based AIDS vaccine. Heterologous prime-boost vaccine regimens using multiple viral vectors are a promising protocol for efficient induction of HIV-specific T-cell responses, and the development of a variety of potent viral vectors have been attempted. This review describes the current progress of the development of T cell-based AIDS vaccines using viral vectors, focusing on Sendai virus vectors, whose phase I clinical trials have been performed.
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Affiliation(s)
- Sayuri Seki
- a AIDS Research Center , National Institute of Infectious Diseases , Tokyo , Japan
| | - Tetsuro Matano
- a AIDS Research Center , National Institute of Infectious Diseases , Tokyo , Japan.,b The Institute of Medical Science , The University of Tokyo , Tokyo , Japan
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19
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Qin M, Brummel S, Singh KK, Fenton T, Spector SA. Associations of host genetic variants on CD4⁺ lymphocyte count and plasma HIV-1 RNA in antiretroviral naïve children. Pediatr Infect Dis J 2014; 33:946-52. [PMID: 24797997 PMCID: PMC4216611 DOI: 10.1097/inf.0000000000000330] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND CD4 T-lymphocyte (CD4) counts and HIV plasma RNA concentration (RNA) are 2 key HIV disease markers. The complex interplay between virus and host genetics may contribute to differences in viral set point and CD4 status. Determining the effects of host genetic variation on HIV disease markers is often complicated by the use of antiretroviral therapy. In this study, the association between genetic variants and baseline HIV RNA and CD4 counts was examined in a large cohort of antiretroviral naïve children. METHODS Specimens from 1053 HIV-infected children were screened for single nucleotide polymorphisms in 78 regions from 17 genes. Linear regression with a robust variance estimator was used to test the association between genetic markers with HIV RNA and CD4 count, controlling for age, race/ethnicity and study. False discovery rate (FDR) controlling was used to adjust for multiple testing. RESULTS The study population was 60% black, 26% Hispanic and 13% white; median age 2.35 years; 55% female. Baseline median CD4 count was 780/mm; median log10 HIV RNA was 5.17 copies/mL. For analyses of the associations of genetic makers with baseline CD4 count, 6 HLA and 4 additional markers exhibited P < 0.05, but none met the criteria for statistical significance with FDR controlled at 0.05. For baseline HIV RNA, HLA DRB1*15, DRB1*10, B-27/57, B-14, Cw-8, B-57 were statistically significant with FDR controlled at 0.05. CONCLUSIONS These results provide strong evidence that HLA DRB1*15, DRB1*10, B-27/57, B-14, Cw-8, B-57 are associated with HIV RNA and play a role in HIV pathogenesis in infected children.
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Affiliation(s)
- Min Qin
- Center for Biostatistics in AIDS Research, Harvard School of Public Health, Boston, MA
| | - Sean Brummel
- Center for Biostatistics in AIDS Research, Harvard School of Public Health, Boston, MA
| | - Kumud K. Singh
- University of California, San Diego, La Jolla, CA and Rady Children’s Hospital, San Diego, CA
| | - Terry Fenton
- Center for Biostatistics in AIDS Research, Harvard School of Public Health, Boston, MA
| | - Stephen A. Spector
- University of California, San Diego, La Jolla, CA and Rady Children’s Hospital, San Diego, CA
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20
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Ranasinghe S, Cutler S, Davis I, Lu R, Soghoian DZ, Qi Y, Sidney J, Kranias G, Flanders M, Lindqvist M, Kuhl B, Alter G, Deeks SG, Walker BD, Gao X, Sette A, Carrington M, Streeck H. Association of HLA-DRB1-restricted CD4⁺ T cell responses with HIV immune control. Nat Med 2013; 19:930-3. [PMID: 23793098 PMCID: PMC3974408 DOI: 10.1038/nm.3229] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 05/09/2013] [Indexed: 12/13/2022]
Abstract
The contribution of HLA class II-restricted CD4(+) T cell responses to HIV immune control is poorly defined. Here, we delineated previously uncharacterized peptide-DRB1 restrictions in functional assays and analyzed the host genetic effects of HLA-DRB1 alleles on HIV viremia in a large cohort of HIV controllers and progressors. We found distinct stratifications in the effect of HLA-DRB1 alleles on HIV viremia, with HLA-DRB1*15:02 significantly associated with low viremia and HLA-DRB1*03:01 significantly associated with high viremia. Notably, a subgroup of HLA-DRB1 variants linked with low viremia showed the ability to promiscuously present a larger breadth of peptides with lower functional avidity when compared to HLA-DRB1 variants linked with high viremia. Our data provide systematic evidence that HLA-DRB1 variant expression has a considerable impact on the control of HIV replication, an effect that seems to be mediated primarily by the protein specificity of CD4(+) T cell responses to HIV Gag and Nef.
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Affiliation(s)
- Srinika Ranasinghe
- Ragon Institute of MGH, MIT, and Harvard, Massachusetts General Hospital and Harvard Medical School, Cambridge, Massachusetts, USA
| | - Sam Cutler
- Ragon Institute of MGH, MIT, and Harvard, Massachusetts General Hospital and Harvard Medical School, Cambridge, Massachusetts, USA
| | - Isaiah Davis
- Ragon Institute of MGH, MIT, and Harvard, Massachusetts General Hospital and Harvard Medical School, Cambridge, Massachusetts, USA
| | - Richard Lu
- new affiliation: U.S. Military HIV Research Program (MHRP), Henry M. Jackson Foundation, Walter Reed Army Institute of Research (WRAIR), Silver Spring, Maryland, USA
| | - Damien Z. Soghoian
- Ragon Institute of MGH, MIT, and Harvard, Massachusetts General Hospital and Harvard Medical School, Cambridge, Massachusetts, USA
| | - Ying Qi
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, NCI Frederick, Frederick, Maryland, USA
| | - John Sidney
- La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - Gregory Kranias
- new affiliation: U.S. Military HIV Research Program (MHRP), Henry M. Jackson Foundation, Walter Reed Army Institute of Research (WRAIR), Silver Spring, Maryland, USA
| | - Michael Flanders
- Ragon Institute of MGH, MIT, and Harvard, Massachusetts General Hospital and Harvard Medical School, Cambridge, Massachusetts, USA
| | - Madelene Lindqvist
- Ragon Institute of MGH, MIT, and Harvard, Massachusetts General Hospital and Harvard Medical School, Cambridge, Massachusetts, USA
| | - Bjorn Kuhl
- Ragon Institute of MGH, MIT, and Harvard, Massachusetts General Hospital and Harvard Medical School, Cambridge, Massachusetts, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Massachusetts General Hospital and Harvard Medical School, Cambridge, Massachusetts, USA
| | - Steven G. Deeks
- UCSF Department of Medicine at San Francisco General Hospital, San Francisco, California, USA
| | - Bruce D. Walker
- Ragon Institute of MGH, MIT, and Harvard, Massachusetts General Hospital and Harvard Medical School, Cambridge, Massachusetts, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Xiaojiang Gao
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, NCI Frederick, Frederick, Maryland, USA
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - Mary Carrington
- Ragon Institute of MGH, MIT, and Harvard, Massachusetts General Hospital and Harvard Medical School, Cambridge, Massachusetts, USA
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, NCI Frederick, Frederick, Maryland, USA
| | - Hendrik Streeck
- new affiliation: U.S. Military HIV Research Program (MHRP), Henry M. Jackson Foundation, Walter Reed Army Institute of Research (WRAIR), Silver Spring, Maryland, USA
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21
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Abstract
Host genetic factors are a major contributing factor to the inter-individual variation observed in response to human immunodeficiency virus (HIV) infection and are linked to resistance to HIV infection among exposed individuals, as well as rate of disease progression and the likelihood of viral transmission. Of the genetic variants that have been shown to affect the natural history of HIV infection, the human leukocyte antigen (HLA) class I genes exhibit the strongest and most consistent association, underscoring a central role for CD8(+) T cells in resistance to the virus. HLA proteins play important roles in T-cell-mediated adaptive immunity by presenting immunodominant HIV epitopes to cytotoxic T lymphocytes (CTLs) and CD4(+) T cells. Genetic and functional data also indicate a function for HLA in natural killer cell-mediated innate immunity against HIV by interacting with killer cell immunoglobulin-like receptors (KIR). We review the HLA and KIR associations with HIV disease and discuss the mechanisms underlying these associations.
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Affiliation(s)
- Maureen P. Martin
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland, USA
| | - Mary Carrington
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland, USA
- Ragon Institute of MGH, MIT, and Harvard, Boston, Massachusetts, USA
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22
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Castelli FA, Szely N, Olivain A, Casartelli N, Grygar C, Schneider A, Besse A, Levy Y, Schwartz O, Maillère B. Hierarchy of CD4 T cell epitopes of the ANRS Lipo5 synthetic vaccine relies on the frequencies of pre-existing peptide-specific T cells in healthy donors. THE JOURNAL OF IMMUNOLOGY 2013; 190:5757-63. [PMID: 23636059 DOI: 10.4049/jimmunol.1300145] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The Agence National de Recherche sur le SIDA et les hepatitis Lipo5 vaccine is composed by five long fragments of HIV proteins and was recently shown to induce in seronegative volunteers a CD4 T cell response largely dominated by the G2 fragment. To understand this response profile, we submitted the five HIV fragments to HLA-DR-binding assays and evaluated the frequency of naive Lipo5-specific CD4 T lymphocytes in the blood of 22 healthy individuals. We enumerated the Lipo5-specific T cell lines induced in vitro by weekly rounds of specific stimulation. Four peptides and hence not only G2 exhibited a broad specificity for HLA-DR molecules. In contrast, most of the T cell lines specific for Lipo5 reacted with G2, revealing a G2-specific T cell repertoire superior to 2 cells per million, whereas it is close to 0.4 for the other peptides. We also found good cross-reactivity of all the peptides with clade B and C variants and that G2 and P1 are able to recruit T cells that recognize HIV-infected cells. We therefore mainly observed very good concordance between the frequency to individual Lipo5 peptides among vaccinees in a large-scale vaccine trial and the distribution of peptide specificity of the in vitro induced T cell lines. These findings underline the role of the size of the epitope-specific naive repertoire in shaping the CD4 T cell response after vaccination and highlight the value of evaluating the naive repertoire to predict vaccine immunogenicity.
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Affiliation(s)
- Florence Anne Castelli
- Commissariat à l'Energie Atomique, Institut de Biologie et de Technologies, Service d'Ingénierie Moléculaire des Protéines, F-91191 Gif Sur Yvette, France
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23
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Zaunders J, van Bockel D. Innate and Adaptive Immunity in Long-Term Non-Progression in HIV Disease. Front Immunol 2013; 4:95. [PMID: 23630526 PMCID: PMC3633949 DOI: 10.3389/fimmu.2013.00095] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 04/09/2013] [Indexed: 12/20/2022] Open
Abstract
Long-term non-progressors (LTNP) were identified after 10-15 years of the epidemic, and have been the subject of intense investigation ever since. In a small minority of cases, infection with nef/3'LTR deleted attenuated viral strains allowed control over viral replication. A common feature of LTNP is the readily detected proliferation of CD4 T-cells in vitro, in response to p24. In some cases, the responding CD4 T-cells have cytotoxic effector function and may target conserved p24 epitopes, similar to the CD8 T-cells described below. LTNP may also carry much lower HIV DNA burden in key CD4 subsets, presumably resulting from lower viral replication during primary infection. Some studies, but not others, suggest that LTNP have CD4 T-cells that are relatively resistant to HIV infection in vitro. One possible mechanism may involve up-regulation of the cell cycle regulator p21/waf in CD4 T-cells from LTNP. Delayed progression in Caucasian LTNP is also partly associated with heterozygosity of the Δ32 CCR5 allele, probably through decreased expression of CCR5 co-receptor on CD4 T-cells. However, in approximately half of Caucasian LTNP, two host genotypes, namely HLA-B57 and HLA-B27, are associated with viral control. Immunodominant CD8 T-cells from these individuals target epitopes in p24 that are highly conserved, and escape mutations have significant fitness costs to the virus. Furthermore, recent studies have suggested that these CD8 T-cells from LTNP, but not from HLA-B27 or HLA-B57 progressors, can cross-react with intermediate escape mutations, preventing full escape via compensatory mutations. Humoral immunity appears to play little part in LTNP subjects, since broadly neutralizing antibodies are rare, even amongst slow progressors. Recent genome-wide comparisons between LTNP and progressors have confirmed the HLA-B57, HLA-B27, and delta32 CCR5 allelic associations, plus indicated a role for HLA-C/KIR interactions, but have not revealed any new genotypes so far. Nevertheless, it is hoped that studying the mechanisms of intracellular restriction factors, such as the recently identified SAMHD1, will lead to a better understanding of non-progression.
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Affiliation(s)
- John Zaunders
- Centre for Applied Medical Research, St Vincent's Hospital Darlinghurst, NSW, Australia
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24
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Haaland RE, Johnson JA, Tang J. Recent advances in research of HIV infection: implications of viral and host genetics on treatment and prevention. Public Health Genomics 2013; 16:31-6. [PMID: 23548715 DOI: 10.1159/000345935] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The genetic diversity among human immunodeficiency virus (HIV) subtypes as well as the variability of viral sequences found in HIV-infected individuals presents a number of difficult obstacles for the development of universally effective HIV treatment and prevention methods. Here, we present a brief summary of recent developments in the analysis of viral genetics and human genomics to provide insight into future methods for HIV treatment and prevention. Recent studies have mined viral sequences found in newly infected individuals to identify common features of all transmitted viruses that could provide potential targets for HIV vaccine development. Analysis of human immunogenetics has identified specific alleles associated with reduced virus loads in HIV-infected individuals providing valuable information that may influence individual responses to treatment and prevention methods. Increased sensitivity of antiretroviral drug resistance testing has improved the detection of hidden drug resistant virus but also highlighted the potential for drug resistant viruses to reduce the effectiveness of clinical treatment regimens. The rapidly expanding amount of data generated by studies of viral genetics and human immunogenetics will provide valuable information to guide the design of new strategies to improve clinical treatment and enhance HIV vaccine development.
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Affiliation(s)
- R E Haaland
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA.
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25
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Burwitz BJ, Giraldo-Vela JP, Reed J, Newman LP, Bean AT, Nimityongskul FA, Castrovinci PA, Maness NJ, Leon EJ, Rudersdorf R, Sacha JB. CD8+ and CD4+ cytotoxic T cell escape mutations precede breakthrough SIVmac239 viremia in an elite controller. Retrovirology 2012; 9:91. [PMID: 23131037 PMCID: PMC3496649 DOI: 10.1186/1742-4690-9-91] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 10/14/2012] [Indexed: 02/05/2023] Open
Abstract
Background Virus-specific T cells are critical components in the containment of immunodeficiency virus infections. While the protective role of CD8+ T cells is well established by studies of CD8+ T cell-mediated viral escape, it remains unknown if CD4+ T cells can also impose sufficient selective pressure on replicating virus to drive the emergence of high-frequency escape variants. Identifying a high frequency CD4+ T cell driven escape mutation would provide compelling evidence of direct immunological pressure mediated by these cells. Results Here, we studied a SIVmac239-infected elite controller rhesus macaque with a 1,000-fold spontaneous increase in plasma viral load that preceded disease progression and death from AIDS-related complications. We sequenced the viral genome pre- and post-breakthrough and demonstrate that CD8+ T cells drove the majority of the amino acid substitutions outside of Env. However, within a region of Gag p27CA targeted only by CD4+ T cells, we identified a unique post-breakthrough mutation, Gag D205E, which abrogated CD4+ T cell recognition. Further, we demonstrate that the Gag p27CA-specific CD4+ T cells exhibited cytolytic activity and that SIV bearing the Gag D205E mutation escapes this CD4+ T cell effector function ex vivo. Conclusions Cumulatively, these results confirm the importance of virus specific CD8+ T cells and demonstrate that CD4+ T cells can also exert significant selective pressure on immunodeficiency viruses in vivo during low-level viral replication. These results also suggest that further studies of CD4+ T cell escape should focus on cases of elite control with spontaneous viral breakthrough.
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Affiliation(s)
- Benjamin J Burwitz
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, 505 NW 185th, Beaverton, OR 97006, USA
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26
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Abstract
HIV is a disease in which the original clinical observations of severe opportunistic infections gave the first clues regarding the underlying pathology, namely that HIV is essentially an infection of the immune system. HIV infects and deletes CD4(+) T cells that normally coordinate the adaptive T- and B-cell response to defend against intracellular pathogens. The immune defect is immediate and profound: At the time of acute infection with an AIDS virus, typically more than half of the gut-associated CD4(+) T cells are depleted, leaving a damaged immune system to contend with a life-long infection.
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Affiliation(s)
- Bruce Walker
- Ragon Institute of MGH, MIT, and Harvard Mass General Hospital-East, Charlestown, Massachusetts 02129, USA.
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27
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Abstract
The dynamics of HIV-1 viremia is a complex and evolving landscape with clinical and epidemiological (public health) implications. Most studies have relied on the use of set-point viral load (VL) as a readily available proxy of viral dynamics to assess host and viral correlates. This review highlights recent findings from population-based studies of set-point VL, focusing primarily on robust data related to host genetics. A comprehensive understanding of viral dynamics will clearly need to consider both host and viral characteristics, with close attention to (i) the timing of VL measurements, (ii) the biology of viral evolution, (iii) compartments of active viral replication, (iv) the transmission source partner as the immediate past microenvironment, and (v) proper application of statistical models.
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Affiliation(s)
- Heather A. Prentice
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama;
- Author to whom correspondence should be addressed; ; Tel.: +1-720-352-3432
| | - Jianming Tang
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama;
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama;
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28
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Vargas-Inchaustegui DA, Xiao P, Tuero I, Patterson LJ, Robert-Guroff M. NK and CD4+ T cell cooperative immune responses correlate with control of disease in a macaque simian immunodeficiency virus infection model. THE JOURNAL OF IMMUNOLOGY 2012; 189:1878-85. [PMID: 22798665 DOI: 10.4049/jimmunol.1201026] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Control of infectious disease may be accomplished by successful vaccination or by complex immunologic and genetic factors favoring Ag-specific multicellular immune responses. Using a rhesus macaque model, we evaluated Ag-specific T cell-dependent NK cell immune responses in SIV-infected macaques, designated "controlling" or "noncontrolling" based on long-term chronic viremia levels, to determine whether NK cell effector functions contribute to control of SIV infection. We observed that Gag stimulation of macaque PBMCs induced subset-specific NK cell responses in SIV-controlling but not SIV-noncontrolling animals, as well as that circulatory NK cell responses were dependent on Ag-specific IL-2 production by CD4(+) central memory T cells. NK cell activation was blocked by anti-IL-2-neutralizing Ab and by CD4(+) T cell depletion, which abrogated the Gag-specific responses. Among tissue-resident cells, splenic and circulatory NK cells displayed similar activation profiles, whereas liver and mucosal NK cells displayed a decreased activation profile, similar in SIV-controlling and -noncontrolling macaques. Lack of T cell-dependent NK cell function was rescued in SIV-noncontrolling macaques through drug-mediated control of viremia. Our results indicate that control of disease progression in SIV-controlling macaques is associated with cooperation between Ag-specific CD4(+) T cells and NK cell effector function, which highlight the importance of such cell-to-cell cooperativity in adaptive immunity and suggest that this interaction should be further investigated in HIV vaccine development and other prophylactic vaccine approaches.
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29
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Chang HH, Soderberg K, Skinner JA, Banchereau J, Chaussabel D, Haynes BF, Ramoni M, Letvin NL. Transcriptional network predicts viral set point during acute HIV-1 infection. J Am Med Inform Assoc 2012; 19:1103-9. [PMID: 22700869 DOI: 10.1136/amiajnl-2012-000867] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND HIV-1-infected individuals with higher viral set points progress to AIDS more rapidly than those with lower set points. Predicting viral set point early following infection can contribute to our understanding of early control of HIV-1 replication, to predicting long-term clinical outcomes, and to the choice of optimal therapeutic regimens. METHODS In a longitudinal study of 10 untreated HIV-1-infected patients, we used gene expression profiling of peripheral blood mononuclear cells to identify transcriptional networks for viral set point prediction. At each sampling time, a statistical analysis inferred the optimal transcriptional network that best predicted viral set point. We then assessed the accuracy of this transcriptional model by predicting viral set point in an independent cohort of 10 untreated HIV-1-infected patients from Malawi. RESULTS The gene network inferred at time of enrollment predicted viral set point 24 weeks later in the independent Malawian cohort with an accuracy of 87.5%. As expected, the predictive accuracy of the networks inferred at later time points was even greater, exceeding 90% after week 4. The composition of the inferred networks was largely conserved between time points. The 12 genes comprising this dynamic signature of viral set point implicated the involvement of two major canonical pathways: interferon signaling (p<0.0003) and membrane fraction (p<0.02). A silico knockout study showed that HLA-DRB1 and C4BPA may contribute to restricting HIV-1 replication. CONCLUSIONS Longitudinal gene expression profiling of peripheral blood mononuclear cells from patients with acute HIV-1 infection can be used to create transcriptional network models to early predict viral set point with a high degree of accuracy.
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Affiliation(s)
- Hsun-Hsien Chang
- Children's Hospital Informatics Program, Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, Massachusetts, USA.
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Interplay between HIV-1 and Host Genetic Variation: A Snapshot into Its Impact on AIDS and Therapy Response. Adv Virol 2012; 2012:508967. [PMID: 22666249 PMCID: PMC3361994 DOI: 10.1155/2012/508967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 02/26/2012] [Accepted: 03/11/2012] [Indexed: 11/18/2022] Open
Abstract
As of February 2012, 50 circulating recombinant forms (CRFs) have been reported for HIV-1 while one CRF for HIV-2. Also according to HIV sequence compendium 2011, the HIV sequence database is replete with 414,398 sequences. The fact that there are CRFs, which are an amalgamation of sequences derived from six or more subtypes (CRF27_cpx (cpx refers to complex) is a mosaic with sequences from 6 different subtypes besides an unclassified fragment), serves as a testimony to the continual divergent evolution of the virus with its approximate 1% per year rate of evolution, and this phenomena per se poses tremendous challenge for vaccine development against HIV/AIDS, a devastating disease that has killed 1.8 million patients in 2010. Here, we explore the interaction between HIV-1 and host genetic variation in the context of HIV/AIDS and antiretroviral therapy response.
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31
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Wright JK, Brumme ZL, Julg B, van der Stok M, Mncube Z, Gao X, Carlson JM, Goulder PJR, Walker BD, Brockman MA, Ndung'u T. Lack of association between HLA class II alleles and in vitro replication capacities of recombinant viruses encoding HIV-1 subtype C Gag-protease from chronically infected individuals. J Virol 2012; 86:1273-6. [PMID: 22090116 PMCID: PMC3255856 DOI: 10.1128/jvi.06533-11] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Accepted: 11/03/2011] [Indexed: 01/08/2023] Open
Abstract
It is unknown whether favorable HLA class II alleles may attenuate HIV-1 through selection pressure in a manner similar to that of protective HLA class I alleles. We investigated the relationship between HLA class II alleles and in vitro replication capacities of recombinant viruses encoding HIV-1 subtype C Gag-protease from chronically infected individuals. No associations were found between individual alleles and lower replication capacity, suggesting no significant HIV-1 attenuation by HLA class II-restricted Gag-specific CD4(+) T cell immune pressure.
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Affiliation(s)
- Jaclyn K. Wright
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Zabrina L. Brumme
- Simon Fraser University, Burnaby, Canada
- BC Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Boris Julg
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Boston, Massachusetts, USA
| | - Mary van der Stok
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Zenele Mncube
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Xiaojiang Gao
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, NCI-Frederick, Frederick, Massachusetts, USA
| | | | - Philip J. R. Goulder
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Boston, Massachusetts, USA
- Department of Paediatrics, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Bruce D. Walker
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Mark A. Brockman
- Simon Fraser University, Burnaby, Canada
- BC Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Boston, Massachusetts, USA
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Eberle J, Gürtler LG. HIV Types, Groups, Subtypes and Recombinant Forms: Errors in Replication, Selection Pressure and Quasispecies. Intervirology 2012; 55:79-83. [DOI: 10.1159/000331993] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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Thèze J, Chakrabarti LA, Vingert B, Porichis F, Kaufmann DE. HIV controllers: a multifactorial phenotype of spontaneous viral suppression. Clin Immunol 2011; 141:15-30. [PMID: 21865089 DOI: 10.1016/j.clim.2011.07.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Revised: 07/23/2011] [Accepted: 07/26/2011] [Indexed: 02/02/2023]
Abstract
A small minority of HIV-infected individuals, known as HIV controllers, is able to exert long-term control over HIV replication in the absence of treatment. Increasing evidence suggests that the adaptive immune system plays a critical role in this control but also that a combination of several host and/or viral factors, rather than a single cause, leads to this rare phenotype. Here, we review recent advances in the study of these remarkable individuals. We summarize the epidemiology and clinical characteristics of HIV controllers, and subsequently describe contributing roles of host genetic factors, innate and adaptive immune responses, and viral factors to this phenotype. We emphasize distinctive characteristics of HIV-specific CD4 T cell responses and of CD4 T cell subpopulations that are frequently found in HIV controllers. We discuss major controversies in the field and the relevance of the study of HIV controllers for the development of novel therapeutic strategies and vaccines.
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Affiliation(s)
- Jacques Thèze
- Unité d'Immunogénétique Cellulaire, Institut Pasteur, 75015, Paris, France.
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