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Rutten L, Swart M, Koornneef A, Bouchier P, Blokland S, Sadi A, Juraszek J, Vijayan A, Schmit-Tillemans S, Verspuij J, Choi Y, Daal CE, Perkasa A, Torres Morales S, Myeni SK, Kikkert M, Tolboom J, van Manen D, Kuipers H, Schuitemaker H, Zahn R, Langedijk JPM. Impact of SARS-CoV-2 spike stability and RBD exposure on antigenicity and immunogenicity. Sci Rep 2024; 14:5735. [PMID: 38459086 PMCID: PMC10923862 DOI: 10.1038/s41598-024-56293-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/05/2024] [Indexed: 03/10/2024] Open
Abstract
The spike protein (S) of SARS-CoV-2 induces neutralizing antibodies and is the key component of current COVID-19 vaccines. The most efficacious COVID-19 vaccines are genetically-encoded spikes with a double proline substitution in the hinge region to stabilize S in the prefusion conformation (S-2P). A subunit vaccine can be a valuable addition to mRNA and viral vector-based vaccines but requires high stability of spike. In addition, further stabilization of the prefusion conformation of spike might improve immunogenicity. To test this, five spike proteins were designed and characterized, ranging from low to high stability. The immunogenicity of these proteins was assessed in mice, demonstrating that a spike (S-closed-2) with a high melting temperature, which still allowed ACE2 binding, induced the highest neutralization titers against homologous and heterologous strains (up to 16-fold higher than the least stabilized spike). In contrast, the most stable spike variant (S-locked), in which the receptor binding domains (RBDs) were locked in a closed conformation and thus not able to breathe, induced relatively low neutralizing antibody titers against heterologous strains. These data demonstrate that S protein stabilization with RBDs exposing highly conserved epitopes may be needed to increase the immunogenicity of spike proteins for future COVID-19 vaccines.
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Affiliation(s)
- Lucy Rutten
- Janssen Vaccines and Prevention B.V., Archimedesweg 4-6, Leiden, The Netherlands
| | - Maarten Swart
- Janssen Vaccines and Prevention B.V., Archimedesweg 4-6, Leiden, The Netherlands
| | - Annemart Koornneef
- Janssen Vaccines and Prevention B.V., Archimedesweg 4-6, Leiden, The Netherlands
| | - Pascale Bouchier
- Janssen Vaccines and Prevention B.V., Archimedesweg 4-6, Leiden, The Netherlands
| | - Sven Blokland
- Janssen Vaccines and Prevention B.V., Archimedesweg 4-6, Leiden, The Netherlands
| | - Ava Sadi
- Janssen Vaccines and Prevention B.V., Archimedesweg 4-6, Leiden, The Netherlands
| | - Jarek Juraszek
- Janssen Vaccines and Prevention B.V., Archimedesweg 4-6, Leiden, The Netherlands
| | - Aneesh Vijayan
- Janssen Vaccines and Prevention B.V., Archimedesweg 4-6, Leiden, The Netherlands
| | | | - Johan Verspuij
- Janssen Vaccines and Prevention B.V., Archimedesweg 4-6, Leiden, The Netherlands
| | - Ying Choi
- Janssen Vaccines and Prevention B.V., Archimedesweg 4-6, Leiden, The Netherlands
| | - Chenandly E Daal
- Janssen Vaccines and Prevention B.V., Archimedesweg 4-6, Leiden, The Netherlands
| | - Aditya Perkasa
- Janssen Vaccines and Prevention B.V., Archimedesweg 4-6, Leiden, The Netherlands
| | - Shessy Torres Morales
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Sebenzile K Myeni
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Marjolein Kikkert
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jeroen Tolboom
- Janssen Vaccines and Prevention B.V., Archimedesweg 4-6, Leiden, The Netherlands
| | - Daniëlle van Manen
- Janssen Vaccines and Prevention B.V., Archimedesweg 4-6, Leiden, The Netherlands
| | - Harmjan Kuipers
- Janssen Vaccines and Prevention B.V., Archimedesweg 4-6, Leiden, The Netherlands
| | - Hanneke Schuitemaker
- Janssen Vaccines and Prevention B.V., Archimedesweg 4-6, Leiden, The Netherlands
| | - Roland Zahn
- Janssen Vaccines and Prevention B.V., Archimedesweg 4-6, Leiden, The Netherlands
| | - Johannes P M Langedijk
- Janssen Vaccines and Prevention B.V., Archimedesweg 4-6, Leiden, The Netherlands.
- ForgeBio, Amsterdam, The Netherlands.
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Barouch DH, Tomaka FL, Wegmann F, Stieh DJ, Alter G, Robb ML, Michael NL, Peter L, Nkolola JP, Borducchi EN, Chandrashekar A, Jetton D, Stephenson KE, Li W, Korber B, Tomaras GD, Montefiori DC, Gray G, Frahm N, McElrath MJ, Baden L, Johnson J, Hutter J, Swann E, Karita E, Kibuuka H, Mpendo J, Garrett N, Mngadi K, Chinyenze K, Priddy F, Lazarus E, Laher F, Nitayapan S, Pitisuttithum P, Bart S, Campbell T, Feldman R, Lucksinger G, Borremans C, Callewaert K, Roten R, Sadoff J, Scheppler L, Weijtens M, Feddes-de Boer K, van Manen D, Vreugdenhil J, Zahn R, Lavreys L, Nijs S, Tolboom J, Hendriks J, Euler Z, Pau MG, Schuitemaker H. Evaluation of a mosaic HIV-1 vaccine in a multicentre, randomised, double-blind, placebo-controlled, phase 1/2a clinical trial (APPROACH) and in rhesus monkeys (NHP 13-19). Lancet 2018; 392:232-243. [PMID: 30047376 PMCID: PMC6192527 DOI: 10.1016/s0140-6736(18)31364-3] [Citation(s) in RCA: 225] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 06/07/2018] [Accepted: 06/08/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND More than 1·8 million new cases of HIV-1 infection were diagnosed worldwide in 2016. No licensed prophylactic HIV-1 vaccine exists. A major limitation to date has been the lack of direct comparability between clinical trials and preclinical studies. We aimed to evaluate mosaic adenovirus serotype 26 (Ad26)-based HIV-1 vaccine candidates in parallel studies in humans and rhesus monkeys to define the optimal vaccine regimen to advance into clinical efficacy trials. METHODS We conducted a multicentre, randomised, double-blind, placebo-controlled phase 1/2a trial (APPROACH). Participants were recruited from 12 clinics in east Africa, South Africa, Thailand, and the USA. We included healthy, HIV-1-uninfected participants (aged 18-50 years) who were considered at low risk for HIV-1 infection. We randomly assigned participants to one of eight study groups, stratified by region. Participants and investigators were blinded to the treatment allocation throughout the study. We primed participants at weeks 0 and 12 with Ad26.Mos.HIV (5 × 1010 viral particles per 0·5 mL) expressing mosaic HIV-1 envelope (Env)/Gag/Pol antigens and gave boosters at weeks 24 and 48 with Ad26.Mos.HIV or modified vaccinia Ankara (MVA; 108 plaque-forming units per 0·5 mL) vectors with or without high-dose (250 μg) or low-dose (50 μg) aluminium adjuvanted clade C Env gp140 protein. Those in the control group received 0·9% saline. All study interventions were administered intramuscularly. Primary endpoints were safety and tolerability of the vaccine regimens and Env-specific binding antibody responses at week 28. Safety and immunogenicity were also assessed at week 52. All participants who received at least one vaccine dose or placebo were included in the safety analysis; immunogenicity was analysed using the per-protocol population. We also did a parallel study in rhesus monkeys (NHP 13-19) to assess the immunogenicity and protective efficacy of these vaccine regimens against a series of six repetitive, heterologous, intrarectal challenges with a rhesus peripheral blood mononuclear cell-derived challenge stock of simian-human immunodeficiency virus (SHIV-SF162P3). The APPROACH trial is registered with ClinicalTrials.gov, number NCT02315703. FINDINGS Between Feb 24, 2015, and Oct 16, 2015, we randomly assigned 393 participants to receive at least one dose of study vaccine or placebo in the APPROACH trial. All vaccine regimens demonstrated favourable safety and tolerability. The most commonly reported solicited local adverse event was mild-to-moderate pain at the injection site (varying from 69% to 88% between the different active groups vs 49% in the placebo group). Five (1%) of 393 participants reported at least one grade 3 adverse event considered related to the vaccines: abdominal pain and diarrhoea (in the same participant), increased aspartate aminotransferase, postural dizziness, back pain, and malaise. The mosaic Ad26/Ad26 plus high-dose gp140 boost vaccine was the most immunogenic in humans; it elicited Env-specific binding antibody responses (100%) and antibody-dependent cellular phagocytosis responses (80%) at week 52, and T-cell responses at week 50 (83%). We also randomly assigned 72 rhesus monkeys to receive one of five different vaccine regimens or placebo in the NHP 13-19 study. Ad26/Ad26 plus gp140 boost induced similar magnitude, durability, and phenotype of immune responses in rhesus monkeys as compared with humans and afforded 67% protection against acquisition of SHIV-SF162P3 infection (two-sided Fisher's exact test p=0·007). Env-specific ELISA and enzyme-linked immunospot assay responses were the principal immune correlates of protection against SHIV challenge in monkeys. INTERPRETATION The mosaic Ad26/Ad26 plus gp140 HIV-1 vaccine induced comparable and robust immune responses in humans and rhesus monkeys, and it provided significant protection against repetitive heterologous SHIV challenges in rhesus monkeys. This vaccine concept is currently being evaluated in a phase 2b clinical efficacy study in sub-Saharan Africa (NCT03060629). FUNDING Janssen Vaccines & Prevention BV, National Institutes of Health, Ragon Institute of MGH, MIT and Harvard, Henry M Jackson Foundation for the Advancement of Military Medicine, US Department of Defense, and International AIDS Vaccine Initiative.
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Affiliation(s)
- Dan H Barouch
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
| | | | - Frank Wegmann
- Janssen Vaccines & Prevention BV, Leiden, Netherlands
| | | | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Merlin L Robb
- Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Nelson L Michael
- Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Lauren Peter
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Joseph P Nkolola
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Erica N Borducchi
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | | | - David Jetton
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Kathryn E Stephenson
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Wenjun Li
- University of Massachusetts Medical School, Worcester, MA, USA
| | - Bette Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Georgia D Tomaras
- Department of Surgery and Duke Human Vaccine Institute, Duke University, Durham, NC, USA
| | - David C Montefiori
- Department of Surgery and Duke Human Vaccine Institute, Duke University, Durham, NC, USA
| | - Glenda Gray
- Perinatal HIV Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicole Frahm
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Lindsey Baden
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jennifer Johnson
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Julia Hutter
- Vaccine Clinical Research Branch, Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Edith Swann
- Vaccine Clinical Research Branch, Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Etienne Karita
- Project San Francisco, Rwanda-Zambia HIV Research Group, Kigali, Rwanda
| | - Hannah Kibuuka
- Makerere University Walter Reed Project, Kampala, Uganda
| | - Juliet Mpendo
- Uganda Virus Research Institute, International AIDS Vaccine Initiative HIV Vaccine Program, Entebbe, Uganda
| | - Nigel Garrett
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Kathy Mngadi
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | | | - Frances Priddy
- International AIDS Vaccine Initiative, New York City, NY, USA
| | - Erica Lazarus
- Department of Surgery and Duke Human Vaccine Institute, Duke University, Durham, NC, USA
| | - Fatima Laher
- Department of Surgery and Duke Human Vaccine Institute, Duke University, Durham, NC, USA
| | - Sorachai Nitayapan
- Royal Thai Army, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Punnee Pitisuttithum
- The Vaccine Trial Center, Faculty of Tropical Medicine, Mahidol University, Bangkok
| | | | | | | | | | | | | | | | - Jerald Sadoff
- Janssen Vaccines & Prevention BV, Leiden, Netherlands
| | - Lorenz Scheppler
- Janssen Vaccines & Prevention BV, Leiden, Netherlands; Janssen Infectious Diseases BV, Beerse, Belgium
| | - Mo Weijtens
- Janssen Vaccines & Prevention BV, Leiden, Netherlands
| | | | | | | | - Roland Zahn
- Janssen Vaccines & Prevention BV, Leiden, Netherlands
| | | | - Steven Nijs
- Janssen Infectious Diseases BV, Beerse, Belgium
| | | | | | - Zelda Euler
- Janssen Vaccines & Prevention BV, Leiden, Netherlands
| | - Maria G Pau
- Janssen Vaccines & Prevention BV, Leiden, Netherlands
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Spadoni JL, Rucart P, Le Clerc S, van Manen D, Coulonges C, Ulveling D, Laville V, Labib T, Taing L, Delaneau O, Montes M, Schuitemaker H, Noirel J, Zagury JF. Identification of Genes Whose Expression Profile Is Associated with Non-Progression towards AIDS Using eQTLs. PLoS One 2015; 10:e0136989. [PMID: 26367535 PMCID: PMC4569262 DOI: 10.1371/journal.pone.0136989] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 08/12/2015] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Many genome-wide association studies have been performed on progression towards the acquired immune deficiency syndrome (AIDS) and they mainly identified associations within the HLA loci. In this study, we demonstrate that the integration of biological information, namely gene expression data, can enhance the sensitivity of genetic studies to unravel new genetic associations relevant to AIDS. METHODS We collated the biological information compiled from three databases of expression quantitative trait loci (eQTLs) involved in cells of the immune system. We derived a list of single nucleotide polymorphisms (SNPs) that are functional in that they correlate with differential expression of genes in at least two of the databases. We tested the association of those SNPs with AIDS progression in two cohorts, GRIV and ACS. Tests on permuted phenotypes of the GRIV and ACS cohorts or on randomised sets of equivalent SNPs allowed us to assess the statistical robustness of this method and to estimate the true positive rate. RESULTS Eight genes were identified with high confidence (p = 0.001, rate of true positives 75%). Some of those genes had previously been linked with HIV infection. Notably, ENTPD4 belongs to the same family as CD39, whose expression has already been associated with AIDS progression; while DNAJB12 is part of the HSP90 pathway, which is involved in the control of HIV latency. Our study also drew our attention to lesser-known functions such as mitochondrial ribosomal proteins and a zinc finger protein, ZFP57, which could be central to the effectiveness of HIV infection. Interestingly, for six out of those eight genes, down-regulation is associated with non-progression, which makes them appealing targets to develop drugs against HIV.
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Affiliation(s)
- Jean-Louis Spadoni
- Chaire de Bioinformatique; Laboratoire Génomique, Bioinformatique, et Applications (EA 4627), Conservatoire National des Arts et Métiers, Paris, France
| | - Pierre Rucart
- Chaire de Bioinformatique; Laboratoire Génomique, Bioinformatique, et Applications (EA 4627), Conservatoire National des Arts et Métiers, Paris, France
| | - Sigrid Le Clerc
- Chaire de Bioinformatique; Laboratoire Génomique, Bioinformatique, et Applications (EA 4627), Conservatoire National des Arts et Métiers, Paris, France
| | - Daniëlle van Manen
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
- Crucell Holland B.V., Archimedesweg 4–6, 2333 CN, Leiden, The Netherlands
| | - Cédric Coulonges
- Chaire de Bioinformatique; Laboratoire Génomique, Bioinformatique, et Applications (EA 4627), Conservatoire National des Arts et Métiers, Paris, France
| | - Damien Ulveling
- Chaire de Bioinformatique; Laboratoire Génomique, Bioinformatique, et Applications (EA 4627), Conservatoire National des Arts et Métiers, Paris, France
| | - Vincent Laville
- Chaire de Bioinformatique; Laboratoire Génomique, Bioinformatique, et Applications (EA 4627), Conservatoire National des Arts et Métiers, Paris, France
| | - Taoufik Labib
- Chaire de Bioinformatique; Laboratoire Génomique, Bioinformatique, et Applications (EA 4627), Conservatoire National des Arts et Métiers, Paris, France
| | - Lieng Taing
- Chaire de Bioinformatique; Laboratoire Génomique, Bioinformatique, et Applications (EA 4627), Conservatoire National des Arts et Métiers, Paris, France
| | - Olivier Delaneau
- Département de Génétique et Développement, Faculté de Médecine, Université de Genève, Switzerland
| | - Matthieu Montes
- Chaire de Bioinformatique; Laboratoire Génomique, Bioinformatique, et Applications (EA 4627), Conservatoire National des Arts et Métiers, Paris, France
| | - Hanneke Schuitemaker
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
- Crucell Holland B.V., Archimedesweg 4–6, 2333 CN, Leiden, The Netherlands
| | - Josselin Noirel
- Chaire de Bioinformatique; Laboratoire Génomique, Bioinformatique, et Applications (EA 4627), Conservatoire National des Arts et Métiers, Paris, France
| | - Jean-François Zagury
- Chaire de Bioinformatique; Laboratoire Génomique, Bioinformatique, et Applications (EA 4627), Conservatoire National des Arts et Métiers, Paris, France
- * E-mail:
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McLaren PJ, Coulonges C, Ripke S, van den Berg L, Buchbinder S, Carrington M, Cossarizza A, Dalmau J, Deeks SG, Delaneau O, De Luca A, Goedert JJ, Haas D, Herbeck JT, Kathiresan S, Kirk GD, Lambotte O, Luo M, Mallal S, van Manen D, Martinez-Picado J, Meyer L, Miro JM, Mullins JI, Obel N, O'Brien SJ, Pereyra F, Plummer FA, Poli G, Qi Y, Rucart P, Sandhu MS, Shea PR, Schuitemaker H, Theodorou I, Vannberg F, Veldink J, Walker BD, Weintrob A, Winkler CA, Wolinsky S, Telenti A, Goldstein DB, de Bakker PIW, Zagury JF, Fellay J. Association study of common genetic variants and HIV-1 acquisition in 6,300 infected cases and 7,200 controls. PLoS Pathog 2013; 9:e1003515. [PMID: 23935489 PMCID: PMC3723635 DOI: 10.1371/journal.ppat.1003515] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 06/07/2013] [Indexed: 11/18/2022] Open
Abstract
Multiple genome-wide association studies (GWAS) have been performed in HIV-1 infected individuals, identifying common genetic influences on viral control and disease course. Similarly, common genetic correlates of acquisition of HIV-1 after exposure have been interrogated using GWAS, although in generally small samples. Under the auspices of the International Collaboration for the Genomics of HIV, we have combined the genome-wide single nucleotide polymorphism (SNP) data collected by 25 cohorts, studies, or institutions on HIV-1 infected individuals and compared them to carefully matched population-level data sets (a list of all collaborators appears in Note S1 in Text S1). After imputation using the 1,000 Genomes Project reference panel, we tested approximately 8 million common DNA variants (SNPs and indels) for association with HIV-1 acquisition in 6,334 infected patients and 7,247 population samples of European ancestry. Initial association testing identified the SNP rs4418214, the C allele of which is known to tag the HLA-B*57:01 and B*27:05 alleles, as genome-wide significant (p = 3.6×10−11). However, restricting analysis to individuals with a known date of seroconversion suggested that this association was due to the frailty bias in studies of lethal diseases. Further analyses including testing recessive genetic models, testing for bulk effects of non-genome-wide significant variants, stratifying by sexual or parenteral transmission risk and testing previously reported associations showed no evidence for genetic influence on HIV-1 acquisition (with the exception of CCR5Δ32 homozygosity). Thus, these data suggest that genetic influences on HIV acquisition are either rare or have smaller effects than can be detected by this sample size. Comparing the frequency differences between common DNA variants in disease-affected cases and in unaffected controls has been successful in uncovering the genetic component of multiple diseases. This approach is most effective when large samples of cases and controls are available. Here we combine information from multiple studies of HIV infected patients, including more than 6,300 HIV+ individuals, with data from 7,200 general population samples of European ancestry to test nearly 8 million common DNA variants for an impact on HIV acquisition. With this large sample we did not observe any single common genetic variant that significantly associated with HIV acquisition. We further tested 22 variants previously identified by smaller studies as influencing HIV acquisition. With the exception of a deletion polymorphism in the CCR5 gene (CCR5Δ32) we found no convincing evidence to support these previous associations. Taken together these data suggest that genetic influences on HIV acquisition are either rare or have smaller effects than can be detected by this sample size.
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Affiliation(s)
- Paul J. McLaren
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Cédric Coulonges
- Laboratoire Génomique, Bioinformatique, et Applications, EA4627, Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
- ANRS Genomic Group (French Agency for Research on AIDS and Hepatitis), Paris, France
| | - Stephan Ripke
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Leonard van den Berg
- Department of Neurology, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Susan Buchbinder
- Bridge HIV, San Francisco Department of Public Health, San Francisco, California, United States of America
| | - Mary Carrington
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America
| | - Andrea Cossarizza
- Department of Surgery, Medicine, Dentistry and Morphological Sciences University of Modena and Reggio Emilia School of Medicine, Modena, Italy
| | - Judith Dalmau
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Steven G. Deeks
- Department of Medicine, University of California, San Francisco, California, United States of America
| | - Olivier Delaneau
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Andrea De Luca
- University Division of Infectious Diseases, Siena University Hospital, Siena, Italy
- Institute of Clinical infectious Diseases, Università Cattolica del Sacro Cuore, Roma, Italy
| | - James J. Goedert
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, United States of America
| | - David Haas
- Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Joshua T. Herbeck
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Sekar Kathiresan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Cardiovascular Research Center and Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Gregory D. Kirk
- Department of Epidemiology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Olivier Lambotte
- INSERM U1012, Bicêtre, France
- University Paris-Sud, Bicêtre, France
- AP-HP, Department of Internal Medicine and Infectious Diseases, Bicêtre Hospital, Bicêtre, France
| | - Ma Luo
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - Simon Mallal
- Institute for Immunology & Infectious Diseases, Murdoch University and Pathwest, Perth, Australia
| | - Daniëlle van Manen
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Javier Martinez-Picado
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Laurence Meyer
- ANRS Genomic Group (French Agency for Research on AIDS and Hepatitis), Paris, France
- Inserm, CESP U1018, University Paris-Sud, UMRS 1018, Faculté de Médecine Paris-Sud; AP-HP, Hopital Bicêtre, Epidemiology and Public Health Service, Le Kremlin Bicêtre, France
| | - José M. Miro
- Infectious Diseases Service. Hospital Clinic – IDIBAPS, University of Barcelona, Barcelona, Spain
| | - James I. Mullins
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Niels Obel
- Department of Infectious Diseases, The National University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Stephen J. O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
| | - Florencia Pereyra
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America
- Division of Infectious Disease, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Francis A. Plummer
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - Guido Poli
- Division of Immunology, Transplantation and Infectious Diseases, Vita-Salute San Raffaele University, School of Medicine & San Raffaele Scientific Institute, Milan, Italy
| | - Ying Qi
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Pierre Rucart
- Laboratoire Génomique, Bioinformatique, et Applications, EA4627, Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
- ANRS Genomic Group (French Agency for Research on AIDS and Hepatitis), Paris, France
| | - Manj S. Sandhu
- Genetic Epidemiology Group, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Non-Communicable Disease Research Group, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Patrick R. Shea
- Center for Human Genome Variation, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Hanneke Schuitemaker
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Ioannis Theodorou
- ANRS Genomic Group (French Agency for Research on AIDS and Hepatitis), Paris, France
- INSERM UMRS 945, Paris, France
| | - Fredrik Vannberg
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Jan Veldink
- Department of Neurology, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bruce D. Walker
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Amy Weintrob
- Infectious Disease Clinical Research Program, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - Cheryl A. Winkler
- Basic Research Laboratory, Molecular Genetic Epidemiology Section, Center for Cancer Research, NCI, SAIC-Frederick, Inc., Frederick National Laboratory, Frederick, Maryland, United States of America
| | - Steven Wolinsky
- Division of Infectious Diseases, The Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Amalio Telenti
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | - David B. Goldstein
- Center for Human Genome Variation, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Paul I. W. de Bakker
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Division of Genetics Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Epidemiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jean-François Zagury
- Laboratoire Génomique, Bioinformatique, et Applications, EA4627, Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
- ANRS Genomic Group (French Agency for Research on AIDS and Hepatitis), Paris, France
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
- * E-mail:
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Euler Z, van Gils MJ, Boeser-Nunnink BD, Schuitemaker H, van Manen D. Genome-wide association study on the development of cross-reactive neutralizing antibodies in HIV-1 infected individuals. PLoS One 2013; 8:e54684. [PMID: 23372753 PMCID: PMC3553002 DOI: 10.1371/journal.pone.0054684] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Accepted: 12/17/2012] [Indexed: 11/19/2022] Open
Abstract
Broadly neutralizing antibodies may protect against HIV-1 acquisition. In natural infection, only 10–30% of patients have cross-reactive neutralizing humoral immunity which may relate to viral and or host factors. To explore the role of host genetic markers in the formation of cross-reactive neutralizing activity (CrNA) in HIV-1 infected individuals, we performed a genome-wide association study (GWAS), in participants of the Amsterdam Cohort Studies with known CrNA in their sera. Single-nucleotide polymorphisms (SNPs) with the strongest P-values are located in the major histocompatibility complex (MHC) region, close to MICA (P = 7.68×10−7), HLA-B (P = 6.96×10−6) and in the coding region of HCP5 (P = 1.34×10−5). However, none of the signals reached genome-wide significance. Our findings underline the potential involvement of genes close or within the MHC region with the development of CrNA.
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Affiliation(s)
- Zelda Euler
- Department Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Marit J. van Gils
- Department Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Brigitte D. Boeser-Nunnink
- Department Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Hanneke Schuitemaker
- Department Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
- * E-mail:
| | - Daniëlle van Manen
- Department Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
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van Manen D, van 't Wout AB, Schuitemaker H. Genome-wide association studies on HIV susceptibility, pathogenesis and pharmacogenomics. Retrovirology 2012; 9:70. [PMID: 22920050 PMCID: PMC3468375 DOI: 10.1186/1742-4690-9-70] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Accepted: 07/31/2012] [Indexed: 11/22/2022] Open
Abstract
Susceptibility to HIV-1 and the clinical course after infection show a substantial heterogeneity between individuals. Part of this variability can be attributed to host genetic variation. Initial candidate gene studies have revealed interesting host factors that influence HIV infection, replication and pathogenesis. Recently, genome-wide association studies (GWAS) were utilized for unbiased searches at a genome-wide level to discover novel genetic factors and pathways involved in HIV-1 infection. This review gives an overview of findings from the GWAS performed on HIV infection, within different cohorts, with variable patient and phenotype selection. Furthermore, novel techniques and strategies in research that might contribute to the complete understanding of virus-host interactions and its role on the pathogenesis of HIV infection are discussed.
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Affiliation(s)
- Daniëlle van Manen
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, Center for Infectious Diseases and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
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7
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Limou S, Delaneau O, van Manen D, An P, Sezgin E, Le Clerc S, Coulonges C, Troyer JL, Veldink JH, van den Berg LH, Spadoni JL, Taing L, Labib T, Montes M, Delfraissy JF, Schachter F, O'Brien SJ, Buchbinder S, van Natta ML, Jabs DA, Froguel P, Schuitemaker H, Winkler CA, Zagury JF. Multicohort genomewide association study reveals a new signal of protection against HIV-1 acquisition. J Infect Dis 2012; 205:1155-62. [PMID: 22362864 DOI: 10.1093/infdis/jis028] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND To date, only mutations in CCR5 have been shown to confer resistance to human immunodeficiency virus type 1 (HIV-1) infection, and these explain only a small fraction of the observed variability in HIV susceptibility. METHODS We performed a meta-analysis between 2 independent European genomewide association studies, each comparing HIV-1 seropositive cases with normal population controls known to be HIV uninfected, to identify single-nucleotide polymorphisms (SNPs) associated with the HIV-1 acquisition phenotype. SNPs exhibiting P < 10(-5) in this first stage underwent second-stage analysis in 2 independent US cohorts of European descent. RESULTS After the first stage, a single highly significant association was revealed for the chromosome 8 rs6996198 with HIV-1 acquisition and was replicated in both second-stage cohorts. Across the 4 groups, the rs6996198-T allele was consistently associated with a significant reduced risk of HIV-1 infection, and the global meta-analysis reached genomewide significance: P(combined) = 7.76 × 10(-8). CONCLUSIONS We provide strong evidence of association for a common variant with HIV-1 acquisition in populations of European ancestry. This protective signal against HIV-1 infection is the first identified outside the CCR5 nexus. First clues point to a potential functional role for a nearby candidate gene, CYP7B1, but this locus warrants further investigation.
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Affiliation(s)
- Sophie Limou
- Laboratoire Génomique, Bioinformatique, et Applications, EA4627, Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
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8
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Bol SM, Booiman T, van Manen D, Bunnik EM, van Sighem AI, Sieberer M, Boeser-Nunnink B, de Wolf F, Schuitemaker H, Portegies P, Kootstra NA, van 't Wout AB. Single nucleotide polymorphism in gene encoding transcription factor Prep1 is associated with HIV-1-associated dementia. PLoS One 2012; 7:e30990. [PMID: 22347417 PMCID: PMC3274517 DOI: 10.1371/journal.pone.0030990] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Accepted: 12/29/2011] [Indexed: 11/18/2022] Open
Abstract
Background Infection with HIV-1 may result in severe cognitive and motor impairment, referred to as HIV-1-associated dementia (HAD). While its prevalence has dropped significantly in the era of combination antiretroviral therapy, milder neurocognitive disorders persist with a high prevalence. To identify additional therapeutic targets for treating HIV-associated neurocognitive disorders, several candidate gene polymorphisms have been evaluated, but few have been replicated across multiple studies. Methods We here tested 7 candidate gene polymorphisms for association with HAD in a case-control study consisting of 86 HAD cases and 246 non-HAD AIDS patients as controls. Since infected monocytes and macrophages are thought to play an important role in the infection of the brain, 5 recently identified single nucleotide polymorphisms (SNPs) affecting HIV-1 replication in macrophages in vitro were also tested. Results The CCR5 wt/Δ32 genotype was only associated with HAD in individuals who developed AIDS prior to 1991, in agreement with the observed fading effect of this genotype on viral load set point. A significant difference in genotype distribution among all cases and controls irrespective of year of AIDS diagnosis was found only for a SNP in candidate gene PREP1 (p = 1.2×10−5). Prep1 has recently been identified as a transcription factor preferentially binding the −2,518 G allele in the promoter of the gene encoding MCP-1, a protein with a well established role in the etiology of HAD. Conclusion These results support previous findings suggesting an important role for MCP-1 in the onset of HIV-1-associated neurocognitive disorders.
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Affiliation(s)
- Sebastiaan M. Bol
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Thijs Booiman
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Daniëlle van Manen
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Evelien M. Bunnik
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Ard I. van Sighem
- HIV Monitoring Foundation, Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Margit Sieberer
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Brigitte Boeser-Nunnink
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Frank de Wolf
- HIV Monitoring Foundation, Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
- Department of Infectious Disease Epidemiology, Imperial College, London, United Kingdom
| | - Hanneke Schuitemaker
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Peter Portegies
- Department of Neurology at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
- Department of Neurology at the OLVG Hospital, Amsterdam, The Netherlands
| | - Neeltje A. Kootstra
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Angélique B. van 't Wout
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
- * E-mail:
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9
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van Manen D, Delaneau O, Kootstra NA, Boeser-Nunnink BD, Limou S, Bol SM, Burger JA, Zwinderman AH, Moerland PD, van 't Slot R, Zagury JF, van 't Wout AB, Schuitemaker H. Genome-wide association scan in HIV-1-infected individuals identifying variants influencing disease course. PLoS One 2011; 6:e22208. [PMID: 21811574 PMCID: PMC3141012 DOI: 10.1371/journal.pone.0022208] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 06/17/2011] [Indexed: 01/20/2023] Open
Abstract
Background AIDS develops typically after 7–11 years of untreated HIV-1 infection, with extremes of very rapid disease progression (<2 years) and long-term non-progression (>15 years). To reveal additional host genetic factors that may impact on the clinical course of HIV-1 infection, we designed a genome-wide association study (GWAS) in 404 participants of the Amsterdam Cohort Studies on HIV-1 infection and AIDS. Methods The association of SNP genotypes with the clinical course of HIV-1 infection was tested in Cox regression survival analyses using AIDS-diagnosis and AIDS-related death as endpoints. Results Multiple, not previously identified SNPs, were identified to be strongly associated with disease progression after HIV-1 infection, albeit not genome-wide significant. However, three independent SNPs in the top ten associations between SNP genotypes and time between seroconversion and AIDS-diagnosis, and one from the top ten associations between SNP genotypes and time between seroconversion and AIDS-related death, had P-values smaller than 0.05 in the French Genomics of Resistance to Immunodeficiency Virus cohort on disease progression. Conclusions Our study emphasizes that the use of different phenotypes in GWAS may be useful to unravel the full spectrum of host genetic factors that may be associated with the clinical course of HIV-1 infection.
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Affiliation(s)
- Daniëlle van Manen
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Olivier Delaneau
- Chaire de Bioinformatique, Conservatoire National des Arts et Métiers and ANRS Genomic Group, Paris, France
| | - Neeltje A. Kootstra
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Brigitte D. Boeser-Nunnink
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Sophie Limou
- Chaire de Bioinformatique, Conservatoire National des Arts et Métiers and ANRS Genomic Group, Paris, France
| | - Sebastiaan M. Bol
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Judith A. Burger
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Aeilko H. Zwinderman
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Perry D. Moerland
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
- Netherlands Bioinformatics Center (NBIC), Nijmegen, The Netherlands
| | - Ruben van 't Slot
- Complex Genetics Section, Department of Biomedical Genetics at the University Medical Center, Utrecht, The Netherlands
| | - Jean-François Zagury
- Chaire de Bioinformatique, Conservatoire National des Arts et Métiers and ANRS Genomic Group, Paris, France
| | - Angélique B. van 't Wout
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Hanneke Schuitemaker
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
- * E-mail:
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Troyer JL, Nelson GW, Lautenberger JA, Chinn L, McIntosh C, Johnson RC, Sezgin E, Kessing B, Malasky M, Hendrickson SL, Li G, Pontius J, Tang M, An P, Winkler CA, Limou S, Le Clerc S, Delaneau O, Zagury JF, Schuitemaker H, van Manen D, Bream JH, Gomperts ED, Buchbinder S, Goedert JJ, Kirk GD, O'Brien SJ. Genome-wide association study implicates PARD3B-based AIDS restriction. J Infect Dis 2011; 203:1491-502. [PMID: 21502085 PMCID: PMC3080910 DOI: 10.1093/infdis/jir046] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Accepted: 12/22/2010] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Host genetic variation influences human immunodeficiency virus (HIV) infection and progression to AIDS. Here we used clinically well-characterized subjects from 5 pretreatment HIV/AIDS cohorts for a genome-wide association study to identify gene associations with rate of AIDS progression. METHODS European American HIV seroconverters (n = 755) were interrogated for single-nucleotide polymorphisms (SNPs) (n = 700,022) associated with progression to AIDS 1987 (Cox proportional hazards regression analysis, co-dominant model). RESULTS Association with slower progression was observed for SNPs in the gene PARD3B. One of these, rs11884476, reached genome-wide significance (relative hazard = 0.3; P =3. 370 × 10(-9)) after statistical correction for 700,022 SNPs and contributes 4.52% of the overall variance in AIDS progression in this study. Nine of the top-ranked SNPs define a PARD3B haplotype that also displays significant association with progression to AIDS (hazard ratio, 0.3; P = 3.220 × 10(-8)). One of these SNPs, rs10185378, is a predicted exonic splicing enhancer; significant alteration in the expression profile of PARD3B splicing transcripts was observed in B cell lines with alternate rs10185378 genotypes. This SNP was typed in European cohorts of rapid progressors and was found to be protective for AIDS 1993 definition (odds ratio, 0.43, P = .025). CONCLUSIONS These observations suggest a potential unsuspected pathway of host genetic influence on the dynamics of AIDS progression.
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Affiliation(s)
- Jennifer L Troyer
- Laboratory of Genomic Diversity, SAIC-Frederick, Inc., Frederick, MD 21702, USA.
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11
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Bol SM, Moerland PD, Limou S, van Remmerden Y, Coulonges C, van Manen D, Herbeck JT, Fellay J, Sieberer M, Sietzema JG, van 't Slot R, Martinson J, Zagury JF, Schuitemaker H, van 't Wout AB. Genome-wide association study identifies single nucleotide polymorphism in DYRK1A associated with replication of HIV-1 in monocyte-derived macrophages. PLoS One 2011; 6:e17190. [PMID: 21364930 PMCID: PMC3045405 DOI: 10.1371/journal.pone.0017190] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Accepted: 01/21/2011] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND HIV-1 infected macrophages play an important role in rendering resting T cells permissive for infection, in spreading HIV-1 to T cells, and in the pathogenesis of AIDS dementia. During highly active anti-retroviral treatment (HAART), macrophages keep producing virus because tissue penetration of antiretrovirals is suboptimal and the efficacy of some is reduced. Thus, to cure HIV-1 infection with antiretrovirals we will also need to efficiently inhibit viral replication in macrophages. The majority of the current drugs block the action of viral enzymes, whereas there is an abundance of yet unidentified host factors that could be targeted. We here present results from a genome-wide association study identifying novel genetic polymorphisms that affect in vitro HIV-1 replication in macrophages. METHODOLOGY/PRINCIPAL FINDINGS Monocyte-derived macrophages from 393 blood donors were infected with HIV-1 and viral replication was determined using Gag p24 antigen levels. Genomic DNA from individuals with macrophages that had relatively low (n = 96) or high (n = 96) p24 production was used for SNP genotyping with the Illumina 610 Quad beadchip. A total of 494,656 SNPs that passed quality control were tested for association with HIV-1 replication in macrophages, using linear regression. We found a strong association between in vitro HIV-1 replication in monocyte-derived macrophages and SNP rs12483205 in DYRK1A (p = 2.16 × 10(-5)). While the association was not genome-wide significant (p<1 × 10(-7)), we could replicate this association using monocyte-derived macrophages from an independent group of 31 individuals (p = 0.0034). Combined analysis of the initial and replication cohort increased the strength of the association (p = 4.84 × 10(-6)). In addition, we found this SNP to be associated with HIV-1 disease progression in vivo in two independent cohort studies (p = 0.035 and p = 0.0048). CONCLUSIONS/SIGNIFICANCE These findings suggest that the kinase DYRK1A is involved in the replication of HIV-1, in vitro in macrophages as well as in vivo.
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Affiliation(s)
- Sebastiaan M. Bol
- Landsteiner Laboratory, Sanquin Research, Department of Experimental Immunology, and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Perry D. Moerland
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center of the University of Amsterdam, The Netherlands
- Netherlands Bioinformatics Center (NBIC), Nijmegen, The Netherlands
| | - Sophie Limou
- Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
- Université Paris 12, INSERM U955, Paris, France
| | - Yvonne van Remmerden
- Landsteiner Laboratory, Sanquin Research, Department of Experimental Immunology, and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Cédric Coulonges
- Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
- Université Paris 12, INSERM U955, Paris, France
| | - Daniëlle van Manen
- Landsteiner Laboratory, Sanquin Research, Department of Experimental Immunology, and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Joshua T. Herbeck
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Jacques Fellay
- Center for Human Genome Variation, Duke University, Durham, North Carolina, United States of America
| | - Margit Sieberer
- Landsteiner Laboratory, Sanquin Research, Department of Experimental Immunology, and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Jantine G. Sietzema
- Landsteiner Laboratory, Sanquin Research, Department of Experimental Immunology, and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Ruben van 't Slot
- Complex Genetics Section, Department of Biomedical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jeremy Martinson
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jean-François Zagury
- Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
- Université Paris 12, INSERM U955, Paris, France
| | - Hanneke Schuitemaker
- Landsteiner Laboratory, Sanquin Research, Department of Experimental Immunology, and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Angélique B. van 't Wout
- Landsteiner Laboratory, Sanquin Research, Department of Experimental Immunology, and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
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12
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Limou S, Coulonges C, Herbeck JT, van Manen D, An P, Le Clerc S, Delaneau O, Diop G, Taing L, Montes M, van't Wout AB, Gottlieb GS, Therwath A, Rouzioux C, Delfraissy JF, Lelièvre JD, Lévy Y, Hercberg S, Dina C, Phair J, Donfield S, Goedert JJ, Buchbinder S, Estaquier J, Schächter F, Gut I, Froguel P, Mullins JI, Schuitemaker H, Winkler C, Zagury JF. Multiple-cohort genetic association study reveals CXCR6 as a new chemokine receptor involved in long-term nonprogression to AIDS. J Infect Dis 2010; 202:908-15. [PMID: 20704485 DOI: 10.1086/655782] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND The compilation of previous genomewide association studies of AIDS shows a major polymorphism in the HCP5 gene associated with both control of the viral load and long-term nonprogression (LTNP) to AIDS. METHODS To look for genetic variants that affect LTNP without necessary control of the viral load, we reanalyzed the genomewide data of the unique LTNP Genomics of Resistance to Immunodeficiency Virus (GRIV) cohort by excluding "elite controller" patients, who were controlling the viral load at very low levels (<100 copies/mL). RESULTS The rs2234358 polymorphism in the CXCR6 gene was the strongest signal (P=2.5 x 10(-7); odds ratio, 1.85) obtained for the genomewide association study comparing the 186 GRIV LTNPs who were not elite controllers with 697 uninfected control subjects. This association was replicated in 3 additional independent European studies, reaching genomewide significance of P(combined)=9.7 x 10(-10). This association with LTNP is independent of the CCR2-CCR5 locus and the HCP5 polymorphisms. CONCLUSIONS The statistical significance, the replication, and the magnitude of the association demonstrate that CXCR6 is likely involved in the molecular etiology of AIDS and, in particular, in LTNP, emphasizing the power of extreme-phenotype cohorts. CXCR6 is a chemokine receptor that is known as a minor coreceptor in human immunodeficiency virus type 1 infection but could participate in disease progression through its role as a mediator of inflammation.
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Affiliation(s)
- Sophie Limou
- Chaire de Bioinformatique, Conservatoire National des Arts et Métiers
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van Loo KMJ, van Schijndel JE, van Zweeden M, van Manen D, Trip MD, Petersen DC, Schuitemaker H, Hayes VM, Martens GJM. Correlation between HIV-1 seropositivity and prevalence of a gamma-secretase polymorphism in two distinct ethnic populations. J Med Virol 2009; 81:1847-51. [PMID: 19774691 DOI: 10.1002/jmv.21601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Susceptibility for human immunodeficiency virus type 1 (HIV-1) infection may be influenced by host genetics. Recent findings with a Wistar rat model raised the possibility that the gamma-secretase pathway may be associated with an individual's susceptibility to infection. A functional single-nucleotide polymorphism (SNP) in the gamma-secretase component APH1B (Phe217Leu; rs1047552) was therefore analyzed for association with HIV-1 infection. The SNP showed a tendency for association with HIV-1 infection in a Xhosa indigenous South African Bantu study (P = 0.087), and associated significantly in a Caucasian Dutch study (P = 0.049). Together, the results suggest a role for the gamma-secretase pathway in susceptibility to HIV-1 infection.
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Affiliation(s)
- Karen M J van Loo
- Department of Molecular Animal Physiology, Radboud University Nijmegen, Donders Institute for Brain, Cognition and Behaviour and Nijmegen Center for Molecular Life Sciences, Nijmegen 6525 GA , The Netherlands
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van Manen D, Rits MAN, Beugeling C, van Dort K, Schuitemaker H, Kootstra NA. The effect of Trim5 polymorphisms on the clinical course of HIV-1 infection. PLoS Pathog 2008; 4:e18. [PMID: 18248091 PMCID: PMC2222955 DOI: 10.1371/journal.ppat.0040018] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2007] [Accepted: 12/17/2007] [Indexed: 01/13/2023] Open
Abstract
The antiviral factor tripartite interaction motif 5α (Trim5α) restricts a broad range of retroviruses in a species-specific manner. Although human Trim5α is unable to block HIV-1 infection in human cells, a modest inhibition of HIV-1 replication has been reported. Recently two polymorphisms in the Trim5 gene (H43Y and R136Q) were shown to affect the antiviral activity of Trim5α in vitro. In this study, participants of the Amsterdam Cohort studies were screened for polymorphisms at amino acid residue 43 and 136 of the Trim5 gene, and the potential effects of these polymorphisms on the clinical course of HIV-1 infection were analyzed. In agreement with the reported decreased antiviral activity of Trim5α that contains a Y at amino acid residue 43 in vitro, an accelerated disease progression was observed for individuals who were homozygous for the 43Y genotype as compared to individuals who were heterozygous or homozygous for the 43H genotype. A protective effect of the 136Q genotype was observed but only after the emergence of CXCR4-using (X4) HIV-1 variants and when a viral load of 104.5 copies per ml plasma was used as an endpoint in survival analysis. Interestingly, naive CD4 T cells, which are selectively targeted by X4 HIV-1, revealed a significantly higher expression of Trim5α than memory CD4 T cells. In addition, we observed that the 136Q allele in combination with the −2GG genotype in the 5′UTR was associated with an accelerated disease progression. Thus, polymorphisms in the Trim5 gene may influence the clinical course of HIV-1 infection also underscoring the antiviral effect of Trim5α on HIV-1 in vivo. The clinical course of HIV-1 infection is highly variable between individuals, and host genetic variations may at least account for part of these differences. Recently two single nucleotide polymorphisms in the tripartite interaction motif 5 gene (Trim5) have been reported to affect the antiviral activity of the Trim5α protein. Here we analyzed the effect of these polymorphisms on the clinical course of HIV-1 infection in participants of the Amsterdam Cohort studies. We observed an accelerated disease progression for individuals who were homozygous for the 43Y genotype that has been associated with a decreased antiviral activity of Trim5α in vitro. The 136Q genotype has in vitro been associated with a slightly higher anti-HIV-1 activity. We observed a protective effect of the 136Q genotype only after the emergence of CXCR4-using HIV-1 variants using viral load above 104.5 copies per ml plasma as an endpoint in survival analysis. These results suggest that genetic variations in the Trim5 gene may influence the clinical course of HIV-1 infection and confirm a role of Trim5α on HIV-1 in vivo.
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Affiliation(s)
- Daniëlle van Manen
- Department of Clinical Viro Immunology, Sanquin Research, Landsteiner Laboratory, University of Amsterdam, Amsterdam, The Netherlands
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