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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 PMCID: PMC3601691 DOI: 10.1086/655782] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Accepted: 04/09/2010] [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
- Université Paris 12, Institut National de la Santé et de la Recherche Médicale (INSERM) U955
- Commissariat à l'Énergie Atomique/Institut de Génomique, Centre National de GénotypageEvry
| | - Cédric Coulonges
- Chaire de Bioinformatique, Conservatoire National des Arts et Métiers
- Agence Nationale de Recherches sur le SIDA et les Hépatites Virales Genomic Group (French Agency for Research on AIDS and Hepatitis)
| | - Joshua T. Herbeck
- Department of Microbiology, University of Washington School of MedicineSeattle
| | - Daniëlle van Manen
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, Center for Infectious Diseases and Immunity Amsterdam Academic Medical Center, University of AmsterdamAmsterdam, the Netherlands
| | - Ping An
- Laboratory of Genomic Diversity, Science Applications International Corporation-Frederick, National Cancer Institute-FrederickFrederick
| | - Sigrid Le Clerc
- Chaire de Bioinformatique, Conservatoire National des Arts et Métiers
- Agence Nationale de Recherches sur le SIDA et les Hépatites Virales Genomic Group (French Agency for Research on AIDS and Hepatitis)
- Université Paris 12, Institut National de la Santé et de la Recherche Médicale (INSERM) U955
| | - Olivier Delaneau
- Chaire de Bioinformatique, Conservatoire National des Arts et Métiers
| | - Gora Diop
- Chaire de Bioinformatique, Conservatoire National des Arts et Métiers
| | - Lieng Taing
- Chaire de Bioinformatique, Conservatoire National des Arts et Métiers
| | - Matthieu Montes
- Chaire de Bioinformatique, Conservatoire National des Arts et Métiers
| | - Angélique B. van't Wout
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, Center for Infectious Diseases and Immunity Amsterdam Academic Medical Center, University of AmsterdamAmsterdam, the Netherlands
| | | | - Amu Therwath
- Laboratoire d'Oncologie Moléculaire, Université Paris 7Paris
| | - Christine Rouzioux
- Agence Nationale de Recherches sur le SIDA et les Hépatites Virales Genomic Group (French Agency for Research on AIDS and Hepatitis)
| | - Jean-François Delfraissy
- Agence Nationale de Recherches sur le SIDA et les Hépatites Virales Genomic Group (French Agency for Research on AIDS and Hepatitis)
| | - Jean-Daniel Lelièvre
- Université Paris 12, Institut National de la Santé et de la Recherche Médicale (INSERM) U955
| | - Yves Lévy
- Université Paris 12, Institut National de la Santé et de la Recherche Médicale (INSERM) U955
| | - Serge Hercberg
- Unite Mixte de Recherche (UMR) U557 INSERM/U1125 Inra/Conservatoire National des Arts et Métiers/UP13, Centre de Recherche en Nutrition Humaine Ile-de-France, Santé-Médecine-Biologie Humaine Paris 13Bobigny
| | - Christian Dina
- UMR Centre National de la Recherche Scientifique 8090, Institut Pasteur de LilleLille, France
| | - John Phair
- Feinberg School of Medicine, Division of Infectious Diseases, Northwestern UniversityChicago, Illinois
| | | | - James J. Goedert
- Infections and Immunoepidemiology Branch, National Cancer Institute-Bethesda, Division of Cancer Epidemiology and GeneticsRockville, Maryland
| | - Susan Buchbinder
- San Francisco Department of Public Health, HIV Research SectionSan Francisco, California
| | - Jérôme Estaquier
- Université Paris 12, Institut National de la Santé et de la Recherche Médicale (INSERM) U955
- Assistance Publique Hôpitaux de Paris, Hôpital Henri MondorCréteil
| | | | - Ivo Gut
- Commissariat à l'Énergie Atomique/Institut de Génomique, Centre National de GénotypageEvry
| | - Philippe Froguel
- UMR Centre National de la Recherche Scientifique 8090, Institut Pasteur de LilleLille, France
- Genomic Medicine, Hammersmith Hospital, Imperial College LondonLondon, United Kingdom
| | - James I. Mullins
- Department of Microbiology, University of Washington School of MedicineSeattle
| | - Hanneke Schuitemaker
- Chaire de Bioinformatique, Conservatoire National des Arts et Métiers
- Agence Nationale de Recherches sur le SIDA et les Hépatites Virales Genomic Group (French Agency for Research on AIDS and Hepatitis)
- Laboratoire d'Oncologie Moléculaire, Université Paris 7Paris
- Université Paris 12, Institut National de la Santé et de la Recherche Médicale (INSERM) U955
- Assistance Publique Hôpitaux de Paris, Hôpital Henri MondorCréteil
- Commissariat à l'Énergie Atomique/Institut de Génomique, Centre National de GénotypageEvry
- Unite Mixte de Recherche (UMR) U557 INSERM/U1125 Inra/Conservatoire National des Arts et Métiers/UP13, Centre de Recherche en Nutrition Humaine Ile-de-France, Santé-Médecine-Biologie Humaine Paris 13Bobigny
- UMR Centre National de la Recherche Scientifique 8090, Institut Pasteur de LilleLille, France
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, Center for Infectious Diseases and Immunity Amsterdam Academic Medical Center, University of AmsterdamAmsterdam, the Netherlands
- Genomic Medicine, Hammersmith Hospital, Imperial College LondonLondon, United Kingdom
- Department of Microbiology, University of Washington School of MedicineSeattle
- Laboratory of Genomic Diversity, Science Applications International Corporation-Frederick, National Cancer Institute-FrederickFrederick
- Infections and Immunoepidemiology Branch, National Cancer Institute-Bethesda, Division of Cancer Epidemiology and GeneticsRockville, Maryland
- Feinberg School of Medicine, Division of Infectious Diseases, Northwestern UniversityChicago, Illinois
- Department of Biostatistics, RhoChapel Hill, North Carolina
- San Francisco Department of Public Health, HIV Research SectionSan Francisco, California
| | - Cheryl Winkler
- Laboratory of Genomic Diversity, Science Applications International Corporation-Frederick, National Cancer Institute-FrederickFrederick
| | - Jean-François Zagury
- Chaire de Bioinformatique, Conservatoire National des Arts et Métiers
- Agence Nationale de Recherches sur le SIDA et les Hépatites Virales Genomic Group (French Agency for Research on AIDS and Hepatitis)
- Université Paris 12, Institut National de la Santé et de la Recherche Médicale (INSERM) U955
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Diop G, Hirtzig T, Do H, Coulonges C, Vasilescu A, Labib T, Spadoni JL, Therwath A, Lathrop M, Matsuda F, Zagury JF. Exhaustive genotyping of the interferon alpha receptor 1 (IFNAR1) gene and association of an IFNAR1 protein variant with AIDS progression or susceptibility to HIV-1 infection in a French AIDS cohort. Biomed Pharmacother 2006; 60:569-77. [PMID: 17027223 DOI: 10.1016/j.biopha.2006.08.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2006] [Accepted: 08/09/2006] [Indexed: 11/28/2022] Open
Abstract
We have undertaken a systematic genomic approach in order to explore the role of the interferon alpha (IFN-alpha) pathway in AIDS disease development. As it is very difficult to genotype the IFN-alpha gene itself since it has many pseudo-genes, we have focused our interest on the genetic polymorphisms of the IFN-alpha receptor 1 (IFNAR1). We genotyped the Genetics of Resistance to Immunodeficiency Virus (GRIV) cohort composed of patients with extreme profiles of progression to AIDS, slow progressors (SP) and rapid progressors (RP), as well as seronegative controls (CTR). We identified 19 single nucleotide polymorphisms (SNPs) with a minor allele frequency (MAF) greater than 1% among which two were newly characterized by our study. We found putative associations with AIDS disease development for four SNP alleles and for three haplotypes. The most interesting signals were found for two SNPs in linkage disequilibrium, the SNP IFNAR1_18339 corresponding to a Val168Leu mutation in the extracellular domain of the protein and the intronic SNP, IFNAR1_30127. The intronic SNP IFNAR1_30127 yielded a strong signal both when comparing SP with CTR (P=0.002) and RP with CTR (P=0.005) while IFNAR1_18339 yielded a smaller signal because less patients were analyzed; these SNPs could thus be involved in AIDS progression or in susceptibility to human immunodeficiency virus 1 (HIV-1) infection. Interestingly, two independent studies have previously pointed out the SNP IFNAR1_18339 in susceptibility to multiple sclerosis and to malaria. This is the first work investigating the polymorphisms of the IFNAR1 gene in AIDS. Our results which point out a possible role for the IFN-alpha pathway in susceptibility to HIV-1 infection or progression to AIDS need a necessary confirmation by genomic studies in other AIDS cohorts.
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Affiliation(s)
- G Diop
- Equipe génomique, bio-informatique et pathologies du système immunitaire, Inserm U736, 15, rue de l'Ecole-de-Médecine, 75006 Paris, France
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Do H, Vasilescu A, Diop G, Hirtzig T, Coulonges C, Labib T, Heath SC, Spadoni JL, Therwath A, Lathrop M, Matsuda F, Zagury JF. Associations of the IL2Ralpha, IL4Ralpha, IL10Ralpha, and IFN (gamma) R1 cytokine receptor genes with AIDS progression in a French AIDS cohort. Immunogenetics 2006; 58:89-98. [PMID: 16491350 DOI: 10.1007/s00251-005-0072-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2005] [Accepted: 11/28/2005] [Indexed: 10/25/2022]
Abstract
We have performed an extensive analysis of Th1/Th2 cytokine receptors IL2Ralpha, IL4Ralpha, IL10Ralpha, and IFNgammaR1 gene polymorphisms to evaluate their impact on AIDS progression. The coding regions and promoters of these genes were sequenced in the genetics of resistance to immunodeficiency virus cohort, composed of 327 HIV-1-positive patients with extreme progression phenotypes, slow and rapid progressors, and of 446 healthy control subjects, all of them of Caucasian descent. Overall, 104 single nucleotide polymorphisms and four insertions/deletions with a minor allelic frequency higher than 1% were identified, 21 of them being newly characterized. We observed weak associations for 13 polymorphisms of IL2Ralpha, IL4Ralpha, IL10Ralpha, and IFNgammaR1, and 11 haplotypes of IL2Ralpha, IL4Ralpha, and IFNgammaR1. However, we could not relate these positive signals to any relevant biological information on the gene function. To affirm these putative associations in AIDS, further confirmation on other AIDS cohorts will be needed. This complete catalog of polymorphisms in IL2Ralpha, IL4Ralpha, IL10Ralpha, and IFNgammaR1 cytokine receptor genes should also be useful for investigating associations in other immune-related diseases.
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Affiliation(s)
- Hervé Do
- Equipe génomique, bioinformatique et pathologies du système immunitaire, INSERM U736, 15 rue de l'Ecole de Médecine, 75006, Paris, France
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Diop G, Spadoni JL, Do H, Hirtzig T, Coulonges C, Labib T, Issing W, Rappaport J, Therwath A, Lathrop M, Matsuda F, Zagury JF. Genomic approach of AIDS pathogenesis: exhaustive genotyping of the TNFR1 gene in a French AIDS cohort. Biomed Pharmacother 2006; 59:474-80. [PMID: 16153798 DOI: 10.1016/j.biopha.2005.07.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2005] [Indexed: 12/30/2022] Open
Abstract
Large-scale genomic studies in cohorts have been made possible for the last few years thanks to the progress of molecular biology and bioinformatics. This systematic approach allows a better understanding of the molecular mechanisms of disease development and as a consequence can contribute to the rational design of new diagnostic and therapeutic tools. We present here the exhaustive genotyping of a candidate gene, tumor necrosis factor receptor 1 (TNFR1), in the genetic of resistance to immunodeficiency virus (GRIV) AIDS cohort. This gene was chosen because it is likely to be involved in the apoptosis pathways of CD4+ and CD8+ T-cells during human immunodeficiency virus 1 (HIV-1) infection. Seven frequent polymorphisms were characterized in 319 HIV-1 seropositive patients from the GRIV cohort with extreme disease progression phenotypes, slow progression or rapid progression, and in 427 healthy controls. The TNFR1 gene locus does not appear to be part of any haploblock and contains only a small haploblock of two successive SNPs. One promoter SNP (TNFR1_17444594, position -581) and one intronic SNP (TNFR1_27223241, position +11511) gave weak positive signals of association (resp. P=0.03 and P=0.04) as well as two haplotypes. To our knowledge, this is the first genetic association study dealing with the TNFR1 gene in AIDS and the putative associations identified will need to be validated through other AIDS cohort analyses or by further biological experimentation.
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Affiliation(s)
- Gora Diop
- Equipe génomique, bioinformatique et pathologies du système immunitaire, Inserm EMI0355, 15, rue de l'Ecole-de-Médecine, 75006 Paris, France
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Hao K, Niu T, Xu X, Fang Z, Xu X. Single-nucleotide polymorphisms of the KCNS3 gene are significantly associated with airway hyperresponsiveness. Hum Genet 2005; 116:378-83. [PMID: 15714333 DOI: 10.1007/s00439-005-1256-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2004] [Accepted: 12/23/2004] [Indexed: 10/25/2022]
Abstract
Airway hyperresponsiveness (AHR) is one of the major clinical symptoms and intermediate phenotypes of asthma. A recent genome-wide search for asthma quantitative trait loci has revealed a significant linkage signal between a p-terminal region of chromosome 2 and AHR. Thus, the gene encoding the potassium voltage-gated channel delayed-rectifier protein S3 (KCNS3) in this region is considered a positional candidate for asthma. We have evaluated a total of 12 single-nucleotide polymorphisms (SNPs) of the KCNS3 gene in a validation panel of 48 lymphoblastoid cell line DNA samples of Chinese origin. Three SNPs were found to be polymorphic and were tested. Two independent sets (an initial screening set and a replication set) of cases and controls from the original linkage study sample were collected. In the initial screening set, two SNPs (rs1031771 and rs1031772) showed suggestive association and were further confirmed by the replication set. In combined single-SNP analysis, the rs1031771 G allele (odds ratio=1.42, P=0.006) and rs1031772 T allele (odds ratio=1.40, P=0.018) were associated with a significantly higher risk of AHR. Haplotype analysis also detected significant association (P=0.006). Our findings suggest that SNPs located at the 3' downstream region of KCNS3 have a significant role in the etiology of AHR.
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Affiliation(s)
- Ke Hao
- Program for Population Genetics, Harvard School of Public Health, 665 Huntington Avenue FXB-101, Boston, MA 02115, USA
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Winkler CA, Hendel H, Carrington M, Smith MW, Nelson GW, O'brien SJ, Phair J, Vlahov D, Jacobson LP, Rappaport J, Vasilescu A, Bertin-Maghit S, An P, Lu W, Andrieu JM, Schächter F, Therwath A, Zagury JF. Dominant Effects of CCR2-CCR5 Haplotypes in HIV-1 Disease Progression. J Acquir Immune Defic Syndr 2004; 37:1534-8. [PMID: 15602133 DOI: 10.1097/01.qai.0000127353.01578.63] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Three haplotypes for the CCR2-CCR5 region previously have been shown to affect AIDS progression; however, it is not known if the protective and accelerating effects of the haplotypes are relatively constant throughout infection or exert their effects early or late in HIV type 1 infection. The authors report the relative contributions to AIDS progression of CCR2 64I, CCR5 Delta32, and the CCR5 promoter haplotype +.P1.+ in the GRIV cohort, which included patients representing the extremes of the distribution for AIDS progression: rapid progressors (RP) who developed CD4 T-cell counts of <300/ mm within 3 years after the last HIV-1-seronegative test and slow progressors (SP) who were HIV-1 infected for > or =8 years with CD4 T-cell counts of >500/mm. Comparing the RP with a seroconverter control group including intermediate progressors to AIDS, we observed the early protective effect of CCR5 Delta32 (odds ratio = 0.25; P = 0.007) was similar in strength to the early susceptible effect of CCR5 +.P1.+ (odds ratio = 2.1, P = 0.01). Comparison of the intermediate control group to the SP showed weaker and less significant odd ratios, suggesting that the effect of these factors tended to be stronger on early progression; the tendency towards a disproportionately early effect was significant for CCR5 Delta32 (P = 0.04) but not for CCR5 +.P1.+ (P = 0.12). Follow-up of SP demonstrated that these polymorphisms have little effect after 8 years, because the subset of SP who had progression after study entry had the same genotype distribution as the global population of SP, suggesting that factors other than CCR5 or CCR2 genetic variants must be responsible for the long-term maintenance of nonprogression.
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Affiliation(s)
- Cheryl A Winkler
- Laboratory of Genomic Diversity, Division of Basic Research, SAIC-Frederick, NCI, Frederick, MD, USA
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Vasilescu A, Heath SC, Diop G, Do H, Hirtzig T, Hendel H, Bertin-Maghit S, Rappaport J, Therwath A, Lathrop GM, Matsuda F, Zagury JF. Genomic analysis of Fas and FasL genes and absence of correlation with disease progression in AIDS. Immunogenetics 2004; 56:56-60. [PMID: 15042330 DOI: 10.1007/s00251-004-0664-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2004] [Revised: 02/26/2004] [Indexed: 10/26/2022]
Abstract
Apoptosis has been suggested as a major mechanism for the CD4(+) T-lymphocyte depletion observed in patients infected with human immunodeficiency virus 1 (HIV-1). To evaluate the impact of genetic variations to apoptosis during progression of acquired immunodeficiency syndrome (AIDS), we have performed an extensive genetic analysis of Fas and Fas ligand ( FasL) genes. The coding regions and promoters of these genes were resequenced in a cohort of 212 HIV-1-seropositive patients presenting extreme disease phenotypes and 155 healthy controls of Caucasian origin. Overall, 33 single nucleotide polymorphisms (SNPs) with an allele frequency >1% were identified and evaluated for their association with disease progression. Among them, 14 polymorphisms were newly characterized. We did not find any statistically significant association of Fas and FasL polymorphisms and haplotypes with AIDS progression.
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Affiliation(s)
- A Vasilescu
- Centre National de Génotypage, 2 rue Gaston Crémieux, 91000 Evry, France
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