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Aarnink A, Dereuddre-Bosquet N, Vaslin B, Le Grand R, Winterton P, Apoil PA, Blancher A. Influence of the MHC genotype on the progression of experimental SIV infection in the Mauritian cynomolgus macaque. Immunogenetics 2011; 63:267-74. [DOI: 10.1007/s00251-010-0504-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Accepted: 12/15/2010] [Indexed: 11/30/2022]
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302
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Shapshak P, Kangueane P, Fujimura RK, Commins D, Chiappelli F, Singer E, Levine AJ, Minagar A, Novembre FJ, Somboonwit C, Nath A, Sinnott JT. Editorial neuroAIDS review. AIDS 2011; 25:123-41. [PMID: 21076277 PMCID: PMC4464840 DOI: 10.1097/qad.0b013e328340fd42] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Paul Shapshak
- Division of Infectious Disease, Department of Internal Medicine, Tampa General Hospital, Tampa, Florida, USA
- Department of Psychiatry and Behavioral Medicine, University of South Florida, College of Medicine, Tampa, Florida, USA
| | - Pandjassarame Kangueane
- Biomedical Informatics, 17A lrulan Sundai Annex, Pondicherry, India
- AIMST University, Kedha, Malaysia
| | - Robert K. Fujimura
- Geriatric Research Education and Clinical Centers, Veterans Administration, Puget Sound Healthcare System, Seattle, Washington
| | - Deborah Commins
- Department of Pathology, University of Southern California Keck School of Medicine, Los Angeles
| | | | - Elyse Singer
- Department of Neurology and National Neurological AIDS Bank, UCLA School of Medicine, Westwood, California
| | - Andrew J. Levine
- Department of Neurology and National Neurological AIDS Bank, UCLA School of Medicine, Westwood, California
| | - Alireza Minagar
- Department of Neurology, Louisiana State University Health Sciences Center, Shreveport, Louisiana
| | | | - Charurut Somboonwit
- Division of Infectious Disease, Department of Internal Medicine, Tampa General Hospital, Tampa, Florida, USA
- Clinical Research Unit, Hillsborough Health Department, Tampa, Florida
| | - Avindra Nath
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - John T. Sinnott
- Division of Infectious Disease, Department of Internal Medicine, Tampa General Hospital, Tampa, Florida, USA
- Clinical Research Unit, Hillsborough Health Department, Tampa, Florida
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303
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Casto AM, Feldman MW. Genome-wide association study SNPs in the human genome diversity project populations: does selection affect unlinked SNPs with shared trait associations? PLoS Genet 2011; 7:e1001266. [PMID: 21253569 PMCID: PMC3017115 DOI: 10.1371/journal.pgen.1001266] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2010] [Accepted: 12/02/2010] [Indexed: 01/11/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified more than 2,000 trait-SNP associations, and the number continues to increase. GWAS have focused on traits with potential consequences for human fitness, including many immunological, metabolic, cardiovascular, and behavioral phenotypes. Given the polygenic nature of complex traits, selection may exert its influence on them by altering allele frequencies at many associated loci, a possibility which has yet to be explored empirically. Here we use 38 different measures of allele frequency variation and 8 iHS scores to characterize over 1,300 GWAS SNPs in 53 globally distributed human populations. We apply these same techniques to evaluate SNPs grouped by trait association. We find that groups of SNPs associated with pigmentation, blood pressure, infectious disease, and autoimmune disease traits exhibit unusual allele frequency patterns and elevated iHS scores in certain geographical locations. We also find that GWAS SNPs have generally elevated scores for measures of allele frequency variation and for iHS in Eurasia and East Asia. Overall, we believe that our results provide evidence for selection on several complex traits that has caused changes in allele frequencies and/or elevated iHS scores at a number of associated loci. Since GWAS SNPs collectively exhibit elevated allele frequency measures and iHS scores, selection on complex traits may be quite widespread. Our findings are most consistent with this selection being either positive or negative, although the relative contributions of the two are difficult to discern. Our results also suggest that trait-SNP associations identified in Eurasian samples may not be present in Africa, Oceania, and the Americas, possibly due to differences in linkage disequilibrium patterns. This observation suggests that non-Eurasian and non-East Asian sample populations should be included in future GWAS.
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Affiliation(s)
- Amanda M Casto
- Department of Genetics, Stanford University, Stanford, California, United States of America.
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304
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Abstract
Multiple epidemiological studies have demonstrated associations between the human leukocyte antigen (HLA) loci and human immunodeficiency virus (HIV) disease, and more recently the killer cell immunoglobulin-like (KIR) locus has been implicated in differential responses to the virus. Genome-wide association studies have convincingly shown that the HLA class I locus is the most significant host genetic contributor to the variation in HIV control, underscoring a central role for CD8 T cells in resistance to the virus. However, both genetic and functional data indicate that part of the HLA effect on HIV is due to interactions between KIR and HLA genes, also implicating natural killer cells in defense against viral infection and viral expansion prior to initiation of an adaptive response. We review the HLA and KIR associations with HIV disease and the progress that has been made in understanding the mechanisms that explain these associations.
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Affiliation(s)
- Arman A Bashirova
- Ragon Institute of Massachusetts General Hospital, MIT, Boston, Massachusetts 02129, USA.
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305
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Affiliation(s)
- Andrew J McMichael
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OS3 9DS, UK.
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306
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Chinn LW, Tang M, Kessing BD, Lautenberger JA, Troyer JL, Malasky MJ, McIntosh C, Kirk GD, Wolinsky SM, Buchbinder SP, Gomperts ED, Goedert JJ, O'Brien SJ. Genetic associations of variants in genes encoding HIV-dependency factors required for HIV-1 infection. J Infect Dis 2010; 202:1836-45. [PMID: 21083371 PMCID: PMC3107555 DOI: 10.1086/657322] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Accepted: 07/14/2010] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND High-throughput genome-wide techniques have facilitated the identification of previously unknown host proteins involved in cellular human immunodeficiency virus (HIV) infection. Recently, 3 independent studies have used small interfering RNA technology to silence each gene in the human genome to determine the importance of each in HIV infection. Genes conferring a significant effect were termed HIV-dependency factors (HDFs). METHODS We assembled high-density panels of 6380 single-nucleotide polymorphisms (SNPs) in 278 HDF genes and tested for genotype associations with HIV infection and AIDS progression in 1633 individuals from clinical AIDS cohorts. RESULTS After statistical correction for multiple tests, significant associations with HIV acquisition were found for SNPs in 2 genes, NCOR2 and IDH1. Weaker associations with AIDS progression were revealed for SNPs within the TM9SF2 and EGFR genes. CONCLUSIONS This study independently verifies the influence of NCOR2 and IDH1 on HIV transmission, and its findings suggest that variation in these genes affects susceptibility to HIV infection in exposed individuals.
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Affiliation(s)
| | | | | | | | | | | | | | - Gregory D. Kirk
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | | | | | - Edward D. Gomperts
- Childrens Hospital Los Angeles and University of Southern California, Los Angeles, California
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307
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Graw F, Magnus C, Regoes RR. Theoretical analysis of the evolution of immune memory. BMC Evol Biol 2010; 10:380. [PMID: 21143840 PMCID: PMC3018457 DOI: 10.1186/1471-2148-10-380] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Accepted: 12/08/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The ability of an immune system to remember pathogens improves the chance of the host to survive a second exposure to the same pathogen. This immunological memory has evolved in response to the pathogen environment of the hosts. In vertebrates, the memory of previous infection is physiologically accomplished by the development of memory T and B cells. Many questions concerning the generation and maintenance of immunological memory are still debated. Is there a limit to how many memory cells a host can generate and maintain? If there is a limit, how should new cells be incorporated into a filled memory compartment? And how many different pathogens should the immune system remember? RESULTS In this study, we examine how memory traits evolve as a response to different pathogen environments using an individual-based model. We find that even without a cost related to the maintenance of a memory pool, the positive effect of bigger memory pool sizes saturates. The optimal diversity of a limited memory pool is determined by the probability of re-infection, rather than by the prevalence of a pathogen in the environment, or the frequency of exposure. CONCLUSIONS Relating immune memory traits to the pathogen environment of the hosts, our population biological framework sheds light on the evolutionary determinants of immune memory.
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308
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Martin MP, Qi Y, Goedert JJ, Hussain SK, Kirk GD, Keith Hoots W, Buchbinder S, Carrington M, Thio CL. IL28B polymorphism does not determine outcomes of hepatitis B virus or HIV infection. J Infect Dis 2010; 202:1749-53. [PMID: 20977343 PMCID: PMC2974014 DOI: 10.1086/657146] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2010] [Accepted: 07/08/2010] [Indexed: 12/22/2022] Open
Abstract
An IL28B haplotype strongly determines the outcome of natural and interferon-α treated hepatitis C virus (HCV) infection. To assess whether the polymorphism marking the haplotype (rs12979860) also affects other interferon-α responsive chronic viral illnesses, namely hepatitis B virus (HBV) and human immunodeficiency virus (HIV) type 1 infections, we genotyped 226 individuals with HBV persistence, 384 with HBV recovery, and 2548 with or at high risk for HIV infection. The C/C genotype of rs12979860 was not associated with HBV recovery (odds ratio, 0.99), resistance to HIV infection (odds ratio, 0.97), or HIV disease progression (P > .05). This IL28B single-nucleotide polymorphism affects the immune response to HCV but not to HBV or HIV.
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Affiliation(s)
- Maureen P. Martin
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, NCI-Frederick, Frederick
| | - Ying Qi
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, NCI-Frederick, Frederick
| | - James J. Goedert
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville
| | | | | | - W. Keith Hoots
- Division of Blood Diseases and Resources, National Heart Lung and Blood Institute, Bethesda, Maryland
| | | | - Mary Carrington
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, NCI-Frederick, Frederick
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309
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Alcaïs A, Quintana-Murci L, Thaler DS, Schurr E, Abel L, Casanova JL. Life-threatening infectious diseases of childhood: single-gene inborn errors of immunity? Ann N Y Acad Sci 2010; 1214:18-33. [PMID: 21091717 DOI: 10.1111/j.1749-6632.2010.05834.x] [Citation(s) in RCA: 130] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The hypothesis that inborn errors of immunity underlie infectious diseases is gaining experimental support. However, the apparent modes of inheritance of predisposition or resistance differ considerably among diseases and among studies. A coherent genetic architecture of infectious diseases is lacking. We suggest here that life-threatening infectious diseases in childhood, occurring in the course of primary infection, result mostly from individually rare but collectively diverse single-gene variations of variable clinical penetrance, whereas the genetic component of predisposition to secondary or reactivation infections in adults is more complex. This model is consistent with (i) the high incidence of most infectious diseases in early childhood, followed by a steady decline; (ii) theoretical modeling of the impact of monogenic or polygenic predisposition on the incidence distribution of infectious diseases before reproductive age; (iii) available molecular evidence from both monogenic and complex genetics of infectious diseases in children and adults; (iv) current knowledge of immunity to primary and secondary or latent infections; (v) the state of the art in the clinical genetics of noninfectious pediatric and adult diseases; and (vi) evolutionary data for the genes underlying single-gene and complex disease risk. With the recent advent of new-generation deep resequencing, this model of single-gene variations underlying severe pediatric infectious diseases is experimentally testable.
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Affiliation(s)
- Alexandre Alcaïs
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale, University Paris Descartes, Paris, France
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310
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Chakrabarti LA, Simon V. Immune mechanisms of HIV control. Curr Opin Immunol 2010; 22:488-96. [PMID: 20650621 DOI: 10.1016/j.coi.2010.06.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Revised: 06/16/2010] [Accepted: 06/17/2010] [Indexed: 12/20/2022]
Abstract
HIV-1 can be contained by the immune system, as demonstrated by the existence of rare individuals who spontaneously control HIV-1 replication in the absence of antiretroviral therapy. Emerging evidence points to the importance of a very active cellular immune response in mediating HIV-1 control. The rapid induction of interferon-dependent HIV restriction factors, the presence of protective MHC class I alleles, and the development of a high avidity T-cell response may all cooperate in limiting HIV replication at an early stage. This review will focus on recent advances in understanding the immune mechanisms of HIV control, and on the lessons that may be drawn for the development of candidate HIV vaccines.
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Affiliation(s)
- Lisa A Chakrabarti
- Institut Pasteur, Unité d'Immunogénétique Cellulaire, 25 rue du Dr Roux, 75724 Paris Cedex 15, France.
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311
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Abstract
On 16 and 17 July 2010, immediately prior to the XVIII International AIDS Conference in Vienna, Austria, the International AIDS Society held a workshop on the important topic of moving beyond antiretroviral therapy and addressing HIV persistence. “Towards a Cure: HIV Reservoirs and Strategies to Control Them” was chaired by Nobel laureate Françoise Barré-Sinoussi and co-sponsored by the French National Agency for Research on AIDS and Viral Hepatitis, Bundesministerium für Wissenschaft und Forschung, the National Institutes of Health, Sidaction and the Treatment Action Group. This article gives an overview of the findings presented at the workshop; complete abstracts are included in this supplement to the Journal of the International AIDS Society.
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312
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313
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314
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Abstract
This is a crucial transition time for human genetics in general, and for HIV host genetics in particular. After years of equivocal results from candidate gene analyses, several genome-wide association studies have been published that looked at plasma viral load or disease progression. Results from other studies that used various large-scale approaches (siRNA screens, transcriptome or proteome analysis, comparative genomics) have also shed new light on retroviral pathogenesis. However, most of the inter-individual variability in response to HIV-1 infection remains to be explained: genome resequencing and systems biology approaches are now required to progress toward a better understanding of the complex interactions between HIV-1 and its human host.
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Affiliation(s)
- Jacques Fellay
- Center for Human Genome Variation, Duke University School of Medicine, Durham, North Carolina, United States of America.
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315
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Phylogenetic approach reveals that virus genotype largely determines HIV set-point viral load. PLoS Pathog 2010; 6:e1001123. [PMID: 20941398 PMCID: PMC2947993 DOI: 10.1371/journal.ppat.1001123] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Accepted: 08/27/2010] [Indexed: 11/19/2022] Open
Abstract
HIV virulence, i.e. the time of progression to AIDS, varies greatly among patients. As for other rapidly evolving pathogens of humans, it is difficult to know if this variance is controlled by the genotype of the host or that of the virus because the transmission chain is usually unknown. We apply the phylogenetic comparative approach (PCA) to estimate the heritability of a trait from one infection to the next, which indicates the control of the virus genotype over this trait. The idea is to use viral RNA sequences obtained from patients infected by HIV-1 subtype B to build a phylogeny, which approximately reflects the transmission chain. Heritability is measured statistically as the propensity for patients close in the phylogeny to exhibit similar infection trait values. The approach reveals that up to half of the variance in set-point viral load, a trait associated with virulence, can be heritable. Our estimate is significant and robust to noise in the phylogeny. We also check for the consistency of our approach by showing that a trait related to drug resistance is almost entirely heritable. Finally, we show the importance of taking into account the transmission chain when estimating correlations between infection traits. The fact that HIV virulence is, at least partially, heritable from one infection to the next has clinical and epidemiological implications. The difference between earlier studies and ours comes from the quality of our dataset and from the power of the PCA, which can be applied to large datasets and accounts for within-host evolution. The PCA opens new perspectives for approaches linking clinical data and evolutionary biology because it can be extended to study other traits or other infectious diseases. Some untreated patients infected by HIV die within a couple of years, while others survive more than 25 years. To date, it is still unclear whether this variance in the virulence of the infection is due to the host or to the virus genotype. One of the main difficulties in answering this question is that, as for most human diseases, we tend not to know who infected whom. Here, we solve this problem by adopting a phylogenetic approach, which estimates the heritability of species traits on a phylogeny. In our case, species correspond to infected patients and the trait is an infection trait. The phylogeny is obtained from the HIV RNA sequences isolated in each patient. We find that more than half of the variance observed in the set-point viral load—a trait that predicts virulence—is heritable from one infection to the next. This implies that set-point viral load is strongly controlled by the virus genotype. This application of the phylogenetic comparative approach to infectious diseases yields major results for the deciphering of HIV pathogenesis. Future applications to other traits and/or other pathogens will help us to better understand rapidly evolving diseases of humans.
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316
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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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317
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Abstract
This report describes a meeting organized by Ken Smith and Jim Kaufman, entitled Evolution and Immunity, which took place at the University of Cambridge on 24 September 2009 to honour the anniversaries of the birth of Darwin and the first publication of The Origin of Species. Ten internationally-known speakers described the effects of evolution on immunity, ranging in timescales from the deep-time evolution of adaptive immune systems in vertebrates and invertebrates to the evolution of pathogens and lymphocytes within a single individual. The final talk explored the application of phylogenetic analysis to non-biological systems.
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Affiliation(s)
- Jim Kaufman
- Department of Pathology, University of Cambridge, Cambridge, UK.
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318
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Pasternak AO, Jurriaans S, Bakker M, Berkhout B, Lukashov VV. Steady increase in cellular HIV-1 load during the asymptomatic phase of untreated infection despite stable plasma viremia. AIDS 2010; 24:1641-9. [PMID: 20543660 DOI: 10.1097/qad.0b013e32833b3171] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
OBJECTIVE To compare the dynamics of HIV-1 molecular markers in peripheral blood mononuclear cells (PBMCs) and in plasma during the asymptomatic phase of untreated HIV-1 infection. DESIGN AND METHODS Using seminested real-time PCR assays, we measured the levels of HIV-1 proviral (pr) DNA, unspliced (us) RNA, and multiply spliced RNA in the PBMCs of 10 untreated HIV-1-infected men at multiple time points during the asymptomatic phase of infection and compared the longitudinal trends of these markers with those of viral RNA in plasma. RESULTS Whereas plasma RNA levels did not significantly change in any of the individuals, levels of usRNA significantly increased with time in six out of 10 persons, and levels of prDNA in four. Slopes, changes, and time-weighted changes from baseline of usRNA, prDNA, and CD4 cell count, but not of plasma RNA, were significantly different from zero (P < 0.01). No significant longitudinal trend of plasma RNA was observed in the study group using linear mixed models, whereas the trends of usRNA, prDNA, and CD4 cell count were highly significant (P < 0.001). usRNA levels increased significantly faster than those of plasma RNA or prDNA, suggesting a temporal increase in viral replication rates in PBMCs. Finally, CD4 cell count inversely correlated with levels of usRNA and prDNA, but not with plasma RNA level. CONCLUSION During the asymptomatic phase of untreated HIV-1 infection, when virion production and clearance are balanced, resulting in stable plasma viremia, viral load in PBMCs steadily increases and is a sensitive and direct longitudinal virological marker of infection progression.
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Specht A, Telenti A, Martinez R, Fellay J, Bailes E, Evans DT, Carrington M, Hahn BH, Goldstein DB, Kirchhoff F. Counteraction of HLA-C-mediated immune control of HIV-1 by Nef. J Virol 2010; 84:7300-11. [PMID: 20463068 PMCID: PMC2898263 DOI: 10.1128/jvi.00619-10] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2010] [Accepted: 05/04/2010] [Indexed: 11/20/2022] Open
Abstract
A host genetic variant (-35C/T) correlates with increased human leukocyte antigen C (HLA-C) expression and improved control of HIV-1. HLA-C-mediated immunity may be particularly protective because HIV-1 is unable to remove HLA-C from the cell surface, whereas it can avoid HLA-A- and HLA-B-mediated immunity by Nef-mediated down-modulation. However, some individuals with the protective -35CC genotype exhibit high viral loads. Here, we investigated whether the ability of HIV-1 to replicate efficiently in the "protective" high-HLA-C-expression host environment correlates with specific functional properties of Nef. We found that high set point viral loads (sVLs) were not associated with the emergence of Nef variants that had acquired the ability to down-modulate HLA-C or were more effective in removing HLA-A and HLA-B from the cell surface. However, in individuals with the protective -35CC genotype we found a significant association between sVLs and the efficiency of Nef-mediated enhancement of virion infectivity and modulation of CD4, CD28, and the major histocompatibility complex class II (MHC-II)-associated invariant chain (Ii), while this was not observed in subjects with the -35TT genotype. Since the latter Nef functions all influence the stimulation of CD4(+) T helper cells by antigen-presenting cells, they may cooperate to affect both the activation status of infected T cells and the generation of an antiviral cytotoxic T-lymphocyte (CTL) response. In comparison, different levels of viremia in individuals with the common -35TT genotype were not associated with differences in Nef function but with differences in HLA-C mRNA expression levels. Thus, while high HLA-C expression may generally facilitate control of HIV-1, Nef may counteract HLA-C-mediated immune control in some individuals indirectly, by manipulating T-cell function and MHC-II antigen presentation.
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Affiliation(s)
- Anke Specht
- Institute of Molecular Virology, University Hospital of Ulm, 89081 Ulm, Germany, Institute of Microbiology, University Hospital Center and University of Lausanne, 1011 Lausanne, Switzerland, Center for Human Genome Variation, Duke Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina 27710, Institute of Genetics, University of Nottingham, Queens Medical Centre, NH7 2UH, Nottingham, United Kingdom, Department of Microbiology and Molecular Genetics, Harvard Medical School, New England Primate Research Center, Southborough, Massachusetts 01772, Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts 02114, Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Amalio Telenti
- Institute of Molecular Virology, University Hospital of Ulm, 89081 Ulm, Germany, Institute of Microbiology, University Hospital Center and University of Lausanne, 1011 Lausanne, Switzerland, Center for Human Genome Variation, Duke Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina 27710, Institute of Genetics, University of Nottingham, Queens Medical Centre, NH7 2UH, Nottingham, United Kingdom, Department of Microbiology and Molecular Genetics, Harvard Medical School, New England Primate Research Center, Southborough, Massachusetts 01772, Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts 02114, Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Raquel Martinez
- Institute of Molecular Virology, University Hospital of Ulm, 89081 Ulm, Germany, Institute of Microbiology, University Hospital Center and University of Lausanne, 1011 Lausanne, Switzerland, Center for Human Genome Variation, Duke Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina 27710, Institute of Genetics, University of Nottingham, Queens Medical Centre, NH7 2UH, Nottingham, United Kingdom, Department of Microbiology and Molecular Genetics, Harvard Medical School, New England Primate Research Center, Southborough, Massachusetts 01772, Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts 02114, Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Jacques Fellay
- Institute of Molecular Virology, University Hospital of Ulm, 89081 Ulm, Germany, Institute of Microbiology, University Hospital Center and University of Lausanne, 1011 Lausanne, Switzerland, Center for Human Genome Variation, Duke Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina 27710, Institute of Genetics, University of Nottingham, Queens Medical Centre, NH7 2UH, Nottingham, United Kingdom, Department of Microbiology and Molecular Genetics, Harvard Medical School, New England Primate Research Center, Southborough, Massachusetts 01772, Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts 02114, Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Elizabeth Bailes
- Institute of Molecular Virology, University Hospital of Ulm, 89081 Ulm, Germany, Institute of Microbiology, University Hospital Center and University of Lausanne, 1011 Lausanne, Switzerland, Center for Human Genome Variation, Duke Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina 27710, Institute of Genetics, University of Nottingham, Queens Medical Centre, NH7 2UH, Nottingham, United Kingdom, Department of Microbiology and Molecular Genetics, Harvard Medical School, New England Primate Research Center, Southborough, Massachusetts 01772, Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts 02114, Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - David T. Evans
- Institute of Molecular Virology, University Hospital of Ulm, 89081 Ulm, Germany, Institute of Microbiology, University Hospital Center and University of Lausanne, 1011 Lausanne, Switzerland, Center for Human Genome Variation, Duke Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina 27710, Institute of Genetics, University of Nottingham, Queens Medical Centre, NH7 2UH, Nottingham, United Kingdom, Department of Microbiology and Molecular Genetics, Harvard Medical School, New England Primate Research Center, Southborough, Massachusetts 01772, Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts 02114, Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Mary Carrington
- Institute of Molecular Virology, University Hospital of Ulm, 89081 Ulm, Germany, Institute of Microbiology, University Hospital Center and University of Lausanne, 1011 Lausanne, Switzerland, Center for Human Genome Variation, Duke Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina 27710, Institute of Genetics, University of Nottingham, Queens Medical Centre, NH7 2UH, Nottingham, United Kingdom, Department of Microbiology and Molecular Genetics, Harvard Medical School, New England Primate Research Center, Southborough, Massachusetts 01772, Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts 02114, Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Beatrice H. Hahn
- Institute of Molecular Virology, University Hospital of Ulm, 89081 Ulm, Germany, Institute of Microbiology, University Hospital Center and University of Lausanne, 1011 Lausanne, Switzerland, Center for Human Genome Variation, Duke Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina 27710, Institute of Genetics, University of Nottingham, Queens Medical Centre, NH7 2UH, Nottingham, United Kingdom, Department of Microbiology and Molecular Genetics, Harvard Medical School, New England Primate Research Center, Southborough, Massachusetts 01772, Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts 02114, Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - David B. Goldstein
- Institute of Molecular Virology, University Hospital of Ulm, 89081 Ulm, Germany, Institute of Microbiology, University Hospital Center and University of Lausanne, 1011 Lausanne, Switzerland, Center for Human Genome Variation, Duke Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina 27710, Institute of Genetics, University of Nottingham, Queens Medical Centre, NH7 2UH, Nottingham, United Kingdom, Department of Microbiology and Molecular Genetics, Harvard Medical School, New England Primate Research Center, Southborough, Massachusetts 01772, Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts 02114, Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Frank Kirchhoff
- Institute of Molecular Virology, University Hospital of Ulm, 89081 Ulm, Germany, Institute of Microbiology, University Hospital Center and University of Lausanne, 1011 Lausanne, Switzerland, Center for Human Genome Variation, Duke Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina 27710, Institute of Genetics, University of Nottingham, Queens Medical Centre, NH7 2UH, Nottingham, United Kingdom, Department of Microbiology and Molecular Genetics, Harvard Medical School, New England Primate Research Center, Southborough, Massachusetts 01772, Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts 02114, Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294
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320
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Casado C, Colombo S, Rauch A, Martínez R, Günthard HF, Garcia S, Rodríguez C, del Romero J, Telenti A, López-Galíndez C. Host and viral genetic correlates of clinical definitions of HIV-1 disease progression. PLoS One 2010; 5:e11079. [PMID: 20552027 PMCID: PMC2884031 DOI: 10.1371/journal.pone.0011079] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Accepted: 05/21/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Various patterns of HIV-1 disease progression are described in clinical practice and in research. There is a need to assess the specificity of commonly used definitions of long term non-progressor (LTNP) elite controllers (LTNP-EC), viremic controllers (LTNP-VC), and viremic non controllers (LTNP-NC), as well as of chronic progressors (P) and rapid progressors (RP). METHODOLOGY AND PRINCIPAL FINDINGS We re-evaluated the HIV-1 clinical definitions, summarized in Table 1, using the information provided by a selected number of host genetic markers and viral factors. There is a continuous decrease of protective factors and an accumulation of risk factors from LTNP-EC to RP. Statistical differences in frequency of protective HLA-B alleles (p-0.01), HLA-C rs9264942 (p-0.06), and protective CCR5/CCR2 haplotypes (p-0.02) across groups, and the presence of viruses with an ancestral genotype in the "viral dating" (i.e., nucleotide sequences with low viral divergence from the most recent common ancestor) support the differences among principal clinical groups of HIV-1 infected individuals. CONCLUSIONS A combination of host genetic and viral factors supports current clinical definitions that discriminate among patterns of HIV-1 progression. The study also emphasizes the need to apply a standardized and accepted set of clinical definitions for the purpose of disease stratification and research.
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Affiliation(s)
- Concepción Casado
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Sara Colombo
- Institute of Microbiology, University Hospital Center, University of Lausanne, Lausanne, Switzerland
| | - Andri Rauch
- University Clinic of Infectious Diseases, University Hospital Bern and University of Bern, Bern, Switzerland
| | - Raquel Martínez
- Institute of Microbiology, University Hospital Center, University of Lausanne, Lausanne, Switzerland
| | - Huldrych F. Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University of Zurich, Zurich, Switzerland
| | - Soledad Garcia
- Centro Sanitario Sandoval, IMSALUD Comunidad Autónoma de Madrid, Madrid, Spain
| | - Carmen Rodríguez
- Centro Sanitario Sandoval, IMSALUD Comunidad Autónoma de Madrid, Madrid, Spain
| | - Jorge del Romero
- Centro Sanitario Sandoval, IMSALUD Comunidad Autónoma de Madrid, Madrid, Spain
| | - Amalio Telenti
- Institute of Microbiology, University Hospital Center, University of Lausanne, Lausanne, Switzerland
- * E-mail: (AT); (CLG)
| | - Cecilio López-Galíndez
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
- * E-mail: (AT); (CLG)
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321
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Zhang K, Cui S, Chang S, Zhang L, Wang J. i-GSEA4GWAS: a web server for identification of pathways/gene sets associated with traits by applying an improved gene set enrichment analysis to genome-wide association study. Nucleic Acids Res 2010; 38:W90-5. [PMID: 20435672 PMCID: PMC2896119 DOI: 10.1093/nar/gkq324] [Citation(s) in RCA: 154] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Genome-wide association study (GWAS) is nowadays widely used to identify genes involved in human complex disease. The standard GWAS analysis examines SNPs/genes independently and identifies only a number of the most significant SNPs. It ignores the combined effect of weaker SNPs/genes, which leads to difficulties to explore biological function and mechanism from a systems point of view. Although gene set enrichment analysis (GSEA) has been introduced to GWAS to overcome these limitations by identifying the correlation between pathways/gene sets and traits, the heavy dependence on genotype data, which is not easily available for most published GWAS investigations, has led to limited application of it. In order to perform GSEA on a simple list of GWAS SNP P-values, we implemented GSEA by using SNP label permutation. We further improved GSEA (i-GSEA) by focusing on pathways/gene sets with high proportion of significant genes. To provide researchers an open platform to analyze GWAS data, we developed the i-GSEA4GWAS (improved GSEA for GWAS) web server. i-GSEA4GWAS implements the i-GSEA approach and aims to provide new insights in complex disease studies. i-GSEA4GWAS is freely available at http://gsea4gwas.psych.ac.cn/.
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Affiliation(s)
- Kunlin Zhang
- Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, 100101, Beijing, China
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322
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Tang J, Malhotra R, Song W, Brill I, Hu L, Farmer PK, Mulenga J, Allen S, Hunter E, Kaslow RA. Human leukocyte antigens and HIV type 1 viral load in early and chronic infection: predominance of evolving relationships. PLoS One 2010; 5:e9629. [PMID: 20224785 PMCID: PMC2835758 DOI: 10.1371/journal.pone.0009629] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Accepted: 02/18/2010] [Indexed: 11/18/2022] Open
Abstract
Background During untreated, chronic HIV-1 infection, plasma viral load (VL) is a relatively stable quantitative trait that has clinical and epidemiological implications. Immunogenetic research has established various human genetic factors, especially human leukocyte antigen (HLA) variants, as independent determinants of VL set-point. Methodology/Principal Findings To identify and clarify HLA alleles that are associated with either transient or durable immune control of HIV-1 infection, we evaluated the relationships of HLA class I and class II alleles with VL among 563 seroprevalent Zambians (SPs) who were seropositive at enrollment and 221 seroconverters (SCs) who became seropositive during quarterly follow-up visits. After statistical adjustments for non-genetic factors (sex and age), two unfavorable alleles (A*3601 and DRB1*0102) were independently associated with high VL in SPs (p<0.01) but not in SCs. In contrast, favorable HLA variants, mainly A*74, B*13, B*57 (or Cw*18), and one HLA-A and HLA-C combination (A*30+Cw*03), dominated in SCs; their independent associations with low VL were reflected in regression beta estimates that ranged from −0.47±0.23 to −0.92±0.32 log10 in SCs (p<0.05). Except for Cw*18, all favorable variants had diminishing or vanishing association with VL in SPs (p≤0.86). Conclusions/Significance Overall, each of the three HLA class I genes had at least one allele that might contribute to effective immune control, especially during the early course of HIV-1 infection. These observations can provide a useful framework for ongoing analyses of viral mutations induced by protective immune responses.
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Affiliation(s)
- Jianming Tang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America.
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323
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Rotger M, Dang KK, Fellay J, Heinzen EL, Feng S, Descombes P, Shianna KV, Ge D, Günthard HF, Goldstein DB, Telenti A. Genome-wide mRNA expression correlates of viral control in CD4+ T-cells from HIV-1-infected individuals. PLoS Pathog 2010; 6:e1000781. [PMID: 20195503 PMCID: PMC2829051 DOI: 10.1371/journal.ppat.1000781] [Citation(s) in RCA: 144] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Accepted: 01/20/2010] [Indexed: 12/17/2022] Open
Abstract
There is great interindividual variability in HIV-1 viral setpoint after seroconversion, some of which is known to be due to genetic differences among infected individuals. Here, our focus is on determining, genome-wide, the contribution of variable gene expression to viral control, and to relate it to genomic DNA polymorphism. RNA was extracted from purified CD4+ T-cells from 137 HIV-1 seroconverters, 16 elite controllers, and 3 healthy blood donors. Expression levels of more than 48,000 mRNA transcripts were assessed by the Human-6 v3 Expression BeadChips (Illumina). Genome-wide SNP data was generated from genomic DNA using the HumanHap550 Genotyping BeadChip (Illumina). We observed two distinct profiles with 260 genes differentially expressed depending on HIV-1 viral load. There was significant upregulation of expression of interferon stimulated genes with increasing viral load, including genes of the intrinsic antiretroviral defense. Upon successful antiretroviral treatment, the transcriptome profile of previously viremic individuals reverted to a pattern comparable to that of elite controllers and of uninfected individuals. Genome-wide evaluation of cis-acting SNPs identified genetic variants modulating expression of 190 genes. Those were compared to the genes whose expression was found associated with viral load: expression of one interferon stimulated gene, OAS1, was found to be regulated by a SNP (rs3177979, p = 4.9E-12); however, we could not detect an independent association of the SNP with viral setpoint. Thus, this study represents an attempt to integrate genome-wide SNP signals with genome-wide expression profiles in the search for biological correlates of HIV-1 control. It underscores the paradox of the association between increasing levels of viral load and greater expression of antiviral defense pathways. It also shows that elite controllers do not have a fully distinctive mRNA expression pattern in CD4+ T cells. Overall, changes in global RNA expression reflect responses to viral replication rather than a mechanism that might explain viral control.
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Affiliation(s)
- Margalida Rotger
- Institute of Microbiology, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Kristen K. Dang
- Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina, United States of America
| | - Jacques Fellay
- Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina, United States of America
| | - Erin L. Heinzen
- Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina, United States of America
| | - Sheng Feng
- Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina, United States of America
- Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina, United States of America
| | | | - Kevin V. Shianna
- Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina, United States of America
| | - Dongliang Ge
- Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina, United States of America
| | - Huldrych F. Günthard
- Division of Infectious Diseases, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - David B. Goldstein
- Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina, United States of America
| | - Amalio Telenti
- Institute of Microbiology, University Hospital and University of Lausanne, Lausanne, Switzerland
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