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Neuner-Jehle N, Zeeb M, Thorball CW, Fellay J, Metzner KJ, Frischknecht P, Neumann K, Leeman C, Rauch A, Stöckle M, Huber M, Perreau M, Bernasconi E, Notter J, Hoffmann M, Leuzinger K, Günthard HF, Pasin C, Kouyos RD. Using viral diversity to identify HIV-1 variants under HLA-dependent selection in a systematic viral genome-wide screen. PLoS Pathog 2024; 20:e1012385. [PMID: 39116192 PMCID: PMC11335148 DOI: 10.1371/journal.ppat.1012385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 08/20/2024] [Accepted: 07/02/2024] [Indexed: 08/10/2024] Open
Abstract
The pathogenesis of HIV-1 infection is governed by a highly dynamic, time-dependent interaction between the host and the viral genome. In this study, we developed a novel systematic approach to assess the host-virus interaction, using average pairwise viral diversity as a proxy for time since infection, and applied this method to nearly whole viral genome sequences (n = 4,464), human leukocyte antigen (HLA) genotyping data (n = 1,044), and viral RNA load (VL) measurements during the untreated chronic phase (n = 829) of Swiss HIV Cohort Study participants. Our systematic genome-wide screen revealed for 98 HLA/viral-variant pairs a signature of immune-driven selection in the form of an HLA-dependent effect of infection time on the presence of HIV amino acid variants. Of these pairs, 12 were found to have an effect on VL. Furthermore, 28/58 pairs were validated by time-to-event analyses and 48/92 by computational HLA-epitope predictions. Our diversity-based approach allows a powerful and systematic investigation of the interaction between the virus and cellular immunity, revealing a notable subset of such interaction effects. From an evolutionary perspective, these observations underscore the complexity of HLA-mediated selection pressures on the virus that shape viral evolution and pathogenesis.
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Affiliation(s)
- Nadia Neuner-Jehle
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Marius Zeeb
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Christian W. Thorball
- Precision Medicine Unit, Biomedical Data Science Center, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Jacques Fellay
- Precision Medicine Unit, Biomedical Data Science Center, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Karin J. Metzner
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Paul Frischknecht
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Kathrin Neumann
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Christine Leeman
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Marcel Stöckle
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Matthieu Perreau
- Divisions of Immunology and Allergy, Lausanne University Hospital, Lausanne, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Ente Ospedaliero Cantonale, Lugano, University of Geneva and University of Southern Switzerland, Lugano, Switzerland
| | - Julia Notter
- Division of Infectious Diseases, Infection Prevention and Travel Medicine, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Matthias Hoffmann
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital Olten, Olten, Switzerland
| | | | - Huldrych F. Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Chloé Pasin
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
- Collegium Helveticum, Zurich, Switzerland
| | - Roger D. Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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Murray DD, Grund B, MacPherson CR, Ekenberg C, Zucco AG, Reekie J, Dominguez-Dominguez L, Leung P, Fusco D, Gras J, Gerstoft J, Helleberg M, Borges ÁH, Polizzotto MN, Lundgren JD. Association between ten-eleven methylcytosine dioxygenase 2 genetic variation and viral load in people with HIV. AIDS 2023; 37:379-387. [PMID: 36473831 PMCID: PMC9894145 DOI: 10.1097/qad.0000000000003427] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 09/29/2022] [Accepted: 11/02/2022] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Identifying genetic factors that influence HIV-pathogenesis is critical for understanding disease pathways. Previous studies have suggested a role for the human gene ten-eleven methylcytosine dioxygenase 2 (TET2) in modulating HIV-pathogenesis. METHODS We assessed whether genetic variation in TET2 was associated with markers of HIV-pathogenesis using both gene level and single nucleotide polymorphism (SNP) level association in 8512 HIV-positive persons across five clinical trial cohorts. RESULTS Variation at both the gene and SNP-level of TET2 was found to be associated with levels of HIV viral load (HIV-VL) consistently in the two cohorts that recruited antiretroviral-naïve participants. The SNPs occurred in two clusters of high linkage disequilibrium (LD), one associated with high HIV-VL and the other low HIV-VL, and were predominantly found in Black participants. CONCLUSION Genetic variation in TET2 was associated with HIV-VL in two large antiretroviral therapy (ART)-naive clinical trial cohorts. The role of TET2 in HIV-pathogenesis warrants further investigation.
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Affiliation(s)
- Daniel D. Murray
- Centre of Excellence for Health, Immunity and Infections (CHIP), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Birgit Grund
- School of Statistics, University of Minnesota, Minneapolis, MN, USA
| | - Cameron R. MacPherson
- Centre of Excellence for Health, Immunity and Infections (CHIP), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Christina Ekenberg
- Centre of Excellence for Health, Immunity and Infections (CHIP), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Adrian G. Zucco
- Centre of Excellence for Health, Immunity and Infections (CHIP), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Joanne Reekie
- Centre of Excellence for Health, Immunity and Infections (CHIP), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Lourdes Dominguez-Dominguez
- Centre of Excellence for Health, Immunity and Infections (CHIP), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Preston Leung
- Centre of Excellence for Health, Immunity and Infections (CHIP), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Dahlene Fusco
- Tulane University Medical Center, Tulane University, New Orleans, LA, USA
| | - Julien Gras
- Service de Maladies infectieuses et tropicales, APHP-Hôpital Saint Louis, Paris, France
| | - Jan Gerstoft
- Department of Infectious Diseases, Copenhagen University Hospital, Rigshospitalet
| | - Marie Helleberg
- Centre of Excellence for Health, Immunity and Infections (CHIP), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital, Rigshospitalet
| | - Álvaro H. Borges
- Centre of Excellence for Health, Immunity and Infections (CHIP), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases Immunology, Statens Serum Institut, Copenhagen, Denmark
| | - Mark N. Polizzotto
- Clinical Hub for Interventional Research, College of Health and Medicine, The Australian National University, Canberra, Australia
| | - Jens D. Lundgren
- Centre of Excellence for Health, Immunity and Infections (CHIP), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
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Genome-wide association study reveals genetic variants associated with HIV-1C infection in a Botswana study population. Proc Natl Acad Sci U S A 2021; 118:2107830118. [PMID: 34782459 DOI: 10.1073/pnas.2107830118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2021] [Indexed: 11/18/2022] Open
Abstract
Although there have been many studies of gene variant association with different stages of HIV/AIDS progression in United States and European cohorts, few gene-association studies have assessed genic determinants in sub-Saharan African populations, which have the highest density of HIV infections worldwide. We carried out genome-wide association studies on 766 study participants at risk for HIV-1 subtype C (HIV-1C) infection in Botswana. Three gene associations (AP3B1, PTPRA, and NEO1) were shown to have significant association with HIV-1C acquisition. Each gene association was replicated within Botswana or in the United States-African American or United States-European American AIDS cohorts or in both. Each associated gene has a prior reported influence on HIV/AIDS pathogenesis. Thirteen previously discovered AIDS restriction genes were further replicated in the Botswana cohorts, extending our confidence in these prior AIDS restriction gene reports. This work presents an early step toward the identification of genetic variants associated with and affecting HIV acquisition or AIDS progression in the understudied HIV-1C afflicted Botswana population.
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Le Clerc S, Limou S, Zagury JF. Large-Scale "OMICS" Studies to Explore the Physiopatholgy of HIV-1 Infection. Front Genet 2019; 10:799. [PMID: 31572435 PMCID: PMC6754074 DOI: 10.3389/fgene.2019.00799] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 07/30/2019] [Indexed: 12/23/2022] Open
Abstract
In this review, we present the main large-scale experimental studies that have been performed in the HIV/AIDS field. These “omics” studies are based on several technologies including genotyping, RNA interference, and transcriptome or epigenome analysis. Due to the direct connection with disease evolution, there has been a large focus on genotyping cohorts of well-characterized patients through genome-wide association studies (GWASs), but there have also been several invitro studies such as small interfering RNA (siRNA) interference or transcriptome analyses of HIV-1–infected cells. After describing the major results obtained with these omics technologies—including some with a high relevance for HIV-1 treatment—we discuss the next steps that the community needs to embrace in order to derive new actionable therapeutic or diagnostic targets. Only integrative approaches that combine all big data results and consider their complex interactions will allow us to capture the global picture of HIV molecular pathogenesis. This novel challenge will require large collaborative efforts and represents a huge open field for innovative bioinformatics approaches.
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Affiliation(s)
- Sigrid Le Clerc
- Laboratoire GBCM, EA7528, Conservatoire National des Arts et Métiers, HESAM Université, Paris, France
| | - Sophie Limou
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation en Urologie et Néphrologie (ITUN), CHU de Nantes, Nantes, France.,Computer Sciences and Mathematics Department, Ecole Centrale de Nantes, Nantes, France
| | - Jean-François Zagury
- Laboratoire GBCM, EA7528, Conservatoire National des Arts et Métiers, HESAM Université, Paris, France
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Tsiara CG, Nikolopoulos GK, Dimou NL, Pantavou KG, Bagos PG, Mensah B, Talias M, Braliou GG, Paraskeva D, Bonovas S, Hatzakis A. Interleukin gene polymorphisms and susceptibility to HIV-1 infection: a meta-analysis. J Genet 2018; 97:235-251. [PMID: 29666343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Some subjects are repeatedly exposed to human immunodeficiency virus (HIV), yet they remain uninfected. This suggests the existence of host-resistance mechanisms. The current study synthesizes the evidence regarding the association between interleukin (IL) gene polymorphisms and HIV susceptibility. Medline, Scopus and the Web of Science databases were systematically searched, and a meta-analysis of case-control studies was conducted. Univariate and bivariate methods were used. The literature search identified 42 eligible studies involving 15,727 subjects. Evidence was obtained on eight single-nucleotide polymorphisms (SNPs): IL1A -889 C>T (rs1800587), IL1B +3953/4 C>T (rs1143634), IL4 -589/90 C>T (rs2243250), IL6 -174 G>C (rs1800795), IL10 -592 C>A (rs1800872), IL10-1082 A>G (rs1800896), IL12B -1188 A>C (rs3212227) and IL28B C>T (rs12979860). The IL1B +3953/4 C>T variant appears to increase the risk of HIV acquisition, under the assumption of a recessive genetic model (odds ratio (OR): 4.47, 95% CI: 2.35-8.52). The AA homozygotes of the IL10 -592 C>A SNP had an increased, marginally nonsignificant, risk (OR: 1.39, 95% CI: 0.97-2.01). It reached, however, significance in sub analyses (OR: 1.49, 95% CI: 1.04-2.12). Finally, the well-studied hepatitis C virus (HCV) infection IL28B (rs12979860) CT/TT genotypes were associated with a 27% decrease in HIV infection risk, especially in populations infected with HCV (OR: 0.73, 95% CI: 0.57-0.95). Interleukin signalling is perhaps important in HIV infection and some interleukin genetic variants may affect the risk of HIV acquisition. Approaches targeting specific genes and genome wide association studies should be conducted to decipher the effect of these polymorphisms.
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Affiliation(s)
- Chrissa G Tsiara
- Hellenic Centre for Disease Control and Prevention, 15123 Athens, Greece. ,
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Carignano HA, Roldan DL, Beribe MJ, Raschia MA, Amadio A, Nani JP, Gutierrez G, Alvarez I, Trono K, Poli MA, Miretti MM. Genome-wide scan for commons SNPs affecting bovine leukemia virus infection level in dairy cattle. BMC Genomics 2018; 19:142. [PMID: 29439661 PMCID: PMC5812220 DOI: 10.1186/s12864-018-4523-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 02/01/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Bovine leukemia virus (BLV) infection is omnipresent in dairy herds causing direct economic losses due to trade restrictions and lymphosarcoma-related deaths. Milk production drops and increase in the culling rate are also relevant and usually neglected. The BLV provirus persists throughout a lifetime and an inter-individual variation is observed in the level of infection (LI) in vivo. High LI is strongly correlated with disease progression and BLV transmission among herd mates. In a context of high prevalence, classical control strategies are economically prohibitive. Alternatively, host genomics studies aiming to dissect loci associated with LI are potentially useful tools for genetic selection programs tending to abrogate the viral spreading. The LI was measured through the proviral load (PVL) set-point and white blood cells (WBC) counts. The goals of this work were to gain insight into the contribution of SNPs (bovine 50KSNP panel) on LI variability and to identify genomics regions underlying this trait. RESULTS We quantified anti-p24 response and total leukocytes count in peripheral blood from 1800 cows and used these to select 800 individuals with extreme phenotypes in WBCs and PVL. Two case-control genomic association studies using linear mixed models (LMMs) considering population stratification were performed. The proportion of the variance captured by all QC-passed SNPs represented 0.63 (SE ± 0.14) of the phenotypic variance for PVL and 0.56 (SE ± 0.15) for WBCs. Overall, significant associations (Bonferroni's corrected -log10p > 5.94) were shared for both phenotypes by 24 SNPs within the Bovine MHC. Founder haplotypes were used to measure the linkage disequilibrium (LD) extent (r2 = 0.22 ± 0.27 at inter-SNP distance of 25-50 kb). The SNPs and LD blocks indicated genes potentially associated with LI in infected cows: i.e. relevant immune response related genes (DQA1, DRB3, BOLA-A, LTA, LTB, TNF, IER3, GRP111, CRISP1), several genes involved in cell cytoskeletal reorganization (CD2AP, PKHD1, FLOT1, TUBB5) and modelling of the extracellular matrix (TRAM2, TNXB). Host transcription factors (TFs) were also highlighted (TFAP2D; ABT1, GCM1, PRRC2A). CONCLUSIONS Data obtained represent a step forward to understand the biology of BLV-bovine interaction, and provide genetic information potentially applicable to selective breeding programs.
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Affiliation(s)
- Hugo A. Carignano
- Instituto Nacional de Tecnología Agropecuaria (INTA). Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA). Instituto de Genética, B1686 Hurlingham, Argentina
| | - Dana L. Roldan
- Instituto Nacional de Tecnología Agropecuaria (INTA). Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA). Instituto de Genética, B1686 Hurlingham, Argentina
| | - María J. Beribe
- Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Pergamino, B2700 Pergamino, Argentina
| | - María A. Raschia
- Instituto Nacional de Tecnología Agropecuaria (INTA). Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA). Instituto de Genética, B1686 Hurlingham, Argentina
| | - Ariel Amadio
- Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Rafaela, S2300, Rafaela, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1033AAJ Ciudad Autónoma de Buenos Aires, Argentina
| | - Juan P. Nani
- Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Rafaela, S2300, Rafaela, Argentina
| | - Gerónimo Gutierrez
- Instituto Nacional de Tecnología Agropecuaria (INTA). Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA). Instituto de Virología, B686 Hurlingham, Argentina
| | - Irene Alvarez
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1033AAJ Ciudad Autónoma de Buenos Aires, Argentina
- Instituto Nacional de Tecnología Agropecuaria (INTA). Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA). Instituto de Virología, B686 Hurlingham, Argentina
| | - Karina Trono
- Instituto Nacional de Tecnología Agropecuaria (INTA). Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA). Instituto de Virología, B686 Hurlingham, Argentina
| | - Mario A. Poli
- Instituto Nacional de Tecnología Agropecuaria (INTA). Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA). Instituto de Genética, B1686 Hurlingham, Argentina
| | - Marcos M. Miretti
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1033AAJ Ciudad Autónoma de Buenos Aires, Argentina
- Grupo de Investigación en Genética Aplicada, Instituto de Biología Subtropical (GIGA - IBS), Universidad Nacional de Misiones, N3300 Posadas, Argentina
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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] [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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Grotto RMT, Picelli N, de Souza LDR, Silva GF, Ferrasi AC, Silveira LVDA, Pardini MIDMC. Human Platelet Polymorphism can be a genetic marker associated with HIV/HCV coinfection. J Med Virol 2015; 87:1677-81. [PMID: 25976501 DOI: 10.1002/jmv.24233] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2015] [Indexed: 11/10/2022]
Abstract
To evaluate the associations of HPA polymorphisms -1, -3, and -5 with HIV/HCV coinfection were included in this study 60 HIV/HCV-coinfected patients from the Sao Paulo State health service centers. Data reported by Verdichio-Moraes et al. (2009: J. Med Virol 81:757-759) were used as the non-infected and HCV monoinfected groups. Human Platelet Polymorphism genotyping was performed in 60 Patients co-infected with HIV/HCV by PCR-SSP or PCR-RFLP. HIV subtyping and HCV genotyping was performed by RT-PCR followed sequencing. The data analyses were performed using the χ2 test or Fisher's Exact Test and the logistic regression model. Patients coinfected with HIV/HCV presented HCV either genotype 1 (78.3%) or non-1 (21.7%) and HIV either subtype B (85.0%) or non-B (15%). The Human Platelet Polymorphism-1a/1b genotype was more frequent (P < 0.05) in HIV/HCV coinfection than in HCV monoinfection and the allelic frequency of Human Platelet Polymorphism-5b in the Patients coinfected with HIV/HCV was higher (P < 0.05) than in HCV monoinfected cases and non-infected individuals. These data suggest that the presence of specific HPA allele on platelets could favor the existence of coinfection. On the other hand, Human Platelet Polymorphism-5a/5b was more frequent (P < 0.05) in HIV/HCV coinfected and HCV monoinfected groups than in the non-infected individuals, suggesting that this platelet genotype is related to HCV infection, regardless of HIV presence. Results suggest that the Human Platelet Polymorphism profile in HIV/HCV coinfected individuals differs from the one of both HCV monoinfected and non-infected population. So, the Human Platelet Polymorphism can be a genetic marker associated with HIV/HCV coinfection.
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Affiliation(s)
- Rejane Maria Tommasini Grotto
- Molecular Biology Laboratory, Blood Transfusion Center, Botucatu Medical School, Sao Paulo State University, UNESP, São Paulo, Brazil.,Department of Bioprocess and Biotechnology, School of Agricultural Sciences, Lageado Experiment Station. Sao Paulo State University, UNESP, Botucatu-SP, Brazil
| | - Natália Picelli
- Molecular Biology Laboratory, Blood Transfusion Center, Botucatu Medical School, Sao Paulo State University, UNESP, São Paulo, Brazil
| | - Lenice do Rosário de Souza
- Tropical Diseases Department, Botucatu Medical School, Sao Paulo State University UNESP, São Paulo, Brazil
| | - Giovanni Faria Silva
- Department of Internal Medicine, Botucatu Medical School, Sao Paulo State University UNESP, São Paulo, Brazil
| | - Adriana Camargo Ferrasi
- Molecular Biology Laboratory, Blood Transfusion Center, Botucatu Medical School, Sao Paulo State University, UNESP, São Paulo, Brazil.,Department of Internal Medicine, Botucatu Medical School, Sao Paulo State University UNESP, São Paulo, Brazil
| | | | - Maria Inês de Moura Campos Pardini
- Molecular Biology Laboratory, Blood Transfusion Center, Botucatu Medical School, Sao Paulo State University, UNESP, São Paulo, Brazil.,Department of Internal Medicine, Botucatu Medical School, Sao Paulo State University UNESP, São Paulo, Brazil
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Qin M, Brummel S, Singh KK, Fenton T, Spector SA. Associations of host genetic variants on CD4⁺ lymphocyte count and plasma HIV-1 RNA in antiretroviral naïve children. Pediatr Infect Dis J 2014; 33:946-52. [PMID: 24797997 PMCID: PMC4216611 DOI: 10.1097/inf.0000000000000330] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND CD4 T-lymphocyte (CD4) counts and HIV plasma RNA concentration (RNA) are 2 key HIV disease markers. The complex interplay between virus and host genetics may contribute to differences in viral set point and CD4 status. Determining the effects of host genetic variation on HIV disease markers is often complicated by the use of antiretroviral therapy. In this study, the association between genetic variants and baseline HIV RNA and CD4 counts was examined in a large cohort of antiretroviral naïve children. METHODS Specimens from 1053 HIV-infected children were screened for single nucleotide polymorphisms in 78 regions from 17 genes. Linear regression with a robust variance estimator was used to test the association between genetic markers with HIV RNA and CD4 count, controlling for age, race/ethnicity and study. False discovery rate (FDR) controlling was used to adjust for multiple testing. RESULTS The study population was 60% black, 26% Hispanic and 13% white; median age 2.35 years; 55% female. Baseline median CD4 count was 780/mm; median log10 HIV RNA was 5.17 copies/mL. For analyses of the associations of genetic makers with baseline CD4 count, 6 HLA and 4 additional markers exhibited P < 0.05, but none met the criteria for statistical significance with FDR controlled at 0.05. For baseline HIV RNA, HLA DRB1*15, DRB1*10, B-27/57, B-14, Cw-8, B-57 were statistically significant with FDR controlled at 0.05. CONCLUSIONS These results provide strong evidence that HLA DRB1*15, DRB1*10, B-27/57, B-14, Cw-8, B-57 are associated with HIV RNA and play a role in HIV pathogenesis in infected children.
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Affiliation(s)
- Min Qin
- Center for Biostatistics in AIDS Research, Harvard School of Public Health, Boston, MA
| | - Sean Brummel
- Center for Biostatistics in AIDS Research, Harvard School of Public Health, Boston, MA
| | - Kumud K. Singh
- University of California, San Diego, La Jolla, CA and Rady Children’s Hospital, San Diego, CA
| | - Terry Fenton
- Center for Biostatistics in AIDS Research, Harvard School of Public Health, Boston, MA
| | - Stephen A. Spector
- University of California, San Diego, La Jolla, CA and Rady Children’s Hospital, San Diego, CA
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11
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Karlsson EK, Sigurdsson S, Ivansson E, Thomas R, Elvers I, Wright J, Howald C, Tonomura N, Perloski M, Swofford R, Biagi T, Fryc S, Anderson N, Courtay-Cahen C, Youell L, Ricketts SL, Mandlebaum S, Rivera P, von Euler H, Kisseberth WC, London CA, Lander ES, Couto G, Comstock K, Starkey MP, Modiano JF, Breen M, Lindblad-Toh K. Genome-wide analyses implicate 33 loci in heritable dog osteosarcoma, including regulatory variants near CDKN2A/B. Genome Biol 2013; 14:R132. [PMID: 24330828 PMCID: PMC4053774 DOI: 10.1186/gb-2013-14-12-r132] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 12/12/2013] [Indexed: 11/16/2022] Open
Abstract
Background Canine osteosarcoma is clinically nearly identical to the human disease, but is common and highly heritable, making genetic dissection feasible. Results Through genome-wide association analyses in three breeds (greyhounds, Rottweilers, and Irish wolfhounds), we identify 33 inherited risk loci explaining 55% to 85% of phenotype variance in each breed. The greyhound locus exhibiting the strongest association, located 150 kilobases upstream of the genes CDKN2A/B, is also the most rearranged locus in canine osteosarcoma tumors. The top germline candidate variant is found at a >90% frequency in Rottweilers and Irish wolfhounds, and alters an evolutionarily constrained element that we show has strong enhancer activity in human osteosarcoma cells. In all three breeds, osteosarcoma-associated loci and regions of reduced heterozygosity are enriched for genes in pathways connected to bone differentiation and growth. Several pathways, including one of genes regulated by miR124, are also enriched for somatic copy-number changes in tumors. Conclusions Mapping a complex cancer in multiple dog breeds reveals a polygenic spectrum of germline risk factors pointing to specific pathways as drivers of disease.
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12
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Limou S, Zagury JF. Immunogenetics: Genome-Wide Association of Non-Progressive HIV and Viral Load Control: HLA Genes and Beyond. Front Immunol 2013; 4:118. [PMID: 23750159 PMCID: PMC3664380 DOI: 10.3389/fimmu.2013.00118] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 05/04/2013] [Indexed: 01/11/2023] Open
Abstract
Very early after the identification of the human immunodeficiency virus (HIV), host genetics factors were anticipated to play a role in viral control and disease progression. As early as the mid-1990s, candidate gene studies demonstrated a central role for the chemokine co-receptor/ligand (e.g., CCR5) and human leukocyte antigen (HLA) systems. In the last decade, the advent of genome-wide arrays opened a new era for unbiased genetic exploration of the genome and brought big expectations for the identification of new unexpected genes and pathways involved in HIV/AIDS. More than 15 genome-wide association studies targeting various HIV-linked phenotypes have been published since 2007. Surprisingly, only the two HIV-chemokine co-receptors and HLA loci have exhibited consistent and reproducible statistically significant genetic associations. In this chapter, we will review the findings from the genome-wide studies focusing especially on non-progressive and HIV control phenotypes, and discuss the current perspectives.
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Affiliation(s)
- Sophie Limou
- Basic Science Program, Basic Research Laboratory, Frederick National Laboratory for Cancer ResearchFrederick, MD, USA
| | - Jean-François Zagury
- Chaire de Bioinformatique, Laboratoire Génomique Bioinformatique et Applications (EA 4627), Conservatoire National des Arts et MétiersParis, France
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13
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Messiaen P, De Spiegelaere W, Alcami J, Vervisch K, Van Acker P, Verhasselt B, Meuwissen P, Calonge E, Gonzalez N, Gutierrez-Rodero F, Rodriguez-Martín C, Sermijn E, Poppe B, Vogelaers D, Verhofstede C, Vandekerckhove L. Characterization of LEDGF/p75 genetic variants and association with HIV-1 disease progression. PLoS One 2012; 7:e50204. [PMID: 23226247 PMCID: PMC3511443 DOI: 10.1371/journal.pone.0050204] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 10/16/2012] [Indexed: 12/24/2022] Open
Abstract
Background As Lens epithelium-derived growth factor (LEDGF/p75) is an important co-factor involved in HIV-1 integration, the LEDGF/p75-IN interaction is a promising target for the new class of allosteric HIV integrase inhibitors (LEDGINs). Few data are available on the genetic variability of LEDGF/p75 and the influence on HIV disease in vivo. This study evaluated the relation between LEDGF/p75 genetic variation, mRNA expression and HIV-1 disease progression in order to guide future clinical use of LEDGINs. Methods Samples were derived from a therapy-naïve cohort at Ghent University Hospital and a Spanish long-term-non-progressor cohort. High-resolution melting curve analysis and Sanger sequencing were used to identify all single nucleotide polymorphisms (SNPs) in the coding region, flanking intronic regions and full 3′UTR of LEDGF/p75. In addition, two intronic tagSNPs were screened based on previous indication of influencing HIV disease. LEDGF/p75 mRNA was quantified in patient peripheral blood mononuclear cells (PBMC) using RT-qPCR. Results 325 samples were investigated from patients of Caucasian (n = 291) and African (n = 34) origin, including Elite (n = 49) and Viremic controllers (n = 62). 21 SNPs were identified, comprising five in the coding region and 16 in the non-coding regions and 3′UTR. The variants in the coding region were infrequent and had no major impact on protein structure according to SIFT and PolyPhen score. One intronic SNP (rs2737828) was significantly under-represented in Caucasian patients (P<0.0001) compared to healthy controls (HapMap). Two SNPs showed a non-significant trend towards association with slower disease progression but not with LEDGF/p75 expression. The observed variation in LEDGF/p75 expression was not correlated with disease progression. Conclusions LEDGF/p75 is a highly conserved protein. Two non-coding polymorphisms were identified indicating a correlation with disease outcome, but further research is needed to clarify phenotypic impact. The conserved coding region and the observed variation in LEDGF/p75 expression are important characteristics for clinical use of LEDGINs.
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Affiliation(s)
- Peter Messiaen
- HIV Translational Research Unit, Department of General Internal Medicine and Infectious Diseases, Ghent University Hospital, Ghent, Belgium
| | - Ward De Spiegelaere
- HIV Translational Research Unit, Department of General Internal Medicine and Infectious Diseases, Ghent University Hospital, Ghent, Belgium
| | - Jose Alcami
- Unidad de Inmunopatología del SIDA, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Karen Vervisch
- HIV Translational Research Unit, Department of General Internal Medicine and Infectious Diseases, Ghent University Hospital, Ghent, Belgium
| | - Petra Van Acker
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Bruno Verhasselt
- Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium
| | - Pieter Meuwissen
- Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium
| | - Esther Calonge
- Unidad de Inmunopatología del SIDA, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Nuria Gonzalez
- Unidad de Inmunopatología del SIDA, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | | | | | - Erica Sermijn
- HIV Translational Research Unit, Department of General Internal Medicine and Infectious Diseases, Ghent University Hospital, Ghent, Belgium
| | - Bruce Poppe
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Dirk Vogelaers
- HIV Translational Research Unit, Department of General Internal Medicine and Infectious Diseases, Ghent University Hospital, Ghent, Belgium
| | - Chris Verhofstede
- Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium
| | - Linos Vandekerckhove
- HIV Translational Research Unit, Department of General Internal Medicine and Infectious Diseases, Ghent University Hospital, Ghent, Belgium
- Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium
- * E-mail:
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14
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Pinnetti C, Bandera A, Mangioni D, Gori A. Viral, host and therapeutic factors affecting T-cell recovery in virologically controlled HIV patients. Future Virol 2012. [DOI: 10.2217/fvl.12.80] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Despite suppressive combination antiretroviral therapy, a considerable proportion of HIV-infected patients do not achieve adequate immune recovery in terms of the CD4+ T-cell count, although they have controlled viremia values. Many questions remain for clinicians in the management of these patients, defined as immunological nonresponders, including questions about the mechanisms underlying the lack of immune restoration and possible therapeutic approaches to this particular group of patients.
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Affiliation(s)
- Carmela Pinnetti
- Division of Infectious Diseases, Department of Internal Medicine, ‘San Gerardo’ Hospital, University of Milan-Bicocca, Via Pergolesi 33, 20052 Monza, Milan, Italy
| | - Alessandra Bandera
- Division of Infectious Diseases, Department of Internal Medicine, ‘San Gerardo’ Hospital, University of Milan-Bicocca, Via Pergolesi 33, 20052 Monza, Milan, Italy
| | - Davide Mangioni
- Division of Infectious Diseases, Department of Internal Medicine, ‘San Gerardo’ Hospital, University of Milan-Bicocca, Via Pergolesi 33, 20052 Monza, Milan, Italy
| | - Andrea Gori
- Division of Infectious Diseases, Department of Internal Medicine, ‘San Gerardo’ Hospital, University of Milan-Bicocca, Via Pergolesi 33, 20052 Monza, Milan, Italy
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15
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Simpson PD, Moysi E, Wicks K, Sudan K, Rowland-Jones SL, McMichael AJ, Knight J, Gillespie GM. Functional differences exist between TNFα promoters encoding the common -237G SNP and the rarer HLA-B*5701-linked A variant. PLoS One 2012; 7:e40100. [PMID: 22808100 PMCID: PMC3396654 DOI: 10.1371/journal.pone.0040100] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 05/31/2012] [Indexed: 11/18/2022] Open
Abstract
A large body of functional and epidemiological evidence have previously illustrated the impact of specific MHC class I subtypes on clinical outcome during HIV-1 infection, and these observations have recently been re-iterated in genome wide association studies (GWAS). Yet because of the complexities surrounding GWAS-based approaches and the lack of knowledge relating to the identity of rarer single nucleotide polymorphism (SNP) variants, it has proved difficult to discover independent causal variants associated with favourable immune control. This is especially true of the candidate variants within the HLA region where many of the recently proposed disease influencing SNPs appear to reflect linkage with ‘protective’ MHC class I alleles. Yet causal MHC-linked SNPs may exist but remain overlooked owing to the complexities associated with their identification. Here we focus on the ancestral TNFα promoter −237A variant (rs361525), shown historically to be in complete linkage disequilibrium with the ‘protective’ HLA-B*5701 allele. Many of the ancestral SNPs within the extended TNFα promoter have been associated with both autoimmune conditions and disease outcomes, however, the direct role of these variants on TNFα expression remains controversial. Yet, because of the important role played by TNFα in HIV-1 infection, and given the proximity of the −237 SNP to the core promoter, its location within a putative repressor region previously characterized in mice, and its disruption of a methylation-susceptible CpG dinucleotide motif, we chose to carefully evaluate its impact on TNFα production. Using a variety of approaches we now demonstrate that carriage of the A SNP is associated with lower TNFα production, via a mechanism not readily explained by promoter methylation nor the binding of transcription factors or repressors. We propose that the −237A variant could represent a minor causal SNP that additionally contributes to the HLA-B*5701-mediated ‘protective’ effect during HIV-1 infection.
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Affiliation(s)
- Peter D Simpson
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital University of Oxford, Oxford, Oxfordshire, United Kingdom.
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What did we learn on host's genetics by studying large cohorts of HIV-1-infected patients in the genome-wide association era? Curr Opin HIV AIDS 2011; 6:290-6. [PMID: 21546832 DOI: 10.1097/coh.0b013e3283478449] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
PURPOSE OF REVIEW Genome-wide association studies (GWASs) performed in large cohorts of HIV-1-infected patients have shown that high throughput genomics can add valuable information in understanding disease progression. We report recent information gathered in the international field during the last few years and revisit the importance of well documented cohorts for genotype-phenotype association studies. RECENT FINDINGS The majority of GWASs in the HIV-1 field found that viral loads and disease progression are under the control of variants located in the major histocompatibility complex (MHC) in untreated patients. Although these experiments brought a new and more objective vision of genotype-phenotype correlations in HIV-1 disease, they also pointed out that less than 15% of the observed phenotypic variability can be explained as common genetic variants. Most of the studies have included mainly white patients and the few studies performed in Africans are underpowered but suggest that MHC is probably not the only genetic determinant influencing disease progression in this population. SUMMARY Although the first results of the GWASs in HIV disease look as a confirmation of previous findings, high throughput agnostic genomics entered the field of chronic infectious diseases and will probably unveil new genotype-phenotype associations in the future. Networks between existing cohorts leading to 'virtual mega-cohorts' will be necessary to increase the probability to discover new genetic pathways important for HIV disease. Finally, predictive models including genetic information for clinical usage is another challenge in HIV disease genetics.
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17
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Winkler C. Is there a genetic basis for health disparities in human immunodeficiency virus disease? ACTA ACUST UNITED AC 2011; 77:149-59. [PMID: 20309925 DOI: 10.1002/msj.20172] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The highest global prevalence rates for human immunodeficiency virus and acquired immune deficiency syndrome have been recorded in southern Africa; in the United States, individuals of African descent are disproportionately affected by human immunodeficiency virus infection. Human immunodeficiency virus-infected individuals with African ancestry are also estimated to have a 17-fold or greater risk for developing human immunodeficiency virus-associated nephropathy in comparison with their counterparts of non-African descent. Several recent studies have implicated genetic alleles that are more frequent in populations of African descent and increase the risk of human immunodeficiency virus infection and the risk of human immunodeficiency virus-associated neuropathy (HIVAN). The supposition that persons of African descent are more susceptible to human immunodeficiency virus infection because of an underlying genetic predisposition is not supported by available evidence. However, strong, replicated data show that the increased risk for human immunodeficiency virus-associated nephropathy, as well as other major forms of kidney disease in individuals of African descent, is due in part to MYH9 (myosin, heavy chain 9, non-muscle) renal disease susceptibility alleles that are very frequent throughout sub-Saharan Africa but are infrequent or absent in non-Africans. Selection, drift, and demographic events shape the allelic architecture of the human genome: it is expected that these events will be reflected in geographic-specific differentiation in allele frequencies for a small subset of alleles that may be associated with either increased or reduced risk for complex and infectious diseases.
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Affiliation(s)
- Cheryl Winkler
- Laboratory of Genomic Diversity, National Cancer Institute at Frederick, Frederick, MD, USA.
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18
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Keane N, John M. Biomarkers of natural and vaccine immunity against HIV. Biomark Med 2011; 5:113-6. [DOI: 10.2217/bmm.11.23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Niamh Keane
- Institute for Immunology & Infectious Diseases, Murdoch University, Perth, Western Australia
| | - Mina John
- Institute for Immunology & Infectious Diseases, Murdoch University, Perth, Western Australia and Department of Clinical Immunology, PathWest Laboratory Medicine WA, Royal Perth Hospital, Perth, Western Australia
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Mendelian randomization: potential use of genetics to enable causal inferences regarding HIV-associated biomarkers and outcomes. Curr Opin HIV AIDS 2011; 5:545-59. [PMID: 20978399 DOI: 10.1097/coh.0b013e32833f2087] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
PURPOSE OF REVIEW It is unknown whether biomarkers simply correlate with or are causal for HIV-associated outcomes. Mendelian randomization is a genetic epidemiologic approach used to disentangle causation from association. Here, we discuss the potential use of Mendelian randomization for differentiating whether biomarkers are correlating with or causal for HIV-associated outcomes. RECENT FINDINGS Mendelian randomization refers to the random allocation of alleles at the time of gamete formation. In observational epidemiology, this refers to the use of genetic variants to estimate a causal effect between a modifiable risk factor and an outcome of interest. A formal Mendelian randomization study using a genetic marker as a proxy for the biomarker has not been conducted in the HIV field. However, in the postgenomic era, this approach is being used increasingly. Examples are evidence for the causal role of BMI in blood pressure and noncausal role of C-reactive protein in coronary heart disease. We discuss the conceptual framework, uses, and limitations of Mendelian randomization in the context of HIV infection as well as specific biomarkers (IL-6, C-reactive protein) and genetic determinants (e.g., in CCR5, chemokine, and DARC genes) that associate with HIV-related outcomes. SUMMARY Making the distinction between correlation and causality has particular relevance when a biomarker (e.g., IL-6) is potentially modifiable, in which case a biomarker-guided targeted treatment strategy may be feasible. Although the tenets of Mendelian randomization rest on strong assumptions, and conducting a Mendelian randomization study in HIV infection presents many challenges, it may offer the potential to identify causal biomarkers for HIV-associated outcomes.
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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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