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Singh M, Leddy SM, Iñiguez LP, Bendall ML, Nixon DF, Feschotte C. Transposable elements may enhance antiviral resistance in HIV-1 elite controllers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.11.571123. [PMID: 38168352 PMCID: PMC10760019 DOI: 10.1101/2023.12.11.571123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Less than 0.5% of people living with HIV-1 are elite controllers (ECs) - individuals who have a replication-competent viral reservoir in their CD4+ T cells but maintain undetectable plasma viremia without the help of antiretroviral therapy. While the EC CD4+ T cell transcriptome has been investigated for gene expression signatures associated with disease progression (or, in this case, a lack thereof), the expression and regulatory activity of transposable elements (TEs) in ECs has not been explored. Yet previous studies have established that TEs can directly impact the immune response to pathogens, including HIV-1. Thus, we hypothesize that the regulatory activities of TEs could contribute to the natural resistance of ECs against HIV-1. We perform a TE-centric analysis of previously published multi-omics data derived from EC individuals and other populations. We find that the CD4+ T cell transcriptome and retrotranscriptome of ECs are distinct from healthy controls, treated patients, and viremic progressors. However, there is a substantial level of transcriptomic heterogeneity among ECs. We categorize individuals with distinct chromatin accessibility and expression profiles into four clusters within the EC group, each possessing unique repertoires of TEs and antiviral factors. Notably, several TE families with known immuno-regulatory activity are differentially expressed among ECs. Their transcript levels in ECs positively correlate with their chromatin accessibility and negatively correlate with the expression of their KRAB zinc-finger (KZNF) repressors. This coordinated variation is seen at the level of individual TE loci likely acting or, in some cases, known to act as cis-regulatory elements for nearby genes involved in the immune response and HIV-1 restriction. Based on these results, we propose that the EC phenotype is driven in part by the reduced availability of specific KZNF proteins to repress TE-derived cis-regulatory elements for antiviral genes, thereby heightening their basal level of resistance to HIV-1 infection. Our study reveals considerable heterogeneity in the CD4+ T cell transcriptome of ECs, including variable expression of TEs and their KZNF controllers, that must be taken into consideration to decipher the mechanisms enabling HIV-1 control.
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Affiliation(s)
- Manvendra Singh
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
- Clinical Neuroscience, Max Planck Institute for Multidisciplinary Sciences, City Campus, Göttingen, Germany
| | - Sabrina M Leddy
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Luis Pedro Iñiguez
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Matthew L Bendall
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Douglas F Nixon
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
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Ellinger B, Pohlmann D, Woens J, Jäkel FM, Reinshagen J, Stocking C, Prassolov VS, Fehse B, Riecken K. A High-Throughput HIV-1 Drug Screening Platform, Based on Lentiviral Vectors and Compatible with Biosafety Level-1. Viruses 2020; 12:E580. [PMID: 32466195 PMCID: PMC7290285 DOI: 10.3390/v12050580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/19/2020] [Accepted: 05/20/2020] [Indexed: 11/17/2022] Open
Abstract
HIV-1 infection is a complex, multi-step process involving not only viral, but also multiple cellular factors. To date, drug discovery methods have primarily focused on the inhibition of single viral proteins. We present an efficient and unbiased approach, compatible with biosafety level 1 (BSL-1) conditions, to identify inhibitors of HIV-1 reverse transcription, intracellular trafficking, nuclear entry and genome integration. Starting with a fluorescent assay setup, we systematically improved the screening methodology in terms of stability, efficiency and pharmacological relevance. Stability and throughput were optimized by switching to a luciferase-based readout. BSL-1 compliance was achieved without sacrificing pharmacological relevance by using lentiviral particles pseudo-typed with the mouse ecotropic envelope protein to transduce human PM1 T cells gene-modified to express the corresponding murine receptor. The cellular assay was used to screen 26,048 compounds selected for maximum diversity from a 200,640-compound in-house library. This yielded z' values greater than 0.8 with a hit rate of 3.3% and a confirmation rate of 50%. We selected 93 hits and enriched the collection with 279 similar compounds from the in-house library to identify promising structural features. The most active compounds were validated using orthogonal assay formats. The similarity of the compound profiles across the different platforms demonstrated that the reported lentiviral assay system is a robust and versatile tool for the identification of novel HIV-1 inhibitors.
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Affiliation(s)
- Bernhard Ellinger
- Department ScreeningPort, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, 22525 Hamburg, Germany; (B.E.); (J.R.)
- Fraunhofer Cluster of Excellence Immune-Mediated Diseases CIMD, Partner site Hamburg, 22525 Hamburg, Germany
| | - Daniel Pohlmann
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.P.); (J.W.); (F.M.J.); (C.S.)
| | - Jannis Woens
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.P.); (J.W.); (F.M.J.); (C.S.)
| | - Felix M. Jäkel
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.P.); (J.W.); (F.M.J.); (C.S.)
| | - Jeanette Reinshagen
- Department ScreeningPort, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, 22525 Hamburg, Germany; (B.E.); (J.R.)
- Fraunhofer Cluster of Excellence Immune-Mediated Diseases CIMD, Partner site Hamburg, 22525 Hamburg, Germany
| | - Carol Stocking
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.P.); (J.W.); (F.M.J.); (C.S.)
- Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | - Vladimir S. Prassolov
- Engelhardt-Institute of Molecular Biology, Russian Academy of Sciences, 117984 Moscow, Russia;
| | - Boris Fehse
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.P.); (J.W.); (F.M.J.); (C.S.)
- German Center for Infection Research (DZIF), Partner site Hamburg, 20246 Hamburg, Germany
| | - Kristoffer Riecken
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.P.); (J.W.); (F.M.J.); (C.S.)
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Ramsuran V, Ewy R, Nguyen H, Kulkarni S. Variation in the Untranslated Genome and Susceptibility to Infections. Front Immunol 2018; 9:2046. [PMID: 30245696 PMCID: PMC6137953 DOI: 10.3389/fimmu.2018.02046] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 08/20/2018] [Indexed: 12/11/2022] Open
Abstract
The clinical outcomes of infections are highly variable among individuals and are determined by complex host-pathogen interactions. Genome-wide association studies (GWAS) are powerful tools to unravel common genetic variations that are associated with disease risk and clinical outcomes. However, GWAS has only rarely revealed information on the exact genetic elements and their effects underlying an association because the majority of the hits are within non-coding regions. Some of the variants or the linked polymorphisms are now being discovered to have functional significance, such as regulatory elements in the promoter and enhancer regions or the microRNA binding sites in the 3′untranslated region of the protein-coding genes, which influence transcription, RNA stability, and translation of the protein-coding genes. However, only 3% of the entire transcriptome is protein-coding, signifying that non-coding RNAs represent most of the transcripts. Thus, a large portion of previously identified intergenic GWAS single nucleotide polymorphisms (SNPs) is in the non-coding RNAs. The non-coding RNAs form a large-scale regulatory network across the transcriptome, greatly expanding the complexity of gene regulation. Accumulating evidence also suggests that the “non-coding” genome regions actively regulate the highly dynamic three dimensional (3D) chromatin structures, which are critical for genome function. Epigenetic modulation like DNA methylation and histone modifications further affect chromatin accessibility and gene expression adding another layer of complexity to the functional interpretation of genetic variation associated with disease outcomes. We provide an overview of the current information on the influence of variation in these “untranslated” regions of the human genome on infectious diseases. The focus of this review is infectious disease-associated polymorphisms and gene regulatory mechanisms of pathophysiological relevance.
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Affiliation(s)
- Veron Ramsuran
- Centre for the AIDS Programme of Research in South Africa, KwaZulu-Natal Research Innovation and Sequencing Platform, School of Laboratory Medicine and Medical Sciences, Nelson R. Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Rodger Ewy
- Genetics Department, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Hoang Nguyen
- Genetics Department, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Smita Kulkarni
- Genetics Department, Texas Biomedical Research Institute, San Antonio, TX, United States
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HLA-C Alleles and Cytomegalovirus Retinitis in Brazilian Patients with AIDS. J Ophthalmol 2018; 2018:3830104. [PMID: 30245869 PMCID: PMC6139195 DOI: 10.1155/2018/3830104] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 06/13/2018] [Accepted: 07/08/2018] [Indexed: 11/17/2022] Open
Abstract
Purpose Since cytomegalovirus retinitis (CR) is an important cause of visual impairment among AIDS patients and HLA-C alleles have been associated with AIDS disease outcome, we typed HLA-C locus in patients with AIDS exhibiting or not CR. Methods Three groups of individuals were studied: (i) 49 patients with AIDS and CR (Group I), (ii) 161 patients with AIDS without CR (Group II), and (iii) 202 healthy HIV-negative individuals (Group III). HLA-C typing was performed using commercial kits. Results The HLA-C∗07 allele group was underrepresented in AIDS patients with CR (P=0.005) when compared to controls or when compared to AIDS patients without CR (P=0.006). The HLA-C∗05 allele group was overrepresented in Group II in comparison to Group III (P=0.017). The frequency of the HLA-C∗16 allele group was increased in Group III in comparison to Group II (P=0.004). Conclusion The HLA-C∗07 allele group conferred protection against the development of CR in Brazilian AIDS patients, whereas the HLA-C∗05 and HLA-C∗16 allele groups were associated with AIDS susceptibility or protection, respectively.
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Zupin L, Polesello V, Segat L, Kamada AJ, Kuhn L, Crovella S. DEFB1 polymorphisms and HIV-1 mother-to-child transmission in Zambian population. J Matern Fetal Neonatal Med 2018; 32:2805-2811. [PMID: 29506422 DOI: 10.1080/14767058.2018.1449206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Introduction: Human Beta Defensin-1 (hBD-1) is a component of the innate immune system, the first line of defence against pathogens, already reported as involved in the susceptibility to HIV-1 infection and HIV-1 mother-to-child transmission (MTCT) in different populations. We investigated the role of DEFB1 gene (encoding for hBD-1) functional polymorphisms in the susceptibility to HIV-1 MTCT in a population from Zambia. Methods: Four selected polymorphisms within DEFB1 gene, three at the 5' untranslated region (UTR), namely -52G > A (rs1799946), -44C > G (rs1800972) and -20G > A (rs11362) and one in the 3'UTR, c.*87A > G (rs1800972), were genotyped in 101 HIV-1 positive mothers (26 transmitters -27% and 75 not transmitters -73%) and 331 infants born to HIV-1 infected mothers (85 HIV-1 positive -26% and 246 exposed but not infected -74%). Results: DEFB1 c.*87-A allele was more frequent among HIV- children with respect to HIV+ (with intrauterine MTCT). Concerning DEFB1 haplotypes, GCGA haplotype resulted more represented in HIV- than HIV+ infants and DEFB1 ACGG haplotype presented increased frequency in HIV- children respect to HIV+ (with intra-partum MTCT) (p = .02, p = .002 and p = .006, respectively). Conclusions: DEFB1 polymorphisms were significantly associated with decreased risk of HIV-1 infection acquisition in the studied Zambian population suggesting that they may play a role in HIV-1 MTCT.
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Affiliation(s)
- Luisa Zupin
- a Department of Medicine, Surgery and Health Sciences , University of Trieste , Trieste , Italy
| | - Vania Polesello
- b Institute for Maternal and Child Health - IRCCS "Burlo Garofolo" , Trieste , Italy
| | - Ludovica Segat
- b Institute for Maternal and Child Health - IRCCS "Burlo Garofolo" , Trieste , Italy
| | - Anselmo Jiro Kamada
- c Department of Genetics , Federal University of Pernambuco , Recife , Brazil
| | - Louise Kuhn
- d Gertrude H. Sergievsky Center and Department of Epidemiology, Mailman School of Public Health , Columbia University , NY , USA
| | - Sergio Crovella
- b Institute for Maternal and Child Health - IRCCS "Burlo Garofolo" , Trieste , Italy
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Impact of the Polymorphism rs9264942 near the HLA-C Gene on HIV-1 DNA Reservoirs in Asymptomatic Chronically Infected Patients Initiating Antiviral Therapy. J Immunol Res 2017; 2017:8689313. [PMID: 29445759 PMCID: PMC5763112 DOI: 10.1155/2017/8689313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 10/17/2017] [Indexed: 11/17/2022] Open
Abstract
Several genome-wide association studies have identified a polymorphism located 35 kb upstream of the coding region of HLA-C gene (rs9264942; termed -35 C/T) as a host factor significantly associated with the control of HIV-1 viremia in untreated patients. The potential association of this host genetic polymorphism with the viral reservoirs has never been investigated, nor the association with the viral control in response to the treatment. In this study, we assess the influence of the polymorphism -35 C/T on the outcome of virus burden in 183 antiretroviral-naïve HIV-1-infected individuals who initiated antiviral treatment (study STIR-2102), analyzing HIV-1 RNA viremia and HIV-1 DNA reservoirs. The rs9264942 genotyping was investigated retrospectively, and plasma levels of HIV-1 RNA and peripheral blood mononuclear cell- (PBMC-) associated HIV-1 DNA were compared between carriers and noncarriers of the protective allele -35 C before antiretroviral therapy (ART), one month after ART and at the end of the study (36 months). HIV-1 RNA and HIV-1 DNA levels were both variables significantly different between carriers and noncarriers of the allele -35 C before ART. HIV-1 DNA levels remained also significantly different one month posttherapy. However, this protective effect of the -35 C allele was not maintained after long-term ART.
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Moura Rodrigues R, Plana M, Garcia F, Zupin L, Kuhn L, Crovella S. Genome-wide scan in two groups of HIV-infected patients treated with dendritic cell-based immunotherapy. Immunol Res 2017; 64:1207-1215. [PMID: 27704462 DOI: 10.1007/s12026-016-8875-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We performed a retrospective genome-wide association study in HIV-infected individuals who were treated with dendritic cell-based immunotherapy in clinical trials performed by two research groups (Spain and Brazil). We aimed to identify host genetic variants influencing treatment response. The Illumina Human Core Exome 12 v 1.0 Bead Chip with over 250,000 markers was used to analyze genetic factors affecting treatment response. Additionally, we performed a meta-analysis of the results obtained from Spanish and Brazilian patients. We identified a genetic variation (rs7935564 G allele) in TRIM22 gene, which encodes TRIM22 protein acting like a HIV restriction factor, as being associated with good response to dendritic cell-based immunotherapy. We then verified the impact of TRIM22 rs7935564 SNP in susceptibility to HIV infection and disease progression by assessing the influence of biogeographic ancestry in the distribution of allelic and genotype frequencies in three populations from Italy, Brazil and Zambia. TRIM22 rs7935564 genotyping indicated association of G rs7935564 allele with long-term non-progression of HIV disease in Italian patients, thus corroborating our hypothesis that it is involved as a restriction factor in dendritic cell-based immunotherapy response. TRIM22 rs7935564 polymorphism was associated with good response to dendritic cell-based immunotherapy. We hypothesize that in selecting patients for treatment, there is a possible bias related to the natural presence of restriction factors that are genetically determined and could influence final outcome of therapy.
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Affiliation(s)
- Ronald Moura Rodrigues
- Department of Genetics, Federal University of Pernambuco, Recife, Brazil.,Laboratory of Immunopathology Keizo Azami (LIKA), Federal University of Pernambuco, Recife, Brazil
| | - Monserrat Plana
- Retrovirology and Cellular Immunopathology Laboratory, AIDS Research Group, Catalan Project for the Development of an HIV Vaccine (HIVACAT), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Barcelona, Spain
| | - Felipe Garcia
- Infectious Diseases Unit, AIDS Research Group, Catalan Project for the Development of an HIV Vaccine (HIVACAT), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Barcelona, Spain
| | - Luisa Zupin
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Via dell'Istria 65/1, Zip code: 34137, Trieste, Italy.,Department of Medicine, Surgery and Health Sciences,, University of Trieste, Trieste, Italy
| | - Louise Kuhn
- Department of Epidemiology, Columbia University, New York, NY, USA
| | - Sergio Crovella
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Via dell'Istria 65/1, Zip code: 34137, Trieste, Italy. .,Department of Medicine, Surgery and Health Sciences,, University of Trieste, Trieste, Italy.
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Mehlotra RK, Zimmerman PA, Weinberg A. Defensin gene variation and HIV/AIDS: a comprehensive perspective needed. J Leukoc Biol 2016; 99:687-92. [PMID: 26957215 DOI: 10.1189/jlb.6ru1215-560r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 02/02/2016] [Indexed: 01/24/2023] Open
Abstract
Both α- and β-defensins have anti-human immunodeficiency virus activity. These defensins achieve human immunodeficiency virus inhibition through a variety of mechanisms, including direct binding with virions, binding to and modulation of host cell-surface receptors with disruption of intracellular signaling, and functioning as chemokines or cytokines to augment and alter adaptive immune responses. Polymorphisms in the defensin genes have been associated with susceptibility to human immunodeficiency virus infection and disease progression. However, the roles that these defensins and their genetic polymorphisms have in influencing human immunodeficiency virus/acquired immunodeficiency syndrome outcomes are not straightforward and, at times, appear contradictory. Differences in populations, study designs, and techniques for genotyping defensin gene polymorphisms may have contributed to this lack of clarity. In addition, a comprehensive approach, where both subfamilies of defensins and their all-inclusive genetic polymorphism profiles are analyzed, is lacking. Such an approach may reveal whether the human immunodeficiency virus inhibitory activities of α- and β-defensins are based on parallel or divergent mechanisms and may provide further insights into how the genetic predisposition for susceptibility or resistance to human immunodeficiency virus/acquired immunodeficiency syndrome is orchestrated between these molecules.
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Affiliation(s)
- Rajeev K Mehlotra
- Center for Global Health and Diseases, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Peter A Zimmerman
- Center for Global Health and Diseases, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Aaron Weinberg
- Department of Biological Sciences, Case Western Reserve University School of Dental Medicine, Cleveland, Ohio, USA
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McLaren PJ, Carrington M. The impact of host genetic variation on infection with HIV-1. Nat Immunol 2015; 16:577-83. [PMID: 25988890 PMCID: PMC6296468 DOI: 10.1038/ni.3147] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 03/12/2015] [Indexed: 12/16/2022]
Abstract
The outcome after infection with the human immunodeficiency virus type 1 (HIV-1) is a complex phenotype determined by interactions among the pathogen, the human host and the surrounding environment. An impact of host genetic variation on HIV-1 susceptibility was identified early in the pandemic, with a major role attributed to the genes encoding class I human leukocyte antigens (HLA) and the chemokine receptor CCR5. Studies using genome-wide data sets have underscored the strength of these associations relative to variants located throughout the rest of the genome. However, the extent to which additional polymorphisms influence HIV-1 disease progression, and how much of the variability in outcome can be attributed to host genetics, remain largely unclear. Here we discuss findings concerning the functional impact of associated variants, outline methods for quantifying the host genetic component and examine how available genome-wide data sets may be leveraged to discover gene variants that affect the outcome of HIV-1 infection.
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Affiliation(s)
- Paul J McLaren
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Mary Carrington
- 1] Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA. [2] The Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
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Vince N, Bashirova AA, Lied A, Gao X, Dorrell L, McLaren PJ, Fellay J, Carrington M. HLA class I and KIR genes do not protect against HIV type 1 infection in highly exposed uninfected individuals with hemophilia A. J Infect Dis 2014; 210:1047-51. [PMID: 24719475 PMCID: PMC4215081 DOI: 10.1093/infdis/jiu214] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 03/26/2014] [Indexed: 01/15/2023] Open
Abstract
A recent genome-wide association study (GWAS) involving patients with hemophilia A who were exposed to but uninfected with human immunodeficiency virus type 1 (HIV-1) did not reveal genetic variants associated with resistance to HIV-1 infection, beyond homozygosity for CCR5-Δ32. Since variation in HLA class I and KIR genes is not well interrogated by standard GWAS techniques, we tested whether these 2 loci were involved in protection from HIV-1 infection in the same hemophilia cohort, using controls from the general population. Our data indicate that HLA class I alleles, presence or absence of KIR genes, and functionally relevant combinations of the HLA/KIR genotypes are not involved in resistance to parenterally transmitted HIV-1 infection.
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Affiliation(s)
- Nicolas Vince
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Maryland
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts
| | - Arman A. Bashirova
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Maryland
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts
| | - Alexandra Lied
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts
| | - Xiaojiang Gao
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Maryland
| | - Lucy Dorrell
- Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Paul J. McLaren
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jacques Fellay
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Mary Carrington
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Maryland
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts
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