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Naruse TK, Konishi-Takemura M, Yanagida R, Sharma G, Vajpayee M, Terunuma H, Mehra NK, Kaur G, Kimura A. Killer cell immunoglobulin-like receptor three domains long cytoplasmic tail 1 gene *007 may modulate disease progression of human immunodeficiency virus-1 infection in the Japanese population. Int J Immunogenet 2023; 50:48-52. [PMID: 36807537 DOI: 10.1111/iji.12617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/19/2023] [Accepted: 02/06/2023] [Indexed: 02/19/2023]
Abstract
One of the KIR allele, KIR3DL1*007, was associated with the progression to acquired immunodeficiency syndrome and not with the susceptibility to HIV-1 infection in the Japanese and Indian populations, implying that KIR3DL1*007-positive NK cells might eliminate HIV-infected cells less effectively than NK cells bearing the other KIR3DL1 alleles or KIR3DS1 alleles.
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Affiliation(s)
- Taeko K Naruse
- Department of Molecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.,Department of Protozoology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Makiko Konishi-Takemura
- Department of Molecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Risa Yanagida
- Department of Molecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Gaurav Sharma
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Madhu Vajpayee
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | | | - Narinder K Mehra
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Gurvinder Kaur
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Akinori Kimura
- Department of Molecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.,Institute of Research, Tokyo Medical and Dental University, Tokyo, Japan
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2
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Douillard V, Castelli EC, Mack SJ, Hollenbach JA, Gourraud PA, Vince N, Limou S. Approaching Genetics Through the MHC Lens: Tools and Methods for HLA Research. Front Genet 2021; 12:774916. [PMID: 34925459 PMCID: PMC8677840 DOI: 10.3389/fgene.2021.774916] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/08/2021] [Indexed: 01/11/2023] Open
Abstract
The current SARS-CoV-2 pandemic era launched an immediate and broad response of the research community with studies both about the virus and host genetics. Research in genetics investigated HLA association with COVID-19 based on in silico, population, and individual data. However, they were conducted with variable scale and success; convincing results were mostly obtained with broader whole-genome association studies. Here, we propose a technical review of HLA analysis, including basic HLA knowledge as well as available tools and advice. We notably describe recent algorithms to infer and call HLA genotypes from GWAS SNPs and NGS data, respectively, which opens the possibility to investigate HLA from large datasets without a specific initial focus on this region. We thus hope this overview will empower geneticists who were unfamiliar with HLA to run MHC-focused analyses following the footsteps of the Covid-19|HLA & Immunogenetics Consortium.
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Affiliation(s)
- Venceslas Douillard
- Centre de Recherche en Transplantation et Immunologie, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Université de Nantes, Nantes, France
| | | | - Steven J. Mack
- Division of Allergy, Immunology and Bone Marrow Transplantation, Department of Pediatrics, School of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Jill A. Hollenbach
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, United States
| | - Pierre-Antoine Gourraud
- Centre de Recherche en Transplantation et Immunologie, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Université de Nantes, Nantes, France
| | - Nicolas Vince
- Centre de Recherche en Transplantation et Immunologie, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Université de Nantes, Nantes, France
| | - Sophie Limou
- Centre de Recherche en Transplantation et Immunologie, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Université de Nantes, Nantes, France
- Ecole Centrale de Nantes, Department of Computer Sciences and Mathematics in Biology, Nantes, France
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3
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Vince N, Limou S, Daya M, Morii W, Rafaels N, Geffard E, Douillard V, Walencik A, Boorgula MP, Chavan S, Vergara C, Ortega VE, Wilson JG, Lange LA, Watson H, Nicolae DL, Meyers DA, Hansel NN, Ford JG, Faruque MU, Bleecker ER, Campbell M, Beaty TH, Ruczinski I, Mathias RA, Taub MA, Ober C, Noguchi E, Barnes KC, Torgerson D, Gourraud PA. Association of HLA-DRB1∗09:01 with tIgE levels among African-ancestry individuals with asthma. J Allergy Clin Immunol 2020; 146:147-155. [PMID: 31981624 DOI: 10.1016/j.jaci.2020.01.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 12/05/2019] [Accepted: 01/08/2020] [Indexed: 12/21/2022]
Abstract
BACKGROUND Asthma is a complex chronic inflammatory disease of the airways. Association studies between HLA and asthma were first reported in the 1970s, and yet, the precise role of HLA alleles in asthma is not fully understood. Numerous genome-wide association studies were recently conducted on asthma, but were always limited to simple genetic markers (single nucleotide polymorphisms) and not complex HLA gene polymorphisms (alleles/haplotypes), therefore not capturing the biological relevance of this complex locus for asthma pathogenesis. OBJECTIVE To run the first HLA-centric association study with asthma and specific asthma-related phenotypes in a large cohort of African-ancestry individuals. METHODS We collected high-density genomics data for the Consortium on Asthma among African-ancestry Populations in the Americas (N = 4993) participants. Using computer-intensive machine-learning attribute bagging methods to infer HLA alleles, and Easy-HLA to infer HLA 5-gene haplotypes, we conducted a high-throughput HLA-centric association study of asthma susceptibility and total serum IgE (tIgE) levels in subjects with and without asthma. RESULTS Among the 1607 individuals with asthma, 972 had available tIgE levels, with a mean tIgE level of 198.7 IU/mL. We could not identify any association with asthma susceptibility. However, we showed that HLA-DRB1∗09:01 was associated with increased tIgE levels (P = 8.5 × 10-4; weighted effect size, 0.51 [0.15-0.87]). CONCLUSIONS We identified for the first time an HLA allele associated with tIgE levels in African-ancestry individuals with asthma. Our report emphasizes that by leveraging powerful computational machine-learning methods, specific/extreme phenotypes, and population diversity, we can explore HLA gene polymorphisms in depth and reveal the full extent of complex disease associations.
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Affiliation(s)
- Nicolas Vince
- Université de Nantes, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Nantes, France
| | - Sophie Limou
- Université de Nantes, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Nantes, France; Ecole Centrale de Nantes, Nantes, France
| | - Michelle Daya
- Department of Medicine, University of Colorado Denver, Aurora, Colo
| | - Wataru Morii
- Department of Medical Genetics, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Nicholas Rafaels
- Department of Medicine, University of Colorado Denver, Aurora, Colo
| | - Estelle Geffard
- Université de Nantes, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Nantes, France
| | - Venceslas Douillard
- Université de Nantes, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Nantes, France
| | - Alexandre Walencik
- Université de Nantes, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Nantes, France
| | | | - Sameer Chavan
- Department of Medicine, University of Colorado Denver, Aurora, Colo
| | | | - Victor E Ortega
- Department of Internal Medicine, Section on Pulmonary, Critical Care, Allergy and Immunologic Diseases, Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, Miss
| | - Leslie A Lange
- Department of Medicine, University of Colorado Denver, Aurora, Colo
| | - Harold Watson
- Faculty of Medical Sciences Cave Hill Campus, The University of the West Indies, Bridgetown, Barbados
| | - Dan L Nicolae
- Department of Medicine, University of Chicago, Chicago, Ill
| | - Deborah A Meyers
- Department of Medicine, University of Arizona College of Medicine, Tucson, Ariz
| | - Nadia N Hansel
- Department of Medicine, Johns Hopkins University, Baltimore, Md
| | - Jean G Ford
- Department of Medicine, Einstein Medical Center, Philadelphia, Pa
| | - Mezbah U Faruque
- National Human Genome Center, Howard University College of Medicine, Washington, DC
| | - Eugene R Bleecker
- Department of Medicine, University of Arizona College of Medicine, Tucson, Ariz
| | - Monica Campbell
- Department of Medicine, University of Colorado Denver, Aurora, Colo
| | - Terri H Beaty
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Md
| | - Ingo Ruczinski
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Md
| | - Rasika A Mathias
- Department of Medicine, Johns Hopkins University, Baltimore, Md; Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Md
| | - Margaret A Taub
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Md
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, Ill
| | - Emiko Noguchi
- Department of Medical Genetics, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | | | - Dara Torgerson
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Pierre-Antoine Gourraud
- Université de Nantes, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Nantes, France.
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4
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Debebe BJ, Boelen L, Lee JC, Thio CL, Astemborski J, Kirk G, Khakoo SI, Donfield SM, Goedert JJ, Asquith B. Identifying the immune interactions underlying HLA class I disease associations. eLife 2020; 9:54558. [PMID: 32238263 PMCID: PMC7253178 DOI: 10.7554/elife.54558] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/06/2020] [Indexed: 12/11/2022] Open
Abstract
Variation in the risk and severity of many autoimmune diseases, malignancies and infections is strongly associated with polymorphisms at the HLA class I loci. These genetic associations provide a powerful opportunity for understanding the etiology of human disease. HLA class I associations are often interpreted in the light of 'protective' or 'detrimental' CD8+ T cell responses which are restricted by the host HLA class I allotype. However, given the diverse receptors which are bound by HLA class I molecules, alternative interpretations are possible. As well as binding T cell receptors on CD8+ T cells, HLA class I molecules are important ligands for inhibitory and activating killer immunoglobulin-like receptors (KIRs) which are found on natural killer cells and some T cells; for the CD94:NKG2 family of receptors also expressed mainly by NK cells and for leukocyte immunoglobulin-like receptors (LILRs) on myeloid cells. The aim of this study is to develop an immunogenetic approach for identifying and quantifying the relative contribution of different receptor-ligand interactions to a given HLA class I disease association and then to use this approach to investigate the immune interactions underlying HLA class I disease associations in three viral infections: Human T cell Leukemia Virus type 1, Human Immunodeficiency Virus type 1 and Hepatitis C Virus as well as in the inflammatory condition Crohn's disease.
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Affiliation(s)
- Bisrat J Debebe
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Lies Boelen
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - James C Lee
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | -
- Johns Hopkins University, Baltimore, United States.,Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Chloe L Thio
- Johns Hopkins University, Baltimore, United States
| | | | - Gregory Kirk
- Johns Hopkins University, Baltimore, United States
| | - Salim I Khakoo
- Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | | | - James J Goedert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, United States
| | - Becca Asquith
- Department of Infectious Disease, Imperial College London, London, United Kingdom
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5
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Geffard E, Limou S, Walencik A, Daya M, Watson H, Torgerson D, Barnes KC, Cesbron Gautier A, Gourraud PA, Vince N. Easy-HLA: a validated web application suite to reveal the full details of HLA typing. Bioinformatics 2020; 36:2157-2164. [PMID: 31750874 PMCID: PMC8248894 DOI: 10.1093/bioinformatics/btz875] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 09/19/2019] [Accepted: 11/20/2019] [Indexed: 01/10/2023] Open
Abstract
MOTIVATION The HLA system plays a pivotal role in both clinical applications and immunology research. Typing HLA genes in patient and donor is indeed required in hematopoietic stem cell and solid-organ transplantation, and the histocompatibility complex region exhibits countless genetic associations with immune-related pathologies. Since the discovery of HLA antigens, the HLA system nomenclature and typing methods have constantly evolved, which leads to difficulties in using data generated with older methodologies. RESULTS Here, we present Easy-HLA, a web-based software suite designed to facilitate analysis and gain knowledge from HLA typing, regardless of nomenclature or typing method. Easy-HLA implements a computational and statistical method of HLA haplotypes inference based on published reference populations containing over 600 000 haplotypes to upgrade missing or partial HLA information: 'HLA-Upgrade' tool infers high-resolution HLA typing and 'HLA-2-Haplo' imputes haplotype pairs and provides additional functional annotations (e.g. amino acids and KIR ligands). We validated both tools using two independent cohorts (total n = 2500). For HLA-Upgrade, we reached a prediction accuracy of 92% from low- to high-resolution of European genotypes. We observed a 96% call rate and 76% accuracy with HLA-2-Haplo European haplotype pairs prediction. In conclusion, Easy-HLA tools facilitate large-scale immunogenetic analysis and promotes the multi-faceted HLA expertise beyond allelic associations by providing new functional immunogenomics parameters. AVAILABILITY AND IMPLEMENTATION Easy-HLA is a web application freely available (free account) at: https://hla.univ-nantes.fr. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Estelle Geffard
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche en
Transplantation et Immunologie, UMR 1064, ITUN, Nantes F-44000, France
| | - Sophie Limou
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche en
Transplantation et Immunologie, UMR 1064, ITUN, Nantes F-44000, France
| | - Alexandre Walencik
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche en
Transplantation et Immunologie, UMR 1064, ITUN, Nantes F-44000, France
- Laboratoire d’Histocompatibilité et d’Immunogénétique, EFS Centre—Pays de la
Loire, Nantes F-44000, France
| | - Michelle Daya
- Department of Medicine, University of Colorado Denver, Aurora, CO
80045, USA
| | - Harold Watson
- Faculty of Medical Sciences Cave Hill Campus, The University of the West
Indies, Bridgetown BB11000, Barbados
| | - Dara Torgerson
- McGill University and Genome Quebec Innovation Centre, Montreal,
QC H3A 0G1, Canada
| | | | - on behalf of CAAPA
- Department of Medicine, University of Colorado Denver, Aurora, CO
80045, USA
| | - Anne Cesbron Gautier
- Laboratoire d’Histocompatibilité et d’Immunogénétique, EFS Centre—Pays de la
Loire, Nantes F-44000, France
| | - Pierre-Antoine Gourraud
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche en
Transplantation et Immunologie, UMR 1064, ITUN, Nantes F-44000, France
| | - Nicolas Vince
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche en
Transplantation et Immunologie, UMR 1064, ITUN, Nantes F-44000, France
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6
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Chaisri S, Pabalan N, Tabunhan S, Tharabenjasin P, Sankuntaw N, Leelayuwat C. Effects of the killer immunoglobulin-like receptor (KIR) polymorphisms on HIV acquisition: A meta-analysis. PLoS One 2019; 14:e0225151. [PMID: 31790432 PMCID: PMC6886768 DOI: 10.1371/journal.pone.0225151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 10/29/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Genetic involvement of Killer Immunoglobulin-like Receptor (KIR) polymorphisms and Human Immunodeficiency Virus (HIV)-exposed seronegative (HESN) compared to HIV-infected (HIVI) individuals has been reported. However, inconsistency of the outcomes reduces precision of the estimates. A meta-analysis was applied to obtain more precise estimates of association. METHODS A multi-database literature search yielded thirteen case-control studies. Risks were expressed as odds ratios (ORs) and 95% confidence intervals (CIs) with significance set at a two-tailed P-value of ≤ 0.05. We used two levels of analyses: (1) gene content that included 13 KIR polymorphisms (2DL1-3, 2DL5A, 2DL5B, 2DS1-3, 2DS4F, 2DS4D, 2DS5, 3DL1 and 3DS1); and (2) 3DL1/S1 genotypes. Subgroup analysis was ethnicity-based (Caucasians, Asians and Africans). Outlier treatment was applied to heterogeneous effects which dichotomized the outcomes into pre-outlier (PRO) and post-outlier (PSO). Multiple comparisons were addressed with the Bonferroni correction. RESULTS We generated 52 and 18 comparisons from gene content and genotype analyses, respectively. Of the 70 comparisons, 13 yielded significant outcomes, two (indicating reduced risk) of which survived the Bonferroni correction (Pc). These protective effects pointed to the Caucasian subgroup in 2DL3 (OR 0.19, 95% CI 0.09, 0.40, Pc < 10-3) and 3DS1S1 (OR 0.37, 95% CI 0.24, 0.56, Pc < 10-3). These two PSO outcomes yielded effects of increased magnitude and precision, as well as raised significance and deemed robust by sensitivity analysis. Of the two, the 2DL3 effect was improved with a test of interaction (Pc interaction < 10-4). CONCLUSION Multiple meta-analytical treatments presented strong evidence of the protective effect (up to 81%) of the KIR polymorphisms (2DL3 and 3DS1S1) among Caucasians. The Asian and African outcomes were inconclusive due to the low number of studies.
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Affiliation(s)
- Suwit Chaisri
- Chulabhorn International College of Medicine, Thammasat University, Pathum Thani, Thailand
- The Centre for Research and Development of Medical Diagnostic Laboratories (CMDL), Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Noel Pabalan
- Chulabhorn International College of Medicine, Thammasat University, Pathum Thani, Thailand
- * E-mail:
| | - Sompong Tabunhan
- Chulabhorn International College of Medicine, Thammasat University, Pathum Thani, Thailand
| | - Phuntila Tharabenjasin
- Chulabhorn International College of Medicine, Thammasat University, Pathum Thani, Thailand
| | - Nipaporn Sankuntaw
- Chulabhorn International College of Medicine, Thammasat University, Pathum Thani, Thailand
| | - Chanvit Leelayuwat
- The Centre for Research and Development of Medical Diagnostic Laboratories (CMDL), Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
- Department of Clinical Immunology and Transfusion Sciences, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
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23rd Nantes Actualités Transplantation: "Genomics and Immunogenetics of Kidney and Inflammatory Diseases-Lessons for Transplantation". Transplantation 2019; 103:857-861. [PMID: 30399125 DOI: 10.1097/tp.0000000000002517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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8
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Mori M, Leitman E, Walker B, Ndung’u T, Carrington M, Goulder P. Impact of HLA Allele-KIR Pairs on HIV Clinical Outcome in South Africa. J Infect Dis 2019; 219:1456-1463. [PMID: 30520960 PMCID: PMC6467198 DOI: 10.1093/infdis/jiy692] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 11/30/2018] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND HLA class I contributes to HIV immune control through antigen presentation to cytotoxic T lymphocytes (CTLs) and natural killer (NK) cells. In contrast to investigations of CTL, studies of NK cells in HIV control through HLA-killer immunoglobulin-like receptor (KIR) interactions remain sparse in African cohorts. METHODS Treatment-naive, chronically HIV-infected adults (N = 312) were recruited from South Africa, and the effects of HLA-KIR pairs on clinical outcome were analyzed. RESULTS There was no significant difference in viral load among all subjects with HLA alleles from the HLA-C1 group (P = .1). However, differences in HLA-C type significantly influenced viremia among 247 KIR2DL3 positives (P = .04), suggesting that specific HLA-KIR interactions contribute to immune control. Higher viral load (P = .02) and lower CD4+ T-cell counts (P = .008) were observed in subjects with HLA-C*16:01+KIR2DL3+. Longitudinal analysis showed more rapid progression to AIDS among HLA-C*16:01+KIR2DL3+ subjects (adjusted hazard ratio 1.9, P = .03) than those without this genotype, independent of CD4+ T-cell count and viral load. CONCLUSIONS These results highlight the existence of unique anti-HIV innate immunity within distinct populations and the contribution of KIR on NK cells and some CTLs to the well-described HLA-mediated impact on HIV disease progression.
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Affiliation(s)
- Masahiko Mori
- Department of Paediatrics, University of Oxford
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Japan
| | | | - Bruce Walker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge
| | - Thumbi Ndung’u
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal
- Africa Health Research Institute, Durban, South Africa
- Max Planck Institute for Infection Biology, Berlin, Germany
| | - Mary Carrington
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge
- Cancer and Inflammation Program, Frederick National Laboratory for Cancer Research, Maryland
| | - Philip Goulder
- Department of Paediatrics, University of Oxford
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal
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9
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Boelen L, Debebe B, Silveira M, Salam A, Makinde J, Roberts CH, Wang ECY, Frater J, Gilmour J, Twigger K, Ladell K, Miners KL, Jayaraman J, Traherne JA, Price DA, Qi Y, Martin MP, Macallan DC, Thio CL, Astemborski J, Kirk G, Donfield SM, Buchbinder S, Khakoo SI, Goedert JJ, Trowsdale J, Carrington M, Kollnberger S, Asquith B. Inhibitory killer cell immunoglobulin-like receptors strengthen CD8 + T cell-mediated control of HIV-1, HCV, and HTLV-1. Sci Immunol 2018; 3:eaao2892. [PMID: 30413420 PMCID: PMC6277004 DOI: 10.1126/sciimmunol.aao2892] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 06/06/2018] [Accepted: 10/09/2018] [Indexed: 01/05/2023]
Abstract
Killer cell immunoglobulin-like receptors (KIRs) are expressed predominantly on natural killer cells, where they play a key role in the regulation of innate immune responses. Recent studies show that inhibitory KIRs can also affect adaptive T cell-mediated immunity. In mice and in human T cells in vitro, inhibitory KIR ligation enhanced CD8+ T cell survival. To investigate the clinical relevance of these observations, we conducted an extensive immunogenetic analysis of multiple independent cohorts of HIV-1-, hepatitis C virus (HCV)-, and human T cell leukemia virus type 1 (HTLV-1)-infected individuals in conjunction with in vitro assays of T cell survival, analysis of ex vivo KIR expression, and mathematical modeling of host-virus dynamics. Our data suggest that functional engagement of inhibitory KIRs enhances the CD8+ T cell response against HIV-1, HCV, and HTLV-1 and is a significant determinant of clinical outcome in all three viral infections.
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Affiliation(s)
- Lies Boelen
- Department of Medicine, Imperial College London, London, UK
| | - Bisrat Debebe
- Department of Medicine, Imperial College London, London, UK
| | - Marcos Silveira
- Department of Medicine, Imperial College London, London, UK
- Faculty of Engineering, São Paulo State University-UNESP, São Paulo, Brazil
| | - Arafa Salam
- Institute for Infection and Immunity, St. George's, University of London, London, UK
| | - Julia Makinde
- International AIDS Vaccine Initiative Human Immunology Laboratory, London, UK
| | - Chrissy H Roberts
- Clinical Research Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Eddie C Y Wang
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - John Frater
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre, Oxford, UK
| | - Jill Gilmour
- International AIDS Vaccine Initiative Human Immunology Laboratory, London, UK
| | - Katie Twigger
- Department of Medicine, Imperial College London, London, UK
| | - Kristin Ladell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Kelly L Miners
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Jyothi Jayaraman
- Immunology Division, Department of Pathology, University of Cambridge, Cambridge, UK
| | - James A Traherne
- Immunology Division, Department of Pathology, University of Cambridge, Cambridge, UK
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Ying Qi
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Maureen P Martin
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Derek C Macallan
- Institute for Infection and Immunity, St. George's, University of London, London, UK
| | | | | | | | | | - Susan Buchbinder
- San Francisco Department of Public Health, San Francisco, CA, USA
| | - Salim I Khakoo
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - James J Goedert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - John Trowsdale
- Immunology Division, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Mary Carrington
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
| | - Simon Kollnberger
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Becca Asquith
- Department of Medicine, Imperial College London, London, UK.
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Hens J, Jennes W, Kestens L. The role of NK cells in HIV-1 protection: autologous, allogeneic or both? AIDS Res Ther 2016; 13:15. [PMID: 26997965 PMCID: PMC4799629 DOI: 10.1186/s12981-016-0099-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 03/09/2016] [Indexed: 12/03/2022] Open
Abstract
Natural killer (NK) cells specialize in killing virally infected- or tumor cells and are part of the innate immune system. The activational state of NK cells is determined by the balance of incoming activating and inhibitory signals mediated by receptor-ligand binding with the target cell. These receptor-ligand bonds mainly consist of the killer immunoglobulin-like receptors (KIR), which are expressed at the cell surface of NK cells, and their ligands: the highly variable human leukocyte antigen -class I molecules (HLA). Absence of an inhibitory receptor-ligand bond lowers the NK cell activation threshold, whereas an activating receptor-ligand bond stimulates the cell, potentially overcoming this threshold and triggering NK cell activation. NK cells influence the course of infection as well as the acquisition of HIV-1. Several lines of evidence relate the activating NK cell receptor KIR3DS1, in the presence or absence of its putative ligand HLA-Bw4, with slower disease progression as well as resistance to HIV-1 infection. Overall, resistance to HIV-1 infection predominantly correlates with activating KIR/HLA profiles, consisting of e.g. activating KIRs, group B haplotypes, or inhibitory KIRs in absence of their ligands. Such a conclusion is less evident for studies of HIV-1 disease progression, with studies reporting beneficial as well as detrimental effects of activating KIR/HLA genotypes. It is likely that KIR/HLA association studies are complicated by the complexity of the KIR and HLA loci and their mutual interactions, as well as by additional factors like route of HIV exposure, immune activation, presence of co-infections, and the effect of anti-HIV-1 antibodies. One newly discovered NK cell activation pathway associated with resistance to HIV-1 infection involves the presence of an iKIR/HLA mismatch between partners. The absence of such an iKIR/HLA bond renders donor-derived allogeneic HIV-1 infected cells vulnerable to NK cell responses during HIV-1 transmission. Therefore, theoretically, HIV-1 would be eliminated before it has the chance to infect the autologous cells in the recipient. While this “alloreactive” NK cell mechanism is especially relevant to HIV transmission in monogamous couples, it would be interesting to investigate how it could influence resistance to HIV in other settings. The objective of this review is to summarize the knowledge about these autologous and alloreactive NK cell responses with regard to HIV-1 outcome.
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Leitman EM, Hurst J, Mori M, Kublin J, Ndung'u T, Walker BD, Carlson J, Gray GE, Matthews PC, Frahm N, Goulder PJR. Lower Viral Loads and Slower CD4+ T-Cell Count Decline in MRKAd5 HIV-1 Vaccinees Expressing Disease-Susceptible HLA-B*58:02. J Infect Dis 2016; 214:379-89. [PMID: 26951820 PMCID: PMC4936641 DOI: 10.1093/infdis/jiw093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 03/02/2016] [Indexed: 11/18/2022] Open
Abstract
Background. HLA strongly influences human immunodeficiency virus type 1 (HIV-1) disease progression. A major contributory mechanism is via the particular HLA-presented HIV-1 epitopes that are recognized by CD8+ T-cells. Different populations vary considerably in the HLA alleles expressed. We investigated the HLA-specific impact of the MRKAd5 HIV-1 Gag/Pol/Nef vaccine in a subset of the infected Phambili cohort in whom the disease-susceptible HLA-B*58:02 is highly prevalent. Methods. Viral loads, CD4+ T-cell counts, and enzyme-linked immunospot assay–determined anti-HIV-1 CD8+ T-cell responses for a subset of infected antiretroviral-naive Phambili participants, selected according to sample availability, were analyzed. Results. Among those expressing disease-susceptible HLA-B*58:02, vaccinees had a lower chronic viral set point than placebo recipients (median, 7240 vs 122 500 copies/mL; P = .01), a 0.76 log10 lower longitudinal viremia level (P = .01), and slower progression to a CD4+ T-cell count of <350 cells/mm3 (P = .02). These differences were accompanied by a higher Gag-specific breadth (4.5 vs 1 responses; P = .04) and magnitude (2300 vs 70 spot-forming cells/106 peripheral blood mononuclear cells; P = .06) in vaccinees versus placebo recipients. Conclusions. In addition to the known enhancement of HIV-1 acquisition resulting from the MRKAd5 HIV-1 vaccine, these findings in a nonrandomized subset of enrollees show an HLA-specific vaccine effect on the time to CD4+ T-cell count decline and viremia level after infection and the potential for vaccines to differentially alter disease outcome according to population HLA composition. Clinical Trials Registration. NCT00413725, DOH-27-0207-1539.
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Affiliation(s)
| | - Jacob Hurst
- Nuffield Department of Medicine, University of Oxford, United Kingdom
| | | | - James Kublin
- HIV-1 Vaccine Trials Network, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center
| | - Thumbi Ndung'u
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts HIV-1 Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal KwaZulu-Natal Research Institute for Tuberculosis and HIV-1, University of KwaZulu-Natal, Durban Max Planck Institute for Infection Biology, Berlin, Germany
| | - Bruce D Walker
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts HIV-1 Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal
| | | | - Glenda E Gray
- South African Medical Research Council, Cape Town Perinatal HIV-1 Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Nicole Frahm
- HIV-1 Vaccine Trials Network, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center Department of Global Health, University of Washington, Seattle
| | - Philip J R Goulder
- Department of Paediatrics HIV-1 Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal
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Salie M, Daya M, Möller M, Hoal EG. Activating KIRs alter susceptibility to pulmonary tuberculosis in a South African population. Tuberculosis (Edinb) 2015; 95:817-821. [PMID: 26542219 DOI: 10.1016/j.tube.2015.09.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 08/31/2015] [Accepted: 09/07/2015] [Indexed: 11/16/2022]
Abstract
We investigate the role of killer immunoglobulin-like receptor (KIR) genes and human leukocyte antigen class-I (HLA) variants in susceptibility to tuberculosis in a South African population. In a sample set comprising 408 TB cases and 351 healthy controls, we show that the KIR3DS1 gene and KIR genotypes with five or more activating KIRs, and the presence of 3DS1, protect against developing active TB in the South African Coloured population. Several HLA class-I alleles were identified as susceptibility factors for TB disease. However, none of the KIR-HLA compound genotypes were found to be associated with TB. Our data suggests that the KIR genes may play an important role in TB disease.
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Affiliation(s)
- Muneeb Salie
- SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical TB Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
| | - Michelle Daya
- SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical TB Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Marlo Möller
- SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical TB Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Eileen G Hoal
- SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical TB Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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Olesen R, Vigano S, Rasmussen TA, Søgaard OS, Ouyang Z, Buzon M, Bashirova A, Carrington M, Palmer S, Brinkmann CR, Yu XG, Østergaard L, Tolstrup M, Lichterfeld M. Innate Immune Activity Correlates with CD4 T Cell-Associated HIV-1 DNA Decline during Latency-Reversing Treatment with Panobinostat. J Virol 2015; 89:10176-89. [PMID: 26223643 PMCID: PMC4580197 DOI: 10.1128/jvi.01484-15] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 07/21/2015] [Indexed: 01/09/2023] Open
Abstract
UNLABELLED The pharmaceutical reactivation of dormant HIV-1 proviruses by histone deacetylase inhibitors (HDACi) represents a possible strategy to reduce the reservoir of HIV-1-infected cells in individuals treated with suppressive combination antiretroviral therapy (cART). However, the effects of such latency-reversing agents on the viral reservoir size are likely to be influenced by host immune responses. Here, we analyzed the immune factors associated with changes in proviral HIV-1 DNA levels during treatment with the potent HDACi panobinostat in a human clinical trial involving 15 cART-treated HIV-1-infected patients. We observed that the magnitude, breadth, and cytokine secretion profile of HIV-1-specific CD8 T cell responses were unrelated to changes in HIV-1 DNA levels in CD4 T cells during panobinostat treatment. In contrast, the proportions of CD3(-) CD56(+) total NK cells and CD16(+) CD56(dim) NK cells were inversely correlated with HIV-1 DNA levels throughout the study, and changes in HIV-1 DNA levels during panobinostat treatment were negatively associated with the corresponding changes in CD69(+) NK cells. Decreasing levels of HIV-1 DNA during latency-reversing treatment were also related to the proportions of plasmacytoid dendritic cells, to distinct expression patterns of interferon-stimulated genes, and to the expression of the IL28B CC genotype. Together, these data suggest that innate immune activity can critically modulate the effects of latency-reversing agents on the viral reservoir and may represent a target for future immunotherapeutic interventions in HIV-1 eradication studies. IMPORTANCE Currently available antiretroviral drugs are highly effective in suppressing HIV-1 replication, but the virus persists, despite treatment, in a latent form that does not actively express HIV-1 gene products. One approach to eliminate these cells, colloquially termed the "shock-and-kill" strategy, focuses on the use of latency-reversing agents that induce active viral gene expression in latently infected cells, followed by immune-mediated killing. Panobinostat, a histone deacetylase inhibitor, demonstrated potent activities in reversing HIV-1 latency in a recent pilot clinical trial and reduced HIV-1 DNA levels in a subset of patients. Interestingly, we found that innate immune factors, such as natural killer cells, plasmacytoid dendritic cells, and the expression patterns of interferon-stimulated genes, were most closely linked to a decline in the HIV-1 DNA level during treatment with panobinostat. These data suggest that innate immune activity may play an important role in reducing the residual reservoir of HIV-1-infected cells.
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MESH Headings
- Antigens, CD/genetics
- Antigens, CD/immunology
- Antiretroviral Therapy, Highly Active
- CD4-Positive T-Lymphocytes/drug effects
- CD4-Positive T-Lymphocytes/enzymology
- CD4-Positive T-Lymphocytes/immunology
- CD4-Positive T-Lymphocytes/virology
- CD8-Positive T-Lymphocytes/drug effects
- CD8-Positive T-Lymphocytes/enzymology
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/virology
- Cell Count
- DNA, Viral/antagonists & inhibitors
- DNA, Viral/genetics
- DNA, Viral/immunology
- Dendritic Cells/drug effects
- Dendritic Cells/enzymology
- Dendritic Cells/immunology
- Dendritic Cells/virology
- Drug Administration Schedule
- Gene Expression
- Genotype
- HIV Infections/drug therapy
- HIV Infections/enzymology
- HIV Infections/immunology
- HIV Infections/virology
- HIV-1/drug effects
- HIV-1/growth & development
- HIV-1/immunology
- Histone Deacetylase Inhibitors/therapeutic use
- Histone Deacetylases/genetics
- Histone Deacetylases/immunology
- Humans
- Hydroxamic Acids/therapeutic use
- Immunity, Innate/drug effects
- Indoles/therapeutic use
- Interferons
- Interleukins/genetics
- Interleukins/immunology
- Killer Cells, Natural/drug effects
- Killer Cells, Natural/enzymology
- Killer Cells, Natural/immunology
- Killer Cells, Natural/virology
- Panobinostat
- Virus Latency/drug effects
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Affiliation(s)
- Rikke Olesen
- Infectious Disease Division, Aarhus University Hospital, Aarhus, Denmark
| | - Selena Vigano
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA Harvard Medical School, Boston, Massachusetts, USA
| | - Thomas A Rasmussen
- Infectious Disease Division, Aarhus University Hospital, Aarhus, Denmark
| | - Ole S Søgaard
- Infectious Disease Division, Aarhus University Hospital, Aarhus, Denmark
| | - Zhengyu Ouyang
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
| | - Maria Buzon
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA Harvard Medical School, Boston, Massachusetts, USA
| | - Arman Bashirova
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Mary Carrington
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Sarah Palmer
- Westmead Millennium Institute for Medical Research, University of Sydney, Sydney, Australia
| | | | - Xu G Yu
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA Harvard Medical School, Boston, Massachusetts, USA
| | - Lars Østergaard
- Infectious Disease Division, Aarhus University Hospital, Aarhus, Denmark
| | - Martin Tolstrup
- Infectious Disease Division, Aarhus University Hospital, Aarhus, Denmark
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA Harvard Medical School, Boston, Massachusetts, USA Infectious Disease Division, Massachusetts General Hospital, Boston, Massachusetts, USA Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts, USA
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Abstract
PURPOSE OF REVIEW Rapid expansion of genomic technologies has resulted in an unprecedented ability to interrogate the impact of human genetic variation on disease. HIV-1 infection is a unique model for studying this impact because host genetic variation influences both clinical outcome and the genetic sequence and evolution of the pathogen itself. RECENT FINDINGS Several candidate gene studies have proposed novel associations with HIV acquisition and/or disease progression; however, many of these are not supported by larger genome-wide association studies. Thus, controversy remains as to which host and viral genetic factors truly impact HIV infection. Novel methods for assessing the genetic (viral and host) component of disease progression are becoming important areas of investigation. SUMMARY To fully understand the impact of human genetic variation in HIV disease, the field will need to come together to set a standard for discovery of new genes. Additionally, novel avenues of investigation such as sequencing studies (to define the role of rare variants), studies of epistasis and host/viral genome interaction will be of great value.
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Immunogenetic influences on acquisition of HIV-1 infection: consensus findings from two African cohorts point to an enhancer element in IL19 (1q32.2). Genes Immun 2015; 16:213-20. [PMID: 25633979 PMCID: PMC4409473 DOI: 10.1038/gene.2014.84] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 12/19/2014] [Accepted: 12/19/2014] [Indexed: 12/12/2022]
Abstract
Numerous reports have suggested that immunogenetic factors may influence HIV-1 acquisition, yet replicated findings that translate between study cohorts remain elusive. Our work aimed to test several hypotheses about genetic variants within the IL10-IL24 gene cluster that encodes interleukin (IL)-10, IL-19, IL-20, and IL-24. In aggregated data from 515 Rwandans and 762 Zambians with up to 12 years of follow-up, 190 single nucleotide polymorphisms (SNPs) passed quality control procedures. When HIV-1-exposed seronegative subjects (n = 486) were compared with newly seroconverted individuals (n = 313) and seroprevalent subjects (n = 478) who were already infected at enrollment, rs12407485 (G>A) in IL19 showed a robust association signal in adjusted logistic regression models (odds ratio = 0.64, P = 1.7 × 10−4, and q = 0.033). Sensitivity analyses demonstrated that (i) results from both cohorts and subgroups within each cohort were highly consistent; (ii) verification of HIV-1 infection status after enrollment was critical; and (iii) supporting evidence was readily obtained from Cox proportional hazards models. Data from public databases indicate that rs12407485 is part of an enhancer element for three transcription factors. Overall, these findings suggest that molecular features at the IL19 locus may modestly alter the establishment of HIV-1 infection.
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