1
|
Gutiérrez-Bautista JF, Sampedro A, Ballesta-Alcaraz L, Aguilera-Franco M, Olivares-Durán MJ, Cobo F, Reguera JA, Rodríguez-Granger J, Torres-Llamas A, Martín-Sánchez J, Aznar-Peralta I, Vilchez JR, López-Nevot MÁ, Sampedro-Martínez A. Analysis of HLA Alleles in Different Cohorts of Patients Infected by L. infantum from Southern Spain. Int J Mol Sci 2024; 25:8205. [PMID: 39125781 PMCID: PMC11311343 DOI: 10.3390/ijms25158205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 07/15/2024] [Accepted: 07/25/2024] [Indexed: 08/12/2024] Open
Abstract
Leishmaniasis is an infectious disease caused by protozoa of the genus Leishmania, which is endemic in certain areas of Europe, such as southern Spain. The disease manifests in various clinical phenotypes, including visceral, cutaneous, mucosal, or asymptomatic leishmaniasis. This diversity in clinical outcomes may be influenced by the host immune response, with human leukocyte antigen (HLA) molecules playing a crucial role in determining susceptibility and progression of the infection. This study explores the association between specific HLA variants and Leishmania infantum infection. We recruited four cohorts: a control group, asymptomatic individuals, patients with symptomatic disease, and cohabitants of infected individuals. HLA typing was performed for all participants, followed by an association analysis with infection status and disease progression. Our findings indicate that the HLA-B*38 and HLA-C*03 alleles are associated with protection against L. infantum infection. These results contribute to a better understanding of the disease's progression, offer potential for new therapeutic approaches such as vaccines, and expand the existing knowledge in the literature.
Collapse
Affiliation(s)
- Juan Francisco Gutiérrez-Bautista
- Departamento de Bioquímica, Biología Molecular e Inmunología III, University of Granada, 18016 Granada, Spain
- Servicio de Análisis Clínicos e Inmunología, University Hospital Virgen de las Nieves, 18014 Granada, Spain; (L.B.-A.); (M.J.O.-D.); (J.R.V.)
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain;
| | - Antonio Sampedro
- Centro de Salud Zaidín Sur, Distrito Granada Metropolitano, Servicio Andaluz de Salud, 18007 Granada, Spain;
| | - Lucia Ballesta-Alcaraz
- Servicio de Análisis Clínicos e Inmunología, University Hospital Virgen de las Nieves, 18014 Granada, Spain; (L.B.-A.); (M.J.O.-D.); (J.R.V.)
| | - María Aguilera-Franco
- Servicio de Microbiología, University Hospital Virgen de las Nieves, 18014 Granada, Spain; (M.A.-F.); (F.C.); (J.A.R.); (J.R.-G.)
| | - María José Olivares-Durán
- Servicio de Análisis Clínicos e Inmunología, University Hospital Virgen de las Nieves, 18014 Granada, Spain; (L.B.-A.); (M.J.O.-D.); (J.R.V.)
| | - Fernando Cobo
- Servicio de Microbiología, University Hospital Virgen de las Nieves, 18014 Granada, Spain; (M.A.-F.); (F.C.); (J.A.R.); (J.R.-G.)
| | - Juan Antonio Reguera
- Servicio de Microbiología, University Hospital Virgen de las Nieves, 18014 Granada, Spain; (M.A.-F.); (F.C.); (J.A.R.); (J.R.-G.)
| | - Javier Rodríguez-Granger
- Servicio de Microbiología, University Hospital Virgen de las Nieves, 18014 Granada, Spain; (M.A.-F.); (F.C.); (J.A.R.); (J.R.-G.)
| | - Andrés Torres-Llamas
- Departamento de Parasitología, University of Granada, 18016 Granada, Spain; (A.T.-L.); (J.M.-S.)
| | - Joaquina Martín-Sánchez
- Departamento de Parasitología, University of Granada, 18016 Granada, Spain; (A.T.-L.); (J.M.-S.)
| | - Inés Aznar-Peralta
- GENYO Centre for Genomics and Oncological Research, Pfizer, University of Granada, Andalusian, 18016 Granada, Spain
| | - Jose Ramon Vilchez
- Servicio de Análisis Clínicos e Inmunología, University Hospital Virgen de las Nieves, 18014 Granada, Spain; (L.B.-A.); (M.J.O.-D.); (J.R.V.)
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain;
| | - Miguel Ángel López-Nevot
- Departamento de Bioquímica, Biología Molecular e Inmunología III, University of Granada, 18016 Granada, Spain
- Servicio de Análisis Clínicos e Inmunología, University Hospital Virgen de las Nieves, 18014 Granada, Spain; (L.B.-A.); (M.J.O.-D.); (J.R.V.)
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain;
| | - Antonio Sampedro-Martínez
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain;
- Servicio de Microbiología, University Hospital Virgen de las Nieves, 18014 Granada, Spain; (M.A.-F.); (F.C.); (J.A.R.); (J.R.-G.)
| |
Collapse
|
2
|
Viard M, O'hUigin C, Yuki Y, Bashirova AA, Collins DR, Urbach JM, Wolinsky S, Buchbinder S, Kirk GD, Goedert JJ, Michael NL, Haas DW, Deeks SG, Walker BD, Yu X, Carrington M. Impact of HLA class I functional divergence on HIV control. Science 2024; 383:319-325. [PMID: 38236978 DOI: 10.1126/science.adk0777] [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: 08/01/2023] [Accepted: 12/07/2023] [Indexed: 01/23/2024]
Abstract
Heterozygosity of Human leukocyte antigen (HLA) class I genes is linked to beneficial outcomes after HIV infection, presumably through greater breadth of HIV epitope presentation and cytotoxic T cell response. Distinct allotype pairs, however, differ in the extent to which they bind shared sets of peptides. We developed a functional divergence metric that measures pairwise complementarity of allotype-associated peptide binding profiles. Greater functional divergence for pairs of HLA-A and/or HLA-B allotypes was associated with slower AIDS progression and independently with enhanced viral load control. The metric predicts immune breadth at the peptide level rather than gene level and redefines HLA heterozygosity as a continuum differentially affecting disease outcome. Functional divergence may affect response to additional infections, vaccination, immunotherapy, and other diseases where HLA heterozygote advantage occurs.
Collapse
Affiliation(s)
- Mathias Viard
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute Bethesda, MD, USA
| | - Colm O'hUigin
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute Bethesda, MD, USA
| | - Yuko Yuki
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute Bethesda, MD, USA
| | - Arman A Bashirova
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute Bethesda, MD, USA
| | - David R Collins
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Jonathan M Urbach
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Steven Wolinsky
- Division of Infectious Diseases, Department of Medicine, The Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Susan Buchbinder
- Bridge HIV, San Francisco Department of Public Health, San Francisco, CA, USA
- Department of Medicine, Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Gregory D Kirk
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - James J Goedert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nelson L Michael
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - David W Haas
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Steven G Deeks
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Bruce D Walker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Xu Yu
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute Bethesda, MD, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| |
Collapse
|
3
|
Increased Prevalence of Unstable HLA-C Variants in HIV-1 Rapid-Progressor Patients. Int J Mol Sci 2022; 23:ijms232314852. [PMID: 36499177 PMCID: PMC9741376 DOI: 10.3390/ijms232314852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022] Open
Abstract
HIV-1 infection in the absence of treatment results in progression toward AIDS. Host genetic factors play a role in HIV-1 pathogenesis, but complete knowledge is not yet available. Since less-expressed HLA-C variants are associated with poor HIV-1 control and unstable HLA-C variants are associated with higher HIV-1 infectivity, we investigated whether there was a correlation between the different stages of HIV-1 progression and the presence of specific HLA-C allotypes. HLA-C genotyping was performed using allele-specific PCR by analyzing a treatment-naïve cohort of 96 HIV-1-infected patients from multicentric cohorts in the USA, Canada, and Brazil. HIV-1-positive subjects were classified according to their different disease progression status as progressors (Ps, n = 48), long-term non-progressors (LTNPs, n = 37), and elite controllers (ECs, n = 11). HLA-C variants were classified as stable or unstable according to their binding stability to β2-microglobulin/peptide complex. Our results showed a significant correlation between rapid progression to AIDS and the presence of two or one unstable HLA-C variants (p-value: 0.0078, p-value: 0.0143, respectively). These findings strongly suggest a link between unstable HLA-C variants both at genotype and at allele levels and rapid progression to AIDS. This work provides further insights into the impact of host genetic factors on AIDS progression.
Collapse
|
4
|
Aguiar VRC, Augusto DG, Castelli EC, Hollenbach JA, Meyer D, Nunes K, Petzl-Erler ML. An immunogenetic view of COVID-19. Genet Mol Biol 2021; 44:e20210036. [PMID: 34436508 PMCID: PMC8388242 DOI: 10.1590/1678-4685-gmb-2021-0036] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 06/12/2021] [Indexed: 02/06/2023] Open
Abstract
Meeting the challenges brought by the COVID-19 pandemic requires an interdisciplinary approach. In this context, integrating knowledge of immune function with an understanding of how genetic variation influences the nature of immunity is a key challenge. Immunogenetics can help explain the heterogeneity of susceptibility and protection to the viral infection and disease progression. Here, we review the knowledge developed so far, discussing fundamental genes for triggering the innate and adaptive immune responses associated with a viral infection, especially with the SARS-CoV-2 mechanisms. We emphasize the role of the HLA and KIR genes, discussing what has been uncovered about their role in COVID-19 and addressing methodological challenges of studying these genes. Finally, we comment on questions that arise when studying admixed populations, highlighting the case of Brazil. We argue that the interplay between immunology and an understanding of genetic associations can provide an important contribution to our knowledge of COVID-19.
Collapse
Affiliation(s)
- Vitor R. C. Aguiar
- Universidade de São Paulo, Departamento de Genética e Biologia
Evolutiva, São Paulo, SP, Brazil
| | - Danillo G. Augusto
- University of California, UCSF Weill Institute for Neurosciences,
Department of Neurology, San Francisco, CA, USA
- Universidade Federal do Paraná, Departamento de Genética, Curitiba,
PR, Brazil
| | - Erick C. Castelli
- Universidade Estadual Paulista, Faculdade de Medicina de Botucatu,
Departamento de Patologia, Botucatu, SP, Brazil
| | - Jill A. Hollenbach
- University of California, UCSF Weill Institute for Neurosciences,
Department of Neurology, San Francisco, CA, USA
| | - Diogo Meyer
- Universidade de São Paulo, Departamento de Genética e Biologia
Evolutiva, São Paulo, SP, Brazil
| | - Kelly Nunes
- Universidade de São Paulo, Departamento de Genética e Biologia
Evolutiva, São Paulo, SP, Brazil
| | | |
Collapse
|
5
|
Sng XYX, Li J, Zareie P, Assmus LM, Lee JKC, Jones CM, Turner SJ, Daley SR, Quinn KM, La Gruta NL. The Impact of MHC Class I Dose on Development and Maintenance of the Polyclonal Naive CD8+ T Cell Repertoire. THE JOURNAL OF IMMUNOLOGY 2020; 204:3108-3116. [DOI: 10.4049/jimmunol.2000081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/02/2020] [Indexed: 12/14/2022]
|
6
|
Gartner MJ, Roche M, Churchill MJ, Gorry PR, Flynn JK. Understanding the mechanisms driving the spread of subtype C HIV-1. EBioMedicine 2020; 53:102682. [PMID: 32114391 PMCID: PMC7047180 DOI: 10.1016/j.ebiom.2020.102682] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/29/2020] [Accepted: 02/05/2020] [Indexed: 12/12/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) subtype C (C-HIV) is the most prevalent form of HIV-1 globally, accounting for approximately 50% of infections worldwide. C-HIV is the predominant and near-exclusive subtype in the low resource regions of India and Southern Africa. Given the vast diversity of HIV-1 subtypes, it is curious as to why C-HIV constitutes such a large proportion of global infections. This enriched prevalence may be due to phenotypic differences between C-HIV isolates and other viral strains that permit enhanced transmission efficiency or, pathogenicity, or might due to the socio-demographics of the regions where C-HIV is endemic. Here, we compare the mechanisms of C-HIV pathogenesis to less prominent HIV-1 subtypes, including viral genetic and phenotypic characteristics, and host genetic variability, to understand whether evolutionary factors drove C-HIV to predominance.
Collapse
Affiliation(s)
- Matthew J Gartner
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia
| | - Michael Roche
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia; The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
| | - Melissa J Churchill
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia; Department of Microbiology, Monash University, Melbourne, Australia
| | - Paul R Gorry
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia.
| | - Jacqueline K Flynn
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia; The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia; School of Clinical Sciences at Monash Health, Monash University, Melbourne, Australia.
| |
Collapse
|
7
|
Does MHC heterozygosity influence microbiota form and function? PLoS One 2019; 14:e0215946. [PMID: 31095603 PMCID: PMC6522005 DOI: 10.1371/journal.pone.0215946] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 04/11/2019] [Indexed: 12/14/2022] Open
Abstract
MHC molecules are essential for the adaptive immune response, and they are the most polymorphic genetic loci in vertebrates. Extreme genetic variation at these loci is paradoxical given their central importance to host health. Classic models of MHC gene evolution center on antagonistic host-pathogen interactions to promote gene diversification and allelic diversity in host populations. However, all multicellular organisms are persistently colonized by their microbiota that perform essential metabolic functions for their host and protect from infection. Here, we provide data to support the hypothesis that MHC heterozygote advantage (a main force of selection thought to drive MHC gene evolution), may operate by enhancing fitness advantages conferred by the host’s microbiome. We utilized fecal 16S rRNA gene sequences and their predicted metagenome datasets collected from multiple MHC congenic homozygote and heterozygote mouse strains to describe the influence of MHC heterozygosity on microbiome form and function. We find that in contrast to homozygosity at MHC loci, MHC heterozygosity promotes functional diversification of the microbiome, enhances microbial network connectivity, and results in enrichment for a variety of microbial functions that are positively associated with host fitness. We demonstrate that taxonomic and functional diversity of the microbiome is positively correlated in MHC heterozygote but not homozygote animals, suggesting that heterozygote microbiomes are more functionally adaptive under similar environmental conditions than homozygote microbiomes. Our data complement previous observations on the role of MHC polymorphism in sculpting microbiota composition, but also provide functional insights into how MHC heterozygosity may enhance host health by modulating microbiome form and function. We also provide evidence to support that MHC heterozygosity limits functional redundancy among commensal microbes and may enhance the metabolic versatility of their microbiome. Results from our analyses yield multiple testable predictions regarding the role of MHC heterozygosity on the microbiome that will help guide future research in the area of MHC-microbiome interactions.
Collapse
|
8
|
Naranbhai V, Carrington M. Host genetic variation and HIV disease: from mapping to mechanism. Immunogenetics 2017; 69:489-498. [PMID: 28695282 PMCID: PMC5537324 DOI: 10.1007/s00251-017-1000-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 05/07/2017] [Indexed: 12/12/2022]
Abstract
This review aims to provide a summary of current knowledge of host genetic effects on human immunodeficiency virus (HIV) disease. Mapping of simple single nucleotide polymorphisms (SNP) has been largely successful in HIV, but more complex genetic associations involving haplotypic or epigenetic variation, for example, remain elusive. Mechanistic insights explaining SNP associations are incomplete, but continue to be forthcoming. The number of robust immunogenetic correlates of HIV is modest and their discovery mostly predates the genome-wide era. Nevertheless, genome-wide evaluations have nicely validated the impact of HLA and CCR5 variants on HIV disease, and importantly, made clear the many false positive associations that were previously suggested by studies using the candidate gene approach. We describe how multiple HIV outcome measures such as acquisition, viral control, and immune decline have been studied in adults and in children, but that collectively these identify only the two replicable loci responsible for modifying HIV disease, CCR5, and HLA. Recent heritability estimates in this disease corroborate the modest impact of genetic determinants and their oligogenic nature. While the mechanism of protection afforded by genetic variants that diminish CCR5 expression is clear, new aspects of HLA class I-mediated protection continue to be uncovered. We describe how these genetic findings have enhanced insights into immunobiology, been clinically translated into CCR5 antagonists, allowed prioritization of antigens for vaccination efforts, and identified targets for genome-editing interventions. Finally, we describe how studies of genetically complex parts of the genome using new tools may begin revealing additional correlates.
Collapse
Affiliation(s)
- Vivek Naranbhai
- 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.
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa.
| | - 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
| |
Collapse
|
9
|
Vesa J, Chaillon A, Wagner GA, Anderson CM, Richman DD, Smith DM, Little SJ. Increased HIV-1 superinfection risk in carriers of specific human leukocyte antigen alleles. AIDS 2017; 31:1149-1158. [PMID: 28244954 PMCID: PMC5559224 DOI: 10.1097/qad.0000000000001445] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
OBJECTIVE The aim of this study was to characterize the demographic, behavioural, clinical and immunogenetic determinants of HIV-1 superinfection in a high-risk cohort of MSM. DESIGN A retrospective cohort study of prospectively followed MSM. METHODS Ninety-eight MSM with acute or early HIV-1 monoinfection were followed for a median of 15.6 months. Demographic and human leukocyte antigen (HLA) genotype data were collected at enrolment. Sexual behaviour, clinical and the infection status (monoinfection or superinfection) data were recorded at each visit (at enrolment and thereafter at a median of 4.2-month intervals). HIV-1 superinfection risk was determined by Cox regression and Kaplan-Meier survival analysis. RESULTS Ten individuals (10.2%) had superinfection during follow-up. Cox regression did not show significantly increased superinfection risk for individuals with an increased amount of condomless anal intercourse, lower CD4 T-cell count or higher viral load, but higher number of sexual contacts demonstrated a trend towards significance [hazard ratio, 4.74; 95% confidence interval (95% CI), 0.87-25.97; P = 0.073]. HLA-A*29 (hazard ratio, 4.10; 95% CI, 0.88-14.76; P = 0.069), HLA-B*35 (hazard ratio, 4.64; 95% CI, 1.33-18.17; P = 0.017), HLA-C*04 (hazard ratio, 5.30; 95% CI, 1.51-20.77; P = 0.010), HLA-C*16 (hazard ratio, 4.05; 95% CI, 0.87-14.62; P = 0.071), HLA-DRB1*07 (hazard ratio, 3.29; 95% CI, 0.94-12.90; P = 0.062) and HLA-DRB1*08 (hazard ratio, 15.37; 95% CI, 2.11-79.80; P = 0.011) were associated with an increased risk of superinfection at α = 0.10, whereas HLA-DRB1*11 was associated with decreased superinfection risk (hazard ratio, 0.13; 95% CI, 0.00-1.03; P = 0.054). CONCLUSION HLA genes may, in part, elucidate the genetic basis of differential superinfection risk, and provide important information for the development of efficient prevention and treatment strategies of HIV-1 superinfection.
Collapse
Affiliation(s)
- Jouni Vesa
- University of California San Diego, La Jolla
| | | | | | | | - Douglas D. Richman
- University of California San Diego, La Jolla
- Veterans Affairs San Diego Healthcare System, San Diego, California, USA
| | - Davey M. Smith
- University of California San Diego, La Jolla
- Veterans Affairs San Diego Healthcare System, San Diego, California, USA
| | | |
Collapse
|
10
|
Angin M, Wong G, Papagno L, Versmisse P, David A, Bayard C, Charmeteau-De Muylder B, Besseghir A, Thiébaut R, Boufassa F, Pancino G, Sauce D, Lambotte O, Brun-Vézinet F, Matheron S, Rowland-Jones SL, Cheynier R, Sáez-Cirión A, Appay V. Preservation of Lymphopoietic Potential and Virus Suppressive Capacity by CD8+ T Cells in HIV-2-Infected Controllers. THE JOURNAL OF IMMUNOLOGY 2016; 197:2787-95. [PMID: 27566819 DOI: 10.4049/jimmunol.1600693] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 07/23/2016] [Indexed: 12/14/2022]
Abstract
Compared with HIV-1, HIV-2 infection is characterized by a larger proportion of slow or nonprogressors. A better understanding of HIV-2 pathogenesis should open new therapeutic avenues to establish control of HIV-1 replication in infected patients. In this study, we studied the production of CD8(+) T cells and their capacity for viral control in HIV-2 controllers from the French ANRS CO5 HIV-2 cohort. HIV-2 controllers display a robust capacity to support long-term renewal of the CD8(+) T cell compartment by preserving immune resources, including hematopoietic progenitors and thymic activity, which could contribute to the long-term maintenance of the CD8(+) T cell response and the avoidance of premature immune aging. Our data support the presence of HIV-2 Gag-specific CD8(+) T cells that display an early memory differentiation phenotype and robust effector potential in HIV-2 controllers. Accordingly, to our knowledge, we show for the first time that HIV-2 controllers possess CD8(+) T cells that show an unusually strong capacity to suppress HIV-2 infection in autologous CD4(+) T cells ex vivo, an ability that likely depends on the preservation of host immune resources. This effective and durable antiviral response probably participates in a virtuous circle, during which controlled viral replication permits the preservation of potent immune functions, thus preventing HIV-2 disease progression.
Collapse
Affiliation(s)
- Mathieu Angin
- Institut Pasteur, Unité HIV Inflammation et Persistance, Paris 75015, France
| | - Glenn Wong
- Sorbonne Universités, Université Pierre et Marie Curie, Université Paris 06, DHU FAST, CR7, Centre d'Immunologie et des Maladies Infectieuses, INSERM U1135, Paris 75005, France; Nuffield Department of Medicine, Headington, Oxford OX3 7FZ, United Kingdom
| | - Laura Papagno
- Sorbonne Universités, Université Pierre et Marie Curie, Université Paris 06, DHU FAST, CR7, Centre d'Immunologie et des Maladies Infectieuses, INSERM U1135, Paris 75005, France
| | - Pierre Versmisse
- Institut Pasteur, Unité HIV Inflammation et Persistance, Paris 75015, France
| | - Annie David
- Institut Pasteur, Unité HIV Inflammation et Persistance, Paris 75015, France
| | - Charles Bayard
- Sorbonne Universités, Université Pierre et Marie Curie, Université Paris 06, DHU FAST, CR7, Centre d'Immunologie et des Maladies Infectieuses, INSERM U1135, Paris 75005, France
| | - Bénédicte Charmeteau-De Muylder
- INSERM U1016, Institut Cochin, Cytokines and Viral Infections Team, Paris 75014, France; CNRS UMR 8104, Université Paris Descartes, Sorbonne Paris Cité, Paris 75014, France
| | - Amel Besseghir
- Centre de Méthodologie et de Gestion des Essais Cliniques de l'INSERM U1219, Virus de l'Immunodéficience Humaine, Hépatites Virales et Comorbidités, Épidémiologie Clinique et Santé Publique, Bordeaux 33076, France
| | - Rodolphe Thiébaut
- Centre de Méthodologie et de Gestion des Essais Cliniques de l'INSERM U1219, Virus de l'Immunodéficience Humaine, Hépatites Virales et Comorbidités, Épidémiologie Clinique et Santé Publique, Bordeaux 33076, France
| | - Faroudy Boufassa
- INSERM U1018, Centre de Recherche en Epidémiologie et Santé des Populations, Université Paris Sud, Le Kremlin Bicêtre 94270, France
| | - Gianfranco Pancino
- Institut Pasteur, Unité HIV Inflammation et Persistance, Paris 75015, France
| | - Delphine Sauce
- Sorbonne Universités, Université Pierre et Marie Curie, Université Paris 06, DHU FAST, CR7, Centre d'Immunologie et des Maladies Infectieuses, INSERM U1135, Paris 75005, France
| | - Olivier Lambotte
- INSERM UMR 1184, Immunologie des Maladies Virales et Autoimmunes, Le Kremlin Bicêtre 94270, France; Assistance Publique-Hôpitaux de Paris, Service de Médecine Interne, Hôpitaux Universitaires, Le Kremlin Bicêtre 94270, France; Université Paris Sud, Le Kremlin Bicêtre 94270, France
| | - Françoise Brun-Vézinet
- Assistance Publique-Hôpitaux de Paris, Laboratoire de Virologie, Hôpital Bichat, Paris 75018, France
| | - Sophie Matheron
- INSERM UMR 1137, Infections, Antimicrobiens, Modélisation, Evolution, Université Paris Diderot, Sorbonne Paris Cité, Paris 75018, France; and Assistance Publique-Hôpitaux de Paris, Service des Maladies Infectieuses et Tropicales, Hôpital Bichat, Paris 75018, France
| | | | - Rémi Cheynier
- INSERM U1016, Institut Cochin, Cytokines and Viral Infections Team, Paris 75014, France; CNRS UMR 8104, Université Paris Descartes, Sorbonne Paris Cité, Paris 75014, France
| | - Asier Sáez-Cirión
- Institut Pasteur, Unité HIV Inflammation et Persistance, Paris 75015, France;
| | - Victor Appay
- Sorbonne Universités, Université Pierre et Marie Curie, Université Paris 06, DHU FAST, CR7, Centre d'Immunologie et des Maladies Infectieuses, INSERM U1135, Paris 75005, France;
| | | |
Collapse
|
11
|
Frange P, Faye A, Avettand-Fenoël V, Bellaton E, Descamps D, Angin M, David A, Caillat-Zucman S, Peytavin G, Dollfus C, Le Chenadec J, Warszawski J, Rouzioux C, Sáez-Cirión A. HIV-1 virological remission lasting more than 12 years after interruption of early antiretroviral therapy in a perinatally infected teenager enrolled in the French ANRS EPF-CO10 paediatric cohort: a case report. LANCET HIV 2016; 3:e49-54. [DOI: 10.1016/s2352-3018(15)00232-5] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 11/11/2015] [Accepted: 11/12/2015] [Indexed: 12/20/2022]
|
12
|
Consequences of HLA-B*13-Associated Escape Mutations on HIV-1 Replication and Nef Function. J Virol 2015; 89:11557-71. [PMID: 26355081 DOI: 10.1128/jvi.01955-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 08/31/2015] [Indexed: 01/05/2023] Open
Abstract
UNLABELLED HLA-B*13 is associated with superior in vivo HIV-1 viremia control. Protection is thought to be mediated by sustained targeting of key cytotoxic T lymphocyte (CTL) epitopes and viral fitness costs of CTL escape in Gag although additional factors may contribute. We assessed the impact of 10 published B*13-associated polymorphisms in Gag, Pol, and Nef, in 23 biologically relevant combinations, on HIV-1 replication capacity and Nef-mediated reduction of cell surface CD4 and HLA class I expression. Mutations were engineered into HIV-1NL4.3, and replication capacity was measured using a green fluorescent protein (GFP) reporter T cell line. Nef-mediated CD4 and HLA-A*02 downregulation was assessed by flow cytometry, and T cell recognition of infected target cells was measured via coculture with an HIV-specific luciferase reporter cell line. When tested individually, only Gag-I147L and Gag-I437L incurred replicative costs (5% and 17%, respectively), consistent with prior reports. The Gag-I437L-mediated replication defect was rescued to wild-type levels by the adjacent K436R mutation. A novel B*13 epitope, comprising 8 residues and terminating at Gag147, was identified in p24(Gag) (GQMVHQAIGag140-147). No other single or combination Gag, Pol, or Nef mutant impaired viral replication. Single Nef mutations did not affect CD4 or HLA downregulation; however, the Nef double mutant E24Q-Q107R showed 40% impairment in HLA downregulation with no evidence of Nef stability defects. Moreover, target cells infected with HIV-1-NefE24Q-Q107R were recognized better by HIV-specific T cells than those infected with HIV-1NL4.3 or single Nef mutants. Our results indicate that CTL escape in Gag and Nef can be functionally costly and suggest that these effects may contribute to long-term HIV-1 control by HLA-B*13. IMPORTANCE Protective effects of HLA-B*13 on HIV-1 disease progression are mediated in part by fitness costs of CTL escape mutations in conserved Gag epitopes, but other mechanisms remain incompletely known. We extend our knowledge of the impact of B*13-driven escape on HIV-1 replication by identifying Gag-K436R as a compensatory mutation for the fitness-costly Gag-I437L. We also identify Gag-I147L, the most rapidly and commonly selected B*13-driven substitution in HIV-1, as a putative C-terminal anchor residue mutation in a novel B*13 epitope. Most notably, we identify a novel escape-driven fitness defect: B*13-driven substitutions E24Q and Q107R in Nef, when present together, substantially impair this protein's ability to downregulate HLA class I. This, in turn, increases the visibility of infected cells to HIV-specific T cells. Our results suggest that B*13-associated escape mutations impair HIV-1 replication by two distinct mechanisms, that is, by reducing Gag fitness and dampening Nef immune evasion function.
Collapse
|
13
|
Keynan Y, Rueda ZV, Bresler K, Becker M, Kasper K. HLA B51 is associated with faster AIDS progression among newly diagnosed HIV-infected individuals in Manitoba, Canada. Int J Immunogenet 2015; 42:336-40. [PMID: 26263514 DOI: 10.1111/iji.12219] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 05/05/2015] [Accepted: 06/21/2015] [Indexed: 11/29/2022]
Abstract
Human leucocyte antigen (HLA) alleles influence the rate of CD4 decline among HIV-infected individuals. We investigated the association between HLA B35 and HLA B51 and the rate of CD4 decline and/or opportunistic infections, among 294 HIV-positive individuals from Manitoba, Canada. All individuals presenting with a CD4 count >200 cells μL(-1) , who had at least two CD4 counts, and no evidence of co-infection were included. Individuals bearing HLA B35 or HLA B51 were compared to controls. A multivariate model demonstrated that HLA B35 allele was associated with a hazard ratio of 2.05 (95% CI 1.31-3.18) for reaching AIDS and HLA B51 allele with HR of 2.03 (95% CI 1.18-3.49) for reaching the same end-point. High prevalence of HLA B35 was seen in the patient population receiving care in Manitoba. Our observations confirm the association of HLA B35 with rapid disease progression. We report, for the first time, faster CD4 decline among individuals with HLA B51 allele.
Collapse
Affiliation(s)
- Y Keynan
- Manitoba HIV Program, Winnipeg, MB, Canada.,Department of Medical Microbiology, University of Manitoba, Winnipeg, MB, Canada.,Department of Community Health Sciences, University of Manitoba, Winnipeg, MB, Canada.,Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - Z V Rueda
- Universidad Pontificia Bolivariana, Medellin, Colombia
| | - K Bresler
- Manitoba HIV Program, Winnipeg, MB, Canada
| | - M Becker
- Manitoba HIV Program, Winnipeg, MB, Canada.,Department of Medical Microbiology, University of Manitoba, Winnipeg, MB, Canada.,Department of Community Health Sciences, University of Manitoba, Winnipeg, MB, Canada.,Centre for Global Public Health, University of Manitoba, Winnipeg, MB, Canada
| | - K Kasper
- Manitoba HIV Program, Winnipeg, MB, Canada.,Department of Medical Microbiology, University of Manitoba, Winnipeg, MB, Canada.,Department of Community Health Sciences, University of Manitoba, Winnipeg, MB, Canada.,Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| |
Collapse
|
14
|
Velasco C, Parker E, Pastor L, Nhama A, Macuacua S, Mandomando I, Blanco J, Naniche D. Rapid HIV progression during acute HIV-1 subtype C infection in a Mozambican patient with atypical seroconversion. Am J Trop Med Hyg 2015; 92:681-3. [PMID: 25624400 DOI: 10.4269/ajtmh.14-0554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 12/16/2014] [Indexed: 01/31/2023] Open
Abstract
Acute human immunodeficiency virus (HIV) infection (AHI) refers to the period between viral transmission and development of an adaptive immune response to HIV antigens (seroconversion) usually lasting 6-8 weeks. Rare cases have been described in which HIV-infected patients fail to seroconvert and instead, develop rapid HIV-mediated clinical decline. We report the case of a Mozambican woman with AHI and malaria coinfection who showed atypical seroconversion and experienced rapid deterioration and death within 14 weeks of diagnosis with AHI. Atypical seroconversion may be associated with rapid progression. Fourth generation rapid tests could lead to earlier identification and intervention for this vulnerable subgroup.
Collapse
Affiliation(s)
- Cesar Velasco
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain; Department of Preventive Medicine and Epidemiology, Hospital Clinic, Barcelona, Spain; School of Paediatrics and Child Health, University of Western Australia, Perth, Australia; IrsiCaixa Institute for AIDS Research, Institut Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, UAB, Badalona, Spain; Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique; Instituto Nacional de Saúde, Ministério de Saúde, Maputo, Mozambique; Universitat de Vic- Universitat Central de Catalunya, Vic, Spain
| | - Erica Parker
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain; Department of Preventive Medicine and Epidemiology, Hospital Clinic, Barcelona, Spain; School of Paediatrics and Child Health, University of Western Australia, Perth, Australia; IrsiCaixa Institute for AIDS Research, Institut Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, UAB, Badalona, Spain; Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique; Instituto Nacional de Saúde, Ministério de Saúde, Maputo, Mozambique; Universitat de Vic- Universitat Central de Catalunya, Vic, Spain
| | - Lucia Pastor
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain; Department of Preventive Medicine and Epidemiology, Hospital Clinic, Barcelona, Spain; School of Paediatrics and Child Health, University of Western Australia, Perth, Australia; IrsiCaixa Institute for AIDS Research, Institut Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, UAB, Badalona, Spain; Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique; Instituto Nacional de Saúde, Ministério de Saúde, Maputo, Mozambique; Universitat de Vic- Universitat Central de Catalunya, Vic, Spain
| | - Abel Nhama
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain; Department of Preventive Medicine and Epidemiology, Hospital Clinic, Barcelona, Spain; School of Paediatrics and Child Health, University of Western Australia, Perth, Australia; IrsiCaixa Institute for AIDS Research, Institut Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, UAB, Badalona, Spain; Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique; Instituto Nacional de Saúde, Ministério de Saúde, Maputo, Mozambique; Universitat de Vic- Universitat Central de Catalunya, Vic, Spain
| | - Salesio Macuacua
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain; Department of Preventive Medicine and Epidemiology, Hospital Clinic, Barcelona, Spain; School of Paediatrics and Child Health, University of Western Australia, Perth, Australia; IrsiCaixa Institute for AIDS Research, Institut Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, UAB, Badalona, Spain; Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique; Instituto Nacional de Saúde, Ministério de Saúde, Maputo, Mozambique; Universitat de Vic- Universitat Central de Catalunya, Vic, Spain
| | - Inácio Mandomando
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain; Department of Preventive Medicine and Epidemiology, Hospital Clinic, Barcelona, Spain; School of Paediatrics and Child Health, University of Western Australia, Perth, Australia; IrsiCaixa Institute for AIDS Research, Institut Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, UAB, Badalona, Spain; Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique; Instituto Nacional de Saúde, Ministério de Saúde, Maputo, Mozambique; Universitat de Vic- Universitat Central de Catalunya, Vic, Spain
| | - Julià Blanco
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain; Department of Preventive Medicine and Epidemiology, Hospital Clinic, Barcelona, Spain; School of Paediatrics and Child Health, University of Western Australia, Perth, Australia; IrsiCaixa Institute for AIDS Research, Institut Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, UAB, Badalona, Spain; Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique; Instituto Nacional de Saúde, Ministério de Saúde, Maputo, Mozambique; Universitat de Vic- Universitat Central de Catalunya, Vic, Spain
| | - Denise Naniche
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain; Department of Preventive Medicine and Epidemiology, Hospital Clinic, Barcelona, Spain; School of Paediatrics and Child Health, University of Western Australia, Perth, Australia; IrsiCaixa Institute for AIDS Research, Institut Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, UAB, Badalona, Spain; Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique; Instituto Nacional de Saúde, Ministério de Saúde, Maputo, Mozambique; Universitat de Vic- Universitat Central de Catalunya, Vic, Spain
| |
Collapse
|
15
|
Regoes RR, McLaren PJ, Battegay M, Bernasconi E, Calmy A, Günthard HF, Hoffmann M, Rauch A, Telenti A, Fellay J. Disentangling human tolerance and resistance against HIV. PLoS Biol 2014; 12:e1001951. [PMID: 25226169 PMCID: PMC4165755 DOI: 10.1371/journal.pbio.1001951] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 08/08/2014] [Indexed: 12/20/2022] Open
Abstract
Title: Human tolerance against HIV An evolutionary ecology perspective on clinical data reveals that human traits can affect how well an individual tolerates HIV infection, and identifies host immunity factors associated with disease tolerance. In ecology, “disease tolerance” is defined as an evolutionary strategy of hosts against pathogens, characterized by reduced or absent pathogenesis despite high pathogen load. To our knowledge, tolerance has to date not been quantified and disentangled from host resistance to disease in any clinically relevant human infection. Using data from the Swiss HIV Cohort Study, we investigated if there is variation in tolerance to HIV in humans and if this variation is associated with polymorphisms in the human genome. In particular, we tested for associations between tolerance and alleles of the Human Leukocyte Antigen (HLA) genes, the CC chemokine receptor 5 (CCR5), the age at which individuals were infected, and their sex. We found that HLA-B alleles associated with better HIV control do not confer tolerance. The slower disease progression associated with these alleles can be fully attributed to the extent of viral load reduction in carriers. However, we observed that tolerance significantly varies across HLA-B genotypes with a relative standard deviation of 34%. Furthermore, we found that HLA-B homozygotes are less tolerant than heterozygotes. Lastly, tolerance was observed to decrease with age, resulting in a 1.7-fold difference in disease progression between 20 and 60-y-old individuals with the same viral load. Thus, disease tolerance is a feature of infection with HIV, and the identification of the mechanisms involved may pave the way to a better understanding of pathogenesis. When confronted with pathogens, hosts can either evolve to fight them or learn to live with them. The first of these two strategies is called “resistance” and the second “tolerance”. In the context of HIV, many genes conferring resistance have been identified, but no tolerance genes are known. Using statistical techniques originating from plant ecology, we analyzed data from an HIV cohort to look for differences in tolerance between HIV-infected individuals and tested whether they go hand in hand with genetic differences. We found that younger people are more tolerant to HIV infection. We also observed that individuals who carry two different alleles of HLA-B, an important immunity gene, are more tolerant. These findings add to our understanding of how hosts tolerate infections and could open new avenues for treating infections.
Collapse
Affiliation(s)
- Roland R. Regoes
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- * E-mail:
| | - Paul J. McLaren
- Global Health Institute, EPF Lausanne, Lausanne, Switzerland
- Institute of Microbiology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Manuel Battegay
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland
| | - Alexandra Calmy
- Geneva University Hospital, HIV Unit, Department of Internal Medicine, Geneva, Switzerland
| | - Huldrych F. Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Matthias Hoffmann
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St.Gallen, St.Gallen, Switzerland
| | - Andri Rauch
- University Clinic of Infectious Diseases, University Hospital Bern and University of Bern, Bern, Switzerland
| | - Amalio Telenti
- Institute of Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Jacques Fellay
- Global Health Institute, EPF Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | |
Collapse
|
16
|
Abstract
OBJECTIVE To evaluate the impact of mitochondrial DNA (mtDNA) haplogroups on virologic and immunological outcomes of HIV infection. DESIGN HAART-naive African American adolescent participants to the Reaching for Excellence in Adolescent Care and Health study. METHODS The mtDNA haplogroups were inferred from sequenced mtDNA hypervariable regions HV1 and HV2 and their predictive value on HIV outcomes were evaluated in linear mixed models, controlled for human leukocyte antigen (HLA)-B27, HLA-B57 and HLA-B35-Px alleles and other covariates. RESULTS We report data showing that the mtDNA L2 lineage, a group composed of L2a, L2b and L2e mtDNA haplogroups in the studied population, is significantly associated (beta = -0.08; Bonferroni-adjusted P = 0.004) with decline of CD4 T cells (median loss of 8 ± 1 cells per month) in HAART-naive HIV-infected individuals of African American descent (n = 133). No significant association (P < 0.05) with set-point viral load was observed with any of the tested mtDNA haplogroups. The present data concur with previous findings in the AIDS Clinical Trials Group study 384, implicating the L2 lineage with slower CD4 T-cell recovery after antiretroviral therapy in African Americans. CONCLUSIONS Whereas the L2 lineage showed an association with unfavorable immunological outcomes of HIV infection, its phylogenetic divergence from J and U5a, two lineages associated with accelerated HIV progression in European Americans, raises the possibility that interactions with common nucleus-encoded variants drive HIV progression. Disentangling the effects of mitochondrial and nuclear gene variants on the outcomes of HIV infection is an important step to be taken toward a better understanding of HIV/AIDS pathogenesis and pharmacogenomics.
Collapse
|
17
|
Zhang H, Zhao B, Han X, Wang Z, Liu B, Lu C, Zhang M, Liu J, Chen O, Hu Q, Jiang F, Shang H. Associations of HLA class I antigen specificities and haplotypes with disease progression in HIV-1-infected Hans in Northern China. Hum Immunol 2013; 74:1636-42. [PMID: 24012585 DOI: 10.1016/j.humimm.2013.08.287] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 07/17/2013] [Accepted: 08/10/2013] [Indexed: 12/11/2022]
Abstract
The human leukocyte antigen (HLA) allele frequencies, which differ among various ethnic populations, may result in population-specific effects on HIV-1 disease progression. No large-scale study has yet been conducted on the Chinese population. In this study, HLA class I antigen specificities were determined in a cohort including 105 long-term non-progressors (LTNPs) and 321 typical progressors (TPs), who were recruited from HIV-1-infected Northern Han Chinese, to determine the associations between certain HLA types and HIV-1 disease progression. The frequencies of HLA class I specificities and haplotypes among the two groups were compared using binary logistic stepwise regression. Results showed that HLA-A(∗)30-B(∗)13-C(∗)06 (OR = 0.387, P = 0.019) and B(∗)67 (OR = 0.134, P = 0.005) were associated with a long-term non-progressing condition, and C(∗)01 (OR = 2.539, P = 0.050) was overrepresented in TPs after adjusting for non-genetic factors (sex, age, the location of patients, HIV subtype and the route of infection). The influence of HLA homozygosity on HIV disease progression was also analyzed. However, homozygosity at HLA-A, HLA-B or HLA-C conferred no observable disadvantage in our study population (P = 0.730, 0.246 and 0.445, respectively). These findings suggest that the host's genetics make important contributions to HIV viral control and may help to develop peptide-based vaccines for this population.
Collapse
Affiliation(s)
- Hui Zhang
- Key Laboratory of AIDS Immunology of the Ministry of Health, Department of Laboratory Medicine, The First Hospital of China Medical University, Shenyang, China
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Ovsyannikova IG, Pankratz VS, Vierkant RA, Pajewski NM, Quinn CP, Kaslow RA, Jacobson RM, Poland GA. Human leukocyte antigens and cellular immune responses to anthrax vaccine adsorbed. Infect Immun 2013; 81:2584-91. [PMID: 23649091 PMCID: PMC3697592 DOI: 10.1128/iai.00269-13] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 04/28/2013] [Indexed: 01/21/2023] Open
Abstract
Interindividual variations in vaccine-induced immune responses are in part due to host genetic polymorphisms in the human leukocyte antigen (HLA) and other gene families. This study examined associations between HLA genotypes, haplotypes, and homozygosity and protective antigen (PA)-specific cellular immune responses in healthy subjects following immunization with Anthrax Vaccine Adsorbed (AVA). While limited associations were observed between individual HLA alleles or haplotypes and variable lymphocyte proliferative (LP) responses to AVA, analyses of homozygosity supported the hypothesis of a "heterozygote advantage." Individuals who were homozygous for any HLA locus demonstrated significantly lower PA-specific LP than subjects who were heterozygous at all eight loci (median stimulation indices [SI], 1.84 versus 2.95, P = 0.009). Similarly, we found that class I (HLA-A) and class II (HLA-DQA1 and HLA-DQB1) homozygosity was significantly associated with an overall decrease in LP compared with heterozygosity at those three loci. Specifically, individuals who were homozygous at these loci had significantly lower PA-specific LP than subjects heterozygous for HLA-A (median SI, 1.48 versus 2.13, P = 0.005), HLA-DQA1 (median SI, 1.75 versus 2.11, P = 0.007), and HLA-DQB1 (median SI, 1.48 versus 2.13, P = 0.002) loci, respectively. Finally, homozygosity at an increasing number (≥ 4) of HLA loci was significantly correlated with a reduction in LP response (P < 0.001) in a dose-dependent manner. Additional studies are needed to reproduce these findings and determine whether HLA-heterozygous individuals generate stronger cellular immune response to other virulence factors (Bacillus anthracis LF and EF) than HLA-homozygous subjects.
Collapse
Affiliation(s)
- Inna G. Ovsyannikova
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, Minnesota, USA
- Program in Translational Immunovirology and Biodefense, Mayo Clinic, Rochester, Minnesota, USA
| | - V. Shane Pankratz
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Robert A. Vierkant
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Nicholas M. Pajewski
- Department of Biostatistical Sciences, Wake Forest University Health Sciences, Winston Salem, North Carolina, USA
| | - Conrad P. Quinn
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Richard A. Kaslow
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Robert M. Jacobson
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, Minnesota, USA
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Gregory A. Poland
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, Minnesota, USA
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Program in Translational Immunovirology and Biodefense, Mayo Clinic, Rochester, Minnesota, USA
| |
Collapse
|
19
|
Abstract
Host genetic factors are a major contributing factor to the inter-individual variation observed in response to human immunodeficiency virus (HIV) infection and are linked to resistance to HIV infection among exposed individuals, as well as rate of disease progression and the likelihood of viral transmission. Of the genetic variants that have been shown to affect the natural history of HIV infection, the human leukocyte antigen (HLA) class I genes exhibit the strongest and most consistent association, underscoring a central role for CD8(+) T cells in resistance to the virus. HLA proteins play important roles in T-cell-mediated adaptive immunity by presenting immunodominant HIV epitopes to cytotoxic T lymphocytes (CTLs) and CD4(+) T cells. Genetic and functional data also indicate a function for HLA in natural killer cell-mediated innate immunity against HIV by interacting with killer cell immunoglobulin-like receptors (KIR). We review the HLA and KIR associations with HIV disease and discuss the mechanisms underlying these associations.
Collapse
Affiliation(s)
- Maureen P. Martin
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland, USA
| | - Mary Carrington
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland, USA
- Ragon Institute of MGH, MIT, and Harvard, Boston, Massachusetts, USA
| |
Collapse
|
20
|
Poland GA, Kennedy RB, McKinney BA, Ovsyannikova IG, Lambert ND, Jacobson RM, Oberg AL. Vaccinomics, adversomics, and the immune response network theory: individualized vaccinology in the 21st century. Semin Immunol 2013; 25:89-103. [PMID: 23755893 DOI: 10.1016/j.smim.2013.04.007] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 03/23/2013] [Accepted: 04/18/2013] [Indexed: 02/08/2023]
Abstract
Vaccines, like drugs and medical procedures, are increasingly amenable to individualization or personalization, often based on novel data resulting from high throughput "omics" technologies. As a result of these technologies, 21st century vaccinology will increasingly see the abandonment of a "one size fits all" approach to vaccine dosing and delivery, as well as the abandonment of the empiric "isolate-inactivate-inject" paradigm for vaccine development. In this review, we discuss the immune response network theory and its application to the new field of vaccinomics and adversomics, and illustrate how vaccinomics can lead to new vaccine candidates, new understandings of how vaccines stimulate immune responses, new biomarkers for vaccine response, and facilitate the understanding of what genetic and other factors might be responsible for rare side effects due to vaccines. Perhaps most exciting will be the ability, at a systems biology level, to integrate increasingly complex high throughput data into descriptive and predictive equations for immune responses to vaccines. Herein, we discuss the above with a view toward the future of vaccinology.
Collapse
|
21
|
Rapid, complex adaptation of transmitted HIV-1 full-length genomes in subtype C-infected individuals with differing disease progression. AIDS 2013; 27:507-18. [PMID: 23370465 DOI: 10.1097/qad.0b013e32835cab64] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
OBJECTIVE(S) There is limited information on full-length genome sequences and the early evolution of transmitted HIV-1 subtype C viruses, which constitute the majority of viruses spread in Africa. The purpose of this study was to characterize the earliest changes across the genome of subtype C viruses following transmission, to better understand early control of viremia. DESIGN We derived the near full-length genome sequence responsible for clinical infection from five HIV subtype C-infected individuals with different disease progression profiles and tracked adaptation to immune responses in the first 6 months of infection. METHODS Near full-length genomes were generated by single genome amplification and direct sequencing. Sequences were analyzed for amino acid mutations associated with cytotoxic T lymphocyte (CTL) or antibody-mediated immune pressure, and for reversion. RESULTS Fifty-five sequence changes associated with adaptation to the new host were identified, with 38% attributed to CTL pressure, 35% to antibody pressure, 16% to reversions and the remainder were unclassified. Mutations in CTL epitopes were most frequent in the first 5 weeks of infection, with the frequency declining over time with the decline in viral load. CTL escape predominantly occurred in nef, followed by pol and env. Shuffling/toggling of mutations was identified in 81% of CTL epitopes, with only 7% reaching fixation within the 6-month period. CONCLUSION There was rapid virus adaptation following transmission, predominantly driven by CTL pressure, with most changes occurring during high viremia. Rapid escape and complex escape pathways provide further challenges for vaccine protection.
Collapse
|
22
|
Lingappa JR, Thomas KK, Hughes JP, Baeten JM, Wald A, Farquhar C, de Bruyn G, Fife KH, Campbell MS, Kapiga S, Mullins JI, Celum, for the Partners in Preventi C. Partner characteristics predicting HIV-1 set point in sexually acquired HIV-1 among African seroconverters. AIDS Res Hum Retroviruses 2013; 29:164-71. [PMID: 23061422 DOI: 10.1089/aid.2012.0206] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Plasma HIV-1 RNA set point is an important predictor of HIV-1 disease progression. We hypothesized that inoculum size and HIV-1 exposure prior to HIV-1 transmission may modulate set point. We evaluated predictors of set point among 141 African HIV-1 seroconverters and their HIV-1-infected study partners. We compared characteristics of seroconverters and their HIV-1-infected partners and HIV-1 set point. Data were from a clinical trial of genital HSV-2 suppression with acyclovir to reduce HIV-1 transmission in HIV-1 serodiscordant couples with HIV-1 transmission linkage assigned through virus sequencing. Our analysis includes data from all transmissions including those with transmission linkage to the HIV-1-infected "source partner" and those that were not linked to their HIV-1-infected study partner. In multivariable analysis, higher plasma HIV-1 in source partners was associated with higher seroconverter set point ( + 0.44 log10 copies/ml per log(10) source partner plasma HIV-1, p < 0.001). In addition, bacterial vaginosis (BV) among female source partners near the time of infection was associated with higher set point in their male seroconverters ( + 0.49 log(10), p = 0.04). Source partner characteristics associated with lower set point included male circumcision ( - 0.63 log(10), p = 0.03) and assignment to acyclovir ( - 0.44 log10, p = 0.02). The proportion of variation in set point explained by plasma HIV-1 RNA of the source partner, after controlling for other factors, was 0.06. Source partner plasma HIV-1 level is the most significant predictor of seroconverter set point, possibly reflecting characteristics of the transmitted virus. Acyclovir use, BV among women source partners, and circumcision among male source partners may alter the set point by affecting transmitted virus inoculum in the source partners' genital compartment.
Collapse
Affiliation(s)
- Jairam R. Lingappa
- Department of Global Health, University of Washington, Seattle, Washington
- Department of Medicine, University of Washington, Seattle, Washington
- Department of Pediatrics, University of Washington, Seattle, Washington
| | | | - James P. Hughes
- Department of Biostatistics, University of Washington, Seattle, Washington
| | - Jared M. Baeten
- Department of Global Health, University of Washington, Seattle, Washington
- Department of Medicine, University of Washington, Seattle, Washington
- Department of Epidemiology, University of Washington, Seattle, Washington
| | - Anna Wald
- Department of Medicine, University of Washington, Seattle, Washington
- Department of Epidemiology, University of Washington, Seattle, Washington
- Laboratory Medicine, University of Washington, Seattle, Washington
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Carey Farquhar
- Department of Global Health, University of Washington, Seattle, Washington
- Department of Medicine, University of Washington, Seattle, Washington
- Department of Epidemiology, University of Washington, Seattle, Washington
| | - Guy de Bruyn
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, Republic of South Africa
| | - Kenneth H. Fife
- Department of Medicine, Indiana University, Indianapolis, Indiana
| | - Mary S. Campbell
- Department of Medicine, University of Washington, Seattle, Washington
| | - Saidi Kapiga
- Department of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - James I. Mullins
- Department of Medicine, University of Washington, Seattle, Washington
- Laboratory Medicine, University of Washington, Seattle, Washington
- Department of Microbiology, University of Washington, Seattle, Washington
| | - Connie Celum, for the Partners in Preventi
- Department of Global Health, University of Washington, Seattle, Washington
- Department of Medicine, University of Washington, Seattle, Washington
- Department of Epidemiology, University of Washington, Seattle, Washington
| | | |
Collapse
|
23
|
Abstract
Human immunodeficiency virus (HIV) pathogenesis has proven to be quite complex and dynamic with most of the critical events (e.g., transmission, CD4(+) T-cell destruction) occurring in mucosal tissues. In addition, although the resulting disease can progress over years, it is clear that many critical events happen within the first few weeks of infection when most patients are unaware that they are infected. These events occur predominantly in tissues other than the peripheral blood, particularly the gastrointestinal tract, where massive depletion of CD4(+) T cells occurs long before adverse consequences of HIV infection are otherwise apparent. Profound insights into these early events have been gained through the use of nonhuman primate models, which offer the opportunity to examine the early stages of infection with the simian immunodeficiency virus (SIV), a close relative of HIV that induces an indistinguishable clinical picture from AIDS in Asian primate species, but importantly, fails to cause disease in its natural African hosts, such as sooty mangabeys and African green monkeys. This article draws from data derived from both human and nonhuman primate studies.
Collapse
Affiliation(s)
- A A Lackner
- Tulane National Primate Research Center, Tulane University Health Science Center, Covington, LA 70443, USA.
| | | | | |
Collapse
|
24
|
Budde ML, Greene JM, Chin EN, Ericsen AJ, Scarlotta M, Cain BT, Pham NH, Becker EA, Harris M, Weinfurter JT, O'Connor SL, Piatak M, Lifson JD, Gostick E, Price DA, Friedrich TC, O'Connor DH. Specific CD8+ T cell responses correlate with control of simian immunodeficiency virus replication in Mauritian cynomolgus macaques. J Virol 2012; 86:7596-604. [PMID: 22573864 PMCID: PMC3416303 DOI: 10.1128/jvi.00716-12] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 04/30/2012] [Indexed: 11/20/2022] Open
Abstract
Specific major histocompatibility complex (MHC) class I alleles are associated with an increased frequency of spontaneous control of human and simian immunodeficiency viruses (HIV and SIV). The mechanism of control is thought to involve MHC class I-restricted CD8(+) T cells, but it is not clear whether particular CD8(+) T cell responses or a broad repertoire of epitope-specific CD8(+) T cell populations (termed T cell breadth) are principally responsible for mediating immunologic control. To test the hypothesis that heterozygous macaques control SIV replication as a function of superior T cell breadth, we infected MHC-homozygous and MHC-heterozygous cynomolgus macaques with the pathogenic virus SIVmac239. As measured by a gamma interferon enzyme-linked immunosorbent spot assay (IFN-γ ELISPOT) using blood, T cell breadth did not differ significantly between homozygotes and heterozygotes. Surprisingly, macaques that controlled SIV replication, regardless of their MHC zygosity, shared durable T cell responses against similar regions of Nef. While the limited genetic variability in these animals prevents us from making generalizations about the importance of Nef-specific T cell responses in controlling HIV, these results suggest that the T cell-mediated control of virus replication that we observed is more likely the consequence of targeting specificity rather than T cell breadth.
Collapse
Affiliation(s)
- Melisa L. Budde
- Wisconsin National Primate Research Center, Madison, Wisconsin, USA
| | - Justin M. Greene
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, Wisconsin, USA
| | - Emily N. Chin
- Department of Cellular and Molecular Biology, University of Wisconsin, Madison, Wisconsin, USA
| | - Adam J. Ericsen
- Wisconsin National Primate Research Center, Madison, Wisconsin, USA
| | - Matthew Scarlotta
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, Wisconsin, USA
| | - Brian T. Cain
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, Wisconsin, USA
| | - Ngoc H. Pham
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, Wisconsin, USA
| | - Ericka A. Becker
- Wisconsin National Primate Research Center, Madison, Wisconsin, USA
| | - Max Harris
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, Wisconsin, USA
| | - Jason T. Weinfurter
- Wisconsin National Primate Research Center, Madison, Wisconsin, USA
- Department of Pathobiological Sciences, University of Wisconsin, Madison, Wisconsin, USA
| | - Shelby L. O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, Madison, Wisconsin, USA
| | - Michael Piatak
- AIDS and Cancer Virus Program, Science Applications International Corporation-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Jeffrey D. Lifson
- AIDS and Cancer Virus Program, Science Applications International Corporation-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Emma Gostick
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom
| | - David A. Price
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom
| | - Thomas C. Friedrich
- Wisconsin National Primate Research Center, Madison, Wisconsin, USA
- Department of Pathobiological Sciences, University of Wisconsin, Madison, Wisconsin, USA
| | - David H. O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, Madison, Wisconsin, USA
| |
Collapse
|
25
|
Stephens HAF. Immunogenetic surveillance of HIV/AIDS. INFECTION GENETICS AND EVOLUTION 2012; 12:1481-91. [PMID: 22575339 DOI: 10.1016/j.meegid.2012.04.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Revised: 04/05/2012] [Accepted: 04/06/2012] [Indexed: 11/28/2022]
Abstract
Evolutionary pressure by viruses is most likely responsible for the extraordinary allelic polymorphism of genes encoding class I human leukocyte antigens (HLA) and killer immunoglobulin-like receptors (KIR). Such genetic diversity has functional implications for the immune response to viruses and generates population-based variations in HLA class I allele frequencies and KIR gene profiles. The HIV-1 virus has relatively recently established itself as a major human pathogen, rapidly diversifying into a variety of phylogenetic subtypes or clades (A-G) and recombinants in different populations. HIV-1 clade C is the most common subtype in circulation accounting for 48% of all infections, followed by HIV-1 clades A and B which are responsible for 13% and 11% of infections in the current pandemic, respectively. Candidate gene studies of large cohorts of predominantly HIV-1 clade B but also clades C and A infected patients, have consistently shown significant associations between certain HLA class I alleles namely HLA-B*57, B*58, B*27, B*51 and relatively low viraemia. However, there is evidence that other associations between HLA-B*15, B*18 or B*53 and levels of HIV-1 viraemia are clade-specific. Recent genome-wide association studies of HIV-1 clade B exposed cohorts have confirmed that HLA-B, which is the most polymorphic locus in the human genome, is the major genetic locus contributing to immune control of viraemia. Moreover, the presence of natural killer cell receptors encoded by KIR-3DL1 and 3DS1 genes together with certain HLA class I alleles carrying the KIR target motif Bw4Ile80, provides an enhanced ability to control HIV-1 viraemia in some individuals. It is likely that rapid co-evolution of HIV-1 immune escape variants together with an adjustment of human immune response gene profiles has occurred in some exposed populations. Taken together, immunogenetic surveillance of HIV-1 exposed cohorts has revealed important correlates of natural immunity, which could provide a rational platform for the design and testing of future vaccines aimed at controlling the current AIDS pandemic.
Collapse
Affiliation(s)
- Henry A F Stephens
- UCL Centre for Nephrology and the Anthony Nolan Laboratories, Royal Free Hospital, Rowland Hill Street, London NW3 2PF, UK.
| |
Collapse
|
26
|
Abstract
Recent years have seen a significant increase in understanding of the host genetic and genomic determinants of susceptibility to HIV-1 infection and disease progression, driven in large part by candidate gene studies, genome-wide association studies, genome-wide transcriptome analyses, and large-scale in vitro genome screens. These studies have identified common variants in some host loci that clearly influence disease progression, characterized the scale and dynamics of gene and protein expression changes in response to infection, and provided the first comprehensive catalogs of genes and pathways involved in viral replication. Experimental models of AIDS and studies in natural hosts of primate lentiviruses have complemented and in some cases extended these findings. As the relevant technology continues to progress, the expectation is that such studies will increase in depth (e.g., to include host whole exome and whole genome sequencing) and in breadth (in particular, by integrating multiple data types).
Collapse
Affiliation(s)
- Amalio Telenti
- Institute of Microbiology, University Hospital and University of Lausanne, 1011 Lausanne, Switzerland.
| | | |
Collapse
|
27
|
Mehta SR, Kosakovsky Pond SL, Young JA, Richman D, Little S, Smith DM. Associations between phylogenetic clustering and HLA profile among HIV-infected individuals in San Diego, California. J Infect Dis 2012; 205:1529-33. [PMID: 22448013 DOI: 10.1093/infdis/jis231] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Specific sequence changes of human immunodeficiency virus type 1 (HIV-1) in the presence of specific HLA molecules may alter the composition and processing of viral peptides, leading to immune escape. Persistence of these mutations after transmission may leave the genetic fingerprint of the transmitter's HLA profile. Here, we evaluated the associations between HLA profiles and the phylogenetic relationships of HIV sequences sampled from a cohort of recently infected individuals in San Diego, California. METHODS We identified transmission clusters within the study cohort, using phylogenetic analysis of sampled HIV pol genotypes at a genetic distance of <1.5%. We then evaluated the association of specific HLA alleles, HLA homozygosity, HLA concordance, race and ethnicity, and mutational patterns within the clustering and nonclustering groups. RESULTS From 350 cohort participants, we identified 162 clustering individuals and 188 nonclustering individuals. We identified trends for enrichment of particular alleles within individual clusters and evidence of viral escape within those clusters. We also found that discordance of HLA alleles was significantly associated with clustering individuals. CONCLUSIONS Some transmission clusters demonstrate HLA enrichment, and viruses in these HLA-associated clusters often show evidence of escape to enriched alleles. Interestingly, HLA discordance was associated with clustering in our predominantly MSM population.
Collapse
Affiliation(s)
- Sanjay R Mehta
- Department of Medicine, University of California, San Diego, CA 92093-0711, USA.
| | | | | | | | | | | |
Collapse
|
28
|
Protocol for analyzing human leukocyte antigen variants and sexually transmitted infections: from genotyping to immunoassays. Methods Mol Biol 2012; 903:359-80. [PMID: 22782832 DOI: 10.1007/978-1-61779-937-2_25] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This chapter describes experimental and analytical procedures that can be used to decipher the specific role of human leukocyte antigen (HLA) variants in infectious diseases. The techniques are distilled from more than one decade of active immunogenetics research, primarily on sexually transmitted infections (STIs) caused by viral and bacterial pathogens, including human immunodeficiency virus type 1 (HIV-1), hepatitis B virus (HBV), and Chlamydia trachomatis. The specific approaches cover (1) sequence-specific oligonucleotide (SSO) probe hybridization for low-resolution genotyping, (2) sequencing-based typing (SBT) for high-resolution, (3) statistical methods for testing associations between HLA variants and phenotypic traits, and (4) enzyme-linked immunospot (ELISpot) assay for enumerating HLA-restricted and epitope-specific T-lymphocyte responses. Proper application of these mature and robust techniques should help establish the importance of individual HLA alleles, haplotypes, and supertypes to host-pathogen interactions.
Collapse
|
29
|
Kuniholm MH, Gao X, Xue X, Kovacs A, Anastos K, Marti D, Greenblatt RM, Cohen MH, Minkoff H, Gange SJ, Fazzari M, Young MA, Strickler HD, Carrington M. Human leukocyte antigen genotype and risk of HIV disease progression before and after initiation of antiretroviral therapy. J Virol 2011; 85:10826-33. [PMID: 21849458 PMCID: PMC3187522 DOI: 10.1128/jvi.00804-11] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Accepted: 08/05/2011] [Indexed: 01/11/2023] Open
Abstract
While the human leukocyte antigen (HLA) genotype has been associated with the rate of HIV disease progression in untreated patients, little is known regarding these relationships in patients using highly active antiretroviral therapy (HAART). The limited data reported to date identified few HLA-HIV disease associations in patients using HAART and even occasional associations that were opposite of those found in untreated patients. We conducted high-resolution HLA class I and II genotyping in a random sample (n = 860) of HIV-seropositive women enrolled in a long-term cohort initiated in 1994. HLA-HIV disease associations before and after initiation of HAART were examined using multivariate analyses. In untreated HIV-seropositive patients, we observed many of the predicted associations, consistent with prior studies. For example, HLA-B*57 (β = -0.7; 95% confidence interval [CI] = -0.9 to -0.5; P = 5 × 10⁻¹¹) and Bw4 (β = -0.2; 95% CI = -0.4 to -0.1; P = 0.009) were inversely associated with baseline HIV viral load, and B*57 was associated with a low risk of rapid CD4+ decline (odds ratio [OR] = 0.2; 95% CI = 0.1 to 0.6; P = 0.002). Conversely, in treated patients, the odds of a virological response to HAART were lower for B*57:01 (OR = 0.2; 95% CI = 0.0 to 0.9; P = 0.03), and Bw4 (OR = 0.4; 95% CI = 0.1 to 1.0; P = 0.04) was associated with low odds of an immunological response. The associations of HLA genotype with HIV disease are different and sometimes even opposite in treated and untreated patients.
Collapse
Affiliation(s)
- Mark H Kuniholm
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Belfer Building, Room 1308, 1300 Morris Park Ave., Bronx, NY 10461, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Peretz Y, Marra O, Thomas R, Legault D, Côté P, Boulassel MR, Rouleau D, Routy JP, Sékaly RP, Tsoukas CM, Tremblay C, Bernard NF. Relative contribution of HIV-specific functional lymphocyte subsets restricted by protective and non-protective HLA alleles. Viral Immunol 2011; 24:189-98. [PMID: 21668360 DOI: 10.1089/vim.2010.0117] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Expression of major histocompatibility complex (MHC) class I alleles such as B*57 and B*27 are associated with slow HIV disease progression. HIV-specific immune responses in slow progressors (SP) are characterized by a poly-functional profile. We previously observed within infected subjects that HIV peptide-specific responses could differ from each other in their functional composition. We investigate here whether responses restricted by MHC class I alleles associated with slow disease progression have a more poly-functional profile than responses restricted by other alleles. We stimulated peripheral blood mononuclear cells (PBMCs) isolated from 36 chronically HIV-infected individuals with a panel of optimal peptides restricted by the HLA alleles expressed by each subject, and assessed the contribution of single IL-2-, single IFN-γ-, and IFN-γ/IL-2-secreting lymphocytes to the total response measured using a dual color ELISPOT assay. The contribution of functional subsets to responses restricted by HLA B*57/B*27 was similar in SP and progressors. For responses restricted by other MHC class I alleles, dual IFN-γ/IL-2-secreting lymphocytes contributed significantly more to the total response in SP than progressors. Within SP subjects, peptides restricted by both B*57/B*27 and other alleles stimulated responses with similar functional profiles. In progressors, peptides restricted by B*57/B*27 stimulated responses composed of a significantly greater proportion of IFN-γ/IL-2-secreting cells than peptides restricted by other alleles. Within progressors, the contribution of IFN-γ/IL-2-secreting lymphocytes was greater to epitopes restricted by protective HLA alleles compared with responses restricted by other alleles. HLA haplotypes influence the relative functional composition of HIV-specific responses.
Collapse
Affiliation(s)
- Yoav Peretz
- National Immune Monitoring Laboratory (NIML), Genome Québec, Montreal, Québec, Canada
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Wang W, Cong Z, Liu X, Tong W, Qiao H, Jiang H, Wei Q, Qin C. Frequency of the major histocompatibility complex Mamu-A*01 allele in experimental rhesus macaques in China. J Med Primatol 2011; 39:374-80. [PMID: 20444001 DOI: 10.1111/j.1600-0684.2010.00420.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND In Indian rhesus macaques, the major histocompatibility complex Mamu gene, especially the Mamu-A*01 allele, plays an important role in simian immunodeficiency virus susceptibility and disease progression. The Mamu-A*01 allele is one of the protective genes mostly being studied in simian acquired immunodeficiency syndrome. METHODS PCR was used to amplify the Mamu-A*01 allele in 130 Chinese-origin rhesus macaques. Identification of the allele was then confirmed by sequencing and IFN-γ ELISPOT assay. RESULTS The Mamu-A*01 allele was detected in 3.85% (5 of 130) of the experimental Chinese-origin rhesus macaques. The sequence homology reached 99.1% in comparison with Indian rhesus macaques. A significantly large number of spots were observed in Mamu-A*01-positive monkeys when analyzed by ELISPOT with Gag181-189 epitope stimulation. CONCLUSIONS Our study suggests that Mamu-A*01-positive Chinese-origin rhesus monkeys are suitable for use in AIDS studies.
Collapse
Affiliation(s)
- Wei Wang
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medical Center, Peking Union Medical College, Beijing, China
| | | | | | | | | | | | | | | |
Collapse
|
32
|
Lazaryan A, Song W, Lobashevsky E, Tang J, Shrestha S, Zhang K, McNicholl JM, Gardner LI, Wilson CM, Klein RS, Rompalo A, Mayer K, Sobel J, Kaslow RA. The influence of human leukocyte antigen class I alleles and their population frequencies on human immunodeficiency virus type 1 control among African Americans. Hum Immunol 2011; 72:312-8. [PMID: 21262311 DOI: 10.1016/j.humimm.2011.01.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Revised: 12/09/2010] [Accepted: 01/13/2011] [Indexed: 11/17/2022]
Abstract
Populations of African ancestry continue to account for a disproportionate burden of the human immunodeficiency virus type 1 (HIV-1) epidemic in the United States. We investigated the effects of human leukocyte antigen (HLA) class I markers in association with virologic and immunologic control of HIV-1 infection among 338 HIV-1 subtype B-infected African Americans in 2 cohorts: Reaching for Excellence in Adolescent Care and Health (REACH) and HIV Epidemiology Research Study (HERS). One-year treatment-free interval measurements of HIV-1 RNA viral loads and CD4(+) T cells were examined both separately and combined to represent 3 categories of HIV-1 disease control (76 controllers, 169 intermediates, and 93 noncontrollers). Certain previously or newly implicated HLA class I alleles (A*32, A*36, A*74, B*14, B*1510, B*3501, B*45, B*53, B*57, Cw*04, Cw*08, Cw*12, and Cw*18) were associated with 1 or more of the endpoints in univariate analyses. After multivariable adjustments for other genetic and nongenetic risk factors of HIV-1 progression, the subset of alleles more strongly or consistently associated with HIV-1 disease control included A*32, A*74, B*14, B*45, B*53, B*57, and Cw*08. Carriage of infrequent HLA-B but not HLA-A alleles was associated with more favorable disease outcomes. Certain HLA class I associations with control of HIV-1 infection cross the boundaries of race and viral subtype, whereas others appear confined within one or the other of those boundaries.
Collapse
|
33
|
Abstract
Multiple epidemiological studies have demonstrated associations between the human leukocyte antigen (HLA) loci and human immunodeficiency virus (HIV) disease, and more recently the killer cell immunoglobulin-like (KIR) locus has been implicated in differential responses to the virus. Genome-wide association studies have convincingly shown that the HLA class I locus is the most significant host genetic contributor to the variation in HIV control, underscoring a central role for CD8 T cells in resistance to the virus. However, both genetic and functional data indicate that part of the HLA effect on HIV is due to interactions between KIR and HLA genes, also implicating natural killer cells in defense against viral infection and viral expansion prior to initiation of an adaptive response. We review the HLA and KIR associations with HIV disease and the progress that has been made in understanding the mechanisms that explain these associations.
Collapse
Affiliation(s)
- Arman A Bashirova
- Ragon Institute of Massachusetts General Hospital, MIT, Boston, Massachusetts 02129, USA.
| | | | | |
Collapse
|
34
|
Kaufman L, Ross MJ. Biomarkers of HIV. Biomarkers 2010. [DOI: 10.1002/9780470918562.ch15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
35
|
Chatterjee K. Host genetic factors in susceptibility to HIV-1 infection and progression to AIDS. J Genet 2010; 89:109-16. [DOI: 10.1007/s12041-010-0003-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
36
|
O'Connor SL, Lhost JJ, Becker EA, Detmer AM, Johnson RC, MacNair CE, Wiseman RW, Karl JA, Greene JM, Burwitz BJ, Bimber BN, Lank SM, Tuscher JJ, Mee ET, Rose NJ, Desrosiers RC, Hughes AL, Friedrich TC, Carrington M, O'Connor DH. MHC heterozygote advantage in simian immunodeficiency virus-infected Mauritian cynomolgus macaques. Sci Transl Med 2010; 2:22ra18. [PMID: 20375000 PMCID: PMC2865159 DOI: 10.1126/scitranslmed.3000524] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The importance of a broad CD8 T lymphocyte (CD8-TL) immune response to HIV is unknown. Ex vivo measurements of immunological activity directed at a limited number of defined epitopes provide an incomplete portrait of the actual immune response. We examined viral loads in simian immunodeficiency virus (SIV)-infected major histocompatibility complex (MHC)-homozygous and MHC-heterozygous Mauritian cynomolgus macaques. Chronic viremia in MHC-homozygous macaques was 80 times that in MHC-heterozygous macaques. Virus from MHC-homozygous macaques accumulated 11 to 14 variants, consistent with escape from CD8-TL responses after 1 year of SIV infection. The pattern of mutations detected in MHC-heterozygous macaques suggests that their epitope-specific CD8-TL responses are a composite of those present in their MHC-homozygous counterparts. These results provide the clearest example of MHC heterozygote advantage among individuals infected with the same immunodeficiency virus strain, suggesting that broad recognition of multiple CD8-TL epitopes should be a key feature of HIV vaccines.
Collapse
Affiliation(s)
- Shelby L. O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Jennifer J. Lhost
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Ericka A. Becker
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Ann M. Detmer
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Randall C. Johnson
- Laboratory of Genomic Diversity, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702
- Chaire de Bioinformatique, Conservatoire National des Arts et Metiers, 75003, Paris, France
| | - Caitlin E. MacNair
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Roger W. Wiseman
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Julie A. Karl
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Justin M. Greene
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Benjamin J. Burwitz
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Benjamin N. Bimber
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Simon M. Lank
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Jennifer J. Tuscher
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Edward T. Mee
- Division of Retrovirology, National Institute for Biological Standards and Control, South Mimms, Potters Bar, Hertfordshire EN6 3QG, UK
| | - Nicola J. Rose
- Division of Retrovirology, National Institute for Biological Standards and Control, South Mimms, Potters Bar, Hertfordshire EN6 3QG, UK
| | - Ronald C. Desrosiers
- New England Primate Research Center, Harvard Medical School, Southborough, Massachusetts 01772
| | - Austin L. Hughes
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208
| | - Thomas C. Friedrich
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Mary Carrington
- Cancer and Inflammation Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702 and Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts 02114
| | - David H. O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53706
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706
| |
Collapse
|
37
|
Hu SP, Zhou GB, Luan JA, Chen YP, Xiao DW, Deng YJ, Huang LQ, Cai KL. Polymorphisms of HLA-A and HLA-B genes in genetic susceptibility to esophageal carcinoma in Chaoshan Han Chinese. Dis Esophagus 2010; 23:46-52. [PMID: 19392852 DOI: 10.1111/j.1442-2050.2009.00965.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Esophageal carcinoma (EC) occurs at high rate in Chaoshan region of southern China. Human leukocyte antigen (HLA) polymorphism has been implicated in risk for various cancers. To investigate the impact of HLA-A and HLA-B polymorphisms on susceptibility to EC, a case-control study was conducted among 206 patients with esophageal squamous cell carcinoma and 524 controls from Chaoshan Han population. HLA-A and HLA-B polymorphisms were genotyped by polymerase chain reaction-sequence-specific primers. Genotypic association tests for dominant, recessive, and additive models, and haplotypic association were calculated using unconditional logistic regression. A*11 was identified in a recessive model as an only allele strongly associated with EC risk (odds ratios [OR]=2.10, 95% confidence interval [CI]=1.33-3.31) even after correction for multiple test. The haplotypes A*02-B*46 (OR=1.53, 95% CI=1.04-2.24) and A*11-B*51 (OR=2.29, 95% CI=1.20-4.40) showed association with increased risk for EC, whereas A*11-B*58 (OR=0.00, 95% CI=0.00-0.82) was associated with decreased risk, though the significance of these haplotypes was lost after correction. This is a first association study at genetic level identifying HLA-A and HLA-B-related variations in genetic susceptibility to EC among Chaoshan population. The variation pattern is likely to be EC-specific because it is different from that observed for nasopharyngeal carcinoma in the same study population and might, at least in part, explain the high rate of EC in this ethnic group.
Collapse
Affiliation(s)
- Sheng-Ping Hu
- Department of Thoracic Surgery, First Affiliated Hospital, and Center for Molecular Biology and Forensic Genetics Laboratory, Shantou University Medical College, Shantou, China.
| | | | | | | | | | | | | | | |
Collapse
|
38
|
Abstract
PURPOSE OF REVIEW This review will discuss the current challenges facing the development of a successful AIDS vaccine and approaches being pursued to overcome them, with an emphasis on vaccines designed to elicit primarily cellular, rather than humoral, antiviral immune responses. RECENT FINDINGS Recent insights into the biology of mucosal virus transmission, CD4 T-cell depletion dynamics, the character of virus-specific CD8 T-cell responses, and the dynamic effects that CD8 T cells exert on virus evolution and genetic diversity manifest during lentivirus infections have engendered an improved understanding of the anatomical, physiological, and immunological aspects of HIV infection. These advances help frame the key scientific hurdles to development of a safe and effective AIDS vaccine that an expanding number and diversity of experimental approaches in vaccine design, administration, and evaluation are now seeking to overcome. SUMMARY The development of an effective AIDS vaccine remains elusive. Our increasing knowledge regarding the biology of HIV infection, mechanisms of AIDS pathogenesis, and correlates of protective immunity, however, suggest new hypotheses which, when critically evaluated, should bring us closer to the realization of an AIDS vaccine - or at least an improved understanding of the true nature and magnitude of the obstacles ahead.
Collapse
|
39
|
Abstract
HIV host genetic studies seek to describe as comprehensively as possible the effect of human genetic variation on the individual response to HIV type-1 (HIV-1) infection. Many associations between specific gene variants and HIV-1 disease outcomes have been reported over the past 15 years. Although most of them have yet to be confirmed or have been proven false-positives, the identification of several definitive genotype-phenotype associations has shed new light on HIV-1 pathogenesis. This review discusses these results in the context of the new genome-wide approaches that now make it possible to globally assess the influence of the host genome on HIV-1-related outcomes.
Collapse
Affiliation(s)
- Jacques Fellay
- Center for Human Genome Variation, Institute for Genome Sciences & Policy, Duke University, Durham, NC, USA.
| |
Collapse
|
40
|
Polymorphisms in toll-like receptor 4 and toll-like receptor 9 influence viral load in a seroincident cohort of HIV-1-infected individuals. AIDS 2009; 23:2387-95. [PMID: 19855253 DOI: 10.1097/qad.0b013e328330b489] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
OBJECTIVES Toll-like receptors (TLRs) are innate immune sensors that are integral to resisting chronic and opportunistic infections. Mounting evidence implicates TLR polymorphisms in susceptibilities to various infectious diseases, including HIV-1. We investigated the impact of TLR single nucleotide polymorphisms (SNPs) on clinical outcome in a seroincident cohort of HIV-1-infected volunteers. DESIGN We analyzed TLR SNPs in 201 antiretroviral treatment-naive HIV-1-infected volunteers from a longitudinal seroincident cohort with regular follow-up intervals (median follow-up 4.2 years, interquartile range 4.4). Participants were stratified into two groups according to either disease progression, defined as peripheral blood CD4(+) T-cell decline over time, or peak and setpoint viral load. METHODS Haplotype tagging SNPs from TLR2, TLR3, TLR4, and TLR9 were detected by mass array genotyping, and CD4(+) T-cell counts and viral load measurements were determined prior to antiretroviral therapy initiation. The association of TLR haplotypes with viral load and rapid progression was assessed by multivariate regression models using age and sex as covariates. RESULTS Two TLR4 SNPs in strong linkage disequilibrium [1063 A/G (D299G) and 1363 C/T (T399I)] were more frequent among individuals with high peak viral load compared with low/moderate peak viral load (odds ratio 6.65, 95% confidence interval 2.19-20.46, P < 0.001; adjusted P = 0.002 for 1063 A/G). In addition, a TLR9 SNP previously associated with slow progression was found less frequently among individuals with high viral setpoint compared with low/moderate setpoint (odds ratio 0.29, 95% confidence interval 0.13-0.65, P = 0.003, adjusted P = 0.04). CONCLUSION This study suggests a potentially new role for TLR4 polymorphisms in HIV-1 peak viral load and confirms a role for TLR9 polymorphisms in disease progression.
Collapse
|
41
|
Kennedy RB, Ovsyannikova IG, Vierkant RA, Jacobson RM, Poland GA. Effect of human leukocyte antigen homozygosity on rubella vaccine-induced humoral and cell-mediated immune responses. Hum Immunol 2009; 71:128-35. [PMID: 19896518 DOI: 10.1016/j.humimm.2009.11.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2009] [Revised: 10/23/2009] [Accepted: 11/02/2009] [Indexed: 01/22/2023]
Abstract
Human leukocyte antigen (HLA) genes play a critical role in host immunity, including vaccine responses. HLA molecules present antigenic peptides to T cells and provide inhibitory signals to NK cells, and polymorphisms within HLA genes allow binding and presentation of a diverse array of self and foreign peptides. Heterozygosity across HLA alleles has been found to play a positive role in host defense for a variety of infections. Homozygosity within one or more HLA loci may restrict this epitope repertoire and limit T-cell responses to infection or vaccination. Here we report that homozygosity within the HLA DPB1 locus is associated with increased levels of rubella-specific IgG, an effect driven by a common allele DPB1*0401. We also show that homozygosity within different HLA class I and class II loci is correlated with variations (but not necessarily decreases) in interleukin (IL)-2, IL-5, and IL-10 secretion after rubella virus stimulation.
Collapse
Affiliation(s)
- Richard B Kennedy
- Mayo Clinic, Vaccine Research Group, Mayo Clinic, Rochester, Minnesota, USA
| | | | | | | | | |
Collapse
|
42
|
Huang X, Ling H, Feng L, Ding X, Zhou Q, Han M, Mao W, Xiong H. Human leukocyte antigen profile in HIV-1 infected individuals and AIDS patients from Chongqing, China. Microbiol Immunol 2009; 53:512-23. [DOI: 10.1111/j.1348-0421.2009.00150.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
43
|
Hoppe C, Klitz W, Vichinsky E, Styles L. HLA type and risk of alloimmunization in sickle cell disease. Am J Hematol 2009; 84:462-4. [PMID: 19484735 DOI: 10.1002/ajh.21442] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
44
|
Williams KC, Burdo TH. HIV and SIV infection: the role of cellular restriction and immune responses in viral replication and pathogenesis. APMIS 2009; 117:400-12. [PMID: 19400864 DOI: 10.1111/j.1600-0463.2009.02450.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) have a long biological history. Both viruses evolved from Africa and remnants of them can be found in the 'fossil record' of several species in which they are not endemic. SIV remains endemic in several species of monkeys in Africa where it does not cause immune deficiency. HIV and SIV actively replicate within humans and Asian non-human primates, despite cellular and genetic viral restriction factors and genes, and at times robust innate and adaptive immune responses. While Lentiviruses are considered 'slow viruses' it is clear in humans and susceptible Asian monkeys that virus production is rapid and highly active. This results in a massive loss of CD4+ memory effector T cells early after infection and a continued race between viral evolution, cytotoxic lymphocytes, and failed neutralizing antibody responses. Concurrently, HIV and SIV can infect monocyte/macrophage populations in blood and more importantly in tissues, including the central nervous system, where the virus can remain sequestered and not cleared by anti-retroviral therapy, and hide for years. This review will discuss species and cellular barriers to infection, and the role of innate and acquired immunity with infection and pathogenesis of HIV and SIV in select species.
Collapse
|
45
|
Gurunathan S, Habib RE, Baglyos L, Meric C, Plotkin S, Dodet B, Corey L, Tartaglia J. Use of predictive markers of HIV disease progression in vaccine trials. Vaccine 2009; 27:1997-2015. [DOI: 10.1016/j.vaccine.2009.01.039] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2008] [Revised: 12/19/2008] [Accepted: 01/08/2009] [Indexed: 10/21/2022]
|
46
|
Kohaar I, Hussain S, Thakur N, Tiwari P, Nasare V, Batra S, Singh V, Bhambani S, Das BC, Sarkar DP, Bharadwaj M. Association between human leukocyte antigen class II alleles and human papillomavirus-mediated cervical cancer in Indian women. Hum Immunol 2009; 70:222-9. [PMID: 19272325 DOI: 10.1016/j.humimm.2009.01.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2008] [Revised: 11/14/2008] [Accepted: 01/10/2009] [Indexed: 01/17/2023]
Abstract
We investigated the association of human leukocyte antigen (HLA) II (DRB1 and DQB1) alleles with susceptibility to human papillomavirus (HPV)-associated cervical precancer and cancer cases in a hospital-based case-control study in a northern Indian population. A total of 202 subjects, including 100 patients comprising 31 cervical precancer (cervical intraepithelial neoplasia [CIN] 2/3) and 69 invasive cervical cancer cases, and 102 healthy controls participated in the study. Both patients and controls were screened for HPV infection using a polymerase chain reaction (PCR-based approach. Low-resolution PCR-sequence specific priming (PCR-SSP) was used to genotype HLA II (DRB1 and DQB1). Our results demonstrate that the DRB1*15 allele/DRB1*15-DQB1*06 haplotype may have a predisposition for HPV infection (p(c) < 0.05) or cervical cancer/precancer (p(c) < 0.05) development, whereas the DRB1*04 allele/DRB1*04-DQB1*03 haplotype might exhibit susceptibility to cervical precancerous lesions (p(c) < 0.05). The DRB1*13 allele/DRB1*13-DQB1*06 haplotype was strongly protective against risk to HPV infection (p(c) < 0.002) as well as cervical cancer (p(c) 0.01). Therefore, we have demonstrated that HLA DR-DQ polymorphisms are involved in genetic susceptibility to cervical cancer or HPV infection in a northern Indian population.
Collapse
Affiliation(s)
- Indu Kohaar
- Division of Molecular Genetics and Biochemistry, Institute of Cytology and Preventive Oncology (ICMR), I-7, Sector 39, Noida 201 301, India
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Piacentini L, Biasin M, Fenizia C, Clerici M. Genetic correlates of protection against HIV infection: the ally within. J Intern Med 2009; 265:110-24. [PMID: 19093964 DOI: 10.1111/j.1365-2796.2008.02041.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Repeated exposure to HIV does not necessarily result in infection and HIV infection does not inevitably lead to the development of the AIDS. Multiple immunological and genetic features can confer resistance to HIV acquisition and progression at different steps in viral infection; a full understanding of these mechanisms could result in the development of novel therapeutic and vaccine approaches for HIV infection. In this review, we focus on the genetic mechanisms associated with resistance to HIV infection and to the progression to AIDS.
Collapse
Affiliation(s)
- L Piacentini
- Department of Preclinical Sciences, University of Milan, Segrate, Milan, Italy
| | | | | | | |
Collapse
|
48
|
Carrington M, Martin MP, van Bergen J. KIR-HLA intercourse in HIV disease. Trends Microbiol 2008; 16:620-7. [PMID: 18976921 DOI: 10.1016/j.tim.2008.09.002] [Citation(s) in RCA: 114] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2008] [Revised: 09/10/2008] [Accepted: 09/15/2008] [Indexed: 11/29/2022]
Abstract
Human leukocyte antigen (HLA) class I loci are essential to an effective immune response against a wide variety of pathogenic microorganisms, and they represent the prototypes for genetic polymorphism that are sustained through balancing selection. The functional significance of HLA class I variation is better exemplified by studies involving HIV type 1 (HIV-1) than any other infectious organism. HLA class I molecules are essential to the acquired immune response, but they are also important in innate immunity as ligands for the killer cell immunoglobulin-like receptors (KIR), which modulate natural killer cell activity. Here we concentrate on the interaction between the HLA-B and KIR3DL1/KIR3DS1 genes, describe the effects of these loci on HIV disease, and discuss questions that remain unresolved.
Collapse
Affiliation(s)
- Mary Carrington
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD 21702, USA.
| | | | | |
Collapse
|
49
|
Goulder PJR, Watkins DI. Impact of MHC class I diversity on immune control of immunodeficiency virus replication. Nat Rev Immunol 2008; 8:619-30. [PMID: 18617886 PMCID: PMC2963026 DOI: 10.1038/nri2357] [Citation(s) in RCA: 365] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The recent failure of the T-cell-based HIV vaccine trial led by Merck & Co., Inc. prompts the urgent need to refocus on the question of which T-cell responses are required to control HIV replication. The well-described association between the expression of particular MHC class I molecules and successful containment of HIV or, in the macaque model, SIV replication provide a valuable starting point from which to evaluate more precisely what might constitute effective CD8(+) T-cell responses. Here, we review recent studies of T-cell-mediated control of HIV and SIV infection, and offer insight for the design of a successful T-cell-based HIV vaccine in the future.
Collapse
Affiliation(s)
- Philip J R Goulder
- Department of Paediatrics, Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, South Parks Road, Oxford OX1 3SY, UK.
| | | |
Collapse
|
50
|
Mackelprang RD, John-Stewart G, Carrington M, Richardson B, Rowland-Jones S, Gao X, Mbori-Ngacha D, Mabuka J, Lohman-Payne B, Farquhar C. Maternal HLA homozygosity and mother-child HLA concordance increase the risk of vertical transmission of HIV-1. J Infect Dis 2008; 197:1156-61. [PMID: 18462163 DOI: 10.1086/529528] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Mother-child human leukocyte antigen (HLA) concordance and maternal HLA homozygosity may increase the risk of vertical transmission of human immunodeficiency virus type 1 (HIV-1) risk by reducing infant immune responses. METHODS We analyzed mother-child HLA concordance and maternal HLA homozygosity in a Kenyan perinatal cohort receiving antenatal zidovudine. HLA concordance was scored as the number of shared class I alleles, and relative risk estimates were adjusted for maternal HIV-1 load. RESULTS Among 277 mother-infant pairs, HIV-1 transmission occurred in 58 infants (21%), with in utero transmission in 21 (36%), peripartum transmission in 26 (45%), and transmission via breast-feeding in 11 (19%). With increased concordance, we observed a significant increase in the risk of transmission overall (adjusted hazard ratio [aHR], 1.3 [95% confidence interval {CI}, 1.0-1.7]; P = .04 in utero (adjusted odds ratio, 1.72 [95% CI, 1.0-1.7]; P = .04), and via breast-feeding (aHR, 1.6 [95% CI, 1.0-2.5]; P = .04). Women with homozygosity had higher plasma HIV-1 RNA levels at 32 weeks of gestation (5.1 vs. 4.8 log(10) copies/mL; P = .03) and an increased risk of transmission overall (aHR, 1.7 [95% CI, 1.1-2.7]; P = .03) and via breast-feeding (aHR, 5.8 [95% CI, 1.9-17.7]; P = .002). CONCLUSION The risks of overall, in utero, and breast milk HIV-1 transmission increased with HLA concordance and homozygosity. The increased risk may be due to reduced alloimmunity or less diverse protective immune responses.
Collapse
|