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Siegel DA, Thanh C, Wan E, Hoh R, Hobbs K, Pan T, Gibson EA, Kroetz DL, Martin J, Hecht F, Pilcher C, Martin M, Carrington M, Pillai S, Busch MP, Stone M, Levy CN, Huang ML, Roychoudhury P, Hladik F, Jerome KR, Kiem HP, Henrich TJ, Deeks SG, Lee SA. Host variation in type I interferon signaling genes (MX1), C-C chemokine receptor type 5 gene, and major histocompatibility complex class I alleles in treated HIV+ noncontrollers predict viral reservoir size. AIDS 2023; 37:477-488. [PMID: 36695358 PMCID: PMC9894159 DOI: 10.1097/qad.0000000000003428] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 10/28/2022] [Indexed: 01/26/2023]
Abstract
OBJECTIVE Prior genomewide association studies have identified variation in major histocompatibility complex (MHC) class I alleles and C-C chemokine receptor type 5 gene (CCR5Δ32) as genetic predictors of viral control, especially in 'elite' controllers, individuals who remain virally suppressed in the absence of therapy. DESIGN Cross-sectional genomewide association study. METHODS We analyzed custom whole exome sequencing and direct human leukocyte antigen (HLA) typing from 202 antiretroviral therapy (ART)-suppressed HIV+ noncontrollers in relation to four measures of the peripheral CD4+ T-cell reservoir: HIV intact DNA, total (t)DNA, unspliced (us)RNA, and RNA/DNA. Linear mixed models were adjusted for potential covariates including age, sex, nadir CD4+ T-cell count, pre-ART HIV RNA, timing of ART initiation, and duration of ART suppression. RESULTS Previously reported 'protective' host genetic mutations related to viral setpoint (e.g. among elite controllers) were found to predict smaller HIV reservoir size. The HLA 'protective' B∗57:01 was associated with significantly lower HIV usRNA (q = 3.3 × 10-3), and among the largest subgroup, European ancestry individuals, the CCR5Δ32 deletion was associated with smaller HIV tDNA (P = 4.3 × 10-3) and usRNA (P = 8.7 × 10-3). In addition, genomewide analysis identified several single nucleotide polymorphisms in MX1 (an interferon stimulated gene) that were significantly associated with HIV tDNA (q = 0.02), and the direction of these associations paralleled MX1 gene eQTL expression. CONCLUSIONS We observed a significant association between previously reported 'protective' MHC class I alleles and CCR5Δ32 with the HIV reservoir size in noncontrollers. We also found a novel association between MX1 and HIV total DNA (in addition to other interferon signaling relevant genes, PPP1CB, DDX3X). These findings warrant further investigation in future validation studies.
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Affiliation(s)
- David A. Siegel
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine
| | | | | | - Rebecca Hoh
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine
| | - Kristen Hobbs
- Department of Medicine, Division of Experimental Medicine
| | - Tony Pan
- Department of Medicine, Division of Experimental Medicine
| | | | | | - Jeffrey Martin
- Department of Biostatistics & Epidemiology, University of California San Francisco, California
| | - Frederick Hecht
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine
| | - Christopher Pilcher
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine
| | - Maureen Martin
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts
| | | | | | - Mars Stone
- Vitalant Blood Bank, San Francisco, California
| | | | - Meei-Li Huang
- Department of Laboratory Medicine and Pathology, University of Washington
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine and Pathology, University of Washington
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Florian Hladik
- Department of Obstetrics and Gynecology
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Keith R. Jerome
- Department of Laboratory Medicine and Pathology, University of Washington
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Hans-Peter Kiem
- Department of Laboratory Medicine and Pathology, University of Washington
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Steven G. Deeks
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine
| | - Sulggi A. Lee
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine
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Tuo S, Li C, Liu F, Zhu Y, Chen T, Feng Z, Liu H, Li A. A Novel Multitasking Ant Colony Optimization Method for Detecting Multiorder SNP Interactions. Interdiscip Sci 2022; 14:814-832. [PMID: 35788965 DOI: 10.1007/s12539-022-00530-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 05/29/2022] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
MOTIVATION Linear or nonlinear interactions of multiple single-nucleotide polymorphisms (SNPs) play an important role in understanding the genetic basis of complex human diseases. However, combinatorial analytics in high-dimensional space makes it extremely challenging to detect multiorder SNP interactions. Most classic approaches can only perform one task (for detecting k-order SNP interactions) in each run. Since prior knowledge of a complex disease is usually not available, it is difficult to determine the value of k for detecting k-order SNP interactions. METHODS A novel multitasking ant colony optimization algorithm (named MTACO-DMSI) is proposed to detect multiorder SNP interactions, and it is divided into two stages: searching and testing. In the searching stage, multiple multiorder SNP interaction detection tasks (from 2nd-order to kth-order) are executed in parallel, and two subpopulations that separately adopt the Bayesian network-based K2-score and Jensen-Shannon divergence (JS-score) as evaluation criteria are generated for each task to improve the global search capability and the discrimination ability for various disease models. In the testing stage, the G test statistical test is adopted to further verify the authenticity of candidate solutions to reduce the error rate. RESULT Three multiorder simulated disease models with different interaction effects and three real age-related macular degeneration (AMD), rheumatoid arthritis (RA) and type 1 diabetes (T1D) datasets were used to investigate the performance of the proposed MTACO-DMSI. The experimental results show that the MTACO-DMSI has a faster search speed and higher discriminatory power for diverse simulation disease models than traditional single-task algorithms. The results on real AMD data and RA and T1D datasets indicate that MTACO-DMSI has the ability to detect multiorder SNP interactions at a genome-wide scale. Availability and implementation: https://github.com/shouhengtuo/MTACO-DMSI/.
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Affiliation(s)
- Shouheng Tuo
- School of Computer Science and Technology, Xi'an University of Posts and Telecommunications, Xi'an, 710121, Shaanxi, China.
- Shaanxi Key Laboratory of Network Data Analysis and Intelligent Processing, Xi'an, 710121, Shaanxi, China.
- Xi'an Key Laboratory of Big Data and Intelligent Computing, Xi'an, 710121, Shaanxi, China.
| | - Chao Li
- School of Computer Science and Technology, Xi'an University of Posts and Telecommunications, Xi'an, 710121, Shaanxi, China
- Shaanxi Key Laboratory of Network Data Analysis and Intelligent Processing, Xi'an, 710121, Shaanxi, China
- Xi'an Key Laboratory of Big Data and Intelligent Computing, Xi'an, 710121, Shaanxi, China
| | - Fan Liu
- School of Computer Science and Technology, Xi'an University of Posts and Telecommunications, Xi'an, 710121, Shaanxi, China
- Shaanxi Key Laboratory of Network Data Analysis and Intelligent Processing, Xi'an, 710121, Shaanxi, China
- Xi'an Key Laboratory of Big Data and Intelligent Computing, Xi'an, 710121, Shaanxi, China
| | - YanLing Zhu
- School of Computer Science and Technology, Xi'an University of Posts and Telecommunications, Xi'an, 710121, Shaanxi, China
- Shaanxi Key Laboratory of Network Data Analysis and Intelligent Processing, Xi'an, 710121, Shaanxi, China
- Xi'an Key Laboratory of Big Data and Intelligent Computing, Xi'an, 710121, Shaanxi, China
| | - TianRui Chen
- School of Computer Science and Technology, Xi'an University of Posts and Telecommunications, Xi'an, 710121, Shaanxi, China
- Shaanxi Key Laboratory of Network Data Analysis and Intelligent Processing, Xi'an, 710121, Shaanxi, China
- Xi'an Key Laboratory of Big Data and Intelligent Computing, Xi'an, 710121, Shaanxi, China
| | - ZengYu Feng
- School of Computer Science and Technology, Xi'an University of Posts and Telecommunications, Xi'an, 710121, Shaanxi, China
- Shaanxi Key Laboratory of Network Data Analysis and Intelligent Processing, Xi'an, 710121, Shaanxi, China
- Xi'an Key Laboratory of Big Data and Intelligent Computing, Xi'an, 710121, Shaanxi, China
| | - Haiyan Liu
- School of Computer Science and Technology, Xi'an University of Posts and Telecommunications, Xi'an, 710121, Shaanxi, China
- Shaanxi Key Laboratory of Network Data Analysis and Intelligent Processing, Xi'an, 710121, Shaanxi, China
- Xi'an Key Laboratory of Big Data and Intelligent Computing, Xi'an, 710121, Shaanxi, China
| | - Aimin Li
- School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, 710048, Shaanxi, China
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Genome-wide association study reveals genetic variants associated with HIV-1C infection in a Botswana study population. Proc Natl Acad Sci U S A 2021; 118:2107830118. [PMID: 34782459 DOI: 10.1073/pnas.2107830118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2021] [Indexed: 11/18/2022] Open
Abstract
Although there have been many studies of gene variant association with different stages of HIV/AIDS progression in United States and European cohorts, few gene-association studies have assessed genic determinants in sub-Saharan African populations, which have the highest density of HIV infections worldwide. We carried out genome-wide association studies on 766 study participants at risk for HIV-1 subtype C (HIV-1C) infection in Botswana. Three gene associations (AP3B1, PTPRA, and NEO1) were shown to have significant association with HIV-1C acquisition. Each gene association was replicated within Botswana or in the United States-African American or United States-European American AIDS cohorts or in both. Each associated gene has a prior reported influence on HIV/AIDS pathogenesis. Thirteen previously discovered AIDS restriction genes were further replicated in the Botswana cohorts, extending our confidence in these prior AIDS restriction gene reports. This work presents an early step toward the identification of genetic variants associated with and affecting HIV acquisition or AIDS progression in the understudied HIV-1C afflicted Botswana population.
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Thorball CW, Borghesi A, Bachmann N, Von Siebenthal C, Vongrad V, Turk T, Neumann K, Beerenwinkel N, Bogojeska J, Roth V, Kok YL, Parbhoo S, Wieser M, Böni J, Perreau M, Klimkait T, Yerly S, Battegay M, Rauch A, Schmid P, Bernasconi E, Cavassini M, Kouyos RD, Günthard HF, Metzner KJ, Fellay J. Host Genomics of the HIV-1 Reservoir Size and Its Decay Rate During Suppressive Antiretroviral Treatment. J Acquir Immune Defic Syndr 2020; 85:517-524. [PMID: 33136754 DOI: 10.1097/qai.0000000000002473] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND The primary hurdle for the eradication of HIV-1 is the establishment of a latent viral reservoir early after primary infection. Here, we investigated the potential influence of human genetic variation on the HIV-1 reservoir size and its decay rate during suppressive antiretroviral treatment. SETTING Genome-wide association study and exome sequencing study to look for host genetic determinants of HIV-1 reservoir measurements in patients enrolled in the Swiss HIV Cohort Study, a nation-wide prospective observational study. METHODS We measured total HIV-1 DNA in peripheral blood mononuclear cells from study participants, as a proxy for the reservoir size at 3 time points over a median of 5.4 years, and searched for associations between human genetic variation and 2 phenotypic readouts: the reservoir size at the first time point and its decay rate over the study period. We assessed the contribution of common genetic variants using genome-wide genotyping data from 797 patients with European ancestry enrolled in the Swiss HIV Cohort Study and searched for a potential impact of rare variants and exonic copy number variants using exome sequencing data generated in a subset of 194 study participants. RESULTS Genome-wide and exome-wide analyses did not reveal any significant association with the size of the HIV-1 reservoir or its decay rate on suppressive antiretroviral treatment. CONCLUSIONS Our results point to a limited influence of human genetics on the size of the HIV-1 reservoir and its long-term dynamics in successfully treated individuals.
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Affiliation(s)
- Christian W Thorball
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Alessandro Borghesi
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Neonatal Intensive Care Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Nadine Bachmann
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Chantal Von Siebenthal
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Valentina Vongrad
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Teja Turk
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Kathrin Neumann
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | | | - Volker Roth
- Department of Mathematics and Computer Science, University of Basel, Basel, Switzerland
| | - Yik Lim Kok
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Sonali Parbhoo
- Department of Mathematics and Computer Science, University of Basel, Basel, Switzerland
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA
| | - Mario Wieser
- Department of Mathematics and Computer Science, University of Basel, Basel, Switzerland
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Matthieu Perreau
- Division of Immunology and Allergy, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Thomas Klimkait
- Division Infection Diagnostics, Department Biomedicine-Petersplatz, University of Basel, Basel, Switzerland
| | - Sabine Yerly
- Division of Infectious Diseases and Laboratory of Virology, University Hospital Geneva, University of Geneva, Geneva, Switzerland
| | - Manuel Battegay
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, University Hospital Bern, Bern, Switzerland
| | - Patrick Schmid
- Division of Infectious Diseases, Cantonal Hospital of St. Gallen, St. Gallen, Switzerland
| | - Enos Bernasconi
- Infectious Diseases Service, Regional Hospital of Lugano, Lugano, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland; and
| | - Roger D Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Huldrych F Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Karin J Metzner
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
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5
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Gingras SN, Tang D, Tuff J, McLaren PJ. Minding the gap in HIV host genetics: opportunities and challenges. Hum Genet 2020; 139:865-875. [PMID: 32409920 PMCID: PMC7272494 DOI: 10.1007/s00439-020-02177-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 03/12/2020] [Indexed: 12/15/2022]
Abstract
Genome-wide association studies (GWAS) have been successful in identifying and confirming novel genetic variants that are associated with diverse HIV phenotypes. However, these studies have predominantly focused on European cohorts. HLA molecules have been consistently associated with HIV outcomes, some of which have been found to be population specific, underscoring the need for diversity in GWAS. Recently, there has been a concerted effort to address this gap that leads to health care (disease prevention, diagnosis, treatment) disparities with marginal improvement. As precision medicine becomes more utilized, non-European individuals will be more and more disadvantaged, as the genetic variants identified in genomic research based on European populations may not accurately reflect that of non-European individuals. Leveraging pre-existing, large, multiethnic cohorts, such as the UK Biobank, 23andMe, and the National Institute of Health's All of Us Research Program, can contribute in raising genomic research in non-European populations and ultimately lead to better health outcomes.
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Affiliation(s)
- Shanelle N. Gingras
- JC Wilt Infectious Diseases Research Centre, National HIV and Retrovirology Lab, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - David Tang
- JC Wilt Infectious Diseases Research Centre, National HIV and Retrovirology Lab, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Jeffrey Tuff
- JC Wilt Infectious Diseases Research Centre, National HIV and Retrovirology Lab, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Paul J. McLaren
- JC Wilt Infectious Diseases Research Centre, National HIV and Retrovirology Lab, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
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6
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Thami PK, Chimusa ER. Population Structure and Implications on the Genetic Architecture of HIV-1 Phenotypes Within Southern Africa. Front Genet 2019; 10:905. [PMID: 31611910 PMCID: PMC6777512 DOI: 10.3389/fgene.2019.00905] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 08/26/2019] [Indexed: 12/12/2022] Open
Abstract
The interesting history of Southern Africa has put the region in the spotlight for population medical genetics. Major events including the Bantu expansion and European colonialism have imprinted unique genetic signatures within autochthonous populations of Southern Africa, this resulting in differential allele frequencies across the region. This genetic structure has potential implications on susceptibility and resistance to infectious diseases such as human immunodeficiency virus (HIV) infection. Southern Africa is the region affected worst by HIV. Here, we discuss advances made in genome-wide association studies (GWAS) of HIV-1 in the past 12 years and dissect population diversity within Southern Africa. Our findings accentuate that a plethora of factors such as migration, language and culture, admixture, and natural selection have profiled the genetics of the people of Southern Africa. Genetic structure has been observed among the Khoe-San, among Bantu speakers, and between the Khoe-San, Coloureds, and Bantu speakers. Moreover, Southern African populations have complex admixture scenarios. Few GWAS of HIV-1 have been conducted in Southern Africa, with only one of these identifying two novel variants (HCG22rs2535307 and CCNG1kgp22385164) significantly associated with HIV-1 acquisition and progression. High genetic diversity, multi-wave genetic mixture and low linkage disequilibrium of Southern African populations constitute a challenge in identifying genetic variants with modest risk or protective effect against HIV-1. We therefore posit that it is compelling to assess genome-wide contribution of ancestry to HIV-1 infection. We further suggest robust methods that can pin-point population-specific variants that may contribute to the control of HIV-1 in Southern Africa.
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Affiliation(s)
- Prisca K Thami
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa.,Research Laboratory, Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Emile R Chimusa
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
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Le Clerc S, Limou S, Zagury JF. Large-Scale "OMICS" Studies to Explore the Physiopatholgy of HIV-1 Infection. Front Genet 2019; 10:799. [PMID: 31572435 PMCID: PMC6754074 DOI: 10.3389/fgene.2019.00799] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 07/30/2019] [Indexed: 12/23/2022] Open
Abstract
In this review, we present the main large-scale experimental studies that have been performed in the HIV/AIDS field. These “omics” studies are based on several technologies including genotyping, RNA interference, and transcriptome or epigenome analysis. Due to the direct connection with disease evolution, there has been a large focus on genotyping cohorts of well-characterized patients through genome-wide association studies (GWASs), but there have also been several invitro studies such as small interfering RNA (siRNA) interference or transcriptome analyses of HIV-1–infected cells. After describing the major results obtained with these omics technologies—including some with a high relevance for HIV-1 treatment—we discuss the next steps that the community needs to embrace in order to derive new actionable therapeutic or diagnostic targets. Only integrative approaches that combine all big data results and consider their complex interactions will allow us to capture the global picture of HIV molecular pathogenesis. This novel challenge will require large collaborative efforts and represents a huge open field for innovative bioinformatics approaches.
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Affiliation(s)
- Sigrid Le Clerc
- Laboratoire GBCM, EA7528, Conservatoire National des Arts et Métiers, HESAM Université, Paris, France
| | - Sophie Limou
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation en Urologie et Néphrologie (ITUN), CHU de Nantes, Nantes, France.,Computer Sciences and Mathematics Department, Ecole Centrale de Nantes, Nantes, France
| | - Jean-François Zagury
- Laboratoire GBCM, EA7528, Conservatoire National des Arts et Métiers, HESAM Université, Paris, France
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8
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Díez-Fuertes F, De La Torre-Tarazona HE, Calonge E, Pernas M, Bermejo M, García-Pérez J, Álvarez A, Capa L, García-García F, Saumoy M, Riera M, Boland-Auge A, López-Galíndez C, Lathrop M, Dopazo J, Sakuntabhai A, Alcamí J. Association of a single nucleotide polymorphism in the ubxn6 gene with long-term non-progression phenotype in HIV-positive individuals. Clin Microbiol Infect 2019; 26:107-114. [PMID: 31158522 DOI: 10.1016/j.cmi.2019.05.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 05/07/2019] [Accepted: 05/19/2019] [Indexed: 11/17/2022]
Abstract
OBJECTIVES The long-term non-progressors (LTNPs) are a heterogeneous group of HIV-positive individuals characterized by their ability to maintain high CD4+ T-cell counts and partially control viral replication for years in the absence of antiretroviral therapy. The present study aims to identify host single nucleotide polymorphisms (SNPs) associated with non-progression in a cohort of 352 individuals. METHODS DNA microarrays and exome sequencing were used for genotyping about 240 000 functional polymorphisms throughout more than 20 000 human genes. The allele frequencies of 85 LTNPs were compared with a control population. SNPs associated with LTNPs were confirmed in a population of typical progressors. Functional analyses in the affected gene were carried out through knockdown experiments in HeLa-P4, macrophages and dendritic cells. RESULTS Several SNPs located within the major histocompatibility complex region previously related to LTNPs were confirmed in this new cohort. The SNP rs1127888 (UBXN6) surpassed the statistical significance of these markers after Bonferroni correction (q = 2.11 × 10-6). An uncommon allelic frequency of rs1127888 among LTNPs was confirmed by comparison with typical progressors and other publicly available populations. UBXN6 knockdown experiments caused an increase in CAV1 expression and its accumulation in the plasma membrane. In vitro infection of different cell types with HIV-1 replication-competent recombinant viruses caused a reduction of the viral replication capacity compared with their corresponding wild-type cells expressing UBXN6. CONCLUSIONS A higher prevalence of Ala31Thr in UBXN6 was found among LTNPs within its N-terminal region, which is crucial for UBXN6/VCP protein complex formation. UBXN6 knockdown affected CAV1 turnover and HIV-1 replication capacity.
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Affiliation(s)
- F Díez-Fuertes
- AIDS Immunopathology Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain; Hospital Clínic- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
| | - H E De La Torre-Tarazona
- AIDS Immunopathology Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - E Calonge
- AIDS Immunopathology Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - M Pernas
- Molecular Virology Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - M Bermejo
- AIDS Immunopathology Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - J García-Pérez
- AIDS Immunopathology Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - A Álvarez
- AIDS Immunopathology Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - L Capa
- AIDS Immunopathology Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - F García-García
- Unidad de Bioinformática y Bioestadística, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - M Saumoy
- HIV Unit, Infectious Disease Service, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - M Riera
- Servicio de Medicina Interna-Infecciosas, Hospital Universitario "Son Espases", Palma de Mallorca, Spain
| | - A Boland-Auge
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - C López-Galíndez
- Molecular Virology Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - M Lathrop
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - J Dopazo
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocio, Sevilla, Spain; Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocío, Sevilla, Spain; INB-ELIXIR-es, FPS, Hospital Virgen del Rocío, Sevilla, Spain
| | - A Sakuntabhai
- Functional Genetics of Infectious Diseases, Pasteur Institute, Paris, France
| | - J Alcamí
- AIDS Immunopathology Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain; Hospital Clínic- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
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Polymorphisms in the 3'-UTR of SCD5 gene are associated with hepatocellular carcinoma in Korean population. Mol Biol Rep 2018; 45:1705-1714. [PMID: 30168096 DOI: 10.1007/s11033-018-4313-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 08/17/2018] [Indexed: 12/28/2022]
Abstract
The purpose of the study was to assess the relationship between polymorphisms of the SCD5 and MMP1 gene and hepatocellular carcinoma (HCC). The gene polymorphisms with a minor allele frequency (MAF) > 0.05 were selected eight SNPs (rs6840, rs1065403, rs3821974, and rs3733230 in 3'-UTR; rs4693472, rs3733227, rs1848067, and rs6535374 in intron region) of SCD5 gene and two SNPs (rs1799750 and rs1144393 in promoter region) of MMP1 gene. The genotype of SCD5 and MMP1 gene SNPs were determined by direct sequencing and pyrosequencing, respectively. One hundred sixty-two patients with HCC and two hundred twenty-five control subjects were recruited in Korean male population. In terms of genotype frequencies, SCD5 genotype TC, GA, AG, and CG of rs6840, rs1065403, rs3821974, and rs3733230, respectively were higher in control group than HCC. In addition, these genotype decreased the risk (rs6840; OR 0.55, 95% CI 0.31-0.99; rs1065403; OR 0.46, 95% CI 0.26-0.83; rs3821974; OR 0.56, 95% CI 0.31-0.99; rs3733230; OR 0.62, 95% CI 0.34-1.12) of HCC, which may work as a prevention of HCC. At least one minor allele carrier of SCD5 gene polymorphisms were related to decreased risk of HCC for AFP cut-point levels > 200 or > 400 ng/ml, respectively. Our results indicate that polymorphisms in the 3'-UTR of the SCD5 gene may associated with HCC in the Korean male population.
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10
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Eybpoosh S, Haghdoost AA, Mostafavi E, Bahrampour A, Azadmanesh K, Zolala F. Molecular epidemiology of infectious diseases. Electron Physician 2017; 9:5149-5158. [PMID: 28979755 PMCID: PMC5614305 DOI: 10.19082/5149] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 05/02/2017] [Indexed: 12/12/2022] Open
Abstract
Molecular epidemiology (ME) is a branch of epidemiology developed by merging molecular biology into epidemiological studies. In this paper, the authors try to discuss the ways that molecular epidemiology studies identify infectious diseases' causation and pathogenesis, and unravel infectious agents' sources, reservoirs, circulation pattern, transmission pattern, transmission probability, and transmission order. They bring real-world examples of research works in each area to make each study design more understandable. They also address some research areas and study design aspects that need further attention in future. They close with some thoughts about future directions in this field and emphasize on the need for training competent molecular epidemiology specialists that are capable of dealing with rapid advances in the field.
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Affiliation(s)
- Sana Eybpoosh
- HIV/STI Surveillance Research Center, and WHO Collaborating Center for HIV Surveillance, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran
| | - Ali Akbar Haghdoost
- HIV/STI Surveillance Research Center, and WHO Collaborating Center for HIV Surveillance, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran
| | - Ehsan Mostafavi
- Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging infectious diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Abbas Bahrampour
- Modeling in Health Research Center, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran
| | | | - Farzaneh Zolala
- Modeling in Health Research Center, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran
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11
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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.
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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
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12
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Nititham J, Gupta R, Zeng X, Hartogensis W, Nixon DF, Deeks SG, Hecht FM, Liao W. Psoriasis risk SNPs and their association with HIV-1 control. Hum Immunol 2017; 78:179-184. [PMID: 27810495 PMCID: PMC5253078 DOI: 10.1016/j.humimm.2016.10.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 10/14/2016] [Accepted: 10/28/2016] [Indexed: 12/12/2022]
Abstract
Human evolution has resulted in selection for genetic polymorphisms beneficial in the defense against pathogens. However, such polymorphisms may have the potential to heighten the risk of autoimmune disease. Here, we investigated whether psoriasis-associated single nucleotide polymorphisms influence host control of HIV-1 infection. We studied psoriasis and viral immune response variants in three HIV-positive cohorts: (1) HIV-1 controllers and non-controllers in the Study of the Consequences of the Protease Inhibitor Era (SCOPE) cohort (n=366), (2) Individuals with primary HIV infection in the Options cohort (n=675), and (3) HIV-positive injection drug users from the Urban Health Study (UHS) (n=987). We found a strong association of two psoriasis MHC variants, rs9264942 and rs3021366, with both HIV-1 controller status and viral load, and identified another Class III MHC variant rs9368699 to be strongly associated with viral load. A number of genetic variants outside the MHC (SOX5, TLR9, SDC4, PROX1, IL12B, TLR4, MBL-2, TYK2, IFIH1) demonstrated nominal significance. Overall, our data suggest that several psoriasis variants within the MHC have a robust impact on HIV-1 control, while variants outside the MHC require further investigation.
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Affiliation(s)
- Joanne Nititham
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
| | - Rashmi Gupta
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
| | - Xue Zeng
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
| | - Wendy Hartogensis
- Division of HIV/AIDS, Department of Medicine, San Francisco General Hospital, University of California San Francisco, San Francisco, CA, USA
| | - Douglas F Nixon
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington, DC, USA
| | - Steven G Deeks
- Division of HIV/AIDS, Department of Medicine, San Francisco General Hospital, University of California San Francisco, San Francisco, CA, USA
| | - Frederick M Hecht
- Division of HIV/AIDS, Department of Medicine, San Francisco General Hospital, University of California San Francisco, San Francisco, CA, USA
| | - Wilson Liao
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA.
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Jiang W, Yu W. Jointly determining significance levels of primary and replication studies by controlling the false discovery rate in two-stage genome-wide association studies. Stat Methods Med Res 2017; 27:2795-2808. [PMID: 28067114 DOI: 10.1177/0962280216687168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In genome-wide association studies, we normally discover associations between genetic variants and diseases/traits in primary studies, and validate the findings in replication studies. We consider the associations identified in both primary and replication studies as true findings. An important question under this two-stage setting is how to determine significance levels in both studies. In traditional methods, significance levels of the primary and replication studies are determined separately. We argue that the separate determination strategy reduces the power in the overall two-stage study. Therefore, we propose a novel method to determine significance levels jointly. Our method is a reanalysis method that needs summary statistics from both studies. We find the most powerful significance levels when controlling the false discovery rate in the two-stage study. To enjoy the power improvement from the joint determination method, we need to select single nucleotide polymorphisms for replication at a less stringent significance level. This is a common practice in studies designed for discovery purpose. We suggest this practice is also suitable in studies with validation purpose in order to identify more true findings. Simulation experiments show that our method can provide more power than traditional methods and that the false discovery rate is well-controlled. Empirical experiments on datasets of five diseases/traits demonstrate that our method can help identify more associations. The R-package is available at: http://bioinformatics.ust.hk/RFdr.html .
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Affiliation(s)
- Wei Jiang
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Weichuan Yu
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
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14
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Bustamante M, Standl M, Bassat Q, Vilor-Tejedor N, Medina-Gomez C, Bonilla C, Ahluwalia TS, Bacelis J, Bradfield JP, Tiesler CMT, Rivadeneira F, Ring S, Vissing NH, Fink NR, Jugessur A, Mentch FD, Ballester F, Kriebel J, Kiefte-de Jong JC, Wolsk HM, Llop S, Thiering E, Beth SA, Timpson NJ, Andersen J, Schulz H, Jaddoe VWV, Evans DM, Waage J, Hakonarson H, Grant SFA, Jacobsson B, Bønnelykke K, Bisgaard H, Davey Smith G, Moll HA, Heinrich J, Estivill X, Sunyer J. A genome-wide association meta-analysis of diarrhoeal disease in young children identifies FUT2 locus and provides plausible biological pathways. Hum Mol Genet 2016; 25:4127-4142. [PMID: 27559109 PMCID: PMC5291237 DOI: 10.1093/hmg/ddw264] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 07/21/2016] [Accepted: 07/28/2016] [Indexed: 02/02/2023] Open
Abstract
More than a million childhood diarrhoeal episodes occur worldwide each year, and in developed countries a considerable part of them are caused by viral infections. In this study, we aimed to search for genetic variants associated with diarrhoeal disease in young children by meta-analyzing genome-wide association studies, and to elucidate plausible biological mechanisms. The study was conducted in the context of the Early Genetics and Lifecourse Epidemiology (EAGLE) consortium. Data about diarrhoeal disease in two time windows (around 1 year of age and around 2 years of age) was obtained via parental questionnaires, doctor interviews or medical records. Standard quality control and statistical tests were applied to the 1000 Genomes imputed genotypic data. The meta-analysis (N = 5758) followed by replication (N = 3784) identified a genome-wide significant association between rs8111874 and diarrhoea at age 1 year. Conditional analysis suggested that the causal variant could be rs601338 (W154X) in the FUT2 gene. Children with the A allele, which results in a truncated FUT2 protein, had lower risk of diarrhoea. FUT2 participates in the production of histo-blood group antigens and has previously been implicated in the susceptibility to infections, including Rotavirus and Norovirus Gene-set enrichment analysis suggested pathways related to the histo-blood group antigen production, and the regulation of ion transport and blood pressure. Among others, the gastrointestinal tract, and the immune and neuro-secretory systems were detected as relevant organs. In summary, this genome-wide association meta-analysis suggests the implication of the FUT2 gene in diarrhoeal disease in young children from the general population.
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Affiliation(s)
- Mariona Bustamante
- ISGlobal, Center for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Pompeu Fabra University (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Marie Standl
- Institute of Epidemiology I, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Quique Bassat
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Natalia Vilor-Tejedor
- ISGlobal, Center for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- Pompeu Fabra University (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Carolina Medina-Gomez
- The Generation R Study Group, Erasmus MC, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Carolina Bonilla
- MRC/University of Bristol Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Tarunveer S Ahluwalia
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Jonas Bacelis
- Department of Obstetrics and Gynecology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Jonathan P Bradfield
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Carla M T Tiesler
- Institute of Epidemiology I, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Ludwig-Maximilians-University of Munich, Dr. von Hauner Children's Hospital, Division of Metabolic Diseases and Nutritional Medicine, Munich, Germany
| | - Fernando Rivadeneira
- The Generation R Study Group, Erasmus MC, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Susan Ring
- MRC/University of Bristol Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Nadja H Vissing
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Nadia R Fink
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Astanand Jugessur
- Department of Genetics and Bioinformatics, Area of Health Data and Digitalisation, Institute of Public Health, Oslo, Norway
| | - Frank D Mentch
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ferran Ballester
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-Universitat Jaume I-Universitat de València, València, Spain
| | - Jennifer Kriebel
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Jessica C Kiefte-de Jong
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, Rotterdam, The Netherlands
- Leiden University College, The Hague, The Netherlands
| | - Helene M Wolsk
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Sabrina Llop
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-Universitat Jaume I-Universitat de València, València, Spain
| | - Elisabeth Thiering
- Institute of Epidemiology I, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Ludwig-Maximilians-University of Munich, Dr. von Hauner Children's Hospital, Division of Metabolic Diseases and Nutritional Medicine, Munich, Germany
| | - Systke A Beth
- The Generation R Study Group, Erasmus MC, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, Rotterdam, The Netherlands
| | - Nicholas J Timpson
- MRC/University of Bristol Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Josefine Andersen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Holger Schulz
- Institute of Epidemiology I, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Vincent W V Jaddoe
- The Generation R Study Group, Erasmus MC, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, Rotterdam, The Netherlands
| | - David M Evans
- MRC/University of Bristol Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Bristol, UK
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
| | - Johannes Waage
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Struan F A Grant
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Endocrinology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Genetics and Bioinformatics, Area of Health Data and Digitalisation, Institute of Public Health, Oslo, Norway
| | - Klaus Bønnelykke
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Hans Bisgaard
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - George Davey Smith
- MRC/University of Bristol Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Henriette A Moll
- Department of Pediatrics, Erasmus MC, Rotterdam, The Netherlands
| | - Joachim Heinrich
- Institute of Epidemiology I, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, Inner City Clinic, University Hospital of Munich (LMU), Munich, Germany
| | - Xavier Estivill
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Pompeu Fabra University (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
- Experimental Genetics, Sidra Medical and Research Centre, Doha, Qatar
| | - Jordi Sunyer
- ISGlobal, Center for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- Pompeu Fabra University (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
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Thørner LW, Erikstrup C, Harritshøj LH, Larsen MH, Kronborg G, Pedersen C, Larsen CS, Pedersen G, Gerstoft J, Obel N, Ullum H. Impact of polymorphisms in the HCP5 and HLA-C, and ZNRD1 genes on HIV viral load. INFECTION GENETICS AND EVOLUTION 2016; 41:185-190. [PMID: 27083073 DOI: 10.1016/j.meegid.2016.03.037] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 03/11/2016] [Accepted: 03/30/2016] [Indexed: 01/16/2023]
Abstract
AIMS Single nucleotide polymorphisms (SNPs) in the human leucocyte antigen (HLA) complex P5 (HCP5), HLA-C, and near the zinc ribbon domain containing 1 (ZNRD1) have been shown to influence viral load (VL) set point in HIV-infected individuals with a known seroconversion onset. We aimed to determine the influence of HCP5 rs2395029, HLA-C rs9264942, and ZNRD1 rs3869068 on VL in antiretroviral-naïve individuals and on time to the first VL<51 copies/ml and on CD4(+) T-cell recovery after initiation of combination antiretroviral therapy (cART). MATERIAL AND METHODS We genotyped the rs2395029 (A>C), rs9264942 (T>C), and rs3869068 (C>T) SNPs in 1897 Caucasians from The Danish HIV Cohort Study - a prospective, nationwide, population-based study of HIV-infected individuals in Denmark. General linear models evaluated the effect of SNPs on VL in antiretroviral-naïve individuals 0-18months after diagnosis and on CD4(+) T-cell recovery during cART. Cox proportional hazard regression analysis assessed the association with time to first VL<51 copies/ml. All models were assuming additive genetic effects. RESULTS The rs2395029, rs9264942, and rs3869068 minor alleles were associated with lower VL in antiretroviral-naïve individuals (rs2395029: [mean VL (copies/ml)], A/A: 70,795 [61,660-79,433], A/C: 33,884 [19,498-58,884], P=0.002; rs9264942: TT: 81,283 [67,608-97,724], T/C: 63,096 [54,954-75,858], CC: 38,905 [25,119-58,884], P<0.0001; rs3869068, CC: 72,444 [63,096-83,176], C/T: 45,709 [33,113-64,565], TT: 58,884 [20,417-169,824], P=0.01). Moreover, the C-alleles of rs2395029 and rs9264942 were associated with shorter time to VL<51 copies/ml: (HR [95% confidence interval], 1.67 [1.09-1.72], P=0.008; 1.16 [1.06-1.28], P=0.002; 1.30 [1.08-1.53], P=0.005, respectively, adjusted for last VL before cART). None of the SNPs predicted CD4(+) T-cell recovery during cART. CONCLUSIONS The minor alleles of rs2395029, rs9264942, and rs3689068 associate with lower VL among antiretroviral-naïve individuals and with shorter time to first VL<51copies/ml during cART even after adjustment for VL before cART.
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Affiliation(s)
- Lise Wegner Thørner
- Dept. of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark.
| | - Christian Erikstrup
- Dept. of Clinical Immunology, Aarhus University Hospital, Skejby, Aarhus, Denmark
| | - Lene Holm Harritshøj
- Dept. of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Margit Hørup Larsen
- Dept. of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Gitte Kronborg
- Dept. of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| | - Court Pedersen
- Dept. of Infectious Diseases, Odense University Hospital, Odense, Denmark
| | | | - Gitte Pedersen
- Dept. of Infectious Diseases, Aarhus University Hospital, Aalborg, Denmark
| | - Jan Gerstoft
- Dept. of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
| | - Niels Obel
- Dept. of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
| | - Henrik Ullum
- Dept. of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
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Polymorphisms of large effect explain the majority of the host genetic contribution to variation of HIV-1 virus load. Proc Natl Acad Sci U S A 2015; 112:14658-63. [PMID: 26553974 DOI: 10.1073/pnas.1514867112] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Previous genome-wide association studies (GWAS) of HIV-1-infected populations have been underpowered to detect common variants with moderate impact on disease outcome and have not assessed the phenotypic variance explained by genome-wide additive effects. By combining the majority of available genome-wide genotyping data in HIV-infected populations, we tested for association between ∼8 million variants and viral load (HIV RNA copies per milliliter of plasma) in 6,315 individuals of European ancestry. The strongest signal of association was observed in the HLA class I region that was fully explained by independent effects mapping to five variable amino acid positions in the peptide binding grooves of the HLA-B and HLA-A proteins. We observed a second genome-wide significant association signal in the chemokine (C-C motif) receptor (CCR) gene cluster on chromosome 3. Conditional analysis showed that this signal could not be fully attributed to the known protective CCR5Δ32 allele and the risk P1 haplotype, suggesting further causal variants in this region. Heritability analysis demonstrated that common human genetic variation-mostly in the HLA and CCR5 regions-explains 25% of the variability in viral load. This study suggests that analyses in non-European populations and of variant classes not assessed by GWAS should be priorities for the field going forward.
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17
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GWATCH: a web platform for automated gene association discovery analysis. Gigascience 2014; 3:18. [PMID: 25374661 PMCID: PMC4220276 DOI: 10.1186/2047-217x-3-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 09/30/2014] [Indexed: 01/08/2023] Open
Abstract
Background As genome-wide sequence analyses for complex human disease determinants are expanding, it is increasingly necessary to develop strategies to promote discovery and validation of potential disease-gene associations. Findings Here we present a dynamic web-based platform – GWATCH – that automates and facilitates four steps in genetic epidemiological discovery: 1) Rapid gene association search and discovery analysis of large genome-wide datasets; 2) Expanded visual display of gene associations for genome-wide variants (SNPs, indels, CNVs), including Manhattan plots, 2D and 3D snapshots of any gene region, and a dynamic genome browser illustrating gene association chromosomal regions; 3) Real-time validation/replication of candidate or putative genes suggested from other sources, limiting Bonferroni genome-wide association study (GWAS) penalties; 4) Open data release and sharing by eliminating privacy constraints (The National Human Genome Research Institute (NHGRI) Institutional Review Board (IRB), informed consent, The Health Insurance Portability and Accountability Act (HIPAA) of 1996 etc.) on unabridged results, which allows for open access comparative and meta-analysis. Conclusions GWATCH is suitable for both GWAS and whole genome sequence association datasets. We illustrate the utility of GWATCH with three large genome-wide association studies for HIV-AIDS resistance genes screened in large multicenter cohorts; however, association datasets from any study can be uploaded and analyzed by GWATCH.
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Murray CJL, Ortblad KF, Guinovart C, Lim SS, Wolock TM, Roberts DA, Dansereau EA, Graetz N, Barber RM, Brown JC, Wang H, Duber HC, Naghavi M, Dicker D, Dandona L, Salomon JA, Heuton KR, Foreman K, Phillips DE, Fleming TD, Flaxman AD, Phillips BK, Johnson EK, Coggeshall MS, Abd-Allah F, Abera SF, Abraham JP, Abubakar I, Abu-Raddad LJ, Abu-Rmeileh NM, Achoki T, Adeyemo AO, Adou AK, Adsuar JC, Agardh EE, Akena D, Al Kahbouri MJ, Alasfoor D, Albittar MI, Alcalá-Cerra G, Alegretti MA, Alemu ZA, Alfonso-Cristancho R, Alhabib S, Ali R, Alla F, Allen PJ, Alsharif U, Alvarez E, Alvis-Guzman N, Amankwaa AA, Amare AT, Amini H, Ammar W, Anderson BO, Antonio CAT, Anwari P, Arnlöv J, Arsenijevic VSA, Artaman A, Asghar RJ, Assadi R, Atkins LS, Badawi A, Balakrishnan K, Banerjee A, Basu S, Beardsley J, Bekele T, Bell ML, Bernabe E, Beyene TJ, Bhala N, Bhalla A, Bhutta ZA, Abdulhak AB, Binagwaho A, Blore JD, Basara BB, Bose D, Brainin M, Breitborde N, Castañeda-Orjuela CA, Catalá-López F, Chadha VK, Chang JC, Chiang PPC, Chuang TW, Colomar M, Cooper LT, Cooper C, Courville KJ, Cowie BC, Criqui MH, Dandona R, Dayama A, De Leo D, Degenhardt L, Del Pozo-Cruz B, Deribe K, Des Jarlais DC, Dessalegn M, Dharmaratne SD, Dilmen U, Ding EL, Driscoll TR, Durrani AM, Ellenbogen RG, Ermakov SP, Esteghamati A, Faraon EJA, Farzadfar F, Fereshtehnejad SM, Fijabi DO, Forouzanfar MH, Fra Paleo U, Gaffikin L, Gamkrelidze A, Gankpé FG, Geleijnse JM, Gessner BD, Gibney KB, Ginawi IAM, Glaser EL, Gona P, Goto A, Gouda HN, Gugnani HC, Gupta R, Gupta R, Hafezi-Nejad N, Hamadeh RR, Hammami M, Hankey GJ, Harb HL, Haro JM, Havmoeller R, Hay SI, Hedayati MT, Pi IBH, Hoek HW, Hornberger JC, Hosgood HD, Hotez PJ, Hoy DG, Huang JJ, Iburg KM, Idrisov BT, Innos K, Jacobsen KH, Jeemon P, Jensen PN, Jha V, Jiang G, Jonas JB, Juel K, Kan H, Kankindi I, Karam NE, Karch A, Karema CK, Kaul A, Kawakami N, Kazi DS, Kemp AH, Kengne AP, Keren A, Kereselidze M, Khader YS, Khalifa SEAH, Khan EA, Khang YH, Khonelidze I, Kinfu Y, Kinge JM, Knibbs L, Kokubo Y, Kosen S, Defo BK, Kulkarni VS, Kulkarni C, Kumar K, Kumar RB, Kumar GA, Kwan GF, Lai T, Balaji AL, Lam H, Lan Q, Lansingh VC, Larson HJ, Larsson A, Lee JT, Leigh J, Leinsalu M, Leung R, Li Y, Li Y, De Lima GMF, Lin HH, Lipshultz SE, Liu S, Liu Y, Lloyd BK, Lotufo PA, Machado VMP, Maclachlan JH, Magis-Rodriguez C, Majdan M, Mapoma CC, Marcenes W, Marzan MB, Masci JR, Mashal MT, Mason-Jones AJ, Mayosi BM, Mazorodze TT, Mckay AC, Meaney PA, Mehndiratta MM, Mejia-Rodriguez F, Melaku YA, Memish ZA, Mendoza W, Miller TR, Mills EJ, Mohammad KA, Mokdad AH, Mola GL, Monasta L, Montico M, Moore AR, Mori R, Moturi WN, Mukaigawara M, Murthy KS, Naheed A, Naidoo KS, Naldi L, Nangia V, Narayan KMV, Nash D, Nejjari C, Nelson RG, Neupane SP, Newton CR, Ng M, Nisar MI, Nolte S, Norheim OF, Nowaseb V, Nyakarahuka L, Oh IH, Ohkubo T, Olusanya BO, Omer SB, Opio JN, Orisakwe OE, Pandian JD, Papachristou C, Caicedo AJP, Patten SB, Paul VK, Pavlin BI, Pearce N, Pereira DM, Pervaiz A, Pesudovs K, Petzold M, Pourmalek F, Qato D, Quezada AD, Quistberg DA, Rafay A, Rahimi K, Rahimi-Movaghar V, Ur Rahman S, Raju M, Rana SM, Razavi H, Reilly RQ, Remuzzi G, Richardus JH, Ronfani L, Roy N, Sabin N, Saeedi MY, Sahraian MA, Samonte GMJ, Sawhney M, Schneider IJC, Schwebel DC, Seedat S, Sepanlou SG, Servan-Mori EE, Sheikhbahaei S, Shibuya K, Shin HH, Shiue I, Shivakoti R, Sigfusdottir ID, Silberberg DH, Silva AP, Simard EP, Singh JA, Skirbekk V, Sliwa K, Soneji S, Soshnikov SS, Sreeramareddy CT, Stathopoulou VK, Stroumpoulis K, Swaminathan S, Sykes BL, Tabb KM, Talongwa RT, Tenkorang EY, Terkawi AS, Thomson AJ, Thorne-Lyman AL, Towbin JA, Traebert J, Tran BX, Dimbuene ZT, Tsilimbaris M, Uchendu US, Ukwaja KN, Uzun SB, Vallely AJ, Vasankari TJ, Venketasubramanian N, Violante FS, Vlassov VV, Vollset SE, Waller S, Wallin MT, Wang L, Wang X, Wang Y, Weichenthal S, Weiderpass E, Weintraub RG, Westerman R, White RA, Wilkinson JD, Williams TN, Woldeyohannes SM, Wong JQ, Xu G, Yang YC, Yano Y, Yentur GK, Yip P, Yonemoto N, Yoon SJ, Younis M, Yu C, Jin KY, El Sayed Zaki M, Zhao Y, Zheng Y, Zhou M, Zhu J, Zou XN, Lopez AD, Vos T. Global, regional, and national incidence and mortality for HIV, tuberculosis, and malaria during 1990-2013: a systematic analysis for the Global Burden of Disease Study 2013. Lancet 2014; 384:1005-70. [PMID: 25059949 PMCID: PMC4202387 DOI: 10.1016/s0140-6736(14)60844-8] [Citation(s) in RCA: 668] [Impact Index Per Article: 66.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
BACKGROUND The Millennium Declaration in 2000 brought special global attention to HIV, tuberculosis, and malaria through the formulation of Millennium Development Goal (MDG) 6. The Global Burden of Disease 2013 study provides a consistent and comprehensive approach to disease estimation for between 1990 and 2013, and an opportunity to assess whether accelerated progress has occured since the Millennium Declaration. METHODS To estimate incidence and mortality for HIV, we used the UNAIDS Spectrum model appropriately modified based on a systematic review of available studies of mortality with and without antiretroviral therapy (ART). For concentrated epidemics, we calibrated Spectrum models to fit vital registration data corrected for misclassification of HIV deaths. In generalised epidemics, we minimised a loss function to select epidemic curves most consistent with prevalence data and demographic data for all-cause mortality. We analysed counterfactual scenarios for HIV to assess years of life saved through prevention of mother-to-child transmission (PMTCT) and ART. For tuberculosis, we analysed vital registration and verbal autopsy data to estimate mortality using cause of death ensemble modelling. We analysed data for corrected case-notifications, expert opinions on the case-detection rate, prevalence surveys, and estimated cause-specific mortality using Bayesian meta-regression to generate consistent trends in all parameters. We analysed malaria mortality and incidence using an updated cause of death database, a systematic analysis of verbal autopsy validation studies for malaria, and recent studies (2010-13) of incidence, drug resistance, and coverage of insecticide-treated bednets. FINDINGS Globally in 2013, there were 1·8 million new HIV infections (95% uncertainty interval 1·7 million to 2·1 million), 29·2 million prevalent HIV cases (28·1 to 31·7), and 1·3 million HIV deaths (1·3 to 1·5). At the peak of the epidemic in 2005, HIV caused 1·7 million deaths (1·6 million to 1·9 million). Concentrated epidemics in Latin America and eastern Europe are substantially smaller than previously estimated. Through interventions including PMTCT and ART, 19·1 million life-years (16·6 million to 21·5 million) have been saved, 70·3% (65·4 to 76·1) in developing countries. From 2000 to 2011, the ratio of development assistance for health for HIV to years of life saved through intervention was US$4498 in developing countries. Including in HIV-positive individuals, all-form tuberculosis incidence was 7·5 million (7·4 million to 7·7 million), prevalence was 11·9 million (11·6 million to 12·2 million), and number of deaths was 1·4 million (1·3 million to 1·5 million) in 2013. In the same year and in only individuals who were HIV-negative, all-form tuberculosis incidence was 7·1 million (6·9 million to 7·3 million), prevalence was 11·2 million (10·8 million to 11·6 million), and number of deaths was 1·3 million (1·2 million to 1·4 million). Annualised rates of change (ARC) for incidence, prevalence, and death became negative after 2000. Tuberculosis in HIV-negative individuals disproportionately occurs in men and boys (versus women and girls); 64·0% of cases (63·6 to 64·3) and 64·7% of deaths (60·8 to 70·3). Globally, malaria cases and deaths grew rapidly from 1990 reaching a peak of 232 million cases (143 million to 387 million) in 2003 and 1·2 million deaths (1·1 million to 1·4 million) in 2004. Since 2004, child deaths from malaria in sub-Saharan Africa have decreased by 31·5% (15·7 to 44·1). Outside of Africa, malaria mortality has been steadily decreasing since 1990. INTERPRETATION Our estimates of the number of people living with HIV are 18·7% smaller than UNAIDS's estimates in 2012. The number of people living with malaria is larger than estimated by WHO. The number of people living with HIV, tuberculosis, or malaria have all decreased since 2000. At the global level, upward trends for malaria and HIV deaths have been reversed and declines in tuberculosis deaths have accelerated. 101 countries (74 of which are developing) still have increasing HIV incidence. Substantial progress since the Millennium Declaration is an encouraging sign of the effect of global action. FUNDING Bill & Melinda Gates Foundation.
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Affiliation(s)
| | | | | | - Stephen S Lim
- Institute for Health Metrics and Evaluation, Seattle, WA, USA
| | | | - D Allen Roberts
- Institute for Health Metrics and Evaluation, Seattle, WA, USA
| | | | - Nicholas Graetz
- Institute for Health Metrics and Evaluation, Seattle, WA, USA
| | - Ryan M Barber
- Institute for Health Metrics and Evaluation, Seattle, WA, USA
| | | | - Haidong Wang
- Institute for Health Metrics and Evaluation, Seattle, WA, USA
| | - Herbert C Duber
- Institute for Health Metrics and Evaluation, Seattle, WA, USA
| | - Mohsen Naghavi
- Institute for Health Metrics and Evaluation, Seattle, WA, USA
| | - Daniel Dicker
- Institute for Health Metrics and Evaluation, Seattle, WA, USA
| | - Lalit Dandona
- Institute for Health Metrics and Evaluation, Seattle, WA, USA; Public Health Foundation of India, New Delhi, India
| | | | - Kyle R Heuton
- Institute for Health Metrics and Evaluation, Seattle, WA, USA
| | | | | | | | | | | | | | | | | | | | - Jerry P Abraham
- University of Texas School of Medicine San Antonio, San Antonio, TX, USA
| | | | | | - Niveen Me Abu-Rmeileh
- Institute of Community and Public Health-Birzeti University, Ramallah, West Bank, Occupied Palestinian Territory
| | | | | | | | | | | | | | | | | | | | - Gabriel Alcalá-Cerra
- Grupo de Investigación en Ciencias de la Salud y Neurociencias (CISNEURO), Cartagena de Indias, Colombia
| | - Miguel Angel Alegretti
- Facultad de Medicina, Departamento de Medicina Preventiva y Social, Universidad de la República, Montevideo, Uruguay
| | | | | | | | | | - Francois Alla
- School of Public Health, University of Lorraine, Nancy, France
| | | | | | | | | | | | - Azmeraw T Amare
- Department of Epidemiology, University of Groningen, Groningen, The Netherlands; College of Medicine and Health Sciences, Bahir Dar University, Bahir Dar, Ethiopia
| | - Hassan Amini
- Kurdistan Environmental Health Research Center, Kurdistan University of Medical Sciences, Sanandaj, Kurdistan, Iran
| | | | | | | | | | | | | | | | - Rana J Asghar
- South Asian Public Health Forum, Islamabad, Pakistan
| | - Reza Assadi
- Mashhad University of Medical Sciences, Mashhad, Iran
| | - Lydia S Atkins
- Ministry of Health, Wellness, Human Services and Gender Relations, Castries, St. Lucia
| | - Alaa Badawi
- Public Health Agency of Canada, Toronto, ON, Canada
| | | | | | | | | | | | | | | | | | | | - Ashish Bhalla
- Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | | | | | | | - Jed D Blore
- University of Melbourne, Melbourne, VIC, Australia
| | | | | | | | | | | | - Ferrán Catalá-López
- Division of Pharmacoepidemiology and Pharmacovigilance, Spanish Medicines and Healthcare Products Agency (AEMPS), Ministry of Health, Madrid, Spain
| | | | | | | | - Ting-Wu Chuang
- Department of Parasitology, College of Medicine, Taipei Medical University, Taipei, Taiwan; Center for International Tropical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | | | | | - Cyrus Cooper
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
| | | | - Benjamin C Cowie
- Victorian Infectious Diseases Reference Laboratory, North Melbourne, VIC, Australia
| | | | | | - Anand Dayama
- Emory University School of Medicine, Atlanta, GA, USA
| | | | | | | | | | | | - Muluken Dessalegn
- Africa Medical and Research Foundation in Ethiopia, Addis Ababa, Ethiopia
| | | | | | - Eric L Ding
- Harvard School of Public Health, Cambridge, MA, USA
| | | | | | | | - Sergey Petrovich Ermakov
- The Institute of Social and Economic Studies of Population at the Russian Academy of Sciences, Moscow, Russia
| | - Alireza Esteghamati
- Endocrinology and Metabolism Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Farshad Farzadfar
- Non-Communicable Diseases Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | | | | | | | | | - Lynne Gaffikin
- Stanford University School of Medicine, Stanford, CA, USA
| | | | | | | | | | | | | | | | - Philimon Gona
- University of Massachusetts Medical School, Worcester, MA, USA
| | - Atsushi Goto
- Department of Diabetes Research, National Center for Global Health and Medicine, Tokyo, Japan
| | - Hebe N Gouda
- University of Queensland, Brisbane, QLD, Australia
| | | | | | - Rahul Gupta
- Kanawha Charleston Health Department, Charleston, WV, USA
| | - Nima Hafezi-Nejad
- Endocrinology and Metabolism Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Mouhanad Hammami
- Wayne County Department of Health and Human Services, Detroit, MI, USA
| | - Graeme J Hankey
- School of Medicine and Pharmacology, University of Western Australia, Perth, WA, Australia
| | | | - Josep Maria Haro
- Parc Sanitari Sant Joan de Déu, CIBERSAM, University of Barcelona, Sant Boi de Llobregat, Barcelona, Spain
| | | | | | | | | | - Hans W Hoek
- Parnassia Psychiatric Institute, The Hague, Netherlands
| | | | | | | | - Damian G Hoy
- School of Population Health, Brisbane, QLD, Australia; Public Health Division, Secretariat of the Pacific Community, Noumea, New Caledonia
| | | | | | | | - Kaire Innos
- National Institute for Health Development, Tallinn, Estonia
| | | | | | | | - Vivekanand Jha
- Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Guohong Jiang
- Tianjin Centers for Diseases Control and Prevention, Tianjin, China
| | - Jost B Jonas
- Department of Ophthalmology, Medical Faculty Mannheim of the University of Heidelberg, Mannheim, Germany
| | - Knud Juel
- The National Institute of Public Health, Copenhagen, Denmark
| | | | | | | | - André Karch
- Helmholtz Centre for Infection Research, Braunschweig, Germany; German Center for Infection Research (DZIF), Hannover-Braunschweig site, Germany
| | | | - Anil Kaul
- Oklahoma State University, Tulsa, OK, USA
| | | | - Dhruv S Kazi
- University of California San Francisco, San Francisco, CA, USA
| | | | - Andre Pascal Kengne
- South African Medical Research Council, Cape Town, Western Cape, South Africa
| | - Andre Keren
- Cardiology, Hadassah Ein Kerem University Hospital, Jerusalem, Israel
| | - Maia Kereselidze
- National Centre for Disease Control and Public Health, Tbilisi, Georgia
| | | | | | | | - Young-Ho Khang
- Institute of Health Policy and Management, Seoul National University College of Medicine, Seoul, South Korea
| | - Irma Khonelidze
- National Centre for Disease Control and Public Health, Tbilisi, Georgia
| | | | | | - Luke Knibbs
- University of Queensland, Brisbane, QLD, Australia
| | - Yoshihiro Kokubo
- Department of Preventive Cardiology, Department of Preventive Medicine and Epidemiologic Informatics, National Cerebral and Cardiovascular Center, Suita, Osaka, Japan
| | - S Kosen
- Center for Community Empowerment, Health Policy & Humanities, NIHRD, Jakarta, Indonesia
| | | | | | - Chanda Kulkarni
- Rajrajeshwari Medical College & Hospital, Bangalore, Karnataka, India
| | - Kaushalendra Kumar
- International Institute for Population Sciences, Mumbai, Maharashtra, India
| | - Ravi B Kumar
- Indian Institute of Public Health, Public Health Foundation of India, Gurgaon, Haryana, India
| | - G Anil Kumar
- Public Health Foundation of India, New Delhi, India
| | | | - Taavi Lai
- Fourth View Consulting, Tallinn, Estonia
| | | | - Hilton Lam
- Institute of Health Policy and Development Studies, National Institutes of Health, Manila, Philippines
| | - Qing Lan
- National Cancer Institute, Rockville, MD, USA
| | | | - Heidi J Larson
- London School of Hygiene and Tropical Medicine, Bloomsbury, UK
| | | | | | - James Leigh
- University of Sydney, Sydney, NSW, Australia
| | - Mall Leinsalu
- National Institute for Health Development, Tallinn, Estonia
| | - Ricky Leung
- University at Albany, The State University of New York, Rensselaer, NY, USA
| | - Yichong Li
- Genentech, Inc, South San Francisco, CA, USA
| | - Yongmei Li
- Genentech, Inc, South San Francisco, CA, USA
| | | | - Hsien-Ho Lin
- Institute of Epidemiology and Preventive Medicine, Taipei, Taiwan
| | | | - Shiwei Liu
- National Center for Chronic and Non-communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yang Liu
- Emory University, Atlanta, GA, USA
| | - Belinda K Lloyd
- Eastern Health Clinical School, VIC, Australia; Turning Point, Eastern Health, Fitzroy, VIC, Australia
| | | | | | | | | | - Marek Majdan
- Department of Public Health, Faculty of Health Sciences and Social Work, Trnava University, Trnava, Slovakia
| | | | | | | | - Joseph R Masci
- Elmhurst Hospital Center, Mount Sinai Services, Elmhurst, NY, USA
| | | | | | | | | | | | | | | | | | | | | | | | - Ted R Miller
- Pacific Institute for Research & Evaluation, Calverton MD, USA; Centre for Population Health Research, Curtin University, Perth, WA, Australia
| | | | | | - Ali H Mokdad
- Institute for Health Metrics and Evaluation, Seattle, WA, USA
| | | | - Lorenzo Monasta
- Institute for Maternal and Child Health-IRCCS "Burlo Garofolo," Trieste, Italy
| | - Marcella Montico
- Institute for Maternal and Child Health-IRCCS "Burlo Garofolo," Trieste, Italy
| | | | - Rintaro Mori
- National Center for Child Health and Development, Setagaya, Tokyo, Japan
| | | | | | | | - Aliya Naheed
- International Centre for Diarrhoeal Diseases Research, Dhaka, Bangladesh
| | - Kovin S Naidoo
- University of KwaZulu-Natal, Durban, KwaZulu-Natal, South Africa
| | - Luigi Naldi
- Azienda Ospedaliera papa Giovanni XXIII, Bergamo, Italy
| | | | | | - Denis Nash
- School of Public Health, City University of New York, New York, NY, USA
| | | | - Robert G Nelson
- National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - Sudan Prasad Neupane
- Norwegian Center for Addiction Research (SERAF), University of Oslo, Oslo, Norway
| | - Charles R Newton
- Kenya Medical Research Institute Wellcome Trust Programme, Kilifi, Kenya
| | - Marie Ng
- Institute for Health Metrics and Evaluation, Seattle, WA, USA
| | | | - Sandra Nolte
- Charité Universitätsmedizin Berlin, Berlin, Germany
| | | | | | | | | | | | | | | | - John Nelson Opio
- Lira District Local Government, Lira Municipal Council, Northern Uganda, Uganda
| | - Orish Ebere Orisakwe
- Toxicology Unit, Faculty of Pharmacy, University of Port Harcourt, Port Harcourt, Rivers State, Nigeria
| | | | | | | | | | | | | | - Neil Pearce
- London School of Hygiene and Tropical Medicine, Bloomsbury, UK
| | - David M Pereira
- 3B's Research Group-Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine and ICVS/3B's-PT Government Associate Laboratory, Braga, Portugal
| | - Aslam Pervaiz
- Postgraduate Medical Institute, Lahore, Punjab, Pakistan
| | | | - Max Petzold
- Centre for Applied Biostatistics, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | | | - Dima Qato
- College of Pharmacy, University of Illinois, Chicago, IL, USA
| | - Amado D Quezada
- National Institute of Public Health of Mexico, Cuernavaca, Morelos, Mexico
| | | | | | | | - Vafa Rahimi-Movaghar
- Sina Trauma and Surgery Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | | | | | - Saleem M Rana
- Department of Public Health, University of the Punjab, Lahore, Punjab, Pakistan
| | - Homie Razavi
- Center for Disease Analysis, Louisville, CO, USA
| | | | - Giuseppe Remuzzi
- IRCCS Mario Negri Institute for Pharmacological Research, Centro Anna Maria Astori, Bergamo, Italy
| | | | - Luca Ronfani
- Institute for Maternal and Child Health-IRCCS "Burlo Garofolo," Trieste, Italy
| | | | | | | | | | - Genesis May J Samonte
- National HIV/AIDS & STI Surveillance and Strategic Information Unit, National Epidemiology Center, Department of Health, Manila, National Capital Region, Philippines
| | | | | | | | - Soraya Seedat
- Stellenbosch University, Cape Town, Western Cape, South Africa
| | - Sadaf G Sepanlou
- Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Sara Sheikhbahaei
- Endocrinology and Metabolism Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | | | | | - Ivy Shiue
- Heriot-Watt University, Edinburgh, UK
| | - Rupak Shivakoti
- Center for Clinical Global Health Education, Johns Hopkins University, Baltimore, MD, USA
| | | | | | - Andrea P Silva
- Instituto Nacional de Epidemiología Dr Juan H Jara, Mar del Plata, Buenos Aires, Argentina
| | - Edgar P Simard
- Surveillance and Health Services Research Program American Cancer Society, Atlanta, GA, USA
| | | | | | - Karen Sliwa
- Faculty of Health Sciences, Hatter Institute for Cardiovascular Research in Africa, Cape Town, Western Cape, South Africa
| | | | - Sergey S Soshnikov
- Federal Research Institute for Health Organization and Informatics of Ministry of Health of the Russian Federation, Moscow, Russia
| | | | | | - Konstantinos Stroumpoulis
- KEELPNO (Centre for Disease Control, Greece, dispatched to "Alexandra" General Hospital of Athens), Athens, Greece
| | - Soumya Swaminathan
- National Institute for Research in Tuberculosis, Chennai, Tamil Nadu, India
| | - Bryan L Sykes
- Department of Criminology, Law and Society (and Sociology), University of California-Irvine, Chicago, IL, USA
| | | | | | | | - Abdullah Sulieman Terkawi
- Department of Anesthesiology, University of Virginia, Charlottesville, VA, USA; Department of Anesthesiology, King Fahad Medical City, Riyadh, Saudi Arabia
| | | | | | - Jeffrey A Towbin
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | | | - Bach X Tran
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Zacharie Tsala Dimbuene
- Department of Population Sciences and Development, Faculty of Economics and Management, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | | | | | - Kingsley N Ukwaja
- Department of Internal Medicine, Federal Teaching Hospital Abakaliki, Abakailiki, Ebonyi State, Nigeria
| | | | | | | | | | | | | | - Stein Emil Vollset
- Norwegian Institute of Public Health, Oslo, Norway; University of Bergen, Bergen, Norway
| | - Stephen Waller
- Uniformed Services University of Health Sciences, Bethesda, MD, USA
| | - Mitchell T Wallin
- VA Medical Center and Georgetown University Neurology Department, Washington, DC, USA
| | - Linhong Wang
- National Center for Chronic and Non-communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - XiaoRong Wang
- Shandong University Affiliated Jinan Central Hospital, Jinan, China
| | - Yanping Wang
- National Office for Maternal and Child Health Surveillance, Chengdu, China
| | | | | | - Robert G Weintraub
- University of Melbourne, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, Australia
| | | | - Richard A White
- Department of Infectious Disease Epidemiology, Division of Infectious Disease Control and Department of Health Statistics, Division of Epidemiology, Oslo, Norway
| | | | | | | | - John Q Wong
- Ateneo School of Medicine and Public Health, Pasig City, Metro Manila, Philippines
| | - Gelin Xu
- Nanjing University School of Medicine, Jinling Hospital, Nanjing, China
| | - Yang C Yang
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yuichiro Yano
- Division of Cardiovascular Medicine, Jichi Medical University School of Medicine, Shimotsuke, Tochigi, Japan
| | | | - Paul Yip
- The University of Hong Kong, Hong Kong, Hong Kong
| | - Naohiro Yonemoto
- National Center of Neurology and Psychiatry, Kodira, Tokyo, Japan
| | | | | | - Chuanhua Yu
- Department of Epidemiology and Biostatistics, School of Public Health and Global Health Institute, Wuhan University, Wuhan, China
| | - Kim Yun Jin
- TCM MEDICAL TK SDN BHD, Nusajaya, Johor Bahru, Malaysia
| | | | - Yong Zhao
- Chongqing Medical University, Chongqing, China
| | - Yingfeng Zheng
- Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Maigeng Zhou
- National Center for Chronic and Non-communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jun Zhu
- National Office for Maternal and Child Health Surveillance, Chengdu, China
| | - Xiao Nong Zou
- Cancer Institute/Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Alan D Lopez
- University of Melbourne, Melbourne, VIC, Australia
| | - Theo Vos
- Institute for Health Metrics and Evaluation, Seattle, WA, USA
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Prentice HA, Pajewski NM, He D, Zhang K, Brown EE, Kilembe W, Allen S, Hunter E, Kaslow RA, Tang J. Host genetics and immune control of HIV-1 infection: fine mapping for the extended human MHC region in an African cohort. Genes Immun 2014; 15:275-81. [PMID: 24784026 PMCID: PMC4111776 DOI: 10.1038/gene.2014.16] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Revised: 03/28/2014] [Accepted: 03/28/2014] [Indexed: 12/31/2022]
Abstract
Multiple MHC loci encoding human leukocyte antigens (HLA) have allelic variants unequivocally associated with differential immune control of HIV-1 infection. Fine mapping based on single nucleotide polymorphisms (SNPs) in the extended MHC (xMHC) region is expected to reveal causal or novel factors and to justify a search for functional mechanisms. We have tested the utility of a custom fine-mapping platform (the ImmunoChip) for 172 HIV-1 seroconverters (SCs) and 449 seroprevalent individuals (SPs) from Lusaka, Zambia, with a focus on more than 6,400 informative xMHC SNPs. When conditioned on HLA and non-genetic factors previously associated with HIV-1 viral load (VL) in the study cohort, penalized approaches (HyperLasso models) identified an intergenic SNP (rs3094626 between RPP21 and HLA-E) and an intronic SNP (rs3134931 in NOTCH4) as novel correlates of early set-point VL in SCs. The minor allele of rs2857114 (downstream from HLA-DOB) was an unfavorable factor in SPs. Joint models based on demographic features, HLA alleles and the newly identified SNP variants could explain 29% and 15% of VL variance in SCs and SPs, respectively. These findings and bioinformatics strongly suggest that both classic and non-classic MHC genes deserve further investigation, especially in Africans with relatively short haplotype blocks.
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Affiliation(s)
- H A Prentice
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - N M Pajewski
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - D He
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - K Zhang
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - E E Brown
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - W Kilembe
- Zambia-Emory HIV-1 Research Project, Lusaka, Zambia
| | - S Allen
- 1] Zambia-Emory HIV-1 Research Project, Lusaka, Zambia [2] Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - E Hunter
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - R A Kaslow
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - J Tang
- 1] Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA [2] Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
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20
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Hartwig FP, Entiauspe LG, Nunes EM, Rodrigues FM, Collares T, Seixas FK, da Silveira MF. Evidence for an epistatic effect between TP53 R72P and MDM2 T309G SNPs in HIV infection: a cross-sectional study in women from South Brazil. PLoS One 2014; 9:e89489. [PMID: 24586820 PMCID: PMC3938491 DOI: 10.1371/journal.pone.0089489] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 01/22/2014] [Indexed: 12/29/2022] Open
Abstract
OBJECTIVE To investigate the associations of TP53 R72P and MDM2 T309G SNPs with HPV infection status, HPV oncogenic risk and HIV infection status. DESIGN Cross-sectional study combining two groups (150 HIV-negative and 100 HIV-positive) of women. METHODS Data was collected using a closed questionnaire. DNA was extracted from cervical samples. HPV infection status was determined by nested-PCR, and HPV oncogenic risk group by Sanger sequencing. Both SNPS were genotyped by PCR-RFLP. Crude and adjusted associations involving each exposure (R72P and T309G SNPs, as well as 13 models of epistasis) and each outcome (HPV status, HPV oncogenic risk group and HIV infection) were assessed using logistic regression. RESULTS R72P SNP was protectively associated with HPV status (overdominant model), as well as T309G SNP with HPV oncogenic risk (strongest in the overdominant model). No epistatic model was associated with HPV status, but a dominant (R72P over T309G) protective epistatic effect was observed for HPV oncogenic risk. HIV status was strongly associated (risk factor) with different epistatic models, especially in models based on a visual inspection of the results. Moreover, HIV status was evidenced to be an effect mediator of the associations involving HPV oncogenic risk. CONCLUSIONS We found evidence for a role of R72P and T309G SNPs in HPV status and HPV oncogenic risk (respectively), and strong associations were found for an epistatic effect in HIV status. Prospective studies in larger samples are warranted to validate our findings, which point to a novel role of these SNPs in HIV infection.
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Affiliation(s)
- Fernando Pires Hartwig
- Postgraduate Program in Epidemiology, Department of Social Medicine, Faculty of Medicine, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
- Molecular and Cellular Oncology Research Group, Biotechnology Unit, Technology Development Center, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Ludmila Gonçalves Entiauspe
- Postgraduate Program in Biotechnology, Technology Development Center (Biotechnology Unit), Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
- Molecular and Cellular Oncology Research Group, Biotechnology Unit, Technology Development Center, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Emily Montosa Nunes
- Molecular and Cellular Oncology Research Group, Biotechnology Unit, Technology Development Center, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Fernanda Martins Rodrigues
- Molecular and Cellular Oncology Research Group, Biotechnology Unit, Technology Development Center, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Tiago Collares
- Postgraduate Program in Biotechnology, Technology Development Center (Biotechnology Unit), Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
- Molecular and Cellular Oncology Research Group, Biotechnology Unit, Technology Development Center, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Fabiana Kömmling Seixas
- Postgraduate Program in Biotechnology, Technology Development Center (Biotechnology Unit), Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
- Molecular and Cellular Oncology Research Group, Biotechnology Unit, Technology Development Center, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Mariângela Freitas da Silveira
- Postgraduate Program in Epidemiology, Department of Social Medicine, Faculty of Medicine, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
- Maternal and Child Department, Faculty of Medicine, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
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21
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Cespedes MS, Kerns SL, Holzman RS, McLaren PJ, Ostrer H, Aberg JA. Genetic predictors of cervical dysplasia in African American HIV-infected women: ACTG DACS 268. HIV CLINICAL TRIALS 2013; 14:292-302. [PMID: 24334182 DOI: 10.1310/hct1406-292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
OBJECTIVE To examine genome-wide associations in HIV-infected women with a history of cervical dysplasia compared with HIV-infected women with no history of abnormal Papanicolaou (Pap) tests. DESIGN Case-control study using data from women analyzed for the HIV Controllers Study and enrolled in HIV treatment-naïve studies in the AIDS Clinical Trials Group (ACTG). METHODS Genotyping utilized Illumina HumanHap 650 Y or 1MDuo platforms. After quality control and principal component analysis, ~610,000 significant single nucleotide polymorphisms (SNPs) were tested for association. Threshold for significance was P < 5 × 10(-8) for genome-wide associations. RESULTS No significant genomic association was observed between women with low-grade dysplasia and controls. The genome-wide association study (GWAS) analysis between women with high-grade dysplasia or invasive cervical cancer and normal controls identified significant SNPs. In the analyses limited to African American women, 11 SNPs were significantly associated with the development of high-grade dysplasia or cancer after correcting for multiple comparisons. The model using significant SNPs alone had improved accuracy in predicting high-grade dysplasia in African American women compared to the use of clinical data (area under the receiver operating characteristic curve for genetic and clinical model = 0.9 and 0.747, respectively). CONCLUSIONS These preliminary data serve as proof of concept that there may be a genetic predisposition to developing high-grade cervical dysplasia in African American HIV-infected women. Given the small sample size, the results need to be validated in a separate cohort.
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Affiliation(s)
| | | | | | - Paul J McLaren
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Harry Ostrer
- Albert Einstein College of Medicine, Bronx, New York
| | - Judith A Aberg
- New York University School of Medicine, New York, New York
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22
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Dahiya S, Irish BP, Nonnemacher MR, Wigdahl B. Genetic variation and HIV-associated neurologic disease. Adv Virus Res 2013; 87:183-240. [PMID: 23809924 DOI: 10.1016/b978-0-12-407698-3.00006-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
HIV-associated neurologic disease continues to be a significant complication in the era of highly active antiretroviral therapy. A substantial subset of the HIV-infected population shows impaired neuropsychological performance as a result of HIV-mediated neuroinflammation and eventual central nervous system (CNS) injury. CNS compartmentalization of HIV, coupled with the evolution of genetically isolated populations in the CNS, is responsible for poor prognosis in patients with AIDS, warranting further investigation and possible additions to the current therapeutic strategy. This chapter reviews key advances in the field of neuropathogenesis and studies that have highlighted how molecular diversity within the HIV genome may impact HIV-associated neurologic disease. We also discuss the possible functional implications of genetic variation within the viral promoter and possibly other regions of the viral genome, especially in the cells of monocyte-macrophage lineage, which are arguably key cellular players in HIV-associated CNS disease.
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Affiliation(s)
- Satinder Dahiya
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Bryan P Irish
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Michael R Nonnemacher
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
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23
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Ballana E, Esté JA. Insights from host genomics into HIV infection and disease: Identification of host targets for drug development. Antiviral Res 2013; 100:473-86. [PMID: 24084487 DOI: 10.1016/j.antiviral.2013.09.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 09/17/2013] [Accepted: 09/20/2013] [Indexed: 01/11/2023]
Abstract
HIV susceptibility and disease progression show a substantial degree of individual heterogeneity, ranging from fast progressors to long-term non progressors or elite controllers, that is, subjects that control infection in the absence of therapy. Recent years have seen a significant increase in understanding of the host genetic determinants of susceptibility to HIV infection and disease progression, driven in large part by candidate gene studies, genome-wide association studies, genome-wide transcriptome analyses, and large-scale functional screens. These studies have identified common variants in 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 catalogue of genes and pathways involved in viral replication. This review highlights the potential of host genomic influences in antiviral therapy by pointing to promising novel drug targets but also providing the basis of the identification and validation of host mechanisms that might be susceptible targets for novel antiviral therapies.
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Affiliation(s)
- Ester Ballana
- IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain.
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24
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McLaren PJ, Coulonges C, Ripke S, van den Berg L, Buchbinder S, Carrington M, Cossarizza A, Dalmau J, Deeks SG, Delaneau O, De Luca A, Goedert JJ, Haas D, Herbeck JT, Kathiresan S, Kirk GD, Lambotte O, Luo M, Mallal S, van Manen D, Martinez-Picado J, Meyer L, Miro JM, Mullins JI, Obel N, O'Brien SJ, Pereyra F, Plummer FA, Poli G, Qi Y, Rucart P, Sandhu MS, Shea PR, Schuitemaker H, Theodorou I, Vannberg F, Veldink J, Walker BD, Weintrob A, Winkler CA, Wolinsky S, Telenti A, Goldstein DB, de Bakker PIW, Zagury JF, Fellay J. Association study of common genetic variants and HIV-1 acquisition in 6,300 infected cases and 7,200 controls. PLoS Pathog 2013; 9:e1003515. [PMID: 23935489 PMCID: PMC3723635 DOI: 10.1371/journal.ppat.1003515] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 06/07/2013] [Indexed: 11/18/2022] Open
Abstract
Multiple genome-wide association studies (GWAS) have been performed in HIV-1 infected individuals, identifying common genetic influences on viral control and disease course. Similarly, common genetic correlates of acquisition of HIV-1 after exposure have been interrogated using GWAS, although in generally small samples. Under the auspices of the International Collaboration for the Genomics of HIV, we have combined the genome-wide single nucleotide polymorphism (SNP) data collected by 25 cohorts, studies, or institutions on HIV-1 infected individuals and compared them to carefully matched population-level data sets (a list of all collaborators appears in Note S1 in Text S1). After imputation using the 1,000 Genomes Project reference panel, we tested approximately 8 million common DNA variants (SNPs and indels) for association with HIV-1 acquisition in 6,334 infected patients and 7,247 population samples of European ancestry. Initial association testing identified the SNP rs4418214, the C allele of which is known to tag the HLA-B*57:01 and B*27:05 alleles, as genome-wide significant (p = 3.6×10−11). However, restricting analysis to individuals with a known date of seroconversion suggested that this association was due to the frailty bias in studies of lethal diseases. Further analyses including testing recessive genetic models, testing for bulk effects of non-genome-wide significant variants, stratifying by sexual or parenteral transmission risk and testing previously reported associations showed no evidence for genetic influence on HIV-1 acquisition (with the exception of CCR5Δ32 homozygosity). Thus, these data suggest that genetic influences on HIV acquisition are either rare or have smaller effects than can be detected by this sample size. Comparing the frequency differences between common DNA variants in disease-affected cases and in unaffected controls has been successful in uncovering the genetic component of multiple diseases. This approach is most effective when large samples of cases and controls are available. Here we combine information from multiple studies of HIV infected patients, including more than 6,300 HIV+ individuals, with data from 7,200 general population samples of European ancestry to test nearly 8 million common DNA variants for an impact on HIV acquisition. With this large sample we did not observe any single common genetic variant that significantly associated with HIV acquisition. We further tested 22 variants previously identified by smaller studies as influencing HIV acquisition. With the exception of a deletion polymorphism in the CCR5 gene (CCR5Δ32) we found no convincing evidence to support these previous associations. Taken together these data suggest that genetic influences on HIV acquisition are either rare or have smaller effects than can be detected by this sample size.
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Affiliation(s)
- Paul J. McLaren
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Cédric Coulonges
- Laboratoire Génomique, Bioinformatique, et Applications, EA4627, Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
- ANRS Genomic Group (French Agency for Research on AIDS and Hepatitis), Paris, France
| | - Stephan Ripke
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Leonard van den Berg
- Department of Neurology, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Susan Buchbinder
- Bridge HIV, San Francisco Department of Public Health, San Francisco, California, United States of America
| | - Mary Carrington
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America
| | - Andrea Cossarizza
- Department of Surgery, Medicine, Dentistry and Morphological Sciences University of Modena and Reggio Emilia School of Medicine, Modena, Italy
| | - Judith Dalmau
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Steven G. Deeks
- Department of Medicine, University of California, San Francisco, California, United States of America
| | - Olivier Delaneau
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Andrea De Luca
- University Division of Infectious Diseases, Siena University Hospital, Siena, Italy
- Institute of Clinical infectious Diseases, Università Cattolica del Sacro Cuore, Roma, Italy
| | - James J. Goedert
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, United States of America
| | - David Haas
- Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Joshua T. Herbeck
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Sekar Kathiresan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Cardiovascular Research Center and Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Gregory D. Kirk
- Department of Epidemiology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Olivier Lambotte
- INSERM U1012, Bicêtre, France
- University Paris-Sud, Bicêtre, France
- AP-HP, Department of Internal Medicine and Infectious Diseases, Bicêtre Hospital, Bicêtre, France
| | - Ma Luo
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - Simon Mallal
- Institute for Immunology & Infectious Diseases, Murdoch University and Pathwest, Perth, Australia
| | - Daniëlle van Manen
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Javier Martinez-Picado
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Laurence Meyer
- ANRS Genomic Group (French Agency for Research on AIDS and Hepatitis), Paris, France
- Inserm, CESP U1018, University Paris-Sud, UMRS 1018, Faculté de Médecine Paris-Sud; AP-HP, Hopital Bicêtre, Epidemiology and Public Health Service, Le Kremlin Bicêtre, France
| | - José M. Miro
- Infectious Diseases Service. Hospital Clinic – IDIBAPS, University of Barcelona, Barcelona, Spain
| | - James I. Mullins
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Niels Obel
- Department of Infectious Diseases, The National University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Stephen J. O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
| | - Florencia Pereyra
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America
- Division of Infectious Disease, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Francis A. Plummer
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - Guido Poli
- Division of Immunology, Transplantation and Infectious Diseases, Vita-Salute San Raffaele University, School of Medicine & San Raffaele Scientific Institute, Milan, Italy
| | - Ying Qi
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Pierre Rucart
- Laboratoire Génomique, Bioinformatique, et Applications, EA4627, Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
- ANRS Genomic Group (French Agency for Research on AIDS and Hepatitis), Paris, France
| | - Manj S. Sandhu
- Genetic Epidemiology Group, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Non-Communicable Disease Research Group, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Patrick R. Shea
- Center for Human Genome Variation, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Hanneke Schuitemaker
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Ioannis Theodorou
- ANRS Genomic Group (French Agency for Research on AIDS and Hepatitis), Paris, France
- INSERM UMRS 945, Paris, France
| | - Fredrik Vannberg
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Jan Veldink
- Department of Neurology, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bruce D. Walker
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Amy Weintrob
- Infectious Disease Clinical Research Program, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - Cheryl A. Winkler
- Basic Research Laboratory, Molecular Genetic Epidemiology Section, Center for Cancer Research, NCI, SAIC-Frederick, Inc., Frederick National Laboratory, Frederick, Maryland, United States of America
| | - Steven Wolinsky
- Division of Infectious Diseases, The Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Amalio Telenti
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | - David B. Goldstein
- Center for Human Genome Variation, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Paul I. W. de Bakker
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Division of Genetics Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Epidemiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jean-François Zagury
- Laboratoire Génomique, Bioinformatique, et Applications, EA4627, Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
- ANRS Genomic Group (French Agency for Research on AIDS and Hepatitis), Paris, France
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
- * E-mail:
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25
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Abstract
Untreated HIV-1 infection typically progresses to AIDS within 10 years, but less than 1% of infected individuals remain healthy and have normal CD4(+) T cell counts and undetectable viral loads; some individuals have remained this way for 35 years and counting. Through a combination of large population studies of cohorts of these 'HIV-1 controllers' and detailed studies of individual patients, a heterogeneous picture has emerged regarding the basis for this remarkable resistance to AIDS progression. In this Review, we highlight the host genetic factors, the viral genetic factors and the immunological factors that are associated with the controller phenotype, we discuss emerging methodological approaches that could facilitate a better understanding of spontaneous HIV-1 immune control in the future, and we delineate implications for a 'functional cure' of HIV-1 infection.
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Affiliation(s)
- Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Massachusetts General Hospital, Cambridge, Massachusetts 02139, USA.
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26
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Duskova K, Nagilla P, Le HS, Iyer P, Thalamuthu A, Martinson J, Bar-Joseph Z, Buchanan W, Rinaldo C, Ayyavoo V. MicroRNA regulation and its effects on cellular transcriptome in human immunodeficiency virus-1 (HIV-1) infected individuals with distinct viral load and CD4 cell counts. BMC Infect Dis 2013; 13:250. [PMID: 23721325 PMCID: PMC3680326 DOI: 10.1186/1471-2334-13-250] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 05/16/2013] [Indexed: 12/13/2022] Open
Abstract
Background Disease progression in the absence of therapy varies significantly in HIV-1 infected individuals. Both viral and host cellular molecules are implicated; however, the exact role of these factors and/or the mechanism involved remains elusive. To understand how microRNAs (miRNAs), which are regulators of transcription and translation, influence host cellular gene expression (mRNA) during HIV-1 infection, we performed a comparative miRNA and mRNA microarray analysis using PBMCs obtained from infected individuals with distinct viral load and CD4 counts. Methods RNA isolated from PBMCs obtained from HIV-1 seronegative and HIV-1 positive individuals with distinct viral load and CD4 counts were assessed for miRNA and mRNA profile. Selected miRNA and mRNA transcripts were validated using in vivo and in vitro infection model. Results Our results indicate that HIV-1 positive individuals with high viral load (HVL) showed a dysregulation of 191 miRNAs and 309 mRNA transcripts compared to the uninfected age and sex matched controls. The miRNAs miR-19b, 146a, 615-3p, 382, 34a, 144 and 155, that are known to target innate and inflammatory factors, were significantly upregulated in PBMCs with high viral load, as were the inflammatory molecules CXCL5, CCL2, IL6 and IL8, whereas defensin, CD4, ALDH1, and Neurogranin (NRGN) were significantly downregulated. Using the transcriptome profile and predicted target genes, we constructed the regulatory networks of miRNA-mRNA pairs that were differentially expressed between control, LVL and HVL subjects. The regulatory network revealed an inverse correlation of several miRNA-mRNA pair expression patterns, suggesting HIV-1 mediated transcriptional regulation is in part likely through miRNA regulation. Conclusions Results from our studies indicate that gene expression is significantly altered in PBMCs in response to virus replication. It is interesting to note that the infected individuals with low or undetectable viral load exhibit a gene expression profile very similar to control or uninfected subjects. Importantly, we identified several new mRNA targets (Defensin, Neurogranin, AIF) as well as the miRNAs that could be involved in regulating their expression through the miRNA-mRNA interaction.
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Affiliation(s)
- Karolina Duskova
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, 425 Parran Hall, 130 Desoto Street, Pittsburgh, PA 15261, USA
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27
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Limou S, Zagury JF. Immunogenetics: Genome-Wide Association of Non-Progressive HIV and Viral Load Control: HLA Genes and Beyond. Front Immunol 2013; 4:118. [PMID: 23750159 PMCID: PMC3664380 DOI: 10.3389/fimmu.2013.00118] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 05/04/2013] [Indexed: 01/11/2023] Open
Abstract
Very early after the identification of the human immunodeficiency virus (HIV), host genetics factors were anticipated to play a role in viral control and disease progression. As early as the mid-1990s, candidate gene studies demonstrated a central role for the chemokine co-receptor/ligand (e.g., CCR5) and human leukocyte antigen (HLA) systems. In the last decade, the advent of genome-wide arrays opened a new era for unbiased genetic exploration of the genome and brought big expectations for the identification of new unexpected genes and pathways involved in HIV/AIDS. More than 15 genome-wide association studies targeting various HIV-linked phenotypes have been published since 2007. Surprisingly, only the two HIV-chemokine co-receptors and HLA loci have exhibited consistent and reproducible statistically significant genetic associations. In this chapter, we will review the findings from the genome-wide studies focusing especially on non-progressive and HIV control phenotypes, and discuss the current perspectives.
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Affiliation(s)
- Sophie Limou
- Basic Science Program, Basic Research Laboratory, Frederick National Laboratory for Cancer ResearchFrederick, MD, USA
| | - Jean-François Zagury
- Chaire de Bioinformatique, Laboratoire Génomique Bioinformatique et Applications (EA 4627), Conservatoire National des Arts et MétiersParis, France
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Abstract
The AIDS era has seen multiple advances in the power of genetics research; scores of host genetic protective factors have been nominated and several have translated to the bedside. We discuss how genomics may inform HIV/AIDS prevention, treatment and eradication.
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Yang Y, Ellis MK, McManus DP. Immunogenetics of human echinococcosis. Trends Parasitol 2012; 28:447-54. [PMID: 22951425 DOI: 10.1016/j.pt.2012.08.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 07/31/2012] [Accepted: 08/01/2012] [Indexed: 01/28/2023]
Abstract
Susceptibility and resistance to human Echinococcus infection and disease, although poorly understood, appear to reflect a complex interaction of parasite and host immunological and genetic factors. Disease stage, progression, and prognosis following treatment appear to be strongly influenced by cytokine and antibody profiles, and more recent evidence has suggested an important role of dendritic cells (DCs) and T regulatory cells (Tregs) in immunomodulation. Microarrays have supported these findings, highlighting both known and novel pathways involved in chronic murine disease. Genetic studies to date have been few and with limited success. Advanced genomic approaches, such as genome-wide association studies (GWAS), may provide further insight to identify the relevant pathways involved, thereby facilitating a new approach for the development of new clinical therapies.
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Affiliation(s)
- YuRong Yang
- Molecular Parasitology Laboratory, Queensland Institute of Medical Research, Brisbane, QLD, Australia.
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van Manen D, van 't Wout AB, Schuitemaker H. Genome-wide association studies on HIV susceptibility, pathogenesis and pharmacogenomics. Retrovirology 2012; 9:70. [PMID: 22920050 PMCID: PMC3468375 DOI: 10.1186/1742-4690-9-70] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Accepted: 07/31/2012] [Indexed: 11/22/2022] Open
Abstract
Susceptibility to HIV-1 and the clinical course after infection show a substantial heterogeneity between individuals. Part of this variability can be attributed to host genetic variation. Initial candidate gene studies have revealed interesting host factors that influence HIV infection, replication and pathogenesis. Recently, genome-wide association studies (GWAS) were utilized for unbiased searches at a genome-wide level to discover novel genetic factors and pathways involved in HIV-1 infection. This review gives an overview of findings from the GWAS performed on HIV infection, within different cohorts, with variable patient and phenotype selection. Furthermore, novel techniques and strategies in research that might contribute to the complete understanding of virus-host interactions and its role on the pathogenesis of HIV infection are discussed.
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Affiliation(s)
- Daniëlle van Manen
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, Center for Infectious Diseases and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
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31
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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).
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Affiliation(s)
- Amalio Telenti
- Institute of Microbiology, University Hospital and University of Lausanne, 1011 Lausanne, Switzerland.
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32
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Limou S, Delaneau O, van Manen D, An P, Sezgin E, Le Clerc S, Coulonges C, Troyer JL, Veldink JH, van den Berg LH, Spadoni JL, Taing L, Labib T, Montes M, Delfraissy JF, Schachter F, O'Brien SJ, Buchbinder S, van Natta ML, Jabs DA, Froguel P, Schuitemaker H, Winkler CA, Zagury JF. Multicohort genomewide association study reveals a new signal of protection against HIV-1 acquisition. J Infect Dis 2012; 205:1155-62. [PMID: 22362864 DOI: 10.1093/infdis/jis028] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND To date, only mutations in CCR5 have been shown to confer resistance to human immunodeficiency virus type 1 (HIV-1) infection, and these explain only a small fraction of the observed variability in HIV susceptibility. METHODS We performed a meta-analysis between 2 independent European genomewide association studies, each comparing HIV-1 seropositive cases with normal population controls known to be HIV uninfected, to identify single-nucleotide polymorphisms (SNPs) associated with the HIV-1 acquisition phenotype. SNPs exhibiting P < 10(-5) in this first stage underwent second-stage analysis in 2 independent US cohorts of European descent. RESULTS After the first stage, a single highly significant association was revealed for the chromosome 8 rs6996198 with HIV-1 acquisition and was replicated in both second-stage cohorts. Across the 4 groups, the rs6996198-T allele was consistently associated with a significant reduced risk of HIV-1 infection, and the global meta-analysis reached genomewide significance: P(combined) = 7.76 × 10(-8). CONCLUSIONS We provide strong evidence of association for a common variant with HIV-1 acquisition in populations of European ancestry. This protective signal against HIV-1 infection is the first identified outside the CCR5 nexus. First clues point to a potential functional role for a nearby candidate gene, CYP7B1, but this locus warrants further investigation.
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Affiliation(s)
- Sophie Limou
- Laboratoire Génomique, Bioinformatique, et Applications, EA4627, Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
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Ansari AA, Mayne AE, Takahashi Y, Pattanapanyasat K. Incorporation of innate immune effector mechanisms in the formulation of a vaccine against HIV-1. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 780:143-59. [PMID: 21842371 DOI: 10.1007/978-1-4419-5632-3_12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The realization of a major role for events that occur during acute viremia that dictate the course of disease both in HIV-1 infected humans and susceptible SIV infected non-human primates has prompted an intense interest in studies of the contribution of innate immune effector mechanisms. It is reasoned that findings from such studies may be important and need to be incorporated into the design and formulation of potential candidate vaccines against HIV-1. This review serves to outline the various non-human primate models that can best serve to address this issue, a summary of our knowledge on the various subsets of NK cells (one of the major innate immune cell lineage) that have an impact on the course of disease, the potential pathways that regulate their function and the potential role of the KIRs on SIV-induced disease course. Finally, the major points from this report and the data presented on similar subjects by other investigators is utilized to provide a summary of the potential future directions that we need to take in efforts to move this field forward.
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Affiliation(s)
- Aftab A Ansari
- Department of Pathology, Emory University School of Medicine, Atlanta, GA 30322, USA.
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35
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Newport MJ, Finan C. Genome-wide association studies and susceptibility to infectious diseases. Brief Funct Genomics 2011; 10:98-107. [PMID: 21436306 DOI: 10.1093/bfgp/elq037] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Progress in genomics and the associated technological, statistical and bioinformatics advances have facilitated the successful implementation of genome-wide association studies (GWAS) towards understanding the genetic basis of common diseases. Infectious diseases contribute significantly to the global burden of disease and there is robust epidemiological evidence that host genetic factors are important determinants of the outcome of interactions between host and pathogen. Indeed, infectious diseases have exerted profound selective pressure on human evolution. However, the application of GWAS to infectious diseases has been relatively limited compared with non-communicable diseases. Here we review GWAS findings for important infectious diseases, including malaria, tuberculosis and HIV. We highlight some of the pitfalls recognized more generally for GWAS, as well as issues specific to infection, including the role of the pathogen which also has a genome. We also discuss the challenges encountered when studying African populations which are genetically more ancient and more diverse that other populations and disproportionately bear the main global burden of serious infectious diseases.
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Affiliation(s)
- Melanie J Newport
- Infectious Diseases and Global Health at Brighton and Sussex Medical School, UK.
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36
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An P, Li R, Wang JM, Yoshimura T, Takahashi M, Samudralal R, O'Brien SJ, Phair J, Goedert JJ, Kirk GD, Troyer JL, Sezgin E, Buchbinder SP, Donfield S, Nelson GW, Winkler CA. Role of exonic variation in chemokine receptor genes on AIDS: CCRL2 F167Y association with pneumocystis pneumonia. PLoS Genet 2011; 7:e1002328. [PMID: 22046140 PMCID: PMC3203199 DOI: 10.1371/journal.pgen.1002328] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 08/03/2011] [Indexed: 02/04/2023] Open
Abstract
Chromosome 3p21-22 harbors two clusters of chemokine receptor genes, several of which serve as major or minor coreceptors of HIV-1. Although the genetic association of CCR5 and CCR2 variants with HIV-1 pathogenesis is well known, the role of variation in other nearby chemokine receptor genes remain unresolved. We genotyped exonic single nucleotide polymorphisms (SNPs) in chemokine receptor genes: CCR3, CCRL2, and CXCR6 (at 3p21) and CCR8 and CX3CR1 (at 3p22), the majority of which were non-synonymous. The individual SNPs were tested for their effects on disease progression and outcomes in five treatment-naïve HIV-1/AIDS natural history cohorts. In addition to the known CCR5 and CCR2 associations, significant associations were identified for CCR3, CCR8, and CCRL2 on progression to AIDS. A multivariate survival analysis pointed to a previously undetected association of a non-conservative amino acid change F167Y in CCRL2 with AIDS progression: 167F is associated with accelerated progression to AIDS (RH = 1.90, P = 0.002, corrected). Further analysis indicated that CCRL2-167F was specifically associated with more rapid development of pneumocystis pneumonia (PCP) (RH = 2.84, 95% CI 1.28-6.31) among four major AIDS-defining conditions. Considering the newly defined role of CCRL2 in lung dendritic cell trafficking, this atypical chemokine receptor may affect PCP through immune regulation and inducing inflammation.
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MESH Headings
- Acquired Immunodeficiency Syndrome/complications
- Chromosomes, Human, Pair 3/genetics
- Cohort Studies
- Disease Progression
- Exons
- Genetic Association Studies
- HEK293 Cells
- HIV-1
- Humans
- Linkage Disequilibrium
- Pneumonia, Pneumocystis/etiology
- Pneumonia, Pneumocystis/genetics
- Polymorphism, Single Nucleotide
- Receptors, CCR/chemistry
- Receptors, CCR/genetics
- Receptors, CCR3/genetics
- Receptors, CCR8/genetics
- Receptors, CXCR6
- Receptors, Chemokine/genetics
- Receptors, Virus/genetics
- Survival Analysis
- Treatment Outcome
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Affiliation(s)
- Ping An
- Basic Research Laboratory, SAIC–Frederick, National Cancer Institute–Frederick, Frederick, Maryland, United States of America
| | - Rongling Li
- Office of Population Genomics, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Ji Ming Wang
- Laboratory of Molecular Immunoregulation, National Cancer Institute–Frederick, Frederick, Maryland, United States of America
| | - Teizo Yoshimura
- Laboratory of Molecular Immunoregulation, National Cancer Institute–Frederick, Frederick, Maryland, United States of America
| | - Munehisa Takahashi
- Laboratory of Molecular Immunoregulation, National Cancer Institute–Frederick, Frederick, Maryland, United States of America
| | - Ram Samudralal
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Stephen J. O'Brien
- Laboratory of Genomic Diversity, National Cancer Institute–Frederick, Frederick, Maryland, United States of America
| | - John Phair
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University Medical School, Chicago, Illinois, United States of America
| | - James J. Goedert
- Infections and Immunoepidemiology Branch, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Gregory D. Kirk
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Jennifer L. Troyer
- BSP/CCR Genetics Core, SAIC–Frederick, National Cancer Institute–Frederick, Frederick, Maryland, United States of America
| | - Efe Sezgin
- Laboratory of Genomic Diversity, National Cancer Institute–Frederick, Frederick, Maryland, United States of America
| | - Susan P. Buchbinder
- San Francisco Department of Public Health, San Francisco, California, United States of America
| | | | - George W. Nelson
- BSP/CCR Genetics Core, SAIC–Frederick, National Cancer Institute–Frederick, Frederick, Maryland, United States of America
| | - Cheryl A. Winkler
- Basic Research Laboratory, SAIC–Frederick, National Cancer Institute–Frederick, Frederick, Maryland, United States of America
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37
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Bol SM, Booiman T, Bunnik EM, Moerland PD, van Dort K, Strauss JF, Sieberer M, Schuitemaker H, Kootstra NA, van 't Wout AB. Polymorphism in HIV-1 dependency factor PDE8A affects mRNA level and HIV-1 replication in primary macrophages. Virology 2011; 420:32-42. [PMID: 21920574 DOI: 10.1016/j.virol.2011.08.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Revised: 04/27/2011] [Accepted: 08/18/2011] [Indexed: 12/29/2022]
Abstract
Four genome-wide RNAi screens have recently identified hundreds of HIV-1 dependency factors (HDFs). Previously, we reported a large variation in the ability of HIV-1 to replicate in monocyte-derived macrophages (MDM) derived from >400 healthy seronegative blood donors. Here we determined whether SNPs in genes encoding newly identified HDFs were associated with this variation in HIV-1 replication. We found a significant association between the minor allele of SNP rs2304418 in phosphodiesterase 8A (PDE8A) and lower HIV-1 replication (p=2.4×10(-6)). The minor allele of SNP rs2304418 was also significantly associated with lower PDE8A mRNA levels in MDM (p=8.3×10(-5)). In accordance with this, overexpression of PDE8A in HEK293T cells resulted in increased HIV-1 replication, while subsequent knock-down of PDE8A decreased replication. This study links host genetic variation in a newly identified HDF to variation in HIV-1 replication in a relevant primary target cell for HIV-1 and may provide new leads for treatment of this infection.
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Affiliation(s)
- Sebastiaan M Bol
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
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Comparative expression profile of miRNA and mRNA in primary peripheral blood mononuclear cells infected with human immunodeficiency virus (HIV-1). PLoS One 2011; 6:e22730. [PMID: 21829495 PMCID: PMC3145673 DOI: 10.1371/journal.pone.0022730] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Accepted: 06/29/2011] [Indexed: 12/31/2022] Open
Abstract
Host cells respond to exogenous infectious agents such as viruses, including HIV-1. Studies have evaluated the changes associated with virus infection at the transcriptional and translational levels of the cellular genes involved in specific pathways. While this approach is useful, in our view it provides only a partial view of genome-wide changes. Recently, technological advances in the expression profiling at the microRNA (miRNA) and mRNA levels have made it possible to evaluate the changes in the components of multiple pathways. To understand the role of miRNA and its interplay with host cellular gene expression (mRNA) during HIV-1 infection, we performed a comparative global miRNA and mRNA microarray using human PBMCs infected with HIV-1. The PBMCs were derived from multiple donors and were infected with virus generated from the molecular clone pNL4-3. The results showed that HIV-1 infection led to altered regulation of 21 miRNAs and 444 mRNA more than 2-fold, with a statistical significance of p<0.05. Furthermore, the differentially regulated miRNA and mRNA were shown to be associated with host cellular pathways involved in cell cycle/proliferation, apoptosis, T-cell signaling, and immune activation. We also observed a number of inverse correlations of miRNA and mRNA expression in infected PBMCs, further confirming the interrelationship between miRNA and mRNA regulation during HIV-1 infection. These results for the first time provide evidence that the miRNA profile could be an early indicator of host cellular dysfunction induced by HIV-1.
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39
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van Manen D, Delaneau O, Kootstra NA, Boeser-Nunnink BD, Limou S, Bol SM, Burger JA, Zwinderman AH, Moerland PD, van 't Slot R, Zagury JF, van 't Wout AB, Schuitemaker H. Genome-wide association scan in HIV-1-infected individuals identifying variants influencing disease course. PLoS One 2011; 6:e22208. [PMID: 21811574 PMCID: PMC3141012 DOI: 10.1371/journal.pone.0022208] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 06/17/2011] [Indexed: 01/20/2023] Open
Abstract
Background AIDS develops typically after 7–11 years of untreated HIV-1 infection, with extremes of very rapid disease progression (<2 years) and long-term non-progression (>15 years). To reveal additional host genetic factors that may impact on the clinical course of HIV-1 infection, we designed a genome-wide association study (GWAS) in 404 participants of the Amsterdam Cohort Studies on HIV-1 infection and AIDS. Methods The association of SNP genotypes with the clinical course of HIV-1 infection was tested in Cox regression survival analyses using AIDS-diagnosis and AIDS-related death as endpoints. Results Multiple, not previously identified SNPs, were identified to be strongly associated with disease progression after HIV-1 infection, albeit not genome-wide significant. However, three independent SNPs in the top ten associations between SNP genotypes and time between seroconversion and AIDS-diagnosis, and one from the top ten associations between SNP genotypes and time between seroconversion and AIDS-related death, had P-values smaller than 0.05 in the French Genomics of Resistance to Immunodeficiency Virus cohort on disease progression. Conclusions Our study emphasizes that the use of different phenotypes in GWAS may be useful to unravel the full spectrum of host genetic factors that may be associated with the clinical course of HIV-1 infection.
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Affiliation(s)
- Daniëlle van Manen
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Olivier Delaneau
- Chaire de Bioinformatique, Conservatoire National des Arts et Métiers and ANRS Genomic Group, Paris, France
| | - Neeltje A. Kootstra
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Brigitte D. Boeser-Nunnink
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Sophie Limou
- Chaire de Bioinformatique, Conservatoire National des Arts et Métiers and ANRS Genomic Group, Paris, France
| | - Sebastiaan M. Bol
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Judith A. Burger
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Aeilko H. Zwinderman
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Perry D. Moerland
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
- Netherlands Bioinformatics Center (NBIC), Nijmegen, The Netherlands
| | - Ruben van 't Slot
- Complex Genetics Section, Department of Biomedical Genetics at the University Medical Center, Utrecht, The Netherlands
| | - Jean-François Zagury
- Chaire de Bioinformatique, Conservatoire National des Arts et Métiers and ANRS Genomic Group, Paris, France
| | - Angélique B. van 't Wout
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Hanneke Schuitemaker
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
- * E-mail:
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40
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Nikolova M, Carriere M, Jenabian MA, Limou S, Younas M, Kök A, Huë S, Seddiki N, Hulin A, Delaneau O, Schuitemaker H, Herbeck JT, Mullins JI, Muhtarova M, Bensussan A, Zagury JF, Lelievre JD, Lévy Y. CD39/adenosine pathway is involved in AIDS progression. PLoS Pathog 2011; 7:e1002110. [PMID: 21750674 PMCID: PMC3131268 DOI: 10.1371/journal.ppat.1002110] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Accepted: 04/23/2011] [Indexed: 12/20/2022] Open
Abstract
HIV-1 infection is characterized by a chronic activation of the immune system and suppressed function of T lymphocytes. Regulatory CD4+ CD25(high) FoxP3+CD127(low) T cells (Treg) play a key role in both conditions. Here, we show that HIV-1 positive patients have a significant increase of Treg-associated expression of CD39/ENTPD1, an ectoenzyme which in concert with CD73 generates adenosine. We show in vitro that the CD39/adenosine axis is involved in Treg suppression in HIV infection. Treg inhibitory effects are relieved by CD39 down modulation and are reproduced by an adenosine-agonist in accordance with a higher expression of the adenosine A2A receptor on patients' T cells. Notably, the expansion of the Treg CD39+ correlates with the level of immune activation and lower CD4+ counts in HIV-1 infected patients. Finally, in a genetic association study performed in three different cohorts, we identified a CD39 gene polymorphism that was associated with down-modulated CD39 expression and a slower progression to AIDS.
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Affiliation(s)
- Maria Nikolova
- INSERM, Unite U955, Creteil, France
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | | | | | - Sophie Limou
- INSERM, Unite U955, Creteil, France
- Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
| | | | | | | | | | - Anne Hulin
- AP-HP, Groupe Henri-Mondor Albert-Chenevier, Laboratory of Pharmacology and Toxicology, Creteil, France
| | - Olivier Delaneau
- Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
| | - Hanneke Schuitemaker
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, Center for Infectious Diseases and Immunity Amsterdam (CINIMA) Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Joshua T. Herbeck
- University of Washington, School of Medicine, Department of Microbiology, Seattle, Washington, United States of America
| | - James I. Mullins
- University of Washington, School of Medicine, Department of Microbiology, Seattle, Washington, United States of America
| | - Maria Muhtarova
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Armand Bensussan
- INSERM UMR 976 and Universite Denis-Diderot-Paris 7, Hopital Saint-Louis, Paris, France
| | - Jean-François Zagury
- INSERM, Unite U955, Creteil, France
- Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
| | - Jean-Daniel Lelievre
- INSERM, Unite U955, Creteil, France
- Université Paris Est Créteil, Faculté de Médecine, Creteil, France
- AP-HP, Groupe Henri-Mondor Albert-Chenevier, Immunologie clinique, Creteil, France
| | - Yves Lévy
- INSERM, Unite U955, Creteil, France
- Université Paris Est Créteil, Faculté de Médecine, Creteil, France
- AP-HP, Groupe Henri-Mondor Albert-Chenevier, Immunologie clinique, Creteil, France
- * E-mail:
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Replication-competent simian immunodeficiency virus (SIV) Gag escape mutations archived in latent reservoirs during antiretroviral treatment of SIV-infected macaques. J Virol 2011; 85:9167-75. [PMID: 21715484 DOI: 10.1128/jvi.00366-11] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In response to pressure exerted by major histocompatibility complex (MHC) class I-mediated CD8(+) T cell control, human immunodeficiency virus (HIV) escape mutations often arise in immunodominant epitopes recognized by MHC class I alleles. While the current standard of care for HIV-infected patients is treatment with highly active antiretroviral therapy (HAART), suppression of viral replication in these patients is not absolute and latently infected cells persist as lifelong reservoirs. To determine whether HIV escape from MHC class I-restricted CD8(+) T cell control develops during HAART treatment and then enters latent reservoirs in the periphery and central nervous system (CNS), with the potential to emerge as replication-competent virus, we tracked the longitudinal development of the simian immunodeficiency virus (SIV) Gag escape mutation K165R in HAART-treated SIV-infected pigtailed macaques. Key findings of these studies included: (i) SIV Gag K165R escape mutations emerged in both plasma and cerebrospinal fluid (CSF) during the decaying phase of viremia after HAART initiation before suppression of viral replication, (ii) SIV K165R Gag escape mutations were archived in latent proviral DNA reservoirs, including the brain in animals receiving HAART that suppressed viral replication, and (iii) replication-competent SIV Gag K165R escape mutations were present in the resting CD4(+) T cell reservoir in HAART-treated SIV-infected macaques. Despite early administration of aggressive antiretroviral treatment, HIV immune escape from CD8(+) T cell control can still develop during the decaying phases of viremia and then persist in latent reservoirs, including the brain, with the potential to emerge if HAART therapy is interrupted.
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Troyer JL, Nelson GW, Lautenberger JA, Chinn L, McIntosh C, Johnson RC, Sezgin E, Kessing B, Malasky M, Hendrickson SL, Li G, Pontius J, Tang M, An P, Winkler CA, Limou S, Le Clerc S, Delaneau O, Zagury JF, Schuitemaker H, van Manen D, Bream JH, Gomperts ED, Buchbinder S, Goedert JJ, Kirk GD, O'Brien SJ. Genome-wide association study implicates PARD3B-based AIDS restriction. J Infect Dis 2011; 203:1491-502. [PMID: 21502085 PMCID: PMC3080910 DOI: 10.1093/infdis/jir046] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Accepted: 12/22/2010] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Host genetic variation influences human immunodeficiency virus (HIV) infection and progression to AIDS. Here we used clinically well-characterized subjects from 5 pretreatment HIV/AIDS cohorts for a genome-wide association study to identify gene associations with rate of AIDS progression. METHODS European American HIV seroconverters (n = 755) were interrogated for single-nucleotide polymorphisms (SNPs) (n = 700,022) associated with progression to AIDS 1987 (Cox proportional hazards regression analysis, co-dominant model). RESULTS Association with slower progression was observed for SNPs in the gene PARD3B. One of these, rs11884476, reached genome-wide significance (relative hazard = 0.3; P =3. 370 × 10(-9)) after statistical correction for 700,022 SNPs and contributes 4.52% of the overall variance in AIDS progression in this study. Nine of the top-ranked SNPs define a PARD3B haplotype that also displays significant association with progression to AIDS (hazard ratio, 0.3; P = 3.220 × 10(-8)). One of these SNPs, rs10185378, is a predicted exonic splicing enhancer; significant alteration in the expression profile of PARD3B splicing transcripts was observed in B cell lines with alternate rs10185378 genotypes. This SNP was typed in European cohorts of rapid progressors and was found to be protective for AIDS 1993 definition (odds ratio, 0.43, P = .025). CONCLUSIONS These observations suggest a potential unsuspected pathway of host genetic influence on the dynamics of AIDS progression.
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Affiliation(s)
- Jennifer L Troyer
- Laboratory of Genomic Diversity, SAIC-Frederick, Inc., Frederick, MD 21702, USA.
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43
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Huang KHG, Goedhals D, Carlson JM, Brockman MA, Mishra S, Brumme ZL, Hickling S, Tang CSW, Miura T, Seebregts C, Heckerman D, Ndung'u T, Walker B, Klenerman P, Steyn D, Goulder P, Phillips R, van Vuuren C, Frater J. Progression to AIDS in South Africa is associated with both reverting and compensatory viral mutations. PLoS One 2011; 6:e19018. [PMID: 21544209 PMCID: PMC3081339 DOI: 10.1371/journal.pone.0019018] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Accepted: 03/13/2011] [Indexed: 11/18/2022] Open
Abstract
We lack the understanding of why HIV-infected individuals in South Africa progress to AIDS. We hypothesised that in end-stage disease there is a shifting dynamic between T cell imposed immunity and viral immune escape, which, through both compensatory and reverting viral mutations, results in increased viral fitness, elevated plasma viral loads and disease progression. We explored how T cell responses, viral adaptation and viral fitness inter-relate in South African cohorts recruited from Bloemfontein, the Free State (n = 278) and Durban, KwaZulu-Natal (n = 775). Immune responses were measured by γ-interferon ELISPOT assays. HLA-associated viral polymorphisms were determined using phylogenetically corrected techniques, and viral replication capacity (VRC) was measured by comparing the growth rate of gag-protease recombinant viruses against recombinant NL4-3 viruses. We report that in advanced disease (CD4 counts <100 cells/µl), T cell responses narrow, with a relative decline in Gag-directed responses (p<0.0001). This is associated with preserved selection pressure at specific viral amino acids (e.g., the T242N polymorphism within the HLA-B*57/5801 restricted TW10 epitope), but with reversion at other sites (e.g., the T186S polymorphism within the HLA-B*8101 restricted TL9 epitope), most notably in Gag and suggestive of "immune relaxation". The median VRC from patients with CD4 counts <100 cells/µl was higher than from patients with CD4 counts ≥ 500 cells/µl (91.15% versus 85.19%, p = 0.0004), potentially explaining the rise in viral load associated with disease progression. Mutations at HIV Gag T186S and T242N reduced VRC, however, in advanced disease only the T242N mutants demonstrated increasing VRC, and were associated with compensatory mutations (p = 0.013). These data provide novel insights into the mechanisms of HIV disease progression in South Africa. Restoration of fitness correlates with loss of viral control in late disease, with evidence for both preserved and relaxed selection pressure across the HIV genome. Interventions that maintain viral fitness costs could potentially slow progression.
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Affiliation(s)
- Kuan-Hsiang Gary Huang
- Nuffield Department of Clinical Medicine,
Oxford University, Oxford, United Kingdom
- The James Martin 21st Century School,
Oxford, United Kingdom
| | - Dominique Goedhals
- University of Free State, Bloemfontein, South
Africa
- National Health Laboratory Services (NHLS),
Johannesburg, South Africa
| | - Jonathan M. Carlson
- eScience Group, Microsoft Research, Los
Angeles, California, United States of America
| | - Mark A. Brockman
- Simon Fraser University, Burnaby, British
Columbia, Canada
- British Columbia Centre for Excellence in
HIV/AIDS, Vancouver, British Columbia, Canada
- Ragon Institute of Massachusetts General
Hospital, Harvard University and Massachusetts Institute of Technology (MIT),
Boston, Massachusetts, United States of America
| | - Swati Mishra
- Nuffield Department of Clinical Medicine,
Oxford University, Oxford, United Kingdom
| | - Zabrina L. Brumme
- Simon Fraser University, Burnaby, British
Columbia, Canada
- British Columbia Centre for Excellence in
HIV/AIDS, Vancouver, British Columbia, Canada
- Ragon Institute of Massachusetts General
Hospital, Harvard University and Massachusetts Institute of Technology (MIT),
Boston, Massachusetts, United States of America
| | - Stephen Hickling
- Nuffield Department of Clinical Medicine,
Oxford University, Oxford, United Kingdom
| | | | - Toshiyuki Miura
- Ragon Institute of Massachusetts General
Hospital, Harvard University and Massachusetts Institute of Technology (MIT),
Boston, Massachusetts, United States of America
- Institute of Medical Science, University of
Tokyo, Tokyo, Japan
| | - Chris Seebregts
- Biomedical Informatics Research Division,
Medical Research Council, Cape Town, South Africa
| | - David Heckerman
- eScience Group, Microsoft Research, Los
Angeles, California, United States of America
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, The Doris Duke
Medical Research Institute, University of KwaZulu-Natal, Durban, South
Africa
| | - Bruce Walker
- HIV Pathogenesis Programme, The Doris Duke
Medical Research Institute, University of KwaZulu-Natal, Durban, South
Africa
- Infectious Disease, Massachusetts General
Hospital, Boston, Massachusetts, United States of America
- Division of AIDS, Harvard University,
Boston, Massachusetts, United States of America
| | - Paul Klenerman
- Nuffield Department of Clinical Medicine,
Oxford University, Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre,
Oxford, United Kingdom
| | - Dewald Steyn
- University of Free State, Bloemfontein, South
Africa
| | - Philip Goulder
- Department of Paediatrics, University of
Oxford, Oxford, United Kingdom
| | - Rodney Phillips
- Nuffield Department of Clinical Medicine,
Oxford University, Oxford, United Kingdom
- The James Martin 21st Century School,
Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre,
Oxford, United Kingdom
| | | | | | - John Frater
- Nuffield Department of Clinical Medicine,
Oxford University, Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre,
Oxford, United Kingdom
- * E-mail:
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Riva A, Vicenzi E, Galli M, Poli G. Strenuous resistance to natural HIV-1 disease progression: viral controllers and long-term nonprogressors. Future Virol 2011. [DOI: 10.2217/fvl.11.25] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
HIV-1 infection leads to AIDS and death within 8–10 years for most individuals in the absence of antiretroviral therapy (ART). However, a minority of infected individuals show the unusual capacity to spontaneously control disease progression after infection in the absence of any ART. So-called ‘long-term nonprogressors’ are defined by maintenance of peripheral CD4+ T-cell counts >500 cells/µl and good health without ART for >7 years since infection. More recently, ART-naive individuals who spontaneously control their viremia levels at either <50 or <2000 copies of RNA/ml for at least 12 months in the absence of ART have been named ‘elite controllers’ and ‘HIV controllers’, respectively. The overlap between long-term nonprogressors and elite controllers/HIV controllers is partial, and both groups collectively account for <5% of all infected individuals. Unraveling the nature of their relative resistance to HIV-1 disease progression would be of great value for HIV-prevention strategies.
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Affiliation(s)
- Agostino Riva
- Infectious Diseases & Immunopathology Section, Department of Clinical Sciences, L Sacco Hospital, Università di Milano, Italy
| | - Elisa Vicenzi
- Viral Pathogens & Biosafety & AIDS Immunopathogenesis Units, Division of Immunology, Transplantation & Infectious Diseases, San Raffaele Scientific Institute, Milano, Italy; P2/P3 Laboratories, Via Olgettina n 58, 20132, Milano, Italy
| | - Massimo Galli
- Infectious Diseases & Immunopathology Section, Department of Clinical Sciences, L Sacco Hospital, Università di Milano, Italy
| | - Guido Poli
- Vita-Salute San Raffaele University, School of Medicine, Milano, Italy
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Müller V, Fraser C, Herbeck JT. A strong case for viral genetic factors in HIV virulence. Viruses 2011; 3:204-216. [PMID: 21994727 PMCID: PMC3185695 DOI: 10.3390/v3030204] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Revised: 02/28/2011] [Accepted: 02/28/2011] [Indexed: 12/23/2022] Open
Abstract
HIV infections show great variation in the rate of progression to disease, and the role of viral genetic factors in this variation had remained poorly characterized until recently. Now a series of four studies [1-4] published within a year has filled this important gap and has demonstrated a robust effect of the viral genotype on HIV virulence.
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Affiliation(s)
- Viktor Müller
- Institute of Biology, Eötvös Loránd University, Pázmány P. s. 1/C, 1117 Budapest, Hungary
| | - Christophe Fraser
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London W2 1PG, UK; E-Mail:
| | - Joshua T. Herbeck
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA; E-Mail:
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46
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Le Clerc S, Coulonges C, Delaneau O, Van Manen D, Herbeck JT, Limou S, An P, Martinson JJ, Spadoni JL, Therwath A, Veldink JH, van den Berg LH, Taing L, Labib T, Mellak S, Montes M, Delfraissy JF, Schächter F, Winkler C, Froguel P, Mullins JI, Schuitemaker H, Zagury JF. Screening low-frequency SNPS from genome-wide association study reveals a new risk allele for progression to AIDS. J Acquir Immune Defic Syndr 2011; 56:279-84. [PMID: 21107268 PMCID: PMC3386792 DOI: 10.1097/qai.0b013e318204982b] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Seven genome-wide association studies (GWAS) have been published in AIDS, and only associations in the HLA region on chromosome 6 and CXCR6 have passed genome-wide significance. METHODS We reanalyzed the data from 3 previously published GWAS, targeting specifically low-frequency SNPs (minor allele frequency <5%). Two groups composed of 365 slow progressors and 147 rapid progressors from Europe and the United States were compared with a control group of 1394 seronegative individuals using Eigenstrat corrections. RESULTS Of the 8584 SNPs with minor allele frequency <5% in cases and controls (Bonferroni threshold = 5.8 × 10⁻⁶), 4 SNPs showed statistical evidence of association with the slow progressor phenotype. The best result was for HCP5 rs2395029 [P = 8.54 × 10⁻¹⁵, odds ratio (OR) = 3.41] in the HLA locus, in partial linkage disequilibrium with 2 additional chromosome 6 associations in C6orf48 (P = 3.03 × 10⁻¹⁰, OR = 2.9) and NOTCH4 (9.08 × 10⁻⁰⁷, OR = 2.32). The fourth association corresponded to rs2072255 located in RICH2 (P = 3.30 × 10⁻⁰⁶, OR = 0.43) in chromosome 17. Using HCP5 rs2395029 as a covariate, the C6orf48 and NOTCH4 signals disappeared, but the RICH2 signal still remained significant. CONCLUSIONS Besides the already known chromosome 6 associations, the analysis of low-frequency SNPs brought up a new association in the RICH2 gene. Interestingly, RICH2 interacts with BST-2 known to be a major restriction factor for HIV-1 infection. Our study has thus identified a new candidate gene for AIDS molecular etiology and confirms the interest of singling out low-frequency SNPs to exploit GWAS data.
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Affiliation(s)
- Sigrid Le Clerc
- Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
- Université Paris 12, INSERM U955, Créteil, France
- ANRS Genomic Group (French Agency for Research on AIDS and Hepatitis), Paris, France
| | - Cédric Coulonges
- Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
- ANRS Genomic Group (French Agency for Research on AIDS and Hepatitis), Paris, France
| | - Olivier Delaneau
- Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
| | - Danielle Van Manen
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, Center for Infectious Diseases and Immunity Amsterdam (CINIMA) Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Joshua T. Herbeck
- University of Washington School of Medicine, Department of Microbiology, Seattle, WA, USA
| | - Sophie Limou
- Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
- Université Paris 12, INSERM U955, Créteil, France
- ANRS Genomic Group (French Agency for Research on AIDS and Hepatitis), Paris, France
- CEA/Institut de Génomique, Centre National de Génotypage, Evry, France
| | - Ping An
- Laboratory of Genomic Diversity, SAIC-Frederick, Inc., National Cancer Institute-Frederick, Frederick, MD, USA
| | | | - Jean-Louis Spadoni
- Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
| | - Amu Therwath
- Laboratoire d’Oncologie Moléculaire, Université Paris 7, Paris, France
| | - Jan H. Veldink
- Rudolf Magnus Institute of Neuroscience, Department of Neurology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Leonard H. van den Berg
- Rudolf Magnus Institute of Neuroscience, Department of Neurology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Lieng Taing
- Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
| | - Taoufik Labib
- Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
| | - Safa Mellak
- Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
| | - Matthieu Montes
- Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
| | | | - François Schächter
- Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
| | - Cheryl Winkler
- Laboratory of Genomic Diversity, SAIC-Frederick, Inc., National Cancer Institute-Frederick, Frederick, MD, USA
| | - Philippe Froguel
- UMR CNRS 8090, Institut Pasteur de Lille, Lille, France
- Genomic Medicine, Hammersmith Hospital, Imperial College London, London, UK
| | - James I. Mullins
- University of Washington School of Medicine, Department of Microbiology, Seattle, WA, USA
| | - Hanneke Schuitemaker
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, Center for Infectious Diseases and Immunity Amsterdam (CINIMA) Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Jean-François Zagury
- Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
- Université Paris 12, INSERM U955, Créteil, France
- ANRS Genomic Group (French Agency for Research on AIDS and Hepatitis), Paris, France
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Aouizerat BE, Pearce CL, Miaskowski C. The search for host genetic factors of HIV/AIDS pathogenesis in the post-genome era: progress to date and new avenues for discovery. Curr HIV/AIDS Rep 2011; 8:38-44. [PMID: 21221856 PMCID: PMC3035795 DOI: 10.1007/s11904-010-0065-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Though pursuit of host genetic factors that influence the pathogenesis of HIV began over two decades ago, progress has been slow. Initial genome-level searches for variations associated with HIV-related traits have yielded interesting candidates, but less in the way of novel pathways to be exploited for therapeutic targets. More recent genome-wide association studies (GWAS) that include different phenotypes, novel designs, and that have examined different population characteristics suggest novel targets and affirm the utility of additional searches. Recent findings from these GWAS are reviewed, new directions for research are identified, and the promise of systems biology to yield novel insights is discussed.
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Affiliation(s)
- Bradley E. Aouizerat
- Department of Physiological Nursing and Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143-0610 USA
| | - C. Leigh Pearce
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 USA
| | - Christine Miaskowski
- Department of Physiological Nursing, University of California San Francisco, San Francisco, CA 94143-0610 USA
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48
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Bol SM, Moerland PD, Limou S, van Remmerden Y, Coulonges C, van Manen D, Herbeck JT, Fellay J, Sieberer M, Sietzema JG, van 't Slot R, Martinson J, Zagury JF, Schuitemaker H, van 't Wout AB. Genome-wide association study identifies single nucleotide polymorphism in DYRK1A associated with replication of HIV-1 in monocyte-derived macrophages. PLoS One 2011; 6:e17190. [PMID: 21364930 PMCID: PMC3045405 DOI: 10.1371/journal.pone.0017190] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Accepted: 01/21/2011] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND HIV-1 infected macrophages play an important role in rendering resting T cells permissive for infection, in spreading HIV-1 to T cells, and in the pathogenesis of AIDS dementia. During highly active anti-retroviral treatment (HAART), macrophages keep producing virus because tissue penetration of antiretrovirals is suboptimal and the efficacy of some is reduced. Thus, to cure HIV-1 infection with antiretrovirals we will also need to efficiently inhibit viral replication in macrophages. The majority of the current drugs block the action of viral enzymes, whereas there is an abundance of yet unidentified host factors that could be targeted. We here present results from a genome-wide association study identifying novel genetic polymorphisms that affect in vitro HIV-1 replication in macrophages. METHODOLOGY/PRINCIPAL FINDINGS Monocyte-derived macrophages from 393 blood donors were infected with HIV-1 and viral replication was determined using Gag p24 antigen levels. Genomic DNA from individuals with macrophages that had relatively low (n = 96) or high (n = 96) p24 production was used for SNP genotyping with the Illumina 610 Quad beadchip. A total of 494,656 SNPs that passed quality control were tested for association with HIV-1 replication in macrophages, using linear regression. We found a strong association between in vitro HIV-1 replication in monocyte-derived macrophages and SNP rs12483205 in DYRK1A (p = 2.16 × 10(-5)). While the association was not genome-wide significant (p<1 × 10(-7)), we could replicate this association using monocyte-derived macrophages from an independent group of 31 individuals (p = 0.0034). Combined analysis of the initial and replication cohort increased the strength of the association (p = 4.84 × 10(-6)). In addition, we found this SNP to be associated with HIV-1 disease progression in vivo in two independent cohort studies (p = 0.035 and p = 0.0048). CONCLUSIONS/SIGNIFICANCE These findings suggest that the kinase DYRK1A is involved in the replication of HIV-1, in vitro in macrophages as well as in vivo.
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Affiliation(s)
- Sebastiaan M. Bol
- Landsteiner Laboratory, Sanquin Research, Department of Experimental Immunology, and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Perry D. Moerland
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center of the University of Amsterdam, The Netherlands
- Netherlands Bioinformatics Center (NBIC), Nijmegen, The Netherlands
| | - Sophie Limou
- Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
- Université Paris 12, INSERM U955, Paris, France
| | - Yvonne van Remmerden
- Landsteiner Laboratory, Sanquin Research, Department of Experimental Immunology, and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Cédric Coulonges
- Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
- Université Paris 12, INSERM U955, Paris, France
| | - Daniëlle van Manen
- Landsteiner Laboratory, Sanquin Research, Department of Experimental Immunology, and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Joshua T. Herbeck
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Jacques Fellay
- Center for Human Genome Variation, Duke University, Durham, North Carolina, United States of America
| | - Margit Sieberer
- Landsteiner Laboratory, Sanquin Research, Department of Experimental Immunology, and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Jantine G. Sietzema
- Landsteiner Laboratory, Sanquin Research, Department of Experimental Immunology, and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Ruben van 't Slot
- Complex Genetics Section, Department of Biomedical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jeremy Martinson
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jean-François Zagury
- Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
- Université Paris 12, INSERM U955, Paris, France
| | - Hanneke Schuitemaker
- Landsteiner Laboratory, Sanquin Research, Department of Experimental Immunology, and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Angélique B. van 't Wout
- Landsteiner Laboratory, Sanquin Research, Department of Experimental Immunology, and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
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Abstract
Despite the availability of effective treatment for several decades, leprosy remains an important medical problem in many regions of the world. Infection with Mycobacterium leprae can produce paucibacillary disease, characterized by well-formed granulomas and a Th1 T-cell response, or multibacillary disease, characterized by poorly organized cellular infiltrates and Th2 cytokines. These diametric immune responses confer states of relative resistance or susceptibility to leprosy, respectively, and have well-defined clinical manifestations. As a result, leprosy provides a unique opportunity to dissect the genetic basis of human in vivo immunity. A series of studies over the past 40 years suggests that host genes influence the risk of leprosy acquisition and the predilection for different clinical forms of the disease. However, a comprehensive, cellular, and molecular view of the genes and variants involved is still being assembled. In this article, we review several decades of human genetic studies of leprosy, including a number of recent investigations. We emphasize genetic analyses that are validated by the replication of the same phenotype in independent studies or supported by functional experiments demonstrating biological mechanisms of action for specific polymorphisms. Identifying and functionally exploring the genetic and immunological factors that underlie human susceptibility to leprosy have yielded important insights into M. leprae pathogenesis and are likely to advance our understanding of the immune response to other pathogenic mycobacteria. This knowledge may inform new treatment or vaccine strategies for leprosy or tuberculosis.
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50
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Murcray CE, Lewinger JP, Conti DV, Thomas DC, Gauderman WJ. Sample size requirements to detect gene-environment interactions in genome-wide association studies. Genet Epidemiol 2011; 35:201-10. [PMID: 21308767 DOI: 10.1002/gepi.20569] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2010] [Revised: 01/05/2011] [Accepted: 01/10/2011] [Indexed: 11/07/2022]
Abstract
Many complex diseases are likely to be a result of the interplay of genes and environmental exposures. The standard analysis in a genome-wide association study (GWAS) scans for main effects and ignores the potentially useful information in the available exposure data. Two recently proposed methods that exploit environmental exposure information involve a two-step analysis aimed at prioritizing the large number of SNPs tested to highlight those most likely to be involved in a GE interaction. For example, Murcray et al. ([2009] Am J Epidemiol 169:219–226) proposed screening on a test that models the G-E association induced by an interaction in the combined case-control sample. Alternatively, Kooperberg and LeBlanc ([2008] Genet Epidemiol 32:255–263) suggested screening on genetic marginal effects. In both methods, SNPs that pass the respective screening step at a pre-specified significance threshold are followed up with a formal test of interaction in the second step. We propose a hybrid method that combines these two screening approaches by allocating a proportion of the overall genomewide significance level to each test. We show that the Murcray et al. approach is often the most efficient method, but that the hybrid approach is a powerful and robust method for nearly any underlying model. As an example, for a GWAS of 1 million markers including a single true disease SNP with minor allele frequency of 0.15, and a binary exposure with prevalence 0.3, the Murcray, Kooperberg and hybrid methods are 1.90, 1.27, and 1.87 times as efficient, respectively, as the traditional case-control analysis to detect an interaction effect size of 2.0.
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Affiliation(s)
- Cassandra E Murcray
- Department of Preventive Medicine, University of Southern California, Los Angeles, California 90089-9010, USA.
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