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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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Tavares LA, Januário YC, daSilva LLP. HIV-1 Hijacking of Host ATPases and GTPases That Control Protein Trafficking. Front Cell Dev Biol 2021; 9:622610. [PMID: 34307340 PMCID: PMC8295591 DOI: 10.3389/fcell.2021.622610] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 06/07/2021] [Indexed: 12/22/2022] Open
Abstract
The human immunodeficiency virus (HIV-1) modifies the host cell environment to ensure efficient and sustained viral replication. Key to these processes is the capacity of the virus to hijack ATPases, GTPases and the associated proteins that control intracellular protein trafficking. The functions of these energy-harnessing enzymes can be seized by HIV-1 to allow the intracellular transport of viral components within the host cell or to change the subcellular distribution of antiviral factors, leading to immune evasion. Here, we summarize how energy-related proteins deviate from their normal functions in host protein trafficking to aid the virus in different phases of its replicative cycle. Recent discoveries regarding the interplay among HIV-1 and host ATPases and GTPases may shed light on potential targets for pharmacological intervention.
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Affiliation(s)
- Lucas A Tavares
- Department of Cell and Molecular Biology, Center for Virology Research, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Yunan C Januário
- Department of Cell and Molecular Biology, Center for Virology Research, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Luis L P daSilva
- Department of Cell and Molecular Biology, Center for Virology Research, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
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Amanya SB, Nyiro B, Waswa F, Obura B, Nakaziba R, Nabulime E, Katabazi AF, Nabatanzi R, Bayiyana A, Mboowa G, Kayongo A, Wayengera M, Sande OJ. Variations in Trim5α and Cyclophilin A genes among HIV-1 elite controllers and non controllers in Uganda: a laboratory-based cross-sectional study. Retrovirology 2020; 17:19. [PMID: 32631377 PMCID: PMC7339491 DOI: 10.1186/s12977-020-00527-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 06/27/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tripartite Motif Containing 5 alpha (TRIM5α), a restriction factor produced ubiquitously in cells and tissues of the body plays an important role in the immune response against HIV. TRIM5α targets the HIV capsid for proteosomal destruction. Cyclophilin A, an intracellular protein has also been reported to influence HIV infectivity in a cell-specific manner. Accordingly, variations in TRIM5α and Cyclophilin A genes have been documented to influence HIV-1 disease progression. However, these variations have not been documented among Elite controllers in Uganda and whether they play a role in viral suppression remains largely undocumented. Our study focused on identifying the variations in TRIM5α and Cyclophilin A genes among HIV-1 Elite controllers and non-controllers in Uganda. RESULTS From the sequence analysis, the rs10838525 G > A mutation in exon 2 of TRIM5α was only found among elite controllers (30%) while the rs3824949 in the 5'UTR was seen among 25% of the non-controllers. In the Cyclophilin A promoter, rs6850 was seen among 62.5% of the non-controllers and only among 10% elite controllers. Furthermore, rs17860048 in the Cyclophillin A promoter was predominantly seen among elite controllers (30%) and 12.5% non-controllers. From gene expression analysis, we noted that the respective genes were generally elevated among elite controllers, however, this difference was not statistically significant (TRIM5α p = 0.6095; Cyclophilin A p = 0.6389). CONCLUSION Variations in TRIM5α and Cyclophillin A promoter may influence HIV viral suppression. The rs10838525 SNP in TRIM5α may contribute to viral suppression among HIV-1 elite controllers. The rs6850 in the cyclophillin A gene may be responsible for HIV-1 rapid progression among HIV-1 non-controllers. These SNPs should be investigated mechanistically to determine their precise role in HIV-1 viral suppression.
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Affiliation(s)
- Sharon Bright Amanya
- Faculty of Health Sciences, Lira University, Lira, Uganda ,grid.11194.3c0000 0004 0620 0548Department of Immunology and Molecular Biology, Makerere University College of Health Sciences, Kampala, Uganda
| | - Brian Nyiro
- grid.11194.3c0000 0004 0620 0548Department of Immunology and Molecular Biology, Makerere University College of Health Sciences, Kampala, Uganda
| | - Francis Waswa
- grid.11194.3c0000 0004 0620 0548Department of Immunology and Molecular Biology, Makerere University College of Health Sciences, Kampala, Uganda
| | | | | | - Eva Nabulime
- grid.436163.50000 0004 0648 1108Center for AIDS Research (CFAR) Lab, Joint Clinical Research Center, Kampala, Uganda
| | - Ashaba Fred Katabazi
- grid.11194.3c0000 0004 0620 0548Department of Immunology and Molecular Biology, Makerere University College of Health Sciences, Kampala, Uganda
| | - Rose Nabatanzi
- grid.11194.3c0000 0004 0620 0548Department of Immunology and Molecular Biology, Makerere University College of Health Sciences, Kampala, Uganda
| | - Alice Bayiyana
- grid.11194.3c0000 0004 0620 0548Department of Immunology and Molecular Biology, Makerere University College of Health Sciences, Kampala, Uganda
| | - Gerald Mboowa
- grid.11194.3c0000 0004 0620 0548Department of Immunology and Molecular Biology, Makerere University College of Health Sciences, Kampala, Uganda ,grid.11194.3c0000 0004 0620 0548The African Center of Excellence in Bioinformatics and Data Intensive Sciences, the Infectious Diseases Institute, McKinnell Knowledge Centre, Makerere University, Kampala, Uganda
| | - Alex Kayongo
- grid.11194.3c0000 0004 0620 0548Makerere University Lung Institute, Kampala, Uganda
| | - Misaki Wayengera
- grid.11194.3c0000 0004 0620 0548Department of Immunology and Molecular Biology, Makerere University College of Health Sciences, Kampala, Uganda
| | - Obondo J. Sande
- grid.11194.3c0000 0004 0620 0548Department of Immunology and Molecular Biology, Makerere University College of Health Sciences, Kampala, Uganda
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Badillo-Vargas IE, Chen Y, Martin KM, Rotenberg D, Whitfield AE. Discovery of Novel Thrips Vector Proteins That Bind to the Viral Attachment Protein of the Plant Bunyavirus Tomato Spotted Wilt Virus. J Virol 2019; 93:e00699-19. [PMID: 31413126 PMCID: PMC6803271 DOI: 10.1128/jvi.00699-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 08/02/2019] [Indexed: 01/05/2023] Open
Abstract
The plant-pathogenic virus tomato spotted wilt virus (TSWV) encodes a structural glycoprotein (GN) that, like with other bunyavirus/vector interactions, serves a role in viral attachment and possibly in entry into arthropod vector host cells. It is well documented that Frankliniella occidentalis is one of nine competent thrips vectors of TSWV transmission to plant hosts. However, the insect molecules that interact with viral proteins, such as GN, during infection and dissemination in thrips vector tissues are unknown. The goals of this project were to identify TSWV-interacting proteins (TIPs) that interact directly with TSWV GN and to localize the expression of these proteins in relation to virus in thrips tissues of principal importance along the route of dissemination. We report here the identification of six TIPs from first-instar larvae (L1), the most acquisition-efficient developmental stage of the thrips vector. Sequence analyses of these TIPs revealed homology to proteins associated with the infection cycle of other vector-borne viruses. Immunolocalization of the TIPs in L1 revealed robust expression in the midgut and salivary glands of F. occidentalis, the tissues most important during virus infection, replication, and plant inoculation. The TIPs and GN interactions were validated using protein-protein interaction assays. Two of the thrips proteins, endocuticle structural glycoprotein and cyclophilin, were found to be consistent interactors with GN These newly discovered thrips protein-GN interactions are important for a better understanding of the transmission mechanism of persistent propagative plant viruses by their vectors, as well as for developing new strategies of insect pest management and virus resistance in plants.IMPORTANCE Thrips-transmitted viruses cause devastating losses to numerous food crops worldwide. For negative-sense RNA viruses that infect plants, the arthropod serves as a host as well by supporting virus replication in specific tissues and organs of the vector. The goal of this work was to identify thrips proteins that bind directly to the viral attachment protein and thus may play a role in the infection cycle in the insect. Using the model plant bunyavirus tomato spotted wilt virus (TSWV), and the most efficient thrips vector, we identified and validated six TSWV-interacting proteins from Frankliniella occidentalis first-instar larvae. Two proteins, an endocuticle structural glycoprotein and cyclophilin, were able to interact directly with the TSWV attachment protein, GN, in insect cells. The TSWV GN-interacting proteins provide new targets for disrupting the viral disease cycle in the arthropod vector and could be putative determinants of vector competence.
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Affiliation(s)
| | - Yuting Chen
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, USA
| | - Kathleen M Martin
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, USA
| | - Dorith Rotenberg
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, USA
| | - Anna E Whitfield
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, USA
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Madlala P, Singh R, An P, Werner L, Mlisana K, Abdool Karim SS, Winkler CA, Ndung’u T. Association of Polymorphisms in the Regulatory Region of the Cyclophilin a Gene (PPIA) with Gene Expression and HIV/AIDS Disease Progression. J Acquir Immune Defic Syndr 2016; 72:465-73. [PMID: 27088296 PMCID: PMC4942341 DOI: 10.1097/qai.0000000000001028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Human cyclophilin A (CypA) encoded by peptidyl prolyl isomerase A gene (PPIA), enhances HIV-1 replication by aiding capsid uncoating. The association of genetic variation in the PPIA regulatory region with susceptibility to HIV-1 infection, disease progression, and gene expression among black South Africans at risk for infection or infected with HIV-1 is unknown. METHODS We genotyped 539 participants from 2 longitudinal study cohorts of black South Africans at high risk for infection or infected with HIV-1 for PPIA regulatory single nucleotide polymorphisms by polymerase chain reaction-restriction fragment length polymorphism. RESULTS Minor allele (G) of SNP rs6850 (rs6850 G) significantly associated with higher viral loads (mean 4.85 versus 4.46 log copies/mL, P = 0.0006) and lower CD4 T-cell counts (mean 506 versus 557 cells/μL, P = 0.0256) during the acute phase of infection in the Centre for the AIDS Programme of Research in South Africa (CAPRISA) 002 cohort. Consistently, rs6850 G significantly associated with higher viral loads (mean 4.49 versus 4.01 log copies/mL, P < 0.0001) and lower CD4 T-cell counts (mean 442 versus 494 cells/μL, P = 0.0002) during the early chronic phase of infection in the CAPRISA 002 cohort; rs6850 G further associated significantly with rapid CD4 T-cell decline in the CAPRISA 002 cohort (P = 0.0481) and Sinikithemba chronic infection cohort (P = 0.0156). Interestingly, rs6850 G significantly associated with elevated CypA mRNA levels in HIV-1-positive individuals (P = 0.0061). CONCLUSIONS These data suggest that rs6850 G enhances HIV-1 replication through upregulation of CypA expression following HIV-1 infection. The data support ongoing efforts to develop anti-HIV-1 drugs that block interaction of HIV-1 and cellular proteins.
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Affiliation(s)
- Paradise Madlala
- HIV Pathogenesis Programme, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Ravesh Singh
- HIV Pathogenesis Programme, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Ping An
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, United States of America
| | - Lise Werner
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Koleka Mlisana
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Salim S. Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Cheryl A. Winkler
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, United States of America
| | - Thumbi Ndung’u
- HIV Pathogenesis Programme, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- KwaZulu-Natal Research Institute for Tuberculosis and HIV, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
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Herrero R, Pineda JA, Rivero-Juarez A, Echbarthi M, Real LM, Camacho A, Macias J, Fibla J, Rivero A, Caruz A. Common haplotypes in CD209 promoter and susceptibility to HIV-1 infection in intravenous drug users. INFECTION GENETICS AND EVOLUTION 2016; 45:20-25. [PMID: 27539513 DOI: 10.1016/j.meegid.2016.08.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 08/10/2016] [Accepted: 08/14/2016] [Indexed: 12/30/2022]
Abstract
INTRODUCTION CD209 is a receptor expressed in the dendritic cells involved in recognition of oligosaccharides present in several pathogens with a relevant impact on human health. SNPs located in the promoter region have been associated with HIV-1 susceptibility, although this finding has not been replicated in other populations. The objective of this study is to evaluate the association of CD209 promoter haplotypes with risk of HIV-1 infection in a cohort of Spanish male intravenous drug users (IDU) infected with hepatitis C virus (HCV) and to characterize the phenotypic effects of the associated variants. METHODS We genotyped 4 SNPs of CD209 promoter in 295 HCV males exposed to HIV-1 infection by IDU, 165 HIV-1-infected and 130 exposed uninfected (EUI) and 142 healthy controls (HC). We have cloned the promoter variants in a reporter vector and evaluated the promoter activities in a cell culture model. CD209 mRNAs were measured in PBMC. RESULTS Single-marker analysis revealed no significant allelic association with the risk of HIV-1 infection by parenteral route. Nevertheless, one haplotype was significantly overrepresented in EUI compared with HIV-1 positive patients and was associated with HIV-1 status (P=0.0008; OR: 0.43). Functional experiments suggested that the protective haplotype displayed lower transcriptional activity in vitro (P<0.05) and this was correlated with lower CD209 mRNA expression in PBMC (P=0.014). CONCLUSIONS This study suggests that the promoter haplotypes of CD209 influence the risk of HIV-1 acquisition in IDU and that this association is correlated with the mRNA expression level.
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Affiliation(s)
- Rocio Herrero
- Immunogenetics Unit, Department of Experimental Biology, University of Jaen, 23071 Jaén, Spain.
| | - Juan A Pineda
- Infectious Diseases and Microbiology Clinical Unit, Valme Hospital, 41014 Seville, Spain.
| | - Antonio Rivero-Juarez
- Maimonides Institute for Research in Biomedicine of Cordoba (IMIBIC)/Reina Sofia University Hospital, 14004 Cordoba, Spain.
| | - Meriem Echbarthi
- Immunogenetics Unit, Department of Experimental Biology, University of Jaen, 23071 Jaén, Spain.
| | - Luis-Miguel Real
- Infectious Diseases and Microbiology Clinical Unit, Valme Hospital, 41014 Seville, Spain.
| | - Angela Camacho
- Maimonides Institute for Research in Biomedicine of Cordoba (IMIBIC)/Reina Sofia University Hospital, 14004 Cordoba, Spain.
| | - Juan Macias
- Infectious Diseases and Microbiology Clinical Unit, Valme Hospital, 41014 Seville, Spain.
| | - Joan Fibla
- Human Genetics Unit, Department of Basic Medical Sciences, University of Lleida IRBLleida, 25003, Lleida, Catalonia, Spain.
| | - Antonio Rivero
- Maimonides Institute for Research in Biomedicine of Cordoba (IMIBIC)/Reina Sofia University Hospital, 14004 Cordoba, Spain.
| | - Antonio Caruz
- Immunogenetics Unit, Department of Experimental Biology, University of Jaen, 23071 Jaén, Spain.
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Pouché L, Stojanova J, Marquet P, Picard N. New challenges and promises in solid organ transplantation pharmacogenetics: the genetic variability of proteins involved in the pharmacodynamics of immunosuppressive drugs. Pharmacogenomics 2016; 17:277-96. [PMID: 26799749 DOI: 10.2217/pgs.15.169] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Interindividual variability in immunosuppressive drug responses might be partly explained by genetic variants in proteins involved in the immune response or associated with IS pharmacodynamics. On a general basis, the pharmacogenetics of drug target proteins is less known and understood than that of proteins involved in drug disposition pathways. The aim of this review is to facilitate research related to the pharmacodynamics of the main immunosuppressive drugs used in solid organ transplantation. We elaborated a quality of evidence grading system based on a literature review and identified 'highly recommended', 'recommended' or 'potential' candidates for further research. It is likely that a number of additional rare variants might further explain drug response phenotypes in transplantation, and particularly the most severe ones. The advent of next-generation sequencing will help to identify those variants.
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Affiliation(s)
- Lucie Pouché
- Inserm, UMR 850, 2 Avenue Martin-Luther King, F-87042 Limoges, France.,CHU Limoges, Department of Pharmacology, Toxicology & Pharmacovigilance, 2 Avenue Martin-Luther King, F-87042 Limoges, France
| | - Jana Stojanova
- Laboratory of Chemical Carcinogenesis & Pharmacogenetics, University of Chile, Santiago, Chile
| | - Pierre Marquet
- Inserm, UMR 850, 2 Avenue Martin-Luther King, F-87042 Limoges, France.,CHU Limoges, Department of Pharmacology, Toxicology & Pharmacovigilance, 2 Avenue Martin-Luther King, F-87042 Limoges, France.,Univ. Limoges, Faculty of Medicine & Pharmacy, 2 rue du Dr Marcland, F-87025 Limoges, France.,FHU SUPORT, 87000 Limoges, France
| | - Nicolas Picard
- Inserm, UMR 850, 2 Avenue Martin-Luther King, F-87042 Limoges, France.,CHU Limoges, Department of Pharmacology, Toxicology & Pharmacovigilance, 2 Avenue Martin-Luther King, F-87042 Limoges, France.,Univ. Limoges, Faculty of Medicine & Pharmacy, 2 rue du Dr Marcland, F-87025 Limoges, France.,FHU SUPORT, 87000 Limoges, France
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Zhang W, Zhang ZZ, Tang LY, Lin Y, Su FX, Xie XM, Su XF, Ren ZF. Genetic variants in EBV reactivation-related genes and the risk and survival of breast cancer. Tumour Biol 2016; 37:8337-47. [PMID: 26729199 DOI: 10.1007/s13277-015-4562-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 12/01/2015] [Indexed: 12/27/2022] Open
Abstract
Tumor susceptibility gene 101 (TSG101) and activating transcription factor 2 (ATF2) have been suggested to involve in the reactivation of EBV which has implications in the development and progression of breast cancer. Therefore, the polymorphisms of TSG101 and ATF2 may associate with breast cancer risk and prognosis. A case-control study with 1551 breast cancer cases and 1605 age-matched controls were conducted in Guangzhou, China. We have also successfully followed up 1168 cases until December 31, 2014. The variant allele of TSG101 rs2292179 was associated with a non-significant reduced risk of breast cancer, particularly among women with BMI < 24 (kg/m(2)) (P for interaction <0.05). For ATF2 rs3845744, the variant allele was also associated with a significantly reduced breast cancer risk [odds ratio (OR) (95 % confidence interval (CI)) 0.86 (0.74∼1.00)], and the association occurred among only postmenopausal women [OR (95 % CI) 0.69 (0.54∼0.88)] (P for interaction <0.05). Breast cancer risk was further reduced with the increasing numbers of the variant G alleles of the two polymorphisms (P for trend <0.05). We did not find an overall association of the two loci with breast cancer prognosis, while the hazard ratios of the two loci (AG/GG vs. AA) were significantly higher among postmenopausal women than premenopausal women (P = 0.046, 0.016 for TSG101 rs2292179 and ATF2 rs3845744, respectively). In summary, the variant alleles of TSG101 rs2292179 and ATF2 rs3845744 were associated with a reduced risk of breast cancer, particularly for subjects with BMI <24 (kg/m(2)) and postmenopausal women, respectively. The two SNPs and menopausal status may have a significant interaction on breast cancer progression.
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Affiliation(s)
- Wei Zhang
- The School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China
| | - Zheng-Zheng Zhang
- The School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China
- Aviation Hygiene Management Division, China Southern Airlines Company Limited, 9/F, Kangda Building, 278 Airport Road, Guangzhou, China
| | - Lu-Ying Tang
- The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
| | - Ying Lin
- The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Feng-Xi Su
- The Second Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Xiao-Ming Xie
- The Sun Yat-Sen University Cancer Center, Guangzhou, 510080, China
| | - Xue-Fen Su
- School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.
| | - Ze-Fang Ren
- The School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China.
- Department of Statistics and Epidemiology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-sen University, 74 Zhongshan 2nd Rd, Guangzhou, 510080, China.
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PPIA rs6850: A > G single-nucleotide polymorphism is associated with raised plasma cyclophilin A levels in patients with coronary artery disease. Mol Cell Biochem 2015; 412:259-68. [DOI: 10.1007/s11010-015-2632-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 12/15/2015] [Indexed: 12/20/2022]
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10
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Verstrepen L, Carpentier I, Beyaert R. The biology of A20-binding inhibitors of NF-kappaB activation (ABINs). ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 809:13-31. [PMID: 25302363 DOI: 10.1007/978-1-4939-0398-6_2] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The family of A20-Binding Inhibitors of NF-kappaB (ABINs) consists of three proteins, ABIN-1, ABIN-2 and ABIN-3, which were originally identified as A20-binding proteins and inhibitors of cytokines and Lipopolysaccharide (LPS) induced NF-kappaB activation. ABIN family members have limited sequence homology in a number of short regions that mediate A20-binding, ubiquitin-binding, and NF-kappaB inhibition. The functional role of A20 binding to ABINs remains unclear, although an adaptor function has been suggested. ABIN-1 and ABIN-3 expression is upregulated when cells are triggered by NF-kappaB-activating stimuli, suggesting a role for these ABINs in a negative feedback regulation of NF-kappaB signaling. Additional ABIN functions have been reported such as inhibition of TNF-induced hepatocyte apoptosis, regulation of HIV-1 replication for ABIN-1, and Tumor Progression Locus 2 (TPL-2)-mediated Extracellular signal-Regulated Kinase (ERK) activation for ABIN-2. In mice, ABIN-1 overexpression reduces allergic airway inflammation and TNF-mediated liver injury, ABIN-2 overexpression delays liver regeneration, and ABIN-3 overexpression partially protects against LPS-induced acute liver failure. Analysis of mice deficient in ABIN-1 or ABIN-2 demonstrates the important immune regulatory function of ABINs. Future studies should clarify the functional implication of the A20-ABIN interaction in supporting ABINs' mechanisms of action.
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How HIV-1 Gag assembles in cells: Putting together pieces of the puzzle. Virus Res 2014; 193:89-107. [PMID: 25066606 DOI: 10.1016/j.virusres.2014.07.001] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 07/02/2014] [Accepted: 07/02/2014] [Indexed: 11/21/2022]
Abstract
During the late stage of the viral life cycle, HIV-1 Gag assembles into a spherical immature capsid, and undergoes budding, release, and maturation. Here we review events involved in immature capsid assembly from the perspective of five different approaches used to study this process: mutational analysis, structural studies, assembly of purified recombinant Gag, assembly of newly translated Gag in a cell-free system, and studies in cells using biochemical and imaging techniques. We summarize key findings obtained using each approach, point out where there is consensus, and highlight unanswered questions. Particular emphasis is placed on reconciling data suggesting that Gag assembles by two different paths, depending on the assembly environment. Specifically, in assembly systems that lack cellular proteins, high concentrations of Gag can spontaneously assemble using purified nucleic acid as a scaffold. However, in the more complex intracellular environment, barriers that limit self-assembly are present in the form of cellular proteins, organelles, host defenses, and the absence of free nucleic acid. To overcome these barriers and promote efficient immature capsid formation in an unfavorable environment, Gag appears to utilize an energy-dependent, host-catalyzed, pathway of assembly intermediates in cells. Overall, we show how data obtained using a variety of techniques has led to our current understanding of HIV assembly.
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Shah VB, Aiken C. Gene expression analysis of a panel of cell lines that differentially restrict HIV-1 CA mutants infection in a cyclophilin a-dependent manner. PLoS One 2014; 9:e92724. [PMID: 24663101 PMCID: PMC3963944 DOI: 10.1371/journal.pone.0092724] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 02/25/2014] [Indexed: 12/31/2022] Open
Abstract
HIV-1 replication is dependent on binding of the viral capsid to the host protein cyclophilin A (CypA). Interference with cyclophilin A binding, either by mutations in the HIV-1 capsid protein (CA) or by the drug cyclosporine A (CsA), inhibits HIV-1 replication in cell culture. Resistance to CsA is conferred by A92E or G94D substitutions in CA. The mutant viruses are also dependent on CsA for their replication. Interestingly, infection of some cell lines by these mutants is enhanced by CsA, while infection of others is not affected by the drug. The cells are thus termed nonpermissive and permissive, respectively, for infection by CsA-dependent mutants. The mechanistic basis for the cell type dependence is not well understood, but has been hypothesized to result from a dominant-acting host factor that blocks HIV-1 infection by a mechanism that requires CypA binding to the viral capsid. In an effort to identify a CypA-dependent host restriction factor, we adopted a strategy involving comparative gene expression analysis in three permissive and three non-permissive cell types. We ranked the genes based on their relative overexpression in non-permissive cell types compared to the permissive cell types. Based on specific selection criteria, 26 candidate genes were selected and targeted using siRNA in nonpermissive (HeLa) cells. Depletion of none of the selected candidate genes led to the reversal of CsA-dependent phenotype of the A92E mutant. Our data suggest that none of the 26 genes tested is responsible for the dependence of the A92E mutant on CsA. Our study provides gene expression data that may be useful for future efforts to identify the putative CypA-dependent HIV-1 restriction factor and in studies of other cell-specific phenotypes.
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Affiliation(s)
- Vaibhav B. Shah
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Christopher Aiken
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- * E-mail:
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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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14
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Cyclophilins as modulators of viral replication. Viruses 2013; 5:1684-701. [PMID: 23852270 PMCID: PMC3738956 DOI: 10.3390/v5071684] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 06/26/2013] [Accepted: 07/03/2013] [Indexed: 01/11/2023] Open
Abstract
Cyclophilins are peptidyl‐prolyl cis/trans isomerases important in the proper folding of certain proteins. Mounting evidence supports varied roles of cyclophilins, either positive or negative, in the life cycles of diverse viruses, but the nature and mechanisms of these roles are yet to be defined. The potential for cyclophilins to serve as a drug target for antiviral therapy is evidenced by the success of non-immunosuppressive cyclophilin inhibitors (CPIs), including Alisporivir, in clinical trials targeting hepatitis C virus infection. In addition, as cyclophilins are implicated in the predisposition to, or severity of, various diseases, the ability to specifically and effectively modulate their function will prove increasingly useful for disease intervention. In this review, we will summarize the evidence of cyclophilins as key mediators of viral infection and prospective drug targets.
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15
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Telenti A. Host polymorphism in steps of the HIV-1 lifecycle after entry and other genetic variants influencing HIV-1 pathogenesis. Curr Opin HIV AIDS 2012; 1:232-40. [PMID: 19372815 DOI: 10.1097/01.coh.0000221598.79906.12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW Dominant host factors modifying the susceptibility to HIV-1 include diversity in the major histocompatibility complex class I, and alleles of chemokine and chemokine receptor genes. Additional host factors, particularly those determining cell permissiveness to viral replication, are expected to play a significant role in HIV-1 pathogenesis. RECENT FINDINGS A growing number of publications (n = 32) propose new variants (n = 27) modifying HIV-1 susceptibility in genes (n = 17) needed for the viral lifecycle, in antiviral innate defense, and in a number of soluble and membrane proteins. SUMMARY Although there are multiple publications describing putative associations of host genetic variants and susceptibility to HIV-1, most reports are yet to be confirmed by subsequent publications, or have led to conflicting data among laboratories.
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Affiliation(s)
- Amalio Telenti
- Institute of Microbiology and University Hospital, University of Lausanne, Lausanne, Switzerland
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16
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17
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Tang YW, Ou CY. Past, present and future molecular diagnosis and characterization of human immunodeficiency virus infections. Emerg Microbes Infect 2012; 1:e19. [PMID: 26038427 PMCID: PMC3630918 DOI: 10.1038/emi.2012.15] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 05/08/2012] [Accepted: 05/21/2012] [Indexed: 12/31/2022]
Abstract
Substantive and significant advances have been made in the last two decades in the characterization of human immunodeficiency virus (HIV) infections using molecular techniques. These advances include the use of real-time measurements, isothermal amplification, the inclusion of internal quality assurance protocols, device miniaturization and the automation of specimen processing. The result has been a significant increase in the availability of results to a high level of accuracy and quality. Molecular assays are currently widely used for diagnostics, antiretroviral monitoring and drug resistance characterization in developed countries. Simple and cost-effective point-of-care versions are also being vigorously developed with the eventual goal of providing timely healthcare services to patients residing in remote areas and those in resource-constrained countries. In this review, we discuss the evolution of these molecular technologies, not only in the context of the virus, but also in the context of tests focused on human genomics and transcriptomics.
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Affiliation(s)
- Yi-Wei Tang
- Memorial Sloan-Kettering Cancer Center , New York, NY 10065, USA
| | - Chin-Yih Ou
- Centers for Disease Control and Prevention , Atlanta, GA 30333, USA
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18
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Raghavan S, Alagarasu K, Selvaraj P. Immunogenetics of HIV and HIV associated tuberculosis. Tuberculosis (Edinb) 2012; 92:18-30. [PMID: 21943869 DOI: 10.1016/j.tube.2011.08.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Accepted: 08/08/2011] [Indexed: 11/28/2022]
Affiliation(s)
- S Raghavan
- Department of Immunology, Tuberculosis Research Centre (ICMR), Mayor V.R. Ramanathan Road, Chetput, Chennai 600031, India
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19
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Gijsbers EF, Schuitemaker H, Kootstra NA. HIV-1 transmission and viral adaptation to the host. Future Virol 2012. [DOI: 10.2217/fvl.11.134] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
HIV-1 transmission predominantly occurs via mucosal transmission and blood–blood contact. In most newly infected individuals, outgrowth of a single virus variant has been described. This indicates that HIV-1 transmission is a very inefficient process and is restricted by an extensive transmission bottleneck. The transmission rate is directly correlated to the viral load in the donor and the susceptibility of the recipient, which is influenced by factors such as the integrity of mucosal barriers, target cell availability and genetic host factors. After establishment of infection in the new host, the viral population remains very homogenous until the host immune response drives evolution of the viral quasispecies. This review describes our current knowledge on HIV-1 transmission and recent insights in viral adaption to its host.
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Affiliation(s)
- Esther F Gijsbers
- Department of Experimental Immunology, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Hanneke Schuitemaker
- Department of Experimental Immunology, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
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20
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Host Genomic Profiling in Human Immunodeficiency Virus Infection. Mol Microbiol 2011. [DOI: 10.1128/9781555816834.ch53] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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21
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Bergamaschi A, Pancino G. Host hindrance to HIV-1 replication in monocytes and macrophages. Retrovirology 2010; 7:31. [PMID: 20374633 PMCID: PMC2868797 DOI: 10.1186/1742-4690-7-31] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2009] [Accepted: 04/07/2010] [Indexed: 11/29/2022] Open
Abstract
Monocytes and macrophages are targets of HIV-1 infection and play critical roles in multiple aspects of viral pathogenesis. HIV-1 can replicate in blood monocytes, although only a minor proportion of circulating monocytes harbor viral DNA. Resident macrophages in tissues can be infected and function as viral reservoirs. However, their susceptibility to infection, and their capacity to actively replicate the virus, varies greatly depending on the tissue localization and cytokine environment. The susceptibility of monocytes to HIV-1 infection in vitro depends on their differentiation status. Monocytes are refractory to infection and become permissive upon differentiation into macrophages. In addition, the capacity of monocyte-derived macrophages to sustain viral replication varies between individuals. Host determinants regulate HIV-1 replication in monocytes and macrophages, limiting several steps of the viral life-cycle, from viral entry to virus release. Some host factors responsible for HIV-1 restriction are shared with T lymphocytes, but several anti-viral mechanisms are specific to either monocytes or macrophages. Whilst a number of these mechanisms have been identified in monocytes or in monocyte-derived macrophages in vitro, some of them have also been implicated in the regulation of HIV-1 infection in vivo, in particular in the brain and the lung where macrophages are the main cell type infected by HIV-1. This review focuses on cellular factors that have been reported to interfere with HIV-1 infection in monocytes and macrophages, and examines the evidences supporting their role in vivo, highlighting unique aspects of HIV-1 restriction in these two cell types.
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Affiliation(s)
- Anna Bergamaschi
- Institut Pasteur, Unité de Régulation des Infections Rétrovirales, Paris, France.
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22
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Chatterjee K. Host genetic factors in susceptibility to HIV-1 infection and progression to AIDS. J Genet 2010; 89:109-16. [DOI: 10.1007/s12041-010-0003-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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23
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An P, Winkler CA. Host genes associated with HIV/AIDS: advances in gene discovery. Trends Genet 2010; 26:119-31. [PMID: 20149939 PMCID: PMC3792714 DOI: 10.1016/j.tig.2010.01.002] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Revised: 12/31/2009] [Accepted: 01/03/2010] [Indexed: 02/06/2023]
Abstract
Twenty-five years after the discovery of HIV as the cause of AIDS there is still no effective vaccine and no cure for this disease. HIV susceptibility shows a substantial degree of individual heterogeneity, much of which can be conferred by host genetic variation. In an effort to discover host factors required for HIV replication, identify crucial pathogenic pathways, and reveal the full armament of host defenses, there has been a shift from candidate-gene studies to unbiased genome-wide genetic and functional studies. However, the number of securely identified host factors involved in HIV disease remains small, explaining only approximately 15-20% of the observed heterogeneity - most of which is attributable to human lymphocyte antigen (HLA) variants. Multidisciplinary approaches integrating genetic epidemiology to systems biology will be required to fully understand virus-host interactions to effectively combat HIV/AIDS.
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Affiliation(s)
| | - Cheryl A. Winkler
- Laboratory of Genomic Diversity, SAIC-Frederick, Inc., National Cancer Institute- Frederick, Frederick, MD
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24
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Abstract
HIV host genetic studies seek to describe as comprehensively as possible the effect of human genetic variation on the individual response to HIV type-1 (HIV-1) infection. Many associations between specific gene variants and HIV-1 disease outcomes have been reported over the past 15 years. Although most of them have yet to be confirmed or have been proven false-positives, the identification of several definitive genotype-phenotype associations has shed new light on HIV-1 pathogenesis. This review discusses these results in the context of the new genome-wide approaches that now make it possible to globally assess the influence of the host genome on HIV-1-related outcomes.
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Affiliation(s)
- Jacques Fellay
- Center for Human Genome Variation, Institute for Genome Sciences & Policy, Duke University, Durham, NC, USA.
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25
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Crawford DC, Zheng N, Speelmon EC, Stanaway I, Rieder MJ, Nickerson DA, McElrath MJ, Lingappa J. An excess of rare genetic variation in ABCE1 among Yorubans and African-American individuals with HIV-1. Genes Immun 2009; 10:715-21. [PMID: 19657357 DOI: 10.1038/gene.2009.57] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Signatures of natural selection occur throughout the human genome and can be detected at the sequence level. We have re-sequenced ABCE1, a host candidate gene essential for HIV-1 capsid assembly, in European- (n=23) and African-descent (Yoruban; n=24) reference populations for genetic variation discovery. We identified an excess of rare genetic variation in Yoruban samples, and the resulting Tajima's D was low (-2.27). The trend of excess rare variation persisted in flanking candidate genes ANAPC10 and OTUD4, suggesting that this pattern of positive selection can be detected across the 184.5 kb examined on chromosome 4. Owing to ABCE1's role in HIV-1 replication, we re-sequenced the candidate gene in three small cohorts of HIV-1-infected or resistant individuals. We were able to confirm the excess of rare genetic variation among HIV-1-positive African-American individuals (n=53; Tajima's D=-2.34). These results highlight the potential importance of ABCE1's role in infectious diseases such as HIV-1.
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Affiliation(s)
- D C Crawford
- Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University, Nashville, TN, USA
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26
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Bol SM, van Remmerden Y, Sietzema JG, Kootstra NA, Schuitemaker H, van't Wout AB. Donor variation in in vitro HIV-1 susceptibility of monocyte-derived macrophages. Virology 2009; 390:205-11. [PMID: 19535121 DOI: 10.1016/j.virol.2009.05.027] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2009] [Revised: 03/15/2009] [Accepted: 05/24/2009] [Indexed: 11/17/2022]
Abstract
Primary human cells from different donors vary in their susceptibility to in vitro infection with HIV-1. In order to perform genetic analysis to identify host factors that affect HIV-1 susceptibility, it is important that a clear phenotype is defined. Here, we report a standardized method to study variation for in vitro HIV-1 infection in monocyte-derived macrophages (MDM) from large numbers of individuals. With this assay, HIV-1 susceptibility of MDM from 489 different donors shows more than 3 log variation and a good correlation with the 32 base pair deletion in the CCR5 co-receptor (ccr5 Delta 32 genotype) of the donors. However, in 7 of 12 donors completely resistant to infection with CCR5-using HIV-1, this was not explained by the ccr5 Delta 32 genotype, showing evidence that other host factors are likely to influence HIV-1 replication in MDM. Infections with VSV-G pseudotyped HIV-1 indeed confirmed the existence of post-entry level restrictions in MDM.
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Affiliation(s)
- Sebastiaan M Bol
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infectious Diseases and Immunity Amsterdam (CINIMA), Academic Medical Center of The University of Amsterdam, Amsterdam, The Netherlands
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27
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Verstrepen L, Carpentier I, Verhelst K, Beyaert R. ABINs: A20 binding inhibitors of NF-kappa B and apoptosis signaling. Biochem Pharmacol 2009; 78:105-14. [PMID: 19464428 DOI: 10.1016/j.bcp.2009.02.009] [Citation(s) in RCA: 142] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2008] [Revised: 02/12/2009] [Accepted: 02/16/2009] [Indexed: 01/09/2023]
Abstract
ABINs have been described as three different proteins (ABIN-1, ABIN-2, ABIN-3) that bind the ubiquitin-editing nuclear factor-kappaB (NF-kappaB) inhibitor protein A20 and which show limited sequence homology. Overexpression of ABINs inhibits NF-kappaB activation by tumor necrosis factor (TNF) and several other stimuli. Similar to A20, ABIN-1 and ABIN-3 expression is NF-kappaB dependent, implicating a potential role for the A20/ABIN complex in the negative feedback regulation of NF-kappaB activation. Adenoviral gene transfer of ABIN-1 has been shown to reduce NF-kappaB activation in mouse liver and lungs. However, ABIN-1 as well as ABIN-2 deficient mice exhibit only slightly increased or normal NF-kappaB activation, respectively, possibly reflecting redundant NF-kappaB inhibitory activities of multiple ABINs. Other functions of ABINs might be non-redundant. For example, ABIN-1 shares with A20 the ability to inhibit TNF-induced apoptosis and as a result ABIN-1 deficient mice die during embryogenesis due to TNF-dependent fetal liver apoptosis. On the other hand, ABIN-2 is required for optimal TPL-2 dependent extracellularly regulated kinase activation in macrophages treated with TNF or Toll-like receptor ligands. ABINs have recently been shown to contain an ubiquitin-binding domain that is essential for their NF-kappaB inhibitory and anti-apoptotic activities. In this context, ABINs were proposed to function as adaptors between ubiquitinated proteins and other regulatory proteins. Alternatively, ABINs might disrupt signaling complexes by competing with other ubiquitin-binding proteins for the binding to specific ubiquitinated targets. Altogether, these findings implicate an important role for ABINs in the regulation of immunity and tissue homeostasis.
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Affiliation(s)
- Lynn Verstrepen
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, B-9052 Zwijnaarde, Belgium
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28
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Rits MAN, van Dort KA, Kootstra NA. Polymorphisms in the regulatory region of the Cyclophilin A gene influence the susceptibility for HIV-1 infection. PLoS One 2008; 3:e3975. [PMID: 19092998 PMCID: PMC2599883 DOI: 10.1371/journal.pone.0003975] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2008] [Accepted: 11/18/2008] [Indexed: 11/18/2022] Open
Abstract
Background Previous studies have demonstrated an association between polymorphisms in the regulatory regions of Cyclophilin A (CypA) and susceptibility to both HIV-1 infection and disease progression. Here we studied whether these polymorphisms are associated with susceptibility to HIV-1 infection and disease progression in the Amsterdam Cohort on HIV-1 infection and AIDS (ACS) in a group of men having sex with men (MSM) and drug users (DU). Methodology/Principal Findings We screened participants of the ACS for the C1604G and A1650G polymorphisms in the regulatory regions of CypA. The prevalence of the 1650G allele was significantly higher in high risk seronegative MSM than in HIV-1 infected MSM. However, C1604G or A1650G were not associated with the clinical course of infection in MSM of the ACS. Interestingly, participants of the ACS-DU who carried the 1604G allele showed a significantly accelerated progression when viral RNA load above 104.5 copies per ml plasma was used as an endpoint in survival analysis. Conclusion/Significance The results obtained in this study suggest that the A1650G polymorphism in the regulatory region of the CypA gene may be associated with protection from HIV-1 infection, while the 1604G allele may have a weak association with the clinical course of infection in DU.
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Affiliation(s)
- Maarten A. N. Rits
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Karel A. van Dort
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Neeltje A. Kootstra
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
- * E-mail:
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29
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The tumor suppressor protein PML controls apoptosis induced by the HIV-1 envelope. Cell Death Differ 2008; 16:298-311. [DOI: 10.1038/cdd.2008.158] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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30
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Affiliation(s)
- Xiaonan Yang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai and National Engineering Center for BioChip at Shanghai, Shanghai 201203, China;
- Laboratory of Microbial Molecular Physiology, Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Hongliang Yang
- Laboratory of Microbial Molecular Physiology, Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- Department of Microbiology and Parasitology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Gangqiao Zhou
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Guo-Ping Zhao
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai and National Engineering Center for BioChip at Shanghai, Shanghai 201203, China;
- Laboratory of Microbial Molecular Physiology, Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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31
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Palacín M, Rodríguez I, García-Castro M, Ortega F, Reguero JR, López-Larrea C, Morís C, Alvarez V, Coto E. A search for cyclophilin-A gene (PPIA) variation and its contribution to the risk of atherosclerosis and myocardial infarction. Int J Immunogenet 2008; 35:159-64. [DOI: 10.1111/j.1744-313x.2008.00755.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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32
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Loeuillet C, Deutsch S, Ciuffi A, Robyr D, Taffé P, Muñoz M, Beckmann JS, Antonarakis SE, Telenti A. In vitro whole-genome analysis identifies a susceptibility locus for HIV-1. PLoS Biol 2008; 6:e32. [PMID: 18288889 PMCID: PMC2245987 DOI: 10.1371/journal.pbio.0060032] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2007] [Accepted: 01/03/2008] [Indexed: 12/13/2022] Open
Abstract
Advances in large-scale analysis of human genomic variability provide unprecedented opportunities to study the genetic basis of susceptibility to infectious agents. We report here the use of an in vitro system for the identification of a locus on HSA8q24.3 associated with cellular susceptibility to HIV-1. This locus was mapped through quantitative linkage analysis using cell lines from multigeneration families, validated in vitro, and followed up by two independent association studies in HIV-positive individuals. Single nucleotide polymorphism rs2572886, which is associated with cellular susceptibility to HIV-1 in lymphoblastoid B cells and in primary T cells, was also associated with accelerated disease progression in one of two cohorts of HIV-1-infected patients. Biological analysis suggests a role of the rs2572886 region in the regulation of the LY6 family of glycosyl-phosphatidyl-inositol (GPI)-anchored proteins. Genetic analysis of in vitro cellular phenotypes provides an attractive approach for the discovery of susceptibility loci to infectious agents.
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Affiliation(s)
- Corinne Loeuillet
- Institute of Microbiology, University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Samuel Deutsch
- Department of Genetic Medicine and Development, University of Geneva Medical School and University Hospital of Geneva, Geneva, Switzerland
| | - Angela Ciuffi
- Institute of Microbiology, University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Daniel Robyr
- Department of Genetic Medicine and Development, University of Geneva Medical School and University Hospital of Geneva, Geneva, Switzerland
| | | | - Miguel Muñoz
- Institute of Microbiology, University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Jacques S Beckmann
- Department of Medical Genetics, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School and University Hospital of Geneva, Geneva, Switzerland
| | - Amalio Telenti
- Institute of Microbiology, University Hospital, University of Lausanne, Lausanne, Switzerland
- Swiss HIV Cohort Study, Lausanne, Switzerland
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Abstract
Pharmacogenetics holds promise in HIV treatment because of the complexity and potential toxicity of multidrug therapies that are prescribed for long periods. Thus far, few candidate genes have been examined for a limited number of allelic variants, but a number of confirmed associations have already emerged. A change in paradigm emerges from the availability of the HapMap, the wealth of data on less-common genetic polymorphisms, and new genotyping technology. This review presents a comprehensive analysis of the existing literature on pharmacogenetic determinants of antiretroviral drug exposure, drug toxicity, as well as genetic markers associated with the rate of disease progression. It is expected that larger-scale comprehensive genome approaches will profoundly change the landscape of knowledge in the future.
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Affiliation(s)
- A Telenti
- Institute of Microbiology, University of Lausanne, Lausanne, Switzerland.
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34
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An P, Wang LH, Hutcheson-Dilks H, Nelson G, Donfield S, Goedert JJ, Rinaldo CR, Buchbinder S, Kirk GD, O'Brien SJ, Winkler CA. Regulatory polymorphisms in the cyclophilin A gene, PPIA, accelerate progression to AIDS. PLoS Pathog 2007; 3:e88. [PMID: 17590083 PMCID: PMC1894826 DOI: 10.1371/journal.ppat.0030088] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2007] [Accepted: 05/11/2007] [Indexed: 11/18/2022] Open
Abstract
Human cyclophilin A, or CypA, encoded by the gene peptidyl prolyl isomerase A (PPIA), is incorporated into the HIV type 1 (HIV-1) virion and promotes HIV-1 infectivity by facilitating virus uncoating. We examined the effect of single nucleotide polymorphisms (SNPs) and haplotypes within the PPIA gene on HIV-1 infection and disease progression in five HIV-1 longitudinal history cohorts. Kaplan-Meier survival statistics and Cox proportional hazards model were used to assess time to AIDS outcomes. Among eight SNPs tested, two promoter SNPs (SNP3 and SNP4) in perfect linkage disequilibrium were associated with more rapid CD4(+) T-cell loss (relative hazard = 3.7, p = 0.003) in African Americans. Among European Americans, these alleles were also associated with a significant trend to more rapid progression to AIDS in a multi-point categorical analysis (p = 0.005). Both SNPs showed differential nuclear protein-binding efficiencies in a gel shift assay. In addition, one SNP (SNP5) located in the 5' UTR previously shown to be associated with higher ex vivo HIV-1 replication was found to be more frequent in HIV-1-positive individuals than in those highly exposed uninfected individuals. These results implicate regulatory PPIA polymorphisms as a component of genetic susceptibility to HIV-1 infection or disease progression, affirming the important role of PPIA in HIV-1 pathogenesis.
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Affiliation(s)
- Ping An
- Laboratory of Genomic Diversity, Science Applications International Corporation-Frederick, National Cancer Institute-Frederick, Frederick, Maryland, United States of America
| | - Li Hua Wang
- Basic Research Program, Science Applications International Corporation-Frederick, National Cancer Institute-Frederick, Frederick, Maryland, United States of America
| | - Holli Hutcheson-Dilks
- Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland, United States of America
| | - George Nelson
- Laboratory of Genomic Diversity, Science Applications International Corporation-Frederick, National Cancer Institute-Frederick, Frederick, Maryland, United States of America
| | - Sharyne Donfield
- Rho Incorporated, Chapel Hill, North Carolina, United States of America
| | - James J Goedert
- Viral Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Charles R Rinaldo
- Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, United States of America
| | - Susan Buchbinder
- San Francisco Department of Public Health, San Francisco, California, United States of America
| | - Gregory D Kirk
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Stephen J O'Brien
- Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland, United States of America
| | - Cheryl A Winkler
- Laboratory of Genomic Diversity, Science Applications International Corporation-Frederick, National Cancer Institute-Frederick, Frederick, Maryland, United States of America
- * To whom correspondence should be addressed. E-mail:
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Lama J, Planelles V. Host factors influencing susceptibility to HIV infection and AIDS progression. Retrovirology 2007; 4:52. [PMID: 17651505 PMCID: PMC1978541 DOI: 10.1186/1742-4690-4-52] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Accepted: 07/25/2007] [Indexed: 12/21/2022] Open
Abstract
Transmission of HIV first results in an acute infection, followed by an apparently asymptomatic period that averages ten years. In the absence of antiretroviral treatment, most patients progress into a generalized immune dysfunction that culminates in death. The length of the asymptomatic period varies, and in rare cases infected individuals never progress to AIDS. Other individuals whose behavioral traits put them at high-risk of HIV transmission, surprisingly appear resistant and never succumb to infection. These unique cases highlight the fact that susceptibility to HIV infection and progression to disease are complex traits modulated by environmental and genetic factors. Recent evidence has indicated that natural variations in host genes can influence the outcome of HIV infection and its transmission. In this review we summarize the available literature on the roles of cellular factors and their genetic variation in modulating HIV infection and disease progression.
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Affiliation(s)
- Juan Lama
- La Jolla Institute for Molecular Medicine, 4570 Executive Drive, Suite 100, San Diego, California 92121, USA
- RetroVirox, Inc. 4570 Executive Drive, Suite 100, San Diego, California 92121, USA
| | - Vicente Planelles
- Department of Pathology, University of Utah School of Medicine, 15 North Medical Drive East #2100 – Room 2520, Salt Lake City, Utah 84112, USA
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Fellay J, Shianna KV, Ge D, Colombo S, Ledergerber B, Weale M, Zhang K, Gumbs C, Castagna A, Cossarizza A, Cozzi-Lepri A, De Luca A, Easterbrook P, Francioli P, Mallal S, Martinez-Picado J, Miro JM, Obel N, Smith JP, Wyniger J, Descombes P, Antonarakis SE, Letvin NL, McMichael AJ, Haynes BF, Telenti A, Goldstein DB. A whole-genome association study of major determinants for host control of HIV-1. Science 2007; 317:944-7. [PMID: 17641165 PMCID: PMC1991296 DOI: 10.1126/science.1143767] [Citation(s) in RCA: 971] [Impact Index Per Article: 57.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Understanding why some people establish and maintain effective control of HIV-1 and others do not is a priority in the effort to develop new treatments for HIV/AIDS. Using a whole-genome association strategy, we identified polymorphisms that explain nearly 15% of the variation among individuals in viral load during the asymptomatic set-point period of infection. One of these is found within an endogenous retroviral element and is associated with major histocompatibility allele human leukocyte antigen (HLA)-B*5701, whereas a second is located near the HLA-C gene. An additional analysis of the time to HIV disease progression implicated two genes, one of which encodes an RNA polymerase I subunit. These findings emphasize the importance of studying human genetic variation as a guide to combating infectious agents.
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Affiliation(s)
- Jacques Fellay
- Center for Population Genomics and Pharmacogenetics, Duke Institute for Genome Sciences and Policy, Duke University, Durham, NC 27710, USA
| | - Kevin V. Shianna
- Duke Institute for Genome Sciences and Policy, Duke University, Durham, NC 27710, USA
| | - Dongliang Ge
- Center for Population Genomics and Pharmacogenetics, Duke Institute for Genome Sciences and Policy, Duke University, Durham, NC 27710, USA
| | - Sara Colombo
- Institute of Microbiology, University Hospital Center; and University of Lausanne, 1011 Lausanne, Switzerland
| | - Bruno Ledergerber
- Division of Infectious Diseases, University Hospital, 8091 Zürich, Switzerland
| | - Mike Weale
- Center for Population Genomics and Pharmacogenetics, Duke Institute for Genome Sciences and Policy, Duke University, Durham, NC 27710, USA
| | - Kunlin Zhang
- Institute of Microbiology, University Hospital Center; and University of Lausanne, 1011 Lausanne, Switzerland
| | - Curtis Gumbs
- Center for Population Genomics and Pharmacogenetics, Duke Institute for Genome Sciences and Policy, Duke University, Durham, NC 27710, USA
| | - Antonella Castagna
- Clinic of Infectious Diseases, Istituto di Ricovero e Cura a Carattere Scientifico, San Raffaele Hospital, 20127 Milan, Italy
| | - Andrea Cossarizza
- Department of Biomedical Sciences, Section of General Pathology, University of Modena and Reggio Emilia, School of Medicine, 41100 Modena, Italy
| | - Alessandro Cozzi-Lepri
- Department of Primary Care and Population Sciences, Royal Free and University College Medical School, University College London, London NW3 2PF, UK
| | - Andrea De Luca
- Institute of Clinical Infectious Diseases, Catholic University of the Sacred Heart, 00168 Rome, Italy
| | - Philippa Easterbrook
- Academic Department of HIV and Genitourinary Medicine, Kings College London, at Guy's, King's, and St. Thomas' Hospitals, London SE5 9RJ, UK
| | - Patrick Francioli
- Service of Infectious Diseases, Department of Medicine and Service of Hospital Preventive Medicine, University Hospital Center, 1011 Lausanne, Switzerland
| | - Simon Mallal
- Centre for Clinical Immunology and Biomedical Statistics, Royal Perth Hospital; and Murdoch University, Perth, WA 6000, Australia
| | - Javier Martinez-Picado
- irsiCaixa Foundation and Hospital Germans Trias i Pujol, 08916 Badalona, Spain; and Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - José M. Miro
- Hospital Clinic–Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, 08036 Barcelona, Spain
| | - Niels Obel
- Department of Infectious Diseases, Copenhagen University Hospital, Rigshospitalet, 2100 Copenhagen, Denmark
| | - Jason P. Smith
- Duke Institute for Genome Sciences and Policy, Duke University, Durham, NC 27710, USA
| | - Josiane Wyniger
- Institute of Microbiology, University Hospital Center; and University of Lausanne, 1011 Lausanne, Switzerland
| | - Patrick Descombes
- Genomics Platform, National Centre of Competence in Research “Frontiers in Genetics,” University of Geneva, 1211 Geneva, Switzerland
| | - Stylianos E. Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Norman L. Letvin
- Division of Viral Pathogenesis, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Andrew J. McMichael
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA
| | - Amalio Telenti
- Institute of Microbiology, University Hospital Center; and University of Lausanne, 1011 Lausanne, Switzerland
- To whom correspondence should be addressed. E-mail: (A.T.); (D.B.G.)
| | - David B. Goldstein
- Center for Population Genomics and Pharmacogenetics, Duke Institute for Genome Sciences and Policy, Duke University, Durham, NC 27710, USA
- To whom correspondence should be addressed. E-mail: (A.T.); (D.B.G.)
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Bochud PY, Hersberger M, Taffé P, Bochud M, Stein CM, Rodrigues SD, Calandra T, Francioli P, Telenti A, Speck RF, Aderem A. Polymorphisms in Toll-like receptor 9 influence the clinical course of HIV-1 infection. AIDS 2007; 21:441-6. [PMID: 17301562 DOI: 10.1097/qad.0b013e328012b8ac] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND The clinical course of HIV-1 infection is highly variable among individuals, at least in part as a result of genetic polymorphisms in the host. Toll-like receptors (TLRs) have a key role in innate immunity and mutations in the genes encoding these receptors have been associated with increased or decreased susceptibility to infections. OBJECTIVES To determine whether single-nucleotide polymorphisms (SNPs) in TLR2-4 and TLR7-9 influenced the natural course of HIV-1 infection. METHODS Twenty-eight SNPs in TLRs were analysed in HAART-naive HIV-positive patients from the Swiss HIV Cohort Study. The SNPs were detected using Sequenom technology. Haplotypes were inferred using an expectation-maximization algorithm. The CD4 T cell decline was calculated using a least-squares regression. Patients with a rapid CD4 cell decline, less than the 15th percentile, were defined as rapid progressors. The risk of rapid progression associated with SNPs was estimated using a logistic regression model. Other candidate risk factors included age, sex and risk groups (heterosexual, homosexual and intravenous drug use). RESULTS Two SNPs in TLR9 (1635A/G and +1174G/A) in linkage disequilibrium were associated with the rapid progressor phenotype: for 1635A/G, odds ratio (OR), 3.9 [95% confidence interval (CI),1.7-9.2] for GA versus AA and OR, 4.7 (95% CI,1.9-12.0) for GG versus AA (P = 0.0008). CONCLUSION Rapid progression of HIV-1 infection was associated with TLR9 polymorphisms. Because of its potential implications for intervention strategies and vaccine developments, additional epidemiological and experimental studies are needed to confirm this association.
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Weiler A, May GE, Qi Y, Wilson N, Watkins DI. Polymorphisms in eight host genes associated with control of HIV replication do not mediate elite control of viral replication in SIV-infected Indian rhesus macaques. Immunogenetics 2006; 58:1003-9. [PMID: 17106666 DOI: 10.1007/s00251-006-0166-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2006] [Accepted: 10/05/2006] [Indexed: 10/23/2022]
Abstract
Polymorphisms in several host genes in HIV-infected individuals facilitate slow progression to AIDS. We have identified several SIV-infected Indian rhesus macaques that naturally control viral replication. We investigated whether spontaneous control of SIV in any of these animals could be explained by mutations in host genes. Such variables could confound studies of associations between MHC class I alleles and control of viral replication. We searched for polymorphisms in CCR5, CXCR6, GPR15, RANTES, IL-10, APOBEC3G, TNF-alpha, and TSG101 and looked for associations with decreased viral replication. We did not detect any correlations between plasma viral concentration and polymorphisms in host genes examined in this study. In addition, we did not find the polymorphisms present in humans in any of our macaques.
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Affiliation(s)
- Andrea Weiler
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715, USA.
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Abstract
Genomics is now a core element in the effort to develop a vaccine against HIV-1. Thanks to unprecedented progress in high-throughput genotyping and sequencing, in knowledge about genetic variation in humans, and in evolutionary genomics, it is finally possible to systematically search the genome for common genetic variants that influence the human response to HIV-1. The identification of such variants would help to determine which aspects of the response to the virus are the most promising targets for intervention. However, a key obstacle to progress remains the scarcity of appropriate human cohorts available for genomic research.
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Affiliation(s)
- Amalio Telenti
- Institute of Microbiology, University Hospital, University of Lausanne, 1011 Lausanne, Switzerland.
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Bashirova AA, Bleiber G, Qi Y, Hutcheson H, Yamashita T, Johnson RC, Cheng J, Alter G, Goedert JJ, Buchbinder S, Hoots K, Vlahov D, May M, Maldarelli F, Jacobson L, O'brien SJ, Telenti A, Carrington M. Consistent effects of TSG101 genetic variability on multiple outcomes of exposure to human immunodeficiency virus type 1. J Virol 2006; 80:6757-63. [PMID: 16809281 PMCID: PMC1489017 DOI: 10.1128/jvi.00094-06] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tumor susceptibility gene 101 (TSG101) encodes a host cellular protein that is appropriated by human immunodeficiency virus type 1 (HIV-1) in the budding process of viral particles from infected cells. Variation in the coding or noncoding regions of the gene could potentially affect the degree of TSG101-mediated release of viral particles. While the coding regions of the gene were found to lack nonsynonymous variants, two polymorphic sites in the TSG101 5' area were identified that were associated with the rate of AIDS progression among Caucasians. These single-nucleotide polymorphisms (SNPs), located at positions -183 and +181 relative to the translation start, specify three haplotypes termed A, B, and C, which occur at frequencies of 67%, 21%, and 12%, respectively. Haplotype C is associated with relatively rapid AIDS progression, while haplotype B is associated with slower disease progression. Both effects were dominant over the intermediate haplotype A. The haplotypes also demonstrated parallel effects on the rate of CD4 T-cell depletion and viral load increase over time, as well as a possible influence on HIV-1 infection. The data raise the hypothesis that noncoding variation in TSG101 affects the efficiency of TSG101-mediated release of viral particles from infected cells, thereby altering levels of plasma viral load and subsequent disease progression.
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Affiliation(s)
- Arman A Bashirova
- Laboratory of Genomic Diversity, SAIC-Frederick, Inc., National Cancer Institute, Frederick, Maryland 21702, USA
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Goldschmidt V, Bleiber G, May M, Martinez R, Ortiz M, Telenti A. Role of common human TRIM5alpha variants in HIV-1 disease progression. Retrovirology 2006; 3:54. [PMID: 16925802 PMCID: PMC1560158 DOI: 10.1186/1742-4690-3-54] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2006] [Accepted: 08/22/2006] [Indexed: 11/30/2022] Open
Abstract
Background The retroviral restriction factor tripartite motif protein (TRIM)5α, is characterized by marked amino acid diversity among primates, including specific clusters of residues under positive selection. The identification of multiple non-synonymous changes in humans suggests that TRIM5α variants might be relevant to retroviral pathogenesis. Previous studies have shown that such variants are unlikely to modify susceptibility to HIV-1 infection, or the course of early infection. However, the longterm effect of carrying Trim5α variants on disease progression in individuals infected with HIV-1 has not previously been investigated. Methods In a cohort of 979 untreated individuals infected with HIV-1 with median follow up 3.2 years and 9,828 CD4 T cell measurements, we analysed common amino acid variations: H43Y, V112F, R136Q, G249D, and H419Y. The rate of CD4 T cell decline before treatment was used as the phenotype. In addition, we extended previous work on the in vitro susceptibility of purified donor CD4 T cells (n = 125) to HIV-1 infection, and on the susceptibility of HeLa cells that were stably transduced with the different TRIM5 variants. Haplotypes were analysed according to the most parsimonious evolutionary structure, where two main human TRIM5α groups can be defined according to the residue at amino acid 136. Humans present both Q136 and R136 at similar frequency, and additional TRIM5α amino acid variants are almost exclusively derived from R136-carrying haplotypes. Results We observed modest differences in disease progression for evolutionary branches carrying R136-derived haplotypes, and with the non-synonymous polymorphisms G249D and H419Y. In vitro analysis of susceptibility of donor CD4 T cells, and of the various transduced HeLa cell lines supported the absence of significant differential restriction of HIV-1 infection by the various huTRIM5α alleles. Conclusion Common human variants of TRIM5α have no effect or modest effect on HIV-1 disease progression. These variants occur at sites conserved throughout evolution, and are remote from clusters of positive selection in the primate lineage. The evolutionary value of the substitutions remains unclear.
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Affiliation(s)
- Valérie Goldschmidt
- Institute of Microbiology and University Hospital, University of Lausanne, Switzerland
| | - Gabriela Bleiber
- Institute of Microbiology and University Hospital, University of Lausanne, Switzerland
| | - Margaret May
- Department of Social Medicine, University of Bristol, UK
| | - Raquel Martinez
- Institute of Microbiology and University Hospital, University of Lausanne, Switzerland
| | - Millàn Ortiz
- Institute of Microbiology and University Hospital, University of Lausanne, Switzerland
| | - Amalio Telenti
- Institute of Microbiology and University Hospital, University of Lausanne, Switzerland
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Abstract
Susceptibility to HIV-1 and the rate of disease progression reflect the influence of the genetic diversity of the virus as well as the variation in host factors. The virus will co-evolve with the host, escaping and adapting to host-determined influences. Dominant host factors currently identified include diversity in the major histocompatibility complex class I, and alleles of chemokine, chemokine receptor and cytokine genes. Recent work proposes new variants in life cycle genes and in antiviral innate defense, which modify HIV-1 susceptibility. Comparative genomics generates information on host cell barriers that may explain the current distribution of these viruses among human and nonhuman primates. A greater understanding of the genetic basis of human susceptibility to HIV-1 contributes to an understanding of the pathogenesis of the disease, helps identify new targets for prophylaxis and vaccine development and will lead to predictive tools to identify those at risk of rapid disease progression.
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Affiliation(s)
- Amalio Telenti
- University of Lausanne, Institute of Microbiology and University Hospital, Bugnon 48 – CHUV,1011 Lausanne, Switzerland
| | - Gabriela Bleiber
- University of Lausanne, Institute of Microbiology and University Hospital, Bugnon 48 – CHUV,1011 Lausanne, Switzerland and GlaxoSmithKline, Infectious Diseases Medicines Development Center, Greenford, UK
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