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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Dominguez-Molina B, Tarancon-Diez L, Hua S, Abad-Molina C, Rodriguez-Gallego E, Machmach K, Vidal F, Tural C, Moreno S, Goñi JM, Ramírez de Arellano E, Del Val M, Gonzalez-Escribano MF, Del Romero J, Rodriguez C, Capa L, Viciana P, Alcamí J, Yu XG, Walker BD, Leal M, Lichterfeld M, Ruiz-Mateos E. HLA-B*57 and IFNL4-related polymorphisms are associated with protection against HIV-1 disease progression in controllers. Clin Infect Dis 2016; 64:621-628. [PMID: 27986689 DOI: 10.1093/cid/ciw833] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Indexed: 12/23/2022] Open
Abstract
Background HIV-1-controllers maintain HIV-1 viremia at low levels (normally <2000 HIV-RNA copies/mL) without antiretroviral treatment. However, some HIV-1-controllers have evidence of immunologic progression with marked CD4+T-cell decline. We investigated host genetic factors associated with protection against CD4+T-cell loss in HIV-1-controllers. Methods We analysed the association of interferon lambda 4 (IFNL4)-related polymorphisms and HLA-B haplotypes within Long Term Non-Progressor HIV-1-controllers ((LTNP-C), defined by maintaining CD4+T-cells counts >500 cells/mm3 for more than 7 years after HIV-1 diagnosis) versus non-LTNP-C, who developed CD4+T-cells counts <500 cells/mm3 Both a Spanish study cohort (n=140) and an international validation cohort (n=914) were examined. Additionally, in a subgroup of individuals HIV-1-specific T-cell responses and soluble cytokines were analysed RESULTS: HLA-B*57 was independently associated with the LTNP-C phenotype (OR=3.056 (1.029-9.069) p=0.044 and OR=1.924 (1.252-2.957) p=0.003) while IFNL4 genotypes represented independent factors for becoming non-LTNP-C (TT/TT, ss469415590, OR=0.401 (0.171-0.942) p=0.036 or A/A, rs12980275, OR=0.637 (0.434-0.934) p=0.021) in the Spanish and validation cohort, respectively, after adjusting for sex, age at HIV-1 diagnosis, IFNL4-related polymorphisms and different HLA-B haplotypes. LTNP-C showed lower plasma IP-10 (p=0.019) and higher IFN-γ (p=0.02) levels than the HIV-1-controllers with diminished CD4+T-cell numbers. Moreover, LTNP-C exhibited higher quantities of IL2+CD57- and IFN-γ+CD57- HIV-1-specific CD8+T-cells (p=0.002 and 0.041, respectively) than non-LTNP-C. Conclusions We have defined genetic markers able to segregate stable HIV-1-controllers from those who experience CD4+T-cell decline. These findings allow for identification of HIV-1-controllers at risk for immunologic progression, and provide avenues for personalized therapeutic interventions and precision medicine for optimizing clinical care of these individuals.
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Affiliation(s)
- B Dominguez-Molina
- Laboratory of Immunovirology, Clinic Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville, IBiS, Virgen del Rocío University Hospital, Seville, Spain
| | - L Tarancon-Diez
- Laboratory of Immunovirology, Clinic Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville, IBiS, Virgen del Rocío University Hospital, Seville, Spain
| | - S Hua
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA Harvard Medical School, Boston, Massachusetts, USA Infectious Disease Division, Massachusetts General Hospital, Boston, Massachusetts, USA Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - C Abad-Molina
- Laboratoy of Immunology, Institute of Biomedicine of Seville, IBiS, Virgen del Rocío University Hospital, Seville, Spain
| | - E Rodriguez-Gallego
- Hospital Universitari de Tarragona Joan XXIII, IISPV, Universitat Rovira i Virgili, Tarragona, Spain
| | - K Machmach
- Department of Medical Microbiology and Immunology, University of California, Davis, Davis, CA, USA
| | - F Vidal
- Hospital Universitari de Tarragona Joan XXIII, IISPV, Universitat Rovira i Virgili, Tarragona, Spain
| | - C Tural
- Fundació Lluita Contra la Sida, Fundacio Irsicaixa, Hospital Universitari Germans Trias i Pujol, Badalona,Spain
| | - S Moreno
- Department of Infectious Diseases, Hospital Ramón y Cajal, Universidad de Alcalá de Henares, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - J M Goñi
- Department of Endocrinology, Complejo Hospitalario de Navarra, Pamplona, Spain
| | - E Ramírez de Arellano
- Unidad de Inmunología Viral, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - M Del Val
- Unidad de Inmunología Viral, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain.,Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Madrid, Spain
| | - M F Gonzalez-Escribano
- Laboratoy of Immunology, Institute of Biomedicine of Seville, IBiS, Virgen del Rocío University Hospital, Seville, Spain
| | - J Del Romero
- Centro Sanitario Sandoval, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain
| | - C Rodriguez
- Centro Sanitario Sandoval, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain
| | - L Capa
- AIDS Immunopathology Unit, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - P Viciana
- Laboratory of Immunovirology, Clinic Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville, IBiS, Virgen del Rocío University Hospital, Seville, Spain
| | - J Alcamí
- AIDS Immunopathology Unit, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - X G Yu
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA Harvard Medical School, Boston, Massachusetts, USA Infectious Disease Division, Massachusetts General Hospital, Boston, Massachusetts, USA Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - B D Walker
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA Harvard Medical School, Boston, Massachusetts, USA Infectious Disease Division, Massachusetts General Hospital, Boston, Massachusetts, USA Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Manuel Leal
- Laboratory of Immunovirology, Clinic Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville, IBiS, Virgen del Rocío University Hospital, Seville, Spain
| | - M Lichterfeld
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA Harvard Medical School, Boston, Massachusetts, USA Infectious Disease Division, Massachusetts General Hospital, Boston, Massachusetts, USA Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - E Ruiz-Mateos
- Laboratory of Immunovirology, Clinic Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville, IBiS, Virgen del Rocío University Hospital, Seville, Spain
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