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Martín-Sierra C, Bravo MJ, Sáez ME, De Rojas I, Santos M, Martín-Carmona J, Corma-Gómez A, González-Serna A, Royo JL, Pineda JA, Rivero A, Rivero-Juárez A, Macías J, Real LM. The absence of seroconversion after exposition to hepatitis C virus is not related to KIR-HLA genotype combinations (GEHEP-012 study). Antiviral Res 2024; 222:105795. [PMID: 38181855 DOI: 10.1016/j.antiviral.2024.105795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/30/2023] [Accepted: 01/02/2024] [Indexed: 01/07/2024]
Abstract
BACKGROUND & AIMS It has been reported that specific killer-cell immunoglobulin-like receptors (KIRs) and HLA genotype combinations, such as KIR2DS4/HLA-C1 with presence of KIRDL2 or KIRDL3, homozygous KIRDL3/HLA-C1 and KIR3DL1/≥2HLA-Bw4, are strongly associated with the lack of active infection and seroconversion after exposition to hepatitis C virus (HCV). OBJECTIVE To determine whether these KIR-HLA combinations are relevant factors involved in that phenotype. PATIENTS AND METHODS In this retrospective case-control study, genotype data from a genome-wide association study previously performed on low susceptibility to HCV-infection carried out on 27 high-risk HCV-seronegative (HRSN) individuals and 743 chronically infected (CI) subjects were used. HLA alleles were imputed using R package HIBAG v1.2223 and KIR genotypes were imputed using the online resource KIR*IMP v1.2.0. RESULTS It was possible to successfully impute at least one KIR-HLA genotype combination previously associated with the lack of infection and seroconversion after exposition to HCV in a total of 23 (85.2%) HRSN individuals and in 650 (87.5%) CI subjects. No KIR-HLA genotype combination analyzed was related to the HRSN condition. CONCLUSIONS Our results suggest that those KIR-HLA genotype combinations are not relevant factors involved in the lack of infection and seroconversion after exposition to HCV. More studies will be needed to completely understand this phenotype.
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Affiliation(s)
- Carmen Martín-Sierra
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain; Instituto de Biomedicina de Sevilla, IBiS/Hospital Universitario Virgen de Valme /CSIC/Universidad de Sevilla, Sevilla, Spain
| | - María José Bravo
- Departamento de Especialidades Quirúrgicas, Bioquímica e Inmunología, Universidad de Málaga, Málaga, Spain
| | | | - Itziar De Rojas
- Research Center and Memory Clinic Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Marta Santos
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain; Instituto de Biomedicina de Sevilla, IBiS/Hospital Universitario Virgen de Valme /CSIC/Universidad de Sevilla, Sevilla, Spain
| | - Jesica Martín-Carmona
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain; Instituto de Biomedicina de Sevilla, IBiS/Hospital Universitario Virgen de Valme /CSIC/Universidad de Sevilla, Sevilla, Spain
| | - Anaïs Corma-Gómez
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain; Instituto de Biomedicina de Sevilla, IBiS/Hospital Universitario Virgen de Valme /CSIC/Universidad de Sevilla, Sevilla, Spain
| | - Alejandro González-Serna
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain; Instituto de Biomedicina de Sevilla, IBiS/Hospital Universitario Virgen de Valme /CSIC/Universidad de Sevilla, Sevilla, Spain; Departamento de Fisiología. Universidad de Sevilla, Sevilla, Spain
| | - José Luis Royo
- Departamento de Especialidades Quirúrgicas, Bioquímica e Inmunología, Universidad de Málaga, Málaga, Spain
| | - Juan A Pineda
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain; Instituto de Biomedicina de Sevilla, IBiS/Hospital Universitario Virgen de Valme /CSIC/Universidad de Sevilla, Sevilla, Spain; Departamento de Medicina. Universidad de Sevilla, Sevilla, Spain
| | - Antonio Rivero
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBC), Hospital Universitario Reina Sofía de Córdoba, Universidad de Córdoba, Córdoba, Spain
| | - Antonio Rivero-Juárez
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBC), Hospital Universitario Reina Sofía de Córdoba, Universidad de Córdoba, Córdoba, Spain
| | - Juan Macías
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain; Instituto de Biomedicina de Sevilla, IBiS/Hospital Universitario Virgen de Valme /CSIC/Universidad de Sevilla, Sevilla, Spain; Departamento de Medicina. Universidad de Sevilla, Sevilla, Spain
| | - Luis Miguel Real
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain; Instituto de Biomedicina de Sevilla, IBiS/Hospital Universitario Virgen de Valme /CSIC/Universidad de Sevilla, Sevilla, Spain; Departamento de Bioquímica Médica, Biología Molecular e Inmunología, Universidad de Sevilla, Sevilla, Spain.
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Real LM, Sáez ME, Corma-Gómez A, Gonzalez-Pérez A, Thorball C, Ruiz R, Jimenez-Leon MR, Gonzalez-Serna A, Gasca-Capote C, Bravo MJ, Royo JL, Perez-Gomez A, Camacho-Sojo MI, Gallego I, Vitalle J, Bachiller S, Gutierrez-Valencia A, Vidal F, Fellay J, Lichterfeld M, Ruiz-Mateos E. A metagenome-wide association study of HIV disease progression in HIV controllers. iScience 2023; 26:107214. [PMID: 37456859 PMCID: PMC10339206 DOI: 10.1016/j.isci.2023.107214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/19/2023] [Accepted: 06/22/2023] [Indexed: 07/18/2023] Open
Abstract
Some HIV controllers experience immunologic progression with CD4+ T cell decline. We aimed to identify genetic factors associated with CD4+ T cell lost in HIV controllers. A total of 561 HIV controllers were included, 442 and 119 from the International HIV controllers Study Cohort and the Swiss HIV Cohort Study, respectively. No SNP or gene was associated with the long-term non-progressor HIV spontaneous control phenotype in the individual GWAS or in the meta-analysis. However, SNPs previously associated with natural HIV control linked to HLA-B (rs2395029 [p = 0.005; OR = 1.70], rs59440261 [p = 0.003; OR = 1.78]), MICA (rs112243036 [p = 0.011; OR = 1.45]), and PSORS1C1 loci (rs3815087 [p = 0.017; OR = 1.39]) showed nominal association with this phenotype. Genetic factors associated with the long-term HIV controllers without risk of immunologic progression are those previously related to the overall HIV controller phenotype.
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Affiliation(s)
- Luis Miguel Real
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen de Valme, Instituto de Biomedicina de Sevilla, IBIS, Sevilla, Spain
- Departamento de Especialidades Quirúrgicas, Bioquímica e Inmunología, Facultad de Medicina, Universidad de Málaga, Málaga, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC)-Instituto de Salud Carlos III, Madrid, Spain
| | - María E. Sáez
- Centro Andaluz de Estudios Bioinformáticos (CAEBI, SL), Sevilla, Spain
| | - Anais Corma-Gómez
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen de Valme, Instituto de Biomedicina de Sevilla, IBIS, Sevilla, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC)-Instituto de Salud Carlos III, Madrid, Spain
| | | | - Christian Thorball
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Rocío Ruiz
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Sevilla/Instituto de Biomedicina de Sevilla-Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41012 Sevilla, Spain
| | - María Reyes Jimenez-Leon
- Institute of Biomedicine of Seville, IBiS/Virgen del Rocío University Hospital/CSIC/University of Seville, Clinic Unit of Infectious Diseases, Microbiology and Preventive Medicine, Seville, Spain
| | - Alejandro Gonzalez-Serna
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen de Valme, Instituto de Biomedicina de Sevilla, IBIS, Sevilla, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC)-Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen Gasca-Capote
- Institute of Biomedicine of Seville, IBiS/Virgen del Rocío University Hospital/CSIC/University of Seville, Clinic Unit of Infectious Diseases, Microbiology and Preventive Medicine, Seville, Spain
| | - María José Bravo
- Departamento de Especialidades Quirúrgicas, Bioquímica e Inmunología, Facultad de Medicina, Universidad de Málaga, Málaga, Spain
| | - José Luis Royo
- Departamento de Especialidades Quirúrgicas, Bioquímica e Inmunología, Facultad de Medicina, Universidad de Málaga, Málaga, Spain
| | - Alberto Perez-Gomez
- Institute of Biomedicine of Seville, IBiS/Virgen del Rocío University Hospital/CSIC/University of Seville, Clinic Unit of Infectious Diseases, Microbiology and Preventive Medicine, Seville, Spain
| | - María Inés Camacho-Sojo
- Institute of Biomedicine of Seville, IBiS/Virgen del Rocío University Hospital/CSIC/University of Seville, Clinic Unit of Infectious Diseases, Microbiology and Preventive Medicine, Seville, Spain
| | - Isabel Gallego
- Institute of Biomedicine of Seville, IBiS/Virgen del Rocío University Hospital/CSIC/University of Seville, Clinic Unit of Infectious Diseases, Microbiology and Preventive Medicine, Seville, Spain
| | - Joana Vitalle
- Institute of Biomedicine of Seville, IBiS/Virgen del Rocío University Hospital/CSIC/University of Seville, Clinic Unit of Infectious Diseases, Microbiology and Preventive Medicine, Seville, Spain
| | - Sara Bachiller
- Institute of Biomedicine of Seville, IBiS/Virgen del Rocío University Hospital/CSIC/University of Seville, Clinic Unit of Infectious Diseases, Microbiology and Preventive Medicine, Seville, Spain
- Department of Medical Biochemistry, Molecular Biology and Immunology, School of Medicine, University of Seville, Seville, Spain
| | - Alicia Gutierrez-Valencia
- Institute of Biomedicine of Seville, IBiS/Virgen del Rocío University Hospital/CSIC/University of Seville, Clinic Unit of Infectious Diseases, Microbiology and Preventive Medicine, Seville, Spain
| | - Francisco Vidal
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC)-Instituto de Salud Carlos III, Madrid, Spain
- Hospital Universitari de Tarragona Joan XXIII (HJ23), Tarragona, Spain
- Institut Investigació Sanitària Pere Virgili (IISPV), Tarragona, Spain
- Universitat Rovira i Virgili (URV), Tarragona, Spain
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Infectious Disease Division, Massachusetts General Hospital, Boston, MA, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, MA, USA
| | - Ezequiel Ruiz-Mateos
- Institute of Biomedicine of Seville, IBiS/Virgen del Rocío University Hospital/CSIC/University of Seville, Clinic Unit of Infectious Diseases, Microbiology and Preventive Medicine, Seville, Spain
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Corma-Gómez A, Macías J, Rivero A, Rivero-Juarez A, de los Santos I, Reus-Bañuls S, Morano L, Merino D, Palacios R, Galera C, Fernández-Fuertes M, González-Serna A, de Rojas I, Ruiz A, Sáez ME, Real LM, Pineda JA. A Genome-Wide Association Study on Liver Stiffness Changes during Hepatitis C Virus Infection Cure. Diagnostics (Basel) 2021; 11:1501. [PMID: 34441435 PMCID: PMC8394459 DOI: 10.3390/diagnostics11081501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/11/2021] [Accepted: 08/16/2021] [Indexed: 02/07/2023] Open
Abstract
Liver stiffness (LS) at sustained virological response (SVR) after direct-acting antivirals (DAA)-based therapy is a predictor of liver events in hepatitis C virus (HCV)-infected patients. The study aim was to identify genetic factors associated with LS changes from the moment of starting anti-HCV therapy to SVR. This prospective study included HCV-infected patients from the GEHEP-011 cohort who achieved SVR with DAA-based therapy, with LS pre-treatment ≥ 9.5 kPa and LS measurement available at SVR. Plink and Magma software were used to carry out genome-wide single-nucleotide polymorphism (SNP)-based and gene-based association analyses, respectively. The ShinyGO application was used for exploring enrichment in Gene Ontology (GO) categories for biological processes. Overall, 242 patients were included. Median (quartile 1, quartile 3) LS values at pre-treatment and at SVR were 16.8 (12, 28) kPa and 12.0 (8.5, 19.3) kPa, respectively. Thirty-five SNPs and three genes reached suggestive association with LS changes from the moment of starting anti-HCV therapy to SVR. GO categories related to DNA packaging complex, DNA conformation change, chromosome organization and chromatin organization were significantly enriched. Our study reports possible genetic factors associated with LS changes during HCV-infection cure. In addition, our results suggest that processes related to DNA conformation are also involved in these changes.
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Affiliation(s)
- Anaïs Corma-Gómez
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital de Valme, 41014 Sevilla, Spain; (A.C.-G.); (J.M.); (M.F.-F.); (A.G.-S.); (J.A.P.)
| | - Juan Macías
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital de Valme, 41014 Sevilla, Spain; (A.C.-G.); (J.M.); (M.F.-F.); (A.G.-S.); (J.A.P.)
- Departamento de Medicina, Universidad de Sevilla, 41009 Sevilla, Spain
| | - Antonio Rivero
- Unidad de Enfermedades Infecciosas, Hospital Universitario Reina Sofía, Instituto Maimonides de Investigación Biomédica de Córdoba (IMIBIC), Universidad de Córdoba, 14004 Córdoba, Spain; (A.R.); (A.R.-J.)
| | - Antonio Rivero-Juarez
- Unidad de Enfermedades Infecciosas, Hospital Universitario Reina Sofía, Instituto Maimonides de Investigación Biomédica de Córdoba (IMIBIC), Universidad de Córdoba, 14004 Córdoba, Spain; (A.R.); (A.R.-J.)
| | - Ignacio de los Santos
- Unidad de Medicina Interna y Enfermedades Infecciosas, Hospital de La Princesa, 28006 Madrid, Spain;
| | - Sergio Reus-Bañuls
- Unidad de Enfermedades Infecciosas, Hospital General Universitario de Alicante, 03010 Alicante, Spain;
| | - Luis Morano
- Unidad de Patología Infecciosa, Hospital Universitario Alvaro Cunqueiro, Instituto de Investigación Sanitaria Galicia Sur (IISGS), 36312 Vigo, Spain;
| | - Dolores Merino
- Unidad de Enfermedades Infecciosas, Hospital Universitario Juan Ramón Jiménez, 21005 Huelva, Spain;
| | - Rosario Palacios
- Unidad de Enfermedades Infecciosas y Microbiología, Hospital Virgen de la Victoria, 29010 Málaga, Spain;
| | - Carlos Galera
- Unidad de Medicina Interna, Hospital Clínico Universitario Virgen de la Arrixaca, 30120 Murcia, Spain;
| | - Marta Fernández-Fuertes
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital de Valme, 41014 Sevilla, Spain; (A.C.-G.); (J.M.); (M.F.-F.); (A.G.-S.); (J.A.P.)
| | - Alejandro González-Serna
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital de Valme, 41014 Sevilla, Spain; (A.C.-G.); (J.M.); (M.F.-F.); (A.G.-S.); (J.A.P.)
| | - Itziar de Rojas
- Fundació ACE—Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya (UIC), 08028 Barcelona, Spain; (I.d.R.); (A.R.)
- CIBERNED Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Agustín Ruiz
- Fundació ACE—Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya (UIC), 08028 Barcelona, Spain; (I.d.R.); (A.R.)
- CIBERNED Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - María E. Sáez
- Centro Andaluz de Estudios Bioinformáticos (CAEBI, SL), 41013 Sevilla, Spain;
| | - Luis M. Real
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital de Valme, 41014 Sevilla, Spain; (A.C.-G.); (J.M.); (M.F.-F.); (A.G.-S.); (J.A.P.)
- Departamento de Especialidades Quirúrgicas, Bioquímica e Inmunología, Universidad de Málaga, 29010 Málaga, Spain
| | - Juan A. Pineda
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital de Valme, 41014 Sevilla, Spain; (A.C.-G.); (J.M.); (M.F.-F.); (A.G.-S.); (J.A.P.)
- Departamento de Medicina, Universidad de Sevilla, 41009 Sevilla, Spain
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