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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Turelli P, Playfoot C, Grun D, Raclot C, Pontis J, Coudray A, Thorball C, Duc J, Pankevich EV, Deplancke B, Busskamp V, Trono D. Primate-restricted KRAB zinc finger proteins and target retrotransposons control gene expression in human neurons. Sci Adv 2020; 6:eaba3200. [PMID: 32923624 PMCID: PMC7455193 DOI: 10.1126/sciadv.aba3200] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 07/16/2020] [Indexed: 05/11/2023]
Abstract
In the first days of embryogenesis, transposable element-embedded regulatory sequences (TEeRS) are silenced by Kruppel-associated box (KRAB) zinc finger proteins (KZFPs). Many TEeRS are subsequently co-opted in transcription networks, but how KZFPs influence this process is largely unknown. We identify ZNF417 and ZNF587 as primate-specific KZFPs repressing HERVK (human endogenous retrovirus K) and SVA (SINE-VNTR-Alu) integrants in human embryonic stem cells (ESCs). Expressed in specific regions of the human developing and adult brain, ZNF417/587 keep controlling TEeRS in ESC-derived neurons and brain organoids, secondarily influencing the differentiation and neurotransmission profile of neurons and preventing the induction of neurotoxic retroviral proteins and an interferon-like response. Thus, evolutionarily recent KZFPs and their TE targets partner up to influence human neuronal differentiation and physiology.
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Affiliation(s)
- Priscilla Turelli
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Christopher Playfoot
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Dephine Grun
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Charlène Raclot
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Julien Pontis
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Alexandre Coudray
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Christian Thorball
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Julien Duc
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Eugenia V. Pankevich
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Bart Deplancke
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Volker Busskamp
- Center for Regenerative Therapies, Technische Universität Dresden, Dresden, Germany
- Faculty of Medicine, Department of Ophthalmology, University of Bonn, Bonn, Germany
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Corresponding author.
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Mohammadi P, di Iulio J, Muñoz M, Martinez R, Bartha I, Cavassini M, Thorball C, Fellay J, Beerenwinkel N, Ciuffi A, Telenti A. Dynamics of HIV latency and reactivation in a primary CD4+ T cell model. PLoS Pathog 2014; 10:e1004156. [PMID: 24875931 PMCID: PMC4038609 DOI: 10.1371/journal.ppat.1004156] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 04/18/2014] [Indexed: 12/11/2022] Open
Abstract
HIV latency is a major obstacle to curing infection. Current strategies to eradicate HIV aim at increasing transcription of the latent provirus. In the present study we observed that latently infected CD4+ T cells from HIV-infected individuals failed to produce viral particles upon ex vivo exposure to SAHA (vorinostat), despite effective inhibition of histone deacetylases. To identify steps that were not susceptible to the action of SAHA or other latency reverting agents, we used a primary CD4+ T cell model, joint host and viral RNA sequencing, and a viral-encoded reporter. This model served to investigate the characteristics of latently infected cells, the dynamics of HIV latency, and the process of reactivation induced by various stimuli. During latency, we observed persistence of viral transcripts but only limited viral translation. Similarly, the reactivating agents SAHA and disulfiram successfully increased viral transcription, but failed to effectively enhance viral translation, mirroring the ex vivo data. This study highlights the importance of post-transcriptional blocks as one mechanism leading to HIV latency that needs to be relieved in order to purge the viral reservoir. HIV-infected individuals must receive lifelong antiviral therapy because treatment discontinuation generally results in rapid viral rebound. The field has identified a state of latency at the level of transcription of the integrated provirus as the major mechanism of persistence. A number of drugs are now tested that aim at inducing viral transcription as a step to purge the reservoir. The assessment of viral production in cells from HIV-infected individuals with optimal viral suppression revealed the failure of SAHA/vorinostat to efficiently generate viral particle production. To further investigate and characterize the process of latency at the transcriptome level, and the response to SAHA as well as various reactivating agents, we use a model of primary CD4+ lymphocytes. The main observation from this study is that viral transcripts persist during latency, and that the accumulation of viral transcripts does not result in efficient viral protein expression upon reactivation with agents such as SAHA. Our data suggest that post-transcriptional blocks also contribute to latency, and that additional strategies need to be explored to efficiently purge the viral reservoir.
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Affiliation(s)
- Pejman Mohammadi
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel and Lausanne, Switzerland
| | - Julia di Iulio
- Swiss Institute of Bioinformatics, Basel and Lausanne, Switzerland
- Institute of Microbiology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Miguel Muñoz
- Institute of Microbiology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Raquel Martinez
- Institute of Microbiology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - István Bartha
- Swiss Institute of Bioinformatics, Basel and Lausanne, Switzerland
- Institute of Microbiology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Matthias Cavassini
- Service of Infectious Diseases, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Christian Thorball
- Institute of Microbiology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Jacques Fellay
- Swiss Institute of Bioinformatics, Basel and Lausanne, Switzerland
- Institute of Microbiology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Service of Infectious Diseases, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel and Lausanne, Switzerland
- * E-mail: (NB); (AC); (AT)
| | - Angela Ciuffi
- Institute of Microbiology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- University of Lausanne, Lausanne, Switzerland
- * E-mail: (NB); (AC); (AT)
| | - Amalio Telenti
- Institute of Microbiology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- University of Lausanne, Lausanne, Switzerland
- * E-mail: (NB); (AC); (AT)
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