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Gasca-Capote C, Lian X, Gao C, Roseto IC, Jiménez-León MR, Gladkov G, Camacho-Sojo MI, Pérez-Gómez A, Gallego I, Lopez-Cortes LE, Bachiller S, Vitalle J, Rafii-El-Idrissi Benhnia M, Ostos FJ, Collado-Romacho AR, Santos J, Palacios R, Gomez-Ayerbe C, Muñoz-Medina L, Ruiz-Sancho A, Frias M, Rivero-Juarez A, Roca-Oporto C, Hidalgo-Tenorio C, Rull A, Olalla J, Lopez-Ruz MA, Vidal F, Viladés C, Mastrangelo A, Cavassini M, Espinosa N, Perreau M, Peraire J, Rivero A, López-Cortes LF, Lichterfeld M, Yu XG, Ruiz-Mateos E. The HIV-1 reservoir landscape in persistent elite controllers and transient elite controllers. J Clin Invest 2024; 134:e174215. [PMID: 38376918 PMCID: PMC11014653 DOI: 10.1172/jci174215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 02/13/2024] [Indexed: 02/21/2024] Open
Abstract
BACKGROUNDPersistent controllers (PCs) maintain antiretroviral-free HIV-1 control indefinitely over time, while transient controllers (TCs) eventually lose virological control. It is essential to characterize the quality of the HIV reservoir in terms of these phenotypes in order to identify the factors that lead to HIV progression and to open new avenues toward an HIV cure.METHODSThe characterization of HIV-1 reservoir from peripheral blood mononuclear cells was performed using next-generation sequencing techniques, such as full-length individual and matched integration site proviral sequencing (FLIP-Seq; MIP-Seq).RESULTSPCs and TCs, before losing virological control, presented significantly lower total, intact, and defective proviruses compared with those of participants on antiretroviral therapy (ART). No differences were found in total and defective proviruses between PCs and TCs. However, intact provirus levels were lower in PCs compared with TCs; indeed the intact/defective HIV-DNA ratio was significantly higher in TCs. Clonally expanded intact proviruses were found only in PCs and located in centromeric satellite DNA or zinc-finger genes, both associated with heterochromatin features. In contrast, sampled intact proviruses were located in permissive genic euchromatic positions in TCs.CONCLUSIONSThese results suggest the need for, and can give guidance to, the design of future research to identify a distinct proviral landscape that may be associated with the persistent control of HIV-1 without ART.FUNDINGInstituto de Salud Carlos III (FI17/00186, FI19/00083, MV20/00057, PI18/01532, PI19/01127 and PI22/01796), Gilead Fellowships (GLD22/00147). NIH grants AI155171, AI116228, AI078799, HL134539, DA047034, MH134823, amfAR ARCHE and the Bill and Melinda Gates Foundation.
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Affiliation(s)
- Carmen Gasca-Capote
- Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital, Spanish National Research Council (CSIC), University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
| | - Xiaodong Lian
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Isabelle C. Roseto
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - María Reyes Jiménez-León
- Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital, Spanish National Research Council (CSIC), University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
| | - Gregory Gladkov
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - María Inés Camacho-Sojo
- Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital, Spanish National Research Council (CSIC), University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
| | - Alberto Pérez-Gómez
- Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital, Spanish National Research Council (CSIC), University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
| | - Isabel Gallego
- Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital, Spanish National Research Council (CSIC), University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
| | - Luis E. Lopez-Cortes
- Clinical Unit of Infectious Diseases and Microbiology, Virgen Macarena University Hospital, Seville, Spain
- Department of Medicine and Microbiology, School of Medicine and
- IBiS, Virgen Macarena University Hospital, CSIC, University of Seville, Seville, Spain
- CIBERINFEC, Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Sara Bachiller
- Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital, Spanish National Research Council (CSIC), University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
- Department of Medical Biochemistry, Molecular Biology, and Immunology, School of Medicine, University of Seville, Seville, Spain
| | - Joana Vitalle
- Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital, Spanish National Research Council (CSIC), University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
| | - Mohamed Rafii-El-Idrissi Benhnia
- Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital, Spanish National Research Council (CSIC), University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
- Department of Medical Biochemistry, Molecular Biology, and Immunology, School of Medicine, University of Seville, Seville, Spain
| | - Francisco J. Ostos
- Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital, Spanish National Research Council (CSIC), University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
- Department of Medical Biochemistry, Molecular Biology, and Immunology, School of Medicine, University of Seville, Seville, Spain
| | | | - Jesús Santos
- Infectious Diseases, Microbiology and Preventive Medicine Unit, Virgen de la Victoria University Hospital, Malaga, Spain
| | - Rosario Palacios
- Infectious Diseases, Microbiology and Preventive Medicine Unit, Virgen de la Victoria University Hospital, Malaga, Spain
| | - Cristina Gomez-Ayerbe
- Infectious Diseases, Microbiology and Preventive Medicine Unit, Virgen de la Victoria University Hospital, Malaga, Spain
| | - Leopoldo Muñoz-Medina
- Unit of Infectious Diseases, San Cecilio University Hospital, Biohealth Research Institute, IBS-Granada, Granada, Spain
| | - Andrés Ruiz-Sancho
- Unit of Infectious Diseases, San Cecilio University Hospital, Biohealth Research Institute, IBS-Granada, Granada, Spain
| | - Mario Frias
- CIBERINFEC, Institute of Health Carlos III (ISCIII), Madrid, Spain
- Service of Infectious Diseases, Reina Sofía University Hospital, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Córdoba University, Cordoba, Spain
| | - Antonio Rivero-Juarez
- CIBERINFEC, Institute of Health Carlos III (ISCIII), Madrid, Spain
- Service of Infectious Diseases, Reina Sofía University Hospital, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Córdoba University, Cordoba, Spain
| | - Cristina Roca-Oporto
- Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital, Spanish National Research Council (CSIC), University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
| | - Carmen Hidalgo-Tenorio
- Unit of Infectious Diseases, Virgen de las Nieves University Hospital, Biohealth Research Institute, IBS-Granada, Granada, Spain
| | - Anna Rull
- CIBERINFEC, Institute of Health Carlos III (ISCIII), Madrid, Spain
- Joan XXIII University Hospital of Tarragona, IISPV, University of Rovira i Virgili, Tarragona, Spain
| | - Julian Olalla
- Internal Medicine Department, Costa Del Sol Hospital, Marbella, Spain
| | - Miguel A. Lopez-Ruz
- Unit of Infectious Diseases, Virgen de las Nieves University Hospital, Biohealth Research Institute, IBS-Granada, Granada, Spain
| | - Francesc Vidal
- CIBERINFEC, Institute of Health Carlos III (ISCIII), Madrid, Spain
- Joan XXIII University Hospital of Tarragona, IISPV, University of Rovira i Virgili, Tarragona, Spain
| | - Consuelo Viladés
- CIBERINFEC, Institute of Health Carlos III (ISCIII), Madrid, Spain
- Joan XXIII University Hospital of Tarragona, IISPV, University of Rovira i Virgili, Tarragona, Spain
| | | | - Matthias Cavassini
- Service of Infectious Diseases, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Nuria Espinosa
- Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital, Spanish National Research Council (CSIC), University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
| | - Matthieu Perreau
- Service of Immunology and Allergy, Lausanne University Hospital and
| | - Joaquin Peraire
- CIBERINFEC, Institute of Health Carlos III (ISCIII), Madrid, Spain
- Joan XXIII University Hospital of Tarragona, IISPV, University of Rovira i Virgili, Tarragona, Spain
| | - Antonio Rivero
- CIBERINFEC, Institute of Health Carlos III (ISCIII), Madrid, Spain
- Service of Infectious Diseases, Reina Sofía University Hospital, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Córdoba University, Cordoba, Spain
| | - Luis F. López-Cortes
- Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital, Spanish National Research Council (CSIC), University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Xu G. Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Ezequiel Ruiz-Mateos
- Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital, Spanish National Research Council (CSIC), University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
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