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Yin L, Wang Q, Liu S, Chen J, Zhang Y, Lu L, Lu H, Song Z, Zhang L. iTRAQ-based proteomic study on monocyte cell model discovered an association of LAMP2 downregulation with HIV-1 latency. Proteome Sci 2024; 22:6. [PMID: 38750478 PMCID: PMC11095035 DOI: 10.1186/s12953-024-00230-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 05/06/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND Patients with immunodeficiency virus-1 (HIV-1) infection are challenging to be cured completely due to the existence of HIV-1 latency reservoirs. However, the knowledge of the mechanisms and biomarkers associated with HIV-1 latency is limited. Therefore, identifying proteins related to HIV-1 latency could provide new insights into the underlying mechanisms of HIV-1 latency, and ultimately contribute to the eradication of HIV reservoirs. METHODS An Isobaric Tags for Relative and Absolute Quantification (iTRAQ)-labeled subcellular proteomic study was performed on an HIV-1 latently infected cell model (U1, a HIV-1-integrated U937 cell line) and its control (U937). Differentially expressed proteins (DEPs) were analyzed using STRING-DB. Selected DEPs were further evaluated by western blotting and multiple reaction monitoring technology in both cell model and patient-derived cluster of differentiation 4 (CD4)+ T cells. Finally, we investigated the relationship between a specific DEP lysosome-associated membrane glycoprotein 2 (LAMP2) and HIV-1 reactivation by panobinostat or lysosome regulation by a lysosomotropic agent hydroxychloroquine in U1 and U937 cells. RESULTS In total, 110 DEPs were identified in U1 cells comparing to U937 control cells. Bioinformatics analysis suggested associations of the altered proteins with the immune response and endosomal/lysosomal pathway. LAMP2, leukocyte surface antigen CD47, CD55, and ITGA6 were downregulated in HIV-1 latent cells. Downregulated LAMP2 was further confirmed in resting CD4+ T cells from patients with latent HIV-1 infection. Furthermore, both HIV-1 reactivation by panobinostat and stimulation with hydroxychloroquine upregulated LAMP2 expression. CONCLUSIONS Our results indicated the involvement of the endosomal/lysosomal pathway in HIV-1 latency in macrophage cell model. The down-modulation of LAMP2 was associated with HIV latency, and the restoration of LAMP2 expression accompanied the transition of viral latency to active infection. This study provides new insights into the mechanism of HIV-1 latency and potential strategies for eradicating HIV-1 reservoirs by targeting LAMP2 expression.
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Affiliation(s)
- Lin Yin
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Qimin Wang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Siyuan Liu
- Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200011, China
| | - Jun Chen
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Yujiao Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Lingqing Lu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Hongzhou Lu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
- Department of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The Third People's Hospital of Shenzhen, Shenzhen, 518112, China
| | - Zhigang Song
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.
| | - Lijun Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.
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Heinz JL, Swagemakers SMA, von Hofsten J, Helleberg M, Thomsen MM, De Keukeleere K, de Boer JH, Ilginis T, Verjans GMGM, van Hagen PM, van der Spek PJ, Mogensen TH. Whole exome sequencing of patients with varicella-zoster virus and herpes simplex virus induced acute retinal necrosis reveals rare disease-associated genetic variants. Front Mol Neurosci 2023; 16:1253040. [PMID: 38025266 PMCID: PMC10630912 DOI: 10.3389/fnmol.2023.1253040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 10/09/2023] [Indexed: 12/01/2023] Open
Abstract
Purpose Herpes simplex virus (HSV) and varicella-zoster virus (VZV) are neurotropic human alphaherpesviruses endemic worldwide. Upon primary infection, both viruses establish lifelong latency in neurons and reactivate intermittently to cause a variety of mild to severe diseases. Acute retinal necrosis (ARN) is a rare, sight-threatening eye disease induced by ocular VZV or HSV infection. The virus and host factors involved in ARN pathogenesis remain incompletely described. We hypothesize an underlying genetic defect in at least part of ARN cases. Methods We collected blood from 17 patients with HSV-or VZV-induced ARN, isolated DNA and performed Whole Exome Sequencing by Illumina followed by analysis in Varseq with criteria of CADD score > 15 and frequency in GnomAD < 0.1% combined with biological filters. Gene modifications relative to healthy control genomes were filtered according to high quality and read-depth, low frequency, high deleteriousness predictions and biological relevance. Results We identified a total of 50 potentially disease-causing genetic variants, including missense, frameshift and splice site variants and on in-frame deletion in 16 of the 17 patients. The vast majority of these genes are involved in innate immunity, followed by adaptive immunity, autophagy, and apoptosis; in several instances variants within a given gene or pathway was identified in several patients. Discussion We propose that the identified variants may contribute to insufficient viral control and increased necrosis ocular disease presentation in the patients and serve as a knowledge base and starting point for the development of improved diagnostic, prophylactic, and therapeutic applications.
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Affiliation(s)
- Johanna L. Heinz
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Sigrid M. A. Swagemakers
- Department of Pathology and Clinical Bioinformatics, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Joanna von Hofsten
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Ophthalmology, Halland Hospital Halmstad, Halmstad, Sweden
| | - Marie Helleberg
- Department of Infectious Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Center of Excellence for Health, Immunity and Infections, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Michelle M. Thomsen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Kerstin De Keukeleere
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Joke H. de Boer
- Department of Ophthalmology, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Tomas Ilginis
- Department of Ophthalmology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Georges M. G. M. Verjans
- HerpeslabNL, Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Peter M. van Hagen
- Department of Internal Medicine and Immunology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Peter J. van der Spek
- Department of Pathology and Clinical Bioinformatics, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Trine H. Mogensen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
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Pesce E, Manfrini N, Cordiglieri C, Santi S, Bandera A, Gobbini A, Gruarin P, Favalli A, Bombaci M, Cuomo A, Collino F, Cricrì G, Ungaro R, Lombardi A, Mangioni D, Muscatello A, Aliberti S, Blasi F, Gori A, Abrignani S, De Francesco R, Biffo S, Grifantini R. Exosomes Recovered From the Plasma of COVID-19 Patients Expose SARS-CoV-2 Spike-Derived Fragments and Contribute to the Adaptive Immune Response. Front Immunol 2022; 12:785941. [PMID: 35111156 PMCID: PMC8801440 DOI: 10.3389/fimmu.2021.785941] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/16/2021] [Indexed: 12/12/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is an infectious disease caused by beta-coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that has rapidly spread across the globe starting from February 2020. It is well established that during viral infection, extracellular vesicles become delivery/presenting vectors of viral material. However, studies regarding extracellular vesicle function in COVID-19 pathology are still scanty. Here, we performed a comparative study on exosomes recovered from the plasma of either MILD or SEVERE COVID-19 patients. We show that although both types of vesicles efficiently display SARS-CoV-2 spike-derived peptides and carry immunomodulatory molecules, only those of MILD patients are capable of efficiently regulating antigen-specific CD4+ T-cell responses. Accordingly, by mass spectrometry, we show that the proteome of exosomes of MILD patients correlates with a proper functioning of the immune system, while that of SEVERE patients is associated with increased and chronic inflammation. Overall, we show that exosomes recovered from the plasma of COVID-19 patients possess SARS-CoV-2-derived protein material, have an active role in enhancing the immune response, and possess a cargo that reflects the pathological state of patients in the acute phase of the disease.
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Affiliation(s)
- Elisa Pesce
- Istituto Nazionale Genetica Molecolare (INGM), Istituto Nazionale Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan, Italy
| | - Nicola Manfrini
- Istituto Nazionale Genetica Molecolare (INGM), Istituto Nazionale Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan, Italy
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Chiara Cordiglieri
- Istituto Nazionale Genetica Molecolare (INGM), Istituto Nazionale Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan, Italy
| | - Spartaco Santi
- Unit of Bologna, Consiglio Nazionale delle Ricerche (CNR) Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza”, Bologna, Italy
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Alessandra Bandera
- Infectious Diseases Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
- Centre for Multidisciplinary Research in Health Science (MACH), Università degli Studi di Milano, Milan, Italy
| | - Andrea Gobbini
- Istituto Nazionale Genetica Molecolare (INGM), Istituto Nazionale Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan, Italy
| | - Paola Gruarin
- Istituto Nazionale Genetica Molecolare (INGM), Istituto Nazionale Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan, Italy
| | - Andrea Favalli
- Istituto Nazionale Genetica Molecolare (INGM), Istituto Nazionale Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan, Italy
| | - Mauro Bombaci
- Istituto Nazionale Genetica Molecolare (INGM), Istituto Nazionale Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan, Italy
| | - Alessandro Cuomo
- Department of Experimental Oncology, Istituto Europeo di Oncologia (IEO), European Institute of Oncology Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
| | - Federica Collino
- Laboratory of Translational Research in Paediatric Nephro-Urology, Fondazione Ca’ Granda IRCCS Ospedale Maggiore Policlinico, Milan, Italy
- Department of Clinical Sciences and Community Health, University of Milano, Milan, Italy
| | - Giulia Cricrì
- Laboratory of Translational Research in Paediatric Nephro-Urology, Fondazione Ca’ Granda IRCCS Ospedale Maggiore Policlinico, Milan, Italy
- Department of Clinical Sciences and Community Health, University of Milano, Milan, Italy
| | - Riccardo Ungaro
- Infectious Diseases Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Andrea Lombardi
- Infectious Diseases Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Davide Mangioni
- Infectious Diseases Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Antonio Muscatello
- Infectious Diseases Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefano Aliberti
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
- Respiratory Unit and Cystic Fibrosis Adult Center, Respiratory Unit and Cystic Fibrosis Adult Center, Milan, Italy
| | - Francesco Blasi
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
- Respiratory Unit and Cystic Fibrosis Adult Center, Respiratory Unit and Cystic Fibrosis Adult Center, Milan, Italy
| | - Andrea Gori
- Infectious Diseases Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
- Centre for Multidisciplinary Research in Health Science (MACH), Università degli Studi di Milano, Milan, Italy
| | - Sergio Abrignani
- Istituto Nazionale Genetica Molecolare (INGM), Istituto Nazionale Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan, Italy
- Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Raffaele De Francesco
- Istituto Nazionale Genetica Molecolare (INGM), Istituto Nazionale Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan, Italy
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy
| | - Stefano Biffo
- Istituto Nazionale Genetica Molecolare (INGM), Istituto Nazionale Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan, Italy
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Renata Grifantini
- Istituto Nazionale Genetica Molecolare (INGM), Istituto Nazionale Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan, Italy
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