1
|
Duran-Castells C, Prats A, Oriol-Tordera B, Llano A, Galvez C, Martinez-Picado J, Ballana E, Garcia-Vidal E, Clotet B, Muñoz-Moreno JA, Hanke T, Moltó J, Mothe B, Brander C, Ruiz-Riol M. Plasma proteomic profiling identifies CD33 as a marker of HIV control in natural infection and after therapeutic vaccination. EBioMedicine 2023; 95:104732. [PMID: 37506557 PMCID: PMC10410179 DOI: 10.1016/j.ebiom.2023.104732] [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: 01/17/2023] [Revised: 07/10/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND Biomarkers predicting the outcome of HIV-1 virus control in natural infection and after therapeutic interventions in HIV-1 cure trials remain poorly defined. The BCN02 trial (NCT02616874), combined a T-cell vaccine with romidepsin (RMD), a cancer-drug that was used to promote HIV-1 latency reversal and which has also been shown to have beneficial effects on neurofunction. We conducted longitudinal plasma proteomics analyses in trial participants to define biomarkers associated with virus control during monitored antiretroviral pause (MAP) and to identify novel therapeutic targets that can improve future cure strategies. METHODS BCN02 was a phase I, open-label, single-arm clinical trial in early-treated, HIV infected individuals. Longitudinal plasma proteomes were analyzed in 11 BCN02 participants, including 8 participants that showed a rapid HIV-1 plasma rebound during a monitored antiretroviral pause (MAP-NC, 'non-controllers') and 3 that remained off ART with sustained plasma viremia <2000 copies/ml (MAP-C, 'controllers'). Inflammatory and neurological proteomes in plasma were evaluated and integration data analysis (viral and neurocognitive parameters) was performed. Validation studies were conducted in a cohort of untreated HIV-1+ individuals (n = 96) and in vitro viral replication assays using an anti-CD33 antibody were used for functional validation. FINDINGS Inflammatory plasma proteomes in BCN02 participants showed marked longitudinal alterations. Strong proteome differences were also observed between MAP-C and MAP-NC, including in baseline timepoints. CD33/Siglec-3 was the unique plasma marker with the ability to discriminate between MAPC-C and MAP-NC at all study timepoints and showed positive correlations with viral parameters. Analyses in an untreated cohort of PLWH confirmed the positive correlation between viral parameters and CD33 plasma levels, as well as PBMC gene expression. Finally, adding an anti-CD33 antibody to in vitro virus cultures significantly reduced HIV-1 replication and proviral levels in T cells and macrophages. INTERPRETATION This study indicates that CD33/Siglec-3 may serve as a predictor of HIV-1 control and as potential therapeutic tool to improve future cure strategies. FUNDING Spanish Science and Innovation Ministry (SAF2017-89726-R and PID2020-119710RB-I00), NIH (P01-AI131568), European Commission (GA101057548) and a Grifols research agreement.
Collapse
Affiliation(s)
- Clara Duran-Castells
- IrsiCaixa AIDS Research Institute Badalona, Hospital Universitari Germans Trias i Pujol, Badalona, Spain; Universitat Autònoma de Barcelona, Spain
| | - Anna Prats
- Fight Infections Foundation and Infectious Diseases Department, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Bruna Oriol-Tordera
- IrsiCaixa AIDS Research Institute Badalona, Hospital Universitari Germans Trias i Pujol, Badalona, Spain; Universitat Autònoma de Barcelona, Spain
| | - Anuska Llano
- IrsiCaixa AIDS Research Institute Badalona, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Cristina Galvez
- IrsiCaixa AIDS Research Institute Badalona, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Javier Martinez-Picado
- IrsiCaixa AIDS Research Institute Badalona, Hospital Universitari Germans Trias i Pujol, Badalona, Spain; University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain; Catalan Institution for Research Advanced Studies (ICREA), Barcelona, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Ester Ballana
- IrsiCaixa AIDS Research Institute Badalona, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Edurne Garcia-Vidal
- IrsiCaixa AIDS Research Institute Badalona, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Bonaventura Clotet
- IrsiCaixa AIDS Research Institute Badalona, Hospital Universitari Germans Trias i Pujol, Badalona, Spain; Fight Infections Foundation and Infectious Diseases Department, Hospital Universitari Germans Trias i Pujol, Badalona, Spain; University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain
| | - Jose A Muñoz-Moreno
- Fight Infections Foundation and Infectious Diseases Department, Hospital Universitari Germans Trias i Pujol, Badalona, Spain; Faculty of Psychology and Education Sciences, Universitat Oberta de Catalunya (UOC), Barcelona, Spain
| | - Thomas Hanke
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK; Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - José Moltó
- Fight Infections Foundation and Infectious Diseases Department, Hospital Universitari Germans Trias i Pujol, Badalona, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Beatriz Mothe
- IrsiCaixa AIDS Research Institute Badalona, Hospital Universitari Germans Trias i Pujol, Badalona, Spain; Fight Infections Foundation and Infectious Diseases Department, Hospital Universitari Germans Trias i Pujol, Badalona, Spain; University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Christian Brander
- IrsiCaixa AIDS Research Institute Badalona, Hospital Universitari Germans Trias i Pujol, Badalona, Spain; Universitat Autònoma de Barcelona, Spain; University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain; Catalan Institution for Research Advanced Studies (ICREA), Barcelona, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Marta Ruiz-Riol
- IrsiCaixa AIDS Research Institute Badalona, Hospital Universitari Germans Trias i Pujol, Badalona, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain.
| |
Collapse
|
2
|
Miller RM, Knoener RA, Benner BE, Frey BL, Scalf M, Shortreed MR, Sherer NM, Smith LM. Discovery of Dehydroamino Acid Residues in the Capsid and Matrix Structural Proteins of HIV-1. J Proteome Res 2022; 21:993-1001. [PMID: 35192358 PMCID: PMC8976760 DOI: 10.1021/acs.jproteome.1c00867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) remains a deadly infectious disease despite existing antiretroviral therapies. A comprehensive understanding of the specific mechanisms of viral infectivity remains elusive and currently limits the development of new and effective therapies. Through in-depth proteomic analysis of HIV-1 virions, we discovered the novel post-translational modification of highly conserved residues within the viral matrix and capsid proteins to the dehydroamino acids, dehydroalanine and dehydrobutyrine. We further confirmed their presence by labeling the reactive alkene, characteristic of dehydroamino acids, with glutathione via Michael addition. Dehydroamino acids are rare, understudied, and have been observed mainly in select bacterial and fungal species. Until now, they have not been observed in HIV proteins. We hypothesize that these residues are important in viral particle maturation and could provide valuable insight into HIV infectivity mechanisms.
Collapse
Affiliation(s)
- Rachel M Miller
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Rachel A Knoener
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States.,McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of Wisconsin, Madison, Wisconsin 53705, United States
| | - Bayleigh E Benner
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of Wisconsin, Madison, Wisconsin 53705, United States
| | - Brian L Frey
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Michael R Shortreed
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Nathan M Sherer
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of Wisconsin, Madison, Wisconsin 53705, United States
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| |
Collapse
|
3
|
Tripathi D, Sodani M, Gupta PK, Kulkarni S. Host directed therapies: COVID-19 and beyond. CURRENT RESEARCH IN PHARMACOLOGY AND DRUG DISCOVERY 2021; 2:100058. [PMID: 34870156 PMCID: PMC8464038 DOI: 10.1016/j.crphar.2021.100058] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/14/2021] [Accepted: 09/19/2021] [Indexed: 12/15/2022] Open
Abstract
The global spread of SARS-CoV-2 has necessitated the development of novel, safe and effective therapeutic agents against this virus to stop the pandemic, however the development of novel antivirals may take years, hence, the best alternative available, is to repurpose the existing antiviral drugs with known safety profile in humans. After more than one year into this pandemic, global efforts have yielded the fruits and with the launch of many vaccines in the market, the world is inching towards the end of this pandemic, nonetheless, future pandemics of this magnitude or even greater cannot be denied. The preparedness against viruses of unknown origin should be maintained and the broad-spectrum antivirals with activity against range of viruses should be developed to curb future viral pandemics. The majority of antivirals developed till date are pathogen specific agents, which target critical viral pathways and lack broad spectrum activity required to target wide range of viruses. The surge in drug resistance among pathogens has rendered a compelling need to shift our focus towards host directed factors in the treatment of infectious diseases. This gains special relevance in the case of viral infections, where the pathogen encodes a handful of genes and predominantly depends on host factors for their propagation and persistence. Therefore, future antiviral drug development should focus more on targeting molecules of host pathways that are often hijacked by many viruses. Such cellular proteins of host pathways offer attractive targets for the development of broad-spectrum anticipatory antivirals. In the present article, we have reviewed the host directed therapies (HDTs) effective against viral infections with a special focus on COVID-19. This article also discusses the strategies involved in identifying novel host targets and subsequent development of broad spectrum HDTs.
Collapse
Affiliation(s)
- Devavrat Tripathi
- Radiation Medicine Centre, Bhabha Atomic Research Centre, C/O Tata Memorial Hospital Annexe, Parel, Mumbai, 400012, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Megha Sodani
- Radiation Medicine Centre, Bhabha Atomic Research Centre, C/O Tata Memorial Hospital Annexe, Parel, Mumbai, 400012, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Pramod Kumar Gupta
- Radiation Medicine Centre, Bhabha Atomic Research Centre, C/O Tata Memorial Hospital Annexe, Parel, Mumbai, 400012, India
- Corresponding author.
| | - Savita Kulkarni
- Radiation Medicine Centre, Bhabha Atomic Research Centre, C/O Tata Memorial Hospital Annexe, Parel, Mumbai, 400012, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
- Corresponding author. Radiation Medicine Centre, Bhabha Atomic Research Centre, C/O Tata Memorial Hospital Annexe, Parel, Mumbai, 400012, India.
| |
Collapse
|
4
|
Rodríguez-Gallego E, Tarancón-Diez L, García F, Del Romero J, Benito JM, Alba V, Herrero P, Rull A, Dominguez-Molina B, Martinez-Madrid O, Martin-Pena L, Pulido F, León A, Rodríguez C, Rallón N, Peraire J, Viladés C, Leal M, Vidal F, Ruiz-Mateos E. Proteomic Profile Associated With Loss of Spontaneous Human Immunodeficiency Virus Type 1 Elite Control. J Infect Dis 2020; 219:867-876. [PMID: 30312441 DOI: 10.1093/infdis/jiy599] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/05/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Elite controllers (ECs) spontaneously control plasma human immunodeficiency virus type 1 (HIV-1) RNA without antiretroviral therapy. However, 25% lose virological control over time. The aim of this work was to study the proteomic profile that preceded this loss of virological control to identify potential biomarkers. METHODS Plasma samples from ECs who spontaneously lost virological control (transient controllers [TCs]), at 2 years and 1 year before the loss of control, were compared with a control group of ECs who persistently maintained virological control during the same follow-up period (persistent controllers [PCs]). Comparative plasma shotgun proteomics was performed with tandem mass tag (TMT) isobaric tag labeling and nanoflow liquid chromatography coupled to Orbitrap mass spectrometry. RESULTS Eighteen proteins exhibited differences comparing PC and preloss TC timepoints. These proteins were involved in proinflammatory mechanisms, and some of them play a role in HIV-1 replication and pathogenesis and interact with structural viral proteins. Coagulation factor XI, α-1-antichymotrypsin, ficolin-2, 14-3-3 protein, and galectin-3-binding protein were considered potential biomarkers. CONCLUSIONS The proteomic signature associated with the spontaneous loss of virological control was characterized by higher levels of inflammation, transendothelial migration, and coagulation. Galectin-3 binding protein could be considered as potential biomarker for the prediction of virological progression and as therapeutic target in ECs.
Collapse
Affiliation(s)
- Esther Rodríguez-Gallego
- Hospital Universitari de Tarragona Joan XXIII, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Tarragona
| | - Laura Tarancón-Diez
- Laboratory of Immunovirology, Clinic Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville, Virgen del Rocío University Hospital/Consejo Superior de Investigaciones Científicas/University of Seville, Spain
| | - Felipe García
- Hospital Clinic-Fundació Clinic, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Centre Català d'Investigació i Desenvolupament de Vacunes contra la Sida, Universidad de Barcelona, Spain
| | - Jorge Del Romero
- Centro Sanitario Sandoval, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos, Madrid, Spain
| | - Jose Miguel Benito
- IIS-Fundación Jiménez Diaz, Universidad Autónoma de Madrid/Madrid Hospital Universitario Rey Juan Carlos, Móstoles, Spain
| | - Verónica Alba
- Hospital Universitari de Tarragona Joan XXIII, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Tarragona
| | - Pol Herrero
- Centre for Omic Sciences, Unitat Mixta Universitat Rovira i Virgili-Eurecat, Reus, Spain
| | - Anna Rull
- Hospital Universitari de Tarragona Joan XXIII, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Tarragona
| | - Beatriz Dominguez-Molina
- Laboratory of Immunovirology, Clinic Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville, Virgen del Rocío University Hospital/Consejo Superior de Investigaciones Científicas/University of Seville, Spain
| | - Onofre Martinez-Madrid
- Unidad Enfermedades Infecciosas, Hospital General Universitario Santa Lucía, Cartagena, Spain
| | - Luisa Martin-Pena
- Infectious Disease Service, Son Espases Hospital, Palma de Mallorca, Illes Balears, Spain.,Multidisciplinary Group for Infectious Disease Service, Institute of Health Sciences Research, Instituto de Investigación Sanitaria de Palma, Health Research Foundation Ramón Llull, Son Espases Hospital, Palma de Mallorca, Illes Balears
| | - Federico Pulido
- HIV Unit, Hospital Universitario 12 de Octubre, Universidad Complutense, Madrid, Spain
| | - Agathe León
- Hospital Clinic-Fundació Clinic, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Centre Català d'Investigació i Desenvolupament de Vacunes contra la Sida, Universidad de Barcelona, Spain
| | - Carmen Rodríguez
- Centro Sanitario Sandoval, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos, Madrid, Spain
| | - Norma Rallón
- IIS-Fundación Jiménez Diaz, Universidad Autónoma de Madrid/Madrid Hospital Universitario Rey Juan Carlos, Móstoles, Spain
| | - Joaquim Peraire
- Hospital Universitari de Tarragona Joan XXIII, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Tarragona
| | - Consuelo Viladés
- Hospital Universitari de Tarragona Joan XXIII, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Tarragona
| | - Manuel Leal
- Laboratory of Immunovirology, Clinic Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville, Virgen del Rocío University Hospital/Consejo Superior de Investigaciones Científicas/University of Seville, Spain.,Servicio de Medicina Interna, Hospital Viamed Santa Ángela de la Cruz, Sevilla, Spain
| | - Francesc Vidal
- Hospital Universitari de Tarragona Joan XXIII, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Tarragona
| | - Ezequiel Ruiz-Mateos
- Laboratory of Immunovirology, Clinic Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville, Virgen del Rocío University Hospital/Consejo Superior de Investigaciones Científicas/University of Seville, Spain
| | | |
Collapse
|
5
|
Ma Y, Zhao X, Jia J, Yang Y, Fan R, Lv M, Ding F, Wu J, Zhang J. Analysis of Protein Expression in Human Cells Cocultured with Porcine Peripheral Blood Mononuclear Cells. Intervirology 2019; 61:237-246. [PMID: 30889573 DOI: 10.1159/000495179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 10/15/2018] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE Porcine endogenous retroviruses (PERV) involved in pig to human xenotransplantation have raised great concerns because of their ubiquitous nature in pigs and their ability of infecting human cells in vitro. Although no significant cytopathic effect attributed to PERV was evident on PERV-infected human embryonic kidney 293 (HEK293) cells, we did proteomic analysis to investigate the differences of protein profile in order to further characterize the effect of PERV infection. METHODS HEK293 cells were cocultured with porcine peripheral blood mononuclear cells (PBMCs). Protein profiles of PERV-infected and -noninfected HEK293 cells were analyzed by two-dimensional gel electrophoresis (2-DE). Protein spots with at least 1.5-fold alteration were identified by high-definition mass spectrometry (HDMS) analysis. Then real-time RT-PCR and Western blotting were performed to validate the proteomic results. RESULTS Differential analysis of PERV-infected and -noninfected HEK293 cells by 2-DE revealed ten differentially regulated proteins. The proteins identified by HDMS were involved in various cellular pathways including signal transduction, cell apoptosis, and protein synthesis. CONCLUSION The results of this study revealed differentially expressed proteins in HEK293 cells cocultured with porcine PBMCs and implied that these changes were probably induced by PERV infection. These results provide clues and potential links to understanding the molecular effect of the infection by human-tropic PERV.
Collapse
Affiliation(s)
- Yuyuan Ma
- Beijing Key Laboratory of Blood Safety and Supply Technologies, Institute of Health Service and Transfusion Medicine, Academy of Military Medical Sciences, Beijing, China,
| | - Xiong Zhao
- Beijing Key Laboratory of Blood Safety and Supply Technologies, Institute of Health Service and Transfusion Medicine, Academy of Military Medical Sciences, Beijing, China
| | - Junting Jia
- Beijing Key Laboratory of Blood Safety and Supply Technologies, Institute of Health Service and Transfusion Medicine, Academy of Military Medical Sciences, Beijing, China.,Department of Blood Transfusion, Chinese PLA General Hospital, Beijing, China
| | - Yongxian Yang
- Beijing Key Laboratory of Blood Safety and Supply Technologies, Institute of Health Service and Transfusion Medicine, Academy of Military Medical Sciences, Beijing, China
| | - Rui Fan
- Beijing Key Laboratory of Blood Safety and Supply Technologies, Institute of Health Service and Transfusion Medicine, Academy of Military Medical Sciences, Beijing, China
| | - Maomin Lv
- Beijing Key Laboratory of Blood Safety and Supply Technologies, Institute of Health Service and Transfusion Medicine, Academy of Military Medical Sciences, Beijing, China
| | - Fang Ding
- Beijing Key Laboratory of Blood Safety and Supply Technologies, Institute of Health Service and Transfusion Medicine, Academy of Military Medical Sciences, Beijing, China
| | - Jianmin Wu
- Beijing Key Laboratory of Blood Safety and Supply Technologies, Institute of Health Service and Transfusion Medicine, Academy of Military Medical Sciences, Beijing, China.,Guangxi Veterinary Research Institute, Nanning, China
| | - Jingang Zhang
- Beijing Key Laboratory of Blood Safety and Supply Technologies, Institute of Health Service and Transfusion Medicine, Academy of Military Medical Sciences, Beijing, China
| |
Collapse
|
6
|
Golumbeanu M, Desfarges S, Hernandez C, Quadroni M, Rato S, Mohammadi P, Telenti A, Beerenwinkel N, Ciuffi A. Proteo-Transcriptomic Dynamics of Cellular Response to HIV-1 Infection. Sci Rep 2019; 9:213. [PMID: 30659199 PMCID: PMC6338737 DOI: 10.1038/s41598-018-36135-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 11/14/2018] [Indexed: 01/19/2023] Open
Abstract
Throughout the HIV-1 replication cycle, complex host-pathogen interactions take place in the infected cell, leading to the production of new virions. The virus modulates the host cellular machinery in order to support its life cycle, while counteracting intracellular defense mechanisms. We investigated the dynamic host response to HIV-1 infection by systematically measuring transcriptomic, proteomic, and phosphoproteomic expression changes in infected and uninfected SupT1 CD4+ T cells at five time points of the viral replication process. By means of a Gaussian mixed-effects model implemented in the new R/Bioconductor package TMixClust, we clustered host genes based on their temporal expression patterns. We identified a proteo-transcriptomic gene expression signature of 388 host genes specific for HIV-1 replication. Comprehensive functional analyses of these genes confirmed the previously described roles of some of the genes and revealed novel key virus-host interactions affecting multiple molecular processes within the host cell, including signal transduction, metabolism, cell cycle, and immune system. The results of our analysis are accessible through a freely available, dedicated and user-friendly R/Shiny application, called PEACHi2.0. This resource constitutes a catalogue of dynamic host responses to HIV-1 infection that provides a basis for a more comprehensive understanding of virus-host interactions.
Collapse
Affiliation(s)
- Monica Golumbeanu
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Sébastien Desfarges
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- InvivoGen, Toulouse, France
| | - Céline Hernandez
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
- Computational Systems Biology Team, Institut de Biologie de I'Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, ENS, PSL Université, Paris, France
| | - Manfredo Quadroni
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Sylvie Rato
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Pejman Mohammadi
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, (CA), USA
| | - Amalio Telenti
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, (CA), USA.
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland.
| | - Angela Ciuffi
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.
| |
Collapse
|
7
|
Saxena R, Vekariya U, Tripathi R. HIV-1 Nef and host proteome analysis: Current perspective. Life Sci 2019; 219:322-328. [PMID: 30664855 DOI: 10.1016/j.lfs.2019.01.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 01/17/2019] [Accepted: 01/17/2019] [Indexed: 01/23/2023]
Abstract
Proteome represents the set of proteins being produced by an organism at a given time. Comparative proteomic profiling of a healthy and diseased state is likely to reflect the dynamics of a disease process. Proteomic techniques are widely used to discover novel biomarkers and decipher mechanisms of HIV-1 pathogenesis. Proteomics is thus emerging as an indispensable tool of monitoring a disease process and intense interactions between HIV-1 and host. Nef is known to regulate various functions in the host to establish the state of infection. This review gives an overview of all proteomic studies done on HIV infection and HIV associated disorders including recent developments in Nef-host proteomic profiling. Here, we propose an emphasis on Nef based proteomic studies. We also discuss the future prospects and the technical and biological challenges involved in proteomic studies. Future studies with Nef related proteomic investigation are likely to identify more targets for diagnosis and therapy.
Collapse
Affiliation(s)
- Reshu Saxena
- Toxicology and Experimental Medicine Division, CSIR-Central Drug Research Institute, Sector-10, Janakipuram Extension, Sitapur Road, Lucknow 226031, U.P., India
| | - Umeshkumar Vekariya
- Toxicology and Experimental Medicine Division, CSIR-Central Drug Research Institute, Sector-10, Janakipuram Extension, Sitapur Road, Lucknow 226031, U.P., India
| | - Rajkamal Tripathi
- Toxicology and Experimental Medicine Division, CSIR-Central Drug Research Institute, Sector-10, Janakipuram Extension, Sitapur Road, Lucknow 226031, U.P., India.
| |
Collapse
|
8
|
Cheruiyot C, Pataki Z, Ramratnam B, Li M. Proteomic Analysis of Exosomes and Its Application in HIV-1 Infection. Proteomics Clin Appl 2018; 12:e1700142. [PMID: 29687643 DOI: 10.1002/prca.201700142] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 03/23/2018] [Indexed: 12/21/2022]
Abstract
Exosomes are 30-100 nm extracellular vesicles secreted from late endosomes by various types of cells. Numerous studies have suggested that exosomes play significant roles in human immunodeficiency virus 1 (HIV-1) biogenesis. Proteomics coupled with exosome fractionation has been successfully used to identify various exosomal proteins and helped to uncover the interactions between exosomes and HIV-1. To inform the current progress in the intersection of exosome, proteomics, and HIV-1, this review is focused on: i) analyzing different exosome isolation, purification methods, and their implications in HIV-1 studies; ii) evaluating the roles of various proteomic techniques in defining exosomal contents; iii) discussing the research and clinical applications of proteomics and exosome in HIV-1 biology.
Collapse
Affiliation(s)
- Collins Cheruiyot
- Department of Medicine, Division of Infectious Diseases, Laboratory of Retrovirology, Alpert Medical School of Brown University, Providence, RI, 02903, USA
| | - Zemplen Pataki
- Department of Medicine, Division of Infectious Diseases, Laboratory of Retrovirology, Alpert Medical School of Brown University, Providence, RI, 02903, USA
| | - Bharat Ramratnam
- Department of Medicine, Division of Infectious Diseases, Laboratory of Retrovirology, Alpert Medical School of Brown University, Providence, RI, 02903, USA.,Centers of Biomedical Research Excellence, Center for Cancer Research, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, RI, 02903, USA.,Clinical Research Center of Lifespan, Providence, RI, 02903, USA
| | - Ming Li
- Department of Medicine, Division of Infectious Diseases, Laboratory of Retrovirology, Alpert Medical School of Brown University, Providence, RI, 02903, USA
| |
Collapse
|
9
|
Butorov EV. Plasma L-Carnitine and L-Lysine Concentrations in HIV-Infected Patients. Open Biochem J 2017; 11:119-131. [PMID: 29387270 PMCID: PMC5750727 DOI: 10.2174/1874091x01711010119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 11/13/2017] [Accepted: 11/14/2017] [Indexed: 01/23/2023] Open
Abstract
Background: Virus infections are associated with significant alterations in host cells amino acids profiles that support biosynthetic demands necessary for production of viral progeny. Amino acids play an important role in the pathogenesis of all virus-related infections both as basic substrates for protein synthesis and as regulators in many metabolic pathways. Objective: Our aim was to determine the changes in plasma L-carnitine levels and its amino acid precursor (L-lysine) in HIV-infected patients. Methods: We performed a case-control study of 430 HIV-1 infected males (non-vegetarians) without any restriction in the
nourishment, before highly active antiretroviral therapy (HAART) and 125 HIV-1 subjects after the introduction of
HAART who were periodically monitored in the Municipal Center of HIV/AIDS prophylaxis, Surgut, Russian
Federation Results: The plasma total (TC) and free (FC) L-carnitine concentrations markedly decreased with the clinical stages of HIV infection. The mean plasma TC, FC and L-lysine levels were significantly lower in asymptomatic stage (A) and advanced CDC stages (B, C) HIV-infected patients compared with our reference values. The total and free L-carnitine and its amino acid precursor concentrations mild increased in HIV-infected subjects after the introduction of HAART. Our data revealed that L-lysine amino acid and its derivative (TC) levels were negatively correlated with viral load and inversely with CD4 count lymphocytes in the total cohort. Conclusion: The study results show that there was evidence for an association between plasma L-carnitine, L-lysine and HIV-1 RNA levels, immunological markers and clinical stages of HIV infection. The obtained data indicate that level changes of these host essential nutritional elements can play an important role in the HIV life cycle. These findings are important for understanding the pathophysiology of HIV infection and must be considered in further research for the development of new approaches in the treatment of the disease.
Collapse
Affiliation(s)
- Evgeny V Butorov
- The Municipal Center of HIV/AIDS prophylaxis, Surgut, Russian Federation
| |
Collapse
|
10
|
Lapek JD, Lewinski MK, Wozniak JM, Guatelli J, Gonzalez DJ. Quantitative Temporal Viromics of an Inducible HIV-1 Model Yields Insight to Global Host Targets and Phospho-Dynamics Associated with Protein Vpr. Mol Cell Proteomics 2017; 16:1447-1461. [PMID: 28606917 DOI: 10.1074/mcp.m116.066019] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 05/22/2017] [Indexed: 12/12/2022] Open
Abstract
The mechanisms by which human immunodeficiency virus (HIV) circumvents and coopts cellular machinery to replicate and persist in cells are not fully understood. HIV accessory proteins play key roles in the HIV life cycle by altering host pathways that are often dependent on post-translational modifications (PTMs). Thus, the identification of HIV accessory protein host targets and their PTM status is critical to fully understand how HIV invades, avoids detection and replicates to spread infection. To date, a comprehensive characterization of HIV accessory protein host targets and modulation of their PTM status does not exist. The significant gap in knowledge regarding the identity and PTMs of HIV host targets is due, in part, to technological limitations. Here, we applied current mass spectrometry techniques to define mechanisms of viral protein action by identifying host proteins whose abundance is affected by the accessory protein Vpr and the corresponding modulation of down-stream signaling pathways, specifically those regulated by phosphorylation. By utilizing a novel, inducible HIV-1 CD4+ T-cell model system expressing either the wild type or a vpr-negative viral genome, we overcame challenges associated with synchronization and infection-levels present in other models. We report identification and abundance dynamics of over 7000 proteins and 28,000 phospho-peptides. Consistent with Vpr's ability to impair cell-cycle progression, we observed Vpr-mediated modulation of spindle and centromere proteins, as well as Aurora kinase A and cyclin-dependent kinase 4 (CDK4). Unexpectedly, we observed evidence of Vpr-mediated modulation of the activity of serine/arginine-rich protein-specific kinases (SRPKs), suggesting a possible role for Vpr in the regulation of RNA splicing. This study presents a new experimental system and provides a data-resource that lays the foundation for validating host proteins and phosphorylation-pathways affected by HIV-1 and its accessory protein Vpr.
Collapse
Affiliation(s)
- John D Lapek
- From the ‡Department of Pharmacology.,§Skaggs School of Pharmacy and Pharmaceutical Sciences
| | - Mary K Lewinski
- §Skaggs School of Pharmacy and Pharmaceutical Sciences.,¶San Diego Veterans Affairs Healthcare System, San Diego, California 92161, and
| | - Jacob M Wozniak
- From the ‡Department of Pharmacology.,§Skaggs School of Pharmacy and Pharmaceutical Sciences
| | - John Guatelli
- ¶San Diego Veterans Affairs Healthcare System, San Diego, California 92161, and.,the ‖Department of Medicine, University of California San Diego, La Jolla, California 92093
| | - David J Gonzalez
- From the ‡Department of Pharmacology, .,§Skaggs School of Pharmacy and Pharmaceutical Sciences
| |
Collapse
|
11
|
Zhang L, Jia X, Jin JO, Lu H, Tan Z. Recent 5-year Findings and Technological Advances in the Proteomic Study of HIV-associated Disorders. GENOMICS, PROTEOMICS & BIOINFORMATICS 2017; 15:110-120. [PMID: 28391008 PMCID: PMC5415375 DOI: 10.1016/j.gpb.2016.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 11/03/2016] [Accepted: 11/24/2016] [Indexed: 12/24/2022]
Abstract
Human immunodeficiency virus-1 (HIV-1) mainly relies on host factors to complete its life cycle. Hence, it is very important to identify HIV-regulated host proteins. Proteomics is an excellent technique for this purpose because of its high throughput and sensitivity. In this review, we summarized current technological advances in proteomics, including general isobaric tags for relative and absolute quantitation (iTRAQ) and stable isotope labeling by amino acids in cell culture (SILAC), as well as subcellular proteomics and investigation of posttranslational modifications. Furthermore, we reviewed the applications of proteomics in the discovery of HIV-related diseases and HIV infection mechanisms. Proteins identified by proteomic studies might offer new avenues for the diagnosis and treatment of HIV infection and the related diseases.
Collapse
Affiliation(s)
- Lijun Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China.
| | - Xiaofang Jia
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Jun-O Jin
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Hongzhou Lu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Zhimi Tan
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| |
Collapse
|
12
|
Exosome-associated release, uptake, and neurotoxicity of HIV-1 Tat protein. J Neurovirol 2016; 22:774-788. [PMID: 27173397 DOI: 10.1007/s13365-016-0451-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 04/18/2016] [Accepted: 05/02/2016] [Indexed: 12/17/2022]
Abstract
HIV-1 Tat is an indispensible transactivator for HIV gene transcription and replication. It has been shown to exit cells as a free protein and enter neighboring cells or interact with surface receptors of neighboring cells to regulate gene expression and cell function. In this study, we report, for the first time, exosome-associated Tat release and uptake. Using a HIV-1 LTR-driven luciferase reporter-based cell assay and Western blotting or in combination with exosome inhibitor, OptiPrep gradient fractionation, and exosome depletion, we demonstrated significant presence of HIV-1 Tat in exosomes derived from Tat-expressing primary astrocytes, Tat-transfected U373.MG and 293T, and HIV-infected MT4. We further showed that exosome-associated Tat from Tat-expressing astrocytes was capable of causing neurite shortening and neuron death, further supporting that this new form of extracellular Tat is biologically active. Lastly, we constructed a Tat mutant deleted of its basic domain and determined the role of the basic domain in Tat trafficking into exosomes. Basic domain-deleted Tat exhibited no apparent effects on Tat trafficking into exosomes, while maintained its dominant-negative function in Tat-mediated LTR transactivation. Taken together, these results show a significant fraction of Tat is secreted and present in the form of exosomes and may contribute to the stability of extracellular Tat and broaden the spectrum of its target cells.
Collapse
|