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Liu J, Ding C, Shi Y, Wang Y, Zhang X, Huang L, Fang Q, Shuai C, Gao Y, Wu J. Advances in Mechanism of HIV-1 Immune Reconstitution Failure: Understanding Lymphocyte Subpopulations and Interventions for Immunological Nonresponders. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:1609-1620. [PMID: 38768409 DOI: 10.4049/jimmunol.2300777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 04/08/2024] [Indexed: 05/22/2024]
Abstract
In individuals diagnosed with AIDS, the primary method of sustained suppression of HIV-1 replication is antiretroviral therapy, which systematically increases CD4+ T cell levels and restores immune function. However, there is still a subset of 10-40% of people living with HIV who not only fail to reach normal CD4+ T cell counts but also experience severe immune dysfunction. These individuals are referred to as immunological nonresponders (INRs). INRs have a higher susceptibility to opportunistic infections and non-AIDS-related illnesses, resulting in increased morbidity and mortality rates. Therefore, it is crucial to gain new insights into the primary mechanisms of immune reconstitution failure to enable early and effective treatment for individuals at risk. This review provides an overview of the dynamics of key lymphocyte subpopulations, the main molecular mechanisms of INRs, clinical diagnosis, and intervention strategies during immune reconstitution failure, primarily from a multiomics perspective.
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Affiliation(s)
- Jiamin Liu
- School of Public Health, Anhui Medical University, Hefei, China
| | - Chengchao Ding
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yu Shi
- School of Public Health, Anhui Medical University, Hefei, China
| | - Yiyu Wang
- School of Public Health, Anhui Medical University, Hefei, China
| | - Xiangyu Zhang
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Lina Huang
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Qin Fang
- Central Laboratory of HIV Molecular and Immunology, Anhui Provincial Center for Disease Control and Prevention, Hefei, China
| | - Chenxi Shuai
- Central Laboratory of HIV Molecular and Immunology, Anhui Provincial Center for Disease Control and Prevention, Hefei, China
| | - Yong Gao
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Jianjun Wu
- School of Public Health, Anhui Medical University, Hefei, China
- Central Laboratory of HIV Molecular and Immunology, Anhui Provincial Center for Disease Control and Prevention, Hefei, China
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Espineira S, Flores-Piñas M, Chafino S, Viladés C, Negredo E, Fernández-Arroyo S, Mallolas J, Villar B, Moreno S, Vidal F, Rull A, Peraire J. Multi-omics in HIV: searching insights to understand immunological non-response in PLHIV. Front Immunol 2023; 14:1228795. [PMID: 37649488 PMCID: PMC10465175 DOI: 10.3389/fimmu.2023.1228795] [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: 05/25/2023] [Accepted: 07/25/2023] [Indexed: 09/01/2023] Open
Abstract
Antiretroviral therapy (ART) induces persistent suppression of HIV-1 replication and gradual recovery of T-cell counts, and consequently, morbidity and mortality from HIV-related illnesses have been significantly reduced. However, in approximately 30% of people living with HIV (PLHIV) on ART, CD4+ T-cell counts fail to normalize despite ART and complete suppression of HIV viral load, resulting in severe immune dysfunction, which may represent an increased risk of clinical progression to AIDS and non-AIDS events as well as increased mortality. These patients are referred to as "immune inadequate responders", "immunodiscordant responders" or "immune nonresponders (INR)". The molecular mechanisms underlying poor CD4+ T-cell recovery are still unclear. In this sense, the use of omics sciences has shed light on possible factors involved in the activity and metabolic dysregulation of immune cells during the failure of CD4+ T-cell recovery in INR. Moreover, identification of key molecules by omics approaches allows for the proposal of potential biomarkers or therapeutic targets to improve CD4+ T-cell recovery and the quality of life of these patients. Hence, this review aimed to summarize the information obtained through different omics concerning the molecular factors and pathways associated with the INR phenotype to better understand the complexity of this immunological status in HIV infection.
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Affiliation(s)
- Sonia Espineira
- Infection and Immunity Research Group (INIM), Institut Investigació Sanitària Pere Virgili (IISPV), Tarragona, Spain
- Infection and Immunity Research Group (INIM), Hospital Universitari de Tarragona Joan XXIII (HJ23), Tarragona, Spain
- Universitat Rovira i Virgili (URV), Tarragona, Spain
| | - Marina Flores-Piñas
- Infection and Immunity Research Group (INIM), Institut Investigació Sanitària Pere Virgili (IISPV), Tarragona, Spain
- Infection and Immunity Research Group (INIM), Hospital Universitari de Tarragona Joan XXIII (HJ23), Tarragona, Spain
| | - Silvia Chafino
- Infection and Immunity Research Group (INIM), Hospital Universitari de Tarragona Joan XXIII (HJ23), Tarragona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Consuelo Viladés
- Infection and Immunity Research Group (INIM), Institut Investigació Sanitària Pere Virgili (IISPV), Tarragona, Spain
- Infection and Immunity Research Group (INIM), Hospital Universitari de Tarragona Joan XXIII (HJ23), Tarragona, Spain
- Universitat Rovira i Virgili (URV), Tarragona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Eugenia Negredo
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Lluita contra les Infeccions, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
- Universitat Autònoma de Barcelona, Barcelona, Spain
- Universitat de Vic - Universitat Central de Catalunya, Vic, Spain
| | - Salvador Fernández-Arroyo
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences, Joint Unit Eurecat-Universitat Rovira i Virgili, Unique Scientific and Technical Infrastructure (ICTS), Reus, Spain
| | - Josep Mallolas
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- HIV Unit, Hospital Clínic-Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Beatriz Villar
- Infection and Immunity Research Group (INIM), Institut Investigació Sanitària Pere Virgili (IISPV), Tarragona, Spain
- Infection and Immunity Research Group (INIM), Hospital Universitari de Tarragona Joan XXIII (HJ23), Tarragona, Spain
- Universitat Rovira i Virgili (URV), Tarragona, Spain
| | - Santiago Moreno
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Department of Infectious Diseases, University Hospital Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Universidad de Alcalá (UAH), Madrid, Spain
| | - Francesc Vidal
- Infection and Immunity Research Group (INIM), Institut Investigació Sanitària Pere Virgili (IISPV), Tarragona, Spain
- Infection and Immunity Research Group (INIM), Hospital Universitari de Tarragona Joan XXIII (HJ23), Tarragona, Spain
- Universitat Rovira i Virgili (URV), Tarragona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Anna Rull
- Infection and Immunity Research Group (INIM), Institut Investigació Sanitària Pere Virgili (IISPV), Tarragona, Spain
- Infection and Immunity Research Group (INIM), Hospital Universitari de Tarragona Joan XXIII (HJ23), Tarragona, Spain
- Universitat Rovira i Virgili (URV), Tarragona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Joaquim Peraire
- Infection and Immunity Research Group (INIM), Institut Investigació Sanitària Pere Virgili (IISPV), Tarragona, Spain
- Infection and Immunity Research Group (INIM), Hospital Universitari de Tarragona Joan XXIII (HJ23), Tarragona, Spain
- Universitat Rovira i Virgili (URV), Tarragona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
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Beliakova-Bethell N, Manousopoulou A, Deshmukh S, Mukim A, Richman DD, Garbis SD, Spina CA. Integrated proteomics and transcriptomics analyses identify novel cell surface markers of HIV latency. Virology 2022; 573:50-58. [PMID: 35714458 PMCID: PMC10427345 DOI: 10.1016/j.virol.2022.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/19/2022] [Accepted: 06/01/2022] [Indexed: 10/18/2022]
Abstract
Elimination of the latent HIV cell reservoir may be possible, if the molecular identity of latently infected cells were fully elucidated. We conducted comprehensive molecular profiling, at the protein and RNA levels, of primary T cells latently infected with HIV in vitro. Isobaric labelling quantitative proteomics and RNA sequencing identified 1453 proteins and 618 genes, altered in latently infected cells compared to mock-infected controls (p < 0.05). Biomarker selection was based on results from integrated data analysis. Relative enrichment for latently infected cells was monitored using flow cytometric sorting and the HIV integrant assay. Antibodies against selected proteins, encoded by CEACAM1 and PLXNB2, enabled enrichment of latently infected cells from cell mixtures by 3-10 fold (5.8 average, p < 0.001), comparable to levels obtained with biomarkers reported previously. Individual biomarkers are likely linked to subsets of latently infected cells, and an extended antibody panel will be required to inclusively target the latent HIV reservoir.
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Affiliation(s)
- Nadejda Beliakova-Bethell
- VA San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, CA, USA; University of California at San Diego, CA, USA.
| | - Antigoni Manousopoulou
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK; Proteas Bioanalytics Inc., BioLabs at the Lundquist Institute, Torrance, CA, USA
| | | | - Amey Mukim
- University of California at San Diego, CA, USA
| | - Douglas D Richman
- VA San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, CA, USA; University of California at San Diego, CA, USA
| | - Spiros D Garbis
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK; Proteas Bioanalytics Inc., BioLabs at the Lundquist Institute, Torrance, CA, USA
| | - Celsa A Spina
- VA San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, CA, USA; University of California at San Diego, CA, USA
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4
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Rodchenkov I, Babur O, Luna A, Aksoy BA, Wong JV, Fong D, Franz M, Siper MC, Cheung M, Wrana M, Mistry H, Mosier L, Dlin J, Wen Q, O’Callaghan C, Li W, Elder G, Smith PT, Dallago C, Cerami E, Gross B, Dogrusoz U, Demir E, Bader GD, Sander C. Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. Nucleic Acids Res 2020; 48:D489-D497. [PMID: 31647099 PMCID: PMC7145667 DOI: 10.1093/nar/gkz946] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 10/07/2019] [Accepted: 10/10/2019] [Indexed: 12/14/2022] Open
Abstract
Pathway Commons (https://www.pathwaycommons.org) is an integrated resource of publicly available information about biological pathways including biochemical reactions, assembly of biomolecular complexes, transport and catalysis events and physical interactions involving proteins, DNA, RNA, and small molecules (e.g. metabolites and drug compounds). Data is collected from multiple providers in standard formats, including the Biological Pathway Exchange (BioPAX) language and the Proteomics Standards Initiative Molecular Interactions format, and then integrated. Pathway Commons provides biologists with (i) tools to search this comprehensive resource, (ii) a download site offering integrated bulk sets of pathway data (e.g. tables of interactions and gene sets), (iii) reusable software libraries for working with pathway information in several programming languages (Java, R, Python and Javascript) and (iv) a web service for programmatically querying the entire dataset. Visualization of pathways is supported using the Systems Biological Graphical Notation (SBGN). Pathway Commons currently contains data from 22 databases with 4794 detailed human biochemical processes (i.e. pathways) and ∼2.3 million interactions. To enhance the usability of this large resource for end-users, we develop and maintain interactive web applications and training materials that enable pathway exploration and advanced analysis.
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Affiliation(s)
- Igor Rodchenkov
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Ozgun Babur
- Department of Molecular and Medical Genetics, School of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Augustin Luna
- cBio Center, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA 02215, USA
| | - Bulent Arman Aksoy
- Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY 10065, USA
| | - Jeffrey V Wong
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Dylan Fong
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Max Franz
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Metin Can Siper
- Department of Molecular and Medical Genetics, School of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Manfred Cheung
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Michael Wrana
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Harsh Mistry
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Logan Mosier
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Jonah Dlin
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Qizhi Wen
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Caitlin O’Callaghan
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Wanxin Li
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Geoffrey Elder
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Peter T Smith
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Christian Dallago
- Department of Cell Biology, Harvard Medical School, Boston, MA 02215, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA 02215, USA
- Department of Informatics, Technische Universität München, 85748 Garching, Germany
| | - Ethan Cerami
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Benjamin Gross
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ugur Dogrusoz
- Department of Computer Engineering, Bilkent University, Ankara 06800, Turkey
| | - Emek Demir
- Department of Molecular and Medical Genetics, School of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Gary D Bader
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Chris Sander
- cBio Center, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA 02215, USA
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5
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Wang C, Beiss V, Steinmetz NF. Cowpea Mosaic Virus Nanoparticles and Empty Virus-Like Particles Show Distinct but Overlapping Immunostimulatory Properties. J Virol 2019; 93:e00129-19. [PMID: 31375592 PMCID: PMC6803287 DOI: 10.1128/jvi.00129-19] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 07/16/2019] [Indexed: 12/30/2022] Open
Abstract
Cowpea mosaic virus (CPMV) is a plant virus that has been developed for multiple biomedical and nanotechnology applications, including immunotherapy. Two key platforms are available: virus nanoparticles (VNPs) based on the complete CMPV virion, including the genomic RNA, and virus-like nanoparticles (VLPs) based on the empty CPMV (eCPMV) virion. It is unclear whether these platforms differ in terms of immunotherapeutic potential. We therefore compared their physicochemical properties and immunomodulatory activities following in situ vaccination of an aggressive ovarian tumor mouse model (ID8-Defb29/Vegf-A). In physicochemical terms, CPMV and eCPMV were very similar, and both significantly increased the survival of tumor-bearing mice and showed promising antitumor efficacy. However, they demonstrated distinct yet overlapping immunostimulatory effects due to the presence of virus RNA in wild-type particles, indicating their suitability for different immunotherapeutic strategies. Specifically, we found that the formulations had similar effects on most secreted cytokines and immune cells, but the RNA-containing CPMV particles were uniquely able to boost populations of potent antigen-presenting cells, such as tumor-infiltrating neutrophils and activated dendritic cells. Our results will facilitate the development of CPMV and eCPMV as immunotherapeutic vaccine platforms with tailored responses.IMPORTANCE The engagement of antiviral effector responses caused by viral infection is essential when using viruses or virus-like particles (VLPs) as an immunotherapeutic agent. Here, we compare the chemophysical and immunostimulatory properties of wild-type cowpea mosaic virus (CPMV) (RNA containing) and eCPMV (RNA-free VLPs) produced from two expression systems (agrobacterium-based plant expression system and baculovirus-insect cell expression). CPMV and eCPMV could each be developed as novel adjuvants to overcome immunosuppression and thus promote tumor regression in ovarian cancer (and other tumor types). To our knowledge, this is the first study to define the immunotherapeutic differences between CPMV and eCPMV, which is essential for the further development of biomedical applications for plant viruses and the selection of rational combinations of immunomodulatory reagents.
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Affiliation(s)
- Chao Wang
- Department of NanoEngineering, University of California, San Diego, La Jolla, California, USA
- Department of Biomedical Engineering, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Veronique Beiss
- Department of NanoEngineering, University of California, San Diego, La Jolla, California, USA
- Department of Biomedical Engineering, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Nicole F Steinmetz
- Department of NanoEngineering, University of California, San Diego, La Jolla, California, USA
- Moores Cancer Center, University of California, San Diego, La Jolla, California, USA
- Department of Radiology, University of California, San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
- Department of Biomedical Engineering, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
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Mozhgani SH, Zarei Ghobadi M, Behnam Rad M, Farzanehpour M, Behzadian F. Reconnaissance of the candidate genes involved in the pathogenesis of human immunodeficiency virus and targeted by antiretroviral therapy. J Med Virol 2019; 91:2134-2141. [PMID: 31317550 DOI: 10.1002/jmv.25549] [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: 04/07/2019] [Accepted: 07/06/2019] [Indexed: 11/11/2022]
Abstract
The expression levels of many genes change after treatment of human immunodeficiency virus (HIV)-infected subjects by antiretroviral drugs. High-throughput analysis of tremendous datasets led to the discovery of genes that are implicated in the treatment pathways. In this study, we performed a gene-enrichment analysis after determining the differentially expressed genes (DEGs) between untreated HIV-positive and HIV-negative subjects and also between treated HIV-positive subjects with antiretroviral therapy (ART; who receiving nucleoside reverse transcriptase inhibitor-based ART) and untreated HIV-positive cases in the peripheral blood mononuclear cells (PBMCs), adipose, and muscle tissues. In sum, the genes that activate inflammatory, immune response, proliferation, metabolism, and viral involvement pathways have different expression patterns in the untreated HIV-positive subjects and treated HIV-positive cases. Moreover, the expression levels of the genes including ACLY, ALDH18A1, HADHA, and YARS in the PBMCs tissue and HBEGF, PKN3, DEGS2, and EDN3 in the fat tissue were found to be different in the HIV-infected patients, which can be considered as new biomarkers for HIV infection.
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Affiliation(s)
- Sayed-Hamidreza Mozhgani
- Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran.,Non-communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Mohadeseh Zarei Ghobadi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.,Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Mohammad Behnam Rad
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Mahdieh Farzanehpour
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Farida Behzadian
- Department of Bioscience and Biotechnology, Malek Ashtar University of Technology, Tehran, Iran
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7
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Saadane A, Petrov A, Mast N, El-Darzi N, Dao T, Alnemri A, Song Y, Dunaief JL, Pikuleva IA. Mechanisms that minimize retinal impact of apolipoprotein E absence. J Lipid Res 2018; 59:2368-2382. [PMID: 30333155 DOI: 10.1194/jlr.m090043] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 10/17/2018] [Indexed: 01/28/2023] Open
Abstract
Apolipoprotein E (APOE) is a component of lipid-transporting particles and a recognition ligand for receptors, which bind these particles. The APOE isoform ε2 is a risk factor for age-related macular degeneration; nevertheless, APOE absence in humans and mice does not significantly affect the retina. We found that retinal cholesterol biosynthesis and the levels of retinal cholesterol were increased in Apoe-/- mice, whereas cholesterol elimination by metabolism was decreased. No focal cholesterol deposits were observed in the Apoe-/- retina. Retinal proteomics identified the most abundant cholesterol-related proteins in WT mice and revealed that, of these cholesterol-related proteins, only APOA4 had increased expression in the Apoe-/- retina. In addition, there were changes in retinal abundance of proteins involved in proinflammatory and antiinflammatory responses, cellular cytoskeleton maintenance, vesicular traffic, and retinal iron homeostasis. The data obtained indicate that when APOE is absent, particles containing APOA1, APOA4, and APOJ still transport cholesterol in the intraretinal space, but these particles are not taken up by retinal cells. Therefore, cholesterol biosynthesis inside retinal cells increase, whereas metabolism to oxysterols decreases to prevent cells from cholesterol depletion. These and other compensatory changes underlie only a minor retinal phenotype in Apoe-/- mice.
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Affiliation(s)
- Aicha Saadane
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH
| | - Alexey Petrov
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH
| | - Natalia Mast
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH
| | - Nicole El-Darzi
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH
| | - Tung Dao
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH
| | - Ahab Alnemri
- F. M. Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Ying Song
- F. M. Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Joshua L Dunaief
- F. M. Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Irina A Pikuleva
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH
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8
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Karim AF, Sande OJ, Tomechko SE, Ding X, Li M, Maxwell S, Ewing RM, Harding CV, Rojas RE, Chance MR, Boom WH. Proteomics and Network Analyses Reveal Inhibition of Akt-mTOR Signaling in CD4 + T Cells by Mycobacterium tuberculosis Mannose-Capped Lipoarabinomannan. Proteomics 2017; 17:1700233. [PMID: 28994205 PMCID: PMC5725663 DOI: 10.1002/pmic.201700233] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 09/13/2017] [Indexed: 11/10/2022]
Abstract
Mycobacterium tuberculosis (Mtb) cell wall glycolipid mannose-capped lipoarabinomannan (ManLAM) inhibits CD4+ T-cell activation by inhibiting proximal T-cell receptor (TCR) signaling when activated by anti-CD3. To understand the impact of ManLAM on CD4+ T-cell function when both the TCR-CD3 complex and major costimulator CD28 are engaged, we performed label-free quantitative MS and network analysis. Mixed-effect model analysis of peptide intensity identified 149 unique peptides representing 131 proteins that were differentially regulated by ManLAM in anti-CD3- and anti-CD28-activated CD4+ T cells. Crosstalker, a novel network analysis tool identified dysregulated translation, TCA cycle, and RNA metabolism network modules. PCNA, Akt, mTOR, and UBC were found to be bridge node proteins connecting these modules of dysregulated proteins. Altered PCNA expression and cell cycle analysis showed arrest at the G2M phase. Western blot confirmed that ManLAM inhibited Akt and mTOR phosphorylation, and decreased expression of deubiquitinating enzymes Usp9x and Otub1. Decreased NF-κB phosphorylation suggested interference with CD28 signaling through inhibition of the Usp9x-Akt-mTOR pathway. Thus, ManLAM induced global changes in the CD4+ T-cell proteome by affecting Akt-mTOR signaling, resulting in broad functional impairment of CD4+ T-cell activation beyond inhibition of proximal TCR-CD3 signaling.
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Affiliation(s)
- Ahmad F. Karim
- Department of MedicineUniversity Hospitals Cleveland Medical CenterCase Western Reserve UniversityClevelandOHUSA
- Department of Molecular Biology & MicrobiologyCase Western Reserve UniversityClevelandOHUSA
| | - Obondo J. Sande
- Department of MedicineUniversity Hospitals Cleveland Medical CenterCase Western Reserve UniversityClevelandOHUSA
| | - Sara E. Tomechko
- Center for Proteomics & BioinformaticsCase Western Reserve UniversityClevelandOHUSA
| | - Xuedong Ding
- Department of MedicineUniversity Hospitals Cleveland Medical CenterCase Western Reserve UniversityClevelandOHUSA
| | - Ming Li
- Center for Proteomics & BioinformaticsCase Western Reserve UniversityClevelandOHUSA
| | - Sean Maxwell
- Center for Proteomics & BioinformaticsCase Western Reserve UniversityClevelandOHUSA
| | - Rob M. Ewing
- Centre for Biological SciencesUniversity of SouthamptonSouthamptonUK
| | - Clifford V. Harding
- Department of Molecular Biology & MicrobiologyCase Western Reserve UniversityClevelandOHUSA
- Department of PathologyUniversity Hospitals Cleveland Medical CenterCase Western Reserve UniversityClevelandOHUSA
| | - Roxana E. Rojas
- Department of Molecular Biology & MicrobiologyCase Western Reserve UniversityClevelandOHUSA
| | - Mark R. Chance
- Center for Proteomics & BioinformaticsCase Western Reserve UniversityClevelandOHUSA
- Department of NutritionSchool of MedicineCase Western Reserve UniversityClevelandOHUSA
| | - W. Henry Boom
- Department of MedicineUniversity Hospitals Cleveland Medical CenterCase Western Reserve UniversityClevelandOHUSA
- Department of Molecular Biology & MicrobiologyCase Western Reserve UniversityClevelandOHUSA
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9
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Seabra CM, Szoko N, Erdin S, Ragavendran A, Stortchevoi A, Maciel P, Lundberg K, Schlatzer D, Smith J, Talkowski ME, Gusella JF, Natowicz MR. A novel microduplication of ARID1B: Clinical, genetic, and proteomic findings. Am J Med Genet A 2017; 173:2478-2484. [PMID: 28691782 PMCID: PMC5561488 DOI: 10.1002/ajmg.a.38327] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 05/21/2017] [Indexed: 11/10/2022]
Abstract
Genetic alterations of ARID1B have been recently recognized as one of the most common mendelian causes of intellectual disability and are associated with both syndromic and non-syndromic phenotypes. The ARID1B protein, a subunit of the chromatin remodeling complex SWI/SNF-A, is involved in the regulation of transcription and multiple downstream cellular processes. We report here the clinical, genetic, and proteomic phenotypes of an individual with a unique apparent de novo mutation of ARID1B due to an intragenic duplication. His neurodevelopmental phenotype includes a severe speech/language disorder with full scale IQ scores 78-98 and scattered academic skill levels, expanding the phenotypic spectrum of ARID1B mutations. Haploinsufficiency of ARID1B was determined both by RNA sequencing and quantitative RT-PCR. Fluorescence in situ hybridization analysis supported an intragenic localization of the ARID1B copy number gain. Principal component analysis revealed marked differentiation of the subject's lymphoblast proteome from that of controls. Of 3426 proteins quantified, 1014 were significantly up- or down-regulated compared to controls (q < 0.01). Pathway analysis revealed highly significant enrichment for canonical pathways of EIF2 and EIF4 signaling, protein ubiquitination, tRNA charging and chromosomal replication, among others. Network analyses revealed down-regulation of: (1) intracellular components involved in organization of membranes, organelles, and vesicles; (2) aspects of cell cycle control, signal transduction, and nuclear protein export; (3) ubiquitination and proteosomal function; and (4) aspects of mRNA synthesis/splicing. Further studies are needed to determine the detailed molecular and cellular mechanisms by which constitutional haploinsufficiency of ARID1B causes syndromic and non-syndromic developmental disabilities.
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Affiliation(s)
- Catarina M. Seabra
- GABBA - Institute of Biomedical Sciences Abel Salazar of the University of Porto, Portugal
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard Medical School, Boston, MA, USA
| | - Nicholas Szoko
- Cleveland Clinic Lerner College of Medicine, Cleveland, OH, USA
| | - Serkan Erdin
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard Medical School, Boston, MA, USA
| | - Ashok Ragavendran
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard Medical School, Boston, MA, USA
| | - Alexei Stortchevoi
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Patrícia Maciel
- Life and Health Sciences Research Institute, School of Medicine, University of Minho, Braga, Portugal
- ICVS/3Bs - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Kathleen Lundberg
- Center for Proteomics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Daniela Schlatzer
- Center for Proteomics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Janice Smith
- Baylor Genetics Laboratories, Baylor College of Medicine, Houston, TX, USA
| | - Michael E. Talkowski
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard Medical School, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Harvard University, Cambridge, MA, USA
| | - James F. Gusella
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Harvard University, Cambridge, MA, USA
| | - Marvin R. Natowicz
- Cleveland Clinic Lerner College of Medicine, Cleveland, OH, USA
- Pathology & Laboratory Medicine, Genomic Medicine, Neurology and Pediatrics Institutes, Cleveland Clinic, OH, USA and Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
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10
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Unravelling HIV-1 Latency, One Cell at a Time. Trends Microbiol 2017; 25:932-941. [PMID: 28668335 DOI: 10.1016/j.tim.2017.06.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 05/22/2017] [Accepted: 06/01/2017] [Indexed: 12/14/2022]
Abstract
A single virus is capable of infecting and replicating in a single cell. Recent advances across single-cell omics technologies - genomics, epigenomics, transcriptomics, epitranscriptomics, proteomics, and metabolomics - will offer unprecedented opportunities to gain more insights into the various aspects of the life cycle of viruses and their impact on the host cell. Here, using the human immunodeficiency virus type 1 (HIV-1) as an example, we summarize the current knowledge and the future potential of single-cell omics in the investigation of an important aspect of the life cycle of HIV-1 that represents a major hurdle in achieving viral eradication, HIV-1 latency.
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11
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Azzam S, Schlatzer D, Nethery D, Saleh D, Li X, Akladious A, Chance MR, Strohl KP. Proteomic profiling of the hypothalamus in two mouse models of narcolepsy. Proteomics 2017; 17. [PMID: 28544614 DOI: 10.1002/pmic.201600478] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 05/15/2017] [Accepted: 05/16/2017] [Indexed: 12/21/2022]
Abstract
Narcolepsy is a disabling neurological disorder of sleepiness linked to the loss of neurons producing orexin neuropeptides in the hypothalamus. Two well-characterized phenotypic mouse models of narcolepsy, loss-of-function (orexin-knockout), and progressive loss of orexin (orexin/ataxin-3) exist. The open question is whether the proteomics signatures of the hypothalamus would be different between the two models. To address this gap, we utilized a label-free proteomics approach and conducted a hypothalamic proteome analysis by comparing each disease model to that of wild type. Following data processing and statistical analysis, 14 484 peptides mapping to 2282 nonredundant proteins were identified, of which 39 proteins showed significant differences in protein expression across groups. Altered proteins in both models showed commonalties in pathways for mitochondrial dysfunction and neuronal degeneration, as well as altered proteins related to inflammatory demyelination, insulin resistance, metabolic responses, and the dopaminergic and monoaminergic systems. Model-specific alterations in insulin degraded enzyme (IDE) and synaptosomal-associated protein-25 were unique to orexin-KO and orexin/ataxin-3, respectively. For both models, proteomics not only identified clinically suspected consequences of orexin loss on energy homeostasis and neurotransmitter systems, but also identified commonalities in inflammation and degeneration despite the entirely different genetic basis of the two mouse models.
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Affiliation(s)
- Sausan Azzam
- Center for Proteomics and Bioinformatics, Department of Nutrition, Case Western Reserve University, Cleveland, OH, USA.,Pulmonary Critical Care and Sleep Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Daniela Schlatzer
- Center for Proteomics and Bioinformatics, Department of Nutrition, Case Western Reserve University, Cleveland, OH, USA
| | - David Nethery
- Pulmonary Critical Care and Sleep Medicine, Case Western Reserve University, Cleveland, OH, USA
| | | | - Xiaolin Li
- Center for Proteomics and Bioinformatics, Department of Nutrition, Case Western Reserve University, Cleveland, OH, USA
| | - Afaf Akladious
- Medical Service, Louis Stokes Cleveland DVA Medical Center, Cleveland, OH, USA
| | - Mark R Chance
- Center for Proteomics and Bioinformatics, Department of Nutrition, Case Western Reserve University, Cleveland, OH, USA
| | - Kingman P Strohl
- Pulmonary Critical Care and Sleep Medicine, Case Western Reserve University, Cleveland, OH, USA.,Medical Service, Louis Stokes Cleveland DVA Medical Center, Cleveland, OH, USA.,Department of Medicine, University Hospitals Case Medical Center, Cleveland, OH, USA
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