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Yero A, Goulet JP, Shi T, Costiniuk CT, Routy JP, Tremblay C, Mboumba Bouassa RS, Alexandrova Y, Pagliuzza A, Chomont N, Ancuta P, Jenabian MA. Altered memory CCR6 + Th17-polarised T-cell function and biology in people with HIV under successful antiretroviral therapy and HIV elite controllers. EBioMedicine 2024; 107:105274. [PMID: 39178742 PMCID: PMC11388266 DOI: 10.1016/j.ebiom.2024.105274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 07/17/2024] [Accepted: 07/27/2024] [Indexed: 08/26/2024] Open
Abstract
BACKGROUND Despite successful antiretroviral therapy (ART), frequencies and immunological functions of memory CCR6+ Th17-polarised CD4+ T-cells are not fully restored in people with HIV (PWH). Moreover, long-lived Th17 cells contribute to HIV persistence under ART. However, the molecular mechanisms underlying these observations remain understudied. METHODS mRNA-sequencing was performed using Illumina technology on freshly FACS-sorted memory CCR6+CD4+ T-cells from successfully ART-treated (ST), elite controllers (EC), and uninfected donors (HD). Gene expression validation was performed by RT-PCR, flow cytometry, and in vitro functional assays. FINDINGS Decreased Th17 cell frequencies in STs and ECs versus HDs coincided with reduced Th17-lineage cytokine production in vitro. Accordingly, the RORγt/RORC2 repressor NR1D1 was upregulated, while the RORγt/RORC2 inducer Semaphorin 4D was decreased in memory CCR6+ T-cells of STs and ECs versus HDs. The presence of HIV-DNA in memory CCR6+ T-cells of ST and EC corresponded with the downregulation of HIV restriction factors (SERINC3, KLF3, and RNF125) and HIV inhibitors (tetraspanins), along with increased expression of the HIV-dependency factor MRE11, indicative of higher susceptibility/permissiveness to HIV-1 infection. Furthermore, markers of DNA damage/modification were elevated in memory CCR6+ T-cells of STs and ECs versus HDs, in line with their increased activation (CD38/HLA-DR), senescence/exhaustion phenotype (CTLA-4/PD-1/CD57) and their decreased expression of proliferation marker Ki-67. INTERPRETATION These results reveal new molecular mechanisms of Th17 cell deficit in ST and EC PWH despite a successful control of HIV-1 replication. This knowledge points to potential therapeutic interventions to limit HIV-1 infection and restore frequencies, effector functions, and senescence/exhaustion in Th17 cells. FUNDING This study was funded by the Canadian Institutes of Health Research (CIHR, operating grant MOP 142294, and the Canadian HIV Cure Enterprise [CanCURE 2.0] Team Grant HB2 164064), and in part, by the Réseau SIDA et maladies infectieuses du Fonds de recherche du Québec-Santé (FRQ-S).
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Affiliation(s)
- Alexis Yero
- Department of Biological Sciences and CERMO-FC Research Centre, Université du Québec à Montréal (UQAM), Montreal, QC, Canada
| | | | - Tao Shi
- Department of Biological Sciences and CERMO-FC Research Centre, Université du Québec à Montréal (UQAM), Montreal, QC, Canada
| | - Cecilia T Costiniuk
- Chronic Viral Illness Service and Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Jean-Pierre Routy
- Chronic Viral Illness Service and Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Cecile Tremblay
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CR-CHUM), Montreal, QC, Canada; Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université de Montréal, Montreal, QC, Canada
| | - Ralph-Sydney Mboumba Bouassa
- Department of Biological Sciences and CERMO-FC Research Centre, Université du Québec à Montréal (UQAM), Montreal, QC, Canada
| | - Yulia Alexandrova
- Department of Biological Sciences and CERMO-FC Research Centre, Université du Québec à Montréal (UQAM), Montreal, QC, Canada
| | - Amélie Pagliuzza
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CR-CHUM), Montreal, QC, Canada
| | - Nicolas Chomont
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CR-CHUM), Montreal, QC, Canada; Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université de Montréal, Montreal, QC, Canada
| | - Petronela Ancuta
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CR-CHUM), Montreal, QC, Canada; Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université de Montréal, Montreal, QC, Canada
| | - Mohammad-Ali Jenabian
- Department of Biological Sciences and CERMO-FC Research Centre, Université du Québec à Montréal (UQAM), Montreal, QC, Canada; Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université de Montréal, Montreal, QC, Canada.
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Ghone DA, Evans EL, Bandini M, Stephenson KG, Sherer NM, Suzuki A. HIV-1 Vif disrupts phosphatase feedback regulation at the kinetochore, leading to a pronounced pseudo-metaphase arrest. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.30.605839. [PMID: 39131328 PMCID: PMC11312601 DOI: 10.1101/2024.07.30.605839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
The human immunodeficiency virus type 1 (HIV-1) Virion Infectivity Factor (Vif) targets and degrades cellular APOBEC3 proteins, key regulators of intrinsic and innate antiretroviral immune responses, thereby facilitating HIV-1 infection. While Vif's role in degrading APOBEC3G is well-studied, Vif is also known to cause cell cycle arrest but the detailed nature of Vif's effects on the cell cycle has yet to be delineated. In this study, we employed high-temporal single-cell live imaging and super-resolution microscopy to monitor individual cells during Vif-induced cell cycle arrest. Our findings reveal that Vif does not affect the G2/M boundary as previously thought. Instead, Vif triggers a unique and robust pseudo-metaphase arrest, which is markedly distinct from the mild prometaphase arrest induced by the HIV-1 accessory protein, Vpr, known for modulating the cell cycle. During Vif-mediated arrest, chromosomes align properly to form a metaphase plate but later disassemble, resulting in polar chromosomes. Notably, unlike Vpr, Vif significantly reduces the levels of both Phosphatase 1 (PP1) and 2 (PP2) at kinetochores, which are key regulators of chromosome-microtubule interactions. These results reveal a novel function of Vif in kinetochore regulation that governs the spatial organization of chromosomes during mitosis.
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Affiliation(s)
- Dhaval A Ghone
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Biophysics Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
- These authors contributed equally
| | - Edward L Evans
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Cancer Biology Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- These authors contributed equally
- Present address: Laboratory for Optical and Computational Instrumentation, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - Madison Bandini
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Cancer Biology Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Kaelyn G Stephenson
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Nathan M Sherer
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Carbone Comprehensive Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Aussie Suzuki
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Carbone Comprehensive Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
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3
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Kmiec D, Kirchhoff F. Antiviral factors and their counteraction by HIV-1: many uncovered and more to be discovered. J Mol Cell Biol 2024; 16:mjae005. [PMID: 38318650 PMCID: PMC11334937 DOI: 10.1093/jmcb/mjae005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/13/2023] [Accepted: 02/04/2024] [Indexed: 02/07/2024] Open
Abstract
Extensive studies on HIV-1 have led to the discovery of a variety of structurally and functionally diverse innate defense factors that target various steps of the retroviral replication cycle. Some of them, such as APOBEC3, tetherin, and SERINC5, are well established. Their importance is evident from the fact that HIV-1 uses its accessory proteins Vif, Vpu, and Nef to counteract them. However, the list of antiviral factors is constantly increasing, and accumulating evidence suggests that innate defense mechanisms, which restrict HIV-1 and/or are counteracted by viral proteins, remain to be discovered. These antiviral factors are relevant to diseases other than HIV/AIDS, since they are commonly active against various viral pathogens. In this review, we provide an overview of recently reported antiretroviral factors and viral countermeasures, present the evidence suggesting that more innate defense mechanisms remain to be discovered, and discuss why this is a challenging but rewarding task.
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Affiliation(s)
- Dorota Kmiec
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
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4
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Hu Y, Delviks-Frankenberry KA, Wu C, Arizaga F, Pathak VK, Xiong Y. Structural insights into PPP2R5A degradation by HIV-1 Vif. Nat Struct Mol Biol 2024:10.1038/s41594-024-01314-6. [PMID: 38789685 DOI: 10.1038/s41594-024-01314-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 04/11/2024] [Indexed: 05/26/2024]
Abstract
HIV-1 Vif recruits host cullin-RING-E3 ubiquitin ligase and CBFβ to degrade the cellular APOBEC3 antiviral proteins through diverse interactions. Recent evidence has shown that Vif also degrades the regulatory subunits PPP2R5(A-E) of cellular protein phosphatase 2A to induce G2/M cell cycle arrest. As PPP2R5 proteins bear no functional or structural resemblance to A3s, it is unclear how Vif can recognize different sets of proteins. Here we report the cryogenic-electron microscopy structure of PPP2R5A in complex with HIV-1 Vif-CBFβ-elongin B-elongin C at 3.58 Å resolution. The structure shows PPP2R5A binds across the Vif molecule, with biochemical and cellular studies confirming a distinct Vif-PPP2R5A interface that partially overlaps with those for A3s. Vif also blocks a canonical PPP2R5A substrate-binding site, indicating that it suppresses the phosphatase activities through both degradation-dependent and degradation-independent mechanisms. Our work identifies critical Vif motifs regulating the recognition of diverse A3 and PPP2R5A substrates, whereby disruption of these host-virus protein interactions could serve as potential targets for HIV-1 therapeutics.
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Affiliation(s)
- Yingxia Hu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Krista A Delviks-Frankenberry
- Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, USA
| | - Chunxiang Wu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Fidel Arizaga
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Vinay K Pathak
- Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, USA.
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
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5
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Ikeda T, Shimizu R, Nasser H, Carpenter MA, Cheng AZ, Brown WL, Sauter D, Harris RS. APOBEC3 degradation is the primary function of HIV-1 Vif determining virion infectivity in the myeloid cell line THP-1. mBio 2023; 14:e0078223. [PMID: 37555667 PMCID: PMC10470580 DOI: 10.1128/mbio.00782-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/22/2023] [Indexed: 08/10/2023] Open
Abstract
HIV-1 must overcome multiple innate antiviral mechanisms to replicate in CD4+ T lymphocytes and macrophages. Previous studies have demonstrated that the apolipoprotein B mRNA editing enzyme polypeptide-like 3 (APOBEC3, A3) family of proteins (at least A3D, A3F, A3G, and stable A3H haplotypes) contribute to HIV-1 restriction in CD4+ T lymphocytes. Virus-encoded virion infectivity factor (Vif) counteracts this antiviral activity by degrading A3 enzymes allowing HIV-1 replication in infected cells. In addition to A3 proteins, Vif also targets other cellular proteins in CD4+ T lymphocytes, including PPP2R5 proteins. However, whether Vif primarily degrades only A3 proteins during viral replication is currently unknown. Herein, we describe the development and characterization of A3F-, A3F/A3G-, and A3A-to-A3G-null THP-1 cells. In comparison to Vif-proficient HIV-1, Vif-deficient viruses have substantially reduced infectivity in parental and A3F-null THP-1 cells, and a more modest decrease in infectivity in A3F/A3G-null cells. Remarkably, disruption of A3A-A3G protein expression completely restores the infectivity of Vif-deficient viruses in THP-1 cells. These results indicate that the primary function of Vif during infectious HIV-1 production from THP-1 cells is the targeting and degradation of A3 enzymes. IMPORTANCE HIV-1 Vif neutralizes the HIV-1 restriction activity of A3 proteins. However, it is currently unclear whether Vif has additional essential cellular targets. To address this question, we disrupted A3A to A3G genes in the THP-1 myeloid cell line using CRISPR and compared the infectivity of wild-type HIV-1 and Vif mutants with the selective A3 neutralization activities. Our results demonstrate that the infectivity of Vif-deficient HIV-1 and the other Vif mutants is fully restored by ablating the expression of cellular A3A to A3G proteins. These results indicate that A3 proteins are the only essential target of Vif that is required for fully infectious HIV-1 production from THP-1 cells.
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Affiliation(s)
- Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Ryo Shimizu
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
- Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Hesham Nasser
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
- Department of Clinical Pathology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Michael A. Carpenter
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Adam Z. Cheng
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA
| | - William L. Brown
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Daniel Sauter
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Reuben S. Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas, USA
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6
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Ikeda T, Shimizu R, Nasser H, Carpenter MA, Cheng AZ, Brown WL, Sauter D, Harris RS. APOBEC3 degradation is the primary function of HIV-1 Vif for virus replication in the myeloid cell line THP-1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.28.534666. [PMID: 37034786 PMCID: PMC10081227 DOI: 10.1101/2023.03.28.534666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
HIV-1 must overcome multiple innate antiviral mechanisms to replicate in CD4 + T lymphocytes and macrophages. Previous studies have demonstrated that the APOBEC3 (A3) family of proteins (at least A3D, A3F, A3G, and stable A3H haplotypes) contribute to HIV-1 restriction in CD4 + T lymphocytes. Virus-encoded virion infectivity factor (Vif) counteracts this antiviral activity by degrading A3 enzymes allowing HIV-1 replication in infected cells. In addition to A3 proteins, Vif also targets other cellular proteins in CD4 + T lymphocytes, including PPP2R5 proteins. However, whether Vif primarily degrades only A3 proteins or has additional essential targets during viral replication is currently unknown. Herein, we describe the development and characterization of A3F -, A3F/A3G -, and A3A -to- A3G -null THP-1 cells. In comparison to Vif-proficient HIV-1, Vif-deficient viruses have substantially reduced infectivity in parental and A3F -null THP-1 cells, and a more modest decrease in infectivity in A3F/A3G -null cells. Remarkably, disruption of A3Aâ€"A3G protein expression completely restores the infectivity of Vif-deficient viruses in THP-1 cells. These results indicate that the primary function of Vif during HIV-1 replication in THP-1 cells is the targeting and degradation of A3 enzymes. Importance HIV-1 Vif neutralizes the HIV-1 restriction activity of A3 proteins. However, it is currently unclear whether Vif has additional essential cellular targets. To address this question, we disrupted A3A to A3G genes in the THP-1 myeloid cell line using CRISPR and compared the infectivity of wildtype HIV-1 and Vif mutants with the selective A3 neutralization activities. Our results demonstrate that the infectivity of Vif-deficient HIV-1 and the other Vif mutants is fully restored by ablating the expression of cellular A3A to A3G proteins. These results indicate that A3 proteins are the only essential target of Vif that is required for HIV-1 replication in THP-1 cells.
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Affiliation(s)
- Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan
| | - Ryo Shimizu
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan
- Graduate School of Medical Sciences, Kumamoto University, Kumamoto 8600811, Japan
| | - Hesham Nasser
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan
- Department of Clinical Pathology, Faculty of Medicine, Suez Canal University, Ismailia 41511, Egypt
| | - Michael A. Carpenter
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas 78229, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas 78229, USA
| | - Adam Z. Cheng
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - William L. Brown
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Daniel Sauter
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen 72076, Germany
| | - Reuben S. Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas 78229, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas 78229, USA
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7
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Albarnaz JD, Weekes MP. Proteomic analysis of antiviral innate immunity. Curr Opin Virol 2023; 58:101291. [PMID: 36529073 DOI: 10.1016/j.coviro.2022.101291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/03/2022] [Accepted: 11/17/2022] [Indexed: 12/23/2022]
Abstract
The capacity of host cells to detect and restrict an infecting virus rests on an array of cell-autonomous antiviral effectors and innate immune receptors that can trigger inflammatory processes at tissue and organismal levels. Dynamic changes in protein abundance, subcellular localisation, post-translational modifications and interactions with other biomolecules govern these processes. Proteomics is therefore an ideal experimental tool to discover novel mechanisms of host antiviral immunity. Additional information can be gleaned both about host and virus by systematic analysis of viral immune evasion strategies. In this review, we summarise recent advances in proteomic technologies and their application to antiviral innate immunity.
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Affiliation(s)
- Jonas D Albarnaz
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, CB2 0XY Cambridge, UK
| | - Michael P Weekes
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, CB2 0XY Cambridge, UK.
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8
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Rashid MU, Glover KKM, Lao Y, Spicer V, Coombs KM. Temporal proteomic analyses of human lung cells distinguish high pathogenicity influenza viruses and coronaviruses from low pathogenicity viruses. Front Microbiol 2022; 13:994512. [PMID: 36299731 PMCID: PMC9589293 DOI: 10.3389/fmicb.2022.994512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/23/2022] [Indexed: 11/29/2022] Open
Abstract
Newly re-emerging viruses are of significant global concern. In late 2019, a new coronavirus, SARS-CoV-2, emerged in China and soon spread worldwide, causing the COVID-19 pandemic, which to date has caused >6 M deaths. There has been a wealth of studies on this new virus since its emergence. The coronaviruses consist of many animal and human pathogens, with some of the human coronavirus, such as strain OC43, normally causing only mild cold-like symptoms. Viruses usurp host cellular processes to successfully replicate. We used tandem mass tag mass spectrometry-based proteomic analyses of human lung MRC-5 cells infected with OC43 for various periods of time to delineate virus-induced host cell alterations. Numerous proteins involved in lipid metabolism, molecular transport, small molecule biochemistry, cell death and survival, humoral immune response, and inflammatory response were dysregulated. Comparison of our findings to previous studies that examined a range of differentially pathogenic influenza A viruses (IAV), and to SARS-CoV-2 data, revealed that proteins involved in the cell cycle, cytokine signaling, DNA replication, and anti-inflammatory responses were generally similarly affected by virtually all tested IAV and CoV. However, proteins involved in necrosis, protein metabolism, ECM regulation, and signal transduction were generally different. In addition, the more pathogenic CoV and IAV activated Rb-dependent repression of E2F-mediated transcription, whereas less pathogenic influenza and coronaviruses either inhibited or had no effect on this pathway.
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Affiliation(s)
- Mahamud-ur Rashid
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
- Manitoba Center for Proteomics and Systems Biology, Winnipeg, MB, Canada
| | - Kathleen K. M. Glover
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
- Manitoba Center for Proteomics and Systems Biology, Winnipeg, MB, Canada
| | - Ying Lao
- Manitoba Center for Proteomics and Systems Biology, Winnipeg, MB, Canada
| | - Victor Spicer
- Manitoba Center for Proteomics and Systems Biology, Winnipeg, MB, Canada
| | - Kevin M. Coombs
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
- Manitoba Center for Proteomics and Systems Biology, Winnipeg, MB, Canada
- Children’s Hospital Research Institute of Manitoba, John Buhler Research Center, Winnipeg, MB, Canada
- *Correspondence: Kevin M. Coombs,
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Zhao Y, Li L, Wang X, He S, Shi W, Chen S. Temporal Proteomic and Phosphoproteomic Analysis of EV-A71-Infected Human Cells. J Proteome Res 2022; 21:2367-2384. [DOI: 10.1021/acs.jproteome.2c00237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yue Zhao
- College of Biological Sciences, China Agricultural University, Beijing 100193, China
- Proteomics Center, National Institute of Biological Sciences, Beijing 102206, China
| | - Lin Li
- Proteomics Center, National Institute of Biological Sciences, Beijing 102206, China
| | - Xinhui Wang
- CAMS Key Laboratory of Synthetic Biology Regulatory Elements, Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, Jiangsu, China
- Suzhou Institute of Systems Medicine, Suzhou 215123, Jiangsu, China
| | - Sudan He
- CAMS Key Laboratory of Synthetic Biology Regulatory Elements, Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, Jiangsu, China
- Suzhou Institute of Systems Medicine, Suzhou 215123, Jiangsu, China
| | - Weifeng Shi
- Department of Laboratory Medicine, The Third Affiliated Hospital of Soochow University, Changzhou 213003, Jiangsu, China
| | - She Chen
- Proteomics Center, National Institute of Biological Sciences, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
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Crozier TW, Greenwood EJ, Williamson JC, Guo W, Porter LM, Gabaev I, Teixeira-Silva A, Grice GL, Wickenhagen A, Stanton RJ, Wang ECY, Wilson SJ, Matheson NJ, Nathan JA, McCaughan F, Lehner PJ. Quantitative proteomic analysis of SARS-CoV-2 infection of primary human airway ciliated cells and lung epithelial cells demonstrates the effectiveness of SARS-CoV-2 innate immune evasion. Wellcome Open Res 2022; 7:224. [PMID: 36483314 PMCID: PMC9706147 DOI: 10.12688/wellcomeopenres.17946.1] [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] [Accepted: 08/26/2022] [Indexed: 02/02/2023] Open
Abstract
Background: Quantitative proteomics is able to provide a comprehensive, unbiased description of changes to cells caused by viral infection, but interpretation may be complicated by differential changes in infected and uninfected 'bystander' cells, or the use of non-physiological cellular models. Methods: In this paper, we use fluorescence-activated cell sorting (FACS) and quantitative proteomics to analyse cell-autonomous changes caused by authentic SARS-CoV-2 infection of respiratory epithelial cells, the main target of viral infection in vivo. First, we determine the relative abundance of proteins in primary human airway epithelial cells differentiated at the air-liquid interface (basal, secretory and ciliated cells). Next, we specifically characterise changes caused by SARS-CoV-2 infection of ciliated cells. Finally, we compare temporal proteomic changes in infected and uninfected 'bystander' Calu-3 lung epithelial cells and compare infection with B.29 and B.1.1.7 (Alpha) variants. Results: Amongst 5,709 quantified proteins in primary human airway ciliated cells, the abundance of 226 changed significantly in the presence of SARS-CoV-2 infection (q <0.05 and >1.5-fold). Notably, viral replication proceeded without inducing a type-I interferon response. Amongst 6,996 quantified proteins in Calu-3 cells, the abundance of 645 proteins changed significantly in the presence of SARS-CoV-2 infection (q < 0.05 and > 1.5-fold). In contrast to the primary cell model, a clear type I interferon (IFN) response was observed. Nonetheless, induction of IFN-inducible proteins was markedly attenuated in infected cells, compared with uninfected 'bystander' cells. Infection with B.29 and B.1.1.7 (Alpha) variants gave similar results. Conclusions: Taken together, our data provide a detailed proteomic map of changes in SARS-CoV-2-infected respiratory epithelial cells in two widely used, physiologically relevant models of infection. As well as identifying dysregulated cellular proteins and processes, the effectiveness of strategies employed by SARS-CoV-2 to avoid the type I IFN response is illustrated in both models.
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Affiliation(s)
- Thomas W.M. Crozier
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Edward J.D. Greenwood
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| | - James C. Williamson
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Wenrui Guo
- Department of Medicine, Addenbrookes Hospital, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Linsey M. Porter
- Department of Medicine, Addenbrookes Hospital, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Ildar Gabaev
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Ana Teixeira-Silva
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Guinevere L. Grice
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Arthur Wickenhagen
- MRC - University of Glasgow Centre for Virus Research, Glasgow, G61 1QH, UK
| | - Richard J. Stanton
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Eddie C. Y. Wang
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Sam J. Wilson
- MRC - University of Glasgow Centre for Virus Research, Glasgow, G61 1QH, UK
| | - Nicholas J. Matheson
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
- NHS Blood and Transplant, Cambridge, CB2 0PT, UK
| | - James A. Nathan
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Frank McCaughan
- Department of Medicine, Addenbrookes Hospital, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Paul J. Lehner
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
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11
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Luperchio AM, Jónsson SR, Salamango DJ. Evolutionary Conservation of PP2A Antagonism and G2/M Cell Cycle Arrest in Maedi-Visna Virus Vif. Viruses 2022; 14:1701. [PMID: 36016323 PMCID: PMC9413702 DOI: 10.3390/v14081701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/29/2022] [Accepted: 07/29/2022] [Indexed: 11/18/2022] Open
Abstract
The canonical function of lentiviral Vif proteins is to counteract the mutagenic potential of APOBEC3 antiviral restriction factors. However, recent studies have discovered that Vif proteins from diverse HIV-1 and simian immunodeficiency virus (SIV) isolates degrade cellular B56 phosphoregulators to remodel the host phosphoproteome and induce G2/M cell cycle arrest. Here, we evaluate the conservation of this activity among non-primate lentiviral Vif proteins using fluorescence-based degradation assays and demonstrate that maedi-visna virus (MVV) Vif efficiently degrades all five B56 family members. Testing an extensive panel of single amino acid substitution mutants revealed that MVV Vif recognizes B56 proteins through a conserved network of electrostatic interactions. Furthermore, experiments using genetic and pharmacologic approaches demonstrate that degradation of B56 proteins requires the cellular cofactor cyclophilin A. Lastly, MVV Vif-mediated depletion of B56 proteins induces a potent G2/M cell cycle arrest phenotype. Therefore, remodeling of the cellular phosphoproteome and induction of G2/M cell cycle arrest are ancient and conserved functions of lentiviral Vif proteins, which suggests that they are advantageous for lentiviral pathogenesis.
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Affiliation(s)
- Adeline M. Luperchio
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, NY 11794, USA;
| | - Stefán R. Jónsson
- Institute for Experimental Pathology, University of Iceland, Keldur, 112 Reykjavik, Iceland;
| | - Daniel J. Salamango
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, NY 11794, USA;
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12
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Fielding CA, Sabberwal P, Williamson JC, Greenwood EJD, Crozier TWM, Zelek W, Seow J, Graham C, Huettner I, Edgeworth JD, Price DA, Morgan PB, Ladell K, Eberl M, Humphreys IR, Merrick B, Doores K, Wilson SJ, Lehner PJ, Wang ECY, Stanton RJ. SARS-CoV-2 host-shutoff impacts innate NK cell functions, but antibody-dependent NK activity is strongly activated through non-spike antibodies. eLife 2022; 11:e74489. [PMID: 35587364 PMCID: PMC9239683 DOI: 10.7554/elife.74489] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 05/17/2022] [Indexed: 12/15/2022] Open
Abstract
The outcome of infection is dependent on the ability of viruses to manipulate the infected cell to evade immunity, and the ability of the immune response to overcome this evasion. Understanding this process is key to understanding pathogenesis, genetic risk factors, and both natural and vaccine-induced immunity. SARS-CoV-2 antagonises the innate interferon response, but whether it manipulates innate cellular immunity is unclear. An unbiased proteomic analysis determined how cell surface protein expression is altered on SARS-CoV-2-infected lung epithelial cells, showing downregulation of activating NK ligands B7-H6, MICA, ULBP2, and Nectin1, with minimal effects on MHC-I. This occurred at the level of protein synthesis, could be mediated by Nsp1 and Nsp14, and correlated with a reduction in NK cell activation. This identifies a novel mechanism by which SARS-CoV-2 host-shutoff antagonises innate immunity. Later in the disease process, strong antibody-dependent NK cell activation (ADNKA) developed. These responses were sustained for at least 6 months in most patients, and led to high levels of pro-inflammatory cytokine production. Depletion of spike-specific antibodies confirmed their dominant role in neutralisation, but these antibodies played only a minor role in ADNKA compared to antibodies to other proteins, including ORF3a, Membrane, and Nucleocapsid. In contrast, ADNKA induced following vaccination was focussed solely on spike, was weaker than ADNKA following natural infection, and was not boosted by the second dose. These insights have important implications for understanding disease progression, vaccine efficacy, and vaccine design.
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Affiliation(s)
- Ceri Alan Fielding
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Pragati Sabberwal
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - James C Williamson
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of CambridgeCambridgeUnited Kingdom
| | - Edward JD Greenwood
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of CambridgeCambridgeUnited Kingdom
| | - Thomas WM Crozier
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of CambridgeCambridgeUnited Kingdom
| | - Wioleta Zelek
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Jeffrey Seow
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College LondonLondonUnited Kingdom
| | - Carl Graham
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College LondonLondonUnited Kingdom
| | - Isabella Huettner
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College LondonLondonUnited Kingdom
| | - Jonathan D Edgeworth
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College LondonLondonUnited Kingdom
- Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation TrustLondonUnited Kingdom
| | - David A Price
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Paul B Morgan
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Kristin Ladell
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Matthias Eberl
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Ian R Humphreys
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Blair Merrick
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College LondonLondonUnited Kingdom
- Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation TrustLondonUnited Kingdom
| | - Katie Doores
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College LondonLondonUnited Kingdom
| | - Sam J Wilson
- MRC - University of Glasgow Centre for Virus ResearchGlasgowUnited Kingdom
| | - Paul J Lehner
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of CambridgeCambridgeUnited Kingdom
| | - Eddie CY Wang
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Richard J Stanton
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
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13
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Pellegrina D, Bahcheli AT, Krassowski M, Reimand J. Human phospho-signaling networks of SARS-CoV-2 infection are rewired by population genetic variants. Mol Syst Biol 2022; 18:e10823. [PMID: 35579274 PMCID: PMC9112486 DOI: 10.15252/msb.202110823] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 11/23/2022] Open
Abstract
SARS-CoV-2 infection hijacks signaling pathways and induces protein-protein interactions between human and viral proteins. Human genetic variation may impact SARS-CoV-2 infection and COVID-19 pathology; however, the genetic variation in these signaling networks remains uncharacterized. Here, we studied human missense single nucleotide variants (SNVs) altering phosphorylation sites modulated by SARS-CoV-2 infection, using machine learning to identify amino acid substitutions altering kinase-bound sequence motifs. We found 2,033 infrequent phosphorylation-associated SNVs (pSNVs) that are enriched in sequence motif alterations, potentially reflecting the evolution of signaling networks regulating host defenses. Proteins with pSNVs are involved in viral life cycle and host responses, including RNA splicing, interferon response (TRIM28), and glucose homeostasis (TBC1D4) with potential associations with COVID-19 comorbidities. pSNVs disrupt CDK and MAPK substrate motifs and replace these with motifs of Tank Binding Kinase 1 (TBK1) involved in innate immune responses, indicating consistent rewiring of signaling networks. Several pSNVs associate with severe COVID-19 and hospitalization (STARD13, ARFGEF2). Our analysis highlights potential genetic factors contributing to inter-individual variation of SARS-CoV-2 infection and COVID-19 and suggests leads for mechanistic and translational studies.
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Affiliation(s)
- Diogo Pellegrina
- Computational Biology ProgramOntario Institute for Cancer ResearchTorontoONCanada
| | - Alexander T Bahcheli
- Computational Biology ProgramOntario Institute for Cancer ResearchTorontoONCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoONCanada
| | - Michal Krassowski
- Medical Sciences DivisionNuffield Department of Women's and Reproductive HealthUniversity of OxfordOxfordUK
| | - Jüri Reimand
- Computational Biology ProgramOntario Institute for Cancer ResearchTorontoONCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoONCanada
- Department of Medical BiophysicsUniversity of TorontoTorontoONCanada
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14
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Johnson JR, Crosby DC, Hultquist JF, Kurland AP, Adhikary P, Li D, Marlett J, Swann J, Hüttenhain R, Verschueren E, Johnson TL, Newton BW, Shales M, Simon VA, Beltrao P, Frankel AD, Marson A, Cox JS, Fregoso OI, Young JAT, Krogan NJ. Global post-translational modification profiling of HIV-1-infected cells reveals mechanisms of host cellular pathway remodeling. Cell Rep 2022; 39:110690. [PMID: 35417684 PMCID: PMC9429972 DOI: 10.1016/j.celrep.2022.110690] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 03/07/2022] [Accepted: 03/24/2022] [Indexed: 01/03/2023] Open
Abstract
Viruses must effectively remodel host cellular pathways to replicate and evade immune defenses, and they must do so with limited genomic coding capacity. Targeting post-translational modification (PTM) pathways provides a mechanism by which viruses can broadly and rapidly transform a hostile host environment into a hospitable one. We use mass spectrometry-based proteomics to quantify changes in protein abundance and two PTM types-phosphorylation and ubiquitination-in response to HIV-1 infection with viruses harboring targeted deletions of a subset of HIV-1 genes. PTM analysis reveals a requirement for Aurora kinase activity in HIV-1 infection and identified putative substrates of a phosphatase that is degraded during infection. Finally, we demonstrate that the HIV-1 Vpr protein inhibits histone H1 ubiquitination, leading to defects in DNA repair.
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Affiliation(s)
- Jeffrey R Johnson
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA 94158, USA; Gladstone Institute for Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA.
| | - David C Crosby
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Judd F Hultquist
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA 94158, USA; Gladstone Institute for Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Andrew P Kurland
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Prithy Adhikary
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Donna Li
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - John Marlett
- Viral Vector Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Justine Swann
- Viral Vector Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Ruth Hüttenhain
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA 94158, USA; Gladstone Institute for Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Erik Verschueren
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA 94158, USA; Gladstone Institute for Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Tasha L Johnson
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA 94158, USA; Gladstone Institute for Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Billy W Newton
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA 94158, USA; Gladstone Institute for Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Michael Shales
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA 94158, USA; Gladstone Institute for Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Viviana A Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Pedro Beltrao
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CD10 1SD, UK
| | - Alan D Frankel
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Alexander Marson
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA; Diabetes Center, University of California San Francisco, San Francisco, CA 94143, USA; Innovative Genomics Institute, University of California Berkeley, Berkeley, CA 94720, USA; Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
| | - Jeffery S Cox
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Oliver I Fregoso
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - John A T Young
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA 94158, USA; Gladstone Institute for Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA.
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15
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Guillin OM, Vindry C, Ohlmann T, Chavatte L. Interplay between Selenium, Selenoproteins and HIV-1 Replication in Human CD4 T-Lymphocytes. Int J Mol Sci 2022; 23:ijms23031394. [PMID: 35163318 PMCID: PMC8835795 DOI: 10.3390/ijms23031394] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/21/2022] [Accepted: 01/22/2022] [Indexed: 12/12/2022] Open
Abstract
The infection of CD4 T-lymphocytes with human immunodeficiency virus (HIV), the etiological agent of acquired immunodeficiency syndrome (AIDS), disrupts cellular homeostasis, increases oxidative stress and interferes with micronutrient metabolism. Viral replication simultaneously increases the demand for micronutrients and causes their loss, as for selenium (Se). In HIV-infected patients, selenium deficiency was associated with a lower CD4 T-cell count and a shorter life expectancy. Selenium has an important role in antioxidant defense, redox signaling and redox homeostasis, and most of these biological activities are mediated by its incorporation in an essential family of redox enzymes, namely the selenoproteins. Here, we have investigated how selenium and selenoproteins interplay with HIV infection in different cellular models of human CD4 T lymphocytes derived from established cell lines (Jurkat and SupT1) and isolated primary CD4 T cells. First, we characterized the expression of the selenoproteome in various human T-cell models and found it tightly regulated by the selenium level of the culture media, which was in agreement with reports from non-immune cells. Then, we showed that selenium had no significant effect on HIV-1 protein production nor on infectivity, but slightly reduced the percentage of infected cells in a Jurkat cell line and isolated primary CD4 T cells. Finally, in response to HIV-1 infection, the selenoproteome was slightly altered.
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Affiliation(s)
- Olivia M. Guillin
- Centre International de Recherche en Infectiologie (CIRI), 69007 Lyon, France; (O.M.G.); (C.V.)
- Institut National de la Santé et de la Recherche Médicale (INSERM) Unité U1111, 69007 Lyon, France
- Ecole Normale Supérieure de Lyon (ENS), 69007 Lyon, France
- Université Claude Bernard Lyon 1 (UCBL1), 69622 Lyon, France
- Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 5308 (UMR5308), 69007 Lyon, France
| | - Caroline Vindry
- Centre International de Recherche en Infectiologie (CIRI), 69007 Lyon, France; (O.M.G.); (C.V.)
- Institut National de la Santé et de la Recherche Médicale (INSERM) Unité U1111, 69007 Lyon, France
- Ecole Normale Supérieure de Lyon (ENS), 69007 Lyon, France
- Université Claude Bernard Lyon 1 (UCBL1), 69622 Lyon, France
- Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 5308 (UMR5308), 69007 Lyon, France
| | - Théophile Ohlmann
- Centre International de Recherche en Infectiologie (CIRI), 69007 Lyon, France; (O.M.G.); (C.V.)
- Institut National de la Santé et de la Recherche Médicale (INSERM) Unité U1111, 69007 Lyon, France
- Ecole Normale Supérieure de Lyon (ENS), 69007 Lyon, France
- Université Claude Bernard Lyon 1 (UCBL1), 69622 Lyon, France
- Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 5308 (UMR5308), 69007 Lyon, France
- Correspondence: (T.O.); (L.C.); Tel.: +33-4-72-72-89-53 (T.O.); +33-4-72-72-86-24 (L.C.)
| | - Laurent Chavatte
- Centre International de Recherche en Infectiologie (CIRI), 69007 Lyon, France; (O.M.G.); (C.V.)
- Institut National de la Santé et de la Recherche Médicale (INSERM) Unité U1111, 69007 Lyon, France
- Ecole Normale Supérieure de Lyon (ENS), 69007 Lyon, France
- Université Claude Bernard Lyon 1 (UCBL1), 69622 Lyon, France
- Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 5308 (UMR5308), 69007 Lyon, France
- Correspondence: (T.O.); (L.C.); Tel.: +33-4-72-72-89-53 (T.O.); +33-4-72-72-86-24 (L.C.)
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16
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Cakir M, Obernier K, Forget A, Krogan NJ. Target Discovery for Host-Directed Antiviral Therapies: Application of Proteomics Approaches. mSystems 2021; 6:e0038821. [PMID: 34519533 PMCID: PMC8547474 DOI: 10.1128/msystems.00388-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Current epidemics, such as AIDS or flu, and the emergence of new threatening pathogens, such as the one causing the current coronavirus disease 2019 (COVID-19) pandemic, represent major global health challenges. While vaccination is an important part of the arsenal to counter the spread of viral diseases, it presents limitations and needs to be complemented by efficient therapeutic solutions. Intricate knowledge of host-pathogen interactions is a powerful tool to identify host-dependent vulnerabilities that can be exploited to dampen viral replication. Such host-directed antiviral therapies are promising and are less prone to the development of drug-resistant viral strains. Here, we first describe proteomics-based strategies that allow the rapid characterization of host-pathogen interactions. We then discuss how such data can be exploited to help prioritize compounds with potential host-directed antiviral activity that can be tested in preclinical models.
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Affiliation(s)
- Merve Cakir
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, USA
| | - Kirsten Obernier
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, USA
| | - Antoine Forget
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, USA
| | - Nevan J. Krogan
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, USA
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17
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Gao W, Rui Y, Li G, Zhai C, Su J, Liu H, Zheng W, Zheng B, Zhang W, Yang Y, Hua S, Yu X. Specific Deubiquitinating Enzymes Promote Host Restriction Factors Against HIV/SIV Viruses. Front Immunol 2021; 12:740713. [PMID: 34630422 PMCID: PMC8492978 DOI: 10.3389/fimmu.2021.740713] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 08/31/2021] [Indexed: 11/13/2022] Open
Abstract
Hijacking host ubiquitin pathways is essential for the replication of diverse viruses. However, the role of deubiquitinating enzymes (DUBs) in the interplay between viruses and the host is poorly characterized. Here, we demonstrate that specific DUBs are potent inhibitors of viral proteins from HIVs/simian immunodeficiency viruses (SIVs) that are involved in viral evasion of host restriction factors and viral replication. In particular, we discovered that T cell-functioning ubiquitin-specific protease 8 (USP8) is a potent and specific inhibitor of HIV-1 virion infectivity factor (Vif)-mediated apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3)G (A3G) degradation. Ectopic expression of USP8 inhibited Vif-induced A3G degradation and suppressed wild-type HIV-1 infectivity even in the presence of Vif. In addition, specific DUBs repressed Vpr-, Vpu-, and Vpx-triggered host restriction factor degradation. Our study has revealed a previously unrecognized interplay between the host's DUBs and viral replication. Enhancing the antiviral activity of DUBs therefore represents an attractive strategy against HIVs/SIVs.
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Affiliation(s)
- Wenying Gao
- Center for Pathogen Biology and Infectious Diseases, Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, China
| | - Yajuan Rui
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, Ministry of Education), Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Guangquan Li
- Jilin Provincial Key Laboratory on Molecular and Chemical Genetics, The Second Hospital of Jilin University, Changchun, China
| | - Chenyang Zhai
- Center for Pathogen Biology and Infectious Diseases, Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, China
| | - Jiaming Su
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, Ministry of Education), Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Han Liu
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, China
| | - Wenwen Zheng
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, Ministry of Education), Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Baisong Zheng
- Center for Pathogen Biology and Infectious Diseases, Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, China
| | - Wenyan Zhang
- Center for Pathogen Biology and Infectious Diseases, Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, China
| | - Yongjun Yang
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Shucheng Hua
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, China
| | - Xiaofang Yu
- Center for Pathogen Biology and Infectious Diseases, Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, China.,Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, Ministry of Education), Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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18
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Barski MS, Minnell JJ, Maertens GN. PP2A Phosphatase as an Emerging Viral Host Factor. Front Cell Infect Microbiol 2021; 11:725615. [PMID: 34422684 PMCID: PMC8371333 DOI: 10.3389/fcimb.2021.725615] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 07/20/2021] [Indexed: 12/12/2022] Open
Abstract
Protein phosphatase 2A (PP2A) is one of the most ubiquitous cellular proteins and is responsible for the vast majority of Ser/Thr phosphatase activity in eukaryotes. PP2A is a heterotrimer, and its assembly, intracellular localization, enzymatic activity, and substrate specificity are subject to dynamic regulation. Each of its subunits can be targeted by viral proteins to hijack and modulate its activity and downstream signaling to the advantage of the virus. Binding to PP2A is known to be essential to the life cycle of many viruses and seems to play a particularly crucial role for oncogenic viruses, which utilize PP2A to transform infected cells through controlling the cell cycle and apoptosis. Here we summarise the latest developments in the field of PP2A viral targeting; in particular recent discoveries of PP2A hijacking through molecular mimicry of a B56-specific motif by several different viruses. We also discuss the potential as well as shortcomings for therapeutic intervention in the face of our current understanding of viral PP2A targeting.
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Affiliation(s)
| | | | - Goedele Noella Maertens
- Department of Infectious Disease, Section of Molecular Virology, St Mary’s Hospital, Imperial College London, London, United Kingdom
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19
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Barbosa JAF, Sparapani S, Boulais J, Lodge R, Cohen ÉA. Human Immunodeficiency Virus Type 1 Vpr Mediates Degradation of APC1, a Scaffolding Component of the Anaphase-Promoting Complex/Cyclosome. J Virol 2021; 95:e0097120. [PMID: 34011540 PMCID: PMC8274603 DOI: 10.1128/jvi.00971-20] [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: 05/20/2020] [Accepted: 05/05/2021] [Indexed: 11/20/2022] Open
Abstract
HIV-1 encodes several accessory proteins-Nef, Vif, Vpr, and Vpu-whose functions are to modulate the cellular environment to favor immune evasion and viral replication. While Vpr was shown to mediate a G2/M cell cycle arrest and provide a replicative advantage during infection of myeloid cells, the mechanisms underlying these functions remain unclear. In this study, we defined HIV-1 Vpr proximity interaction network using the BioID proximity labeling approach and identified 352 potential Vpr partners/targets, including several complexes, such as the cell cycle-regulatory anaphase-promoting complex/cyclosome (APC/C). Herein, we demonstrate that both the wild type and cell cycle-defective mutants of Vpr induce the degradation of APC1, an essential APC/C scaffolding protein, and show that this activity relies on the recruitment of DCAF1 by Vpr and the presence of a functional proteasome. Vpr forms a complex with APC1, and the APC/C coactivators Cdh1 and Cdc20 are associated with these complexes. Interestingly, we found that Vpr encoded by the prototypic HIV-1 NL4.3 does not interact efficiently with APC1 and is unable to mediate its degradation as a result of a N28S-G41N amino acid substitution. In contrast, we show that APC1 degradation is a conserved feature of several primary Vpr variants from transmitted/founder virus. Functionally, Vpr-mediated APC1 degradation did not impact the ability of the protein to induce a G2 cell cycle arrest during infection of CD4+ T cells or enhance HIV-1 replication in macrophages, suggesting that this conserved activity may be important for other aspects of HIV-1 pathogenesis. IMPORTANCE The function of the Vpr accessory protein during HIV-1 infection remains poorly defined. Several cellular targets of Vpr were previously identified, but their individual degradation does not fully explain the ability of Vpr to impair the cell cycle or promote HIV-1 replication in macrophages. Here, we used the unbiased proximity labeling approach, called BioID, to further define the Vpr proximity interaction network and identified several potentially new Vpr partners/targets. We validated our approach by focusing on a cell cycle master regulator, the APC/C complex, and demonstrated that Vpr mediated the degradation of a critical scaffolding component of APC/C called APC1. Furthermore, we showed that targeting of APC/C by Vpr did not impact the known activity of Vpr. Since degradation of APC1 is a conserved feature of several primary variants of Vpr, it is likely that the interplay between Vpr and APC/C governs other aspects of HIV-1 pathogenesis.
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Affiliation(s)
| | | | | | - Robert Lodge
- Montreal Clinical Research Institute, Montréal, Québec, Canada
| | - Éric A. Cohen
- Montreal Clinical Research Institute, Montréal, Québec, Canada
- Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montréal, Québec, Canada
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20
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Rahmatbakhsh M, Gagarinova A, Babu M. Bioinformatic Analysis of Temporal and Spatial Proteome Alternations During Infections. Front Genet 2021; 12:667936. [PMID: 34276775 PMCID: PMC8283032 DOI: 10.3389/fgene.2021.667936] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 06/08/2021] [Indexed: 12/13/2022] Open
Abstract
Microbial pathogens have evolved numerous mechanisms to hijack host's systems, thus causing disease. This is mediated by alterations in the combined host-pathogen proteome in time and space. Mass spectrometry-based proteomics approaches have been developed and tailored to map disease progression. The result is complex multidimensional data that pose numerous analytic challenges for downstream interpretation. However, a systematic review of approaches for the downstream analysis of such data has been lacking in the field. In this review, we detail the steps of a typical temporal and spatial analysis, including data pre-processing steps (i.e., quality control, data normalization, the imputation of missing values, and dimensionality reduction), different statistical and machine learning approaches, validation, interpretation, and the extraction of biological information from mass spectrometry data. We also discuss current best practices for these steps based on a collection of independent studies to guide users in selecting the most suitable strategies for their dataset and analysis objectives. Moreover, we also compiled the list of commonly used R software packages for each step of the analysis. These could be easily integrated into one's analysis pipeline. Furthermore, we guide readers through various analysis steps by applying these workflows to mock and host-pathogen interaction data from public datasets. The workflows presented in this review will serve as an introduction for data analysis novices, while also helping established users update their data analysis pipelines. We conclude the review by discussing future directions and developments in temporal and spatial proteomics and data analysis approaches. Data analysis codes, prepared for this review are available from https://github.com/BabuLab-UofR/TempSpac, where guidelines and sample datasets are also offered for testing purposes.
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Affiliation(s)
| | - Alla Gagarinova
- Department of Biochemistry, Microbiology, & Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, SK, Canada
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21
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Abstract
The abundance, localization, modifications, and protein-protein interactions of many host cell and virus proteins can change dynamically throughout the course of any viral infection. Studying these changes is critical for a comprehensive understanding of how viruses replicate and cause disease, as well as for the development of antiviral therapeutics and vaccines. Previously, we developed a mass spectrometry-based technique called quantitative temporal viromics (QTV), which employs isobaric tandem mass tags (TMTs) to allow precise comparative quantification of host and virus proteomes through a whole time course of infection. In this review, we discuss the utility and applications of QTV, exemplified by numerous studies that have since used proteomics with a variety of quantitative techniques to study virus infection through time. Expected final online publication date for the Annual Review of Virology, Volume 8 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
| | - Michael P Weekes
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom;
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22
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Mahoney KE, Shabanowitz J, Hunt DF. MHC Phosphopeptides: Promising Targets for Immunotherapy of Cancer and Other Chronic Diseases. Mol Cell Proteomics 2021; 20:100112. [PMID: 34129940 PMCID: PMC8724925 DOI: 10.1016/j.mcpro.2021.100112] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 05/11/2021] [Accepted: 06/02/2021] [Indexed: 12/27/2022] Open
Abstract
Major histocompatibility complex-associated peptides have been considered as potential immunotherapeutic targets for many years. MHC class I phosphopeptides result from dysregulated cell signaling pathways that are common across cancers and both viral and bacterial infections. These antigens are recognized by central memory T cells from healthy donors, indicating that they are considered antigenic by the immune system and that they are presented across different individuals and diseases. Based on these responses and the similar dysregulation, phosphorylated antigens are promising candidates for prevention or treatment of different cancers as well as a number of other chronic diseases.
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Affiliation(s)
- Keira E Mahoney
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA.
| | - Donald F Hunt
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA; Department of Pathology, University of Virginia, Charlottesville, Virginia, USA.
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23
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Dupont L, Bloor S, Williamson JC, Cuesta SM, Shah R, Teixeira-Silva A, Naamati A, Greenwood EJD, Sarafianos SG, Matheson NJ, Lehner PJ. The SMC5/6 complex compacts and silences unintegrated HIV-1 DNA and is antagonized by Vpr. Cell Host Microbe 2021; 29:792-805.e6. [PMID: 33811831 PMCID: PMC8118623 DOI: 10.1016/j.chom.2021.03.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/31/2020] [Accepted: 02/26/2021] [Indexed: 12/16/2022]
Abstract
Silencing of nuclear DNA is an essential feature of innate immune responses to invading pathogens. Early in infection, unintegrated lentiviral cDNA accumulates in the nucleus yet remains poorly expressed. In HIV-1-like lentiviruses, the Vpr accessory protein enhances unintegrated viral DNA expression, suggesting Vpr antagonizes cellular restriction. We previously showed how Vpr remodels the host proteome, identifying multiple cellular targets. We now screen these using a targeted CRISPR-Cas9 library and identify SMC5-SMC6 complex localization factor 2 (SLF2) as the Vpr target responsible for silencing unintegrated HIV-1. SLF2 recruits the SMC5/6 complex to unintegrated lentiviruses, and depletion of SLF2, or the SMC5/6 complex, increases viral expression. ATAC-seq demonstrates that Vpr-mediated SLF2 depletion increases chromatin accessibility of unintegrated virus, suggesting that the SMC5/6 complex compacts viral chromatin to silence gene expression. This work implicates the SMC5/6 complex in nuclear immunosurveillance of extrachromosomal DNA and defines its targeting by Vpr as an evolutionarily conserved antagonism.
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Affiliation(s)
- Liane Dupont
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, UK
| | - Stuart Bloor
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, UK
| | - James C Williamson
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, UK
| | | | - Raven Shah
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Ana Teixeira-Silva
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, UK
| | - Adi Naamati
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, UK
| | - Edward J D Greenwood
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, UK
| | - Stefan G Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Nicholas J Matheson
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, UK
| | - Paul J Lehner
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, UK.
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24
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Jevtić P, Haakonsen DL, Rapé M. An E3 ligase guide to the galaxy of small-molecule-induced protein degradation. Cell Chem Biol 2021; 28:1000-1013. [PMID: 33891901 DOI: 10.1016/j.chembiol.2021.04.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/28/2021] [Accepted: 04/05/2021] [Indexed: 12/13/2022]
Abstract
Induced protein degradation accomplishes elimination, rather than inhibition, of pathological proteins. Key to the success of this novel therapeutic modality is the modification of proteins with ubiquitin chains, which is brought about by molecular glues or bivalent compounds that induce proximity between the target protein and an E3 ligase. The human genome encodes ∼600 E3 ligases that differ widely in their structures, catalytic mechanisms, modes of regulation, and physiological roles. While many of these enzymes hold great promise for drug discovery, few have been successfully engaged by small-molecule degraders. Here, we review E3 ligases that are being used for induced protein degradation. Based on these prior successes and our growing understanding of the biology and biochemistry of E3 ligases, we propose new ubiquitylation enzymes that can be harnessed for drug discovery to firmly establish induced protein degradation as a specific and efficient therapeutic approach.
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Affiliation(s)
- Predrag Jevtić
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, USA
| | - Diane L Haakonsen
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, USA
| | - Michael Rapé
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, USA.
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25
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Duan Z, Yuan C, Han Y, Zhou L, Zhao J, Ruan Y, Chen J, Ni M, Ji X. TMT-based quantitative proteomics analysis reveals the attenuated replication mechanism of Newcastle disease virus caused by nuclear localization signal mutation in viral matrix protein. Virulence 2021; 11:607-635. [PMID: 32420802 PMCID: PMC7549962 DOI: 10.1080/21505594.2020.1770482] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Nuclear localization of cytoplasmic RNA virus proteins mediated by intrinsic nuclear localization signal (NLS) plays essential roles in successful virus replication. We previously reported that NLS mutation in the matrix (M) protein obviously attenuates the replication and pathogenicity of Newcastle disease virus (NDV), but the attenuated replication mechanism remains unclear. In this study, we showed that M/NLS mutation not only disrupted M's nucleocytoplasmic trafficking characteristic but also impaired viral RNA synthesis and transcription. Using TMT-based quantitative proteomics analysis of BSR-T7/5 cells infected with the parental NDV rSS1GFP and the mutant NDV rSS1GFP-M/NLSm harboring M/NLS mutation, we found that rSS1GFP infection stimulated much greater quantities and more expression changes of differentially expressed proteins involved in host cell transcription, ribosomal structure, posttranslational modification, and intracellular trafficking than rSS1GFP-M/NLSm infection. Further in-depth analysis revealed that the dominant nuclear accumulation of M protein inhibited host cell transcription, RNA processing and modification, protein synthesis, posttranscriptional modification and transport; and this kind of inhibition could be weakened when most of M protein was confined outside the nucleus. More importantly, we found that the function of M protein in the cytoplasm effected the inhibition of TIFA expression in a dose-dependent manner, and promoted NDV replication by down-regulating TIFA/TRAF6/NF-κB-mediated production of cytokines. It was the first report about the involvement of M protein in NDV immune evasion. Taken together, our findings demonstrate that NDV replication is closely related to the nucleocytoplasmic trafficking of M protein, which accelerates our understanding of the molecular functions of NDV M protein.
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Affiliation(s)
- Zhiqiang Duan
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University , Guiyang, China.,College of Animal Science, Guizhou University , Guiyang, China
| | - Chao Yuan
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University , Guiyang, China.,College of Animal Science, Guizhou University , Guiyang, China
| | - Yifan Han
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University , Guiyang, China.,College of Animal Science, Guizhou University , Guiyang, China
| | - Lei Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University , Guiyang, China.,College of Animal Science, Guizhou University , Guiyang, China
| | - Jiafu Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University , Guiyang, China.,College of Animal Science, Guizhou University , Guiyang, China
| | - Yong Ruan
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University , Guiyang, China.,College of Animal Science, Guizhou University , Guiyang, China
| | - Jiaqi Chen
- College of Animal Science, Guizhou University , Guiyang, China
| | - Mengmeng Ni
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University , Guiyang, China.,College of Animal Science, Guizhou University , Guiyang, China
| | - Xinqin Ji
- College of Animal Science, Guizhou University , Guiyang, China
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26
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Pavel M, Park SJ, Frake RA, Son SM, Manni MM, Bento CF, Renna M, Ricketts T, Menzies FM, Tanasa R, Rubinsztein DC. α-Catenin levels determine direction of YAP/TAZ response to autophagy perturbation. Nat Commun 2021; 12:1703. [PMID: 33731717 PMCID: PMC7969950 DOI: 10.1038/s41467-021-21882-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 02/18/2021] [Indexed: 12/14/2022] Open
Abstract
The factors regulating cellular identity are critical for understanding the transition from health to disease and responses to therapies. Recent literature suggests that autophagy compromise may cause opposite effects in different contexts by either activating or inhibiting YAP/TAZ co-transcriptional regulators of the Hippo pathway via unrelated mechanisms. Here, we confirm that autophagy perturbation in different cell types can cause opposite responses in growth-promoting oncogenic YAP/TAZ transcriptional signalling. These apparently contradictory responses can be resolved by a feedback loop where autophagy negatively regulates the levels of α-catenins, LC3-interacting proteins that inhibit YAP/TAZ, which, in turn, positively regulate autophagy. High basal levels of α-catenins enable autophagy induction to positively regulate YAP/TAZ, while low α-catenins cause YAP/TAZ activation upon autophagy inhibition. These data reveal how feedback loops enable post-transcriptional determination of cell identity and how levels of a single intermediary protein can dictate the direction of response to external or internal perturbations.
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Affiliation(s)
- Mariana Pavel
- Department of Medical Genetics, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge, UK
- Department of Immunology, Grigore T. Popa University of Medicine and Pharmacy of Iasi, Iasi, Romania
| | - So Jung Park
- Department of Medical Genetics, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge, UK
- UK Dementia Research Institute, Cambridge Biomedical Campus, Cambridge, UK
| | - Rebecca A Frake
- Department of Medical Genetics, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge, UK
| | - Sung Min Son
- Department of Medical Genetics, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge, UK
- UK Dementia Research Institute, Cambridge Biomedical Campus, Cambridge, UK
| | - Marco M Manni
- Department of Medical Genetics, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge, UK
- UK Dementia Research Institute, Cambridge Biomedical Campus, Cambridge, UK
| | - Carla F Bento
- Department of Medical Genetics, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge, UK
| | - Maurizio Renna
- Department of Medical Genetics, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge, UK
| | - Thomas Ricketts
- Department of Medical Genetics, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge, UK
| | - Fiona M Menzies
- Department of Medical Genetics, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge, UK
| | - Radu Tanasa
- Department of Physics, Alexandru Ioan Cuza University of Iasi, Iasi, Romania
| | - David C Rubinsztein
- Department of Medical Genetics, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge, UK.
- UK Dementia Research Institute, Cambridge Biomedical Campus, Cambridge, UK.
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27
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Gao RL, Liu LK, Guo LM, Wang KJ, Liu HP. CqPP2A inhibits white spot syndrome virus infection by up-regulating antimicrobial substances expression in red claw crayfish Cherax quadricarinatus. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 116:103913. [PMID: 33137394 DOI: 10.1016/j.dci.2020.103913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/27/2020] [Accepted: 10/27/2020] [Indexed: 06/11/2023]
Abstract
Protein phosphatase 2A (PP2A) is an important serine/threonine phosphatase, a highly conserved enzyme widely expressed in eukaryotic cells, which accounts for a majority of the serine/threonine phosphatase activity in cells implicated in regulation of immune signaling pathways and antiviral response. However, most of studies about PP2A have been conducted in mammals but few in crustaceans. In this study, two subunits of PP2A (named as CqPP2Ab and CqPP2Ac) were characterized to be involved in white spot syndrome virus (WSSV) infection in the haematopoietic tissue (Hpt) cells from red claw crayfish Cherax quadricarinatus. The open reading frame (ORF) of CqPP2Ab was 1341 bp encoding 446 amino acids with seven WD40 domains, and the ORF of CqPP2Ac was 930 bp encoding 309 amino acids with a PP2Ac domain. Tissue distribution analysis showed that the mRNA transcript of CqPP2Ab and CqPP2Ac were both widely expressed in all the tested tissues with the highest expression in hemocyte, followed by high expression in Hpt. The gene expressions of CqPP2Ab and CqPP2Ac were both significantly down-regulated at 6 h post WSSV infection (6 hpi) in Hpt cells. Importantly, the expression of viral immediate early gene IE1 and late viral gene envelope protein VP28 were both significantly increased post WSSV infection after gene silencing of CqPP2Ab or CqPP2Ac in Hpt cells, suggesting that CqPP2Ab and CqPP2Ac could inhibit WSSV infection in Hpt cells, probably by increasing the antimicrobial substances expression in consideration to the significantly reduced expression of anti-lipopolysaccharide factor, crustin, and lysozyme after gene silencing of CqPP2Ab or CqPP2Ac, respectively. These findings provide a new light on the mechanism of WSSV infection and the antiviral response in crustaceans.
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Affiliation(s)
- Rui-Lin Gao
- State Key Laboratory of Marine Environmental Science, State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Ling-Ke Liu
- State Key Laboratory of Marine Environmental Science, State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Li-Mei Guo
- State Key Laboratory of Marine Environmental Science, State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Ke-Jian Wang
- State Key Laboratory of Marine Environmental Science, State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Hai-Peng Liu
- State Key Laboratory of Marine Environmental Science, State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, Fujian, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China.
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28
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Gan G, Xu X, Chen X, Zhang XF, Wang J, Zhong CQ. SCASP: A Simple and Robust SDS-Aided Sample Preparation Method for Proteomic Research. Mol Cell Proteomics 2021; 20:100051. [PMID: 33549647 PMCID: PMC7970136 DOI: 10.1016/j.mcpro.2021.100051] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/12/2021] [Accepted: 01/15/2021] [Indexed: 11/15/2022] Open
Abstract
SDS is widely used in sample preparation for proteomic research. However, SDS is incompatible with LC and electrospray ionization. SDS depletion is therefore required ahead of LC-MS analysis. Most of current SDS removal strategies are time consuming, laborious, and have low reproducibility. Here, we describe a method, SDS-cyclodextrin (CD)-assisted sample preparation, by which CD can bind to SDS and form CD-SDS complexes in solutions, allowing for direct tryptic digestion. We demonstrate that SDS-CD-assisted sample preparation is a simple, fast, and robust SDS-based sample preparation method for proteomics application.
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Affiliation(s)
- Guohong Gan
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life Sciences, Xiamen University, Xiamen, China
| | - Xiao Xu
- Department of Emergency, Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Xi Chen
- SpecAlly Life Technology Co, Ltd, Wuhan, China; Wuhan Institute of Biotechnology, Wuhan, China
| | - Xiu-Fang Zhang
- Department of Paediatrics, Xiang'an Hospital of Xiamen University, Xiamen, China
| | - Jinling Wang
- Department of Emergency, Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Chuan-Qi Zhong
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life Sciences, Xiamen University, Xiamen, China.
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29
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Haas P, Muralidharan M, Krogan NJ, Kaake RM, Hüttenhain R. Proteomic Approaches to Study SARS-CoV-2 Biology and COVID-19 Pathology. J Proteome Res 2021; 20:1133-1152. [PMID: 33464917 PMCID: PMC7839417 DOI: 10.1021/acs.jproteome.0c00764] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Indexed: 12/17/2022]
Abstract
The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), was declared a pandemic infection in March 2020. As of December 2020, two COVID-19 vaccines have been authorized for emergency use by the U.S. Food and Drug Administration, but there are no effective drugs to treat COVID-19, and pandemic mitigation efforts like physical distancing have had acute social and economic consequences. In this perspective, we discuss how the proteomic research community can leverage technologies and expertise to address the pandemic by investigating four key areas of study in SARS-CoV-2 biology. Specifically, we discuss how (1) mass spectrometry-based structural techniques can overcome limitations and complement traditional structural approaches to inform the dynamic structure of SARS-CoV-2 proteins, complexes, and virions; (2) virus-host protein-protein interaction mapping can identify the cellular machinery required for SARS-CoV-2 replication; (3) global protein abundance and post-translational modification profiling can characterize signaling pathways that are rewired during infection; and (4) proteomic technologies can aid in biomarker identification, diagnostics, and drug development in order to monitor COVID-19 pathology and investigate treatment strategies. Systems-level high-throughput capabilities of proteomic technologies can yield important insights into SARS-CoV-2 biology that are urgently needed during the pandemic, and more broadly, can inform coronavirus virology and host biology.
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Affiliation(s)
- Paige Haas
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Monita Muralidharan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Nevan J. Krogan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Robyn M. Kaake
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ruth Hüttenhain
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
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30
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Salamango DJ, Harris RS. Demystifying Cell Cycle Arrest by HIV-1 Vif. Trends Microbiol 2021; 29:381-384. [PMID: 33478820 DOI: 10.1016/j.tim.2021.01.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/28/2020] [Accepted: 01/04/2021] [Indexed: 11/26/2022]
Abstract
Although APOBEC3 degradation is the canonical function of HIV-1 Vif, this viral protein also induces potent cell cycle arrest through a newly defined mechanism. Here, we review recent advances in this area and propose that the scope of this activity may go beyond subversion of the host cell cycle.
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Affiliation(s)
- Daniel J Salamango
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN 55455, USA.
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31
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Salamango DJ, Harris RS. Dual Functionality of HIV-1 Vif in APOBEC3 Counteraction and Cell Cycle Arrest. Front Microbiol 2021; 11:622012. [PMID: 33510734 PMCID: PMC7835321 DOI: 10.3389/fmicb.2020.622012] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/11/2020] [Indexed: 01/02/2023] Open
Abstract
Accessory proteins are a key feature that distinguishes primate immunodeficiency viruses such as human immunodeficiency virus type I (HIV-1) from other retroviruses. A prime example is the virion infectivity factor, Vif, which hijacks a cellular co-transcription factor (CBF-β) to recruit a ubiquitin ligase complex (CRL5) to bind and degrade antiviral APOBEC3 enzymes including APOBEC3D (A3D), APOBEC3F (A3F), APOBEC3G (A3G), and APOBEC3H (A3H). Although APOBEC3 antagonism is essential for viral pathogenesis, and a more than sufficient functional justification for Vif’s evolution, most viral proteins have evolved multiple functions. Indeed, Vif has long been known to trigger cell cycle arrest and recent studies have shed light on the underlying molecular mechanism. Vif accomplishes this function using the same CBF-β/CRL5 ubiquitin ligase complex to degrade a family of PPP2R5 phospho-regulatory proteins. These advances have helped usher in a new era of accessory protein research and fresh opportunities for drug development.
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Affiliation(s)
- Daniel J Salamango
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, United States.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, United States
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, United States.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, United States.,Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN, United States
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32
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Sperk M, van Domselaar R, Rodriguez JE, Mikaeloff F, Sá Vinhas B, Saccon E, Sönnerborg A, Singh K, Gupta S, Végvári Á, Neogi U. Utility of Proteomics in Emerging and Re-Emerging Infectious Diseases Caused by RNA Viruses. J Proteome Res 2020; 19:4259-4274. [PMID: 33095583 PMCID: PMC7640957 DOI: 10.1021/acs.jproteome.0c00380] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Indexed: 12/21/2022]
Abstract
Emerging and re-emerging infectious diseases due to RNA viruses cause major negative consequences for the quality of life, public health, and overall economic development. Most of the RNA viruses causing illnesses in humans are of zoonotic origin. Zoonotic viruses can directly be transferred from animals to humans through adaptation, followed by human-to-human transmission, such as in human immunodeficiency virus (HIV), severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and, more recently, SARS coronavirus 2 (SARS-CoV-2), or they can be transferred through insects or vectors, as in the case of Crimean-Congo hemorrhagic fever virus (CCHFV), Zika virus (ZIKV), and dengue virus (DENV). At the present, there are no vaccines or antiviral compounds against most of these viruses. Because proteins possess a vast array of functions in all known biological systems, proteomics-based strategies can provide important insights into the investigation of disease pathogenesis and the identification of promising antiviral drug targets during an epidemic or pandemic. Mass spectrometry technology has provided the capacity required for the precise identification and the sensitive and high-throughput analysis of proteins on a large scale and has contributed greatly to unravelling key protein-protein interactions, discovering signaling networks, and understanding disease mechanisms. In this Review, we present an account of quantitative proteomics and its application in some prominent recent examples of emerging and re-emerging RNA virus diseases like HIV-1, CCHFV, ZIKV, and DENV, with more detail with respect to coronaviruses (MERS-CoV and SARS-CoV) as well as the recent SARS-CoV-2 pandemic.
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Affiliation(s)
- Maike Sperk
- Division
of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Campus Flemingsberg, Stockholm 14152, Sweden
| | - Robert van Domselaar
- Division
of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institute, ANA Futura, Campus Flemingsberg, Stockholm 14152, Sweden
| | - Jimmy Esneider Rodriguez
- Division
of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm 14152 Sweden
| | - Flora Mikaeloff
- Division
of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Campus Flemingsberg, Stockholm 14152, Sweden
| | - Beatriz Sá Vinhas
- Division
of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Campus Flemingsberg, Stockholm 14152, Sweden
| | - Elisa Saccon
- Division
of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Campus Flemingsberg, Stockholm 14152, Sweden
| | - Anders Sönnerborg
- Division
of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Campus Flemingsberg, Stockholm 14152, Sweden
- Division
of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institute, ANA Futura, Campus Flemingsberg, Stockholm 14152, Sweden
| | - Kamal Singh
- Department
of Molecular Microbiology and Immunology and the Bond Life Science
Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Soham Gupta
- Division
of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Campus Flemingsberg, Stockholm 14152, Sweden
| | - Ákos Végvári
- Division
of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm 14152 Sweden
| | - Ujjwal Neogi
- Division
of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Campus Flemingsberg, Stockholm 14152, Sweden
- Department
of Molecular Microbiology and Immunology and the Bond Life Science
Center, University of Missouri, Columbia, Missouri 65211, United States
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33
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Saleemi MA, Ahmad B, Benchoula K, Vohra MS, Mea HJ, Chong PP, Palanisamy NK, Wong EH. Emergence and molecular mechanisms of SARS-CoV-2 and HIV to target host cells and potential therapeutics. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 85:104583. [PMID: 33035643 PMCID: PMC7536551 DOI: 10.1016/j.meegid.2020.104583] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 09/24/2020] [Accepted: 10/01/2020] [Indexed: 02/07/2023]
Abstract
The emergence of a new coronavirus, in around late December 2019 which had first been reported in Wuhan, China has now developed into a massive threat to global public health. The World Health Organization (WHO) has named the disease caused by the virus as COVID-19 and the virus which is the culprit was renamed from the initial novel respiratory 2019 coronavirus to SARS-CoV-2. The person-to-person transmission of this virus is ongoing despite drastic public health mitigation measures such as social distancing and movement restrictions implemented in most countries. Understanding the source of such an infectious pathogen is crucial to develop a means of avoiding transmission and further to develop therapeutic drugs and vaccines. To identify the etiological source of a novel human pathogen is a dynamic process that needs comprehensive and extensive scientific validations, such as observed in the Middle East respiratory syndrome (MERS), severe acute respiratory syndrome (SARS), and human immunodeficiency virus (HIV) cases. In this context, this review is devoted to understanding the taxonomic characteristics of SARS-CoV-2 and HIV. Herein, we discuss the emergence and molecular mechanisms of both viral infections. Nevertheless, no vaccine or therapeutic drug is yet to be approved for the treatment of SARS-CoV-2, although it is highly likely that new effective medications that target the virus specifically will take years to establish. Therefore, this review reflects the latest repurpose of existing antiviral therapeutic drug choices available to combat SARS-CoV-2.
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Affiliation(s)
- Mansab Ali Saleemi
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor's University, Lakeside Campus, Subang Jaya, Selangor Darul Ehsan 47500, Malaysia
| | - Bilal Ahmad
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor's University, Lakeside Campus, Subang Jaya, Selangor Darul Ehsan 47500, Malaysia
| | - Khaled Benchoula
- School of Medicine, Faculty of Health and Medical Sciences, Taylor's University, Lakeside Campus, Subang Jaya, Selangor Darul Ehsan 47500, Malaysia
| | - Muhammad Sufyan Vohra
- School of Medicine, Faculty of Health and Medical Sciences, Taylor's University, Lakeside Campus, Subang Jaya, Selangor Darul Ehsan 47500, Malaysia
| | - Hing Jian Mea
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor's University, Lakeside Campus, Subang Jaya, Selangor Darul Ehsan 47500, Malaysia
| | - Pei Pei Chong
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor's University, Lakeside Campus, Subang Jaya, Selangor Darul Ehsan 47500, Malaysia
| | - Navindra Kumari Palanisamy
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, Universiti Teknologi MARA (UiTM), Sungai Buloh Campus, Sungai Buloh, Selangor, Malaysia
| | - Eng Hwa Wong
- School of Medicine, Faculty of Health and Medical Sciences, Taylor's University, Lakeside Campus, Subang Jaya, Selangor Darul Ehsan 47500, Malaysia.
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Duan S, Wang S, Song Y, Gao N, Meng L, Gai Y, Zhang Y, Wang S, Wang C, Yu B, Wu J, Yu X. A novel HIV-1 inhibitor that blocks viral replication and rescues APOBEC3s by interrupting vif/CBFβ interaction. J Biol Chem 2020; 295:14592-14605. [PMID: 32817167 PMCID: PMC7586213 DOI: 10.1074/jbc.ra120.013404] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 08/18/2020] [Indexed: 11/06/2022] Open
Abstract
HIV remains a health challenge worldwide, partly because of the continued development of resistance to drugs. Therefore, it is urgent to find new HIV inhibitors and targets. Apolipoprotein B mRNA-editing catalytic polypeptide-like 3 family members (APOBEC3) are important host restriction factors that inhibit HIV-1 replication by their cytidine deaminase activity. HIV-1 viral infectivity factor (Vif) promotes proteasomal degradation of APOBEC3 proteins by recruiting the E3 ubiquitin ligase complex, in which core-binding factor β (CBFβ) is a necessary molecular chaperone. Interrupting the interaction between Vif and CBFβ can release APOBEC3 proteins to inhibit HIV-1 replication and may be useful for developing new drug targets for HIV-1. In this study, we identified a potent small molecule inhibitor CBFβ/Vif-3 (CV-3) of HIV-1 replication by employing structure-based virtual screening using the crystal structure of Vif and CBFβ (PDB: 4N9F) and validated CV-3's antiviral activity. We found that CV-3 specifically inhibited HIV-1 replication (IC50 = 8.16 µm; 50% cytotoxic concentration >100 µm) in nonpermissive lymphocytes. Furthermore, CV-3 treatment rescued APOBEC3 family members (human APOBEC3G (hA3G), hA3C, and hA3F) in the presence of Vif and enabled hA3G packaging into HIV-1 virions, which resulted in Gly-to-Ala hypermutations in viral genomes. Finally, we used FRET to demonstrate that CV-3 inhibited the interaction between Vif and CBFβ by simultaneously forming hydrogen bonds with residues Gln-67, Ile-102, and Arg-131 of CBFβ. These findings demonstrate that CV-3 can effectively inhibit HIV-1 by blocking the interaction between Vif and CBFβ and that this interaction can serve as a new target for developing HIV-1 inhibitors.
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Affiliation(s)
- Sizhu Duan
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin Province, China
| | - Shiqi Wang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin Province, China
| | - Yanan Song
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin Province, China
| | - Nan Gao
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin Province, China
| | - Lina Meng
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin Province, China
| | - Yanxin Gai
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin Province, China
| | - Ying Zhang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin Province, China
| | - Song Wang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, Jilin Province, China
| | - Chu Wang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin Province, China
| | - Bin Yu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin Province, China; Key Laboratory for Molecular Enzymology and Engineering, the Ministry of Education, School of Life Sciences, Jilin University, Changchun, Jilin Province, China
| | - Jiaxin Wu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin Province, China; Key Laboratory for Molecular Enzymology and Engineering, the Ministry of Education, School of Life Sciences, Jilin University, Changchun, Jilin Province, China
| | - Xianghui Yu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin Province, China; Key Laboratory for Molecular Enzymology and Engineering, the Ministry of Education, School of Life Sciences, Jilin University, Changchun, Jilin Province, China.
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35
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Functional and Structural Insights into a Vif/PPP2R5 Complex Elucidated Using Patient HIV-1 Isolates and Computational Modeling. J Virol 2020; 94:JVI.00631-20. [PMID: 32847850 DOI: 10.1128/jvi.00631-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 08/17/2020] [Indexed: 02/06/2023] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) Vif recruits a cellular ubiquitin ligase complex to degrade antiviral APOBEC3 enzymes (APOBEC3C-H) and PP2A phosphatase regulators (PPP2R5A to PPP2R5E). While APOBEC3 antagonism is the canonical function of HIV-1 Vif, this viral accessory protein is also known to trigger G2/M cell cycle arrest. Vif initiates G2/M arrest by degrading multiple PPP2R5 family members, an activity prevalent among diverse HIV-1 and simian immunodeficiency virus (SIV) isolates. Here, computational protein-protein docking was used to delineate a Vif/CBF-β/PPP2R5 complex in which Vif is predicted to bind the same PPP2R5 surface as physiologic phosphatase targets. This model was tested using targeted mutagenesis of amino acid residues within or adjacent to the putative interface to show loss or retention, respectively, of Vif-induced PPP2R5 degradation activity. Additionally, expression of a peptide that mimics cellular targets of PPP2R5s robustly inhibited Vif-mediated degradation of PPP2R5A but not APOBEC3G. Moreover, live-cell imaging studies examining Vif-mediated degradation of PPP2R5A and APOBEC3G within the same cell revealed that PPP2R5A degradation kinetics are comparable to those of APOBEC3G with a half-life of roughly 6 h postinfection, demonstrating that Vif can concurrently mediate the degradation of distinct cellular substrates. Finally, experiments with a panel of patient-derived Vif isolates indicated that PPP2R5A degradation activity is common in patient-derived isolates. Taken together, these results support a model in which PPP2R5 degradation and global changes in the cellular phosphoproteome are likely to be advantageous for viral pathogenesis.IMPORTANCE A critical function of HIV-1 Vif is to counteract the family of APOBEC3 innate immune proteins. It is also widely accepted that Vif induces G2/M cell cycle arrest in several different cell types. Recently, it has been shown that Vif degrades multiple PPP2R5 phosphoregulators to induce the G2/M arrest phenotype. Here, computational approaches are used to test a structural model of the Vif/PPP2R5 complex. In addition, imaging studies are used to show that Vif degrades these PPP2R5 substrates in roughly the same time frame as APOBEC3 degradation and that this activity is prevalent in patient-derived Vif isolates. These studies are important by further defining PPP2R5 proteins as a bona fide substrate of HIV-1 Vif.
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36
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HIV-1 Vif Triggers Cell Cycle Arrest by Degrading Cellular PPP2R5 Phospho-regulators. Cell Rep 2020; 29:1057-1065.e4. [PMID: 31665623 PMCID: PMC6903395 DOI: 10.1016/j.celrep.2019.09.057] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/10/2019] [Accepted: 09/18/2019] [Indexed: 02/07/2023] Open
Abstract
HIV-1 Vif hijacks a cellular ubiquitin ligase complex to degrade antiviral APOBEC3 enzymes and PP2A phosphatase regulators (PPP2R5A–E). APOBEC3 counteraction is essential for viral pathogenesis. However, Vif also functions through an unknown mechanism to induce G2 cell cycle arrest. Here, deep mutagenesis is used to define the Vif surface required for PPP2R5 degradation and isolate a panel of separation-of-function mutants (PPP2R5 degradation-deficient and APOBEC3G degradation-proficient). Functional studies with Vif and PPP2R5 mutants were combined to demonstrate that PPP2R5 is, in fact, the target Vif degrades to induce G2 arrest. Pharmacologic and genetic approaches show that direct modulation of PP2A function or depletion of specific PPP2R5 proteins causes an indistinguishable arrest phenotype. Vif function in the cell cycle checkpoint is present in common HIV-1 subtypes worldwide and likely advantageous for viral pathogenesis. Salamango et al. discovered that the HIV-1 accessory protein Vif degrades several PP2A phospho-regulators to induce G2 cell cycle arrest. This activity is prevalent among diverse HIV-1 subtypes and global viral populations, suggesting that virus-induced G2 arrest is advantageous for pathogenesis.
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37
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Ferreira IATM, Porterfield JZ, Gupta RK, Mlcochova P. Cell Cycle Regulation in Macrophages and Susceptibility to HIV-1. Viruses 2020; 12:v12080839. [PMID: 32751972 PMCID: PMC7472357 DOI: 10.3390/v12080839] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 07/24/2020] [Accepted: 07/28/2020] [Indexed: 02/07/2023] Open
Abstract
Macrophages are the first line of defence against invading pathogens. They play a crucial role in immunity but also in regeneration and homeostasis. Their remarkable plasticity in their phenotypes and function provides them with the ability to quickly respond to environmental changes and infection. Recent work shows that macrophages undergo cell cycle transition from a G0/terminally differentiated state to a G1 state. This G0-to-G1 transition presents a window of opportunity for HIV-1 infection. Macrophages are an important target for HIV-1 but express high levels of the deoxynucleotide-triphosphate hydrolase SAMHD1, which restricts viral DNA synthesis by decreasing levels of dNTPs. While the G0 state is non-permissive to HIV-1 infection, a G1 state is very permissive to HIV-1 infection. This is because macrophages in a G1 state switch off the antiviral restriction factor SAMHD1 by phosphorylation, thereby allowing productive HIV-1 infection. Here, we explore the macrophage cell cycle and the interplay between its regulation and permissivity to HIV-1 infection.
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Affiliation(s)
- Isabella A. T. M. Ferreira
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge CB20AW, UK; (I.A.T.M.F.); (R.K.G.)
- Department of Medicine, University of Cambridge, Cambridge CB20QQ, UK
| | - J. Zachary Porterfield
- Department of Microbiology, University of Kentucky, Lexington, KY 40536, USA;
- Africa Health Research Institute, Durban 4001, South Africa
| | - Ravindra K. Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge CB20AW, UK; (I.A.T.M.F.); (R.K.G.)
- Department of Medicine, University of Cambridge, Cambridge CB20QQ, UK
- Africa Health Research Institute, Durban 4001, South Africa
| | - Petra Mlcochova
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge CB20AW, UK; (I.A.T.M.F.); (R.K.G.)
- Department of Medicine, University of Cambridge, Cambridge CB20QQ, UK
- Correspondence:
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38
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Greenwood EJD, Williamson JC, Sienkiewicz A, Naamati A, Matheson NJ, Lehner PJ. Promiscuous Targeting of Cellular Proteins by Vpr Drives Systems-Level Proteomic Remodeling in HIV-1 Infection. Cell Rep 2020; 27:1579-1596.e7. [PMID: 31042482 PMCID: PMC6506760 DOI: 10.1016/j.celrep.2019.04.025] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 03/19/2019] [Accepted: 04/02/2019] [Indexed: 12/26/2022] Open
Abstract
HIV-1 encodes four “accessory proteins” (Vif, Vpr, Vpu, and Nef), dispensable for viral replication in vitro but essential for viral pathogenesis in vivo. Well characterized cellular targets have been associated with Vif, Vpu, and Nef, which counteract host restriction and promote viral replication. Conversely, although several substrates of Vpr have been described, their biological significance remains unclear. Here, we use complementary unbiased mass spectrometry-based approaches to demonstrate that Vpr is both necessary and sufficient for the DCAF1/DDB1/CUL4 E3 ubiquitin ligase-mediated degradation of at least 38 cellular proteins, causing systems-level changes to the cellular proteome. We therefore propose that promiscuous targeting of multiple host factors underpins complex Vpr-dependent cellular phenotypes and validate this in the case of G2/M cell cycle arrest. Our model explains how Vpr modulates so many cell biological processes and why the functional consequences of previously described Vpr targets, identified and studied in isolation, have proved elusive. HIV-1 Vpr is responsible for almost all proteomic changes in HIV-1-infected cells Vpr directly targets multiple nuclear proteins for degradation Vpr cellular phenotypes (e.g., cell cycle arrest) stem from broad substrate targeting Targeting of a few proteins is conserved across diverse primate lentiviral species
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Affiliation(s)
- Edward J D Greenwood
- Department of Medicine, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0QQ, UK; Cambridge Institute for Medical Research, Keith Peters Building, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0XY, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, UK.
| | - James C Williamson
- Department of Medicine, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0QQ, UK; Cambridge Institute for Medical Research, Keith Peters Building, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0XY, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, UK.
| | - Agata Sienkiewicz
- Department of Medicine, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0QQ, UK; Cambridge Institute for Medical Research, Keith Peters Building, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0XY, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, UK
| | - Adi Naamati
- Department of Medicine, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0QQ, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, UK
| | - Nicholas J Matheson
- Department of Medicine, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0QQ, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, UK
| | - Paul J Lehner
- Department of Medicine, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0QQ, UK; Cambridge Institute for Medical Research, Keith Peters Building, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0XY, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, UK.
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39
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Ivanov S, Lagunin A, Filimonov D, Tarasova O. Network-Based Analysis of OMICs Data to Understand the HIV-Host Interaction. Front Microbiol 2020; 11:1314. [PMID: 32625189 PMCID: PMC7311653 DOI: 10.3389/fmicb.2020.01314] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 05/25/2020] [Indexed: 12/22/2022] Open
Abstract
The interaction of human immunodeficiency virus with human cells is responsible for all stages of the viral life cycle, from the infection of CD4+ cells to reverse transcription, integration, and the assembly of new viral particles. To date, a large amount of OMICs data as well as information from functional genomics screenings regarding the HIV–host interaction has been accumulated in the literature and in public databases. We processed databases containing HIV–host interactions and found 2910 HIV-1-human protein-protein interactions, mostly related to viral group M subtype B, 137 interactions between human and HIV-1 coding and non-coding RNAs, essential for viral lifecycle and cell defense mechanisms, 232 transcriptomics, 27 proteomics, and 34 epigenomics HIV-related experiments. Numerous studies regarding network-based analysis of corresponding OMICs data have been published in recent years. We overview various types of molecular networks, which can be created using OMICs data, including HIV–human protein–protein interaction networks, co-expression networks, gene regulatory and signaling networks, and approaches for the analysis of their topology and dynamics. The network-based analysis can be used to determine the critical pathways and key proteins involved in the HIV life cycle, cellular and immune responses to infection, viral escape from host defense mechanisms, and mechanisms mediating different susceptibility of humans to infection. The proteins and pathways identified in these studies represent a basis for developing new anti-HIV therapeutic strategies such as new drugs preventing infection of CD4+ cells and viral replication, effective vaccines, “shock and kill” and “block and lock” approaches to cure latent infection.
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Affiliation(s)
- Sergey Ivanov
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia.,Department of Bioinformatics, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Alexey Lagunin
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia.,Department of Bioinformatics, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitry Filimonov
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia
| | - Olga Tarasova
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia
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Critical role of PP2A-B56 family protein degradation in HIV-1 Vif mediated G2 cell cycle arrest. Biochem Biophys Res Commun 2020; 527:257-263. [DOI: 10.1016/j.bbrc.2020.04.123] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 04/22/2020] [Indexed: 11/21/2022]
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41
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Marelli S, Williamson JC, Protasio AV, Naamati A, Greenwood EJD, Deane JE, Lehner PJ, Matheson NJ. Antagonism of PP2A is an independent and conserved function of HIV-1 Vif and causes cell cycle arrest. eLife 2020; 9:e53036. [PMID: 32292164 PMCID: PMC7920553 DOI: 10.7554/elife.53036] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/17/2020] [Indexed: 01/01/2023] Open
Abstract
The seminal description of the cellular restriction factor APOBEC3G and its antagonism by HIV-1 Vif has underpinned two decades of research on the host-virus interaction. We recently reported that HIV-1 Vif is also able to degrade the PPP2R5 family of regulatory subunits of key cellular phosphatase PP2A (PPP2R5A-E; Greenwood et al., 2016; Naamati et al., 2019). We now identify amino acid polymorphisms at positions 31 and 128 of HIV-1 Vif which selectively regulate the degradation of PPP2R5 family proteins. These residues covary across HIV-1 viruses in vivo, favouring depletion of PPP2R5A-E. Through analysis of point mutants and naturally occurring Vif variants, we further show that degradation of PPP2R5 family subunits is both necessary and sufficient for Vif-dependent G2/M cell cycle arrest. Antagonism of PP2A by HIV-1 Vif is therefore independent of APOBEC3 family proteins, and regulates cell cycle progression in HIV-infected cells.
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Affiliation(s)
- Sara Marelli
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of CambridgeCambridgeUnited Kingdom
| | - James C Williamson
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of CambridgeCambridgeUnited Kingdom
| | - Anna V Protasio
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of CambridgeCambridgeUnited Kingdom
| | - Adi Naamati
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of CambridgeCambridgeUnited Kingdom
| | - Edward JD Greenwood
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of CambridgeCambridgeUnited Kingdom
| | - Janet E Deane
- Department of Clinical Neuroscience, University of CambridgeCambridgeUnited Kingdom
- Cambridge Institute for Medical Research (CIMR), University of CambridgeCambridgeUnited Kingdom
| | - Paul J Lehner
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of CambridgeCambridgeUnited Kingdom
| | - Nicholas J Matheson
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of CambridgeCambridgeUnited Kingdom
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42
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Park E, Chen J, Moore A, Mangolini M, Santoro A, Boyd JR, Schjerven H, Ecker V, Buchner M, Williamson JC, Lehner PJ, Gasparoli L, Williams O, Bloehdorn J, Stilgenbauer S, Leitges M, Egle A, Schmidt-Supprian M, Frietze S, Ringshausen I. Stromal cell protein kinase C-β inhibition enhances chemosensitivity in B cell malignancies and overcomes drug resistance. Sci Transl Med 2020; 12:eaax9340. [PMID: 31941829 PMCID: PMC7116365 DOI: 10.1126/scitranslmed.aax9340] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 11/15/2019] [Indexed: 12/15/2022]
Abstract
Overcoming drug resistance remains a key challenge to cure patients with acute and chronic B cell malignancies. Here, we describe a stromal cell-autonomous signaling pathway, which contributes to drug resistance of malignant B cells. We show that protein kinase C (PKC)-β-dependent signals from bone marrow-derived stromal cells markedly decrease the efficacy of cytotoxic therapies. Conversely, small-molecule PKC-β inhibitors antagonize prosurvival signals from stromal cells and sensitize tumor cells to targeted and nontargeted chemotherapy, resulting in enhanced cytotoxicity and prolonged survival in vivo. Mechanistically, stromal PKC-β controls the expression of adhesion and matrix proteins, required for activation of phosphoinositide 3-kinases (PI3Ks) and the extracellular signal-regulated kinase (ERK)-mediated stabilization of B cell lymphoma-extra large (BCL-XL) in tumor cells. Central to the stroma-mediated drug resistance is the PKC-β-dependent activation of transcription factor EB, regulating lysosome biogenesis and plasma membrane integrity. Stroma-directed therapies, enabled by direct inhibition of PKC-β, enhance the effectiveness of many antileukemic therapies.
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Affiliation(s)
- Eugene Park
- Wellcome Trust/MRC Cambridge Stem Cell Institute and Department of Haematology, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AH, UK
| | - Jingyu Chen
- Wellcome Trust/MRC Cambridge Stem Cell Institute and Department of Haematology, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AH, UK
| | - Andrew Moore
- Wellcome Trust/MRC Cambridge Stem Cell Institute and Department of Haematology, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AH, UK
| | - Maurizio Mangolini
- Wellcome Trust/MRC Cambridge Stem Cell Institute and Department of Haematology, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AH, UK
| | - Antonella Santoro
- Wellcome Trust/MRC Cambridge Stem Cell Institute and Department of Haematology, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AH, UK
| | - Joseph R Boyd
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, VT 05405, USA
| | - Hilde Schjerven
- Department of Laboratory Medicine, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA
- KG Jebsen Centre for B cell Malignancies, IMM, OUH, 0424 Oslo, Norway
| | - Veronika Ecker
- Institut für Klinische Chemie und Pathobiochemie, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
- TranslaTUM, Center for Translational Cancer Research, Technische Universität München, 81675 Munich, Germany
| | - Maike Buchner
- Institut für Klinische Chemie und Pathobiochemie, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
- TranslaTUM, Center for Translational Cancer Research, Technische Universität München, 81675 Munich, Germany
| | - James C Williamson
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
| | - Paul J Lehner
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
| | - Luca Gasparoli
- University College London (UCL) GOS-ICH, London WC1N 1EH, UK
| | - Owen Williams
- University College London (UCL) GOS-ICH, London WC1N 1EH, UK
| | - Johannes Bloehdorn
- Department of Internal Medicine III, University of Ulm, 89081 Ulm, Germany
| | | | - Michael Leitges
- Faculty of Medicine, Craig L. Dobbin Genetics Research Centre, Memorial University of Newfoundland, St. John's, Newfoundland A1B 3V6, Canada
| | - Alexander Egle
- IIIrd Medical Department with Hematology, Medical Oncology, Hemostaseology, Infectious Diseases and Rheumatology, Oncologic Center, Paracelsus Medical University, Cancer Cluster Salzburg, 5020 Salzburg, Austria
- Salzburg Cancer Research Institute (SCRI) with Laboratory of Immunological and Molecular Cancer Research (LIMCR), 5020 Salzburg, Austria
- Cancer Cluster Salzburg, 5020 Salzburg, Austria
| | - Marc Schmidt-Supprian
- German Cancer Consortium, DKFZ, 69120 Heidelberg, Germany
- Institute of Experimental Hematology, School of Medicine, Technical University Munich, 81675 Munich, Germany
| | - Seth Frietze
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA
| | - Ingo Ringshausen
- Wellcome Trust/MRC Cambridge Stem Cell Institute and Department of Haematology, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AH, UK.
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EWI-2 Inhibits Cell-Cell Fusion at the HIV-1 Virological Presynapse. Viruses 2019; 11:v11121082. [PMID: 31757023 PMCID: PMC6950393 DOI: 10.3390/v11121082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/14/2019] [Accepted: 11/16/2019] [Indexed: 12/13/2022] Open
Abstract
Cell-to-cell transfer of virus particles at the Env-dependent virological synapse (VS) is a highly efficient mode of HIV-1 transmission. While cell–cell fusion could be triggered at the VS, leading to the formation of syncytia and preventing exponential growth of the infected cell population, this is strongly inhibited by both viral (Gag) and host (ezrin and tetraspanins) proteins. Here, we identify EWI-2, a protein that was previously shown to associate with ezrin and tetraspanins, as a host factor that contributes to the inhibition of Env-mediated cell–cell fusion. Using quantitative fluorescence microscopy, shRNA knockdowns, and cell–cell fusion assays, we show that EWI-2 accumulates at the presynaptic terminal (i.e., the producer cell side of the VS), where it contributes to the fusion-preventing activities of the other viral and cellular components. We also find that EWI-2, like tetraspanins, is downregulated upon HIV-1 infection, most likely by Vpu. Despite the strong inhibition of fusion at the VS, T cell-based syncytia do form in vivo and in physiologically relevant culture systems, but they remain small. In regard to that, we demonstrate that EWI-2 and CD81 levels are restored on the surface of syncytia, where they (presumably) continue to act as fusion inhibitors. This study documents a new role for EWI-2 as an inhibitor of HIV-1-induced cell–cell fusion and provides novel insight into how syncytia are prevented from fusing indefinitely.
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44
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Sadowski I, Hashemi FB. Strategies to eradicate HIV from infected patients: elimination of latent provirus reservoirs. Cell Mol Life Sci 2019; 76:3583-3600. [PMID: 31129856 PMCID: PMC6697715 DOI: 10.1007/s00018-019-03156-8] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 04/29/2019] [Accepted: 05/20/2019] [Indexed: 02/06/2023]
Abstract
35 years since identification of HIV as the causative agent of AIDS, and 35 million deaths associated with this disease, significant effort is now directed towards the development of potential cures. Current anti-retroviral (ART) therapies for HIV/AIDS can suppress virus replication to undetectable levels, and infected individuals can live symptom free so long as treatment is maintained. However, removal of therapy allows rapid re-emergence of virus from a highly stable reservoir of latently infected cells that exist as a barrier to elimination of the infection with current ART. Prospects of a cure for HIV infection are significantly encouraged by two serendipitous cases where individuals have entered remission following stem cell transplantation from compatible HIV-resistant donors. However, development of a routine cure that could become available to millions of infected individuals will require a means of specifically purging cells harboring latent HIV, preventing replication of latent provirus, or destruction of provirus genomes by gene editing. Elimination of latently infected cells will require a means of exposing this population, which may involve identification of a natural specific biomarker or therapeutic intervention to force their exposure by reactivation of virus expression. Accordingly, the proposed "Shock and Kill" strategy involves treatment with latency-reversing agents (LRA) to induce HIV provirus expression thus exposing these cells to killing by cellular immunity or apoptosis. Current efforts to enable this strategy are directed at developing improved combinations of LRA to produce broad and robust induction of HIV provirus and enhancing the elimination of cells where replication has been reactivated by targeted immune modulation. Alternative strategies may involve preventing re-emergence virus from latently infected cells by "Lock and Block" intervention, where transcription of provirus is inhibited to prevent virus spread or disruption of the HIV provirus genome by genome editing.
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Affiliation(s)
- Ivan Sadowski
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada.
| | - Farhad B Hashemi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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45
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Naamati A, Williamson JC, Greenwood EJ, Marelli S, Lehner PJ, Matheson NJ. Functional proteomic atlas of HIV infection in primary human CD4+ T cells. eLife 2019; 8:41431. [PMID: 30857592 PMCID: PMC6414203 DOI: 10.7554/elife.41431] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 02/10/2019] [Indexed: 12/19/2022] Open
Abstract
Viruses manipulate host cells to enhance their replication, and the identification of cellular factors targeted by viruses has led to key insights into both viral pathogenesis and cell biology. In this study, we develop an HIV reporter virus (HIV-AFMACS) displaying a streptavidin-binding affinity tag at the surface of infected cells, allowing facile one-step selection with streptavidin-conjugated magnetic beads. We use this system to obtain pure populations of HIV-infected primary human CD4+ T cells for detailed proteomic analysis, and quantitate approximately 9000 proteins across multiple donors on a dynamic background of T cell activation. Amongst 650 HIV-dependent changes (q < 0.05), we describe novel Vif-dependent targets FMR1 and DPH7, and 192 proteins not identified and/or regulated in T cell lines, such as ARID5A and PTPN22. We therefore provide a high-coverage functional proteomic atlas of HIV infection, and a mechanistic account of host factors subverted by the virus in its natural target cell.
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Affiliation(s)
- Adi Naamati
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - James C Williamson
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom.,Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Edward Jd Greenwood
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom.,Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Sara Marelli
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Paul J Lehner
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
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Liu Y, Fu Y, Wang Q, Li M, Zhou Z, Dabbagh D, Fu C, Zhang H, Li S, Zhang T, Gong J, Kong X, Zhai W, Su J, Sun J, Zhang Y, Yu XF, Shao Z, Zhou F, Wu Y, Tan X. Proteomic profiling of HIV-1 infection of human CD4 + T cells identifies PSGL-1 as an HIV restriction factor. Nat Microbiol 2019; 4:813-825. [PMID: 30833724 DOI: 10.1038/s41564-019-0372-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 01/16/2019] [Indexed: 12/17/2022]
Abstract
Human immunodeficiency virus (HIV) actively modulates the protein stability of host cells to optimize viral replication. To systematically examine this modulation in HIV infection, we used isobaric tag-based mass spectrometry to quantify changes in the abundance of over 14,000 proteins during HIV-1 infection of human primary CD4+ T cells. We identified P-selectin glycoprotein ligand 1 (PSGL-1) as an HIV-1 restriction factor downregulated by HIV-1 Vpu, which binds to PSGL-1 and induces its ubiquitination and degradation through the ubiquitin ligase SCFβ-TrCP2. PSGL-1 is induced by interferon-γ in activated CD4+ T cells to inhibit HIV-1 reverse transcription and potently block viral infectivity by incorporating in progeny virions. This infectivity block is antagonized by Vpu via PSGL-1 degradation. We further show that PSGL-1 knockdown can significantly abolish the anti-HIV activity of interferon-γ in primary CD4+ T cells. Our study identifies an HIV restriction factor and a key mediator of interferon-γ's anti-HIV activity.
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Affiliation(s)
- Ying Liu
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Advanced Innovation Center for Structural Biology, School of Pharmaceutical Sciences, Tsinghua-Peking Center for Life Sciences, Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Yajing Fu
- Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, Department of Laboratory Medicine, The First Affiliated Hospital, China Medical University, Shenyang, China.,School of System Biology, George Mason University, Manassas, VA, USA
| | - Qian Wang
- Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Mushan Li
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zheng Zhou
- School of System Biology, George Mason University, Manassas, VA, USA
| | - Deemah Dabbagh
- School of System Biology, George Mason University, Manassas, VA, USA
| | - Chunyan Fu
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Advanced Innovation Center for Structural Biology, School of Pharmaceutical Sciences, Tsinghua-Peking Center for Life Sciences, Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Hang Zhang
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Advanced Innovation Center for Structural Biology, School of Pharmaceutical Sciences, Tsinghua-Peking Center for Life Sciences, Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Shuo Li
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Advanced Innovation Center for Structural Biology, School of Pharmaceutical Sciences, Tsinghua-Peking Center for Life Sciences, Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Tengjiang Zhang
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Advanced Innovation Center for Structural Biology, School of Pharmaceutical Sciences, Tsinghua-Peking Center for Life Sciences, Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Jing Gong
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Advanced Innovation Center for Structural Biology, School of Pharmaceutical Sciences, Tsinghua-Peking Center for Life Sciences, Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Xiaohui Kong
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Advanced Innovation Center for Structural Biology, School of Pharmaceutical Sciences, Tsinghua-Peking Center for Life Sciences, Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Weiwei Zhai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Jiaming Su
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jianping Sun
- Beijing You'an Hospital, Capital Medical University, Beijing, China
| | - Yonghong Zhang
- Beijing You'an Hospital, Capital Medical University, Beijing, China
| | - Xiao-Fang Yu
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhen Shao
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Feng Zhou
- Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
| | - Yuntao Wu
- School of System Biology, George Mason University, Manassas, VA, USA.
| | - Xu Tan
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Advanced Innovation Center for Structural Biology, School of Pharmaceutical Sciences, Tsinghua-Peking Center for Life Sciences, Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China.
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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.
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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.
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48
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Harman JC, Guidry JJ, Gidday JM. Comprehensive characterization of the adult ND4 Swiss Webster mouse retina: Using discovery-based mass spectrometry to decipher the total proteome and phosphoproteome. Mol Vis 2018; 24:875-889. [PMID: 30713425 PMCID: PMC6334985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 12/31/2018] [Indexed: 11/05/2022] Open
Abstract
Purpose Diverse groups of proteins play integral roles in both the physiology and pathophysiology of the retina. However, thorough proteomic analyses of retinas of experimental species are currently unavailable. The purpose of the present paper is providing the field with a comprehensive proteomic characterization of the retina of a commonly used laboratory mouse using a discovery-based mass spectrometry (MS) approach. Methods Retinas from eight male and eight female 30-week-old outbred ND4 Swiss Webster mice were harvested and immediately processed for MS analysis on a Thermo Fisher (TF) Fusion Orbitrap MS. The retinal proteome and phosphoproteome were identified and subsequently analyzed using Proteome Discoverer 2.2 and Panther-GeneGo. SEQUEST-HT scoring was used for analysis, and the reference protein FASTA database was from Mus musculus. Specifically, three technical repeats were performed for each biological sample. For characterization, only high-scoring peptides were considered, with a false discovery rate (FDR) of <1%. Downstream bioinformatic analysis used Ingenuity Pathway Analysis (IPA; Qiagen). Results Using Proteome Discoverer 2.2, 4,767 different proteins were identified and segregated into 26 major protein classes, 9 functional molecular classes, and 12 categories of biological processes. The five largest protein classes included the following: nucleic acid binding (17%), hydrolases (13%), enzyme modulators (10%), transferases (9%), and oxidoreductases (6%). "Binding" and "catalytic" proteins contributed to 81% of the molecular function class at 37% and 42%, respectively. "Cellular processing" and "metabolic processes" contributed the most to biologic activity, at 31% and 26%, respectively. Phosphopeptide enrichment yielded the identification of 610 additional unique proteins that were not originally identified. The two datasets combined produced an adult mouse retinal proteome consisting of 5,377 unique proteins. Overall, 41% of the retinal proteome was phosphorylated. The overwhelming diversity of retinal protein functionality was reflected through further analyses revealing 2,086 unique pathway hits across 241 different pathways (TF). A core analysis summary report was performed in IPA (Qiagen) to analyze the top signaling networks, protein-protein interaction (PPI) enrichments, and canonical pathways. Conclusions Using this high-throughput technique, we have further deciphered and updated the diverse proteome of the mouse retina, including the phosphoproteome, thereby providing the most comprehensive proteomic profile for this tissue known to date. These findings, and the bioinformatic analyses we also provided, establish a platform for future studies, facilitating the elucidation of the relevance of these proteins to the molecular and cellular pathologies that underlie retinal function and disease.
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Affiliation(s)
- Jarrod C. Harman
- Department of Ophthalmology, Louisiana State University Health Science Center (LSUHSC), New Orleans, LA,Department of Physiology, LSUHSC, New Orleans, LA,Neuroscience Center of Excellence, LSUHSC, New Orleans, LA
| | - Jessie J. Guidry
- Department of Biochemistry and Molecular Biology, LSUHSC, New Orleans, LA,Proteomics Core Facility, LSUHSC, New Orleans, LA
| | - Jeffrey M. Gidday
- Department of Ophthalmology, Louisiana State University Health Science Center (LSUHSC), New Orleans, LA,Department of Physiology, LSUHSC, New Orleans, LA,Neuroscience Center of Excellence, LSUHSC, New Orleans, LA
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49
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Nilsson J. Protein phosphatases in the regulation of mitosis. J Cell Biol 2018; 218:395-409. [PMID: 30446607 PMCID: PMC6363451 DOI: 10.1083/jcb.201809138] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 10/29/2018] [Accepted: 10/29/2018] [Indexed: 12/15/2022] Open
Abstract
The accurate segregation of genetic material to daughter cells during mitosis depends on the precise coordination and regulation of hundreds of proteins by dynamic phosphorylation. Mitotic kinases are major regulators of protein function, but equally important are protein phosphatases that balance their actions, their coordinated activity being essential for accurate chromosome segregation. Phosphoprotein phosphatases (PPPs) that dephosphorylate phosphoserine and phosphothreonine residues are increasingly understood as essential regulators of mitosis. In contrast to kinases, the lack of a pronounced peptide-binding cleft on the catalytic subunit of PPPs suggests that these enzymes are unlikely to be specific. However, recent exciting insights into how mitotic PPPs recognize specific substrates have revealed that they are as specific as kinases. Furthermore, the activities of PPPs are tightly controlled at many levels to ensure that they are active only at the proper time and place. Here, I will discuss substrate selection and regulation of mitotic PPPs focusing mainly on animal cells and explore how these actions control mitosis, as well as important unanswered questions.
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Affiliation(s)
- Jakob Nilsson
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
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50
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Mangolini M, Götte F, Moore A, Ammon T, Oelsner M, Lutzny-Geier G, Klein-Hitpass L, Williamson JC, Lehner PJ, Dürig J, Möllmann M, Rásó-Barnett L, Hughes K, Santoro A, Méndez-Ferrer S, Oostendorp RAJ, Zimber-Strobl U, Peschel C, Hodson DJ, Schmidt-Supprian M, Ringshausen I. Notch2 controls non-autonomous Wnt-signalling in chronic lymphocytic leukaemia. Nat Commun 2018; 9:3839. [PMID: 30242258 PMCID: PMC6155045 DOI: 10.1038/s41467-018-06069-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 07/31/2018] [Indexed: 01/05/2023] Open
Abstract
The Wnt signalling pathway, one of the core de-regulated pathways in chronic lymphocytic leukaemia (CLL), is activated in only a subset of patients through somatic mutations. Here we describe alternative, microenvironment-dependent mechanisms of Wnt activation in malignant B cells. We show that tumour cells specifically induce Notch2 activity in mesenchymal stromal cells (MSCs) required for the transcription of the complement factor C1q. MSC-derived C1q in turn inhibits Gsk3-β mediated degradation of β-catenin in CLL cells. Additionally, stromal Notch2 activity regulates N-cadherin expression in CLL cells, which interacts with and further stabilises β-catenin. Together, these stroma Notch2-dependent mechanisms induce strong activation of canonical Wnt signalling in CLL cells. Pharmacological inhibition of the Wnt pathway impairs microenvironment-mediated survival of tumour cells. Similarly, inhibition of Notch signalling diminishes survival of stroma-protected CLL cells in vitro and disease engraftment in vivo. Notch2 activation in the microenvironment is a pre-requisite for the activation of canonical Wnt signalling in tumour cells.
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Affiliation(s)
- Maurizio Mangolini
- Wellcome Trust/ MRC Cambridge Stem Cell Institute & Department of Haematology, University of Cambridge, Cambridge, CB2 0AH, UK
| | - Frederik Götte
- Department of Hematology and Medical Oncology, Klinikum rechts der Isar der Technischen Universität München, Munich, 81675, Germany
| | - Andrew Moore
- Wellcome Trust/ MRC Cambridge Stem Cell Institute & Department of Haematology, University of Cambridge, Cambridge, CB2 0AH, UK
| | - Tim Ammon
- Department of Hematology and Medical Oncology, Klinikum rechts der Isar der Technischen Universität München, Munich, 81675, Germany
| | - Madlen Oelsner
- Department of Hematology and Medical Oncology, Klinikum rechts der Isar der Technischen Universität München, Munich, 81675, Germany
| | - Gloria Lutzny-Geier
- Department of Internal Medicine 5, Haematology and Oncology, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, 91054, Germany
| | - Ludger Klein-Hitpass
- Institute of Cell Biology, Faculty of Medicine, University of Duisburg-Essen, Essen, 45122, Germany
| | - James C Williamson
- Cambridge Institute for Medical Research (CIMR), University of Cambridge, Cambridge, CB2 0XY, UK
| | - Paul J Lehner
- Cambridge Institute for Medical Research (CIMR), University of Cambridge, Cambridge, CB2 0XY, UK
| | - Jan Dürig
- Department of Hematology, University Hospital Essen,, University of Duisburg-Essen, Essen, 45122, Germany
| | - Michael Möllmann
- Department of Hematology, University Hospital Essen,, University of Duisburg-Essen, Essen, 45122, Germany
| | - Lívia Rásó-Barnett
- Haematopathology and Oncology Diagnostic Service (HODS), Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Katherine Hughes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Antonella Santoro
- Wellcome Trust/ MRC Cambridge Stem Cell Institute & Department of Haematology, University of Cambridge, Cambridge, CB2 0AH, UK
| | - Simón Méndez-Ferrer
- Wellcome Trust/ MRC Cambridge Stem Cell Institute & Department of Haematology, University of Cambridge, Cambridge, CB2 0AH, UK
- NHS Blood and Transplant, Cambridge, CB2 0PT, UK
| | - Robert A J Oostendorp
- Department of Hematology and Medical Oncology, Klinikum rechts der Isar der Technischen Universität München, Munich, 81675, Germany
| | | | - Christian Peschel
- Department of Hematology and Medical Oncology, Klinikum rechts der Isar der Technischen Universität München, Munich, 81675, Germany
- German Cancer Consortium, DKFZ, Heidelberg, 69120, Germany
| | - Daniel J Hodson
- Wellcome Trust/ MRC Cambridge Stem Cell Institute & Department of Haematology, University of Cambridge, Cambridge, CB2 0AH, UK
| | - Marc Schmidt-Supprian
- Department of Hematology and Medical Oncology, Klinikum rechts der Isar der Technischen Universität München, Munich, 81675, Germany
- German Cancer Consortium, DKFZ, Heidelberg, 69120, Germany
| | - Ingo Ringshausen
- Wellcome Trust/ MRC Cambridge Stem Cell Institute & Department of Haematology, University of Cambridge, Cambridge, CB2 0AH, UK.
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