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McGowan J, Peter C, Kim J, Popli S, Veerman B, Saul-McBeth J, Conti H, Pruett-Miller SM, Chattopadhyay S, Chakravarti R. 14-3-3ζ-TRAF5 axis governs interleukin-17A signaling. Proc Natl Acad Sci U S A 2020; 117:25008-25017. [PMID: 32968020 PMCID: PMC7547158 DOI: 10.1073/pnas.2008214117] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
IL-17A is a therapeutic target in many autoimmune diseases. Most nonhematopoietic cells express IL-17A receptors and respond to extracellular IL-17A by inducing proinflammatory cytokines. The IL-17A signal transduction triggers two broad, TRAF6- and TRAF5-dependent, intracellular signaling pathways to produce representative cytokines (IL-6) and chemokines (CXCL-1), respectively. Our limited understanding of the cross-talk between these two branches has generated a crucial gap of knowledge, leading to therapeutics indiscriminately blocking IL-17A and global inhibition of its target genes. In previous work, we discovered an elevated expression of 14-3-3 proteins in inflammatory aortic disease, a rare human autoimmune disorder with increased levels of IL-17A. Here we report that 14-3-3ζ is essential for IL-17 signaling by differentially regulating the signal-induced IL-6 and CXCL-1. Using genetically manipulated human and mouse cells, and ex vivo and in vivo rat models, we uncovered a function of 14-3-3ζ. As a part of the molecular mechanism, we show that 14-3-3ζ interacts with several TRAF proteins; in particular, its interaction with TRAF5 and TRAF6 is increased in the presence of IL-17A. In contrast to TRAF6, we found TRAF5 to be an endogenous suppressor of IL-17A-induced IL-6 production, an effect countered by 14-3-3ζ. Furthermore, we observed that 14-3-3ζ interaction with TRAF proteins is required for the IL-17A-induced IL-6 levels. Together, our results show that 14-3-3ζ is an essential component of IL-17A signaling and IL-6 production, an effect that is suppressed by TRAF5. To the best of our knowledge, this report of the 14-3-3ζ-TRAF5 axis, which differentially regulates IL-17A-induced IL-6 and CXCL-1 production, is unique.
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Affiliation(s)
- Jenna McGowan
- Department of Physiology & Pharmacology, College of Medicine & Life Sciences, University of Toledo, Toledo, OH 43614
| | - Cara Peter
- Department of Physiology & Pharmacology, College of Medicine & Life Sciences, University of Toledo, Toledo, OH 43614
| | - Joshua Kim
- Department of Physiology & Pharmacology, College of Medicine & Life Sciences, University of Toledo, Toledo, OH 43614
| | - Sonam Popli
- Department of Medical Microbiology & Immunology, College of Medicine & Life Sciences, University of Toledo, Toledo, OH 43614
| | - Brent Veerman
- Department of Physiology & Pharmacology, College of Medicine & Life Sciences, University of Toledo, Toledo, OH 43614
| | - Jessica Saul-McBeth
- Department of Biological Sciences, College of Natural Sciences & Mathematics, University of Toledo, Toledo, OH 43614
| | - Heather Conti
- Department of Biological Sciences, College of Natural Sciences & Mathematics, University of Toledo, Toledo, OH 43614
| | - Shondra M Pruett-Miller
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Saurabh Chattopadhyay
- Department of Medical Microbiology & Immunology, College of Medicine & Life Sciences, University of Toledo, Toledo, OH 43614
| | - Ritu Chakravarti
- Department of Physiology & Pharmacology, College of Medicine & Life Sciences, University of Toledo, Toledo, OH 43614;
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Yu DS, Weng TH, Hu CY, Wu ZG, Li YH, Cheng LF, Wu NP, Li LJ, Yao HP. Chaperones, Membrane Trafficking and Signal Transduction Proteins Regulate Zaire Ebola Virus trVLPs and Interact With trVLP Elements. Front Microbiol 2018; 9:2724. [PMID: 30483236 PMCID: PMC6240689 DOI: 10.3389/fmicb.2018.02724] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 10/24/2018] [Indexed: 01/19/2023] Open
Abstract
Ebolavirus (EBOV) life cycle involves interactions with numerous host factors, but it remains poorly understood, as does pathogenesis. Herein, we synthesized 65 siRNAs targeting host genes mostly connected with aspects of the negative-sense RNA virus life cycle (including viral entry, uncoating, fusion, replication, assembly, and budding). We produced EBOV transcription- and replication-competent virus-like particles (trVLPs) to mimic the EBOV life cycle. After screening host factors associated with the trVLP life cycle, we assessed interactions of host proteins with trVLP glycoprotein (GP), VP40, and RNA by co-immunoprecipitation (Co-IP) and chromatin immunoprecipitation (ChIP). The results demonstrate that RNAi silencing with 11 siRNAs (ANXA5, ARFGAP1, FLT4, GRP78, HSPA1A, HSP90AB1, HSPA8, MAPK11, MEK2, NTRK1, and YWHAZ) decreased the replication efficiency of trVLPs. Co-IP revealed nine candidate host proteins (FLT4, GRP78, HSPA1A, HSP90AB1, HSPA8, MAPK11, MEK2, NTRK1, and YWHAZ) potentially interacting with trVLP GP, and four (ANXA5, GRP78, HSPA1A, and HSP90AB1) potentially interacting with trVLP VP40. Ch-IP identified nine candidate host proteins (ANXA5, ARFGAP1, FLT4, GRP78, HSPA1A, HSP90AB1, MAPK11, MEK2, and NTRK1) interacting with trVLP RNA. This study was based on trVLP and could not replace live ebolavirus entirely; in particular, the interaction between trVLP RNA and host proteins cannot be assumed to be identical in live virus. However, the results provide valuable information for further studies and deepen our understanding of essential host factors involved in the EBOV life cycle.
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Affiliation(s)
- Dong-Shan Yu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Tian-Hao Weng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Chen-Yu Hu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Zhi-Gang Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yan-Hua Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Lin-Fang Cheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Nan-Ping Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Lan-Juan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Hang-Ping Yao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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Herrera-Uribe J, Jiménez-Marín Á, Lacasta A, Monteagudo PL, Pina-Pedrero S, Rodríguez F, Moreno Á, Garrido JJ. Comparative proteomic analysis reveals different responses in porcine lymph nodes to virulent and attenuated homologous African swine fever virus strains. Vet Res 2018; 49:90. [PMID: 30208957 PMCID: PMC6134756 DOI: 10.1186/s13567-018-0585-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/05/2018] [Indexed: 01/07/2023] Open
Abstract
African swine fever (ASF) is a pathology of pigs against which there is no treatment or vaccine. Understanding the equilibrium between innate and adaptive protective responses and immune pathology might contribute to the development of strategies against ASFV. Here we compare, using a proteomic approach, the course of the in vivo infection caused by two homologous strains: the virulent E75 and the attenuated E75CV1. Our results show a progressive loss of proteins by day 7 post-infection (pi) with E75, reflecting tissue destruction. Many signal pathways were affected by both infections but in different ways and extensions. Cytoskeletal remodelling and clathrin-endocytosis were affected by both isolates, while a greater number of proteins involved on inflammatory and immunological pathways were altered by E75CV1. 14-3-3 mediated signalling, related to immunity and apoptosis, was inhibited by both isolates. The implication of the Rho GTPases by E75CV1 throughout infection is also evident. Early events reflected the lack of E75 recognition by the immune system, an evasion strategy acquired by the virulent strains, and significant changes at 7 days post-infection (dpi), coinciding with the peak of infection and the time of death. The protein signature at day 31 pi with E75CV1 seems to reflect events observed at 1 dpi, including the upregulation of proteosomal subunits and molecules described as autoantigens (vimentin, HSPB1, enolase and lymphocyte cytosolic protein 1), which allow the speculation that auto-antibodies could contribute to chronic ASFV infections. Therefore, the use of proteomics could help understand ASFV pathogenesis and immune protection, opening new avenues for future research.
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Affiliation(s)
- Júber Herrera-Uribe
- Grupo de Genómica y Mejora Animal, Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
| | - Ángeles Jiménez-Marín
- Grupo de Genómica y Mejora Animal, Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
| | - Anna Lacasta
- International Livestock Research Intitute (ILRI), Nairobi, 00100, Kenya.,Centre de Recerca En Sanitat Animal (CReSA), Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Campus UAB, Bellaterra, 08193, Barcelona, Spain
| | - Paula L Monteagudo
- Centre de Recerca En Sanitat Animal (CReSA), Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Campus UAB, Bellaterra, 08193, Barcelona, Spain
| | - Sonia Pina-Pedrero
- Centre de Recerca En Sanitat Animal (CReSA), Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Campus UAB, Bellaterra, 08193, Barcelona, Spain
| | - Fernando Rodríguez
- Centre de Recerca En Sanitat Animal (CReSA), Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Campus UAB, Bellaterra, 08193, Barcelona, Spain
| | - Ángela Moreno
- Grupo de Genómica y Mejora Animal, Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain.,Instituto de Agricultura Sostenible, Campus Alameda del Obispo, 14080 CSIC, Córdoba, Spain
| | - Juan J Garrido
- Grupo de Genómica y Mejora Animal, Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain.
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Nyman TA, Lorey MB, Cypryk W, Matikainen S. Mass spectrometry-based proteomic exploration of the human immune system: focus on the inflammasome, global protein secretion, and T cells. Expert Rev Proteomics 2017; 14:395-407. [PMID: 28406322 DOI: 10.1080/14789450.2017.1319768] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION The immune system is our defense system against microbial infections and tissue injury, and understanding how it works in detail is essential for developing drugs for different diseases. Mass spectrometry-based proteomics can provide in-depth information on the molecular mechanisms involved in immune responses. Areas covered: Summarized are the key immunology findings obtained with MS-based proteomics in the past five years, with a focus on inflammasome activation, global protein secretion, mucosal immunology, immunopeptidome and T cells. Special focus is on extracellular vesicle-mediated protein secretion and its role in immune responses. Expert commentary: Proteomics is an essential part of modern omics-scale immunology research. To date, MS-based proteomics has been used in immunology to study protein expression levels, their subcellular localization, secretion, post-translational modifications, and interactions in immune cells upon activation by different stimuli. These studies have made major contributions to understanding the molecular mechanisms involved in innate and adaptive immune responses. New developments in proteomics offer constantly novel possibilities for exploring the immune system. Examples of these techniques include mass cytometry and different MS-based imaging approaches which can be widely used in immunology.
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Affiliation(s)
- Tuula A Nyman
- a Department of Immunology , Institute of Clinical Medicine, University of Oslo and Rikshospitalet Oslo , Oslo , Norway
| | - Martina B Lorey
- b Rheumatology , University of Helsinki and Helsinki University Hospital , Helsinki , Finland
| | - Wojciech Cypryk
- c Department of Bioorganic Chemistry , Center of Molecular and Macromolecular Studies , Lodz , Poland
| | - Sampsa Matikainen
- b Rheumatology , University of Helsinki and Helsinki University Hospital , Helsinki , Finland
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Chattopadhyay S, Mukherjee A, Patra U, Bhowmick R, Basak T, Sengupta S, Chawla-Sarkar M. Tyrosine phosphorylation modulates mitochondrial chaperonin Hsp60 and delays rotavirus NSP4-mediated apoptotic signaling in host cells. Cell Microbiol 2016; 19. [PMID: 27665089 DOI: 10.1111/cmi.12670] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Revised: 09/12/2016] [Accepted: 09/13/2016] [Indexed: 12/29/2022]
Abstract
Phosphoproteomics-based platforms have been widely used to identify post translational dynamics of cellular proteins in response to viral infection. The present study was undertaken to assess differential tyrosine phosphorylation during early hours of rotavirus (RV) SA11 infection. Heat shock proteins (Hsp60) were found to be enriched in the data set of RV-SA11 induced differentially tyrosine-phosphorylated proteins at 2 hr post infection (hpi). Hsp60 was further found to be phosphorylated by an activated form of Src kinase on 227th tyrosine residue, and tyrosine phosphorylation of mitochondrial chaperonin Hsp60 correlated with its proteasomal degradation at 2-2.5hpi. Interestingly, mitochondrial Hsp60 positively influenced translocation of the rotaviral nonstructural protein 4 to mitochondria during RV infections. Phosphorylation and subsequent transient degradation of mitochondrial Hsp60 during early hours of RV-SA11 infection resulted in inhibition of premature import of nonstructural protein 4 into mitochondria, thereby delaying early apoptosis. Overall, the study highlighted one of the many strategies rotavirus undertakes to prevent early apoptosis and subsequent reduced viral progeny yield.
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Affiliation(s)
- Shiladitya Chattopadhyay
- Division of Virology, National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road SchemeP- XM, Beliaghata, Kolkata, 700010, India
| | - Arpita Mukherjee
- Division of Virology, National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road SchemeP- XM, Beliaghata, Kolkata, 700010, India
| | - Upayan Patra
- Division of Virology, National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road SchemeP- XM, Beliaghata, Kolkata, 700010, India
| | - Rahul Bhowmick
- Division of Virology, National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road SchemeP- XM, Beliaghata, Kolkata, 700010, India
| | - Trayambak Basak
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110020, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-IGIB campus, New Delhi, India
| | - Shantanu Sengupta
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110020, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-IGIB campus, New Delhi, India
| | - Mamta Chawla-Sarkar
- Division of Virology, National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road SchemeP- XM, Beliaghata, Kolkata, 700010, India
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Söderholm S, Kainov DE, Öhman T, Denisova OV, Schepens B, Kulesskiy E, Imanishi SY, Corthals G, Hintsanen P, Aittokallio T, Saelens X, Matikainen S, Nyman TA. Phosphoproteomics to Characterize Host Response During Influenza A Virus Infection of Human Macrophages. Mol Cell Proteomics 2016; 15:3203-3219. [PMID: 27486199 DOI: 10.1074/mcp.m116.057984] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Indexed: 12/18/2022] Open
Abstract
Influenza A viruses cause infections in the human respiratory tract and give rise to annual seasonal outbreaks, as well as more rarely dreaded pandemics. Influenza A viruses become quickly resistant to the virus-directed antiviral treatments, which are the current main treatment options. A promising alternative approach is to target host cell factors that are exploited by influenza viruses. To this end, we characterized the phosphoproteome of influenza A virus infected primary human macrophages to elucidate the intracellular signaling pathways and critical host factors activated upon influenza infection. We identified 1675 phosphoproteins, 4004 phosphopeptides and 4146 nonredundant phosphosites. The phosphorylation of 1113 proteins (66%) was regulated upon infection, highlighting the importance of such global phosphoproteomic profiling in primary cells. Notably, 285 of the identified phosphorylation sites have not been previously described in publicly available phosphorylation databases, despite many published large-scale phosphoproteome studies using human and mouse cell lines. Systematic bioinformatics analysis of the phosphoproteome data indicated that the phosphorylation of proteins involved in the ubiquitin/proteasome pathway (such as TRIM22 and TRIM25) and antiviral responses (such as MAVS) changed in infected macrophages. Proteins known to play roles in small GTPase-, mitogen-activated protein kinase-, and cyclin-dependent kinase- signaling were also regulated by phosphorylation upon infection. In particular, the influenza infection had a major influence on the phosphorylation profiles of a large number of cyclin-dependent kinase substrates. Functional studies using cyclin-dependent kinase inhibitors showed that the cyclin-dependent kinase activity is required for efficient viral replication and for activation of the host antiviral responses. In addition, we show that cyclin-dependent kinase inhibitors protect IAV-infected mice from death. In conclusion, we provide the first comprehensive phosphoproteome characterization of influenza A virus infection in primary human macrophages, and provide evidence that cyclin-dependent kinases represent potential therapeutic targets for more effective treatment of influenza infections.
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Affiliation(s)
- Sandra Söderholm
- From the ‡Institute of Biotechnology, FI-00014 University of Helsinki, Helsinki, Finland; §Unit of Systems Toxicology, Finnish Institute of Occupational Health, FI-00250 Helsinki, Finland
| | - Denis E Kainov
- ¶Institute for Molecular Medicine Finland (FIMM), FI-00014 University of Helsinki, Helsinki, Finland
| | - Tiina Öhman
- From the ‡Institute of Biotechnology, FI-00014 University of Helsinki, Helsinki, Finland
| | - Oxana V Denisova
- ¶Institute for Molecular Medicine Finland (FIMM), FI-00014 University of Helsinki, Helsinki, Finland
| | - Bert Schepens
- ‖Medical Biotechnology Center, VIB, B-9052 Ghent (Zwijnaarde), Belgium; **Department of Biomedical Molecular Biology, B-9052 Ghent University, Ghent, Belgium
| | - Evgeny Kulesskiy
- ¶Institute for Molecular Medicine Finland (FIMM), FI-00014 University of Helsinki, Helsinki, Finland
| | - Susumu Y Imanishi
- ‡‡Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland
| | - Garry Corthals
- ‡‡Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland
| | - Petteri Hintsanen
- ¶Institute for Molecular Medicine Finland (FIMM), FI-00014 University of Helsinki, Helsinki, Finland
| | - Tero Aittokallio
- ¶Institute for Molecular Medicine Finland (FIMM), FI-00014 University of Helsinki, Helsinki, Finland
| | - Xavier Saelens
- ‖Medical Biotechnology Center, VIB, B-9052 Ghent (Zwijnaarde), Belgium; **Department of Biomedical Molecular Biology, B-9052 Ghent University, Ghent, Belgium
| | - Sampsa Matikainen
- §§Department of Rheumatology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Tuula A Nyman
- From the ‡Institute of Biotechnology, FI-00014 University of Helsinki, Helsinki, Finland; ¶¶Institute of Clinical Medicine, University of Oslo, Norway
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Kauko O, Laajala TD, Jumppanen M, Hintsanen P, Suni V, Haapaniemi P, Corthals G, Aittokallio T, Westermarck J, Imanishi SY. Label-free quantitative phosphoproteomics with novel pairwise abundance normalization reveals synergistic RAS and CIP2A signaling. Sci Rep 2015; 5:13099. [PMID: 26278961 PMCID: PMC4642524 DOI: 10.1038/srep13099] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 07/06/2015] [Indexed: 11/11/2022] Open
Abstract
Hyperactivated RAS drives progression of many human malignancies. However, oncogenic activity of RAS is dependent on simultaneous inactivation of protein phosphatase 2A (PP2A) activity. Although PP2A is known to regulate some of the RAS effector pathways, it has not been systematically assessed how these proteins functionally interact. Here we have analyzed phosphoproteomes regulated by either RAS or PP2A, by phosphopeptide enrichment followed by mass-spectrometry-based label-free quantification. To allow data normalization in situations where depletion of RAS or PP2A inhibitor CIP2A causes a large uni-directional change in the phosphopeptide abundance, we developed a novel normalization strategy, named pairwise normalization. This normalization is based on adjusting phosphopeptide abundances measured before and after the enrichment. The superior performance of the pairwise normalization was verified by various independent methods. Additionally, we demonstrate how the selected normalization method influences the downstream analyses and interpretation of pathway activities. Consequently, bioinformatics analysis of RAS and CIP2A regulated phosphoproteomes revealed a significant overlap in their functional pathways. This is most likely biologically meaningful as we observed a synergistic survival effect between CIP2A and RAS expression as well as KRAS activating mutations in TCGA pan-cancer data set, and synergistic relationship between CIP2A and KRAS depletion in colony growth assays.
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Affiliation(s)
- Otto Kauko
- 1] Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistokatu 6, FI-20520 Turku, Finland [2] Department of Pathology, University of Turku, FI-20520 Turku, Finland [3] Turku Doctoral Program of Biomedical Sciences (TuBS), Turku, Finland
| | - Teemu Daniel Laajala
- 1] Department of Mathematics and Statistics, University of Turku, FI-20014 Turku, Finland [2] Drug Research Doctoral Programme (DRDP), Turku, Finland
| | - Mikael Jumppanen
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistokatu 6, FI-20520 Turku, Finland
| | - Petteri Hintsanen
- Institute for Molecular Medicine Finland, Tukholmankatu 8, FI-00290 Helsinki, Finland
| | - Veronika Suni
- 1] Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistokatu 6, FI-20520 Turku, Finland [2] Turku Centre for Computer Science, FI-20520 Turku, Finland
| | - Pekka Haapaniemi
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistokatu 6, FI-20520 Turku, Finland
| | - Garry Corthals
- 1] Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistokatu 6, FI-20520 Turku, Finland [2] Van 't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland, Tukholmankatu 8, FI-00290 Helsinki, Finland
| | - Jukka Westermarck
- 1] Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistokatu 6, FI-20520 Turku, Finland [2] Department of Pathology, University of Turku, FI-20520 Turku, Finland
| | - Susumu Y Imanishi
- 1] Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistokatu 6, FI-20520 Turku, Finland [2] Faculty of Pharmacy, Meijo University, Yagotoyama 150, Tempaku, Nagoya 468-8503, Japan
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Öhman T, Söderholm S, Paidikondala M, Lietzén N, Matikainen S, Nyman TA. Phosphoproteome characterization reveals that Sendai virus infection activates mTOR signaling in human epithelial cells. Proteomics 2015; 15:2087-97. [PMID: 25764225 DOI: 10.1002/pmic.201400586] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 02/24/2015] [Accepted: 03/06/2015] [Indexed: 12/12/2022]
Abstract
Sendai virus (SeV) is a common respiratory pathogen in mice, rats, and hamsters. Host cell recognition of SeV is mediated by pathogen recognition receptors, which recognize viral components and induce intracellular signal transduction pathways that activate the antiviral innate immune response. Viruses use host proteins to control the activities of signaling proteins and their downstream targets, and one of the most important host protein modifications regulated by viral infection is phosphorylation. In this study, we used phosphoproteomics combined with bioinformatics to get a global view of the signaling pathways activated during SeV infection in human lung epithelial cells. We identified altogether 1347 phosphoproteins, and our data shows that SeV infection induces major changes in protein phosphorylation affecting the phosphorylation of almost one thousand host proteins. Bioinformatics analysis showed that SeV infection activates known pathways including MAPK signaling, as well as signaling pathways previously not linked to SeV infection including Rho family of GTPases, HIPPO signaling, and mammalian target of rapamycin (mTOR)-signaling pathway. Further, we performed functional studies with mTOR inhibitors and siRNA approach, which revealed that mTOR signaling is needed for both the host IFN response as well as viral protein synthesis in SeV-infected human lung epithelial cells.
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Affiliation(s)
- Tiina Öhman
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Sandra Söderholm
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Finnish Institute of Occupational Health, Helsinki, Finland
| | | | - Niina Lietzén
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | | | - Tuula A Nyman
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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DeBlasio SL, Johnson R, Mahoney J, Karasev A, Gray SM, MacCoss MJ, Cilia M. Insights into the polerovirus-plant interactome revealed by coimmunoprecipitation and mass spectrometry. Mol Plant Microbe Interact 2015; 28:467-81. [PMID: 25496593 DOI: 10.1094/mpmi-11-14-0363-r] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Identification of host proteins interacting with the aphidborne Potato leafroll virus (PLRV) from the genus Polerovirus, family Luteoviridae, is a critical step toward understanding how PLRV and related viruses infect plants. However, the tight spatial distribution of PLRV to phloem tissues poses challenges. A polyclonal antibody raised against purified PLRV virions was used to coimmunoprecipitate virus-host protein complexes from Nicotiana benthamiana tissue inoculated with an infectious PLRV cDNA clone using Agrobacterium tumefaciens. A. tumefaciens-mediated delivery of PLRV enabled infection and production of assembled, insect-transmissible virus in most leaf cells, overcoming the dynamic range constraint posed by a systemically infected host. Isolated protein complexes were characterized using high-resolution mass spectrometry and consisted of host proteins interacting directly or indirectly with virions, as well as the nonincorporated readthrough protein (RTP) and three phosphorylated positional isomers of the RTP. A bioinformatics analysis using ClueGO and STRING showed that plant proteins in the PLRV protein interaction network regulate key biochemical processes, including carbon fixation, amino acid biosynthesis, ion transport, protein folding, and trafficking.
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Affiliation(s)
- Stacy L DeBlasio
- 1 Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, U.S.A
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