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Kennedy PH, Alborzian Deh Sheikh A, Balakar M, Jones AC, Olive ME, Hegde M, Matias MI, Pirete N, Burt R, Levy J, Little T, Hogan PG, Liu DR, Doench JG, Newton AC, Gottschalk RA, de Boer CG, Alarcón S, Newby GA, Myers SA. Post-translational modification-centric base editor screens to assess phosphorylation site functionality in high throughput. Nat Methods 2024; 21:1033-1043. [PMID: 38684783 DOI: 10.1038/s41592-024-02256-z] [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: 10/16/2023] [Accepted: 03/20/2024] [Indexed: 05/02/2024]
Abstract
Signaling pathways that drive gene expression are typically depicted as having a dozen or so landmark phosphorylation and transcriptional events. In reality, thousands of dynamic post-translational modifications (PTMs) orchestrate nearly every cellular function, and we lack technologies to find causal links between these vast biochemical pathways and genetic circuits at scale. Here we describe the high-throughput, functional assessment of phosphorylation sites through the development of PTM-centric base editing coupled to phenotypic screens, directed by temporally resolved phosphoproteomics. Using T cell activation as a model, we observe hundreds of unstudied phosphorylation sites that modulate NFAT transcriptional activity. We identify the phosphorylation-mediated nuclear localization of PHLPP1, which promotes NFAT but inhibits NFκB activity. We also find that specific phosphosite mutants can alter gene expression in subtle yet distinct patterns, demonstrating the potential for fine-tuning transcriptional responses. Overall, base editor screening of PTM sites provides a powerful platform to dissect PTM function within signaling pathways.
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Affiliation(s)
- Patrick H Kennedy
- Laboratory for Immunochemical Circuits, La Jolla Institute for Immunology, La Jolla, CA, USA
- Center of Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Amin Alborzian Deh Sheikh
- Laboratory for Immunochemical Circuits, La Jolla Institute for Immunology, La Jolla, CA, USA
- Center of Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - Alexander C Jones
- Department of Pharmacology, University of California San Diego, San Diego, CA, USA
- Biomedical Sciences Graduate Program, University of California San Diego, San Diego, CA, USA
| | | | - Mudra Hegde
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Maria I Matias
- Laboratory for Immunochemical Circuits, La Jolla Institute for Immunology, La Jolla, CA, USA
- Center of Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Natan Pirete
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rajan Burt
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jonathan Levy
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Tamia Little
- Laboratory for Immunochemical Circuits, La Jolla Institute for Immunology, La Jolla, CA, USA
- Center of Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Patrick G Hogan
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA
- Program in Immunology, University of California San Diego, San Diego, CA, USA
- Moores Cancer Center, University of California San Diego Health, La Jolla, CA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - John G Doench
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alexandra C Newton
- Department of Pharmacology, University of California San Diego, San Diego, CA, USA
| | - Rachel A Gottschalk
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Carl G de Boer
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Suzie Alarcón
- La Jolla Institute for Immunology, La Jolla, CA, USA
- AUGenomics, San Diego, CA, USA
| | - Gregory A Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Samuel A Myers
- Laboratory for Immunochemical Circuits, La Jolla Institute for Immunology, La Jolla, CA, USA.
- Center of Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA, USA.
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA.
- Department of Pharmacology, University of California San Diego, San Diego, CA, USA.
- Program in Immunology, University of California San Diego, San Diego, CA, USA.
- Moores Cancer Center, University of California San Diego Health, La Jolla, CA, USA.
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Benz PM, Frömel T, Laban H, Zink J, Ulrich L, Groneberg D, Boon RA, Poley P, Renne T, de Wit C, Fleming I. Cardiovascular Functions of Ena/VASP Proteins: Past, Present and Beyond. Cells 2023; 12:1740. [PMID: 37443774 PMCID: PMC10340426 DOI: 10.3390/cells12131740] [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: 04/26/2023] [Revised: 06/18/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
Actin binding proteins are of crucial importance for the spatiotemporal regulation of actin cytoskeletal dynamics, thereby mediating a tremendous range of cellular processes. Since their initial discovery more than 30 years ago, the enabled/vasodilator-stimulated phosphoprotein (Ena/VASP) family has evolved as one of the most fascinating and versatile family of actin regulating proteins. The proteins directly enhance actin filament assembly, but they also organize higher order actin networks and link kinase signaling pathways to actin filament assembly. Thereby, Ena/VASP proteins regulate dynamic cellular processes ranging from membrane protrusions and trafficking, and cell-cell and cell-matrix adhesions, to the generation of mechanical tension and contractile force. Important insights have been gained into the physiological functions of Ena/VASP proteins in platelets, leukocytes, endothelial cells, smooth muscle cells and cardiomyocytes. In this review, we summarize the unique and redundant functions of Ena/VASP proteins in cardiovascular cells and discuss the underlying molecular mechanisms.
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Affiliation(s)
- Peter M. Benz
- Institute for Vascular Signalling, Centre for Molecular Medicine, Goethe University, 60596 Frankfurt am Main, Germany
- German Centre of Cardiovascular Research (DZHK), Partner Site Rhein-Main, 60596 Frankfurt am Main, Germany
| | - Timo Frömel
- Institute for Vascular Signalling, Centre for Molecular Medicine, Goethe University, 60596 Frankfurt am Main, Germany
| | - Hebatullah Laban
- Institute for Vascular Signalling, Centre for Molecular Medicine, Goethe University, 60596 Frankfurt am Main, Germany
| | - Joana Zink
- Institute for Vascular Signalling, Centre for Molecular Medicine, Goethe University, 60596 Frankfurt am Main, Germany
| | - Lea Ulrich
- Institute for Vascular Signalling, Centre for Molecular Medicine, Goethe University, 60596 Frankfurt am Main, Germany
| | - Dieter Groneberg
- Institute of Physiology I, University of Würzburg, 97070 Würzburg, Germany
| | - Reinier A. Boon
- German Centre of Cardiovascular Research (DZHK), Partner Site Rhein-Main, 60596 Frankfurt am Main, Germany
- Cardiopulmonary Institute, 60596 Frankfurt am Main, Germany
- Centre of Molecular Medicine, Institute of Cardiovascular Regeneration, Goethe-University, 60596 Frankfurt am Main, Germany
- Department of Physiology, Amsterdam Cardiovascular Sciences, VU University Medical Centre, 1081 HZ Amsterdam, The Netherlands
| | - Philip Poley
- Institut für Physiologie, Universität zu Lübeck, 23562 Lübeck, Germany
- German Centre of Cardiovascular Research (DZHK), Partner Site Hamburg/Kiel/Lübeck, 23562 Lübeck, Germany
| | - Thomas Renne
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- Center for Thrombosis and Hemostasis (CTH), Johannes Gutenberg University Medical Center, 55131 Mainz, Germany
- Irish Centre for Vascular Biology, School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, D02 VN51 Dublin, Ireland
| | - Cor de Wit
- Institut für Physiologie, Universität zu Lübeck, 23562 Lübeck, Germany
- German Centre of Cardiovascular Research (DZHK), Partner Site Hamburg/Kiel/Lübeck, 23562 Lübeck, Germany
| | - Ingrid Fleming
- Institute for Vascular Signalling, Centre for Molecular Medicine, Goethe University, 60596 Frankfurt am Main, Germany
- German Centre of Cardiovascular Research (DZHK), Partner Site Rhein-Main, 60596 Frankfurt am Main, Germany
- Cardiopulmonary Institute, 60596 Frankfurt am Main, Germany
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3
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Griffith AA, Callahan KP, King NG, Xiao Q, Su X, Salomon AR. SILAC Phosphoproteomics Reveals Unique Signaling Circuits in CAR-T Cells and the Inhibition of B Cell-Activating Phosphorylation in Target Cells. J Proteome Res 2022; 21:395-409. [PMID: 35014847 PMCID: PMC8830406 DOI: 10.1021/acs.jproteome.1c00735] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Chimeric antigen receptor (CAR) is a single-pass transmembrane receptor designed to specifically target and eliminate cancers. While CARs prove highly efficacious against B cell malignancies, the intracellular signaling events which promote CAR T cell activity remain elusive. To gain further insight into both CAR T cell signaling and the potential signaling response of cells targeted by CAR, we analyzed phosphopeptides captured by two separate phosphoenrichment strategies from third generation CD19-CAR T cells cocultured with SILAC labeled Raji B cells by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Here, we report that CD19-CAR T cells upregulated several key phosphorylation events also observed in canonical T cell receptor (TCR) signaling, while Raji B cells exhibited a significant decrease in B cell receptor-signaling related phosphorylation events in response to coculture. Our data suggest that CD19-CAR stimulation activates a mixture of unique CD19-CAR-specific signaling pathways and canonical TCR signaling, while global phosphorylation in Raji B cells is reduced after association with the CD19-CAR T cells.
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Affiliation(s)
- Alijah A. Griffith
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI, 02912
| | - Kenneth P. Callahan
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI, 02912
| | - Nathan Gordo King
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI, 02912
| | - Qian Xiao
- Department of Cell Biology, Yale School of Medicine, Yale University, New Haven, CT, 06520
| | - Xiaolei Su
- Department of Cell Biology, Yale School of Medicine, Yale University, New Haven, CT, 06520
| | - Arthur R. Salomon
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI, 02912,
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4
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Zhou XX, Bracken CJ, Zhang K, Zhou J, Mou Y, Wang L, Cheng Y, Leung KK, Wells JA. Targeting Phosphotyrosine in Native Proteins with Conditional, Bispecific Antibody Traps. J Am Chem Soc 2020; 142:17703-17713. [PMID: 32924468 DOI: 10.1021/jacs.0c08458] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Engineering sequence-specific antibodies (Abs) against phosphotyrosine (pY) motifs embedded in folded polypeptides remains highly challenging because of the stringent requirement for simultaneous recognition of the pY motif and the surrounding folded protein epitope. Here, we present a method named phosphotyrosine Targeting by Recombinant Ab Pair, or pY-TRAP, for in vitro engineering of binders for native pY proteins. Specifically, we create the pY protein by unnatural amino acid misincorporation, mutagenize a universal pY-binding Ab to create a first binder B1 for the pY motif on the pY protein, and then select against the B1-pY protein complex for a second binder B2 that recognizes the composite epitope of B1 and the pY-containing protein complex. We applied pY-TRAP to create highly specific binders to folded Ub-pY59, a rarely studied Ub phosphoform exclusively observed in cancerous tissues, and ZAP70-pY248, a kinase phosphoform regulated in feedback signaling pathways in T cells. The pY-TRAPs do not have detectable binding to wild-type proteins or to other pY peptides or proteins tested. This pY-TRAP approach serves as a generalizable method for engineering sequence-specific Ab binders to native pY proteins.
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Affiliation(s)
- Xin X Zhou
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Colton J Bracken
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Kaihua Zhang
- Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158, United States
| | - Jie Zhou
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Yun Mou
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Lei Wang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158, United States.,Howard Hughes Medical Institute, University of California, San Francisco, California 94158, United States
| | - Kevin K Leung
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States.,Chan Zuckerberg Biohub, San Francisco, California 94158, United States.,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158, United States
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5
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Zmuda F, Chamberlain LH. Regulatory effects of post-translational modifications on zDHHC S-acyltransferases. J Biol Chem 2020; 295:14640-14652. [PMID: 32817054 PMCID: PMC7586229 DOI: 10.1074/jbc.rev120.014717] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/15/2020] [Indexed: 01/09/2023] Open
Abstract
The human zDHHC S-acyltransferase family comprises 23 enzymes that mediate the S-acylation of a multitude of cellular proteins, including channels, receptors, transporters, signaling molecules, scaffolds, and chaperones. This reversible post-transitional modification (PTM) involves the attachment of a fatty acyl chain, usually derived from palmitoyl-CoA, to specific cysteine residues on target proteins, which affects their stability, localization, and function. These outcomes are essential to control many processes, including synaptic transmission and plasticity, cell growth and differentiation, and infectivity of viruses and other pathogens. Given the physiological importance of S-acylation, it is unsurprising that perturbations in this process, including mutations in ZDHHC genes, have been linked to different neurological pathologies and cancers, and there is growing interest in zDHHC enzymes as novel drug targets. Although zDHHC enzymes control a diverse array of cellular processes and are associated with major disorders, our understanding of these enzymes is surprisingly incomplete, particularly with regard to the regulatory mechanisms controlling these enzymes. However, there is growing evidence highlighting the role of different PTMs in this process. In this review, we discuss how PTMs, including phosphorylation, S-acylation, and ubiquitination, affect the stability, localization, and function of zDHHC enzymes and speculate on possible effects of PTMs that have emerged from larger screening studies. Developing a better understanding of the regulatory effects of PTMs on zDHHC enzymes will provide new insight into the intracellular dynamics of S-acylation and may also highlight novel approaches to modulate S-acylation for clinical gain.
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Affiliation(s)
- Filip Zmuda
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, United Kingdom.
| | - Luke H Chamberlain
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, United Kingdom.
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6
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The role of competing mechanisms on Lck regulation. Immunol Res 2020; 68:289-295. [PMID: 32794043 DOI: 10.1007/s12026-020-09148-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 08/10/2020] [Indexed: 10/23/2022]
Abstract
Lck is a Src-related protein tyrosine kinase that associates with CD4 and CD8 molecules and is essential to T cell development and T cell activation. Regulatory mechanisms of Lck are diverse and controversy exists regarding the importance of each mechanism. The balance of phosphorylation at the inhibitory and activating Tyr residues is maintained by a balance between CD45 and Csk and is dependent upon intact intracellular trafficking machinery. Current evidence shows that lipid-binding changes depending on Lck conformation and that phosphorylation-induced conformational changes in Lck modulate its kinase activity potentially through regulation of Lck clustering at the plasma membrane. Downstream regulators such as ZAP-70 mediate negative feedback that is dependent on Tyr192 phosphorylation. This review examines the diverse regulation of Lck in detail, highlighting the role of each mechanism on maintaining an appropriate amount of Lck in each conformational state, thus allowing for an efficient, appropriate, and controlled amount of T cell activation following TCR stimulation.
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7
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The Influence of Reactive Oxygen Species in the Immune System and Pathogenesis of Multiple Sclerosis. Autoimmune Dis 2020; 2020:5793817. [PMID: 32789026 PMCID: PMC7334772 DOI: 10.1155/2020/5793817] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 04/14/2020] [Accepted: 05/22/2020] [Indexed: 02/08/2023] Open
Abstract
Multiple roles have been indicated for reactive oxygen species (ROS) in the immune system in recent years. ROS have been extensively studied due to their ability to damage DNA and other subcellular structures. Noticeably, they have been identified as a pivotal second messenger for T-cell receptor signaling and T-cell activation and participate in antigen cross-presentation and chemotaxis. As an agent with direct toxic effects on cells, ROS lead to the initiation of the autoimmune response. Moreover, ROS levels are regulated by antioxidant systems, which include enzymatic and nonenzymatic antioxidants. Enzymatic antioxidants include superoxide dismutase, catalase, glutathione peroxidase, and glutathione reductase. Nonenzymatic antioxidants contain vitamins C, A, and E, glutathione, and thioredoxin. Particularly, cellular antioxidant systems have important functions in maintaining the redox system homeostasis. This review will discuss the significant roles of ROS generation and antioxidant systems under normal conditions, in the immune system, and pathogenesis of multiple sclerosis.
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Curtis M, Kenny HA, Ashcroft B, Mukherjee A, Johnson A, Zhang Y, Helou Y, Batlle R, Liu X, Gutierrez N, Gao X, Yamada SD, Lastra R, Montag A, Ahsan N, Locasale JW, Salomon AR, Nebreda AR, Lengyel E. Fibroblasts Mobilize Tumor Cell Glycogen to Promote Proliferation and Metastasis. Cell Metab 2019; 29:141-155.e9. [PMID: 30174305 PMCID: PMC6326875 DOI: 10.1016/j.cmet.2018.08.007] [Citation(s) in RCA: 181] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 06/22/2018] [Accepted: 08/02/2018] [Indexed: 12/29/2022]
Abstract
Successful metastasis requires the co-evolution of stromal and cancer cells. We used stable isotope labeling of amino acids in cell culture coupled with quantitative, label-free phosphoproteomics to study the bidirectional signaling in ovarian cancer cells and human-derived, cancer-associated fibroblasts (CAFs) after co-culture. In cancer cells, the interaction with CAFs supported glycogenolysis under normoxic conditions and induced phosphorylation and activation of phosphoglucomutase 1, an enzyme involved in glycogen metabolism. Glycogen was funneled into glycolysis, leading to increased proliferation, invasion, and metastasis of cancer cells co-cultured with human CAFs. Glycogen mobilization in cancer cells was dependent on p38α MAPK activation in CAFs. In vivo, deletion of p38α in CAFs and glycogen phosphorylase inhibition in cancer cells reduced metastasis, suggesting that glycogen is an energy source used by cancer cells to facilitate metastatic tumor growth.
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Affiliation(s)
- Marion Curtis
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL 60637, USA
| | - Hilary A Kenny
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL 60637, USA
| | - Bradley Ashcroft
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL 60637, USA
| | - Abir Mukherjee
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL 60637, USA
| | - Alyssa Johnson
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL 60637, USA
| | - Yilin Zhang
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL 60637, USA
| | - Ynes Helou
- Department of Molecular Biology, Cell Biology, and Biochemistry/Center of Genomics and Proteomics, Brown University, Providence, RI 02903, USA
| | - Raquel Batlle
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Xiaojing Liu
- Department of Pharmacology and Cancer Biology, Duke Cancer Institute, Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27705, USA
| | - Nuria Gutierrez
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Xia Gao
- Department of Pharmacology and Cancer Biology, Duke Cancer Institute, Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27705, USA
| | - S Diane Yamada
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL 60637, USA
| | - Ricardo Lastra
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Anthony Montag
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Nagib Ahsan
- Division of Biology and Medicine, Alpert Medical School, Brown University, Providence, RI 02903, USA; Center for Cancer Research Development, Proteomics Core Facility, Rhode Island Hospital, Providence, RI 02903, USA
| | - Jason W Locasale
- Department of Pharmacology and Cancer Biology, Duke Cancer Institute, Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27705, USA
| | - Arthur R Salomon
- Department of Molecular Biology, Cell Biology, and Biochemistry/Center of Genomics and Proteomics, Brown University, Providence, RI 02903, USA; Center for Cancer Research Development, Proteomics Core Facility, Rhode Island Hospital, Providence, RI 02903, USA
| | - Angel R Nebreda
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Ernst Lengyel
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL 60637, USA.
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9
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G protein subunit phosphorylation as a regulatory mechanism in heterotrimeric G protein signaling in mammals, yeast, and plants. Biochem J 2018; 475:3331-3357. [PMID: 30413679 DOI: 10.1042/bcj20160819] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 09/28/2018] [Accepted: 10/02/2018] [Indexed: 12/15/2022]
Abstract
Heterotrimeric G proteins composed of Gα, Gβ, and Gγ subunits are vital eukaryotic signaling elements that convey information from ligand-regulated G protein-coupled receptors (GPCRs) to cellular effectors. Heterotrimeric G protein-based signaling pathways are fundamental to human health [Biochimica et Biophysica Acta (2007) 1768, 994-1005] and are the target of >30% of pharmaceuticals in clinical use [Biotechnology Advances (2013) 31, 1676-1694; Nature Reviews Drug Discovery (2017) 16, 829-842]. This review focuses on phosphorylation of G protein subunits as a regulatory mechanism in mammals, budding yeast, and plants. This is a re-emerging field, as evidence for phosphoregulation of mammalian G protein subunits from biochemical studies in the early 1990s can now be complemented with contemporary phosphoproteomics and genetic approaches applied to a diversity of model systems. In addition, new evidence implicates a family of plant kinases, the receptor-like kinases, which are monophyletic with the interleukin-1 receptor-associated kinase/Pelle kinases of metazoans, as possible GPCRs that signal via subunit phosphorylation. We describe early and modern observations on G protein subunit phosphorylation and its functional consequences in these three classes of organisms, and suggest future research directions.
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10
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Dimitrova P, Alipieva K, Grozdanova T, Simova S, Bankova V, Georgiev MI, Popova MP. New iridoids from Verbascum nobile and their effect on lectin-induced T cell activation and proliferation. Food Chem Toxicol 2017; 111:605-615. [PMID: 29208506 DOI: 10.1016/j.fct.2017.11.060] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 11/27/2017] [Accepted: 11/30/2017] [Indexed: 02/06/2023]
Abstract
The Verbascum species are widely used traditional herb remedies against respiratory, inflammatory conditions and disorders. In the present study methanol extract of the aerial parts of the endemic Verbascum nobile Velen, was investigated and two novel iridoid glycosides 1 and 2, together with nine known constituents: iridoids, phenylethanoids, and saponins characteristic of Verbascum genus were identified. Further, the biological activity of the extract and selected isolated compounds on concanavalin (Con A)-induced T cell proliferation and activation of human Jurkat T cell line and splenic murine CD3 T cells was evaluated. T cell growth was studied by colorimetric-based WST proliferation assay while DNA content, cell cycling, dynamic of cell proliferation, expression of activation markers, intracellular expression of cytokine IFN-γ, and phosphorylation of ERK were analyzed by flow cytometry. Caspase-mediated apoptosis resulting in a poly (ADP-ribose) polymerase (PARP) cleavage was assessed by colorimetric in-cell kit. It was found that the extract, and all tested compounds (1, 2, 3 and 9) inhibited lectin-induced cell growth of Jurkat T cell line. The novel compounds decreased the frequencies of cells in S phase without causing a significant cell cycle arrest at G1 phase, caspases-mediated apoptosis and/or a profound change in the dynamic of splenic murine CD3+ T cell proliferation. Both compounds showed stronger inhibitory effect on Con A-induced ERK phosphorylation than the known bioactive compounds 3 and 9, and suppressed the expression of early activation marker CD69, the intracellular level of IFN-γ, and the generation of CD3+IFN-γ+ effectors. Our data suggest that the novel iridoid glycosides might have a potential to modulate T cell-related pathologies.
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Affiliation(s)
- Petya Dimitrova
- Department of Immunology, The Stefan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, bl. 26 Acad. Georgi Bonchev Str., 1113 Sofia, Bulgaria
| | - Kalina Alipieva
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, bl. 9 Acad Georgi Bonchev Str., 1113 Sofia, Bulgaria.
| | - Tsvetinka Grozdanova
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, bl. 9 Acad Georgi Bonchev Str., 1113 Sofia, Bulgaria
| | - Svetlana Simova
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, bl. 9 Acad Georgi Bonchev Str., 1113 Sofia, Bulgaria
| | - Vassya Bankova
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, bl. 9 Acad Georgi Bonchev Str., 1113 Sofia, Bulgaria
| | - Milen I Georgiev
- Group of Plant Cell Biotechnology and Metabolomics, The Stefan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 139 Ruski Blvd., 4000 Plovdiv, Bulgaria
| | - Milena P Popova
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, bl. 9 Acad Georgi Bonchev Str., 1113 Sofia, Bulgaria
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11
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Verdina A, Di Rocco G, Virdia I, Monteonofrio L, Gatti V, Policicchio E, Bruselles A, Tartaglia M, Soddu S. HIPK2-T566 autophosphorylation diversely contributes to UV- and doxorubicin-induced HIPK2 activation. Oncotarget 2017; 8:16744-16754. [PMID: 28060750 PMCID: PMC5369998 DOI: 10.18632/oncotarget.14421] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 12/15/2016] [Indexed: 12/30/2022] Open
Abstract
HIPK2 is a Y-regulated S/T kinase involved in various cellular processes, including cell-fate decision during development and DNA damage response. Cis-autophosphorylation in the activation-loop and trans-autophosphorylation at several S/T sites along the protein are required for HIPK2 activation, subcellular localization, and subsequent posttranslational modifications. The specific function of a few of these autophosphorylations has been recently clarified; however, most of the sites found phosphorylated by mass spectrometry in human and/or mouse HIPK2 are still uncharacterized. In the process of studying HIPK2 in human colorectal cancers, we identified a mutation (T566P) in a site we previously found autophosphorylated in mouse Hipk2. Biochemical and functional characterization of this site showed that compared to wild type (wt) HIPK2, HIPK2-T566P maintains nuclear-speckle localization and has only a mild reduction in kinase and growth arresting activities upon overexpression. Next, we assessed cell response following UV-irradiation or treatment with doxorubicin, two well-known HIPK2 activators, by evaluating cell number and viability, p53-Ser46 phosphorylation, p21 induction, and caspase cleavage. Interestingly, cells expressing HIPK2-T566P mutant did not respond to UV-irradiation, while behaved similarly to wt HIPK2 upon doxorubicin-treatment. Evaluation of HIPK2-T566 phosphorylation status by a T566-phospho-specific antibody showed constitutive phosphorylation in unstressed cells, which was maintained after doxorubicin-treatment but inhibited by UV-irradiation. Taken together, these data show that HIPK2-T566 phosphorylation contributes to UV-induced HIPK2 activity but it is dispensable for doxorubicin response.
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Affiliation(s)
- Alessandra Verdina
- Unit of Cellular Networks and Molecular Therapeutic Targets, Department of Research, Advanced Diagnostics, and Technological Innovation, Regina Elena National Cancer Institute - IRCCS, Rome, Italy
| | - Giuliana Di Rocco
- Unit of Cellular Networks and Molecular Therapeutic Targets, Department of Research, Advanced Diagnostics, and Technological Innovation, Regina Elena National Cancer Institute - IRCCS, Rome, Italy
| | - Ilaria Virdia
- Unit of Cellular Networks and Molecular Therapeutic Targets, Department of Research, Advanced Diagnostics, and Technological Innovation, Regina Elena National Cancer Institute - IRCCS, Rome, Italy
| | - Laura Monteonofrio
- Unit of Cellular Networks and Molecular Therapeutic Targets, Department of Research, Advanced Diagnostics, and Technological Innovation, Regina Elena National Cancer Institute - IRCCS, Rome, Italy
| | - Veronica Gatti
- Unit of Cellular Networks and Molecular Therapeutic Targets, Department of Research, Advanced Diagnostics, and Technological Innovation, Regina Elena National Cancer Institute - IRCCS, Rome, Italy.,Present address: Istituto di Biologia Cellulare e Neurobiologia, CNR, Monterotondo Scalo, Rome, Italy
| | - Eleonora Policicchio
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Alessandro Bruselles
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù - IRCCS, Rome, Italy
| | - Silvia Soddu
- Unit of Cellular Networks and Molecular Therapeutic Targets, Department of Research, Advanced Diagnostics, and Technological Innovation, Regina Elena National Cancer Institute - IRCCS, Rome, Italy
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12
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Álvarez-Salamero C, Castillo-González R, Navarro MN. Lighting Up T Lymphocyte Signaling with Quantitative Phosphoproteomics. Front Immunol 2017; 8:938. [PMID: 28848546 PMCID: PMC5552657 DOI: 10.3389/fimmu.2017.00938] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 07/21/2017] [Indexed: 12/31/2022] Open
Abstract
Phosphorylation is the most abundant post-translational modification, regulating several aspects of protein and cell function. Quantitative phosphoproteomics approaches have expanded the scope of phosphorylation analysis enabling the quantification of changes in thousands of phosphorylation sites simultaneously in two or more conditions. These approaches offer a global view of the impact of cellular perturbations such as extracellular stimuli or gene ablation in intracellular signaling networks. Such great potential also brings on a new challenge: to identify, among the thousands of phosphorylations found in global phosphoproteomics studies, the small subset of site-specific phosphorylations expected to be functionally relevant. This review focus on updating and integrating findings on T lymphocyte signaling generated using global phosphoproteomics approaches, drawing attention on the biological relevance of the obtained data.
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Affiliation(s)
- Candelas Álvarez-Salamero
- Departamento de Medicina, Universidad Autónoma de Madrid, Madrid, Spain.,Instituto de Investigación Sanitaria del Hospital Universitario de La Princesa, Madrid, Spain
| | | | - María N Navarro
- Departamento de Medicina, Universidad Autónoma de Madrid, Madrid, Spain.,Instituto de Investigación Sanitaria del Hospital Universitario de La Princesa, Madrid, Spain.,Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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13
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Belmont J, Gu T, Mudd A, Salomon AR. A PLC-γ1 Feedback Pathway Regulates Lck Substrate Phosphorylation at the T-Cell Receptor and SLP-76 Complex. J Proteome Res 2017. [PMID: 28644030 DOI: 10.1021/acs.jproteome.6b01026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Phospholipase C gamma 1 (PLC-γ1) occupies a critically important position in the T-cell signaling pathway. While its functions as a regulator of both Ca2+ signaling and PKC-family kinases are well characterized, PLC-γ1's role in the regulation of early T-cell receptor signaling events is incompletely understood. Activation of the T-cell receptor leads to the formation of a signalosome complex between SLP-76, LAT, PLC-γ1, Itk, and Vav1. Recent studies have revealed the existence of both positive and negative feedback pathways from SLP-76 to the apical kinase in the pathway, Lck. To determine if PLC-γ1 contributes to the regulation of these feedback networks, we performed a quantitative phosphoproteomic analysis of PLC-γ1-deficient T cells. These data revealed a previously unappreciated role for PLC-γ1 in the positive regulation of Zap-70 and T-cell receptor tyrosine phosphorylation. Conversely, PLC-γ1 negatively regulated the phosphorylation of SLP-76-associated proteins, including previously established Lck substrate phosphorylation sites within this complex. While the positive and negative regulatory phosphorylation sites on Lck were largely unchanged, Tyr192 phosphorylation was elevated in Jgamma1. The data supports a model wherein Lck's targeting, but not its kinase activity, is altered by PLC-γ1, possibly through Lck Tyr192 phosphorylation and increased association of the kinase with protein scaffolds SLP-76 and TSAd.
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Affiliation(s)
- Judson Belmont
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University , Providence, Rhode Island 02912, United States
| | - Tao Gu
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University , Providence, Rhode Island 02912, United States
| | - Ashley Mudd
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University , Providence, Rhode Island 02912, United States
| | - Arthur R Salomon
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University , Providence, Rhode Island 02912, United States.,Department of Chemistry, Brown University , Providence, Rhode Island 02912, United States
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14
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Abstract
TCR signaling critically depends on protein phosphorylation across many proteins. Localization of each phosphorylation event relative to the T-cell receptor (TCR) and canonical T-cell signaling proteins will provide clues about the structure of TCR signaling networks. Quantitative phosphoproteomic analysis by mass spectrometry provides a wide-scale view of cellular phosphorylation networks. However, analysis of phosphorylation by mass spectrometry is still challenging due to the relative low abundance of phosphorylated proteins relative to all proteins and the extraordinary diversity of phosphorylation sites across the proteome. Highly selective enrichment of phosphorylated peptides is essential to provide the most comprehensive view of the phosphoproteome. Optimization of phosphopeptide enrichment methods coupled with highly sensitive mass spectrometry workflows significantly improves the sequencing depth of the phosphoproteome to over 10,000 unique phosphorylation sites from complex cell lysates. Here we describe a step-by-step method for phosphoproteomic analysis that has achieved widespread success for identification of serine, threonine, and tyrosine phosphorylation. Reproducible quantification of relative phosphopeptide abundance is provided by intensity-based label-free quantitation. An ideal set of mass spectrometry analysis parameters is also provided that optimize the yield of identified sites. We also provide guidelines for the bioinformatic analysis of this type of data to assess the quality of the data and to comply with proteomic data reporting requirements.
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Affiliation(s)
- Nagib Ahsan
- Division of Biology and Medicine, Alpert Medical School, Brown University, Providence, RI, 02903, USA
- Center for Cancer Research and Development, Proteomics Core Facility, Rhode Island Hospital, Providence, RI, 02903, USA
| | - Arthur R Salomon
- Center for Cancer Research and Development, Proteomics Core Facility, Rhode Island Hospital, Providence, RI, 02903, USA.
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, 02903, USA.
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15
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Hatano A, Matsumoto M, Nakayama KI. Phosphoproteomics analyses show subnetwork systems in T-cell receptor signaling. Genes Cells 2016; 21:1095-1112. [DOI: 10.1111/gtc.12406] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 08/02/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Atsushi Hatano
- Department of Molecular and Cellular Biology; Medical Institute of Bioregulation; Kyushu University; 3-1-1 Maidashi Higashi-ku Fukuoka 812-8582 Japan
| | - Masaki Matsumoto
- Department of Molecular and Cellular Biology; Medical Institute of Bioregulation; Kyushu University; 3-1-1 Maidashi Higashi-ku Fukuoka 812-8582 Japan
| | - Keiichi I. Nakayama
- Department of Molecular and Cellular Biology; Medical Institute of Bioregulation; Kyushu University; 3-1-1 Maidashi Higashi-ku Fukuoka 812-8582 Japan
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16
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Kwon B, Gamache T, Lee HK, Querfurth HW. Synergistic effects of β-amyloid and ceramide-induced insulin resistance on mitochondrial metabolism in neuronal cells. Biochim Biophys Acta Mol Basis Dis 2015; 1852:1810-23. [DOI: 10.1016/j.bbadis.2015.05.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 05/18/2015] [Accepted: 05/19/2015] [Indexed: 12/16/2022]
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17
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Helou YA, Petrashen AP, Salomon AR. Vav1 Regulates T-Cell Activation through a Feedback Mechanism and Crosstalk between the T-Cell Receptor and CD28. J Proteome Res 2015; 14:2963-75. [PMID: 26043137 DOI: 10.1021/acs.jproteome.5b00340] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Vav1, a Rac/Rho guanine nucleotide exchange factor and a critical component of the T-cell receptor (TCR) signaling cascade is tyrosine phosphorylated rapidly in response to T-cell activation. Vav1 has established roles in proliferation, cytokine secretion, Ca(2+) responses, and actin cytoskeleton regulation; however, its function in the regulation of phosphorylation of TCR components, including the ζ chain, the CD3 δ, ε, γ chains, and the associated kinases Lck and ZAP-70, is not well established. To obtain a more comprehensive picture of the role of Vav1 in receptor proximal signaling, we performed a wide-scale characterization of Vav1-dependent tyrosine phosphorylation events using quantitative phosphoproteomic analysis of Vav1-deficient T cells across a time course of TCR stimulation. Importantly, this study revealed a new function for Vav1 in the negative feedback regulation of the phosphorylation of immunoreceptor tyrosine-based activation motifs within the ζ chains, CD3 δ, ε, γ chains, as well as activation sites on the critical T cell tyrosine kinases Itk, Lck, and ZAP-70. Our study also uncovered a previously unappreciated role for Vav1 in crosstalk between the CD28 and TCR signaling pathways.
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Affiliation(s)
- Ynes A Helou
- †Department of Molecular Pharmacology, Physiology, and Biotechnology and ‡Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 02903, United States
| | - Anna P Petrashen
- †Department of Molecular Pharmacology, Physiology, and Biotechnology and ‡Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 02903, United States
| | - Arthur R Salomon
- †Department of Molecular Pharmacology, Physiology, and Biotechnology and ‡Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 02903, United States
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18
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Webb JT, Behar M. Topology, dynamics, and heterogeneity in immune signaling. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2015; 7:285-300. [DOI: 10.1002/wsbm.1306] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 04/14/2015] [Accepted: 04/21/2015] [Indexed: 12/28/2022]
Affiliation(s)
- J. Taylor Webb
- Department of Biomedical Engineering; The University of Texas at Austin; Austin TX USA
| | - Marcelo Behar
- Department of Biomedical Engineering; The University of Texas at Austin; Austin TX USA
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19
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Goodfellow HS, Frushicheva MP, Ji Q, Cheng DA, Kadlecek TA, Cantor AJ, Kuriyan J, Chakraborty AK, Salomon A, Weiss A. The catalytic activity of the kinase ZAP-70 mediates basal signaling and negative feedback of the T cell receptor pathway. Sci Signal 2015; 8:ra49. [PMID: 25990959 DOI: 10.1126/scisignal.2005596] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
T cell activation by antigens binding to the T cell receptor (TCR) must be properly regulated to ensure normal T cell development and effective immune responses to pathogens and transformed cells while avoiding autoimmunity. The Src family kinase Lck and the Syk family kinase ZAP-70 (ζ chain-associated protein kinase of 70 kD) are sequentially activated in response to TCR engagement and serve as critical components of the TCR signaling machinery that leads to T cell activation. We performed a mass spectrometry-based phosphoproteomic study comparing the quantitative differences in the temporal dynamics of phosphorylation in stimulated and unstimulated T cells with or without inhibition of ZAP-70 catalytic activity. The data indicated that the kinase activity of ZAP-70 stimulates negative feedback pathways that target Lck and thereby modulate the phosphorylation patterns of the immunoreceptor tyrosine-based activation motifs (ITAMs) of the CD3 and ζ chain components of the TCR and of signaling molecules downstream of Lck, including ZAP-70. We developed a computational model that provides a mechanistic explanation for the experimental findings on ITAM phosphorylation in wild-type cells, ZAP-70-deficient cells, and cells with inhibited ZAP-70 catalytic activity. This model incorporated negative feedback regulation of Lck activity by the kinase activity of ZAP-70 and predicted the order in which tyrosines in the ITAMs of TCR ζ chains must be phosphorylated to be consistent with the experimental data.
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Affiliation(s)
- Hanna Sjölin Goodfellow
- Howard Hughes Medical Institute, UCSF, San Francisco, CA 94143, USA.,Department of Medicine, UCSF, San Francisco, CA 94143, USA
| | - Maria P Frushicheva
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Qinqin Ji
- Department of Chemistry, Brown University, Providence, RI 02912, USA
| | - Debra A Cheng
- Howard Hughes Medical Institute, UCSF, San Francisco, CA 94143, USA.,Department of Medicine, UCSF, San Francisco, CA 94143, USA
| | - Theresa A Kadlecek
- Howard Hughes Medical Institute, UCSF, San Francisco, CA 94143, USA.,Department of Medicine, UCSF, San Francisco, CA 94143, USA
| | - Aaron J Cantor
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.,California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
| | - John Kuriyan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.,California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA.,Department of Chemistry, University of California, Berkeley, CA 94720, USA.,Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Arup K Chakraborty
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Arthur Salomon
- Department of Chemistry, Brown University, Providence, RI 02912, USA.,Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Arthur Weiss
- Howard Hughes Medical Institute, UCSF, San Francisco, CA 94143, USA.,Department of Medicine, UCSF, San Francisco, CA 94143, USA
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20
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Boylan JM, Salomon AR, Tantravahi U, Gruppuso PA. Adaptation of HepG2 cells to a steady-state reduction in the content of protein phosphatase 6 (PP6) catalytic subunit. Exp Cell Res 2015; 335:224-37. [PMID: 25999147 DOI: 10.1016/j.yexcr.2015.05.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 05/06/2015] [Accepted: 05/08/2015] [Indexed: 11/27/2022]
Abstract
Protein phosphatase 6 (PP6) is a ubiquitous Ser/Thr phosphatase involved in an array of cellular processes. To assess the potential of PP6 as a therapeutic target in liver disorders, we attenuated expression of the PP6 catalytic subunit in HepG2 cells using lentiviral-transduced shRNA. Two PP6 knock-down (PP6KD) cell lines (90% reduction of PP6-C protein content) were studied in depth. Both proliferated at a rate similar to control cells. However, flow cytometry indicated G2/M cell cycle arrest that was accounted for by a shift of the cells from a diploid to tetraploid state. PP6KD cells did not show an increase in apoptosis, nor did they exhibit reduced viability in the presence of bleomycin or taxol. Gene expression analysis by microarray showed attenuated anti-inflammatory signaling. Genes associated with DNA replication were downregulated. Mass spectrometry-based phosphoproteomic analysis yielded 80 phosphopeptides representing 56 proteins that were significantly affected by a stable reduction in PP6-C. Proteins involved in DNA replication, DNA damage repair and pre-mRNA splicing were overrepresented among these. PP6KD cells showed intact mTOR signaling. Our studies demonstrated involvement of PP6 in a diverse set of biological pathways and an adaptive response that may limit the effectiveness of targeting PP6 in liver disorders.
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Affiliation(s)
- Joan M Boylan
- Department of Pediatrics, Brown University and Rhode Island Hospital, Providence, RI, USA
| | - Arthur R Salomon
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA; Department of Chemistry, Brown University, Providence, RI, USA
| | - Umadevi Tantravahi
- Division of Genetics, Department of Pathology, Brown University and Women and Infants Hospital, Providence, RI, USA
| | - Philip A Gruppuso
- Department of Pediatrics, Brown University and Rhode Island Hospital, Providence, RI, USA; Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA.
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21
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Ortutay Z, Oksanen A, Aittomäki S, Ortutay C, Pesu M. Proprotein convertase FURIN regulates T cell receptor-induced transactivation. J Leukoc Biol 2015; 98:73-83. [PMID: 25926688 DOI: 10.1189/jlb.2a0514-257rr] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 04/08/2015] [Indexed: 12/23/2022] Open
Abstract
Antigen emergence rapidly stimulates T cells, which leads to changes in cytokine production, cell proliferation, and differentiation. Some of the key molecules involved in these events, such as TGF-β1 and NOTCH1, are synthesized initially as inactive precursors and are proteolytically activated during T cell activation. PCSKs regulate proprotein maturation by catalyzing the proteolytic cleavage of their substrates. The prototype PCSK FURIN is induced upon TCR activation, and its expression in T cells is critical for the maintenance of peripheral immune tolerance. In this study, we tested the hypothesis that FURIN regulates T cell activation. Our data demonstrate that IL-2 is increased initially in FURIN-deficient mouse CD4(+) T cells, but the TCR-induced IL-2 mRNA expression is not sustained in the absence of FURIN. Accordingly, the inhibition of FURIN in human Jurkat T cell lines also results in a decrease in IL-2 production, whereas the overexpression of WT FURIN is associated with elevated IL-2 levels. In Jurkat cells, FURIN is dispensable for immediate TCR signaling steps, such as ERK, ZAP70, or LAT phosphorylation. However, with the use of gene reporter assays, we demonstrate that FURIN regulates the AP-1, NFAT, and NF-κB transcription factors. Finally, by performing a transcription factor-binding site enrichment analysis on FURIN-dependent transcriptomes, we identify the FURIN-regulated transcription factors in mouse CD4(+) T cell subsets. Collectively, our work confirms the hypothesis that the TCR-regulated protease FURIN plays an important role in T cell activation and that it can specifically modulate TCR-activated transactivation.
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Affiliation(s)
- Zsuzsanna Ortutay
- *Immunoregulation, BioMediTech, University of Tampere, Finland; HiDucator Oy, Kangasala, Finland; and Department of Dermatology and Fimlab Laboratories, Tampere University Hospital, Pirkanmaa Hospital District, Tampere, Finland
| | - Anna Oksanen
- *Immunoregulation, BioMediTech, University of Tampere, Finland; HiDucator Oy, Kangasala, Finland; and Department of Dermatology and Fimlab Laboratories, Tampere University Hospital, Pirkanmaa Hospital District, Tampere, Finland
| | - Saara Aittomäki
- *Immunoregulation, BioMediTech, University of Tampere, Finland; HiDucator Oy, Kangasala, Finland; and Department of Dermatology and Fimlab Laboratories, Tampere University Hospital, Pirkanmaa Hospital District, Tampere, Finland
| | - Csaba Ortutay
- *Immunoregulation, BioMediTech, University of Tampere, Finland; HiDucator Oy, Kangasala, Finland; and Department of Dermatology and Fimlab Laboratories, Tampere University Hospital, Pirkanmaa Hospital District, Tampere, Finland
| | - Marko Pesu
- *Immunoregulation, BioMediTech, University of Tampere, Finland; HiDucator Oy, Kangasala, Finland; and Department of Dermatology and Fimlab Laboratories, Tampere University Hospital, Pirkanmaa Hospital District, Tampere, Finland
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22
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Ji Q, Salomon AR. Wide-scale quantitative phosphoproteomic analysis reveals that cold treatment of T cells closely mimics soluble antibody stimulation. J Proteome Res 2015; 14:2082-9. [PMID: 25839225 DOI: 10.1021/pr501172u] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The activation of T lymphocytes through antigen-mediated T cell receptor (TCR) clustering is vital in regulating the adaptive immune response. Although T cell receptor signaling has been extensively studied, the fundamental mechanisms for signal initiation are not fully understood. Reduced temperatures have initiated some of the hallmarks of TCR signaling, such as increased phosphorylation and activation on ERK and calcium release from the endoplasmic reticulum, as well as coalesced the T cell membrane microdomains. The precise mechanism of the TCR signaling initiation due to temperature change remains obscure. One critical question is whether the signaling initiated by the cold treatment of T cells differs from the signaling initiated by the cross-linking of the T cell receptor. To address this uncertainty, we performed a wide-scale, quantitative mass-spectrometry-based phosphoproteomic analysis on T cells stimulated either by temperature shifts or through the cross-linking of the TCR. Careful statistical comparisons between the two stimulations revealed a striking level of identity among the subset of 339 sites that changed significantly with both stimulations. This study demonstrates for the first time, in unprecedented detail, that T cell cold treatment was sufficient to initiate signaling patterns that were nearly identical to those of soluble antibody stimulation, shedding new light on the mechanism of activation of these critically important immune cells.
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Affiliation(s)
- Qinqin Ji
- †Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Arthur R Salomon
- †Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States.,‡Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 02903, United States
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23
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Helou YA, Salomon AR. Protein networks and activation of lymphocytes. Curr Opin Immunol 2015; 33:78-85. [PMID: 25687331 DOI: 10.1016/j.coi.2015.01.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 01/30/2015] [Accepted: 01/30/2015] [Indexed: 12/30/2022]
Abstract
The signal transduction pathways initiated by lymphocyte activation play a critical role in regulating host immunity. High-resolution mass spectrometry has accelerated the investigation of these complex and dynamic pathways by enabling the qualitative and quantitative investigation of thousands of proteins and phosphoproteins simultaneously. In addition, the unbiased and wide-scale identification of protein-protein interaction networks and protein kinase substrates in lymphocyte signaling pathways can be achieved by mass spectrometry-based approaches. Critically, the integration of these discovery-driven strategies with single-cell analysis using mass cytometry can facilitate the understanding of complex signaling phenotypes in distinct immunophenotypes.
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Affiliation(s)
- Ynes A Helou
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02912, USA
| | - Arthur R Salomon
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912, USA.
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24
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Chiang YJ, Hodes RJ. Regulation of T cell development by c-Cbl: essential role of Lck. Int Immunol 2014; 27:245-51. [PMID: 25477210 DOI: 10.1093/intimm/dxu105] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Accepted: 11/21/2014] [Indexed: 12/19/2022] Open
Abstract
A canonical pre-TCR/TCR signaling pathway critical for thymic T cell development involves sequential phosphorylation and signaling through Lck, Zap70, Lat and Slp76. However, we and others have previously reported that genomic deletion of c-Cbl (Cbl) partially or completely reverses the defects in thymic development in mice deficient in Zap70, Slp76, Lat or Vav1, indicating the presence of alternative pathways normally suppressed by Cbl. To further elucidate pre-TCR/TCR signaling pathways involved in thymic development, we characterized the effect of Cbl inactivation on developmental and signaling defects in mice deficient in proximal signaling molecules Lck and Zap70. Inactivation of Cbl partially reversed defective T cell development in Zap70 (-/-) mice and reversed defects in phosphorylation of Erk, Plc-γ1, Vav1 and Akt, in TCR-stimulated Cbl (-/-) Zap70 (-/-) thymocytes. Recent reports identified an essential role of Lck in associating with CD4 and CD8 coreceptors and mediating the requirement for MHC restriction in TCR recognition. Since TCR recognition has been shown to be MHC-restricted in Cbl (-/-) mice, it was of interest to determine whether the requirement for Lck remained unmodified by Cbl deletion. Indeed, in contrast to the effect of Cbl inactivation in partially or fully bypassing requirements for other TCR signaling components, inactivation of Cbl did not reverse either defective T cell development or defective phosphorylation of TCR signaling molecules in Lck (-/-) mice. Thus, Lck, which plays a unique role in enforcing MHC restriction, is essential for thymic development in presence or absence of Cbl, ensuring MHC restriction of T cells derived from either pathway.
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Affiliation(s)
- Y Jeffrey Chiang
- Experimental Immunology Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Richard J Hodes
- Experimental Immunology Branch, National Cancer Institute, Bethesda, MD 20892, USA National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
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Ji Q, Ding Y, Salomon AR. SRC homology 2 domain-containing leukocyte phosphoprotein of 76 kDa (SLP-76) N-terminal tyrosine residues regulate a dynamic signaling equilibrium involving feedback of proximal T-cell receptor (TCR) signaling. Mol Cell Proteomics 2014; 14:30-40. [PMID: 25316710 DOI: 10.1074/mcp.m114.037861] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
SRC homology 2 domain-containing leukocyte phosphoprotein of 76 kDa (SLP-76) is a cytosolic adaptor protein that plays an important role in the T-cell receptor-mediated T-cell signaling pathway. SLP-76 links proximal receptor stimulation to downstream effectors through interaction with many signaling proteins. Previous studies showed that mutation of three tyrosine residues, Tyr(112), Tyr(128), and Tyr(145), in the N terminus of SLP-76 results in severely impaired phosphorylation and activation of Itk and PLCγ1, which leads to defective calcium mobilization, Erk activation, and NFAT activation. To expand our knowledge of the role of N-terminal phosphorylation of SLP-76 from these three tyrosine sites, we characterized nearly 1000 tyrosine phosphorylation sites via mass spectrometry in SLP-76 reconstituted wild-type cells and SLP-76 mutant cells in which three tyrosine residues were replaced with phenylalanines (Y3F mutant). Mutation of the three N-terminal tyrosine residues of SLP-76 phenocopied SLP-76-deficient cells for the majority of tyrosine phosphorylation sites observed, including feedback on proximal T-cell receptor signaling proteins. Meanwhile, reversed phosphorylation changes were observed on Tyr(192) of Lck when we compared mutants to the complete removal of SLP-76. In addition, N-terminal tyrosine sites of SLP-76 also perturbed phosphorylation of Tyr(440) of Fyn, Tyr(702) of PLCγ1, Tyr(204), Tyr(397), and Tyr(69) of ZAP-70, revealing new modes of regulation on these sites. All these findings confirmed the central role of N-terminal tyrosine sites of SLP-76 in the pathway and also shed light on novel signaling events that are uniquely regulated by SLP-76 N-terminal tyrosine residues.
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Affiliation(s)
- Qinqin Ji
- From the ‡Department of Chemistry, Brown University Providence, RI 02903
| | - Yiyuan Ding
- From the ‡Department of Chemistry, Brown University Providence, RI 02903
| | - Arthur R Salomon
- From the ‡Department of Chemistry, Brown University Providence, RI 02903; §Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University Providence, RI 02903
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DeNardo BD, Holloway MP, Ji Q, Nguyen KT, Cheng Y, Valentine MB, Salomon A, Altura RA. Quantitative phosphoproteomic analysis identifies activation of the RET and IGF-1R/IR signaling pathways in neuroblastoma. PLoS One 2013; 8:e82513. [PMID: 24349301 PMCID: PMC3859635 DOI: 10.1371/journal.pone.0082513] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 10/24/2013] [Indexed: 12/20/2022] Open
Abstract
Neuroblastoma is an embryonal tumor of childhood with a heterogenous clinical presentation that reflects differences in activation of complex biological signaling pathways. Protein phosphorylation is a key component of cellular signal transduction and plays a critical role in processes that control cancer cell growth and survival. We used shotgun LC/MS to compare phosphorylation between a human MYCN amplified neuroblastoma cell line (NB10), modeling a resistant tumor, and a human neural precursor cell line (NPC), modeling a normal baseline neural crest cell. 2181 unique phosphorylation sites representing 1171 proteins and 2598 phosphopeptides were found. Protein kinases accounted for 6% of the proteome, with a predominance of tyrosine kinases, supporting their prominent role in oncogenic signaling pathways. Highly abundant receptor tyrosine kinase (RTK) phosphopeptides in the NB10 cell line relative to the NPC cell line included RET, insulin-like growth factor 1 receptor/insulin receptor (IGF-1R/IR), and fibroblast growth factor receptor 1 (FGFR1). Multiple phosphorylated peptides from downstream mediators of the PI3K/AKT/mTOR and RAS pathways were also highly abundant in NB10 relative to NPC. Our analysis highlights the importance of RET, IGF-1R/IR and FGFR1 as RTKs in neuroblastoma and suggests a methodology that can be used to identify potential novel biological therapeutic targets. Furthermore, application of this previously unexploited technology in the clinic opens the possibility of providing a new wide-scale molecular signature to assess disease progression and prognosis.
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Affiliation(s)
- Bradley D. DeNardo
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, The Warren Albert School of Medicine at Brown University, Providence, Rhode Island, United States of America
| | - Michael P. Holloway
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, The Warren Albert School of Medicine at Brown University, Providence, Rhode Island, United States of America
| | - Qinqin Ji
- Department of Chemistry, Brown University, Providence, Rhode Island, United States of America
| | - Kevin T. Nguyen
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, The Warren Albert School of Medicine at Brown University, Providence, Rhode Island, United States of America
| | - Yan Cheng
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, The Warren Albert School of Medicine at Brown University, Providence, Rhode Island, United States of America
| | - Marcus B. Valentine
- St. Jude Comprehensive Cancer Center Cytogenetic Shared Resource, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Arthur Salomon
- Department of Molecular and Cellular Biochemistry, Brown University, Providence, Rhode Island, United States of America
| | - Rachel A. Altura
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, The Warren Albert School of Medicine at Brown University, Providence, Rhode Island, United States of America
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