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Kunová N, Ondrovičová G, Bauer JA, Krajčovičová V, Pinkas M, Stojkovičová B, Havalová H, Lukáčová V, Kohútová L, Košťan J, Martináková L, Baráth P, Nováček J, Zoll S, Kereϊche S, Kutejová E, Pevala V. Polyphosphate and tyrosine phosphorylation in the N-terminal domain of the human mitochondrial Lon protease disrupts its functions. Sci Rep 2024; 14:9923. [PMID: 38688959 PMCID: PMC11061198 DOI: 10.1038/s41598-024-60030-9] [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: 12/18/2023] [Accepted: 04/18/2024] [Indexed: 05/02/2024] Open
Abstract
Phosphorylation plays a crucial role in the regulation of many fundamental cellular processes. Phosphorylation levels are increased in many cancer cells where they may promote changes in mitochondrial homeostasis. Proteomic studies on various types of cancer identified 17 phosphorylation sites within the human ATP-dependent protease Lon, which degrades misfolded, unassembled and oxidatively damaged proteins in mitochondria. Most of these sites were found in Lon's N-terminal (NTD) and ATPase domains, though little is known about the effects on their function. By combining the biochemical and cryo-electron microscopy studies, we show the effect of Tyr186 and Tyr394 phosphorylations in Lon's NTD, which greatly reduce all Lon activities without affecting its ability to bind substrates or perturbing its tertiary structure. A substantial reduction in Lon's activities is also observed in the presence of polyphosphate, whose amount significantly increases in cancer cells. Our study thus provides an insight into the possible fine-tuning of Lon activities in human diseases, which highlights Lon's importance in maintaining proteostasis in mitochondria.
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Grants
- 894 Grant No. 1825144Y Grantová Agentura České Republiky
- 894 Grant No. 1825144Y Grantová Agentura České Republiky
- 894 Grant No. 1825144Y Grantová Agentura České Republiky
- StruBioMol, ITMS: 305011X666 Interreg
- StruBioMol, ITMS: 305011X666 Interreg
- StruBioMol, ITMS: 305011X666 Interreg
- StruBioMol, ITMS: 305011X666 Interreg
- StruBioMol, ITMS: 305011X666 Interreg
- UP CIISB (No. CZ.02.1.01/0.0/0.0/18_046/0015974) European Regional Development Fund, European Union
- UP CIISB (No. CZ.02.1.01/0.0/0.0/18_046/0015974) European Regional Development Fund, European Union
- BIOMEDIRES - II. stage, ITMS: 313011W428 European Regional Development Fund
- APVV-15-0375, APVV-19-0298 Agentúra na Podporu Výskumu a Vývoja
- APVV-15-0375, APVV-19-0298 Agentúra na Podporu Výskumu a Vývoja
- 2/0069/23 Vedecká Grantová Agentúra MŠVVaŠ SR a SAV
- 2/0069/23 Vedecká Grantová Agentúra MŠVVaŠ SR a SAV
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Affiliation(s)
- Nina Kunová
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Gabriela Ondrovičová
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia
| | - Jacob A Bauer
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia
| | - Veronika Krajčovičová
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia
- Laboratory of Clinical and Molecular Genetics, National Institute of Children's Diseases, Limbová 1, 833 40, Bratislava, Slovakia
| | - Matyáš Pinkas
- CEITEC, Masaryk University in Brno, Brno, Czech Republic
| | - Barbora Stojkovičová
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Henrieta Havalová
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia
| | | | - Lenka Kohútová
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Július Košťan
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna, Biocenter 5, 1030, Vienna, Austria
| | - Lucia Martináková
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia
| | - Peter Baráth
- Medirex Group Academy, Nitra, Slovakia
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jiří Nováček
- CEITEC, Masaryk University in Brno, Brno, Czech Republic
| | - Sebastian Zoll
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Namesti 542/2, 16000, Prague, Czech Republic
| | - Sami Kereϊche
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic.
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Namesti 542/2, 16000, Prague, Czech Republic.
| | - Eva Kutejová
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia.
| | - Vladimír Pevala
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia.
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2
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Chatzikalil E, Stergiou IE, Papadakos SP, Konstantinidis I, Theocharis S. The Clinical Relevance of the EPH/Ephrin Signaling Pathway in Pediatric Solid and Hematologic Malignancies. Int J Mol Sci 2024; 25:3834. [PMID: 38612645 PMCID: PMC11011407 DOI: 10.3390/ijms25073834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/26/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
Pediatric neoplasms represent a complex group of malignancies that pose unique challenges in terms of diagnosis, treatment, and understanding of the underlying molecular pathogenetic mechanisms. Erythropoietin-producing hepatocellular receptors (EPHs), the largest family of receptor tyrosine kinases and their membrane-tethered ligands, ephrins, orchestrate short-distance cell-cell signaling and are intricately involved in cell-pattern morphogenesis and various developmental processes. Unraveling the role of the EPH/ephrin signaling pathway in the pathophysiology of pediatric neoplasms and its clinical implications can contribute to deciphering the intricate landscape of these malignancies. The bidirectional nature of the EPH/ephrin axis is underscored by emerging evidence revealing its capacity to drive tumorigenesis, fostering cell-cell communication within the tumor microenvironment. In the context of carcinogenesis, the EPH/ephrin signaling pathway prompts a reevaluation of treatment strategies, particularly in pediatric oncology, where the modest progress in survival rates and enduring treatment toxicity necessitate novel approaches. Molecularly targeted agents have emerged as promising alternatives, prompting a shift in focus. Through a nuanced understanding of the pathway's intricacies, we aim to lay the groundwork for personalized diagnostic and therapeutic strategies, ultimately contributing to improved outcomes for young patients grappling with neoplastic challenges.
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Affiliation(s)
- Elena Chatzikalil
- Division of Pediatric Hematology-Oncology, First Department of Pediatrics, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | - Ioanna E. Stergiou
- Department of Pathophysiology, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | - Stavros P. Papadakos
- First Department of Pathology, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | | | - Stamatios Theocharis
- First Department of Pathology, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece;
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3
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Codenotti S, Sandrini L, Mandracchia D, Lorenzi L, Corsetti G, Poli M, Asperti M, Salvi V, Bosisio D, Monti E, Mitola S, Triggiani L, Guescini M, Pozzo E, Sampaolesi M, Gastaldello S, Cassandri M, Marampon F, Fanzani A. Statin-Sensitive Akt1/Src/Caveolin-1 Signaling Enhances Oxidative Stress Resistance in Rhabdomyosarcoma. Cancers (Basel) 2024; 16:853. [PMID: 38473215 PMCID: PMC11154391 DOI: 10.3390/cancers16050853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/07/2024] [Accepted: 02/14/2024] [Indexed: 03/14/2024] Open
Abstract
Identifying the molecular mechanisms underlying radioresistance is a priority for the treatment of RMS, a myogenic tumor accounting for approximately 50% of all pediatric soft tissue sarcomas. We found that irradiation (IR) transiently increased phosphorylation of Akt1, Src, and Cav1 in human RD and RH30 lines. Synthetic inhibition of Akt1 and Src phosphorylation increased ROS levels in all RMS lines, promoting cellular radiosensitization. Accordingly, the elevated activation of the Akt1/Src/Cav1 pathway, as detected in two RD lines characterized by overexpression of a myristoylated Akt1 form (myrAkt1) or Cav1 (RDCav1), was correlated with reduced levels of ROS, higher expression of catalase, and increased radioresistance. We found that treatment with cholesterol-lowering drugs such as lovastatin and simvastatin promoted cell apoptosis in all RMS lines by reducing Akt1 and Cav1 levels and increasing intracellular ROS levels. Combining statins with IR significantly increased DNA damage and cell apoptosis as assessed by γ histone 2AX (γH2AX) staining and FACS analysis. Furthermore, in combination with the chemotherapeutic agent actinomycin D, statins were effective in reducing cell survival through increased apoptosis. Taken together, our findings suggest that the molecularly linked signature formed by Akt1, Src, Cav1, and catalase may represent a prognostic determinant for identifying subgroups of RMS patients with higher probability of recurrence after radiotherapy. Furthermore, statin-induced oxidative stress could represent a treatment option to improve the success of radiotherapy.
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Affiliation(s)
- Silvia Codenotti
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (L.S.); (D.M.); (M.P.); (M.A.); (V.S.); (D.B.); (E.M.); (S.M.)
| | - Leonardo Sandrini
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (L.S.); (D.M.); (M.P.); (M.A.); (V.S.); (D.B.); (E.M.); (S.M.)
| | - Delia Mandracchia
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (L.S.); (D.M.); (M.P.); (M.A.); (V.S.); (D.B.); (E.M.); (S.M.)
| | - Luisa Lorenzi
- Department of Molecular and Translational Medicine, University of Brescia, and ASST Spedali Civili di Brescia, 25123 Brescia, Italy;
| | - Giovanni Corsetti
- Department of Clinical and Experimental Sciences, University of Brescia, 25123 Brescia, Italy;
| | - Maura Poli
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (L.S.); (D.M.); (M.P.); (M.A.); (V.S.); (D.B.); (E.M.); (S.M.)
| | - Michela Asperti
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (L.S.); (D.M.); (M.P.); (M.A.); (V.S.); (D.B.); (E.M.); (S.M.)
| | - Valentina Salvi
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (L.S.); (D.M.); (M.P.); (M.A.); (V.S.); (D.B.); (E.M.); (S.M.)
| | - Daniela Bosisio
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (L.S.); (D.M.); (M.P.); (M.A.); (V.S.); (D.B.); (E.M.); (S.M.)
| | - Eugenio Monti
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (L.S.); (D.M.); (M.P.); (M.A.); (V.S.); (D.B.); (E.M.); (S.M.)
| | - Stefania Mitola
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (L.S.); (D.M.); (M.P.); (M.A.); (V.S.); (D.B.); (E.M.); (S.M.)
| | - Luca Triggiani
- Department of Radiation Oncology, ASST Spedali Civili di Brescia, University of Brescia, 25123 Brescia, Italy;
| | - Michele Guescini
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy;
| | - Enrico Pozzo
- Department of Development and Regeneration, KU Leuven, 3000 Leuven, Belgium; (E.P.); (M.S.)
| | - Maurilio Sampaolesi
- Department of Development and Regeneration, KU Leuven, 3000 Leuven, Belgium; (E.P.); (M.S.)
| | - Stefano Gastaldello
- Department of Physiology and Pharmacology, Karolinska Institutet, 17177 Stockholm, Sweden;
| | - Matteo Cassandri
- Department of Radiological Sciences, Oncology and Anatomic Pathology, “Sapienza” University of Rome, 00161 Rome, Italy; (M.C.); (F.M.)
| | - Francesco Marampon
- Department of Radiological Sciences, Oncology and Anatomic Pathology, “Sapienza” University of Rome, 00161 Rome, Italy; (M.C.); (F.M.)
| | - Alessandro Fanzani
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (L.S.); (D.M.); (M.P.); (M.A.); (V.S.); (D.B.); (E.M.); (S.M.)
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4
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Repici A, Ardizzone A, De Luca F, Colarossi L, Prestifilippo A, Pizzino G, Paterniti I, Esposito E, Capra AP. Signaling Pathways of AXL Receptor Tyrosine Kinase Contribute to the Pathogenetic Mechanisms of Glioblastoma. Cells 2024; 13:361. [PMID: 38391974 PMCID: PMC10886920 DOI: 10.3390/cells13040361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/05/2024] [Accepted: 02/16/2024] [Indexed: 02/24/2024] Open
Abstract
Brain tumors are a diverse collection of neoplasms affecting the brain with a high prevalence rate in people of all ages around the globe. In this pathological context, glioblastoma, a form of glioma that belongs to the IV-grade astrocytoma group, is the most common and most aggressive form of the primary brain tumors. Indeed, despite the best treatments available including surgery, radiotherapy or a pharmacological approach with Temozolomide, glioblastoma patients' mortality is still high, within a few months of diagnosis. Therefore, to increase the chances of these patients surviving, it is critical to keep finding novel treatment opportunities. In the past, efforts to treat glioblastoma have mostly concentrated on customized treatment plans that target specific mutations such as epidermal growth factor receptor (EGFR) mutations, Neurotrophic Tyrosine Receptor Kinase (NTRK) fusions, or multiple receptors using multi-kinase inhibitors like Sunitinib and Regorafenib, with varying degrees of success. Here, we focused on the receptor tyrosine kinase AXL that has been identified as a mediator for tumor progression and therapy resistance in various cancer types, including squamous cell tumors, small cell lung cancer, and breast cancer. Activated AXL leads to a significant increase in tumor proliferation, tumor cell migration, and angiogenesis in different in vitro and in vivo models of cancer since this receptor regulates interplay with apoptotic, angiogenic and inflammatory pathways. Based on these premises, in this review we mainly focused on the role of AXL in the course of glioblastoma, considering its primary biological mechanisms and as a possible target for the application of the most recent treatments.
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Affiliation(s)
- Alberto Repici
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno D’Alcontres, 31, 98166 Messina, Italy; (A.R.); (A.A.); (F.D.L.); (I.P.); (A.P.C.)
| | - Alessio Ardizzone
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno D’Alcontres, 31, 98166 Messina, Italy; (A.R.); (A.A.); (F.D.L.); (I.P.); (A.P.C.)
| | - Fabiola De Luca
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno D’Alcontres, 31, 98166 Messina, Italy; (A.R.); (A.A.); (F.D.L.); (I.P.); (A.P.C.)
| | - Lorenzo Colarossi
- Istituto Oncologico del Mediterraneo, Via Penninazzo 7, 95029 Viagrande, Italy; (L.C.); (A.P.); (G.P.)
| | - Angela Prestifilippo
- Istituto Oncologico del Mediterraneo, Via Penninazzo 7, 95029 Viagrande, Italy; (L.C.); (A.P.); (G.P.)
| | - Gabriele Pizzino
- Istituto Oncologico del Mediterraneo, Via Penninazzo 7, 95029 Viagrande, Italy; (L.C.); (A.P.); (G.P.)
| | - Irene Paterniti
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno D’Alcontres, 31, 98166 Messina, Italy; (A.R.); (A.A.); (F.D.L.); (I.P.); (A.P.C.)
| | - Emanuela Esposito
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno D’Alcontres, 31, 98166 Messina, Italy; (A.R.); (A.A.); (F.D.L.); (I.P.); (A.P.C.)
| | - Anna Paola Capra
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno D’Alcontres, 31, 98166 Messina, Italy; (A.R.); (A.A.); (F.D.L.); (I.P.); (A.P.C.)
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Lee CY, The M, Meng C, Bayer FP, Putzker K, Müller J, Streubel J, Woortman J, Sakhteman A, Resch M, Schneider A, Wilhelm S, Kuster B. Illuminating phenotypic drug responses of sarcoma cells to kinase inhibitors by phosphoproteomics. Mol Syst Biol 2024; 20:28-55. [PMID: 38177929 PMCID: PMC10883282 DOI: 10.1038/s44320-023-00004-7] [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: 12/23/2022] [Revised: 11/06/2023] [Accepted: 11/30/2023] [Indexed: 01/06/2024] Open
Abstract
Kinase inhibitors (KIs) are important cancer drugs but often feature polypharmacology that is molecularly not understood. This disconnect is particularly apparent in cancer entities such as sarcomas for which the oncogenic drivers are often not clear. To investigate more systematically how the cellular proteotypes of sarcoma cells shape their response to molecularly targeted drugs, we profiled the proteomes and phosphoproteomes of 17 sarcoma cell lines and screened the same against 150 cancer drugs. The resulting 2550 phenotypic profiles revealed distinct drug responses and the cellular activity landscapes derived from deep (phospho)proteomes (9-10,000 proteins and 10-27,000 phosphorylation sites per cell line) enabled several lines of analysis. For instance, connecting the (phospho)proteomic data with drug responses revealed known and novel mechanisms of action (MoAs) of KIs and identified markers of drug sensitivity or resistance. All data is publicly accessible via an interactive web application that enables exploration of this rich molecular resource for a better understanding of active signalling pathways in sarcoma cells, identifying treatment response predictors and revealing novel MoA of clinical KIs.
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Affiliation(s)
- Chien-Yun Lee
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Matthew The
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Chen Meng
- Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Technical University of Munich, Freising, Germany
| | - Florian P Bayer
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Kerstin Putzker
- Chemical Biology Core Facility, EMBL Heidelberg, Heidelberg, Germany
| | - Julian Müller
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Johanna Streubel
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Julia Woortman
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Amirhossein Sakhteman
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Moritz Resch
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Annika Schneider
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Stephanie Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.
- Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Technical University of Munich, Freising, Germany.
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany.
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6
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Wang T, Sun L, Chen C, Zhang Y, He B, Zhang Y, Wang Z, Xue H, Hao Y. Phosphorylation at tyrosine 317 and 508 are crucial for PIK3CA/p110α to promote CRC tumorigenesis. Cell Biosci 2023; 13:164. [PMID: 37689735 PMCID: PMC10493024 DOI: 10.1186/s13578-023-01102-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 08/07/2023] [Indexed: 09/11/2023] Open
Abstract
BACKGROUND PI3K/AKT signaling pathway plays important role in tumorigenesis of human cancer. Protein phosphorylation is crucial for signaling transduction of this pathway. PIK3CA, encoding the catalytic subunit p110α of PI3K complex, is one of the most frequently mutated oncogenes in human cancers. However, phosphorylation sites of PIK3CA/p110α and their underlying mechanism in tumorigenesis are largely unknown. METHODS Tyrosine phosphorylation sites of PIK3CA/p110α are identified with Mass-Spectrum. Crispr/CAS9 strategy is applied to generate Y317F and Y508F mutant knock-in cell clones. The growth and metastasis abilities of cells are evaluated in vitro and in vivo. Phospho-proteomics analysis and Western blots are used to demonstrate downstream signaling pathways of PIK3CA/p110α tyrosine phosphorylation. In vitro kinase assay is applied to identify the kinase of PIK3CA/p110α tyrosine phosphorylation. RESULTS Tyrosine phosphorylation of PIK3CA/p110α is stimulated by growth factors such as EGF, HGF and PDGF. Two tyrosine residues, Y317 and Y508, are identified on PIK3CA/p110α. Either Y317 or Y508 phosphorylation is essential for tumorigenesis of CRC. Mutation at Y317 of p110α reduces the proliferation, migration, and invasion of cancer cells through Src-MLC2 pathway, while mutation at Y508 of p110α impairs AKT signaling. Moreover, Src interacts with and phosphorylates p110α. CONCLUSIONS PIK3CA/p110α phosphorylation at Y317 and Y508 play important role in tumorigenesis of colorectal cancer through two independent pathways.
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Affiliation(s)
- Ting Wang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200032, China
| | - Longci Sun
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Chengkun Chen
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200032, China
| | - Yingchao Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200032, China
| | - Baoyu He
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200032, China
- Department of Laboratory Medicine, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, 272029, Shandong, China
| | - Yanhua Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200032, China
| | - Zhenghe Wang
- Department of Genetics and Genome Sciences, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Hanbing Xue
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Ministry of Health, Shanghai Jiao Tong University, Shanghai, 200127, China.
| | - Yujun Hao
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200032, China.
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7
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Rodriguez G, Martinez GS, Negrete OD, Sun S, Guo W, Xie Y, Li L, Xiao C, Ross JA, Kirken RA. JAK3 Y841 Autophosphorylation Is Critical for STAT5B Activation, Kinase Domain Stability and Dimer Formation. Int J Mol Sci 2023; 24:11928. [PMID: 37569303 PMCID: PMC10418363 DOI: 10.3390/ijms241511928] [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: 06/01/2023] [Revised: 07/15/2023] [Accepted: 07/20/2023] [Indexed: 08/13/2023] Open
Abstract
Janus tyrosine kinase 3 (JAK3) is primarily expressed in immune cells and is needed for signaling by the common gamma chain (γc) family of cytokines. Abnormal JAK3 signal transduction can manifest as hematological disorders, e.g., leukemia, severe combined immunodeficiency (SCID) and autoimmune disease states. While regulatory JAK3 phosphosites have been well studied, here a functional proteomics approach coupling a JAK3 autokinase assay to mass spectrometry revealed ten previously unreported autophosphorylation sites (Y105, Y190, Y238, Y399, Y633, Y637, Y738, Y762, Y824, and Y841). Of interest, Y841 was determined to be evolutionarily conserved across multiple species and JAK family members, suggesting a broader role for this residue. Phospho-substitution mutants confirmed that Y841 is also required for STAT5 tyrosine phosphorylation. The homologous JAK1 residue Y894 elicited a similar response to mutagenesis, indicating the shared importance for this site in JAK family members. Phospho-specific Y841-JAK3 antibodies recognized activated kinase from various T-cell lines and transforming JAK3 mutants. Computational biophysics analysis linked Y841 phosphorylation to enhanced JAK3 JH1 domain stability across pH environments, as well as to facilitated complementary electrostatic JH1 dimer formation. Interestingly, Y841 is not limited to tyrosine kinases, suggesting it represents a conserved ubiquitous enzymatic function that may hold therapeutic potential across multiple kinase families.
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Affiliation(s)
- Georgialina Rodriguez
- Department of Biological Sciences, The University of Texas at El Paso, 500 W University Ave., El Paso, TX 79968, USA
- Border Biomedical Research Center, The University of Texas at El Paso, 500 W University Ave., El Paso, TX 79968, USA
| | - George Steven Martinez
- Department of Biological Sciences, The University of Texas at El Paso, 500 W University Ave., El Paso, TX 79968, USA
- Border Biomedical Research Center, The University of Texas at El Paso, 500 W University Ave., El Paso, TX 79968, USA
| | - Omar Daniel Negrete
- Department of Biological Sciences, The University of Texas at El Paso, 500 W University Ave., El Paso, TX 79968, USA
- Border Biomedical Research Center, The University of Texas at El Paso, 500 W University Ave., El Paso, TX 79968, USA
| | - Shengjie Sun
- Department of Physics, The University of Texas at El Paso, 500 W University Ave., El Paso, TX 79968, USA
- Computational Science Program, The University of Texas at El Paso, 500 W University Ave., El Paso, TX 79968, USA
| | - Wenhan Guo
- Department of Physics, The University of Texas at El Paso, 500 W University Ave., El Paso, TX 79968, USA
- Computational Science Program, The University of Texas at El Paso, 500 W University Ave., El Paso, TX 79968, USA
| | - Yixin Xie
- Department of Physics, The University of Texas at El Paso, 500 W University Ave., El Paso, TX 79968, USA
- Computational Science Program, The University of Texas at El Paso, 500 W University Ave., El Paso, TX 79968, USA
| | - Lin Li
- Department of Physics, The University of Texas at El Paso, 500 W University Ave., El Paso, TX 79968, USA
- Computational Science Program, The University of Texas at El Paso, 500 W University Ave., El Paso, TX 79968, USA
| | - Chuan Xiao
- Computational Science Program, The University of Texas at El Paso, 500 W University Ave., El Paso, TX 79968, USA
- Department of Biochemistry, The University of Texas at El Paso, 500 W University Ave., El Paso, TX 79968, USA
| | - Jeremy Aaron Ross
- Department of Biological Sciences, The University of Texas at El Paso, 500 W University Ave., El Paso, TX 79968, USA
- Border Biomedical Research Center, The University of Texas at El Paso, 500 W University Ave., El Paso, TX 79968, USA
| | - Robert Arthur Kirken
- Department of Biological Sciences, The University of Texas at El Paso, 500 W University Ave., El Paso, TX 79968, USA
- Border Biomedical Research Center, The University of Texas at El Paso, 500 W University Ave., El Paso, TX 79968, USA
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8
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Li Y, Zhu J, Yu Z, Li H, Jin X. The role of Lamin B2 in human diseases. Gene 2023; 870:147423. [PMID: 37044185 DOI: 10.1016/j.gene.2023.147423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 04/02/2023] [Accepted: 04/05/2023] [Indexed: 04/14/2023]
Abstract
Lamin B2 (LMNB2), on the inner side of the nuclear envelope, constitutes the nuclear skeleton by connecting with other nuclear proteins. LMNB2 is involved in a wide range of nuclear functions, including DNA replication and stability, regulation of chromatin, and nuclear stiffness. Moreover, LMNB2 regulates several cellular processes, such as tissue development, cell cycle, cellular proliferation and apoptosis, chromatin localization and stability, and DNA methylation. Besides, the influence of abnormal expression and mutations of LMNB2 has been gradually discovered in cancers and laminopathies. Therefore, this review summarizes the recent advances of LMNB2-associated biological roles in physiological or pathological conditions, with a particular emphasis on cancers and laminopathies, as well as the potential mechanism of LMNB2 in related cancers.
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Affiliation(s)
- Yuxuan Li
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of LiHuiLi Hospital, Ningbo University, Ningbo, Zhejiang 315040, P.R. China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Jie Zhu
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of LiHuiLi Hospital, Ningbo University, Ningbo, Zhejiang 315040, P.R. China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Zongdong Yu
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of LiHuiLi Hospital, Ningbo University, Ningbo, Zhejiang 315040, P.R. China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Hong Li
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of LiHuiLi Hospital, Ningbo University, Ningbo, Zhejiang 315040, P.R. China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, P.R. China.
| | - Xiaofeng Jin
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of LiHuiLi Hospital, Ningbo University, Ningbo, Zhejiang 315040, P.R. China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, P.R. China.
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9
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Xu N, Yu Y, Duan C, Wei J, Sun W, Jiang C, Jian B, Cao W, Jia L, Ma X. Quantitative proteomics identifies and validates urinary biomarkers of rhabdomyosarcoma in children. Clin Proteomics 2023; 20:10. [PMID: 36918772 PMCID: PMC10012572 DOI: 10.1186/s12014-023-09401-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 03/02/2023] [Indexed: 03/16/2023] Open
Abstract
BACKGROUND Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma with poor prognosis in children. The 5-year survival rate for early RMS has improved, whereas it remains unsatisfactory for advanced patients. Urine can rapidly reflect changes in the body and identify low-abundance proteins. Early screening of tumor markers through urine in RMS allows for earlier treatment, which is associated with better outcomes. METHODS RMS patients under 18 years old, including those newly diagnosed and after surgery, were enrolled. Urine samples were collected at the time points of admission and after four cycles of chemotherapy during follow-up. Then, a two-stage workflow was established. (1) In the discovery stage, differential proteins (DPs) were initially identified in 43 RMS patients and 12 healthy controls (HCs) using a data-independent acquisition method. (2) In the verification stage, DPs were further verified as biomarkers in 54 RMS patients and 25 HCs using parallel reaction monitoring analysis. Furthermore, a receiver operating characteristic (ROC) curve was used to construct the protein panels for the diagnosis of RMS. Gene Ontology (GO) and Ingenuity Pathway Analysis (IPA) software were used to perform bioinformatics analysis. RESULTS A total of 251 proteins were significantly altered in the discovery stage, most of which were enriched in the head, neck and urogenital tract, consistent with the most common sites of RMS. The most overrepresented biological processes from GO analysis included immunity, inflammation, tumor invasion and neuronal damage. Pathways engaging the identified proteins revealed 33 common pathways, including WNT/β-catenin signaling and PI3K/AKT signaling. Finally, 39 proteins were confirmed as urinary biomarkers for RMS, and a diagnostic panel composed of 5 candidate proteins (EPS8L2, SPARC, HLA-DRB1, ACAN, and CILP) was constructed for the early screening of RMS (AUC: 0.79, 95%CI = 0.66 ~ 0.92). CONCLUSIONS These findings provide novel biomarkers in urine that are easy to translate into clinical diagnosis of RMS and illustrate the value of global and targeted urine proteomics to identify and qualify candidate biomarkers for noninvasive molecular diagnosis.
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Affiliation(s)
- Na Xu
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Oncology, Key Laboratory of Major Diseases in Children, Ministry of Education, No. 56 Nalishi Road, Beijing, 100045, China.,Department of Pediatrics, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Yuncui Yu
- Clinical Research Center, Department of Pharmacy, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, No. 56 Nanlishi Road, Beijing, 100045, China
| | - Chao Duan
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Oncology, Key Laboratory of Major Diseases in Children, Ministry of Education, No. 56 Nalishi Road, Beijing, 100045, China
| | - Jing Wei
- Clinical Research Center, Department of Pharmacy, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, No. 56 Nanlishi Road, Beijing, 100045, China
| | - Wei Sun
- Proteomics Research Center, Core Facility of Instruments, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chiyi Jiang
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Oncology, Key Laboratory of Major Diseases in Children, Ministry of Education, No. 56 Nalishi Road, Beijing, 100045, China
| | - Binglin Jian
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Oncology, Key Laboratory of Major Diseases in Children, Ministry of Education, No. 56 Nalishi Road, Beijing, 100045, China
| | - Wang Cao
- Clinical Research Center, Department of Pharmacy, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, No. 56 Nanlishi Road, Beijing, 100045, China
| | - Lulu Jia
- Clinical Research Center, Department of Pharmacy, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, No. 56 Nanlishi Road, Beijing, 100045, China.
| | - Xiaoli Ma
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Oncology, Key Laboratory of Major Diseases in Children, Ministry of Education, No. 56 Nalishi Road, Beijing, 100045, China.
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10
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Fleuren EDG, Vlenterie M, van der Graaf WTA. Recent advances on anti-angiogenic multi-receptor tyrosine kinase inhibitors in osteosarcoma and Ewing sarcoma. Front Oncol 2023; 13:1013359. [PMID: 36994209 PMCID: PMC10040783 DOI: 10.3389/fonc.2023.1013359] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 02/06/2023] [Indexed: 03/16/2023] Open
Abstract
Osteosarcoma (OS) and Ewing sarcoma (ES) are the two most common types of primary bone cancer that predominantly affect the young. Despite aggressive multimodal treatment, survival has not improved significantly over the past four decades. Clinical efficacy has historically been observed for some mono-Receptor Tyrosine Kinase (RTK) inhibitors, albeit in small subsets of OS and ES patients. Clinical efficacy in larger groups of OS or ES patients was reported recently with several newer generation multi-RTK inhibitors. All these inhibitors combine a strong anti-angiogenic (VEGFRs) component with simultaneous inhibition of other key RTKs implicated in OS and ES progression (PDGFR, FGFR, KIT and/or MET). However, despite interesting clinical data, none of these agents have obtained a registration for these indications and are thus difficult to implement in routine OS and ES patient care. It is at present also unclear which of these drugs, with largely overlapping molecular inhibition profiles, would work best for which patient or subtype, and treatment resistance almost uniformly occurs. Here, we provide a critical assessment and systemic comparison on the clinical outcomes to the six most tested drugs in this field in OS and ES to date, including pazopanib, sorafenib, regorafenib, anlotinib, lenvatinib and cabozantinib. We pay special attention to clinical response evaluations in bone sarcomas and provide drug comparisons, including drug-related toxicity, to put these drugs into context for OS and ES patients, and describe how future trials utilizing anti-angiogenic multi-RTK targeted drugs could be designed to ultimately improve response rates and decrease toxicity.
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Affiliation(s)
- Emmy D. G. Fleuren
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Clinical Medicine, UNSW Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
- Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
- *Correspondence: Emmy D. G. Fleuren,
| | - Myrella Vlenterie
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Winette T. A. van der Graaf
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, Netherlands
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
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11
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Src heterodimerically activates Lyn or Fyn to serve as targets for the diagnosis and treatment of esophageal squamous cell carcinoma. SCIENCE CHINA. LIFE SCIENCES 2023:10.1007/s11427-022-2216-x. [PMID: 36763244 DOI: 10.1007/s11427-022-2216-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/21/2022] [Indexed: 02/11/2023]
Abstract
Although Src is one of the oldest and most investigated oncoproteins, its function in tumor malignancy remains to be defined further. In this study, we demonstrated that the inhibition of Src activity by ponatinib effectively suppressed several malignant phenotypes of esophageal squamous cell carcinoma (ESCC) both in vitro and in vivo, whereas it did not produce growth-inhibitory effects on normal esophageal epithelial cells (NEECs). Importantly, we combined phosphoproteomics and several cellular and molecular biologic strategies to identify that Src interacted with the members of Src-family kinases (SFKs), such as Fyn or Lyn, to form heterodimers. Src interactions with Fyn and Lyn phosphorylated the tyrosine sites in SH2 (Fyn Tyr185 or Lyn Tyr183) and kinase domains (Fyn Tyr420 or Lyn Tyr397), which critically contributed to ESCC development. By contrast, Src could not form heterodimers with Fyn or Lyn in NEECs. We used RNA sequencing to comprehensively demonstrate that the inhibition of Src activity effectively blocked several critical tumor-promoting pathways, such as JAK/STAT, mTOR, stemness-related, and metabolism-related pathways. Results of the real-time polymerase chain reaction (RT-PCR) assay confirmed that Lyn and Fyn were critical effectors for the Src-mediated expression of tumor growth or metastasis-related molecules. Furthermore, results of the clinical ESCC samples showed that the hyperactivation of pSrc Tyr419, Fyn Tyr185 or Tyr420, and Lyn Tyr183 or Tyr397 could be biomarkers of ESCC prognosis. This study illustrates that Src/Fyn and Src/Lyn heterodimers serve as targets for the treatment of ESCC.
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12
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Najar MA, Arefian M, Sidransky D, Gowda H, Prasad TSK, Modi PK, Chatterjee A. Tyrosine Phosphorylation Profiling Revealed the Signaling Network Characteristics of CAMKK2 in Gastric Adenocarcinoma. Front Genet 2022; 13:854764. [PMID: 35646067 PMCID: PMC9136244 DOI: 10.3389/fgene.2022.854764] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/28/2022] [Indexed: 12/24/2022] Open
Abstract
Calcium/calmodulin-dependent protein kinase kinase 2 (CAMKK2) is a serine/threonine protein kinase which functions via the calcium-triggered signaling cascade with CAMK1, CAMK4, and AMPKα as the immediate downstream substrates. CAMKK2 is reported to be overexpressed in gastric cancer; however, its signaling mechanism is poorly understood. We carried out label-free quantitative tyrosine phosphoproteomics to investigate tyrosine-mediated molecular signaling associated with CAMKK2 in gastric cancer cells. Using a high-resolution Orbitrap Fusion Tribrid Fourier-transform mass spectrometer, we identified 350 phosphotyrosine sites mapping to 157 proteins. We observed significant alterations in 81 phosphopeptides corresponding to 63 proteins upon inhibition of CAMKK2, among which 16 peptides were hyperphosphorylated corresponding to 13 proteins and 65 peptides were hypophosphorylated corresponding to 51 proteins. We report here that the inhibition of CAMKK2 leads to changes in the phosphorylation of several tyrosine kinases such as PKP2, PTK2, EPHA1, EPHA2, PRKCD, MAPK12, among others. Pathway analyses revealed that proteins are differentially phosphorylated in response to CAMKK2 inhibition involved in focal adhesions, actin cytoskeleton, axon guidance, and signaling by VEGF. The western blot analysis upon inhibition and/or silencing of CAMKK2 revealed a decrease in phosphorylation of PTK2 at Y925, c-JUN at S73, and STAT3 at Y705, which was in concordance with the mass spectrometry data. The study indicates that inhibition of CAMKK2 has an anti-oncogenic effect in gastric cells regulating phosphorylation of STAT3 through PTK2/c-JUN in gastric cancer.
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Affiliation(s)
- Mohd. Altaf Najar
- Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, India
| | - Mohammad Arefian
- Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, India
| | - David Sidransky
- Department of Oncology and Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Harsha Gowda
- Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, India
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, India
| | - T. S. Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, India
| | - Prashant Kumar Modi
- Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, India
- *Correspondence: Prashant Kumar Modi, ; Aditi Chatterjee,
| | - Aditi Chatterjee
- Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, India
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- *Correspondence: Prashant Kumar Modi, ; Aditi Chatterjee,
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Abstract
Advances in proteomic and metabolomic technologies have accelerated our understanding of multiple aspects of cancer biology across distinct tumour types. Here we review the current state-of-the-art in the use of proteomics and metabolomics in soft tissue sarcomas. We highlight the utility of these Omics-based methodologies to identify new drug targets, synthetic lethal interactions, candidate therapeutics and novel biomarkers to facilitate patient stratification. Due to the unbiased and global nature of these profiling methods to assess the levels of protein expression, post-translational modifications such as phosphorylation and glycosylation as well as key metabolites, many of these findings have broad applications not just in specific histotypes but across multiple STS subtypes. Specific examples of proteomic and metabolomic findings that have led to the development of early phase clinical trials of investigational agents will be discussed. While promising, the use of these technologies in the study of sarcoma is still limited, and there is a need for further research in this area. In particular, it would be important to integrate these approaches with other Omics strategies such as genomics and epigenomics as well as implement these tools alongside clinical trials in order to maximize the impact of these tools on our biological understanding and treatment of this group of rare diseases of unmet need.
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Affiliation(s)
- Madhumeeta Chadha
- Division of Molecular Pathology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, SM2 5NG, UK
| | - Paul H Huang
- Division of Molecular Pathology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, SM2 5NG, UK.
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14
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Pankova V, Thway K, Jones RL, Huang PH. The Extracellular Matrix in Soft Tissue Sarcomas: Pathobiology and Cellular Signalling. Front Cell Dev Biol 2021; 9:763640. [PMID: 34957097 PMCID: PMC8696013 DOI: 10.3389/fcell.2021.763640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 11/09/2021] [Indexed: 11/22/2022] Open
Abstract
Soft tissue sarcomas are rare cancers of mesenchymal origin or differentiation comprising over 70 different histological subtypes. Due to their mesenchymal differentiation, sarcomas are thought to produce and deposit large quantities of extracellular matrix (ECM) components. Interactions between ECM ligands and their corresponding adhesion receptors such as the integrins and the discoidin domain receptors play key roles in driving many fundamental oncogenic processes including uncontrolled proliferation, cellular invasion and altered metabolism. In this review, we focus on emerging studies that describe the key ECM components commonly found in soft tissue sarcomas and discuss preclinical and clinical evidence outlining the important role that these proteins and their cognate adhesion receptors play in sarcomagenesis. We conclude by providing a perspective on the need for more comprehensive in-depth analyses of both the ECM and adhesion receptor biology in multiple histological subtypes in order to identify new drug targets and prognostic biomarkers for this group of rare diseases of unmet need.
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Affiliation(s)
- Valeriya Pankova
- Division of Molecular Pathology, The Institute of Cancer Research, Sutton, United Kingdom
| | - Khin Thway
- Division of Molecular Pathology, The Institute of Cancer Research, Sutton, United Kingdom
- Sarcoma Unit, The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Robin L. Jones
- Sarcoma Unit, The Royal Marsden NHS Foundation Trust, London, United Kingdom
- Division of Clinical Studies, The Institute of Cancer Research, Sutton, United Kingdom
| | - Paul H. Huang
- Division of Molecular Pathology, The Institute of Cancer Research, Sutton, United Kingdom
- *Correspondence: Paul H. Huang,
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15
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Silva AM, Moniz T, de Castro B, Rangel M. Human transferrin: An inorganic biochemistry perspective. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214186] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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16
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Fleuren EDG, Terry RL, Meyran D, Omer N, Trapani JA, Haber M, Neeson PJ, Ekert PG. Enhancing the Potential of Immunotherapy in Paediatric Sarcomas: Breaking the Immunosuppressive Barrier with Receptor Tyrosine Kinase Inhibitors. Biomedicines 2021; 9:1798. [PMID: 34944614 PMCID: PMC8698536 DOI: 10.3390/biomedicines9121798] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 11/22/2021] [Accepted: 11/24/2021] [Indexed: 12/22/2022] Open
Abstract
Despite aggressive surgery, chemotherapy, and radiotherapy, survival of children and adolescents and young adults (AYAs) with sarcoma has not improved significantly in the past four decades. Immune checkpoint inhibitors (ICIs) are an exciting type of immunotherapy that offer new opportunities for the treatment of paediatric and AYA sarcomas. However, to date, most children do not derive a benefit from this type of treatment as a monotherapy. The immunosuppressive tumour microenvironment is a major barrier limiting their efficacy. Combinations of ICIs, such as anti-PD-1 therapy, with targeted molecular therapies that have immunomodulatory properties may be the key to breaking through immunosuppressive barriers and improving patient outcomes. Preclinical studies have indicated that several receptor tyrosine kinase inhibitors (RTKi) can alter the tumour microenvironment and boost the efficacy of anti-PD-1 therapy. A number of these combinations have entered phase-1/2 clinical trials, mostly in adults, and in most instances have shown efficacy with manageable side-effects. In this review, we discuss the status of ICI therapy in paediatric and AYA sarcomas and the rationale for co-treatment with RTKis. We highlight new opportunities for the integration of ICI therapy with RTK inhibitors, to improve outcomes for children with sarcoma.
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Affiliation(s)
- Emmy D. G. Fleuren
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Randwick 2031, Australia; (R.L.T.); (M.H.); (P.G.E.)
- School of Women’s and Children’s Health, UNSW Sydney, Randwick 2052, Australia
- Centre for Childhood Cancer Research, UNSW Sydney, Randwick 2031, Australia
| | - Rachael L. Terry
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Randwick 2031, Australia; (R.L.T.); (M.H.); (P.G.E.)
- School of Women’s and Children’s Health, UNSW Sydney, Randwick 2052, Australia
| | - Deborah Meyran
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne 3000, Australia; (D.M.); (J.A.T.); (P.J.N.)
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne 3000, Australia
- Inserm, Université de Paris, U976 HIPI Unit, Institut de Recherche Saint-Louis, 75475 Paris, France
| | - Natacha Omer
- Translational Innate Immunotherapy, University of Queensland Diamantina Institute (UQDI), Brisbane 4102, Australia;
- Oncology Services Group, Queensland Children’s Hospital, Brisbane 4101, Australia
| | - Joseph A. Trapani
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne 3000, Australia; (D.M.); (J.A.T.); (P.J.N.)
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne 3000, Australia
| | - Michelle Haber
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Randwick 2031, Australia; (R.L.T.); (M.H.); (P.G.E.)
- School of Women’s and Children’s Health, UNSW Sydney, Randwick 2052, Australia
| | - Paul J. Neeson
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne 3000, Australia; (D.M.); (J.A.T.); (P.J.N.)
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne 3000, Australia
| | - Paul G. Ekert
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Randwick 2031, Australia; (R.L.T.); (M.H.); (P.G.E.)
- School of Women’s and Children’s Health, UNSW Sydney, Randwick 2052, Australia
- Centre for Childhood Cancer Research, UNSW Sydney, Randwick 2031, Australia
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne 3000, Australia; (D.M.); (J.A.T.); (P.J.N.)
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne 3000, Australia
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne 3052, Australia
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Fordham AM, Ekert PG, Fleuren EDG. Precision medicine and phosphoproteomics for the identification of novel targeted therapeutic avenues in sarcomas. Biochim Biophys Acta Rev Cancer 2021; 1876:188613. [PMID: 34390800 DOI: 10.1016/j.bbcan.2021.188613] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 08/09/2021] [Accepted: 08/09/2021] [Indexed: 12/18/2022]
Abstract
Rapid advances in genomic technologies have enabled in-depth interrogation of cancer genomes, revealing novel and unexpected therapeutic targets in many cancer types. Identifying actionable dependencies in the diverse and heterogeneous group of sarcomas, particularly those that occur in children or adolescents and young adults (AYAs), remains especially challenging. These patients rarely harbor actionable genomic aberrations, no targeted agent is approved, and outcomes have remained poor for the past decades. This underlines a clear need to refine our methods for target identification. Phosphoproteomics studies in sarcoma showed the power of such analyses to capture novel actionable drivers that are not accompanied by mutational events or gene amplifications. This Review makes the case that incorporating phosphoproteomic molecular profiling alongside (functional) genomics technologies can significantly expand therapeutic target identification, and pinpoint drug mechanisms of action, in pediatric and AYA sarcoma patients. We explore the utility and prospects of phosphoproteomics in personalized medicine.
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Affiliation(s)
- Ashleigh M Fordham
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Paul G Ekert
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia; School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia; Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia; Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Emmy D G Fleuren
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia; School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia.
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18
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Llorente-González C, González-Rodríguez M, Vicente-Manzanares M. Targeting cytoskeletal phosphorylation in cancer. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2021; 2:292-308. [PMID: 36046434 PMCID: PMC9400739 DOI: 10.37349/etat.2021.00047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 06/01/2021] [Indexed: 11/19/2022] Open
Abstract
Phosphorylation of cytoskeletal proteins regulates the dynamics of polymerization, stability, and disassembly of the different types of cytoskeletal polymers. These control the ability of cells to migrate and divide. Mutations and alterations of the expression levels of multiple protein kinases are hallmarks of most forms of cancer. Thus, altered phosphorylation of cytoskeletal proteins is observed in most cancer cells. These alterations potentially control the ability of cancer cells to divide, invade and form distal metastasis. This review highlights the emergent role of phosphorylation in the control of the function of the different cytoskeletal polymers in cancer cells. It also addresses the potential effect of targeted inhibitors in the normalization of cytoskeletal function.
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Affiliation(s)
- Clara Llorente-González
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007 Salamanca, Spain
| | - Marta González-Rodríguez
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007
| | - Miguel Vicente-Manzanares
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007 Salamanca, Spain
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19
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FAK Signaling in Rhabdomyosarcoma. Int J Mol Sci 2020; 21:ijms21228422. [PMID: 33182556 PMCID: PMC7697003 DOI: 10.3390/ijms21228422] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/07/2020] [Accepted: 11/08/2020] [Indexed: 01/01/2023] Open
Abstract
Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma of children and adolescents. The fusion-positive (FP)-RMS variant expressing chimeric oncoproteins such as PAX3-FOXO1 and PAX7-FOXO1 is at high risk. The fusion negative subgroup, FN-RMS, has a good prognosis when non-metastatic. Despite a multimodal therapeutic approach, FP-RMS and metastatic FN-RMS often show a dismal prognosis with 5-year survival of less than 30%. Therefore, novel targets need to be discovered to develop therapies that halt tumor progression, reducing long-term side effects in young patients. Focal adhesion kinase (FAK) is a non-receptor tyrosine kinase that regulates focal contacts at the cellular edges. It plays a role in cell motility, survival, and proliferation in response to integrin and growth factor receptors’ activation. FAK is often dysregulated in cancer, being upregulated and/or overactivated in several adult and pediatric tumor types. In RMS, both in vitro and preclinical studies point to a role of FAK in tumor cell motility/invasion and proliferation, which is inhibited by FAK inhibitors. In this review, we summarize the data on FAK expression and modulation in RMS. Moreover, we give an overview of the approaches to inhibit FAK in both preclinical and clinical cancer settings.
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20
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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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21
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Sanchez-Martin C, Serapian SA, Colombo G, Rasola A. Dynamically Shaping Chaperones. Allosteric Modulators of HSP90 Family as Regulatory Tools of Cell Metabolism in Neoplastic Progression. Front Oncol 2020; 10:1177. [PMID: 32766157 PMCID: PMC7378685 DOI: 10.3389/fonc.2020.01177] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 06/10/2020] [Indexed: 12/31/2022] Open
Abstract
Molecular chaperones have recently emerged as fundamental regulators of salient biological routines, including metabolic adaptations to environmental changes. Yet, many of the molecular mechanisms at the basis of their functions are still unknown or at least uncertain. This is in part due to the lack of chemical tools that can interact with the chaperones to induce measurable functional perturbations. In this context, the use of small molecules as modulators of protein functions has proven relevant for the investigation of a number of biomolecular systems. Herein, we focus on the functions, interactions and signaling pathways of the HSP90 family of molecular chaperones as possible targets for the discovery of new molecular entities aimed at tuning their activity and interactions. HSP90 and its mitochondrial paralog, TRAP1, regulate the activity of crucial metabolic circuitries, making cells capable of efficiently using available energy sources, with relevant implications both in healthy conditions and in a variety of disease states and especially cancer. The design of small-molecules targeting the chaperone cycle of HSP90 and able to inhibit or stimulate the activity of the protein can provide opportunities to finely dissect their biochemical activities and to obtain lead compounds to develop novel, mechanism-based drugs.
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Affiliation(s)
| | | | - Giorgio Colombo
- Dipartimento di Chimica, Università di Pavia, Pavia, Italy.,Istituto di Chimica del Riconoscimento Molecolare, CNR, Milan, Italy
| | - Andrea Rasola
- Dipartimento di Scienze Biomediche, Università di Padova, Padua, Italy
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22
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Jin W. The Role of Tyrosine Kinases as a Critical Prognostic Parameter and Its Targeted Therapies in Ewing Sarcoma. Front Cell Dev Biol 2020; 8:613. [PMID: 32754598 PMCID: PMC7381324 DOI: 10.3389/fcell.2020.00613] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 06/22/2020] [Indexed: 12/12/2022] Open
Abstract
Ewing sarcoma (ES) is a rare, highly aggressive, bone, or soft tissue-associated tumor. Although this sarcoma often responds well to initial chemotherapy, 40% of the patients develop a lethal recurrence of the disease, with death recorded in 75-80% of patients with metastatic ES within 5 years, despite receiving high-dose chemotherapy. ES is genetically well-characterized, as indicated by the EWS-FLI1 fusion protein encoded as a result of chromosomal translocation in 80-90% of patients with ES, as well as in ES-related cancer cell lines. Recently, tyrosine kinases have been identified in the pathogenesis of ES. These tyrosine kinases, acting as oncoproteins, are associated with the clinical pathogenesis, metastasis, acquisition of self-renewal traits, and chemoresistance of ES, through the activation of various intracellular signaling pathways. This review describes the recent progress related to cellular and molecular functional roles of tyrosine kinases in the progression of ES.
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Affiliation(s)
- Wook Jin
- Laboratory of Molecular Disease and Cell Regulation, Department of Biochemistry, School of Medicine, Gachon University, Incheon, South Korea
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23
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NEK10 tyrosine phosphorylates p53 and controls its transcriptional activity. Oncogene 2020; 39:5252-5266. [DOI: 10.1038/s41388-020-1361-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 06/02/2020] [Accepted: 06/08/2020] [Indexed: 11/09/2022]
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24
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Li W, Feng C, Di W, Hong S, Chen H, Ejaz M, Yang Y, Xu TR. Clinical use of vascular endothelial growth factor receptor inhibitors for the treatment of renal cell carcinoma. Eur J Med Chem 2020; 200:112482. [PMID: 32492594 DOI: 10.1016/j.ejmech.2020.112482] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 05/16/2020] [Accepted: 05/16/2020] [Indexed: 02/08/2023]
Abstract
In recent years, there have been increased incidences of metastatic renal cell carcinoma (RCC), which is refractory to conventional chemotherapy. Owing to the insensitivity to traditional therapy, targeted therapy becomes a possible alternative strategy. Over the past decade, the development of targeted treatments for metastatic RCC has advanced considerably. Several studies have shown that the vascular endothelial growth factor pathway is an important mediator for the occurrence and development of RCC, and tyrosine kinase inhibitors (TKIs) that target vascular endothelial growth factor receptors (VEGFRs) have been considered optimal therapeutic options for RCC. Six small molecules that inhibit VEGFR1/2/3, namely, sunitinib, sorafenib, axitinib, pazopanib, cabozantinib, and lenvatinib, have been approved by the Food and Drug Administration (FDA) for the treatment of RCC. Additionally, clinical trials assessing seven TKIs that target VEGFRs are currently in progress. To some extent, these drugs improve quality of life and prolong the survival of patients. This paper presents a review of the systemic targeted therapies against VEGFRs that have been approved so far or are undergoing trials as treatments for RCC.
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Affiliation(s)
- Wei Li
- Department of Urology, Affiliated Hospital of Kunming University of Science and Technology, The First People's Hospital of Yunnan Province, PR China
| | - Chengguan Feng
- Department of Urology, Affiliated Hospital of Kunming University of Science and Technology, The First People's Hospital of Yunnan Province, PR China; Faculty of Life Science and Technology, Kunming University of Science and Technology, PR China
| | - Weihong Di
- Department of Urology, Affiliated Hospital of Kunming University of Science and Technology, The First People's Hospital of Yunnan Province, PR China
| | - Shanwen Hong
- Department of Urology, Affiliated Hospital of Kunming University of Science and Technology, The First People's Hospital of Yunnan Province, PR China
| | - Hui Chen
- Department of Urology, Affiliated Hospital of Kunming University of Science and Technology, The First People's Hospital of Yunnan Province, PR China; Faculty of Life Science and Technology, Kunming University of Science and Technology, PR China
| | - Mubashir Ejaz
- Faculty of Life Science and Technology, Kunming University of Science and Technology, PR China
| | - Yang Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, PR China.
| | - Tian-Rui Xu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, PR China.
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25
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Bora-Singhal N, Mohankumar D, Saha B, Colin CM, Lee JY, Martin MW, Zheng X, Coppola D, Chellappan S. Novel HDAC11 inhibitors suppress lung adenocarcinoma stem cell self-renewal and overcome drug resistance by suppressing Sox2. Sci Rep 2020; 10:4722. [PMID: 32170113 PMCID: PMC7069992 DOI: 10.1038/s41598-020-61295-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 02/20/2020] [Indexed: 01/06/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) is known to have poor patient outcomes due to development of resistance to chemotherapy agents and the EGFR inhibitors, which results in recurrence of highly aggressive lung tumors. Even with recent success in immunotherapy using the checkpoint inhibitors, additional investigations are essential to identify novel therapeutic strategies for efficacious treatment for NSCLC. Our finding that high levels of histone deacetylase 11 (HDAC11) in human lung tumor tissues correlate with poor patient outcome and that depletion or inhibition of HDAC11 not only significantly reduces self-renewal of cancer stem cells (CSCs) from NSCLC but also decreases Sox2 expression that is essential for maintenance of CSCs, indicates that HDAC11 is a potential target to combat NSCLC. We find that HDAC11 suppresses Sox2 expression through the mediation of Gli1, the Hedgehog pathway transcription factor. In addition, we have used highly selective HDAC11 inhibitors that not only target stemness and adherence independent growth of lung cancer cells but these inhibitors could also efficiently ablate the growth of drug-insensitive stem-like cells as well as therapy resistant lung cancer cells. These inhibitors were found to be efficacious even in presence of cancer associated fibroblasts which have been shown to contribute in therapy resistance. Our study presents a novel role of HDAC11 in lung adenocarcinoma progression and the potential use of highly selective inhibitors of HDAC11 in combating lung cancers.
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Affiliation(s)
- Namrata Bora-Singhal
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Durairaj Mohankumar
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Biswarup Saha
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Christelle M Colin
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Jennifer Y Lee
- FORMA Therapeutics, 500 Arsenal St, Suite 100, Watertown, MA, 02472, USA
| | - Matthew W Martin
- FORMA Therapeutics, 500 Arsenal St, Suite 100, Watertown, MA, 02472, USA
| | - Xiaozhang Zheng
- FORMA Therapeutics, 500 Arsenal St, Suite 100, Watertown, MA, 02472, USA
| | - Domenico Coppola
- Department of Anatomic Pathology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Srikumar Chellappan
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612, USA.
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26
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AXL as a Target in Breast Cancer Therapy. JOURNAL OF ONCOLOGY 2020; 2020:5291952. [PMID: 32148495 PMCID: PMC7042526 DOI: 10.1155/2020/5291952] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 01/18/2020] [Indexed: 12/21/2022]
Abstract
AXL is a receptor tyrosine kinase (RTK) that has been implicated in diverse tumor-promoting processes such as proliferation, migration, invasion, survival, and apoptosis. AXL therefore plays a role in cancer progression, and AXL has been implicated in a wide variety of malignancies from solid tumors to hematopoietic cancers where it is often associated with poor prognosis. In cancer, AXL has been shown to promote epithelial to mesenchymal transition (EMT), metastasis formation, drug resistance, and a role for AXL in modulation of the tumor microenvironment and immune response has been identified. In light of these activities multiple AXL inhibitors have been developed, and several of these have entered clinical trials in the U.S. In breast cancer, high levels of AXL expression have been observed. The role of AXL in cancer with a focus on therapeutic implications for breast cancer is discussed.
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27
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Wasinski B, Sohail A, Bonfil RD, Kim S, Saliganan A, Polin L, Bouhamdan M, Kim HRC, Prunotto M, Fridman R. Discoidin Domain Receptors, DDR1b and DDR2, Promote Tumour Growth within Collagen but DDR1b Suppresses Experimental Lung Metastasis in HT1080 Xenografts. Sci Rep 2020; 10:2309. [PMID: 32047176 PMCID: PMC7012844 DOI: 10.1038/s41598-020-59028-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 01/20/2020] [Indexed: 12/17/2022] Open
Abstract
The Discoidin Domain Receptors (DDRs) constitute a unique set of receptor tyrosine kinases that signal in response to collagen. Using an inducible expression system in human HT1080 fibrosarcoma cells, we investigated the role of DDR1b and DDR2 on primary tumour growth and experimental lung metastases. Neither DDR1b nor DDR2 expression altered tumour growth at the primary site. However, implantation of DDR1b- or DDR2-expressing HT1080 cells with collagen I significantly accelerated tumour growth rate, an effect that could not be observed with collagen I in the absence of DDR induction. Interestingly, DDR1b, but not DDR2, completely hindered the ability of HT1080 cells to form lung colonies after intravenous inoculation, suggesting a differential role for DDR1b in primary tumour growth and lung colonization. Analyses of tumour extracts revealed specific alterations in Hippo pathway core components, as a function of DDR and collagen expression, that were associated with stimulation of tumour growth by DDRs and collagen I. Collectively, these findings identified divergent effects of DDRs on primary tumour growth and experimental lung metastasis in the HT1080 xenograft model and highlight the critical role of fibrillar collagen and DDRs in supporting the growth of tumours thriving within a collagen-rich stroma.
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Affiliation(s)
- Benjamin Wasinski
- Department of Pathology, Wayne State University School of Medicine and Karmanos Cancer Institute, Detroit, MI, 48201, USA
| | - Anjum Sohail
- Department of Pathology, Wayne State University School of Medicine and Karmanos Cancer Institute, Detroit, MI, 48201, USA
| | - R Daniel Bonfil
- Department of Pathology, Wayne State University School of Medicine and Karmanos Cancer Institute, Detroit, MI, 48201, USA.,Department of Urology, Wayne State University School of Medicine and Karmanos Cancer Institute, Detroit, MI, 48201, USA.,Department of Oncology, Wayne State University School of Medicine and Karmanos Cancer Institute, Detroit, MI, 48201, USA.,Department of Pathology, College of Medical Sciences and Dr. Kiran C. Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, 33328-2018, USA
| | - Seongho Kim
- Department of Oncology, Wayne State University School of Medicine and Karmanos Cancer Institute, Detroit, MI, 48201, USA
| | - Allen Saliganan
- Department of Urology, Wayne State University School of Medicine and Karmanos Cancer Institute, Detroit, MI, 48201, USA
| | - Lisa Polin
- Department of Oncology, Wayne State University School of Medicine and Karmanos Cancer Institute, Detroit, MI, 48201, USA
| | - Mohamad Bouhamdan
- Department of Pathology, Wayne State University School of Medicine and Karmanos Cancer Institute, Detroit, MI, 48201, USA
| | - Hyeong-Reh C Kim
- Department of Pathology, Wayne State University School of Medicine and Karmanos Cancer Institute, Detroit, MI, 48201, USA.,Department of Oncology, Wayne State University School of Medicine and Karmanos Cancer Institute, Detroit, MI, 48201, USA
| | - Marco Prunotto
- Hoffmann-La Roche, Basel, Switzerland.,School of Pharmaceutical Sciences, Geneva, Switzerland
| | - Rafael Fridman
- Department of Pathology, Wayne State University School of Medicine and Karmanos Cancer Institute, Detroit, MI, 48201, USA. .,Department of Oncology, Wayne State University School of Medicine and Karmanos Cancer Institute, Detroit, MI, 48201, USA.
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28
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Receptor Tyrosine Kinases in Osteosarcoma: 2019 Update. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1258:141-155. [PMID: 32767239 DOI: 10.1007/978-3-030-43085-6_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The primary conclusions of our 2014 contribution to this series were as follows: Multiple receptor tyrosine kinases (RTKs) likely contribute to aggressive phenotypes in osteosarcoma and, therefore, inhibition of multiple RTKs is likely necessary for successful clinical outcomes. Inhibition of multiple RTKs may also be useful to overcome resistance to inhibitors of individual RTKs as well as resistance to conventional chemotherapies. Different combinations of RTKs are likely important in individual patients. AXL, EPHB2, FGFR2, IGF1R, and RET were identified as promising therapeutic targets by our in vitro phosphoproteomic/siRNA screen of 42 RTKs in the highly metastatic LM7 and 143B human osteosarcoma cell lines. This chapter is intended to provide an update on these topics as well as the large number of osteosarcoma clinical studies of inhibitors of multiple tyrosine kinases (multi-TKIs) that were recently published.
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29
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Intramitochondrial Src kinase links mitochondrial dysfunctions and aggressiveness of breast cancer cells. Cell Death Dis 2019; 10:940. [PMID: 31819039 PMCID: PMC6901437 DOI: 10.1038/s41419-019-2134-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 10/09/2019] [Accepted: 11/06/2019] [Indexed: 12/13/2022]
Abstract
High levels and activity of Src kinase are common among breast cancer subtypes, and several inhibitors of the kinase are currently tested in clinical trials. Alterations in mitochondrial activity is also observed among the different types of breast cancer. Src kinase is localized in several subcellular compartments, including mitochondria where it targets several proteins to modulate the activity of the organelle. Although the subcellular localization of other oncogenes modulates the potency of known treatments, nothing is known about the specific role of intra-mitochondrial Src (mtSrc) in breast cancer. The aim of this work was to determine whether mtSrc kinase has specific impact on breast cancer cells. We first observed that activity of mtSrc is higher in breast cancer cells of the triple negative subtype. Over-expression of Src specifically targeted to mitochondria reduced mtDNA levels, mitochondrial membrane potential and cellular respiration. These alterations of mitochondrial functions led to lower cellular viability, shorter cell cycle and increased invasive capacity. Proteomic analyses revealed that mtSrc targets the mitochondrial single-stranded DNA-binding protein, a regulator of mtDNA replication. Our findings suggest that mtSrc promotes aggressiveness of breast cancer cells via phosphorylation of mitochondrial single-stranded DNA-binding protein leading to reduced mtDNA levels and mitochondrial activity. This study highlights the importance of considering the subcellular localization of Src kinase in the development of potent therapy for breast cancer.
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30
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Antfolk D, Antila C, Kemppainen K, Landor SKJ, Sahlgren C. Decoding the PTM-switchboard of Notch. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:118507. [PMID: 31301363 PMCID: PMC7116576 DOI: 10.1016/j.bbamcr.2019.07.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 07/03/2019] [Accepted: 07/06/2019] [Indexed: 01/08/2023]
Abstract
The developmentally indispensable Notch pathway exhibits a high grade of pleiotropism in its biological output. Emerging evidence supports the notion of post-translational modifications (PTMs) as a modus operandi controlling dynamic fine-tuning of Notch activity. Although, the intricacy of Notch post-translational regulation, as well as how these modifications lead to multiples of divergent Notch phenotypes is still largely unknown, numerous studies show a correlation between the site of modification and the output. These include glycosylation of the extracellular domain of Notch modulating ligand binding, and phosphorylation of the PEST domain controlling half-life of the intracellular domain of Notch. Furthermore, several reports show that multiple PTMs can act in concert, or compete for the same sites to drive opposite outputs. However, further investigation of the complex PTM crosstalk is required for a complete understanding of the PTM-mediated Notch switchboard. In this review, we aim to provide a consistent and up-to-date summary of the currently known PTMs acting on the Notch signaling pathway, their functions in different contexts, as well as explore their implications in physiology and disease. Furthermore, we give an overview of the present state of PTM research methodology, and allude to a future with PTM-targeted Notch therapeutics.
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Affiliation(s)
- Daniel Antfolk
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
| | - Christian Antila
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
| | - Kati Kemppainen
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
| | - Sebastian K-J Landor
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland.
| | - Cecilia Sahlgren
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland; Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands.
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31
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Yin LM, Ulloa L, Yang YQ. Transgelin-2: Biochemical and Clinical Implications in Cancer and Asthma. Trends Biochem Sci 2019; 44:885-896. [PMID: 31256982 DOI: 10.1016/j.tibs.2019.05.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 05/22/2019] [Accepted: 05/30/2019] [Indexed: 12/29/2022]
Abstract
Transgelin-2 has been regarded as an actin-binding protein that induces actin gelation and regulates actin cytoskeleton. However, transgelin-2 has recently been shown to relax the myosin cytoskeleton of the airway smooth muscle cells by acting as a receptor for extracellular metallothionein-2. From a clinical perspective, these results support transgelin-2 as a promising therapeutic target for diseases such as cancer and asthma. The inhibition of transgelin-2 prevents actin gelation and thereby cancer cell proliferation, invasion, and metastasis. Conversely, the activation of transgelin-2 with specific agonists relaxes airway smooth muscles and reduces pulmonary resistance in asthma. Here, we review new studies on the biochemical properties of transgelin-2 and discuss their clinical implications for the treatment of immune, oncogenic, and respiratory disorders.
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Affiliation(s)
- Lei-Miao Yin
- Yueyang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200030, China
| | - Luis Ulloa
- International Laboratory of Neuro-Immunomodulation, Shanghai University of Traditional Chinese Medicine, Shanghai 200030, China; Center of Immunology and Inflammation, Dept. of Surgery. Rutgers University-New Jersey Medical School, Newark, NJ 07101, USA.
| | - Yong-Qing Yang
- Yueyang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200030, China.
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32
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Galliou PA, Verrou KM, Koliakos G. Phosphorylation mapping of laminin α1-chain: Kinases in association with active sites. Comput Biol Chem 2019; 80:480-497. [PMID: 31174160 DOI: 10.1016/j.compbiolchem.2019.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 04/25/2019] [Indexed: 11/25/2022]
Abstract
Laminin-111 is a trimeric glycoprotein of the extracellular matrix (ECM) that holds a significant role in cell adhesion, migration and differentiation. Laminin-111 is the most studied laminin isoform, composed of three chains; α1, β1 and γ1. Phosphorylation is the most common eukaryotic post - translational modification and has regulatory effect on protein function. Using bioinformatic tools we computationally predicted all the possible phosphorylation sites on human laminin α1-chain sequence (LAMA1) according to kinases binding motifs. Thus, we predicted, for the first time, the possibly responsible kinases for fifteen of the nineteen already published experimentally observed phosphorylated residues in LAMA1. Searching the literature extensively, we recorded all the known functional sites (active sites) in LAMA1. We combined the experimentally observed and predicted phosphorylated residues as well as the active sites in LAMA1, generating an analytic phosphorylation map of human laminin α1-chain, which is useful for further analysis. Our results indicated fourteen kinases that might be important for the phosphorylation of human laminin α1-chain, out of which three kinases with reported ecto-phosphorylation activity (PKA, PKC and CKII) were suggested to have a more significant role. Six cancer associated-active sites were correlated with kinases, three out which were correlated with only the above ecto - kinases.
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Affiliation(s)
- Panagiota Angeliki Galliou
- Laboratory of Biological Chemistry, Medical School, Aristotle University of Thessaloniki, 54124, Greece..
| | - Kleio-Maria Verrou
- Laboratory of Biological Chemistry, Medical School, Aristotle University of Thessaloniki, 54124, Greece.; School of Medicine, University of Crete, 71500, Greece..
| | - George Koliakos
- Laboratory of Biological Chemistry, Medical School, Aristotle University of Thessaloniki, 54124, Greece..
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33
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Da Q, Han H, Valladolid C, Fernández M, Khatlani T, Pradhan S, Nolasco J, Matsunami RK, Engler DA, Cruz MA, Vijayan KV. In vitro phosphorylation of von Willebrand factor by FAM20c enhances its ability to support platelet adhesion. J Thromb Haemost 2019; 17:866-877. [PMID: 30864273 PMCID: PMC6545126 DOI: 10.1111/jth.14426] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Indexed: 11/30/2022]
Abstract
Essentials Platelet adhesion to von Willebrand factor (VWF) is critical for hemostasis and thrombosis. Whether VWF can undergo phosphorylation is unknown. Family with sequence similarity 20 kinase phosphorylates VWF A2 domain at S1517 and S1613. Phosphorylation of VWF and VWF A1A2A3 domain at S1613 enhances platelet adhesion. SUMMARY: Background von Willebrand factor (VWF) mediates platelet adhesion and contributes to hemostasis at sites of vascular injury as well as to arterial thrombosis. The A1A2A3 domains of VWF contain important sites that differentially participate in supporting platelet adhesion. FAM20c (family with sequence similarity 20, member C) has emerged as a serine/threonine kinase, which phosphorylates extracellular proteins containing the S-X-E/pS motifs that are also found within the VWF A domains. This is of interest because we and others have shown that structural modifications within these A domains influence the ability of VWF to support platelet adhesion. Objective We assessed if VWF A domains can be phosphorylated and the functional consequence of phosphorylated VWF. Results Here, we show that FAM20c phosphorylated purified plasma VWF, VWF A1A2A3 protein, isolated A2 domain, but not A1 and A3 domain proteins, in vitro. FAM20c phosphorylated the isolated A2 domain at S1517 and S1613 within the S-X-E recognition motif, with S1613 being the major phosphorylation site. Mass spectrometry analysis of purified plasma VWF from healthy donors revealed several phosphorylation sites, including the S1613 in the A2 domain. VWF A1A2A3 domain protein phosphorylated at S1613 promoted stable platelet adhesion and microthrombi at high shear stress. Lastly, under high shear stress VWF treated with FAM20c and ATP robustly supported platelet adhesion, compared to VWF treated with FAM20c in the absence of ATP. Conclusion These outcomes indicate that VWF can be phosphorylated by FAM20c in vitro, and this novel post-translational modification enhances the adhesiveness of VWF to platelets.
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Affiliation(s)
- Qi Da
- Department of Medicine, Houston, TX 77030, U.S.A
- Center for Translational Research on Inflammatory Diseases (CTRID), Michael E. DeBakey Veterans Affairs Medical Center (MEDVAMC), Houston, TX 77030, U.S.A
| | - Hyojeong Han
- Department of Pediatrics, Houston, TX 77030, U.S.A
- Center for Translational Research on Inflammatory Diseases (CTRID), Michael E. DeBakey Veterans Affairs Medical Center (MEDVAMC), Houston, TX 77030, U.S.A
| | - Christian Valladolid
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, U.S.A
- Center for Translational Research on Inflammatory Diseases (CTRID), Michael E. DeBakey Veterans Affairs Medical Center (MEDVAMC), Houston, TX 77030, U.S.A
| | - María Fernández
- Department of Medicine, Houston, TX 77030, U.S.A
- Center for Translational Research on Inflammatory Diseases (CTRID), Michael E. DeBakey Veterans Affairs Medical Center (MEDVAMC), Houston, TX 77030, U.S.A
| | - Tanvir Khatlani
- Department of Medicine, Houston, TX 77030, U.S.A
- Center for Translational Research on Inflammatory Diseases (CTRID), Michael E. DeBakey Veterans Affairs Medical Center (MEDVAMC), Houston, TX 77030, U.S.A
- Present address: King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard Health Affairs, Riyadh, KSA
| | - Subhashree Pradhan
- Department of Medicine, Houston, TX 77030, U.S.A
- Center for Translational Research on Inflammatory Diseases (CTRID), Michael E. DeBakey Veterans Affairs Medical Center (MEDVAMC), Houston, TX 77030, U.S.A
| | - Jennifer Nolasco
- Department of Medicine, Houston, TX 77030, U.S.A
- Center for Translational Research on Inflammatory Diseases (CTRID), Michael E. DeBakey Veterans Affairs Medical Center (MEDVAMC), Houston, TX 77030, U.S.A
| | - Risë K. Matsunami
- Department of Houston Methodist Hospital Research Institute, Houston, TX 77030, U.S.A
| | - David A Engler
- Department of Houston Methodist Hospital Research Institute, Houston, TX 77030, U.S.A
| | - Miguel A. Cruz
- Department of Medicine, Houston, TX 77030, U.S.A
- Department of Pediatrics, Houston, TX 77030, U.S.A
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, U.S.A
- Center for Translational Research on Inflammatory Diseases (CTRID), Michael E. DeBakey Veterans Affairs Medical Center (MEDVAMC), Houston, TX 77030, U.S.A
| | - K. Vinod Vijayan
- Department of Medicine, Houston, TX 77030, U.S.A
- Department of Pediatrics, Houston, TX 77030, U.S.A
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, U.S.A
- Center for Translational Research on Inflammatory Diseases (CTRID), Michael E. DeBakey Veterans Affairs Medical Center (MEDVAMC), Houston, TX 77030, U.S.A
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Beekhof R, van Alphen C, Henneman AA, Knol JC, Pham TV, Rolfs F, Labots M, Henneberry E, Le Large TY, de Haas RR, Piersma SR, Vurchio V, Bertotti A, Trusolino L, Verheul HM, Jimenez CR. INKA, an integrative data analysis pipeline for phosphoproteomic inference of active kinases. Mol Syst Biol 2019; 15:e8250. [PMID: 30979792 PMCID: PMC6461034 DOI: 10.15252/msb.20188250] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 03/15/2019] [Accepted: 03/20/2019] [Indexed: 12/19/2022] Open
Abstract
Identifying hyperactive kinases in cancer is crucial for individualized treatment with specific inhibitors. Kinase activity can be discerned from global protein phosphorylation profiles obtained with mass spectrometry-based phosphoproteomics. A major challenge is to relate such profiles to specific hyperactive kinases fueling growth/progression of individual tumors. Hitherto, the focus has been on phosphorylation of either kinases or their substrates. Here, we combined label-free kinase-centric and substrate-centric information in an Integrative Inferred Kinase Activity (INKA) analysis. This multipronged, stringent analysis enables ranking of kinase activity and visualization of kinase-substrate networks in a single biological sample. To demonstrate utility, we analyzed (i) cancer cell lines with known oncogenes, (ii) cell lines in a differential setting (wild-type versus mutant, +/- drug), (iii) pre- and on-treatment tumor needle biopsies, (iv) cancer cell panel with available drug sensitivity data, and (v) patient-derived tumor xenografts with INKA-guided drug selection and testing. These analyses show superior performance of INKA over its components and substrate-based single-sample tool KARP, and underscore target potential of high-ranking kinases, encouraging further exploration of INKA's functional and clinical value.
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Affiliation(s)
- Robin Beekhof
- Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Carolien van Alphen
- Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Alex A Henneman
- Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Jaco C Knol
- Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Thang V Pham
- Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Frank Rolfs
- Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Mariette Labots
- Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Evan Henneberry
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Tessa Ys Le Large
- Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Richard R de Haas
- Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Sander R Piersma
- Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Valentina Vurchio
- Department of Oncology, Candiolo Cancer Institute IRCCS, University of Torino, Torino, Italy
| | - Andrea Bertotti
- Department of Oncology, Candiolo Cancer Institute IRCCS, University of Torino, Torino, Italy
| | - Livio Trusolino
- Department of Oncology, Candiolo Cancer Institute IRCCS, University of Torino, Torino, Italy
| | - Henk Mw Verheul
- Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Connie R Jimenez
- Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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35
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Signals Getting Crossed in the Entanglement of Redox and Phosphorylation Pathways: Phosphorylation of Peroxiredoxin Proteins Sparks Cell Signaling. Antioxidants (Basel) 2019; 8:antiox8020029. [PMID: 30678096 PMCID: PMC6406269 DOI: 10.3390/antiox8020029] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 01/16/2019] [Accepted: 01/18/2019] [Indexed: 12/13/2022] Open
Abstract
Reactive oxygen and nitrogen species have cell signaling properties and are involved in a multitude of processes beyond redox homeostasis. The peroxiredoxin (Prdx) proteins are highly sensitive intracellular peroxidases that can coordinate cell signaling via direct reactive species scavenging or by acting as a redox sensor that enables control of binding partner activity. Oxidation of the peroxidatic cysteine residue of Prdx proteins are the classical post-translational modification that has been recognized to modulate downstream signaling cascades, but increasing evidence supports that dynamic changes to phosphorylation of Prdx proteins is also an important determinant in redox signaling. Phosphorylation of Prdx proteins affects three-dimensional structure and function to coordinate cell proliferation, wound healing, cell fate and lipid signaling. The advent of large proteomic datasets has shown that there are many opportunities to understand further how phosphorylation of Prdx proteins fit into intracellular signaling cascades in normal or malignant cells and that more research is necessary. This review summarizes the Prdx family of proteins and details how post-translational modification by kinases and phosphatases controls intracellular signaling.
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36
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Brambilla D, Chiari M, Gori A, Cretich M. Towards precision medicine: the role and potential of protein and peptide microarrays. Analyst 2019; 144:5353-5367. [DOI: 10.1039/c9an01142k] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Techniques to comprehensively analyze protein signatures are pivotal to unravel disease mechanisms, develop novel biomarkers and targeted therapies. In this frame, protein and peptide microarrays can play a major role in fuelling precision medicine.
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Affiliation(s)
- Dario Brambilla
- Consiglio Nazionale delle Ricerche
- Istituto di Chimica del Riconoscimento Molecolare (ICRM)
- Milano
- Italy
| | - Marcella Chiari
- Consiglio Nazionale delle Ricerche
- Istituto di Chimica del Riconoscimento Molecolare (ICRM)
- Milano
- Italy
| | - Alessandro Gori
- Consiglio Nazionale delle Ricerche
- Istituto di Chimica del Riconoscimento Molecolare (ICRM)
- Milano
- Italy
| | - Marina Cretich
- Consiglio Nazionale delle Ricerche
- Istituto di Chimica del Riconoscimento Molecolare (ICRM)
- Milano
- Italy
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37
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An N-Terminal Extension to UBA5 Adenylation Domain Boosts UFM1 Activation: Isoform-Specific Differences in Ubiquitin-like Protein Activation. J Mol Biol 2018; 431:463-478. [PMID: 30412706 DOI: 10.1016/j.jmb.2018.10.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/15/2018] [Accepted: 10/17/2018] [Indexed: 01/06/2023]
Abstract
Modification of proteins by the ubiquitin-like protein, UFM1, requires activation of UFM1 by the E1-activating enzyme, UBA5. In humans, UBA5 possesses two isoforms, each comprising an adenylation domain, but only one containing an N-terminal extension. Currently, the role of the N-terminal extension in UFM1 activation is not clear. Here we provide structural and biochemical data on UBA5 N-terminal extension to understand its contribution to UFM1 activation. The crystal structures of the UBA5 long isoform bound to ATP with and without UFM1 show that the N-terminus not only is directly involved in ATP binding but also affects how the adenylation domain interacts with ATP. Surprisingly, in the presence of the N-terminus, UBA5 no longer retains the 1:2 ratio of ATP to UBA5, but rather this becomes a 1:1 ratio. Accordingly, the N-terminus significantly increases the affinity of ATP to UBA5. Finally, the N-terminus, although not directly involved in the E2 binding, stimulates transfer of UFM1 from UBA5 to the E2, UFC1.
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38
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Abstract
Notch signaling is a form of intercellular communication which plays pivotal roles at various stages in development and disease. Previous findings have hinted that integrins and extracellular matrix may regulate Notch signaling, although a mechanistic basis for this interaction had not been identified. Here, we reveal that the regulation of Notch by integrins and extracellular matrix is carried out by Src family kinases (SFKs) working downstream of integrins. We identify a physical interaction between the SFK member, c-Src, and the Notch intracellular domain (NICD) that is enhanced by β3 integrin and the integrin binding ECM protein, MAGP2. Our results demonstrate that c-Src directly phosphorylates the NICD at specific tyrosine residues and that mutation of these phosphorylation sites increases Notch responsive transcriptional activity. Furthermore, we also find that phosphorylation of the NICD by SFKs attenuates Notch mediated transcription by decreasing recruitment of MAML to the Notch co-transcriptional complex. Finally, we also find that SFK activity decreases NICD half-life. Collectively, our results provide important mechanistic data that underlie the emerging role of Notch as a general sensor and responder to extracellular signals.
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39
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Patwardhan PP, Musi E, Schwartz GK. Preclinical Evaluation of Nintedanib, a Triple Angiokinase Inhibitor, in Soft-tissue Sarcoma: Potential Therapeutic Implication for Synovial Sarcoma. Mol Cancer Ther 2018; 17:2329-2340. [PMID: 30166401 DOI: 10.1158/1535-7163.mct-18-0319] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 07/25/2018] [Accepted: 08/21/2018] [Indexed: 11/16/2022]
Abstract
Sarcomas are rare cancers that make up about 1% of all cancers in adults; however, they occur more commonly among children and young adolescents. Sarcomas are genetically complex and are often difficult to treat given the lack of clinical efficacy of any of the currently available therapies. Receptor tyrosine kinases (RTK) such as c-Kit, c-Met, PDGFR, IGF-1R, as well as FGFR have all been reported to be involved in driving tumor development and progression in adult and pediatric soft-tissue sarcoma. These driver kinases often act as critical determinants of tumor cell proliferation and targeting these signal transduction pathways remains an attractive therapeutic approach. Nintedanib, a potent triple angiokinase inhibitor, targets PDGFR, VEGFR, and FGFR pathways critical for tumor angiogenesis and vasculature. In this study, we evaluated the preclinical efficacy of nintedanib in soft-tissue sarcoma cell lines. Nintedanib treatment resulted in significant antiproliferative effect in vitro in cell lines with high expression of RTK drug targets. Furthermore, treatment with nintedanib showed significant downregulation of downstream phosphorylated AKT and ERK1/2. Finally, treatment with nintedanib resulted in significant tumor growth suppression in mouse xenograft model of synovial sarcoma. Notably, both the in vitro and in vivo efficacy of nintedanib was superior to that of imatinib, another multikinase inhibitor, previously tested with minimal success in clinical trials in sarcoma. Overall, the data from this study provide a strong rationale to warrant further clinical exploration of this drug in patients with synovial sarcoma. Mol Cancer Ther; 17(11); 2329-40. ©2018 AACR.
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Affiliation(s)
- Parag P Patwardhan
- Department of Medicine, Columbia University Medical Center, New York, New York.
| | - Elgilda Musi
- Department of Medicine, Columbia University Medical Center, New York, New York
| | - Gary K Schwartz
- Department of Medicine, Columbia University Medical Center, New York, New York.,Herbert Irving Comprehensive Cancer Center, Columbia University College of Medicine, New York, New York
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40
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Steinberg SF. Post-translational modifications at the ATP-positioning G-loop that regulate protein kinase activity. Pharmacol Res 2018; 135:181-187. [PMID: 30048755 DOI: 10.1016/j.phrs.2018.07.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 07/10/2018] [Accepted: 07/11/2018] [Indexed: 12/27/2022]
Abstract
Protein kinases are a superfamily of enzymes that control a wide range of cellular functions. These enzymes share a highly conserved catalytic core that folds into a similar bilobar three-dimensional structure. One highly conserved region in the protein kinase core is the glycine-rich loop (or G-loop), a highly flexible loop that is characterized by a consensus GxGxxG sequence. The G-loop points toward the catalytic cleft and functions to bind and position ATP for phosphotransfer. Of note, in many protein kinases, the second and third glycine residues in the G-loop triad flank residues that can be targets for phosphorylation (Ser, Thr, or Tyr) or other post-translational modifications (ubiquitination, acetylation, O-GlcNAcylation, oxidation). There is considerable evidence that cyclin-dependent kinases are held inactive through inhibitory phosphorylation of the conserved Thr/Tyr residues in this position of the G-loop and that dephosphorylation by cellular phosphatases is required for CDK activation and progression through the cell cycle. This review summarizes literature that identifies residues in or adjacent to the G-loop in other protein kinases that are targets for functionally important post-translational modifications.
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Affiliation(s)
- Susan F Steinberg
- Department of Pharmacology, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY 10032, USA.
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41
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Chen Y, Zhang Y, Guo X. Proteasome dysregulation in human cancer: implications for clinical therapies. Cancer Metastasis Rev 2018; 36:703-716. [PMID: 29039081 DOI: 10.1007/s10555-017-9704-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cancer cells show heightened dependency on the proteasome for their survival, growth, and spread. Proteasome dysregulation is therefore commonly selected in favor of the development of many types of cancer. The vast abnormalities in a cancer cell, on top of the complexity of the proteasome itself, have enabled a plethora of mechanisms gearing the proteasome to the oncogenic process. Here, we use selected examples to highlight some general mechanisms underlying proteasome dysregulation in cancer, including copy number variations, transcriptional control, epigenetic regulation, and post-translational modifications. Research in this field has greatly advanced our understanding of proteasome regulation and will shed new light on proteasome-based combination therapies for cancer treatment.
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Affiliation(s)
- Yulin Chen
- Life Sciences Institute of Zhejiang University, 866 Yuhangtang Rd, Hangzhou, 310058, China
| | - Yanan Zhang
- Life Sciences Institute of Zhejiang University, 866 Yuhangtang Rd, Hangzhou, 310058, China
| | - Xing Guo
- Life Sciences Institute of Zhejiang University, 866 Yuhangtang Rd, Hangzhou, 310058, China.
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42
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Cassinelli G, Favini E, Dal Bo L, Tortoreto M, De Maglie M, Dagrada G, Pilotti S, Zunino F, Zaffaroni N, Lanzi C. Antitumor efficacy of the heparan sulfate mimic roneparstat (SST0001) against sarcoma models involves multi-target inhibition of receptor tyrosine kinases. Oncotarget 2018; 7:47848-47863. [PMID: 27374103 PMCID: PMC5216983 DOI: 10.18632/oncotarget.10292] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 05/08/2016] [Indexed: 12/20/2022] Open
Abstract
The heparan sulfate (HS) mimic/heparanase inhibitor roneparstat (SST0001) shows antitumor activity in preclinical sarcoma models. We hypothesized that this 100% N-acetylated and glycol-split heparin could interfere with the functions of several receptor tyrosine kinases (RTK) coexpressed in sarcomas and activated by heparin-binding growth factors. Using a phospho-proteomic approach, we investigated the drug effects on RTK activation in human cell lines representative of different sarcoma subtypes. Inhibition of FGF, IGF, ERBB and PDGF receptors by the drug was biochemically and functionally validated. Roneparstat counteracted the autocrine loop induced by the COL1A1/PDGFB fusion oncogene, expressed in a human dermatofibrosarcoma protuberans primary culture and in NIH3T3COL1A1/PDGFB transfectants, inhibiting cell anchorage-independent growth and invasion. In addition, roneparstat inhibited the activation of cell surface PDGFR and PDGFR-associated FAK, likely contributing to the reversion of NIH3T3COL1A1/PDGFB cell transformed and pro-invasive phenotype. Biochemical and histological/immunohistochemical ex vivo analyses confirmed a reduced activation of ERBB4, EGFR, INSR, IGF1R, associated with apoptosis induction and angiogenesis inhibition in a drug-treated Ewing's sarcoma family tumor xenograft. The combination of roneparstat with irinotecan significantly improved the antitumor effect against A204 rhabdoid xenografts resulting in a high rate of complete responses and cures. These findings reveal that roneparstat exerts a multi-target inhibition of RTKs relevant in the pathobiology of different sarcoma subtypes. These effects, likely cooperating with heparanase inhibition, contribute to the antitumor efficacy of the drug. The study supports heparanase/HS axis targeting as a valuable approach in combination therapies of different sarcoma subtypes providing a preclinical rationale for clinical investigation.
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Affiliation(s)
- Giuliana Cassinelli
- Molecular Pharmacology Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Enrica Favini
- Molecular Pharmacology Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Laura Dal Bo
- Molecular Pharmacology Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Monica Tortoreto
- Molecular Pharmacology Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Marcella De Maglie
- Department of Veterinary Sciences and Public Health, Università Degli Studi di Milano, Milan, Italy.,Mouse and Animal Pathology Laboratory, Fondazione Filarete, Milan, Italy
| | - Gianpaolo Dagrada
- Laboratory of Experimental Molecular Pathology, Department of Diagnostic Pathology and Laboratory, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Silvana Pilotti
- Laboratory of Experimental Molecular Pathology, Department of Diagnostic Pathology and Laboratory, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Franco Zunino
- Molecular Pharmacology Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Nadia Zaffaroni
- Molecular Pharmacology Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Cinzia Lanzi
- Molecular Pharmacology Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
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43
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Wong JP, Todd JR, Finetti MA, McCarthy F, Broncel M, Vyse S, Luczynski MT, Crosier S, Ryall KA, Holmes K, Payne LS, Daley F, Wai P, Jenks A, Tanos B, Tan AC, Natrajan RC, Williamson D, Huang PH. Dual Targeting of PDGFRα and FGFR1 Displays Synergistic Efficacy in Malignant Rhabdoid Tumors. Cell Rep 2017; 17:1265-1275. [PMID: 27783942 PMCID: PMC5098123 DOI: 10.1016/j.celrep.2016.10.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 08/07/2016] [Accepted: 09/30/2016] [Indexed: 12/13/2022] Open
Abstract
Subunits of the SWI/SNF chromatin remodeling complex are mutated in a significant proportion of human cancers. Malignant rhabdoid tumors (MRTs) are lethal pediatric cancers characterized by a deficiency in the SWI/SNF subunit SMARCB1. Here, we employ an integrated molecular profiling and chemical biology approach to demonstrate that the receptor tyrosine kinases (RTKs) PDGFRα and FGFR1 are coactivated in MRT cells and that dual blockade of these receptors has synergistic efficacy. Inhibitor combinations targeting both receptors and the dual inhibitor ponatinib suppress the AKT and ERK1/2 pathways leading to apoptosis. MRT cells that have acquired resistance to the PDGFRα inhibitor pazopanib are susceptible to FGFR inhibitors. We show that PDGFRα levels are regulated by SMARCB1 expression, and assessment of clinical specimens documents the expression of both PDGFRα and FGFR1 in rhabdoid tumor patients. Our findings support a therapeutic approach in cancers with SWI/SNF deficiencies by exploiting RTK coactivation dependencies. Malignant rhabdoid tumors display coactivation of PDGFRα and FGFR1 Dual inhibition of PDGFRα and FGFR1 leads to synergistic apoptosis FGFR1 inhibition overcomes acquired resistance to pazopanib treatment PDGFRα and FGFR1 are expressed in rhabdoid tumor patient specimens
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Affiliation(s)
- Jocelyn P Wong
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, UK
| | - Jason R Todd
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, UK
| | - Martina A Finetti
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne NE1 4LP, UK
| | - Frank McCarthy
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, UK
| | - Malgorzata Broncel
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, UK
| | - Simon Vyse
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, UK
| | - Maciej T Luczynski
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, UK
| | - Stephen Crosier
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne NE1 4LP, UK
| | - Karen A Ryall
- Translational Bioinformatics and Cancer Systems Biology Laboratory, Division of Medical Oncology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kate Holmes
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, UK
| | - Leo S Payne
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, UK
| | - Frances Daley
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer Research, The Institute of Cancer Research, London SW3 6JB, UK
| | - Patty Wai
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer Research, The Institute of Cancer Research, London SW3 6JB, UK
| | - Andrew Jenks
- Division of Cancer Therapeutics, The Institute of Cancer Research, London SW3 6JB, UK
| | - Barbara Tanos
- Division of Cancer Therapeutics, The Institute of Cancer Research, London SW3 6JB, UK
| | - Aik-Choon Tan
- Translational Bioinformatics and Cancer Systems Biology Laboratory, Division of Medical Oncology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Rachael C Natrajan
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer Research, The Institute of Cancer Research, London SW3 6JB, UK
| | - Daniel Williamson
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne NE1 4LP, UK
| | - Paul H Huang
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, UK.
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44
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Klinghammer K, Keller J, George J, Hoffmann J, Chan EL, Hayman MJ. A phosphoarray platform is capable of personalizing kinase inhibitor therapy in head and neck cancers. Int J Cancer 2017; 142:156-164. [PMID: 28906000 DOI: 10.1002/ijc.31045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 08/06/2017] [Accepted: 08/22/2017] [Indexed: 01/07/2023]
Abstract
Tyrosine kinase inhibitors are effective treatments for cancers. Knowing the specific kinase mutants that drive the underlying cancers predict therapeutic response to these inhibitors. Thus, the current protocol for personalized cancer therapy involves genotyping tumors in search of various driver mutations and subsequently individualizing the tyrosine kinase inhibitor to the patients whose tumors express the corresponding driver mutant. While this approach works when known driver mutations are found, its limitation is the dependence on driver mutations as predictors for response. To complement the genotype approach, we hypothesize that a phosphoarray platform is equally capable of personalizing kinase inhibitor therapy. We selected head and neck squamous cell carcinoma as the cancer model to test our hypothesis. Using the receptor tyrosine kinase phosphoarray, we identified the phosphorylation profiles of 49 different tyrosine kinase receptors in five different head and neck cancer cell lines. Based on these results, we tested the cell line response to the corresponding kinase inhibitor therapy. We found that this phosphoarray accurately informed the kinase inhibitor response profile of the cell lines. Next, we determined the phosphorylation profiles of 39 head and neck cancer patient derived xenografts. We found that absent phosphorylated EGFR signal predicted primary resistance to cetuximab treatment in the xenografts without phosphorylated ErbB2. Meanwhile, absent ErbB2 signaling in the xenografts with phosphorylated EGFR is associated with a higher likelihood of response to cetuximab. In summary, the phosphoarray technology has the potential to become a new diagnostic platform for personalized cancer therapy.
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Affiliation(s)
- Konrad Klinghammer
- Department of Hematology and Oncology, Charite University Medicine, Berlin, Germany
| | - James Keller
- Department of Microbiology and Molecular Genetics, Stony Brook University, Stony Brook, NY, 11794
| | - Jonathan George
- Department of Microbiology and Molecular Genetics, Stony Brook University, Stony Brook, NY, 11794
| | - Jens Hoffmann
- EPO-Experimental Pharmacology and Oncology GmbH, Berlin, Germany
| | - Edward L Chan
- Department of Microbiology and Molecular Genetics, Stony Brook University, Stony Brook, NY, 11794.,Division of Pediatric Hematology/Oncology
| | - Michael J Hayman
- Department of Microbiology and Molecular Genetics, Stony Brook University, Stony Brook, NY, 11794
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45
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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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46
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Weiser BP, Stivers JT, Cole PA. Investigation of N-Terminal Phospho-Regulation of Uracil DNA Glycosylase Using Protein Semisynthesis. Biophys J 2017; 113:393-401. [PMID: 28746850 DOI: 10.1016/j.bpj.2017.06.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 06/09/2017] [Accepted: 06/12/2017] [Indexed: 11/16/2022] Open
Abstract
Uracil DNA Glycosylase (UNG2) is the primary enzyme in humans that prevents the stable incorporation of deoxyuridine monophosphate into DNA in the form of U/A basepairs. During S-phase, UNG2 remains associated with the replication fork through its interactions with two proteins, Proliferating Cell Nuclear Antigen (PCNA) and Replication Protein A (RPA), which are critical for DNA replication and repair. In this work, we used protein semisynthesis and fluorescence anisotropy assays to explore the interactions of UNG2 with PCNA and RPA and to determine the effects of two UNG2 phosphorylation sites (Thr6 and Tyr8) located within its PCNA-interacting motif (PIP-box). In binding assays, we found that phosphorylation of Thr6 or Tyr8 on UNG2 can impede PCNA binding without affecting UNG2 catalytic activity or its RPA interaction. Our data also suggests that unmodified UNG2, PCNA, and RPA can form a ternary protein complex. We propose that the UNG2 N-terminus may serve as a flexible scaffold to tether PCNA and RPA at the replication fork, and that post-translational modifications on the UNG2 N-terminus disrupt formation of the PCNA-UNG2-RPA protein complex.
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Affiliation(s)
- Brian P Weiser
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - James T Stivers
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Philip A Cole
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland.
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47
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Randolph ME, Cleary MM, Bajwa Z, Svalina MN, Young MC, Mansoor A, Kaur P, Bult CJ, Goros MW, Michalek JE, Xiang S, Keck J, Krasnoperov V, Gill P, Keller C. EphB4/EphrinB2 therapeutics in Rhabdomyosarcoma. PLoS One 2017; 12:e0183161. [PMID: 28817624 PMCID: PMC5560593 DOI: 10.1371/journal.pone.0183161] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 07/31/2017] [Indexed: 01/08/2023] Open
Abstract
Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma affecting children and is often diagnosed with concurrent metastases. Unfortunately, few effective therapies have been discovered that improve the long-term survival rate for children with metastatic disease. Here we determined effectiveness of targeting the receptor tyrosine kinase, EphB4, in both alveolar and embryonal RMS either directly through the inhibitory antibody, VasG3, or indirectly by blocking both forward and reverse signaling of EphB4 binding to EphrinB2, cognate ligand of EphB4. Clinically, EphB4 expression in eRMS was correlated with longer survival. Experimentally, inhibition of EphB4 with VasG3 in both aRMS and eRMS orthotopic xenograft and allograft models failed to alter tumor progression. Inhibition of EphB4 forward signaling using soluble EphB4 protein fused with murine serum albumin failed to affect eRMS model tumor progression, but did moderately slow progression in murine aRMS. We conclude that inhibition of EphB4 signaling with these agents is not a viable monotherapy for rhabdomyosarcoma.
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Affiliation(s)
- Matthew E. Randolph
- Children’s Cancer Therapy Development Institute, Beaverton, Oregon, United States of America
| | - Megan M. Cleary
- Children’s Cancer Therapy Development Institute, Beaverton, Oregon, United States of America
- Department of Pediatrics, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Zia Bajwa
- Children’s Cancer Therapy Development Institute, Beaverton, Oregon, United States of America
| | - Matthew N. Svalina
- Children’s Cancer Therapy Development Institute, Beaverton, Oregon, United States of America
- Department of Pediatrics, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Michael C. Young
- Children’s Cancer Therapy Development Institute, Beaverton, Oregon, United States of America
| | - Atiya Mansoor
- Department of Pathology, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Pali Kaur
- The Jackson Laboratory Cancer Center, The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Carol J. Bult
- The Jackson Laboratory Cancer Center, The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Martin W. Goros
- Department of Epidemiology and Biostatistics, University of Texas Health Science Center, San Antonio, Texas, United States of America
| | - Joel E. Michalek
- Department of Epidemiology and Biostatistics, University of Texas Health Science Center, San Antonio, Texas, United States of America
| | - Sunny Xiang
- The Jackson Laboratory Cancer Center, The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - James Keck
- The Jackson Laboratory Cancer Center, The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | | | - Parkash Gill
- Vasgene Therapeutics, Los Angeles, California, United States of America
| | - Charles Keller
- Children’s Cancer Therapy Development Institute, Beaverton, Oregon, United States of America
- Department of Pediatrics, Oregon Health & Science University, Portland, Oregon, United States of America
- * E-mail:
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48
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Fleuren EDG, Vlenterie M, van der Graaf WTA, Hillebrandt-Roeffen MHS, Blackburn J, Ma X, Chan H, Magias MC, van Erp A, van Houdt L, Cebeci SAS, van de Ven A, Flucke UE, Heyer EE, Thomas DM, Lord CJ, Marini KD, Vaghjiani V, Mercer TR, Cain JE, Wu J, Versleijen-Jonkers YMH, Daly RJ. Phosphoproteomic Profiling Reveals ALK and MET as Novel Actionable Targets across Synovial Sarcoma Subtypes. Cancer Res 2017; 77:4279-4292. [PMID: 28634201 DOI: 10.1158/0008-5472.can-16-2550] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 04/21/2017] [Accepted: 06/06/2017] [Indexed: 11/16/2022]
Abstract
Despite intensive multimodal treatment of sarcomas, a heterogeneous group of malignant tumors arising from connective tissue, survival remains poor. Candidate-based targeted treatments have demonstrated limited clinical success, urging an unbiased and comprehensive analysis of oncogenic signaling networks to reveal therapeutic targets and personalized treatment strategies. Here we applied mass spectrometry-based phosphoproteomic profiling to the largest and most heterogeneous set of sarcoma cell lines characterized to date and identified novel tyrosine phosphorylation patterns, enhanced tyrosine kinases in specific subtypes, and potential driver kinases. ALK was identified as a novel driver in the Aska-SS synovial sarcoma (SS) cell line via expression of an ALK variant with a large extracellular domain deletion (ALKΔ2-17). Functional ALK dependency was confirmed in vitro and in vivo with selective inhibitors. Importantly, ALK immunopositivity was detected in 6 of 43 (14%) of SS patient specimens, one of which exhibited an ALK rearrangement. High PDGFRα phosphorylation also characterized SS cell lines, which was accompanied by enhanced MET activation in Yamato-SS cells. Although Yamato-SS cells were sensitive to crizotinib (ALK/MET-inhibitor) but not pazopanib (VEGFR/PDGFR-inhibitor) monotherapy in vitro, synergistic effects were observed upon drug combination. In vivo, both drugs were individually effective, with pazopanib efficacy likely attributable to reduced angiogenesis. MET or PDGFRα expression was detected in 58% and 84% of SS patients, respectively, with coexpression in 56%. Consequently, our integrated approach has led to the identification of ALK and MET as promising therapeutic targets in SS. Cancer Res; 77(16); 4279-92. ©2017 AACR.
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Affiliation(s)
- Emmy D G Fleuren
- Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom.
- The CRUK Gene Function Laboratory and the Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Myrella Vlenterie
- Department of Medical Oncology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Winette T A van der Graaf
- Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
- Royal Marsden NHS Foundation Trust, London, United Kingdom
| | | | - James Blackburn
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St. Vincent's Clinical School, Faculty of Medicine, UNSW, Sydney, New South Wales, Australia
| | - Xiuquan Ma
- Cancer Research Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Howard Chan
- Cancer Research Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Mandy C Magias
- Cancer Research Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Anke van Erp
- Department of Medical Oncology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Laurens van Houdt
- Department of Medical Oncology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Sabri A S Cebeci
- Department of Medical Oncology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Amy van de Ven
- Department of Medical Oncology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Uta E Flucke
- Department of Pathology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Erin E Heyer
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - David M Thomas
- Cancer Division, The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Christopher J Lord
- The CRUK Gene Function Laboratory and the Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Kieren D Marini
- Centre for Cancer Research, Hudson Institute of Medical Research and Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Vijesh Vaghjiani
- Centre for Cancer Research, Hudson Institute of Medical Research and Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Tim R Mercer
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St. Vincent's Clinical School, Faculty of Medicine, UNSW, Sydney, New South Wales, Australia
| | - Jason E Cain
- Centre for Cancer Research, Hudson Institute of Medical Research and Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Jianmin Wu
- Cancer Division, The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Center for Cancer Bioinformatics, Peking University Cancer Hospital & Institute, Hai-Dian District, Beijing, China
| | | | - Roger J Daly
- Cancer Research Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia.
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49
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In GK, Hu JS, Tseng WW. Treatment of advanced, metastatic soft tissue sarcoma: latest evidence and clinical considerations. Ther Adv Med Oncol 2017; 9:533-550. [PMID: 28794805 PMCID: PMC5524246 DOI: 10.1177/1758834017712963] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 05/04/2017] [Indexed: 12/24/2022] Open
Abstract
Soft tissue sarcoma (STS) is a biologically heterogeneous malignancy with over 50 subtypes. Historically, there have been few systemic treatment options for this relatively rare disease. Traditional cytotoxic agents, such as anthracyclines, alkylating agents, and taxanes have limited clinical benefit beyond the first-line setting; across all high-grade STS subtypes, median overall survival remains approximately 12-18 months for advanced metastatic disease. The development of targeted therapies has led to recent US Food and Drug Administration approval of four new treatments for high-grade STS in the advanced metastatic setting. Among these, olaratumab is most notable for its improvement in overall survival for patients with anthracycline-naïve disease. Further progress in STS management will rely on novel trial design, subtype-specific therapies and validation of biomarkers to tailor therapy. Immunotherapy has shown promise as a new, but yet undiscovered frontier in the management of STS.
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Affiliation(s)
- Gino K. In
- Division of Oncology, Norris Comprehensive Cancer Center, Los Angeles, CA, USA
- Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - James S. Hu
- Division of Oncology, Norris Comprehensive Cancer Center, Los Angeles, CA, USA
- Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - William W. Tseng
- Department of Surgery, Section of Surgical Oncology, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
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50
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Integrated analysis of gene expression and copy number identified potential cancer driver genes with amplification-dependent overexpression in 1,454 solid tumors. Sci Rep 2017; 7:641. [PMID: 28377632 PMCID: PMC5428069 DOI: 10.1038/s41598-017-00219-3] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 02/14/2017] [Indexed: 02/03/2023] Open
Abstract
Identification of driver genes contributes to the understanding of cancer etiology and is imperative for the development of individualized therapies. Gene amplification is a major event in oncogenesis. Driver genes with tumor-specific amplification-dependent overexpression can be therapeutic targets. In this study, we aimed to identify amplification-dependent driver genes in 1,454 solid tumors, across more than 15 cancer types, by integrative analysis of gene expression and copy number. Amplification-dependent overexpression of 64 known driver oncogenes were found in 587 tumors (40%); genes frequently observed were MYC (25%) and MET (18%) in colorectal cancer; SKP2 (21%) in lung squamous cell carcinoma; HIST1H3B (19%) and MYCN (13%) in liver cancer; KIT (57%) in gastrointestinal stromal tumors; and FOXL2 (12%) in squamous cell carcinoma across tissues. Genomic aberrations in 138 known cancer driver genes and 491 established fusion genes were found in 1,127 tumors (78%). Further analyses of 820 cancer-related genes revealed 16 as potential driver genes, with amplification-dependent overexpression restricted to the remaining 22% of samples (327 tumors) initially undetermined genetic drivers. Among them, AXL, which encodes a receptor tyrosine kinase, was recurrently overexpressed and amplified in sarcomas. Our studies of amplification-dependent overexpression identified potential drug targets in individual tumors.
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