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Artificial Intelligence-Based Computational Screening and Functional Assays Identify Candidate Small Molecule Antagonists of PTPmu-Dependent Adhesion. Int J Mol Sci 2023; 24:ijms24054274. [PMID: 36901713 PMCID: PMC10001486 DOI: 10.3390/ijms24054274] [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: 11/22/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/25/2023] Open
Abstract
PTPmu (PTPµ) is a member of the receptor protein tyrosine phosphatase IIb family that participates in cell-cell adhesion and signaling. PTPmu is proteolytically downregulated in glioblastoma (glioma), and the resulting extracellular and intracellular fragments are believed to stimulate cancer cell growth and/or migration. Therefore, drugs targeting these fragments may have therapeutic potential. Here, we used the AtomNet® platform, the first deep learning neural network for drug design and discovery, to screen a molecular library of several million compounds and identified 76 candidates predicted to interact with a groove between the MAM and Ig extracellular domains required for PTPmu-mediated cell adhesion. These candidates were screened in two cell-based assays: PTPmu-dependent aggregation of Sf9 cells and a tumor growth assay where glioma cells grow in three-dimensional spheres. Four compounds inhibited PTPmu-mediated aggregation of Sf9 cells, six compounds inhibited glioma sphere formation/growth, while two priority compounds were effective in both assays. The stronger of these two compounds inhibited PTPmu aggregation in Sf9 cells and inhibited glioma sphere formation down to 25 micromolar. Additionally, this compound was able to inhibit the aggregation of beads coated with an extracellular fragment of PTPmu, directly demonstrating an interaction. This compound presents an interesting starting point for the development of PTPmu-targeting agents for treating cancer including glioblastoma.
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2
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Rumman M, Dhawan J. PTPRU, a quiescence-induced receptor tyrosine phosphatase negatively regulates osteogenic differentiation of human mesenchymal stem cells. Biochem Biophys Res Commun 2022; 636:41-49. [DOI: 10.1016/j.bbrc.2022.10.062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 10/18/2022] [Indexed: 11/02/2022]
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3
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Molyneaux K, Wnek MD, Craig SEL, Vincent J, Rucker I, Wnek GE, Brady-Kalnay SM. Physically-cross-linked poly(vinyl alcohol) cell culture plate coatings facilitate preservation of cell-cell interactions, spheroid formation, and stemness. J Biomed Mater Res B Appl Biomater 2021; 109:1744-1753. [PMID: 33847464 DOI: 10.1002/jbm.b.34832] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 02/21/2021] [Accepted: 03/14/2021] [Indexed: 12/19/2022]
Abstract
We employed aqueous solutions of highly-hydrolyzed (>99+%) poly(vinyl alcohol), PVA, to coat plastic dishes as a method to efficiently induce three-dimensional (3D) culturing of cells. The coatings were prepared by simple evaporation of 3 wt/vol% solutions of PVA in water and require no additional processing steps after air drying under sterile conditions. The coating allows spheroids to form in solution. Spheroid formation is usually preferable to two-dimensional (2D) culturing as it creates a more realistic ex vivo model of some human tissues and tumors. Using PVA-coated cell culture plates, we demonstrated that we can grow reproducibly sized spheroids using several human glioma cell lines, including LN229, U87 MG, and Gli36, and the embryonic kidney cell line, 293T. Spheroids formed on PVA-coated plates grow as well as on other commercially-available, low-attachment plates, and have excellent optical imaging properties. As spheroids, LN229 cells express markers of cancer stem cells. Finally, we confirmed that spheroids generated on PVA-coated plates are sensitive to molecular perturbations, as increased expression of the cell adhesion molecule PTPμ significantly increased the size of spheroids. The PVA hydrogel layer is an effective tool for creating a more realistic ex vivo culture system than traditional 2D culture and can be used to generate cell spheroids for potential application in drug screening and personalized medicine for diseases such as cancer.
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Affiliation(s)
- Kathleen Molyneaux
- Department of Molecular Biology & Microbiology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Maria D Wnek
- Department of Molecular Biology & Microbiology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Sonya E L Craig
- Department of Molecular Biology & Microbiology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jason Vincent
- Department of Molecular Biology & Microbiology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Imani Rucker
- Department of Molecular Biology & Microbiology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Gary E Wnek
- Department of Macromolecular Science and Engineering, Case Western Reserve University, Cleveland, Ohio, USA
| | - Susann M Brady-Kalnay
- Department of Molecular Biology & Microbiology, Case Western Reserve University, Cleveland, Ohio, USA
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4
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Ruckert MT, de Andrade PV, Santos VS, Silveira VS. Protein tyrosine phosphatases: promising targets in pancreatic ductal adenocarcinoma. Cell Mol Life Sci 2019; 76:2571-2592. [PMID: 30982078 PMCID: PMC11105579 DOI: 10.1007/s00018-019-03095-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 03/25/2019] [Accepted: 04/08/2019] [Indexed: 12/21/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the most common type of pancreatic cancer. It is the fourth leading cause of cancer-related death and is associated with a very poor prognosis. KRAS driver mutations occur in approximately 95% of PDAC cases and cause the activation of several signaling pathways such as mitogen-activated protein kinase (MAPK) pathways. Regulation of these signaling pathways is orchestrated by feedback loops mediated by the balance between protein tyrosine kinases (PTKs) and protein tyrosine phosphatases (PTPs), leading to activation or inhibition of its downstream targets. The human PTPome comprises 125 members, and these proteins are classified into three distinct families according to their structure. Since PTP activity description, it has become clear that they have both inhibitory and stimulatory effects on cancer-associated signaling processes and that deregulation of PTP function is closely associated with tumorigenesis. Several PTPs have displayed either tumor suppressor or oncogenic characteristics during the development and progression of PDAC. In this sense, PTPs have been presented as promising candidates for the treatment of human pancreatic cancer, and many PTP inhibitors have been developed since these proteins were first associated with cancer. Nevertheless, some challenges persist regarding the development of effective and safe methods to target these molecules and deliver these drugs. In this review, we discuss the role of PTPs in tumorigenesis as tumor suppressor and oncogenic proteins. We have focused on the differential expression of these proteins in PDAC, as well as their clinical implications and possible targeting for pharmacological inhibition in cancer therapy.
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Affiliation(s)
- Mariana Tannús Ruckert
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, São Paulo, Brazil
| | - Pamela Viani de Andrade
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, São Paulo, Brazil
| | - Verena Silva Santos
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, São Paulo, Brazil
| | - Vanessa Silva Silveira
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, São Paulo, Brazil.
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5
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Narla G, Sangodkar J, Ryder CB. The impact of phosphatases on proliferative and survival signaling in cancer. Cell Mol Life Sci 2018; 75:2695-2718. [PMID: 29725697 PMCID: PMC6023766 DOI: 10.1007/s00018-018-2826-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 03/24/2018] [Accepted: 04/23/2018] [Indexed: 02/06/2023]
Abstract
The dynamic and stringent coordination of kinase and phosphatase activity controls a myriad of physiologic processes. Aberrations that disrupt the balance of this interplay represent the basis of numerous diseases. For a variety of reasons, early work in this area portrayed kinases as the dominant actors in these signaling events with phosphatases playing a secondary role. In oncology, these efforts led to breakthroughs that have dramatically altered the course of certain diseases and directed vast resources toward the development of additional kinase-targeted therapies. Yet, more recent scientific efforts have demonstrated a prominent and sometimes driving role for phosphatases across numerous malignancies. This maturation of the phosphatase field has brought with it the promise of further therapeutic advances in the field of oncology. In this review, we discuss the role of phosphatases in the regulation of cellular proliferation and survival signaling using the examples of the MAPK and PI3K/AKT pathways, c-Myc and the apoptosis machinery. Emphasis is placed on instances where these signaling networks are perturbed by dysregulation of specific phosphatases to favor growth and persistence of human cancer.
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Affiliation(s)
| | - Jaya Sangodkar
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
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Elson A. Stepping out of the shadows: Oncogenic and tumor-promoting protein tyrosine phosphatases. Int J Biochem Cell Biol 2017; 96:135-147. [PMID: 28941747 DOI: 10.1016/j.biocel.2017.09.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 09/15/2017] [Accepted: 09/16/2017] [Indexed: 12/18/2022]
Abstract
Protein tyrosine phosphorylation is critical for proper function of cells and organisms. Phosphorylation is regulated by the concerted but generically opposing activities of tyrosine kinases (PTKs) and tyrosine phosphatases (PTPs), which ensure its proper regulation, reversibility, and ability to respond to changing physiological situations. Historically, PTKs have been associated mainly with oncogenic and pro-tumorigenic activities, leading to the generalization that protein dephosphorylation is anti-oncogenic and hence that PTPs are tumor-suppressors. In many cases PTPs do suppress tumorigenesis. However, a growing body of evidence indicates that PTPs act as dominant oncogenes and drive cell transformation in a number of contexts, while in others PTPs support transformation that is driven by other oncogenes. This review summarizes the known transforming and tumor-promoting activities of the classical, tyrosine specific PTPs and highlights their potential as drug targets for cancer therapy.
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Affiliation(s)
- Ari Elson
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, 76100, Israel.
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7
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Sun PH, Chen G, Mason M, Jiang WG, Ye L. Dual roles of protein tyrosine phosphatase kappa in coordinating angiogenesis induced by pro-angiogenic factors. Int J Oncol 2017; 50:1127-1135. [PMID: 28259897 PMCID: PMC5363875 DOI: 10.3892/ijo.2017.3884] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 01/18/2017] [Indexed: 11/09/2022] Open
Abstract
A potential role may be played by receptor-type protein tyrosine phosphatase kappa (PTPRK) in angiogenesis due to its critical function in coordinating intracellular signal transduction from various receptors reliant on tyrosine phosphorylation. In the present study, we investigated the involvement of PTPRK in the cellular functions of vascular endothelial cells (HECV) and its role in angiogenesis using in vitro assays and a PTPRK knockdown vascular endothelial cell model. PTPRK knockdown in HECV cells (HECVPTPRKkd) resulted in a decrease of cell proliferation and cell-matrix adhesion; however, increased cell spreading and motility were seen. Reduced focal adhesion kinase (FAK) and paxillin protein levels were seen in the PTPRK knockdown cells which may contribute to the inhibitory effect on adhesion. HECVPTPRKkd cells were more responsive to the treatment of fibroblast growth factor (FGF) in their migration compared with the untreated control and cells treated with VEGF. Moreover, elevated c-Src and Akt1 were seen in the PTPRK knockdown cells. The FGF-promoted cell migration was remarkably suppressed by an addition of PLCγ inhibitor compared with other small inhibitors. Knockdown of PTPRK suppressed the ability of HECV cells to form tubules and also impaired the tubule formation that was induced by FGF and conditioned medium of cancer cells. Taken together, it suggests that PTPRK plays dual roles in coordinating angiogenesis. It plays a positive role in cell proliferation, adhesion and tubule formation, but suppresses cell migration, in particular, the FGF-promoted migration. PTPRK bears potential to be targeted for the prevention of tumour associated angiogenesis.
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Affiliation(s)
- Ping-Hui Sun
- Cardiff China Medical Research Collaborative Institute of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, CF14 4XN, UK
| | - Gang Chen
- Cardiff China Medical Research Collaborative Institute of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, CF14 4XN, UK
| | - Malcolm Mason
- Cardiff China Medical Research Collaborative Institute of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, CF14 4XN, UK
| | - Wen G Jiang
- Cardiff China Medical Research Collaborative Institute of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, CF14 4XN, UK
| | - Lin Ye
- Cardiff China Medical Research Collaborative Institute of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, CF14 4XN, UK
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Bourgonje AM, Verrijp K, Schepens JTG, Navis AC, Piepers JAF, Palmen CBC, van den Eijnden M, Hooft van Huijsduijnen R, Wesseling P, Leenders WPJ, Hendriks WJAJ. Comprehensive protein tyrosine phosphatase mRNA profiling identifies new regulators in the progression of glioma. Acta Neuropathol Commun 2016; 4:96. [PMID: 27586084 PMCID: PMC5009684 DOI: 10.1186/s40478-016-0372-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 08/19/2016] [Indexed: 12/20/2022] Open
Abstract
The infiltrative behavior of diffuse gliomas severely reduces therapeutic potential of surgical resection and radiotherapy, and urges for the identification of new drug-targets affecting glioma growth and migration. To address the potential role of protein tyrosine phosphatases (PTPs), we performed mRNA expression profiling for 91 of the 109 known human PTP genes on a series of clinical diffuse glioma samples of different grades and compared our findings with in silico knowledge from REMBRANDT and TCGA databases. Overall PTP family expression levels appeared independent of characteristic genetic aberrations associated with lower grade or high grade gliomas. Notably, seven PTP genes (DUSP26, MTMR4, PTEN, PTPRM, PTPRN2, PTPRT and PTPRZ1) were differentially expressed between grade II-III gliomas and (grade IV) glioblastomas. For DUSP26, PTEN, PTPRM and PTPRT, lower expression levels correlated with poor prognosis, and overexpression of DUSP26 or PTPRT in E98 glioblastoma cells reduced tumorigenicity. Our study represents the first in-depth analysis of PTP family expression in diffuse glioma subtypes and warrants further investigations into PTP-dependent signaling events as new entry points for improved therapy.
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Malhotra M, Toulouse A, Godinho BMDC, Mc Carthy DJ, Cryan JF, O'Driscoll CM. RNAi therapeutics for brain cancer: current advancements in RNAi delivery strategies. MOLECULAR BIOSYSTEMS 2016; 11:2635-57. [PMID: 26135606 DOI: 10.1039/c5mb00278h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Malignant primary brain tumors are aggressive cancerous cells that invade the surrounding tissues of the central nervous system. The current treatment options for malignant brain tumors are limited due to the inability to cross the blood-brain barrier. The advancements in current research has identified and characterized certain molecular markers that are essential for tumor survival, progression, metastasis and angiogenesis. These molecular markers have served as therapeutic targets for the RNAi based therapies, which enable site-specific silencing of the gene responsible for tumor proliferation. However, to bring about therapeutic success, an efficient delivery carrier that can cross the blood-brain barrier and reach the targeted site is essential. The current review focuses on the potential of targeted, non-viral and viral particles containing RNAi therapeutic molecules as delivery strategies specifically for brain tumors.
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Affiliation(s)
- Meenakshi Malhotra
- Pharmacodelivery Group, School of Pharmacy, University College Cork, Cork, Ireland
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10
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Craig SEL, Brady-Kalnay SM. Regulation of development and cancer by the R2B subfamily of RPTPs and the implications of proteolysis. Semin Cell Dev Biol 2014; 37:108-18. [PMID: 25223585 DOI: 10.1016/j.semcdb.2014.09.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 09/04/2014] [Accepted: 09/05/2014] [Indexed: 01/04/2023]
Abstract
The initial cloning of receptor protein tyrosine phosphatases (RPTPs) was met with excitement because of their hypothesized function in counterbalancing receptor tyrosine kinase signaling. In recent years, members of a subfamily of RPTPs with homophilic cell-cell adhesion capabilities, known as the R2B subfamily, have been shown to have functions beyond that of counteracting tyrosine kinase activity, by independently influencing cell signaling in their own right and by regulating cell adhesion. The R2B subfamily is composed of four members: PTPmu (PTPRM), PTPrho (PTPRT), PTPkappa (PTPRK), and PCP-2 (PTPRU). The effects of this small subfamily of RPTPs is far reaching, influencing several developmental processes and cancer. In fact, R2B RPTPs are predicted to be tumor suppressors and are among the most frequently mutated protein tyrosine phosphatases (PTPs) in cancer. Confounding these conclusions are more recent studies suggesting that proteolysis of the full-length R2B RPTPs result in oncogenic extracellular and intracellular protein fragments. This review discusses the current knowledge of the role of R2B RPTPs in development and cancer, with special detail given to the mechanisms and implications that proteolysis has on R2B RPTP function. We also touch upon the concept of exploiting R2B proteolysis to develop cancer imaging tools, and consider the effects of R2B proteolysis on axon guidance, perineural invasion and collective cell migration.
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Affiliation(s)
- Sonya E L Craig
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4960, USA
| | - Susann M Brady-Kalnay
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4960, USA; Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.
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11
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Liu Y, Zhu Z, Xiong Z, Zheng J, Hu Z, Qiu J. Knockdown of protein tyrosine phosphatase receptor U inhibits growth and motility of gastric cancer cells. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2014; 7:5750-61. [PMID: 25337216 PMCID: PMC4203187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Accepted: 08/23/2014] [Indexed: 06/04/2023]
Abstract
Protein tyrosine phosphatase receptor U (PTPRU) has been shown to be a tumor suppressor in colon cancer by dephosphorylating β-catenin and reducing the activation of β-catenin signaling. Here, we investigate the expression of PTPRU protein in gastric cancer cell lines, gastric cancer tissues and respective adjacent non-cancer tissues and find that the 130 kDa nuclear-localized PTPRU fragment is the main PTPRU isoform in gastric cancer cells, whereas the full-length PTPRU is relatively lowly expressed. The level of the 130 kDa PTPRU is higher in gastric cancer tissues than in adjacent non-cancer tissues. Knockdown of endogenous PTPRU in gastric cancer cells using lentivirus-delivered specific shRNA results in the attenuation of cell growth, migration, invasion and adhesion. Knockdown of PTPRU also inhibits tyrosine phosphorylation and transcriptional activity of β-catenin as well as levels of focal adhesion proteins and lysine methylation of histone H3. These results indicate that PTPRU is required for gastric cancer progression and may serve as a potential therapeutic target.
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Affiliation(s)
- Yongjie Liu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and TechnologyShanghai 200237, P. R. China
| | - Zhichuan Zhu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and TechnologyShanghai 200237, P. R. China
| | - Zhiqi Xiong
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and TechnologyShanghai 200237, P. R. China
| | - Jing Zheng
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and TechnologyShanghai 200237, P. R. China
| | - Zelan Hu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and TechnologyShanghai 200237, P. R. China
| | - Jiangfeng Qiu
- Department of Gastrointestinal Surgery, Ningbo First HospitalNingbo 315010, P. R. China
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12
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Zhu Z, Liu Y, Li K, Liu J, Wang H, Sun B, Xiong Z, Jiang H, Zheng J, Hu Z. Protein tyrosine phosphatase receptor U (PTPRU) is required for glioma growth and motility. Carcinogenesis 2014; 35:1901-10. [PMID: 24876153 DOI: 10.1093/carcin/bgu123] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The membrane protein tyrosine phosphatase receptor U (PTPRU) has been shown to function as a negative regulator of adhesion and proliferation in certain cancer cell types, primarily through its dephosphorylation of β-catenin and inhibition of subsequent downstream signaling. In the present study, we set out to characterize the role of PTPRU in glioma and found that, while the expression of full-length PTPRU protein is low in these tumors, a number of non-full-length PTPRU isoforms are highly expressed. Among these isoforms, one in particular is localized to the nucleus, and its expression is increased in glioma tissues in a manner that positively correlates with malignancy grade. Short hairpin RNA knockdown of endogenous PTPRU in human and rat glioma cell lines suppressed proliferation, survival, invasion, migration, adhesion and vasculogenic tube formation in vitro, as well as intracranial tumor progression in vivo. In addition, knocking down PTPRU reduced tyrosine phosphorylation (pY) and transcriptional activity of β-catenin, and we were able to specifically rescue the cell migration defect by expressing a LEF1-β-catenin fusion protein in PTPRU-depleted cells. PTPRU knockdown also led to increased tyrosine pY of the E3 ubiquitin ligase c-Cbl and to the destabilization of several focal adhesion proteins. Taken together, our findings demonstrate that endogenous PTPRU promote glioma progression through their effect on β-catenin and focal adhesion signaling.
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Affiliation(s)
- Zhichuan Zhu
- School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China, Department of Neurosurgery, Shanghai Neurosurgical Center, Huashan Hospital, Fudan University, Shanghai 200030, China and Institute of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yongjie Liu
- School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China, Department of Neurosurgery, Shanghai Neurosurgical Center, Huashan Hospital, Fudan University, Shanghai 200030, China and Institute of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Kui Li
- School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China, Department of Neurosurgery, Shanghai Neurosurgical Center, Huashan Hospital, Fudan University, Shanghai 200030, China and Institute of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jiwei Liu
- School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China, Department of Neurosurgery, Shanghai Neurosurgical Center, Huashan Hospital, Fudan University, Shanghai 200030, China and Institute of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hongtao Wang
- School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China, Department of Neurosurgery, Shanghai Neurosurgical Center, Huashan Hospital, Fudan University, Shanghai 200030, China and Institute of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Bing Sun
- Department of Neurosurgery, Shanghai Neurosurgical Center, Huashan Hospital, Fudan University, Shanghai 200030, China and
| | - Zhiqi Xiong
- Institute of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hualiang Jiang
- School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China, Department of Neurosurgery, Shanghai Neurosurgical Center, Huashan Hospital, Fudan University, Shanghai 200030, China and Institute of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jing Zheng
- School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China, Department of Neurosurgery, Shanghai Neurosurgical Center, Huashan Hospital, Fudan University, Shanghai 200030, China and Institute of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zelan Hu
- School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China, Department of Neurosurgery, Shanghai Neurosurgical Center, Huashan Hospital, Fudan University, Shanghai 200030, China and Institute of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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Zheng CL, Kawane S, Bottomly D, Wilmot B. Analysis considerations for utilizing RNA-Seq to characterize the brain transcriptome. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2014; 116:21-54. [PMID: 25172470 DOI: 10.1016/b978-0-12-801105-8.00002-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
RNA-Seq allows one to examine only gene expression as well as expression of noncoding RNAs, alternative splicing, and allele-specific expression. With this increased sensitivity and dynamic range, there are computational and statistical considerations that need to be contemplated, which are highly dependent on the biological question being asked. We highlight these to provide an overview of their importance and the impact they can have on downstream interpretation of the brain transcriptome.
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Affiliation(s)
- Christina L Zheng
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, Oregon, USA; Knight Cancer Institute, Oregon Health, Oregon Health and Science University, Portland, Oregon, USA.
| | - Sunita Kawane
- Clinical & Translational Research Institute, Oregon Health and Science University, Portland, Oregon, USA
| | - Daniel Bottomly
- Clinical & Translational Research Institute, Oregon Health and Science University, Portland, Oregon, USA
| | - Beth Wilmot
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, Oregon, USA; Clinical & Translational Research Institute, Oregon Health and Science University, Portland, Oregon, USA
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14
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Hale JS, Li M, Lathia JD. The malignant social network: cell-cell adhesion and communication in cancer stem cells. Cell Adh Migr 2012; 6:346-55. [PMID: 22796941 DOI: 10.4161/cam.21294] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Tumors contain a vastly complicated cellular network that relies on local communication to execute malignant programs. The molecular cues that are involved in cell-cell adhesion orchestrate large-scale tumor behaviors such as proliferation and invasion. We have recently begun to appreciate that many tumors contain a high degree of cellular heterogeneity and are organized in a cellular hierarchy, with a cancer stem cell (CSC) population identified at the apex in multiple cancer types. CSCs reside in unique microenvironments or niches that are responsible for directing their behavior through cellular interactions between CSCs and stromal cells, generating a malignant social network. Identifying cell-cell adhesion mechanisms in this network has implications for the basic understanding of tumorigenesis and the development of more effective therapies. In this review, we will discuss our current understanding of cell-cell adhesion mechanisms used by CSCs and how these local interactions have global consequences for tumor biology.
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Affiliation(s)
- James S Hale
- Department of Cell Biology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
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