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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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Ba Q, Li X, Huang C, Li J, Fu Y, Chen P, Duan J, Hao M, Zhang Y, Li J, Sun C, Ying H, Song H, Zhang R, Shen Z, Wang H. BCCIPβ modulates the ribosomal and extraribosomal function of S7 through a direct interaction. J Mol Cell Biol 2018; 9:209-219. [PMID: 28510697 PMCID: PMC5907838 DOI: 10.1093/jmcb/mjx019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 05/14/2017] [Indexed: 11/14/2022] Open
Abstract
Extraribosomal functions of ribosomal proteins (RPs) have gained much attention for their implications in tumorigenesis and progression. However, the regulations for transition between the ribosomal and extraribosomal functions of RPs are rarely reported. Herein, we identified a ribosomal protein S7-interacting partner, BCCIPβ, which modulates the functional conversion of S7. Through the N-terminal acidic domain, BCCIPβ interacts with the central basic region in S7 and regulates the extraribosomal distribution of S7. BCCIPβ deficiency abrogates the ribosomal accumulation but enhances the ribosome-free location of S7. This translocation further impairs protein synthesis and triggers ribosomal stress. Consequently, BCCIPβ deficiency suppresses the ribosomal function and initiates the extraribosomal function of S7, resulting in restriction of cell proliferation. Moreover, clinically relevant S7 mutations were found to dampen the interaction with BCCIPβ and facilitate the functional transition of S7. In conclusion, BCCIPβ, as a S7 modulator, contributes to the regulation of ribosomal and extraribosomal functions of S7 and has implications in cell growth and tumor development.
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Affiliation(s)
- Qian Ba
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiaoguang Li
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Chao Huang
- Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Junyang Li
- Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yijing Fu
- Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Peizhan Chen
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Juan Duan
- Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Miao Hao
- Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yinghua Zhang
- Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jingquan Li
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Chuanqi Sun
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Hao Ying
- Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Haiyun Song
- Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ruiwen Zhang
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, TX 79106, USA
| | - Zhiyuan Shen
- Rutgers Cancer Institute of New Jersey, Department of Radiation Oncology of Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA
| | - Hui Wang
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- Correspondence to: Hui Wang, E-mail:
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Meeusen B, Janssens V. Tumor suppressive protein phosphatases in human cancer: Emerging targets for therapeutic intervention and tumor stratification. Int J Biochem Cell Biol 2017; 96:98-134. [PMID: 29031806 DOI: 10.1016/j.biocel.2017.10.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 10/04/2017] [Accepted: 10/05/2017] [Indexed: 02/06/2023]
Abstract
Aberrant protein phosphorylation is one of the hallmarks of cancer cells, and in many cases a prerequisite to sustain tumor development and progression. Like protein kinases, protein phosphatases are key regulators of cell signaling. However, their contribution to aberrant signaling in cancer cells is overall less well appreciated, and therefore, their clinical potential remains largely unexploited. In this review, we provide an overview of tumor suppressive protein phosphatases in human cancer. Along their mechanisms of inactivation in defined cancer contexts, we give an overview of their functional roles in diverse signaling pathways that contribute to their tumor suppressive abilities. Finally, we discuss their emerging roles as predictive or prognostic markers, their potential as synthetic lethality targets, and the current feasibility of their reactivation with pharmacologic compounds as promising new cancer therapies. We conclude that their inclusion in clinical practice has obvious potential to significantly improve therapeutic outcome in various ways, and should now definitely be pushed forward.
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Affiliation(s)
- Bob Meeusen
- Laboratory of Protein Phosphorylation & Proteomics, Dept. of Cellular & Molecular Medicine, Faculty of Medicine, KU Leuven & Leuven Cancer Institute (LKI), KU Leuven, Belgium
| | - Veerle Janssens
- Laboratory of Protein Phosphorylation & Proteomics, Dept. of Cellular & Molecular Medicine, Faculty of Medicine, KU Leuven & Leuven Cancer Institute (LKI), KU Leuven, Belgium.
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Zhao S, Sedwick D, Wang Z. Genetic alterations of protein tyrosine phosphatases in human cancers. Oncogene 2014; 34:3885-94. [PMID: 25263441 PMCID: PMC4377308 DOI: 10.1038/onc.2014.326] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Revised: 08/20/2014] [Accepted: 08/21/2014] [Indexed: 12/12/2022]
Abstract
Protein tyrosine phosphatases (PTPs) are enzymes that remove phosphate from tyrosine residues in proteins. Recent whole-exome sequencing of human cancer genomes reveals that many PTPs are frequently mutated in a variety of cancers. Among these mutated PTPs, protein tyrosine phosphatase T (PTPRT) appears to be the most frequently mutated PTP in human cancers. Beside PTPN11 which functions as an oncogene in leukemia, genetic and functional studies indicate that most of mutant PTPs are tumor suppressor genes. Identification of the substrates and corresponding kinases of the mutant PTPs may provide novel therapeutic targets for cancers harboring these mutant PTPs.
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Affiliation(s)
- S Zhao
- 1] Division of Gastroenterology and Hepatology and Shanghai Institution of Digestive Disease, Shanghai Jiao-Tong University School of Medicine Renji Hospital, Shanghai, China [2] Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA [3] Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - D Sedwick
- 1] Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA [2] Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Z Wang
- 1] Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA [2] Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
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Huang YY, Lu H, Liu S, Droz-Rosario R, Shen Z. Requirement of mouse BCCIP for neural development and progenitor proliferation. PLoS One 2012; 7:e30638. [PMID: 22292003 PMCID: PMC3265516 DOI: 10.1371/journal.pone.0030638] [Citation(s) in RCA: 15] [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: 11/01/2011] [Accepted: 12/19/2011] [Indexed: 11/18/2022] Open
Abstract
Multiple DNA repair pathways are involved in the orderly development of neural systems at distinct stages. The homologous recombination (HR) pathway is required to resolve stalled replication forks and critical for the proliferation of progenitor cells during neural development. BCCIP is a BRCA2 and CDKN1A interacting protein implicated in HR and inhibition of DNA replication stress. In this study, we determined the role of BCCIP in neural development using a conditional BCCIP knock-down mouse model. BCCIP deficiency impaired embryonic and postnatal neural development, causing severe ataxia, cerebral and cerebellar defects, and microcephaly. These development defects are associated with spontaneous DNA damage and subsequent cell death in the proliferative cell populations of the neural system during embryogenesis. With in vitro neural spheroid cultures, BCCIP deficiency impaired neural progenitor's self-renewal capability, and spontaneously activated p53. These data suggest that BCCIP and its anti-replication stress functions are essential for normal neural development by maintaining an orderly proliferation of neural progenitors.
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Affiliation(s)
- Yi-Yuan Huang
- The Cancer Institute of New Jersey, Department of Radiation Oncology, Robert Wood Johnson Medical School, New Brunswick, New Jersey, United States of America
| | - Huimei Lu
- The Cancer Institute of New Jersey, Department of Radiation Oncology, Robert Wood Johnson Medical School, New Brunswick, New Jersey, United States of America
| | - Stephany Liu
- The Cancer Institute of New Jersey, Department of Radiation Oncology, Robert Wood Johnson Medical School, New Brunswick, New Jersey, United States of America
| | - Roberto Droz-Rosario
- The Cancer Institute of New Jersey, Department of Radiation Oncology, Robert Wood Johnson Medical School, New Brunswick, New Jersey, United States of America
| | - Zhiyuan Shen
- The Cancer Institute of New Jersey, Department of Radiation Oncology, Robert Wood Johnson Medical School, New Brunswick, New Jersey, United States of America
- * E-mail:
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Phillips-Mason PJ, Kaur H, Burden-Gulley SM, Craig SEL, Brady-Kalnay SM. Identification of phospholipase C gamma1 as a protein tyrosine phosphatase mu substrate that regulates cell migration. J Cell Biochem 2011; 112:39-48. [PMID: 20506511 DOI: 10.1002/jcb.22710] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The receptor protein tyrosine phosphatase PTPµ has a cell-adhesion molecule-like extracellular segment and a catalytically active intracellular segment. This structure gives PTPµ the ability to transduce signals in response to cell-cell adhesion. Full-length PTPµ is down-regulated in glioma cells by proteolysis which is linked to increased migration of these cells in the brain. To gain insight into the substrates PTPµ may be dephosphorylating to suppress glioma cell migration, we used a substrate trapping method to identify PTPµ substrates in tumor cell lines. We identified both PKCδ and PLCγ1 as PTPµ substrates. As PLCγ1 activation is linked to increased invasion of cancer cells, we set out to determine whether PTPµ may be upstream of PLCγ1 in regulating glioma cell migration. We conducted brain slice assays using U87-MG human glioma cells in which PTPµ expression was reduced by shRNA to induce migration. Treatment of the same cells with PTPµ shRNA and a PLCγ1 inhibitor prevented migration of the cells within the brain slice. These data suggest that PLCγ1 is downstream of PTPµ and that dephosphorylation of PLCγ1 is likely to be a major pathway through which PTPµ suppresses glioma cell migration.
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Affiliation(s)
- Polly J Phillips-Mason
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH 44106-4960, USA
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Abu-Amero KK, Hellani A, Salih MA, Alorainy IA, Zidan G, Kern KC, Sicotte NL, Bosley TM. Optic disk and white matter abnormalities in a patient with a de novo 18p partial monosomy. Ophthalmic Genet 2010; 31:147-54. [PMID: 20565246 DOI: 10.3109/13816810.2010.492817] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
PURPOSE Neuro-ophthalmologic and neuroimaging features of partial chromosome 18p deletion syndromes have not yet been fully described. METHODS Careful neuro-ophthalmologic and neuroimaging evaluation of a young woman with a partial 18p deletion, including 3 Tesla MRI and diffusion tensor imaging, cytogenetic analysis on GTG-banded chromosomes, and 244K array CGH analysis. RESULTS This 17-year-old girl had modest mental retardation, facial dysmorphism, other characteristics typical of 18p deletion syndrome, and anomalous optic disks. MRI showed enlarged third and lateral ventricles, a thin corpus callosum and patchy white matter signal hyperintensities without enhancement, while diffusion tensor imaging (DTI) revealed significant abnormalities of the corpus callosum with relative sparing of the corticospinal tracts. She had a de novo 14.6 Mb deletion on chromosome 18p [del(18)(p11.2>pter)], a region including 143 genes, only 10 of which were likely candidates for phenotypic expression. CONCLUSIONS This young woman had clinical features similar to those described previously with the 18p deletion syndrome, including moderate mental retardation and dysmorphism without focal neurologic signs. She was myopic, like other 18p deletion patients, supporting the concept that 18p contains a candidate locus for myopia. She also had anomalous optic disks, a feature that may be more common in this syndrome than previously recognized. MRI revealed enlarged ventricles and white matter abnormalities that may be explained in part by haploinsufficiency of ADCYAP1 and LPIN2 in the deleted region of chromosome 18.
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Affiliation(s)
- Khaled K Abu-Amero
- Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia.
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Wilson BT, Douglas SF, Polvikoski T. Astrocytoma in a Breast Cancer Lineage: Part of the BRCA2 Phenotype? J Clin Oncol 2010; 28:e596-8. [DOI: 10.1200/jco.2010.28.9173] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Brian T. Wilson
- Northern Genetics Service, Institute of Human Genetics, International Centre for Life, Newcastle upon Tyne, United Kingdom
| | - S. Fiona Douglas
- Northern Genetics Service, Institute of Human Genetics, International Centre for Life, Newcastle upon Tyne, United Kingdom
| | - Tuomo Polvikoski
- Institute for Ageing and Health, Newcastle University, Campus of Ageing and Vitality, Newcastle upon Tyne, United Kingdom
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Becka S, Zhang P, Craig SEL, Lodowski DT, Wang Z, Brady-Kalnay SM. Characterization of the adhesive properties of the type IIb subfamily receptor protein tyrosine phosphatases. ACTA ACUST UNITED AC 2010; 17:34-47. [PMID: 20521994 DOI: 10.3109/15419061.2010.487957] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Receptor protein tyrosine phosphatases (RPTPs) have cell adhesion molecule-like extracellular domains coupled to cytoplasmic tyrosine phosphatase domains. PTPmu is the prototypical member of the type IIb subfamily of RPTPs, which includes PTPrho, PTPkappa, and PCP-2. The authors performed the first comprehensive analysis of the subfamily in one system, examining adhesion and antibody recognition. The authors evaluated if antibodies that they developed to detect PTPmu also recognized other subfamily members. Notably, each antibody recognizes distinct subsets of type IIb RPTPs. PTPmu, PTPrho, and PTPkappa have all been shown to mediate cell-cell aggregation, and prior work with PCP-2 indicated that it can mediate bead aggregation in vitro. This study reveals that PCP-2 is unique among the type IIb RPTPs in that it does not mediate cell-cell aggregation via homophilic binding. The authors conclude from these experiments that PCP-2 is likely to have a distinct biological function other than cell-cell aggregation.
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Affiliation(s)
- Scott Becka
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio, USA
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Burgoyne AM, Phillips-Mason PJ, Burden-Gulley SM, Robinson S, Sloan AE, Miller RH, Brady-Kalnay SM. Proteolytic cleavage of protein tyrosine phosphatase mu regulates glioblastoma cell migration. Cancer Res 2009; 69:6960-8. [PMID: 19690139 DOI: 10.1158/0008-5472.can-09-0863] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Glioblastoma multiforme (GBM), the most common malignant primary brain tumor, represents a significant disease burden. GBM tumor cells disperse extensively throughout the brain parenchyma, and the need for tumor-specific drug targets and pharmacologic agents to inhibit cell migration and dispersal is great. The receptor protein tyrosine phosphatase mu (PTPmu) is a homophilic cell adhesion molecule. The full-length form of PTPmu is down-regulated in human glioblastoma. In this article, overexpression of full-length PTPmu is shown to suppress migration and survival of glioblastoma cells. Additionally, proteolytic cleavage is shown to be the mechanism of PTPmu down-regulation in glioblastoma cells. Proteolysis of PTPmu generates a series of proteolytic fragments, including a soluble catalytic intracellular domain fragment that translocates to the nucleus. Only proteolyzed PTPmu fragments are detected in human glioblastomas. Short hairpin RNA-mediated down-regulation of PTPmu fragments decreases glioblastoma cell migration and survival. A peptide inhibitor of PTPmu function blocks fragment-induced glioblastoma cell migration, which may prove to be of therapeutic value in GBM treatment. These data suggest that loss of cell surface PTPmu by proteolysis generates catalytically active PTPmu fragments that contribute to migration and survival of glioblastoma cells.
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Affiliation(s)
- Adam M Burgoyne
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106-4960, USA
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