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Ulke J, Chopra S, Kadiri OLJ, Geserick P, Stein V, Cheshmeh S, Kleinridders A, Kappert K. PTPRJ is a negative regulator of insulin signaling in neuronal cells, impacting protein biosynthesis, and neurite outgrowth. J Neuroendocrinol 2024:e13446. [PMID: 39253900 DOI: 10.1111/jne.13446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 07/29/2024] [Accepted: 08/28/2024] [Indexed: 09/11/2024]
Abstract
Central insulin resistance has been linked to the development of neurodegenerative diseases and mood disorders. Various proteins belonging to the enzyme family of protein tyrosine phosphatases (PTPs) act as inhibitors of insulin signaling. Protein tyrosine phosphatase receptor type J (PTPRJ) has been identified as a negative regulator in insulin signaling in the periphery. However, the impact of PTPRJ on insulin signaling and its functional role in neuronal cells is largely unknown. Therefore, we generated a Ptprj knockout (KO) cell model in the murine neuroblast cell line Neuro2a by CRISPR-Cas9 gene editing. Ptprj KO cells displayed enhanced insulin signaling, as shown by increased phosphorylation of the insulin receptor (INSR), IRS-1, AKT, and ERK1/2. Further, proximity ligation assays (PLA) revealed both direct interaction of PTPRJ with the INSR and recruitment of this phosphatase to the receptor upon insulin stimulation. By RNA sequencing gene expression analysis, we identified multiple gene clusters responsible for glucose uptake and metabolism, and genes involved in the synthesis of various lipids being mainly upregulated under PTPRJ deficiency. Furthermore, multiple Ca2+ transporters were differentially expressed along with decreased protein biosynthesis. This was accompanied by an increase in endoplasmic reticulum (ER) stress markers. On a functional level, PTPRJ deficiency compromised cell differentiation and neurite outgrowth, suggesting a role in nervous system development. Taken together, PTPRJ emerges as a negative regulator of central insulin signaling, impacting neuronal metabolism and neurite outgrowth.
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Affiliation(s)
- Jannis Ulke
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Diagnostic Laboratory Medicine, Clinical Chemistry and Pathobiochemistry, Berlin, Germany
- Max Rubner Center (MRC) for Cardiovascular Metabolic Renal Research, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Simran Chopra
- Department of Molecular and Experimental Nutritional Medicine, Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany
| | - Otsuware Linda-Josephine Kadiri
- Department of Molecular and Experimental Nutritional Medicine, Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany
| | - Peter Geserick
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Diagnostic Laboratory Medicine, Clinical Chemistry and Pathobiochemistry, Berlin, Germany
- Max Rubner Center (MRC) for Cardiovascular Metabolic Renal Research, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Vanessa Stein
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Diagnostic Laboratory Medicine, Clinical Chemistry and Pathobiochemistry, Berlin, Germany
- Max Rubner Center (MRC) for Cardiovascular Metabolic Renal Research, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Sahar Cheshmeh
- Department of Molecular and Experimental Nutritional Medicine, Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany
| | - André Kleinridders
- Department of Molecular and Experimental Nutritional Medicine, Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany
| | - Kai Kappert
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Diagnostic Laboratory Medicine, Clinical Chemistry and Pathobiochemistry, Berlin, Germany
- Max Rubner Center (MRC) for Cardiovascular Metabolic Renal Research, Charité-Universitätsmedizin Berlin, Berlin, Germany
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2
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Chen Z, Ji W, Feng W, Cui J, Wang Y, Li F, Chen J, Guo Z, Xia L, Zhu X, Niu X, Zhang Y, Li Z, Wong AST, Lu S, Xia W. PTPRT loss enhances anti-PD-1 therapy efficacy by regulation of STING pathway in non-small cell lung cancer. Sci Transl Med 2024; 16:eadl3598. [PMID: 39231239 DOI: 10.1126/scitranslmed.adl3598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 04/18/2024] [Accepted: 08/08/2024] [Indexed: 09/06/2024]
Abstract
With the revolutionary progress of immune checkpoint inhibitors (ICIs) in non-small cell lung cancer, identifying patients with cancer who would benefit from ICIs has become critical and urgent. Here, we report protein tyrosine phosphatase receptor type T (PTPRT) loss as a precise and convenient predictive marker independent of PD-L1 expression for anti-PD-1/PD-L1 axis therapy. Anti-PD-1/PD-L1 axis treatment markedly increased progression-free survival in patients with PTPRT-deficient tumors. PTPRT-deficient tumors displayed cumulative DNA damage, increased cytosolic DNA release, and higher tumor mutation burden. Moreover, the tyrosine residue 240 of STING was identified as a direct substrate of PTPRT. PTPRT loss elevated phosphorylation of STING at Y240 and thus inhibited its proteasome-mediated degradation. PTPRT-deficient tumors released more IFN-β, CCL5, and CXCL10 by activation of STING pathway and increased immune cell infiltration, especially of CD8 T cells and natural killer cells, ultimately enhancing the efficacy of anti-PD-1 therapy in multiple subcutaneous and orthotopic tumor mouse models. The response of PTPRT-deficient tumors to anti-PD-1 therapy depends on the tumor-intrinsic STING pathway. In summary, our findings reveal the mechanism of how PTPRT-deficient tumors become sensitive to anti-PD-1 therapy and highlight the biological function of PTPRT in innate immunity. Considering the prevalence of PTPRT mutations and negative expression, this study has great value for patient stratification and clinical decision-making.
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Affiliation(s)
- Zhuo Chen
- State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Wenxiang Ji
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
| | - Wenxin Feng
- State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Jingchuan Cui
- State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Yuchen Wang
- State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Fan Li
- State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Jiachen Chen
- State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Ziheng Guo
- State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Liliang Xia
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
| | - Xiaokuan Zhu
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
| | - Xiaomin Niu
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
| | - Yanshuang Zhang
- State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Ziming Li
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
| | - Alice S T Wong
- School of Biological Sciences, University of Hong Kong, Pokfulam Road, 999077, Hong Kong
| | - Shun Lu
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
| | - Weiliang Xia
- State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
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The Structure, Function and Regulation of Protein Tyrosine Phosphatase Receptor Type J and Its Role in Diseases. Cells 2022; 12:cells12010008. [PMID: 36611803 PMCID: PMC9818648 DOI: 10.3390/cells12010008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/08/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Protein tyrosine phosphatase receptor type J (PTPRJ), also known as DEP-1, HPTPη, or CD148, belongs to the R3 subfamily of receptor protein tyrosine phosphatases (RPTPs). It was first identified as an antioncogene due to its protein level being significantly downregulated in most epithelial tumors and cancer cell lines (e.g., colon, lung, thyroid, breast, and pancreas). PTPRJ regulates mouse optic nerve projection by inhibiting the phosphorylation of the erythropoietin-producing hepatocellular carcinoma (Eph) receptor and abelson murine leukemia viral oncogene homolog 1 (c-Abl). PTPRJ is crucial for metabolism. Recent studies have demonstrated that PTPRJ dephosphorylates JAK2 at positions Y813 and Y868 to inhibit leptin signaling. Akt is more phosphorylated at the Ser473 and Thr308 sites in Ptprj-/- mice, suggesting that PTPRJ may be a novel negative regulator of insulin signaling. PTPRJ also plays an important role in balancing the pro- and anti-osteoclastogenic activity of the M-CSF receptor (M-CSFR), and in maintaining NFATc1 expression during the late stages of osteoclastogenesis to promote bone-resorbing osteoclast (OCL) maturation. Furthermore, multiple receptor tyrosine kinases (RTKs) as substrates of PTPRJ are probably a potential therapeutic target for many types of diseases, such as cancer, neurodegenerative diseases, and metabolic diseases, by inhibiting their phosphorylation activity. In light of the important roles that PTPRJ plays in many diseases, this review summarizes the structural features of the protein, its expression pattern, and the physiological and pathological functions of PTPRJ, to provide new ideas for treating PTPRJ as a potential therapeutic target for related metabolic diseases and cancer.
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Yarnall MT, Kim SH, Korntner S, Bishop AC. Destabilization of the SHP2 and SHP1 protein tyrosine phosphatase domains by a non-conserved "backdoor" cysteine. Biochem Biophys Rep 2022; 32:101370. [PMID: 36275931 PMCID: PMC9578986 DOI: 10.1016/j.bbrep.2022.101370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 10/11/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
Protein tyrosine phosphatases (PTPs) are critical regulators of cellular signal transduction that catalyze the hydrolytic dephosphorylation of phosphotyrosine in substrate proteins. Among several conserved features in classical PTP domains are an active-site cysteine residue that is necessary for catalysis and a "backdoor" cysteine residue that can serve to protect the active-site cysteine from irreversible oxidation. Curiously, two biologically important phosphatases, Src homology domain-containing PTPs 2 and 1 (SHP2 and SHP1), each contain an additional backdoor cysteine residue at a position of the PTP domain that is occupied by proline in almost all other classical PTPs (position 333 in human SHP2 numbering). Here we show that the presence of cysteine 333 significantly destabilizes the fold of the PTP domains in the SHPs. We find that replacement of cysteine 333 with proline confers increased thermal stability on the SHP2 and SHP1 PTP domains, as measured by temperature-dependent activity assays and differential scanning fluorimetry. Conversely, we show that substantial destabilization of the PTP-domain fold is conferred by introduction of a non-natural cysteine residue in a non-SHP PTP that contains proline at the 333 position. It has previously been suggested that the extra backdoor cysteine of the SHP PTPs may work in tandem with the conserved backdoor cysteine to provide protection from irreversible oxidative enzyme inactivation. If so, our current results suggest that, during the course of mammalian evolution, the SHP proteins have developed extra protection from oxidation at the cost of the thermal instability that is conferred by the presence of their PTP domains' second backdoor cysteine.
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Affiliation(s)
| | - Sean H. Kim
- Amherst College, Department of Chemistry, Amherst, MA, 01002, USA
| | - Samuel Korntner
- Amherst College, Department of Chemistry, Amherst, MA, 01002, USA
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Wang CC, Shen WJ, Anuraga G, Khoa Ta HD, Xuan DTM, Chen ST, Shen CF, Jiang JZ, Sun Z, Wang CY, Wang WJ. Novel Potential Therapeutic Targets of PTPN Families for Lung Cancer. J Pers Med 2022; 12:jpm12121947. [PMID: 36556168 PMCID: PMC9784538 DOI: 10.3390/jpm12121947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/13/2022] [Accepted: 11/14/2022] [Indexed: 11/25/2022] Open
Abstract
Despite the treatment of lung adenocarcinoma (LUAD) having partially improved in recent years, LUAD patients still have poor prognosis rates. Therefore, it is especially important to explore effective biomarkers and exploit novel therapeutic developments. High-throughput technologies are widely used as systematic approaches to explore differences in expressions of thousands of genes for both biological and genomic systems. Recently, using big data analyses in biomedicine research by integrating several high-throughput databases and tools, including The Cancer Genome Atlas (TCGA), cBioportal, Oncomine, and Kaplan-Meier plotter, is an important strategy to identify novel biomarkers for cancer therapy. Here, we used two different comprehensive bioinformatics analysis and revealed protein tyrosine phosphatase non-receptor type (PTPN) family genes, especially PTPN1 and PTPN22, were downregulated in lung cancer tissue in comparison with normal samples. The survival curves indicated that LUAD patients with high transcription levels of PTPN5 were significantly associated with a good prognosis. Meanwhile, Gene Ontology (GO) and MetaCore analyses indicated that co-expression of the PTPN1, PTPN5, and PTPN21 genes was significantly enriched in cancer development-related pathways, including GTPase activity, regulation of small GTPase-mediated signal transduction, response to mechanical stimuli, vasculogenesis, organ morphogenesis, regulation of stress fiber assembly, mitogen-activated protein kinase (MAPK) cascade, cell migration, and angiogenesis. Collectively, this study revealed that PTPN family members are both significant prognostic biomarkers for lung cancer progression and promising clinical therapeutic targets, which provide new targets for treating LUAD patients.
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Affiliation(s)
- Chin-Chou Wang
- Divisions of Pulmonary & Critical Care Medicine, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan
- Department of Respiratory Therapy, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan
- Department of Respiratory Care, Chang Gung University of Science and Technology, Chiayi 613016, Taiwan
| | - Wan-Jou Shen
- Department of Biological Science and Technology, China Medical University, Taichung 40676, Taiwan
| | - Gangga Anuraga
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan
- Department of Statistics, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, Indonesia
| | - Hoang Dang Khoa Ta
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan
| | - Do Thi Minh Xuan
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Sih-Tong Chen
- Department of Biological Science and Technology, China Medical University, Taichung 40676, Taiwan
| | - Chiu-Fan Shen
- Divisions of Pulmonary & Critical Care Medicine, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan
| | - Jia-Zhen Jiang
- Emergency Department, Huashan Hospital North, Fudan University, Shanghai 201508, China
| | - Zhengda Sun
- Kaiser Permanente, Northern California Regional Laboratories, The Permanente Medical Group, 1725 Eastshore Hwy, Berkeley, CA 94710, USA
| | - Chih-Yang Wang
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei 11031, Taiwan
- Correspondence: (C.-Y.W.); (W.-J.W.)
| | - Wei-Jan Wang
- Department of Biological Science and Technology, China Medical University, Taichung 40676, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung 40676, Taiwan
- Correspondence: (C.-Y.W.); (W.-J.W.)
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Wang J, Li S, Zhang X, Zhu N, Yiminniyaze R, Dong L, Li C, Gulinuer W, Xia J, Li J, Zhou D, Liu X, Zhang Y, Zhang Y, Li S. Protein tyrosine phosphatase PTPL1 suppresses lung cancer through Src/ERK/YAP1 signaling. Thorac Cancer 2022; 13:3042-3051. [PMID: 36193770 PMCID: PMC9626330 DOI: 10.1111/1759-7714.14657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND To reveal the function of protein tyrosine phosphatase-L1 (PTPL1) in lung adenocarcinoma. METHODS Lung cancer cell lines were transfected with short hairpin RNA against PTPL1 (shPTPL1 group) or negative control (shmock group). Quantitative real-time polymerase chain reaction (qRT-PCR) and western blotting were used to verify the transfection efficacy. Cell proliferation was analyzed by ethynyldeoxyuridine (EdU), Cell counting kit 8 (CCK8), and colony formation assay after PTPL1 or PTPL1 and yes-associated protein (YAP1) knockdown. The effect of PTPL1 on tumor growth was examined in a xenograft lung cancer model. RESULTS PTPL1 was downregulated in various types of lung cancer cell lines. The EdU, CCK8, colony formation assays and investigation using a xenograft lung cancer model indicated that PTPL1 knockdown increased the proliferation of lung cancer cells. Mechanistically, PTPL1 knockdown induced the activation of the Proto-oncogene tyrosine-protein kinase SRC (Src)/Extracellular regulated MAP kinase (ERK) pathway and thereby promoted yes-associated protein (YAP1) nuclear translocation and activation. CONCLUSIONS In our study, PTPL1 played a crucial suppressive role in the pathogenesis of lung cancer potentially through counteracting the Src/ERK/YAP1 pathway.
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Affiliation(s)
- Jing Wang
- Department of Pulmonary and Critical Care Medicine, Huashan HospitalFudan UniversityShanghaiChina
| | - Shuanghui Li
- Department of Pulmonary and Critical Care Medicine, Huashan HospitalFudan UniversityShanghaiChina
| | - Xiujuan Zhang
- Department of Pulmonary and Critical Care Medicine, Huashan HospitalFudan UniversityShanghaiChina
| | - Ning Zhu
- Department of Pulmonary and Critical Care Medicine, Huashan HospitalFudan UniversityShanghaiChina
| | - Ruzetuoheti Yiminniyaze
- Department of Pulmonary and Critical Care Medicine, Huashan HospitalFudan UniversityShanghaiChina
| | - Liang Dong
- Department of Pulmonary and Critical Care Medicine, Huashan HospitalFudan UniversityShanghaiChina
| | - Chengwei Li
- Department of Pulmonary and Critical Care Medicine, Huashan HospitalFudan UniversityShanghaiChina
| | - Wumaier Gulinuer
- Department of Pulmonary and Critical Care Medicine, Huashan HospitalFudan UniversityShanghaiChina
| | - Jingwen Xia
- Department of Pulmonary and Critical Care Medicine, Huashan HospitalFudan UniversityShanghaiChina
| | - Jing Li
- Department of Pulmonary and Critical Care Medicine, Huashan HospitalFudan UniversityShanghaiChina
| | - Daibing Zhou
- Department of Pulmonary and Critical Care Medicine, Huashan HospitalFudan UniversityShanghaiChina
| | - Xinning Liu
- Department of Pulmonary and Critical Care Medicine, Huashan HospitalFudan UniversityShanghaiChina
| | - Youzhi Zhang
- Department of Pulmonary and Critical Care Medicine, Huashan HospitalFudan UniversityShanghaiChina
| | - Yuanyuan Zhang
- Department of Pulmonary and Critical Care Medicine, Huashan HospitalFudan UniversityShanghaiChina
| | - Shengqing Li
- Department of Pulmonary and Critical Care Medicine, Huashan HospitalFudan UniversityShanghaiChina
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Wang T, Ba X, Zhang X, Zhang N, Wang G, Bai B, Li T, Zhao J, Zhao Y, Yu Y, Wang B. Pan-cancer analyses of classical protein tyrosine phosphatases and phosphatase-targeted therapy in cancer. Front Immunol 2022; 13:976996. [PMID: 36341348 PMCID: PMC9630847 DOI: 10.3389/fimmu.2022.976996] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 10/04/2022] [Indexed: 09/23/2023] Open
Abstract
Protein tyrosine phosphatases function in dephosphorylating target proteins to regulate signaling pathways that control a broad spectrum of fundamental physiological and pathological processes. Detailed knowledge concerning the roles of classical PTPs in human cancer merits in-depth investigation. We comprehensively analyzed the regulatory mechanisms and clinical relevance of classical PTPs in more than 9000 tumor patients across 33 types of cancer. The independent datasets and functional experiments were employed to validate our findings. We exhibited the extensive dysregulation of classical PTPs and constructed the gene regulatory network in human cancer. Moreover, we characterized the correlation of classical PTPs with both drug-resistant and drug-sensitive responses to anti-cancer drugs. To evaluate the PTP activity in cancer prognosis, we generated a PTPscore based on the expression and hazard ratio of classical PTPs. Our study highlights the notable role of classical PTPs in cancer biology and provides novel intelligence to improve potential therapeutic strategies based on pTyr regulation.
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Affiliation(s)
- Tao Wang
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Xinlei Ba
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Xiaonan Zhang
- College of Life and Health Sciences, Northeastern University, Shenyang, China
- Department of Pathophysiology, Bengbu Medical College, Bengbu, China
| | - Na Zhang
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Guowen Wang
- Department of Thoracic surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Bin Bai
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Tong Li
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Jiahui Zhao
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Yanjiao Zhao
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Yang Yu
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Bing Wang
- College of Life and Health Sciences, Northeastern University, Shenyang, China
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8
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Gong T, Jaratlerdsiri W, Jiang J, Willet C, Chew T, Patrick SM, Lyons RJ, Haynes AM, Pasqualim G, Brum IS, Stricker PD, Mutambirwa SBA, Sadsad R, Papenfuss AT, Bornman RMS, Chan EKF, Hayes VM. Genome-wide interrogation of structural variation reveals novel African-specific prostate cancer oncogenic drivers. Genome Med 2022; 14:100. [PMID: 36045381 PMCID: PMC9434886 DOI: 10.1186/s13073-022-01096-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 07/28/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND African ancestry is a significant risk factor for advanced prostate cancer (PCa). Mortality rates in sub-Saharan Africa are 2.5-fold greater than global averages. However, the region has largely been excluded from the benefits of whole genome interrogation studies. Additionally, while structural variation (SV) is highly prevalent, PCa genomic studies are still biased towards small variant interrogation. METHODS Using whole genome sequencing and best practice workflows, we performed a comprehensive analysis of SVs for 180 (predominantly Gleason score ≥ 8) prostate tumours derived from 115 African, 61 European and four ancestrally admixed patients. We investigated the landscape and relationship of somatic SVs in driving ethnic disparity (African versus European), with a focus on African men from southern Africa. RESULTS Duplication events showed the greatest ethnic disparity, with a 1.6- (relative frequency) to 2.5-fold (count) increase in African-derived tumours. Furthermore, we found duplication events to be associated with CDK12 inactivation and MYC copy number gain, and deletion events associated with SPOP mutation. Overall, African-derived tumours were 2-fold more likely to present with a hyper-SV subtype. In addition to hyper-duplication and deletion subtypes, we describe a new hyper-translocation subtype. While we confirm a lower TMPRSS2-ERG fusion-positive rate in tumours from African cases (10% versus 33%), novel African-specific PCa ETS family member and TMPRSS2 fusion partners were identified, including LINC01525, FBXO7, GTF3C2, NTNG1 and YPEL5. Notably, we found 74 somatic SV hotspots impacting 18 new candidate driver genes, with CADM2, LSAMP, PTPRD, PDE4D and PACRG having therapeutic implications for African patients. CONCLUSIONS In this first African-inclusive SV study for high-risk PCa, we demonstrate the power of SV interrogation for the identification of novel subtypes, oncogenic drivers and therapeutic targets. Identifying a novel spectrum of SVs in tumours derived from African patients provides a mechanism that may contribute, at least in part, to the observed ethnic disparity in advanced PCa presentation in men of African ancestry.
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Affiliation(s)
- Tingting Gong
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, Australia
- Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Human Phenome Institute, Fudan University, Shanghai, China
| | - Weerachai Jaratlerdsiri
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, Australia
- Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Jue Jiang
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, Australia
- Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Cali Willet
- Sydney Informatics Hub, University of Sydney, Sydney, NSW, Australia
| | - Tracy Chew
- Sydney Informatics Hub, University of Sydney, Sydney, NSW, Australia
| | - Sean M Patrick
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - Ruth J Lyons
- Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Anne-Maree Haynes
- Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Gabriela Pasqualim
- Endocrine and Tumor Molecular Biology Laboratory, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratory of Genetics, Instituto de Ciências Biológicas, Universidade Federal do Rio Grande, Rio Grande, Brazil
| | - Ilma Simoni Brum
- Endocrine and Tumor Molecular Biology Laboratory, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Phillip D Stricker
- Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Department of Urology, St. Vincent's Hospital, Darlinghurst, NSW, Australia
| | - Shingai B A Mutambirwa
- Department of Urology, Sefako Makgatho Health Science University, Dr George Mukhari Academic Hospital, Medunsa, Ga-Rankuwa, South Africa
| | - Rosemarie Sadsad
- Sydney Informatics Hub, University of Sydney, Sydney, NSW, Australia
| | - Anthony T Papenfuss
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Riana M S Bornman
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - Eva K F Chan
- Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- NSW Health Pathology, Sydney, Australia
| | - Vanessa M Hayes
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, Australia.
- Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa.
- Faculty of Health Sciences, University of Limpopo, Turfloop Campus, Mankweng, South Africa.
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Zhao J, Dai K, Xie J, Fang C, Chen N, Dai J, Xu D. Case Report: Clinical complete response of advanced renal cell carcinoma associated with Xp11.2 translocation/TFE3 gene fusion by treated by camrelizumab and axitinib: A rare case report. Front Pharmacol 2022; 13:927299. [PMID: 36034832 PMCID: PMC9403306 DOI: 10.3389/fphar.2022.927299] [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: 04/24/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
Renal cell carcinoma (RCC) associated with Xp11.2 translocation/TFE3 gene fusions is a rare subtype of renal tumor. This entity predominantly occurs in juveniles, but rarely in adults. Xp11.2 translocation RCC (tRCC) patients with lymph node or organ metastasis are associated with poor prognosis, and the strategy remains controversial. Herein, we presented our experience with the diagnosis and treatment of an adult case of Xp11.2 tRCC. In our clinical practice, a 32-year-old male manifested fever and right flank paroxysmal blunt pain, and computed tomography showed an inhomogeneous mass, 6 cm in diameter, in the right kidney. Then right partial nephrectomy (PN) and renal hilar lymph node dissection by laparoscopic surgery were performed. Pathology revealed that the tumor cells were positive for TFE3 immunohistologically and positive for TFE3 break-apart fluorescence in situ hybridization assay. A splice site mutation c.1544-1G>T of protein tyrosine phosphatase receptor delta (PTPRD) was detected by next-generation sequencing and weak PTPRD expression was confirmed in tumor tissues compared to tumor periphery. This patient was diagnosed with stage III RCC and received immune checkpoint inhibitor (camrelizumab) in combination with tyrosine kinase inhibitor (axitinib) treatment for 1 year. He achieved a clinical complete response with no sign of recurrence or metastasis. PTPRD mutation might be a favorable indicator for Xp11.2 tRCC patients managed by PN and followed by the adjuvant therapy of immune checkpoint inhibitor and tyrosine kinase inhibitor.
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Affiliation(s)
- Juping Zhao
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Juping Zhao, ; Jun Dai, ; Danfeng Xu,
| | - Kun Dai
- Hangzhou Jichenjunchuang Medical Laboratory Co.Ltd, Hangzhou, China
| | - Jialing Xie
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chen Fang
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Na Chen
- Hangzhou Jichenjunchuang Medical Laboratory Co.Ltd, Hangzhou, China
| | - Jun Dai
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Juping Zhao, ; Jun Dai, ; Danfeng Xu,
| | - Danfeng Xu
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Juping Zhao, ; Jun Dai, ; Danfeng Xu,
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10
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Liu R, Sun Y, Berthelet J, Bui LC, Xu X, Viguier M, Dupret JM, Deshayes F, Rodrigues Lima F. Biochemical, Enzymatic, and Computational Characterization of Recurrent Somatic Mutations of the Human Protein Tyrosine Phosphatase PTP1B in Primary Mediastinal B Cell Lymphoma. Int J Mol Sci 2022; 23:ijms23137060. [PMID: 35806064 PMCID: PMC9266312 DOI: 10.3390/ijms23137060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/23/2022] [Accepted: 06/23/2022] [Indexed: 12/16/2022] Open
Abstract
Human protein tyrosine phosphatase 1B (PTP1B) is a ubiquitous non-receptor tyrosine phosphatase that serves as a major negative regulator of tyrosine phosphorylation cascades of metabolic and oncogenic importance such as the insulin, epidermal growth factor receptor (EGFR), and JAK/STAT pathways. Increasing evidence point to a key role of PTP1B-dependent signaling in cancer. Interestingly, genetic defects in PTP1B have been found in different human malignancies. Notably, recurrent somatic mutations and splice variants of PTP1B were identified in human B cell and Hodgkin lymphomas. In this work, we analyzed the molecular and functional levels of three PTP1B mutations identified in primary mediastinal B cell lymphoma (PMBCL) patients and located in the WPD-loop (V184D), P-loop (R221G), and Q-loop (G259V). Using biochemical, enzymatic, and molecular dynamics approaches, we show that these mutations lead to PTP1B mutants with extremely low intrinsic tyrosine phosphatase activity that display alterations in overall protein stability and in the flexibility of the active site loops of the enzyme. This is in agreement with the key role of the active site loop regions, which are preorganized to interact with the substrate and to enable catalysis. Our study provides molecular and enzymatic evidence for the loss of protein tyrosine phosphatase activity of PTP1B active-site loop mutants identified in human lymphoma.
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Affiliation(s)
- Rongxing Liu
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France; (R.L.); (L.-C.B.); (M.V.); (J.-M.D.); (F.D.)
| | - Yujie Sun
- School of Medicine and Pharmacy, Ocean University of China, Qingdao 266071, China; (Y.S.); (X.X.)
| | - Jérémy Berthelet
- Université Paris Cité, CNRS, Centre d’Epigénétique et Destin Cellulaire, F-75013 Paris, France;
| | - Linh-Chi Bui
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France; (R.L.); (L.-C.B.); (M.V.); (J.-M.D.); (F.D.)
| | - Ximing Xu
- School of Medicine and Pharmacy, Ocean University of China, Qingdao 266071, China; (Y.S.); (X.X.)
| | - Mireille Viguier
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France; (R.L.); (L.-C.B.); (M.V.); (J.-M.D.); (F.D.)
| | - Jean-Marie Dupret
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France; (R.L.); (L.-C.B.); (M.V.); (J.-M.D.); (F.D.)
| | - Frédérique Deshayes
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France; (R.L.); (L.-C.B.); (M.V.); (J.-M.D.); (F.D.)
| | - Fernando Rodrigues Lima
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France; (R.L.); (L.-C.B.); (M.V.); (J.-M.D.); (F.D.)
- Correspondence:
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11
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Sain A, Khamrai D, Kandasamy T, Naskar D. Targeting protein tyrosine phosphatase 1B in obesity-associated colon cancer: Possible role of sweet potato (Ipomoea batatas). Proteins 2022; 90:1346-1362. [PMID: 35119127 DOI: 10.1002/prot.26316] [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: 09/28/2021] [Revised: 01/21/2022] [Accepted: 01/27/2022] [Indexed: 11/05/2022]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) has emerged as one of the links between obesity and colon cancer (CC). Anti-obesity and anti-CC attributes of sweet potato (Ipomoea batatas) reported sparsely. Here, we aimed to study the potential of PTP1B as a target in CC, particularly in obese population. Expression and genomic alteration frequency of PTPN1 (PTP1B) were checked in CC. Interacting partners of PTP1B through STRING and hub genes through Cytoscape (MCODE) were identified. Hub genes were subjected to functional enrichment analyses (via Metascape), differential gene expression, copy number variation, and single nucleotide variation analyses (GSCA database). Cancer-related pathways and associated immune infiltrates of the hub genes were checked too. Eleven sweet potato-derived compounds selected through drug likeness (DL) and toxicity filters were explored via molecular docking (AutoDock Vina) to reveal the interactions with PTP1B. Genomic alteration frequency of the PTPN1 was highest in CC compared to all the other TCGA cancers, and a high expression (RNA and protein) is also observed in CC that correlated well to a poor overall survival (OS). Furthermore, PTP1B and related proteins were enriched in different biological processes and signaling pathways related to carcinogenesis including epithelial-mesenchymal transition. Overall, PTP1B identified as a potential target in obesity-linked CC and sweet potato might exert its protective action by targeting the PTP1B. Sweet potato compounds (e.g., pelargonidin and luteolin) interacted with the catalytic P loop and the WPD loop of the PTP1B. Furthermore, MD simulation study ascertained that luteolin has the highest affinity against the PTP1B, whereas pelargonidin and quercetin showed good binding affinity too, thus can be explored further.
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Affiliation(s)
- Arindam Sain
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, Nadia, West Bengal, India
| | - Dipshikha Khamrai
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, Nadia, West Bengal, India
| | - Thirukumaran Kandasamy
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Debdut Naskar
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, Nadia, West Bengal, India
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12
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Moshiri H, Cabrera Riofrío DA, Lim YJ, Lauhasurayotin S, Manisterski M, Elhasid R, Bonilla FA, Dhanraj S, Armstrong RN, Li H, Scherer SW, Hernández-Hernández A, Dror Y. Germline PTPN13 mutations in patients with bone marrow failure and acute lymphoblastic leukemia. Leukemia 2022; 36:2132-2135. [DOI: 10.1038/s41375-022-01610-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/05/2022] [Accepted: 05/17/2022] [Indexed: 11/09/2022]
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13
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Li Y, Jia A, Yang H, Wang Y, Wang Y, Yang Q, Cao Y, Bi Y, Liu G. Protein Tyrosine Phosphatase PTPRO Signaling Couples Metabolic States to Control the Development of Granulocyte Progenitor Cells. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:1434-1444. [PMID: 35246496 DOI: 10.4049/jimmunol.2100878] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 12/30/2021] [Indexed: 06/14/2023]
Abstract
Protein tyrosine phosphatase (PTPase) is critically involved in the regulation of hematopoietic stem cell development and differentiation. Roles of novel isolated receptor PTPase PTPRO from bone marrow hematopoietic stem cells in granulopoiesis have not been investigated. PTPRO expression is correlated with granulocytic differentiation, and Ptpro -/- mice developed neutrophilia, with an expanded granulocytic compartment resulting from a cell-autonomous increase in the number of granulocyte progenitors under steady-state and potentiated innate immune responses against Listeria monocytogenes infection. Mechanistically, mTOR and HIF1α signaling engaged glucose metabolism and initiated a transcriptional program involving the lineage decision factor C/EBPα, which is critically required for the PTPRO deficiency-directed granulopoiesis. Genetic ablation of mTOR or HIF1α or perturbation of glucose metabolism suppresses progenitor expansion, neutrophilia, and higher glycolytic activities by Ptpro -/- In addition, Ptpro -/- upregulated HIF1α regulates the lineage decision factor C/EBPα promoter activities. Thus, our findings identify a previously unrecognized interplay between receptor PTPase PTPRO signaling and mTOR-HIF1α metabolic reprogramming in progenitor cells of granulocytes that underlies granulopoiesis.
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Affiliation(s)
- Yan Li
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Anna Jia
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Hui Yang
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai, China; and
| | - Yuexin Wang
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yufei Wang
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Qiuli Yang
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yejin Cao
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yujing Bi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Guangwei Liu
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China;
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14
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Bhattacharjee S, Chakraborty T, Bhaumik A. A Ce-MOF as an alkaline phosphatase mimic: Ce-OH 2 sites in catalytic dephosphorylation. Inorg Chem Front 2022. [DOI: 10.1039/d2qi01443b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
For the first time, a metal–organic framework (Ce-MOF) bearing a Ce–OH2–Ce motif was used to mimic the active sites of alkaline phosphatase.
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Affiliation(s)
- Sudip Bhattacharjee
- School of Materials Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Tonmoy Chakraborty
- School of Materials Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Asim Bhaumik
- School of Materials Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
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15
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Ismail MA, Nasrallah GK, Monne M, AlSayab A, Yassin MA, Varadharaj G, Younes S, Sorio C, Cook R, Modjtahedi H, Al-Dewik NI. Description of PTPRG genetic variants identified in a cohort of Chronic Myeloid Leukemia patients and their ability to influence response to Tyrosine kinase Inhibitors. Gene 2021; 813:146101. [PMID: 34906644 DOI: 10.1016/j.gene.2021.146101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 10/07/2021] [Accepted: 11/16/2021] [Indexed: 12/25/2022]
Abstract
Tyrosine kinase inhibitors (TKIs) have remarkably transformed Ph+ chronic myeloid leukemia (CML) management; however, TKI resistance remains a major clinical challenge. Mutations in BCR-ABL1 are well studied but fail to explain 20-40% of resistant cases, suggesting the activation of alternative, BCR-ABL1-independent pathways. Protein Tyrosine Phosphatase Receptor Gamma (PTPRG), a tumor suppressor, was found to be well expressed in CML patients responsive to TKIs and down-regulated in resistant patients. In this study, we aimed to identify genetic variants in PTPRG that could potentially modulate TKIs response in CML patients. DNA was extracted from peripheral blood samples collected from two CML cohorts (Qatar and Italy) and targeted exome sequencing was performed. Among 31 CML patients, six were TKI-responders and 25 were TKI-resistant. Sequencing identified ten variants, seven were annotated and three were novel SNPs (c.1602_1603insC, c.85+86delC, and c.2289-129delA). Among them, five variants were identified in 15 resistant cases. Of these, one novel exon variant (c.1602_1603insC), c.841-29C>T (rs199917960) and c.1378-224A>G (rs2063204) were found to be significantly different between the resistant cases compared to responders. Our findings suggest that PTPRG variants may act as an indirect resistance mechanism of BCR-ABL1 to affect TKI treatment.
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Affiliation(s)
- Mohamed A Ismail
- School of Life Science, Pharmacy and Chemistry, Faculty of science, engineering & computing-Kingston University London, United Kingdom; Interim Translational Research Institute (iTRI), Hamad Medical Corporation (HMC), Doha, Qatar
| | - Gheyath K Nasrallah
- Department of Biomedical Science, College of Health Sciences, Member of QU Health, Qatar University, Doha, Qatar
| | - Maria Monne
- Centro di Diagnostica Biomolecolare e Citogenetica Emato-Oncologica, "San Francesco" Hospital, Nuoro, Italy
| | - Ali AlSayab
- Interim Translational Research Institute (iTRI), Hamad Medical Corporation (HMC), Doha, Qatar
| | - Mohamed A Yassin
- Department of Medical Oncology, National Centre for Cancer Care and Research, Hamad Medical Corporation (HMC), Doha, Qatar
| | | | - Salma Younes
- Department of Research, Women's Wellness and Research Center, Hamad Medical Corporation, Qatar
| | - Claudio Sorio
- Department of Medicine, University of Verona, Verona, Italy
| | - Richard Cook
- School of Life Science, Pharmacy and Chemistry, Faculty of science, engineering & computing-Kingston University London, United Kingdom
| | - Helmout Modjtahedi
- School of Life Science, Pharmacy and Chemistry, Faculty of science, engineering & computing-Kingston University London, United Kingdom
| | - Nader I Al-Dewik
- Interim Translational Research Institute (iTRI), Hamad Medical Corporation (HMC), Doha, Qatar; Faculty of Health and Social Care Sciences, Kingston University, St. George's University of London, UK; Clinical and Metabolic Genetics, Department of Pediatrics, Hamad General Hospital, Hamad Medical Corporation, Doha, Qatar; College of Health and Life Science (CHLS), Hamad Bin Khalifa University (HBKU), Doha, Qatar.
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16
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Turdo A, D'Accardo C, Glaviano A, Porcelli G, Colarossi C, Colarossi L, Mare M, Faldetta N, Modica C, Pistone G, Bongiorno MR, Todaro M, Stassi G. Targeting Phosphatases and Kinases: How to Checkmate Cancer. Front Cell Dev Biol 2021; 9:690306. [PMID: 34778245 PMCID: PMC8581442 DOI: 10.3389/fcell.2021.690306] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 10/04/2021] [Indexed: 12/21/2022] Open
Abstract
Metastatic disease represents the major cause of death in oncologic patients worldwide. Accumulating evidence have highlighted the relevance of a small population of cancer cells, named cancer stem cells (CSCs), in the resistance to therapies, as well as cancer recurrence and metastasis. Standard anti-cancer treatments are not always conclusively curative, posing an urgent need to discover new targets for an effective therapy. Kinases and phosphatases are implicated in many cellular processes, such as proliferation, differentiation and oncogenic transformation. These proteins are crucial regulators of intracellular signaling pathways mediating multiple cellular activities. Therefore, alterations in kinases and phosphatases functionality is a hallmark of cancer. Notwithstanding the role of kinases and phosphatases in cancer has been widely investigated, their aberrant activation in the compartment of CSCs is nowadays being explored as new potential Achille's heel to strike. Here, we provide a comprehensive overview of the major protein kinases and phosphatases pathways by which CSCs can evade normal physiological constraints on survival, growth, and invasion. Moreover, we discuss the potential of inhibitors of these proteins in counteracting CSCs expansion during cancer development and progression.
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Affiliation(s)
- Alice Turdo
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties (PROMISE), University of Palermo, Palermo, Italy
| | - Caterina D'Accardo
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties (PROMISE), University of Palermo, Palermo, Italy
| | - Antonino Glaviano
- Department of Surgical, Oncological and Stomatological Sciences (DICHIRONS), University of Palermo, Palermo, Italy
| | - Gaetana Porcelli
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties (PROMISE), University of Palermo, Palermo, Italy
| | - Cristina Colarossi
- Department of Experimental Oncology, Mediterranean Institute of Oncology (IOM), Catania, Italy
| | - Lorenzo Colarossi
- Department of Experimental Oncology, Mediterranean Institute of Oncology (IOM), Catania, Italy
| | - Marzia Mare
- Department of Experimental Oncology, Mediterranean Institute of Oncology (IOM), Catania, Italy
| | | | - Chiara Modica
- Department of Surgical, Oncological and Stomatological Sciences (DICHIRONS), University of Palermo, Palermo, Italy
| | - Giuseppe Pistone
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties (PROMISE), University of Palermo, Palermo, Italy
| | - Maria Rita Bongiorno
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties (PROMISE), University of Palermo, Palermo, Italy
| | - Matilde Todaro
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties (PROMISE), University of Palermo, Palermo, Italy.,Azienda Ospedaliera Universitaria Policlinico (AOUP), Palermo, Italy
| | - Giorgio Stassi
- Department of Surgical, Oncological and Stomatological Sciences (DICHIRONS), University of Palermo, Palermo, Italy
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17
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Watt AT, Head B, Leonard SW, Tanguay RL, Traber MG. Gene Expression of CRAL_TRIO Family Proteins modulated by Vitamin E Deficiency in Zebrafish (Danio Rerio). J Nutr Biochem 2021; 97:108801. [PMID: 34119630 PMCID: PMC10129037 DOI: 10.1016/j.jnutbio.2021.108801] [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: 08/12/2020] [Revised: 04/19/2021] [Accepted: 06/01/2021] [Indexed: 11/15/2022]
Abstract
An evaluation of the impact of vitamin E deficiency on expression of the alpha-tocopherol transfer protein (α-TTP) and related CRAL_TRIO genes was undertaken using livers from adult zebrafish based on the hypothesis that increased lipid peroxidation would modulate gene expression. Zebrafish were fed either a vitamin E sufficient (E+) or deficient (E-) diet for 9 months, then fish were euthanized, and livers were harvested. Livers from the E+ relative to E- fish contained 40-times more α-tocopherol (P <0.0001) and one fourth the malondialdehyde (P = 0.0153). RNA was extracted from E+ and E- livers, then subject to evaluation of gene expression of ttpa and other genes of the CRAL_TRIO family, genes of antioxidant markers, and genes related to lipid metabolism. Ttpa expression was not altered by vitamin E status. However, one member of the CRAL_TRIO family, tyrosine-protein phosphatase non-receptor type 9 gene (ptpn9a), showed a 2.4-fold increase (P = 0.029) in E- relative to E+ livers. Further, we identified that the gene for choline kinase alpha (chka) showed a 3.0-fold increase (P = 0.010) in E- livers. These outcomes are consistent with our previous findings that show vitamin E deficiency increased lipid peroxidation causing increases in phospholipid turnover.
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Affiliation(s)
- Alexander T Watt
- Linus Pauling Institute, Oregon State University, Corvallis, Oregon; Integrative Biology Program, Oregon State University, Corvallis, Oregon
| | - Brian Head
- Linus Pauling Institute, Oregon State University, Corvallis, Oregon; Molecular and Cell Biology Program
| | - Scott W Leonard
- Linus Pauling Institute, Oregon State University, Corvallis, Oregon
| | - Robyn L Tanguay
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, Oregon
| | - Maret G Traber
- Linus Pauling Institute, Oregon State University, Corvallis, Oregon; School of Biological and Population Health Sciences, Oregon State University, Corvallis, Oregon.
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18
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He Z, Li A, Lin D, Gu Y, Chen Y, Ou Q, Li L, Yao H, Yu Y. Association of immune checkpoint inhibitor with survival in patients with cancers with protein tyrosine phosphatase receptor T mutation. Clin Transl Med 2020; 10:e214. [PMID: 33135355 PMCID: PMC7591738 DOI: 10.1002/ctm2.214] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/07/2020] [Accepted: 10/12/2020] [Indexed: 12/24/2022] Open
Affiliation(s)
- Zifan He
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Medical Oncology, Phase I Clinical Trial Centre, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Anlin Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Medical Oncology, Phase I Clinical Trial Centre, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,The First Clinical Medical College, Guangdong Medical University, Zhanjiang, China
| | - Dagui Lin
- Department of Colorectal Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yang Gu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Medical Oncology, Phase I Clinical Trial Centre, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yongjian Chen
- Department of Medical Oncology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Qiyun Ou
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Medical Oncology, Phase I Clinical Trial Centre, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Liren Li
- Department of Colorectal Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Herui Yao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Medical Oncology, Phase I Clinical Trial Centre, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yunfang Yu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Medical Oncology, Phase I Clinical Trial Centre, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
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19
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Structural Insights into the Active Site Formation of DUSP22 in N-loop-containing Protein Tyrosine Phosphatases. Int J Mol Sci 2020; 21:ijms21207515. [PMID: 33053837 PMCID: PMC7589817 DOI: 10.3390/ijms21207515] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/07/2020] [Accepted: 10/09/2020] [Indexed: 02/07/2023] Open
Abstract
Cysteine-based protein tyrosine phosphatases (Cys-based PTPs) perform dephosphorylation to regulate signaling pathways in cellular responses. The hydrogen bonding network in their active site plays an important conformational role and supports the phosphatase activity. Nearly half of dual-specificity phosphatases (DUSPs) use three conserved residues, including aspartate in the D-loop, serine in the P-loop, and asparagine in the N-loop, to form the hydrogen bonding network, the D-, P-, N-triloop interaction (DPN-triloop interaction). In this study, DUSP22 is used to investigate the importance of the DPN-triloop interaction in active site formation. Alanine mutations and somatic mutations of the conserved residues, D57, S93, and N128 substantially decrease catalytic efficiency (kcat/KM) by more than 102-fold. Structural studies by NMR and crystallography reveal that each residue can perturb the three loops and induce conformational changes, indicating that the hydrogen bonding network aligns the residues in the correct positions for substrate interaction and catalysis. Studying the DPN-triloop interaction reveals the mechanism maintaining phosphatase activity in N-loop-containing PTPs and provides a foundation for further investigation of active site formation in different members of this protein class.
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20
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Long Q, Sun J, Lv J, Liang Y, Li H, Li X. PTPN13 acts as a tumor suppressor in clear cell renal cell carcinoma by inactivating Akt signaling. Exp Cell Res 2020; 396:112286. [PMID: 32919955 DOI: 10.1016/j.yexcr.2020.112286] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/04/2020] [Accepted: 09/09/2020] [Indexed: 01/24/2023]
Abstract
Protein tyrosine phosphatase, nonreceptor type 13 (PTPN13), has emerged as a critical cancer-related gene that is implicated in a wide range of cancer types. However, the role of PTPN13 in clear cell renal cell carcinoma (ccRCC) is poorly understood. In the present study, we aimed to evaluate whether PTPN13 participates in the progression of ccRCC. Decreased expression of PTPN13 was found in ccRCC tissues, which predicted a shorter survival rate in ccRCC patients. PTPN13 expression was also lower in ccRCC cell lines, and the upregulation of PTPN13 repressed the proliferation, colony formation and invasion, but enhanced the apoptosis of ccRCC cells. In contrast, the silencing of PTPN13 produced the opposite effects. Further data showed that PTPN13 overexpression decreased the phosphorylation of Akt, while PTPN13 silencing increased the phosphorylation of Akt. Treatment with Akt inhibitor markedly abrogated the PTPN13 silencing-evoked oncogenic effect in ccRCC cells. Xenograft tumor experiments revealed that overexpression of PTPN13 remarkably restricted the tumor formation and growth of ccRCC cells in vivo associated with inactivation of Akt. In conclusion, our data demonstrated that overexpression of PTPN13 restricts the proliferation and invasion of ccRCC cells through inactivation of Akt. Our study suggests a tumor suppressive function of PTPN13 in ccRCC and highlights the potential role of PTPN13 in the progression of ccRCC.
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Affiliation(s)
- Qingzhi Long
- Department of Urology, The First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Jiping Sun
- Department of Nephrology, The First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Jia Lv
- Department of Nephrology, The First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yu Liang
- Department of Nephrology, The First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Huixian Li
- Department of Nephrology, The First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Xudong Li
- Department of Urology, The First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an, 710061, China.
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21
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Lou J, Best MD. A General Approach to Enzyme‐Responsive Liposomes. Chemistry 2020; 26:8597-8607. [DOI: 10.1002/chem.202000529] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/14/2020] [Indexed: 01/06/2023]
Affiliation(s)
- Jinchao Lou
- Department of Chemistry University of Tennessee 1420 Circle Drive Knoxville TN 37996 USA
| | - Michael D. Best
- Department of Chemistry University of Tennessee 1420 Circle Drive Knoxville TN 37996 USA
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22
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Jahejo AR, Rajput N, Kashif J, Kalhoro DH, Niu S, Qiao ML, Zhang D, Qadir MF, Mangi RA, Khan A, Ahsan A, Khan A, Tian WX. Recombinant glutathione-S-transferase A3 protein regulates the angiogenesis-related genes of erythrocytes in thiram induced tibial lesions. Res Vet Sci 2020; 131:244-253. [PMID: 32438067 DOI: 10.1016/j.rvsc.2020.05.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/06/2020] [Accepted: 05/07/2020] [Indexed: 12/13/2022]
Abstract
Tibial dyschondroplasia (TD) is a skeletal deformity disease in broilers that occurs when vascularization in the growth plate (GP) is below normal. Although, blood vessels have been reported to contribute significantly in bone formation. Therefore, in the current study, we have examined the mRNA expression of angiogenesis-related genes in erythrocytes of thiram induced TD chickens by qRT-PCR and performed histopathological analysis to determine regulatory effect of recombinant Glutathione-S-Transferase A3 (rGSTA3) protein in response to the destructive effect of thiram following the injection of rGSTA3 protein. Histopathology results suggested that, blood vessels of GPs were damaged in thiram induced TD chicken group (D), it also affected the area and density of blood vessels. In the 20 and 50 μg·kg-1 of rGSTA3 protein-administered groups, E and F vessels appeared to be normal and improved on day 6 and 15. Furthermore, qRT-PCR results showed that rGSTA3 protein significantly (P < .05) up-regulated the expression of the most important angiogenesis-related integrin family genes ITGA2, ITGA5, ITGB2, ITGB3, ITGAV. The expression level of other genes including TBXA2R, FYN, IQGAP2, IL1R1, GIT1, RAP1B, RPL17, RAC2, MAML3, PTPN11, VAV1, PTCH1, NCOR2, CLU and ITGB3 up-regulated on dosage of rGSTA3 protein. In conclusion, angiogenesis is destroyed in thiram induced TD broilers, and rGSTA3 protein injection improved the vascularization of GPs by upregulating the angiogenesis related genes most importantly integrin family genes ITGAV, ITGA2, ITGB2, ITGB3, ITGA5.
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Affiliation(s)
- Ali Raza Jahejo
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, China
| | - Nasir Rajput
- Faculty of Animal Husbandry and Veterinary Sciences, Sindh Agriculture University Tandojam, Sindh 70060, Pakistan
| | - Jam Kashif
- Faculty of Animal Husbandry and Veterinary Sciences, Sindh Agriculture University Tandojam, Sindh 70060, Pakistan
| | - Dildar Hussain Kalhoro
- Faculty of Animal Husbandry and Veterinary Sciences, Sindh Agriculture University Tandojam, Sindh 70060, Pakistan
| | - Sheng Niu
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, China
| | - Meng-Li Qiao
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, China
| | - Ding Zhang
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, China
| | - Muhammad Farhan Qadir
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, China
| | - Raza Ali Mangi
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, China
| | - Afrasyab Khan
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, China
| | - Anam Ahsan
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, China
| | - Ajab Khan
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, China
| | - Wen-Xia Tian
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, China.
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23
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Jahejo AR, Zhang D, Niu S, Mangi RA, Khan A, Qadir MF, Khan A, Chen HC, Tian WX. Transcriptome-based screening of intracellular pathways and angiogenesis related genes at different stages of thiram induced tibial lesions in broiler chickens. BMC Genomics 2020; 21:50. [PMID: 31941444 PMCID: PMC6964038 DOI: 10.1186/s12864-020-6456-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 01/07/2020] [Indexed: 01/21/2023] Open
Abstract
Background The Tibial dyschondroplasia (TD) in fast-growing chickens is mainly caused by improper blood circulation. The exact mechanism underlying angiogenesis and vascularization in tibial growth plate of broiler chickens remains unclear. Therefore, this research attempts to study genes involved in the regulation of angiogenesis in chicken red blood cells. Twenty-four broiler chickens were allotted into a control and thiram (Tetramethyl thiuram disulfide) group. Blood samples were collected on day 2, 6 (8- and 14-days old chickens) and 15 (23 days old chickens). Results Histopathology and hematoxylin and eosin (H&E) results showed that angiogenesis decreased on the 6th day of the experiment but started to recover on the 15th day of the experiment. Immunohistochemistry (IHC) results confirmed the expressions of integrin alpha-v precursor (ITGAV) and clusterin precursor (CLU). Transcriptome sequencing analysis evaluated 293 differentially expressed genes (DEGs), of which 103 up-regulated genes and 190 down-regulated genes were enriched in the pathways of neuroactive ligand receptor interaction, mitogen-activated protein kinase (MAPK), ribosome, regulation of actin cytoskeleton, focal adhesion, natural killer cell mediated cytotoxicity and the notch signalling pathways. DEGs (n = 20) related to angiogenesis of chicken erythrocytes in the enriched pathways were thromboxane A2 receptor (TBXA2R), interleukin-1 receptor type 1 precursor (IL1R1), ribosomal protein L17 (RPL17), integrin beta-3 precursor (ITGB3), ITGAV, integrin beta-2 precursor (ITGB2), ras-related C3 botulinum toxin substrate 2 (RAC2), integrin alpha-2 (ITGA2), IQ motif containing GTPase activating protein 2 (IQGAP2), ARF GTPase-activating protein (GIT1), proto-oncogene vav (VAV1), integrin alpha-IIb-like (ITGA5), ras-related protein Rap-1b precursor (RAP1B), tyrosine protein kinase Fyn-like (FYN), tyrosine-protein phosphatase non-receptor type 11 (PTPN11), protein patched homolog 1 (PTCH1), nuclear receptor corepressor 2 (NCOR2) and mastermind like protein 3 (MAML3) selected for further confirmation with qPCR. However, commonly DEGs were sarcoplasmic/endoplasmic reticulum calcium ATPase 3 (ATP2A3), ubiquitin-conjugating enzyme E2 R2 (UBE2R2), centriole cilia and spindle-associated protein (CCSAP), coagulation factor XIII A chain protein (F13A1), shroom 2 isoform X6 (SHROOM2), ras GTPase-activating protein 3 (RASA3) and CLU. Conclusion We have found potential therapeutic genes concerned to erythrocytes and blood regulation, which regulated the angiogenesis in thiram induced TD chickens. This study also revealed the potential functions of erythrocytes. Graphical abstract 1. Tibial dyschondroplasia (TD) in chickens were more on day 6, which started recovering on day 15. 2. The enriched pathway observed in TD chickens on day 6 was ribosome pathway, on day 15 were regulation of actin cytoskeleton and focal adhesion pathway. 3. The genes involved in the ribosome pathways was ribosomal protein L17 (RPL17). regulation of actin cytoskeleton pathway were Ras-related C3 botulinum toxin substrate 2 (RAC2), Ras-related protein Rap-1b precursor (RAP1B), ARF GTPase-activating protein (GIT1), IQ motif containing GTPase activating protein 2 (IQGAP2), Integrin alpha-v precursor (ITGAV), Integrin alpha-2 (ITGA2), Integrin beta-2 precursor (ITGB2), Integrin beta-3 precursor (ITGB3), Integrin alpha-IIb-like (ITGA5). Focal adhesion Proto-oncogene vav (Vav-like), Tyrosine-protein kinase Fyn-like (FYN).
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Affiliation(s)
- Ali Raza Jahejo
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, China
| | - Ding Zhang
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, China
| | - Sheng Niu
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, China
| | - Raza Ali Mangi
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, China
| | - Afrasyab Khan
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, China
| | - Muhammad Farhan Qadir
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, China
| | - Ajab Khan
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, China
| | - Huan-Chun Chen
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wen-Xia Tian
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, China.
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24
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Lin L, Lu L, Du R, Yuan C, Zhu M, Fu X, Xing S. A Ce(iii) complex potently inhibits the activity and expression of tyrosine phosphatase SHP-2. Dalton Trans 2019; 48:17673-17682. [PMID: 31763642 DOI: 10.1039/c9dt03200b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Four new Ce(iii) complexes 1-4 with tridentate NNO-donor Schiff base ligands have been designed and successfully synthesized. These complexes were characterized by elemental analysis, IR, and ESI-MS, with formulas of [Ce(HL1)2(NO3)3]·2CH3OH (1), [Ce(L2)2(NO3)]·3H2O (2), [Ce(HL3)(L3)(NO3)Br]·H2O (3) and [Ce(L4)2(NO3)]·3H2O (4), in which ligands HL1-HL4 are respectively N'-[(1E)-pyridin-2-ylmethylidene]pyrazine-2-carbohydrazide (HL1), 2-(1-(salicyloylhydrazono)ethyl)pyrazine (HL2), N'-[(1E)-pyridin-2-ylmethylidene]pyridine-2-carbohydrazide (HL3) and 2-(1-(salicyloylhydrazono)ethyl) pyridine (HL4). X-ray single crystal diffraction analysis indicates that complex 1 crystallizes in the monoclinic system with the space group C2/c and the structure of complex 1 consists of a monomeric Ce(iii) species with a Ce(iii) moiety bonded to two tridentate Schiff base ligands, three nitrates and solvents. These complexes effectively inhibit the enzyme activities of PTPs (SHP-1, SHP-2, TCPTP and PTP1B), among which complex 3 shows the most potent inhibition of SHP-2 with the lowest IC50 value of 0.61 μM and displays obvious selectivity towards SHP-2. Its inhibition potency against SHP-2 was approximately 17, 4, and 5 fold higher than that against SHP-1, TCPTP and PTP1B, respectively. Further study discloses that complex 3 inhibits SHP-2 in a competitive manner. Fluorescence measurements indicate that complex 3 tightly binds to SHP-2 with a molar ratio of 1 : 1 and a binding constant of 5.45 × 105 M-1. Western blot experiments show that complex 3 promotes the phosphorylation of the SHP-2 substrate by the combination of the inhibition of the activity and expression of SHP-2. Moreover, complex 3 decreases the survival rate of A549 cells to 35.12% at 100 μM and induces apoptosis with an apoptosis rate of 12.06% at 50 μM. All these results suggest that complex 3 is a potential bi-functional inhibitor of the activity and expression of tyrosine phosphatase SHP-2.
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Affiliation(s)
- Lixia Lin
- Institute of Molecular Science, Key Laboratory of Chemical Biology and Molecular Engineering of the Education Ministry, Shanxi University, Taiyuan, Shanxi 030006, People's Republic of China.
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25
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Ilska-Warner JJ, Psifidi A, Seeker LA, Wilbourn RV, Underwood SL, Fairlie J, Whitelaw B, Nussey DH, Coffey MP, Banos G. The Genetic Architecture of Bovine Telomere Length in Early Life and Association With Animal Fitness. Front Genet 2019; 10:1048. [PMID: 31749836 PMCID: PMC6843005 DOI: 10.3389/fgene.2019.01048] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/30/2019] [Indexed: 12/19/2022] Open
Abstract
Health and survival are key goals for selective breeding in farm animals. Progress, however, is often limited by the low heritability of these animal fitness traits in addition to measurement difficulties. In this respect, relevant early-life biomarkers may be useful for breeding purposes. Telomere length (TL), measured in leukocytes, is a good candidate biomarker since TL has been associated with health, ageing, and stress in humans and other species. However, telomere studies are very limited in farm animals. Here, we examined the genetic background, genomic architecture, and factors affecting bovine TL measurements in early life, and the association of the latter with animal fitness traits expressed later in life associated with survival, longevity, health, and reproduction. We studied two TL measurements, one at birth (TLB) and another during the first lactation (TLFL) of a cow. We performed a genome-wide association study of dairy cattle TL, the first in a non-human species, and found that TLB and TLFL are complex, polygenic, moderately heritable, and highly correlated traits. However, genomic associations with distinct chromosomal regions were identified for the two traits suggesting that their genomic architecture is not identical. This is reflected in changes in TL throughout an individual’s life. TLB had a significant association with survival, length of productive life and future health status of the animal, and could be potentially used as an early-life biomarker for disease predisposition and longevity in dairy cattle.
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Affiliation(s)
- Joanna J Ilska-Warner
- Animal and Veterinary Sciences, Scotland's Rural College, Edinburgh, United Kingdom.,The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Androniki Psifidi
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom.,Royal Veterinary College, University of London, London, United Kingdom
| | - Luise A Seeker
- Animal and Veterinary Sciences, Scotland's Rural College, Edinburgh, United Kingdom.,MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Rachael V Wilbourn
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Sarah L Underwood
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Jennifer Fairlie
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Bruce Whitelaw
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Daniel H Nussey
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Mike P Coffey
- Animal and Veterinary Sciences, Scotland's Rural College, Edinburgh, United Kingdom
| | - Georgios Banos
- Animal and Veterinary Sciences, Scotland's Rural College, Edinburgh, United Kingdom.,The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
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26
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Gu J, Zhang Z, Lang T, Ma X, Yang L, Xu J, Tian C, Han K, Qiu J. PTPRU, As A Tumor Suppressor, Inhibits Cancer Stemness By Attenuating Hippo/YAP Signaling Pathway. Onco Targets Ther 2019; 12:8095-8104. [PMID: 31632062 PMCID: PMC6782031 DOI: 10.2147/ott.s218125] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 09/13/2019] [Indexed: 12/11/2022] Open
Abstract
Background PTPRU is an important signaling molecule that regulates a variety of cellular processes; however, the role of PTPRU in cancer development has remained elusive. Here, we report that PTPRU serves as a tumor suppressor that inhibits cancer stemness by attenuating Hippo/YAP signaling pathway. Methods Primary cancer cells and cell line cells were used in the study. The gene expression data were downloaded from R2 analysis and visualization platform and Kaplan–Meier analysis was performed to study the relationship between survival and PTPRU expression. qRT-PCR and Western blot were employed to study the expression of target genes in tissues and cells. Sphere and colony formation, proliferation, migration activities and the expression of stem cell and EMT markers were employed for characterizing the stemness. Gene manipulation was achieved by lentivirus-mediated gene delivery system. Luciferase reporter gene assay was used to study the transcriptional activity of the promoter, and ChIP-qPCR was employed to study the target binding sequence of the protein. Spearman correlation analysis was performed to study the correlation between two genes. Student’s t-test was used for determination of the significance between two experimental groups. Results PTPRU is downregulated in colorectal and gastric cancer tissues and cancer stem cells. High expression of PTPRU predicts poor prognosis. Overexpression of PTPRU attenuates the stemness of gastric cancer stem cells and knockdown of PTRPU improves the maintenance of the stemness of cancer stem cells. Mechanistic analysis showed that PTPRU inhibits Hippo/YAP signaling by suppressing the expression of YAP in a transcriptional level. Overexpression of YAP restored PTPRU-induced inhibited stemness of gastric cancer stem cells. Conclusion PTPRU serves as a tumor suppressor that inhibits the stemness of cancer stem cell by inhibiting Hippo/YAP signaling pathway.
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Affiliation(s)
- Jiayi Gu
- Department of Gastrointestinal Surgery, Renji Hospital Shanghai Jiao Tong University School of Medicine, Shanghai 200127, People's Republic of China
| | - Zhiqi Zhang
- Department of General Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, People's Republic of China
| | - Tingyuan Lang
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital and Chongqing Cancer Institute and Chongqing Cancer Hospital, Chongqing 400030, People's Republic of China
| | - Xinlin Ma
- Department of Gastrointestinal Surgery, Renji Hospital Shanghai Jiao Tong University School of Medicine, Shanghai 200127, People's Republic of China
| | - Linxi Yang
- Department of Gastrointestinal Surgery, Renji Hospital Shanghai Jiao Tong University School of Medicine, Shanghai 200127, People's Republic of China
| | - Jia Xu
- Department of Gastrointestinal Surgery, Renji Hospital Shanghai Jiao Tong University School of Medicine, Shanghai 200127, People's Republic of China
| | - Cong Tian
- Department of Medical Oncology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, People's Republic of China
| | - Kun Han
- Department of Medical Oncology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, People's Republic of China
| | - Jiangfeng Qiu
- Department of Gastrointestinal Surgery, Renji Hospital Shanghai Jiao Tong University School of Medicine, Shanghai 200127, People's Republic of China
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27
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Hao HX, Wang H, Liu C, Kovats S, Velazquez R, Lu H, Pant B, Shirley M, Meyer MJ, Pu M, Lim J, Fleming M, Alexander L, Farsidjani A, LaMarche MJ, Moody S, Silver SJ, Caponigro G, Stuart DD, Abrams TJ, Hammerman PS, Williams J, Engelman JA, Goldoni S, Mohseni M. Tumor Intrinsic Efficacy by SHP2 and RTK Inhibitors in KRAS-Mutant Cancers. Mol Cancer Ther 2019; 18:2368-2380. [DOI: 10.1158/1535-7163.mct-19-0170] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 07/10/2019] [Accepted: 08/16/2019] [Indexed: 11/16/2022]
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28
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Liu X, Huang J, Liu L, Liu R. MPZL1 is highly expressed in advanced gallbladder carcinoma and promotes the aggressive behavior of human gallbladder carcinoma GBC‑SD cells. Mol Med Rep 2019; 20:2725-2733. [PMID: 31322261 PMCID: PMC6691252 DOI: 10.3892/mmr.2019.10506] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 05/09/2019] [Indexed: 01/17/2023] Open
Abstract
Myelin protein 0‑like 1 (MPZL1) has been reported to have a role in hepatocellular carcinoma. However, to the best of our knowledge, there have been no studies on the function and molecular mechanism of MPZL1 gene in gallbladder carcinoma. The present study confirmed that MPZL1 was upregulated in four gallbladder carcinoma tissues according to the mRNA microarray analysis. The results of the immunohistochemical analysis of tissues from 82 patients with gallbladder carcinoma demonstrated that patients with advanced tumor stages (both T and N stage) had higher positive expression of MPZL1. Moreover, a total of 20 cases of gallbladder carcinoma and matched paired paracarcinoma tissues along with 20 samples of healthy gallbladder tissue from patients with cholecystitis were analyzed using reverse transcription‑quantitative PCR and western blotting. The results demonstrated that the expression of MPZL1 in gallbladder carcinoma tissues was significantly higher than that of paired paracarcinoma tissues and randomly matched normal gallbladder epithelial tissues. According to the Tumor‑Node‑Metastasis classification, the expression level of MPZL1 protein in stage IV gallbladder carcinoma was significantly higher than that in stage III gallbladder carcinoma. The enhanced expression of MPZL1 gene appeared to improve the migration ability of GBC‑SD cells. Conversely, GBC‑SD cells that transfected with MPZL1 siRNA exhibited decreased migration ability. The results of proliferation experiments showed that the knockdown of MPZL1 siRNA caused impairments in GBC‑SD cell proliferation. On the contrary, the overexpression of MPZL1 increased the proliferation ability of GBC‑SD cells. The results of flow cytometry analyses indicated that the upregulation of MPZL1 had an anti‑apoptotic effect on GBC‑SD cells. In conclusion, the present study showed that the expression and protein levels of MPZL1 were significantly higher in gallbladder carcinoma tissues, especially in patients diagnosed with advanced tumor stages. Overexpression of MPZL1 may have promoted the invasion, metastasis, proliferation and survival of GBC‑SD cells.
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Affiliation(s)
- Xiaolei Liu
- Department of Hepato‑Pancreato‑Biliary Surgical Oncology, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Jia Huang
- Department of General Surgery, China‑Japan Friendship Hospital, Beijing 100029, P.R. China
| | - Liguo Liu
- Department of General Surgery, China‑Japan Friendship Hospital, Beijing 100029, P.R. China
| | - Rong Liu
- Department of Hepato‑Pancreato‑Biliary Surgical Oncology, Chinese PLA General Hospital, Beijing 100853, P.R. China
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29
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Wang D, Cheng Z, Zhao M, Jiao C, Meng Q, Pan H, Xie Y, Li L, Zhu Y, Wang W, Qu C, Liang D. PTPN9 induces cell apoptosis by mitigating the activation of Stat3 and acts as a tumor suppressor in colorectal cancer. Cancer Manag Res 2019; 11:1309-1319. [PMID: 30804683 PMCID: PMC6371942 DOI: 10.2147/cmar.s187001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Accumulating evidence has shown that protein tyrosine phosphatases (PTPs) are involved in regulating the transduction of many signaling pathways and play important roles in modulating the progression of some cancers, but the functions of PTPs in cancers have not been well elucidated until now. Here, we aimed to identify the roles of protein tyrosine phosphatase nonreceptor type 9 (PTPN9), a cytoplasmic PTP, in the development of colorectal cancer and elucidate the regulatory mechanism involved. Materials and methods Cell viability assessment, colony formation assay, caspase-3 and caspase-9 activity assay, real-time PCR, and Western blot analysis were applied. Results Our results showed that PTPN9 expression was frequently downregulated in colorectal cancer tissues compared with adjacent normal tissues. Overexpression of PTPN9 mitigated cell growth and colony formation and induced cell apoptosis in colorectal cancer. Conversely, PTPN9 knockdown promoted cell growth and survival. Moreover, PTPN9 negatively regulated the activation of Stat3 and depressed its nuclear translocation in colorectal cancer. The effects of PTPN9 knockdown on cell apoptosis were attenuated by inhibition of the Stat3 pathway. Conclusion These results indicate that PTPN9 inhibits cell growth and survival by repressing the activation of Stat3 in colorectal cancer, which suggests an important underlying mechanism of regulating cell growth and provides a novel candidate therapeutic target for colorectal cancer.
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Affiliation(s)
- Dawei Wang
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, People's Republic of China,
| | - Zhuoxin Cheng
- Department of General Surgery, The First Affiliated Hospital of Jiamusi University, Jiamusi 154002, People's Republic of China.,Heilongjiang Provincial Key Laboratory of Metabolic Disease, Jiamusi 154002, People's Republic of China
| | - Ming Zhao
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, People's Republic of China,
| | - Chengbin Jiao
- Department of General Surgery, The First Affiliated Hospital of Jiamusi University, Jiamusi 154002, People's Republic of China
| | - Qinghui Meng
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, People's Republic of China,
| | - Huayang Pan
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, People's Republic of China,
| | - Yu Xie
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, People's Republic of China,
| | - Long Li
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, People's Republic of China,
| | - Yexing Zhu
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, People's Republic of China,
| | - Wei Wang
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, People's Republic of China,
| | - Chunlei Qu
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, People's Republic of China,
| | - Deshen Liang
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, People's Republic of China,
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Meta-analysis of association between Arg326Gln (rs1503185) and Gln276Pro (rs1566734) polymorphisms of PTPRJ gene and cancer risk. J Appl Genet 2019; 60:57-62. [PMID: 30661225 PMCID: PMC6373398 DOI: 10.1007/s13353-019-00481-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 12/21/2018] [Accepted: 01/04/2019] [Indexed: 12/12/2022]
Abstract
Protein tyrosine phosphatase receptor type J (PTPRJ, DEP1) is a tumour suppressor gene that negatively regulates such processes as angiogenesis, cell proliferation and migration and is one of the genes important for tumour development. Similar to other phosphatase genes, PTPRJ is also described as an oncogene. Among various genetic changes characteristic for this gene, single nucleotide polymorphisms (SNPs) constituting benign genetic variants that can modulate its function have been described. We focused on Gln276Pro and Arg326Gln missense polymorphisms and performed a meta-analysis using data from 2930 and 852 patients for Gln276Pro and Arg326Gln respectively in different cancers. A meta-analysis was performed based on five articles accessed via the PubMed and Research Gate databases. Our meta-analysis revealed that for Arg326Gln, the presence of the Arg (C) allele was associated with lower risk of some cancers, the strongest association was observed for colorectal cancer patients, and there was no association between Gln276Pro (G>T) polymorphism and cancer risk. The polymorphisms Arg326Gln and Gln276Pro of the PTPRJ gene are not associated with an increased risk of cancer except for the Arg326Gln polymorphism in colorectal cancer. Large-scale studies should be performed to verify the impact of this SNP on individual susceptibility to colorectal cancer for given individuals.
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Dupain C, Harttrampf AC, Boursin Y, Lebeurrier M, Rondof W, Robert-Siegwald G, Khoueiry P, Geoerger B, Massaad-Massade L. Discovery of New Fusion Transcripts in a Cohort of Pediatric Solid Cancers at Relapse and Relevance for Personalized Medicine. Mol Ther 2018; 27:200-218. [PMID: 30509566 DOI: 10.1016/j.ymthe.2018.10.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 10/18/2018] [Accepted: 10/26/2018] [Indexed: 12/16/2022] Open
Abstract
We hypothetized that pediatric cancers would more likely harbor fusion transcripts. To dissect the complexity of the fusions landscape in recurrent solid pediatric cancers, we conducted a study on 48 patients with different relapsing or resistant malignancies. By analyzing RNA sequencing data with a new in-house pipeline for fusions detection named ChimComp, followed by verification by real-time PCR, we identified and classified the most confident fusion transcripts (FTs) according to their potential biological function and druggability. The majority of FTs were predicted to affect key cancer pathways and described to be involved in oncogenesis. Contrary to previous descriptions, we found no significant correlation between the number of fusions and mutations, emphasizing the particularity to study pre-treated pediatric patients. A considerable proportion of FTs containing tumor suppressor genes was detected, reflecting their importance in pediatric cancers. FTs containing non-receptor tyrosine kinases occurred at low incidence and predominantly in brain tumors. Remarkably, more than 30% of patients presented a potentially druggable high-confidence fusion. In conclusion, we detected new oncogenic FTs in relapsing pediatric cancer patients by establishing a robust pipeline that can be applied to other malignancies, to detect and prioritize experimental validation studies leading to the development of new therapeutic options.
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Affiliation(s)
- Célia Dupain
- Université Paris-Sud 11, Laboratoire de Vectorologie et Thérapeutiques Anticancéreuses, UMR 8203, Villejuif 94805, France; CNRS, Villejuif, Laboratoire de Vectorologie et Thérapeutiques Anticancéreuses, UMR 8203, Villejuif 94805, France; Gustave Roussy, Laboratoire de Vectorologie et Thérapeutiques Anticancéreuses, UMR 8203, Villejuif 94805, France
| | - Anne C Harttrampf
- Université Paris-Sud 11, Laboratoire de Vectorologie et Thérapeutiques Anticancéreuses, UMR 8203, Villejuif 94805, France; CNRS, Villejuif, Laboratoire de Vectorologie et Thérapeutiques Anticancéreuses, UMR 8203, Villejuif 94805, France; Gustave Roussy, Laboratoire de Vectorologie et Thérapeutiques Anticancéreuses, UMR 8203, Villejuif 94805, France; Gustave Roussy, Department of Pediatric and Adolescent Oncology, Villejuif 94805, France
| | - Yannick Boursin
- Gustave Roussy, Bioinformatics Platform, AMMICA, INSERM US23/CNRS UMS3655, Villejuif 94805, France
| | - Manuel Lebeurrier
- Gustave Roussy, Bioinformatics Platform, AMMICA, INSERM US23/CNRS UMS3655, Villejuif 94805, France
| | - Windy Rondof
- Université Paris-Sud 11, Laboratoire de Vectorologie et Thérapeutiques Anticancéreuses, UMR 8203, Villejuif 94805, France; CNRS, Villejuif, Laboratoire de Vectorologie et Thérapeutiques Anticancéreuses, UMR 8203, Villejuif 94805, France; Gustave Roussy, Laboratoire de Vectorologie et Thérapeutiques Anticancéreuses, UMR 8203, Villejuif 94805, France; Gustave Roussy, Bioinformatics Platform, AMMICA, INSERM US23/CNRS UMS3655, Villejuif 94805, France
| | | | - Pierre Khoueiry
- American University of Beirut, Faculty of Medicine, Department of Biochemistry and Molecular Genetics, P.O. Box 11-0236 DTS 419-B, Bliss Street, Beirut, Lebanon
| | - Birgit Geoerger
- Université Paris-Sud 11, Laboratoire de Vectorologie et Thérapeutiques Anticancéreuses, UMR 8203, Villejuif 94805, France; CNRS, Villejuif, Laboratoire de Vectorologie et Thérapeutiques Anticancéreuses, UMR 8203, Villejuif 94805, France; Gustave Roussy, Laboratoire de Vectorologie et Thérapeutiques Anticancéreuses, UMR 8203, Villejuif 94805, France; Gustave Roussy, Department of Pediatric and Adolescent Oncology, Villejuif 94805, France
| | - Liliane Massaad-Massade
- Université Paris-Sud 11, Laboratoire de Vectorologie et Thérapeutiques Anticancéreuses, UMR 8203, Villejuif 94805, France; CNRS, Villejuif, Laboratoire de Vectorologie et Thérapeutiques Anticancéreuses, UMR 8203, Villejuif 94805, France; Gustave Roussy, Laboratoire de Vectorologie et Thérapeutiques Anticancéreuses, UMR 8203, Villejuif 94805, France.
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32
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Luo J, Ma K, Shi Y, Chen Z, Zhao M, Huang Y, Wang S, Xi J, Zhan C, Xu S, Wang Q. Genetic analyses of differences between solid and nonsolid predominant lung adenocarcinomas. Thorac Cancer 2018; 9:1656-1663. [PMID: 30276966 PMCID: PMC6275839 DOI: 10.1111/1759-7714.12876] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 08/22/2018] [Accepted: 08/23/2018] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Solid predominant lung adenocarcinomas (LUAD) have distinct histopathological and clinical characteristics compared with nonsolid subtypes. A comprehensive comparison of altered genes found in solid and nonsolid subtypes has not previously been performed. In this study, we analyzed differences in gene expression, genetic mutations, and DNA methylation to better understand the risk factors for these two subtypes of LUAD. METHODS Differentially expressed genes (DEGs) and differentially mutated genes (DMGs) were analyzed from RNA-seq data downloaded from The Cancer Genome Atlas (TCGA) and Broad Institute database. To understand the functional significance of molecular changes, we examined the DEGs and DMGs with Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis. RESULTS A total of 184 patients in the TCGA cohort and 140 patients in the Broad Institute cohort were included in this study. We identified 75 DEGs, of which 15 were upregulated and 56 downregulated in the solid group relative to the nonsolid group. The DEGs were mainly involved in the regulation of water and fluid transport. We discovered 38 significantly differentially expressed genes that overlapped in the two groups. The DMGs were mainly enriched for pathways involved in cell-cell adhesion, cell adhesion, biological adhesion, and hemophilic cell adhesion. We additionally discovered nine significantly methylated genes between solid and nonsolid LUAD. CONCLUSIONS Our study identified distinct DEGs, DMGs, and methylation genes for solid and nonsolid LUAD subtypes. These findings improve our understanding of the different carcinogenesis mechanisms in LUAD and will help to develop new therapeutic strategies.
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Affiliation(s)
- Jizhuang Luo
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ke Ma
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yu Shi
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zongwei Chen
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Mengnan Zhao
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yiwei Huang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Shuai Wang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Junjie Xi
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Cheng Zhan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Songtao Xu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qun Wang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
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The Cooperative Relationship between STAT5 and Reactive Oxygen Species in Leukemia: Mechanism and Therapeutic Potential. Cancers (Basel) 2018; 10:cancers10100359. [PMID: 30262727 PMCID: PMC6210354 DOI: 10.3390/cancers10100359] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 09/21/2018] [Accepted: 09/24/2018] [Indexed: 02/07/2023] Open
Abstract
Reactive oxygen species (ROS) are now recognized as important second messengers with roles in many aspects of signaling during leukemogenesis. They serve as critical cell signaling molecules that regulate the activity of various enzymes including tyrosine phosphatases. ROS can induce inactivation of tyrosine phosphatases, which counteract the effects of tyrosine kinases. ROS increase phosphorylation of many proteins including signal transducer and activator of transcription-5 (STAT5) via Janus kinases (JAKs). STAT5 is aberrantly activated through phosphorylation in many types of cancer and this constitutive activation is associated with cell survival, proliferation, and self-renewal. Such leukemic activation of STAT5 is rarely caused by mutation of the STAT5 gene itself but instead by overactive mutant receptors with tyrosine kinase activity as well as JAK, SRC family protein tyrosine kinases (SFKs), and Abelson murine leukemia viral oncogene homolog (ABL) kinases. Interestingly, STAT5 suppresses transcription of several genes encoding antioxidant enzymes while simultaneously enhancing transcription of NADPH oxidase. By doing so, STAT5 activation promotes an overall elevation of ROS level, which acts as a feed-forward loop, especially in high risk Fms-related tyrosine kinase 3 (FLT3) mutant leukemia. Therefore, efforts have been made recently to target ROS in cancer cells. Drugs that are able to either quench ROS production or inversely augment ROS-related signaling pathways both have potential as cancer therapies and may afford some selectivity by activating feedback inhibition of the ROS-STAT5 kinome. This review summarizes the cooperative relationship between ROS and STAT5 and explores the pros and cons of emerging ROS-targeting therapies that are selective for leukemia characterized by persistent STAT5 phosphorylation.
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34
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Kim M, Baek M, Kim DJ. Protein Tyrosine Signaling and its Potential Therapeutic Implications in Carcinogenesis. Curr Pharm Des 2018. [PMID: 28625132 DOI: 10.2174/1381612823666170616082125] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Protein tyrosine phosphorylation is a crucial signaling mechanism that plays a role in epithelial carcinogenesis. Protein tyrosine kinases (PTKs) control various cellular processes including growth, differentiation, metabolism, and motility by activating major signaling pathways including STAT3, AKT, and MAPK. Genetic mutation of PTKs and/or prolonged activation of PTKs and their downstream pathways can lead to the development of epithelial cancer. Therefore, PTKs became an attractive target for cancer prevention. PTK inhibitors are continuously being developed, and they are currently used for the treatment of cancers that show a high expression of PTKs. Protein tyrosine phosphatases (PTPs), the homeostatic counterpart of PTKs, negatively regulate the rate and duration of phosphotyrosine signaling. PTPs initially were considered to be only housekeeping enzymes with low specificity. However, recent studies have demonstrated that PTPs can function as either tumor suppressors or tumor promoters, depending on their target substrates. Together, both PTK and PTP signal transduction pathways are potential therapeutic targets for cancer prevention and treatment.
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Affiliation(s)
- Mihwa Kim
- Department of Biomedical Sciences, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Minwoo Baek
- Department of Biomedical Sciences, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Dae Joon Kim
- Department of Biomedical Sciences, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA
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35
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Nunes-Xavier CE, Mingo J, López JI, Pulido R. The role of protein tyrosine phosphatases in prostate cancer biology. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1866:102-113. [PMID: 30401533 DOI: 10.1016/j.bbamcr.2018.06.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 06/18/2018] [Accepted: 06/28/2018] [Indexed: 02/07/2023]
Abstract
Prostate cancer (PCa) is the most frequent malignancy in the male population of Western countries. Although earlier detection and more active surveillance have improved survival, it is still a challenge how to treat advanced cases. Since androgen receptor (AR) and AR-related signaling pathways are fundamental in the growth of normal and neoplastic prostate cells, targeting androgen synthesis or AR activity constitutes the basis of the current hormonal therapies in PCa. However, resistance to these treatments develops, both by AR-dependent and -independent mechanisms. Thus, alternative therapeutic approaches should be developed to target more efficiently advanced disease. Protein tyrosine phosphatases (PTPs) are direct regulators of the protein- and residue-specific phosphotyrosine (pTyr) content of cells, and dysregulation of the cellular Tyr phosphorylation/dephosphorylation balance is a major driving event in cancer, including PCa. Here, we review the current knowledge on the role of classical PTPs in the growth, differentiation, and survival of epithelial prostate cells, and their potential as important players and therapeutic targets for modulation in PCa.
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Affiliation(s)
- Caroline E Nunes-Xavier
- Department of Tumor Biology, Institute of Cancer Research, Oslo University Hospital Radiumhospitalet, N-0310 Oslo, Norway; Biomarkers in Cancer Unit, Biocruces Health Research Institute, 48903 Barakaldo, Bizkaia, Spain
| | - Janire Mingo
- Biomarkers in Cancer Unit, Biocruces Health Research Institute, 48903 Barakaldo, Bizkaia, Spain
| | - José I López
- Biomarkers in Cancer Unit, Biocruces Health Research Institute, 48903 Barakaldo, Bizkaia, Spain; Department of Pathology, Cruces University Hospital, University of the Basque Country (UPV/EHU), 48903 Barakaldo, Bizkaia, Spain
| | - Rafael Pulido
- Biomarkers in Cancer Unit, Biocruces Health Research Institute, 48903 Barakaldo, Bizkaia, Spain; Ikerbasque, Basque Foundation for Science, 48011 Bilbao, Spain.
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36
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Vazhappilly CG, Saleh E, Ramadan W, Menon V, Al-Azawi AM, Tarazi H, Abdu-Allah H, El-Shorbagi AN, El-Awady R. Inhibition of SHP2 by new compounds induces differential effects on RAS/RAF/ERK and PI3K/AKT pathways in different cancer cell types. Invest New Drugs 2018; 37:252-261. [PMID: 29947013 DOI: 10.1007/s10637-018-0626-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 06/20/2018] [Indexed: 10/28/2022]
Abstract
Kinases and phosphatases are important players in growth signaling and are involved in cancer development. For development of targeted cancer therapy, attention is given to kinases rather than phosphatases inhibitors. Src homology region 2 domain-containing protein tyrosine phosphatase2 (SHP2) is overexpressed in different types of cancers. We investigated the SHP2-inhibitory effects of two new 5-aminosalicylate-4-thiazolinones in human cervical (HeLa) and breast (MCF-7 & MDA-MB-231) cancer cells. In-silico molecular docking showed preferential affinity of the two compounds towards the catalytic over the allosteric site of SHP2. An enzymatic assay confirmed the docking results whereby 0.01 μM of both compounds reduced SHP2 activity to 50%. On cellular level, the two compounds significantly reduced the expression of SHP2, KRAS, p-ERK and p-STAT3 in HeLa but not in the other two cell lines. Phosphorylation of AKT and JNK was enhanced in HeLa and MCF7. Both compounds exhibited anti-proliferative/anti-migratory effects on HeLa and MCF7 but not in MDA-MB-231 cells. These results indicate that inhibition of SHP2 and its downstream pathways by the two compounds might be a promising strategy for cancer therapy in some but not all cancer types.
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Affiliation(s)
- Cijo George Vazhappilly
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Ekram Saleh
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates.,Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Wafaa Ramadan
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Varsha Menon
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Aya Mudhafar Al-Azawi
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Hamadeh Tarazi
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates.,College of Pharmacy, University of Sharjah, University City Road, 27272, Sharjah, United Arab Emirates
| | - Hajjaj Abdu-Allah
- Medicinal Chemistry Department, College of Pharmacy, Assuit University, Assuit, Egypt
| | - Abdel-Nasser El-Shorbagi
- College of Pharmacy, University of Sharjah, University City Road, 27272, Sharjah, United Arab Emirates.,Medicinal Chemistry Department, College of Pharmacy, Assuit University, Assuit, Egypt
| | - Raafat El-Awady
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates. .,College of Pharmacy, University of Sharjah, University City Road, 27272, Sharjah, United Arab Emirates.
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37
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Painter JN, O'Mara TA, Morris AP, Cheng THT, Gorman M, Martin L, Hodson S, Jones A, Martin NG, Gordon S, Henders AK, Attia J, McEvoy M, Holliday EG, Scott RJ, Webb PM, Fasching PA, Beckmann MW, Ekici AB, Hein A, Rübner M, Hall P, Czene K, Dörk T, Dürst M, Hillemanns P, Runnebaum I, Lambrechts D, Amant F, Annibali D, Depreeuw J, Vanderstichele A, Goode EL, Cunningham JM, Dowdy SC, Winham SJ, Trovik J, Hoivik E, Werner HMJ, Krakstad C, Ashton K, Otton G, Proietto T, Tham E, Mints M, Ahmed S, Healey CS, Shah M, Pharoah PDP, Dunning AM, Dennis J, Bolla MK, Michailidou K, Wang Q, Tyrer JP, Hopper JL, Peto J, Swerdlow AJ, Burwinkel B, Brenner H, Meindl A, Brauch H, Lindblom A, Chang‐Claude J, Couch FJ, Giles GG, Kristensen VN, Cox A, Zondervan KT, Nyholt DR, MacGregor S, Montgomery GW, Tomlinson I, Easton DF, Thompson DJ, Spurdle AB. Genetic overlap between endometriosis and endometrial cancer: evidence from cross-disease genetic correlation and GWAS meta-analyses. Cancer Med 2018; 7:1978-1987. [PMID: 29608257 PMCID: PMC5943470 DOI: 10.1002/cam4.1445] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 01/17/2018] [Accepted: 01/21/2018] [Indexed: 12/27/2022] Open
Abstract
Epidemiological, biological, and molecular data suggest links between endometriosis and endometrial cancer, with recent epidemiological studies providing evidence for an association between a previous diagnosis of endometriosis and risk of endometrial cancer. We used genetic data as an alternative approach to investigate shared biological etiology of these two diseases. Genetic correlation analysis of summary level statistics from genomewide association studies (GWAS) using LD Score regression revealed moderate but significant genetic correlation (rg = 0.23, P = 9.3 × 10-3 ), and SNP effect concordance analysis provided evidence for significant SNP pleiotropy (P = 6.0 × 10-3 ) and concordance in effect direction (P = 2.0 × 10-3 ) between the two diseases. Cross-disease GWAS meta-analysis highlighted 13 distinct loci associated at P ≤ 10-5 with both endometriosis and endometrial cancer, with one locus (SNP rs2475335) located within PTPRD associated at a genomewide significant level (P = 4.9 × 10-8 , OR = 1.11, 95% CI = 1.07-1.15). PTPRD acts in the STAT3 pathway, which has been implicated in both endometriosis and endometrial cancer. This study demonstrates the value of cross-disease genetic analysis to support epidemiological observations and to identify biological pathways of relevance to multiple diseases.
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38
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Zhao Y, Scott A, Zhang P, Hao Y, Feng X, Somasundaram S, Khalil AM, Willis J, Wang Z. Regulation of paxillin-p130-PI3K-AKT signaling axis by Src and PTPRT impacts colon tumorigenesis. Oncotarget 2018; 8:48782-48793. [PMID: 27447856 PMCID: PMC5564724 DOI: 10.18632/oncotarget.10654] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 06/03/2016] [Indexed: 01/31/2023] Open
Abstract
Protein tyrosine phosphatase receptor T (PTPRT) is frequently mutated in a variety of human cancers including colorectal cancer. Here we report that PTPRT knockout increases the size of mouse colon tumors in the Apcmin+/− genetic background, suggesting that inactivation of PTPRT promotes tumor progression. We previously demonstrated that PTPRT dephosphorylates paxillin at tyrosine-Y88 residue. Consistently, phosphorylation of Y88 paxillin (pY88) is up-regulated in colon tumors derived from Apcmin+/− Ptprt−/− mice. An important downstream effector of pY88 paxillin is the oncogene Akt. Here, we show that pY88 paxillin impacts the Akt pathway by regulating the interaction between p130cas and the p85 regulatory subunit of PI3-Kinase. Additionally, while pY88 paxillin is a substrate of the tumor suppressor phosphatase PTPRT, the corresponding kinase has not been previously identified. In this study, we demonstrate that the oncogenic kinase Src directly phosphorylates paxillin at Y88. Moreover, colorectal cancer cells that express high levels of pY88 paxillin are sensitive to dasatinib treatment, suggesting that pY88 paxillin may serve as a predictive biomarker for Src family kinase inhibitors.
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Affiliation(s)
- Yiqing Zhao
- Department of Genetics and Genome Sciences, Case Medical Center and Case Western Reserve University, Cleveland, Ohio 44106, USA.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Anthony Scott
- Department of Genetics and Genome Sciences, Case Medical Center and Case Western Reserve University, Cleveland, Ohio 44106, USA.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Peng Zhang
- Department of Genetics and Genome Sciences, Case Medical Center and Case Western Reserve University, Cleveland, Ohio 44106, USA.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Yujun Hao
- Department of Genetics and Genome Sciences, Case Medical Center and Case Western Reserve University, Cleveland, Ohio 44106, USA.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Xiujing Feng
- Department of Genetics and Genome Sciences, Case Medical Center and Case Western Reserve University, Cleveland, Ohio 44106, USA.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Saigopal Somasundaram
- Department of Genetics and Genome Sciences, Case Medical Center and Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Ahmad M Khalil
- Department of Genetics and Genome Sciences, Case Medical Center and Case Western Reserve University, Cleveland, Ohio 44106, USA.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Joseph Willis
- Department of Pathology, Case Medical Center and Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Zhenghe Wang
- Department of Genetics and Genome Sciences, Case Medical Center and Case Western Reserve University, Cleveland, Ohio 44106, USA.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio 44106, USA
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Tayou J. Identification of subsets of actionable genetic alterations in KRAS-mutant lung cancers using association rule mining. Cell Oncol (Dordr) 2018; 41:395-408. [DOI: 10.1007/s13402-018-0377-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/16/2018] [Indexed: 12/21/2022] Open
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40
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Abstract
In higher eukaryotes, the Tyr phosphorylation status of cellular proteins results from the coordinated action of Protein Tyrosine Kinases (PTKs) and Protein Tyrosine Phosphatases (PTPs). PTPs have emerged as highly regulated enzymes with diverse substrate specificity, and proteins with Tyr-dephosphorylation or Tyr-dephosphorylation-like properties can be clustered as the PTPome. This includes proteins from the PTP superfamily, which display a Cys-based catalytic mechanism, as well as enzymes from other gene families (Asp-based phosphatases, His-based phosphatases) that have converged in protein Tyr-dephosphorylation-related functions by using non-Cys-based catalytic mechanisms. Within the Cys-based members of the PTPome, classical PTPs dephosphorylate specific phosphoTyr (pTyr) residues from protein substrates, whereas VH1-like dual-specificity PTPs dephosphorylate pTyr, pSer, and pThr residues, as well as nonproteinaceous substrates, including phosphoinositides and phosphorylated carbohydrates. In addition, several PTPs have impaired catalytic activity as a result of amino acid substitutions at their active sites, but retain regulatory functions related with pTyr signaling. As a result of their relevant biological activity, many PTPs are linked to human disease, including cancer, neurodevelopmental, and metabolic diseases, making these proteins important drug targets and molecular markers in the clinic. Here, a brief overview on the biochemistry and physiology of the different groups of proteins that belong to the mammalian PTPome is presented.
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41
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Caldieri G, Malabarba MG, Di Fiore PP, Sigismund S. EGFR Trafficking in Physiology and Cancer. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2018; 57:235-272. [PMID: 30097778 DOI: 10.1007/978-3-319-96704-2_9] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Signaling from the epidermal growth factor receptor (EGFR) elicits multiple biological responses, including cell proliferation, migration, and survival. Receptor endocytosis and trafficking are critical physiological processes that control the strength, duration, diversification, and spatial restriction of EGFR signaling through multiple mechanisms, which we review in this chapter. These mechanisms include: (i) regulation of receptor density and activation at the cell surface; (ii) concentration of receptors into distinct nascent endocytic structures; (iii) commitment of the receptor to different endocytic routes; (iv) endosomal sorting and postendocytic trafficking of the receptor through distinct pathways, and (v) recycling to restricted regions of the cell surface. We also highlight how communication between organelles controls EGFR activity along the endocytic route. Finally, we illustrate how abnormal trafficking of EGFR oncogenic mutants, as well as alterations of the endocytic machinery, contributes to aberrant EGFR signaling in cancer.
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Affiliation(s)
- Giusi Caldieri
- Dipartimento di Oncologia ed Emato-oncologia, Università degli Studi di Milano, Via Santa Sofia 9/1, 20122, Milan, Italy
- Istituto Europeo di Oncologia, Via Ripamonti 435, 20141, Milan, Italy
| | - Maria Grazia Malabarba
- Dipartimento di Oncologia ed Emato-oncologia, Università degli Studi di Milano, Via Santa Sofia 9/1, 20122, Milan, Italy
- Istituto Europeo di Oncologia, Via Ripamonti 435, 20141, Milan, Italy
| | - Pier Paolo Di Fiore
- Dipartimento di Oncologia ed Emato-oncologia, Università degli Studi di Milano, Via Santa Sofia 9/1, 20122, Milan, Italy
- Istituto Europeo di Oncologia, Via Ripamonti 435, 20141, Milan, Italy
| | - Sara Sigismund
- Dipartimento di Oncologia ed Emato-oncologia, Università degli Studi di Milano, Via Santa Sofia 9/1, 20122, Milan, Italy.
- Istituto Europeo di Oncologia, Via Ripamonti 435, 20141, Milan, Italy.
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Zhang S, Fan G, Hao Y, Hammell M, Wilkinson JE, Tonks NK. Suppression of protein tyrosine phosphatase N23 predisposes to breast tumorigenesis via activation of FYN kinase. Genes Dev 2017; 31:1939-1957. [PMID: 29066500 PMCID: PMC5710140 DOI: 10.1101/gad.304261.117] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 10/06/2017] [Indexed: 12/18/2022]
Abstract
Zhang et al. identified PTPN23 as a suppressor of cell motility and invasion in mammary epithelial and breast cancer cells. They validated the underlying mechanism of PTPN23 function in breast tumorigenesis as that of a key phosphatase that normally suppresses the activity of FYN in two different models. Disruption of the balanced modulation of reversible tyrosine phosphorylation has been implicated in the etiology of various human cancers, including breast cancer. Protein Tyrosine Phosphatase N23 (PTPN23) resides in chromosomal region 3p21.3, which is hemizygously or homozygously lost in some breast cancer patients. In a loss-of-function PTPome screen, our laboratory identified PTPN23 as a suppressor of cell motility and invasion in mammary epithelial and breast cancer cells. Now, our TCGA (The Cancer Genome Atlas) database analyses illustrate a correlation between low PTPN23 expression and poor survival in breast cancers of various subtypes. Therefore, we investigated the tumor-suppressive function of PTPN23 in an orthotopic transplantation mouse model. Suppression of PTPN23 in Comma 1Dβ cells induced breast tumors within 56 wk. In PTPN23-depleted tumors, we detected hyperphosphorylation of the autophosphorylation site tyrosine in the SRC family kinase (SFK) FYN as well as Tyr142 in β-catenin. We validated the underlying mechanism of PTPN23 function in breast tumorigenesis as that of a key phosphatase that normally suppresses the activity of FYN in two different models. We demonstrated that tumor outgrowth from PTPN23-deficient BT474 cells was suppressed in a xenograft model in vivo upon treatment with AZD0530, an SFK inhibitor. Furthermore, double knockout of FYN and PTPN23 via CRISPR/CAS9 also attenuated tumor outgrowth from PTPN23 knockout Cal51 cells. Overall, this mechanistic analysis of the tumor-suppressive function of PTPN23 in breast cancer supports the identification of FYN as a therapeutic target for breast tumors with heterozygous or homozygous loss of PTPN23.
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Affiliation(s)
- Siwei Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.,Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York 11794, USA
| | - Gaofeng Fan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Yuan Hao
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Molly Hammell
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - John Erby Wilkinson
- Unit for Laboratory Animal Medicine, Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Nicholas K Tonks
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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43
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Rossi UA, Hasenauer FC, Caffaro ME, Neumann R, Salatin A, Poli MA, Rossetti CA. A haplotype at intron 8 of PTPRT gene is associated with resistance to Brucella infection in Argentinian creole goats. Vet Microbiol 2017; 207:133-137. [DOI: 10.1016/j.vetmic.2017.06.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 05/31/2017] [Accepted: 06/01/2017] [Indexed: 11/25/2022]
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44
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Laczmanska I, Karpinski P, Gil J, Laczmanski L, Makowska I, Bebenek M, Ramsey D, Sasiadek MM. The PTPN13 Y2081D (T>G) (rs989902) polymorphism is associated with an increased risk of sporadic colorectal cancer. Colorectal Dis 2017; 19:O272-O278. [PMID: 28504867 DOI: 10.1111/codi.13727] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 03/24/2017] [Indexed: 12/26/2022]
Abstract
AIM Colorectal cancer (CRC) is one of the most common cancers worldwide and, although the majority of cases are sporadic, its development and progression depends on a range of factors: environmental, genetic and epigenetic. A variety of genetic pathways have been described as being crucial in CRC, including protein tyrosine phosphatases (PTPs). PTPN13 (also called FAP-1) is a non-receptor PTP and interacts with a number of important components of growth and apoptosis pathways. It is also involved in the inhibition of Fas-induced apoptosis. METHOD The single nucleotide polymorphism genotype at Y2081D (T>G) (rs989902) of PTPN13 exon 39 was determined in DNA extracted from blood samples from 174 sporadic CRC patients and 176 healthy individuals. Also, a meta-analysis was performed based on three articles accessed via the PubMed and ResearchGate databases. RESULTS The risk of CRC was 2.087 times greater for patients with the GG genotype than for those with the TT genotype (P = 0.0475). In the meta-analysis, a significantly increased risk of cancer associated with the G allele was observed in the squamous cell carcinoma of the head and neck subgroup (TT vs GG+GT, OR 1.23, 95% CI [1.02, 1.47], P = 0.0258), and a significantly decreased risk in the breast cancer subgroup (TT vs GG+GT, OR 0.63, 95% CI [0.41, 0.96], P = 0.0334) and in the CRC subgroup (GT+TT vs GG, OR 0.51, 95% CI [0.41, 0.95], P = 0.0333). CONCLUSION PTPN13 rs989902 is significantly associated with the risk of CRC in the Polish population. Given that this report provides the first evidence of an association of PTPN13 rs989902 with the risk of CRC in a Caucasian population, further large scale studies are necessary to confirm this finding.
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Affiliation(s)
- I Laczmanska
- Genetics Department, Wroclaw Medical University, Wroclaw, Poland
| | - P Karpinski
- Genetics Department, Wroclaw Medical University, Wroclaw, Poland
| | - J Gil
- Genetics Department, Wroclaw Medical University, Wroclaw, Poland
| | - L Laczmanski
- Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland.,Research and Development Center of Lower Silesian Regional Specialist Hospital, Wroclaw, Poland
| | - I Makowska
- Genetics Department, Wroclaw Medical University, Wroclaw, Poland
| | - M Bebenek
- First Department of Surgical Oncology, Lower Silesian Oncology Center, Wroclaw, Poland
| | - D Ramsey
- Department of Operations Research, Wroclaw University of Technology, Wroclaw, Poland
| | - M M Sasiadek
- Genetics Department, Wroclaw Medical University, Wroclaw, Poland
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45
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Gu Z, Fang X, Li C, Chen C, Liang G, Zheng X, Fan Q. Increased PTPRA expression leads to poor prognosis through c-Src activation and G1 phase progression in squamous cell lung cancer. Int J Oncol 2017; 51:489-497. [PMID: 28656243 PMCID: PMC5505127 DOI: 10.3892/ijo.2017.4055] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 06/19/2017] [Indexed: 01/02/2023] Open
Abstract
PTPRA is reported to be involved in cancer development and progression through activating the Src family kinase (SFK) signaling pathways, however, the roles of PTPRA in the squamous cell lung cancer (SCC) development are unclear. The purpose of this study was to clarify the clinical relevance and biological roles of PTPRA in SCC. We found that PTPRA was upregulated in squamous cell lung cancer compared to matched normal tissues at the mRNA (N=20, P=0.004) and protein expression levels (N=75, P<0.001). Notably, high mRNA level of PTPRA was significantly correlated with poorer prognosis in 675 SCC patients from the Kaplan-Meier plotter database. With 75 cases, we found that PTPRA protein expression was significantly correlated with tumor size (P=0.002), lymph node metastasis (P=0.008), depth of tumor invasion (P<0.001) and clinical stage (P<0.001). The Kaplan-Meier plot suggested that high expression of PTPRA had poorer overall survival in SCC patients (P=0.009). Multivariate Cox regression analysis suggested that PTPRA expression was an independent prognostic factor in SCC patients. In the cellular models, PTPRA promotes SCC cell proliferation through modulating Src activation as well as cell cycle progression. In conclusion, higher PTPRA level was associated with worse prognosis of SCC patients and PTPRA could promote the cell cycle progression through stimulating the c-Src signaling pathways.
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Affiliation(s)
- Zhidong Gu
- Department of Clinical Medicine, Ruijin Hospital, Jiaotong University School of Medicine, Shanghai 200025, P.R. China
| | - Xuqian Fang
- Department of Clinical Medicine, Ruijin Hospital North, Jiaotong University School of Medicine, Shanghai 201801, P.R. China
| | - Chang Li
- Department of Clinical Medicine, Ruijin Hospital, Jiaotong University School of Medicine, Shanghai 200025, P.R. China
| | - Changqiang Chen
- Department of Clinical Medicine, Ruijin Hospital North, Jiaotong University School of Medicine, Shanghai 201801, P.R. China
| | - Guangshu Liang
- Department of Clinical Medicine, Ruijin Hospital, Jiaotong University School of Medicine, Shanghai 200025, P.R. China
| | - Xinming Zheng
- Department of Clinical Medicine, Ruijin Hospital, Jiaotong University School of Medicine, Shanghai 200025, P.R. China
| | - Qishi Fan
- Department of Clinical Medicine, Ruijin Hospital North, Jiaotong University School of Medicine, Shanghai 201801, P.R. China
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46
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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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Dong H, Ma L, Gan J, Lin W, Chen C, Yao Z, Du L, Zheng L, Ke C, Huang X, Song H, Kumar R, Yeung SC, Zhang H. PTPRO represses ERBB2-driven breast oncogenesis by dephosphorylation and endosomal internalization of ERBB2. Oncogene 2017; 36:410-422. [PMID: 27345410 PMCID: PMC5269534 DOI: 10.1038/onc.2016.213] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 05/05/2016] [Accepted: 05/08/2016] [Indexed: 02/05/2023]
Abstract
The plasma membrane-associated tyrosine phosphatase PTPRO is frequently transcriptionally repressed in cancers and signifies poor prognosis of breast cancer patients. In this study, deletion of Ptpro in MMTV-Erbb2 transgenic mice dramatically shortened the mammary tumor latency and accelerated tumor growth due to loss of Ptpro within the breast cancer cells but not in surrounding tissue as confirmed by hetero-transplantation studies. Both in vitro and in vivo data demonstrated that the phosphatase activity was required for the inactivation of ERBB2 and its downstream signaling. PTPRO regulated the phosphorylation status of ERBB2 at Y1248. Co-immunoprecipitation and proximity ligation assay (Duolink) indicated that PTPRO directly physically interacted with ERBB2. Moreover, PTPRO phosphatase activity shortened the half-life of ERBB2 by increasing endocytotic degradation. PTPRO reexpression by demethylation treatment using 5-azacytidine reduced the proliferation and colony formation potential in ERBB2-positive breast cancer cells. Taken together, PTPRO inhibited ERBB2-driven breast cancer through dephosphorylation leading to dual effects of ERBB2 signaling suppression and endosomal internalization of ERBB2, Therefore, reexpression of PTPRO may be a potential therapy for ERBB2-overexpressing breast cancer.
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Affiliation(s)
- H Dong
- Cancer Research Center, Shantou University Medical College, Shantou, China
| | - L Ma
- Department of Gastroenterology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - J Gan
- Cancer Research Center, Shantou University Medical College, Shantou, China
| | - W Lin
- Cancer Research Center, Shantou University Medical College, Shantou, China
| | - C Chen
- Cancer Research Center, Shantou University Medical College, Shantou, China
| | - Z Yao
- Cancer Research Center, Shantou University Medical College, Shantou, China
| | - L Du
- Cancer Research Center, Shantou University Medical College, Shantou, China
| | - L Zheng
- Cancer Research Center, Shantou University Medical College, Shantou, China
| | - C Ke
- Cancer Research Center, Shantou University Medical College, Shantou, China
| | - X Huang
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center of Nanjing University, Nanjing, China
| | - H Song
- Department of Cell Biology, Xi'an Jiaotong University Suzhou Academy, Suzhou, China
| | - R Kumar
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, George Washington University, Washington DC, USA
| | - S C Yeung
- Cancer Research Center, Shantou University Medical College, Shantou, China
- Department of Emergency Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Endocrine Neoplasia and Hormonal Disorders, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Endocrine Neoplasia and Hormonal Disorders, University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA. E-mail:
| | - H Zhang
- Cancer Research Center, Shantou University Medical College, Shantou, China
- Department of Biotherapy, Affiliated Cancer Hospital of Shantou University Medical College, Shantou, China
- Cancer Research Center, Shantou University Medical College, Xinling Road No. 22, Shantou 515041, ChinaE-mail:
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48
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Bishop AC. A missense methionine mutation augments catalytic activity but reduces thermal stability in two protein tyrosine phosphatases. Biochem Biophys Res Commun 2016; 481:153-158. [PMID: 27816449 PMCID: PMC5118098 DOI: 10.1016/j.bbrc.2016.11.001] [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: 10/20/2016] [Accepted: 11/01/2016] [Indexed: 11/23/2022]
Abstract
Recent data sets that catalog the missense mutations in thousands of human genomes have revealed a vast and largely unexplored world of non-canonical protein sequences that are expressed in humans. The functional consequences of most human missense mutations, however, are unknown, and the accuracy with which their effects can be predicted by computational algorithms remains unclear. Among humans of European descent, the most common missense mutation in the catalytic domain of SH2-containing protein tyrosine phosphatase 1 (SHP-1) converts the enzyme's canonical valine 451 to methionine (V451M). The V451M mutation lies in a conserved motif adjacent to the protein tyrosine phosphatase (PTP) consensus sequence and is predicted to compromise catalytic function. In this study it is shown that, counter to prediction, V451M SHP-1 possesses increased catalytic activity as compared to the wild-type enzyme. Additionally, a PTP-wide search of missense-mutation data revealed a variant of one other PTP, Fas-associated PTP (FAP-1), that contains a methionine mutation at the position corresponding to 451 of SHP-1 (T2406M FAP-1). It is shown here that the T2406M mutation increases FAP-1's PTP activity, to a degree that is comparable to the activation deriving from the V451M mutation in SHP-1. Although the two non-canonical methionine residues confer increased activity at moderate temperatures, both V451M SHP-1 and T2406M FAP-1 are less thermally stable than their canonical counterparts, as demonstrated by the mutants' strongly reduced activities at high temperatures. These results highlight the challenges in predicting the functional consequences of missense mutations, which can differ under varying conditions, and suggest that, with regard to position 451/2406, canonical PTP domains have "chosen" stability over optimized activity during the course of evolution.
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Affiliation(s)
- Anthony C Bishop
- Amherst College, Department of Chemistry, Amherst, MA 01002, USA.
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49
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Rahmati S, Abovsky M, Pastrello C, Jurisica I. pathDIP: an annotated resource for known and predicted human gene-pathway associations and pathway enrichment analysis. Nucleic Acids Res 2016; 45:D419-D426. [PMID: 27899558 PMCID: PMC5210562 DOI: 10.1093/nar/gkw1082] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 09/30/2016] [Accepted: 10/25/2016] [Indexed: 01/06/2023] Open
Abstract
Molecular pathway data are essential in current computational and systems biology research. While there are many primary and integrated pathway databases, several challenges remain, including low proteome coverage (57%), low overlap across different databases, unavailability of direct information about underlying physical connectivity of pathway members, and high fraction of protein-coding genes without any pathway annotations, i.e. ‘pathway orphans’. In order to address all these challenges, we developed pathDIP, which integrates data from 20 source pathway databases, ‘core pathways’, with physical protein–protein interactions to predict biologically relevant protein–pathway associations, referred to as ‘extended pathways’. Cross-validation determined 71% recovery rate of our predictions. Data integration and predictions increase coverage of pathway annotations for protein-coding genes to 86%, and provide novel annotations for 5732 pathway orphans. PathDIP (http://ophid.utoronto.ca/pathdip) annotates 17 070 protein-coding genes with 4678 pathways, and provides multiple query, analysis and output options.
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Affiliation(s)
- Sara Rahmati
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Mark Abovsky
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, TMDT, Room 11-314, Toronto, ON M5G 1L7, Canada
| | - Chiara Pastrello
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, TMDT, Room 11-314, Toronto, ON M5G 1L7, Canada
| | - Igor Jurisica
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada .,Princess Margaret Cancer Centre, University Health Network, 101 College Street, TMDT, Room 11-314, Toronto, ON M5G 1L7, Canada.,Department of Computer Science, University of Toronto, Toronto, ON, Canada.,Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
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50
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Morotti A, Rocca S, Carrà G, Saglio G, Brancaccio M. Modeling myeloproliferative neoplasms: From mutations to mouse models and back again. Blood Rev 2016; 31:139-150. [PMID: 27899218 DOI: 10.1016/j.blre.2016.11.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 10/28/2016] [Accepted: 11/22/2016] [Indexed: 02/07/2023]
Abstract
Myeloproliferative neoplasms (MPNs) are defined according to the 2008 World Health Organization (WHO) classification and the recent 2016 revision. Over the years, several genetic lesions have been associated with the development of MPNs, with important consequences for identifying unique biomarkers associated with specific neoplasms and for developing targeted therapies. Defining the genotype-phenotype relationship in MPNs is essential to identify driver somatic mutations that promote MPN development and maintenance in order to develop curative targeted therapies. While studies with human samples can identify putative driver mutations, murine models are mandatory to demonstrate the causative role of mutations and for pre-clinical testing of specific therapeutic interventions. This review focuses on MPN mouse models specifically developed to assess the pathogenetic roles of gene mutations found in human patients, as well as murine MPN-like phenotypes identified in genetically modified mice.
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Affiliation(s)
- Alessandro Morotti
- Department of Clinical and Biological Sciences, University of Torino, Regione Gonzole, 10, 10043 Orbassano, Italy.
| | - Stefania Rocca
- Department of Molecular Biotechnology and Health Sciences, University of Torino, via Nizza, 52, 10126 Torino, Italy.
| | - Giovanna Carrà
- Department of Clinical and Biological Sciences, University of Torino, Regione Gonzole, 10, 10043 Orbassano, Italy.
| | - Giuseppe Saglio
- Department of Clinical and Biological Sciences, University of Torino, Regione Gonzole, 10, 10043 Orbassano, Italy.
| | - Mara Brancaccio
- Department of Molecular Biotechnology and Health Sciences, University of Torino, via Nizza, 52, 10126 Torino, Italy.
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