1
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Papadimitriou E, Kanellopoulou VK. Protein Tyrosine Phosphatase Receptor Zeta 1 as a Potential Target in Cancer Therapy and Diagnosis. Int J Mol Sci 2023; 24:ijms24098093. [PMID: 37175798 PMCID: PMC10178973 DOI: 10.3390/ijms24098093] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/25/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
Protein tyrosine phosphatase receptor zeta 1 (PTPRZ1) is a type V transmembrane tyrosine phosphatase that is highly expressed during embryonic development, while its expression during adulthood is limited. PTPRZ1 is highly detected in the central nervous system, affecting oligodendrocytes' survival and maturation. In gliomas, PTPRZ1 expression is significantly upregulated and is being studied as a potential cancer driver and as a target for therapy. PTPRZ1 expression is also increased in other cancer types, but there are no data on the potential functional significance of this finding. On the other hand, low PTPRZ1 expression seems to be related to a worse prognosis in some cancer types, suggesting that in some cases, it may act as a tumor-suppressor gene. These discrepancies may be due to our limited understanding of PTPRZ1 signaling and tumor microenvironments. In this review, we present evidence on the role of PTPRZ1 in angiogenesis and cancer and discuss the phenomenal differences among the different types of cancer, depending on the regulation of its tyrosine phosphatase activity or ligand binding. Clarifying the involved signaling pathways will lead to its efficient exploitation as a novel therapeutic target or as a biomarker, and the development of proper therapeutic approaches.
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Affiliation(s)
- Evangelia Papadimitriou
- Laboratory of Molecular Pharmacology, Department of Pharmacy, University of Patras, 26504 Patras, Greece
| | - Vasiliki K Kanellopoulou
- Laboratory of Molecular Pharmacology, Department of Pharmacy, University of Patras, 26504 Patras, Greece
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2
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Kanao E, Wada S, Nishida H, Kubo T, Tanigawa T, Imami K, Shimoda A, Umezaki K, Sasaki Y, Akiyoshi K, Adachi J, Otsuka K, Ishihama Y. Classification of Extracellular Vesicles Based on Surface Glycan Structures by Spongy-like Separation Media. Anal Chem 2022; 94:18025-18033. [PMID: 36511577 DOI: 10.1021/acs.analchem.2c04391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Extracellular vesicles (EVs) are lipid bilayer vesicles that enclose various biomolecules. EVs hold promise as sensitive biomarkers to detect and monitor various diseases. However, they have heterogeneous molecular compositions. The compositions of EVs from identical donor cells obtained using the same purification methods may differ, which is a significant obstacle for elucidating objective biological functions. Herein, the potential of a novel lectin-based affinity chromatography (LAC) method to classify EVs based on their glycan structures is demonstrated. The proposed method utilizes a spongy-like monolithic polymer (spongy monolith, SPM), which consists of poly(ethylene-co-glycidyl methacrylate) with continuous micropores and allows an efficient in situ protein reaction with epoxy groups. Two distinct lectins with different specificities, Sambucus sieboldiana agglutinin and concanavalin A, are effectively immobilized on SPM without impacting the binding activity. Moreover, high recovery rates of liposomal nanoparticles as a model of EVs are achieved due to the large flow-through pores (>10 μm) of SPM compared to a typical agarose gel. Finally, lectin-immobilized SPMs are employed to classify EVs based on the surface glycan structures and demonstrate different subpopulations by proteome profiling. This is the first approach to clarify the variation of protein contents in EVs by the difference of surface glycans via lectin immobilized media.
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Affiliation(s)
- Eisuke Kanao
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto606-8501, Japan.,National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka567-0085, Japan
| | - Shuntaro Wada
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto615-8510, Japan
| | - Hiroshi Nishida
- National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka567-0085, Japan
| | - Takuya Kubo
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto615-8510, Japan
| | - Tetsuya Tanigawa
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto615-8510, Japan
| | - Koshi Imami
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto606-8501, Japan.,Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama332-0012, Japan
| | - Asako Shimoda
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto615-8510, Japan
| | - Kaori Umezaki
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto615-8510, Japan
| | - Yoshihiro Sasaki
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto615-8510, Japan
| | - Kazunari Akiyoshi
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto615-8510, Japan
| | - Jun Adachi
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto606-8501, Japan.,National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka567-0085, Japan
| | - Koji Otsuka
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto615-8510, Japan
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto606-8501, Japan.,National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka567-0085, Japan
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3
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Zwaig M, Baguette A, Hu B, Johnston M, Lakkis H, Nakada EM, Faury D, Juretic N, Ellezam B, Weil AG, Karamchandani J, Majewski J, Blanchette M, Taylor MD, Gallo M, Kleinman CL, Jabado N, Ragoussis J. Detection and genomic analysis of BRAF fusions in Juvenile Pilocytic Astrocytoma through the combination and integration of multi-omic data. BMC Cancer 2022; 22:1297. [PMID: 36503484 PMCID: PMC9743522 DOI: 10.1186/s12885-022-10359-z] [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: 07/26/2022] [Accepted: 11/22/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Juvenile Pilocytic Astrocytomas (JPAs) are one of the most common pediatric brain tumors, and they are driven by aberrant activation of the mitogen-activated protein kinase (MAPK) signaling pathway. RAF-fusions are the most common genetic alterations identified in JPAs, with the prototypical KIAA1549-BRAF fusion leading to loss of BRAF's auto-inhibitory domain and subsequent constitutive kinase activation. JPAs are highly vascular and show pervasive immune infiltration, which can lead to low tumor cell purity in clinical samples. This can result in gene fusions that are difficult to detect with conventional omics approaches including RNA-Seq. METHODS To this effect, we applied RNA-Seq as well as linked-read whole-genome sequencing and in situ Hi-C as new approaches to detect and characterize low-frequency gene fusions at the genomic, transcriptomic and spatial level. RESULTS Integration of these datasets allowed the identification and detailed characterization of two novel BRAF fusion partners, PTPRZ1 and TOP2B, in addition to the canonical fusion with partner KIAA1549. Additionally, our Hi-C datasets enabled investigations of 3D genome architecture in JPAs which showed a high level of correlation in 3D compartment annotations between JPAs compared to other pediatric tumors, and high similarity to normal adult astrocytes. We detected interactions between BRAF and its fusion partners exclusively in tumor samples containing BRAF fusions. CONCLUSIONS We demonstrate the power of integrating multi-omic datasets to identify low frequency fusions and characterize the JPA genome at high resolution. We suggest that linked-reads and Hi-C could be used in clinic for the detection and characterization of JPAs.
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Affiliation(s)
- Melissa Zwaig
- grid.14709.3b0000 0004 1936 8649McGill Genome Centre and Department of Human Genetics, McGill University, Montreal, Canada
| | - Audrey Baguette
- grid.414980.00000 0000 9401 2774Quantitative Life Sciences and Lady Davis Institute for Medical Research, Montreal, Quebec Canada
| | - Bo Hu
- grid.14709.3b0000 0004 1936 8649McGill Genome Centre and Department of Human Genetics, McGill University, Montreal, Canada
| | - Michael Johnston
- grid.22072.350000 0004 1936 7697Alberta Children‘s Hospital Research Institute, Charbonneau Cancer Institute, and Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB Canada
| | - Hussein Lakkis
- grid.414980.00000 0000 9401 2774Department of Human Genetics and Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec Canada
| | - Emily M. Nakada
- grid.63984.300000 0000 9064 4811The Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Damien Faury
- grid.63984.300000 0000 9064 4811The Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Nikoleta Juretic
- grid.63984.300000 0000 9064 4811The Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Benjamin Ellezam
- grid.14848.310000 0001 2292 3357Department of Pathology, Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, QC, H3T 1C5 Canada
| | - Alexandre G. Weil
- grid.14848.310000 0001 2292 3357Department of Pediatric Neurosurgery, Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, QC H3T 1C5 Canada
| | - Jason Karamchandani
- grid.14709.3b0000 0004 1936 8649Department of Pathology, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4 Canada
| | - Jacek Majewski
- grid.14709.3b0000 0004 1936 8649McGill Genome Centre and Department of Human Genetics, McGill University, Montreal, Canada
| | - Mathieu Blanchette
- grid.14709.3b0000 0004 1936 8649School of Computer Science and McGill Center for Bioinformatics, McGill University, Montréal, Québec Canada
| | - Michael D. Taylor
- grid.42327.300000 0004 0473 9646Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children Research Institute, Toronto, Canada
| | - Marco Gallo
- grid.22072.350000 0004 1936 7697Alberta Children‘s Hospital Research Institute, Charbonneau Cancer Institute, and Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB Canada
| | - Claudia L. Kleinman
- grid.414980.00000 0000 9401 2774Department of Human Genetics and Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec Canada
| | - Nada Jabado
- grid.63984.300000 0000 9064 4811Department of Human Genetics, Department of Pediatrics, and The Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Jiannis Ragoussis
- grid.14709.3b0000 0004 1936 8649McGill Genome Centre and Department of Human Genetics, McGill University, Montreal, Canada
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4
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Cameron AP, Zeng B, Liu Y, Wang H, Soheilmoghaddam F, Cooper-White J, Zhao CX. Biophysical properties of hydrogels for mimicking tumor extracellular matrix. BIOMATERIALS ADVANCES 2022; 136:212782. [PMID: 35929332 DOI: 10.1016/j.bioadv.2022.212782] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 03/01/2022] [Accepted: 03/26/2022] [Indexed: 06/15/2023]
Abstract
The extracellular matrix (ECM) is an essential component of the tumor microenvironment. It plays a critical role in regulating cell-cell and cell-matrix interactions. However, there is lack of systematic and comparative studies on different widely-used ECM mimicking hydrogels and their properties, making the selection of suitable hydrogels for mimicking different in vivo conditions quite random. This study systematically evaluates the biophysical attributes of three widely used natural hydrogels (Matrigel, collagen gel and agarose gel) including complex modulus, loss tangent, diffusive permeability and pore size. A new and facile method was developed combining Critical Point Drying, Scanning Electron Microscopy imaging and a MATLAB image processing program (CSM method) for the characterization of hydrogel microstructures. This CSM method allows accurate measurement of the hydrogel pore size down to nanometer resolution. Furthermore, a microfluidic device was implemented to measure the hydrogel permeability (Pd) as a function of particle size and gel concentration. Among the three gels, collagen gel has the lowest complex modulus, medium pore size, and the highest loss tangent. Agarose gel exhibits the highest complex modulus, the lowest loss tangent and the smallest pore size. Collagen gel and Matrigel produced complex moduli close to that estimated for cancer ECM. The Pd of these hydrogels decreases significantly with the increase of particle size. By assessing different hydrogels' biophysical characteristics, this study provides valuable insights for tailoring their properties for various three-dimensional cancer models.
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Affiliation(s)
- Anna P Cameron
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Bijun Zeng
- Diamantina Institute, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Yun Liu
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Haofei Wang
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Farhad Soheilmoghaddam
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Justin Cooper-White
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia; School of Chemical Engineering, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Chun-Xia Zhao
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia.
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5
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The landscape of receptor-mediated precision cancer combination therapy via a single-cell perspective. Nat Commun 2022; 13:1613. [PMID: 35338126 PMCID: PMC8956718 DOI: 10.1038/s41467-022-29154-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 02/22/2022] [Indexed: 02/08/2023] Open
Abstract
Mining a large cohort of single-cell transcriptomics data, here we employ combinatorial optimization techniques to chart the landscape of optimal combination therapies in cancer. We assume that each individual therapy can target any one of 1269 genes encoding cell surface receptors, which may be targets of CAR-T, conjugated antibodies or coated nanoparticle therapies. We find that in most cancer types, personalized combinations composed of at most four targets are then sufficient for killing at least 80% of tumor cells while sparing at least 90% of nontumor cells in the tumor microenvironment. However, as more stringent and selective killing is required, the number of targets needed rises rapidly. Emerging individual targets include PTPRZ1 for brain and head and neck cancers and EGFR in multiple tumor types. In sum, this study provides a computational estimate of the identity and number of targets needed in combination to target cancers selectively and precisely. Intra-tumor heterogeneity is often associated with resistance to targeted therapy, requiring the design of combinatorial therapies. Here, based on tumor single-cell transcriptomic datasets, the authors develop a computational approach to identify optimal combinatorial treatments targeting membrane receptors for cancer therapy.
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6
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Seguin L, Odouard S, Corlazzoli F, Haddad SA, Moindrot L, Calvo Tardón M, Yebra M, Koval A, Marinari E, Bes V, Guérin A, Allard M, Ilmjärv S, Katanaev VL, Walker PR, Krause KH, Dutoit V, Sarkaria JN, Dietrich PY, Cosset É. Macropinocytosis requires Gal-3 in a subset of patient-derived glioblastoma stem cells. Commun Biol 2021; 4:718. [PMID: 34112916 PMCID: PMC8192788 DOI: 10.1038/s42003-021-02258-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 05/21/2021] [Indexed: 12/11/2022] Open
Abstract
Recently, we involved the carbohydrate-binding protein Galectin-3 (Gal-3) as a druggable target for KRAS-mutant-addicted lung and pancreatic cancers. Here, using glioblastoma patient-derived stem cells (GSCs), we identify and characterize a subset of Gal-3high glioblastoma (GBM) tumors mainly within the mesenchymal subtype that are addicted to Gal-3-mediated macropinocytosis. Using both genetic and pharmacologic inhibition of Gal-3, we showed a significant decrease of GSC macropinocytosis activity, cell survival and invasion, in vitro and in vivo. Mechanistically, we demonstrate that Gal-3 binds to RAB10, a member of the RAS superfamily of small GTPases, and β1 integrin, which are both required for macropinocytosis activity and cell survival. Finally, by defining a Gal-3/macropinocytosis molecular signature, we could predict sensitivity to this dependency pathway and provide proof-of-principle for innovative therapeutic strategies to exploit this Achilles' heel for a significant and unique subset of GBM patients.
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Affiliation(s)
- Laetitia Seguin
- University Côte d'Azur, CNRS UMR7284, INSERM U1081, Institute for Research on Cancer and Aging (IRCAN), Nice, France
| | - Soline Odouard
- Laboratory of Tumor Immunology, Department of Oncology, Center for Translational Research in Onco-Hematology, Swiss Cancer Center Léman (SCCL), Geneva University Hospitals, University of Geneva, Geneva, Switzerland
| | - Francesca Corlazzoli
- Laboratory of Tumor Immunology, Department of Oncology, Center for Translational Research in Onco-Hematology, Swiss Cancer Center Léman (SCCL), Geneva University Hospitals, University of Geneva, Geneva, Switzerland
| | - Sarah Al Haddad
- Laboratory of Tumor Immunology, Department of Oncology, Center for Translational Research in Onco-Hematology, Swiss Cancer Center Léman (SCCL), Geneva University Hospitals, University of Geneva, Geneva, Switzerland
| | - Laurine Moindrot
- Laboratory of Tumor Immunology, Department of Oncology, Center for Translational Research in Onco-Hematology, Swiss Cancer Center Léman (SCCL), Geneva University Hospitals, University of Geneva, Geneva, Switzerland
| | - Marta Calvo Tardón
- Laboratory of Immunobiology of brain tumors, Center for Translational Research in Onco-Hematology, Geneva University Hospitals, and University of Geneva, Geneva, Switzerland
| | - Mayra Yebra
- Department of Surgery, Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Alexey Koval
- Department of Cell Physiology and Metabolism, Medical School, University of Geneva, Geneva, Switzerland
| | - Eliana Marinari
- Laboratory of Tumor Immunology, Department of Oncology, Center for Translational Research in Onco-Hematology, Swiss Cancer Center Léman (SCCL), Geneva University Hospitals, University of Geneva, Geneva, Switzerland
| | - Viviane Bes
- Laboratory of Immunobiology of brain tumors, Center for Translational Research in Onco-Hematology, Geneva University Hospitals, and University of Geneva, Geneva, Switzerland
| | - Alexandre Guérin
- Department of Pathology and Immunology, Medical School, University of Geneva, Geneva, Geneva, Switzerland
| | - Mathilde Allard
- Laboratory of Tumor Immunology, Department of Oncology, Center for Translational Research in Onco-Hematology, Swiss Cancer Center Léman (SCCL), Geneva University Hospitals, University of Geneva, Geneva, Switzerland
| | - Sten Ilmjärv
- Department of Pathology and Immunology, Medical School, University of Geneva, Geneva, Geneva, Switzerland
| | - Vladimir L Katanaev
- Department of Cell Physiology and Metabolism, Medical School, University of Geneva, Geneva, Switzerland
| | - Paul R Walker
- Laboratory of Immunobiology of brain tumors, Center for Translational Research in Onco-Hematology, Geneva University Hospitals, and University of Geneva, Geneva, Switzerland
| | - Karl-Heinz Krause
- Department of Pathology and Immunology, Medical School, University of Geneva, Geneva, Geneva, Switzerland
| | - Valérie Dutoit
- Laboratory of Tumor Immunology, Department of Oncology, Center for Translational Research in Onco-Hematology, Swiss Cancer Center Léman (SCCL), Geneva University Hospitals, University of Geneva, Geneva, Switzerland
| | - Jann N Sarkaria
- Department of Radiation Oncology, Mayo Clinic, Rochester, MN, USA
| | - Pierre-Yves Dietrich
- Laboratory of Tumor Immunology, Department of Oncology, Center for Translational Research in Onco-Hematology, Swiss Cancer Center Léman (SCCL), Geneva University Hospitals, University of Geneva, Geneva, Switzerland
| | - Érika Cosset
- Laboratory of Tumor Immunology, Department of Oncology, Center for Translational Research in Onco-Hematology, Swiss Cancer Center Léman (SCCL), Geneva University Hospitals, University of Geneva, Geneva, Switzerland.
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7
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Smedley NF, El-Saden S, Hsu W. Discovering and interpreting transcriptomic drivers of imaging traits using neural networks. Bioinformatics 2020; 36:3537-3548. [PMID: 32101278 DOI: 10.1093/bioinformatics/btaa126] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 01/07/2020] [Accepted: 02/19/2020] [Indexed: 12/20/2022] Open
Abstract
MOTIVATION Cancer heterogeneity is observed at multiple biological levels. To improve our understanding of these differences and their relevance in medicine, approaches to link organ- and tissue-level information from diagnostic images and cellular-level information from genomics are needed. However, these 'radiogenomic' studies often use linear or shallow models, depend on feature selection, or consider one gene at a time to map images to genes. Moreover, no study has systematically attempted to understand the molecular basis of imaging traits based on the interpretation of what the neural network has learned. These studies are thus limited in their ability to understand the transcriptomic drivers of imaging traits, which could provide additional context for determining clinical outcomes. RESULTS We present a neural network-based approach that takes high-dimensional gene expression data as input and performs non-linear mapping to an imaging trait. To interpret the models, we propose gene masking and gene saliency to extract learned relationships from radiogenomic neural networks. In glioblastoma patients, our models outperformed comparable classifiers (>0.10 AUC) and our interpretation methods were validated using a similar model to identify known relationships between genes and molecular subtypes. We found that tumor imaging traits had specific transcription patterns, e.g. edema and genes related to cellular invasion, and 10 radiogenomic traits were significantly predictive of survival. We demonstrate that neural networks can model transcriptomic heterogeneity to reflect differences in imaging and can be used to derive radiogenomic traits with clinical value. AVAILABILITY AND IMPLEMENTATION https://github.com/novasmedley/deepRadiogenomics. CONTACT whsu@mednet.ucla.edu. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Nova F Smedley
- Medical & Imaging Informatics.,Department of Radiological Sciences.,Department of Bioengineering
| | - Suzie El-Saden
- Medical & Imaging Informatics.,Department of Radiological Sciences
| | - William Hsu
- Medical & Imaging Informatics.,Department of Radiological Sciences.,Department of Bioengineering.,Bioinformatics IDP, University of California Los Angeles, Los Angeles, CA 90024, USA
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8
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Dong Z, Li C, Coates D. PTN-PTPRZ signalling is involved in deer antler stem cell regulation during tissue regeneration. J Cell Physiol 2020; 236:3752-3769. [PMID: 33111346 DOI: 10.1002/jcp.30115] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 10/06/2020] [Accepted: 10/08/2020] [Indexed: 12/22/2022]
Abstract
A growing deer antler contains a stem cell niche that can drive endochondral bone regeneration at up to 2 cm/day. Pleiotrophin (PTN), as a multifunctional growth factor, is found highly expressed at the messenger RNA level within the active antler stem cell tissues. This study aims to map the expression patterns of PTN protein and its receptors in a growing antler and investigate the effects of PTN on antler stem cells in vitro. Immunohistochemistry was employed to localise PTN/midkine (MDK) and their functional receptors, protein tyrosine phosphatase receptor type Z (PTPRZ), anaplastic lymphoma kinase (ALK), NOTCH2, and integrin αV β3, on serial slides of the antler growth centre. PTN was found to be the dominantly expressed growth factor in the PTN/MDK family. High expression of PTPRZ and ALK co-localised with PTN was found suggesting a potential interaction. The high levels of PTN and PTPRZ reflected the antler stem cell activation status during the regenerative process. When antler stem cells were cultured in vitro under the normoxic condition, no PTN protein was detected and exogenous PTN did not induce differentiation or proliferation but rather stem cell maintenance. Collectively, the antler stem cell niche appears to upregulate PTN and PTPRZ in vivo, and PTN-PTPRZ signalling may be involved in regulating antler stem cell behaviour during rapid antler regeneration.
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Affiliation(s)
- Zhen Dong
- Faculty of Dentistry, Sir John Walsh Research Institute, University of Otago, Dunedin, New Zealand
| | - Chunyi Li
- Institute of Antler Science and Product Technology, Changchun Sci-Tech University, Changchun, China
| | - Dawn Coates
- Faculty of Dentistry, Sir John Walsh Research Institute, University of Otago, Dunedin, New Zealand
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9
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Krause M, Yang FW, te Lindert M, Isermann P, Schepens J, Maas RJA, Venkataraman C, Lammerding J, Madzvamuse A, Hendriks W, te Riet J, Wolf K. Cell migration through three-dimensional confining pores: speed accelerations by deformation and recoil of the nucleus. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180225. [PMID: 31431171 PMCID: PMC6627020 DOI: 10.1098/rstb.2018.0225] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2019] [Indexed: 01/22/2023] Open
Abstract
Directional cell migration in dense three-dimensional (3D) environments critically depends upon shape adaptation and is impeded depending on the size and rigidity of the nucleus. Accordingly, the nucleus is primarily understood as a physical obstacle; however, its pro-migratory functions by stepwise deformation and reshaping remain unclear. Using atomic force spectroscopy, time-lapse fluorescence microscopy and shape change analysis tools, we determined the nuclear size, deformability, morphology and shape change of HT1080 fibrosarcoma cells expressing the Fucci cell cycle indicator or being pre-treated with chromatin-decondensating agent TSA. We show oscillating peak accelerations during migration through 3D collagen matrices and microdevices that occur during shape reversion of deformed nuclei (recoil), and increase with confinement. During G1 cell-cycle phase, nucleus stiffness was increased and yielded further increased speed fluctuations together with sustained cell migration rates in confinement when compared to interphase populations or to periods of intrinsic nuclear softening in the S/G2 cell-cycle phase. Likewise, nuclear softening by pharmacological chromatin decondensation or after lamin A/C depletion reduced peak oscillations in confinement. In conclusion, deformation and recoil of the stiff nucleus contributes to saltatory locomotion in dense tissues. This article is part of a discussion meeting issue 'Forces in cancer: interdisciplinary approaches in tumour mechanobiology'.
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Affiliation(s)
- Marina Krause
- Department of Cell Biology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Feng Wei Yang
- Department of Mathematics, School of Mathematical and Physical Sciences, University of Sussex, Falmer, Brighton BN1 9QH, UK
| | - Mariska te Lindert
- Department of Cell Biology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Philipp Isermann
- Meinig School of Biomedical Engineering, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jan Schepens
- Department of Cell Biology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Ralph J. A. Maas
- Department of Cell Biology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Chandrasekhar Venkataraman
- Department of Mathematics, School of Mathematical and Physical Sciences, University of Sussex, Falmer, Brighton BN1 9QH, UK
| | - Jan Lammerding
- Meinig School of Biomedical Engineering, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Anotida Madzvamuse
- Department of Mathematics, School of Mathematical and Physical Sciences, University of Sussex, Falmer, Brighton BN1 9QH, UK
| | - Wiljan Hendriks
- Department of Cell Biology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Joost te Riet
- Department of Tumor Immunology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Katarina Wolf
- Department of Cell Biology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
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10
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Ruckert MT, de Andrade PV, Santos VS, Silveira VS. Protein tyrosine phosphatases: promising targets in pancreatic ductal adenocarcinoma. Cell Mol Life Sci 2019; 76:2571-2592. [PMID: 30982078 PMCID: PMC11105579 DOI: 10.1007/s00018-019-03095-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 03/25/2019] [Accepted: 04/08/2019] [Indexed: 12/21/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the most common type of pancreatic cancer. It is the fourth leading cause of cancer-related death and is associated with a very poor prognosis. KRAS driver mutations occur in approximately 95% of PDAC cases and cause the activation of several signaling pathways such as mitogen-activated protein kinase (MAPK) pathways. Regulation of these signaling pathways is orchestrated by feedback loops mediated by the balance between protein tyrosine kinases (PTKs) and protein tyrosine phosphatases (PTPs), leading to activation or inhibition of its downstream targets. The human PTPome comprises 125 members, and these proteins are classified into three distinct families according to their structure. Since PTP activity description, it has become clear that they have both inhibitory and stimulatory effects on cancer-associated signaling processes and that deregulation of PTP function is closely associated with tumorigenesis. Several PTPs have displayed either tumor suppressor or oncogenic characteristics during the development and progression of PDAC. In this sense, PTPs have been presented as promising candidates for the treatment of human pancreatic cancer, and many PTP inhibitors have been developed since these proteins were first associated with cancer. Nevertheless, some challenges persist regarding the development of effective and safe methods to target these molecules and deliver these drugs. In this review, we discuss the role of PTPs in tumorigenesis as tumor suppressor and oncogenic proteins. We have focused on the differential expression of these proteins in PDAC, as well as their clinical implications and possible targeting for pharmacological inhibition in cancer therapy.
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Affiliation(s)
- Mariana Tannús Ruckert
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, São Paulo, Brazil
| | - Pamela Viani de Andrade
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, São Paulo, Brazil
| | - Verena Silva Santos
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, São Paulo, Brazil
| | - Vanessa Silva Silveira
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, São Paulo, Brazil.
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11
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Protein Phosphatases-A Touchy Enemy in the Battle Against Glioblastomas: A Review. Cancers (Basel) 2019; 11:cancers11020241. [PMID: 30791455 PMCID: PMC6406705 DOI: 10.3390/cancers11020241] [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: 12/31/2018] [Revised: 02/15/2019] [Accepted: 02/16/2019] [Indexed: 12/19/2022] Open
Abstract
Glioblastoma (GBM) is the most common malignant tumor arising from brain parenchyma. Although many efforts have been made to develop therapies for GBM, the prognosis still remains poor, mainly because of the difficulty in total resection of the tumor mass from brain tissue and the resistance of the residual tumor against standard chemoradiotherapy. Therefore, novel adjuvant therapies are urgently needed. Recent genome-wide analyses of GBM cases have clarified molecular signaling mechanisms underlying GBM biology. However, results of clinical trials targeting phosphorylation-mediated signaling have been unsatisfactory to date. Protein phosphatases are enzymes that antagonize phosphorylation signaling by dephosphorylating phosphorylated signaling molecules. Recently, the critical roles of phosphatases in the regulation of oncogenic signaling in malignant tumor cells have been reported, and tumorigenic roles of deregulated phosphatases have been demonstrated in GBM. However, a detailed mechanism underlying phosphatase-mediated signaling transduction in the regulation of GBM has not been elucidated, and such information is necessary to apply phosphatases as a therapeutic target for GBM. This review highlights and summarizes the phosphatases that have crucial roles in the regulation of oncogenic signaling in GBM cells.
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12
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Shalev M, Elson A. The roles of protein tyrosine phosphatases in bone-resorbing osteoclasts. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1866:114-123. [PMID: 30026076 DOI: 10.1016/j.bbamcr.2018.07.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 07/08/2018] [Accepted: 07/11/2018] [Indexed: 12/20/2022]
Abstract
Maintaining the proper balance between osteoblast-mediated production of bone and its degradation by osteoclasts is essential for health. Osteoclasts are giant phagocytic cells that are formed by fusion of monocyte-macrophage precursor cells; mature osteoclasts adhere to bone tightly and secrete protons and proteases that degrade its matrix. Phosphorylation of tyrosine residues in proteins, which is regulated by the biochemically-antagonistic activities of protein tyrosine kinases and protein tyrosine phosphatases (PTPs), is central in regulating the production of osteoclasts and their bone-resorbing activity. Here we review the roles of individual PTPs of the classical and dual-specificity sub-families that are known to support these processes (SHP2, cyt-PTPe, PTPRO, PTP-PEST, CD45) or to inhibit them (SHP1, PTEN, MKP1). Characterizing the functions of PTPs in osteoclasts is essential for complete molecular level understanding of bone resorption and for designing novel therapeutic approaches for treating bone disease.
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Affiliation(s)
- Moran Shalev
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ari Elson
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot 76100, Israel.
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13
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Hendriks W, Bourgonje A, Leenders W, Pulido R. Proteinaceous Regulators and Inhibitors of Protein Tyrosine Phosphatases. Molecules 2018; 23:molecules23020395. [PMID: 29439552 PMCID: PMC6016963 DOI: 10.3390/molecules23020395] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 02/09/2018] [Accepted: 02/09/2018] [Indexed: 12/18/2022] Open
Abstract
Proper control of the phosphotyrosine content in signal transduction proteins is essential for normal cell behavior and is lost in many pathologies. Attempts to normalize aberrant tyrosine phosphorylation levels in disease states currently involve either the application of small compounds that inhibit tyrosine kinases (TKs) or the addition of growth factors or their mimetics to boost receptor-type TK activity. Therapies that target the TK enzymatic counterparts, the multi-enzyme family of protein tyrosine phosphatases (PTPs), are still lacking despite their undisputed involvement in human diseases. Efforts to pharmacologically modulate PTP activity have been frustrated by the conserved structure of the PTP catalytic core, providing a daunting problem with respect to target specificity. Over the years, however, many different protein interaction-based regulatory mechanisms that control PTP activity have been uncovered, providing alternative possibilities to control PTPs individually. Here, we review these regulatory principles, discuss existing biologics and proteinaceous compounds that affect PTP activity, and mention future opportunities to drug PTPs via these regulatory concepts.
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Affiliation(s)
- Wiljan Hendriks
- Department of Cell Biology, Radboud University Medical Center, Geert Grooteplein 26, 6525 GA Nijmegen, The Netherlands.
| | - Annika Bourgonje
- Department of Cell Biology, Radboud University Medical Center, Geert Grooteplein 26, 6525 GA Nijmegen, The Netherlands.
| | - William Leenders
- Department of Biochemistry, Radboud University Medical Center, Geert Grooteplein 26, 6525 GA Nijmegen, The Netherlands.
| | - Rafael Pulido
- Biomarkers in Cancer Unit, Biocruces Health Research Institute, 48903 Barakaldo, Spain.
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain.
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14
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Jaime-Ramirez AC, Dmitrieva N, Yoo JY, Banasavadi-Siddegowda Y, Zhang J, Relation T, Bolyard C, Wojton J, Kaur B. Humanized chondroitinase ABC sensitizes glioblastoma cells to temozolomide. J Gene Med 2018; 19. [PMID: 28087981 DOI: 10.1002/jgm.2942] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 01/06/2017] [Accepted: 01/08/2017] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Malignant gliomas (glioblastomas; GBMs) are extremely aggressive and have a median survival of approximately 15 months. Current treatment modalities, which include surgical resection, radiation and chemotherapy, have done little to prolong the lives of GBM patients. Chondroitin sulfate proteoglycans (CSPG) are critical for cell-cell and cell-extracellular matrix (ECM) interactions and are implicated in glioma growth and invasion. Chondroitinase (Chase) ABC is a bacterial enzyme that cleaves chondroitin sulfate disaccharide chains from CSPGs in the tumor ECM. Wild-type Chase ABC has limited stability and/or activity in mammalian cells; therefore, we created a mutant humanized version (Chase M) with enhanced function in mammalian cells. METHODS We hypothesized that disruption of cell-cell and cell-ECM interactions by ChaseM and temozolomide (TMZ) will enhance the chemotherapeutic availability and sensitivity of glioma cells. RESULTS Utilizing primary patient-derived neurospheres, we found that ChaseM decreases glioma neurosphere aggregation in vitro. Furthermore, an oncolytic HSV-1 virus expressing secreted ChaseM (OV-ChaseM) enhanced viral spread and glioma cell killing compared to OV-Control, in vitro. OV-ChaseM plus TMZ combinatorial treatment resulted in a significant synergistic enhancement of glioma cell killing accompanied by an increase in apoptotic cell death. Intracellular flow cytometric analysis revealed a significant reduction in the phosphorylation of the pro-survival AKT protein following OV-ChaseM plus TMZ treatment. Lastly, in nude mice bearing intracranial GBM30 glioma xenografts, intratumoral OV-ChaseM plus TMZ (10 mg/kg by oral gavage) combination therapy resulted in a significant (p < 0.02) enhancement of survival compared to each individual treatment alone. CONCLUSIONS These data reveal that OV-ChaseM enhances glioma cell viral susceptibility and sensitivity to TMZ.
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Affiliation(s)
- Alena Cristina Jaime-Ramirez
- Department of Neurological Surgery, The Ohio State University Comprehensive Cancer Center, The James Cancer Hospital, and Solove Research Institute, Columbus, OH, USA
| | - Nina Dmitrieva
- Department of Neurological Surgery, The Ohio State University Comprehensive Cancer Center, The James Cancer Hospital, and Solove Research Institute, Columbus, OH, USA
| | - Ji Young Yoo
- Department of Neurological Surgery, The Ohio State University Comprehensive Cancer Center, The James Cancer Hospital, and Solove Research Institute, Columbus, OH, USA
| | - Yeshavanth Banasavadi-Siddegowda
- Department of Neurological Surgery, The Ohio State University Comprehensive Cancer Center, The James Cancer Hospital, and Solove Research Institute, Columbus, OH, USA
| | - Jianying Zhang
- Center for Biostatistics Biomedical Informatics Department, The Ohio State University Comprehensive Cancer Center, The James Cancer Hospital, and Solove Research Institute, Columbus, OH, USA
| | - Theresa Relation
- Neuroscience Graduate Program and The Medical Scientist Training Program, The Ohio State University Comprehensive Cancer Center, The James Cancer Hospital, and Solove Research Institute, Columbus, OH, USA
| | - Chelsea Bolyard
- Department of Neurological Surgery, The Ohio State University Comprehensive Cancer Center, The James Cancer Hospital, and Solove Research Institute, Columbus, OH, USA
| | - Jeffrey Wojton
- Department of Neurological Surgery, The Ohio State University Comprehensive Cancer Center, The James Cancer Hospital, and Solove Research Institute, Columbus, OH, USA
| | - Balveen Kaur
- Department of Neurological Surgery, The Ohio State University Comprehensive Cancer Center, The James Cancer Hospital, and Solove Research Institute, Columbus, OH, USA
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15
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Elson A. Stepping out of the shadows: Oncogenic and tumor-promoting protein tyrosine phosphatases. Int J Biochem Cell Biol 2017; 96:135-147. [PMID: 28941747 DOI: 10.1016/j.biocel.2017.09.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 09/15/2017] [Accepted: 09/16/2017] [Indexed: 12/18/2022]
Abstract
Protein tyrosine phosphorylation is critical for proper function of cells and organisms. Phosphorylation is regulated by the concerted but generically opposing activities of tyrosine kinases (PTKs) and tyrosine phosphatases (PTPs), which ensure its proper regulation, reversibility, and ability to respond to changing physiological situations. Historically, PTKs have been associated mainly with oncogenic and pro-tumorigenic activities, leading to the generalization that protein dephosphorylation is anti-oncogenic and hence that PTPs are tumor-suppressors. In many cases PTPs do suppress tumorigenesis. However, a growing body of evidence indicates that PTPs act as dominant oncogenes and drive cell transformation in a number of contexts, while in others PTPs support transformation that is driven by other oncogenes. This review summarizes the known transforming and tumor-promoting activities of the classical, tyrosine specific PTPs and highlights their potential as drug targets for cancer therapy.
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Affiliation(s)
- Ari Elson
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, 76100, Israel.
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16
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van den Heuvel CNAM, Navis AC, de Bitter T, Amiri H, Verrijp K, Heerschap A, Rex K, Dussault I, Caenepeel S, Coxon A, Span PN, Wesseling P, Hendriks W, Leenders WPJ. Selective MET Kinase Inhibition in MET-Dependent Glioma Models Alters Gene Expression and Induces Tumor Plasticity. Mol Cancer Res 2017; 15:1587-1597. [PMID: 28751462 DOI: 10.1158/1541-7786.mcr-17-0177] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 06/15/2017] [Accepted: 07/24/2017] [Indexed: 11/16/2022]
Abstract
The receptor tyrosine kinase (RTK) MET represents a promising tumor target in a subset of glioblastomas. Most RTK inhibitors available in the clinic today, including those inhibiting MET, affect multiple targets simultaneously. Previously, it was demonstrated that treatment with cabozantinib (MET/VEGFR2/RET inhibitor) prolonged survival of mice carrying orthotopic patient-derived xenografts (PDX) of the MET-addicted glioblastoma model E98, yet did not prevent development of recurrent and cabozantinib-resistant tumors. To exclude VEGFR2 inhibition-inflicted blood-brain barrier normalization and diminished tumor distribution of the drug, we have now investigated the effects of the novel MET-selective inhibitor Compound A in the orthotopic E98 xenograft model. In vitro, Compound A proved a highly potent inhibitor of proliferation of MET-addicted cell lines. In line with its target selectivity, Compound A did not restore the leaky blood-brain barrier and was more effective than cabozantinib in inhibiting MET phosphorylation in vivo Compound A treatment significantly prolonged survival of mice carrying E98 tumor xenografts, but did not prevent eventual progression. Contrasting in vitro results, the Compound A-treated xenografts displayed high levels of AKT phosphorylation despite the absence of phosphorylated MET. Profiling by RNA sequencing showed that in vivo transcriptomes differed significantly from those in control xenografts.Implications: Collectively, these findings demonstrate the plasticity of paracrine growth factor receptor signaling in vivo and urge for prudency with in vitro drug-testing strategies to validate monotherapies. Mol Cancer Res; 15(11); 1587-97. ©2017 AACR.
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Affiliation(s)
| | - Anna C Navis
- Department of Pathology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Tessa de Bitter
- Department of Pathology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Houshang Amiri
- Department of Radiology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Kiek Verrijp
- Department of Pathology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Arend Heerschap
- Department of Radiology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Karen Rex
- Department of Oncology Research, Amgen Inc., Thousand Oaks, California
| | - Isabelle Dussault
- Department of Oncology Research, Amgen Inc., Thousand Oaks, California
| | - Sean Caenepeel
- Department of Oncology Research, Amgen Inc., Thousand Oaks, California
| | - Angela Coxon
- Department of Oncology Research, Amgen Inc., Thousand Oaks, California
| | - Paul N Span
- Department of Radiation Oncology, Radboud University Medical Centre, Radiotherapy and Oncoimmunology Laboratory, Nijmegen, the Netherlands
| | - Pieter Wesseling
- Department of Pathology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Wiljan Hendriks
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - William P J Leenders
- Department of Pathology, Radboud University Medical Centre, Nijmegen, the Netherlands.
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17
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Lenting K, Verhaak R, Ter Laan M, Wesseling P, Leenders W. Glioma: experimental models and reality. Acta Neuropathol 2017; 133:263-282. [PMID: 28074274 PMCID: PMC5250671 DOI: 10.1007/s00401-017-1671-4] [Citation(s) in RCA: 185] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 01/06/2017] [Accepted: 01/06/2017] [Indexed: 12/12/2022]
Abstract
In theory, in vitro and in vivo models for human gliomas have great potential to not only enhance our understanding of glioma biology, but also to facilitate the development of novel treatment strategies for these tumors. For reliable prediction and validation of the effects of different therapeutic modalities, however, glioma models need to comply with specific and more strict demands than other models of cancer, and these demands are directly related to the combination of genetic aberrations and the specific brain micro-environment gliomas grow in. This review starts with a brief introduction on the pathological and molecular characteristics of gliomas, followed by an overview of the models that have been used in the last decades in glioma research. Next, we will discuss how these models may play a role in better understanding glioma development and especially in how they can aid in the design and optimization of novel therapies. The strengths and weaknesses of the different models will be discussed in light of genotypic, phenotypic and metabolic characteristics of human gliomas. The last part of this review provides some examples of how therapy experiments using glioma models can lead to deceptive results when such characteristics are not properly taken into account.
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Affiliation(s)
- Krissie Lenting
- Department of Pathology, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Roel Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Mark Ter Laan
- Department of Neurosurgery, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Pieter Wesseling
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
- Department of Pathology, Princess Máxima Center for Pediatric Oncology and University Medical Center Utrecht, Utrecht, The Netherlands
| | - William Leenders
- Department of Pathology, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands.
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18
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Papadimitriou E, Pantazaka E, Castana P, Tsalios T, Polyzos A, Beis D. Pleiotrophin and its receptor protein tyrosine phosphatase beta/zeta as regulators of angiogenesis and cancer. Biochim Biophys Acta Rev Cancer 2016; 1866:252-265. [DOI: 10.1016/j.bbcan.2016.09.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 09/26/2016] [Accepted: 09/28/2016] [Indexed: 02/06/2023]
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19
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Bourgonje AM, Verrijp K, Schepens JTG, Navis AC, Piepers JAF, Palmen CBC, van den Eijnden M, Hooft van Huijsduijnen R, Wesseling P, Leenders WPJ, Hendriks WJAJ. Comprehensive protein tyrosine phosphatase mRNA profiling identifies new regulators in the progression of glioma. Acta Neuropathol Commun 2016; 4:96. [PMID: 27586084 PMCID: PMC5009684 DOI: 10.1186/s40478-016-0372-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 08/19/2016] [Indexed: 12/20/2022] Open
Abstract
The infiltrative behavior of diffuse gliomas severely reduces therapeutic potential of surgical resection and radiotherapy, and urges for the identification of new drug-targets affecting glioma growth and migration. To address the potential role of protein tyrosine phosphatases (PTPs), we performed mRNA expression profiling for 91 of the 109 known human PTP genes on a series of clinical diffuse glioma samples of different grades and compared our findings with in silico knowledge from REMBRANDT and TCGA databases. Overall PTP family expression levels appeared independent of characteristic genetic aberrations associated with lower grade or high grade gliomas. Notably, seven PTP genes (DUSP26, MTMR4, PTEN, PTPRM, PTPRN2, PTPRT and PTPRZ1) were differentially expressed between grade II-III gliomas and (grade IV) glioblastomas. For DUSP26, PTEN, PTPRM and PTPRT, lower expression levels correlated with poor prognosis, and overexpression of DUSP26 or PTPRT in E98 glioblastoma cells reduced tumorigenicity. Our study represents the first in-depth analysis of PTP family expression in diffuse glioma subtypes and warrants further investigations into PTP-dependent signaling events as new entry points for improved therapy.
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20
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Bao G, Wang N, Li R, Xu G, Liu P, He B. Glycoprotein non-metastaticmelanoma protein B promotes glioma motility and angiogenesis through the Wnt/β-catenin signaling pathway. Exp Biol Med (Maywood) 2016; 241:1968-1976. [PMID: 27334625 DOI: 10.1177/1535370216654224] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 05/11/2016] [Indexed: 02/03/2023] Open
Abstract
Glioma is a common tumor with high mortality and poor overall survival. However, the regulatory mechanisms of glioma tumorigenesis and glioma cell motility are completely unknown. Here, we investigated the role of glycoprotein non-metastatic melanoma protein B in glioma. The expression of glycoprotein non-metastatic melanoma protein B is observed to be aberrantly regulated in glioma tissues and cells, and high levels of glycoprotein non-metastatic melanoma protein B present an inverse correlation with the survival of glioma patients. Compared with the control, glycoprotein non-metastatic melanoma protein B inhibition significantly retarded the proliferation and migration of human glioma cells. The tube formation ability of HBMECs induced by glioma cells was also remarkably reduced by glycoprotein non-metastatic melanoma protein B silencing. Increased levels of VEGF-C and TEM7 were down-regulated by the suppression of glycoprotein non-metastatic melanoma protein B in glioma cells. Additionally, the activity of MMP-2/3/9 was assessed in glioma cells using Western blotting and gelatin zymography assay; their activities were strongly decreased following the suppression of glycoprotein non-metastatic melanoma protein B. Further studies suggested that canonical Wnt/β-catenin pathway was activated, but was inactivated by glycoprotein non-metastatic melanoma protein B suppression in glioma cells. In conclusion, we demonstrate that glycoprotein non-metastatic melanoma protein B might be an inducer for glioma and could enhance matrix metalloproteinase activity through Wnt/β-catenin pathway to contribute to glioma tumorigenesis. This may represent a new understanding for malignant glioma.
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Affiliation(s)
- Gang Bao
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Ning Wang
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Ruichun Li
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Gaofeng Xu
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Peijun Liu
- Centre for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Baixiang He
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
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21
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Small-molecule inhibition of PTPRZ reduces tumor growth in a rat model of glioblastoma. Sci Rep 2016; 6:20473. [PMID: 26857455 PMCID: PMC4746629 DOI: 10.1038/srep20473] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 01/04/2016] [Indexed: 01/02/2023] Open
Abstract
Protein tyrosine phosphatase receptor-type Z (PTPRZ) is aberrantly over-expressed in glioblastoma and a causative factor for its malignancy. However, small molecules that selectively inhibit the catalytic activity of PTPRZ have not been discovered. We herein performed an in vitro screening of a chemical library, and identified SCB4380 as the first potent inhibitor for PTPRZ. The stoichiometric binding of SCB4380 to the catalytic pocket was demonstrated by biochemical and mass spectrometric analyses. We determined the crystal structure of the catalytic domain of PTPRZ, and the structural basis of the binding of SCB4380 elucidated by a molecular docking method was validated by site-directed mutagenesis studies. The intracellular delivery of SCB4380 by liposome carriers inhibited PTPRZ activity in C6 glioblastoma cells, and thereby suppressed their migration and proliferation in vitro and tumor growth in a rat allograft model. Therefore, selective inhibition of PTPRZ represents a promising approach for glioma therapy.
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22
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Kuban-Jankowska A, Sahu KK, Gorska M, Tuszynski JA, Wozniak M. Chicoric acid binds to two sites and decreases the activity of the YopH bacterial virulence factor. Oncotarget 2016; 7:2229-38. [PMID: 26735581 PMCID: PMC4823031 DOI: 10.18632/oncotarget.6812] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 11/26/2015] [Indexed: 11/25/2022] Open
Abstract
Chicoric acid (CA) is a phenolic compound present in dietary supplements with a large spectrum of biological properties reported ranging from antioxidant, to antiviral, to immunostimulatory properties. Due to the fact that chicoric acid promotes phagocytic activity and was reported as an allosteric inhibitor of the PTP1B phosphatase, we examined the effect of CA on YopH phosphatase from pathogenic bacteria, which block phagocytic processes of a host cell. We performed computational studies of chicoric acid binding to YopH as well as validation experiments with recombinant enzymes. In addition, we performed similar studies for caffeic and chlorogenic acids to compare the results. Docking experiments demonstrated that, from the tested compounds, only CA binds to both catalytic and secondary binding sites of YopH. Our experimental results showed that CA reduces activity of recombinant YopH phosphatase from Yersinia enterocolitica and human CD45 phosphatase. The inhibition caused by CA was irreversible and did not induce oxidation of catalytic cysteine. We proposed that inactivation of YopH induced by CA is involved with allosteric inhibition by interacting with essential regions responsible for ligand binding.
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Affiliation(s)
| | - Kamlesh K. Sahu
- Department of Physics, University of Alberta, Edmonton, Canada
| | - Magdalena Gorska
- Department of Medical Chemistry, Medical University of Gdansk, Gdansk, Poland
| | - Jack A. Tuszynski
- Department of Physics, University of Alberta, Edmonton, Canada
- Division of Experimental Oncology, Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Canada
| | - Michal Wozniak
- Department of Medical Chemistry, Medical University of Gdansk, Gdansk, Poland
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23
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Luna S, Mingo J, Aurtenetxe O, Blanco L, Amo L, Schepens J, Hendriks WJ, Pulido R. Tailor-Made Protein Tyrosine Phosphatases: In Vitro Site-Directed Mutagenesis of PTEN and PTPRZ-B. Methods Mol Biol 2016; 1447:79-93. [PMID: 27514801 DOI: 10.1007/978-1-4939-3746-2_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In vitro site-directed mutagenesis (SDM) of protein tyrosine phosphatases (PTPs) is a commonly used approach to experimentally analyze PTP functions at the molecular and cellular level and to establish functional correlations with PTP alterations found in human disease. Here, using the tumor-suppressor PTEN and the receptor-type PTPRZ-B (short isoform from PTPRZ1 gene) phosphatases as examples, we provide a brief insight into the utility of specific mutations in the experimental analysis of PTP functions. We describe a standardized, rapid, and simple method of mutagenesis to perform single and multiple amino acid substitutions, as well as deletions of short nucleotide sequences, based on one-step inverse PCR and DpnI restriction enzyme treatment. This method of SDM is generally applicable to any other protein of interest.
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Affiliation(s)
- Sandra Luna
- Biocruces Health Research Institute, Pza Cruces s/n, 48903, Barakaldo, Spain
| | - Janire Mingo
- Biocruces Health Research Institute, Pza Cruces s/n, 48903, Barakaldo, Spain
| | - Olaia Aurtenetxe
- Biocruces Health Research Institute, Pza Cruces s/n, 48903, Barakaldo, Spain
| | - Lorena Blanco
- Biocruces Health Research Institute, Pza Cruces s/n, 48903, Barakaldo, Spain
| | - Laura Amo
- Biocruces Health Research Institute, Pza Cruces s/n, 48903, Barakaldo, Spain
| | - Jan Schepens
- Department of Cell Biology, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, 6525 GA, Nijmegen, The Netherlands
| | - Wiljan J Hendriks
- Department of Cell Biology, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, 6525 GA, Nijmegen, The Netherlands
| | - Rafael Pulido
- Biocruces Health Research Institute, Pza Cruces s/n, 48903, Barakaldo, Spain.
- IKERBASQUE, Basque Foundation for Science, 48013, Bilbao, Spain.
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Identification of a novel MET mutation in high-grade glioma resulting in an auto-active intracellular protein. Acta Neuropathol 2015; 130:131-44. [PMID: 25862637 PMCID: PMC4469304 DOI: 10.1007/s00401-015-1420-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 03/13/2015] [Accepted: 03/25/2015] [Indexed: 01/03/2023]
Abstract
MET has gained interest as a therapeutic target for a number of malignancies because of its involvement in tumorigenesis, invasion and metastasis. At present, a number of inhibitors, both antibodies against MET or its ligand hepatocyte growth factor, and small molecule MET tyrosine kinase inhibitors are in clinical trials. We here describe a novel variant of MET that is expressed in 6 % of high-grade gliomas. Characterization of this mutation in a glioma cell line revealed that it consists of an intronic deletion, resulting in a splice event connecting an intact splice donor site in exon 6 with the next splice acceptor site being that of exon 9. The encoded protein lacks parts of the extracellular IPT domains 1 and 2, encoded by exons 7 and 8, resulting in a novel pseudo-IPT and is named METΔ7−8. METΔ7−8 is located predominantly in the cytosol and is constitutively active. The auto-activating nature of METΔ7−8, in combination with a lack of transmembrane localization, renders METΔ7−8 not targetable using antibodies, although the protein is efficiently deactivated by MET-specific tyrosine kinase inhibitors. Testing of MET-expressing tumors for the presence of this variant may be important for treatment decision making.
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