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Rademaker G, Costanza B, Pyr Dit Ruys S, Peiffer R, Agirman F, Maloujahmoum N, Vertommen D, Turtoi A, Bellahcène A, Castronovo V, Peulen O. Paladin, overexpressed in colon cancer, is required for actin polymerisation and liver metastasis dissemination. Oncogenesis 2022; 11:42. [PMID: 35882839 PMCID: PMC9325978 DOI: 10.1038/s41389-022-00416-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 07/06/2022] [Accepted: 07/08/2022] [Indexed: 11/23/2022] Open
Abstract
Introduction Colorectal cancer remains a public health issue and most colon cancer patients succumb to the development of metastases. Using a specific protocol of pressure-assisted interstitial fluid extrusion to recover soluble biomarkers, we identified paladin as a potential colon cancer liver metastases biomarker. Methods Using shRNA gene knockdown, we explored the biological function of paladin in colon cancer cells and investigated the phospho-proteome within colon cancer cells. We successively applied in vitro migration assays, in vivo metastasis models and co-immunoprecipitation experiments. Results We discovered that paladin is required for colon cancer cell migration and metastasis, and that paladin depletion altered the phospho-proteome within colon cancer cells. Data are available via ProteomeXchange with identifier PXD030803. Thanks to immunoprecipitation experiments, we demonstrated that paladin, was interacting with SSH1, a phosphatase involved in colon cancer metastasis. Finally, we showed that paladin depletion in cancer cells results in a less dynamic actin cytoskeleton. Conclusions Paladin is an undervalued protein in oncology. This study highlights for the first time that, paladin is participating in actin cytoskeleton remodelling and is required for efficient cancer cell migration. ![]()
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Affiliation(s)
- Gilles Rademaker
- Metastasis Research Laboratory, Giga Cancer University of Liège, Liège, Belgium.,Department of Anatomy, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Brunella Costanza
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, Milan, 20139, Italy
| | - Sébastien Pyr Dit Ruys
- MassProt platform, de Duve Institute, Université Catholique de Louvain (UCLouvain), Brussels, Belgium
| | - Raphaël Peiffer
- Metastasis Research Laboratory, Giga Cancer University of Liège, Liège, Belgium
| | - Ferman Agirman
- Metastasis Research Laboratory, Giga Cancer University of Liège, Liège, Belgium
| | - Naïma Maloujahmoum
- Metastasis Research Laboratory, Giga Cancer University of Liège, Liège, Belgium
| | - Didier Vertommen
- MassProt platform, de Duve Institute, Université Catholique de Louvain (UCLouvain), Brussels, Belgium
| | - Andrei Turtoi
- Tumor microenvironment and resistance to treatment Laboratory, Institut de Recherche en Cancérologie de Montpellier (IRCM), Université de Montpellier (UM), Institut Régional du Cancer de Montpellier (ICM), Montpellier, France
| | - Akeila Bellahcène
- Metastasis Research Laboratory, Giga Cancer University of Liège, Liège, Belgium
| | - Vincent Castronovo
- Metastasis Research Laboratory, Giga Cancer University of Liège, Liège, Belgium
| | - Olivier Peulen
- Metastasis Research Laboratory, Giga Cancer University of Liège, Liège, Belgium.
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2
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Nitzsche A, Pietilä R, Love DT, Testini C, Ninchoji T, Smith RO, Ekvärn E, Larsson J, Roche FP, Egaña I, Jauhiainen S, Berger P, Claesson‐Welsh L, Hellström M. Paladin is a phosphoinositide phosphatase regulating endosomal VEGFR2 signalling and angiogenesis. EMBO Rep 2021; 22:e50218. [PMID: 33369848 PMCID: PMC7857541 DOI: 10.15252/embr.202050218] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 11/07/2020] [Accepted: 11/18/2020] [Indexed: 12/19/2022] Open
Abstract
Cell signalling governs cellular behaviour and is therefore subject to tight spatiotemporal regulation. Signalling output is modulated by specialized cell membranes and vesicles which contain unique combinations of lipids and proteins. The phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2 ), an important component of the plasma membrane as well as other subcellular membranes, is involved in multiple processes, including signalling. However, which enzymes control the turnover of non-plasma membrane PI(4,5)P2 , and their impact on cell signalling and function at the organismal level are unknown. Here, we identify Paladin as a vascular PI(4,5)P2 phosphatase regulating VEGFR2 endosomal signalling and angiogenesis. Paladin is localized to endosomal and Golgi compartments and interacts with vascular endothelial growth factor receptor 2 (VEGFR2) in vitro and in vivo. Loss of Paladin results in increased internalization of VEGFR2, over-activation of extracellular regulated kinase 1/2, and hypersprouting of endothelial cells in the developing retina of mice. These findings suggest that inhibition of Paladin, or other endosomal PI(4,5)P2 phosphatases, could be exploited to modulate VEGFR2 signalling and angiogenesis, when direct and full inhibition of the receptor is undesirable.
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Affiliation(s)
- Anja Nitzsche
- Science for Life LaboratoryThe Rudbeck LaboratoryDepartment of Immunology, Genetics and PathologyUppsala UniversityUppsalaSweden
- Present address:
Université de ParisParis Cardiovascular Research CenterINSERM U970ParisFrance
| | - Riikka Pietilä
- Science for Life LaboratoryThe Rudbeck LaboratoryDepartment of Immunology, Genetics and PathologyUppsala UniversityUppsalaSweden
| | - Dominic T Love
- Science for Life LaboratoryThe Rudbeck LaboratoryDepartment of Immunology, Genetics and PathologyUppsala UniversityUppsalaSweden
| | - Chiara Testini
- Science for Life LaboratoryThe Rudbeck LaboratoryDepartment of Immunology, Genetics and PathologyUppsala UniversityUppsalaSweden
- Present address:
Division of NephrologyDepartment of MedicineBoston Children’s HospitalBostonMAUSA
| | - Takeshi Ninchoji
- Science for Life LaboratoryThe Rudbeck LaboratoryDepartment of Immunology, Genetics and PathologyUppsala UniversityUppsalaSweden
| | - Ross O Smith
- Science for Life LaboratoryThe Rudbeck LaboratoryDepartment of Immunology, Genetics and PathologyUppsala UniversityUppsalaSweden
| | - Elisabet Ekvärn
- Science for Life LaboratoryThe Rudbeck LaboratoryDepartment of Immunology, Genetics and PathologyUppsala UniversityUppsalaSweden
- Present address:
Cepheid ABSolnaSweden
| | - Jimmy Larsson
- Science for Life LaboratoryThe Rudbeck LaboratoryDepartment of Immunology, Genetics and PathologyUppsala UniversityUppsalaSweden
- Present address:
Department of Cell and Molecular BiologyUppsala UniversityUppsalaSweden
| | - Francis P Roche
- Science for Life LaboratoryThe Rudbeck LaboratoryDepartment of Immunology, Genetics and PathologyUppsala UniversityUppsalaSweden
| | - Isabel Egaña
- Science for Life LaboratoryThe Rudbeck LaboratoryDepartment of Immunology, Genetics and PathologyUppsala UniversityUppsalaSweden
| | - Suvi Jauhiainen
- Science for Life LaboratoryThe Rudbeck LaboratoryDepartment of Immunology, Genetics and PathologyUppsala UniversityUppsalaSweden
| | - Philipp Berger
- Laboratory of Nanoscale BiologyPaul‐Scherrer InstituteVilligenSwitzerland
| | - Lena Claesson‐Welsh
- Science for Life LaboratoryThe Rudbeck LaboratoryDepartment of Immunology, Genetics and PathologyUppsala UniversityUppsalaSweden
| | - Mats Hellström
- Science for Life LaboratoryThe Rudbeck LaboratoryDepartment of Immunology, Genetics and PathologyUppsala UniversityUppsalaSweden
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3
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Hao X, Pang J, Li R, Lv L, Liu G, Li Y, Cheng G, Zhang J. Exome sequencing study revealed novel susceptibility loci in subarachnoid hemorrhage (SAH). Mol Brain 2020; 13:82. [PMID: 32450902 PMCID: PMC7249693 DOI: 10.1186/s13041-020-00620-6] [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: 12/30/2019] [Accepted: 05/11/2020] [Indexed: 11/10/2022] Open
Abstract
Aim To expand our current understanding of the genetic basis of subarachnoid hemorrhage (SAH), and reveal the susceptibility genes in SAH risk. Methods We conducted whole-exome sequencing (WES) in a cohort of 196 individuals, including 94 SAH patients and 94 controls, as well as 8 samples that belong to two pedigrees. Systematically examination for rare variations (through direct genotyping) and common variations (through genotyping and imputation) for SAHs were performed in this study. Results A total of 16,029 single-nucleotide polymorphisms (SNPs) and 108,999 short indels were detected in all samples, and among them, 30 SNPs distributed on 17 genes presented a strong association signal with SAH. Two novel pathogenic gene variants were identified as associated risk loci, including mutation in TPO and PALD1. The statistical analysis for rare, damaging variations in SAHs identified several susceptibility genes which were involved in degradation of the extracellular matrix and transcription factor signal pathways. And 25 putative pathogenic genes for SAH were also identified basic on functional interaction network analysis with the published SAH-associated genes. Additionally, pedigree analysis revealed autosomal dominant inheritance of pathogenic genes. Conclusion Systematical analysis revealed a key role for rare variations in SAH risk and discovered SNPs in new complex loci. Our study expanded the list of candidate genes associated with SAH risk, and will facilitate the investigation of disease-related mechanisms and potential clinical therapies.
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Affiliation(s)
- Xiwa Hao
- Department of Neurology, Baotou Central Hospital, Baotou, China
| | - Jiangxia Pang
- Department of Neurology, Baotou Central Hospital, Baotou, China
| | - Ruiming Li
- Department of Neurology, Baotou Central Hospital, Baotou, China
| | - Lin Lv
- Department of Neurology, Baotou Central Hospital, Baotou, China
| | - Guorong Liu
- Department of Neurology, Baotou Central Hospital, Baotou, China
| | - Yuechun Li
- Department of Neurology, Baotou Central Hospital, Baotou, China
| | - Guojuan Cheng
- Department of Neurology, Baotou Central Hospital, Baotou, China
| | - Jingfen Zhang
- Department of Neurology, Baotou Central Hospital, Baotou, China.
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4
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Grangeon L, Guey S, Schwitalla JC, Bergametti F, Arnould M, Corpechot M, Hadjadj J, Riant F, Aloui C, Drunat S, Vidaud D, Tournier-Lasserve E, Kraemer M. Clinical and Molecular Features of 5 European Multigenerational Families With Moyamoya Angiopathy. Stroke 2020; 50:789-796. [PMID: 30908154 DOI: 10.1161/strokeaha.118.023972] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background and Purpose Moyamoya angiopathy (MMA) is a rare cerebral vasculopathy outside of Asia. In Japanese patients, a vast majority of patients carry the founder p.R4810K variant in the RNF213 gene, and familial cases are around 10%. In European patients, data about familial occurrence are limited. The aim of this study was to characterize the clinical and molecular features of several European families with a parent-to-child transmission of MMA. Methods Out of 126 MMA probands referred, we identified 113 sporadic probands and 13 familial probands. Segregation analysis showed a vertical parent-to-child pattern of inheritance in the families of 5 of these probands. All 5 families were of German or Dutch ancestry. We investigated the clinical features of affected members and used whole-exome sequencing to screen RNF213 and 13 genes involved in Mendelian MMA and to identify genes recurrently mutated in these families. Results Twelve affected MMA patients were identified, including 9 females and 3 males. Age at clinical onset ranged from 11 to 65 years. In 3 of 5 families, associated livedo racemosa was found. We did not detect any deleterious variants in the 13 known MMA genes. RNF213 rare missense variants predicted to be pathogenic were detected in all affected members of 2 of these families, as well as 2 candidate variants of the PALD1 gene. Conclusions Nonsyndromic MMA was identified in 5 European families, including 2 to 3 clinically affected cases segregating with a parent-to-child pattern of inheritance in each family. Molecular screening detected rare deleterious variants within RNF213 and PALD1 in all affected members of 2 of these 5 families, as well as in some clinically unaffected members. Altogether these data raise the difficult and, to date unanswered, question of the medical indication of presymptomatic screening.
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Affiliation(s)
- Lou Grangeon
- From the Sorbonne Paris Cité, Inserm UMR-S1161, Génétique et physiopathologie des maladies cérébro-vasculaires, Université Paris Diderot, France (L.G., S.G., F.B., M.A., C.A. E.T.-L.)
| | - Stéphanie Guey
- From the Sorbonne Paris Cité, Inserm UMR-S1161, Génétique et physiopathologie des maladies cérébro-vasculaires, Université Paris Diderot, France (L.G., S.G., F.B., M.A., C.A. E.T.-L.)
| | | | - Françoise Bergametti
- From the Sorbonne Paris Cité, Inserm UMR-S1161, Génétique et physiopathologie des maladies cérébro-vasculaires, Université Paris Diderot, France (L.G., S.G., F.B., M.A., C.A. E.T.-L.)
| | - Minh Arnould
- From the Sorbonne Paris Cité, Inserm UMR-S1161, Génétique et physiopathologie des maladies cérébro-vasculaires, Université Paris Diderot, France (L.G., S.G., F.B., M.A., C.A. E.T.-L.)
| | - Michaelle Corpechot
- AP-HP, Service de génétique moléculaire neurovasculaire, Centre de Référence des Maladies Vasculaires Rares du Cerveau et de l'œil, Groupe Hospitalier Saint-Louis Lariboisière, Paris, France (M.C., J.H., F.R., E.T.-L.)
| | - Jessica Hadjadj
- AP-HP, Service de génétique moléculaire neurovasculaire, Centre de Référence des Maladies Vasculaires Rares du Cerveau et de l'œil, Groupe Hospitalier Saint-Louis Lariboisière, Paris, France (M.C., J.H., F.R., E.T.-L.)
| | - Florence Riant
- AP-HP, Service de génétique moléculaire neurovasculaire, Centre de Référence des Maladies Vasculaires Rares du Cerveau et de l'œil, Groupe Hospitalier Saint-Louis Lariboisière, Paris, France (M.C., J.H., F.R., E.T.-L.)
| | - Chaker Aloui
- From the Sorbonne Paris Cité, Inserm UMR-S1161, Génétique et physiopathologie des maladies cérébro-vasculaires, Université Paris Diderot, France (L.G., S.G., F.B., M.A., C.A. E.T.-L.)
| | - Severine Drunat
- AP-HP, Service de génétique, Groupe Hospitalier Robert Debré, Paris, France (S.D.)
| | - Dominique Vidaud
- AP-HP, Service de génétique, Groupe hospitalier Cochin, Paris, France (D.V.)
| | - Elisabeth Tournier-Lasserve
- From the Sorbonne Paris Cité, Inserm UMR-S1161, Génétique et physiopathologie des maladies cérébro-vasculaires, Université Paris Diderot, France (L.G., S.G., F.B., M.A., C.A. E.T.-L.).,AP-HP, Service de génétique moléculaire neurovasculaire, Centre de Référence des Maladies Vasculaires Rares du Cerveau et de l'œil, Groupe Hospitalier Saint-Louis Lariboisière, Paris, France (M.C., J.H., F.R., E.T.-L.)
| | - Markus Kraemer
- Department of Neurology, Alfried Krupp Hospital Essen, Germany (J.C.S., M.K.).,Department of Neurology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Germany (M.K.)
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5
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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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6
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Female mice lacking Pald1 exhibit endothelial cell apoptosis and emphysema. Sci Rep 2017; 7:15453. [PMID: 29133847 PMCID: PMC5684320 DOI: 10.1038/s41598-017-14894-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 10/18/2017] [Indexed: 12/16/2022] Open
Abstract
Paladin (Pald1, mKIAA1274 or x99384) was identified in screens for vascular-specific genes and is a putative phosphatase. Paladin has also been proposed to be involved in various biological processes such as insulin signaling, innate immunity and neural crest migration. To determine the role of paladin we have now characterized the Pald1 knock-out mouse in a broad array of behavioral, physiological and biochemical tests. Here, we show that female, but not male, Pald1 heterozygous and homozygous knock-out mice display an emphysema-like histology with increased alveolar air spaces and impaired lung function with an obstructive phenotype. In contrast to many other tissues where Pald1 is restricted to the vascular compartment, Pald1 is expressed in both the epithelial and mesenchymal compartments of the postnatal lung. However, in Pald1 knock-out females, there is a specific increase in apoptosis and proliferation of endothelial cells, but not in non-endothelial cells. This results in a transient reduction of endothelial cells in the maturing lung. Our data suggests that Pald1 is required during lung vascular development and for normal function of the developing and adult lung in a sex-specific manner. To our knowledge, this is the first report of a sex-specific effect on endothelial cell apoptosis.
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7
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Toivanen PI, Nieminen T, Laakkonen JP, Heikura T, Kaikkonen MU, Ylä-Herttuala S. Snake venom VEGF Vammin induces a highly efficient angiogenic response in skeletal muscle via VEGFR-2/NRP specific signaling. Sci Rep 2017; 7:5525. [PMID: 28717175 PMCID: PMC5514023 DOI: 10.1038/s41598-017-05876-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 06/05/2017] [Indexed: 01/13/2023] Open
Abstract
Vascular Endothelial Growth Factors (VEGFs) are promising molecules for the treatment of ischemic diseases by pro-angiogenic therapy. Snake venom VEGFs are a novel subgroup with unique receptor binding profiles and as such are potential new therapeutic agents. We determined the ligand-receptor interactions, gene regulation and angiogenic properties of Vipera ammodytes venom VEGF, Vammin, and compared it to the canonical angiogenic factor VEGF-A to evaluate the use of Vammin for therapeutic angiogenesis. Vammin efficiently induced VEGFR-2 mediated proliferation and expression of genes associated with proliferation, migration and angiogenesis. VEGF-A165 and especially VEGF-A109 induced less pronounced effects. Vammin regulates a number of signaling pathways by inducing the expression of NR4A family nuclear receptors and regulators of calcium signaling and MAP kinase pathways. Interestingly, MARC1, which encodes an enzyme discovered to catalyze reduction of nitrate to NO, was identified as a novel VEGFR-2 regulated gene. In rabbit skeletal muscle adenoviral delivery of Vammin induced prominent angiogenic responses. Both the vector dose and the co-receptor binding of the ligand were critical parameters controlling the type of angiogenic response from sprouting angiogenesis to vessel enlargement. Vammin induced VEGFR-2/NRP-1 mediated signaling more effectively than VEGF-A, consequently it is a promising candidate for development of pro-angiogenic therapies.
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Affiliation(s)
- Pyry I Toivanen
- Department of Biotechnology and Molecular Medicine, A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Tiina Nieminen
- Department of Biotechnology and Molecular Medicine, A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Johanna P Laakkonen
- Department of Biotechnology and Molecular Medicine, A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Tommi Heikura
- Department of Biotechnology and Molecular Medicine, A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Minna U Kaikkonen
- Department of Biotechnology and Molecular Medicine, A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Seppo Ylä-Herttuala
- Department of Biotechnology and Molecular Medicine, A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland. .,Heart Center and Gene Therapy Unit, Kuopio University Hospital, Kuopio, Finland.
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8
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Shil S, Joshi RS, Joshi CG, Patel AK, Shah RK, Patel N, Jakhesara SJ, Kundu S, Reddy B, Koringa PG, Rank DN. Transcriptomic comparison of primary bovine horn core carcinoma culture and parental tissue at early stage. Vet World 2017; 10:38-55. [PMID: 28246447 PMCID: PMC5301178 DOI: 10.14202/vetworld.2017.38-55] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 11/29/2016] [Indexed: 12/18/2022] Open
Abstract
Aim: Squamous cell carcinoma or SCC of horn in bovines (bovine horn core carcinoma) frequently observed in Bos indicus affecting almost 1% of cattle population. Freshly isolated primary epithelial cells may be closely related to the malignant epithelial cells of the tumor. Comparison of gene expression in between horn’s SCC tissue and its early passage primary culture using next generation sequencing was the aim of this study. Materials and Methods: Whole transcriptome sequencing of horn’s SCC tissue and its early passage cells using Ion Torrent PGM were done. Comparative expression and analysis of different genes and pathways related to cancer and biological processes associated with malignancy, proliferating capacity, differentiation, apoptosis, senescence, adhesion, cohesion, migration, invasion, angiogenesis, and metabolic pathways were identified. Results: Up-regulated genes in SCC of horn’s early passage cells were involved in transporter activity, catalytic activity, nucleic acid binding transcription factor activity, biogenesis, cellular processes, biological regulation and localization and the down-regulated genes mainly were involved in focal adhesion, extracellular matrix receptor interaction and spliceosome activity. Conclusion: The experiment revealed similar transcriptomic nature of horn’s SCC tissue and its early passage cells.
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Affiliation(s)
- Sharadindu Shil
- Veterinary Officer (WBAH & VS), West Bengal Animal Resources Development Department, Bankura - 772 152, West Bengal, India; Department of Animal Genetics & Breeding, College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, India
| | - R S Joshi
- Department of Animal Genetics & Breeding, College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, India
| | - C G Joshi
- Department of Animal Biotechnology, College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, India
| | - A K Patel
- Hester Biosciences Limited, Ahmedabad, Gujarat, India
| | - Ravi K Shah
- Department of Animal Biotechnology, College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, India
| | - Namrata Patel
- Department of Animal Biotechnology, College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, India
| | - Subhash J Jakhesara
- Department of Animal Biotechnology, College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, India
| | - Sumana Kundu
- Veterinary Officer, MVC Sarenga, Government of West Bengal, Bankura, West Bengal, India
| | - Bhaskar Reddy
- Department of Animal Biotechnology, College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, India
| | - P G Koringa
- Department of Animal Biotechnology, College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, India
| | - D N Rank
- Department of Animal Biotechnology, College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, India; Department of Animal Genetics & Breeding, College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, India
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9
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Tsolis KC, Bagli E, Kanaki K, Zografou S, Carpentier S, Bei ES, Christoforidis S, Zervakis M, Murphy C, Fotsis T, Economou A. Proteome Changes during Transition from Human Embryonic to Vascular Progenitor Cells. J Proteome Res 2016; 15:1995-2007. [DOI: 10.1021/acs.jproteome.6b00180] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Konstantinos C. Tsolis
- Department
of Protein structure and Proteomics Facility, Institute of Molecular Biology and Biotechnology - FORTH, 70013 Iraklio, Crete, Greece
- Department
of Biology, University of Crete, 70013 Iraklio, Crete, Greece
| | - Eleni Bagli
- Division
of Biomedical Research, Institute of Molecular Biology and Biotechnology - FORTH, 45110 Ioaninna, Greece
| | - Katerina Kanaki
- Department
of Protein structure and Proteomics Facility, Institute of Molecular Biology and Biotechnology - FORTH, 70013 Iraklio, Crete, Greece
| | - Sofia Zografou
- Division
of Biomedical Research, Institute of Molecular Biology and Biotechnology - FORTH, 45110 Ioaninna, Greece
| | - Sebastien Carpentier
- SYBIOMA, KU Leuven facility for Systems Biology Based Mass Spectrometry, B-3000 Leuven Belgium
| | - Ekaterini S. Bei
- School
of Electronic and Computer Engineering, Technical University of Crete, 73100 Chania, Greece
| | - Savvas Christoforidis
- Division
of Biomedical Research, Institute of Molecular Biology and Biotechnology - FORTH, 45110 Ioaninna, Greece
- Laboratory
of Biological Chemistry, Medical School, University of Ioannina, 45110 Ioannina, Greece
| | - Michalis Zervakis
- School
of Electronic and Computer Engineering, Technical University of Crete, 73100 Chania, Greece
| | - Carol Murphy
- Division
of Biomedical Research, Institute of Molecular Biology and Biotechnology - FORTH, 45110 Ioaninna, Greece
- School
of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
| | - Theodore Fotsis
- Division
of Biomedical Research, Institute of Molecular Biology and Biotechnology - FORTH, 45110 Ioaninna, Greece
- Laboratory
of Biological Chemistry, Medical School, University of Ioannina, 45110 Ioannina, Greece
- School
of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
| | - Anastassios Economou
- Department
of Protein structure and Proteomics Facility, Institute of Molecular Biology and Biotechnology - FORTH, 70013 Iraklio, Crete, Greece
- Department
of Biology, University of Crete, 70013 Iraklio, Crete, Greece
- SYBIOMA, KU Leuven facility for Systems Biology Based Mass Spectrometry, B-3000 Leuven Belgium
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10
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Alonso A, Pulido R. The extended human PTPome: a growing tyrosine phosphatase family. FEBS J 2015; 283:1404-29. [PMID: 26573778 DOI: 10.1111/febs.13600] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 10/02/2015] [Accepted: 11/13/2015] [Indexed: 12/13/2022]
Abstract
Tyr phosphatases are, by definition, enzymes that dephosphorylate phospho-Tyr (pTyr) from proteins. This activity is found in several structurally diverse protein families, including the protein Tyr phosphatase (PTP), arsenate reductase, rhodanese, haloacid dehalogenase (HAD) and His phosphatase (HP) families. Most of these families include members with substrate specificity for non-pTyr substrates, such as phospho-Ser/phospho-Thr, phosphoinositides, phosphorylated carbohydrates, mRNAs, or inorganic moieties. A Cys is essential for catalysis in PTPs, rhodanese and arsenate reductase enzymes, whereas this work is performed by an Asp in HAD phosphatases and by a His in HPs, via a catalytic mechanism shared by all of the different families. The category that contains most Tyr phosphatases is the PTP family, which, although it received its name from this activity, includes Ser, Thr, inositide, carbohydrate and RNA phosphatases, as well as some inactive pseudophosphatase proteins. Here, we propose an extended collection of human Tyr phosphatases, which we call the extended human PTPome. The addition of new members (SACs, paladin, INPP4s, TMEM55s, SSU72, and acid phosphatases) to the currently categorized PTP group of enzymes means that the extended human PTPome contains up to 125 proteins, of which ~ 40 are selective for pTyr. We set criteria to ascribe proteins to the extended PTPome, and summarize the more important features of the new PTPome members in the context of their phosphatase activity and their relationship with human disease.
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Affiliation(s)
- Andrés Alonso
- Instituto de Biología y Genética Molecular (IBGM), CSIC-Universidad de Valladolid, Valladolid, Spain
| | - Rafael Pulido
- Biocruces Health Research Institute, Barakaldo, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
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Reiterer V, Eyers PA, Farhan H. Day of the dead: pseudokinases and pseudophosphatases in physiology and disease. Trends Cell Biol 2014; 24:489-505. [PMID: 24818526 DOI: 10.1016/j.tcb.2014.03.008] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 03/25/2014] [Accepted: 03/27/2014] [Indexed: 12/19/2022]
Abstract
Pseudophosphatases and pseudokinases are increasingly viewed as integral elements of signaling pathways, and there is mounting evidence that they have frequently retained the ability to interact with cellular 'substrates', and can exert important roles in different diseases. However, these pseudoenzymes have traditionally received scant attention compared to classical kinases and phosphatases. In this review we explore new findings in the emerging pseudokinase and pseudophosphatase fields, and discuss their different modes of action which include exciting new roles as scaffolds, anchors, spatial modulators, traps, and ligand-driven regulators of canonical kinases and phosphatases. Thus, it is now apparent that pseudokinases and pseudophosphatases both support and drive a panoply of signaling networks. Finally, we highlight recent evidence on their involvement in human pathologies, marking them as potential novel drug targets.
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Affiliation(s)
- Veronika Reiterer
- Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen, Switzerland
| | - Patrick A Eyers
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK.
| | - Hesso Farhan
- Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen, Switzerland; Department of Biology, University of Konstanz, Konstanz, Germany.
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PTP-central: a comprehensive resource of protein tyrosine phosphatases in eukaryotic genomes. Methods 2013; 65:156-64. [PMID: 23911837 DOI: 10.1016/j.ymeth.2013.07.031] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 07/18/2013] [Accepted: 07/21/2013] [Indexed: 12/28/2022] Open
Abstract
Reversible tyrosine phosphorylation is a fundamental signaling mechanism controlling a diversity of cellular processes. Whereas protein tyrosine kinases have long been implicated in many diseases, aberrant protein tyrosine phosphatase (PTP) activity is also increasingly being associated with a wide spectrum of conditions. PTPs are now regarded as key regulators of biochemical processes instead of simple "off" switches operating in tyrosine kinase signaling pathways. Despite the central importance that PTPs play in the cell's biochemistry, the tyrosine phosphatomes of most species remain uncharted. Here we present a highly sensitive and specific sequence-based method for the automatic classification of PTPs. As proof of principle we re-annotated the human tyrosine phosphatome, and discovered four new PTP genes that had not been reported before. Our method and the predicted tyrosine phosphatomes of 65 eukaryotic genomes are accessible online through the user-friendly PTP-central resource (http://www.PTP-central.org/), where users can also submit their own sequences for prediction. PTP-central is a comprehensive and continually developing resource that currently integrates the predicted tyrosine phosphatomes with structural data and genetic association disease studies, as well as homology relationships. PTP-central thus fills an important void for the systematic study of PTPs, both in model organisms and from an evolutionary perspective.
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