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Antwi FD, Awad T, Larin M, Heesom K, Lewis P, Reddell P, Poghosyan Z, Dewitt S, Moseley R, Knäuper V. Tigilanol Tiglate-Induced Changes in Secretome Profiles Alter C-Met Phosphorylation and Cell Surface Protein Expression in H357 Head and Neck Cancer Cells. Cells 2024; 13:982. [PMID: 38891113 PMCID: PMC11171882 DOI: 10.3390/cells13110982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 05/31/2024] [Accepted: 06/01/2024] [Indexed: 06/21/2024] Open
Abstract
Tigilanol tiglate (TT, also known as EBC-46) is a novel, plant-derived diterpene ester possessing anticancer and wound-healing properties. Here, we show that TT-evoked PKC-dependent S985 phosphorylation of the tyrosine kinase MET leads to subsequent degradation of tyrosine phosphorylated p-Y1003 and p-Y1234/5 MET species. PKC inhibition with BIM-1 blocked S985 phosphorylation of MET and led to MET cell surface accumulation. Treatment with metalloproteinase inhibitors prevented MET-ECD release into cell culture media, which was also blocked by PKC inhibitors. Furthermore, unbiased secretome analysis, performed using TMT-technology, identified additional targets of TT-dependent release of cell surface proteins from H357 head and neck cancer cells. We confirm that the MET co-signalling receptor syndecan-1 was cleaved from the cell surface in response to TT treatment. This was accompanied by rapid cleavage of the cellular junction adhesion protein Nectin-1 and the nerve growth factor receptor NGFRp75/TNFR16. These findings, that TT is a novel negative regulator of protumorigenic c-MET and NGFRp75/TNFR16 signalling, as well as regulating Nectin-1-mediated cell adhesion, further contribute to our understanding of the mode of action and efficacy of TT in the treatment of solid tumours.
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Affiliation(s)
- Frank Dickson Antwi
- School of Dentistry, College of Biomedical and Life Sciences, Cardiff University, Cardiff CF14 4XY, UK (S.D.); (R.M.)
| | - Tufaha Awad
- School of Dentistry, College of Biomedical and Life Sciences, Cardiff University, Cardiff CF14 4XY, UK (S.D.); (R.M.)
| | - Meghan Larin
- School of Dentistry, College of Biomedical and Life Sciences, Cardiff University, Cardiff CF14 4XY, UK (S.D.); (R.M.)
| | - Kate Heesom
- Bristol Proteomics Facility, Biomedical Sciences Building, University Walk, University of Bristol, Bristol BS8 1TD, UK
| | - Phil Lewis
- Bristol Proteomics Facility, Biomedical Sciences Building, University Walk, University of Bristol, Bristol BS8 1TD, UK
| | | | - Zaruhi Poghosyan
- School of Medicine, College of Biomedical and Life Sciences, Cardiff University, Cardiff CF14 4XN, UK
| | - Sharon Dewitt
- School of Dentistry, College of Biomedical and Life Sciences, Cardiff University, Cardiff CF14 4XY, UK (S.D.); (R.M.)
| | - Ryan Moseley
- School of Dentistry, College of Biomedical and Life Sciences, Cardiff University, Cardiff CF14 4XY, UK (S.D.); (R.M.)
| | - Vera Knäuper
- School of Dentistry, College of Biomedical and Life Sciences, Cardiff University, Cardiff CF14 4XY, UK (S.D.); (R.M.)
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Welsh CL, Madan LK. Protein Tyrosine Phosphatase regulation by Reactive Oxygen Species. Adv Cancer Res 2024; 162:45-74. [PMID: 39069369 DOI: 10.1016/bs.acr.2024.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Protein Tyrosine Phosphatases (PTPs) help to maintain the balance of protein phosphorylation signals that drive cell division, proliferation, and differentiation. These enzymes are also well-suited to redox-dependent signaling and oxidative stress response due to their cysteine-based catalytic mechanism, which requires a deprotonated thiol group at the active site. This review focuses on PTP structural characteristics, active site chemical properties, and vulnerability to change by reactive oxygen species (ROS). PTPs can be oxidized and inactivated by H2O2 through three non-exclusive mechanisms. These pathways are dependent on the coordinated actions of other H2O2-sensitive proteins, such as peroxidases like Peroxiredoxins (Prx) and Thioredoxins (Trx). PTPs undergo reversible oxidation by converting their active site cysteine from thiol to sulfenic acid. This sulfenic acid can then react with adjacent cysteines to form disulfide bonds or with nearby amides to form sulfenyl-amide linkages. Further oxidation of the sulfenic acid form to the sulfonic or sulfinic acid forms causes irreversible deactivation. Understanding the structural changes involved in both reversible and irreversible PTP oxidation can help with their chemical manipulation for therapeutic intervention. Nonetheless, more information remains unidentified than is presently known about the precise dynamics of proteins participating in oxidation events, as well as the specific oxidation states that can be targeted for PTPs. This review summarizes current information on PTP-specific oxidation patterns and explains how ROS-mediated signal transmission interacts with phosphorylation-based signaling machinery controlled by growth factor receptors and PTPs.
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Affiliation(s)
- Colin L Welsh
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, College of Medicine, Medical University of South Carolina, Charleston, SC, United States
| | - Lalima K Madan
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, College of Medicine, Medical University of South Carolina, Charleston, SC, United States; Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, United States.
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Chen L, Qian Z, Zheng Y, Zhang J, Sun J, Zhou C, Xiao H. Structural analysis of PTPN21 reveals a dominant-negative effect of the FERM domain on its phosphatase activity. SCIENCE ADVANCES 2024; 10:eadi7404. [PMID: 38416831 PMCID: PMC10901363 DOI: 10.1126/sciadv.adi7404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 01/24/2024] [Indexed: 03/01/2024]
Abstract
PTPN21 belongs to the four-point-one, ezrin, radixin, moesin (FERM) domain-containing protein tyrosine phosphatases (PTP) and plays important roles in cytoskeleton-associated cellular processes like cell adhesion, motility, and cargo transport. Because of the presence of a WPE loop instead of a WPD loop in the phosphatase domain, it is often considered to lack phosphatase activity. However, many of PTPN21's biological functions require its catalytic activity. To reconcile these findings, we have determined the structures of individual PTPN21 FERM, PTP domains, and a complex between FERM-PTP. Combined with biochemical analysis, we have found that PTPN21 PTP is weakly active and is autoinhibited by association with its FERM domain. Disruption of FERM-PTP interaction results in enhanced ERK activation. The oncogenic HPV18 E7 protein binds to PTP at the same location as PTPN21 FERM, indicating that it may act by displacing the FERM domain from PTP. Our results provide mechanistic insight into PTPN21 and benefit functional studies of PTPN21-mediated processes.
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Affiliation(s)
- Lu Chen
- Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
- School of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Zijun Qian
- Department of Hematology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Yuyuan Zheng
- School of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Jie Zhang
- Department of Hematology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Jie Sun
- Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Chun Zhou
- Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
- School of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Haowen Xiao
- Department of Hematology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
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4
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El Badaoui L, Barr AJ. Analysis of Receptor-Type Protein Tyrosine Phosphatase Extracellular Regions with Insights from AlphaFold. Int J Mol Sci 2024; 25:820. [PMID: 38255894 PMCID: PMC10815196 DOI: 10.3390/ijms25020820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/04/2024] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
The receptor-type protein tyrosine phosphatases (RPTPs) are involved in a wide variety of physiological functions which are mediated via their diverse extracellular regions. They play key roles in cell-cell contacts, bind various ligands and are regulated by dimerization and other processes. Depending on the subgroup, they have been described as everything from 'rigid rods' to 'floppy tentacles'. Here, we review current experimental structural knowledge on the extracellular region of RPTPs and draw on AlphaFold structural predictions to provide further insights into structure and function of these cellular signalling molecules, which are often mutated in disease and are recognised as drug targets. In agreement with experimental data, AlphaFold predicted structures for extracellular regions of R1, and R2B subgroup RPTPs have an extended conformation, whereas R2B RPTPs are twisted, reflecting their high flexibility. For the R3 PTPs, AlphaFold predicts that members of this subgroup adopt an extended conformation while others are twisted, and that certain members, such as CD148, have one or more large, disordered loop regions in place of fibronectin type 3 domains suggested by sequence analysis.
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Affiliation(s)
| | - Alastair J. Barr
- School of Life Sciences, University of Westminster, 115 New Cavendish Street, London W1W 6UW, UK;
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Zhao P, Li H, Bu W. A Forward Vision for Chemodynamic Therapy: Issues and Opportunities. Angew Chem Int Ed Engl 2023; 62:e202210415. [PMID: 36650984 DOI: 10.1002/anie.202210415] [Citation(s) in RCA: 68] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Indexed: 01/19/2023]
Abstract
Since the insight to fuse Fenton chemistry and nanomedicine into cancer therapy, great signs of progress have been made in the field of chemodynamic therapy (CDT). However, the exact mechanism of CDT is obscured by the unique tumor chemical environment and inevitable nanoparticle-cell interactions, thus impeding further development. In this Scientific Perspective, the significance of CDT is clarified, the complex mechanism is deconstructed into primitive chemical and biological interactions, and the mechanism research directions based on the chemical kinetics and biological signaling pathways are discussed in detail. Moreover, beneficial outlooks are presented to enlighten the evolution of next-generation CDT. Hopefully, this Scientific Perspective can inspire new ideas and advances for CDT and provide a reference for breaking down the interdisciplinary barriers in the field of nanomedicine.
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Affiliation(s)
- Peiran Zhao
- Department of Materials Science and State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, 200433, P.R. China
| | - Huiyan Li
- Department of Materials Science and State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, 200433, P.R. China
| | - Wenbo Bu
- Department of Materials Science and State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, 200433, P.R. China
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Hendriks WJAJ, van Cruchten RTP, Pulido R. Hereditable variants of classical protein tyrosine phosphatase genes: Will they prove innocent or guilty? Front Cell Dev Biol 2023; 10:1051311. [PMID: 36755664 PMCID: PMC9900141 DOI: 10.3389/fcell.2022.1051311] [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: 09/22/2022] [Accepted: 12/28/2022] [Indexed: 01/24/2023] Open
Abstract
Protein tyrosine phosphatases, together with protein tyrosine kinases, control many molecular signaling steps that control life at cellular and organismal levels. Impairing alterations in the genes encoding the involved proteins is expected to profoundly affect the quality of life-if compatible with life at all. Here, we review the current knowledge on the effects of germline variants that have been reported for genes encoding a subset of the protein tyrosine phosphatase superfamily; that of the thirty seven classical members. The conclusion must be that the newest genome research tools produced an avalanche of data that suggest 'guilt by association' for individual genes to specific disorders. Future research should face the challenge to investigate these accusations thoroughly and convincingly, to reach a mature genotype-phenotype map for this intriguing protein family.
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Affiliation(s)
- Wiljan J. A. J. Hendriks
- Department of Cell Biology, Radboud University Medical Centre, Nijmegen, The Netherlands,*Correspondence: Wiljan J. A. J. Hendriks,
| | | | - Rafael Pulido
- Biomarkers in Cancer Unit, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
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7
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Zhao P, Li H, Bu W. A Forward Vision for Chemodynamic Therapy: Issues and Opportunities. Angew Chem Int Ed Engl 2023. [DOI: 10.1002/ange.202210415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Peiran Zhao
- Department of Materials Science and State Key Laboratory of Molecular Engineering of Polymers Fudan University Shanghai 200433 P.R. China
| | - Huiyan Li
- Department of Materials Science and State Key Laboratory of Molecular Engineering of Polymers Fudan University Shanghai 200433 P.R. China
| | - Wenbo Bu
- Department of Materials Science and State Key Laboratory of Molecular Engineering of Polymers Fudan University Shanghai 200433 P.R. China
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Lv Z, Wang T, Cao X, Sun M, Qu Y. The role of receptor‐type protein tyrosine phosphatases in cancer. PRECISION MEDICAL SCIENCES 2023. [DOI: 10.1002/prm2.12090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Zhengyuan Lv
- Department of Medical Genetics, School of Basic Medical Science Nanjing Medical University Nanjing China
| | - Tianming Wang
- Department of Medical Genetics, School of Basic Medical Science Nanjing Medical University Nanjing China
- Central Laboratory, Translational Medicine Research Center The Affiliated Jiangning Hospital with Nanjing Medical University Nanjing China
| | - Xin Cao
- Department of Medical Genetics, School of Basic Medical Science Nanjing Medical University Nanjing China
| | - Mengting Sun
- Biobank of Jiangsu Institute of Cancer Research The Affiliated Cancer Hospital of Nanjing Medical University Nanjing China
| | - Yuan Qu
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research The Affiliated Cancer Hospital of Nanjing Medical University Nanjing China
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Rumman M, Dhawan J. PTPRU, a quiescence-induced receptor tyrosine phosphatase negatively regulates osteogenic differentiation of human mesenchymal stem cells. Biochem Biophys Res Commun 2022; 636:41-49. [DOI: 10.1016/j.bbrc.2022.10.062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 10/18/2022] [Indexed: 11/02/2022]
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10
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Siepe DH, Henneberg LT, Wilson SC, Hess GT, Bassik MC, Zinn K, Garcia KC. Identification of orphan ligand-receptor relationships using a cell-based CRISPRa enrichment screening platform. eLife 2022; 11:e81398. [PMID: 36178190 PMCID: PMC9578707 DOI: 10.7554/elife.81398] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 09/29/2022] [Indexed: 11/20/2022] Open
Abstract
Secreted proteins, which include cytokines, hormones, and growth factors, are extracellular ligands that control key signaling pathways mediating cell-cell communication within and between tissues and organs. Many drugs target secreted ligands and their cell surface receptors. Still, there are hundreds of secreted human proteins that either have no identified receptors ('orphans') or are likely to act through cell surface receptors that have not yet been characterized. Discovery of secreted ligand-receptor interactions by high-throughput screening has been problematic, because the most commonly used high-throughput methods for protein-protein interaction (PPI) screening are not optimized for extracellular interactions. Cell-based screening is a promising technology for the deorphanization of ligand-receptor interactions, because multimerized ligands can enrich for cells expressing low affinity cell surface receptors, and such methods do not require purification of receptor extracellular domains. Here, we present a proteo-genomic cell-based CRISPR activation (CRISPRa) enrichment screening platform employing customized pooled cell surface receptor sgRNA libraries in combination with a magnetic bead selection-based enrichment workflow for rapid, parallel ligand-receptor deorphanization. We curated 80 potentially high-value orphan secreted proteins and ultimately screened 20 secreted ligands against two cell sgRNA libraries with targeted expression of all single-pass (TM1) or multi-pass transmembrane (TM2+) receptors by CRISPRa. We identified previously unknown interactions in 12 of these screens, and validated several of them using surface plasmon resonance and/or cell binding assays. The newly deorphanized ligands include three receptor protein tyrosine phosphatase (RPTP) ligands and a chemokine-like protein that binds to killer immunoglobulin-like receptors (KIRs). These new interactions provide a resource for future investigations of interactions between the human-secreted and membrane proteomes.
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Affiliation(s)
- Dirk H Siepe
- Department of Molecular and Cellular Physiology, Stanford UniversityStanfordUnited States
| | - Lukas T Henneberg
- Department of Molecular and Cellular Physiology, Stanford UniversityStanfordUnited States
| | - Steven C Wilson
- Department of Molecular and Cellular Physiology, Stanford UniversityStanfordUnited States
| | - Gaelen T Hess
- Stanford ChEM-H, Department of Genetics, Stanford UniversityStanfordUnited States
| | - Michael C Bassik
- Stanford ChEM-H, Department of Genetics, Stanford UniversityStanfordUnited States
| | - Kai Zinn
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford UniversityStanfordUnited States
- Howard Hughes Medical Institute, Stanford University School of MedicineStanfordUnited States
- Department of Structural Biology, Stanford University School of MedicineStanfordUnited States
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Klymus KE, Hrabik RA, Thompson NL, Cornman RS. Genome resequencing clarifies phylogeny and reveals patterns of selection in the toxicogenomics model Pimephales promelas. PeerJ 2022; 10:e13954. [PMID: 36042859 PMCID: PMC9420404 DOI: 10.7717/peerj.13954] [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: 04/04/2022] [Accepted: 08/05/2022] [Indexed: 01/19/2023] Open
Abstract
Background The fathead minnow (Pimephales promelas) is a model species for toxicological research. A high-quality genome reference sequence is available, and genomic methods are increasingly used in toxicological studies of the species. However, phylogenetic relationships within the genus remain incompletely known and little population-genomic data are available for fathead minnow despite the potential effects of genetic background on toxicological responses. On the other hand, a wealth of extant samples is stored in museum collections that in principle allow fine-scale analysis of contemporary and historical genetic variation. Methods Here we use short-read shotgun resequencing to investigate sequence variation among and within Pimephales species. At the genus level, our objectives were to resolve phylogenetic relationships and identify genes with signatures of positive diversifying selection. At the species level, our objective was to evaluate the utility of archived-sample resequencing for detecting selective sweeps within fathead minnow, applied to a population introduced to the San Juan River of the southwestern United States sometime prior to 1950. Results We recovered well-supported but discordant phylogenetic topologies for nuclear and mitochondrial sequences that we hypothesize arose from mitochondrial transfer among species. The nuclear tree supported bluntnose minnow (P. notatus) as sister to fathead minnow, with the slim minnow (P. tenellus) and bullhead minnow (P. vigilax) more closely related to each other. Using multiple methods, we identified 11 genes that have diversified under positive selection within the genus. Within the San Juan River population, we identified selective-sweep regions overlapping several sets of related genes, including both genes that encode the giant sarcomere protein titin and the two genes encoding the MTORC1 complex, a key metabolic regulator. We also observed elevated polymorphism and reduced differentation among populations (FST) in genomic regions containing certain immune-gene clusters, similar to what has been reported in other taxa. Collectively, our data clarify evolutionary relationships and selective pressures within the genus and establish museum archives as a fruitful resource for characterizing genomic variation. We anticipate that large-scale resequencing will enable the detection of genetic variants associated with environmental toxicants such as heavy metals, high salinity, estrogens, and agrichemicals, which could be exploited as efficient biomarkers of exposure in natural populations.
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Affiliation(s)
- Katy E. Klymus
- U.S. Geological Survey, Columbia Ecological Research Center, Columbia, MO, USA
| | | | - Nathan L. Thompson
- U.S. Geological Survey, Columbia Ecological Research Center, Columbia, MO, USA
| | - Robert S. Cornman
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, CO, USA
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Konigorski S, Janke J, Patone G, Bergmann MM, Lippert C, Hübner N, Kaaks R, Boeing H, Pischon T. Identification of novel genes whose expression in adipose tissue affects body fat mass and distribution: an RNA-Seq and Mendelian Randomization study. Eur J Hum Genet 2022:10.1038/s41431-022-01161-3. [PMID: 35953519 DOI: 10.1038/s41431-022-01161-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 06/26/2022] [Accepted: 07/19/2022] [Indexed: 10/15/2022] Open
Abstract
Many studies have shown that abdominal adiposity is more strongly related to health risks than peripheral adiposity. However, the underlying pathways are still poorly understood. In this cross-sectional study using data from RNA-sequencing experiments and whole-body MRI scans of 200 participants in the EPIC-Potsdam cohort, our aim was to identify novel genes whose gene expression in subcutaneous adipose tissue has an effect on body fat mass (BFM) and body fat distribution (BFD). The analysis identified 625 genes associated with adiposity, of which 531 encode a known protein and 487 are novel candidate genes for obesity. Enrichment analyses indicated that BFM-associated genes were characterized by their higher than expected involvement in cellular, regulatory and immune system processes, and BFD-associated genes by their involvement in cellular, metabolic, and regulatory processes. Mendelian Randomization analyses suggested that the gene expression of 69 genes was causally related to BFM and BFD. Six genes were replicated in UK Biobank. In this study, we identified novel genes for BFM and BFD that are BFM- and BFD-specific, involved in different molecular processes, and whose up-/downregulated gene expression may causally contribute to obesity.
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Affiliation(s)
- Stefan Konigorski
- Digital Health & Machine Learning Research Group, Hasso Plattner Institute for Digital Engineering, University of Potsdam, Potsdam, Germany.
- Molecular Epidemiology Research Group, Max Delbrück Center (MDC) for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Jürgen Janke
- Molecular Epidemiology Research Group, Max Delbrück Center (MDC) for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Giannino Patone
- Genetics and Genomics of Cardiovascular Diseases Research Group, Max Delbrück Center (MDC) for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Manuela M Bergmann
- German Institute of Human Nutrition Potsdam-Rehbrücke (DIfE), Nuthetal, Germany
| | - Christoph Lippert
- Digital Health & Machine Learning Research Group, Hasso Plattner Institute for Digital Engineering, University of Potsdam, Potsdam, Germany
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Norbert Hübner
- Genetics and Genomics of Cardiovascular Diseases Research Group, Max Delbrück Center (MDC) for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- DZHK (German Center for Cardiovascular Research) partner site Berlin, Berlin, Germany
- Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Rudolf Kaaks
- Department of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Heiner Boeing
- German Institute of Human Nutrition Potsdam-Rehbrücke (DIfE), Nuthetal, Germany
| | - Tobias Pischon
- Molecular Epidemiology Research Group, Max Delbrück Center (MDC) for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
- DZHK (German Center for Cardiovascular Research) partner site Berlin, Berlin, Germany.
- Charité Universitätsmedizin Berlin, Berlin, Germany.
- MDC Biobank, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany.
- BIH Biobank, Berlin Institute of Health, Berlin, Germany.
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Liu J, Yang L, Li H, Cai Y, Feng J, Hu Z. Conditional ablation of protein tyrosine phosphatase receptor U in midbrain dopaminergic neurons results in reduced neuronal size. J Chem Neuroanat 2022; 124:102135. [DOI: 10.1016/j.jchemneu.2022.102135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 06/17/2022] [Accepted: 07/01/2022] [Indexed: 11/30/2022]
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14
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Sampadi B, Mullenders LHF, Vrieling H. Low and high doses of ionizing radiation evoke discrete global (phospho)proteome responses. DNA Repair (Amst) 2022; 113:103305. [PMID: 35255311 DOI: 10.1016/j.dnarep.2022.103305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/02/2022] [Accepted: 02/22/2022] [Indexed: 12/16/2022]
Abstract
BACKGROUND Although cancer risk is assumed to be linear with ionizing radiation (IR) dose, it is unclear to what extent low doses (LD) of IR from medical and occupational exposures pose a cancer risk for humans. Improved mechanistic understanding of the signaling responses to LD may help to clarify this uncertainty. Here, we performed quantitative mass spectrometry-based proteomics and phosphoproteomics experiments, using mouse embryonic stem cells, at 0.5 h and 4 h after exposure to LD (0.1 Gy) and high doses (HD; 1 Gy) of IR. RESULTS The proteome remained relatively stable (29; 0.5% proteins responded), whereas the phosphoproteome changed dynamically (819; 7% phosphosites changed) upon irradiation. Dose-dependent alterations of 25 IR-responsive proteins were identified, with only four in common between LD and HD. Mitochondrial metabolic proteins and pathways responded to LD, whereas transporter proteins and mitochondrial uncoupling pathways responded to HD. Congruently, mitochondrial respiration increased after LD exposure but decreased after HD exposure. While the bulk of the phosphoproteome response to LD (76%) occurred already at 0.5 h, an equivalent proportion of the phosphosites responded to HD at both time points. Motif, kinome/phosphatome, kinase-substrate, and pathway analyses revealed a robust DNA damage response (DDR) activation after HD exposure but not after LD exposure. Instead, LD-irradiation induced (de)phosphorylation of kinases, kinase-substrates and phosphatases that predominantly respond to reactive oxygen species (ROS) production. CONCLUSION Our analyses identify discrete global proteome and phosphoproteome responses after LD and HD, uncovering novel proteins and protein (de)phosphorylation events involved in the dose-dependent ionizing radiation responses.
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Affiliation(s)
- Bharath Sampadi
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333ZC Leiden, The Netherlands.
| | - Leon H F Mullenders
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333ZC Leiden, The Netherlands; Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan
| | - Harry Vrieling
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333ZC Leiden, The Netherlands.
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Grad M, Nir A, Levy G, Trangle SS, Shapira G, Shomron N, Assaf Y, Barak B. Altered White Matter and microRNA Expression in a Murine Model Related to Williams Syndrome Suggests That miR-34b/c Affects Brain Development via Ptpru and Dcx Modulation. Cells 2022; 11:cells11010158. [PMID: 35011720 PMCID: PMC8750756 DOI: 10.3390/cells11010158] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/15/2021] [Accepted: 12/28/2021] [Indexed: 11/16/2022] Open
Abstract
Williams syndrome (WS) is a multisystem neurodevelopmental disorder caused by a de novo hemizygous deletion of ~26 genes from chromosome 7q11.23, among them the general transcription factor II-I (GTF2I). By studying a novel murine model for the hypersociability phenotype associated with WS, we previously revealed surprising aberrations in myelination and cell differentiation properties in the cortices of mutant mice compared to controls. These mutant mice had selective deletion of Gtf2i in the excitatory neurons of the forebrain. Here, we applied diffusion magnetic resonance imaging and fiber tracking, which showed a reduction in the number of streamlines in limbic outputs such as the fimbria/fornix fibers and the stria terminalis, as well as the corpus callosum of these mutant mice compared to controls. Furthermore, we utilized next-generation sequencing (NGS) analysis of cortical small RNAs' expression (RNA-Seq) levels to identify altered expression of microRNAs (miRNAs), including two from the miR-34 cluster, known to be involved in prominent processes in the developing nervous system. Luciferase reporter assay confirmed the direct binding of miR-34c-5p to the 3'UTR of PTPRU-a gene involved in neural development that was elevated in the cortices of mutant mice relative to controls. Moreover, we found an age-dependent variation in the expression levels of doublecortin (Dcx)-a verified miR-34 target. Thus, we demonstrate the substantial effect a single gene deletion can exert on miRNA regulation and brain structure, and advance our understanding and, hopefully, treatment of WS.
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Affiliation(s)
- Meitar Grad
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel; (M.G.); (A.N.); (G.L.); (N.S.); (Y.A.)
| | - Ariel Nir
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel; (M.G.); (A.N.); (G.L.); (N.S.); (Y.A.)
| | - Gilad Levy
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel; (M.G.); (A.N.); (G.L.); (N.S.); (Y.A.)
| | - Sari Schokoroy Trangle
- Faculty of Social Sciences, School of Psychological Sciences, Tel Aviv University, Tel Aviv 6997801, Israel;
| | - Guy Shapira
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel;
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Noam Shomron
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel; (M.G.); (A.N.); (G.L.); (N.S.); (Y.A.)
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel;
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yaniv Assaf
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel; (M.G.); (A.N.); (G.L.); (N.S.); (Y.A.)
- Faculty of Life Sciences, School of Neurobiology, Biochemistry & Biophysics, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Boaz Barak
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel; (M.G.); (A.N.); (G.L.); (N.S.); (Y.A.)
- Faculty of Social Sciences, School of Psychological Sciences, Tel Aviv University, Tel Aviv 6997801, Israel;
- Correspondence:
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Mattei AM, Smailys JD, Hepworth EMW, Hinton SD. The Roles of Pseudophosphatases in Disease. Int J Mol Sci 2021; 22:ijms22136924. [PMID: 34203203 PMCID: PMC8269279 DOI: 10.3390/ijms22136924] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/10/2021] [Accepted: 06/24/2021] [Indexed: 01/07/2023] Open
Abstract
The pseudophosphatases, atypical members of the protein tyrosine phosphatase family, have emerged as bona fide signaling regulators within the past two decades. Their roles as regulators have led to a renaissance of the pseudophosphatase and pseudoenyme fields, catapulting interest from a mere curiosity to intriguing and relevant proteins to investigate. Pseudophosphatases make up approximately fourteen percent of the phosphatase family, and are conserved throughout evolution. Pseudophosphatases, along with pseudokinases, are important players in physiology and pathophysiology. These atypical members of the protein tyrosine phosphatase and protein tyrosine kinase superfamily, respectively, are rendered catalytically inactive through mutations within their catalytic active signature motif and/or other important domains required for catalysis. This new interest in the pursuit of the relevant functions of these proteins has resulted in an elucidation of their roles in signaling cascades and diseases. There is a rapid accumulation of knowledge of diseases linked to their dysregulation, such as neuropathies and various cancers. This review analyzes the involvement of pseudophosphatases in diseases, highlighting the function of various role(s) of pseudophosphatases involvement in pathologies, and thus providing a platform to strongly consider them as key therapeutic drug targets.
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Young KA, Biggins L, Sharpe HJ. Protein tyrosine phosphatases in cell adhesion. Biochem J 2021; 478:1061-1083. [PMID: 33710332 PMCID: PMC7959691 DOI: 10.1042/bcj20200511] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 02/10/2021] [Accepted: 02/12/2021] [Indexed: 02/07/2023]
Abstract
Adhesive structures between cells and with the surrounding matrix are essential for the development of multicellular organisms. In addition to providing mechanical integrity, they are key signalling centres providing feedback on the extracellular environment to the cell interior, and vice versa. During development, mitosis and repair, cell adhesions must undergo extensive remodelling. Post-translational modifications of proteins within these complexes serve as switches for activity. Tyrosine phosphorylation is an important modification in cell adhesion that is dynamically regulated by the protein tyrosine phosphatases (PTPs) and protein tyrosine kinases. Several PTPs are implicated in the assembly and maintenance of cell adhesions, however, their signalling functions remain poorly defined. The PTPs can act by directly dephosphorylating adhesive complex components or function as scaffolds. In this review, we will focus on human PTPs and discuss their individual roles in major adhesion complexes, as well as Hippo signalling. We have collated PTP interactome and cell adhesome datasets, which reveal extensive connections between PTPs and cell adhesions that are relatively unexplored. Finally, we reflect on the dysregulation of PTPs and cell adhesions in disease.
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Affiliation(s)
- Katherine A. Young
- Signalling Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, U.K
| | - Laura Biggins
- Bioinformatics, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, U.K
| | - Hayley J. Sharpe
- Signalling Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, U.K
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Lee HS, Mo Y, Shin HC, Kim SJ, Ku B. Structural and Biochemical Characterization of the Two Drosophila Low Molecular Weight-Protein Tyrosine Phosphatases DARP and Primo-1. Mol Cells 2020; 43:1035-1045. [PMID: 33372666 PMCID: PMC7772506 DOI: 10.14348/molcells.2020.0192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/18/2020] [Accepted: 11/19/2020] [Indexed: 11/27/2022] Open
Abstract
The Drosophila genome contains four low molecular weightprotein tyrosine phosphatase (LMW-PTP) members: Primo-1, Primo-2, CG14297, and CG31469. The lack of intensive biochemical analysis has limited our understanding of these proteins. Primo-1 and CG31469 were previously classified as pseudophosphatases, but CG31469 was also suggested to be a putative protein arginine phosphatase. Herein, we present the crystal structures of CG31469 and Primo-1, which are the first Drosophila LMW-PTP structures. Structural analysis showed that the two proteins adopt the typical LMW-PTP fold and have a canonically arranged P-loop. Intriguingly, while Primo-1 is presumed to be a canonical LMW-PTP, CG31469 is unique as it contains a threonine residue at the fifth position of the P-loop motif instead of highly conserved isoleucine and a characteristically narrow active site pocket, which should facilitate the accommodation of phosphoarginine. Subsequent biochemical analysis revealed that Primo-1 and CG31469 are enzymatically active on phosphotyrosine and phosphoarginine, respectively, refuting their classification as pseudophosphatases. Collectively, we provide structural and biochemical data on two Drosophila proteins: Primo-1, the canonical LMW-PTP protein, and CG31469, the first investigated eukaryotic protein arginine phosphatase. We named CG31469 as DARP, which stands for Drosophila ARginine Phosphatase.
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Affiliation(s)
- Hye Seon Lee
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Yeajin Mo
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Ho-Chul Shin
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Seung Jun Kim
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Bonsu Ku
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
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