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Tritto V, Capitanio D, Gelfi C, Riva P. Changes of RAS Pathway Phosphorylation in Lymphoblastoid Cell Lines from Noonan Syndrome Patients Carrying Hypomorphic Variants in Two NS Genes. Int J Mol Sci 2023; 24:4035. [PMID: 36835447 PMCID: PMC9959625 DOI: 10.3390/ijms24044035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 02/10/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
Noonan syndrome (NS) is an autosomal dominant multisystem disorder, characterized by variable expressivity and locus heterogeneity, being caused by mutations in one of a subset of RAS pathway genes. Nevertheless, for 20-30% of patients it is not possible to provide molecular diagnosis, suggesting that further unknown genes or mechanisms are involved in NS pathogenesis. Recently, we proposed a digenic inheritance of subclinical variants as an alternative NS pathogenic model in two NS patients negative for molecular diagnosis. They showed hypomorphic variants of RAS pathway genes co-inherited from both their healthy parents that we hypothesized to generate an additive effect. Here, we report on the phosphoproteome and proteome analysis by liquid chromatography tandem mass spectrometry (LC-MS/MS) performed on the immortalized peripheral blood mononuclear cells (PBMCs) from the two above trios. Our results indicate that the two unrelated patients show overlapped profiles in both protein abundances and their phosphorylation levels not reached by their parents. IPA software predicted RAS-related pathways as significantly activated in the two patients. Interestingly, they remained unchanged or only slightly activated in both patients' parents. These findings suggest that the presence of one subclinical variant can activate the RAS pathway below the pathological threshold, which can instead be exceeded by the additive effect due to the co-presence of two subclinical variants causing NS, supporting our digenic inheritance hypothesis.
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Affiliation(s)
- Viviana Tritto
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, 20054 Segrate, Italy
| | - Daniele Capitanio
- Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, 20133 Milan, Italy
| | - Cecilia Gelfi
- Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, 20133 Milan, Italy
- IRCCS Istituto Ortopedico Galeazzi, 20161 Milan, Italy
| | - Paola Riva
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, 20054 Segrate, Italy
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The Tyrosine Phosphatase SHP2: A New Target for Insulin Resistance? Biomedicines 2022; 10:biomedicines10092139. [PMID: 36140242 PMCID: PMC9495760 DOI: 10.3390/biomedicines10092139] [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: 07/15/2022] [Revised: 08/26/2022] [Accepted: 08/28/2022] [Indexed: 11/17/2022] Open
Abstract
The SH2 containing protein tyrosine phosphatase 2(SHP2) plays essential roles in fundamental signaling pathways, conferring on it versatile physiological functions during development and in homeostasis maintenance, and leading to major pathological outcomes when dysregulated. Many studies have documented that SHP2 modulation disrupted glucose homeostasis, pointing out a relationship between its dysfunction and insulin resistance, and the therapeutic potential of its targeting. While studies from cellular or tissue-specific models concluded on both pros-and-cons effects of SHP2 on insulin resistance, recent data from integrated systems argued for an insulin resistance promoting role for SHP2, and therefore a therapeutic benefit of its inhibition. In this review, we will summarize the general knowledge of SHP2’s molecular, cellular, and physiological functions, explaining the pathophysiological impact of its dysfunctions, then discuss its protective or promoting roles in insulin resistance as well as the potency and limitations of its pharmacological modulation.
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Henderson IM, Marez C, Dokladny K, Smoake J, Martinez M, Johnson D, Uhl GR. Substrate-selective positive allosteric modulation of PTPRD’s phosphatase by flavonols. Biochem Pharmacol 2022; 202:115109. [PMID: 35636503 PMCID: PMC10184881 DOI: 10.1016/j.bcp.2022.115109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 05/23/2022] [Accepted: 05/23/2022] [Indexed: 11/30/2022]
Abstract
The receptor type protein tyrosine phosphatase D (PTPRD) is expressed by neurons and implicated in interesting phenotypes that include reward from addictive substances, restless leg syndrome and neurofibrillary tangle densities in Alzheimer's disease (AD-NFTs). However, the brain phosphotyrosine phosphoprotein (PTPP) substrates for PTPRD's phosphatase have not been clearly defined. Although we have identified small molecule inhibitors of PTPRD's phosphatase that are candidates for reducing reward from addictive substances, no positive allosteric modulators of this phosphatase that might be candidates for reducing AD-NFTs have been reported. We now report identification of candidate brain substrates for PTPRD based on their increased phosphorylation in knockout vs wildtype animals, coexpression with PTPRD in neuronal subtypes and brisk dephosphorylation by recombinant human PTPRD phosphatase. We also report discovery that quercetin and other flavonols, though not closely-related flavones, enhance rates of PTPRD's dephosphorylation of a group of these candidate substrate PTPPs but not others. This substrate-selective positive allosteric modulation provides a novel pharmacological action. Flavonol-mediated increases in PTPRD's dephosphorylation of the GSK3 β and α kinases that hyperphosphorylate tau, the major component of AD-NFTs, could help to explain recent data concerning genetic and dietary impacts on Alzheimer's disease.
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Affiliation(s)
- Ian M Henderson
- Biomedical Research Institute of New Mexico, Albuquerque, NM 87108, United States; New Mexico VA Healthcare System, Albuquerque, NM 87108, United States
| | - Carlissa Marez
- Biomedical Research Institute of New Mexico, Albuquerque, NM 87108, United States; New Mexico VA Healthcare System, Albuquerque, NM 87108, United States
| | - Karol Dokladny
- Department of Medicine, University of New Mexico, Albuquerque, NM 87131, United States
| | - Jane Smoake
- Biomedical Research Institute of New Mexico, Albuquerque, NM 87108, United States; New Mexico VA Healthcare System, Albuquerque, NM 87108, United States
| | - Maria Martinez
- Biomedical Research Institute of New Mexico, Albuquerque, NM 87108, United States; New Mexico VA Healthcare System, Albuquerque, NM 87108, United States
| | - David Johnson
- College of Pharmacy, University of Kansas, Lawrence, KS 66045, United States
| | - George R Uhl
- Biomedical Research Institute of New Mexico, Albuquerque, NM 87108, United States; New Mexico VA Healthcare System, Albuquerque, NM 87108, United States; Departments of Neurology, Neuroscience and Molecular Genetics and Microbiology, University of New Mexico, Albuquerque, NM 87131, United States; Departments of Neurology and Pharmacology, University of Maryland School of Medicine, Baltimore, MD 21201, United States; Maryland VA Healthcare System, Baltimore, MD 21201, United States.
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Montero-Bullón JF, González-Velasco Ó, Isidoro-García M, Lacal J. Integrated in silico MS-based phosphoproteomics and network enrichment analysis of RASopathy proteins. Orphanet J Rare Dis 2021; 16:303. [PMID: 34229750 PMCID: PMC8258961 DOI: 10.1186/s13023-021-01934-x] [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: 09/29/2020] [Accepted: 06/27/2021] [Indexed: 11/30/2022] Open
Abstract
Background RASopathies are a group of syndromes showing clinical overlap caused by mutations in genes affecting the RAS-MAPK pathway. Consequent disruption on cellular signaling leads and is driven by phosphoproteome remodeling. However, we still lack a comprehensive picture of the different key players and altered downstream effectors. Methods An in silico interactome of RASopathy proteins was generated using pathway enrichment analysis/STRING tool, including identification of main hub proteins. We also integrated phosphoproteomic and immunoblotting studies using previous published information on RASopathy proteins and their neighbors in the context of RASopathy syndromes. Data from Phosphosite database (www.phosphosite.org) was collected in order to obtain the potential phosphosites subjected to regulation in the 27 causative RASopathy proteins. We compiled a dataset of dysregulated phosphosites in RASopathies, searched for commonalities between syndromes in harmonized data, and analyzed the role of phosphorylation in the syndromes by the identification of key players between the causative RASopathy proteins and the associated interactome. Results In this study, we provide a curated data set of 27 causative RASopathy genes, identify up to 511 protein–protein associations using pathway enrichment analysis/STRING tool, and identify 12 nodes as main hub proteins. We found that a large group of proteins contain tyrosine residues and their biological processes include but are not limited to the nervous system. Harmonizing published RASopathy phosphoproteomic and immunoblotting studies we identified a total of 147 phosphosites with increased phosphorylation, whereas 47 have reduced phosphorylation. The PKB signaling pathway is the most represented among the dysregulated phosphoproteins within the RASopathy proteins and their neighbors, followed by phosphoproteins implicated in the regulation of cell proliferation and the MAPK pathway. Conclusions This work illustrates the complex network underlying the RASopathies and the potential of phosphoproteomics for dissecting the molecular mechanisms in these syndromes. A combined study of associated genes, their interactome and phosphorylation events in RASopathies, elucidates key players and mechanisms to direct future research, diagnosis and therapeutic windows. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-021-01934-x.
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Affiliation(s)
- Javier-Fernando Montero-Bullón
- Metabolic Engineering Group, Department of Microbiology and Genetics, Faculty of Biology, University of Salamanca, 37007, Salamanca, Spain
| | - Óscar González-Velasco
- Bioinformatics and Functional Genomics Group, IBMCC Cancer Research Center, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - María Isidoro-García
- Institute for Biomedical Research of Salamanca (IBSAL), 37007, Salamanca, Spain.,Network for Cooperative Research in Health-RETICS ARADyAL, 37007, Salamanca, Spain.,Department of Clinical Biochemistry, University Hospital of Salamanca, 37007, Salamanca, Spain.,Department of Medicine, University of Salamanca, 37007, Salamanca, Spain
| | - Jesus Lacal
- Institute for Biomedical Research of Salamanca (IBSAL), 37007, Salamanca, Spain. .,Molecular Genetics of Human Diseases Group, Department of Microbiology and Genetics, Faculty of Biology, University of Salamanca, 37007, Salamanca, Spain.
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Yang H, Jiang H, Song Y, Chen DJ, Shen XJ, Chen JH. Neutrophil CD16b crosslinking induces lipid raft-mediated activation of SHP-2 and affects cytokine expression and retarded neutrophil apoptosis. Exp Cell Res 2017; 362:121-131. [PMID: 29137913 DOI: 10.1016/j.yexcr.2017.11.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 11/07/2017] [Accepted: 11/08/2017] [Indexed: 01/11/2023]
Abstract
Two different types of FcRs for IgG are constitutively expressed on the surface of human neutrophils, namely, FcγRIIA (CD32a) and FcγRIIIB (CD16b). Unlike FcγRIIA, FcγRIIIb is GPI anchored to the cell membrane and its signal transduction is still ambiguous. To further understand the signal transduction of CD16b, we compared neutrophil cytokine expression and apoptosis by the cross-linking of CD32a and CD16b respectively. We found that both CD32a and CD16b crosslinking can activate neutrophils, but did not exactly share cytokine expression profiles. On the other hand, CD16b cross-linking retarded neutrophil apoptosis while CD32a promoted it. By interrupting the lipid raft with methyl-β-cyclodextrin (MβCD) and inhibiting the ITAM-SYK pathway with an SYK inhibitor (piceatannol), we found reduced apoptosis was at least partially mediated by lipid raft structure, but not the ITAM-SYK pathway. Additionally, CD16b but not CD32a cross-linking triggered SHP-2 phosphorylation and led to its translocation into lipid rafts. SHP-2 phosphorylation and translocation were inhibited by MβCD. Moreover, pre-inhibition of SHP-2 by a specific inhibitor (SHP099) converted IL-10 and SOCS3 expression level and promoted neutrophil apoptosis after CD16b crosslinking. In conclusion, these results, for the first time, collectively indicate that SHP-2 is activated by CD16b crosslinking in neutrophils and functions as a component of the raft-mediated signaling pathway.
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Affiliation(s)
- H Yang
- Kidney Disease Center, First Affiliated Hospital, Zhejiang University, School of Medicine, Key Laboratory of Nephropathy, Zhejiang Province, Hangzhou, Zhejiang, China; National Clinical Research Base of Traditional Chinese Medicine, Zhejiang Hospital of Traditional Chinese Medicine, Zhejiang Chinese Medical University, Hangzhou, China
| | - H Jiang
- Kidney Disease Center, First Affiliated Hospital, Zhejiang University, School of Medicine, Key Laboratory of Nephropathy, Zhejiang Province, Hangzhou, Zhejiang, China; National Clinical Research Base of Traditional Chinese Medicine, Zhejiang Hospital of Traditional Chinese Medicine, Zhejiang Chinese Medical University, Hangzhou, China
| | - Y Song
- Kidney Disease Center, First Affiliated Hospital, Zhejiang University, School of Medicine, Key Laboratory of Nephropathy, Zhejiang Province, Hangzhou, Zhejiang, China; National Clinical Research Base of Traditional Chinese Medicine, Zhejiang Hospital of Traditional Chinese Medicine, Zhejiang Chinese Medical University, Hangzhou, China
| | - D J Chen
- Kidney Disease Center, First Affiliated Hospital, Zhejiang University, School of Medicine, Key Laboratory of Nephropathy, Zhejiang Province, Hangzhou, Zhejiang, China; National Clinical Research Base of Traditional Chinese Medicine, Zhejiang Hospital of Traditional Chinese Medicine, Zhejiang Chinese Medical University, Hangzhou, China
| | - X J Shen
- Kidney Disease Center, First Affiliated Hospital, Zhejiang University, School of Medicine, Key Laboratory of Nephropathy, Zhejiang Province, Hangzhou, Zhejiang, China; National Clinical Research Base of Traditional Chinese Medicine, Zhejiang Hospital of Traditional Chinese Medicine, Zhejiang Chinese Medical University, Hangzhou, China
| | - J H Chen
- Kidney Disease Center, First Affiliated Hospital, Zhejiang University, School of Medicine, Key Laboratory of Nephropathy, Zhejiang Province, Hangzhou, Zhejiang, China; National Clinical Research Base of Traditional Chinese Medicine, Zhejiang Hospital of Traditional Chinese Medicine, Zhejiang Chinese Medical University, Hangzhou, China.
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Payne LS, Huang PH. Targeted Analysis of Phosphotyrosine Signaling by Multiple Reaction Monitoring Mass Spectrometry. Methods Mol Biol 2017; 1636:263-281. [PMID: 28730485 DOI: 10.1007/978-1-4939-7154-1_17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Phosphoproteomics is an important tool for the unbiased investigation of signaling network activation and has particular application to unraveling aberrant signaling driving cancer progression. However, validating the behavior of specific phosphosites across multiple experimental conditions remains challenging, due to limitations inherent in discovery-based proteomic workflows and the limited availability of high-quality antibodies required for alternative, immunoaffinity-based methods. Targeted phosphoproteomics enables specific phosphosites to be quantified reproducibly across multiple experimental conditions. Importantly, targeted phosphoproteomic assays can be designed rapidly on the basis of data acquired in discovery proteomic experiments and circumvent the requirement of immunoaffinity techniques for reliable antibodies raised to specific, potentially poorly immunogenic phosphopeptides. In the following protocol, we present a method for the relative quantification of phosphosites across multiple experimental conditions and/or technical and biological replicates.
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Affiliation(s)
- Leo S Payne
- Auckland Science Analytical Services, School of Biological Sciences, The University of Auckland, Thomas Building, 3A Symonds Street, Auckland, 1010, New Zealand.
| | - Paul H Huang
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
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