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Pugliese A, Della Marina A, de Paula Estephan E, Zanoteli E, Roos A, Schara-Schmidt U, Hentschel A, Azuma Y, Töpf A, Thompson R, Polavarapu K, Lochmüller H. Mutations in PTPN11 could lead to a congenital myasthenic syndrome phenotype: a Noonan syndrome case series. J Neurol 2024; 271:1331-1341. [PMID: 37923938 DOI: 10.1007/s00415-023-12070-w] [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: 09/02/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 11/06/2023]
Abstract
The RASopathies are a group of genetic rare diseases caused by mutations affecting genes involved in the RAS/MAPK (RAS-mitogen activated protein kinase) pathway. Among them, PTPN11 pathogenic variants are responsible for approximately 50% of Noonan syndrome (NS) cases and, albeit to a lesser extent, of Leopard syndrome (LPRD1), which present a few overlapping clinical features, such as facial dysmorphism, developmental delay, cardiac defects, and skeletal deformities. Motor impairment and decreased muscle strength have been recently reported. The etiology of the muscle involvement in these disorders is still not clear but probably multifactorial, considering the role of the RAS/MAPK pathway in skeletal muscle development and Acetylcholine Receptors (AChR) clustering at the neuromuscular junction (NMJ). We report, herein, four unrelated children carrying three different heterozygous mutations in the PTPN11 gene. Intriguingly, their phenotypic features first led to a clinical suspicion of congenital myasthenic syndrome (CMS), due to exercise-induced fatigability with a variable degree of muscle weakness, and serum proteomic profiling compatible with a NMJ defect. Moreover, muscle fatigue improved after treatment with CMS-specific medication. Although the link between PTPN11 gene and neuromuscular transmission is unconfirmed, an increasing number of patients with RASopathies are affected by muscle weakness and fatigability. Hence, NS or LPDR1 should be considered in children with suspected CMS but negative genetic workup for known CMS genes or additional symptoms indicative of NS, such as facial dysmorphism or intellectual disability.
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Affiliation(s)
- Alessia Pugliese
- IRCCS Centro Neurolesi "Bonino Pulejo", Messina, Italy
- Children's Hospital of Eastern Ontario Research Institute, 401 Smyth Rd., Ottawa, ON, K1H 8L1, Canada
| | - Adela Della Marina
- Department of Pediatric Neurology, Centre for Neuromuscular Disorders, Centre for Translational Neuro- and Behavioral Sciences, University Duisburg-Essen, 45147, Essen, Germany
| | - Eduardo de Paula Estephan
- Department of Neurology, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Brazil
- Department of Neurological Sciences, Psychiatry, and Medical Psychology, Sao Jose do Rio Preto State Medical School, Sao Jose do Rio Preto, São Paulo, Brazil
| | - Edmar Zanoteli
- Department of Neurology, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Brazil
| | - Andreas Roos
- Children's Hospital of Eastern Ontario Research Institute, 401 Smyth Rd., Ottawa, ON, K1H 8L1, Canada
- Department of Pediatric Neurology, Centre for Neuromuscular Disorders, Centre for Translational Neuro- and Behavioral Sciences, University Duisburg-Essen, 45147, Essen, Germany
- Department of Neurology, Heimer Institute for Muscle Research, University Hospital Bergmannsheil, Ruhr-University Bochum, 44789, Bochum, Germany
- Leibniz-Institut Für Analytische Wissenschaften-ISAS-e.V., 44227, Dortmund, Germany
| | - Ulrike Schara-Schmidt
- Department of Pediatric Neurology, Centre for Neuromuscular Disorders, Centre for Translational Neuro- and Behavioral Sciences, University Duisburg-Essen, 45147, Essen, Germany
| | - Andreas Hentschel
- Leibniz-Institut Für Analytische Wissenschaften-ISAS-e.V., 44227, Dortmund, Germany
| | - Yoshiteru Azuma
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Ana Töpf
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, University of Newcastle, Newcastle Upon Tyne, UK
| | - Rachel Thompson
- Children's Hospital of Eastern Ontario Research Institute, 401 Smyth Rd., Ottawa, ON, K1H 8L1, Canada
| | - Kiran Polavarapu
- Children's Hospital of Eastern Ontario Research Institute, 401 Smyth Rd., Ottawa, ON, K1H 8L1, Canada
| | - Hanns Lochmüller
- Children's Hospital of Eastern Ontario Research Institute, 401 Smyth Rd., Ottawa, ON, K1H 8L1, Canada.
- Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, Canada.
- Brain and Mind Research Institute, University of Ottawa, Ottawa, Canada.
- Department of Neuropediatrics and Muscle Disorders, Faculty of Medicine, Medical Center-University of Freiburg, Freiburg, Germany.
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Catalonia, Spain.
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2
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Kim SH, Bulos ML, Adams JA, Yun BK, Bishop AC. Single Ion Pair Is Essential for Stabilizing SHP2's Open Conformation. Biochemistry 2024; 63:273-281. [PMID: 38251939 DOI: 10.1021/acs.biochem.3c00609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
Src-homology-2-domain-containing PTP-2 (SHP2) is a widely expressed signaling enzyme whose misregulation is associated with multiple human pathologies. SHP2's enzymatic activity is controlled by a conformational equilibrium between its autoinhibited ("closed") state and its activated ("open") state. Although SHP2's closed state has been extensively characterized, the putative structure of its open form has only been revealed in the context of a highly activated mutant (E76K), and no systematic studies of the biochemical determinants of SHP2's open-state stabilization have been reported. To identify amino-acid interactions that are critical for stabilizing SHP2's active state, we carried out a mutagenic study of residues that lie at potentially important interdomain interfaces of the open conformation. The open/closed equilibria of the mutants were evaluated, and we identified several interactions that contribute to the stabilization of SHP2's open state. In particular, our findings establish that an ion pair between glutamate 249 on SHP2's PTP domain and arginine 111 on an interdomain loop is the key determinant of SHP2's open-state stabilization. Mutations that disrupt the R111/E249 ion pair substantially shift SHP2's open/closed equilibrium to the closed state, even compared to wild-type SHP2's basal-state equilibrium, which strongly favors the closed state. To the best of our knowledge, the ion-pair variants uncovered in this study are the first known SHP2 mutants in which autoinhibition is augmented with respect to the wild-type protein. Such "hyperinhibited" mutants may provide useful tools for signaling studies that investigate the connections between SHP2 inhibition and the suppression of human disease progression.
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Affiliation(s)
- Sean H Kim
- Department of Chemistry and Program in Biochemistry & Biophysics, Amherst College, Amherst, Massachusetts 01002, United States
| | - Maya L Bulos
- Department of Chemistry and Program in Biochemistry & Biophysics, Amherst College, Amherst, Massachusetts 01002, United States
| | - Jennifer A Adams
- Department of Chemistry and Program in Biochemistry & Biophysics, Amherst College, Amherst, Massachusetts 01002, United States
| | - B Koun Yun
- Department of Chemistry and Program in Biochemistry & Biophysics, Amherst College, Amherst, Massachusetts 01002, United States
| | - Anthony C Bishop
- Department of Chemistry and Program in Biochemistry & Biophysics, Amherst College, Amherst, Massachusetts 01002, United States
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3
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Bishop AC, Serbina A. Targeting Nonconserved and Pathogenic Cysteines of Protein Tyrosine Phosphatases with Small Molecules. Methods Mol Biol 2024; 2743:271-283. [PMID: 38147221 DOI: 10.1007/978-1-0716-3569-8_17] [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: 12/27/2023]
Abstract
Protein tyrosine phosphatases (PTPs) are important therapeutic targets for a range of human pathologies. However, the common architecture of PTP active sites impedes the discovery of selective PTP inhibitors. Our laboratory has recently developed methods to inhibit PTPs allosterically by targeting cysteine residues that either (i) are not conserved in the PTP family or (ii) result from pathogenic mutations. Here, we describe screening protocols for the identification of selective inhibitors that covalently engage such "rare" cysteines in target PTPs. Moreover, to elucidate the breadth of possible applications of our cysteine-directed screening protocols, we provide a brief overview of the nonconserved cysteines present in all human classical PTP domains.
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Affiliation(s)
| | - Anna Serbina
- Department of Chemistry, Amherst College, Amherst, MA, USA
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4
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Anselmi M, Hub JS. Atomistic ensemble of active SHP2 phosphatase. Commun Biol 2023; 6:1289. [PMID: 38129686 PMCID: PMC10739809 DOI: 10.1038/s42003-023-05682-5] [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: 07/05/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
SHP2 phosphatase plays an important role in regulating several intracellular signaling pathways. Pathogenic mutations of SHP2 cause developmental disorders and are linked to hematological malignancies and cancer. SHP2 comprises two tandemly-arranged SH2 domains, a catalytic PTP domain, and a disordered C-terminal tail. Under physiological, non-stimulating conditions, the catalytic site of PTP is occluded by the N-SH2 domain, so that the basal activity of SHP2 is low. Whereas the autoinhibited structure of SHP2 has been known for two decades, its active, open structure still represents a conundrum. Since the oncogenic mutant SHP2E76K almost completely populates the active, open state, this mutant has been extensively studied as a model for activated SHP2. By molecular dynamics simulations and accurate explicit-solvent SAXS curve predictions, we present the heterogeneous atomistic ensemble of constitutively active SHP2E76K in solution, encompassing a set of conformational arrangements and radii of gyration in agreement with experimental SAXS data.
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Affiliation(s)
- Massimiliano Anselmi
- Theoretical Physics and Center for Biophysics, Saarland University, 66123, Saarbrücken, Germany.
| | - Jochen S Hub
- Theoretical Physics and Center for Biophysics, Saarland University, 66123, Saarbrücken, Germany.
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5
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Zhao S, Mekbib KY, van der Ent MA, Allington G, Prendergast A, Chau JE, Smith H, Shohfi J, Ocken J, Duran D, Furey CG, Hao LT, Duy PQ, Reeves BC, Zhang J, Nelson-Williams C, Chen D, Li B, Nottoli T, Bai S, Rolle M, Zeng X, Dong W, Fu PY, Wang YC, Mane S, Piwowarczyk P, Fehnel KP, See AP, Iskandar BJ, Aagaard-Kienitz B, Moyer QJ, Dennis E, Kiziltug E, Kundishora AJ, DeSpenza T, Greenberg ABW, Kidanemariam SM, Hale AT, Johnston JM, Jackson EM, Storm PB, Lang SS, Butler WE, Carter BS, Chapman P, Stapleton CJ, Patel AB, Rodesch G, Smajda S, Berenstein A, Barak T, Erson-Omay EZ, Zhao H, Moreno-De-Luca A, Proctor MR, Smith ER, Orbach DB, Alper SL, Nicoli S, Boggon TJ, Lifton RP, Gunel M, King PD, Jin SC, Kahle KT. Mutation of key signaling regulators of cerebrovascular development in vein of Galen malformations. Nat Commun 2023; 14:7452. [PMID: 37978175 PMCID: PMC10656524 DOI: 10.1038/s41467-023-43062-z] [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: 11/07/2022] [Accepted: 10/30/2023] [Indexed: 11/19/2023] Open
Abstract
To elucidate the pathogenesis of vein of Galen malformations (VOGMs), the most common and most severe of congenital brain arteriovenous malformations, we performed an integrated analysis of 310 VOGM proband-family exomes and 336,326 human cerebrovasculature single-cell transcriptomes. We found the Ras suppressor p120 RasGAP (RASA1) harbored a genome-wide significant burden of loss-of-function de novo variants (2042.5-fold, p = 4.79 x 10-7). Rare, damaging transmitted variants were enriched in Ephrin receptor-B4 (EPHB4) (17.5-fold, p = 1.22 x 10-5), which cooperates with p120 RasGAP to regulate vascular development. Additional probands had damaging variants in ACVRL1, NOTCH1, ITGB1, and PTPN11. ACVRL1 variants were also identified in a multi-generational VOGM pedigree. Integrative genomic analysis defined developing endothelial cells as a likely spatio-temporal locus of VOGM pathophysiology. Mice expressing a VOGM-specific EPHB4 kinase-domain missense variant (Phe867Leu) exhibited disrupted developmental angiogenesis and impaired hierarchical development of arterial-capillary-venous networks, but only in the presence of a "second-hit" allele. These results illuminate human arterio-venous development and VOGM pathobiology and have implications for patients and their families.
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Affiliation(s)
- Shujuan Zhao
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Kedous Y Mekbib
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Martijn A van der Ent
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Garrett Allington
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Andrew Prendergast
- Yale Zebrafish Research Core, Yale School of Medicine, New Haven, CT, USA
| | - Jocelyn E Chau
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT, USA
| | - Hannah Smith
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - John Shohfi
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Jack Ocken
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Daniel Duran
- Department of Neurosurgery, University of Mississippi Medical Center, Jackson, MS, USA
| | - Charuta G Furey
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
- Department of Neurosurgery, Barrow Neurological Institute, Phoenix, AZ, USA
- Ivy Brain Tumor Center, Department of Translational Neuroscience, Barrow Neurological Institute, Phoenix, AZ, USA
| | - Le Thi Hao
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Phan Q Duy
- Department of Neurosurgery, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Benjamin C Reeves
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Junhui Zhang
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | | | - Di Chen
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Boyang Li
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Timothy Nottoli
- Yale Genome Editing Center, Department of Comparative Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Suxia Bai
- Yale Genome Editing Center, Department of Comparative Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Myron Rolle
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Xue Zeng
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT, USA
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Weilai Dong
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Po-Ying Fu
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Yung-Chun Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Shrikant Mane
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Paulina Piwowarczyk
- Department of Neurosurgery, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Katie Pricola Fehnel
- Department of Neurosurgery, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Alfred Pokmeng See
- Department of Neurosurgery, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Bermans J Iskandar
- Department of Neurological Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Beverly Aagaard-Kienitz
- Department of Neurological Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Radiology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Quentin J Moyer
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Evan Dennis
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Emre Kiziltug
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Adam J Kundishora
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Tyrone DeSpenza
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Ana B W Greenberg
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Andrew T Hale
- Department of Neurosurgery, University of Alabama School of Medicine, Birmingham, AL, USA
| | - James M Johnston
- Department of Neurosurgery, University of Alabama School of Medicine, Birmingham, AL, USA
| | - Eric M Jackson
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Phillip B Storm
- Department of Neurosurgery, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Shih-Shan Lang
- Department of Neurosurgery, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - William E Butler
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Bob S Carter
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Paul Chapman
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Christopher J Stapleton
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Aman B Patel
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Georges Rodesch
- Service de Neuroradiologie Diagnostique et Thérapeutique, Hôpital Foch, Suresnes, France
- Department of Interventional Neuroradiology, Hôpital Fondation A. de Rothschild, Paris, France
| | - Stanislas Smajda
- Department of Interventional Neuroradiology, Hôpital Fondation A. de Rothschild, Paris, France
| | - Alejandro Berenstein
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tanyeri Barak
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | | | - Hongyu Zhao
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Andres Moreno-De-Luca
- Department of Radiology, Autism & Developmental Medicine Institute, Genomic Medicine Institute, Geisinger, Danville, PA, USA
| | - Mark R Proctor
- Department of Neurosurgery, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Edward R Smith
- Department of Neurosurgery, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Darren B Orbach
- Department of Neurosurgery, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurointerventional Radiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Seth L Alper
- Division of Nephrology and Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Stefania Nicoli
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA
- Yale Cardiovascular Research Center, Department of Internal Medicine, Section of Cardiology, Yale School of Medicine, New Haven, CT, USA
| | - Titus J Boggon
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT, USA
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA
| | - Richard P Lifton
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Murat Gunel
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Philip D King
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA.
| | - Sheng Chih Jin
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA.
| | - Kristopher T Kahle
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA.
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, US.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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6
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Serbina A, Bishop AC. Quantitation of autoinhibitory defects in pathogenic SHP2 mutants by differential scanning fluorimetry. Anal Biochem 2023; 680:115300. [PMID: 37659706 PMCID: PMC10530186 DOI: 10.1016/j.ab.2023.115300] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 07/26/2023] [Accepted: 08/25/2023] [Indexed: 09/04/2023]
Abstract
Src-homology-2-domain-containing protein tyrosine phosphatase-2 (SHP2) is a signaling enzyme whose activity is governed by an equilibrium between autoinhibited and activated states. Regulation of SHP2 activity is critical for cellular homeostasis, and mutations that alter its autoregulatory equilibrium cause cancers and developmental disorders. Several methods for assessing the strength of autoinhibitory interactions in SHP2 mutants have been previously reported, but each has limitations. We show that differential scanning fluorimetry provides a rapid, quantitative measure of SHP2 autoinhibition that is independent of the intrinsic activity of the SHP2 mutant being analyzed, does not involve protein labeling, and does not require specialized instrumentation.
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Affiliation(s)
- Anna Serbina
- Amherst College, Department of Chemistry, Amherst, MA, 01002, United States
| | - Anthony C Bishop
- Amherst College, Department of Chemistry, Amherst, MA, 01002, United States.
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7
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Lee JJ, Ramadesikan S, Black AF, Christoffer C, Pacheco AFP, Subramanian S, Hanna CB, Barth G, Stauffacher CV, Kihara D, Aguilar RC. Heterogeneity in Lowe Syndrome: Mutations Affecting the Phosphatase Domain of OCRL1 Differ in Impact on Enzymatic Activity and Severity of Cellular Phenotypes. Biomolecules 2023; 13:615. [PMID: 37189363 PMCID: PMC10135975 DOI: 10.3390/biom13040615] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/23/2023] [Accepted: 03/25/2023] [Indexed: 04/01/2023] Open
Abstract
Lowe Syndrome (LS) is a condition due to mutations in the OCRL1 gene, characterized by congenital cataracts, intellectual disability, and kidney malfunction. Unfortunately, patients succumb to renal failure after adolescence. This study is centered in investigating the biochemical and phenotypic impact of patient's OCRL1 variants (OCRL1VAR). Specifically, we tested the hypothesis that some OCRL1VAR are stabilized in a non-functional conformation by focusing on missense mutations affecting the phosphatase domain, but not changing residues involved in binding/catalysis. The pathogenic and conformational characteristics of the selected variants were evaluated in silico and our results revealed some OCRL1VAR to be benign, while others are pathogenic. Then we proceeded to monitor the enzymatic activity and function in kidney cells of the different OCRL1VAR. Based on their enzymatic activity and presence/absence of phenotypes, the variants segregated into two categories that also correlated with the severity of the condition they induce. Overall, these two groups mapped to opposite sides of the phosphatase domain. In summary, our findings highlight that not every mutation affecting the catalytic domain impairs OCRL1's enzymatic activity. Importantly, data support the inactive-conformation hypothesis. Finally, our results contribute to establishing the molecular and structural basis for the observed heterogeneity in severity/symptomatology displayed by patients.
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Affiliation(s)
- Jennifer J. Lee
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; (J.J.L.); (A.F.B.); (A.F.P.P.); (S.S.); (C.B.H.); (G.B.); (C.V.S.); (D.K.)
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Swetha Ramadesikan
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; (J.J.L.); (A.F.B.); (A.F.P.P.); (S.S.); (C.B.H.); (G.B.); (C.V.S.); (D.K.)
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Adrianna F. Black
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; (J.J.L.); (A.F.B.); (A.F.P.P.); (S.S.); (C.B.H.); (G.B.); (C.V.S.); (D.K.)
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Charles Christoffer
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA;
| | - Andres F. Pacheco Pacheco
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; (J.J.L.); (A.F.B.); (A.F.P.P.); (S.S.); (C.B.H.); (G.B.); (C.V.S.); (D.K.)
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Sneha Subramanian
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; (J.J.L.); (A.F.B.); (A.F.P.P.); (S.S.); (C.B.H.); (G.B.); (C.V.S.); (D.K.)
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Claudia B. Hanna
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; (J.J.L.); (A.F.B.); (A.F.P.P.); (S.S.); (C.B.H.); (G.B.); (C.V.S.); (D.K.)
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Gillian Barth
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; (J.J.L.); (A.F.B.); (A.F.P.P.); (S.S.); (C.B.H.); (G.B.); (C.V.S.); (D.K.)
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Cynthia V. Stauffacher
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; (J.J.L.); (A.F.B.); (A.F.P.P.); (S.S.); (C.B.H.); (G.B.); (C.V.S.); (D.K.)
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Daisuke Kihara
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; (J.J.L.); (A.F.B.); (A.F.P.P.); (S.S.); (C.B.H.); (G.B.); (C.V.S.); (D.K.)
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA;
| | - Ruben Claudio Aguilar
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; (J.J.L.); (A.F.B.); (A.F.P.P.); (S.S.); (C.B.H.); (G.B.); (C.V.S.); (D.K.)
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
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8
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Zhao S, Mekbib KY, van der Ent MA, Allington G, Prendergast A, Chau JE, Smith H, Shohfi J, Ocken J, Duran D, Furey CG, Le HT, Duy PQ, Reeves BC, Zhang J, Nelson-Williams C, Chen D, Li B, Nottoli T, Bai S, Rolle M, Zeng X, Dong W, Fu PY, Wang YC, Mane S, Piwowarczyk P, Fehnel KP, See AP, Iskandar BJ, Aagaard-Kienitz B, Kundishora AJ, DeSpenza T, Greenberg ABW, Kidanemariam SM, Hale AT, Johnston JM, Jackson EM, Storm PB, Lang SS, Butler WE, Carter BS, Chapman P, Stapleton CJ, Patel AB, Rodesch G, Smajda S, Berenstein A, Barak T, Erson-Omay EZ, Zhao H, Moreno-De-Luca A, Proctor MR, Smith ER, Orbach DB, Alper SL, Nicoli S, Boggon TJ, Lifton RP, Gunel M, King PD, Jin SC, Kahle KT. Genetic dysregulation of an endothelial Ras signaling network in vein of Galen malformations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.18.532837. [PMID: 36993588 PMCID: PMC10055230 DOI: 10.1101/2023.03.18.532837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
To elucidate the pathogenesis of vein of Galen malformations (VOGMs), the most common and severe congenital brain arteriovenous malformation, we performed an integrated analysis of 310 VOGM proband-family exomes and 336,326 human cerebrovasculature single-cell transcriptomes. We found the Ras suppressor p120 RasGAP ( RASA1 ) harbored a genome-wide significant burden of loss-of-function de novo variants (p=4.79×10 -7 ). Rare, damaging transmitted variants were enriched in Ephrin receptor-B4 ( EPHB4 ) (p=1.22×10 -5 ), which cooperates with p120 RasGAP to limit Ras activation. Other probands had pathogenic variants in ACVRL1 , NOTCH1 , ITGB1 , and PTPN11 . ACVRL1 variants were also identified in a multi-generational VOGM pedigree. Integrative genomics defined developing endothelial cells as a key spatio-temporal locus of VOGM pathophysiology. Mice expressing a VOGM-specific EPHB4 kinase-domain missense variant exhibited constitutive endothelial Ras/ERK/MAPK activation and impaired hierarchical development of angiogenesis-regulated arterial-capillary-venous networks, but only when carrying a "second-hit" allele. These results illuminate human arterio-venous development and VOGM pathobiology and have clinical implications.
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9
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Calligari P, Stella L, Bocchinfuso G. Computational Evaluation of Peptide-Protein Binding Affinities: Application of Potential of Mean Force Calculations to SH2 Domains. Methods Mol Biol 2023; 2705:113-133. [PMID: 37668972 DOI: 10.1007/978-1-0716-3393-9_7] [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: 09/06/2023]
Abstract
Many biological functions are mediated by protein-protein interactions (PPIs), often involving specific structural modules, such as SH2 domains. Inhibition of PPIs is a pharmaceutical strategy of growing importance. However, a major challenge in the design of PPI inhibitors is the large interface involved in these interactions, which, in many cases, makes inhibition by small organic molecules ineffective. Peptides, which cover a wide range of dimensions and can be opportunely designed to mimic protein sequences at PPI interfaces, represent a valuable alternative to small molecules. Computational techniques able to predict the binding affinity of peptides for the target domain or protein represent a crucial stage in the workflow for the design of peptide-based drugs. This chapter describes a protocol to obtain the potential of mean force (PMF) for peptide-SH2 domain binding, starting from umbrella sampling (US) molecular dynamics (MD) simulations. The PMF profiles can be effectively used to predict the relative standard binding free energies of different peptide sequences.
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Affiliation(s)
- Paolo Calligari
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome, Italy
| | - Lorenzo Stella
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome, Italy
| | - Gianfranco Bocchinfuso
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome, Italy.
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10
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Eboreime J, Choi SK, Yoon SR, Sadybekov A, Katritch V, Calabrese P, Arnheim N. Germline selection of PTPN11 (HGNC:9644) variants make a major contribution to both Noonan syndrome's high birth rate and the transmission of sporadic cancer variants resulting in fetal abnormality. Hum Mutat 2022; 43:2205-2221. [PMID: 36349709 PMCID: PMC10099774 DOI: 10.1002/humu.24493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 09/20/2022] [Accepted: 10/12/2022] [Indexed: 11/10/2022]
Abstract
Some spontaneous germline gain-of-function mutations promote spermatogonial stem cell clonal expansion and disproportionate variant sperm production leading to unexpectedly high transmission rates for some human genetic conditions. To measure the frequency and spatial distribution of de novo mutations we divided three testes into 192 pieces each and used error-corrected deep-sequencing on each piece. We focused on PTPN11 (HGNC:9644) Exon 3 that contains 30 different PTPN11 Noonan syndrome (NS) mutation sites. We found 14 of these variants formed clusters among the testes; one testis had 11 different variant clusters. The mutation frequencies of these different clusters were not correlated with their case-recurrence rates nor were case recurrence rates of PTPN11 variants correlated with their tyrosine phosphatase levels thereby confusing PTPN11's role in germline clonal expansion. Six of the PTPN11 exon 3 de novo variants associated with somatic mutation-induced sporadic cancers (but not NS) also formed testis clusters. Further, three of these six variants were observed among fetuses that underwent prenatal ultrasound screening for NS-like features. Mathematical modeling showed that germline selection can explain both the mutation clusters and the high incidence of NS (1/1000-1/2500).
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Affiliation(s)
- Jordan Eboreime
- Department of Biological Sciences, Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, USA
| | - Soo-Kyung Choi
- Department of Biological Sciences, Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, USA
| | - Song-Ro Yoon
- Department of Biological Sciences, Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, USA
| | - Anastasiia Sadybekov
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, California, USA
| | - Vsevolod Katritch
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, California, USA
| | - Peter Calabrese
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California, USA
| | - Norman Arnheim
- Department of Biological Sciences, Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, USA
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11
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Yarnall MT, Kim SH, Korntner S, Bishop AC. Destabilization of the SHP2 and SHP1 protein tyrosine phosphatase domains by a non-conserved "backdoor" cysteine. Biochem Biophys Rep 2022; 32:101370. [PMID: 36275931 PMCID: PMC9578986 DOI: 10.1016/j.bbrep.2022.101370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 10/11/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
Protein tyrosine phosphatases (PTPs) are critical regulators of cellular signal transduction that catalyze the hydrolytic dephosphorylation of phosphotyrosine in substrate proteins. Among several conserved features in classical PTP domains are an active-site cysteine residue that is necessary for catalysis and a "backdoor" cysteine residue that can serve to protect the active-site cysteine from irreversible oxidation. Curiously, two biologically important phosphatases, Src homology domain-containing PTPs 2 and 1 (SHP2 and SHP1), each contain an additional backdoor cysteine residue at a position of the PTP domain that is occupied by proline in almost all other classical PTPs (position 333 in human SHP2 numbering). Here we show that the presence of cysteine 333 significantly destabilizes the fold of the PTP domains in the SHPs. We find that replacement of cysteine 333 with proline confers increased thermal stability on the SHP2 and SHP1 PTP domains, as measured by temperature-dependent activity assays and differential scanning fluorimetry. Conversely, we show that substantial destabilization of the PTP-domain fold is conferred by introduction of a non-natural cysteine residue in a non-SHP PTP that contains proline at the 333 position. It has previously been suggested that the extra backdoor cysteine of the SHP PTPs may work in tandem with the conserved backdoor cysteine to provide protection from irreversible oxidative enzyme inactivation. If so, our current results suggest that, during the course of mammalian evolution, the SHP proteins have developed extra protection from oxidation at the cost of the thermal instability that is conferred by the presence of their PTP domains' second backdoor cysteine.
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Affiliation(s)
| | - Sean H. Kim
- Amherst College, Department of Chemistry, Amherst, MA, 01002, USA
| | - Samuel Korntner
- Amherst College, Department of Chemistry, Amherst, MA, 01002, USA
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12
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Kong J, Long YQ. Recent advances in the discovery of protein tyrosine phosphatase SHP2 inhibitors. RSC Med Chem 2022; 13:246-257. [PMID: 35434626 PMCID: PMC8942255 DOI: 10.1039/d1md00386k] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/14/2022] [Indexed: 01/17/2023] Open
Abstract
Src homology 2 domain-containing protein tyrosine phosphatase (SHP2) is a non-receptor protein tyrosine phosphatase encoded by the Ptpn11 gene, which regulates cell growth, differentiation and apoptosis via modulating various signaling pathways, such as the RAS/ERK signaling pathway, and participates in the PD-1/PD-L1 pathway governing immune surveillance. It has been recognized as a breakthrough antitumor therapeutic target. Besides, numerous studies have shown that SHP2 plays an important role in the regulation of inflammatory diseases. However, inhibitors targeting the active site of SHP2 lack drug-likeness due to their low selectivity and poor bioavailability, thus none has advanced to clinical development. Recently, allosteric inhibitors that stabilize the inactive conformation of SHP2 have achieved breakthrough progress, providing the clinical proof for the druggability of SHP2 as an antitumor drug target. This paper reviews the recently reported design and discovery of SHP2 small molecule inhibitors, focused on the structure-activity relationship (SAR) analysis of several representative SHP2 inhibitors, outlining the evolution and therapeutic potential of the small molecule inhibitors targeting SHP2.
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Affiliation(s)
- Jiao Kong
- Laboratory of Medicinal Chemical Biology, Department of Medicinal Chemistry, College of Pharmaceutical Sciences, Soochow University Medical College Suzhou 215123 China
| | - Ya-Qiu Long
- Laboratory of Medicinal Chemical Biology, Department of Medicinal Chemistry, College of Pharmaceutical Sciences, Soochow University Medical College Suzhou 215123 China
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13
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Pfeiffer A, Franciosa G, Locard-Paulet M, Piga I, Reckzeh K, Vemulapalli V, Blacklow SC, Theilgaard-Mönch K, Jensen LJ, Olsen JV. Phosphorylation of SHP2 at Tyr62 enables acquired resistance to SHP2 allosteric inhibitors in FLT3-ITD-driven AML. Cancer Res 2022; 82:2141-2155. [PMID: 35311954 DOI: 10.1158/0008-5472.can-21-0548] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 12/17/2021] [Accepted: 03/17/2022] [Indexed: 11/16/2022]
Abstract
The protein tyrosine phosphatase SHP2 is crucial for oncogenic transformation of acute myeloid leukemia (AML) cells expressing mutated receptor tyrosine kinases (RTK). SHP2 is required for full RAS-ERK activation to promote cell proliferation and survival programs. Allosteric SHP2 inhibitors act by stabilizing SHP2 in its auto-inhibited conformation and are currently being tested in clinical trials for tumors with overactivation of the RAS/ERK pathway, alone and in various drug combinations. In this study, we established cells with acquired resistance to the allosteric SHP2 inhibitor SHP099 from two FLT3-ITD-positive AML cell lines. Label-free and isobaric labeling quantitative mass spectrometry-based phosphoproteomics of these resistant models demonstrated that AML cells can restore phosphorylated ERK (pERK) in the presence of SHP099, thus developing adaptive resistance. Mechanistically, SHP2 inhibition induced tyrosine phosphorylation and feedback-driven activation of the FLT3 receptor, which in turn phosphorylated SHP2 on tyrosine 62. This phosphorylation stabilized SHP2 in its open conformation, preventing SHP099 binding and conferring resistance. Combinatorial inhibition of SHP2 and MEK or FLT3 prevented pERK rebound and resistant cell growth. The same mechanism was observed in a FLT3-mutated B-ALL cell line and in the inv(16)/KitD816Y AML mouse model, but allosteric inhibition of Shp2 did not impair the clonogenic ability of normal bone marrow progenitors. Together, these results support the future use of SHP2 inhibitor combinations for clinical applications.
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Affiliation(s)
| | | | | | - Ilaria Piga
- Istituto Oncologico Veneto IOV - IRCCS, Italy
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14
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Bobone S, Pannone L, Biondi B, Solman M, Flex E, Canale VC, Calligari P, De Faveri C, Gandini T, Quercioli A, Torini G, Venditti M, Lauri A, Fasano G, Hoeksma J, Santucci V, Cattani G, Bocedi A, Carpentieri G, Tirelli V, Sanchez M, Peggion C, Formaggio F, den Hertog J, Martinelli S, Bocchinfuso G, Tartaglia M, Stella L. Targeting Oncogenic Src Homology 2 Domain-Containing Phosphatase 2 (SHP2) by Inhibiting Its Protein-Protein Interactions. J Med Chem 2021; 64:15973-15990. [PMID: 34714648 PMCID: PMC8591604 DOI: 10.1021/acs.jmedchem.1c01371] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We developed a new class of inhibitors of protein-protein interactions of the SHP2 phosphatase, which is pivotal in cell signaling and represents a central target in the therapy of cancer and rare diseases. Currently available SHP2 inhibitors target the catalytic site or an allosteric pocket but lack specificity or are ineffective for disease-associated SHP2 mutants. Considering that pathogenic lesions cause signaling hyperactivation due to increased levels of SHP2 association with cognate proteins, we developed peptide-based molecules with nanomolar affinity for the N-terminal Src homology domain of SHP2, good selectivity, stability to degradation, and an affinity for pathogenic variants of SHP2 that is 2-20 times higher than for the wild-type protein. The best peptide reverted the effects of a pathogenic variant (D61G) in zebrafish embryos. Our results provide a novel route for SHP2-targeted therapies and a tool for investigating the role of protein-protein interactions in the function of SHP2.
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Affiliation(s)
- Sara Bobone
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Luca Pannone
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome 00146, Italy.,Dipartimento di Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Barbara Biondi
- Institute of Biomolecular Chemistry, Padova Unit, CNR, Padova 35131, Italy
| | - Maja Solman
- Hubrecht institute-KNAW and University Medical Center Utrecht, Utrecht 3584 CT, The Netherlands
| | - Elisabetta Flex
- Dipartimento di Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Viviana Claudia Canale
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Paolo Calligari
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Chiara De Faveri
- Department of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Tommaso Gandini
- Department of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Andrea Quercioli
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Giuseppe Torini
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Martina Venditti
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome 00146, Italy
| | - Antonella Lauri
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome 00146, Italy
| | - Giulia Fasano
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome 00146, Italy
| | - Jelmer Hoeksma
- Hubrecht institute-KNAW and University Medical Center Utrecht, Utrecht 3584 CT, The Netherlands
| | - Valerio Santucci
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Giada Cattani
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Alessio Bocedi
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Giovanna Carpentieri
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome 00146, Italy.,Dipartimento di Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Valentina Tirelli
- Centre of Core Facilities, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Massimo Sanchez
- Centre of Core Facilities, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Cristina Peggion
- Department of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Fernando Formaggio
- Institute of Biomolecular Chemistry, Padova Unit, CNR, Padova 35131, Italy.,Department of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Jeroen den Hertog
- Institute of Biomolecular Chemistry, Padova Unit, CNR, Padova 35131, Italy.,Institute of Biology Leiden, Leiden University, Leiden 2333 BE, The Netherlands
| | - Simone Martinelli
- Dipartimento di Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Gianfranco Bocchinfuso
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome 00146, Italy
| | - Lorenzo Stella
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
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15
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Calligari P, Santucci V, Stella L, Bocchinfuso G. Discriminating between competing models for the allosteric regulation of oncogenic phosphatase SHP2 by characterizing its active state. Comput Struct Biotechnol J 2021; 19:6125-6139. [PMID: 34900129 PMCID: PMC8632847 DOI: 10.1016/j.csbj.2021.10.041] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/31/2021] [Accepted: 10/31/2021] [Indexed: 11/07/2022] Open
Abstract
The Src-homology 2 domain containing phosphatase 2 (SHP2) plays a critical role in crucial signaling pathways and is involved in oncogenesis and in developmental disorders. Its structure includes two SH2 domains (N-SH2 and C-SH2), and a protein tyrosine phosphatase (PTP) domain. Under basal conditions, SHP2 is auto-inhibited, with the N-SH2 domain blocking the PTP active site. Activation involves a rearrangement of the domains that makes the catalytic site accessible, coupled to the association between the SH2 domains and cognate proteins containing phosphotyrosines. Several aspects of this transition are debated and competing mechanistic models have been proposed. A crystallographic structure of SHP2 in an active state has been reported (PDB code 6crf), but several lines of evidence suggests that it is not fully representative of the conformations populated in solution. To clarify the structural rearrangements involved in SHP2 activation, enhanced sampling simulations of the autoinhibited and active states have been performed, for wild type SHP2 and its pathogenic E76K variant. Our results demonstrate that the crystallographic conformation of the active state is unstable in solution, and multiple interdomain arrangements are populated, thus allowing association to bisphosphorylated sequences. Contrary to a recent proposal, activation is coupled to the conformational changes of the N-SH2 binding site, which is significantly more accessible in the active sate, rather than to the structure of the central β-sheet of the domain. In this coupling, a previously undescribed role for the N-SH2 BG loop emerged.
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Key Words
- BTLA, B and T lymphocyte attenuator
- CTLA-4, cytotoxic T lymphocyte-associated antigen 4
- FRET, Förster resonance energy transfer
- Inter-domain dynamics
- JMML, juvenile myelomonocytic leukemia
- MD, molecular dynamics
- NS, Noonan syndrome
- NSML, Noonan syndrome with multiple lentigines
- PD-1, programmed cell death protein 1
- PDB, protein data bank
- PMF, potential of mean force
- PTP, protein tyrosine phosphatase
- Protein flexibility
- REMD, replica exchange molecular dynamics
- RMSD, root mean square deviation
- RMSF, root mean square fluctuation
- RTK, receptor tyrosine kinase
- Replica exchange molecular dynamics simulations
- SASA, solvent accessible surface area
- SAXS, small angle X-ray scattering
- SH2, Src homology 2
- SHP2 regulatory mechanism
- SHP2, Src homology 2 domain-containing phosphatase 2
- SIRPalpha, signal regulatory protein alpha
- pY, phosphorylated tyrosine
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Affiliation(s)
- Paolo Calligari
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Rome, Italy
| | - Valerio Santucci
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Rome, Italy
| | - Lorenzo Stella
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Rome, Italy
| | - Gianfranco Bocchinfuso
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Rome, Italy
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16
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The loops of the N-SH2 binding cleft do not serve as allosteric switch in SHP2 activation. Proc Natl Acad Sci U S A 2021; 118:2025107118. [PMID: 33888588 DOI: 10.1073/pnas.2025107118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The Src-homology-2 domain-containing phosphatase SHP2 is a critical regulator of signal transduction, being implicated in cell growth and differentiation. Activating mutations cause developmental disorders and act as oncogenic drivers in hematologic cancers. SHP2 is activated by phosphopeptide binding to the N-SH2 domain, triggering the release of N-SH2 from the catalytic PTP domain. Based on early crystallographic data, it has been widely accepted that opening of the binding cleft of N-SH2 serves as the key "allosteric switch" driving SHP2 activation. To test the putative coupling between binding cleft opening and SHP2 activation as assumed by the allosteric switch model, we critically reviewed structural data of SHP2, and we used extensive molecular dynamics (MD) simulation and free energy calculations of isolated N-SH2 in solution, SHP2 in solution, and SHP2 in a crystal environment. Our results demonstrate that the binding cleft in N-SH2 is constitutively flexible and open in solution and that a closed cleft found in certain structures is a consequence of crystal contacts. The degree of opening of the binding cleft has only a negligible effect on the free energy of SHP2 activation. Instead, SHP2 activation is greatly favored by the opening of the central β-sheet of N-SH2. We conclude that opening of the N-SH2 binding cleft is not the key allosteric switch triggering SHP2 activation.
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17
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Kim JY, Plaman BA, Bishop AC. Targeting a Pathogenic Cysteine Mutation: Discovery of a Specific Inhibitor of Y279C SHP2. Biochemistry 2020; 59:3498-3507. [PMID: 32871078 PMCID: PMC7891893 DOI: 10.1021/acs.biochem.0c00471] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
An
intriguing challenge of drug discovery is targeting pathogenic
mutant proteins that differ from their wild-type counterparts by only
a single amino acid. In particular, pathogenic cysteine mutations
afford promising opportunities for mutant-specific drug discovery,
due to the unique reactivity of cysteine’s sulfhydryl-containing
side chain. Here we describe the first directed discovery effort targeting
a pathogenic cysteine mutant of a protein tyrosine phosphatase (PTP),
namely Y279C Src-homology-2-containing PTP 2 (SHP2), which has been
causatively linked to the developmental disorder Noonan syndrome with
multiple lentigines (NSML). Through a screen of commercially available
compounds that contain cysteine-reactive functional groups, we have
discovered a small-molecule inhibitor of Y279C SHP2 (compound 99; IC50 ≈ 6 μM) that has no appreciable
effect on the phosphatase activity of wild-type SHP2 or that of other
homologous PTPs (IC50 ≫ 100 μM). Compound 99 exerts its specific inhibitory effect through irreversible
engagement of Y279C SHP2’s pathogenic cysteine residue in a
manner that is time-dependent, is substrate-independent, and persists
in the context of a complex proteome. To the best of our knowledge, 99 is the first specific ligand of a disease-causing PTP mutant
to be identified. This study therefore provides both a starting point
for the development of NSML-directed therapeutic agents and a precedent
for the identification of mutant-specific inhibitors of other pathogenic
PTP mutants.
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Affiliation(s)
- Jenny Y Kim
- Department of Chemistry, Amherst College, Amherst, Massachusetts 01002, United States
| | - Bailey A Plaman
- Department of Chemistry, Amherst College, Amherst, Massachusetts 01002, United States
| | - Anthony C Bishop
- Department of Chemistry, Amherst College, Amherst, Massachusetts 01002, United States
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18
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Anselmi M, Calligari P, Hub JS, Tartaglia M, Bocchinfuso G, Stella L. Structural Determinants of Phosphopeptide Binding to the N-Terminal Src Homology 2 Domain of the SHP2 Phosphatase. J Chem Inf Model 2020; 60:3157-3171. [PMID: 32395997 PMCID: PMC8007070 DOI: 10.1021/acs.jcim.0c00307] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Indexed: 11/28/2022]
Abstract
SH2 domain-containing tyrosine phosphatase 2 (SHP2), encoded by PTPN11, plays a fundamental role in the modulation of several signaling pathways. Germline and somatic mutations in PTPN11 are associated with different rare diseases and hematologic malignancies, and recent studies have individuated SHP2 as a central node in oncogenesis and cancer drug resistance. The SHP2 structure includes two Src homology 2 domains (N-SH2 and C-SH2) followed by a catalytic protein tyrosine phosphatase (PTP) domain. Under basal conditions, the N-SH2 domain blocks the active site, inhibiting phosphatase activity. Association of the N-SH2 domain with binding partners containing short amino acid motifs comprising a phosphotyrosine residue (pY) leads to N-SH2/PTP dissociation and SHP2 activation. Considering the relevance of SHP2 in signaling and disease and the central role of the N-SH2 domain in its allosteric regulation mechanism, we performed microsecond-long molecular dynamics (MD) simulations of the N-SH2 domain complexed to 12 different peptides to define the structural and dynamical features determining the binding affinity and specificity of the domain. Phosphopeptide residues at position -2 to +5, with respect to pY, have significant interactions with the SH2 domain. In addition to the strong interaction of the pY residue with its conserved binding pocket, the complex is stabilized hydrophobically by insertion of residues +1, +3, and +5 in an apolar groove of the domain and interaction of residue -2 with both the pY and a protein surface residue. Additional interactions are provided by hydrogen bonds formed by the backbone of residues -1, +1, +2, and +4. Finally, negatively charged residues at positions +2 and +4 are involved in electrostatic interactions with two lysines (Lys89 and Lys91) specific for the SHP2 N-SH2 domain. Interestingly, the MD simulations illustrated a previously undescribed conformational flexibility of the domain, involving the core β sheet and the loop that closes the pY binding pocket.
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Affiliation(s)
- Massimiliano Anselmi
- Department
of Chemical Science and Technologies, University
of Rome Tor Vergata, 00133, Rome, Italy
| | - Paolo Calligari
- Department
of Chemical Science and Technologies, University
of Rome Tor Vergata, 00133, Rome, Italy
| | - Jochen S. Hub
- Theoretical
Physics and Center for Biophysics, Saarland
University, Campus E2 6, 66123 Saarbrücken, Germany
| | - Marco Tartaglia
- Genetics
and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Gianfranco Bocchinfuso
- Department
of Chemical Science and Technologies, University
of Rome Tor Vergata, 00133, Rome, Italy
| | - Lorenzo Stella
- Department
of Chemical Science and Technologies, University
of Rome Tor Vergata, 00133, Rome, Italy
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19
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Martinelli S, Pannone L, Lissewski C, Brinkmann J, Flex E, Schanze D, Calligari P, Anselmi M, Pantaleoni F, Canale VC, Radio FC, Ioannides A, Rahner N, Schanze I, Josifova D, Bocchinfuso G, Ryten M, Stella L, Tartaglia M, Zenker M. Pathogenic PTPN11 variants involving the poly-glutamine Gln 255 -Gln 256 -Gln 257 stretch highlight the relevance of helix B in SHP2's functional regulation. Hum Mutat 2020; 41:1171-1182. [PMID: 32112654 DOI: 10.1002/humu.24007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 02/14/2020] [Accepted: 02/27/2020] [Indexed: 01/28/2023]
Abstract
Germline PTPN11 mutations cause Noonan syndrome (NS), the most common disorder among RASopathies. PTPN11 encodes SHP2, a protein tyrosine-phosphatase controlling signaling through the RAS-MAPK and PI3K-AKT pathways. Generally, NS-causing PTPN11 mutations are missense changes destabilizing the inactive conformation of the protein or enhancing its binding to signaling partners. Here, we report on two PTPN11 variants resulting in the deletion or duplication of one of three adjacent glutamine residues (Gln255 -to-Gln257 ). While p.(Gln257dup) caused a typical NS phenotype in carriers of a first family, p.(Gln257del) had incomplete penetrance in a second family. Missense mutations involving Gln256 had previously been reported in NS. This poly-glutamine stretch is located on helix B of the PTP domain, a region involved in stabilizing SHP2 in its autoinhibited state. Molecular dynamics simulations predicted that changes affecting this motif perturb the SHP2's catalytically inactive conformation and/or substrate recognition. Biochemical data showed that duplication and deletion of Gln257 variably enhance SHP2's catalytic activity, while missense changes involving Gln256 affect substrate specificity. Expression of mutants in HEK293T cells documented their activating role on MAPK signaling, uncoupling catalytic activity and modulation of intracellular signaling. These findings further document the relevance of helix B in the regulation of SHP2's function.
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Affiliation(s)
- Simone Martinelli
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Luca Pannone
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy.,Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Christina Lissewski
- Institute of Human Genetics, University Hospital of Magdeburg, Otto-von-Guericke-University, Magdeburg, Germany
| | - Julia Brinkmann
- Institute of Human Genetics, University Hospital of Magdeburg, Otto-von-Guericke-University, Magdeburg, Germany
| | - Elisabetta Flex
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Denny Schanze
- Institute of Human Genetics, University Hospital of Magdeburg, Otto-von-Guericke-University, Magdeburg, Germany
| | - Paolo Calligari
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Rome, Italy
| | - Massimiliano Anselmi
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Rome, Italy
| | - Francesca Pantaleoni
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Viviana Claudia Canale
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Rome, Italy
| | | | - Adonis Ioannides
- Clinical Genetics, University of Nicosia Medical School, Nicosia, Cyprus.,South East Thames Regional Genetics Service, Guy's Hospital, London, UK
| | - Nils Rahner
- Medical Faculty, Institute of Human Genetics, Heinrich-Heine University, Düsseldorf, Germany
| | - Ina Schanze
- Institute of Human Genetics, University Hospital of Magdeburg, Otto-von-Guericke-University, Magdeburg, Germany
| | - Dragana Josifova
- South East Thames Regional Genetics Service, Guy's Hospital, London, UK
| | - Gianfranco Bocchinfuso
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Rome, Italy
| | - Mina Ryten
- South East Thames Regional Genetics Service, Guy's Hospital, London, UK
| | - Lorenzo Stella
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Rome, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Martin Zenker
- Institute of Human Genetics, University Hospital of Magdeburg, Otto-von-Guericke-University, Magdeburg, Germany
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20
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Schönfeld M, Selig M, Russo A, Lindner C, Kampmann C, Mildenberger E, Whybra C. Rapid detection by hydrops panel of Noonan syndrome with PTPN11 mutation (p.Thr73Ile) and persistent thrombocytopenia. Mol Genet Genomic Med 2020; 8:e1174. [PMID: 32144894 PMCID: PMC7216795 DOI: 10.1002/mgg3.1174] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/21/2020] [Accepted: 01/30/2020] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Nonimmune hydrops fetalis (NIHF) is still a challenging diagnosis. The differential diagnosis is extensive and the success of identifying a cause depends on the thoroughness of efforts to establish a diagnosis. For the early diagnosis of NIHF, a virtual gene panel diagnostic tool was developed. The female premature baby in question was delivered via emergency cesarean at 30 + 1 weeks of gestational age (GA) due to rapidly developing NIHF to a healthy mother. The family history was noncontributory. METHODS DNA of the family was extracted and sequenced by the virtual hydrops panel with whole-exome sequencing. RESULTS The hydrops panel revealed Noonan syndrome (NS) with a germline mutation in PTPN11 c.218C>T (p.Thr73Ile). CONCLUSION The diagnosis of our patient was rapidly confirmed by the hydrops panel. The variant of c.218C>T (p.Thr73Ile) has not yet been described in literature relating to NIHF. Only a few case reports of this variant are known. This particular mutation is associated with Noonan syndrome, congenital heart defect and persistent thrombocytopenia. Few reveal juvenile myelomonocytic leukemia.
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Affiliation(s)
- Mascha Schönfeld
- Neonatology, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Mareike Selig
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Alexandra Russo
- Hematology, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Christine Lindner
- Department of Obstetrics and Gynecology, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Christoph Kampmann
- Pediatric Cardiology, Department of Pediatrics, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Eva Mildenberger
- Neonatology, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Catharina Whybra
- Neonatology, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
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21
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Therapeutic potential of targeting SHP2 in human developmental disorders and cancers. Eur J Med Chem 2020; 190:112117. [PMID: 32061959 DOI: 10.1016/j.ejmech.2020.112117] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/03/2020] [Accepted: 02/03/2020] [Indexed: 02/06/2023]
Abstract
Src homology 2 (SH2)-containing protein tyrosine phosphatase 2 (SHP2), encoded by PTPN11, regulates cell proliferation, differentiation, apoptosis and survival via releasing intramolecular autoinhibition and modulating various signaling pathways, such as mitogen-activated protein kinase (MAPK) pathway. Mutations and aberrant expression of SHP2 are implicated in human developmental disorders, leukemias and several solid tumors. As an oncoprotein in some cancers, SHP2 represents a rational target for inhibitors to interfere. Nevertheless, its tumor suppressive effect has also been uncovered, indicating the context-specificity. Even so, two types of SHP2 inhibitors including targeting catalytic pocket and allosteric sites have been developed associated with resolved cocrystal complexes. Herein, we describe its structure, biological function, deregulation in human diseases and summarize recent advance in development of SHP2 inhibitors, trying to give an insight into the therapeutic potential in future.
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22
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Kanavy DM, McNulty SM, Jairath MK, Brnich SE, Bizon C, Powell BC, Berg JS. Comparative analysis of functional assay evidence use by ClinGen Variant Curation Expert Panels. Genome Med 2019; 11:77. [PMID: 31783775 PMCID: PMC6884856 DOI: 10.1186/s13073-019-0683-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 11/05/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The 2015 American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) guidelines for clinical sequence variant interpretation state that "well-established" functional studies can be used as evidence in variant classification. These guidelines articulated key attributes of functional data, including that assays should reflect the biological environment and be analytically sound; however, details of how to evaluate these attributes were left to expert judgment. The Clinical Genome Resource (ClinGen) designates Variant Curation Expert Panels (VCEPs) in specific disease areas to make gene-centric specifications to the ACMG/AMP guidelines, including more specific definitions of appropriate functional assays. We set out to evaluate the existing VCEP guidelines for functional assays. METHODS We evaluated the functional criteria (PS3/BS3) of six VCEPs (CDH1, Hearing Loss, Inherited Cardiomyopathy-MYH7, PAH, PTEN, RASopathy). We then established criteria for evaluating functional studies based on disease mechanism, general class of assay, and the characteristics of specific assay instances described in the primary literature. Using these criteria, we extensively curated assay instances cited by each VCEP in their pilot variant classification to analyze VCEP recommendations and their use in the interpretation of functional studies. RESULTS Unsurprisingly, our analysis highlighted the breadth of VCEP-approved assays, reflecting the diversity of disease mechanisms among VCEPs. We also noted substantial variability between VCEPs in the method used to select these assays and in the approach used to specify strength modifications, as well as differences in suggested validation parameters. Importantly, we observed discrepancies between the parameters VCEPs specified as required for approved assay instances and the fulfillment of these requirements in the individual assays cited in pilot variant interpretation. CONCLUSIONS Interpretation of the intricacies of functional assays often requires expert-level knowledge of the gene and disease, and current VCEP recommendations for functional assay evidence are a useful tool to improve the accessibility of functional data by providing a starting point for curators to identify approved functional assays and key metrics. However, our analysis suggests that further guidance is needed to standardize this process and ensure consistency in the application of functional evidence.
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Affiliation(s)
- Dona M Kanavy
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Shannon M McNulty
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Meera K Jairath
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sarah E Brnich
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Chris Bizon
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bradford C Powell
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jonathan S Berg
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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23
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Costigan DC, Dong F. The extended spectrum of RAS-MAPK pathway mutations in colorectal cancer. Genes Chromosomes Cancer 2019; 59:152-159. [PMID: 31589789 DOI: 10.1002/gcc.22813] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/01/2019] [Accepted: 10/02/2019] [Indexed: 01/07/2023] Open
Abstract
Current clinical guidelines recommend mutation analysis for select codons in KRAS and NRAS exons 2, 3, and 4 and BRAF V600E to guide therapy selection and prognostic stratification in advanced colorectal cancer. This study evaluates the impact of extended molecular testing on the detection of RAS-MAPK pathway mutations. Panel next-generation sequencing results of colorectal cancer specimens from 5795 individuals from the American Association for Cancer Research Project Genomics Evidence Neoplasia Information Exchange (AACR Project GENIE) were included. Mutations in RAS-MAPK pathway genes were analyzed and functionally annotated. Colorectal cancers had recurrent pathogenic pathway activating mutations in KRAS (44%), NRAS (4%), HRAS (<1%), BRAF (10%), MAP2K1 (1%), RAF1 (<1%), and PTPN11 (<1%). The proportion of colorectal cancers with pathogenic RAS pathway mutations was 37% when only KRAS codon 12 and 13 mutations were considered, 46% when also including select KRAS and NRAS exons 2, 3, and 4 mutations, 53% when including BRAF V600E mutations, and 56% when including all pathogenic mutations. Panel next-generation sequencing testing identifies additional RAS-MAPK pathway driver mutations beyond current guideline recommendations. These mutations have potential implications in treatment selection for patients with advanced colorectal cancer.
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Affiliation(s)
- Danielle C Costigan
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Fei Dong
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
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24
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Sun J, Lei L, Tsai CM, Wang Y, Shi Y, Ouyang M, Lu S, Seong J, Kim TJ, Wang P, Huang M, Xu X, Nizet V, Chien S, Wang Y. Engineered proteins with sensing and activating modules for automated reprogramming of cellular functions. Nat Commun 2017; 8:477. [PMID: 28883531 PMCID: PMC5589908 DOI: 10.1038/s41467-017-00569-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 07/11/2017] [Indexed: 12/31/2022] Open
Abstract
Protein-based biosensors or activators have been engineered to visualize molecular signals or manipulate cellular functions. Here we integrate these two functionalities into one protein molecule, an integrated sensing and activating protein (iSNAP). A prototype that can detect tyrosine phosphorylation and immediately activate auto-inhibited Shp2 phosphatase, Shp2-iSNAP, is designed through modular assembly. When Shp2-iSNAP is fused to the SIRPα receptor which typically transduces anti-phagocytic signals from the 'don't eat me' CD47 ligand through negative Shp1 signaling, the engineered macrophages not only allow visualization of SIRPα phosphorylation upon CD47 engagement but also rewire the CD47-SIRPα axis into the positive Shp2 signaling, which enhances phagocytosis of opsonized tumor cells. A second SIRPα Syk-iSNAP with redesigned sensor and activator modules can likewise rewire the CD47-SIRPα axis to the pro-phagocytic Syk kinase activation. Thus, our approach can be extended to execute a broad range of sensing and automated reprogramming actions for directed therapeutics.Protein-based biosensors have been engineered to interrogate cellular signaling and manipulate function. Here the authors demonstrate iSNAP, a tool to detect tyrosine phosphorylation and activate desired protein enzymes allowing the control of phagocytosis in macrophages.
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Affiliation(s)
- Jie Sun
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Department of Cell Biology, School of Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Lei Lei
- Department of Bioengineering and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Chih-Ming Tsai
- Department of Pediatrics and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Yi Wang
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yiwen Shi
- Department of Bioengineering and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Mingxing Ouyang
- Department of Bioengineering and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Shaoying Lu
- Department of Bioengineering and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Jihye Seong
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Tae-Jin Kim
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Department of Biological Sciences, Pusan National University, Busan, 46241, Republic of Korea
| | - Pengzhi Wang
- Department of Bioengineering and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Min Huang
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Xiangdong Xu
- Department of Pathology, Veterans Affairs San Diego Healthcare System, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Victor Nizet
- Department of Pediatrics and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Shu Chien
- Department of Bioengineering and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Yingxiao Wang
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,Department of Bioengineering and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, 92093, USA. .,Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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25
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Pannone L, Bocchinfuso G, Flex E, Rossi C, Baldassarre G, Lissewski C, Pantaleoni F, Consoli F, Lepri F, Magliozzi M, Anselmi M, Delle Vigne S, Sorge G, Karaer K, Cuturilo G, Sartorio A, Tinschert S, Accadia M, Digilio MC, Zampino G, De Luca A, Cavé H, Zenker M, Gelb BD, Dallapiccola B, Stella L, Ferrero GB, Martinelli S, Tartaglia M. Structural, Functional, and Clinical Characterization of a Novel PTPN11 Mutation Cluster Underlying Noonan Syndrome. Hum Mutat 2017; 38:451-459. [PMID: 28074573 DOI: 10.1002/humu.23175] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 01/06/2017] [Indexed: 01/12/2023]
Abstract
Germline mutations in PTPN11, the gene encoding the Src-homology 2 (SH2) domain-containing protein tyrosine phosphatase (SHP2), cause Noonan syndrome (NS), a relatively common, clinically variable, multisystem disorder. Here, we report on the identification of five different PTPN11 missense changes affecting residues Leu261 , Leu262 , and Arg265 in 16 unrelated individuals with clinical diagnosis of NS or with features suggestive for this disorder, specifying a novel disease-causing mutation cluster. Expression of the mutant proteins in HEK293T cells documented their activating role on MAPK signaling. Structural data predicted a gain-of-function role of substitutions at residues Leu262 and Arg265 exerted by disruption of the N-SH2/PTP autoinhibitory interaction. Molecular dynamics simulations suggested a more complex behavior for changes affecting Leu261 , with possible impact on SHP2's catalytic activity/selectivity and proper interaction of the PTP domain with the regulatory SH2 domains. Consistent with that, biochemical data indicated that substitutions at codons 262 and 265 increased the catalytic activity of the phosphatase, while those affecting codon 261 were only moderately activating but impacted substrate specificity. Remarkably, these mutations underlie a relatively mild form of NS characterized by low prevalence of cardiac defects, short stature, and cognitive and behavioral issues, as well as less evident typical facial features.
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Affiliation(s)
- Luca Pannone
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy.,Dipartimento di Ematologia, Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, Rome, Italy.,Dipartimento di Medicina Sperimentale, Sapienza Università di Roma, Rome, Italy
| | - Gianfranco Bocchinfuso
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Rome, Italy
| | - Elisabetta Flex
- Dipartimento di Ematologia, Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, Rome, Italy
| | - Cesare Rossi
- Genetica Medica, Policlinico S. Orsola-Malpighi, Bologna, Italy
| | | | - Christina Lissewski
- Institute of Human Genetics, University Hospital of Magdeburg, Otto-von-Guericke-University, Magdeburg, Germany
| | - Francesca Pantaleoni
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Federica Consoli
- Ospedale Casa Sollievo della Sofferenza, IRCCS, San Giovanni Rotondo, Italy
| | - Francesca Lepri
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Monia Magliozzi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy.,Ospedale Casa Sollievo della Sofferenza, IRCCS, San Giovanni Rotondo, Italy
| | - Massimiliano Anselmi
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Rome, Italy
| | - Silvia Delle Vigne
- Dipartimento di Ematologia, Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, Rome, Italy
| | - Giovanni Sorge
- Unità Operativa Complessa di Clinica Pediatrica, Dipartimento di Medicina Clinica e Sperimentale, Università di Catania, Catania, Italy
| | - Kadri Karaer
- Dr. Ersin Arslan Research and Training Hospital, Department of Medical Genetics, Gaziantep, Turkey
| | - Goran Cuturilo
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia.,University Children's Hospital, Belgrade, Serbia
| | - Alessandro Sartorio
- Istituto Auxologico Italiano, Experimental Laboratory for Auxo-Endocrinological Research, Milan and Verbania, Italy.,Istituto Auxologico Italiano, Division of Auxology, Verbania, Italy
| | - Sigrid Tinschert
- Institute of Clinical Genetics, Technical University of Dresden, Dresden, Germany
| | - Maria Accadia
- Ospedale Casa Sollievo della Sofferenza, IRCCS, San Giovanni Rotondo, Italy
| | - Maria C Digilio
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Giuseppe Zampino
- Istituto di Clinica Pediatrica, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Alessandro De Luca
- Ospedale Casa Sollievo della Sofferenza, IRCCS, San Giovanni Rotondo, Italy
| | - Hélène Cavé
- Département de Génétique, Hôpital Robert Debré, Paris, France.,INSERM UMR_S1131, Institut Universitaire d'Hématologie, Université Paris Diderot, Paris-Sorbonne-Cité, Paris, France
| | - Martin Zenker
- Institute of Human Genetics, University Hospital of Magdeburg, Otto-von-Guericke-University, Magdeburg, Germany
| | - Bruce D Gelb
- Mindich Child Health and Development Institute and Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York
| | - Bruno Dallapiccola
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Lorenzo Stella
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Rome, Italy
| | - Giovanni B Ferrero
- Department of Pediatric and Public Health Sciences, University of Torino, Torino, Italy
| | - Simone Martinelli
- Dipartimento di Ematologia, Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, Rome, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
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26
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SHP2 sails from physiology to pathology. Eur J Med Genet 2015; 58:509-25. [PMID: 26341048 DOI: 10.1016/j.ejmg.2015.08.005] [Citation(s) in RCA: 165] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 07/24/2015] [Accepted: 08/30/2015] [Indexed: 02/08/2023]
Abstract
Over the two past decades, mutations of the PTPN11 gene, encoding the ubiquitous protein tyrosine phosphatase SHP2 (SH2 domain-containing tyrosine phosphatase 2), have been identified as the causal factor of several developmental diseases (Noonan syndrome (NS), Noonan syndrome with multiple lentigines (NS-ML), and metachondromatosis), and malignancies (juvenile myelomonocytic leukemia). SHP2 plays essential physiological functions in organism development and homeostasis maintenance by regulating fundamental intracellular signaling pathways in response to a wide range of growth factors and hormones, notably the pleiotropic Ras/Mitogen-Activated Protein Kinase (MAPK) and the Phosphoinositide-3 Kinase (PI3K)/AKT cascades. Analysis of the biochemical impacts of PTPN11 mutations first identified both loss-of-function and gain-of-function mutations, as well as more subtle defects, highlighting the major pathophysiological consequences of SHP2 dysregulation. Then, functional genetic studies provided insights into the molecular dysregulations that link SHP2 mutants to the development of specific traits of the diseases, paving the way for the design of specific therapies for affected patients. In this review, we first provide an overview of SHP2's structure and regulation, then describe its molecular roles, notably its functions in modulating the Ras/MAPK and PI3K/AKT signaling pathways, and its physiological roles in organism development and homeostasis. In the second part, we describe the different PTPN11 mutation-associated pathologies and their clinical manifestations, with particular focus on the biochemical and signaling outcomes of NS and NS-ML-associated mutations, and on the recent advances regarding the pathophysiology of these diseases.
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Lnk adaptor suppresses radiation resistance and radiation-induced B-cell malignancies by inhibiting IL-11 signaling. Proc Natl Acad Sci U S A 2013; 110:20599-604. [PMID: 24297922 DOI: 10.1073/pnas.1319665110] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The Lnk (Sh2b3) adaptor protein dampens the response of hematopoietic stem cells and progenitors (HSPCs) to a variety of cytokines by inhibiting JAK2 signaling. As a consequence, Lnk(-/-) mice develop hematopoietic hyperplasia, which progresses to a phenotype resembling the nonacute phase of myeloproliferative neoplasm. In addition, Lnk mutations have been identified in human myeloproliferative neoplasms and acute leukemia. We find that Lnk suppresses the development of radiation-induced acute B-cell malignancies in mice. Lnk-deficient HSPCs recover more effectively from irradiation than their wild-type counterparts, and this resistance of Lnk(-/-) HSPCs to radiation underlies the subsequent emergence of leukemia. A search for the mechanism responsible for radiation resistance identified the cytokine IL-11 as being critical for the ability of Lnk(-/-) HSPCs to recover from irradiation and subsequently become leukemic. In IL-11 signaling, wild-type Lnk suppresses tyrosine phosphorylation of the Src homology region 2 domain-containing phosphatase-2/protein tyrosine phosphatase nonreceptor type 11 and its association with the growth factor receptor-bound protein 2, as well as activation of the Erk MAP kinase pathway. Indeed, Src homology region 2 domain-containing phosphatase-2 has a binding motif for the Lnk Src Homology 2 domain that is phosphorylated in response to IL-11 stimulation. IL-11 therefore drives a pathway that enhances HSPC radioresistance and radiation-induced B-cell malignancies, but is normally attenuated by the inhibitory adaptor Lnk.
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Müller PJ, Rigbolt KTG, Paterok D, Piehler J, Vanselow J, Lasonder E, Andersen JS, Schaper F, Sobota RM. Protein tyrosine phosphatase SHP2/PTPN11 mistargeting as a consequence of SH2-domain point mutations associated with Noonan Syndrome and leukemia. J Proteomics 2013; 84:132-47. [PMID: 23584145 DOI: 10.1016/j.jprot.2013.04.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 04/02/2013] [Accepted: 04/04/2013] [Indexed: 11/25/2022]
Abstract
UNLABELLED SHP2/PTPN11 is a key regulator of cytokine, growth factor and integrin signaling. SHP2 influences cell survival, proliferation and differentiation by regulating major signaling pathways. Mutations in PTPN11 cause severe diseases like Noonan, LEOPARD syndrome or leukemia. Whereas several of these mutations result in altered enzymatic activity due to impaired auto-inhibition, not all disease patterns can be explained by this mechanism. In this study we analyzed altered binding properties of disease-related SHP2-mutants bearing point mutations within the SH2-domain (T42A, E139D, and R138Q). Mutants were chosen according to SPR assays, which revealed different binding properties of mutated SH2 towards phosphorylated receptor peptides. To analyze global changes in mutant binding properties we applied quantitative mass spectrometry (SILAC). Using an in vitro approach we identified overall more than 1000 protein candidates, which specifically bind to the SH2-domain of SHP2. We discovered that mutations in the SH2-domain selectively affected protein enrichment by altering the binding capacity of the SH2-domain. Mutation-dependent, enhanced or reduced exposure of SHP2 to its binding partners could have an impact on the dynamics of signaling networks. Thus, disease-associated mutants of SHP2 should not only be discussed in the context of deregulated auto-inhibition but also with respect to deregulated protein targeting of the SHP2 mutants. BIOLOGICAL SIGNIFICANCE Using quantitative mass spectrometry based proteomics we provided evidence that disease related mutations in SHP2 domains of SHP2 are able to influence SHP2 recruitment to its targets in mutation dependent manner. We discovered that mutations in the SH2-domain selectively affected protein enrichment ratios suggesting altered binding properties of the SH2-domain. We demonstrated that mutations within SHP2, which had been attributed to affect the enzymatic activity (i.e. affect the open/close status of SHP2), also differ in respect to binding properties. Our study indicates that SHP2 mutations need to be discussed not only in terms of deregulated auto-inhibition but also with respect to deregulated protein targeting properties of the SHP2 mutants. Discovery of the new binding partners for disease-related SHP2 mutants might provide a fruitful foundation for developing strategies targeting Noonan-associated leukemia.
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Affiliation(s)
- Pia J Müller
- Department of Biochemistry, RWTH Aachen University, Pauwelsstrasse 30, D-52074 Aachen, Germany
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