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Rodríguez-Martín M, Báez-Flores J, Ribes V, Isidoro-García M, Lacal J, Prieto-Matos P. Non-Mammalian Models for Understanding Neurological Defects in RASopathies. Biomedicines 2024; 12:841. [PMID: 38672195 PMCID: PMC11048513 DOI: 10.3390/biomedicines12040841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/27/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
RASopathies, a group of neurodevelopmental congenital disorders stemming from mutations in the RAS/MAPK pathway, present a unique opportunity to delve into the intricacies of complex neurological disorders. Afflicting approximately one in a thousand newborns, RASopathies manifest as abnormalities across multiple organ systems, with a pronounced impact on the central and peripheral nervous system. In the pursuit of understanding RASopathies' neurobiology and establishing phenotype-genotype relationships, in vivo non-mammalian models have emerged as indispensable tools. Species such as Danio rerio, Drosophila melanogaster, Caenorhabditis elegans, Xenopus species and Gallus gallus embryos have proven to be invaluable in shedding light on the intricate pathways implicated in RASopathies. Despite some inherent weaknesses, these genetic models offer distinct advantages over traditional rodent models, providing a holistic perspective on complex genetics, multi-organ involvement, and the interplay among various pathway components, offering insights into the pathophysiological aspects of mutations-driven symptoms. This review underscores the value of investigating the genetic basis of RASopathies for unraveling the underlying mechanisms contributing to broader neurological complexities. It also emphasizes the pivotal role of non-mammalian models in serving as a crucial preliminary step for the development of innovative therapeutic strategies.
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Affiliation(s)
- Mario Rodríguez-Martín
- Laboratory of Functional Genetics of Rare Diseases, Department of Microbiology and Genetics, University of Salamanca, 37007 Salamanca, Spain; (M.R.-M.); (J.B.-F.)
- Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain; (M.I.-G.); (P.P.-M.)
| | - Juan Báez-Flores
- Laboratory of Functional Genetics of Rare Diseases, Department of Microbiology and Genetics, University of Salamanca, 37007 Salamanca, Spain; (M.R.-M.); (J.B.-F.)
- Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain; (M.I.-G.); (P.P.-M.)
| | - Vanessa Ribes
- Institut Jacques Monod, Université Paris Cité, CNRS, F-75013 Paris, France;
| | - María Isidoro-García
- Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain; (M.I.-G.); (P.P.-M.)
- Clinical Biochemistry Department, Hospital Universitario de Salamanca, 37007 Salamanca, Spain
- Clinical Rare Diseases Reference Unit DiERCyL, 37007 Castilla y León, Spain
- Department of Medicine, University of Salamanca, 37007 Salamanca, Spain
| | - Jesus Lacal
- Laboratory of Functional Genetics of Rare Diseases, Department of Microbiology and Genetics, University of Salamanca, 37007 Salamanca, Spain; (M.R.-M.); (J.B.-F.)
- Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain; (M.I.-G.); (P.P.-M.)
| | - Pablo Prieto-Matos
- Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain; (M.I.-G.); (P.P.-M.)
- Clinical Rare Diseases Reference Unit DiERCyL, 37007 Castilla y León, Spain
- Department of Pediatrics, Hospital Universitario de Salamanca, 37007 Salamanca, Spain
- Department of Biomedical and Diagnostics Science, University of Salamanca, 37007 Salamanca, Spain
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2
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Fasano G, Petrini S, Bonavolontà V, Paradisi G, Pedalino C, Tartaglia M, Lauri A. Assessment of the FRET-based Teen sensor to monitor ERK activation changes preceding morphological defects in a RASopathy zebrafish model and phenotypic rescue by MEK inhibitor. Mol Med 2024; 30:47. [PMID: 38594640 PMCID: PMC11005195 DOI: 10.1186/s10020-024-00807-w] [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: 09/15/2023] [Accepted: 03/12/2024] [Indexed: 04/11/2024] Open
Abstract
BACKGROUND RASopathies are genetic syndromes affecting development and having variable cancer predisposition. These disorders are clinically related and are caused by germline mutations affecting key players and regulators of the RAS-MAPK signaling pathway generally leading to an upregulated ERK activity. Gain-of-function (GOF) mutations in PTPN11, encoding SHP2, a cytosolic protein tyrosine phosphatase positively controlling RAS function, underlie approximately 50% of Noonan syndromes (NS), the most common RASopathy. A different class of these activating mutations occurs as somatic events in childhood leukemias. METHOD Here, we evaluated the application of a FRET-based zebrafish ERK reporter, Teen, and used quantitative FRET protocols to monitor non-physiological RASopathy-associated changes in ERK activation. In a multi-level experimental workflow, we tested the suitability of the Teen reporter to detect pan-embryo ERK activity correlates of morphometric alterations driven by the NS-causing Shp2D61G allele. RESULTS Spectral unmixing- and acceptor photobleaching (AB)-FRET analyses captured pathological ERK activity preceding the manifestation of quantifiable body axes defects, a morphological pillar used to test the strength of SHP2 GoF mutations. Last, the work shows that by multi-modal FRET analysis, we can quantitatively trace back the modulation of ERK phosphorylation obtained by low-dose MEK inhibitor treatment to early development, before the onset of morphological defects. CONCLUSION This work proves the usefulness of FRET imaging protocols on both live and fixed Teen ERK reporter fish to readily monitor and quantify pharmacologically- and genetically-induced ERK activity modulations in early embryos, representing a useful tool in pre-clinical applications targeting RAS-MAPK signaling.
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Affiliation(s)
- Giulia Fasano
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, 00146, Italy
| | - Stefania Petrini
- Microscopy facility, Research laboratories, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, 00146, Italy
| | - Valeria Bonavolontà
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, 00146, Italy
| | - Graziamaria Paradisi
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, 00146, Italy
- Department for Innovation in Biological Agro-food and Forest systems (DIBAF), University of Tuscia, Viterbo, 01100, Italy
| | - Catia Pedalino
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, 00146, Italy
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, 00146, Italy.
| | - Antonella Lauri
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, 00146, Italy.
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3
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Ram A, Murphy D, DeCuzzi N, Patankar M, Hu J, Pargett M, Albeck JG. A guide to ERK dynamics, part 2: downstream decoding. Biochem J 2023; 480:1909-1928. [PMID: 38038975 PMCID: PMC10754290 DOI: 10.1042/bcj20230277] [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: 07/09/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 12/02/2023]
Abstract
Signaling by the extracellular signal-regulated kinase (ERK) pathway controls many cellular processes, including cell division, death, and differentiation. In this second installment of a two-part review, we address the question of how the ERK pathway exerts distinct and context-specific effects on multiple processes. We discuss how the dynamics of ERK activity induce selective changes in gene expression programs, with insights from both experiments and computational models. With a focus on single-cell biosensor-based studies, we summarize four major functional modes for ERK signaling in tissues: adjusting the size of cell populations, gradient-based patterning, wave propagation of morphological changes, and diversification of cellular gene expression states. These modes of operation are disrupted in cancer and other related diseases and represent potential targets for therapeutic intervention. By understanding the dynamic mechanisms involved in ERK signaling, there is potential for pharmacological strategies that not only simply inhibit ERK, but also restore functional activity patterns and improve disease outcomes.
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Affiliation(s)
- Abhineet Ram
- Department of Molecular and Cellular Biology, University of California, Davis, CA, U.S.A
| | - Devan Murphy
- Department of Molecular and Cellular Biology, University of California, Davis, CA, U.S.A
| | - Nicholaus DeCuzzi
- Department of Molecular and Cellular Biology, University of California, Davis, CA, U.S.A
| | - Madhura Patankar
- Department of Molecular and Cellular Biology, University of California, Davis, CA, U.S.A
| | - Jason Hu
- Department of Molecular and Cellular Biology, University of California, Davis, CA, U.S.A
| | - Michael Pargett
- Department of Molecular and Cellular Biology, University of California, Davis, CA, U.S.A
| | - John G. Albeck
- Department of Molecular and Cellular Biology, University of California, Davis, CA, U.S.A
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4
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Patil K, Wang Y, Chen Z, Suresh K, Radhakrishnan R. Activating mutations drive human MEK1 kinase using a gear-shifting mechanism. Biochem J 2023; 480:1733-1751. [PMID: 37869794 PMCID: PMC10872882 DOI: 10.1042/bcj20230281] [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: 07/11/2023] [Revised: 09/30/2023] [Accepted: 10/20/2023] [Indexed: 10/24/2023]
Abstract
There is an unmet need to classify cancer-promoting kinase mutations in a mechanistically cognizant way. The challenge is to understand how mutations stabilize different kinase configurations to alter function, and how this influences pathogenic potential of the kinase and its responses to therapeutic inhibitors. This goal is made more challenging by the complexity of the mutational landscape of diseases, and is further compounded by the conformational plasticity of each variant where multiple conformations coexist. We focus here on the human MEK1 kinase, a vital component of the RAS/MAPK pathway in which mutations cause cancers and developmental disorders called RASopathies. We sought to explore how these mutations alter the human MEK1 kinase at atomic resolution by utilizing enhanced sampling simulations and free energy calculations. We computationally mapped the different conformational stabilities of individual mutated systems by delineating the free energy landscapes, and showed how this relates directly to experimentally quantified developmental transformation potentials of the mutations. We conclude that mutations leverage variations in the hydrogen bonding network associated with the conformational plasticity to progressively stabilize the active-like conformational state of the kinase while destabilizing the inactive-like state. The mutations alter residue-level internal molecular correlations by differentially prioritizing different conformational states, delineating the various modes of MEK1 activation reminiscent of a gear-shifting mechanism. We define the molecular basis of conversion of this kinase from its inactive to its active state, connecting structure, dynamics, and function by delineating the energy landscape and conformational plasticity, thus augmenting our understanding of MEK1 regulation.
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Affiliation(s)
- Keshav Patil
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA, U.S.A
| | - Yiming Wang
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA, U.S.A
| | - Zhangtao Chen
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, U.S.A
| | - Krishna Suresh
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, U.S.A
| | - Ravi Radhakrishnan
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA, U.S.A
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, U.S.A
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5
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Shvartsman SY, McFann S, Wühr M, Rubinstein BY. Phase plane dynamics of ERK phosphorylation. J Biol Chem 2023; 299:105234. [PMID: 37690685 PMCID: PMC10616409 DOI: 10.1016/j.jbc.2023.105234] [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: 01/23/2023] [Revised: 08/27/2023] [Accepted: 08/29/2023] [Indexed: 09/12/2023] Open
Abstract
The extracellular signal-regulated kinase (ERK) controls multiple critical processes in the cell and is deregulated in human cancers, congenital abnormalities, immune diseases, and neurodevelopmental syndromes. Catalytic activity of ERK requires dual phosphorylation by an upstream kinase, in a mechanism that can be described by two sequential Michaelis-Menten steps. The estimation of individual reaction rate constants from kinetic data in the full mechanism has proved challenging. Here, we present an analytically tractable approach to parameter estimation that is based on the phase plane representation of ERK activation and yields two combinations of six reaction rate constants in the detailed mechanism. These combinations correspond to the ratio of the specificities of two consecutive phosphorylations and the probability that monophosphorylated substrate does not dissociate from the enzyme before the second phosphorylation. The presented approach offers a language for comparing the effects of mutations that disrupt ERK activation and function in vivo. As an illustration, we use phase plane representation to analyze dual phosphorylation under heterozygous conditions, when two enzyme variants compete for the same substrate.
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Affiliation(s)
- Stanislav Y Shvartsman
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA; Center for Computational Biology, Flatiron Institute, New York, New York, USA.
| | - Sarah McFann
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA; Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, USA
| | - Martin Wühr
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
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6
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Zhang L, Zhou J. Zebrafish: A smart tool for heart disease research. JOURNAL OF FISH BIOLOGY 2023. [PMID: 37824489 DOI: 10.1111/jfb.15585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 09/07/2023] [Accepted: 10/09/2023] [Indexed: 10/14/2023]
Abstract
The increasing prevalence of heart disease poses a significant threat to human survival and safety. However, the current treatments available for heart disease are quite limited. Therefore, it is of great importance to utilize suitable animal models that can accurately simulate the physiological characteristics of heart disease. This would help improve our understanding of this disease and aid in the development of new treatment methods and drugs. Zebrafish hearts not only exhibit similarities to mammalian hearts, but they also share ~70% of homologous genes with humans. Utilizing zebrafish as an alternative to costly and time-consuming mammalian models offers numerous advantages. Zebrafish models can be easily established and maintained, and compound screening and genetic methods allow for the creation of various economical and easily controlled zebrafish and zebrafish embryonic heart disease models in a short period of time. Consequently, zebrafish have become a powerful tool for exploring the pathological mechanisms of heart disease and identifying new effective genes. In this review, we summarize recent studies on different zebrafish models of heart disease. We also describe the techniques and protocols used to develop zebrafish models of myocardial infarction, heart failure, and congenital heart disease, including surgical procedures, forward and reverse genetics, as well as drug and combination screening. This review aims to promote the utilization of zebrafish models in investigating diverse pathological mechanisms of heart disease, enhancing our knowledge and comprehension of heart disease, and offering novel insights and objectives for exploring the prevention and treatment of heart disease.
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Affiliation(s)
- Lantian Zhang
- Education Branch, Chongqing Publishing Group, Chongqing, China
| | - Jinrun Zhou
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Science, Shandong University, Qingdao, China
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7
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Andrianova EP, Marmion RA, Shvartsman SY, Zhulin IB. Evolutionary history of MEK1 illuminates the nature of deleterious mutations. Proc Natl Acad Sci U S A 2023; 120:e2304184120. [PMID: 37579140 PMCID: PMC10450672 DOI: 10.1073/pnas.2304184120] [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: 03/13/2023] [Accepted: 07/24/2023] [Indexed: 08/16/2023] Open
Abstract
Mutations in signal transduction pathways lead to various diseases including cancers. MEK1 kinase, encoded by the human MAP2K1 gene, is one of the central components of the MAPK pathway and more than a hundred somatic mutations in the MAP2K1 gene were identified in various tumors. Germline mutations deregulating MEK1 also lead to congenital abnormalities, such as the cardiofaciocutaneous syndrome and arteriovenous malformation. Evaluating variants associated with a disease is a challenge, and computational genomic approaches aid in this process. Establishing evolutionary history of a gene improves computational prediction of disease-causing mutations; however, the evolutionary history of MEK1 is not well understood. Here, by revealing a precise evolutionary history of MEK1, we construct a well-defined dataset of MEK1 metazoan orthologs, which provides sufficient depth to distinguish between conserved and variable amino acid positions. We matched known and predicted disease-causing and benign mutations to evolutionary changes observed in corresponding amino acid positions and found that all known and many suspected disease-causing mutations are evolutionarily intolerable. We selected several variants that cannot be unambiguously assessed by automated prediction tools but that are confidently identified as "damaging" by our approach, for experimental validation in Drosophila. In all cases, evolutionary intolerant variants caused increased mortality and severe defects in fruit fly embryos confirming their damaging nature. We anticipate that our analysis will serve as a blueprint to help evaluate known and novel missense variants in MEK1 and that our approach will contribute to improving automated tools for disease-associated variant interpretation.
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Affiliation(s)
- Ekaterina P. Andrianova
- Department of Microbiology, The Ohio State University, Columbus, OH43210
- Translational Data Analytics Institute, The Ohio State University, Columbus, OH43210
| | - Robert A. Marmion
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ08544
| | - Stanislav Y. Shvartsman
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ08544
- Department of Molecular Biology, Princeton University, Princeton, NJ08544
- Flatiron Institute, Simons Foundation, New York, NY10010
| | - Igor B. Zhulin
- Department of Microbiology, The Ohio State University, Columbus, OH43210
- Translational Data Analytics Institute, The Ohio State University, Columbus, OH43210
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8
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Brown W, Wesalo J, Samanta S, Luo J, Caldwell SE, Tsang M, Deiters A. Genetically Encoded Aminocoumarin Lysine for Optical Control of Protein-Nucleotide Interactions in Zebrafish Embryos. ACS Chem Biol 2023; 18:1305-1314. [PMID: 37272594 PMCID: PMC10278064 DOI: 10.1021/acschembio.3c00028] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 05/17/2023] [Indexed: 06/06/2023]
Abstract
The strategic placement of unnatural amino acids into the active site of kinases and phosphatases has allowed for the generation of photocaged signaling proteins that offer spatiotemporal control over activation of these pathways through precise light exposure. However, deploying this technology to study cell signaling in the context of embryo development has been limited. The promise of optical control is especially useful in the early stages of an embryo where development is driven by tightly orchestrated signaling events. Here, we demonstrate light-induced activation of Protein Kinase A and a RASopathy mutant of NRAS in the zebrafish embryo using a new light-activated amino acid. We applied this approach to gain insight into the roles of these proteins in gastrulation and heart development and forge a path for further investigation of RASopathy mutant proteins in animals.
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Affiliation(s)
- Wes Brown
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Joshua Wesalo
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Subhas Samanta
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Ji Luo
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Steven E. Caldwell
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Michael Tsang
- Department
of Developmental Biology, University of
Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Alexander Deiters
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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9
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Patterson V, Ullah F, Bryant L, Griffin JN, Sidhu A, Saliganan S, Blaile M, Saenz MS, Smith R, Ellingwood S, Grange DK, Hu X, Mireguli M, Luo Y, Shen Y, Mulhern M, Zackai E, Ritter A, Izumi K, Hoefele J, Wagner M, Riedhammer KM, Seitz B, Robin NH, Goodloe D, Mignot C, Keren B, Cox H, Jarvis J, Hempel M, Gibson CF, Tran Mau-Them F, Vitobello A, Bruel AL, Sorlin A, Mehta S, Raymond FL, Gilmore K, Powell BC, Weck K, Li C, Vulto-van Silfhout AT, Giacomini T, Mancardi MM, Accogli A, Salpietro V, Zara F, Vora NL, Davis EE, Burdine R, Bhoj E. Abrogation of MAP4K4 protein function causes congenital anomalies in humans and zebrafish. SCIENCE ADVANCES 2023; 9:eade0631. [PMID: 37126546 PMCID: PMC10132768 DOI: 10.1126/sciadv.ade0631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 03/24/2023] [Indexed: 05/03/2023]
Abstract
We report 21 families displaying neurodevelopmental differences and multiple congenital anomalies while bearing a series of rare variants in mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4). MAP4K4 has been implicated in many signaling pathways including c-Jun N-terminal and RAS kinases and is currently under investigation as a druggable target for multiple disorders. Using several zebrafish models, we demonstrate that these human variants are either loss-of-function or dominant-negative alleles and show that decreasing Map4k4 activity causes developmental defects. Furthermore, MAP4K4 can restrain hyperactive RAS signaling in early embryonic stages. Together, our data demonstrate that MAP4K4 negatively regulates RAS signaling in the early embryo and that variants identified in affected humans abrogate its function, establishing MAP4K4 as a causal locus for individuals with syndromic neurodevelopmental differences.
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Affiliation(s)
- Victoria Patterson
- Princeton University, Princeton, NJ 08544, USA
- Department of Biology, University of York, York, UK
| | - Farid Ullah
- Stanley Manne Children’s Research Institute, Ann & Robert H. Lurie Children’s Hospital of Chicago, Departments of Pediatrics and Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Laura Bryant
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - John N. Griffin
- University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Alpa Sidhu
- The Stead Family Department of Pediatrics, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA
| | | | - Mackenzie Blaile
- University of Colorado Anschutz Medical Campus, 13001 E 17th Pl, Aurora, CO 80045, USA
| | - Margarita S. Saenz
- University of Colorado Anschutz Medical Campus, 13001 E 17th Pl, Aurora, CO 80045, USA
| | - Rosemarie Smith
- Maine Medical Center, 22 Bramhall St, Portland, ME 04102, USA
| | - Sara Ellingwood
- Maine Medical Center, 22 Bramhall St, Portland, ME 04102, USA
| | - Dorothy K. Grange
- St. Louis Children’s Hospital, Washington University School of Medicine, 660 S Euclid Ave, St. Louis, MO 63110, USA
| | - Xuyun Hu
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, MOE Key Laboratory of Major Diseases in Children, Genetics and Birth Defects Control Center, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Maimaiti Mireguli
- First Affiliated Hospital of Xinjiang Medical University, Department of Pediatrics, Xinjiang Uygur Autonomous Region, China
| | - Yanfei Luo
- First Affiliated Hospital of Xinjiang Medical University, Department of Pediatrics, Xinjiang Uygur Autonomous Region, China
| | - Yiping Shen
- Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Maternal and Child Care Hospital of Guangxi Zhuang Autonomous Region, Guangxi, Nanning, China
| | - Maureen Mulhern
- Columbia University Irving Medical Center, 630 W. 168th St, New York, NY 10032, USA
| | - Elaine Zackai
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alyssa Ritter
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kosaki Izumi
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Julia Hoefele
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Matias Wagner
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Pediatrics, Division of Pediatric Neurology, Developmental Medicine and Social Pediatrics, University Hospital of Munich, Ludwig Maximilians University, Munich, Germany
| | - Korbinian M. Riedhammer
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Department of Nephrology, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | | | - Nathaniel H. Robin
- University of Alabama at Birmingham, 1720 University Blvd, Birmingham, AL 35233, USA
| | - Dana Goodloe
- University of Alabama at Birmingham, 1720 University Blvd, Birmingham, AL 35233, USA
| | - Cyril Mignot
- APHP-Sorbonne Université, GH Pitié-Salpêtrière, Paris, France
| | - Boris Keren
- Clinical Genetics Unit, Birmingham Women’s and Children’s NHS Foundation Trust, Mindelsohn Way, Birmingham B15 2TG, UK
| | - Helen Cox
- Clinical Genetics Unit, Birmingham Women’s and Children’s NHS Foundation Trust, Mindelsohn Way, Birmingham B15 2TG, UK
| | - Joanna Jarvis
- Clinical Genetics Unit, Birmingham Women’s and Children’s NHS Foundation Trust, Mindelsohn Way, Birmingham B15 2TG, UK
| | - Maja Hempel
- University Hospital Hamburg-Eppendorf, Martinistraße 52, 20251 Hamburg, Germany
| | | | | | - Antonio Vitobello
- UMR1231 GAD, Inserm, Université Bourgogne-Franche-Comté, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | | | | | | | | | - Kelly Gilmore
- Department of Ob/Gyn, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Bradford C. Powell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Karen Weck
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Chumei Li
- McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | | | - Thea Giacomini
- Unit of Child Neuropsychiatry, University of Genova, EpiCARE Network, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | | | - Andrea Accogli
- Division of Medical Genetics, Department of Medicine, McGill University Health Centre, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Vincenzo Salpietro
- Department of Biotechnological and Applied Clinical Science, University of L’Aquila, 67100 L’Aquila, Italy
| | - Federico Zara
- Department of Biotechnological and Applied Clinical Science, University of L’Aquila, 67100 L’Aquila, Italy
| | - Neeta L. Vora
- Department of Ob/Gyn, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Erica E. Davis
- Stanley Manne Children’s Research Institute, Ann & Robert H. Lurie Children’s Hospital of Chicago, Departments of Pediatrics and Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | | | - Elizabeth Bhoj
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
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10
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Marmion RA, Simpkins AG, Barrett LA, Denberg DW, Zusman S, Schottenfeld-Roames J, Schüpbach T, Shvartsman SY. Stochastic phenotypes in RAS-dependent developmental diseases. Curr Biol 2023; 33:807-816.e4. [PMID: 36706752 PMCID: PMC10026697 DOI: 10.1016/j.cub.2023.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 12/02/2022] [Accepted: 01/05/2023] [Indexed: 01/27/2023]
Abstract
Germline mutations upregulating RAS signaling are associated with multiple developmental disorders. A hallmark of these conditions is that the same mutation may present vastly different phenotypes in different individuals, even in monozygotic twins. Here, we demonstrate how the origins of such largely unexplained phenotypic variations may be dissected using highly controlled studies in Drosophila that have been gene edited to carry activating variants of MEK, a core enzyme in the RAS pathway. This allowed us to measure the small but consistent increase in signaling output of such alleles in vivo. The fraction of mutation carriers reaching adulthood was strongly reduced, but most surviving animals had normal RAS-dependent structures. We rationalize these results using a stochastic signaling model and support it by quantifying cell fate specification errors in bilaterally symmetric larval trachea, a RAS-dependent structure that allows us to isolate the effects of mutations from potential contributions of genetic modifiers and environmental differences. We propose that the small increase in signaling output shifts the distribution of phenotypes into a regime, where stochastic variation causes defects in some individuals, but not in others. Our findings shed light on phenotypic heterogeneity of developmental disorders caused by deregulated RAS signaling and offer a framework for investigating causal effects of other pathogenic alleles and mild mutations in general.
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Affiliation(s)
- Robert A Marmion
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
| | - Alison G Simpkins
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
| | - Lena A Barrett
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA.
| | - David W Denberg
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
| | - Susan Zusman
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
| | | | - Trudi Schüpbach
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
| | - Stanislav Y Shvartsman
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Flatiron Institute, Simons Foundation, New York, NY 10010, USA.
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11
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Tzen EYL, Lim JY, Cheah SM, Choo JT, Kam S, Ng ZM, Thomas B, Jamuar S, Koh AL, Tan EC. Diverse Clinical Manifestations of Cardiofaciocutaneous Syndrome Type 3 in Two Patients from South East Asia. Mol Syndromol 2023; 14:21-29. [PMID: 36777711 PMCID: PMC9911993 DOI: 10.1159/000525434] [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: 02/09/2022] [Accepted: 06/07/2022] [Indexed: 11/19/2022] Open
Abstract
Background Cardiofaciocutaneous syndrome (CFCS) is a rare genetic condition caused by mutations in BRAF, KRAS, MAP2K1, or MAP2K2. It is characterized by ectodermal abnormalities, cardiac defects, intellectual disability, and distinct craniofacial features. CFCS falls under a group of conditions caused by mutations in the RAS/MAPK pathway called RASopathies which share many features. In particular, CFCS has significant phenotypic overlaps with Costello syndrome (CS) and Noonan syndrome (NS). Objective The aim of this study was to assess the patients‧ phenotypic features for syndromic disorders and evaluate the use of molecular testing to clarify the clinical diagnosis. Method The patients were recruited for genetic testing with written informed consent. Genomic DNA from venous blood was sequenced and potential variants were identified via targeted next-generation sequencing. Their phenotypic features were compared with other CFCS cases carrying pathogenic variants in the same gene. Results and Discussion One patient had a de novo variant (c.370C>T; p.P124S) in MAP2K1 and presented with mild and typical features which do not significantly affect her quality of life. The second patient presented with severe features, including failure to thrive, feeding difficulties, epileptic spasms, septal hypertrophy, and global developmental delay, and developed chronic lung disease and sequelae from multiple infections. She had a severe disease course and severe global developmental delay. The discovery of a de novo variant (c.371C>A; p.P124Q) in MAP2K1, which had been reported in another patient with a similar phenotype, clarifies her clinical diagnosis. Her presentations add to existing reports that support expanding the CFCS phenotype to include features previously thought to be more suggestive of CS. Conclusion The genetic findings for the 2 patients affirm the use of identified gene mutations to confirm the clinical diagnosis of syndromic disorders and add to the phenotypic spectrum of CFCS.
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Affiliation(s)
- Elyn Y.-L. Tzen
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Jiin Yin Lim
- Genetics Service, KK Women‧s and Children‧s Hospital, Singapore, Singapore
| | - Sue Mei Cheah
- Complex Care Service, KK Women‧s and Children‧s Hospital, Singapore, Singapore
| | - Jonathan T.L. Choo
- Cardiology Service, KK Women‧s and Children‧s Hospital, Singapore, Singapore
| | - Sylvia Kam
- Genetics Service, KK Women‧s and Children‧s Hospital, Singapore, Singapore
| | - Zhi Min Ng
- Neurology Service, KK Women‧s and Children‧s Hospital, Singapore, Singapore
| | - Biju Thomas
- Respiratory Service, KK Women‧s and Children‧s Hospital, Singapore, Singapore
| | - Saumya Jamuar
- Genetics Service, KK Women‧s and Children‧s Hospital, Singapore, Singapore
| | - Ai Ling Koh
- Genetics Service, KK Women‧s and Children‧s Hospital, Singapore, Singapore
| | - Ene-Choo Tan
- KK Research Centre, KK Women‧s and Children‧s Hospital, Singapore, Singapore,*Ene-Choo Tan,
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12
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Zakharova V, Raykina E, Mersiyanova I, Deordieva E, Pershin D, Vedmedskia V, Rodina Y, Kuzmenko N, Maschan M, Shcherbina A. Cancer-causing MAP2K1 mutation in a mosaic patient with cardio-facio-cutaneous syndrome and immunodeficiency. Hum Mutat 2022; 43:1852-1855. [PMID: 36054331 DOI: 10.1002/humu.24463] [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: 06/09/2022] [Revised: 08/24/2022] [Accepted: 08/30/2022] [Indexed: 01/24/2023]
Abstract
RASopathies are disorders caused by germline mutations in genes that encode components of the RAS/mitogen-activated protein kinase (MAPK) pathway. These syndromes share features of developmental delay, facial dysmorphisms, and defects in various organs, as well as cancer predisposition. Somatic mutations of the same pathway are one of the primary causes of cancer. It is thought that germline cancer-causing mutations would be embryonic lethal, as a more severe phenotype was shown in Drosophila and zebrafish embryos with cancer MAP2K1 mutations than in those with RASopathy mutations. Here we report the case of a patient with RASopathy caused by a cancer-associated MAP2K1 p.Phe53Leu mutation. The postzygotic mosaic nature of this mutation could explain the patient's survival.
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Affiliation(s)
- Victorya Zakharova
- Clinical Data Analysis Department, National Medical Research Center for Endocrinology, Moscow, Russian Federation
| | - Elena Raykina
- Laboratory of Molecular Biology, Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Irina Mersiyanova
- Laboratory of Molecular Biology, Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Ekaterina Deordieva
- Department of Immunology, Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Dmitry Pershin
- Laboratory of Transplant Immunology and Immunotherapy of Hemoblastosis, Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Victorya Vedmedskia
- Laboratory of Transplant Immunology and Immunotherapy of Hemoblastosis, Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Yulia Rodina
- Department of Immunology, Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Natalia Kuzmenko
- Department of Immunology, Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Michael Maschan
- High School of Molecular and Experimental Medicine, Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Anna Shcherbina
- Department of Immunology, Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
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13
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Spencer-Smith R, Terrell EM, Insinna C, Agamasu C, Wagner ME, Ritt DA, Stauffer J, Stephen AG, Morrison DK. RASopathy mutations provide functional insight into the BRAF cysteine-rich domain and reveal the importance of autoinhibition in BRAF regulation. Mol Cell 2022; 82:4262-4276.e5. [PMID: 36347258 PMCID: PMC9677513 DOI: 10.1016/j.molcel.2022.10.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 07/16/2022] [Accepted: 10/14/2022] [Indexed: 11/09/2022]
Abstract
BRAF is frequently mutated in human cancer and the RASopathy syndromes, with RASopathy mutations often observed in the cysteine-rich domain (CRD). Although the CRD participates in phosphatidylserine (PS) binding, the RAS-RAF interaction, and RAF autoinhibition, the impact of these activities on RAF function in normal and disease states is not well characterized. Here, we analyze a panel of CRD mutations and show that they increase BRAF activity by relieving autoinhibition and/or enhancing PS binding, with relief of autoinhibition being the major factor determining mutation severity. Further, we show that CRD-mediated autoinhibition prevents the constitutive plasma membrane localization of BRAF that causes increased RAS-dependent and RAS-independent function. Comparison of the BRAF- and CRAF-CRDs also indicates that the BRAF-CRD is a stronger mediator of autoinhibition and PS binding, and given the increased catalytic activity of BRAF, our studies reveal a more critical role for CRD-mediated autoinhibition in BRAF regulation.
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Affiliation(s)
- Russell Spencer-Smith
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD 21702 USA
| | - Elizabeth M Terrell
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD 21702 USA
| | - Christine Insinna
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD 21702 USA
| | - Constance Agamasu
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702 USA
| | - Morgan E Wagner
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702 USA
| | - Daniel A Ritt
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD 21702 USA
| | - Jim Stauffer
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD 21702 USA
| | - Andrew G Stephen
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702 USA
| | - Deborah K Morrison
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD 21702 USA.
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14
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Russo I, Sartor E, Fagotto L, Colombo A, Tiso N, Alaibac M. The Zebrafish model in dermatology: an update for clinicians. Discov Oncol 2022; 13:48. [PMID: 35713744 PMCID: PMC9206045 DOI: 10.1007/s12672-022-00511-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 06/08/2022] [Indexed: 11/04/2022] Open
Abstract
Recently, the zebrafish has been established as one of the most important model organisms for medical research. Several studies have proved that there is a high level of similarity between human and zebrafish genomes, which encourages the use of zebrafish as a model for understanding human genetic disorders, including cancer. Interestingly, zebrafish skin shows several similarities to human skin, suggesting that this model organism is particularly suitable for the study of neoplastic and inflammatory skin disorders. This paper appraises the specific characteristics of zebrafish skin and describes the major applications of the zebrafish model in dermatological research.
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Affiliation(s)
- Irene Russo
- Unit of Dermatology, University of Padua, Via Gallucci 4, 35128, Padua, Italy
| | - Emma Sartor
- Unit of Dermatology, University of Padua, Via Gallucci 4, 35128, Padua, Italy
| | - Laura Fagotto
- Unit of Dermatology, University of Padua, Via Gallucci 4, 35128, Padua, Italy
| | - Anna Colombo
- Unit of Dermatology, University of Padua, Via Gallucci 4, 35128, Padua, Italy
| | - Natascia Tiso
- Department of Biology, University of Padua, Via U. Bassi 58/B, 35131, Padua, Italy
| | - Mauro Alaibac
- Unit of Dermatology, University of Padua, Via Gallucci 4, 35128, Padua, Italy.
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15
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Motta M, Solman M, Bonnard AA, Kuechler A, Pantaleoni F, Priolo M, Chandramouli B, Coppola S, Pizzi S, Zara E, Ferilli M, Kayserili H, Onesimo R, Leoni C, Brinkmann J, Vial Y, Kamphausen SB, Thomas-Teinturier C, Guimier A, Cordeddu V, Mazzanti L, Zampino G, Chillemi G, Zenker M, Cavé H, Hertog J, Tartaglia M. Expanding the molecular spectrum of pathogenic SHOC2 variants underlying Mazzanti syndrome. Hum Mol Genet 2022; 31:2766-2778. [PMID: 35348676 PMCID: PMC9402240 DOI: 10.1093/hmg/ddac071] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/15/2022] [Accepted: 03/18/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
We previously molecularly and clinically characterized Mazzanti syndrome, a RASopathy related to Noonan syndrome that is mostly caused by a single recurrent missense variant (c.4A > G, p.Ser2Gly) in SHOC2, which encodes a leucine-rich repeat (LRR)-containing protein facilitating signal flow through the RAS-mitogen-associated protein kinase (MAPK) pathway. We also documented that the pathogenic p.Ser2Gly substitution causes upregulation of MAPK signaling and constitutive targeting of SHOC2 to the plasma membrane due to the introduction of an N-myristoylation recognition motif. The almost invariant occurrence of the pathogenic c.4A > G missense change in SHOC2 is mirrored by a relatively homogeneous clinical phenotype of Mazzanti syndrome. Here we provide new data on the clinical spectrum and molecular diversity of this disorder, and functionally characterize new pathogenic variants. The clinical phenotype of six unrelated individuals carrying novel disease-causing SHOC2 variants is delineated, and public and newly collected clinical data are utilized to profile the disorder. In silico, in vitro and in vivo characterization of the newly identified variants provides evidence that the consequences of these missense changes on SHOC2 functional behavior differ from what had been observed for the canonical p.Ser2Gly change but converge towards an enhanced activation of the RAS-MAPK pathway. Our findings expand the molecular spectrum of pathogenic SHOC2 variants, provide a more accurate picture of the phenotypic expression associated with variants in this gene, and definitively establish a GoF behavior as the mechanism of disease.
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Affiliation(s)
- Marialetizia Motta
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Maja Solman
- Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Adeline A Bonnard
- Assistance Publique des Hôpitaux de Paris (AP-HP), Hôpital Robert Debré, Département de Génétique, 75019 Paris, France
- INSERM UMR 1131, Institut de Recherche Saint-Louis, Université de Paris, 75010 Paris, France
| | - Alma Kuechler
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, 45147 Essen, Germany
| | - Francesca Pantaleoni
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Manuela Priolo
- UOSD Genetica Medica, Grandeospedale Metropolitano “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italia
| | | | - Simona Coppola
- National Centre Rare Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Simone Pizzi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Erika Zara
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy
| | - Marco Ferilli
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Hülya Kayserili
- Genetic Diseases Evaluation Center, Medical Genetics Department, Koç University School of Medicine, 34010 İstanbul, Turkey
| | - Roberta Onesimo
- Center for Rare Diseases and Birth Defects, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168 Rome, Italy
| | - Chiara Leoni
- Center for Rare Diseases and Birth Defects, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168 Rome, Italy
| | - Julia Brinkmann
- Institute of Human Genetics, University Hospital Magdeburg, 39120 Magdeburg, Germany
| | - Yoann Vial
- Assistance Publique des Hôpitaux de Paris (AP-HP), Hôpital Robert Debré, Département de Génétique, 75019 Paris, France
- INSERM UMR 1131, Institut de Recherche Saint-Louis, Université de Paris, 75010 Paris, France
| | - Susanne B Kamphausen
- Institute of Human Genetics, University Hospital Magdeburg, 39120 Magdeburg, Germany
| | - Cécile Thomas-Teinturier
- Assistance Publique-Hôpitaux de Paris, Université Paris-Saclay, Hôpital Bicêtre, Department of Pediatric Endocrinology, 94270 Le Kremlin Bicêtre, France
- INSERM UMR 1018, Cancer and Radiation team, CESP, 94800 Villejuif, France
| | - Anne Guimier
- Service de Médecine Genomique des Maladies Rares, CRMR Anomalies du développement, Hôpital Necker-Enfants Malades, Assistance Publique des Hôpitaux de Paris, 75015 Paris, France
| | - Viviana Cordeddu
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Laura Mazzanti
- Alma Mater Studiorum, University of Bologna, 40125 Bologna, Italy
| | - Giuseppe Zampino
- Center for Rare Diseases and Birth Defects, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168 Rome, Italy
- Department of Woman and Child Health and Public Health, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Giovanni Chillemi
- Department for Innovation in Biological, Agro-food and Forest systems, Università della Tuscia, 01100 Viterbo, Italy
- Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari, Centro Nazionale delle Ricerche, 70126 Bari, Italy
| | - Martin Zenker
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, 45147 Essen, Germany
| | - Hélène Cavé
- Assistance Publique des Hôpitaux de Paris (AP-HP), Hôpital Robert Debré, Département de Génétique, 75019 Paris, France
- INSERM UMR 1131, Institut de Recherche Saint-Louis, Université de Paris, 75010 Paris, France
| | - Jeroen Hertog
- Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
- Lead contact
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16
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Barnaby W, Dorman Barclay HE, Nagarkar A, Perkins M, Teicher G, Trapani JG, Downes GB. GABAA α subunit control of hyperactive behavior in developing zebrafish. Genetics 2022; 220:6519832. [PMID: 35106556 PMCID: PMC8982038 DOI: 10.1093/genetics/iyac011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 01/03/2022] [Indexed: 02/04/2023] Open
Abstract
GABAA receptors mediate rapid responses to the neurotransmitter gamma-aminobutyric acid and are robust regulators of the brain and spinal cord neural networks that control locomotor behaviors, such as walking and swimming. In developing zebrafish, gross pharmacological blockade of these receptors causes hyperactive swimming, which is also a feature of many zebrafish epilepsy models. Although GABAA receptors are important to control locomotor behavior, the large number of subunits and homeostatic compensatory mechanisms have challenged efforts to determine subunit-selective roles. To address this issue, we mutated each of the 8 zebrafish GABAA α subunit genes individually and in pairs using a CRISPR-Cas9 somatic inactivation approach and, then, we examined the swimming behavior of the mutants at 2 developmental stages, 48 and 96 h postfertilization. We found that disrupting the expression of specific pairs of subunits resulted in different abnormalities in swimming behavior at 48 h postfertilization. Mutation of α4 and α5 selectively resulted in longer duration swimming episodes, mutations in α3 and α4 selectively caused excess, large-amplitude body flexions (C-bends), and mutation of α3 and α5 resulted in increases in both of these measures of hyperactivity. At 96 h postfertilization, hyperactive phenotypes were nearly absent, suggesting that homeostatic compensation was able to overcome the disruption of even multiple subunits. Taken together, our results identify subunit-selective roles for GABAA α3, α4, and α5 in regulating locomotion. Given that these subunits exhibit spatially restricted expression patterns, these results provide a foundation to identify neurons and GABAergic networks that control discrete aspects of locomotor behavior.
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Affiliation(s)
- Wayne Barnaby
- Neuroscience and Behavior Graduate Program, University of Massachusetts Amherst, Amherst, MA 01003, USA,Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | | | - Akanksha Nagarkar
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Matthew Perkins
- Biology Department and Neuroscience Program, Amherst College, Amherst, MA 01002, USA
| | - Gregory Teicher
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003, USA,Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Josef G Trapani
- Neuroscience and Behavior Graduate Program, University of Massachusetts Amherst, Amherst, MA 01003, USA,Biology Department and Neuroscience Program, Amherst College, Amherst, MA 01002, USA
| | - Gerald B Downes
- Neuroscience and Behavior Graduate Program, University of Massachusetts Amherst, Amherst, MA 01003, USA,Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003, USA,Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA,Corresponding author: Biology Department, Neuroscience and Behavior Graduate Program, and Molecular and Cellular Biology Graduate Program, 611 North Pleasant St., Morrill Science Center, Building 4 North, Amherst, MA 01003, USA.
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17
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Abstract
The RASopathies are a group of disorders caused by a germline mutation in one of the genes encoding a component of the RAS/MAPK pathway. These disorders, including neurofibromatosis type 1, Noonan syndrome, cardiofaciocutaneous syndrome, Costello syndrome and Legius syndrome, among others, have overlapping clinical features due to RAS/MAPK dysfunction. Although several of the RASopathies are very rare, collectively, these disorders are relatively common. In this Review, we discuss the pathogenesis of the RASopathy-associated genetic variants and the knowledge gained about RAS/MAPK signaling that resulted from studying RASopathies. We also describe the cell and animal models of the RASopathies and explore emerging RASopathy genes. Preclinical and clinical experiences with targeted agents as therapeutics for RASopathies are also discussed. Finally, we review how the recently developed drugs targeting RAS/MAPK-driven malignancies, such as inhibitors of RAS activation, direct RAS inhibitors and RAS/MAPK pathway inhibitors, might be leveraged for patients with RASopathies.
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Affiliation(s)
- Katie E Hebron
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Edjay Ralph Hernandez
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Marielle E Yohe
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
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18
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Motta M, Fasano G, Gredy S, Brinkmann J, Bonnard AA, Simsek-Kiper PO, Gulec EY, Essaddam L, Utine GE, Guarnetti Prandi I, Venditti M, Pantaleoni F, Radio FC, Ciolfi A, Petrini S, Consoli F, Vignal C, Hepbasli D, Ullrich M, de Boer E, Vissers LELM, Gritli S, Rossi C, De Luca A, Ben Becher S, Gelb BD, Dallapiccola B, Lauri A, Chillemi G, Schuh K, Cavé H, Zenker M, Tartaglia M. SPRED2 loss-of-function causes a recessive Noonan syndrome-like phenotype. Am J Hum Genet 2021; 108:2112-2129. [PMID: 34626534 DOI: 10.1016/j.ajhg.2021.09.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/14/2021] [Indexed: 12/16/2022] Open
Abstract
Upregulated signal flow through RAS and the mitogen-associated protein kinase (MAPK) cascade is the unifying mechanistic theme of the RASopathies, a family of disorders affecting development and growth. Pathogenic variants in more than 20 genes have been causally linked to RASopathies, the majority having a dominant role in promoting enhanced signaling. Here, we report that SPRED2 loss of function is causally linked to a recessive phenotype evocative of Noonan syndrome. Homozygosity for three different variants-c.187C>T (p.Arg63∗), c.299T>C (p.Leu100Pro), and c.1142_1143delTT (p.Leu381Hisfs∗95)-were identified in four subjects from three families. All variants severely affected protein stability, causing accelerated degradation, and variably perturbed SPRED2 functional behavior. When overexpressed in cells, all variants were unable to negatively modulate EGF-promoted RAF1, MEK, and ERK phosphorylation, and time-course experiments in primary fibroblasts (p.Leu100Pro and p.Leu381Hisfs∗95) documented an increased and prolonged activation of the MAPK cascade in response to EGF stimulation. Morpholino-mediated knockdown of spred2a and spred2b in zebrafish induced defects in convergence and extension cell movements indicating upregulated RAS-MAPK signaling, which were rescued by expressing wild-type SPRED2 but not the SPRED2Leu381Hisfs∗95 protein. The clinical phenotype of the four affected individuals included developmental delay, intellectual disability, cardiac defects, short stature, skeletal anomalies, and a typical facial gestalt as major features, without the occurrence of the distinctive skin signs characterizing Legius syndrome. These features, in part, characterize the phenotype of Spred2-/- mice. Our findings identify the second recessive form of Noonan syndrome and document pleiotropic consequences of SPRED2 loss of function in development.
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Affiliation(s)
- Marialetizia Motta
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Giulia Fasano
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Sina Gredy
- Institute of Physiology, University of Wuerzburg, 97070 Wuerzburg, Germany
| | - Julia Brinkmann
- Institute of Human Genetics, University Hospital Magdeburg, 39120 Magdeburg, Germany
| | - Adeline Alice Bonnard
- Assistance Publique des Hôpitaux de Paris (AP-HP), Hôpital Robert Debré, Département de Génétique, 75019 Paris, France; INSERM UMR 1131, Institut de Recherche Saint-Louis, Université de Paris, Paris, France
| | - Pelin Ozlem Simsek-Kiper
- Department of Pediatric Genetics, Hacettepe University Faculty of Medicine, Sihhiye, 06100 Ankara, Turkey
| | - Elif Yilmaz Gulec
- Department of Medical Genetics, Health Sciences University, Istanbul Kanuni Sultan Suleyman Training and Research Hospital, 34303 Istanbul, Turkey
| | - Leila Essaddam
- Department of Pediatrics-PUC, Béchir Hamza Children's Hospital, Faculty of Medicine, University of Tunis El Manar, Jebbari 1007, Tunis, Tunisia
| | - Gulen Eda Utine
- Department of Pediatric Genetics, Hacettepe University Faculty of Medicine, Sihhiye, 06100 Ankara, Turkey
| | - Ingrid Guarnetti Prandi
- Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali, Università Della Tuscia, 01100 Viterbo, Italy
| | - Martina Venditti
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Francesca Pantaleoni
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Francesca Clementina Radio
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Stefania Petrini
- Confocal Microscopy Core Facility, Ospedale Pediatrico Bambino Gesù, 00146 Rome, Italy
| | - Federica Consoli
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy
| | - Cédric Vignal
- Assistance Publique des Hôpitaux de Paris (AP-HP), Hôpital Robert Debré, Département de Génétique, 75019 Paris, France
| | - Denis Hepbasli
- Institute of Physiology, University of Wuerzburg, 97070 Wuerzburg, Germany
| | - Melanie Ullrich
- Institute of Physiology, University of Wuerzburg, 97070 Wuerzburg, Germany
| | - Elke de Boer
- Department of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Sami Gritli
- Department of Immunology, Pasteur Institute of Tunis, 1002 Tunis-Belvédère, Tunisia
| | - Cesare Rossi
- Genetica Medica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
| | - Alessandro De Luca
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy
| | - Saayda Ben Becher
- Department of Pediatrics-PUC, Béchir Hamza Children's Hospital, Faculty of Medicine, University of Tunis El Manar, Jebbari 1007, Tunis, Tunisia
| | - Bruce D Gelb
- Mindich Child Health and Development Institute and Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bruno Dallapiccola
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Antonella Lauri
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Giovanni Chillemi
- Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali, Università Della Tuscia, 01100 Viterbo, Italy; Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari, Centro Nazionale Delle Ricerche, 70126 Bari, Italy
| | - Kai Schuh
- Institute of Physiology, University of Wuerzburg, 97070 Wuerzburg, Germany
| | - Hélène Cavé
- Assistance Publique des Hôpitaux de Paris (AP-HP), Hôpital Robert Debré, Département de Génétique, 75019 Paris, France; INSERM UMR 1131, Institut de Recherche Saint-Louis, Université de Paris, Paris, France
| | - Martin Zenker
- Institute of Human Genetics, University Hospital Magdeburg, 39120 Magdeburg, Germany
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy.
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19
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Wilson P, Abdelmoti L, Norcross R, Jang ER, Palayam M, Galperin E. The role of USP7 in the Shoc2-ERK1/2 signaling axis and Noonan-like syndrome with loose anagen hair. J Cell Sci 2021; 134:272259. [PMID: 34553755 DOI: 10.1242/jcs.258922] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 09/09/2021] [Indexed: 01/04/2023] Open
Abstract
The ERK1/2 (also known as MAPK3 and MAPK1, respectively) signaling pathway is critical in organismal development and tissue morphogenesis. Deregulation of this pathway leads to congenital abnormalities with severe developmental dysmorphisms. The core ERK1/2 cascade relies on scaffold proteins, such as Shoc2 to guide and fine-tune its signals. Mutations in SHOC2 lead to the development of the pathology termed Noonan-like Syndrome with Loose Anagen Hair (NSLAH). However, the mechanisms underlying the functions of Shoc2 and its contributions to disease progression remain unclear. Here, we show that ERK1/2 pathway activation triggers the interaction of Shoc2 with the ubiquitin-specific protease USP7. We reveal that, in the Shoc2 module, USP7 functions as a molecular 'switch' that controls the E3 ligase HUWE1 and the HUWE1-induced regulatory feedback loop. We also demonstrate that disruption of Shoc2-USP7 binding leads to aberrant activation of the Shoc2-ERK1/2 axis. Importantly, our studies reveal a possible role for USP7 in the pathogenic mechanisms underlying NSLAH, thereby extending our understanding of how ubiquitin-specific proteases regulate intracellular signaling.
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Affiliation(s)
- Patricia Wilson
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Lina Abdelmoti
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Rebecca Norcross
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Eun Ryoung Jang
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Malathy Palayam
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Emilia Galperin
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
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20
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Patton EE, Zon LI, Langenau DM. Zebrafish disease models in drug discovery: from preclinical modelling to clinical trials. Nat Rev Drug Discov 2021; 20:611-628. [PMID: 34117457 PMCID: PMC9210578 DOI: 10.1038/s41573-021-00210-8] [Citation(s) in RCA: 180] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2021] [Indexed: 02/03/2023]
Abstract
Numerous drug treatments that have recently entered the clinic or clinical trials have their genesis in zebrafish. Zebrafish are well established for their contribution to developmental biology and have now emerged as a powerful preclinical model for human disease, as their disease characteristics, aetiology and progression, and molecular mechanisms are clinically relevant and highly conserved. Zebrafish respond to small molecules and drug treatments at physiologically relevant dose ranges and, when combined with cell-specific or tissue-specific reporters and gene editing technologies, drug activity can be studied at single-cell resolution within the complexity of a whole animal, across tissues and over an extended timescale. These features enable high-throughput and high-content phenotypic drug screening, repurposing of available drugs for personalized and compassionate use, and even the development of new drug classes. Often, drugs and drug leads explored in zebrafish have an inter-organ mechanism of action and would otherwise not be identified through targeted screening approaches. Here, we discuss how zebrafish is an important model for drug discovery, the process of how these discoveries emerge and future opportunities for maximizing zebrafish potential in medical discoveries.
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Affiliation(s)
- E Elizabeth Patton
- MRC Human Genetics Unit and Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Cancer, Western General Hospital Campus, University of Edinburgh, Edinburgh, UK.
| | - Leonard I Zon
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Medical School; Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Boston, MA, USA.
| | - David M Langenau
- Department of Pathology, Massachusetts General Research Institute, Boston, MA, USA.
- Center of Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA.
- Harvard Stem Cell Institute, Harvard University, Boston, MA, USA.
- Center of Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA.
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21
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Watanabe M. Introduction to the special issue on "RASopathies: Misregulation of signaling". Birth Defects Res 2021; 112:703-707. [PMID: 32558382 DOI: 10.1002/bdr2.1701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 04/18/2020] [Indexed: 11/10/2022]
Affiliation(s)
- Michiko Watanabe
- Department of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
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22
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Das TK, Gatto J, Mirmira R, Hourizadeh E, Kaufman D, Gelb BD, Cagan R. Drosophila RASopathy models identify disease subtype differences and biomarkers of drug efficacy. iScience 2021; 24:102306. [PMID: 33855281 PMCID: PMC8026909 DOI: 10.1016/j.isci.2021.102306] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 10/30/2020] [Accepted: 03/10/2021] [Indexed: 12/13/2022] Open
Abstract
RASopathies represent a family of mostly autosomal dominant diseases that are caused by missense variants in the rat sarcoma viral oncogene/mitogen activated protein kinase (RAS/MAPK) pathway including KRAS, NRAS, BRAF, RAF1, and SHP2. These variants are associated with overlapping but distinct phenotypes that affect the heart, craniofacial, skeletal, lymphatic, and nervous systems. Here, we report an analysis of 13 Drosophila transgenic lines, each expressing a different human RASopathy isoform. Similar to their human counterparts, each Drosophila line displayed common aspects but also important differences including distinct signaling pathways such as the Hippo and SAPK/JNK signaling networks. We identified multiple classes of clinically relevant drugs-including statins and histone deacetylase inhibitors-that improved viability across most RASopathy lines; in contrast, several canonical RAS pathway inhibitors proved less broadly effective. Overall, our study compares and contrasts a large number of RASopathy-associated variants including their therapeutic responses.
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Affiliation(s)
- Tirtha K. Das
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York NY, USA
- The Mindich Child Health and Development Institute, Department of Pediatrics, Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York NY, USA
| | - Jared Gatto
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York NY, USA
- The Mindich Child Health and Development Institute, Department of Pediatrics, Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York NY, USA
| | - Rupa Mirmira
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York NY, USA
| | - Ethan Hourizadeh
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York NY, USA
| | - Dalia Kaufman
- The Mindich Child Health and Development Institute, Department of Pediatrics, Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York NY, USA
| | - Bruce D. Gelb
- The Mindich Child Health and Development Institute, Department of Pediatrics, Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York NY, USA
| | - Ross Cagan
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York NY, USA
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23
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Marmion RA, Yang L, Goyal Y, Jindal GA, Wetzel JL, Singh M, Schüpbach T, Shvartsman SY. Molecular mechanisms underlying cellular effects of human MEK1 mutations. Mol Biol Cell 2021; 32:974-983. [PMID: 33476180 PMCID: PMC8108529 DOI: 10.1091/mbc.e20-10-0625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Terminal regions of Drosophila embryos are patterned by signaling through ERK, which is genetically deregulated in multiple human diseases. Quantitative studies of terminal patterning have been recently used to investigate gain-of-function variants of human MEK1, encoding the MEK kinase that directly activates ERK by dual phosphorylation. Unexpectedly, several mutations reduced ERK activation by extracellular signals, possibly through a negative feedback triggered by signal-independent activity of the mutant variants. Here we present experimental evidence supporting this model. Using a MEK variant that combines a mutation within the negative regulatory region with alanine substitutions in the activation loop, we prove that pathogenic variants indeed acquire signal-independent kinase activity. We also demonstrate that signal-dependent activation of these variants is independent of kinase suppressor of Ras, a conserved adaptor that is indispensable for activation of normal MEK. Finally, we show that attenuation of ERK activation by extracellular signals stems from transcriptional induction of Mkp3, a dual specificity phosphatase that deactivates ERK by dephosphorylation. These findings in the Drosophila embryo highlight its power for investigating diverse effects of human disease mutations.
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Affiliation(s)
- Robert A Marmion
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Liu Yang
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Yogesh Goyal
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544.,Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104
| | - Granton A Jindal
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544.,Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Joshua L Wetzel
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Department of Computer Science, Princeton University, Princeton, NJ 08540
| | - Mona Singh
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Department of Computer Science, Princeton University, Princeton, NJ 08540
| | - Trudi Schüpbach
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Stanislav Y Shvartsman
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544.,Department of Molecular Biology, Princeton University, Princeton, NJ 08544.,Flatiron Institute, Simons Foundation, New York, NY 10010
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24
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Zhang M, Jang H, Nussinov R. PI3K Driver Mutations: A Biophysical Membrane-Centric Perspective. Cancer Res 2021; 81:237-247. [PMID: 33046444 PMCID: PMC7855922 DOI: 10.1158/0008-5472.can-20-0911] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/24/2020] [Accepted: 10/07/2020] [Indexed: 11/16/2022]
Abstract
Ras activates its effectors at the membrane. Active PI3Kα and its associated kinases/phosphatases assemble at membrane regions enriched in signaling lipids. In contrast, the Raf kinase domain extends into the cytoplasm and its assembly is away from the crowded membrane surface. Our structural membrane-centric outlook underscores the spatiotemporal principles of membrane and signaling lipids, which helps clarify PI3Kα activation. Here we focus on mechanisms of activation driven by PI3Kα driver mutations, spotlighting the PI3Kα double (multiple) activating mutations. Single mutations can be potent, but double mutations are stronger: their combination is specific, a single strong driver cannot fully activate PI3K, and two weak drivers may or may not do so. In contrast, two strong drivers may successfully activate PI3K, where one, for example, H1047R, modulates membrane interactions facilitating substrate binding at the active site (km) and the other, for example, E542K and E545K, reduces the transition state barrier (ka), releasing autoinhibition by nSH2. Although mostly unidentified, weak drivers are expected to be common, so we ask here how common double mutations are likely to be and why PI3Kα with double mutations responds effectively to inhibitors. We provide a structural view of hotspot and weak driver mutations in PI3Kα activation, explain their mechanisms, compare these with mechanisms of Raf activation, and point to targeting cell-specific, chromatin-accessible, and parallel (or redundant) pathways to thwart the expected emergence of drug resistance. Collectively, our biophysical outlook delineates activation and highlights the challenges of drug resistance.
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Affiliation(s)
- Mingzhen Zhang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland
| | - Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland.
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
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25
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Pax2a is expressed in oocytes and is responsible for early development and oogenesis in zebrafish. Biochem Biophys Res Commun 2020; 533:592-599. [PMID: 32981680 DOI: 10.1016/j.bbrc.2020.09.059] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 09/15/2020] [Indexed: 11/23/2022]
Abstract
Eleven genes, including pax2a, were selected as candidate ovulation-inducing genes on the basis of microarray analysis and RNA sequencing in our previous study. The purpose of this study was to investigate the role of the pax2a gene in the ovulation-inducing process. F2 pax2a homozygous mutant zebrafish possessing a deletion of 6 nucleotides were established in this study. However, the deletion included the start codon (ATG) of the pax2a gene, and the Pax2a protein was still detected, which indicated that the deletion caused a shift in the start codon to the next ATG, resulting in a 12-amino acid deletion. F2 pax2a homozygous mutant zebrafish showed ovulation. However, the embryos showed an abnormal oval shape at the epiboly stage that resulted in yolk and tail formation abnormalities and heart edema. The surviving F3 homozygous mutants did not develop ovaries. Pax2a was detected in oocytes and eggs but not after the Prim-22 stage. It is suggested that pax2a is expressed as a maternal gene in oocytes and is necessary for oogenesis and early development.
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26
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Patterson VL, Burdine RD. Swimming toward solutions: Using fish and frogs as models for understanding RASopathies. Birth Defects Res 2020; 112:749-765. [PMID: 32506834 DOI: 10.1002/bdr2.1707] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 04/25/2020] [Indexed: 12/16/2022]
Abstract
The RAS signaling pathway regulates cell growth, survival, and differentiation, and its inappropriate activation is associated with disease in humans. The RASopathies, a set of developmental syndromes, arise when the pathway is overactive during development. Patients share a core set of symptoms, including congenital heart disease, craniofacial anomalies, and neurocognitive delay. Due to the conserved nature of the pathway, animal models are highly informative for understanding disease etiology, and zebrafish and Xenopus are emerging as advantageous model systems. Here we discuss these aquatic models of RASopathies, which recapitulate many of the core symptoms observed in patients. Craniofacial structures become dysmorphic upon expression of disease-associated mutations, resulting in wider heads. Heart defects manifest as delays in cardiac development and changes in heart size, and behavioral deficits are beginning to be explored. Furthermore, early convergence and extension defects cause elongation of developing embryos: this phenotype can be quantitatively assayed as a readout of mutation strength, raising interesting questions regarding the relationship between pathway activation and disease. Additionally, the observation that RAS signaling may be simultaneously hyperactive and attenuated suggests that downregulation of signaling may also contribute to etiology. We propose that models should be characterized using a standardized approach to allow easier comparison between models, and a better understanding of the interplay between mutation and disease presentation.
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Affiliation(s)
- Victoria L Patterson
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Rebecca D Burdine
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
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27
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Yeung E, McFann S, Marsh L, Dufresne E, Filippi S, Harrington HA, Shvartsman SY, Wühr M. Inference of Multisite Phosphorylation Rate Constants and Their Modulation by Pathogenic Mutations. Curr Biol 2020; 30:877-882.e6. [PMID: 32059766 PMCID: PMC7085240 DOI: 10.1016/j.cub.2019.12.052] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 11/03/2019] [Accepted: 12/16/2019] [Indexed: 01/03/2023]
Abstract
Multisite protein phosphorylation plays a critical role in cell regulation [1-3]. It is widely appreciated that the functional capabilities of multisite phosphorylation depend on the order and kinetics of phosphorylation steps, but kinetic aspects of multisite phosphorylation remain poorly understood [4-6]. Here, we focus on what appears to be the simplest scenario, when a protein is phosphorylated on only two sites in a strict, well-defined order. This scenario describes the activation of ERK, a highly conserved cell-signaling enzyme. We use Bayesian parameter inference in a structurally identifiable kinetic model to dissect dual phosphorylation of ERK by MEK, a kinase that is mutated in a large number of human diseases [7-12]. Our results reveal how enzyme processivity and efficiencies of individual phosphorylation steps are altered by pathogenic mutations. The presented approach, which connects specific mutations to kinetic parameters of multisite phosphorylation mechanisms, provides a systematic framework for closing the gap between studies with purified enzymes and their effects in the living organism.
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Affiliation(s)
- Eyan Yeung
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Carl Icahn Laboratory, Washington Road, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Sarah McFann
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Carl Icahn Laboratory, Washington Road, Princeton, NJ 08544, USA; Department of Chemical and Biological Engineering, Engineering Quad, Princeton University, Princeton, NJ 08544, USA
| | - Lewis Marsh
- Mathematical Institute, University of Oxford, Andrew Wiles Building, Woodstock Road, Oxford OX2 6GG, UK
| | - Emilie Dufresne
- Department of Mathematics, James College, Campus West, University of York, York YO10 5DD, UK
| | - Sarah Filippi
- Department of Epidemiology and Biostatistics, Imperial College London, Medical School Building, St Mary's Campus, Norfolk Place, London W2 1PG, UK; Department of Mathematics, South Kensington Campus, Imperial College London, London SW7 2AZ, UK
| | - Heather A Harrington
- Mathematical Institute, University of Oxford, Andrew Wiles Building, Woodstock Road, Oxford OX2 6GG, UK
| | - Stanislav Y Shvartsman
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Carl Icahn Laboratory, Washington Road, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA; Flatiron Institute, Simons Foundation, New York, NY 10010, USA.
| | - Martin Wühr
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Carl Icahn Laboratory, Washington Road, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA.
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28
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Gripp KW, Schill L, Schoyer L, Stronach B, Bennett AM, Blaser S, Brown A, Burdine R, Burkitt-Wright E, Castel P, Darilek S, Dias A, Dyer T, Ellis M, Erickson G, Gelb BD, Green T, Gross A, Ho A, Holder JL, Inoue SI, Jelin AC, Kennedy A, Klein R, Kontaridis MI, Magoulas P, McConnell DB, McCormick F, Neel BG, Prada CE, Rauen KA, Roberts A, Rodriguez-Viciana P, Rosen N, Rumbaugh G, Sablina A, Solman M, Tartaglia M, Thomas A, Timmer WC, Venkatachalam K, Walsh KS, Wolters PL, Yi JS, Zenker M, Ratner N. The sixth international RASopathies symposium: Precision medicine-From promise to practice. Am J Med Genet A 2019; 182:597-606. [PMID: 31825160 DOI: 10.1002/ajmg.a.61434] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 11/05/2019] [Indexed: 12/19/2022]
Abstract
The RASopathies are a group of genetic disorders that result from germline pathogenic variants affecting RAS-mitogen activated protein kinase (MAPK) pathway genes. RASopathies share RAS/MAPK pathway dysregulation and share phenotypic manifestations affecting numerous organ systems, causing lifelong and at times life-limiting medical complications. RASopathies may benefit from precision medicine approaches. For this reason, the Sixth International RASopathies Symposium focused on exploring precision medicine. This meeting brought together basic science researchers, clinicians, clinician scientists, patient advocates, and representatives from pharmaceutical companies and the National Institutes of Health. Novel RASopathy genes, variants, and animal models were discussed in the context of medication trials and drug development. Attempts to define and measure meaningful endpoints for treatment trials were discussed, as was drug availability to patients after trial completion.
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Affiliation(s)
- Karen W Gripp
- Al duPont Hospital for Children, Wilmington, Delaware
| | - Lisa Schill
- RASopathies Network USA, Altadena, California
| | | | | | | | - Susan Blaser
- Hospital for Sick Children, Toronto, Ontario, Canada
| | - Amanda Brown
- Noonan Syndrome Foundation, Farmington, Connecticut
| | | | - Emma Burkitt-Wright
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust and University of Manchester, Manchester, UK
| | - Pau Castel
- UCSF, Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | | | - Alwyn Dias
- Bridge Group Consulting, Morristown, New Jersey
| | - Tuesdi Dyer
- CFC International, Saint Petersburg, Florida
| | | | | | - Bruce D Gelb
- Department of Pediatrics, Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York.,Department of Genetics and Genomic Sciences, Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | | | | | - Alan Ho
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | | | | | - Annie Kennedy
- Parent Project Muscular Dystrophy, Hackensack, New Jersey
| | | | | | | | | | - Frank McCormick
- UCSF, Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - Benjamin G Neel
- Perlmutter Cancer Center and NYU School of Medicine, NYU Langone Health, New York, New York
| | - Carlos E Prada
- Cincinnati Children's Hospital Medical Center and University of Cincinnati, School of Medicine, Cincinnati, Ohio
| | - Katherine A Rauen
- Department of Pediatrics, Division of Genomic Medicine, University of California Davis, Sacramento, California
| | - Amy Roberts
- Department of Cardiology, Division of Genetics, Boston Children's Hospital, Boston, Massachusetts.,Department of Pediatrics, Division of Genetics, Boston Children's Hospital, Boston, Massachusetts
| | | | - Neal Rosen
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Anna Sablina
- VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium
| | - Maja Solman
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù-IRCCS, Rome, Italy
| | | | | | - Kartik Venkatachalam
- McGovern Medical School, University of Texas Health Science Center, Houston, Texas
| | - Karin S Walsh
- Children's National Hospital & The George Washington School of Medicine, Washington, District of Columbia
| | - Pamela L Wolters
- Pediatric Oncology Branch, National Cancer Institute, Bethesda, Maryland
| | - Jae-Sung Yi
- Yale University School of Medicine, New Haven, Connecticut
| | - Martin Zenker
- University Hospital Magdeburg, Institute of Human Genetics, Magdeburg, Germany
| | - Nancy Ratner
- Cincinnati Children's Hospital Medical Center and University of Cincinnati, School of Medicine, Cincinnati, Ohio
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29
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Abstract
Optogenetic approaches are transforming quantitative studies of cell-signaling systems. A recently developed photoswitchable mitogen-activated protein kinase kinase 1 (MEK1) enzyme (psMEK) short-circuits the highly conserved Extracellular Signal-Regulated Kinase (ERK)-signaling cascade at the most proximal step of effector kinase activation. However, since this optogenetic tool relies on phosphorylation-mimicking substitutions in the activation loop of MEK, its catalytic activity is predicted to be substantially lower than that of wild-type MEK that has been phosphorylated at these residues. Here, we present evidence that psMEK indeed has suboptimal functionality in vivo and propose a strategy to circumvent this limitation by harnessing gain-of-function, destabilizing mutations in MEK. Specifically, we demonstrate that combining phosphomimetic mutations with additional mutations in MEK, chosen for their activating potential, restores maximal kinase activity in vitro. We establish that this modification can be tuned by the choice of the destabilizing mutation and does not interfere with reversible activation of psMEK in vivo in both Drosophila and zebrafish. To illustrate the types of perturbations enabled by optimized psMEK, we use it to deliver pulses of ERK activation during zebrafish embryogenesis, revealing rheostat-like responses of an ERK-dependent morphogenetic event.
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30
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Nissim S, Leshchiner I, Mancias JD, Greenblatt MB, Maertens O, Cassa CA, Rosenfeld JA, Cox AG, Hedgepeth J, Wucherpfennig JI, Kim AJ, Henderson JE, Gonyo P, Brandt A, Lorimer E, Unger B, Prokop JW, Heidel JR, Wang XX, Ukaegbu CI, Jennings BC, Paulo JA, Gableske S, Fierke CA, Getz G, Sunyaev SR, Wade Harper J, Cichowski K, Kimmelman AC, Houvras Y, Syngal S, Williams C, Goessling W. Mutations in RABL3 alter KRAS prenylation and are associated with hereditary pancreatic cancer. Nat Genet 2019; 51:1308-1314. [PMID: 31406347 DOI: 10.1038/s41588-019-0475-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 07/01/2019] [Indexed: 12/16/2022]
Abstract
Pancreatic ductal adenocarcinoma is an aggressive cancer with limited treatment options1. Approximately 10% of cases exhibit familial predisposition, but causative genes are not known in most families2. We perform whole-genome sequence analysis in a family with multiple cases of pancreatic ductal adenocarcinoma and identify a germline truncating mutation in the member of the RAS oncogene family-like 3 (RABL3) gene. Heterozygous rabl3 mutant zebrafish show increased susceptibility to cancer formation. Transcriptomic and mass spectrometry approaches implicate RABL3 in RAS pathway regulation and identify an interaction with RAP1GDS1 (SmgGDS), a chaperone regulating prenylation of RAS GTPases3. Indeed, the truncated mutant RABL3 protein accelerates KRAS prenylation and requires RAS proteins to promote cell proliferation. Finally, evidence in patient cohorts with developmental disorders implicates germline RABL3 mutations in RASopathy syndromes. Our studies identify RABL3 mutations as a target for genetic testing in cancer families and uncover a mechanism for dysregulated RAS activity in development and cancer.
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Affiliation(s)
- Sahar Nissim
- Gastroenterology Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Dana-Farber Cancer Institute, Boston, MA, USA.,Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA, USA
| | - Ignaty Leshchiner
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,The Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joseph D Mancias
- Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Matthew B Greenblatt
- Department of Pathology and Laboratory Medicine and the Hospital for Special Surgery, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Ophélia Maertens
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Christopher A Cassa
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jill A Rosenfeld
- The Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Andrew G Cox
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, Australia
| | - John Hedgepeth
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Julia I Wucherpfennig
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Andrew J Kim
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jake E Henderson
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Patrick Gonyo
- Cancer Center and Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Anthony Brandt
- Cancer Center and Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Ellen Lorimer
- Cancer Center and Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Bethany Unger
- Cancer Center and Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jeremy W Prokop
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jerry R Heidel
- Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | | | | | | | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | | | - Carol A Fierke
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Gad Getz
- The Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Cancer Center and Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Shamil R Sunyaev
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Karen Cichowski
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alec C Kimmelman
- Department of Radiation Oncology, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Yariv Houvras
- Weill Cornell Medical College and New York Presbyterian Hospital, New York, NY, USA
| | - Sapna Syngal
- Gastroenterology Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Dana-Farber Cancer Institute, Boston, MA, USA
| | - Carol Williams
- Cancer Center and Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Wolfram Goessling
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. .,Dana-Farber Cancer Institute, Boston, MA, USA. .,Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA, USA. .,The Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Harvard Stem Cell Institute, Cambridge, MA, USA. .,Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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31
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Holter MC, Hewitt LT, Koebele SV, Judd JM, Xing L, Bimonte-Nelson HA, Conrad CD, Araki T, Neel BG, Snider WD, Newbern JM. The Noonan Syndrome-linked Raf1L613V mutation drives increased glial number in the mouse cortex and enhanced learning. PLoS Genet 2019; 15:e1008108. [PMID: 31017896 PMCID: PMC6502435 DOI: 10.1371/journal.pgen.1008108] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 05/06/2019] [Accepted: 03/22/2019] [Indexed: 12/19/2022] Open
Abstract
RASopathies are a family of related syndromes caused by mutations in regulators of the RAS/Extracellular Regulated Kinase 1/2 (ERK1/2) signaling cascade that often result in neurological deficits. RASopathy mutations in upstream regulatory components, such as NF1, PTPN11/SHP2, and RAS have been well-characterized, but mutation-specific differences in the pathogenesis of nervous system abnormalities remain poorly understood, especially those involving mutations downstream of RAS. Here, we assessed cellular and behavioral phenotypes in mice expressing a Raf1L613V gain-of-function mutation associated with the RASopathy, Noonan Syndrome. We report that Raf1L613V/wt mutants do not exhibit a significantly altered number of excitatory or inhibitory neurons in the cortex. However, we observed a significant increase in the number of specific glial subtypes in the forebrain. The density of GFAP+ astrocytes was significantly increased in the adult Raf1L613V/wt cortex and hippocampus relative to controls. OLIG2+ oligodendrocyte progenitor cells were also increased in number in mutant cortices, but we detected no significant change in myelination. Behavioral analyses revealed no significant changes in voluntary locomotor activity, anxiety-like behavior, or sociability. Surprisingly, Raf1L613V/wt mice performed better than controls in select aspects of the water radial-arm maze, Morris water maze, and cued fear conditioning tasks. Overall, these data show that increased astrocyte and oligodendrocyte progenitor cell (OPC) density in the cortex coincides with enhanced cognition in Raf1L613V/wt mutants and further highlight the distinct effects of RASopathy mutations on nervous system development and function. The RASopathies are a large and complex family of syndromes caused by mutations in the RAS/MAPK signaling cascade with no known cure. Individuals with these syndromes often present with heart defects, craniofacial differences, and neurological abnormalities, such as developmental delay, cognitive changes, epilepsy, and an increased risk of autism. However, there is wide variation in the extent of intellectual ability between individuals. It is currently unclear how different RASopathy mutations affect brain development. Here, we describe the cellular and behavioral consequences of a mutation in a gene called Raf1 that is associated with a common RASopathy, Noonan Syndrome. We find that mice harboring a mutation in Raf1 show moderate increases in the number of two subsets of glial cells, which is also observed in a number of other RASopathy brain samples. Surprisingly, we found that Raf1 mutant mice show improved performance in several learning and memory tasks. Our work highlights potential mutation-specific changes in RASopathy brain function and helps set the framework for future personalized therapeutic approaches.
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Affiliation(s)
- Michael C. Holter
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Lauren. T. Hewitt
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Stephanie V. Koebele
- Department of Psychology, Arizona State University, Tempe, Arizona, United States of America
- Arizona Alzheimer’s Consortium, Phoenix, Arizona, United States of America
| | - Jessica M. Judd
- Department of Psychology, Arizona State University, Tempe, Arizona, United States of America
| | - Lei Xing
- Neuroscience Center, The University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Heather A. Bimonte-Nelson
- Department of Psychology, Arizona State University, Tempe, Arizona, United States of America
- Arizona Alzheimer’s Consortium, Phoenix, Arizona, United States of America
| | - Cheryl D. Conrad
- Department of Psychology, Arizona State University, Tempe, Arizona, United States of America
| | - Toshiyuki Araki
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, New York, United States of America
| | - Benjamin G. Neel
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, New York, United States of America
| | - William D. Snider
- Neuroscience Center, The University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Jason M. Newbern
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
- * E-mail:
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32
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Bustelo XR, Crespo P, Fernández-Pisonero I, Rodríguez-Fdez S. RAS GTPase-dependent pathways in developmental diseases: old guys, new lads, and current challenges. Curr Opin Cell Biol 2018; 55:42-51. [PMID: 30007125 PMCID: PMC7615762 DOI: 10.1016/j.ceb.2018.06.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 05/14/2018] [Accepted: 06/14/2018] [Indexed: 10/28/2022]
Abstract
Deregulated RAS signaling is associated with increasing numbers of congenital diseases usually referred to as RASopathies. The spectrum of genes and mutant alleles causing these diseases has been significantly expanded in recent years. This progress has triggered new challenges, including the origin and subsequent selection of the mutations driving these diseases, the specific pathobiological programs triggered by those mutations, the type of correlations that exist between the genotype and the clinical features of patients, and the ancillary genetic factors that influence the severity of the disease in patients. These issues also directly impinge on the feasibility of using RAS pathway drugs to treat RASopathy patients. Here, we will review the main developments and pending challenges in this research topic.
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Affiliation(s)
- Xosé R Bustelo
- Centro de Investigación del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007 Salamanca, Spain; Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007 Salamanca, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007 Salamanca, Spain.
| | - Piero Crespo
- CIBERONC, CSIC-University of Cantabria, 39011 Santander, Spain; Instituto de Biomedicina y Biotecnología de Cantabria, CSIC-University of Cantabria, 39011 Santander, Spain
| | - Isabel Fernández-Pisonero
- Centro de Investigación del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007 Salamanca, Spain; Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007 Salamanca, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007 Salamanca, Spain
| | - Sonia Rodríguez-Fdez
- Centro de Investigación del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007 Salamanca, Spain; Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007 Salamanca, Spain
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33
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Ordan M, Pallara C, Maik-Rachline G, Hanoch T, Gervasio FL, Glaser F, Fernandez-Recio J, Seger R. Intrinsically active MEK variants are differentially regulated by proteinases and phosphatases. Sci Rep 2018; 8:11830. [PMID: 30087384 PMCID: PMC6081382 DOI: 10.1038/s41598-018-30202-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 07/25/2018] [Indexed: 12/14/2022] Open
Abstract
MAPK/ERK kinase (MEK) 1/2 are central signaling proteins that serve as specificity determinants of the MAPK/ERK cascade. More than twenty activating mutations have been reported for MEK1/2, and many of them are known to cause diseases such as cancers, arteriovenous malformation and RASopathies. Changes in their intrinsic activity do not seem to correlate with the severity of the diseases. Here we studied four MEK1/2 mutations using biochemical and molecular dynamic methods. Although the studied mutants elevated the activating phosphorylation of MEK they had no effect on the stimulated ERK1/2 phosphorylation. Studying the regulatory mechanism that may explain this lack of effect, we found that one type of mutation affects MEK stability and two types of mutations demonstrate a reduced sensitivity to PP2A. Together, our results indicate that some MEK mutations exert their function not only by their elevated intrinsic activity, but also by modulation of regulatory elements such as protein stability or dephosphorylation.
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Affiliation(s)
- Merav Ordan
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Chiara Pallara
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain
| | - Galia Maik-Rachline
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Tamar Hanoch
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | | | - Fabian Glaser
- Bioinformatics Knowledge Unit, Technion, Haifa, Israel
| | - Juan Fernandez-Recio
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain.,Institut de Biologia Molecular de Barcelona, CSIC, Barcelona, Spain
| | - Rony Seger
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel.
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34
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Abstract
The extracellular signal-regulated kinase (ERK) pathway leads to activation of the effector molecule ERK, which controls downstream responses by phosphorylating a variety of substrates, including transcription factors. Crucial insights into the regulation and function of this pathway came from studying embryos in which specific phenotypes arise from aberrant ERK activation. Despite decades of research, several important questions remain to be addressed for deeper understanding of this highly conserved signaling system and its function. Answering these questions will require quantifying the first steps of pathway activation, elucidating the mechanisms of transcriptional interpretation and measuring the quantitative limits of ERK signaling within which the system must operate to avoid developmental defects.
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Affiliation(s)
- Aleena L Patel
- Lewis Sigler Institute for Integrative Genomics, Department of Chemical Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Stanislav Y Shvartsman
- Lewis Sigler Institute for Integrative Genomics, Department of Chemical Engineering, Princeton University, Princeton, NJ 08544, USA
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35
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Goyal Y, Schüpbach T, Shvartsman SY. A quantitative model of developmental RTK signaling. Dev Biol 2018; 442:80-86. [PMID: 30026122 DOI: 10.1016/j.ydbio.2018.07.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Revised: 06/22/2018] [Accepted: 07/13/2018] [Indexed: 01/06/2023]
Abstract
Receptor tyrosine kinases (RTKs) control a wide range of developmental processes, from the first stages of embryogenesis to postnatal growth and neurocognitive development in the adult. A significant share of our knowledge about RTKs comes from genetic screens in model organisms, which provided numerous examples demonstrating how specific cell fates and morphologies are abolished when RTK activation is either abrogated or significantly reduced. Aberrant activation of such pathways has also been recognized in many forms of cancer. More recently, studies of human developmental syndromes established that excessive activation of RTKs and their downstream signaling effectors, most notably the Ras signaling pathway, can also lead to structural and functional defects. Given that both insufficient and excessive pathway activation can lead to abnormalities, mechanistic analysis of developmental RTK signaling must address quantitative questions about its regulation and function. Patterning events controlled by the RTK Torso in the early Drosophila embryo are well-suited for this purpose. This mini review summarizes current state of knowledge about Torso-dependent Ras activation and discusses its potential to serve as a quantitative model for studying the general principles of Ras signaling in development and disease.
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Affiliation(s)
- Yogesh Goyal
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, United States; The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, United States
| | - Trudi Schüpbach
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, United States
| | - Stanislav Y Shvartsman
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, United States; The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, United States; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, United States.
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36
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Zebrafish Models of Rare Hereditary Pediatric Diseases. Diseases 2018; 6:diseases6020043. [PMID: 29789451 PMCID: PMC6023479 DOI: 10.3390/diseases6020043] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 05/17/2018] [Accepted: 05/19/2018] [Indexed: 12/12/2022] Open
Abstract
Recent advances in sequencing technologies have made it significantly easier to find the genetic roots of rare hereditary pediatric diseases. These novel methods are not panaceas, however, and they often give ambiguous results, highlighting multiple possible causative mutations in affected patients. Furthermore, even when the mapping results are unambiguous, the affected gene might be of unknown function. In these cases, understanding how a particular genotype can result in a phenotype also needs carefully designed experimental work. Model organism genetics can offer a straightforward experimental setup for hypothesis testing. Containing orthologs for over 80% of the genes involved in human diseases, zebrafish (Danio rerio) has emerged as one of the top disease models over the past decade. A plethora of genetic tools makes it easy to create mutations in almost any gene of the zebrafish genome and these mutant strains can be used in high-throughput preclinical screens for active molecules. As this small vertebrate species offers several other advantages as well, its popularity in biomedical research is bound to increase, with “aquarium to bedside” drug development pipelines taking a more prevalent role in the near future.
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37
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Neben CL, Lo M, Jura N, Klein OD. Feedback regulation of RTK signaling in development. Dev Biol 2017; 447:71-89. [PMID: 29079424 DOI: 10.1016/j.ydbio.2017.10.017] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 10/17/2017] [Accepted: 10/23/2017] [Indexed: 02/07/2023]
Abstract
Precise regulation of the amplitude and duration of receptor tyrosine kinase (RTK) signaling is critical for the execution of cellular programs and behaviors. Understanding these control mechanisms has important implications for the field of developmental biology, and in recent years, the question of how augmentation or attenuation of RTK signaling via feedback loops modulates development has become of increasing interest. RTK feedback regulation is also important for human disease research; for example, germline mutations in genes that encode RTK signaling pathway components cause numerous human congenital syndromes, and somatic alterations contribute to the pathogenesis of diseases such as cancers. In this review, we survey regulators of RTK signaling that tune receptor activity and intracellular transduction cascades, with a focus on the roles of these genes in the developing embryo. We detail the diverse inhibitory mechanisms utilized by negative feedback regulators that, when lost or perturbed, lead to aberrant increases in RTK signaling. We also discuss recent biochemical and genetic insights into positive regulators of RTK signaling and how these proteins function in tandem with negative regulators to guide embryonic development.
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Affiliation(s)
- Cynthia L Neben
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, San Francisco 94143, USA
| | - Megan Lo
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, San Francisco 94143, USA; Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Natalia Jura
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
| | - Ophir D Klein
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, San Francisco 94143, USA; Department of Pediatrics and Institute for Human Genetics, University of California, San Francisco, San Francisco 94143, USA.
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38
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Keenan SE, Shvartsman SY. Mechanisms and causality in molecular diseases. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2017; 39:35. [PMID: 29038918 PMCID: PMC6445273 DOI: 10.1007/s40656-017-0162-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
How is a disease contracted, and how does it progress through the body? Answers to these questions are fundamental to understanding both basic biology and medicine. Advances in the biomedical sciences continue to provide more tools to address these fundamental questions and to uncover questions that have not been thought of before. Despite these major advances, we are still facing conceptual and technical challenges when learning about the etiology of disease, especially for genetic diseases. In this review, we illustrate this point by discussing the causal links between molecular mechanisms and systems-level phenotypes in molecular diseases. We begin with an examination of sickle cell anemia, and how mechanisms of the disease have been comprehended over the last century. While sickle cell anemia involves a mutation in a single protein in a single cell type, other diseases involve mutations in networks with many protein interactions and in diverse cell types. We introduce the challenges that result from these differences and illustrate the current obstacles by discussing the RASopathies, a recently discovered class of developmental syndromes that result from mutations in signaling networks. Methods to study mutant genotypes that lead to mutant phenotypes are discussed, particularly the use of model organisms and mutant proteins to study protein interactions that may be important for development of disease. These studies will point toward the future of diagnosing and treating genetic disease.
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Affiliation(s)
- Shannon E Keenan
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA.
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA.
| | - Stanislav Y Shvartsman
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA
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39
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Jindal GA, Goyal Y, Humphreys JM, Yeung E, Tian K, Patterson VL, He H, Burdine RD, Goldsmith EJ, Shvartsman SY. How activating mutations affect MEK1 regulation and function. J Biol Chem 2017; 292:18814-18820. [PMID: 29018093 DOI: 10.1074/jbc.c117.806067] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 09/19/2017] [Indexed: 01/18/2023] Open
Abstract
The MEK1 kinase directly phosphorylates ERK2, after the activation loop of MEK1 is itself phosphorylated by Raf. Studies over the past decade have revealed a large number of disease-related mutations in the MEK1 gene that lead to tumorigenesis and abnormal development. Several of these mutations result in MEK1 constitutive activity, but how they affect MEK1 regulation and function remains largely unknown. Here, we address these questions focusing on two pathogenic variants of the Phe-53 residue, which maps to the well-characterized negative regulatory region of MEK1. We found that these variants are phosphorylated by Raf faster than the wild-type enzyme, and this phosphorylation further increases their enzymatic activity. However, the maximal activities of fully phosphorylated wild-type and mutant enzymes are indistinguishable. On the basis of available structural information, we propose that the activating substitutions destabilize the inactive conformation of MEK1, resulting in its constitutive activity and making it more prone to Raf-mediated phosphorylation. Experiments in zebrafish revealed that the effects of activating variants on embryonic development reflect the joint control of the negative regulatory region and activating phosphorylation. Our results underscore the complexity of the effects of activating mutations on signaling systems, even at the level of a single protein.
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Affiliation(s)
- Granton A Jindal
- From the Departments of Chemical and Biological Engineering and.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544 and.,Molecular Biology
| | - Yogesh Goyal
- From the Departments of Chemical and Biological Engineering and.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544 and.,Molecular Biology
| | - John M Humphreys
- the Department of Biophysics, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390-8816
| | - Eyan Yeung
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544 and.,Molecular Biology
| | - Kaijia Tian
- From the Departments of Chemical and Biological Engineering and.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544 and
| | - Victoria L Patterson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544 and.,Molecular Biology
| | - Haixia He
- the Department of Biophysics, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390-8816
| | | | - Elizabeth J Goldsmith
- the Department of Biophysics, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390-8816
| | - Stanislav Y Shvartsman
- From the Departments of Chemical and Biological Engineering and .,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544 and.,Molecular Biology
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40
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Zdraljevic S, Andersen EC. Natural diversity facilitates the discovery of conserved chemotherapeutic response mechanisms. Curr Opin Genet Dev 2017; 47:41-47. [PMID: 28892780 DOI: 10.1016/j.gde.2017.08.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 07/15/2017] [Accepted: 08/05/2017] [Indexed: 11/15/2022]
Abstract
Organismal fitness depends on adaptation to complex niches where chemical compounds and pathogens are omnipresent. These stresses can lead to the fixation of alleles in both xenobiotic responses and proliferative signaling pathways that promote survival in these niches. However, both xenobiotic responses and proliferative pathways vary within and among species. For example, genetic differences can accumulate within populations because xenobiotic exposures are not constant and selection is variable. Additionally, neutral genetic variation can accumulate in conserved proliferative pathway genes because these systems are robust to genetic perturbations given their essential roles in normal cell-fate specification. For these reasons, sensitizing mutations or chemical perturbations can disrupt pathways and reveal cryptic variation. With this fundamental view of how organisms respond to cytotoxic compounds and cryptic variation in conserved signaling pathways, it is not surprising that human patients have highly variable responses to chemotherapeutic compounds. These different responses result in the low FDA-approval rates for chemotherapeutics and underscore the need for new approaches to understand these diseases and therapeutic interventions. Model organisms, especially the classic invertebrate systems of Caenorhabditis elegans and Drosophila melanogaster, can be used to combine studies of natural variation across populations with responses to both xenobiotic compounds and chemotherapeutics targeted to conserved proliferative signaling pathways.
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Affiliation(s)
- Stefan Zdraljevic
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA; Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Erik C Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA; Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL 60611, USA.
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Goyal Y, Levario TJ, Mattingly HH, Holmes S, Shvartsman SY, Lu H. Parallel imaging of Drosophila embryos for quantitative analysis of genetic perturbations of the Ras pathway. Dis Model Mech 2017; 10:923-929. [PMID: 28495673 PMCID: PMC5536913 DOI: 10.1242/dmm.030163] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 05/08/2017] [Indexed: 01/06/2023] Open
Abstract
The Ras pathway patterns the poles of the Drosophila embryo by downregulating the levels and activity of a DNA-binding transcriptional repressor Capicua (Cic). We demonstrate that the spatiotemporal pattern of Cic during this signaling event can be harnessed for functional studies of mutations in the Ras pathway in human diseases. Our approach relies on a new microfluidic device that enables parallel imaging of Cic dynamics in dozens of live embryos. We found that although the pattern of Cic in early embryos is complex, it can be accurately approximated by a product of one spatial profile and one time-dependent amplitude. Analysis of these functions of space and time alone reveals the differential effects of mutations within the Ras pathway. Given the highly conserved nature of Ras-dependent control of Cic, our approach provides new opportunities for functional analysis of multiple sequence variants from developmental abnormalities and cancers.
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Affiliation(s)
- Yogesh Goyal
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Thomas J Levario
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Henry H Mattingly
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Susan Holmes
- Department of Statistics, Stanford University, Stanford, CA 94305, USA
| | - Stanislav Y Shvartsman
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA .,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Hang Lu
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
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Baxendale S, van Eeden F, Wilkinson R. The Power of Zebrafish in Personalised Medicine. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1007:179-197. [PMID: 28840558 DOI: 10.1007/978-3-319-60733-7_10] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The goal of personalised medicine is to develop tailor-made therapies for patients in whom currently available therapeutics fail. This approach requires correlating individual patient genotype data to specific disease phenotype data and using these stratified data sets to identify bespoke therapeutics. Applications for personalised medicine include common complex diseases which may have multiple targets, as well as rare monogenic disorders, for which the target may be unknown. In both cases, whole genome sequence analysis (WGS) is discovering large numbers of disease associated mutations in new candidate genes and potential modifier genes. Currently, the main limiting factor is the determination of which mutated genes are important for disease progression and therefore represent potential targets for drug discovery. Zebrafish have gained popularity as a model organism for understanding developmental processes, disease mechanisms and more recently for drug discovery and toxicity testing. In this chapter, we will examine the diverse roles that zebrafish can make in the expanding field of personalised medicine, from generating humanised disease models to xenograft screening of different cancer cell lines, through to finding new drugs via in vivo phenotypic screens. We will discuss the tools available for zebrafish research and recent advances in techniques, highlighting the advantages and potential of using zebrafish for high throughput disease modeling and precision drug discovery.
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Affiliation(s)
- Sarah Baxendale
- The Bateson Centre, Department of Biomedical Science, University of Sheffield, Sheffield, S10 2TN, UK.
| | - Freek van Eeden
- The Bateson Centre, Department of Biomedical Science, University of Sheffield, Sheffield, S10 2TN, UK
| | - Robert Wilkinson
- The Bateson Centre, Department of Biomedical Science, University of Sheffield, Sheffield, S10 2TN, UK.,Department of Infection, Immunity and Cardiovascular Disease, Medical School, Beech Hill Rd, University of Sheffield, Sheffield, S10 2RX, UK
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Grant MG, Patterson VL, Grimes DT, Burdine RD. Modeling Syndromic Congenital Heart Defects in Zebrafish. Curr Top Dev Biol 2017; 124:1-40. [DOI: 10.1016/bs.ctdb.2016.11.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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