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Goret M, Edelweiss E, Jehl J, Reiss D, Aguirre-Pineda P, Friant S, Laporte J. Combining dynamin 2 myopathy and neuropathy mutations rescues both phenotypes. Nat Commun 2025; 16:4667. [PMID: 40393994 PMCID: PMC12092598 DOI: 10.1038/s41467-025-59925-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 05/02/2025] [Indexed: 05/22/2025] Open
Abstract
Mutations within a single gene can lead to diverse human genetic diseases affecting highly specialized tissues. Notably, dominant mutations in the DNM2 gene, encoding the mechanoenzyme dynamin, lead to distinct neuromuscular disorders: centronuclear myopathy (CNM) and Charcot-Marie-Tooth neuropathy (CMT). CNM is characterized by myofiber structural anomalies while CMT presents peripheral nerve defects, both culminating in muscle weakness and atrophy. Despite their shared genetic origin, the mechanisms driving these diseases remain elusive, and no cure is available. Here, we present in vitro assays underlining opposing effects of DNM2 mutations, gain-of-function in CNM and loss-of-function in CMT. In vivo, we explored the potential compensatory effects of CNM and CMT mutations by breeding Dnm2S619L/+ CNM with Dnm2K562E/+ CMT mouse models. Dnm2S619L/K562E offspring exhibit strongly improved motor coordination and muscle strength and mass, compared to single-mutant littermates. Dnm2S619L/K562E mice present normalized muscle structure and nerve fiber organization. This study reveals that two distinct disease-causing mutations within the DNM2 gene compensate each other in vivo, leading to corrections of most individual phenotypes. The inverse modulation of DNM2 activity emerges as a promising therapeutic strategy to address CNM and CMT diseases.
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Affiliation(s)
- Marie Goret
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), INSERM U1258, CNRS UMR7104, University of Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France
| | - Evelina Edelweiss
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), INSERM U1258, CNRS UMR7104, University of Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France
| | - Jérémy Jehl
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), INSERM U1258, CNRS UMR7104, University of Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France
| | - David Reiss
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), INSERM U1258, CNRS UMR7104, University of Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France
| | - Patricio Aguirre-Pineda
- Medical Genetics Laboratory, INSERM UMRS 1112, University of Strasbourg, CRBS, 1 rue Eugène Boeckel, 67000, Strasbourg, France
| | - Sylvie Friant
- Medical Genetics Laboratory, INSERM UMRS 1112, University of Strasbourg, CRBS, 1 rue Eugène Boeckel, 67000, Strasbourg, France
| | - Jocelyn Laporte
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), INSERM U1258, CNRS UMR7104, University of Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France.
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Fries LE, Dharma S, Chakravarti A, Chatterjee S. Variability in proliferative and migratory defects in Hirschsprung disease-associated RET pathogenic variants. Am J Hum Genet 2025; 112:863-875. [PMID: 40010351 DOI: 10.1016/j.ajhg.2025.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2024] [Revised: 02/03/2025] [Accepted: 02/04/2025] [Indexed: 02/28/2025] Open
Abstract
Hirschsprung disease (HSCR) exhibits extensive genetic heterogeneity, with 72% of cases involving pathogenic variants in 10 genes forming a gene regulatory network (GRN) essential for enteric nervous system (ENS) development. The receptor tyrosine kinase gene RET is the most significant contributor, implicated in 12%-50% of individuals depending on the phenotype. RET plays a critical role in ENS precursor proliferation and migration, and defects in these processes lead to HSCR. However, the functional impact of RET pathogenic variants and their mechanisms of disease remain poorly understood. To address this, we investigated proliferative and migratory phenotypes in a RET-dependent neural crest-derived cell line harboring one of five missense (c.166C>A [p.Leu56Met]; c.532G>C [p.Glu178Gln]; c.2372A>T [p.Tyr791Phe]; c.2765C>A [p.Ser922Tyr]; or c.2994T>A [p.Phe998Leu]) or three nonsense (c.612C>A, c.2308C>T, or c.2943C>G) heterozygous pathogenic RET variants. Using cDNA- and CRISPR-based prime reverse insertion mechanism engineering (PRIME) editing coupled with quantitative proliferation and migration assays, we observed significant losses in proliferation and migration in three missense (c.612C>A [p.Tyr204∗]; c.2308C>T [p.Arg770∗]; and c.2943C>G [p.Tyr981∗]) and all nonsense variants. Notably, the c.2372A>T (p.Tyr791Phe) missense variant, whose pathogenicity has been debated, appears benign. Importantly, the severity of migration loss did not consistently correlate with proliferation defects, and the phenotypic severity of nonsense variants was independent of their position within the RET protein. This study highlights the necessity of targeted functional assays to accurately assess the pathogenicity of HSCR-associated variants rather than relying solely on bioinformatics predictions, which could be refined by incorporating functional data.
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Affiliation(s)
- Lauren E Fries
- Center for Human Genetics & Genomics, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Sree Dharma
- Center for Human Genetics & Genomics, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Aravinda Chakravarti
- Center for Human Genetics & Genomics, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, NY 10016, USA.
| | - Sumantra Chatterjee
- Center for Human Genetics & Genomics, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, NY 10016, USA.
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3
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Fries LE, Dharma S, Chakravarti A, Chatterjee S. Variability in proliferative and migratory defects in Hirschsprung disease-associated RET pathogenic variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.24.614825. [PMID: 39372753 PMCID: PMC11451626 DOI: 10.1101/2024.09.24.614825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/08/2024]
Abstract
Despite the extensive genetic heterogeneity of Hirschsprung disease (HSCR; congenital colonic aganglionosis) 72% of patients harbor pathogenic variants in 10 genes that form a gene regulatory network (GRN) controlling the development of the enteric nervous system (ENS). Among these genes, the receptor tyrosine kinase gene RET is the most significant contributor, accounting for pathogenic variants in 12%-50% of patients depending on phenotype. RET plays a critical role in the proliferation and migration of ENS precursors, and defects in these processes lead to HSCR. However, despite the gene's importance in HSCR, the functional consequences of RET pathogenic variants and their mechanism of disease remain poorly understood. To address this, we investigated the proliferative and migratory phenotypes in a RET-dependent neural crest-derived cell line harboring one of five missense (L56M, E178Q, Y791F, S922Y, F998L) or three nonsense (Y204X, R770X, Y981X) pathogenic heterozygous variants. Using a combination of cDNA-based and CRISPR-based PRIME editing coupled with quantitative proliferation and migration assays, we detected significant losses in cell proliferation and migration in three missense (E178Q, S922Y, F998L) and all nonsense variants. Our data suggests that the Y791F variant, whose pathogenicity has been debated, is likely not pathogenic. Importantly, the severity of migration loss did not consistently correlate with proliferation defects, and the phenotypic severity of nonsense variants was independent of their position within the RET protein. This study highlights the necessity and feasibility of targeted functional assays to accurately assess the pathogenicity of HSCR-associated variants, rather than relying solely on machine learning predictions, which could themselves be refined by incorporating such functional data.
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Affiliation(s)
- Lauren E Fries
- Center for Human Genetics & Genomics, New York University Grossman School of Medicine, New York, NY 10016
| | - Sree Dharma
- Center for Human Genetics & Genomics, New York University Grossman School of Medicine, New York, NY 10016
| | - Aravinda Chakravarti
- Center for Human Genetics & Genomics, New York University Grossman School of Medicine, New York, NY 10016
- Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, NY 10016
| | - Sumantra Chatterjee
- Center for Human Genetics & Genomics, New York University Grossman School of Medicine, New York, NY 10016
- Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, NY 10016
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Sunardi M, Ito K, Sato Y, Uesaka T, Iwasaki M, Enomoto H. A Single RET Mutation in Hirschsprung Disease Induces Intestinal Aganglionosis Via a Dominant-Negative Mechanism. Cell Mol Gastroenterol Hepatol 2022; 15:1505-1524. [PMID: 36521661 DOI: 10.1016/j.jcmgh.2022.12.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 12/03/2022] [Accepted: 12/05/2022] [Indexed: 01/02/2023]
Abstract
BACKGROUND & AIMS Hirschsprung disease (HSCR) is a congenital disorder characterized by the absence of the enteric nervous system (ENS). HSCR potentially involves multiple gene aberrations and displays complex patterns of inheritance. Mutations of the RET gene, encoding the RET receptor tyrosine kinase, play a central role in the pathogenesis of HSCR. Although a wide variety of coding RET mutations have been identified, their pathogenetic significance in vivo has remained largely unclear. METHODS We introduced a HSCR-associated RET missense mutation, RET(S811F), into the corresponding region (S812) of the mouse Ret gene. Pathogenetic impact of Ret(S812F) was assessed by histologic and functional analyses of the ENS and by biochemical analyses. Interactions of the Ret(S812F) allele with HSCR susceptibility genes, the RET9 allele and the Ednrb gene, were examined by genetic crossing in mice. RESULTS RetS812F/+ mice displayed intestinal aganglionosis (incidence, 50%) or hypoganglionosis (50%), impaired differentiation of enteric neurons, defecation deficits, and increased lethality. Biochemical analyses revealed that Ret(S811F) protein was not only kinase-deficient but also abrogated function of wild-type RET in trans. Moreover, the Ret(S812F) allele interacted with other HSCR susceptibility genes and caused intestinal aganglionosis with full penetrance. CONCLUSIONS This study demonstrates that a single RET missense mutation alone induces intestinal aganglionosis via a dominant-negative mechanism. The RetS812F/+ mice model HSCR displays dominant inheritance with incomplete penetrance and serves as a valuable platform for better understanding of the pathogenetic mechanism of HSCR caused by coding RET mutations.
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Affiliation(s)
- Mukhamad Sunardi
- Division of Neural Differentiation and Regeneration, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Hyogo, Japan
| | - Keisuke Ito
- Division of Neural Differentiation and Regeneration, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Hyogo, Japan
| | - Yuya Sato
- Division of Neural Differentiation and Regeneration, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Hyogo, Japan
| | - Toshihiro Uesaka
- Division of Neural Differentiation and Regeneration, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Hyogo, Japan
| | - Mitsuhiro Iwasaki
- Division of Neural Differentiation and Regeneration, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Hyogo, Japan
| | - Hideki Enomoto
- Division of Neural Differentiation and Regeneration, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Hyogo, Japan.
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Schultz J, Freibothe I, Haase M, Glatte P, Barreton G, Ziegler A, Görgens H, Fitze G. Distribution of RET proto-oncogene variants in children with appendicitis. Mol Genet Genomic Med 2022; 10:e1864. [PMID: 34981673 PMCID: PMC8830807 DOI: 10.1002/mgg3.1864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 11/15/2021] [Accepted: 12/17/2021] [Indexed: 11/17/2022] Open
Abstract
Background In addition to patient‐related systemic factors directing the immune response, the pathomechanisms of appendicitis (AP) might also include insufficient drainage leading to inflammation caused by decreased peristalsis. Genetic predisposition accounts for 30%–50% of AP. M. Hirschsprung (HSCR), also characterized by disturbed peristalsis, is associated with variants in the RET proto‐oncogene. We thus hypothesized that RET variants contribute to the etiology of AP. Methods DNA from paraffin‐embedded appendices and clinical data of 264 children were analyzed for the RET c.135A>G variant (rs1800858, NC_000010.11:g.43100520A>G). In 46 patients with gangrenous or perforated AP (GAP), peripheral blood DNA was used for RET sequencing. Results Germline mutations were found in 13% of GAP, whereas no RET mutations were found in controls besides the benign variant p.Tyr791Phe (NC_000010.11:g.43118460A>T). In GAP, the polymorphic G‐allele in rs2435352 (NC_000010.11:g.43105241A>G) in intron 4 was underrepresented (p = 0.0317). Conclusion Our results suggest an impact of the RET proto‐oncogene in the etiology of AP. Mutations were similar to patients with HSCR but no clinical features of HSCR were observed. The pathological phenotypes in both populations might thus represent a multigenic etiology including RET germline mutations with phenotypic heterogeneity and incomplete penetrance.
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Affiliation(s)
- Jurek Schultz
- Department of Pediatric Surgery, University of Technology Dresden, Dresden, Germany
| | - Ines Freibothe
- Department of Pediatric Surgery, University of Technology Dresden, Dresden, Germany
| | - Michael Haase
- Department of Pediatric Surgery, University of Technology Dresden, Dresden, Germany
| | - Patrick Glatte
- Department of Pediatric Surgery, University of Technology Dresden, Dresden, Germany
| | - Gustavo Barreton
- Institute of Pathology, University of Technology Dresden, Dresden, Germany
| | - Andreas Ziegler
- Medizincampus Davos, Davos, Switzerland.,School of Mathematics, Statistics and Computer Science, Pietermaritzburg, South Africa.,University Heart Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Heike Görgens
- Department of Surgical Research, University of Technology Dresden, Dresden, Germany
| | - Guido Fitze
- Department of Pediatric Surgery, University of Technology Dresden, Dresden, Germany
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Sarkadi B, Liko I, Nyiro G, Igaz P, Butz H, Patocs A. Analytical Performance of NGS-Based Molecular Genetic Tests Used in the Diagnostic Workflow of Pheochromocytoma/Paraganglioma. Cancers (Basel) 2021; 13:4219. [PMID: 34439371 PMCID: PMC8392134 DOI: 10.3390/cancers13164219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 12/30/2022] Open
Abstract
Next Generation Sequencing (NGS)-based methods are high-throughput and cost-effective molecular genetic diagnostic tools. Targeted gene panel and whole exome sequencing (WES) are applied in clinical practice for assessing mutations of pheochromocytoma/paraganglioma (PPGL) associated genes, but the best strategy is debated. Germline mutations of at the least 18 PPGL genes are present in approximately 20-40% of patients, thus molecular genetic testing is recommended in all cases. We aimed to evaluate the analytical and clinical performances of NGS methods for mutation detection of PPGL-associated genes. WES (three different library preparation and bioinformatics workflows) and an in-house, hybridization based gene panel (endocrine-onco-gene-panel- ENDOGENE) was evaluated on 37 (20 WES and 17 ENDOGENE) samples with known variants. After optimization of the bioinformatic workflow, 61 additional samples were tested prospectively. All clinically relevant variants were validated with Sanger sequencing. Target capture of PPGL genes differed markedly between WES platforms and genes tested. All known variants were correctly identified by all methods, but methods of library preparations, sequencing platforms and bioinformatical settings significantly affected the diagnostic accuracy. The ENDOGENE panel identified several pathogenic mutations and unusual genotype-phenotype associations suggesting that the whole panel should be used for identification of genetic susceptibility of PPGL.
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Affiliation(s)
- Balazs Sarkadi
- MTA-SE Hereditary Tumors Research Group, Eotvos Lorand Research Network, H-1089 Budapest, Hungary; (B.S.); (I.L.); (H.B.)
| | - Istvan Liko
- MTA-SE Hereditary Tumors Research Group, Eotvos Lorand Research Network, H-1089 Budapest, Hungary; (B.S.); (I.L.); (H.B.)
- Bionics Innovation Center, H-1089 Budapest, Hungary;
| | - Gabor Nyiro
- Bionics Innovation Center, H-1089 Budapest, Hungary;
- MTA-SE Molecular Medicine Research Group, Eotvos Lorand Research Network, H-1083 Budapest, Hungary;
| | - Peter Igaz
- MTA-SE Molecular Medicine Research Group, Eotvos Lorand Research Network, H-1083 Budapest, Hungary;
- Department of Endocrinology, Department of Internal Medicine and Oncology, Semmelweis University, H-1083 Budapest, Hungary
| | - Henriett Butz
- MTA-SE Hereditary Tumors Research Group, Eotvos Lorand Research Network, H-1089 Budapest, Hungary; (B.S.); (I.L.); (H.B.)
- Department of Laboratory Medicine, Semmelweis University, H-1089 Budapest, Hungary
- Department of Molecular Genetics, National Institute of Oncology, H-1122 Budapest, Hungary
| | - Attila Patocs
- MTA-SE Hereditary Tumors Research Group, Eotvos Lorand Research Network, H-1089 Budapest, Hungary; (B.S.); (I.L.); (H.B.)
- Bionics Innovation Center, H-1089 Budapest, Hungary;
- Department of Laboratory Medicine, Semmelweis University, H-1089 Budapest, Hungary
- Department of Molecular Genetics, National Institute of Oncology, H-1122 Budapest, Hungary
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Sunardi M, Ito K, Enomoto H. Live visualization of a functional RET-EGFP chimeric receptor in homozygous knock-in mice. Dev Growth Differ 2021; 63:285-294. [PMID: 34324195 DOI: 10.1111/dgd.12740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/07/2021] [Accepted: 06/22/2021] [Indexed: 11/29/2022]
Abstract
The GDNF Family Ligands (GFLs) regulate neural development and kidney organogenesis by activating the RET receptor tyrosine kinase. Many RET-dependent developmental processes involve long-distance cell-cell communications or cell polarity, which includes cell migration and axon guidance. This suggests that spatiotemporally regulated subcellular localization of RET protein and appropriate propagation of RET signaling in cells are essential for the physiological function of the GFLs. Little is known, however, about the dynamics of RET protein in cells. Addressing this issue requires development of a system that allows visualization of RET in living cells. In this study, we report generation of a novel knock-in mouse line in which the RET-EGFP chimeric receptor is expressed under the Ret promoter. Unlike Ret-deficient mice that die after birth due to the absence of the enteric nervous system (ENS) and kidneys, RetRET-EGFP/RET-EGFP mice were viable and grew to adulthood with no overt abnormality, which indicated that RET-EGFP exerts function comparable to RET. In neurons and ENS progenitors, RET-EGFP signals were detected both on the cell membrane and in the cytoplasm, the latter of which appeared as a punctate pattern. Time-lapse imaging of cultured neural cells and embryos revealed active transport of RET-EGFP puncta in neuronal axons and cell bodies. Immunohistochemical analyses detected RET-EGFP signals in early and recycling endosomes, indicating that RET-EGFP is trafficked via the endocytic pathway. RetRET-EGFP/RET-EGFP mice enable visualization of functional RET protein in vivo for the first time and provide a unique platform to examine the dynamics and physiology of RET trafficking.
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Affiliation(s)
- Mukhamad Sunardi
- Division for Neural Differentiation and Regeneration, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Keisuke Ito
- Division for Neural Differentiation and Regeneration, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Hideki Enomoto
- Division for Neural Differentiation and Regeneration, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Kobe, Japan
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Kang YN, Fung C, Vanden Berghe P. Gut innervation and enteric nervous system development: a spatial, temporal and molecular tour de force. Development 2021; 148:148/3/dev182543. [PMID: 33558316 DOI: 10.1242/dev.182543] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
During embryonic development, the gut is innervated by intrinsic (enteric) and extrinsic nerves. Focusing on mammalian ENS development, in this Review we highlight how important the different compartments of this innervation are to assure proper gut function. We specifically address the three-dimensional architecture of the innervation, paying special attention to the differences in development along the longitudinal and circumferential axes of the gut. We review recent information about the formation of both intrinsic innervation, which is fairly well-known, as well as the establishment of the extrinsic innervation, which, despite its importance in gut-brain signaling, has received much less attention. We further discuss how external microbial and nutritional cues or neuroimmune interactions may influence development of gut innervation. Finally, we provide summary tables, describing the location and function of several well-known molecules, along with some newer factors that have more recently been implicated in the development of gut innervation.
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Affiliation(s)
- Yi-Ning Kang
- Laboratory for Enteric NeuroScience (LENS), Translational Research Center for Gastrointestinal Disorders (TARGID), University of Leuven, Leuven 3000, Belgium
| | - Candice Fung
- Laboratory for Enteric NeuroScience (LENS), Translational Research Center for Gastrointestinal Disorders (TARGID), University of Leuven, Leuven 3000, Belgium
| | - Pieter Vanden Berghe
- Laboratory for Enteric NeuroScience (LENS), Translational Research Center for Gastrointestinal Disorders (TARGID), University of Leuven, Leuven 3000, Belgium
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