1
|
Fare CM, Rothstein JD. Nuclear pore dysfunction and disease: a complex opportunity. Nucleus 2024; 15:2314297. [PMID: 38383349 PMCID: PMC10883112 DOI: 10.1080/19491034.2024.2314297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 01/30/2024] [Indexed: 02/23/2024] Open
Abstract
The separation of genetic material from bulk cytoplasm has enabled the evolution of increasingly complex organisms, allowing for the development of sophisticated forms of life. However, this complexity has created new categories of dysfunction, including those related to the movement of material between cellular compartments. In eukaryotic cells, nucleocytoplasmic trafficking is a fundamental biological process, and cumulative disruptions to nuclear integrity and nucleocytoplasmic transport are detrimental to cell survival. This is particularly true in post-mitotic neurons, where nuclear pore injury and errors to nucleocytoplasmic trafficking are strongly associated with neurodegenerative disease. In this review, we summarize the current understanding of nuclear pore biology in physiological and pathological contexts and discuss potential therapeutic approaches for addressing nuclear pore injury and dysfunctional nucleocytoplasmic transport.
Collapse
Affiliation(s)
- Charlotte M Fare
- Department of Neurology and Brain Science Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Jeffrey D Rothstein
- Department of Neurology and Brain Science Institute, Johns Hopkins University, Baltimore, MD, USA
| |
Collapse
|
2
|
Jühlen R, Fahrenkrog B. From the sideline: Tissue-specific nucleoporin function in health and disease, an update. FEBS Lett 2023; 597:2750-2768. [PMID: 37873737 DOI: 10.1002/1873-3468.14761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/26/2023] [Accepted: 10/04/2023] [Indexed: 10/25/2023]
Abstract
The subcellular compartmentalisation of eukaryotic cells requires selective exchange between the cytoplasm and the nucleus. Intact nucleocytoplasmic transport is vital for normal cell function and mutations in the executing machinery have been causally linked to human disease. Central players in nucleocytoplasmic exchange are nuclear pore complexes (NPCs), which are built from ~30 distinct proteins collectively termed nucleoporins. Aberrant nucleoporin expression was detected in human cancers and autoimmune diseases since quite some time, while it was through the increasing use of next generation sequencing that mutations in nucleoporin genes associated with mainly rare hereditary diseases were revealed. The number of newly identified mutations is steadily increasing, as is the number of diseases. Mutational hotspots have emerged: mutations in the scaffold nucleoporins seemingly affect primarily inner organs, such as heart, kidney, and ovaries, whereas genetic alterations in peripheral, cytoplasmic nucleoporins affect primarily the central nervous system and development. In this review, we summarise latest insights on altered nucleoporin function in the context of human hereditary disorders, with a focus on those where mechanistic insights are beginning to emerge.
Collapse
Affiliation(s)
- Ramona Jühlen
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany
| | | |
Collapse
|
3
|
Chen Y, Zhang Y, Zhou X. Non-classical functions of nuclear pore proteins in ciliopathy. Front Mol Biosci 2023; 10:1278976. [PMID: 37908226 PMCID: PMC10614291 DOI: 10.3389/fmolb.2023.1278976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/02/2023] [Indexed: 11/02/2023] Open
Abstract
Nucleoporins (NUPs) constitute integral nuclear pore protein (NPC) elements. Although traditional NUP functions have been extensively researched, evidence of additional vital non-NPC roles, referred to herein as non-classical NUP functions, is also emerging. Several NUPs localise at the ciliary base. Indeed, Nup188, Nup93 or Nup205 knockdown results in cilia loss, impacting cardiac left-right patterning in models and cell lines. Genetic variants of Nup205 and Nup188 have been identified in patients with congenital heart disease and situs inversus totalis or heterotaxy, a prevalent human ciliopathy. These findings link non-classical NUP functions to human diseases. This mini-review summarises pivotal NUP interactions with NIMA-related kinases or nephronophthisis proteins that regulate ciliary function and explores other NUPs potentially implicated in cilia-related disorders. Overall, elucidating the non-classical roles of NUPs will enhance comprehension of ciliopathy aetiology.
Collapse
Affiliation(s)
- Yan Chen
- Obstetrics and Gynecology Hospital of Fudan University, Fudan University Shanghai Medical College, Shanghai, China
| | - Yuan Zhang
- Department of Assisted Reproduction, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiangyu Zhou
- Obstetrics and Gynecology Hospital of Fudan University, Fudan University Shanghai Medical College, Shanghai, China
| |
Collapse
|
4
|
Marquez J, Aslam F, Khokha MK. Expanding EMC foldopathies: Topogenesis deficits alter the neural crest. Genesis 2023; 61:e23520. [PMID: 37318954 PMCID: PMC10524326 DOI: 10.1002/dvg.23520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 04/13/2023] [Accepted: 05/02/2023] [Indexed: 06/17/2023]
Abstract
The endoplasmic reticulum (ER) membrane protein complex (EMC) is essential for the insertion of a wide variety of transmembrane proteins into the plasma membrane across cell types. Each EMC is composed of Emc1-7, Emc10, and either Emc8 or Emc9. Recent human genetics studies have implicated variants in EMC genes as the basis for a group of human congenital diseases. The patient phenotypes are varied but appear to affect a subset of tissues more prominently than others. Namely, craniofacial development seems to be commonly affected. We previously developed an array of assays in Xenopus tropicalis to assess the effects of emc1 depletion on the neural crest, craniofacial cartilage, and neuromuscular function. We sought to extend this approach to additional EMC components identified in patients with congenital malformations. Through this approach, we determine that EMC9 and EMC10 are important for neural crest development and the development of craniofacial structures. The phenotypes observed in patients and our Xenopus model phenotypes similar to EMC1 loss of function likely due to a similar mechanism of dysfunction in transmembrane protein topogenesis.
Collapse
Affiliation(s)
- Jonathan Marquez
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Faiza Aslam
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Mustafa K. Khokha
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, CT, USA
| |
Collapse
|
5
|
Doering L, Cornean A, Thumberger T, Benjaminsen J, Wittbrodt B, Kellner T, Hammouda OT, Gorenflo M, Wittbrodt J, Gierten J. CRISPR-based knockout and base editing confirm the role of MYRF in heart development and congenital heart disease. Dis Model Mech 2023; 16:dmm049811. [PMID: 37584388 PMCID: PMC10445736 DOI: 10.1242/dmm.049811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 07/21/2023] [Indexed: 08/17/2023] Open
Abstract
High-throughput DNA sequencing studies increasingly associate DNA variants with congenital heart disease (CHD). However, functional modeling is a crucial prerequisite for translating genomic data into clinical care. We used CRISPR-Cas9-mediated targeting of 12 candidate genes in the vertebrate model medaka (Oryzias latipes), five of which displayed a novel cardiovascular phenotype spectrum in F0 (crispants): mapre2, smg7, cdc42bpab, ankrd11 and myrf, encoding a transcription factor recently linked to cardiac-urogenital syndrome. Our myrf mutant line showed particularly prominent embryonic cardiac defects recapitulating phenotypes of pediatric patients, including hypoplastic ventricle. Mimicking human mutations, we edited three sites to generate specific myrf single-nucleotide variants via cytosine and adenine base editors. The Glu749Lys missense mutation in the conserved intramolecular chaperon autocleavage domain fully recapitulated the characteristic myrf mutant phenotype with high penetrance, underlining the crucial function of this protein domain. The efficiency and scalability of base editing to model specific point mutations accelerate gene validation studies and the generation of human-relevant disease models.
Collapse
Affiliation(s)
- Lino Doering
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
- Department of Pediatric Cardiology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Alex Cornean
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
- Heidelberg Biosciences International Graduate School, Heidelberg University, 69120 Heidelberg, Germany
| | - Thomas Thumberger
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Joergen Benjaminsen
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Beate Wittbrodt
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Tanja Kellner
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Omar T. Hammouda
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Matthias Gorenflo
- Department of Pediatric Cardiology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - Jakob Gierten
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
- Department of Pediatric Cardiology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| |
Collapse
|
6
|
Tran Mau-Them F, Delanne J, Denommé-Pichon AS, Safraou H, Bruel AL, Vitobello A, Garde A, Nambot S, Bourgon N, Racine C, Sorlin A, Moutton S, Marle N, Rousseau T, Sagot P, Simon E, Vincent-Delorme C, Boute O, Colson C, Petit F, Legendre M, Naudion S, Rooryck C, Prouteau C, Colin E, Guichet A, Ziegler A, Bonneau D, Morel G, Fradin M, Lavillaureix A, Quelin C, Pasquier L, Odent S, Vera G, Goldenberg A, Guerrot AM, Brehin AC, Putoux A, Attia J, Abel C, Blanchet P, Wells CF, Deiller C, Nizon M, Mercier S, Vincent M, Isidor B, Amiel J, Dard R, Godin M, Gruchy N, Jeanne M, Schaeffer E, Maillard PY, Payet F, Jacquemont ML, Francannet C, Sigaudy S, Bergot M, Tisserant E, Ascencio ML, Binquet C, Duffourd Y, Philippe C, Faivre L, Thauvin-Robinet C. Prenatal diagnosis by trio exome sequencing in fetuses with ultrasound anomalies: A powerful diagnostic tool. Front Genet 2023; 14:1099995. [PMID: 37035737 PMCID: PMC10076577 DOI: 10.3389/fgene.2023.1099995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 02/24/2023] [Indexed: 04/11/2023] Open
Abstract
Introduction: Prenatal ultrasound (US) anomalies are detected in around 5%-10% of pregnancies. In prenatal diagnosis, exome sequencing (ES) diagnostic yield ranges from 6% to 80% depending on the inclusion criteria. We describe the first French national multicenter pilot study aiming to implement ES in prenatal diagnosis following the detection of anomalies on US. Patients and methods: We prospectively performed prenatal trio-ES in 150 fetuses with at least two US anomalies or one US anomaly known to be frequently linked to a genetic disorder. Trio-ES was only performed if the results could influence pregnancy management. Chromosomal microarray (CMA) was performed before or in parallel. Results: A causal diagnosis was identified in 52/150 fetuses (34%) with a median time to diagnosis of 28 days, which rose to 56/150 fetuses (37%) after additional investigation. Sporadic occurrences were identified in 34/56 (60%) fetuses and unfavorable vital and/or neurodevelopmental prognosis was made in 13/56 (24%) fetuses. The overall diagnostic yield was 41% (37/89) with first-line trio-ES versus 31% (19/61) after normal CMA. Trio-ES and CMA were systematically concordant for identification of pathogenic CNV. Conclusion: Trio-ES provided a substantial prenatal diagnostic yield, similar to postnatal diagnosis with a median turnaround of approximately 1 month, supporting its routine implementation during the detection of prenatal US anomalies.
Collapse
Affiliation(s)
- Frédéric Tran Mau-Them
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
- INSERM UMR1231 GAD, F-21000, Dijon, France
- *Correspondence: Frédéric Tran Mau-Them,
| | - Julian Delanne
- Centre de Référence Maladies Rares “Anomalies Du Développement et Syndromes Malformatifs”, Centre de Génétique, FHU TRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Anne-Sophie Denommé-Pichon
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
- INSERM UMR1231 GAD, F-21000, Dijon, France
| | - Hana Safraou
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
- INSERM UMR1231 GAD, F-21000, Dijon, France
| | - Ange-Line Bruel
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
- INSERM UMR1231 GAD, F-21000, Dijon, France
| | - Antonio Vitobello
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
- INSERM UMR1231 GAD, F-21000, Dijon, France
| | - Aurore Garde
- Centre de Référence Maladies Rares “Anomalies Du Développement et Syndromes Malformatifs”, Centre de Génétique, FHU TRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Sophie Nambot
- Centre de Référence Maladies Rares “Anomalies Du Développement et Syndromes Malformatifs”, Centre de Génétique, FHU TRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Nicolas Bourgon
- Centre de Référence Maladies Rares “Anomalies Du Développement et Syndromes Malformatifs”, Centre de Génétique, FHU TRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Caroline Racine
- Centre de Référence Maladies Rares “Anomalies Du Développement et Syndromes Malformatifs”, Centre de Génétique, FHU TRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Arthur Sorlin
- INSERM UMR1231 GAD, F-21000, Dijon, France
- Centre de Référence Maladies Rares “Anomalies Du Développement et Syndromes Malformatifs”, Centre de Génétique, FHU TRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Sébastien Moutton
- Centre de Référence Maladies Rares “Anomalies Du Développement et Syndromes Malformatifs”, Centre de Génétique, FHU TRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Nathalie Marle
- Laboratoire Génétique Chromosomique et Moléculaire, CHU Dijon Bourgogne, Dijon, France
| | - Thierry Rousseau
- Service de Gynécologie Obstétrique, Médecine Fœtale et Stérilité Conjugale, Centre Hospitalier Universitaire Dijon Bourgogne, Dijon, France
| | - Paul Sagot
- Service de Gynécologie Obstétrique, Médecine Fœtale et Stérilité Conjugale, Centre Hospitalier Universitaire Dijon Bourgogne, Dijon, France
| | - Emmanuel Simon
- Service de Gynécologie Obstétrique, Médecine Fœtale et Stérilité Conjugale, Centre Hospitalier Universitaire Dijon Bourgogne, Dijon, France
| | - Catherine Vincent-Delorme
- CHU Lille, Clinique de Génétique Guy Fontaine, Centre de Référence Maladies Rares “Anomalies Du Développement et Syndromes Malformatifs” Nord-Ouest, FLille, France
| | - Odile Boute
- CHU Lille, Clinique de Génétique Guy Fontaine, Centre de Référence Maladies Rares “Anomalies Du Développement et Syndromes Malformatifs” Nord-Ouest, FLille, France
| | - Cindy Colson
- CHU Lille, Clinique de Génétique Guy Fontaine, Centre de Référence Maladies Rares “Anomalies Du Développement et Syndromes Malformatifs” Nord-Ouest, FLille, France
| | - Florence Petit
- CHU Lille, Clinique de Génétique Guy Fontaine, Centre de Référence Maladies Rares “Anomalies Du Développement et Syndromes Malformatifs” Nord-Ouest, FLille, France
| | - Marine Legendre
- CHU de Bordeaux, Service de Génétique Médicale, Bordeaux, France
| | - Sophie Naudion
- CHU de Bordeaux, Service de Génétique Médicale, Bordeaux, France
| | - Caroline Rooryck
- CHU de Bordeaux, Service de Génétique Médicale, Bordeaux, France
| | - Clément Prouteau
- Biochemistry and Genetics Department, University Hospital of Angers, Angers, France
| | - Estelle Colin
- Biochemistry and Genetics Department, University Hospital of Angers, Angers, France
| | - Agnès Guichet
- Biochemistry and Genetics Department, University Hospital of Angers, Angers, France
| | - Alban Ziegler
- Biochemistry and Genetics Department, University Hospital of Angers, Angers, France
| | - Dominique Bonneau
- Biochemistry and Genetics Department, University Hospital of Angers, Angers, France
| | - Godelieve Morel
- Service de Génétique Clinique, Centre de Référence Maladies Rares CLAD-Ouest, CHU Hôpital Sud, Rennes, France
| | - Mélanie Fradin
- Service de Génétique Clinique, Centre de Référence Maladies Rares CLAD-Ouest, CHU Hôpital Sud, Rennes, France
| | - Alinoé Lavillaureix
- Service de Génétique Clinique, Centre de Référence Maladies Rares CLAD-Ouest, CHU Hôpital Sud, Rennes, France
| | - Chloé Quelin
- Service de Génétique Clinique, Centre de Référence Maladies Rares CLAD-Ouest, CHU Hôpital Sud, Rennes, France
| | - Laurent Pasquier
- Service de Génétique Clinique, Centre de Référence Maladies Rares CLAD-Ouest, CHU Hôpital Sud, Rennes, France
| | - Sylvie Odent
- Service de Génétique Clinique, Centre de Référence Maladies Rares CLAD-Ouest, CHU Hôpital Sud, Rennes, France
| | - Gabriella Vera
- Service de Génétique—Unité de Génétique Clinique, Rouen, France
| | | | | | | | - Audrey Putoux
- Service de Génétique—GH Est-Hôpital Femme Mère Enfant, Lyon, France
| | | | - Carine Abel
- Service de Génétique et Centre de Diagnostic Anténatal, CHU de Lyon HCL—GH Nord-Hôpital de La Croix Rousse, Lyon, France
| | - Patricia Blanchet
- Equipe Maladies Génétiques de L’Enfant et de L’Adulte, Département Génétique Médicale, Maladies Rares et Médecine Personnalisée, CHU de Montpellier, University Montpellier, Montpellier, France
| | - Constance F. Wells
- Equipe Maladies Génétiques de L’Enfant et de L’Adulte, Département Génétique Médicale, Maladies Rares et Médecine Personnalisée, CHU de Montpellier, University Montpellier, Montpellier, France
| | - Caroline Deiller
- Equipe Maladies Génétiques de L’Enfant et de L’Adulte, Département Génétique Médicale, Maladies Rares et Médecine Personnalisée, CHU de Montpellier, University Montpellier, Montpellier, France
| | - Mathilde Nizon
- CHU Nantes, Service de Génétique Médicale, Nantes, France
- Institut Du Thorax, INSERM, CNRS, UNIV Nantes, Nantes, France
| | - Sandra Mercier
- CHU Nantes, Service de Génétique Médicale, Nantes, France
- Institut Du Thorax, INSERM, CNRS, UNIV Nantes, Nantes, France
| | - Marie Vincent
- CHU Nantes, Service de Génétique Médicale, Nantes, France
- Institut Du Thorax, INSERM, CNRS, UNIV Nantes, Nantes, France
| | - Bertrand Isidor
- CHU Nantes, Service de Génétique Médicale, Nantes, France
- Institut Du Thorax, INSERM, CNRS, UNIV Nantes, Nantes, France
| | - Jeanne Amiel
- Equipe “Embryologie et Génétiques des Malformations Congénitales", Institut Imagine—INSERM U1163, Institut des Maladies Génétiques, Paris, France
- Service de Génétique Médicale et Clinique, Hôpital Necker-Enfants Malades, Paris, France
| | - Rodolphe Dard
- Unité Fonctionnelle de Génétique Médicale, Cytogénétique, Génétique Médicale et Biologie de La Reproduction, Centre Hospitalier Intercommunal Poissy-Saint-Germain-en-Laye, Poissy, France
| | - Manon Godin
- Service de Génétique, CHU Caen Clemenceau, EA 7450 Biotargen, University Caen, Caen, France
| | - Nicolas Gruchy
- Service de Génétique, CHU Caen Clemenceau, EA 7450 Biotargen, University Caen, Caen, France
| | - Médéric Jeanne
- Service de Génétique, CHU de Tours, Tours, France
- UMR 1253, IBrain, Université de Tours, Inserm, Tours, France
| | - Elise Schaeffer
- Service de Génétique Médicale, CHU de Strasbourg—Hôpital de Hautepierre, Strasbourg, France
| | - Pierre-Yves Maillard
- Service de Génétique Médicale, CHU de Strasbourg—Hôpital de Hautepierre, Strasbourg, France
| | - Frédérique Payet
- Service de Génétique Médicale, Pôle Femme, Mère, Enfants CHU de La Réunion—GH Sud Réunion—Saint-Pierre, Saint-Pierre, France
| | - Marie-Line Jacquemont
- Service de Génétique Médicale, Pôle Femme, Mère, Enfants CHU de La Réunion—GH Sud Réunion—Saint-Pierre, Saint-Pierre, France
| | - Christine Francannet
- Service de Génétique Médicale, Pôle Femme et Enfant, CHU de Clermont-Ferrand—Hôpital D'Estaing, Clermont-Ferrand, France
| | - Sabine Sigaudy
- Unité de Génétique Clinique Prénatale, Département de Génétique Médicale, CHU de Marseille—Hôpital de La Timone, Marseille, France
| | - Marine Bergot
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
- INSERM UMR1231 GAD, F-21000, Dijon, France
| | | | - Marie-Laure Ascencio
- Centre D'Investigation Clinique CIC-EC Inserm CIC1432, UFR des Sciences de Santé, Université de Bourgogne-Franche-Comté, Dijon, France
| | - Christine Binquet
- Centre D'Investigation Clinique CIC-EC Inserm CIC1432, UFR des Sciences de Santé, Université de Bourgogne-Franche-Comté, Dijon, France
| | - Yannis Duffourd
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
- INSERM UMR1231 GAD, F-21000, Dijon, France
| | - Christophe Philippe
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
- INSERM UMR1231 GAD, F-21000, Dijon, France
| | - Laurence Faivre
- INSERM UMR1231 GAD, F-21000, Dijon, France
- Centre de Référence Maladies Rares “Anomalies Du Développement et Syndromes Malformatifs”, Centre de Génétique, FHU TRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Christel Thauvin-Robinet
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
- INSERM UMR1231 GAD, F-21000, Dijon, France
- Centre de Référence Maladies Rares “Anomalies Du Développement et Syndromes Malformatifs”, Centre de Génétique, FHU TRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| |
Collapse
|
7
|
Poot M. The Expanding Phenotypic Spectrum of NUP188 Variants Points Toward Multiple Biological Pathways. Mol Syndromol 2022; 13:261-262. [PMID: 36158058 PMCID: PMC9421690 DOI: 10.1159/000525275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 01/03/2023] Open
|
8
|
Petrovic S, Samanta D, Perriches T, Bley CJ, Thierbach K, Brown B, Nie S, Mobbs GW, Stevens TA, Liu X, Tomaleri GP, Schaus L, Hoelz A. Architecture of the linker-scaffold in the nuclear pore. Science 2022; 376:eabm9798. [PMID: 35679425 PMCID: PMC9867570 DOI: 10.1126/science.abm9798] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
INTRODUCTION In eukaryotic cells, the selective bidirectional transport of macromolecules between the nucleus and cytoplasm occurs through the nuclear pore complex (NPC). Embedded in nuclear envelope pores, the ~110-MDa human NPC is an ~1200-Å-wide and ~750-Å-tall assembly of ~1000 proteins, collectively termed nucleoporins. Because of the NPC's eightfold rotational symmetry along the nucleocytoplasmic axis, each of the ~34 different nucleoporins occurs in multiples of eight. Architecturally, the NPC's symmetric core is composed of an inner ring encircling the central transport channel and two outer rings anchored on both sides of the nuclear envelope. Because of its central role in the flow of genetic information from DNA to RNA to protein, the NPC is commonly targeted in viral infections and its nucleoporin constituents are associated with a plethora of diseases. RATIONALE Although the arrangement of most scaffold nucleoporins in the NPC's symmetric core was determined by quantitative docking of crystal structures into cryo-electron tomographic (cryo-ET) maps of intact NPCs, the topology and molecular details of their cohesion by multivalent linker nucleoporins have remained elusive. Recently, in situ cryo-ET reconstructions of NPCs from various species have indicated that the NPC's inner ring is capable of reversible constriction and dilation in response to variations in nuclear envelope membrane tension, thereby modulating the diameter of the central transport channel by ~200 Å. We combined biochemical reconstitution, high-resolution crystal and single-particle cryo-electron microscopy (cryo-EM) structure determination, docking into cryo-ET maps, and physiological validation to elucidate the molecular architecture of the linker-scaffold interaction network that not only is essential for the NPC's integrity but also confers the plasticity and robustness necessary to allow and withstand such large-scale conformational changes. RESULTS By biochemically mapping scaffold-binding regions of all fungal and human linker nucleoporins and determining crystal and single-particle cryo-EM structures of linker-scaffold complexes, we completed the characterization of the biochemically tractable linker-scaffold network and established its evolutionary conservation, despite considerable sequence divergence. We determined a series of crystal and single-particle cryo-EM structures of the intact Nup188 and Nup192 scaffold hubs bound to their Nic96, Nup145N, and Nup53 linker nucleoporin binding regions, revealing that both proteins form distinct question mark-shaped keystones of two evolutionarily conserved hetero‑octameric inner ring complexes. Linkers bind to scaffold surface pockets through short defined motifs, with flanking regions commonly forming additional disperse interactions that reinforce the binding. Using a structure‑guided functional analysis in Saccharomyces cerevisiae, we confirmed the robustness of linker‑scaffold interactions and established the physiological relevance of our biochemical and structural findings. The near-atomic composite structures resulting from quantitative docking of experimental structures into human and S. cerevisiae cryo-ET maps of constricted and dilated NPCs structurally disambiguated the positioning of the Nup188 and Nup192 hubs in the intact fungal and human NPC and revealed the topology of the linker-scaffold network. The linker-scaffold gives rise to eight relatively rigid inner ring spokes that are flexibly interconnected to allow for the formation of lateral channels. Unexpectedly, we uncovered that linker‑scaffold interactions play an opposing role in the outer rings by forming tight cross-link staples between the eight nuclear and cytoplasmic outer ring spokes, thereby limiting the dilatory movements to the inner ring. CONCLUSION We have substantially advanced the structural and biochemical characterization of the symmetric core of the S. cerevisiae and human NPCs and determined near-atomic composite structures. The composite structures uncover the molecular mechanism by which the evolutionarily conserved linker‑scaffold establishes the NPC's integrity while simultaneously allowing for the observed plasticity of the central transport channel. The composite structures are roadmaps for the mechanistic dissection of NPC assembly and disassembly, the etiology of NPC‑associated diseases, the role of NPC dilation in nucleocytoplasmic transport of soluble and integral membrane protein cargos, and the anchoring of asymmetric nucleoporins. [Figure: see text].
Collapse
Affiliation(s)
- Stefan Petrovic
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Dipanjan Samanta
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Thibaud Perriches
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Christopher J. Bley
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Karsten Thierbach
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Bonnie Brown
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Si Nie
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - George W. Mobbs
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Taylor A. Stevens
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Xiaoyu Liu
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Giovani Pinton Tomaleri
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Lucas Schaus
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - André Hoelz
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA,Corresponding author. (A.H.)
| |
Collapse
|
9
|
Deng Y, Song H, Xiao Y, Zhao Y, Chu L, Ding J, Shen X, Qi X. High-Throughput Sequencing to Investigate lncRNA-circRNA-miRNA-mRNA Networks Underlying the Effects of Beta-Amyloid Peptide and Senescence on Astrocytes. Front Genet 2022; 13:868856. [PMID: 35646066 PMCID: PMC9133720 DOI: 10.3389/fgene.2022.868856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/25/2022] [Indexed: 11/21/2022] Open
Abstract
Astrocytes are widely distributed in the central nervous system and play an essential role in the function of neuronal cells. Associations between astrocytes and Alzheimer’s disease (AD) have been noted, and recent work has implicated circular RNA (circRNA) and long non-coding RNA (lncRNA) in the development of AD. However, few reports have investigated which lncRNA and circRNA are involved in the influence of amyloid beta (Aβ) and senescence on astrocytes. This study therefore examines changes at the transcriptome level to explore the effects of Aβ and senescence on astrocytes. Primary cultured astrocytes were treated with Aβ and cultured for 90 days in vitro, and high-throughput sequencing was performed to identify differentially expressed RNAs. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses revealed that differentially expressed genes were associated with the focal adhesion signaling pathway, extracellular matrix receptor signaling pathway, and the extracellular matrix. The protein–protein interaction network was then constructed, and 103 hub genes were screened out; most of these were strongly associated with the expression of the extracellular matrix, extracellular matrix receptor signaling pathway, and focal adhesion. Two competing endogenous RNA networks were constructed based on the selected hub gene and differential RNAs, and we identified multiple competing endogenous RNA regulatory axes that were involved in the effects of Aβ and senescence on astrocytes. This is the first study to explore the molecular regulation mechanism of Aβ and senescence on primary astrocytes from the perspective of the whole transcriptome. In uncovering the signaling pathways and biological processes involved in the effects of Aβ and senescence on astrocytes, this work provides novel insights into the pathogenesis of AD at the level of competing endogenous RNA network regulation.
Collapse
Affiliation(s)
- Yuxin Deng
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education and Key Laboratory of Medical Molecular Biology of Guizhou Province, Guizhou Medical University, Guiyang, China
- School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
| | - Hui Song
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education and Key Laboratory of Medical Molecular Biology of Guizhou Province, Guizhou Medical University, Guiyang, China
| | - Yan Xiao
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education and Key Laboratory of Medical Molecular Biology of Guizhou Province, Guizhou Medical University, Guiyang, China
| | - Yi Zhao
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education and Key Laboratory of Medical Molecular Biology of Guizhou Province, Guizhou Medical University, Guiyang, China
| | - Liangzao Chu
- Department of Neurosurgery, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Jiuyang Ding
- School of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Xiangchun Shen
- School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang, China
- *Correspondence: Xiangchun Shen, ; Xiaolan Qi,
| | - Xiaolan Qi
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education and Key Laboratory of Medical Molecular Biology of Guizhou Province, Guizhou Medical University, Guiyang, China
- School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
- Translational Medicine Research Center, Guizhou Medical University, Guiyang, China
- *Correspondence: Xiangchun Shen, ; Xiaolan Qi,
| |
Collapse
|
10
|
Van Bergen NJ, Bell KM, Carey K, Gear R, Massey S, Murrell EK, Gallacher L, Pope K, Lockhart PJ, Kornberg A, Pais L, Walkiewicz M, Simons C, Wickramasinghe VO, White SM, Christodoulou J. Pathogenic variants in nucleoporin TPR (translocated promoter region, nuclear basket protein) cause severe intellectual disability in humans. Hum Mol Genet 2021; 31:362-375. [PMID: 34494102 DOI: 10.1093/hmg/ddab248] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 08/10/2021] [Accepted: 08/23/2021] [Indexed: 01/16/2023] Open
Abstract
The nuclear pore complex (NPC) is a multi-protein complex that regulates the trafficking of macromolecules between the nucleus and cytoplasm. Genetic variants in components of the NPC have been shown to cause a range of neurological disorders, including intellectual disability and microcephaly. Translocated promoter region, nuclear basket protein (TPR) is a critical scaffolding element of the nuclear facing interior of the NPC. Here we present two siblings with biallelic variants in TPR who present with a phenotype of microcephaly, ataxia and severe intellectual disability. The variants result in a premature truncation variant, and a splice variant leading to a 12-amino acid deletion respectively. Functional analyses in patient fibroblasts demonstrate significantly reduced TPR levels, and decreased TPR-containing NPC density. A compensatory increase in total NPC levels was observed, and decreased global RNA intensity in the nucleus. The discovery of variants that partly disable TPR function provide valuable insight into this essential protein in human disease, and our findings suggest that TPR variants are the cause of the siblings' neurological disorder.
Collapse
Affiliation(s)
- Nicole J Van Bergen
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Katrina M Bell
- Bioinformatics, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia.,Victorian Clinical Genetics Services, Royal Children's Hospital, VIC, Australia
| | - Kirsty Carey
- RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Russell Gear
- Victorian Clinical Genetics Services, Royal Children's Hospital, VIC, Australia
| | - Sean Massey
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia
| | - Edward K Murrell
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia
| | - Lyndon Gallacher
- Department of Paediatrics, University of Melbourne, Melbourne, Australia.,Victorian Clinical Genetics Services, Royal Children's Hospital, VIC, Australia
| | - Kate Pope
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia
| | - Paul J Lockhart
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia
| | - Andrew Kornberg
- Department of Paediatrics, University of Melbourne, Melbourne, Australia.,Neurology Department, Royal Children's Hospital, Melbourne, Australia.,Neurosciences Research, Murdoch Children's Research Institute, Victoria, Australia
| | - Lynn Pais
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Marzena Walkiewicz
- Translational Genomics Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia
| | - Cas Simons
- Victorian Clinical Genetics Services, Royal Children's Hospital, VIC, Australia.,Translational Genomics Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia
| | | | - Vihandha O Wickramasinghe
- RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Susan M White
- Department of Paediatrics, University of Melbourne, Melbourne, Australia.,Victorian Clinical Genetics Services, Royal Children's Hospital, VIC, Australia
| | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia.,Discipline of Child & Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| |
Collapse
|
11
|
Abstract
The development of CRISPR/Cas9 technology has vastly sped up the process of mammalian genome editing by introducing a bacterial system that can be exploited for reverse genetics-based research. However, generating homozygous functional knockout (KO) animals using traditional CRISPR/Cas9-mediated techniques requires three generations of animals. A founder animal with a desired mutation is crossed to produce heterozygous F1 offspring which are subsequently interbred to generate homozygous F2 KO animals. This study describes an adaptation of the CRISPR/Cas9-mediated method to develop a cohort of homozygous gene-targeted KO animals in one generation. A well-characterized ethanol-responsive gene, MyD88, was chosen as a candidate gene for generation of KO mice as proof-of-concept. Previous studies have reported changes in ethanol-related behavioral outcomes in MyD88 KO mice. One-cell mouse embryos were simultaneously electroporated with four gRNAs targeting a critical Exon of MyD88 along with Cas9 protein. DNA and RNA analysis of founder mice revealed a complex mix of genetic alterations, all of which were predicted to ablate MyD88 gene function. Behavioral testing confirmed the hypothesis that successful one-generation KO of MyD88 would reproduce the decreased ethanol-induced sedative/hypnotic effects and increased ethanol consumption in males that were observed in previous studies. This study additionally compared responses of Mock treatment control mice generated through electroporation to controls purchased from a vendor. No substantial behavioral changes were noted between control cohorts. Overall, the CRISPR/Cas9 KO protocol reported here, which we call CRISPR Turbo Accelerated KnockOut (CRISPy TAKO), will be useful for reverse genetic in vivo screens of gene function in whole animals.
Collapse
Affiliation(s)
- Sonja L Plasil
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Amit Seth
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Gregg E Homanics
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.,Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.,Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| |
Collapse
|
12
|
Abstract
Next-generation sequencing has greatly accelerated the discovery of rare human genetic diseases. Nearly 45% of patients have variants associated with known diseases but the unsolved cases remain a conundrum. Moreover, causative mutations can be difficult to pinpoint because variants frequently map to genes with no previous disease associations and, often, only one or a few patients with variants in the same gene are identified. Model organisms, such as Drosophila, can help to identify and characterize these new disease-causing genes. Importantly, Drosophila allow quick and sophisticated genetic manipulations, permit functional testing of human variants, enable the characterization of pathogenic mechanisms and are amenable to drug tests. In this Spotlight, focusing on microcephaly as a case study, we highlight how studies of human genes in Drosophila have aided our understanding of human genetic disorders, allowing the identification of new genes in well-established signaling pathways.
Collapse
Affiliation(s)
- Nichole Link
- Howard Hughes Medical Institute, BCM, Houston, TX, 77030, USA
- Department of Molecular and Human Genetics (MHG), BCM, Houston, TX, 77030, USA
- Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Hugo J Bellen
- Howard Hughes Medical Institute, BCM, Houston, TX, 77030, USA
- Department of Molecular and Human Genetics (MHG), BCM, Houston, TX, 77030, USA
- Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| |
Collapse
|