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2. Integrated clinical and omics approach to rare diseases: novel genes and oligogenic inheritance in holoprosencephaly

Author

Kim, A., Savary, C., Dubourg, C., Carre, W., Mouden, C., Hamdi-Roze, H., Guyodo, H., Douce, J. le, Pasquier, L., Flori, E., Gonzales, M., Beneteau, C., Boute, O., Attie-Bitach, T., Roume, J., Goujon, L., Akloul, L., Odent, S., Watrin, E., Dupe, V., Tayrac, M. de, David, V., Genin, E., Campion, D., Dartigues, J.F.C.O., Deleuze, J.F., Lambert, J.C., Redon, R., Ludwig, T., Grenier-Boley, B., Letort, S., Lindenbaum, P., Meyer, V., Quenez, O., Dina, C., Bellenguez, C., Charbonnier-Le Clezio, C., Giemza, J., Chatel, S., Ferec, C., Marec, H. le, Letenneur, L., Nicolas, G., Rouault, K., Bacq, D., Boland, A., Lechner, D., Wijmenga, C., Swertz, M.A., Slagboom, P.E., Ommen, G.J.B. van, Duijn, C.M. van, Boomsma, D.I., Bakker, P.I.W. de, Bovenberg, J.A., Craen, A.J.M. de, Beekman, M., Hofman, A., Willemsen, G., Wolffenbuttel, B., Platteel, M., Y.P. du, Chen, R.Y., Cao, H.Z., Cao, R., Sun, Y.S., Cao, J.S., Dijk, F. van, Neerincx, P.B.T., Deelen, P., Dijkstra, M., Byelas, G., Kanterakis, A., Bot, J., Ye, K., Lameijer, E.W., Vermaat, M., Laros, J.F.J., Dunnen, J.T. den, Knijff, P. de, Karssen, L.C., Leeuwen, E.M. van, Amin, N., Koval, V., Rivadeneira, F., Estrada, K., Hehirkwa, J.Y., Ligt, J. de, Abdellaoui, A., Hottenga, J.J., Kattenberg, V.M., Enckevort, D. van, Mei, H., Santcroos, M., Schaik, B.D.C. van, Handsaker, R.E., McCarroll, S.A., Eichler, E.E., Ko, A., Sudmant, P., Francioli, L.C., Kloosterman, W.P., Nijman, I.J., Guryev, V., FREX Consortium, GoNL Consortium, Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), Lifestyle Medicine (LM), Nanomedicine & Drug Targeting, Groningen Research Institute for Asthma and COPD (GRIAC), Center for Liver, Digestive and Metabolic Diseases (CLDM), Institut de Génétique et Développement de Rennes (IGDR), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), CHU Pontchaillou [Rennes], Service de génétique et embryologie médicales [CHU Trousseau], CHU Trousseau [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Service de génétique médicale - Unité de génétique clinique [Nantes], Université de Nantes (UN)-Centre hospitalier universitaire de Nantes (CHU Nantes), This work was supported by Fondation Maladie Rares (grant PMO1201204), Agence Nationale de la Recherche (grant ANR-12-BSV1-0007-01) and the Agence de la Biomedecine (AMP2016). This work was supported by La Fondation Maladie Rares and the Agence de la Biomedecine. The authors acknowledge the Centre de Ressources Biologiques (CRB)-Santé (http://www.crbsante-rennes.com) of Rennes for managing patient samples. This Work was supported by France Génomique National infrastructure, funded as part of 'Investissement d'avenir' program managed by Agence Nationale pour la Recherche (contrat ANR-10-INBS-09) https://www.france-genomique.org/spip/spip.php?article158. This study makes use of data generated by the Genome of the Netherlands Project. Funding for the project was provided by the Netherlands Organization for Scientific Research under award number 184 021 007, dated July 9, 2009 and made available as a Rainbow Project of the Biobanking and Biomolecular Research Infrastructure Netherlands (BBMRI-NL). Samples where contributed by LifeLines (http://lifelines.nl/lifelines-research/general), The Leiden Longevity Study (http://www.healthy-ageing.nl, ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), APH - Methodology, APH - Mental Health, Biological Psychology, APH - Health Behaviors & Chronic Diseases, APH - Personalized Medicine, Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)

Subjects
0301 basic medicine, Exome/genetics, Male, Multifactorial Inheritance, MOUSE, PHENOTYPE, GUIDELINES, PATHWAY, 0302 clinical medicine, Holoprosencephaly, Locus heterogeneity, SEQUENCE VARIANTS, oligogenic inheritance, Sonic hedgehog, Exome, Exome sequencing, Genetics, 0303 health sciences, Comparative Genomic Hybridization, Oligogenic Inheritance, Phenotype, 3. Good health, Pedigree, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], Female, FAT1, musculoskeletal diseases, EXPRESSION, congenital, hereditary, and neonatal diseases and abnormalities, Holoprosencephaly/genetics, Clinical Neurology, Biology, MICE LACKING, 03 medical and health sciences, sonic hedgehog, Rare Diseases, Rare Diseases/genetics, primary cilia, DEFICIENT, medicine, Humans, Gene, Multifactorial Inheritance/genetics, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, IDENTIFICATION, Genetic heterogeneity, MUTATIONS, medicine.disease, 030104 developmental biology, holoprosencephaly, Case-Control Studies, Forebrain, Mutation, biology.protein, Neurology (clinical), 030217 neurology & neurosurgery, exome
Abstract

Kim et al. identify novel genes and disease pathways in the forebrain developmental disorder holoprosencephaly, and show that many cases involve oligogenic inheritance. The findings underline the roles of Sonic Hedgehog and primary cilia in forebrain development, and show that integrating clinical phenotyping into genetic studies can uncover relevant mutations.Holoprosencephaly is a pathology of forebrain development characterized by high phenotypic heterogeneity. The disease presents with various clinical manifestations at the cerebral or facial levels. Several genes have been implicated in holoprosencephaly but its genetic basis remains unclear: different transmission patterns have been described including autosomal dominant, recessive and digenic inheritance. Conventional molecular testing approaches result in a very low diagnostic yield and most cases remain unsolved. In our study, we address the possibility that genetically unsolved cases of holoprosencephaly present an oligogenic origin and result from combined inherited mutations in several genes. Twenty-six unrelated families, for whom no genetic cause of holoprosencephaly could be identified in clinical settings [whole exome sequencing and comparative genomic hybridization (CGH)-array analyses], were reanalysed under the hypothesis of oligogenic inheritance. Standard variant analysis was improved with a gene prioritization strategy based on clinical ontologies and gene co-expression networks. Clinical phenotyping and exploration of cross-species similarities were further performed on a family-by-family basis. Statistical validation was performed on 248 ancestrally similar control trios provided by the Genome of the Netherlands project and on 574 ancestrally matched controls provided by the French Exome Project. Variants of clinical interest were identified in 180 genes significantly associated with key pathways of forebrain development including sonic hedgehog (SHH) and primary cilia. Oligogenic events were observed in 10 families and involved both known and novel holoprosencephaly genes including recurrently mutated FAT1, NDST1, COL2A1 and SCUBE2. The incidence of oligogenic combinations was significantly higher in holoprosencephaly patients compared to two control populations (P

Published
2019
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3. Heterozygous Variants in KMT2E Cause a Spectrum of Neurodevelopmental Disorders and Epilepsy

Author

O'Donnell-Luria, A.H., Pais, L.S., Faundes, V., Wood, J.C., Sveden, A., Luria, V., Jamra, R. Abou, Accogli, A., Amburgey, K., Anderlid, B.M., Azzarello-Burri, S., Basinger, A.A., Bianchini, C., Bird, L.M., Buchert, R., Carre, W., Ceulemans, S., Charles, P., Cox, H., Culliton, L., Curro, A., Demurger, F., Dowling, J.J., Duban-Bedu, B., Dubourg, C., Eiset, S.E., Escobar, L.F., Ferrarini, A., Haack, T.B., Hashim, M., Heide, S. van der, Helbig, K.L., Helbig, I., Heredia, R., Heron, D., Isidor, B., Jonasson, A.R., Joset, P., Keren, B., Kok, F., Kroes, H.Y., Lavillaureix, A., Lu, X., Maas, S.M., Maegawa, G.H., Marcelis, C.L.M., Mark, P.R., Masruha, M.R., McLaughlin, H.M., McWalter, K., Melchinger, E.U., Mercimek-Andrews, S., Nava, C., Pendziwiat, M., Person, R., Ramelli, G.P., Ramos, L.L.P., Rauch, A., Reavey, C., Renieri, A., Riess, A., Sanchez-Valle, A., Sattar, S., Saunders, C., Schwarz, N., Smol, T., Srour, M., Steindl, K., Syrbe, S., Taylor, J.C., Telegrafi, A., Thiffault, I., Trauner, D.A., Linden, H., Jr. van der, Koningsbruggen, S. van, Villard, L., Vogel, I., Vogt, J., Weber, Y.G., Wentzensen, I.M., Widjaja, E., Zak, J., Baxter, S., Banka, S., Rodan, L.H., O'Donnell-Luria, A.H., Pais, L.S., Faundes, V., Wood, J.C., Sveden, A., Luria, V., Jamra, R. Abou, Accogli, A., Amburgey, K., Anderlid, B.M., Azzarello-Burri, S., Basinger, A.A., Bianchini, C., Bird, L.M., Buchert, R., Carre, W., Ceulemans, S., Charles, P., Cox, H., Culliton, L., Curro, A., Demurger, F., Dowling, J.J., Duban-Bedu, B., Dubourg, C., Eiset, S.E., Escobar, L.F., Ferrarini, A., Haack, T.B., Hashim, M., Heide, S. van der, Helbig, K.L., Helbig, I., Heredia, R., Heron, D., Isidor, B., Jonasson, A.R., Joset, P., Keren, B., Kok, F., Kroes, H.Y., Lavillaureix, A., Lu, X., Maas, S.M., Maegawa, G.H., Marcelis, C.L.M., Mark, P.R., Masruha, M.R., McLaughlin, H.M., McWalter, K., Melchinger, E.U., Mercimek-Andrews, S., Nava, C., Pendziwiat, M., Person, R., Ramelli, G.P., Ramos, L.L.P., Rauch, A., Reavey, C., Renieri, A., Riess, A., Sanchez-Valle, A., Sattar, S., Saunders, C., Schwarz, N., Smol, T., Srour, M., Steindl, K., Syrbe, S., Taylor, J.C., Telegrafi, A., Thiffault, I., Trauner, D.A., Linden, H., Jr. van der, Koningsbruggen, S. van, Villard, L., Vogel, I., Vogt, J., Weber, Y.G., Wentzensen, I.M., Widjaja, E., Zak, J., Baxter, S., Banka, S., and Rodan, L.H.

Abstract

Contains fulltext : 206572.pdf (publisher's version ) (Open Access), We delineate a KMT2E-related neurodevelopmental disorder on the basis of 38 individuals in 36 families. This study includes 31 distinct heterozygous variants in KMT2E (28 ascertained from Matchmaker Exchange and three previously reported), and four individuals with chromosome 7q22.2-22.23 microdeletions encompassing KMT2E (one previously reported). Almost all variants occurred de novo, and most were truncating. Most affected individuals with protein-truncating variants presented with mild intellectual disability. One-quarter of individuals met criteria for autism. Additional common features include macrocephaly, hypotonia, functional gastrointestinal abnormalities, and a subtle facial gestalt. Epilepsy was present in about one-fifth of individuals with truncating variants and was responsive to treatment with anti-epileptic medications in almost all. More than 70% of the individuals were male, and expressivity was variable by sex; epilepsy was more common in females and autism more common in males. The four individuals with microdeletions encompassing KMT2E generally presented similarly to those with truncating variants, but the degree of developmental delay was greater. The group of four individuals with missense variants in KMT2E presented with the most severe developmental delays. Epilepsy was present in all individuals with missense variants, often manifesting as treatment-resistant infantile epileptic encephalopathy. Microcephaly was also common in this group. Haploinsufficiency versus gain-of-function or dominant-negative effects specific to these missense variants in KMT2E might explain this divergence in phenotype, but requires independent validation. Disruptive variants in KMT2E are an under-recognized cause of neurodevelopmental abnormalities.

Published
2019

4. De Novo Mutations in Protein Kinase Genes CAMK2A and CAMK2B Cause Intellectual Disability

Author

Kury, S., Woerden, G.M. van, Besnard, T., Onori, M.P., Latypova, X., Towne, M.C., Cho, M.T., Prescott, T.E., Ploeg, M.A., Sanders, S., Stessman, H.A.F., Pujol, A., Distel, ben, Robak, L.A., Bernstein, J.A., Denomme-Pichon, A.S., Lesca, G., Sellars, E.A., Berg, J., Carre, W., Busk, O.L., Bon, B.W.M. van, Waugh, J.L., Deardorff, M., Hoganson, G.E., Bosanko, K.B., Johnson, D.S., Dabir, T., Holla, O.L., Sarkar, A., Tveten, K., Bellescize, J. de, Braathen, G.J., Terhal, P.A., Grange, D.K., Haeringen, A. van, Lam, C., Mirzaa, G., Burton, J., Bhoj, E.J., Douglas, J., Santani, A.B., Nesbitt, A.I., Helbig, K.L., Andrews, M.V., Begtrup, A., Tang, S., Gassen, K.L.I. van, Juusola, J., Foss, K., Enns, G.M., Moog, U., Hinderhofer, K., Paramasivam, N., Lincoln, S., Kusako, B.H., Lindenbaum, P., Charpentier, E., Nowak, C.B., Cherot, E., Simonet, T., Ruivenkamp, C.A.L., Hahn, S., Brownstein, C.A., Xia, F., Schmitt, S., Deb, W., Bonneau, D., Nizon, M., Quinquis, D., Chelly, J., Rudolf, G., Sanlaville, D., Parent, P., Gilbert-Dussardier, B., Toutain, A., Sutton, V.R., Thies, J., Peart-Vissers, L.E.L.M., Boisseau, P., Vincent, M., Grabrucker, A.M., Dubourg, C., Tan, W.H., Verbeek, N.E., Granzow, M., Santen, G.W.E., Shendure, J., Isidor, B., Pasquier, L., Redon, R., Yang, Y.P., State, M.W., Kleefstra, T., Cogne, B., Petrovski, S., Retterer, K., Eichler, E.E., Rosenfeld, J.A., Agrawal, P.B., Bezieau, S., Odent, S., Elgersma, Y., Mercier, S., Undiagnosed Dis Network, GEM HUGO, Deciphering Dev Dis Study, Service de génétique médicale [CHU Nantes], Centre hospitalier universitaire de Nantes (CHU Nantes), Department of Neuroscience [Rotterdam, the Netherlands], Erasmus University Medical Center [Rotterdam] (Erasmus MC), Expertise Center for Neurodevelopmental Disorders [Rotterdam, the Netherlands] (ENCORE), Genomics Program and Division of Genetics [Boston, USA], Harvard Medical School [Boston] (HMS)-Boston Children's Hospital-The Manton Center for Orphan Disease Research, Gene Discovery Core [Boston, MA, USA] ( The Manton Center for Orphan Disease Research), Harvard Medical School [Boston] (HMS)-Boston Children's Hospital, GeneDx [Gaithersburg, MD, USA], Department of Medical Genetics [Skien, Norway], Telemark Hospital Trust [Skien, Norway], Department of Psychiatry [San Francisco, CA, USA], University of California [San Francisco] (UCSF), University of California-University of California, Department of Genome Sciences [Seattle] (GS), University of Washington [Seattle], Department of Pharmacology [Omaha, NE, USA], Creighton University Medical School [Omaha, NE, USA], Neurometabolic Diseases Laboratory [Barcelona, Spain], Institut d'Investigació Biomèdica de Bellvitge [Barcelone] (IDIBELL), Centre for Biomedical Research on Rare Diseases [Barcelona, Spain] (CIBERER), Hospital Sant Joan de Déu [Barcelona], Institució Catalana de Recerca i Estudis Avançats (ICREA), Department of Medical Biochemistry [Amsterdam, the Netherlands] (Academic Medical Center), University of Amsterdam [Amsterdam] (UvA), Department of Molecular and Human Genetics [Houston, USA], Baylor College of Medecine, Department of Pediatrics [Stanford], Stanford Medicine, Stanford University-Stanford University, Département de Biochimie et Génétique [Angers], Université d'Angers (UA)-Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM)-PRES Université Nantes Angers Le Mans (UNAM), Biologie Neurovasculaire et Mitochondriale Intégrée (BNMI), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université d'Angers (UA), Service de Génétique [HCL, Lyon] (Centre de Référence des Anomalies du Développement), Hospices civils de Lyon (HCL), Centre de recherche en neurosciences de Lyon (CRNL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet [Saint-Étienne] (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Section of Genetics and Metabolism [Little Rock, AR, USA], University of Arkansas for Medical Sciences (UAMS), Molecular and Clinical Medicine [Dundee, UK] (School of Medicine), University of Dundee [UK]-Ninewells Hospital & Medical School [Dundee, UK], Laboratoire de Génétique Moléculaire & Génomique [CHU Rennes], CHU Pontchaillou [Rennes], Department of Human Genetics [Nijmegen], Radboud University Medical Center [Nijmegen], Department of Neurology [Boston], Harvard Medical School [Boston] (HMS)-Massachusetts General Hospital [Boston], Department of Pediatrics [Philadelphia, PA, USA] (Division of Genetics), Children’s Hospital of Philadelphia (CHOP ), Department of Pediatrics [Chicago, IL, USA] (College of Medicine), University of Illinois [Chicago] (UIC), University of Illinois System-University of Illinois System, Sheffield Children's NHS Foundation Trust, Northern Ireland Regional Genetics Centre [Belfast, UK], Belfast City Hospital-Belfast Health and Social Care Trust, Nottingham Regional Genetics Service [Nottingham, UK], City Hospital Campus [Nottingham, UK]-Nottingham University Hospitals NHS Trust [UK], Département d'Epilepsie, Sommeil et Neurophysiologie Pédiatrique [HCL, Lyon], Hospices Civils de Lyon (HCL), Department of Genetics [Utrecht, the Netherlands], University Medical Center [Utrecht], Department of Pediatrics [Saint Louis, MO, USA] (Division of Genetics and Genomic Medicine), Washington University in Saint Louis (WUSTL), Department of Clinical Genetics [Leiden, the Netherlands], Leiden University Medical Center (LUMC), Department of Pediatrics [Seattle, WA, USA] (Division of Genetic Medicine), University of Washington [Seattle]-Seattle Children’s Hospital, Center for Integrative Brain Research [Seattle, WA, USA], University of Washington [Seattle]-Seattle Children's Research Institute, The Center for Applied Genomics [Philadelphia, PA, USA], Division of Human Genetics [Philadelphia, PA, USA], Department of Pathology and Laboratory Medicine [Philadelphia, PA, USA], University of Pennsylvania [Philadelphia]-Perelman School of Medicine, University of Pennsylvania [Philadelphia], Department of Pathology and Laboratory Medicine [Philadelphia, PA, USA] (Perelman School of Medicine), Division of Clinical Genomics [Aliso Viejo, CA, USA], Ambry Genetics [Aliso Viejo, CA, USA], Division of Neurology [Philadelphia, PA, USA], Institute of Human Genetics [Heidelberg, Germany], Universität Heidelberg [Heidelberg], University of Heidelberg, Medical Faculty, unité de recherche de l'institut du thorax UMR1087 UMR6291 (ITX), Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Diagnostic Génétique [CHU Strasbourg], Université de Strasbourg (UNISTRA)-CHU Strasbourg, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg (UNISTRA), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Service de Neurologie [CHU Strasbourg], Hôpital de Hautepierre [Strasbourg]-Centre Hospitalier Universitaire de Strasbourg (CHU de Strasbourg ), Département de génétique médicale en pédiatrie [CHRU Brest], Centre Hospitalier Régional Universitaire de Brest (CHRU Brest), Service de Génétique [CHU Poitiers], Centre hospitalier universitaire de Poitiers (CHU Poitiers), Service de Génétique [CHRU Tours], Centre Hospitalier Régional Universitaire de Tours (CHRU TOURS), Department of Biological Sciences [Limerick, Ireland], University of Limerick (UL), Bernal Institute [Limerick, Ireland], Howard Hughes Medical Institute [Seattle], Howard Hughes Medical Institute (HHMI), Institut de Génétique et Développement de Rennes (IGDR), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Service de Génétique Clinique [CHU Rennes] (Réseau de Génétique et Génomique Médicale), Hôpitaux Universitaires du Grand Ouest, The Wellcome Trust Sanger Institute [Cambridge], Department of Medicine [Melbourne, Australia], University of Melbourne-Austin Health, Division of Newborn Medicine [Boston, MA, USA], Immunobiology of Human αβ and γδ T Cells and Immunotherapeutic Applications (CRCINA-ÉQUIPE 1), Centre de Recherche en Cancérologie et Immunologie Nantes-Angers (CRCINA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Centre hospitalier universitaire de Nantes (CHU Nantes)-Centre National de la Recherche Scientifique (CNRS)-Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Centre hospitalier universitaire de Nantes (CHU Nantes)-Centre National de la Recherche Scientifique (CNRS)-Université d'Angers (UA), Neurosciences, Physiopathologie Cardiovasculaire et Mitochondriale (MITOVASC), Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre Hospitalier Régional Universitaire de Tours (CHRU Tours), Univ Angers, Okina, University of California [San Francisco] (UC San Francisco), University of California (UC)-University of California (UC), Centre de recherche en neurosciences de Lyon - Lyon Neuroscience Research Center (CRNL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de génétique moléculaire et génomique médicale [CHU Rennes], Nottingham University Hospitals NHS Trust (NUH)-City Hospital Campus [Nottingham, UK], Universiteit Leiden-Universiteit Leiden, Department of Pediatrics [Seattle, WA, USA], University of Pennsylvania-Perelman School of Medicine, University of Pennsylvania, Universität Heidelberg [Heidelberg] = Heidelberg University, Unité de recherche de l'institut du thorax (ITX-lab), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Service de génétique clinique [Rennes], Université de Rennes (UR)-CHU Pontchaillou [Rennes]-hôpital Sud, Université d'Angers (UA)-Université de Nantes (UN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre hospitalier universitaire de Nantes (CHU Nantes)-Université d'Angers (UA)-Université de Nantes (UN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre hospitalier universitaire de Nantes (CHU Nantes), Amsterdam Gastroenterology Endocrinology Metabolism, Medical Biochemistry, and Bernardo, Elizabeth

Subjects
0301 basic medicine, Male, de novo mutations, AMPAR, medicine.disease_cause, Inbred C57BL, Mice, 0302 clinical medicine, Intellectual disability, CAMK2A, Exome, Phosphorylation, Genetics (clinical), Genetics, Neurons, Mutation, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, Brain, Phenotype, NMDAR, intellectual disability, Female, Signal transduction, Rare cancers Radboud Institute for Health Sciences [Radboudumc 9], Signal Transduction, Glutamic Acid, [SDV.CAN]Life Sciences [q-bio]/Cancer, Biology, Article, Cell Line, 03 medical and health sciences, [SDV.CAN] Life Sciences [q-bio]/Cancer, medicine, Journal Article, Animals, Humans, Protein kinase A, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], synaptic plasticity, medicine.disease, Mice, Inbred C57BL, CAMK2, CAMK2B, 030104 developmental biology, HEK293 Cells, Synaptic plasticity, Calcium-Calmodulin-Dependent Protein Kinase Type 2, 030217 neurology & neurosurgery, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract

Contains fulltext : 182539.pdf (Publisher’s version ) (Closed access) Calcium/calmodulin-dependent protein kinase II (CAMK2) is one of the first proteins shown to be essential for normal learning and synaptic plasticity in mice, but its requirement for human brain development has not yet been established. Through a multi-center collaborative study based on a whole-exome sequencing approach, we identified 19 exceedingly rare de novo CAMK2A or CAMK2B variants in 24 unrelated individuals with intellectual disability. Variants were assessed for their effect on CAMK2 function and on neuronal migration. For both CAMK2A and CAMK2B, we identified mutations that decreased or increased CAMK2 auto-phosphorylation at Thr286/Thr287. We further found that all mutations affecting auto-phosphorylation also affected neuronal migration, highlighting the importance of tightly regulated CAMK2 auto-phosphorylation in neuronal function and neurodevelopment. Our data establish the importance of CAMK2A and CAMK2B and their auto-phosphorylation in human brain function and expand the phenotypic spectrum of the disorders caused by variants in key players of the glutamatergic signaling pathway.

Published
2017
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6. Chondrus crispus – A Present and Historical Model Organism for Red Seaweeds

Author

Porcel, B., Carre, W., Ball, S., Chaparro, C., Barbeyron, T., Noel, B., Valentin, K., Elias, M., Artiguenave, François, Arun, A., Aury, J.-M., Barbosa-Neto, J., Bothwell, J., Bouget, F.-Y., Brillet, L., Cabello-Hurtado, F., Capella-Gutierrez, S., Charrier, B., Cladière, L., Cock, J., Coelho, S., Colleoni, C., Czjzek, M., Da Silva, C., Delage, L., Denoeud, France, Deschamps, P., Dittami, S., Gabaldón, T., Gachon, C., Groisillier, A., Jabbari, K., Katinka, M., Kloareg, B., Kowalczyk, N., Labadie, K., Lopez, P., Mclachlan, D., Meslet-Cladiere, L., Moustafa, A., Nehr, Z., Nyvall Collen, P., Panaud, O., Partensky, F., Poulain, J., Rensing, S., Rousvoal, S., Samson, G., Symeonidi, A., Weissenbach, J., Zambounis, A., Wincker, P., Collen, Jonas, Cornish, M. Lynn, Craigie, James, Ficko-Blean, Elizabeth, Hervé, Cécile, Krueger-Hadfield, Stacy, Leblanc, Catherine, Michel, Gurvan, Potin, Philippe, Tonon, Thierry, Boyen, Catherine, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 (UGSF), Institut National de la Recherche Agronomique (INRA)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), inconnu, Inconnu, Centre d'étude spatiale des rayonnements (CESR), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Université Fédérale Toulouse Midi-Pyrénées-Centre National d'Études Spatiales [Toulouse] (CNES)-Météo France-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Météo France, Structure et évolution des génomes (SEG), CNS-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Sylvadour, IUT des Pays de l'Adour, Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie et chimie des protéines [Lyon] (IBCP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Institut de biologie moléculaire des plantes (IBMP), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Institut de Génomique Fonctionnelle de Lyon (IGFL), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, Institut de Génomique d'Evry (IG), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Centre d'études d'océanographie et de biologie marine (CEOBM), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Unité de Recherche Clinique, Hospices Civils de Lyon (HCL), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Bordeaux 2 Laboratoire de Psychologie EA «Santé et qualité de vie», Université Bordeaux Segalen - Bordeaux 2, Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Collège de France (CdF)-Institut national des sciences de l'Univers (INSU - CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), and École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL)

Subjects
biology, Ecology, Ecology (disciplines), [SDV]Life Sciences [q-bio], Population structure, Genomics, biology.organism_classification, Moss, Rocky shore, Algae, Chondrus crispus, Botany, 14. Life underwater, Organism, ComputingMilieux_MISCELLANEOUS
Abstract

Chondrus crispus, or Irish moss, is a common edible red seaweed that can be found on rocky shores in the Northern Atlantic. The cell wall contains carrageenan and C. crispus is the original source of this commercially used thickener. Because of the ecological and economic importance of this red alga a relatively important research literature exists and one of the recent achievements in C. crispus research is the sequencing of its genome. In this chapter we review some of the literature with the aim to promote C. crispus as a model organism for florideophyte red seaweeds. We consider subjects like commercial and historical uses, ecology, genetics, population structure, mating systems, physiology, cell wall biology and genomics. © 2014 Elsevier Ltd.

Published
2014
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8. The Chicken Gene Nomenclature Committee report

Author

Burt, D. W., Carre, W., Fell, Mark, Law, A. S., Antin, P. B., Maglott, D. R., Weber, J. A., Schmidt, C. J., Burgess, S. C., and McCarthy, F. M.

Subjects
animal structures, chicken genetic maps nomenclature
Abstract

Comparative genomics is an essential component of the post-genomic era. The chicken genome is the first avian genome to be sequenced and it will serve as a model for other avian species. Moreover, due to its unique evolutionary niche, the chicken genome can be used to understand evolution of functional elements and gene regulation in mammalian species. However comparative biology both within avian species and within amniotes is hampered due to the difficulty of recognising functional orthologs. This problem is compounded as different databases and sequence repositories proliferate and the names they assign to functional elements proliferate along with them. Currently, genes can be published under more than one name and one name sometimes refers to unrelated genes. Standardized gene nomenclature is necessary to facilitate communication between scientists and genomic resources. Moreover, it is important that this nomenclature be based on existing nomenclature efforts where possible to truly facilitate studies between different species. We report here the formation of the Chicken Gene Nomenclature Committee (CGNC), an international and centralized effort to provide standardized nomenclature for chicken genes. The CGNC works in conjunction with public resources such as NCBI and Ensembl and in consultation with existing nomenclature committees for human and mouse. The CGNC will develop standardized nomenclature in consultation with the research community and relies on the support of the research community to ensure that the nomenclature facilitates comparative and genomic studies.

Published
2009
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9. Systems-wide chicken DNA microarrays, gene expression profiling and discovery of functional genes

Author

Larry Cogburn, Wang, X., Carre, W., Rejto, L., Porter, T. E., Aggrey, S. E., Simon, J., Unité de Recherches Avicoles (URA), and Institut National de la Recherche Agronomique (INRA)

Subjects
GENE EXPRESSION, [SDV.SA.SPA]Life Sciences [q-bio]/Agricultural sciences/Animal production studies, BASE DE DONNEES, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2003

10. Whole genome comparative studies between chicken and turkey and their implications for avian genome evolution

Author

Griffin, D.K., Robertson, L.B., Tempest, H.G., Vignal, A., Fillon, V., Crooijmans, R.P.M.A., Groenen, M.A.M., Deryusheva, S., Gaginskaya, E., Carre, W., Waddington, D., Talbot, R., Völker, M., Masabanda, J.S., Burt, D.W., Griffin, D.K., Robertson, L.B., Tempest, H.G., Vignal, A., Fillon, V., Crooijmans, R.P.M.A., Groenen, M.A.M., Deryusheva, S., Gaginskaya, E., Carre, W., Waddington, D., Talbot, R., Völker, M., Masabanda, J.S., and Burt, D.W.

Abstract

Background Comparative genomics is a powerful means of establishing inter-specific relationships between gene function/location and allows insight into genomic rearrangements, conservation and evolutionary phylogeny. The availability of the complete sequence of the chicken genome has initiated the development of detailed genomic information in other birds including turkey, an agriculturally important species where mapping has hitherto focused on linkage with limited physical information. No molecular study has yet examined conservation of avian microchromosomes, nor differences in copy number variants (CNVs) between birds. Results We present a detailed comparative cytogenetic map between chicken and turkey based on reciprocal chromosome painting and mapping of 338 chicken BACs to turkey metaphases. Two inter-chromosomal changes (both involving centromeres) and three pericentric inversions have been identified between chicken and turkey; and array CGH identified 16 inter-specific CNVs. Conclusion This is the first study to combine the modalities of zoo-FISH and array CGH between different avian species. The first insight into the conservation of microchromosomes, the first comparative cytogenetic map of any bird and the first appraisal of CNVs between birds is provided. Results suggest that avian genomes have remained relatively stable during evolution compared to mammalian equivalents.

Published
2008

12. Dual molecular effects of dominant RORA mutations cause two variants of syndromic intellectual disability with either autistic features or cerebellar ataxia

Author

Latypova, X., Guissart, C., Khan, T. N., Rollier, P., Stamberger, H., Mcwalter, K., Cho, M. T., Kjaergaard, S., Weckhuysen, S., Lesca, G., Besnard, T., KATRIN OUNAP, Schema, L., Chiocchetti, A. G., Mcdonald, M., Bellescize, J., Vincent, M., Esch, H., Sattler, S., Forghani, I., Thiffault, I., Freitag, C. M., Barbouth, D., Cadieux-Dion, M., Saffina, N. P., Grote, L., Carre, W., Saunders, C., Pajusalu, S., Boland, A., Karlowicz, D. Hays, Deleuze, J., Wojcik, M. H., Pressman, R., Isidor, B., Vogels, A., Paesschen, W., Rivier, F., Leboucq, N., Cogne, B., Sasorith, S., Sanlaville, D., Retterer, K., Odent, S., Katsanis, N., Bezieau, S., Koenig, M., Pasquier, L., Davis, E. E., and Kury, S.

15. Functional Genomics in Chickens: Development of Integrated-Systems Microarrays for Transcriptional Profiling and Discovery of Regulatory Pathways

Author

A. Cogburn, L., Wang, X., Carre, W., Rejto, L., E. Aggrey, S., J. Duclos, M., Simon, J., and E. Porter, T.

Abstract

The genetic networks that govern the differentiation and growth of major tissues of economic importance in the chicken are largely unknown. Under a functional genomics project, our consortium has generated 30 609 expressed sequence tags (ESTs) and developed several chicken DNA microarrays, which represent the Chicken Metabolic/Somatic (10 K) and Neuroendocrine/Reproductive (8 K) Systems (http://udgenome.ags.udel.edu/cogburn/). One of the major challenges facing functional genomics is the development of mathematical models to reconstruct functional gene networks and regulatory pathways from vast volumes of microarray data. In initial studies with liver-specific microarrays (3.1 K), we have examined gene expression profiles in liver during the peri-hatch transition and during a strong metabolic perturbation—fasting and re-feeding—in divergently selected broiler chickens (fast vs. slow-growth lines). The expression of many genes controlling metabolic pathways is dramatically altered by these perturbations. Our analysis has revealed a large number of clusters of functionally related genes (mainly metabolic enzymes and transcription factors) that control major metabolic pathways. Currently, we are conducting transcriptional profiling studies of multiple tissues during development of two sets of divergently selected broiler chickens (fast vs. slow growing and fat vs. lean lines). Transcriptional profiling across multiple tissues should permit construction of a detailed genetic blueprint that illustrates the developmental events and hierarchy of genes that govern growth and development of chickens. This review will briefly describe the recent acquisition of chicken genomic resources (ESTs and microarrays) and our consortium's efforts to help launch the new era of functional genomics in the chicken.

Published
2004
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18. FOSL2 truncating variants in the last exon cause a neurodevelopmental disorder with scalp and enamel defects.

Author

Cospain A, Rivera-Barahona A, Dumontet E, Gener B, Bailleul-Forestier I, Meyts I, Jouret G, Isidor B, Brewer C, Wuyts W, Moens L, Delafontaine S, Keung Lam WW, Van Den Bogaert K, Boogaerts A, Scalais E, Besnard T, Cogne B, Guissard C, Rollier P, Carre W, Bouvet R, Tarte K, Gómez-Carmona R, Lapunzina P, Odent S, Faoucher M, Dubourg C, Ruiz-Pérez VL, Devriendt K, Pasquier L, and Pérez-Jurado LA

Subjects
Humans, Scalp abnormalities, Scalp metabolism, HEK293 Cells, Transcription Factor AP-1 genetics, Exons genetics, RNA, Messenger, Fos-Related Antigen-2 genetics, Autism Spectrum Disorder genetics, Ectodermal Dysplasia genetics, Neurodevelopmental Disorders genetics
Abstract

Purpose: We aimed to investigate the molecular basis of a novel recognizable neurodevelopmental syndrome with scalp and enamel anomalies caused by truncating variants in the last exon of the gene FOSL2, encoding a subunit of the AP-1 complex., Methods: Exome sequencing was used to identify genetic variants in all cases, recruited through Matchmaker exchange. Gene expression in blood was analyzed using reverse transcription polymerase chain reaction. In vitro coimmunoprecipitation and proteasome inhibition assays in transfected HEK293 cells were performed to explore protein and AP-1 complex stability., Results: We identified 11 individuals from 10 families with mostly de novo truncating FOSL2 variants sharing a strikingly similar phenotype characterized by prenatal growth retardation, localized cutis scalp aplasia with or without skull defects, neurodevelopmental delay with autism spectrum disorder, enamel hypoplasia, and congenital cataracts. Mutant FOSL2 messenger RNAs escaped nonsense-mediated messenger RNA decay. Truncated FOSL2 interacts with c-JUN, thus mutated AP-1 complexes could be formed., Conclusion: Truncating variants in the last exon of FOSL2 associate a distinct clinical phenotype by altering the regulatory degradation of the AP-1 complex. These findings reveal a new role for FOSL2 in human pathology., Competing Interests: Conflict of Interest L.A.P.-J. is founding partner and scientific advisor of qGenomics Laboratories. All other authors declare no conflicts of interest., (Copyright © 2022 American College of Medical Genetics and Genomics. All rights reserved.)

Published
2022
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19. Fetal Description of the Pancreatic Agenesis and Holoprosencephaly Syndrome Associated to a Specific CNOT1 Variant.

Author

Cospain A, Faoucher M, Cauchois A, Carre W, Quelin C, and Dubourg C

Subjects
Female, Fetus pathology, Humans, Phenotype, Pregnancy, Syndrome, Transcription Factors genetics, Holoprosencephaly diagnosis, Holoprosencephaly genetics, Holoprosencephaly pathology
Abstract

Holoprosencephaly (HPE) is a clinically and genetically heterogeneous disease, which can be associated with various prenatal comorbidities not always detectable on prenatal ultrasound. We report on the case of a foetus carrying a semi-lobar HPE diagnosed at ultrasound, for which a fetal autopsy and a whole exome sequencing were performed following a medical termination of pregnancy. Neuropathological examination confirmed the semi-lobar HPE and general autopsy disclosed a total pancreas agenesis. Whole exome sequencing found the CNOT1 missense c.1603C>T, p.(Arg535Cys), occurring de novo in the foetus. The same variant was previously reported in 5 unrelated children. All individuals had HPE, and 4 out of 5 presented endo- and exocrine pancreatic insufficiency or total pancreas agenesis. CNOT1 encodes a subunit of the CCRN4-NOT complex, expressed at the early stage of embryonic development. This report is the first fetal description of the phenotype associating HPE and pancreatic agenesis linked to the recurrent CNOT1 missense c.1603C>T, p.(Arg535Cys). This finding strengthens the hypothesis of a specific recurrent variant associated with a particular phenotype of HPE and pancreas agenesis. The fetal autopsy that revealed the pancreas agenesis was crucial in guiding the genetic diagnosis and enabling accurate genetic counselling.

Published
2022
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20. Meiotic genes in premature ovarian insufficiency: variants in HROB and REC8 as likely genetic causes.

Author

Tucker EJ, Bell KM, Robevska G, van den Bergen J, Ayers KL, Listyasari N, Faradz SM, Dulon J, Bakhshalizadeh S, Sreenivasan R, Nouyou B, Carre W, Akloul L, Duros S, Domin-Bernhard M, Belaud-Rotureau MA, Touraine P, Jaillard S, and Sinclair AH

Subjects
Animals, Cell Cycle Proteins genetics, Chromosomes, DNA Helicases genetics, DNA-Binding Proteins, Female, Humans, Meiosis genetics, Mice, Phenotype, Exome Sequencing, Primary Ovarian Insufficiency genetics, Primary Ovarian Insufficiency pathology
Abstract

Premature ovarian insufficiency (POI), affecting 1 in 100 women, is characterised by loss of ovarian function associated with elevated gonadotropin, before the age of 40. In addition to infertility, patients face increased risk of comorbidities such as heart disease, osteoporosis, cancer and/or early mortality. We used whole exome sequencing to identify the genetic cause of POI in seven women. Each had biallelic candidate variants in genes with a primary role in DNA damage repair and/or meiosis. This includes two genes, REC8 and HROB, not previously associated with autosomal recessive POI. REC8 encodes a component of the cohesin complex and HROB encodes a factor that recruits MCM8/9 for DNA damage repair. In silico analyses, combined with concordant mouse model phenotypes support these as new genetic causes of POI. We also identified novel variants in MCM8, NUP107, STAG3 and HFM1 and a known variant in POF1B. Our study highlights the pivotal role of meiosis in ovarian function. We identify novel variants, consolidate the pathogenicity of variants previously considered of unknown significance, and propose HROB and REC8 variants as new genetic causes while exploring their link to pathogenesis., (© 2021. The Author(s), under exclusive licence to European Society of Human Genetics.)

Published
2022
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21. Heterozygous Variants in KMT2E Cause a Spectrum of Neurodevelopmental Disorders and Epilepsy.

Author

O'Donnell-Luria AH, Pais LS, Faundes V, Wood JC, Sveden A, Luria V, Abou Jamra R, Accogli A, Amburgey K, Anderlid BM, Azzarello-Burri S, Basinger AA, Bianchini C, Bird LM, Buchert R, Carre W, Ceulemans S, Charles P, Cox H, Culliton L, Currò A, Demurger F, Dowling JJ, Duban-Bedu B, Dubourg C, Eiset SE, Escobar LF, Ferrarini A, Haack TB, Hashim M, Heide S, Helbig KL, Helbig I, Heredia R, Héron D, Isidor B, Jonasson AR, Joset P, Keren B, Kok F, Kroes HY, Lavillaureix A, Lu X, Maas SM, Maegawa GHB, Marcelis CLM, Mark PR, Masruha MR, McLaughlin HM, McWalter K, Melchinger EU, Mercimek-Andrews S, Nava C, Pendziwiat M, Person R, Ramelli GP, Ramos LLP, Rauch A, Reavey C, Renieri A, Rieß A, Sanchez-Valle A, Sattar S, Saunders C, Schwarz N, Smol T, Srour M, Steindl K, Syrbe S, Taylor JC, Telegrafi A, Thiffault I, Trauner DA, van der Linden H Jr, van Koningsbruggen S, Villard L, Vogel I, Vogt J, Weber YG, Wentzensen IM, Widjaja E, Zak J, Baxter S, Banka S, and Rodan LH

Subjects
Adolescent, Adult, Child, Child, Preschool, Epilepsy pathology, Female, Haploinsufficiency, Humans, Infant, Male, Neurodevelopmental Disorders pathology, Pedigree, Phenotype, Young Adult, DNA-Binding Proteins genetics, Epilepsy etiology, Genetic Variation, Heterozygote, Neurodevelopmental Disorders etiology
Abstract

We delineate a KMT2E-related neurodevelopmental disorder on the basis of 38 individuals in 36 families. This study includes 31 distinct heterozygous variants in KMT2E (28 ascertained from Matchmaker Exchange and three previously reported), and four individuals with chromosome 7q22.2-22.23 microdeletions encompassing KMT2E (one previously reported). Almost all variants occurred de novo, and most were truncating. Most affected individuals with protein-truncating variants presented with mild intellectual disability. One-quarter of individuals met criteria for autism. Additional common features include macrocephaly, hypotonia, functional gastrointestinal abnormalities, and a subtle facial gestalt. Epilepsy was present in about one-fifth of individuals with truncating variants and was responsive to treatment with anti-epileptic medications in almost all. More than 70% of the individuals were male, and expressivity was variable by sex; epilepsy was more common in females and autism more common in males. The four individuals with microdeletions encompassing KMT2E generally presented similarly to those with truncating variants, but the degree of developmental delay was greater. The group of four individuals with missense variants in KMT2E presented with the most severe developmental delays. Epilepsy was present in all individuals with missense variants, often manifesting as treatment-resistant infantile epileptic encephalopathy. Microcephaly was also common in this group. Haploinsufficiency versus gain-of-function or dominant-negative effects specific to these missense variants in KMT2E might explain this divergence in phenotype, but requires independent validation. Disruptive variants in KMT2E are an under-recognized cause of neurodevelopmental abnormalities., (Copyright © 2019 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.)

Published
2019
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22. Mechanisms of endoderm formation in a cartilaginous fish reveal ancestral and homoplastic traits in jawed vertebrates.

Author

Godard BG, Coolen M, Le Panse S, Gombault A, Ferreiro-Galve S, Laguerre L, Lagadec R, Wincker P, Poulain J, Da Silva C, Kuraku S, Carre W, Boutet A, and Mazan S

Abstract

In order to gain insight into the impact of yolk increase on endoderm development, we have analyzed the mechanisms of endoderm formation in the catshark S. canicula, a species exhibiting telolecithal eggs and a distinct yolk sac. We show that in this species, endoderm markers are expressed in two distinct tissues, the deep mesenchyme, a mesenchymal population of deep blastomeres lying beneath the epithelial-like superficial layer, already specified at early blastula stages, and the involuting mesendoderm layer, which appears at the blastoderm posterior margin at the onset of gastrulation. Formation of the deep mesenchyme involves cell internalizations from the superficial layer prior to gastrulation, by a movement suggestive of ingressions. These cell movements were observed not only at the posterior margin, where massive internalizations take place prior to the start of involution, but also in the center of the blastoderm, where internalizations of single cells prevail. Like the adjacent involuting mesendoderm, the posterior deep mesenchyme expresses anterior mesendoderm markers under the control of Nodal/activin signaling. Comparisons across vertebrates support the conclusion that endoderm is specified in two distinct temporal phases in the catshark as in all major osteichthyan lineages, in line with an ancient origin of a biphasic mode of endoderm specification in gnathostomes. They also highlight unexpected similarities with amniotes, such as the occurrence of cell ingressions from the superficial layer prior to gastrulation. These similarities may correspond to homoplastic traits fixed separately in amniotes and chondrichthyans and related to the increase in egg yolk mass., (© 2014. Published by The Company of Biologists Ltd.)

Published
2014
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23. Regulation of ANKRD9 expression by lipid metabolic perturbations.

Author

Wang X, Newkirk RF, Carre W, Ghose P, Igobudia B, Townsel JG, and Cogburn LA

Subjects
Amebicides pharmacology, Amino Acid Sequence, Animals, Ankyrin Repeat, Apoptosis, Chick Embryo, Chickens, Fatty Acids, Nonesterified metabolism, Gene Expression Profiling, Gentamicins pharmacology, Molecular Sequence Data, Oligonucleotide Array Sequence Analysis, RNA, Messenger metabolism, Reverse Transcriptase Polymerase Chain Reaction, Sequence Homology, Amino Acid, Gene Expression Regulation, Developmental, Lipid Metabolism, Liver metabolism, Membrane Transport Proteins physiology, Proteins genetics, Proteins metabolism, RNA, Messenger genetics
Abstract

Fatty acid oxidation (FAO) defects cause abnormal lipid accumulation in various tissues, which provides an opportunity to uncover novel genes that are involved in lipid metabolism. During a gene expression study in the riboflavin deficient induced FAO disorder in the chicken, we discovered the dramatic increase in mRNA levels of an uncharacterized gene, ANKRD9. No functions have been ascribed to ANKRD9 and its orthologs, although their sequences are well conserved among vertebrates. To provide insight into the function of ANKRD9, the expression of ANKRD9 mRNA in lipidperturbed paradigms was examined. The hepatic mRNA level of ANKRD9 was repressed by thyroid hormone (T(3)) and fasting, elevated by re-feeding upon fasting. However, ANKRD9 mRNA level is reduced in response to apoptosis. Transient transfection assay with green fluorescent protein tagged- ANKRD9 showed that this protein is localized within the cytoplasm. These findings point to the possibility that ANKRD9 is involved in intracellular lipid accumulation. [BMB reports 2009; 42(9): 568-573].

Published
2009
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24. Chicken genomics resource: sequencing and annotation of 35,407 ESTs from single and multiple tissue cDNA libraries and CAP3 assembly of a chicken gene index.

Author

Carre W, Wang X, Porter TE, Nys Y, Tang J, Bernberg E, Morgan R, Burnside J, Aggrey SE, Simon J, and Cogburn LA

Subjects
Animals, Cluster Analysis, Contig Mapping, Databases, Genetic, Gene Library, Sequence Alignment, Sequence Analysis, DNA, Chickens genetics, Expressed Sequence Tags, Genome
Abstract

Its accessibility, unique evolutionary position, and recently assembled genome sequence have advanced the chicken to the forefront of comparative genomics and developmental biology research as a model organism. Several chicken expressed sequence tag (EST) projects have placed the chicken in 10th place for accrued ESTs among all organisms in GenBank. We have completed the single-pass 5'-end sequencing of 37,557 chicken cDNA clones from several single and multiple tissue cDNA libraries and have entered 35,407 EST sequences into GenBank. Our chicken EST sequences and those found in public databases (on July 1, 2004) provided a total of 517,727 public chicken ESTs and mRNAs. These sequences were used in the CAP3 assembly of a chicken gene index composed of 40,850 contigs and 79,192 unassembled singlets. The CAP3 contigs show a 96.7% match to the chicken genome sequence. The University of Delaware (UD) EST collection (43,928 clones) was assembled into 19,237 nonredundant sequences (13,495 contigs and 5,742 unassembled singlets). The UD collection contains 6,223 unique sequences that are not found in other public EST collections but show a 76% match to the chicken genome sequence. Our chicken contig and singlet sequences were annotated according to the highest BlastX and/or BlastN hits. The UD CAP3 contig assemblies and singlets are searchable by nucleotide sequence or key word (http://cogburn.dbi.udel.edu), and the cDNA clones are readily available for distribution from the chick EST website and clone repository (http://www.chickest.udel.edu). The present paper describes the construction and normalization of single and multiple tissue chicken cDNA libraries, high-throughput EST sequencing from these libraries, the CAP3 assembly of a chicken gene index from all public ESTs, and the identification of several nonredundant chicken gene sets for production of custom DNA microarrays.

Published
2006
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25. Gene expression profiling during cellular differentiation in the embryonic pituitary gland using cDNA microarrays.

Author

Ellestad LE, Carre W, Muchow M, Jenkins SA, Wang X, Cogburn LA, and Porter TE

Subjects
Animals, Chick Embryo, Gene Expression Profiling, Gene Expression Regulation, Developmental, Growth Hormone genetics, Growth Hormone metabolism, Intracellular Signaling Peptides and Proteins genetics, Intracellular Signaling Peptides and Proteins metabolism, Oligonucleotide Array Sequence Analysis, Pituitary Gland, Anterior cytology, Prolactin genetics, Prolactin metabolism, RNA, Messenger metabolism, Reproducibility of Results, Thyrotropin, beta Subunit genetics, Thyrotropin, beta Subunit metabolism, Time Factors, Transcription Factors genetics, Transcription Factors metabolism, Transcription, Genetic, Cell Differentiation genetics, Pituitary Gland, Anterior embryology, Pituitary Gland, Anterior metabolism
Abstract

The anterior pituitary is comprised of five major hormone-secreting cell types that differentiate during embryonic development in a temporally distinct manner. Microarrays containing 5,128 unique cDNAs expressed in the chicken neuroendocrine system were produced and used to identify genes with potential involvement in the onset of thyroid-stimulating hormone beta-subunit (TSHbeta), growth hormone (GH), and prolactin (PRL) mRNA during embryonic development. We identified 352 cDNAs that were differentially expressed (P < or = 0.05) on embryonic day 10 (e10), e12, e14, or e17, the period of thyrotroph, somatotroph, and lactotroph differentiation. Self-organizing maps were used to identify genes that may function to initiate hormone gene transcription. Consistent with cellular ontogeny, TSHbeta mRNA increased steadily between e10 and e17, GH mRNA increased between e12 and e17, and PRL mRNA did not increase until e17. Expression of 141 genes increased in a manner similar to TSHbeta mRNA, and 64 genes decreased between e10 and e17. Although genes with these expression profiles are likely involved in development of the pituitary gland as a whole, some of these could be specifically associated with thyrotroph differentiation. Similarly, the expression profiles of 69 and 61 genes indicate a potential involvement in the induction of GH and PRL mRNA, respectively. Quantitative real-time RT-PCR was used to confirm microarray results for 31 genes. This is the first study to evaluate changes in anterior pituitary gene expression during embryonic development of any species using microarrays, and numerous transcription factors and signaling molecules not previously implicated in pituitary development were identified.

Published
2006
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26. Duplicated Spot 14 genes in the chicken: characterization and identification of polymorphisms associated with abdominal fat traits.

Author

Wang X, Carre W, Zhou H, Lamont SJ, and Cogburn LA

Subjects
Adipose Tissue metabolism, Amino Acid Sequence, Animals, Base Sequence, DNA, Complementary chemistry, DNA, Complementary genetics, Female, Gene Expression, Genes genetics, Genotype, Male, Molecular Sequence Data, Nuclear Proteins, Polymorphism, Genetic, Protein Isoforms genetics, RNA, Messenger genetics, RNA, Messenger metabolism, Sequence Alignment, Sequence Analysis, DNA, Sequence Homology, Amino Acid, Transcription Factors, Chickens genetics, Genes, Duplicate genetics, Proteins genetics
Abstract

In mammals, thyroid hormone responsive Spot 14 (THRSP) is a small acidic protein that is predominately expressed in lipogenic tissue (i.e., liver, abdominal fat and the mammary gland). This gene has been postulated to play a role in lipogenesis, since it responds to thyroid hormone stimulation, high glucose levels and it is localized to a chromosomal region implicated in obesity. In this paper, we report the identification and characterization of duplicated polymorphic paralogs of Spot 14 in the chicken, THRSPalpha and THRSPbeta. Despite low similarity in amino acid (aa) sequence between chickens and mammals, other properties of Spot 14 (i.e., pI, subcellular localization, transcriptional control and functional domains) appear to be highly conserved. Furthermore, a synteny group of THRSP and its flanking genes [NADH dehydrogenase (NDUFC2) and glucosyltransferase (ALG8)] appears to be conserved among chickens, humans, mice and rats. Polymorphic alleles, involving a variable number of tandem repeats (VNTR), were discovered in the putative protein coding region of the duplicated chicken THRSPalpha (9 bp) and THRSPbeta (6 or 12 bp) genes. Our study shows that the THRSPalpha locus is associated with abdominal fat traits in a broilerxLeghorn resource population.

Published
2004
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