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1. Zebrafish as a model to investigate a biallelic gain-of-function variant in MSGN1, associated with a novel skeletal dysplasia syndrome

Author

Asuman Koparir, Caroline Lekszas, Kemal Keseroglu, Thalia Rose, Lena Rappl, Aboulfazl Rad, Reza Maroofian, Nakul Narendran, Atefeh Hasanzadeh, Ehsan Ghayoor Karimiani, Felix Boschann, Uwe Kornak, Eva Klopocki, Ertuğrul M. Özbudak, Barbara Vona, Thomas Haaf, and Daniel Liedtke

Subjects
Medicine, Genetics, QH426-470
Abstract

Abstract Background/Objectives Rare genetic disorders causing specific congenital developmental abnormalities often manifest in single families. Investigation of disease-causing molecular features are most times lacking, although these investigations may open novel therapeutic options for patients. In this study, we aimed to identify the genetic cause in an Iranian patient with severe skeletal dysplasia and to model its molecular function in zebrafish embryos. Results The proband displays short stature and multiple skeletal abnormalities, including mesomelic dysplasia of the arms with complete humero-radio-ulna synostosis, arched clavicles, pelvic dysplasia, short and thin fibulae, proportionally short vertebrae, hyperlordosis and mild kyphosis. Exome sequencing of the patient revealed a novel homozygous c.374G > T, p.(Arg125Leu) missense variant in MSGN1 (NM_001105569). MSGN1, a basic-Helix–Loop–Helix transcription factor, plays a crucial role in formation of presomitic mesoderm progenitor cells/mesodermal stem cells during early developmental processes in vertebrates. Initial in vitro experiments show protein stability and correct intracellular localization of the novel variant in the nucleus and imply retained transcription factor function. To test the pathogenicity of the detected variant, we overexpressed wild-type and mutant msgn1 mRNA in zebrafish embryos and analyzed tbxta (T/brachyury/ntl). Overexpression of wild-type or mutant msgn1 mRNA significantly reduces tbxta expression in the tailbud compared to control embryos. Mutant msgn1 mRNA injected embryos depict a more severe effect, implying a gain-of-function mechanism. In vivo analysis on embryonic development was performed by clonal msgn1 overexpression in zebrafish embryos further demonstrated altered cell compartments in the presomitic mesoderm, notochord and pectoral fin buds. Detection of ectopic tbx6 and bmp2 expression in these embryos hint to affected downstream signals due to Msgn1 gain-of-function. Conclusion In contrast to loss-of-function effects described in animal knockdown models, gain-of-function of MSGN1 explains the only mildly affected axial skeleton of the proband and rather normal vertebrae. In this context we observed notochord bending and potentially disruption of pectoral fin buds/upper extremity after overexpression of msgn1 in zebrafish embryos. The latter might result from Msgn1 function on mesenchymal stem cells or on chondrogenesis in these regions. In addition, we detected ectopic tbx6 and bmp2a expression after gain of Msgn1 function in zebrafish, which are interconnected to short stature, congenital scoliosis, limb shortening and prominent skeletal malformations in patients. Our findings highlight a rare, so far undescribed skeletal dysplasia syndrome associated with a gain-of-function mutation in MSGN1 and hint to its molecular downstream effectors.

Published
2024
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2. Structural and non-coding variants increase the diagnostic yield of clinical whole genome sequencing for rare diseases

Author

Alistair T. Pagnamenta, Carme Camps, Edoardo Giacopuzzi, John M. Taylor, Mona Hashim, Eduardo Calpena, Pamela J. Kaisaki, Akiko Hashimoto, Jing Yu, Edward Sanders, Ron Schwessinger, Jim R. Hughes, Gerton Lunter, Helene Dreau, Matteo Ferla, Lukas Lange, Yesim Kesim, Vassilis Ragoussis, Dimitrios V. Vavoulis, Holger Allroggen, Olaf Ansorge, Christian Babbs, Siddharth Banka, Benito Baños-Piñero, David Beeson, Tal Ben-Ami, David L. Bennett, Celeste Bento, Edward Blair, Charlotte Brasch-Andersen, Katherine R. Bull, Holger Cario, Deirdre Cilliers, Valerio Conti, E. Graham Davies, Fatima Dhalla, Beatriz Diez Dacal, Yin Dong, James E. Dunford, Renzo Guerrini, Adrian L. Harris, Jane Hartley, Georg Hollander, Kassim Javaid, Maureen Kane, Deirdre Kelly, Dominic Kelly, Samantha J. L. Knight, Alexandra Y. Kreins, Erika M. Kvikstad, Craig B. Langman, Tracy Lester, Kate E. Lines, Simon R. Lord, Xin Lu, Sahar Mansour, Adnan Manzur, Reza Maroofian, Brian Marsden, Joanne Mason, Simon J. McGowan, Davide Mei, Hana Mlcochova, Yoshiko Murakami, Andrea H. Németh, Steven Okoli, Elizabeth Ormondroyd, Lilian Bomme Ousager, Jacqueline Palace, Smita Y. Patel, Melissa M. Pentony, Chris Pugh, Aboulfazl Rad, Archana Ramesh, Simone G. Riva, Irene Roberts, Noémi Roy, Outi Salminen, Kyleen D. Schilling, Caroline Scott, Arjune Sen, Conrad Smith, Mark Stevenson, Rajesh V. Thakker, Stephen R. F. Twigg, Holm H. Uhlig, Richard van Wijk, Barbara Vona, Steven Wall, Jing Wang, Hugh Watkins, Jaroslav Zak, Anna H. Schuh, Usha Kini, Andrew O. M. Wilkie, Niko Popitsch, and Jenny C. Taylor

Subjects
Genome sequencing, Rare diseases, Structural variant, Splice site variant, Non-coding, Diagnostic yield, Medicine, Genetics, QH426-470
Abstract

Abstract Background Whole genome sequencing is increasingly being used for the diagnosis of patients with rare diseases. However, the diagnostic yields of many studies, particularly those conducted in a healthcare setting, are often disappointingly low, at 25–30%. This is in part because although entire genomes are sequenced, analysis is often confined to in silico gene panels or coding regions of the genome. Methods We undertook WGS on a cohort of 122 unrelated rare disease patients and their relatives (300 genomes) who had been pre-screened by gene panels or arrays. Patients were recruited from a broad spectrum of clinical specialties. We applied a bioinformatics pipeline that would allow comprehensive analysis of all variant types. We combined established bioinformatics tools for phenotypic and genomic analysis with our novel algorithms (SVRare, ALTSPLICE and GREEN-DB) to detect and annotate structural, splice site and non-coding variants. Results Our diagnostic yield was 43/122 cases (35%), although 47/122 cases (39%) were considered solved when considering novel candidate genes with supporting functional data into account. Structural, splice site and deep intronic variants contributed to 20/47 (43%) of our solved cases. Five genes that are novel, or were novel at the time of discovery, were identified, whilst a further three genes are putative novel disease genes with evidence of causality. We identified variants of uncertain significance in a further fourteen candidate genes. The phenotypic spectrum associated with RMND1 was expanded to include polymicrogyria. Two patients with secondary findings in FBN1 and KCNQ1 were confirmed to have previously unidentified Marfan and long QT syndromes, respectively, and were referred for further clinical interventions. Clinical diagnoses were changed in six patients and treatment adjustments made for eight individuals, which for five patients was considered life-saving. Conclusions Genome sequencing is increasingly being considered as a first-line genetic test in routine clinical settings and can make a substantial contribution to rapidly identifying a causal aetiology for many patients, shortening their diagnostic odyssey. We have demonstrated that structural, splice site and intronic variants make a significant contribution to diagnostic yield and that comprehensive analysis of the entire genome is essential to maximise the value of clinical genome sequencing.

Published
2023
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3. Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity

Author

Sheng-Jia Lin, Barbara Vona, Tracy Lau, Kevin Huang, Maha S. Zaki, Huda Shujaa Aldeen, Ehsan Ghayoor Karimiani, Clarissa Rocca, Mahmoud M. Noureldeen, Ahmed K. Saad, Cassidy Petree, Tobias Bartolomaeus, Rami Abou Jamra, Giovanni Zifarelli, Aditi Gotkhindikar, Ingrid M. Wentzensen, Mingjuan Liao, Emalyn Elise Cork, Pratishtha Varshney, Narges Hashemi, Mohammad Hasan Mohammadi, Aboulfazl Rad, Juanita Neira, Mehran Beiraghi Toosi, Cordula Knopp, Ingo Kurth, Thomas D. Challman, Rebecca Smith, Asmahan Abdalla, Thomas Haaf, Mohnish Suri, Manali Joshi, Wendy K. Chung, Andres Moreno-De-Luca, Henry Houlden, Reza Maroofian, and Gaurav K. Varshney

Subjects
2-oxo acid dehydrogenase, OGDHL, Genetic compensation, Disease model, Zebrafish, Neurodevelopmental disorders, Medicine, Genetics, QH426-470
Abstract

Abstract Background Biallelic variants in OGDHL, encoding part of the α-ketoglutarate dehydrogenase complex, have been associated with highly heterogeneous neurological and neurodevelopmental disorders. However, the validity of this association remains to be confirmed. A second OGDHL patient cohort was recruited to carefully assess the gene-disease relationship. Methods Using an unbiased genotype-first approach, we screened large, multiethnic aggregated sequencing datasets worldwide for biallelic OGDHL variants. We used CRISPR/Cas9 to generate zebrafish knockouts of ogdhl, ogdh paralogs, and dhtkd1 to investigate functional relationships and impact during development. Functional complementation with patient variant transcripts was conducted to systematically assess protein functionality as a readout for pathogenicity. Results A cohort of 14 individuals from 12 unrelated families exhibited highly variable clinical phenotypes, with the majority of them presenting at least one additional variant, potentially accounting for a blended phenotype and complicating phenotypic understanding. We also uncovered extreme clinical heterogeneity and high allele frequencies, occasionally incompatible with a fully penetrant recessive disorder. Human cDNA of previously described and new variants were tested in an ogdhl zebrafish knockout model, adding functional evidence for variant reclassification. We disclosed evidence of hypomorphic alleles as well as a loss-of-function variant without deleterious effects in zebrafish variant testing also showing discordant familial segregation, challenging the relationship of OGDHL as a conventional Mendelian gene. Going further, we uncovered evidence for a complex compensatory relationship among OGDH, OGDHL, and DHTKD1 isoenzymes that are associated with neurodevelopmental disorders and exhibit complex transcriptional compensation patterns with partial functional redundancy. Conclusions Based on the results of genetic, clinical, and functional studies, we formed three hypotheses in which to frame observations: biallelic OGDHL variants lead to a highly variable monogenic disorder, variants in OGDHL are following a complex pattern of inheritance, or they may not be causative at all. Our study further highlights the continuing challenges of assessing the validity of reported disease-gene associations and effects of variants identified in these genes. This is particularly more complicated in making genetic diagnoses based on identification of variants in genes presenting a highly heterogenous phenotype such as “OGDHL-related disorders”.

Published
2023
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4. Identification of three novel homozygous variants in COL9A3 causing autosomal recessive Stickler syndrome

Author

Aboulfazl Rad, Maryam Najafi, Fatemeh Suri, Soheila Abedini, Stephen Loum, Ehsan Ghayoor Karimiani, Narsis Daftarian, David Murphy, Mohammad Doosti, Afrooz Moghaddasi, Hamid Ahmadieh, Hamideh Sabbaghi, Mohsen Rajati, Narges Hashemi, Barbara Vona, and Miriam Schmidts

Subjects
Autosomal recessive Stickler syndrome, COL9A3, Collagen, Hearing loss, Retinal detachment, Medicine
Abstract

Abstract Background Stickler syndrome (STL) is a rare, clinically and molecularly heterogeneous connective tissue disorder. Pathogenic variants occurring in a variety of genes cause STL, mainly inherited in an autosomal dominant fashion. Autosomal recessive STL is ultra-rare with only four families with biallelic COL9A3 variants reported to date. Results Here, we report three unrelated families clinically diagnosed with STL carrying different novel biallelic loss of function variants in COL9A3. Further, we have collected COL9A3 genotype–phenotype associations from the literature. Conclusion Our report substantially expands the molecular genetics and clinical basis of autosomal recessive STL and provides an overview about allelic COL9A3 disorders.

Published
2022
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5. KDM5A mutations identified in autism spectrum disorder using forward genetics

Author

Lauretta El Hayek, Islam Oguz Tuncay, Nadine Nijem, Jamie Russell, Sara Ludwig, Kiran Kaur, Xiaohong Li, Priscilla Anderton, Miao Tang, Amanda Gerard, Anja Heinze, Pia Zacher, Hessa S Alsaif, Aboulfazl Rad, Kazem Hassanpour, Mohammad Reza Abbaszadegan, Camerun Washington, Barbara R DuPont, Raymond J Louie, CAUSES Study, Madeline Couse, Maha Faden, R Curtis Rogers, Rami Abou Jamra, Ellen R Elias, Reza Maroofian, Henry Houlden, Anna Lehman, Bruce Beutler, and Maria H Chahrour

Subjects
autism spectrum disorder, forward genetics, chromatin regulator, vocalization, histone demethylase, Medicine, Science, Biology (General), QH301-705.5
Abstract

Autism spectrum disorder (ASD) is a constellation of neurodevelopmental disorders with high phenotypic and genetic heterogeneity, complicating the discovery of causative genes. Through a forward genetics approach selecting for defective vocalization in mice, we identified Kdm5a as a candidate ASD gene. To validate our discovery, we generated a Kdm5a knockout mouse model (Kdm5a-/-) and confirmed that inactivating Kdm5a disrupts vocalization. In addition, Kdm5a-/- mice displayed repetitive behaviors, sociability deficits, cognitive dysfunction, and abnormal dendritic morphogenesis. Loss of KDM5A also resulted in dysregulation of the hippocampal transcriptome. To determine if KDM5A mutations cause ASD in humans, we screened whole exome sequencing and microarray data from a clinical cohort. We identified pathogenic KDM5A variants in nine patients with ASD and lack of speech. Our findings illustrate the power and efficacy of forward genetics in identifying ASD genes and highlight the importance of KDM5A in normal brain development and function.

Published
2020
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6. A Novel Homozygous <scp> ADCY5 </scp> Variant is Associated with a Neurodevelopmental Disorder and Movement Abnormalities

Author

Maha S. Zaki, Reza Maroofian, Natalia Dominik, Barbara Vona, Aboulfazl Rad, Henry Houlden, and Rauan Kaiyrzhanov

Subjects
Dystonia, ADCY5, Neurodevelopmental disorder, Movement disorders, Neurology, Movement (music), business.industry, medicine, Neurology (clinical), medicine.symptom, medicine.disease, business, Neuroscience
Published
2021
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7. Unraveling the genetic complexities of combined retinal dystrophy and hearing impairment

Author

Susanne Kohl, Asuman Koparir, Hassan Behboudi, Seungbin Han, Thomas Haaf, Hossein Darvish, Rocio Zamora-Ortiz, Cristina Villanueva-Mendoza, Julia Doll, Daniel Villalobos, Reza Maroofian, Vianney Cortés-González, Laura Kuehlewein, Barbara Vona, Michaela A.H. Hofrichter, Narsis Daftarian, Mehraban Mirrahimi, Paulina Bahena, Aboulfazl Rad, Elham Alehabib, Paola Linares, Maria de la Luz Arenas-Sordo, Fatemeh Suri, Tabea Röder, Hamideh Sabbaghi, and Hamid Ahmadieh

Subjects
Proband, Pediatrics, medicine.medical_specialty, Hearing loss, MYO7A, Usher syndrome, Genetic counseling, Retinal Degeneration, Iran, Biology, medicine.disease, Pedigree, Phenotype, Mutation, otorhinolaryngologic diseases, Genetics, medicine, Humans, ddc:610, medicine.symptom, Scheie syndrome, Usher Syndromes, Genetics (clinical), Exome sequencing, Alström syndrome
Abstract

Usher syndrome, the most prevalent cause of combined hereditary vision and hearing impairment, is clinically and genetically heterogeneous. Moreover, several conditions with phenotypes overlapping Usher syndrome have been described. This makes the molecular diagnosis of hereditary deaf–blindness challenging. Here, we performed exome sequencing and analysis on 7 Mexican and 52 Iranian probands with combined retinal degeneration and hearing impairment (without intellectual disability). Clinical assessment involved ophthalmological examination and hearing loss questionnaire. Usher syndrome, most frequently due to biallelic variants in MYO7A (USH1B in 16 probands), USH2A (17 probands), and ADGRV1 (USH2C in 7 probands), was diagnosed in 44 of 59 (75%) unrelated probands. Almost half of the identified variants were novel. Nine of 59 (15%) probands displayed other genetic entities with dual sensory impairment, including Alström syndrome (3 patients), cone-rod dystrophy and hearing loss 1 (2 probands), and Heimler syndrome (1 patient). Unexpected findings included one proband each with Scheie syndrome, coenzyme Q10 deficiency, and pseudoxanthoma elasticum. In four probands, including three Usher cases, dual sensory impairment was either modified/aggravated or caused by variants in distinct genes associated with retinal degeneration and/or hearing loss. The overall diagnostic yield of whole exome analysis in our deaf–blind cohort was 92%. Two (3%) probands were partially solved and only 3 (5%) remained without any molecular diagnosis. In many cases, the molecular diagnosis is important to guide genetic counseling, to support prognostic outcomes and decisions with currently available and evolving treatment modalities.

Published
2021
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8. Aberrant COL11A1 splicing causes prelingual autosomal dominant nonsyndromic hearing loss in the DFNA37 locus

Author

Barbara Vona, Philipp Gamerdinger, Evgeny N. Imyanitov, Thore Schade-Mann, Saskia Biskup, Marcus Müller, Aboulfazl Rad, Grigoriy A. Yanus, Hubert Löwenheim, Björn Schulte, and Anke Tropitzsch

Subjects
Heterozygote, Hearing loss, Hearing Loss, Sensorineural, RNA Splicing, Locus (genetics), Deafness, Biology, Collagen Type XI, 03 medical and health sciences, Genetics, medicine, Humans, Nonsyndromic deafness, Hearing Loss, Gene, Genetics (clinical), Organ system, 030304 developmental biology, Genetic testing, 0303 health sciences, medicine.diagnostic_test, 030305 genetics & heredity, Intron, medicine.disease, Pedigree, RNA splicing, medicine.symptom
Abstract

Alpha-chain collagen molecules encoded by genes that include COL11A1 are essential for skeletal, ocular, and auditory function. COL11A1 variants have been reported in syndromes involving these organ systems. However, a description of the complete clinical spectrum is lacking, as evidenced by a recent association of autosomal dominant nonsyndromic hearing loss due to a splice-altering variant in COL11A1, mapping the DFNA37 locus. Here, we describe two German families presenting prelingual autosomal dominant nonsyndromic hearing loss with novel COL11A1 heterozygous splice-altering variants (c.652-1G>C and c.4338+2T>C) that were molecularly characterized. Interestingly, the c.652-1G>C variant affects the same intron 4 canonical splice site originally reported in the DFNA37 family (c.652-2A>C) but elicits a different splicing outcome. Furthermore, the c.4338+2T>C variant originated de novo. We provide clinical and molecular genetic evidence to unambiguously confirm that COL11A1 splice-altering variants cause DFNA37 hearing loss and affirm that COL11A1 be included in the genetic testing of patients with nonsyndromic deafness.

Published
2020
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9. Biallelic variants in PCDHGC4 cause a novel neurodevelopmental syndrome with progressive microcephaly, seizures, and joint anomalies

Author

M. Tanguy, A. Hamblin, Ehsan Ghayoor Karimiani, Javeria Raza Alvi, Gökhan Yigit, D. Kasperaviciute, Shima Imannezhad, C.R. Boustred, Brigitte Chabrol, Ehtisham Ul Haq Makhdoom, Cécile Mignon-Ravix, Vasiliki Karageorgou, Maria Iqbal, Farah Ashrafzadeh, Sheraz Jamal Khan, Michael Field, Henry Houlden, Adam Jackson, David A. Dyment, J. Pullinger, Yasra Sarwar, S.E.A. Leigh, Jamshaid Mahmood Baig, Zafar Ali, S.C. Smith, A. Stuckey, Muhammad Sajid Hussain, Fatima Rahman, N. Murugaesu, J.C. Ambrose, M. Mueller, K. Sawant, A. Sieghart, E. Walsh, Alistair T. Pagnamenta, Shahid Mahmood Baig, R. Jackson, E.R.A. Thomas, M.B. Pereira, Fowzan S. Alkuraya, K. Witkowska, Augusto Rendon, P. Arumugam, F. Boardman-Pretty, Angelika A. Noegel, Siddharth Banka, Uzma Abdullah, Tim Hubbard, T. Rahim, F.J. Lopez, Dalal K. Bubshait, Louise J. Jones, A. Giess, M.J. Welland, Susanne Motameny, Mehran Beiraghi Toosi, E. Williams, Barbara Vona, Arianna Tucci, K. Savage, Florence Molinari, Florence Riccardi, Mark J. Caulfield, I.U. Leong, M. Kayikci, Muhammad Jameel, Christian Beetz, A. Kousathanas, A. Siddiq, T. Fowler, Yun Li, Jozef Hertecant, M. Bleda, F. Maleady-Crowe, Birgit Budde, Sofia Douzgou, Wolfgang Höhne, C.A. Odhams, Laurent Villard, Janine Altmüller, S.R. Thompson, Lesley C. Adès, Christine Patch, Aboulfazl Rad, P. O’Donovan, A.C. Need, S. M. Wood, L. Lahnstein, L. Moutsianas, Büşranur Çavdarlı, Reza Maroofian, S. Henderson, Tobias Scherf de Almeida, D. Perez-Gil, Tipu Sultan, T. Rogers, Stephanie Efthymiou, Shazia Maqbool, G.C. Chan, A. Sosinsky, Jayne Antony, H. Brittain, R.H. Scott, Peter Nürnberg, Bernd Wollnik, Matthew Osmond, Marseille medical genetics - Centre de génétique médicale de Marseille (MMG), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Département de génétique médicale [Hôpital de la Timone - APHM], Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE)-Institut National de la Santé et de la Recherche Médicale (INSERM), Neurologie, maladies neuro-musculaires [Hôpital de la Timone - APHM], and Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE)

Subjects
0301 basic medicine, In silico, Cadherin Related Proteins, Biology, Article, 03 medical and health sciences, symbols.namesake, 0302 clinical medicine, Neurodevelopmental disorder, Seizures, Intellectual Disability, Intellectual disability, medicine, Missense mutation, Humans, Genetics (clinical), Exome sequencing, Genetics, Progressive microcephaly, [SDV.GEN]Life Sciences [q-bio]/Genetics, medicine.disease, Cadherins, Human genetics, Pedigree, 030104 developmental biology, Phenotype, Neurodevelopmental Disorders, Mendelian inheritance, symbols, Microcephaly, Technology Platforms, 030217 neurology & neurosurgery
Abstract

PURPOSE: We aimed to define a novel autosomal recessive neurodevelopmental disorder, characterize its clinical features, and identify the underlying genetic cause for this condition.METHODS: We performed a detailed clinical characterization of 19 individuals from nine unrelated, consanguineous families with a neurodevelopmental disorder. We used genome/exome sequencing approaches, linkage and cosegregation analyses to identify disease-causing variants, and we performed three-dimensional molecular in silico analysis to predict causality of variants where applicable.RESULTS: In all affected individuals who presented with a neurodevelopmental syndrome with progressive microcephaly, seizures, and intellectual disability we identified biallelic disease-causing variants in Protocadherin-gamma-C4 (PCDHGC4). Five variants were predicted to induce premature protein truncation leading to a loss of PCDHGC4 function. The three detected missense variants were located in extracellular cadherin (EC) domains EC5 and EC6 of PCDHGC4, and in silico analysis of the affected residues showed that two of these substitutions were predicted to influence the Ca2+-binding affinity, which is essential for multimerization of the protein, whereas the third missense variant directly influenced the cis-dimerization interface of PCDHGC4.CONCLUSION: We show that biallelic variants in PCDHGC4 are causing a novel autosomal recessive neurodevelopmental disorder and link PCDHGC4 as a member of the clustered PCDH family to a Mendelian disorder in humans.

Published
2021
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10. Bi-allelic variants in IPO8 cause a connective tissue disorder associated with cardiovascular defects, skeletal abnormalities, and immune dysregulation

Author

Karine Duroure, Estelle Colin, Thomas Edouard, Ludovic Martin, Linda Grimaud, Lyndon Gallacher, George McGillivray, Guy Lenaers, Valérie Desquiret-Dumas, Clarisse Billon, Anne Breton, Mohammed Zarhrate, Emmanuel Mas, Dominique Bonneau, Lynn Pais, Daniel Henrion, Thomas Haaf, Reza Maroofian, Marianna Parlato, Frank M. Ruemmele, Anne-Laure Guihot, Anaïs Philippe, Ehsan Ghayoor Karimiani, Pauline E. Schneeberger, Stanislas Lyonnet, Bernadette Bègue, Bruno Moulin, Rémi Duclaux-Loras, Nicolas Cagnard, Michael Frank, Laurence Faivre, Ruben Attali, Yves Alembik, Filippo Del Bene, Kerstin Kutsche, Céline Revenu, Fabienne Charbit-Henrion, Katta M. Girisha, Aboulfazl Rad, Eyal Reinstein, Shalini S. Nayak, Barbara Vona, Nadine Cerf-Bensussan, Caroline Lekszas, Shay Tzur, Alban Ziegler, Susan M. White, Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM), MitoVasc - 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), Laboratory of Intestinal Immunity (Equipe Inserm U1163), Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Institut de la Vision, Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Institut de Recherche en Santé Digestive (IRSD ), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ingénierie Radioprotection Sûreté Démantèlement (IRSD), Centre National de la Recherche Scientifique (CNRS), Geroscience and rejuvenation research center (RESTORE), Université de Toulouse (UT)-Université de Toulouse (UT)-EFS-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), Embryology and genetics of human malformation, CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), FHU TRANSLAD (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Hôpital de Hautepierre [Strasbourg], Nouvel Hôpital Civil de Strasbourg, Tel Aviv University (TAU), Emedgene Technologies [Tel Aviv], Murdoch Children's Research Institute (MCRI), Universitaetsklinikum Hamburg-Eppendorf = University Medical Center Hamburg-Eppendorf [Hamburg] (UKE), Kasturba Medical College, Manipal, Massachusetts Institute of Technology (MIT), University College of London [London] (UCL), Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, St George's, University of London, University of Würzburg = Universität Würzburg, Fondation Princesse Grace, Fondation Maladies Rares, Harbig Family Foundation, Royal Children's Hospital Foundation, University of Tubingen (2545-1-0), Federal Ministry of Education and Research (01DQ17003 to K.K.), Indian Council of Medical Research (file no. 5/7/1508/2016 to K.M.G), National Human Genome Research Institute, the National Eye Institute, and the National Heart, Lung, and Blood Institute grant UM1 HG008900, National Human Genome Research Institute grant R01 HG009141, Victorian Government's Operational Infrastructure Support Program, ANR-10-IAHU-0001,Imagine,Institut Hospitalo-Universitaire Imagine(2010), ANR-18-IAHU-0001,FOReSIGHT,Enabling Vision Restoration(2018), European Project: 661527,H2020,H2020-MSCA-IF-2014,NMJALS(2015), European Project: 339407,EC:FP7:ERC,ERC-2013-ADG,IMMUNOBIOTA(2014), Service de 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), Autophagie infection et immunité - Autophagy Infection Immunity (APY), Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Génétique et Biologie du Développement, Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Imagine - Institut des maladies génétiques (IMAGINE - U1163), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Physiopathologie Cardiovasculaire et Mitochondriale (MITOVASC), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-EFS-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Embryology and genetics of human malformation (Equipe Inserm U1163), SEGUIN, Nathalie, Instituts Hospitalo-Universitaires - Institut Hospitalo-Universitaire Imagine - - Imagine2010 - ANR-10-IAHU-0001 - IAHU - VALID, Enabling Vision Restoration - - FOReSIGHT2018 - ANR-18-IAHU-0001 - IAHU - VALID, In vivo analysis of neuromuscular junction stability in zebrafish models of amyotrophic lateral sclerosis - NMJALS - - H20202015-11-16 - 2017-11-15 - 661527 - VALID, Host-microbiota interactions across the gut immune system:lessons from early onset inflammatory bowel diseases and from gnotobiotic mice - IMMUNOBIOTA - - EC:FP7:ERC2014-03-01 - 2019-02-28 - 339407 - VALID, École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Male, Connective Tissue Disorder, Loss of Heterozygosity, [SDV.GEN] Life Sciences [q-bio]/Genetics, medicine.disease_cause, IPO8, TGF-β signaling, Pathogenesis, 0302 clinical medicine, Loss of Function Mutation, Transforming Growth Factor beta, connective tissue disorder, Child, Connective Tissue Diseases, Zebrafish, Genetics (clinical), Karyopherin, chemistry.chemical_classification, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Immunity, Cellular, 0303 health sciences, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, Middle Aged, beta Karyopherins, Pedigree, arterial dilatation, Cell biology, [SDV.MHEP.CSC] Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, Phenotype, medicine.anatomical_structure, Cardiovascular Diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Female, Bone Diseases, Signal Transduction, Adult, Adolescent, Connective tissue, Biology, Importin 8, Young Adult, 03 medical and health sciences, [SDV.IMM.VAC] Life Sciences [q-bio]/Immunology/Vaccinology, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, Report, Genetics, medicine, Animals, Humans, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, Infant, Immune dysregulation, Loeys-Dietz syndrome, biology.organism_classification, joint hyperlaxity, chemistry, [SDV.IMM.VAC]Life Sciences [q-bio]/Immunology/Vaccinology, 030217 neurology & neurosurgery, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Transforming growth factor
Abstract

International audience; Dysregulated transforming growth factor TGF-beta signaling underlies the pathogenesis of genetic disorders affecting the connective tissue such as Loeys-Dietz syndrome. Here, we report 12 individuals with bi-allelic loss-of-function variants in IPO8 who presented with a syndromic association characterized by cardio-vascular anomalies, joint hyperlaxity, and various degree of dysmorphic features and developmental delay as well as immune dysregulation; the individuals were from nine unrelated families. Importin 8 belongs to the karyopherin family of nuclear transport receptors and was previously shown to mediate TGF-beta-dependent SMADs trafficking to the nucleus in vitro. The important in vivo role of IPO8 in pSMAD nuclear translocation was demonstrated by CRISPR/Cas9-mediated inactivation in zebrafish. Consistent with IPO8's role in BMP/TGF-beta signaling, ipo8(-/-) zebrafish presented mild to severe dorso-ventral patterning defects during early embryonic development. Moreover, ipo8(-/-) zebrafish displayed severe cardiovascular and skeletal defects that mirrored the human phenotype. Our work thus provides evidence that IPO8 plays a critical and non-redundant role in TGF-beta signaling during development and reinforces the existing link between TGF-beta signaling and connective tissue defects.

Published
2021
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11. Biallelic variants in KARS1 are associated with neurodevelopmental disorders and hearing loss recapitulated by the knockout zebrafish

Author

Sheng-Jia Lin, Barbara Vona, Patricia G. Barbalho, Rauan Kaiyrzhanov, Reza Maroofian, Cassidy Petree, Mariasavina Severino, Valentina Stanley, Pratishtha Varshney, Paulina Bahena, Fatema Alzahrani, Amal Alhashem, Alistair T. Pagnamenta, Gudrun Aubertin, Juvianee I. Estrada-Veras, Héctor Adrián Díaz Hernández, Neda Mazaheri, Andrea Oza, Jenny Thies, Deborah L. Renaud, Sanmati Dugad, Jennifer McEvoy, Tipu Sultan, Lynn S. Pais, Brahim Tabarki, Daniel Villalobos-Ramirez, Aboulfazl Rad, J.C. Ambrose, P. Arumugam, M. Bleda, F. Boardman-Pretty, C.R. Boustred, H. Brittain, M.J. Caulfield, G.C. Chan, T. Fowler, A. Giess, A. Hamblin, S. Henderson, T.J.P. Hubbard, R. Jackson, L.J. Jones, D. Kasperaviciute, M. Kayikci, A. Kousathanas, L. Lahnstein, S.E.A. Leigh, I.U.S. Leong, F.J. Lopez, F. Maleady-Crowe, L. Moutsianas, M. Mueller, N. Murugaesu, A.C. Need, P. O‘Donovan, C.A. Odhams, C. Patch, D. Perez-Gil, M.B. Pereira, J. Pullinger, T. Rahim, A. Rendon, T. Rogers, K. Savage, K. Sawant, R.H. Scott, A. Siddiq, A. Sieghart, S.C. Smith, A. Sosinsky, A. Stuckey, M. Tanguy, E.R.A. Thomas, S.R. Thompson, A. Tucci, E. Walsh, M.J. Welland, E. Williams, K. Witkowska, S.M. Wood, Hamid Galehdari, Farah Ashrafzadeh, Afsaneh Sahebzamani, Kolsoum Saeidi, Erin Torti, Houda Z. Elloumi, Sara Mora, Timothy B. Palculict, Hui Yang, Jonathan D. Wren, null Ben Fowler, Manali Joshi, Martine Behra, Shawn M. Burgess, Swapan K. Nath, Michael G. Hanna, Margaret Kenna, J. Lawrence Merritt, Henry Houlden, Ehsan Ghayoor Karimiani, Maha S. Zaki, Thomas Haaf, Fowzan S. Alkuraya, Joseph G. Gleeson, and Gaurav K. Varshney

Subjects
Genetics, Lysine-tRNA Ligase, biology, Disease, biology.organism_classification, medicine.disease, Phenotype, Human genetics, Disease Models, Animal, Neurodevelopmental Disorders, medicine, Missense mutation, Autism, Animals, Humans, Allele, Hearing Loss, Zebrafish, Genetics (clinical), Gene knockout, Alleles
Abstract

Pathogenic variants in Lysyl-tRNA synthetase 1 (KARS1) have increasingly been recognized as a cause of early-onset complex neurological phenotypes. To advance the timely diagnosis of KARS1-related disorders, we sought to delineate its phenotype and generate a disease model to understand its function in vivo. Through international collaboration, we identified 22 affected individuals from 16 unrelated families harboring biallelic likely pathogenic or pathogenic in KARS1 variants. Sequencing approaches ranged from disease-specific panels to genome sequencing. We generated loss-of-function alleles in zebrafish. We identify ten new and four known biallelic missense variants in KARS1 presenting with a moderate-to-severe developmental delay, progressive neurological and neurosensory abnormalities, and variable white matter involvement. We describe novel KARS1-associated signs such as autism, hyperactive behavior, pontine hypoplasia, and cerebellar atrophy with prevalent vermian involvement. Loss of kars1 leads to upregulation of p53, tissue-specific apoptosis, and downregulation of neurodevelopmental related genes, recapitulating key tissue-specific disease phenotypes of patients. Inhibition of p53 rescued several defects of kars1−/− knockouts. Our work delineates the clinical spectrum associated with KARS1 defects and provides a novel animal model for KARS1-related human diseases revealing p53 signaling components as potential therapeutic targets.

Published
2021

12. Bi-allelic variants in SPATA5L1 lead to intellectual disability, spastic-dystonic cerebral palsy, epilepsy, and hearing loss

Author

Serdal Güngör, Benita Grossmann, Bethany Y. Norton, Zubair M. Ahmed, Wendy K. Chung, John Neidhardt, Julie S. Cohen, Elodie Richard, Yoel Hirsch, Jiankang Li, Jozef Gecz, Ralf A. Husain, Saima Riazuddin, Maria J. Guillen Sacoto, Claudia Steen, Andreas Ziegler, G. Christoph Korenke, Dominic Lenz, Mahim Jain, Urania Kotzaeridou, Henry Houlden, Theresa Brunet, Yavuz Oktay, Semra Hiz, Patricia Cornejo, Sheetal Shetty, Alastair H. MacLennan, Nazira Zharkinbekova, Bader Alhaddad, Dani L. Webber, Mary Alice Abbott, Hanns Lochmüller, Rauan Kaiyrzhanov, Melissa Yelton, Cecilia Mancini, Hakon Hakonarson, Amy Crunk, Simona Amenta, Yiran Guo, Jan Kaslin, Clare L. van Eyk, Richard Webster, Arianna Tucci, Alex M. Pagnozzi, Robert B. Hufnagel, Kirsty McWalter, Sandra M. Nordlie, Kaya Bilguvar, Pasquale Striano, Matias Wagner, Florian Kreuder, Lisa Worgan, Ashley P.L. Marsh, Anna Chassevent, Warren A. Marks, James Liu, Brandon S. Guida, Maria Margherita Mancardi, Kelly Harper, Lance H. Rodan, Rhonda E. Schnur, Dianela Judith Claps Sepulveda, Tzvi Weiden, Michele Pinelli, Marion Rapp, Helen Magee, Jesia G. Berry, Aboulfazl Rad, Michael C. Kruer, Mark A. Corbett, Rita Horvath, Constance Smith-Hicks, Joseph Ekstein, Marta Owczarek-Lipska, Somayeh Bakhtiari, Heinrich Sticht, Thomas Meitinger, Anne M. Comi, Alyssa Blesson, Iris Marquardt, Francesca Clementina Radio, Sergio Padilla-Lopez, Giuseppe Marangi, Christine Makowski, Mona Grimmel, Marco Tartaglia, Sheng Chih Jin, Federico Zara, Andreas Hahn, Shrikant Mane, Michael C Fahey, Marcella Zollino, Barbara Vona, Peter D. Turnpenny, Manuela Morleo, Ute Grasshoff, Amber Begtrup, Richard E. Person, Annalaura Torella, Alexander Münchau, Vincenzo Nigro, Reza Maroofian, John Christodoulou, Tobias B. Haack, Vincenzo Salpietro, Richard, E. M., Bakhtiari, S., Marsh, A. P. L., Kaiyrzhanov, R., Wagner, M., Shetty, S., Pagnozzi, A., Nordlie, S. M., Guida, B. S., Cornejo, P., Magee, H., Liu, J., Norton, B. Y., Webster, R. I., Worgan, L., Hakonarson, H., Li, J., Guo, Y., Jain, M., Blesson, A., Rodan, L. H., Abbott, M. -A., Comi, A., Cohen, J. S., Alhaddad, B., Meitinger, T., Lenz, D., Ziegler, A., Kotzaeridou, U., Brunet, T., Chassevent, A., Smith-Hicks, C., Ekstein, J., Weiden, T., Hahn, A., Zharkinbekova, N., Turnpenny, P., Tucci, A., Yelton, M., Horvath, R., Gungor, S., Hiz, S., Oktay, Y., Lochmuller, H., Zollino, M., Morleo, M., Marangi, G., Nigro, V., Torella, A., Pinelli, M., Amenta, S., Husain, R. A., Grossmann, B., Rapp, M., Steen, C., Marquardt, I., Grimmel, M., Grasshoff, U., Korenke, G. C., Owczarek-Lipska, M., Neidhardt, J., Radio, F. C., Mancini, C., Claps Sepulveda, D. J., Mcwalter, K., Begtrup, A., Crunk, A., Guillen Sacoto, M. J., Person, R., Schnur, R. E., Mancardi, M. M., Kreuder, F., Striano, P., Zara, F., Chung, W. K., Marks, W. A., van Eyk, C. L., Webber, D. L., Corbett, M. A., Harper, K., Berry, J. G., Maclennan, A. H., Gecz, J., Tartaglia, M., Salpietro, V., Christodoulou, J., Kaslin, J., Padilla-Lopez, S., Bilguvar, K., Munchau, A., Ahmed, Z. M., Hufnagel, R. B., Fahey, M. C., Maroofian, R., Houlden, H., Sticht, H., Mane, S. M., Rad, A., Vona, B., Jin, S. C., Haack, T. B., Makowski, C., Hirsch, Y., Riazuddin, S., and Kruer, M. C.

Subjects
Male, Microcephaly, Pathology, Settore MED/03 - GENETICA MEDICA, sensorineural hearing loss, Epilepsy, Neurodevelopmental disorder, sensorineural hearing lo, Genetics (clinical), Allele, ATPases Associated with Diverse Cellular Activitie, medicine.anatomical_structure, Muscle Spasticity, Child, Preschool, Sensorineural hearing loss, Female, movement disorder, medicine.symptom, AAA+ superfamily, Human, Adult, medicine.medical_specialty, Adolescent, Hearing loss, Aaa+ Superfamily, Atpase, Spata5l1, Cerebral Palsy, Intellectual Disability, Movement Disorder, Neurodevelopmental Disorder, Sensorineural Hearing Loss, Biology, Cerebral palsy, White matter, Young Adult, Report, Genetics, medicine, Animals, Humans, ATPase, Genetic Predisposition to Disease, Hearing Loss, SPATA5L1, Hearing Lo, Alleles, cerebral palsy, Periventricular leukomalacia, Animal, Infant, Newborn, Infant, Genetic Variation, medicine.disease, neurodevelopmental disorder, Rats, ATPases Associated with Diverse Cellular Activities, Rat
Abstract

Spermatogenesis-associated 5 like 1 (SPATA5L1) represents an orphan gene encoding a protein of unknown function. We report 28 bi-allelic variants in SPATA5L1 associated with sensorineural hearing loss in 47 individuals from 28 (26 unrelated) families. In addition, 25/47 affected individuals (53%) presented with microcephaly, developmental delay/intellectual disability, cerebral palsy, and/or epilepsy. Modeling indicated damaging effect of variants on the protein, largely via destabilizing effects on protein domains. Brain imaging revealed diminished cerebral volume, thin corpus callosum, and periventricular leukomalacia, and quantitative volumetry demonstrated significantly diminished white matter volumes in several individuals. Immunofluorescent imaging in rat hippocampal neurons revealed localization of Spata511 in neuronal and glial cell nuclei and more prominent expression in neurons. In the rodent inner ear, Spata511 is expressed in the neurosensory hair cells and inner ear supporting cells. Transcriptomic analysis performed with fibroblasts from affected individuals was able to distinguish affected from controls by principal components. Analysis of differentially expressed genes and networks suggested a role for SPATA5L1 in cell surface adhesion receptor function, intracellular focal adhesions, and DNA replication and mitosis. Collectively, our results indicate that bi-allelic SPATA5L1 variants lead to a human disease characterized by sensorineural hearing loss (SNHL) with or without a nonprogressive mixed neurodevelopmental phenotype.

Published
2021

13. A biallelic variant in CLRN2 causes non-syndromic hearing loss in humans

Author

Henry Houlden, Thomas Haaf, Pratishtha Varshney, Christian Beetz, Hamid Galehdari, Lucy A Dunbar, Alireza Sedaghat, Richard J.H. Smith, Michael R. Bowl, Aziz El-Amraoui, Kevin T. Booth, David Murphy, Neda Mazaheri, Sandrine Vitry, Kumar N. Alagramam, Ben Fowler, Shruthi VijayKumar, Aboulfazl Rad, Hela Azaiez, Cassidy Petree, Barbara Vona, Sheng-Jia Lin, Gholamreza Shariati, Reza Maroofian, Franz Rüschendorf, Gaurav K. Varshney, EL-AMRAOUI, Aziz, ECLAIRER LA SURDITÉ : UNE APPROCHE HOLISTIQUE DU SYNDROME D'USHER - - LIGHT4DEAF2015 - ANR-15-RHUS-0001 - RHUS - VALID, Surdité d'apparition tardive et progressive: de la physiopathologie à la thérapie - - HearInNoise2017 - ANR-17-CE16-0017 - AAPG2017 - VALID, Julius-Maximilians-Universität Würzburg (JMU), Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Shahid Chamran University of Ahvaz (SCU), Oklahoma Medical Research Foundation (OMRF), MRC Harwell Institute [UK], University College of London [London] (UCL), University of Iowa [Iowa City], Harvard Medical School [Boston] (HMS), Déficits Sensoriels Progressifs, Pathophysiologie et Thérapie / Progressive Sensory Disorders, Pathophysiology and Therapy (DSP), Sorbonne Université (SU)-Institut de l'Audition [Paris] (IDA), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Max Delbrück Center for Molecular Medicine [Berlin] (MDC), Helmholtz-Gemeinschaft = Helmholtz Association, CENTOGENE AG, Case Western Reserve University [Cleveland], Ahvaz Jundishapur University of Medical Sciences (AJUMS), Narges Medical Genetics and Prenatal Diagnostics, Open Access funding enabled and organized by Projekt DEAL. This work was supported by Intramural Funding (fortüne) at the University of Tübingen (2545-1-0 to BV), the Ministry of Science, Research and Art Baden-Württemberg (to BV), the Medical Research Council (MC_UP_1503/2 to MRB), ANR light4deaf (ANR-15-RHUS-0001), HearInNoise (ANR-17-CE16-0017), LHW-stiftung to AE), and a grant from NIH/COBRE GM103636 (Project 3), the Presbyterian Health Foundation (PHF) Grant to GKV. This study was funded in part by NIDCDs R01s DC002842 and DC012049 to RJS and T32 GM007748 to KTB. LAD is a Medical Research Council DPhil student (1774724)., We would like to extend our gratitude to the family for their participation. We thank Dr. Caroline Lekszas, Dr. Daniel Liedtke, and Dr. Indrajit Nanda from the Institute of Human Genetics at the University of Würzburg for their technical expertise., ANR-15-RHUS-0001,LIGHT4DEAF,ECLAIRER LA SURDITÉ : UNE APPROCHE HOLISTIQUE DU SYNDROME D'USHER(2015), ANR-17-CE16-0017,HearInNoise,Surdité d'apparition tardive et progressive: de la physiopathologie à la thérapie(2017), Julius-Maximilians-Universität Würzburg [Wurtzbourg, Allemagne] (JMU), Carver College of Medicine, University of Iowa, Institut de l'Audition [Paris] (IDA), Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Sorbonne Université - Faculté de Médecine (SU FM), Sorbonne Université (SU), Institute of Neurology - UCL/Queen Square [London, UK] (IN-UCL-QS), Institut Pasteur [Paris], Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), University Hospitals of Cleveland, This work was supported by Intramural Funding (fortüne) at the University of Tübingen (2545-1-0 to B.V.), the Ministry of Science, Research and Art Baden-Württemberg (to B.V.), the Medical Research Council (MC_UP_1503/2 to M.R.B), ANR light4deaf (ANR-15-RHUS-0001), HearInNoise (ANR-17-CE16-0017), LHW-stiftung (to A.E.), and a grant from NIH/COBRE GM103636 (Project 3), the Presbyterian Health Foundation (PHF) Grant to G.K.V. This study was funded in part by NIDCDs R01s DC002842 and DC012049 to R.J.S and T32 GM007748 to K.T.B. L.A.D is a Medical Research Council DPhil student (1774724)., Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), and Déficits Sensoriels Progressifs, Pathophysiologie et Thérapie / Progressive Sensory Disorders, PathoPhysiology and Therapy (DSP)

Subjects
Male, Tetraspanins, [SDV]Life Sciences [q-bio], Gene Expression, MESH: Base Sequence, Consanguinity, Mice, 0302 clinical medicine, Missense mutation, MESH: Animals, Zebrafish, Genetics (clinical), Exome sequencing, Original Investigation, Genetics, 0303 health sciences, Chromosome Mapping, Disease gene identification, MESH: Amino Acid Substitution, Stop codon, Pedigree, [SDV] Life Sciences [q-bio], Female, Sensorineural hearing loss, MESH: Membrane Proteins, Chromosomes, Human, Pair 4, medicine.symptom, Adult, MESH: Chromosomes, Human, Pair 4, MESH: Gene Expression, Hearing loss, MESH: Pedigree, Hearing Loss, Sensorineural, Genes, Recessive, Locus (genetics), Biology, MESH: Hair Cells, Auditory, Inner, 03 medical and health sciences, MESH: Whole Exome Sequencing, Exome Sequencing, medicine, otorhinolaryngologic diseases, Animals, Humans, Point Mutation, ddc:610, MESH: Zebrafish, MESH: Mice, Alleles, MESH: Genes, Recessive, 030304 developmental biology, MESH: Point Mutation, MESH: Consanguinity, Hair Cells, Auditory, Inner, MESH: Humans, Base Sequence, MESH: Alleles, Intron, Membrane Proteins, MESH: Adult, medicine.disease, MESH: Male, Amino Acid Substitution, MESH: Hearing Loss, Sensorineural, Cardiovascular and Metabolic Diseases, MESH: Chromosome Mapping, MESH: Tetraspanins, MESH: Female, 030217 neurology & neurosurgery
Abstract

Deafness, the most frequent sensory deficit in humans, is extremely heterogeneous with hundreds of genes involved. Clinical and genetic analyses of an extended consanguineous family with pre-lingual, moderate-to-profound autosomal recessive sensorineural hearing loss, allowed us to identify CLRN2, encoding a tetraspan protein, as a new deafness gene. Homozygosity mapping followed by exome sequencing identified a 14.96 Mb locus on chromosome 4p15.32p15.1 containing a likely pathogenic missense variant in CLRN2 (c.494C > A, NM_001079827.2) segregating with the disease. Using in vitro RNA splicing analysis, we show that the CLRN2 c.494C > A variant leads to two events: (1) the substitution of a highly conserved threonine (uncharged amino acid) to lysine (charged amino acid) at position 165, p.(Thr165Lys), and (2) aberrant splicing, with the retention of intron 2 resulting in a stop codon after 26 additional amino acids, p.(Gly146Lysfs*26). Expression studies and phenotyping of newly produced zebrafish and mouse models deficient for clarin 2 further confirm that clarin 2, expressed in the inner ear hair cells, is essential for normal organization and maintenance of the auditory hair bundles, and for hearing function. Together, our findings identify CLRN2 as a new deafness gene, which will impact future diagnosis and treatment for deaf patients.

Published
2021
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14. Expanding the phenotype of PIGS-associated early onset epileptic developmental encephalopathy

Author

Javeria Reza Alvi, Henry Houlden, Vincenzo Salpietro, Marina Dutra-Clarke, Rauan Kaiyrzhanov, Pasquale Striano, Barbara Vona, Bianca E Russell, Philippe M. Campeau, Stephanie Efthymiou, Maria J. Guillen Sacoto, Reza Maroofian, Kshitij Mankad, Joseph G. Gleeson, Marcello Scala, Aboulfazl Rad, Tipu Sultan, Marilena Christoforou, Maha S. Zaki, and Thi Tuyet Mai Nguyen

Subjects
0301 basic medicine, Male, Microcephaly, Developmental Disabilities, Bioinformatics, Kidney, Epilepsy, 0302 clinical medicine, PIGS, Global developmental delay, Exome sequencing, medicine.diagnostic_test, neurodevelopmental disorders, Brain, Hypotonia, Phenotype, epileptic encephalopathy, Neurology, Child, Preschool, Muscle Hypotonia, Female, medicine.symptom, Brief Communications, Spasms, Infantile, congenital disorders of glycosylation, epilepsy, exome sequencing, inherited GPI deficiency, phosphatidylinositol glycan class S, Encephalopathy, Vision Disorders, Brief Communication, GPI-Linked Proteins, Nervous System Malformations, 03 medical and health sciences, medicine, Humans, Hearing Loss, Genetic testing, business.industry, Facies, Infant, medicine.disease, 030104 developmental biology, Neurology (clinical), business, Congenital disorder of glycosylation, 030217 neurology & neurosurgery, Acyltransferases
Abstract

The phosphatidylinositol glycan anchor biosynthesis class S protein (PIGS) gene has recently been implicated in a novel congenital disorder of glycosylation resulting in autosomal recessive inherited glycosylphosphatidylinositol‐anchored protein (GPI‐AP) deficiency. Previous studies described seven patients with biallelic variants in the PIGS gene, of whom two presented with fetal akinesia and five with global developmental delay and epileptic developmental encephalopathy. We present the molecular and clinical characteristics of six additional individuals from five families with unreported variants in PIGS. All individuals presented with hypotonia, severe global developmental delay, microcephaly, intractable early infantile epilepsy, and structural brain abnormalities. Additional findings include vision impairment, hearing loss, renal malformation, and hypotonic facial appearances with minor dysmorphic features but without a distinctive facial gestalt. Four individuals died due to neurologic complications. GPI anchoring studies performed on one individual revealed a significant decrease in GPI‐APs. We confirm that biallelic variants in PIGS cause vitamin pyridoxine‐responsive epilepsy due to inherited GPI deficiency and expand the genotype and phenotype of PIGS‐related disorder. Further delineation of the molecular spectrum of PIGS‐related disorders would improve management, help develop treatments, and encourage the expansion of diagnostic genetic testing to include this gene as a potential cause of neurodevelopmental disorders and epilepsy.

Published
2021

15. KDM5A mutations identified in autism spectrum disorder using forward genetics

Author

R. Curtis Rogers, Henry Houlden, Miao Tang, Priscilla Anderton, Jamie Russell, Aboulfazl Rad, Islam Oguz Tuncay, Barbara R. DuPont, Anna Lehman, Maria H. Chahrour, Anja Heinze, Xiaohong Li, Hessa S. Alsaif, Camerun Washington, Amanda Gerard, Rami Abou Jamra, Pia Zacher, Kiran J Kaur, Causes Study, Mohammad Reza Abbaszadegan, Nadine Nijem, Maha Faden, Reza Maroofian, Lauretta El Hayek, Ellen R. Elias, Bruce Beutler, Madeline Couse, Raymond J. Louie, Sara Ludwig, and Kazem Hassanpour

Subjects
0301 basic medicine, Mouse, vocalization, QH301-705.5, Science, Genomics, autism spectrum disorder, Biology, General Biochemistry, Genetics and Molecular Biology, Transcriptome, 03 medical and health sciences, 0302 clinical medicine, chromatin regulator, histone demethylase, mental disorders, medicine, Biology (General), Exome sequencing, Genetics, General Immunology and Microbiology, Genetic heterogeneity, Microarray analysis techniques, General Neuroscience, Genetics and Genomics, General Medicine, medicine.disease, Phenotype, Forward genetics, forward genetics, 030104 developmental biology, Autism spectrum disorder, Medicine, 030217 neurology & neurosurgery, Research Article, Human
Abstract

Autism spectrum disorder (ASD) is a constellation of neurodevelopmental disorders with high phenotypic and genetic heterogeneity, complicating the discovery of causative genes. Through a forward genetics approach selecting for defective vocalization in mice, we identified Kdm5a as a candidate ASD gene. To validate our discovery, we generated a Kdm5a knockout mouse model (Kdm5a-/-) and confirmed that inactivating Kdm5a disrupts vocalization. In addition, Kdm5a-/- mice displayed repetitive behaviors, sociability deficits, cognitive dysfunction, and abnormal dendritic morphogenesis. Loss of KDM5A also resulted in dysregulation of the hippocampal transcriptome. To determine if KDM5A mutations cause ASD in humans, we screened whole exome sequencing and microarray data from a clinical cohort. We identified pathogenic KDM5A variants in nine patients with ASD and lack of speech. Our findings illustrate the power and efficacy of forward genetics in identifying ASD genes and highlight the importance of KDM5A in normal brain development and function.

Published
2020

16. Author response: KDM5A mutations identified in autism spectrum disorder using forward genetics

Author

Priscilla Anderton, Miao Tang, Aboulfazl Rad, Barbara R. DuPont, Xiaohong Li, Bruce Beutler, Kiran J Kaur, Madeline Couse, Islam Oguz Tuncay, R. Curtis Rogers, Henry Houlden, Pia Zacher, Rami Abou Jamra, Anja Heinze, Camerun Washington, Maha Faden, Nadine Nijem, Mohammad Reza Abbaszadegan, Kazem Hassanpour, Reza Maroofian, Amanda Gerard, Hessa S. Alsaif, Lauretta El Hayek, Sara Ludwig, Anna Lehman, Maria H. Chahrour, Jamie Russell, Causes Study, Ellen R. Elias, and Raymond J. Louie

Subjects
Genetics, Autism spectrum disorder, medicine, Psychology, medicine.disease, Forward genetics
Published
2020
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17. Biallelic mutation of CLRN2 causes non-syndromic hearing loss in humans

Author

Barbara Vona, Neda Mazaheri, Sheng-Jia Lin, Lucy A Dunbar, Reza Maroofian, Hela Azaiez, Kevin T. Booth, Sandrine Vitry, Aboulfazl Rad, Pratishtha Varshney, Ben Fowler, Christian Beetz, Kumar N. Alagramam, David Murphy, Gholamreza Shariati, Alireza Sedaghat, Henry Houlden, Shruthi VijayKumar, Richard J. H. Smith, Thomas Haaf, Aziz El-Amraoui, Michael R. Bowl, Gaurav K. Varshney, and Hamid Galehdari

Subjects
Genetics, Biallelic Mutation, Hearing loss, medicine, Intron, Missense mutation, Sensorineural hearing loss, medicine.symptom, Biology, Disease gene identification, medicine.disease, Stop codon, Exome sequencing
Abstract

Deafness, the most frequent sensory deficit in humans, is extremely heterogenous with hundreds of genes probably involved. Clinical and genetic analyses of an extended consanguineous family with pre-lingual, moderate-to-profound autosomal recessive sensorineural hearing loss, allowed us to identify CLRN2, encoding a tetraspan protein as a new deafness gene. Homozygosity mapping followed by exome sequencing identified a 15.2 Mb locus on chromosome 4p15.32p15.1 containing a missense pathogenic variant in CLRN2 (c.494C>A, NM_001079827.2) segregating with the disease. Using in vitro RNA splicing analysis, we show that the CLRN2 c.494C>A mutation leads to two events: 1) the substitution of a highly conserved threonine (uncharged amino acid) to lysine (charged amino acid) at position 165, p.(Thr165Lys), and 2) aberrant splicing, with the retention of intron 2 resulting in a stop codon after 26 additional amino acids, p.(Gly146Lysfs*26). Expression studies and phenotyping of newly produced zebrafish and mouse models deficient for clarin 2 further confirm that clarin 2, expressed in the inner ear hair cells, is essential for normal organization and maintenance of the auditory hair bundles, and for hearing function. Together, our findings identify CLRN2 as a new deafness gene, which will impact future diagnosis and treatment for deaf patients.

Published
2020
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18. Novel loss-of-function variants in CDC14A are associated with recessive sensorineural hearing loss in Iranian and Pakistani patients

Author

Linda Schnapp, Barbara Vona, Thomas Haaf, Imran Khan, Tobias Müller, Franz Rüschendorf, Hyung-Goo Kim, Sabine Knaup, Abolfazl Adli, Michaela A.H. Hofrichter, Daniel Liedtke, Aboulfazl Rad, Susanne M. Kolb, Atefeh Hasanzadeh, Marcus Dittrich, Julia Doll, and Il-Keun Kong

Subjects
Proband, DFNB32, Hearing loss, non-sense mediated mRNA decay, Biology, frameshift, Catalysis, Frameshift mutation, lcsh:Chemistry, Inorganic Chemistry, splicing, medicine, otorhinolaryngologic diseases, ddc:610, Physical and Theoretical Chemistry, lcsh:QH301-705.5, Molecular Biology, Exome, Spectroscopy, Loss function, Exome sequencing, Genetics, Organic Chemistry, CDC14A, General Medicine, medicine.disease, Computer Science Applications, lcsh:Biology (General), lcsh:QD1-999, Cardiovascular and Metabolic Diseases, autosomal recessive hearing loss, Sensorineural hearing loss, medicine.symptom, exome sequencing, Minigene
Abstract

CDC14A encodes the Cell Division Cycle 14A protein and has been associated with autosomal recessive non-syndromic hearing loss (DFNB32), as well as hearing impairment and infertile male syndrome (HIIMS) since 2016. To date, only nine variants have been associated in patients whose initial symptoms included moderate-to-profound hearing impairment. Exome analysis of Iranian and Pakistani probands who both showed bilateral, sensorineural hearing loss revealed a novel splice site variant (c.1421+2T&gt, C, p.?) that disrupts the splice donor site and a novel frameshift variant (c.1041dup, p.Ser348Glnfs*2) in the gene CDC14A, respectively. To evaluate the pathogenicity of both loss-of-function variants, we analyzed the effects of both variants on the RNA-level. The splice variant was characterized using a minigene assay. Altered expression levels due to the c.1041dup variant were assessed using RT-qPCR. In summary, cDNA analysis confirmed that the c.1421+2T&gt, C variant activates a cryptic splice site, resulting in a truncated transcript (c.1414_1421del, p.Val472Leufs*20) and the c.1041dup variant results in a defective transcript that is likely degraded by nonsense-mediated mRNA decay. The present study functionally characterizes two variants and provides further confirmatory evidence that CDC14A is associated with a rare form of hereditary hearing loss.

Published
2020

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