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Yankee TN, Oh S, Winchester EW, Wilderman A, Robinson K, Gordon T, Rosenfeld JA, VanOudenhove J, Scott DA, Leslie EJ, Cotney J. Integrative analysis of transcriptome dynamics during human craniofacial development identifies candidate disease genes. Nat Commun 2023; 14:4623. [PMID: 37532691 PMCID: PMC10397224 DOI: 10.1038/s41467-023-40363-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 07/25/2023] [Indexed: 08/04/2023] Open
Abstract
Craniofacial disorders arise in early pregnancy and are one of the most common congenital defects. To fully understand how craniofacial disorders arise, it is essential to characterize gene expression during the patterning of the craniofacial region. To address this, we performed bulk and single-cell RNA-seq on human craniofacial tissue from 4-8 weeks post conception. Comparisons to dozens of other human tissues revealed 239 genes most strongly expressed during craniofacial development. Craniofacial-biased developmental enhancers were enriched +/- 400 kb surrounding these craniofacial-biased genes. Gene co-expression analysis revealed that regulatory hubs are enriched for known disease causing genes and are resistant to mutation in the normal healthy population. Combining transcriptomic and epigenomic data we identified 539 genes likely to contribute to craniofacial disorders. While most have not been previously implicated in craniofacial disorders, we demonstrate this set of genes has increased levels of de novo mutations in orofacial clefting patients warranting further study.
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Affiliation(s)
- Tara N Yankee
- Graduate Program in Genetics and Developmental Biology, UConn Health, Farmington, CT, 06030, USA
| | - Sungryong Oh
- University of Connecticut School of Medicine, Department of Genetics and Genome Sciences, Farmington, CT, 06030, USA
| | | | - Andrea Wilderman
- Graduate Program in Genetics and Developmental Biology, UConn Health, Farmington, CT, 06030, USA
| | - Kelsey Robinson
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Tia Gordon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Baylor Genetics Laboratory, Houston, TX, 77021, USA
| | - Jennifer VanOudenhove
- University of Connecticut School of Medicine, Department of Genetics and Genome Sciences, Farmington, CT, 06030, USA
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Elizabeth J Leslie
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Justin Cotney
- University of Connecticut School of Medicine, Department of Genetics and Genome Sciences, Farmington, CT, 06030, USA.
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, 06269, USA.
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Ciaccio C, Pantaleoni C, Moscatelli M, Chiapparini L, Nigro V, Valente EM, Sciacca F, Canafoglia L, Bulgheroni S, D'Arrigo S. Neurologic, Neuropsychologic, and Neuroradiologic Features of EBF3-Related Syndrome. NEUROLOGY GENETICS 2023; 9:e200049. [PMID: 37090941 PMCID: PMC10117703 DOI: 10.1212/nxg.0000000000200049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 10/25/2022] [Indexed: 01/24/2023]
Abstract
Background and ObjectivesHeterozygous mutations or deletions of theEBF3gene are known to cause a syndrome characterized by intellectual disability, neurodevelopmental disorders, facial dysmorphisms, hypotonia, and ataxia; the latter is quite common despite in most patients brain MRI is reported to be normal. Despite the predominant neurologic involvement ofEBF3-related syndrome, a systematic definition of neurologic, cognitive/behavioral, and neuroradiologic features is lacking.MethodsWe report on 6 patients (2 females and 4 males, age range 2–12 years), of whom 4 carrying a heterozygous point mutation of theEBF3gene and 2 with 10q26 deletion encompassing the gene, diagnosed at Carlo Besta Neurologic Institute of Milan, Italy. Clinical evaluation was performed by a pediatric neurologist and pediatric dysmorphologist; ataxia severity was rated by Scale for the Assessment and Rating of Ataxia (SARA); brain MRIs were reviewed by expert neuroradiologists; general quotient levels were obtained through standardized Griffiths Mental Development Scales. Patients carrying a 10q26.3 deletion were diagnosed by array-CGH, whereasEBF3variants were detected by whole exome sequencing.ResultsPhenotype was consistent in all patients, but with wide variability in severity. Developmental milestones were invariably delayed and resulted in an extremely variable cognitive impairment. All patients showed ataxic signs, as confirmed by SARA scores, often associated with hypotonia. Brain MRI revealed in all children a cerebellar malformation with vermis hypoplasia and a peculiar foliation anomaly characterized by a radial disposition of cerebellar folia (dandelion sign). Neurophysiologic examinations were unremarkable.DiscussionEBF3-related syndrome has been so far described as a neurodevelopmental condition with dysmorphic traits, with limited emphasis on the neurologic features; we highlight the predominant neurologic involvement of these patients, which can be explained at least in part by the underlying cerebellar malformation. We therefore propose thatEBF3-related syndrome should be classified and treated as a congenital, nonprogressive ataxia.
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Affiliation(s)
- Claudia Ciaccio
- Department of Pediatric Neurosciences (C.C., C.P., S.B., S.D.A.), Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano; Neuroradiology Unit (M.M., Luisa Chiapparini), Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano; Department of Biomedical Sciences for Health (M.M.), University of Milan; Neuroradiology Unit (Luisa Chiapparini), Fondazione IRCCS Policlinico San Matteo, Pavia; Telethon Institute of Genetics and Medicine (TIGEM) (V.N.), Pozzuoli; Department of Precision Medicine (V.N.), Università Della Campania Luigi Vanvitelli, Naples; Department of Molecular Medicine (E.M.V.), University of Pavia, Pavia; Molecular Genetics and Cytogenetics Lab-Neurogenetics Research Center (E.M.V.), IRCCS Mondino Foundation, Pavia; Laboratory of Cytogenetics (F.S.), Unit of Neurological Biochemistry and Neuropharmacology, Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan; and Integrated Diagnostics for Epilepsy (Laura Canafoglia), Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Chiara Pantaleoni
- Department of Pediatric Neurosciences (C.C., C.P., S.B., S.D.A.), Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano; Neuroradiology Unit (M.M., Luisa Chiapparini), Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano; Department of Biomedical Sciences for Health (M.M.), University of Milan; Neuroradiology Unit (Luisa Chiapparini), Fondazione IRCCS Policlinico San Matteo, Pavia; Telethon Institute of Genetics and Medicine (TIGEM) (V.N.), Pozzuoli; Department of Precision Medicine (V.N.), Università Della Campania Luigi Vanvitelli, Naples; Department of Molecular Medicine (E.M.V.), University of Pavia, Pavia; Molecular Genetics and Cytogenetics Lab-Neurogenetics Research Center (E.M.V.), IRCCS Mondino Foundation, Pavia; Laboratory of Cytogenetics (F.S.), Unit of Neurological Biochemistry and Neuropharmacology, Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan; and Integrated Diagnostics for Epilepsy (Laura Canafoglia), Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Marco Moscatelli
- Department of Pediatric Neurosciences (C.C., C.P., S.B., S.D.A.), Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano; Neuroradiology Unit (M.M., Luisa Chiapparini), Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano; Department of Biomedical Sciences for Health (M.M.), University of Milan; Neuroradiology Unit (Luisa Chiapparini), Fondazione IRCCS Policlinico San Matteo, Pavia; Telethon Institute of Genetics and Medicine (TIGEM) (V.N.), Pozzuoli; Department of Precision Medicine (V.N.), Università Della Campania Luigi Vanvitelli, Naples; Department of Molecular Medicine (E.M.V.), University of Pavia, Pavia; Molecular Genetics and Cytogenetics Lab-Neurogenetics Research Center (E.M.V.), IRCCS Mondino Foundation, Pavia; Laboratory of Cytogenetics (F.S.), Unit of Neurological Biochemistry and Neuropharmacology, Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan; and Integrated Diagnostics for Epilepsy (Laura Canafoglia), Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Luisa Chiapparini
- Department of Pediatric Neurosciences (C.C., C.P., S.B., S.D.A.), Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano; Neuroradiology Unit (M.M., Luisa Chiapparini), Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano; Department of Biomedical Sciences for Health (M.M.), University of Milan; Neuroradiology Unit (Luisa Chiapparini), Fondazione IRCCS Policlinico San Matteo, Pavia; Telethon Institute of Genetics and Medicine (TIGEM) (V.N.), Pozzuoli; Department of Precision Medicine (V.N.), Università Della Campania Luigi Vanvitelli, Naples; Department of Molecular Medicine (E.M.V.), University of Pavia, Pavia; Molecular Genetics and Cytogenetics Lab-Neurogenetics Research Center (E.M.V.), IRCCS Mondino Foundation, Pavia; Laboratory of Cytogenetics (F.S.), Unit of Neurological Biochemistry and Neuropharmacology, Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan; and Integrated Diagnostics for Epilepsy (Laura Canafoglia), Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Vincenzo Nigro
- Department of Pediatric Neurosciences (C.C., C.P., S.B., S.D.A.), Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano; Neuroradiology Unit (M.M., Luisa Chiapparini), Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano; Department of Biomedical Sciences for Health (M.M.), University of Milan; Neuroradiology Unit (Luisa Chiapparini), Fondazione IRCCS Policlinico San Matteo, Pavia; Telethon Institute of Genetics and Medicine (TIGEM) (V.N.), Pozzuoli; Department of Precision Medicine (V.N.), Università Della Campania Luigi Vanvitelli, Naples; Department of Molecular Medicine (E.M.V.), University of Pavia, Pavia; Molecular Genetics and Cytogenetics Lab-Neurogenetics Research Center (E.M.V.), IRCCS Mondino Foundation, Pavia; Laboratory of Cytogenetics (F.S.), Unit of Neurological Biochemistry and Neuropharmacology, Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan; and Integrated Diagnostics for Epilepsy (Laura Canafoglia), Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Enza Maria Valente
- Department of Pediatric Neurosciences (C.C., C.P., S.B., S.D.A.), Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano; Neuroradiology Unit (M.M., Luisa Chiapparini), Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano; Department of Biomedical Sciences for Health (M.M.), University of Milan; Neuroradiology Unit (Luisa Chiapparini), Fondazione IRCCS Policlinico San Matteo, Pavia; Telethon Institute of Genetics and Medicine (TIGEM) (V.N.), Pozzuoli; Department of Precision Medicine (V.N.), Università Della Campania Luigi Vanvitelli, Naples; Department of Molecular Medicine (E.M.V.), University of Pavia, Pavia; Molecular Genetics and Cytogenetics Lab-Neurogenetics Research Center (E.M.V.), IRCCS Mondino Foundation, Pavia; Laboratory of Cytogenetics (F.S.), Unit of Neurological Biochemistry and Neuropharmacology, Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan; and Integrated Diagnostics for Epilepsy (Laura Canafoglia), Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Francesca Sciacca
- Department of Pediatric Neurosciences (C.C., C.P., S.B., S.D.A.), Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano; Neuroradiology Unit (M.M., Luisa Chiapparini), Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano; Department of Biomedical Sciences for Health (M.M.), University of Milan; Neuroradiology Unit (Luisa Chiapparini), Fondazione IRCCS Policlinico San Matteo, Pavia; Telethon Institute of Genetics and Medicine (TIGEM) (V.N.), Pozzuoli; Department of Precision Medicine (V.N.), Università Della Campania Luigi Vanvitelli, Naples; Department of Molecular Medicine (E.M.V.), University of Pavia, Pavia; Molecular Genetics and Cytogenetics Lab-Neurogenetics Research Center (E.M.V.), IRCCS Mondino Foundation, Pavia; Laboratory of Cytogenetics (F.S.), Unit of Neurological Biochemistry and Neuropharmacology, Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan; and Integrated Diagnostics for Epilepsy (Laura Canafoglia), Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Laura Canafoglia
- Department of Pediatric Neurosciences (C.C., C.P., S.B., S.D.A.), Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano; Neuroradiology Unit (M.M., Luisa Chiapparini), Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano; Department of Biomedical Sciences for Health (M.M.), University of Milan; Neuroradiology Unit (Luisa Chiapparini), Fondazione IRCCS Policlinico San Matteo, Pavia; Telethon Institute of Genetics and Medicine (TIGEM) (V.N.), Pozzuoli; Department of Precision Medicine (V.N.), Università Della Campania Luigi Vanvitelli, Naples; Department of Molecular Medicine (E.M.V.), University of Pavia, Pavia; Molecular Genetics and Cytogenetics Lab-Neurogenetics Research Center (E.M.V.), IRCCS Mondino Foundation, Pavia; Laboratory of Cytogenetics (F.S.), Unit of Neurological Biochemistry and Neuropharmacology, Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan; and Integrated Diagnostics for Epilepsy (Laura Canafoglia), Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Sara Bulgheroni
- Department of Pediatric Neurosciences (C.C., C.P., S.B., S.D.A.), Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano; Neuroradiology Unit (M.M., Luisa Chiapparini), Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano; Department of Biomedical Sciences for Health (M.M.), University of Milan; Neuroradiology Unit (Luisa Chiapparini), Fondazione IRCCS Policlinico San Matteo, Pavia; Telethon Institute of Genetics and Medicine (TIGEM) (V.N.), Pozzuoli; Department of Precision Medicine (V.N.), Università Della Campania Luigi Vanvitelli, Naples; Department of Molecular Medicine (E.M.V.), University of Pavia, Pavia; Molecular Genetics and Cytogenetics Lab-Neurogenetics Research Center (E.M.V.), IRCCS Mondino Foundation, Pavia; Laboratory of Cytogenetics (F.S.), Unit of Neurological Biochemistry and Neuropharmacology, Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan; and Integrated Diagnostics for Epilepsy (Laura Canafoglia), Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Stefano D'Arrigo
- Department of Pediatric Neurosciences (C.C., C.P., S.B., S.D.A.), Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano; Neuroradiology Unit (M.M., Luisa Chiapparini), Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano; Department of Biomedical Sciences for Health (M.M.), University of Milan; Neuroradiology Unit (Luisa Chiapparini), Fondazione IRCCS Policlinico San Matteo, Pavia; Telethon Institute of Genetics and Medicine (TIGEM) (V.N.), Pozzuoli; Department of Precision Medicine (V.N.), Università Della Campania Luigi Vanvitelli, Naples; Department of Molecular Medicine (E.M.V.), University of Pavia, Pavia; Molecular Genetics and Cytogenetics Lab-Neurogenetics Research Center (E.M.V.), IRCCS Mondino Foundation, Pavia; Laboratory of Cytogenetics (F.S.), Unit of Neurological Biochemistry and Neuropharmacology, Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan; and Integrated Diagnostics for Epilepsy (Laura Canafoglia), Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
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Deisseroth CA, Lerma VC, Magyar CL, Pfliger JM, Nayak A, Bliss ND, LeMaire AW, Narayanan V, Balak C, Zanni G, Valente EM, Bertini E, Benke PJ, Wangler MF, Chao HT. An Integrated Phenotypic and Genotypic Approach Reveals a High-Risk Subtype Association for EBF3 Missense Variants Affecting the Zinc Finger Domain. Ann Neurol 2022; 92:138-153. [PMID: 35340043 DOI: 10.1002/ana.26359] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/28/2022] [Accepted: 03/20/2022] [Indexed: 11/10/2022]
Abstract
OBJECTIVE Collier/Olf/EBF (COE) transcription factors have distinct expression patterns in the developing and mature nervous system. To date, a neurological disease association has been conclusively established for only the Early B-cell Factor-3 (EBF3) COE family member through the identification of heterozygous loss-of-function variants in individuals with autism spectrum/neurodevelopmental disorders (NDD). Here, we identify a symptom severity risk association with missense variants primarily disrupting the zinc finger domain (ZNF) in EBF3-related NDD. METHODS A phenotypic assessment of 41 individuals was combined with a literature meta-analysis for a total of 83 individuals diagnosed with EBF3-related NDD. Quantitative diagnostic phenotypic and symptom severity scales were developed to compare EBF3 variant type and location to identify genotype-phenotype correlations. To stratify the effects of EBF3 variants disrupting either the DNA-binding domain (DBD) or the ZNF, we used in vivo fruit fly UAS-GAL4 expression and in vitro luciferase assays. RESULTS We show that patient symptom severity correlates with EBF3 missense variants perturbing the ZNF, which is a key protein domain required for stabilizing the interaction between EBF3 and the target DNA sequence. We found that ZNF-associated variants failed to restore viability in the fruit fly and impaired transcriptional activation. However, the recurrent variant EBF3 p.Arg209Trp in the DBD is capable of partially rescuing viability in the fly and preserved transcriptional activation. INTERPRETATION We describe a symptom severity risk association with ZNF perturbations and EBF3 loss-of-function in the largest reported cohort to date of EBF3-related NDD patients. This analysis should have potential predictive clinical value for newly identified patients with EBF3 gene variants. ANN NEUROL 2022;92:138-153.
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Affiliation(s)
- Cole A Deisseroth
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Vanesa C Lerma
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
- Department of Pediatrics, Division of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Christina L Magyar
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Graduate Program in Genetics and Genomics, Baylor College of Medicine, Houston, TX, USA
| | - Jessica Mae Pfliger
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
- Department of Pediatrics, Division of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Development, Disease Models, and Therapeutics Training Program, Baylor College of Medicine, Houston, TX, USA
| | - Aarushi Nayak
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA
| | - Nathan D Bliss
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA
| | - Ashley W LeMaire
- Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, TX, USA
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Christopher Balak
- Biomedical Sciences Graduate Program, University of California at San Diego, San Diego, CA, USA
| | - Ginevra Zanni
- Department of Neurosciences, Unit of Neuromuscular and Neurodegenerative Disorders, Bambino Gesu Children's Research Hospital IRCCS, Rome, Italy
| | - Enza Maria Valente
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Neurogenetics Research Centre, IRCCS Mondino Foundation, Pavia, Italy
| | - Enrico Bertini
- Department of Neurosciences, Unit of Neuromuscular and Neurodegenerative Disorders, Bambino Gesu Children's Research Hospital IRCCS, Rome, Italy
| | - Paul J Benke
- Joe DiMaggio Children's Hospital, Hollywood, FL, USA
| | - Michael F Wangler
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Hsiao-Tuan Chao
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
- Department of Pediatrics, Division of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- McNair Medical Institute, The Robert and Janice McNair Foundation, Houston, TX, USA
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4
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Kepler LD, McDiarmid TA, Rankin CH. Rapid assessment of the temporal function and phenotypic reversibility of neurodevelopmental disorder risk genes in Caenorhabditis elegans. Dis Model Mech 2022; 15:274939. [PMID: 35363276 PMCID: PMC9092656 DOI: 10.1242/dmm.049359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 03/22/2022] [Indexed: 11/20/2022] Open
Abstract
Recent studies have indicated that some phenotypes caused by decreased function of select neurodevelopmental disorder (NDD) risk genes can be reversed by restoring gene function in adulthood. However, few of the hundreds of risk genes have been assessed for adult phenotypic reversibility. We developed a strategy to rapidly assess the temporal requirements and phenotypic reversibility of NDD risk gene orthologs using a conditional protein degradation system and machine-vision phenotypic profiling in Caenorhabditis elegans. We measured how degrading and re-expressing orthologs of EBF3, BRN3A and DYNC1H1 at multiple periods throughout development affect 30 morphological, locomotor, sensory and learning phenotypes. We found that phenotypic reversibility was possible for each gene studied. However, the temporal requirements of gene function and degree of rescue varied by gene and phenotype. This work highlights the critical need to assess multiple windows of degradation and re-expression and a large number of phenotypes to understand the many roles a gene can have across the lifespan. This work also demonstrates the benefits of using a high-throughput model system to prioritize NDD risk genes for re-expression studies in other organisms. Summary: We identified diverse temporal functional windows and phenotypic reversibility profiles for three neurodevelopmental disorder risk genes: EBF3•unc-3, BRN3A•unc-86 and DYNC1H1•dhc-1. Re-expression of certain genes could rescue multiple phenotypes later in life, prioritizing them for study.
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Affiliation(s)
- Lexis D Kepler
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2211 Wesbrook Mall, Vancouver, BC V6T 2B5, Canada
| | - Troy A McDiarmid
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2211 Wesbrook Mall, Vancouver, BC V6T 2B5, Canada.,Department of Genome Sciences, University of Washington School of Medicine, Foege Building S-250 3720 15th Ave NE, Seattle, WA 98195, USA
| | - Catharine H Rankin
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2211 Wesbrook Mall, Vancouver, BC V6T 2B5, Canada.,Department of Psychology, University of British Columbia, 2136 West Mall, Vancouver, BC V6T 1Z4, Canada
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5
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Passos-Bueno MR, Costa CIS, Zatz M. Dystrophin genetic variants and autism. DISCOVER MENTAL HEALTH 2022; 2:4. [PMID: 37861890 PMCID: PMC10501027 DOI: 10.1007/s44192-022-00008-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 02/07/2022] [Indexed: 10/21/2023]
Abstract
Loss-of-function variants in the dystrophin gene, a well-known cause of muscular dystrophies, have emerged as a mutational risk mechanism for autism spectrum disorder (ASD), which in turn is a highly prevalent (~ 1%) genetically heterogeneous neurodevelopmental disorder. Although the association of intellectual disability with the dystrophinopathies Duchenne (DMD) and Becker muscular dystrophy (BMD) has been long established, their association with ASD is more recent, and the dystrophin genotype-ASD phenotype correlation is unclear. We therefore present a review of the literature focused on the ASD prevalence among dystrophinopathies, the relevance of the dystrophin isoforms, and most particularly the relevance of the genetic background to the etiology of ASD in these patients. Four families with ASD-DMD/BMD patients are also reported here for the first time. These include a single ASD individual, ASD-discordant and ASD-concordant monozygotic twins, and non-identical ASD triplets. Notably, two unrelated individuals, which were first ascertained because of the ASD phenotype at ages 15 and 5 years respectively, present rare dystrophin variants still poorly characterized, suggesting that some dystrophin variants may compromise the brain more prominently. Whole exome sequencing in these ASD-DMD/BMD individuals together with the literature suggest, although based on preliminary data, a complex and heterogeneous genetic architecture underlying ASD in dystrophinopathies, that include rare variants of large and medium effect. The need for the establishment of a consortia for genomic investigation of ASD-DMD/BMD patients, which may shed light on the genetic architecture of ASD, is discussed.
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Affiliation(s)
- Maria Rita Passos-Bueno
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil.
| | - Claudia Ismania Samogy Costa
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Mayana Zatz
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
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Ignatius E, Puosi R, Palomäki M, Forsbom N, Pohjanpelto M, Alitalo T, Anttonen AK, Avela K, Haataja L, Carroll CJ, Lönnqvist T, Isohanni P. Duplication/triplication mosaicism of EBF3 and expansion of the EBF3 neurodevelopmental disorder phenotype. Eur J Paediatr Neurol 2022; 37:1-7. [PMID: 34999443 DOI: 10.1016/j.ejpn.2021.12.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 12/06/2021] [Accepted: 12/18/2021] [Indexed: 11/15/2022]
Abstract
Deleterious variants in the transcription factor early B-cell factor 3 (EBF3) are known to cause a neurodevelopmental disorder (EBF3-NDD). We report eleven individuals with EBF3 variants, including an individual with a duplication/triplication mosaicism of a region encompassing EBF3 and a phenotype consistent with EBF3-NDD, which may reflect the importance of EBF3 gene-dosage for neurodevelopment. The phenotype of individuals in this cohort was quite mild compared to the core phenotype of previously described individuals. Although ataxia tended to wane with age, we show that cognitive difficulties may increase, and we recommend that individuals with EBF3-NDD have systematic neuropsychological follow-up.
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Affiliation(s)
- Erika Ignatius
- Department of Child Neurology, Children's Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; Research Programs Unit, Stem Cells and Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Riina Puosi
- Department of Child Neurology, Children's Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Maarit Palomäki
- Department of Radiology, HUS Medical Imaging Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Noora Forsbom
- Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Max Pohjanpelto
- Research Programs Unit, Stem Cells and Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Tiina Alitalo
- Laboratory of Genetics, HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Anna-Kaisa Anttonen
- Laboratory of Genetics, HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; Department of Clinical Genetics, HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Kristiina Avela
- Department of Clinical Genetics, HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Leena Haataja
- Department of Child Neurology, Children's Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Christopher J Carroll
- Genetics Research Centre, Molecular and Clinical Sciences Research Institute, St. George's, University of London, London, United Kingdom
| | - Tuula Lönnqvist
- Department of Child Neurology, Children's Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Pirjo Isohanni
- Department of Child Neurology, Children's Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; Research Programs Unit, Stem Cells and Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
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7
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Pruccoli J, Graziano C, Locatelli C, Maltoni L, Sheikh Maye HA, Cordelli DM. Expanding the Neurological Phenotype of Ring Chromosome 10 Syndrome: A Case Report and Review of the Literature. Genes (Basel) 2021; 12:genes12101513. [PMID: 34680908 PMCID: PMC8535287 DOI: 10.3390/genes12101513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 12/05/2022] Open
Abstract
Ring chromosome 10 [r(10)] syndrome is a rare genetic condition, currently described in the medical literature in a small number of case report studies. Typical clinical features include microcephaly, short stature, facial dysmorphisms, ophthalmologic abnormalities and genitourinary malformations. We report a novel case of r(10) syndrome and review the neurological and neuroradiological phenotypes of the previously described cases. Our patient, a 3 year old Italian girl, represents the 20th case of r(10) syndrome described to date. Intellectual disability/developmental delay (ID/DD), microcephaly, strabismus, hypotonia, stereotyped/aggressive behaviors and electroencephalographic abnormalities were identified in our patient, and in a series of previous cases. A brain MRI disclosed a complex malformation involving both the vermis and cerebellar hemispheres; in the literature, posterior cranial fossa abnormalities were documented by CT scan in another case. Two genes deleted in our case (ZMYND11 in 10p and EBF3 in 10q) are involved in autosomal dominant neurodevelopmental disorders, characterized by different expressions of brain and posterior cranial fossa abnormalities, ID/DD, hypotonia and behavioral problems. Our case expands the neurological and neuroradiological phenotype of r(10) syndrome. Although r(10) syndrome represents an extremely rare condition, with a clinical characterization limited to case reports, the recurrence of specific neurological and neuroradiological features suggests the need for specific genotype-phenotype studies.
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Affiliation(s)
- Jacopo Pruccoli
- Child Neurology and Psychiatry Unit, IRCCS Istituto delle Scienze Neurologiche di Bologna, 40138 Bologna, Italy;
- Dipartimento di Scienze Mediche E Chirurgiche (DIMEC), University of Bologna, 40138 Bologna, Italy
| | - Claudio Graziano
- UO Genetica Medica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
| | - Chiara Locatelli
- Neonatal Intensive Care Unit, S.Orsola Malpighi Hospital, 40138 Bologna, Italy;
| | - Lucia Maltoni
- Child Neurology and Psychiatry Unit, Azienda USL della Romagna, 48121 Ravenna, Italy;
| | - Hodman Ahmed Sheikh Maye
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, UOC Neuroradiologia, 40139 Bologna, Italy;
| | - Duccio Maria Cordelli
- Child Neurology and Psychiatry Unit, IRCCS Istituto delle Scienze Neurologiche di Bologna, 40138 Bologna, Italy;
- Dipartimento di Scienze Mediche E Chirurgiche (DIMEC), University of Bologna, 40138 Bologna, Italy
- Correspondence:
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8
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Li Q, Sun C, Guo J, Zhai W, Zhang L. Terminal 10q26.12 deletion is associated with neonatal asymmetric crying facies syndrome: a case report and literature review. Mol Cytogenet 2021; 14:36. [PMID: 34256807 PMCID: PMC8278754 DOI: 10.1186/s13039-021-00554-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 06/24/2021] [Indexed: 11/26/2022] Open
Abstract
Background The terminal 10q26 deletion syndrome is a clinically heterogeneous disorder without identified genotype–phenotype correlations. We reported a case of congenital asymmetric crying facies (ACF) syndrome with 10q26.12qter deletion and discussed their genotype–phenotype correlations and the potentially contributing genes involving the etiology of ACF. Methods and results We reported a case of neonatal 10q26.12qter deletion and summarized the genotype–phenotype correlations and contributing genes of 10q26.12qter deletion from DECIPHER database and published studies. Meanwhile, we analyzed the potential pathogenic genes contributing to 10q26 deletion syndrome. The female preterm infant harboring 10q26.12qter deletion showed symptoms of abnormal craniofacial appearance with rare congenital asymmetric crying facies, developmental retardation, congenital heart disease, and pulmonary artery hypertension. The deleted region was 13.28 Mb in size as detected by G-banding and array comparative genome hybridization, containing 62 Online Mendelian Inheritance in Man (OMIM) catalog genes. We summarized data from 17 other patients with 10q26.12qter deletion, 11 from the DECIPHER database and 6 from published studies. Patients with monoallelic WDR11 and FGFR2 deletions located in 10q26.12q26.2 were predisposed to craniofacial dysmorphisms, growth retardation, intellectual disability and cardiac diseases. Conclusion ACF is a facial dysmorphism frequently accompanied by other systemic deformities. It is a genetic abnormality that may associate with terminal 10q26.12 deletion. Early cardiac, audiologic, cranial examinations and genetic detection are needed to guide early diagnosis and treatment strategy.
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Affiliation(s)
- Qinghong Li
- Department of Neonatology, Northwest Women's and Children's Hospital, Yanta District, No. 1616, Yanxiang Road, Xi'an, 7100061, Shaanxi, People's Republic of China.
| | - Chunmei Sun
- Department of Neonatology, Northwest Women's and Children's Hospital, Yanta District, No. 1616, Yanxiang Road, Xi'an, 7100061, Shaanxi, People's Republic of China
| | - Jinzhen Guo
- Department of Neonatology, Northwest Women's and Children's Hospital, Yanta District, No. 1616, Yanxiang Road, Xi'an, 7100061, Shaanxi, People's Republic of China
| | - Wen Zhai
- Genetic Medical Center, Northwest Women's and Children's Hospital, Xi'an, 7100061, Shaanxi, People's Republic of China
| | - Liping Zhang
- Genetic Medical Center, Northwest Women's and Children's Hospital, Xi'an, 7100061, Shaanxi, People's Republic of China
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9
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Nishi E, Uehara T, Yanagi K, Hasegawa Y, Ueda K, Kaname T, Yamamoto T, Kosaki K, Okamoto N. Clinical spectrum of individuals with de novo EBF3 variants or deletions. Am J Med Genet A 2021; 185:2913-2921. [PMID: 34050706 DOI: 10.1002/ajmg.a.62369] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/30/2022]
Abstract
Hypotonia, ataxia and delayed development syndrome (HADDS) (MIM#617330) is a neurodevelopmental disorder caused by heterozygous pathogenic variants in EBF3 (MIM; 607,407), which is located on chromosome 10q26, and was first reported in 2017. To date, missense, nonsense and frameshift variants have been reported as causes of HADDS, and EBF3 pathogenic variants have been predicted to result in nonsense-mediated mRNA decay and haploinsufficiency. It was also reported that total deletion of EBF3 associated with a 10q26.3 microdeletion also causes HADDS symptoms, supporting the concept that HADDS results from haploinsufficiency of EBF3. Here, we report eight unrelated individuals with heterozygous pathogenic variants of EBF3 or haploinsufficiency of EBF3 due to 10q26 deletion, who exhibit clinical findings including craniofacial features of HADDS. In a detailed examination of clinical manifestations in this study, revealed that neurogenic bladder was diagnosed in infancy (the median 6.5 months), was more frequent than previously reported, and required cystostomy in all but one case. For psychomotor delay, it was also found that their motor/skills values were significantly lower than their cognition/adaptation values (p = 0.0016; paired t-test). Therefore, that HADDS is a recognizable syndrome that shares its characteristic facial features, and that neurogenic bladder diagnosed in infancy and psychomotor delay with marked delay in motor/skills are noteworthy findings in the diagnosis and management of individuals with HADDS.
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Affiliation(s)
- Eriko Nishi
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Tomoko Uehara
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Kumiko Yanagi
- Department of Genome Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Yuiko Hasegawa
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Kimiko Ueda
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Tadashi Kaname
- Department of Genome Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Toshiyuki Yamamoto
- Department of Genomic Medicine, Tokyo Women's Medical University, Tokyo, Japan
| | - Kenjiro Kosaki
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
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10
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Jiménez de la Peña M, Jiménez de Domingo A, Tirado P, Calleja-Pérez B, Alcaraz LA, Álvarez S, Williams J, Hagman JR, Németh AH, Fernández-Jaén A. Neuroimaging Findings in Patients with EBF3 Mutations: Report of Two Cases. Mol Syndromol 2021; 12:186-193. [PMID: 34177436 DOI: 10.1159/000513583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 12/03/2020] [Indexed: 12/27/2022] Open
Abstract
Early B cell factor 3 (EBF3) is a transcription factor involved in brain development. Heterozygous, loss-of-function mutations in EBF3 have been reported in an autosomal dominant neurodevelopmental syndrome characterized by hypotonia, ataxia, and developmental delay (sometimes described as "HADD"s). We report 2 unrelated cases with novel de novo EBF3 mutations: c.455G>T (p.Arg152Leu) and c.962dup (p.Tyr321*) to expand the genotype/phenotype correlations of this disorder; clinical, neuropsychological, and MRI studies were used to define the phenotype. IQ was in the normal range and diffusion tensor imaging revealed asymmetric alterations of the longitudinal fasciculus in both cases. Our results demonstrate that EBF3 mutations can underlie neurodevelopmental disorders without intellectual disability. Long tract abnormalities have not been previously recognized and suggest that they may be an unrecognized and characteristic feature in this syndrome.
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Affiliation(s)
| | | | - Pilar Tirado
- Department of Pediatric Neurology, Hospital Universitario La Paz, Madrid, Spain
| | | | | | - Sara Álvarez
- Genomics and Medicine, NIMGenetics, Madrid, Spain
| | - Jonathan Williams
- Oxford Medical Genetics Laboratories, Churchill Hospital, Oxford, United Kingdom
| | - James R Hagman
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado, USA
| | - Andrea H Németh
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom.,Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Alberto Fernández-Jaén
- Department of Pediatric Neurology, Hospital Universitario Quirónsalud, and Medicine School, Universidad Europea de Madrid, Madrid, Spain
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11
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Quach TT, Stratton HJ, Khanna R, Kolattukudy PE, Honnorat J, Meyer K, Duchemin AM. Intellectual disability: dendritic anomalies and emerging genetic perspectives. Acta Neuropathol 2021; 141:139-158. [PMID: 33226471 PMCID: PMC7855540 DOI: 10.1007/s00401-020-02244-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 12/12/2022]
Abstract
Intellectual disability (ID) corresponds to several neurodevelopmental disorders of heterogeneous origin in which cognitive deficits are commonly associated with abnormalities of dendrites and dendritic spines. These histological changes in the brain serve as a proxy for underlying deficits in neuronal network connectivity, mostly a result of genetic factors. Historically, chromosomal abnormalities have been reported by conventional karyotyping, targeted fluorescence in situ hybridization (FISH), and chromosomal microarray analysis. More recently, cytogenomic mapping, whole-exome sequencing, and bioinformatic mining have led to the identification of novel candidate genes, including genes involved in neuritogenesis, dendrite maintenance, and synaptic plasticity. Greater understanding of the roles of these putative ID genes and their functional interactions might boost investigations into determining the plausible link between cellular and behavioral alterations as well as the mechanisms contributing to the cognitive impairment observed in ID. Genetic data combined with histological abnormalities, clinical presentation, and transgenic animal models provide support for the primacy of dysregulation in dendrite structure and function as the basis for the cognitive deficits observed in ID. In this review, we highlight the importance of dendrite pathophysiology in the etiologies of four prototypical ID syndromes, namely Down Syndrome (DS), Rett Syndrome (RTT), Digeorge Syndrome (DGS) and Fragile X Syndrome (FXS). Clinical characteristics of ID have also been reported in individuals with deletions in the long arm of chromosome 10 (the q26.2/q26.3), a region containing the gene for the collapsin response mediator protein 3 (CRMP3), also known as dihydropyrimidinase-related protein-4 (DRP-4, DPYSL4), which is involved in dendritogenesis. Following a discussion of clinical and genetic findings in these syndromes and their preclinical animal models, we lionize CRMP3/DPYSL4 as a novel candidate gene for ID that may be ripe for therapeutic intervention.
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Affiliation(s)
- Tam T Quach
- Institute for Behavioral Medicine Research, Wexner Medical Center, The Ohio State University, Columbus, OH, 43210, USA
- INSERM U1217/CNRS, UMR5310, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | | | - Rajesh Khanna
- Department of Pharmacology, University of Arizona, Tucson, AZ, 85724, USA
| | | | - Jérome Honnorat
- INSERM U1217/CNRS, UMR5310, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France
- French Reference Center on Paraneoplastic Neurological Syndromes and Autoimmune Encephalitis, Hospices Civils de Lyon, Lyon, France
- SynatAc Team, Institut NeuroMyoGène, Lyon, France
| | - Kathrin Meyer
- The Research Institute of Nationwide Children Hospital, Columbus, OH, 43205, USA
- Department of Pediatric, The Ohio State University, Columbus, OH, 43210, USA
| | - Anne-Marie Duchemin
- Department of Psychiatry and Behavioral Health, The Ohio State University, Columbus, OH, 43210, USA.
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12
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Osei-Owusu IA, Norris AL, Joynt AT, Thorpe J, Cho S, Tierney E, Schmidt J, Hagopian L, Harris J, Pevsner J. Characterization of an unbalanced translocation causing 3q28qter duplication and 10q26.2qter deletion in a patient with global developmental delay and self-injury. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a005884. [PMID: 33335013 PMCID: PMC7784495 DOI: 10.1101/mcs.a005884] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 11/08/2020] [Indexed: 01/17/2023] Open
Abstract
Chromosomal structural variation can cause severe neurodevelopmental and neuropsychiatric phenotypes. Here we present a nonverbal female adolescent with severe stereotypic movement disorder with severe problem behavior (e.g., self-injurious behavior, aggression, and disruptive and destructive behaviors), autism spectrum disorder, severe intellectual disability, attention deficit hyperactivity disorder, and global developmental delay. Previous cytogenetic analysis revealed balanced translocations present in the patient's apparently normal mother. We hypothesized the presence of unbalanced translocations in the patient due to maternal history of spontaneous abortions. Whole-genome sequencing and whole-genome optical mapping, complementary next-generation genomic technologies capable of the accurate and robust detection of structural variants, identified t(3;10), t(10;14), and t(3;14) three-way balanced translocations in the mother and der(10)t(3;14;10) and der(14)t(3;14;10) translocations in the patient. Instead of a t(3;10), she inherited a normal maternal copy of Chromosome 3, resulting in an unbalanced state of a 3q28qter duplication and 10q26.2qter deletion. Copy-imbalanced genes in one or both of these regions, such as DLG1, DOCK1, and EBF3, may contribute to the patient's phenotype that spans neurodevelopmental, musculoskeletal, and psychiatric domains, with the possible contribution of a maternally inherited 15q13.2q13.3 deletion.
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Affiliation(s)
- Ikeoluwa A Osei-Owusu
- Program in Human Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.,Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA
| | - Alexis L Norris
- Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA
| | - Anya T Joynt
- Program in Human Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
| | - Jeremy Thorpe
- Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA.,Program in Biochemistry, Cellular and Molecular Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
| | - Soonweng Cho
- Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA.,Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
| | - Elaine Tierney
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.,Department of Psychiatry, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA
| | - Jonathan Schmidt
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.,Department of Behavioral Psychology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA
| | - Louis Hagopian
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.,Department of Behavioral Psychology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA
| | - Jacqueline Harris
- Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA.,Department of Neurology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
| | - Jonathan Pevsner
- Program in Human Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.,Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA.,Program in Biochemistry, Cellular and Molecular Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.,Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
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13
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Harnish JM, Deal SL, Chao HT, Wangler MF, Yamamoto S. In Vivo Functional Study of Disease-associated Rare Human Variants Using Drosophila. J Vis Exp 2019:10.3791/59658. [PMID: 31498321 PMCID: PMC7418855 DOI: 10.3791/59658] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Advances in sequencing technology have made whole-genome and whole-exome datasets more accessible for both clinical diagnosis and cutting-edge human genetics research. Although a number of in silico algorithms have been developed to predict the pathogenicity of variants identified in these datasets, functional studies are critical to determining how specific genomic variants affect protein function, especially for missense variants. In the Undiagnosed Diseases Network (UDN) and other rare disease research consortia, model organisms (MO) including Drosophila, C. elegans, zebrafish, and mice are actively used to assess the function of putative human disease-causing variants. This protocol describes a method for the functional assessment of rare human variants used in the Model Organisms Screening Center Drosophila Core of the UDN. The workflow begins with gathering human and MO information from multiple public databases, using the MARRVEL web resource to assess whether the variant is likely to contribute to a patient's condition as well as design effective experiments based on available knowledge and resources. Next, genetic tools (e.g., T2A-GAL4 and UAS-human cDNA lines) are generated to assess the functions of variants of interest in Drosophila. Upon development of these reagents, two-pronged functional assays based on rescue and overexpression experiments can be performed to assess variant function. In the rescue branch, the endogenous fly genes are "humanized" by replacing the orthologous Drosophila gene with reference or variant human transgenes. In the overexpression branch, the reference and variant human proteins are exogenously driven in a variety of tissues. In both cases, any scorable phenotype (e.g., lethality, eye morphology, electrophysiology) can be used as a read-out, irrespective of the disease of interest. Differences observed between reference and variant alleles suggest a variant-specific effect, and thus likely pathogenicity. This protocol allows rapid, in vivo assessments of putative human disease-causing variants of genes with known and unknown functions.
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Affiliation(s)
- J Michael Harnish
- Department of Molecular and Human Genetics, Baylor College of Medicine
| | - Samantha L Deal
- Program in Developmental Biology, Baylor College of Medicine
| | - Hsiao-Tuan Chao
- Department of Molecular and Human Genetics, Baylor College of Medicine; Department of Pediatrics, Section of Neurology and Developmental Neuroscience, Baylor College of Medicine; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital; Department of Neuroscience, Baylor College of Medicine
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine; Program in Developmental Biology, Baylor College of Medicine; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine; Program in Developmental Biology, Baylor College of Medicine; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital; Department of Neuroscience, Baylor College of Medicine;
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14
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Lopes F, Torres F, Soares G, Barbosa M, Silva J, Duque F, Rocha M, Sá J, Oliveira G, Sá MJ, Temudo T, Sousa S, Marques C, Lopes S, Gomes C, Barros G, Jorge A, Rocha F, Martins C, Mesquita S, Loureiro S, Cardoso EM, Cálix MJ, Dias A, Martins C, Mota CR, Antunes D, Dupont J, Figueiredo S, Figueiroa S, Gama-de-Sousa S, Cruz S, Sampaio A, Eijk P, Weiss MM, Ylstra B, Rendeiro P, Tavares P, Reis-Lima M, Pinto-Basto J, Fortuna AM, Maciel P. Genomic imbalances defining novel intellectual disability associated loci. Orphanet J Rare Dis 2019; 14:164. [PMID: 31277718 PMCID: PMC6612161 DOI: 10.1186/s13023-019-1135-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 06/12/2019] [Indexed: 11/29/2022] Open
Abstract
Background High resolution genome-wide copy number analysis, routinely used in clinical diagnosis for several years, retrieves new and extremely rare copy number variations (CNVs) that provide novel candidate genes contributing to disease etiology. The aim of this work was to identify novel genetic causes of neurodevelopmental disease, inferred from CNVs detected by array comparative hybridization (aCGH), in a cohort of 325 Portuguese patients with intellectual disability (ID). Results We have detected CNVs in 30.1% of the patients, of which 5.2% corresponded to novel likely pathogenic CNVs. For these 11 rare CNVs (which encompass novel ID candidate genes), we identified those most likely to be relevant, and established genotype-phenotype correlations based on detailed clinical assessment. In the case of duplications, we performed expression analysis to assess the impact of the rearrangement. Interestingly, these novel candidate genes belong to known ID-related pathways. Within the 8% of patients with CNVs in known pathogenic loci, the majority had a clinical presentation fitting the phenotype(s) described in the literature, with a few interesting exceptions that are discussed. Conclusions Identification of such rare CNVs (some of which reported for the first time in ID patients/families) contributes to our understanding of the etiology of ID and for the ever-improving diagnosis of this group of patients. Electronic supplementary material The online version of this article (10.1186/s13023-019-1135-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fátima Lopes
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Fátima Torres
- CGC Genetics, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Gabriela Soares
- Center for Medical Genetics Dr. Jacinto Magalhães, Porto Hospital Center, Praça Pedro Nunes, Porto, Portugal
| | - Mafalda Barbosa
- Center for Medical Genetics Dr. Jacinto Magalhães, Porto Hospital Center, Praça Pedro Nunes, Porto, Portugal.,Unit for Multidisciplinary Research in Biomedicine, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal.,The Mindich Child Health & Development Institute and the Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,The Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - João Silva
- Center for Medical Genetics Dr. Jacinto Magalhães, Porto Hospital Center, Praça Pedro Nunes, Porto, Portugal.,Centro de Genética Preditiva e Preventiva - CGPP, Instituto de Biologia Molecular e Celular - IBMC, Universidade do Porto, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde - i3S, Universidade do Porto, Porto, Portugal
| | - Frederico Duque
- Unidade de Neurodesenvolvimento e Autismo do Serviço do Centro de Desenvolvimento da Criança and Centro de Investigação e Formação Clínica, Pediatric Hospital, Centro Hospitalar e Universitário de Coimbra, 3041-80, Coimbra, Portugal.,University Clinic of Pediatrics and Institute for Biomedical Imaging and Life Science, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Miguel Rocha
- Center for Medical Genetics Dr. Jacinto Magalhães, Porto Hospital Center, Praça Pedro Nunes, Porto, Portugal.,Medical Genetics Unit, Hospital de Braga, Braga, Portugal
| | - Joaquim Sá
- CGC Genetics, Porto, Portugal.,Department of Medical Genetics, Hospital de Faro, Faro, Portugal
| | - Guiomar Oliveira
- Unidade de Neurodesenvolvimento e Autismo do Serviço do Centro de Desenvolvimento da Criança and Centro de Investigação e Formação Clínica, Pediatric Hospital, Centro Hospitalar e Universitário de Coimbra, 3041-80, Coimbra, Portugal.,University Clinic of Pediatrics and Institute for Biomedical Imaging and Life Science, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Maria João Sá
- Center for Medical Genetics Dr. Jacinto Magalhães, Porto Hospital Center, Praça Pedro Nunes, Porto, Portugal.,Unit for Multidisciplinary Research in Biomedicine, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Teresa Temudo
- Pediatric Neurology Department, Centro Materno-Infantil Centro Hospitalar do Porto, Porto, Portugal
| | - Susana Sousa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal.,Centro de Genética Preditiva e Preventiva - CGPP, Instituto de Biologia Molecular e Celular - IBMC, Universidade do Porto, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde - i3S, Universidade do Porto, Porto, Portugal
| | - Carla Marques
- Unidade de Neurodesenvolvimento e Autismo do Serviço do Centro de Desenvolvimento da Criança and Centro de Investigação e Formação Clínica, Pediatric Hospital, Centro Hospitalar e Universitário de Coimbra, 3041-80, Coimbra, Portugal
| | - Sofia Lopes
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Catarina Gomes
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Gisela Barros
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Arminda Jorge
- Development Unit, Pediatrics Service, Hospital Centre of Cova da Beira, Covilhã, Portugal.,CICS - Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
| | - Felisbela Rocha
- Department of Pediatrics, Médio Ave Hospital Center, Vila Nova de Famalicão, Portugal
| | - Cecília Martins
- Department of Pediatrics, Médio Ave Hospital Center, Vila Nova de Famalicão, Portugal
| | - Sandra Mesquita
- Development Unit, Pediatrics Service, Hospital Centre of Cova da Beira, Covilhã, Portugal
| | - Susana Loureiro
- Department of Pediatrics, Hospital S. Teotónio, Tondela/Viseu Hospital Center, Viseu, Portugal
| | - Elisa Maria Cardoso
- Department of Pediatrics, Hospital S. Teotónio, Tondela/Viseu Hospital Center, Viseu, Portugal
| | - Maria José Cálix
- Department of Pediatrics, Hospital S. Teotónio, Tondela/Viseu Hospital Center, Viseu, Portugal
| | - Andreia Dias
- Department of Pediatrics, Hospital S. Teotónio, Tondela/Viseu Hospital Center, Viseu, Portugal
| | - Cristina Martins
- Neuropaediatric Unit - Garcia de Orta Hospital, Almada, Portugal
| | - Céu R Mota
- Pediatric and Neonatal Intensive Care, Department of Pediatrics, Porto Hospital Center, Porto, Portugal
| | - Diana Antunes
- Department of Genetics, Hospital D. Estefânia, Lisboa-Norte Hospital Center, Lisbon, Portugal
| | - Juliette Dupont
- Genetics Service, Paediatric Department, University Hospital Santa Maria, Lisbon, Portugal
| | - Sara Figueiredo
- Department of Pediatrics, Médio Ave Hospital Center, Santo Tirso, Portugal
| | - Sónia Figueiroa
- Division of Pediatric Neurology, Department of Child and Adolescent, Centro Hospitalar do Porto e Hospital de Santo António, Porto, Portugal
| | - Susana Gama-de-Sousa
- Department of Pediatrics, Médio Ave Hospital Center, Vila Nova de Famalicão, Portugal
| | - Sara Cruz
- Neuropsychophysiology Lab, CIPsi, School of Psychology, University of Minho, Braga, Portugal
| | - Adriana Sampaio
- Neuropsychophysiology Lab, CIPsi, School of Psychology, University of Minho, Braga, Portugal
| | - Paul Eijk
- Department of Pathology, VU University Medical Center, Amsterdam, 1007, MB, The Netherlands
| | - Marjan M Weiss
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, 1007, MB, The Netherlands
| | - Bauke Ylstra
- Department of Pathology, VU University Medical Center, Amsterdam, 1007, MB, The Netherlands
| | | | | | - Margarida Reis-Lima
- Center for Medical Genetics Dr. Jacinto Magalhães, Porto Hospital Center, Praça Pedro Nunes, Porto, Portugal.,GDPN- SYNLAB, Porto, Portugal
| | | | - Ana Maria Fortuna
- Center for Medical Genetics Dr. Jacinto Magalhães, Porto Hospital Center, Praça Pedro Nunes, Porto, Portugal
| | - Patrícia Maciel
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057, Braga, Portugal. .,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal.
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