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1. Biallelic variants in CSMD1 are implicated in a neurodevelopmental disorder with intellectual disability and variable cortical malformations

Author

Elizabeth A. Werren, Emily R. Peirent, Henna Jantti, Alba Guxholli, Kinshuk Raj Srivastava, Naama Orenstein, Vinodh Narayanan, Wojciech Wiszniewski, Mateusz Dawidziuk, Pawel Gawlinski, Muhammad Umair, Amjad Khan, Shahid Niaz Khan, David Geneviève, Daphné Lehalle, K. L. I. van Gassen, Jacques C. Giltay, Renske Oegema, Richard H. van Jaarsveld, Rafiullah Rafiullah, Gudrun A. Rappold, Rachel Rabin, John G. Pappas, Marsha M. Wheeler, Michael J. Bamshad, Yao-Chang Tsan, Matthew B. Johnson, Catherine E. Keegan, Anshika Srivastava, and Stephanie L. Bielas

Subjects
Cytology, QH573-671
Abstract

Abstract CSMD1 (Cub and Sushi Multiple Domains 1) is a well-recognized regulator of the complement cascade, an important component of the innate immune response. CSMD1 is highly expressed in the central nervous system (CNS) where emergent functions of the complement pathway modulate neural development and synaptic activity. While a genetic risk factor for neuropsychiatric disorders, the role of CSMD1 in neurodevelopmental disorders is unclear. Through international variant sharing, we identified inherited biallelic CSMD1 variants in eight individuals from six families of diverse ancestry who present with global developmental delay, intellectual disability, microcephaly, and polymicrogyria. We modeled CSMD1 loss-of-function (LOF) pathogenesis in early-stage forebrain organoids differentiated from CSMD1 knockout human embryonic stem cells (hESCs). We show that CSMD1 is necessary for neuroepithelial cytoarchitecture and synchronous differentiation. In summary, we identified a critical role for CSMD1 in brain development and biallelic CSMD1 variants as the molecular basis of a previously undefined neurodevelopmental disorder.

Published
2024
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2. Nuclease-free precise genome editing corrects MECP2 mutations associated with Rett syndrome

Author

Swati Bijlani, Ka Ming Pang, Lakshmi V. Bugga, Sampath Rangasamy, Vinodh Narayanan, and Saswati Chatterjee

Subjects
genome editing, Rett syndrome, MeCP2, adeno-associated virus, homologous recombination, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Rett syndrome is an acquired progressive neurodevelopmental disorder caused by de novo mutations in the X-linked MECP2 gene which encodes a pleiotropic protein that functions as a global transcriptional regulator and a chromatin modifier. Rett syndrome predominantly affects heterozygous females while affected male hemizygotes rarely survive. Gene therapy of Rett syndrome has proven challenging due to a requirement for stringent regulation of expression with either over- or under-expression being toxic. Ectopic expression of MECP2 in conjunction with regulatory miRNA target sequences has achieved some success, but the durability of this approach remains unknown. Here we evaluated a nuclease-free homologous recombination (HR)-based genome editing strategy to correct mutations in the MECP2 gene. The stem cell-derived AAVHSCs have previously been shown to mediate seamless and precise HR-based genome editing. We tested the ability of HR-based genome editing to correct pathogenic mutations in Exons 3 and 4 of the MECP2 gene and restore the wild type sequence while preserving all native genomic regulatory elements associated with MECP2 expression, thus potentially addressing a significant issue in gene therapy for Rett syndrome. Moreover, since the mutations are edited directly at the level of the genome, the corrections are expected to be durable with progeny cells inheriting the edited gene. The AAVHSC MECP2 editing vector was designed to be fully homologous to the target MECP2 region and to insert a promoterless Venus reporter at the end of Exon 4. Evaluation of AAVHSC editing in a panel of Rett cell lines bearing mutations in Exons 3 and 4 demonstrated successful correction and rescue of expression of the edited MECP2 gene. Sequence analysis of edited Rett cells revealed successful and accurate correction of mutations in both Exons 3 and 4 and permitted mapping of HR crossover events. Successful correction was observed only when the mutations were flanked at both the 5′ and 3′ ends by crossover events, but not when both crossovers occurred either exclusively upstream or downstream of the mutation. Importantly, we concluded that pathogenic mutations were successfully corrected in every Rett line analyzed, demonstrating the therapeutic potential of HR-based genome editing.

Published
2024
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3. Family and caregiver perspectives on gene therapy for Rett syndrome

Author

Keri Ramsey, Madison LaFleur, Kiana Robinson, Mark Borgstrom, Ashley Ryan, Vinodh Narayanan, and Valerie Schaibley

Subjects
Rett syndrome, Gene therapy, Risk, Caregiver, Medicine, Genetics, QH426-470
Abstract

Introduction: Rett syndrome (RTT) is a neurodevelopmental disorder that primarily affects females and can result in cognitive impairment, seizures, spasticity, breathing problems, gastrointestinal issues, motor impairment, and behavioral concerns. Gene therapy may be a potential treatment in the future as clinical trials are underway. Aim: This study evaluates the attitudes and opinions of family members and caregivers of patients with RTT towards gene therapy using a mixed-method approach. Methods: Sixty-six caregivers of individuals with RTT completed an online survey asking about their previous experience in research and questions about their understanding of gene therapy, their expectations, as well as their hopes and concerns for treating RTT. Ten respondents also participated in online focus groups, which were evaluated using thematic analysis. Results: Overall, most participants (95.5 %) had heard about gene therapy. More than half of the respondents (68.2 %) reported being somewhat knowledgeable about gene therapy, and 18.2 % reported no understanding of gene therapy. When asked the highest level of risk they would accept when enrolling the individual with Rett syndrome in a gene therapy clinical trial, 47.7 % stated they would accept a low risk, and 7.7 % indicated they would accept a high risk. In the focus groups, individuals discussed barriers to gene therapy, their hopes and concerns regarding gene therapy treatment, and how they would like to receive information about future research and therapies. Participants had concerns about possible side effects of gene therapy, including physical and mental harm, a potential decrease in quality of life, whether individuals with RTT would want to “change who they are,” and the irreversibility of the treatment. Conclusion: Although most participants have heard about gene therapy, many caregivers would only accept a low risk when considering gene therapy for the individual with RTT. This could be in part due to concerns about side effects and potential harm to the patient as well as anticipated barriers related to cost and accessibility to appropriate follow-up care. Understanding caregiver opinions is important in setting goals and evaluating the success of current studies, identifying and addressing barriers to trials and treatment, and in the development and implementation of educational resources for gene therapy in RTT.

Published
2024
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4. Gain and loss of TASK3 channel function and its regulation by novel variation cause KCNK9 imprinting syndrome

Author

Margot A. Cousin, Emma L. Veale, Nikita R. Dsouza, Swarnendu Tripathi, Robyn G. Holden, Maria Arelin, Geoffrey Beek, Mir Reza Bekheirnia, Jasmin Beygo, Vikas Bhambhani, Martin Bialer, Stefania Bigoni, Cyrus Boelman, Jenny Carmichael, Thomas Courtin, Benjamin Cogne, Ivana Dabaj, Diane Doummar, Laura Fazilleau, Alessandra Ferlini, Ralitza H. Gavrilova, John M. Graham, Tobias B. Haack, Jane Juusola, Sarina G. Kant, Saima Kayani, Boris Keren, Petra Ketteler, Chiara Klöckner, Tamara T. Koopmann, Teresa M. Kruisselbrink, Alma Kuechler, Laëtitia Lambert, Xénia Latypova, Robert Roger Lebel, Magalie S. Leduc, Emanuela Leonardi, Andrea M. Lewis, Wendy Liew, Keren Machol, Samir Mardini, Kirsty McWalter, Cyril Mignot, Julie McLaughlin, Alessandra Murgia, Vinodh Narayanan, Caroline Nava, Sonja Neuser, Mathilde Nizon, Davide Ognibene, Joohyun Park, Konrad Platzer, Céline Poirsier, Maximilian Radtke, Keri Ramsey, Cassandra K. Runke, Maria J. Guillen Sacoto, Fernando Scaglia, Marwan Shinawi, Stephanie Spranger, Ee Shien Tan, John Taylor, Anne-Sophie Trentesaux, Filippo Vairo, Rebecca Willaert, Neda Zadeh, Raul Urrutia, Dusica Babovic-Vuksanovic, Michael T. Zimmermann, Alistair Mathie, and Eric W. Klee

Subjects
KCNK9 imprinting syndrome, TASK3 channel, Neurodevelopmental disorder, Electrophysiology, Computational protein modeling, Medicine, Genetics, QH426-470
Abstract

Abstract Background Genomics enables individualized diagnosis and treatment, but large challenges remain to functionally interpret rare variants. To date, only one causative variant has been described for KCNK9 imprinting syndrome (KIS). The genotypic and phenotypic spectrum of KIS has yet to be described and the precise mechanism of disease fully understood. Methods This study discovers mechanisms underlying KCNK9 imprinting syndrome (KIS) by describing 15 novel KCNK9 alterations from 47 KIS-affected individuals. We use clinical genetics and computer-assisted facial phenotyping to describe the phenotypic spectrum of KIS. We then interrogate the functional effects of the variants in the encoded TASK3 channel using sequence-based analysis, 3D molecular mechanic and dynamic protein modeling, and in vitro electrophysiological and functional methodologies. Results We describe the broader genetic and phenotypic variability for KIS in a cohort of individuals identifying an additional mutational hotspot at p.Arg131 and demonstrating the common features of this neurodevelopmental disorder to include motor and speech delay, intellectual disability, early feeding difficulties, muscular hypotonia, behavioral abnormalities, and dysmorphic features. The computational protein modeling and in vitro electrophysiological studies discover variability of the impact of KCNK9 variants on TASK3 channel function identifying variants causing gain and others causing loss of conductance. The most consistent functional impact of KCNK9 genetic variants, however, was altered channel regulation. Conclusions This study extends our understanding of KIS mechanisms demonstrating its complex etiology including gain and loss of channel function and consistent loss of channel regulation. These data are rapidly applicable to diagnostic strategies, as KIS is not identifiable from clinical features alone and thus should be molecularly diagnosed. Furthermore, our data suggests unique therapeutic strategies may be needed to address the specific functional consequences of KCNK9 variation on channel function and regulation.

Published
2022
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5. Gain-of-function variants in the ion channel gene TRPM3 underlie a spectrum of neurodevelopmental disorders

Author

Lydie Burglen, Evelien Van Hoeymissen, Leila Qebibo, Magalie Barth, Newell Belnap, Felix Boschann, Christel Depienne, Katrien De Clercq, Andrew GL Douglas, Mark P Fitzgerald, Nicola Foulds, Catherine Garel, Ingo Helbig, Katharina Held, Denise Horn, Annelies Janssen, Angela M Kaindl, Vinodh Narayanan, Christina Prager, Mailys Rupin-Mas, Alexandra Afenjar, Siyuan Zhao, Vincent Th Ramaekers, Sarah M Ruggiero, Simon Thomas, Stéphanie Valence, Lionel Van Maldergem, Tibor Rohacs, Diana Rodriguez, David Dyment, Thomas Voets, and Joris Vriens

Subjects
TRPM3, neurodevelopment, intellectual disability, gain-of-function, cerebellar atrophy, epilepsy, Medicine, Science, Biology (General), QH301-705.5
Abstract

TRPM3 is a temperature- and neurosteroid-sensitive plasma membrane cation channel expressed in a variety of neuronal and non-neuronal cells. Recently, rare de novo variants in TRPM3 were identified in individuals with developmental and epileptic encephalopathy, but the link between TRPM3 activity and neuronal disease remains poorly understood. We previously reported that two disease-associated variants in TRPM3 lead to a gain of channel function . Here, we report a further 10 patients carrying one of seven additional heterozygous TRPM3 missense variants. These patients present with a broad spectrum of neurodevelopmental symptoms, including global developmental delay, intellectual disability, epilepsy, musculo-skeletal anomalies, and altered pain perception. We describe a cerebellar phenotype with ataxia or severe hypotonia, nystagmus, and cerebellar atrophy in more than half of the patients. All disease-associated variants exhibited a robust gain-of-function phenotype, characterized by increased basal activity leading to cellular calcium overload and by enhanced responses to the neurosteroid ligand pregnenolone sulfate when co-expressed with wild-type TRPM3 in mammalian cells. The antiseizure medication primidone, a known TRPM3 antagonist, reduced the increased basal activity of all mutant channels. These findings establish gain-of-function of TRPM3 as the cause of a spectrum of autosomal dominant neurodevelopmental disorders with frequent cerebellar involvement in humans and provide support for the evaluation of TRPM3 antagonists as a potential therapy.

Published
2023
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6. Deficiency of TET3 leads to a genome-wide DNA hypermethylation episignature in human whole blood

Author

Michael A. Levy, David B. Beck, Kay Metcalfe, Sofia Douzgou, Sivagamy Sithambaram, Trudie Cottrell, Muhammad Ansar, Jennifer Kerkhof, Cyril Mignot, Marie-Christine Nougues, Boris Keren, Hannah W. Moore, Renske Oegema, Jacques C. Giltay, Marleen Simon, Richard H. van Jaarsveld, Jessica Bos, Mieke van Haelst, M. Mahdi Motazacker, Elles M. J. Boon, Gijs W. E. Santen, Claudia A. L. Ruivenkamp, Marielle Alders, Teresa Romeo Luperchio, Leandros Boukas, Keri Ramsey, Vinodh Narayanan, G. Bradley Schaefer, Roberto Bonasio, Kimberly F. Doheny, Roger E. Stevenson, Sidharth Banka, Bekim Sadikovic, and Jill A. Fahrner

Subjects
Medicine, Genetics, QH426-470
Abstract

Abstract TET3 encodes an essential dioxygenase involved in epigenetic regulation through DNA demethylation. TET3 deficiency, or Beck-Fahrner syndrome (BEFAHRS; MIM: 618798), is a recently described neurodevelopmental disorder of the DNA demethylation machinery with a nonspecific phenotype resembling other chromatin-modifying disorders, but inconsistent variant types and inheritance patterns pose diagnostic challenges. Given TET3’s direct role in regulating 5-methylcytosine and recent identification of syndrome-specific DNA methylation profiles, we analyzed genome-wide DNA methylation in whole blood of TET3-deficient individuals and identified an episignature that distinguishes affected and unaffected individuals and those with mono-allelic and bi-allelic pathogenic variants. Validation and testing of the episignature correctly categorized known TET3 variants and determined pathogenicity of variants of uncertain significance. Clinical utility was demonstrated when the episignature alone identified an affected individual from over 1000 undiagnosed cases and was confirmed upon distinguishing TET3-deficient individuals from those with 46 other disorders. The TET3-deficient signature - and the signature resulting from activating mutations in DNMT1 which normally opposes TET3 - are characterized by hypermethylation, which for BEFAHRS involves CpG sites that may be biologically relevant. This work expands the role of epi-phenotyping in molecular diagnosis and reveals genome-wide DNA methylation profiling as a quantitative, functional readout for characterization of this new biochemical category of disease.

Published
2021
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7. Artificial intelligence enables comprehensive genome interpretation and nomination of candidate diagnoses for rare genetic diseases

Author

Francisco M. De La Vega, Shimul Chowdhury, Barry Moore, Erwin Frise, Jeanette McCarthy, Edgar Javier Hernandez, Terence Wong, Kiely James, Lucia Guidugli, Pankaj B. Agrawal, Casie A. Genetti, Catherine A. Brownstein, Alan H. Beggs, Britt-Sabina Löscher, Andre Franke, Braden Boone, Shawn E. Levy, Katrin Õunap, Sander Pajusalu, Matt Huentelman, Keri Ramsey, Marcus Naymik, Vinodh Narayanan, Narayanan Veeraraghavan, Paul Billings, Martin G. Reese, Mark Yandell, and Stephen F. Kingsmore

Subjects
Medicine, Genetics, QH426-470
Abstract

Abstract Background Clinical interpretation of genetic variants in the context of the patient’s phenotype is becoming the largest component of cost and time expenditure for genome-based diagnosis of rare genetic diseases. Artificial intelligence (AI) holds promise to greatly simplify and speed genome interpretation by integrating predictive methods with the growing knowledge of genetic disease. Here we assess the diagnostic performance of Fabric GEM, a new, AI-based, clinical decision support tool for expediting genome interpretation. Methods We benchmarked GEM in a retrospective cohort of 119 probands, mostly NICU infants, diagnosed with rare genetic diseases, who received whole-genome or whole-exome sequencing (WGS, WES). We replicated our analyses in a separate cohort of 60 cases collected from five academic medical centers. For comparison, we also analyzed these cases with current state-of-the-art variant prioritization tools. Included in the comparisons were trio, duo, and singleton cases. Variants underpinning diagnoses spanned diverse modes of inheritance and types, including structural variants (SVs). Patient phenotypes were extracted from clinical notes by two means: manually and using an automated clinical natural language processing (CNLP) tool. Finally, 14 previously unsolved cases were reanalyzed. Results GEM ranked over 90% of the causal genes among the top or second candidate and prioritized for review a median of 3 candidate genes per case, using either manually curated or CNLP-derived phenotype descriptions. Ranking of trios and duos was unchanged when analyzed as singletons. In 17 of 20 cases with diagnostic SVs, GEM identified the causal SVs as the top candidate and in 19/20 within the top five, irrespective of whether SV calls were provided or inferred ab initio by GEM using its own internal SV detection algorithm. GEM showed similar performance in absence of parental genotypes. Analysis of 14 previously unsolved cases resulted in a novel finding for one case, candidates ultimately not advanced upon manual review for 3 cases, and no new findings for 10 cases. Conclusions GEM enabled diagnostic interpretation inclusive of all variant types through automated nomination of a very short list of candidate genes and disorders for final review and reporting. In combination with deep phenotyping by CNLP, GEM enables substantial automation of genetic disease diagnosis, potentially decreasing cost and expediting case review.

Published
2021
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8. Genetic and Protein Network Underlying the Convergence of Rett-Syndrome-like (RTT-L) Phenotype in Neurodevelopmental Disorders

Author

Eric Frankel, Avijit Podder, Megan Sharifi, Roshan Pillai, Newell Belnap, Keri Ramsey, Julius Dodson, Pooja Venugopal, Molly Brzezinski, Lorida Llaci, Brittany Gerald, Gabrielle Mills, Meredith Sanchez-Castillo, Chris D. Balak, Szabolcs Szelinger, Wayne M. Jepsen, Ashley L. Siniard, Ryan Richholt, Marcus Naymik, Isabelle Schrauwen, David W. Craig, Ignazio S. Piras, Matthew J. Huentelman, Nicholas J. Schork, Vinodh Narayanan, and Sampathkumar Rangasamy

Subjects
Rett syndrome, atypical RTT syndrome, Rett-syndrome-like phenotype, methyl-CpG-binding protein 2, neurodevelopmental disorders, overlapping phenotype, Cytology, QH573-671
Abstract

Mutations of the X-linked gene encoding methyl-CpG-binding protein 2 (MECP2) cause classical forms of Rett syndrome (RTT) in girls. A subset of patients who are recognized to have an overlapping neurological phenotype with RTT but are lacking a mutation in a gene that causes classical or atypical RTT can be described as having a ‘Rett-syndrome-like phenotype (RTT-L). Here, we report eight patients from our cohort diagnosed as having RTT-L who carry mutations in genes unrelated to RTT. We annotated the list of genes associated with RTT-L from our patient cohort, considered them in the light of peer-reviewed articles on the genetics of RTT-L, and constructed an integrated protein–protein interaction network (PPIN) consisting of 2871 interactions connecting 2192 neighboring proteins among RTT- and RTT-L-associated genes. Functional enrichment analysis of RTT and RTT-L genes identified a number of intuitive biological processes. We also identified transcription factors (TFs) whose binding sites are common across the set of RTT and RTT-L genes and appear as important regulatory motifs for them. Investigation of the most significant over-represented pathway analysis suggests that HDAC1 and CHD4 likely play a central role in the interactome between RTT and RTT-L genes.

Published
2023
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9. Intellectual disability-associated UNC80 mutations reveal inter-subunit interaction and dendritic function of the NALCN channel complex

Author

Jinhong Wie, Apoorva Bharthur, Morgan Wolfgang, Vinodh Narayanan, Keri Ramsey, C4RCD Research Group, Kimberly Aranda, Qi Zhang, Yandong Zhou, and Dejian Ren

Subjects
Science
Abstract

The sodium-leak channel NALCN controls the resting membrane potentials of neurons. Here, the authors identified two subunits of NALCN, UNC80 and UNC79. Domains in UNC80, which are mutated in individuals with intellectual disability, interact to achieve the dendritic localization of NALCN complex.

Published
2020
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11. GABRG2 Variants Associated with Febrile Seizures

Author

Ciria C. Hernandez, Yanwen Shen, Ningning Hu, Wangzhen Shen, Vinodh Narayanan, Keri Ramsey, Wen He, Liping Zou, and Robert L. Macdonald

Subjects
GABAARs, febrile seizures, mutations, Microbiology, QR1-502
Abstract

Febrile seizures (FS) are the most common form of epilepsy in children between six months and five years of age. FS is a self-limited type of fever-related seizure. However, complicated prolonged FS can lead to complex partial epilepsy. We found that among the GABAA receptor subunit (GABR) genes, most variants associated with FS are harbored in the γ2 subunit (GABRG2). Here, we characterized the effects of eight variants in the GABAA receptor γ2 subunit on receptor biogenesis and channel function. Two-thirds of the GABRG2 variants followed the expected autosomal dominant inheritance in FS and occurred as missense and nonsense variants. The remaining one-third appeared as de novo in the affected probands and occurred only as missense variants. The loss of GABAA receptor function and dominant negative effect on GABAA receptor biogenesis likely caused the FS phenotype. In general, variants in the GABRG2 result in a broad spectrum of phenotypic severity, ranging from asymptomatic, FS, genetic epilepsy with febrile seizures plus (GEFS+), and Dravet syndrome individuals. The data presented here support the link between FS, epilepsy, and GABRG2 variants, shedding light on the relationship between the variant topological occurrence and disease severity.

Published
2023
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12. Biallelic VARS variants cause developmental encephalopathy with microcephaly that is recapitulated in vars knockout zebrafish

Author

Aleksandra Siekierska, Hannah Stamberger, Tine Deconinck, Stephanie N. Oprescu, Michèle Partoens, Yifan Zhang, Jo Sourbron, Elias Adriaenssens, Patrick Mullen, Patrick Wiencek, Katia Hardies, Jeong-Soo Lee, Hoi-Khoanh Giong, Felix Distelmaier, Orly Elpeleg, Katherine L. Helbig, Joseph Hersh, Sedat Isikay, Elizabeth Jordan, Ender Karaca, Angela Kecskes, James R. Lupski, Reka Kovacs-Nagy, Patrick May, Vinodh Narayanan, Manuela Pendziwiat, Keri Ramsey, Sampathkumar Rangasamy, Deepali N. Shinde, Ronen Spiegel, Vincent Timmerman, Sarah von Spiczak, Ingo Helbig, C4RCD Research Group, AR working group of the EuroEPINOMICS RES Consortium, Sarah Weckhuysen, Christopher Francklyn, Anthony Antonellis, Peter de Witte, and Peter De Jonghe

Subjects
Science
Abstract

tRNAs are linked with their cognate amino acid by aminoacyl tRNA synthetases (ARS). Here, the authors report a developmental encephalopathy associated with biallelic VARS variants (valyl-tRNA synthetase) that lead to loss of function, as determined by several in vitro assays and a vars knockout zebrafish model.

Published
2019
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13. Author Correction: Deficiency of TET3 leads to a genome-wide DNA hypermethylation episignature in human whole blood

Author

Michael A. Levy, David B. Beck, Kay Metcalfe, Sofia Douzgou, Sivagamy Sithambaram, Trudie Cottrell, Muhammad Ansar, Jennifer Kerkhof, Cyril Mignot, Marie-Christine Nougues, Boris Keren, Hannah W. Moore, Renske Oegema, Jacques C. Giltay, Marleen Simon, Richard H. van Jaarsveld, Jessica Bos, Mieke van Haelst, M. Mahdi Motazacker, Elles M. J. Boon, Gijs W. E. Santen, Claudia A. L. Ruivenkamp, Marielle Alders, Teresa Romeo Luperchio, Leandros Boukas, Keri Ramsey, Vinodh Narayanan, G. Bradley Schaefer, Roberto Bonasio, Kimberly F. Doheny, Roger E. Stevenson, Siddharth Banka, Bekim Sadikovic, and Jill A. Fahrner

Subjects
Medicine, Genetics, QH426-470
Published
2021
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14. Case Report: Novel mutations in TBC1D24 are associated with autosomal dominant tonic-clonic and myoclonic epilepsy and recessive Parkinsonism, psychosis, and intellectual disability [version 1; referees: 2 approved]

Author

Erika Banuelos, Keri Ramsey, Newell Belnap, Malavika Krishnan, Chris Balak, Szabolcs Szelinger, Ashley L. Siniard, Megan Russell, Ryan Richholt, Matt De Both, Ignazio Piras, Marcus Naymik, Ana M. Claasen, Sampathkumar Rangasamy, Matthew J. Huentelman, David W. Craig, Philippe M. Campeau, Vinodh Narayanan, and Isabelle Schrauwen

Subjects
Medical Genetics, Medicine, Science
Abstract

Mutations disrupting presynaptic protein TBC1D24 are associated with a variable neurological phenotype, including DOORS syndrome, myoclonic epilepsy, early-infantile epileptic encephalopathy, and non-syndromic hearing loss. In this report, we describe a family segregating autosomal dominant epilepsy, and a 37-year-old Caucasian female with a severe neurological phenotype including epilepsy, Parkinsonism, psychosis, visual and auditory hallucinations, gait ataxia and intellectual disability. Whole exome sequencing revealed two missense mutations in the TBC1D24 gene segregating within this family (c.1078C>T; p.Arg360Cys and c.404C>T; p.Pro135Leu). The female proband who presents with a severe neurological phenotype carries both of these mutations in a compound heterozygous state. The p.Pro135Leu variant, however, is present in the proband’s mother and sibling as well, and is consistent with an autosomal dominant pattern linked to tonic-clonic and myoclonic epilepsy. In conclusion, we describe a single family in which TBC1D24 mutations cause expanded dominant and recessive phenotypes. In addition, we discuss and highlight that some variants in TBC1D24 might cause a dominant susceptibility to epilepsy

Published
2017
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15. Reduced neuronal size and mTOR pathway activity in the Mecp2 A140V Rett syndrome mouse model [version 1; referees: 2 approved]

Author

Sampathkumar Rangasamy, Shannon Olfers, Brittany Gerald, Alex Hilbert, Sean Svejda, and Vinodh Narayanan

Subjects
Animal Genetics, Cell Signaling, Neurogenetics, Medicine, Science
Abstract

Rett syndrome (RTT) is a neurodevelopmental disorder caused by mutation in the X-linked MECP2 gene, encoding methyl-CpG-binding protein 2. We have created a mouse model (Mecp2 A140V “knock-in” mutant) expressing the recurrent human MECP2 A140V mutation linked to an X-linked mental retardation/Rett syndrome phenotype. Morphological analyses focused on quantifying soma and nucleus size were performed on primary hippocampus and cerebellum granule neuron (CGN) cultures from mutant (Mecp2A140V/y) and wild type (Mecp2+/y) male mice. Cultured hippocampus and cerebellar granule neurons from mutant animals were significantly smaller than neurons from wild type animals. We also examined soma size in hippocampus neurons from individual female transgenic mice that express both a mutant (maternal allele) and a wild type Mecp2 gene linked to an eGFP transgene (paternal allele). In cultures from such doubly heterozygous female mice, the size of neurons expressing the mutant (A140V) allele also showed a significant reduction compared to neurons expressing wild type MeCP2, supporting a cell-autonomous role for MeCP2 in neuronal development. IGF-1 (insulin growth factor-1) treatment of neuronal cells from Mecp2 mutant mice rescued the soma size phenotype. We also found that Mecp2 mutation leads to down-regulation of the mTOR signaling pathway, known to be involved in neuronal size regulation. Our results suggest that i) reduced neuronal size is an important in vitro cellular phenotype of Mecp2 mutation in mice, and ii) MeCP2 might play a critical role in the maintenance of neuronal structure by modulation of the mTOR pathway. The definition of a quantifiable cellular phenotype supports using neuronal size as a biomarker in the development of a high-throughput, in vitro assay to screen for compounds that rescue small neuronal phenotype (“phenotypic assay”).

Published
2016
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16. Case Report: Compound heterozygous nonsense mutations in TRMT10A are associated with microcephaly, delayed development, and periventricular white matter hyperintensities [version 1; referees: 2 approved]

Author

Mohan Narayanan, Keri Ramsey, Theresa Grebe, Isabelle Schrauwen, Szabolcs Szelinger, Matthew Huentelman, David Craig, Vinodh Narayanan, and C4RCD Research Group

Subjects
Diabetes & Obesity, Genomics, Medicine, Science
Abstract

Microcephaly is a fairly common feature observed in children with delayed development, defined as head circumference less than 2 standard deviations below the mean for age and gender. It may be the result of an acquired insult to the brain, such prenatal or perinatal brain injury (congenital infection or hypoxic ischemic encephalopathy), or be a part of a genetic syndrome. There are over 1000 conditions listed in OMIM (Online Mendelian Inheritance in Man) where microcephaly is a key finding; many of these are associated with specific somatic features and non-CNS anomalies. The term primary microcephaly is used when microcephaly and delayed development are the primary features, and they are not part of another recognized syndrome. In this case report, we present the clinical features of siblings (brother and sister) with primary microcephaly and delayed development, and subtle dysmorphic features. Both children had brain MRI studies that showed periventricular and subcortical T2/FLAIR hyperintensities, without signs of white matter volume loss, and no parenchymal calcifications by CT scan. The family was enrolled in a research study for whole exome sequencing of probands and parents. Analysis of variants determined that the children were compound heterozygotes for nonsense mutations, c.277C>T (p.Arg93*) and c.397C>T (p.Arg133*), in the TRMT10A gene. Mutations in this gene have only recently been reported in children with microcephaly and early onset diabetes mellitus. Our report adds to current knowledge of TRMT10A related neurodevelopmental disorders and demonstrates imaging findings suggestive of delayed or abnormal myelination of the white matter in this disorder. Accurate diagnosis through genomic testing, as in the children described here, allows for early detection and management of medical complications, such as diabetes mellitus.

Published
2015
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17. A Frame-Shift Mutation in CAV1 Is Associated with a Severe Neonatal Progeroid and Lipodystrophy Syndrome.

Author

Isabelle Schrauwen, Szabolcs Szelinger, Ashley L Siniard, Ahmet Kurdoglu, Jason J Corneveaux, Ivana Malenica, Ryan Richholt, Guy Van Camp, Matt De Both, Shanker Swaminathan, Mari Turk, Keri Ramsey, David W Craig, Vinodh Narayanan, and Matthew J Huentelman

Subjects
Medicine, Science
Abstract

A 3-year-old female patient presenting with an unknown syndrome of a neonatal progeroid appearance, lipodystrophy, pulmonary hypertension, cutis marmorata, feeding disorder and failure to thrive was investigated by whole-genome sequencing. This revealed a de novo, heterozygous, frame-shift mutation in the Caveolin1 gene (CAV1) (p.Phe160X). Mutations in CAV1, encoding the main component of the caveolae in plasma membranes, cause Berardinelli-Seip congenital lipodystrophy type 3 (BSCL). Although BSCL is recessive, heterozygous carriers either show a reduced phenotype of partial lipodystrophy, pulmonary hypertension, or no phenotype. To investigate the pathogenic mechanisms underlying this syndrome in more depth, we performed next generation RNA sequencing of peripheral blood, which showed several dysregulated pathways in the patient that might be related to the phenotypic progeroid features (apoptosis, DNA repair/replication, mitochondrial). Secondly, we found a significant down-regulation of known Cav1 interaction partners, verifying the dysfunction of CAV1. Other known progeroid genes and lipodystrophy genes were also dysregulated. Next, western blotting of lysates of cultured fibroblasts showed that the patient shows a significantly decreased expression of wild-type CAV1 protein, demonstrating a loss-of-function mutation, though her phenotype is more severe that other heterozygotes with similar mutations. This phenotypic variety could be explained by differences in genetic background. Indications for this are supported by additional rare variants we found in AGPAT2 and LPIN1 lipodystrophy genes. CAV1, AGPAT2 and LPIN1 all play an important role in triacylglycerol (TAG) biosynthesis in adipose tissue, and the defective function in different parts of this pathway, though not all to the same extend, could contribute to a more severe lipoatrophic phenotype in this patient. In conclusion, we report, for the first time, an association of CAV1 dysfunction with a syndrome of severe premature aging and lipodystrophy. This may contribute to a better understanding of the aging process and pathogenic mechanisms that contribute to premature aging.

Published
2015
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18. Characterization of X chromosome inactivation using integrated analysis of whole-exome and mRNA sequencing.

Author

Szabolcs Szelinger, Ivana Malenica, Jason J Corneveaux, Ashley L Siniard, Ahmet A Kurdoglu, Keri M Ramsey, Isabelle Schrauwen, Jeffrey M Trent, Vinodh Narayanan, Matthew J Huentelman, and David W Craig

Subjects
Medicine, Science
Abstract

In females, X chromosome inactivation (XCI) is an epigenetic, gene dosage compensatory mechanism by inactivation of one copy of X in cells. Random XCI of one of the parental chromosomes results in an approximately equal proportion of cells expressing alleles from either the maternally or paternally inherited active X, and is defined by the XCI ratio. Skewed XCI ratio is suggestive of non-random inactivation, which can play an important role in X-linked genetic conditions. Current methods rely on indirect, semi-quantitative DNA methylation-based assay to estimate XCI ratio. Here we report a direct approach to estimate XCI ratio by integrated, family-trio based whole-exome and mRNA sequencing using phase-by-transmission of alleles coupled with allele-specific expression analysis. We applied this method to in silico data and to a clinical patient with mild cognitive impairment but no clear diagnosis or understanding molecular mechanism underlying the phenotype. Simulation showed that phased and unphased heterozygous allele expression can be used to estimate XCI ratio. Segregation analysis of the patient's exome uncovered a de novo, interstitial, 1.7 Mb deletion on Xp22.31 that originated on the paternally inherited X and previously been associated with heterogeneous, neurological phenotype. Phased, allelic expression data suggested an 83∶20 moderately skewed XCI that favored the expression of the maternally inherited, cytogenetically normal X and suggested that the deleterious affect of the de novo event on the paternal copy may be offset by skewed XCI that favors expression of the wild-type X. This study shows the utility of integrated sequencing approach in XCI ratio estimation.

Published
2014
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19. Gene Expression Profiling in Postmortem Rett Syndrome Brain: Differential Gene Expression and Patient Classification

Author

Carlo Colantuoni, Ok-Hee Jeon, Karim Hyder, Alex Chenchik, Anis H. Khimani, Vinodh Narayanan, Eric P. Hoffman, Walter E. Kaufmann, SakkuBai Naidu, and Jonathan Pevsner

Subjects
Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571
Abstract

The identification of mutations in the transcriptional repressor methyl-CpG-binding protein 2 (MECP2) gene in Rett Syndrome (RTT) suggests that an inappropriate release of transcriptional silencing may give rise to RTT neuropathology. Despite this progress, the molecular basis of RTT neuropathogenesis remains unclear. Using multiple cDNA microarray technologies, subtractive hybridization, and conventional biochemistry, we generated comprehensive gene expression profiles of postmortem brain tissue from RTT patients and matched controls. Many glial transcripts involved in known neuropathological mechanisms were found to have increased expression in RTT brain, while decreases were observed in the expression of multiple neuron-specific mRNAs. Dramatic and consistent decreases in transcripts encoding presynaptic markers indicated a specific deficit in presynaptic development. Employing multiple clustering algorithms, it was possible to accurately segregate RTT from control brain tissue samples based solely on gene expression profile. Although previously achieved in cancers, our results constitute the first report of human disease classification using gene expression profiling in a complex tissue source such as brain.

Published
2001
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20. Simultaneous recordings of ocular microtremor and microsaccades with a piezoelectric sensor and a video-oculography system

Author

Michael B. McCamy, Niamh Collins, Jorge Otero-Millan, Mohammed Al-Kalbani, Stephen L. Macknik, Davis Coakley, Xoana G. Troncoso, Gerard Boyle, Vinodh Narayanan, Thomas R. Wolf, and Susana Martinez-Conde

Subjects
Fixational eye movements, Tremor, Fading, Neural adaptation, Saccadic adaptation, Medicine, Biology (General), QH301-705.5
Abstract

Our eyes are in continuous motion. Even when we attempt to fix our gaze, we produce so called “fixational eye movements”, which include microsaccades, drift, and ocular microtremor (OMT). Microsaccades, the largest and fastest type of fixational eye movement, shift the retinal image from several dozen to several hundred photoreceptors and have equivalent physical characteristics to saccades, only on a smaller scale (Martinez-Conde, Otero-Millan & Macknik, 2013). OMT occurs simultaneously with drift and is the smallest of the fixational eye movements (∼1 photoreceptor width, >0.5 arcmin), with dominant frequencies ranging from 70 Hz to 103 Hz (Martinez-Conde, Macknik & Hubel, 2004). Due to OMT’s small amplitude and high frequency, the most accurate and stringent way to record it is the piezoelectric transduction method. Thus, OMT studies are far rarer than those focusing on microsaccades or drift. Here we conducted simultaneous recordings of OMT and microsaccades with a piezoelectric device and a commercial infrared video tracking system. We set out to determine whether OMT could help to restore perceptually faded targets during attempted fixation, and we also wondered whether the piezoelectric sensor could affect the characteristics of microsaccades. Our results showed that microsaccades, but not OMT, counteracted perceptual fading. We moreover found that the piezoelectric sensor affected microsaccades in a complex way, and that the oculomotor system adjusted to the stress brought on by the sensor by adjusting the magnitudes of microsaccades.

Published
2013
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21. Bi-allelic SNAPC4 variants dysregulate global alternative splicing and lead to neuroregression and progressive spastic paraparesis

Author

F. Graeme Frost, Marie Morimoto, Prashant Sharma, Lyse Ruaud, Newell Belnap, Daniel G. Calame, Yuri Uchiyama, Naomichi Matsumoto, Machteld M. Oud, Elise A. Ferreira, Vinodh Narayanan, Sampath Rangasamy, Matt Huentelman, Lisa T. Emrick, Ikuko Sato-Shirai, Satoko Kumada, Nicole I. Wolf, Peter J. Steinbach, Yan Huang, Barbara N. Pusey, Sandrine Passemard, Jonathan Levy, Séverine Drunat, Marie Vincent, Agnès Guet, Emanuele Agolini, Antonio Novelli, Maria Cristina Digilio, Jill A. Rosenfeld, Jennifer L. Murphy, James R. Lupski, Gilbert Vezina, Ellen F. Macnamara, David R. Adams, Maria T. Acosta, Cynthia J. Tifft, William A. Gahl, and May Christine V. Malicdan

Subjects
All institutes and research themes of the Radboud University Medical Center, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Genetics, Genetics (clinical)
Abstract

Item does not contain fulltext The vast majority of human genes encode multiple isoforms through alternative splicing, and the temporal and spatial regulation of those isoforms is critical for organismal development and function. The spliceosome, which regulates and executes splicing reactions, is primarily composed of small nuclear ribonucleoproteins (snRNPs) that consist of small nuclear RNAs (snRNAs) and protein subunits. snRNA gene transcription is initiated by the snRNA-activating protein complex (SNAPc). Here, we report ten individuals, from eight families, with bi-allelic, deleterious SNAPC4 variants. SNAPC4 encoded one of the five SNAPc subunits that is critical for DNA binding. Most affected individuals presented with delayed motor development and developmental regression after the first year of life, followed by progressive spasticity that led to gait alterations, paraparesis, and oromotor dysfunction. Most individuals had cerebral, cerebellar, or basal ganglia volume loss by brain MRI. In the available cells from affected individuals, SNAPC4 abundance was decreased compared to unaffected controls, suggesting that the bi-allelic variants affect SNAPC4 accumulation. The depletion of SNAPC4 levels in HeLa cell lines via genomic editing led to decreased snRNA expression and global dysregulation of alternative splicing. Analysis of available fibroblasts from affected individuals showed decreased snRNA expression and global dysregulation of alternative splicing compared to unaffected cells. Altogether, these data suggest that these bi-allelic SNAPC4 variants result in loss of function and underlie the neuroregression and progressive spasticity in these affected individuals.

Published
2023
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22. An Integrated Phenotypic and Genotypic Approach Reveals a High‐Risk Subtype Association for <scp> EBF3 </scp> Missense Variants Affecting the Zinc Finger Domain

Author

Cole A. Deisseroth, Vanesa C. Lerma, Christina L. Magyar, Jessica Mae Pfliger, Aarushi Nayak, Nathan D. Bliss, Ashley W. LeMaire, Vinodh Narayanan, Christopher Balak, Ginevra Zanni, Enza Maria Valente, Enrico Bertini, Paul J. Benke, Michael F. Wangler, and Hsiao‐Tuan Chao

Subjects
Neurology, Autism Spectrum Disorder, Neurodevelopmental Disorders, Mutation, Missense, Humans, Zinc Fingers, Neurology (clinical), Transcription Factors
Abstract

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.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.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.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.

Published
2022
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23. Gain-of-function variants in the ion channel gene TRPM3 underlie a spectrum of neurodevelopmental disorders

Author

Evelien Van Hoeymissen, Lydie Burglen, Leila Qebibo, Magalie Barth, Newell Belnap, Felix Boschann, Christel Depienne, Katrien De Clercq, Andrew GL Douglas, Mark P Fitzgerald, Nicola Foulds, Catherine Garel, Ingo Helbig, Katharina Held, Denise Horn, Annelies Janssen, Angela M Kaindl, Vinodh Narayanan, Christina Prager, Mailys Rupin-Mas, Alexandra Afenjar, Siyuan Zhao, Vincent Th Ramaekers, Sarah M Ruggiero, Simon Thomas, Stéphanie Valence, Lionel Van Maldergem, Tibor Rohacs, Diana Rodriguez, David Dyment, Thomas Voets, and Joris Vriens

Subjects
neuroscience, General Immunology and Microbiology, General Neuroscience, cell biology, Medizin, human, General Medicine, General Biochemistry, Genetics and Molecular Biology
Abstract

TRPM3 is a temperature- and neurosteroid-sensitive plasma membrane cation channel expressed in a variety of neuronal and non-neuronal cells. Recently, rare de novo variants in TRPM3 were identified in individuals with developmental and epileptic encephalopathy, but the link between TRPM3 activity and neuronal disease remains poorly understood. We previously reported that two disease-associated variants in TRPM3 lead to a gain of channel function . Here, we report a further 10 patients carrying one of seven additional heterozygous TRPM3 missense variants. These patients present with a broad spectrum of neurodevelopmental symptoms, including global developmental delay, intellectual disability, epilepsy, musculo-skeletal anomalies, and altered pain perception. We describe a cerebellar phenotype with ataxia or severe hypotonia, nystagmus, and cerebellar atrophy in more than half of the patients. All disease-associated variants exhibited a robust gain-of-function phenotype, characterized by increased basal activity leading to cellular calcium overload and by enhanced responses to the neurosteroid ligand pregnenolone sulfate when co-expressed with wild-type TRPM3 in mammalian cells. The antiseizure medication primidone, a known TRPM3 antagonist, reduced the increased basal activity of all mutant channels. These findings establish gain-of-function of TRPM3 as the cause of a spectrum of autosomal dominant neurodevelopmental disorders with frequent cerebellar involvement in humans and provide support for the evaluation of TRPM3 antagonists as a potential therapy.

Published
2023
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24. Author response: Gain-of-function variants in the ion channel gene TRPM3 underlie a spectrum of neurodevelopmental disorders

Author

Evelien Van Hoeymissen, Lydie Burglen, Leila Qebibo, Magalie Barth, Newell Belnap, Felix Boschann, Christel Depienne, Katrien De Clercq, Andrew GL Douglas, Mark P Fitzgerald, Nicola Foulds, Catherine Garel, Ingo Helbig, Katharina Held, Denise Horn, Annelies Janssen, Angela M Kaindl, Vinodh Narayanan, Christina Prager, Mailys Rupin-Mas, Alexandra Afenjar, Siyuan Zhao, Vincent Th Ramaekers, Sarah M Ruggiero, Simon Thomas, Stéphanie Valence, Lionel Van Maldergem, Tibor Rohacs, Diana Rodriguez, David Dyment, Thomas Voets, and Joris Vriens

Published
2022
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25. Neuropsychological and Social Characteristics of a 7 Year Old Child with Hypomelanosis of Ito Followed for 11 Years

Author

George P. Prigatano, Alexandra Novak, and Vinodh Narayanan

Subjects
Hypopigmentation, Neuropsychology and Physiological Psychology, Cognition, Adolescent, Intellectual Disability, Developmental and Educational Psychology, Humans, Child, Pigmentation Disorders, Sociological Factors
Abstract

Hypomelanosis of Ito (HI) is a neurocutaneous disorder associated with central nervous system abnormalities, including speech delay and intellectual disability. The long term neuropsychological and social characteristics of these children are unknown. Neuropsychological observations and parental reports were obtained yearly on a child with HI from ages 7 to 18 years. Serial measures of intelligence revealed stable verbal and perceptual reasoning scores with later improvements in working memory and processing speed performance. Speech articulation improved at age 12, as did the speed of right-hand finger tapping. Improved social integration occurred, but anxiety persisted throughout this developmental period.

Published
2022

26. Expanding allelic and phenotypic spectrum of ZC4H2-related disorder: A novel hypomorphic variant and high prevalence of tethered cord

Author

Parith Wongkittichote, Tae‐Ik Choi, Oc‐Hee Kim, Kacie Riley, Dwight Koeberl, Vinodh Narayanan, Keri Ramsey, Chris Balak, Charles E. Schwartz, Anna Maria Cueto‐Gonzalez, Francina Munell Casadesus, Cheol‐Hee Kim, and Marwan S. Shinawi

Subjects
Genetics, Genetics (clinical)
Abstract

ZC4H2 (MIM# 300897) is a nuclear factor involved in various cellular processes including proliferation and differentiation of neural stem cells, ventral spinal patterning and osteogenic and myogenic processes. Pathogenic variants in ZC4H2 have been associated with Wieacker-Wolff syndrome (MIM# 314580), an X-linked neurodevelopmental disorder characterized by arthrogryposis, development delay, hypotonia, feeding difficulties, poor growth, skeletal abnormalities, and dysmorphic features. Zebrafish zc4h2 null mutants recapitulated the human phenotype, showed complete loss of vsx2 expression in brain, and exhibited abnormal swimming and balance problems. Here we report 7 new patients (four males and three females) with ZC4H2-related disorder from six unrelated families. Four of the 6 ZC4H2 variants are novel: three missense variants, designated as c.142TA (p.Tyr48Asn), c.558GA (p.Met186Ile) and c.602CT (p.Pro201Leu), and a nonsense variant, c.618CA (p.Cys206*). Two variants were previously reported : a nonsense variant c.199CT (p.Arg67*) and a splice site variant (c.225+5GA). Five patients were on the severe spectrum of clinical findings, two of whom had early death. The male patient harboring the p.Met186Ile variant and the female patient that carries the p.Pro201Leu variant have a relatively mild phenotype. Of note, 4/7 patients had a tethered cord that required a surgical repair. We also demonstrate and discuss previously under-recognized phenotypic features including sleep apnea, arrhythmia, hypoglycemia, and unexpected early death. To study the effect of the missense variants, we performed microinjection of human ZC4H2 wild-type or variant mRNAs into zc4h2 null mutant zebrafish embryos. The p.Met186Ile mRNA variant was able to partially rescue vsx2 expression while p.Tyr48Asn and p.Pro201Leu mRNA variants were not. However, swimming and balance problems could not be rescued by any of these variants. These results suggest that the p.Met186Ile is a hypomorphic allele. Our work expands the genotypes and phenotypes associated with ZC4H2-related disorder and demonstrates that the zebrafish system is a reliable method to determine the pathogenicity of ZC4H2 variants.

Published
2022

27. CSNK2B

Author

Judith Bluvstein, Suneeta Madan-Khetarpal, Daniel Groepper, Theodore Sheehan, Michael J. Lyons, Louise Bier, Julie Fleischer, Annapurna Poduri, Lynn Pais, Pascal Joset, Elena Infante, Evan H. Baugh, David Goldstein, Tristan T. Sands, Katharina Steindl, Pim Suwannarat, Cyril Mignot, Boris Keren, Matthew J. Ferber, Laura Schultz-Rogers, Natalie Lippa, Linda Hasadsri, Vinodh Narayanan, Maureen S. Mulhern, Alejandra Vasquez, Claudia A. L. Ruivenkamp, Marleen Simon, Susan M. White, Vimla Aggarwal, Eric W. Klee, Kristine K. Bachman, Lindsay C. Burrage, Caroline Nava, Nicholas Stong, Neil A. Hanchard, Josephine S.C. Chong, Anita Rauch, Renee Bend, Erin L. Heinzen, Sulagna Kushary, Marije Koopmans, Marissa S. Ellingson, Keri Ramsey, Raymond Yeh, Michelle E. Ernst, Ellen van Binsbergen, Sarah S. Barnett, Amanda Thomas, Kristin G. Monaghan, Eva H. Brilstra, Magalie S. Leduc, Weimin Bi, Jennifer A. Lee, Cigdem I. Akman, Sophie Mathieu, Andrea H. Seeley, Grazia M. S. Mancini, and Clinical Genetics

Subjects
0301 basic medicine, Adult, Male, Pediatrics, medicine.medical_specialty, Adolescent, CK2, Developmental Disabilities, Epilepsies, Myoclonic, Status epilepticus, casein kinase II, Article, MSNE, 03 medical and health sciences, Broad spectrum, Epilepsy, Young Adult, 0302 clinical medicine, Status Epilepticus, Intellectual Disability, Intellectual disability, medicine, Humans, Exome, Generalized epilepsy, Age of Onset, generalized epilepsy, Child, Exome sequencing, business.industry, Genetic Variation, Infant, medicine.disease, Young age, 030104 developmental biology, myoclonic status epilepticus, Phenotype, Neurology, Child, Preschool, Mutation, myoclonic seizures, Epilepsy, Generalized, Female, Neurology (clinical), medicine.symptom, Epilepsy severity, business, 030217 neurology & neurosurgery
Abstract

CSNK2B has recently been implicated as a disease gene for neurodevelopmental disability (NDD) and epilepsy. Information about developmental outcomes has been limited by the young age and short follow-up for many of the previously reported cases, and further delineation of the spectrum of associated phenotypes is needed. We present 25 new patients with variants in CSNK2B and refine the associated NDD and epilepsy phenotypes. CSNK2B variants were identified by research or clinical exome sequencing, and investigators from different centers were connected via GeneMatcher. Most individuals had developmental delay and generalized epilepsy with onset in the first 2 years. However, we found a broad spectrum of phenotypic severity, ranging from early normal development with pharmacoresponsive seizures to profound intellectual disability with intractable epilepsy and recurrent refractory status epilepticus. These findings suggest that CSNK2B should be considered in the diagnostic evaluation of patients with a broad range of NDD with treatable or intractable seizures.

Published
2021

28. Okur-Chung neurodevelopmental syndrome-linked CK2α variants have reduced kinase activity

Author

H Rebholz, Sampathkumar Rangasamy, V Corasolla, Vinodh Narayanan, N Dacher, A Urbani, I Dominguez, and J M Cruz-Gamero

Subjects
Genetics, 0303 health sciences, 030305 genetics & heredity, Mutant, Biology, medicine.disease, Phenotype, Human genetics, Hypotonia, 03 medical and health sciences, Neurodevelopmental disorder, medicine, Missense mutation, Kinase activity, medicine.symptom, Protein kinase A, Genetics (clinical), 030304 developmental biology
Abstract

The Okur-Chung neurodevelopmental syndrome, or OCNDS, is a newly discovered rare neurodevelopmental disorder. It is characterized by developmental delay, intellectual disability, behavioral problems (hyperactivity, repetitive movements and social interaction deficits), hypotonia, epilepsy and language/verbalization deficits. OCNDS is linked to de novo mutations in CSNK2A1, that lead to missense or deletion/truncating variants in the encoded protein, the protein kinase CK2α. Eighteen different missense CK2α mutations have been identified to date; however, no biochemical or cell biological studies have yet been performed to clarify the functional impact of such mutations. Here, we show that 15 different missense CK2α mutations lead to varying degrees of loss of kinase activity as recombinant purified proteins and when mutants are ectopically expressed in mammalian cells. We further detect changes in the phosphoproteome of three patient-derived fibroblast lines and show that the subcellular localization of CK2α is altered for some of the OCNDS-linked variants and in patient-derived fibroblasts. Our data argue that reduced kinase activity and abnormal localization of CK2α may underlie the OCNDS phenotype.

Published
2021
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29. Reduced neuronal size and mTOR pathway activity in the Mecp2 A140V Rett syndrome mouse model [version 1; referees: 4 approved]

Author

Sampathkumar Rangasamy, Shannon Olfers, Brittany Gerald, Alex Hilbert, Sean Svejda, and Vinodh Narayanan

Subjects
Research Article, Articles, Animal Genetics, Cell Signaling, Neurogenetics, Rett syndrome, MECP2, Hippocampal neuronal cultures, Cerebellar granule neurons, Neuronal soma size, Neuronal nuclear size, mTOR pathway, IGF-1, Rictor
Abstract

Rett syndrome (RTT) is a neurodevelopmental disorder caused by mutation in the X-linked MECP2 gene, encoding methyl-CpG-binding protein 2. We have created a mouse model ( Mecp2 A140V “knock-in” mutant) expressing the recurrent human MECP2 A140V mutation linked to an X-linked mental retardation/Rett syndrome phenotype. Morphological analyses focused on quantifying soma and nucleus size were performed on primary hippocampus and cerebellum granule neuron (CGN) cultures from mutant ( Mecp2 A140V/y) and wild type ( Mecp2 +/y) male mice. Cultured hippocampus and cerebellar granule neurons from mutant animals were significantly smaller than neurons from wild type animals. We also examined soma size in hippocampus neurons from individual female transgenic mice that express both a mutant (maternal allele) and a wild type Mecp2 gene linked to an eGFP transgene (paternal allele). In cultures from such doubly heterozygous female mice, the size of neurons expressing the mutant (A140V) allele also showed a significant reduction compared to neurons expressing wild type MeCP2, supporting a cell-autonomous role for MeCP2 in neuronal development. IGF-1 (insulin growth factor-1) treatment of neuronal cells from Mecp2 mutant mice rescued the soma size phenotype. We also found that Mecp2 mutation leads to down-regulation of the mTOR signaling pathway, known to be involved in neuronal size regulation. Our results suggest that i) reduced neuronal size is an important in vitro cellular phenotype of Mecp2 mutation in mice, and ii) MeCP2 might play a critical role in the maintenance of neuronal structure by modulation of the mTOR pathway. The definition of a quantifiable cellular phenotype supports using neuronal size as a biomarker in the development of a high-throughput, in vitro assay to screen for compounds that rescue small neuronal phenotype (“phenotypic assay”).

Published
2016
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30. Widening of the genetic and clinical spectrum of Lamb-Shaffer syndrome, a neurodevelopmental disorder due to SOX5 haploinsufficiency

Author

Ashley N. Sigafoos, Salima El Chehadeh, Marcia C. Willing, Ela Akay, Florian Cherik, Anne-Marie E. Goyette, Vinodh Narayanan, Diane Masser-Frye, Catherine Karimov, Rhonda E. Schnur, Rebekah Bressi, Rhys H. Thomas, Gary D. Clark, Tina Barbaro-Dieber, Jill A. Rosenfeld, Carlos A. Bacino, Maria J. Guillen Sacoto, Laura Russell, Kristin Lindstrom, Caroline Schluth-Bolard, Xia Wang, Yvonne Hilhorst-Hofstee, Marcelo Vargas, Zehua Zhu, Ash Zawerton, Boris Keren, Mariëtte J.V. Hoffer, Isabelle Marey, Alice Poisson, Daphné Lehalle, Maries Joseph, Gaetan Lesca, Simon Zwolinski, Laurence Perrin, Rhoda Akilapa, Emilia K. Bijlsma, Christel Depienne, Amélie Piton, Claire G. Salter, Lucie Dupuis, Daryl A. Scott, Jolien S. Klein Wassink-Ruiter, Benjamin Cogné, Mathilde Nizon, Richard Chang, Kirsty McWalter, Myriam Srour, Perrine Charles, Anne-Claude Tabet, Natalie Canham, Sylvie Odent, Caroline Nava, Karl J. Clark, Elizabeth J. Bhoj, Jonathan Levy, Keri Ramsey, Yves Alembik, Lucia Ortega, Sophie Dupuis-Girod, Shoji Ichikawa, Christine Francannet, Marta Bertoli, Christèle Dubourg, Eric W. Klee, Ange-Line Bruel, Sebastien Moutton, Emily Fassi, Anthony Vandersteen, Abdul Haseeb, Antonina Wojcik, Patrick R. Blackburn, Lynne M. Bird, Patrick Rump, Véronique Lefebvre, Alma Kuechler, Sophie Nambot, Keren Machol, Cyril Mignot, Andreas Hartmann, Rossana Sanchez Russo, Erica H. Gerkes, Sylvie Jaillard, Roberto Mendoza-Londono, Trevor Cole, Pauline Monin, Cleveland Clinic, Institut du Cerveau et de la Moëlle Epinière = Brain and Spine Institute (ICM), Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Service de Génétique Cytogénétique et Embryologie [CHU Pitié-Salpêtrière], CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Génétique humaine et fonctions cognitives - Human Genetics and Cognitive Functions (GHFC (UMR_3571 / U-Pasteur_1)), Institut Pasteur [Paris]-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Département de génétique [Robert Debré], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-AP-HP Hôpital universitaire Robert-Debré [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Centre de recherche en neurosciences de Lyon (CRNL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet [Saint-Étienne] (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Hospices Civils de Lyon (HCL), Centre d'Etude et de Recherche Multimodal Et Pluridisciplinaire en imagerie du vivant (CERMEP - imagerie du vivant), Université de Lyon-Université de Lyon-CHU Grenoble-Hospices Civils de Lyon (HCL)-CHU Saint-Etienne-Université Jean Monnet [Saint-Étienne] (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Lipides - Nutrition - Cancer [Dijon - U1231] (LNC), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Centre de génétique - Centre de référence des maladies rares, anomalies du développement et syndromes malformatifs (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), CHU Pontchaillou [Rennes], Institut de recherche en santé, environnement et travail (Irset), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Santé et de la Recherche Médicale (INSERM)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université d'Angers (UA), Center for Human and Clinical Genetics, Leiden University Medical Center (LUMC), Service de génétique médicale - Unité de génétique clinique [Nantes], Université de Nantes (UN)-Centre hospitalier universitaire de Nantes (CHU Nantes), unité de recherche de l'institut du thorax UMR1087 UMR6291 (ITX), Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Department of Health Sciences Research [Mayo Clinic] (HSR), Mayo Clinic, This research was funded in part by the Agence Nationale de la Recherche and European High-Functioning Autism Network (ANR EUHFAUTISM), the Assistance Publique–Hôpitaux de Paris (AP-HP), the Institut National de la Santé et de la Recherche Médicale (INSERM), the BioPsy labex (to Christel Depienne and C.N.) and the Association Française du Syndrome Gilles de la Tourette (AFSGT) to Christel Depienne. It was also funded by the Cleveland Clinic Lerner Research Institute (LRI Chair’s Innovative Research Award to V.L.), and by Harper’s Quest and the LAMSHF Syndrome Research Fund (donations to V.L.) and the Center for Individualized Medicine, Mayo Clinic. This study makes use of data generated by the DECIPHER community and the Deciphering Developmental Disorders (DDD) Study, which is funded by the Wellcome Trust. The DDD study presents independent research commissioned by the Health Innovation Challenge Fund (grant number HICF-1009-003), a parallel funding partnership between Wellcome and the Department of Health, and the Wellcome Sanger Institute (grant number WT098051). The views expressed in this publication are those of the author(s) and not necessarily those of Wellcome or the Department of Health. The study has UK Research Ethics Committee approval (10/H0305/83, granted by the Cambridge South REC, and GEN/284/12 granted by the Republic of Ireland REC). The research team acknowledges the support of the National Institute for Health Research, through the Comprehensive Clinical Research Network., We thank the patients and their families for their participation in this study, and the C4RCD Research Group (Newell Belnap, Amanda Courtright, Ana Claasen, David Craig, Matt Huentelman, Madison LaFleur, Sampathkumar Rangasamy, Ryan Richholt, Isabelle Schrauwen, Ashley L. Siniard, and Szabolics Szelinger) for providing clinical information on patient P18., Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [APHP]-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Service de Génétique et Cytogénétique [CHU Pitié-Salpêtrière], Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Pitié-Salpêtrière [APHP], Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-AP-HP Hôpital universitaire Robert-Debré [Paris], Centre d'Exploration et de Recherche Médicales par Émission de Positons (CERMEP), Université Joseph Fourier - Grenoble 1 (UJF)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-CHU Grenoble-Hospices Civils de Lyon (HCL)-CHU Saint-Etienne-Université Jean Monnet [Saint-Étienne] (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Santé et de la Recherche Médicale (INSERM), Université d'Angers (UA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)

Subjects
Male, Medizin, Haploinsufficiency, L-SOX5, VARIANTS, 0302 clinical medicine, Neurodevelopmental disorder, Intellectual disability, Missense mutation, 2.1 Biological and endogenous factors, Aetiology, Child, Genetics (clinical), Genetics, Pediatric, Genetics & Heredity, 0303 health sciences, Pedigree, FAMILY, DNA-Binding Proteins, developmental delay, TRANSCRIPTION FACTORS, Phenotype, intellectual disability, Child, Preschool, missense variants, Female, SOXD Transcription Factors, Adult, EXPRESSION, Adolescent, Intellectual and Developmental Disabilities (IDD), Clinical Sciences, Mutation, Missense, autism, Cell fate determination, Biology, LONG FORM, SEQUENCE, Article, 03 medical and health sciences, Young Adult, Rare Diseases, Clinical Research, CARTILAGE, Intellectual Disability, medicine, Animals, Humans, Language Development Disorders, Genetic Predisposition to Disease, Preschool, Transcription factor, Gene, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, MUTATIONS, Human Genome, Infant, medicine.disease, Brain Disorders, Neurodevelopmental Disorders, Deciphering Developmental Disorder Study, Mutation, Autism, epilepsy, Missense, 030217 neurology & neurosurgery, GENERATION
Abstract

International audience; PURPOSE: Lamb-Shaffer syndrome (LAMSHF) is a neurodevelopmental disorder described in just over two dozen patients with heterozygous genetic alterations involving SOX5, a gene encoding a transcription factor regulating cell fate and differentiation in neurogenesis and other discrete developmental processes. The genetic alterations described so far are mainly microdeletions. The present study was aimed at increasing our understanding of LAMSHF, its clinical and genetic spectrum, and the pathophysiological mechanisms involved.METHODS: Clinical and genetic data were collected through GeneMatcher and clinical or genetic networks for 41 novel patients harboring various types of SOX5 alterations. Functional consequences of selected substitutions were investigated.RESULTS: Microdeletions and truncating variants occurred throughout SOX5. In contrast, most missense variants clustered in the pivotal SOX-specific high-mobility-group domain. The latter variants prevented SOX5 from binding DNA and promoting transactivation in vitro, whereas missense variants located outside the high-mobility-group domain did not. Clinical manifestations and severity varied among patients. No clear genotype-phenotype correlations were found, except that missense variants outside the high-mobility-group domain were generally better tolerated.CONCLUSIONS:This study extends the clinical and genetic spectrum associated with LAMSHF and consolidates evidence that SOX5 haploinsufficiency leads to variable degrees of intellectual disability, language delay, and other clinical features.

Published
2020
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31. SEMA6B variants cause intellectual disability and alter dendritic spine density and axon guidance

Author

Amélie Cordovado, Martina Schaettin, Médéric Jeanne, Veranika Panasenkava, Anne-Sophie Denommé-Pichon, Boris Keren, Cyril Mignot, Martine Doco-Fenzy, Lance Rodan, Keri Ramsey, Vinodh Narayanan, Julie R Jones, Eloise J Prijoles, Wendy G Mitchell, Jillian R Ozmore, Kali Juliette, Erin Torti, Elizabeth A Normand, Leslie Granger, Andrea K Petersen, Margaret G Au, Juliann P Matheny, Chanika Phornphutkul, Mary-Kathryn Chambers, Joaquín-Alejandro Fernández-Ramos, Eduardo López-Laso, Michael C Kruer, Somayeh Bakhtiari, Marcella Zollino, Manuela Morleo, Giuseppe Marangi, Davide Mei, Tiziana Pisano, Renzo Guerrini, Raymond J Louie, Anna Childers, David B Everman, Betrand Isidor, Séverine Audebert-Bellanger, Sylvie Odent, Dominique Bonneau, Brigitte Gilbert-Dussardier, Richard Redon, Stéphane Bézieau, Frédéric Laumonnier, Esther T Stoeckli, Annick Toutain, Marie-Laure Vuillaume, Jonchère, Laurent, Imagerie et cerveau (iBrain - Inserm U1253 - UNIV Tours ), Université de Tours (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), Universität Zürich [Zürich] = University of Zurich (UZH), FHU TRANSLAD (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Equipe GAD (LNC - U1231), Lipides - Nutrition - Cancer [Dijon - U1231] (LNC), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Agro Dijon, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Agro Dijon, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Hémostase et Remodelage Vasculaire Post-Ischémie (HERVI - EA 3801), Université de Reims Champagne-Ardenne (URCA), Boston Children's Hospital, Harvard Medical School [Boston] (HMS), The Translational Genomics Research Institute (TGen), The Greenwood Genetic Center, Keck School of Medicine [Los Angeles], University of Southern California (USC), Dartmouth Hitchcock Medical Center [Lebanon], Gillette Children's Specialty Healthcare [St Paul], GeneDx [Gaithersburg, MD, USA], Randall Children's Hospital [Portland], University of Kentucky (UK), Warren Alpert Medical School of Brown University, Rhode Island Hospital [Providence, RI, États-Unis], Instituto Maimonides de Investigación Biomédica de Cordoba (IMIBIC), Universidad de Córdoba = University of Córdoba [Córdoba]-Hospital Universitario Reina Sofía, Barrow Neurological Institute, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), Telethon Institute of Genetics and Medicine = Istituto Telethon di Genetica e Medicina (TIGEM), Università degli Studi di Firenze = University of Florence (UniFI), Centre hospitalier universitaire de Nantes (CHU Nantes), Hôpital Morvan - CHRU de Brest (CHU - BREST ), Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), CHU Pontchaillou [Rennes], 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), unité de recherche de l'institut du thorax UMR1087 UMR6291 (ITX), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Nantes Université - UFR de Médecine et des Techniques Médicales (Nantes Univ - UFR MEDECINE), Nantes Université - pôle Santé, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes Université - pôle Santé, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ), Funding for HUGODIMS (Western France exome-based trio approach project to identifygenes involved in intellectual disability) was supported by a grant from the French Ministryof Health and from the Health Regional Agency from Poitou-Charentes [HUGODIMS, 2013,RC14_0107]. [A.C.] is a research student recipient of a grant from the University of Tours., Cordovado, Amélie, Schaettin, Martina, Jeanne, Médéric, Panasenkava, Veranika, Denommé-Pichon, Anne-Sophie, Keren, Bori, Mignot, Cyril, Doco-Fenzy, Martine, Rodan, Lance, Ramsey, Keri, Narayanan, Vinodh, Jones, Julie R, Prijoles, Eloise J, Mitchell, Wendy G, Ozmore, Jillian R, Juliette, Kali, Torti, Erin, Normand, Elizabeth A, Granger, Leslie, Petersen, Andrea K, Au, Margaret G, Matheny, Juliann P, Phornphutkul, Chanika, Chambers, Mary-Kathryn, Fernández-Ramos, Joaquín-Alejandro, López-Laso, Eduardo, Kruer, Michael C, Bakhtiari, Somayeh, Zollino, Marcella, Morleo, Manuela, Marangi, Giuseppe, Mei, Davide, Pisano, Tiziana, Guerrini, Renzo, Louie, Raymond J, Childers, Anna, Everman, David B, Isidor, Betrand, Audebert-Bellanger, Séverine, Odent, Sylvie, Bonneau, Dominique, Gilbert-Dussardier, Brigitte, Redon, Richard, Bézieau, Stéphane, Laumonnier, Frédéric, Stoeckli, Esther T, Toutain, Annick, and Vuillaume, Marie-Laure

Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics, Epilepsy, Dendritic Spines, [SDV]Life Sciences [q-bio], Intellectual disability, Chick Embryo, Semaphorins, [SDV.GEN] Life Sciences [q-bio]/Genetics, General Medicine, Settore MED/03 - GENETICA MEDICA, Axon Guidance, [SDV] Life Sciences [q-bio], HEK293 Cells, SEMA6B, Intellectual Disability, Genetics, Animals, Humans, Original Article, Molecular Biology, Genetics (clinical)
Abstract

Intellectual disability (ID) is a neurodevelopmental disorder frequently caused by monogenic defects. In this study, we collected 14 SEMA6B heterozygous variants in 16 unrelated patients referred for ID to different centers. Whereas, until now, SEMA6B variants have mainly been reported in patients with progressive myoclonic epilepsy, our study indicates that the clinical spectrum is wider and also includes non-syndromic ID without epilepsy or myoclonus. To assess the pathogenicity of these variants, selected mutated forms of Sema6b were overexpressed in Human Embryonic Kidney 293T (HEK293T) cells and in primary neuronal cultures. shRNAs targeting Sema6b were also used in neuronal cultures to measure the impact of the decreased Sema6b expression on morphogenesis and synaptogenesis. The overexpression of some variants leads to a subcellular mislocalization of SEMA6B protein in HEK293T cells and to a reduced spine density owing to loss of mature spines in neuronal cultures. Sema6b knockdown also impairs spine density and spine maturation. In addition, we conducted in vivo rescue experiments in chicken embryos with the selected mutated forms of Sema6b expressed in commissural neurons after knockdown of endogenous SEMA6B. We observed that expression of these variants in commissural neurons fails to rescue the normal axon pathway. In conclusion, identification of SEMA6B variants in patients presenting with an overlapping phenotype with ID and functional studies highlight the important role of SEMA6B in neuronal development, notably in spine formation and maturation and in axon guidance. This study adds SEMA6B to the list of ID-related genes.

Published
2022
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32. Lentiviral haematopoietic stem cell gene therapy for metachromatic leukodystrophy: Results in 5 patients treated under nominal compassionate use

Author

Valeria Calbi, Francesca Fumagalli, Vera Gallo, Salvatore Recupero, Fabiola De Mattia, Elena Sophia Fratini, Ambra Corti, Giulia Tarantola, Marina Sarzana, Alessia Ippolito, Stefano Scarparo, Francesca Ciotti, Maddalena Fraschini, Margherita Levi, Mara Sangalli, Francesco Morena, Sabata Martino, Caroline Sevin, Vinodh Narayanan, Etai Adam, Lisa Emrick, Roberto Giugliani, and Alessandro Aiuti

Subjects
Endocrinology, Endocrinology, Diabetes and Metabolism, Genetics, Molecular Biology, Biochemistry
Published
2023
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33. Deficiency of TET3 leads to a genome-wide DNA hypermethylation episignature in human whole blood

Author

Trudie Cottrell, Jacques C. Giltay, Richard H. van Jaarsveld, Elles M. J. Boon, Roger E. Stevenson, Michael A. Levy, Kimberly F. Doheny, Bekim Sadikovic, G. Bradley Schaefer, Roberto Bonasio, Muhammad Ansar, Vinodh Narayanan, Mieke M. van Haelst, Jill A. Fahrner, Marleen Simon, David B. Beck, Claudia A. L. Ruivenkamp, Sivagamy Sithambaram, Teresa Romeo Luperchio, Leandros Boukas, Marie-Christine Nougues, Hannah W. Moore, Marielle Alders, Renske Oegema, M. Mahdi Motazacker, Kay Metcalfe, Cyril Mignot, Jennifer Kerkhof, Gijs W. E. Santen, Jessica Bos, Sofia Douzgou, Siddharth Banka, Keri Ramsey, Boris Keren, Human Genetics, ACS - Pulmonary hypertension & thrombosis, ANS - Complex Trait Genetics, AR&D - Amsterdam Reproduction & Development, Human genetics, Amsterdam Neuroscience - Complex Trait Genetics, and Amsterdam Reproduction & Development (AR&D)

Subjects
Genetics, Epigenomics, DNA methylation, Neurodevelopmental disorders, Diagnostic markers, QH426-470, Biology, medicine.disease, Phenotype, Genome, Article, Neurodevelopmental disorder, DNA demethylation, CpG site, medicine, DNMT1, Medicine, Epigenetics, Author Correction, Molecular Biology, Genetics (clinical)
Abstract

TET3 encodes an essential dioxygenase involved in epigenetic regulation through DNA demethylation. TET3 deficiency, or Beck-Fahrner syndrome (BEFAHRS; MIM: 618798), is a recently described neurodevelopmental disorder of the DNA demethylation machinery with a nonspecific phenotype resembling other chromatin-modifying disorders, but inconsistent variant types and inheritance patterns pose diagnostic challenges. Given TET3’s direct role in regulating 5-methylcytosine and recent identification of syndrome-specific DNA methylation profiles, we analyzed genome-wide DNA methylation in whole blood of TET3-deficient individuals and identified an episignature that distinguishes affected and unaffected individuals and those with mono-allelic and bi-allelic pathogenic variants. Validation and testing of the episignature correctly categorized known TET3 variants and determined pathogenicity of variants of uncertain significance. Clinical utility was demonstrated when the episignature alone identified an affected individual from over 1000 undiagnosed cases and was confirmed upon distinguishing TET3-deficient individuals from those with 46 other disorders. The TET3-deficient signature - and the signature resulting from activating mutations in DNMT1 which normally opposes TET3 - are characterized by hypermethylation, which for BEFAHRS involves CpG sites that may be biologically relevant. This work expands the role of epi-phenotyping in molecular diagnosis and reveals genome-wide DNA methylation profiling as a quantitative, functional readout for characterization of this new biochemical category of disease.

Published
2021
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34. Author Correction: Deficiency of TET3 leads to a genome-wide DNA hypermethylation episignature in human whole blood

Author

Renske Oegema, Vinodh Narayanan, Marleen Simon, Trudie Cottrell, Marie-Christine Nougues, Mieke M. van Haelst, Gijs W. E. Santen, Roger E. Stevenson, Keri Ramsey, Kay Metcalfe, Jacques C. Giltay, Sivagamy Sithambaram, Teresa Romeo Luperchio, Leandros Boukas, Marielle Alders, Hannah W. Moore, Claudia A. L. Ruivenkamp, Jessica Bos, Richard H. van Jaarsveld, Jill A. Fahrner, David B. Beck, Sofia Douzgou, Jennifer Kerkhof, Muhammad Ansar, Michael A. Levy, G. Bradley Schaefer, Siddharth Banka, Roberto Bonasio, Kimberly F. Doheny, M. Mahdi Motazacker, Cyril Mignot, Elles M. J. Boon, Boris Keren, and Bekim Sadikovic

Subjects
Genetics, Medicine, Dna hypermethylation, QH426-470, Biology, Molecular Biology, Genome, Genetics (clinical), Whole blood
Published
2021
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35. Artificial intelligence enables comprehensive genome interpretation and nomination of candidate diagnoses for rare genetic diseases

Author

Narayanan Veeraraghavan, Pankaj B. Agrawal, Paul Billings, Keri Ramsey, Casie A. Genetti, Martin G. Reese, Jeanette McCarthy, Terence C. Wong, Marcus Naymik, Catherine A. Brownstein, Vinodh Narayanan, Barry Moore, Britt Sabina Löscher, Mark Yandell, Francisco M. De La Vega, Edgar Javier Hernandez, Kiely N. James, Matthew J. Huentelman, Braden E. Boone, Shawn Levy, Stephen F. Kingsmore, Lucia Guidugli, Andre Franke, Erwin Frise, Shimul Chowdhury, Sander Pajusalu, Alan H. Beggs, and Katrin Õunap

Subjects
Male, Candidate gene, Genotype, Context (language use), Disease, QH426-470, Biology, Clinical decision support system, Genome, Rare Diseases, Artificial Intelligence, Databases, Genetic, Exome Sequencing, Genetics, Humans, Medical diagnosis, Molecular Biology, Exome sequencing, Genetics (clinical), Retrospective Studies, Whole genome sequencing, business.industry, Research, Retrospective cohort study, Genomics, Human genetics, Phenotype, Medicine, Molecular Medicine, Female, Artificial intelligence, business
Abstract

Background Clinical interpretation of genetic variants in the context of the patient’s phenotype is becoming the largest component of cost and time expenditure for genome-based diagnosis of rare genetic diseases. Artificial intelligence (AI) holds promise to greatly simplify and speed genome interpretation by integrating predictive methods with the growing knowledge of genetic disease. Here we assess the diagnostic performance of Fabric GEM, a new, AI-based, clinical decision support tool for expediting genome interpretation. Methods We benchmarked GEM in a retrospective cohort of 119 probands, mostly NICU infants, diagnosed with rare genetic diseases, who received whole-genome or whole-exome sequencing (WGS, WES). We replicated our analyses in a separate cohort of 60 cases collected from five academic medical centers. For comparison, we also analyzed these cases with current state-of-the-art variant prioritization tools. Included in the comparisons were trio, duo, and singleton cases. Variants underpinning diagnoses spanned diverse modes of inheritance and types, including structural variants (SVs). Patient phenotypes were extracted from clinical notes by two means: manually and using an automated clinical natural language processing (CNLP) tool. Finally, 14 previously unsolved cases were reanalyzed. Results GEM ranked over 90% of the causal genes among the top or second candidate and prioritized for review a median of 3 candidate genes per case, using either manually curated or CNLP-derived phenotype descriptions. Ranking of trios and duos was unchanged when analyzed as singletons. In 17 of 20 cases with diagnostic SVs, GEM identified the causal SVs as the top candidate and in 19/20 within the top five, irrespective of whether SV calls were provided or inferred ab initio by GEM using its own internal SV detection algorithm. GEM showed similar performance in absence of parental genotypes. Analysis of 14 previously unsolved cases resulted in a novel finding for one case, candidates ultimately not advanced upon manual review for 3 cases, and no new findings for 10 cases. Conclusions GEM enabled diagnostic interpretation inclusive of all variant types through automated nomination of a very short list of candidate genes and disorders for final review and reporting. In combination with deep phenotyping by CNLP, GEM enables substantial automation of genetic disease diagnosis, potentially decreasing cost and expediting case review.

Published
2021
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36. Progressive bilateral nuclear cataracts associated with cerebellar-facial-dental syndrome: case report, literature review, and identification of a new genetic variant

Author

Christopher Balak, Newell Belnap, Matthew J. Huentelman, Brianna Pandey, James Plotnik, Keri Ramsey, and Vinodh Narayanan

Subjects
Pathology, medicine.medical_specialty, TATA-Binding Protein Associated Factors, genetic structures, business.industry, Developmental Disabilities, Genetic disorder, Genetic variants, medicine.disease, eye diseases, Cataract, stomatognathic diseases, Ophthalmology, Cataracts, Cerebellum, Pediatrics, Perinatology and Child Health, Mutation, medicine, Humans, Identification (biology), Dysmorphic facial features, business, Child, Cerebellar hypoplasia
Abstract

Cerebellar-facial-dental syndrome (CFDS) is a newly described autosomal recessive genetic disorder characterized by mutations in the BRF1 gene. CFDS is clinically associated with dysmorphic facial features and cerebellar hypoplasia. We report visually significant progressive bilateral nuclear cataracts in a child with CFDS and identify a new causative genetic variant.

Published
2021

37. List of Contributors

Author

Gregory Aaen, Israel F. Abroms, Ulrika Ådén, Gunnar Ahlsten, Robert B. Aird, Samiah A. Al-Zaidy, Fred Andermann, Banu Anlar, Alexis Arzimanoglou, Stephen Ashwal, Erika Augustine, Karen Ballaban-Gil, Nigel S. Bamford, Charles F. Barlow, Thomas Bast, David Bates, Robert J. Baumann, Enrico Bertini, Alidor Beya, Michael Blaw, John Bodensteiner, Daniel J. Bonthius, Amy E. Brin, Knut Brockmann, John Keith Brown, Stuart B. Brown, Audrey Christine Brumback, Michelle Bureau, James R. Burke, Annie Bye, Carol Camfield, Peter Camfield, Jaume Campistol Plana, Dee James Canale, Onasis Caneris, Roberto H. Caraballo, Alison Chantal Caviness, Hsiao-Tuan Chao, Catherine A. Chapman, Enrique Chaves-Carballo, Yoon-Jae Cho, Hans-Jürgen Christen, Harry T. Chugani, Giovanni Cioni, David Clark, Edward Robert Scheffer Cliff, Frederick B. Cochran, Bruce H. Cohen, Maynard M. Cohen, Kevin Collins, Athanasios Covanis, Macdonald Critchley, J. Helen Cross, Patricia K. Crumrine, Paolo Curatolo, Pamela A. Davies, Gabrielle deVeber, Darryl C. De Vivo, Linda S. de Vries, Liesbeth De Waele, William DeMyer, Anita Devlin, William B. Dobyns, W. Edwin Dodson, Kirsty Donald, Frank H. Duffy, David W. Dunn, Henry G. Dunn, Leon S. Dure, Paul Richard Dyken, Férechté Encha-Razavi, Gerald Erenberg, Melinda L. Estes, Philippe Evrard, Donna Ferriero, Peggy Ferry, Archie Fine, Edward J. Fine, John S. Fine, Richard S. Finkel, Alain Fischer, Christine Fischer, Lance Fogan, Glenn W. Fowler, Yitzchak Frank, Heather J. Fullerton, Tetsuo Furukawa, Ronald S. Gabriel, Aristea S. Galanopoulou, David Gardner-Medwin, Bhuwan Garg, Pierre Genton, Mark S. George, Thierry Gineste, Christopher C. Giza, Nathalie Goemans, Gerald S. Golden, Jeffrey Alan Golden, Gary W. Goldstein, Christopher Gomez, Manuel R. Gomez, Timothy Gomez, Howard P. Goodkin, Neil Gordon, Pierre Gressens, Helmut Groger, Renzo Guerrini, Christina A. Gurnett, Emanuela Gussoni, Richard Haas, Bengt Hagberg, Jerome S. Haller, Adam L. Hartman, Fred Haruda, Deborah Hirtz, Gwendolyn R. Hogan, Guy M. Hunt, Susan T. Iannaccone, Terrie Eleanor Inder, Victor Ionasescu, Katrien Jansen, Yuwu Jiang, Henry J. Kaminski, Shigehiko Kamoshita, Peter B. Kang, David M. Kaufman, Walter E. Kaufmann, Edward M. Kaye, Peter Kellaway, Rhona S. Kelley, Charles Kennedy, Young-Min Kim, Michael Kirby, Adam Kirton, Eliane Kobayashi, Eric H. Kossoff, Michail Koutroumanidis, Lauren Krupp, Bernadette M. Lange, Douglas J. Lanska, Mary Jo Lanska, Paul D. Larsen, Samuel J. Lassoff, John Laterra, Bernard Lemieux, Nicholas J. Lenn, William J. Logan, Elizabeth Lomax, Lawrence D. Longo, A. Lorris Betz, Bala V. Manyam, Warren A. Marks, E. Wayne Massey, Laszlo J. Mate, Ian McKinlay, William T. McLean, Ailsa McLellan, Mark F. Mehler, Johannes C. Melchior, David J. Michelson, Steven P. Miller, Suzanne L. Miller, J. Gordon Millichap, Robert A. Minns, Eli M. Mizrahi, Ann B. Moser, Solomon L. Moshé, Hiltrud Muhle, Francesco Muntoni, Sakkubai Naidu, Vinodh Narayanan, Nardo Nardocci, Jeffrey J. Neil, Ann Neumeyer, Michael J. Noetzel, Yoshiko Nomura, Douglas R. Nordli, Kathryn North, Yoko Ohtsuka, Finbar J.K. O’Callaghan, Roger J. Packer, Gregory M. Pastores, Marc C. Patterson, Phillip L. Pearl, Michel Philippart, Helena S. Pihko, Gordon Piller, Thomas F. Platz, Annapurna Poduri, Michael A. Pollack, Brenda E. Porter, Michèle Provis, Dietz Rating, Harold Reich, Bernd Remler, Jong M. Rho, Peter Richards, Edward P. Richardson, Sylvia O. Richardson, E. Steve Roach, Arthur L. Rose, Marvin P. Rozear, Lucien J. Rubinstein, Robert S. Rust, Arushi Gahlot Saini, Suzanne Saint-Anne Dargassies, Harvey B. Sarnat, Mohammad Sarwar, Richard Satran, Sanford Schneider, Waltraud Schrank, Rodney C. Scott, Syndi Seinfeld, Duygu Selcen, Nenad Sestan, Steven Shapiro, Elliott H. Sherr, Michael Shevell, Lloyd Shield, Richard L. Sidman, Faye S. Silverstein, Michael Sinnreich, O. Carter Snead, Regan Solomons, Emilio Soria-Duran, Carl E. Stafstrom, E. Steven Roach, Harold Stevens, Hans Michael Strassburg, David A. Stumpf, Thomas Sullivan, Herbert M. Swick, Charles N. Swisher, Takao Takahashi, Ingrid Tein, Laura Tochen, Eva E. Thomas, Alan Thompson, Svinder S. Toor, H. Richard Tyler, Peter Uldall, David K. Urion, Ahsan Moosa Naduvil Valappil, Ronald Van Toorn, Jennifer Vermilion, Doris Vidaver, Betty R. Vohr, Brigitte Vollmer, Joseph J. Volpe, Deborah P. Waber, Mark S. Wainwright, Lucius Waites, Christopher Walsh, Adolf Weindl, Mary Anne Whelan, Larry E. White, Vicky Holets Whittemore, Jo Wilmshurst, Elaine Wirrell, Nicole I. Wolf, Paul Youssef, John Zempel, Huda Y. Zoghbi, Sameer M. Zuberi, and Mary Zupanc

Published
2021
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39. Integrated phenotypic and mutational approach defines EBF3-related HADD syndrome genotype-phenotype relationships

Author

Vanesa Lerma, Nathan D. Bliss, Hsiao-Tuan Chao, Paul J. Benke, Michael F. Wangler, Cole A. Deisseroth, Ginevra Zanni, Vinodh Narayanan, Enrico Bertini, Ashley W. LeMaire, Aarushi Nayak, Enza Maria Valente, and Christopher Balak

Subjects
Genetics, Zinc finger, Ataxia, Neurodevelopmental disorder, Cohort, Genotype, medicine, medicine.symptom, Biology, medicine.disease, Phenotype, Hypotonia, Genotype phenotype
Abstract

Hypotonia, Ataxia, and Delayed Development syndrome is a neurodevelopmental disorder caused by heterozygousEarly B-Cell Factor 3(EBF3) loss-of-function variants. Identified in 2016, the full spectrum of clinical findings and the relationship between theEBF3genotype and clinical outcomes has not been determined beyond its namesake features. We combined a phenotypic assessment of 33 individuals molecularly diagnosed withEBF3pathogenic variants with a meta-analysis of 34 previously reported individuals. The combined 62 unique individuals enabled comparative cross-sectional phenotype and genotype analysis in the largest cohort to date of affected individuals. Cardinal distinguishing features were identified that facilitate phenotypic stratification for clinical diagnosis. We developed assessment scales to ascertain individuals at risk for pathogenicEBF3variants, stratify the clinical severity, and connect variant-specific molecular phenotypes to clinical outcomes. Our findings show that a specific class ofEBF3variants affecting the evolutionarily conserved Zinc Finger (ZNF) motif, which is critical for stabilizing the protein interaction with the DNA target sequence, is associated with an increased risk of persistent motor and language impairments. These findings highlight the impact of combining variant-specific molecular phenotypes with comprehensive clinical data to predict neurodevelopmental outcomes and potentially guide personalized decisions for therapeutic interventions.

Published
2020
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41. Complex genetic network underlying the convergent of Rett Syndrome like (RTT-L) phenotype in neurodevelopmental disorders

Author

J. Dodson, Ignazio S. Piras, D. W. Craig, Newell Belnap, G. Mills, Ana M. Claasen, Marcus Naymik, Lorida Llaci, Vinodh Narayanan, B. Gerald, Meredith Sanchez-Castillo, P. Venugopal, Chris Balak, Szabolcs Szelinger, Ryan Richholt, Sampath Rangasamy, Raj Gupta, Isabelle Schrauwen, Ashley L. Siniard, M. Brzezinski, Keri Ramsey, Wayne M. Jepsen, M. D. De Both, R. Pillai, E. S. Frankel, M. J. Huentelman, and M. Sharifi

Subjects
Genetics, FOXG1, congenital, hereditary, and neonatal diseases and abnormalities, CDKL5, medicine, Rett syndrome, Atypical Rett syndrome, TCF4, Biology, medicine.disease, Phenotype, Exome sequencing, MECP2
Abstract

Mutations of the X-linked gene encoding methyl-CpG-binding protein 2 (MECP2) cause classical forms of Rett syndrome (RTT) in girls. Patients with features of classical Rett syndrome, but do not fulfill all the diagnostic criteria (e.g. absence of a MECP2 mutation), are defined as atypical Rett syndrome. Genes encoding for cyclin-dependent kinase-like 5 (CDKL5) and forkhead box G1 (FOXG1) are more commonly found in patients with atypical Rett syndrome. Nevertheless, a subset of patients who are recognized to have an overlapping phenotype with RTT but are lacking a mutation in a gene that causes typical or atypical RTT are described as having Rett syndrome like phenotype (RTT-L). Whole Exome Sequencing (WES) of 8 RTT-L patients from our cohort revealed mutations in the genes GABRG2, GRIN1, ATP1A2, KCNQ2, KCNB1, TCF4, SEMA6B, and GRIN2A, which are seemingly unrelated to Rett syndrome genes. We hypothesized that the phenotypic overlap in RTT and RTT-L is caused by mutations in genes that affect common cellular pathways critical for normal brain development and function. We annotated the list of genes identified causing RTT-L from peer-reviewed articles and performed a protein-protein interaction (PPI) network analysis. We also investigated their interaction with RTT (typical or atypical) genes such as MECP2, CDKL5, NTNG1, and FOXG1. We found that the RTT-L-causing genes were enriched in the biological pathways such as circadian entrainment, the CREB pathway, and RET signaling, and neuronal processes like ion transport, synaptic transmission, and transcription. We conclude that genes that significantly interact with the PPI network established by RTT genes cause RTT-L, explaining the considerable feature overlap between genes that are indicated for RTT-L and RTT.

Published
2020
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42. Front Cover, Volume 41, Issue 2

Author

Carmel G. McCullough, Szabolcs Szelinger, Newell Belnap, Keri Ramsey, Isabelle Schrauwen, Ana M. Claasen, Leah W. Burke, Ashley L. Siniard, Matthew J. Huentelman, Vinodh Narayanan, and David W. Craig

Subjects
Genetics, Genetics (clinical)
Published
2020
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43. Modeling of Pontocerebellar Hypoplasia Type 1B and Chemical Mimicry in Patient-Derived Neural Stem Cells

Author

Ritin Sharma, Jacob M. Carlson, Vinodh Narayanan, Patrick Pirrotte, Kristin Leskoke, Judith A. Tello, Seema Plaisier, Melissa N. Martinez, Matthew J. Huentelman, Liberty François-Moutal, Francesca Vitali, Keri Ramsey, Ben Stansfield, Sampath Rangasamy, May Khanna, Patrick Pirotte, Llorida Llaci, Roberta Diaz Brinton, Jared M. Churko, and Krystine Garcia-Mansfield

Subjects
Mutation, biology, Exosome complex, Pontocerebellar hypoplasia, biology.organism_classification, medicine.disease, Proteomics, medicine.disease_cause, Small molecule, Neural stem cell, Cell biology, medicine, Chemical mimicry, Zebrafish
Abstract

Pontocerebellar Hypoplasia 1B (PCH1B) patients exhibit profound underdevelopment of the neocerebellum and its adjacent structures, leading to severe developmental delays as well as poor survival. Here, we report a new case of PCH1B with a known mutation in EXOSC3, a component of the RNA exosome. We reprogrammed blood from the PCH1B patient and the healthy carrier parents into human induced pluripotent stem cells and differentiated these cells into neural stem cells (NSCs). Proteomic content was analyzed by mass spectrometry to reveal a slight underexpression of mutated EXOSC3 in the PCH1B patient. We discovered that several processes implicated in cell differentiation were impaired. NSCs from the mother were incubated with ERD03, a small molecule rationally developed to model PCH1B in zebrafish and analyzed by high-throughput mass spectrometry-based proteomics. In addition to affecting individual protein expression, we demonstrated the ability of the compound ERD03 to mimic PCH1B-induced protein pathways.

Published
2020
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44. Primrose syndrome: Characterization of the phenotype in42 patients

Author

Erica H. Gerkes, Pietro Strisciuglio, Renata Lazari Sandoval, Todd Waters, A. Rossi, Renata Posmyk, Sheela Unger, Constance T. R. M. Stumpel, Hanne B Hove, Tina Barbaro-Dieber, Marco Tartaglia, Keri Ramsey, Petr E. Jira, Daniel R. Carvalho, Vinodh Narayanan, Leonie A. Menke, Katherine Lachlan, Michael J. Gambello, Viviana Cordeddu, Sandra Jansen, Marrit M. Hitzert, Peter D. Turnpenny, Blanca Gener, Daniela Melis, Raoul C.M. Hennekam, Damara Ortiz, Clare Turnbull, Kyra E. Stuurman, Eline Overwater, Alberto J. Espay, Pediatric surgery, Human genetics, Amsterdam Reproduction & Development (AR&D), Clinical Genetics, Klinische Genetica, MUMC+: DA KG Polikliniek (9), RS: GROW - R4 - Reproductive and Perinatal Medicine, General Paediatrics, ANS - Cellular & Molecular Mechanisms, ARD - Amsterdam Reproduction and Development, Human Genetics, Graduate School, ACS - Heart failure & arrhythmias, APH - Quality of Care, Melis, D., Carvalho, D., Barbaro-Dieber, T., Espay, A. J., Gambello, M. J., Gener, B., Gerkes, E., Hitzert, M. M., Hove, H. B., Jansen, S., Jira, P. E., Lachlan, K., Menke, L. A., Narayanan, V., Ortiz, D., Overwater, E., Posmyk, R., Ramsey, K., Rossi, A., Sandoval, R. L., Stumpel, C., Stuurman, K. E., Cordeddu, V., Turnpenny, P., Strisciuglio, P., Tartaglia, M., Unger, S., Waters, T., Turnbull, C., and Hennekam, R. C.

Subjects
0301 basic medicine, Male, Pathology, alpha‐fetoprotein, Transcription Factor, 030105 genetics & heredity, Carbon-Carbon Double Bond Isomerase, Racemases and Epimerase, Intellectual disability, ectopic calcifications, Primrose syndrome, Child, Wasting, Enoyl-CoA Hydratase, Genetics (clinical), ABNORMALITIES, 3-Hydroxyacyl CoA Dehydrogenases, Calcinosis, ZBTB20, Middle Aged, Ear Disease, Acetyl-CoA C-Acyltransferase, CANCER, Mitochondria, Muscular Atrophy, DIFFERENTIATION, Phenotype, Child, Preschool, Calcinosi, Original Article, Female, medicine.symptom, Human, Adult, medicine.medical_specialty, Heterozygote, Adolescent, alpha-fetoprotein, overgrowth, Mutation, Missense, Racemases and Epimerases, Nerve Tissue Proteins, Genetic Association Studie, 03 medical and health sciences, Frontal Bossing, Young Adult, Testicular Neoplasms, Intellectual Disability, Genetics, medicine, Humans, Abnormalities, Multiple, Genetic Predisposition to Disease, Testicular Neoplasm, Ear Diseases, Genetic Association Studies, Muscle contracture, MUTATIONS, business.industry, ectopic calcification, 3-Hydroxyacyl CoA Dehydrogenase, Macrocephaly, Infant, Original Articles, medicine.disease, Carbon-Carbon Double Bond Isomerases, Megalencephaly, ALPHA, 030104 developmental biology, Palpebral fissure, Face, Nerve Tissue Protein, Mutation, business, FINGER PROTEIN ZBTB20, Calcification, Transcription Factors
Abstract

Primrose syndrome (PS; MIM# 259050) is characterized by intellectual disability (ID), macrocephaly, unusual facial features (frontal bossing, deeply set eyes, down‐slanting palpebral fissures), calcified external ears, sparse body hair and distal muscle wasting. The syndrome is caused by de novo heterozygous missense variants in ZBTB20. Most of the 29 published patients are adults as characteristics appear more recognizable with age. We present 13 hitherto unpublished individuals and summarize the clinical and molecular findings in all 42 patients. Several signs and symptoms of PS develop during childhood, but the cardinal features, such as calcification of the external ears, cystic bone lesions, muscle wasting, and contractures typically develop between 10 and 16 years of age. Biochemically, anemia and increased alpha‐fetoprotein levels are often present. Two adult males with PS developed a testicular tumor. Although PS should be regarded as a progressive entity, there are no indications that cognition becomes more impaired with age. No obvious genotype‐phenotype correlation is present. A subgroup of patients with ZBTB20 variants may be associated with mild, nonspecific ID. Metabolic investigations suggest a disturbed mitochondrial fatty acid oxidation. We suggest a regular surveillance in all adult males with PS until it is clear whether or not there is a truly elevated risk of testicular cancer.

Published
2020
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45. Partial Loss of USP9X Function Leads to a Male Neurodevelopmental and Behavioral Disorder Converging on Transforming Growth Factor beta Signaling

Author

Brett V. Johnson, Raman Kumar, Sabrina Oishi, Suzy Alexander, Maria Kasherman, Michelle Sanchez Vega, Atma Ivancevic, Alison Gardner, Deepti Domingo, Mark Corbett, Euan Parnell, Sehyoun Yoon, Tracey Oh, Matthew Lines, Henrietta Lefroy, Usha Kini, Margot Van Allen, Sabine Grønborg, Sandra Mercier, Sébastien Küry, Stéphane Bézieau, Laurent Pasquier, Martine Raynaud, Alexandra Afenjar, Thierry Billette de Villemeur, Boris Keren, Julie Désir, Lionel Van Maldergem, Martina Marangoni, Nicola Dikow, David A. Koolen, Peter M. VanHasselt, Marjan Weiss, Petra Zwijnenburg, Joaquim Sa, Claudia Falcao Reis, Carlos López-Otín, Olaya Santiago-Fernández, Alberto Fernández-Jaén, Anita Rauch, Katharina Steindl, Pascal Joset, Amy Goldstein, Suneeta Madan-Khetarpal, Elena Infante, Elaine Zackai, Carey Mcdougall, Vinodh Narayanan, Keri Ramsey, Saadet Mercimek-Andrews, Loren Pena, Vandana Shashi, Kelly Schoch, Jennifer A. Sullivan, Filippo Pinto e Vairo, Pavel N. Pichurin, Sarah A. Ewing, Sarah S. Barnett, Eric W. Klee, M. Scott Perry, Mary Kay Koenig, Catherine E. Keegan, Jane L. Schuette, Stephanie Asher, Yezmin Perilla-Young, Laurie D. Smith, Jill A. Rosenfeld, Elizabeth Bhoj, Paige Kaplan, Dong Li, Renske Oegema, Ellen van Binsbergen, Bert van der Zwaag, Marie Falkenberg Smeland, Ioana Cutcutache, Matthew Page, Martin Armstrong, Angela E. Lin, Marcie A. Steeves, Nicolette den Hollander, Mariëtte J.V. Hoffer, Margot R.F. Reijnders, Serwet Demirdas, Daniel C. Koboldt, Dennis Bartholomew, Theresa Mihalic Mosher, Scott E. Hickey, Christine Shieh, Pedro A. Sanchez-Lara, John M. Graham, Kamer Tezcan, G.B. Schaefer, Noelle R. Danylchuk, Alexander Asamoah, Kelly E. Jackson, Naomi Yachelevich, Margaret Au, Luis A. Pérez-Jurado, Tjitske Kleefstra, Peter Penzes, Stephen A. Wood, Thomas Burne, Tyler Mark Pierson, Michael Piper, Jozef Gécz, Lachlan A. Jolly, Maria T. Acosta, David R. Adams, Aaron Aday, Mercedes E. Alejandro, Patrick Allard, Euan A. Ashley, Mahshid S. Azamian, Carlos A. Bacino, Guney Bademci, Eva Baker, Ashok Balasubramanyam, Dustin Baldridge, Deborah Barbouth, Gabriel F. Batzli, Alan H. Beggs, Hugo J. Bellen, Jonathan A. Bernstein, Gerard T. Berry, Anna Bican, David P. Bick, Camille L. Birch, Stephanie Bivona, Carsten Bonnenmann, Devon Bonner, Braden E. Boone, Bret L. Bostwick, Lauren C. Briere, Elly Brokamp, Donna M. Brown, Matthew Brush, Elizabeth A. Burke, Lindsay C. Burrage, Manish J. Butte, Olveen Carrasquillo, Ta Chen Peter Chang, Hsiao-Tuan Chao, Gary D. Clark, Terra R. Coakley, Laurel A. Cobban, Joy D. Cogan, F. Sessions Cole, Heather A. Colley, Cynthia M. Cooper, Heidi Cope, William J. Craigen, Precilla D'Souza, Surendra Dasari, Mariska Davids, Jean M. Davidson, Jyoti G. Dayal, Esteban C. Dell'Angelica, Shweta U. Dhar, Naghmeh Dorrani, Daniel C. Dorset, Emilie D. Douine, David D. Draper, Annika M. Dries, Laura Duncan, David J. Eckstein, Lisa T. Emrick, Christine M. Eng, Gregory M. Enns, Cecilia Esteves, Tyra Estwick, Liliana Fernandez, Carlos Ferreira, Elizabeth L. Fieg, Paul G. Fisher, Brent L. Fogel, Irman Forghani, Noah D. Friedman, William A. Gahl, Rena A. Godfrey, Alica M. Goldman, David B. Goldstein, Jean-Philippe F. Gourdine, Alana Grajewski, Catherine A. Groden, Andrea L. Gropman, Melissa Haendel, Rizwan Hamid, Neil A. Hanchard, Frances High, Ingrid A. Holm, Jason Hom, Alden Huang, Yong Huang, Rosario Isasi, Fariha Jamal, Yong-hui Jiang, Jean M. Johnston, Angela L. Jones, Lefkothea Karaviti, Emily G. Kelley, David M. Koeller, Isaac S. Kohane, Jennefer N. Kohler, Deborah Krakow, Donna M. Krasnewich, Susan Korrick, Mary Koziura, Joel B. Krier, Jennifer E. Kyle, Seema R. Lalani, Byron Lam, Brendan C. Lanpher, Ian R. Lanza, C. Christopher Lau, Jozef Lazar, Kimberly LeBlanc, Brendan H. Lee, Hane Lee, Roy Levitt, Shawn E. Levy, Richard A. Lewis, Sharyn A. Lincoln, Pengfei Liu, Xue Zhong Liu, Sandra K. Loo, Joseph Loscalzo, Richard L. Maas, Ellen F. Macnamara, Calum A. MacRae, Valerie V. Maduro, Marta M. Majcherska, May Christine V. Malicdan, Laura A. Mamounas, Teri A. Manolio, Thomas C. Markello, Ronit Marom, Martin G. Martin, Julian A. Martínez-Agosto, Shruti Marwaha, Thomas May, Jacob McCauley, Allyn McConkie-Rosell, Colleen E. McCormack, Alexa T. McCray, Jason D. Merker, Thomas O. Metz, Matthew Might, Eva Morava-Kozicz, Paolo M. Moretti, Marie Morimoto, John J. Mulvihill, David R. Murdock, Avi Nath, Stan F. Nelson, J. Scott Newberry, John H. Newman, Sarah K. Nicholas, Donna Novacic, Devin Oglesbee, James P. Orengo, Stephen Pak, J. Carl Pallais, Christina GS. Palmer, Jeanette C. Papp, Neil H. Parker, John A. Phillips, Jennifer E. Posey, John H. Postlethwait, Lorraine Potocki, Barbara N. Pusey, Genecee Renteri, Chloe M. Reuter, Lynette Rives, Amy K. Robertson, Lance H. Rodan, Robb K. Rowley, Ralph Sacco, Jacinda B. Sampson, Susan L. Samson, Mario Saporta, Judy Schaechter, Timothy Schedl, Daryl A. Scott, Lisa Shakachite, Prashant Sharma, Kathleen Shields, Jimann Shin, Rebecca Signer, Catherine H. Sillari, Edwin K. Silverman, Janet S. Sinsheimer, Kevin S. Smith, Lilianna Solnica-Krezel, Rebecca C. Spillmann, Joan M. Stoler, Nicholas Stong, David A. Sweetser, Cecelia P. Tamburro, Queenie K.-G. Tan, Mustafa Tekin, Fred Telischi, Willa Thorson, Cynthia J. Tifft, Camilo Toro, Alyssa A. Tran, Tiina K. Urv, Tiphanie P. Vogel, Daryl M. Waggott, Colleen E. Wahl, Nicole M. Walley, Chris A. Walsh, Melissa Walker, Jennifer Wambach, Jijun Wan, Lee-kai Wang, Michael F. Wangler, Patricia A. Ward, Katrina M. Waters, Bobbie-Jo M. Webb-Robertson, Daniel Wegner, Monte Westerfield, Matthew T. Wheeler, Anastasia L. Wise, Lynne A. Wolfe, Jeremy D. Woods, Elizabeth A. Worthey, Shinya Yamamoto, John Yang, Amanda J. Yoon, Guoyun Yu, Diane B. Zastrow, Chunli Zhao, Stephan Zuchner, William Gahl, Clinical Genetics, Human genetics, Amsterdam Reproduction & Development (AR&D), ACS - Atherosclerosis & ischemic syndromes, MUMC+: DA KG Polikliniek (9), and RS: FHML non-thematic output

Subjects
Male, 0301 basic medicine, Brain malformation, Developmental Disabilities, INTERACTS, USP9X, Haploinsufficiency, in-vitro, CELL-MIGRATION, Deubiquitylating enzyme, Biology, Hippocampus, of-function mutations, Article, liquid facets, TGFβ, Mice, 03 medical and health sciences, 0302 clinical medicine, Neurodevelopmental disorder, TGF beta, Transforming Growth Factor beta, Intellectual Disability, Intellectual disability, medicine, Animals, Humans, Missense mutation, deubiquitinating enzyme, Biological Psychiatry, fam/usp9x, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Male Phenotype, medicine.disease, Phenotype, Hypotonia, 030104 developmental biology, Female, medicine.symptom, Ubiquitin Thiolesterase, Neuroscience, 030217 neurology & neurosurgery, Signal Transduction, Rare cancers Radboud Institute for Health Sciences [Radboudumc 9], Transforming growth factor
Abstract

Contains fulltext : 218305.pdf (Publisher’s version ) (Closed access) BACKGROUND: The X-chromosome gene USP9X encodes a deubiquitylating enzyme that has been associated with neurodevelopmental disorders primarily in female subjects. USP9X escapes X inactivation, and in female subjects de novo heterozygous copy number loss or truncating mutations cause haploinsufficiency culminating in a recognizable syndrome with intellectual disability and signature brain and congenital abnormalities. In contrast, the involvement of USP9X in male neurodevelopmental disorders remains tentative. METHODS: We used clinically recommended guidelines to collect and interrogate the pathogenicity of 44 USP9X variants associated with neurodevelopmental disorders in males. Functional studies in patient-derived cell lines and mice were used to determine mechanisms of pathology. RESULTS: Twelve missense variants showed strong evidence of pathogenicity. We define a characteristic phenotype of the central nervous system (white matter disturbances, thin corpus callosum, and widened ventricles); global delay with significant alteration of speech, language, and behavior; hypotonia; joint hypermobility; visual system defects; and other common congenital and dysmorphic features. Comparison of in silico and phenotypical features align additional variants of unknown significance with likely pathogenicity. In support of partial loss-of-function mechanisms, using patient-derived cell lines, we show loss of only specific USP9X substrates that regulate neurodevelopmental signaling pathways and a united defect in transforming growth factor beta signaling. In addition, we find correlates of the male phenotype in Usp9x brain-specific knockout mice, and further resolve loss of hippocampal-dependent learning and memory. CONCLUSIONS: Our data demonstrate the involvement of USP9X variants in a distinctive neurodevelopmental and behavioral syndrome in male subjects and identify plausible mechanisms of pathogenesis centered on disrupted transforming growth factor beta signaling and hippocampal function.

Published
2020
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46. Damaging de novo missense variants in EEF1A2lead to a developmental and degenerative epileptic-dyskinetic encephalopathy

Author

Laurine Perrin, Sha Tang, Brandon S. Guida, Tjitske Kleefstra, Marjolein H. Willemsen, Heather Stickney, Michael C. Kruer, Keri Ramsey, Heather C Mefford, Lynette G. Sadleir, Bobby P. C. Koeleman, Evelyn Sattlegger, Angela E. Lin, Sara A. Lewis, Marcello Scala, Sergio Padilla-Lopez, Luis O. Rohena, Joaquim Sa, Marie Laure Mathieu, Floor E. Jansen, Joy Y. Sebe, David W. Raible, Giorgio Casari, Gemma L. Carvill, Ingrid E. Scheffer, Paul A. Caruso, Robert Huether, Mariasavina Severino, Candace T. Myers, Eva H. Brilstra, Ashwin A. Bhandiwad, Katherine L. Helbig, Somayeh Bakhtiari, Sehribani Ulusoy Oktay, Gaetan Lesca, Vinodh Narayanan, Georgina Hollingsworth, Tyler N. Kruer, Christel Depienne, Valeria Capra, Pasquale Striano, Timothy Feyma, Deepak Gill, Andrea Accogli, Caroline Nava, Carvill, G. L., Helbig, K. L., Myers, C. T., Scala, M., Huether, R., Lewis, S., Kruer, T. N., Guida, B. S., Bakhtiari, S., Sebe, J., Tang, S., Stickney, H., Oktay, S. U., Bhandiwad, A. A., Ramsey, K., Narayanan, V., Feyma, T., Rohena, L. O., Accogli, A., Severino, M., Hollingsworth, G., Gill, D., Depienne, C., Nava, C., Sadleir, L. G., Caruso, P. A., Lin, A. E., Jansen, F. E., Koeleman, B., Brilstra, E., Willemsen, M. H., Kleefstra, T., Sa, J., Mathieu, M. -L., Perrin, L., Lesca, G., Striano, P., Casari, G., Scheffer, I. E., Raible, D., Sattlegger, E., Capra, V., Padilla-Lopez, S., Mefford, H. C., and Kruer, M. C.

Subjects
Adult, Male, de novo, Heterozygote, Adolescent, Encephalopathy, Choreoathetosis, Mutation, Missense, EEF1A2, Haploinsufficiency, Biology, Article, 03 medical and health sciences, Epilepsy, All institutes and research themes of the Radboud University Medical Center, Peptide Elongation Factor 1, Genetics, medicine, Missense mutation, Humans, Child, Genetics (clinical), 030304 developmental biology, Dystonia, 0303 health sciences, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], 030305 genetics & heredity, Genetic Complementation Test, medicine.disease, yeast complementation assay, Protein Structure, Tertiary, dyskinesia, Child, Preschool, epilepsy, Cerebellar atrophy, Epilepsy, Generalized, Female, medicine.symptom, Rare cancers Radboud Institute for Health Sciences [Radboudumc 9]
Abstract

Heterozygous de novo variants in the eukaryotic elongation factor EEF1A2 have previously been described in association with intellectual disability and epilepsy but never functionally validated. Here we report 14 new individuals with heterozygous EEF1A2 variants. We functionally validate multiple variants as protein-damaging using heterologous expression and complementation analysis. Our findings allow us to confirm multiple variants as pathogenic and broaden the phenotypic spectrum to include dystonia/choreoathetosis, and in some cases a degenerative course with cerebral and cerebellar atrophy. Pathogenic variants appear to act via a haploinsufficiency mechanism, disrupting both the protein synthesis and integrated stress response functions of EEF1A2. Our studies provide evidence that EEF1A2 is highly intolerant to variation and that de novo pathogenic variants lead to an epileptic-dyskinetic encephalopathy with both neurodevelopmental and neurodegenerative features. Developmental features may be driven by impaired synaptic protein synthesis during early brain development while progressive symptoms may be linked to an impaired ability to handle cytotoxic stressors.

Published
2020

47. De novo variant in KIF26B is associated with pontocerebellar hypoplasia with infantile spinal muscular atrophy

Author

Chris Balak, Dan W. Nowakowski, Ali Fatemi, Sampath Rangasamy, Catherine A. Brownstein, Pankaj B. Agrawal, Vinodh Narayanan, Keri Ramsey, Ellen Grant, Kyoko Okada, Hsin-Yi Henry Ho, Julie S. Cohen, Sanjay P. Prabhu, Jiahai Shi, Klaus Schmitz-Abe, and Monica H. Wojcik

Subjects
Models, Molecular, 0301 basic medicine, Proband, Nervous system, Microcephaly, Protein Conformation, Gene Expression, Kinesins, Spinal Muscular Atrophies of Childhood, kinesin, Whole Exome Sequencing, Mice, Models, 2.1 Biological and endogenous factors, Missense mutation, microcephaly, Aetiology, Genetics (clinical), Exome sequencing, Pediatric, Arthrogryposis, Genetics, Brain, Magnetic Resonance Imaging, medicine.anatomical_structure, Neurological, Olivopontocerebellar Atrophies, Kinesin, medicine.symptom, Clinical Sciences, Pontocerebellar hypoplasia, Biology, Article, arthrogryposis, 03 medical and health sciences, Rare Diseases, Clinical Research, Exome Sequencing, Cell Adhesion, medicine, Animals, Humans, Amino Acid Sequence, Animal, pontocerebellar hypoplasia, KIF26B, Neurosciences, Molecular, medicine.disease, Brain Disorders, Disease Models, Animal, 030104 developmental biology, Disease Models
Abstract

KIF26B is a member of the kinesin superfamily with evolutionarily conserved functions in controlling aspects of embryogenesis, including the development of the nervous system, though its function is incompletely understood. We describe an infant with progressive microcephaly, pontocerebellar hypoplasia, and arthrogryposis secondary to the involvement of anterior horn cells and ventral (motor) nerves. We performed whole exome sequencing on the trio and identified a de novo KIF26B missense variant, p.Gly546Ser, in the proband. This variant alters a highly conserved amino acid residue that is part of the phosphate-binding loop motif and motor-like domain and is deemed pathogenic by several in silico methods. Functional analysis of the variant protein in cultured cells revealed a reduction in the KIF26B protein's ability to promote cell adhesion, a defect that potentially contributes to its pathogenicity. Overall, KIF26B may play a critical role in the brain development and, when mutated, cause pontocerebellar hypoplasia with arthrogryposis.

Published
2018
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48. Two additional males with X‐linked, syndromic mental retardation carry de novo mutations in HNRNPH2

Author

Chris Balak, Szabolcs Szelinger, Marcus Naymik, Vinodh Narayanan, Meredith Sanchez-Castillo, Ignazio S. Piras, Lorida Llaci, Matthew J. Huentelman, Sampathkumar Rangasamy, Cherae Bilagody, Newell Belnap, Matthew De Both, Keri Ramsey, Wayne M. Jepsen, Raj Gupta, and Richa Pandey

Subjects
Genetics, business.industry, Mutation (genetic algorithm), Intellectual disability, MEDLINE, Medicine, business, medicine.disease, Genetics (clinical), De novo mutations
Published
2019
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49. De Novo Missense Mutations in DHX30 Impair Global Translation and Cause a Neurodevelopmental Disorder

Author

Naomi Meeks, Stefan Kindler, Anya Revah-Politi, Alexander P.A. Stegmann, Vinodh Narayanan, Dominique Bonneau, Claudia Schob, Jill A. Rosenfeld, Jennifer E. Posey, Tim M. Strom, LaDonna Immken, Tjitske Kleefstra, Jolanda H. Schieving, Katherine L. Helbig, Estelle Colin, Magalie Barth, Tamar Harel, Matthew J. Huentelman, James R. Lupski, Benjamin Cogné, Han G. Brunner, Yaping Yang, Sébastien Küry, Jenny Morton, Erica H. Gerkes, Keri Ramsey, Marine Tessarech, Zeynep Coban-Akdemir, Shimon Edvardson, Hans-Jürgen Kreienkamp, Nelly Oundjian, Davor Lessel, Christian Kubisch, Thomas Besnard, Jonas Denecke, Orly Elpeleg, Ana M. Claasen, Kelsey Zegar, Mohammad K. Eldomery, Sandra Mercier, Margot R.F. Reijnders, Stéphane Bézieau, Univ Angers, Okina, MUMC+: DA KG Lab Centraal Lab (9), Klinische Genetica, RS: GROW - R4 - Reproductive and Perinatal Medicine, MUMC+: DA Klinische Genetica (5), Physiopathologie Cardiovasculaire et Mitochondriale (MITOVASC), and Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Central Nervous System, Male, DISRUPTION, INTELLECTUAL DISABILITY, Developmental Disabilities, PROTEIN, DISEASE, 0302 clinical medicine, Neurodevelopmental disorder, Intellectual disability, Missense mutation, Global developmental delay, Amino Acids, Child, Genetics (clinical), Genetics, Adenosine Triphosphatases, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, Translation (biology), Disorders of movement Donders Center for Medical Neuroscience [Radboudumc 3], 3. Good health, FAMILY, Child, Preschool, Female, RNA Helicases, MODULE, Adolescent, Mutation, Missense, RNA GRANULES, Biology, Article, Cell Line, 03 medical and health sciences, Stress granule, Cell Line, Tumor, medicine, Humans, HELICASE, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], STRESS GRANULES, Helicase, RNA, Correction, medicine.disease, GENE, 030104 developmental biology, HEK293 Cells, biology.protein, 030217 neurology & neurosurgery, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract

Contains fulltext : 182457.pdf (Publisher’s version ) (Open Access) DHX30 is a member of the family of DExH-box helicases, which use ATP hydrolysis to unwind RNA secondary structures. Here we identified six different de novo missense mutations in DHX30 in twelve unrelated individuals affected by global developmental delay (GDD), intellectual disability (ID), severe speech impairment and gait abnormalities. While four mutations are recurrent, two are unique with one affecting the codon of one recurrent mutation. All amino acid changes are located within highly conserved helicase motifs and were found to either impair ATPase activity or RNA recognition in different in vitro assays. Moreover, protein variants exhibit an increased propensity to trigger stress granule (SG) formation resulting in global translation inhibition. Thus, our findings highlight the prominent role of translation control in development and function of the central nervous system and also provide molecular insight into how DHX30 dysfunction might cause a neurodevelopmental disorder.

Published
2017
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50. Phenotypic Variability and mTOR Pathway Gene Aberrations in Familial Tuberous Sclerosis

Author

Sampath Rangasamy, Sara Nasser, Winnie S. Liang, Jonathan Adkins, Lori Cuyugan, Shobana Sekar, Daniel Enriquez, and Vinodh Narayanan

Subjects
0301 basic medicine, Genetics, congenital, hereditary, and neonatal diseases and abnormalities, Biology, medicine.disease, Tuberous sclerosis protein, 03 medical and health sciences, Tuberous sclerosis, 030104 developmental biology, 0302 clinical medicine, medicine.anatomical_structure, Pediatrics, Perinatology and Child Health, Cancer research, medicine, Neurology (clinical), TSC1, Allele, TSC2, Gene, Exome, 030217 neurology & neurosurgery, PI3K/AKT/mTOR pathway
Abstract

Tuberous sclerosis complex (TSC) is an autosomal dominant disorder that demonstrates variable severity, such that affected family members may have mild or severe disease. We performed exome and RNA sequencing of blood leukocytes from mild and severe cases across four families to identify mTOR pathway aberrations that may underlie phenotypic variability. In each family, we identified TSC1/TSC2 aberrations along with different mTOR pathway gene alterations, including base substitutions, deletions, and skewed allelic frequencies. Here, we describe the first reported DNA and RNA analysis of TSC families demonstrating mTOR pathway aberrations in mild and severe forms of the disease.

Published
2017
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