1
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Mermet-Meillon F, Mercan S, Bauer-Probst B, Allard C, Bleu M, Calkins K, Knehr J, Altorfer M, Naumann U, Sprouffske K, Barys L, Sesterhenn F, Galli GG. Protein destabilization underlies pathogenic missense mutations in ARID1B. Nat Struct Mol Biol 2024; 31:1018-1022. [PMID: 38347147 DOI: 10.1038/s41594-024-01229-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 01/18/2024] [Indexed: 07/20/2024]
Abstract
ARID1B is a SWI/SNF subunit frequently mutated in human Coffin-Siris syndrome (CSS) and it is necessary for proliferation of ARID1A mutant cancers. While most CSS ARID1B aberrations introduce frameshifts or stop codons, the functional consequence of missense mutations found in ARID1B is unclear. We here perform saturated mutagenesis screens on ARID1B and demonstrate that protein destabilization is the main mechanism associated with pathogenic missense mutations in patients with Coffin-Siris Syndrome.
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Affiliation(s)
| | - Samuele Mercan
- Disease Area Oncology, Novartis Biomedical Research, Basel, Switzerland
| | | | - Cyril Allard
- Disease Area Immunology, Novartis Biomedical Research, Basel, Switzerland
| | - Melusine Bleu
- Disease Area Oncology, Novartis Biomedical Research, Basel, Switzerland
| | - Keith Calkins
- Disease Area Oncology, Novartis Biomedical Research, Basel, Switzerland
| | - Judith Knehr
- Discovery Sciences, Novartis Biomedical Research, Basel, Switzerland
| | - Marc Altorfer
- Discovery Sciences, Novartis Biomedical Research, Basel, Switzerland
| | - Ulrike Naumann
- Discovery Sciences, Novartis Biomedical Research, Basel, Switzerland
| | | | - Louise Barys
- Disease Area Oncology, Novartis Biomedical Research, Basel, Switzerland
| | - Fabian Sesterhenn
- Discovery Sciences, Novartis Biomedical Research, Basel, Switzerland.
| | - Giorgio G Galli
- Disease Area Oncology, Novartis Biomedical Research, Basel, Switzerland.
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2
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Marshall AH, Boyle DJ, Hanson MA, Nagarajan D, Bibi N, Safa A, Johantges AC, Wester JC. Arid1b haploinsufficiency in cortical inhibitory interneurons causes cell-type-dependent changes in cellular and synaptic development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.07.597984. [PMID: 38895260 PMCID: PMC11185764 DOI: 10.1101/2024.06.07.597984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Autism spectrum disorder (ASD) presents with diverse cognitive and behavioral abnormalities beginning during early development. Although the neural circuit mechanisms remain unclear, recent work suggests pathology in cortical inhibitory interneurons (INs) plays a crucial role. However, we lack fundamental information regarding changes in the physiology of synapses to and from INs in ASD. Here, we used transgenic mice to conditionally knockout one copy of the high confidence ASD risk gene Arid1b from the progenitors of parvalbumin-expressing fast-spiking (PV-FS) INs and somatostatin-expressing non-fast-spiking (SST-NFS) INs. In brain slices, we performed paired whole-cell recordings between INs and excitatory projection neurons (PNs) to investigate changes in synaptic physiology. In neonates, we found reduced synaptic input to INs but not PNs, with a concomitant reduction in the frequency of spontaneous network events, which are driven by INs in immature circuits. In mature mice, we found a reduction in the number of PV-FS INs in cortical layers 2/3 and 5. However, changes in PV-FS IN synaptic physiology were cortical layer and PN cell-type dependent. In layer 5, synapses from PV-FS INs to subcortical-projecting PNs were weakened. In contrast, in layer 2/3, synapses to and from PV-FS INs and corticocortical-projecting PNs were strengthened, leading to enhanced feedforward inhibition of input from layer 4. Finally, we found a novel synaptic deficit among SST-NFS INs, in which excitatory synapses from layer 2/3 PNs failed to facilitate. Our data highlight that changes in unitary synaptic dynamics among INs in ASD depend on neuronal cell-type.
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3
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Mourao J, Fabre A, Zamouri I, de Foucaud A, Baud M, Brunelle J, Munnich A, Boddaert N, Cohen D. Short Report: 10-year follow-up of a boy with ARID1B-related disorder. Early intervention, longitudinal dimensional phenotype, brain imaging and outcome. RESEARCH IN DEVELOPMENTAL DISABILITIES 2024; 151:104769. [PMID: 38865789 DOI: 10.1016/j.ridd.2024.104769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 05/21/2024] [Accepted: 05/28/2024] [Indexed: 06/14/2024]
Abstract
ARID1B-related disorders constitute a clinical continuum, from classic Coffin-Siris syndrome to intellectual disability (ID) with or without nonspecific dysmorphic features. Here, we describe an 11-year-old boy with an ARID1B mutation whose phenotype changed from severe developmental delay and ID to a complex neurodevelopmental disorder with multidimensional impairments, including normal intelligence despite heterogeneous IQ scores, severe motor coordination disorder, oral language disorder and attention-deficit/hyperactivity disorder. Phenotypic changes occurred after early intensive remediation and paralleled the normalization of myelination impairments, as evidenced by early brain imaging. WHAT THIS PAPER ADDS?: This report describes a 10-year multidisciplinary follow-up of a child with an ARID1B mutation who received early intensive remediation and whose phenotype changed during development. Clinical improvement paralleled the normalization of myelination impairments. This case supports a dimensional approach for complex neurodevelopmental disorders.
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Affiliation(s)
- Jorge Mourao
- Department of Child and Adolescent Psychiatry, Assistance Publique-Hôpitaux de Paris, Sorbonne University, Paris, France
| | - Aurélie Fabre
- Institut Imagine INSERM U1163 and U1299, Université Paris Cité, Consultation Mobile Régionale de Génétique Fondation Elan Retrouvé, Paris France
| | - Ingrid Zamouri
- Department of Child and Adolescent Psychiatry, Assistance Publique-Hôpitaux de Paris, Sorbonne University, Paris, France; Centre de Référence des Maladies Rares à Expression Psychiatrique, Department of Child and Adolescent Psychiatry, Pitié-Salpêtrière University Hospital, Assistance Publique-Hôpitaux de Paris, Sorbonne University, Paris, France
| | - Astrid de Foucaud
- Department of Child and Adolescent Psychiatry, Assistance Publique-Hôpitaux de Paris, Sorbonne University, Paris, France; Centre de Référence des Maladies Rares à Expression Psychiatrique, Department of Child and Adolescent Psychiatry, Pitié-Salpêtrière University Hospital, Assistance Publique-Hôpitaux de Paris, Sorbonne University, Paris, France
| | - Morgane Baud
- Department of Child and Adolescent Psychiatry, Assistance Publique-Hôpitaux de Paris, Sorbonne University, Paris, France
| | - Julie Brunelle
- Department of Child and Adolescent Psychiatry, Assistance Publique-Hôpitaux de Paris, Sorbonne University, Paris, France
| | - Arnold Munnich
- Institut Imagine, Consultation Mobile Régionale de Génétique Fondation Elan Retrouvé, Paris France
| | - Nathalie Boddaert
- Paediatric Radiology Department, AP-HP, Hôpital Necker Enfants Malades, Université Paris cité, Institut Imagine INSERM U1163 and U1299, F-75015 Paris, France
| | - David Cohen
- Department of Child and Adolescent Psychiatry, Assistance Publique-Hôpitaux de Paris, Sorbonne University, Paris, France; Centre de Référence des Maladies Rares à Expression Psychiatrique, Department of Child and Adolescent Psychiatry, Pitié-Salpêtrière University Hospital, Assistance Publique-Hôpitaux de Paris, Sorbonne University, Paris, France; CNRS UMR 7222, Institute for Intelligent Systems and Robotics, Sorbonne University, Paris, France.
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4
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Martins-Costa C, Wiegers A, Pham VA, Sidhaye J, Doleschall B, Novatchkova M, Lendl T, Piber M, Peer A, Möseneder P, Stuempflen M, Chow SYA, Seidl R, Prayer D, Höftberger R, Kasprian G, Ikeuchi Y, Corsini NS, Knoblich JA. ARID1B controls transcriptional programs of axon projection in an organoid model of the human corpus callosum. Cell Stem Cell 2024; 31:866-885.e14. [PMID: 38718796 DOI: 10.1016/j.stem.2024.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 02/13/2024] [Accepted: 04/17/2024] [Indexed: 06/09/2024]
Abstract
Mutations in ARID1B, a member of the mSWI/SNF complex, cause severe neurodevelopmental phenotypes with elusive mechanisms in humans. The most common structural abnormality in the brain of ARID1B patients is agenesis of the corpus callosum (ACC), characterized by the absence of an interhemispheric white matter tract that connects distant cortical regions. Here, we find that neurons expressing SATB2, a determinant of callosal projection neuron (CPN) identity, show impaired maturation in ARID1B+/- neural organoids. Molecularly, a reduction in chromatin accessibility of genomic regions targeted by TCF-like, NFI-like, and ARID-like transcription factors drives the differential expression of genes required for corpus callosum (CC) development. Through an in vitro model of the CC tract, we demonstrate that this transcriptional dysregulation impairs the formation of long-range axonal projections, causing structural underconnectivity. Our study uncovers new functions of the mSWI/SNF during human corticogenesis, identifying cell-autonomous axonogenesis defects in SATB2+ neurons as a cause of ACC in ARID1B patients.
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Affiliation(s)
- Catarina Martins-Costa
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Andrea Wiegers
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Vincent A Pham
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Jaydeep Sidhaye
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Balint Doleschall
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Maria Novatchkova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Thomas Lendl
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Marielle Piber
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Angela Peer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Paul Möseneder
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Marlene Stuempflen
- Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, 1090 Vienna, Austria
| | - Siu Yu A Chow
- Institute of Industrial Science, The University of Tokyo, 153-8505 Tokyo, Japan; Institute for AI and Beyond, The University of Tokyo, 113-0032 Tokyo, Japan
| | - Rainer Seidl
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Daniela Prayer
- Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, 1090 Vienna, Austria
| | - Romana Höftberger
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, 1090 Vienna, Austria
| | - Gregor Kasprian
- Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, 1090 Vienna, Austria
| | - Yoshiho Ikeuchi
- Institute of Industrial Science, The University of Tokyo, 153-8505 Tokyo, Japan; Institute for AI and Beyond, The University of Tokyo, 113-0032 Tokyo, Japan
| | - Nina S Corsini
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria.
| | - Jürgen A Knoblich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria; Department of Neurology, Medical University of Vienna, 1090 Vienna, Austria.
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5
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Marshall AH, Hanson MA, Boyle DJ, Nagarajan D, Bibi N, Fitzgerald J, Gaitten E, Kokiko-Cochran ON, Gu B, Wester JC. Arid1b haploinsufficiency in pyramidal neurons causes cellular and circuit changes in neocortex but is not sufficient to produce behavioral or seizure phenotypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597344. [PMID: 38895205 PMCID: PMC11185765 DOI: 10.1101/2024.06.04.597344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Arid1b is a high confidence risk gene for autism spectrum disorder that encodes a subunit of a chromatin remodeling complex expressed in neuronal progenitors. Haploinsufficiency causes a broad range of social, behavioral, and intellectual disability phenotypes, including Coffin-Siris syndrome. Recent work using transgenic mouse models suggests pathology is due to deficits in proliferation, survival, and synaptic development of cortical neurons. However, there is conflicting evidence regarding the relative roles of excitatory projection neurons and inhibitory interneurons in generating abnormal cognitive and behavioral phenotypes. Here, we conditionally knocked out either one or both copies of Arid1b from excitatory projection neuron progenitors and systematically investigated the effects on intrinsic membrane properties, synaptic physiology, social behavior, and seizure susceptibility. We found that disrupting Arid1b expression in excitatory neurons alters their membrane properties, including hyperpolarizing action potential threshold; however, these changes depend on neuronal subtype. Using paired whole-cell recordings, we found increased synaptic connectivity rate between projection neurons. Furthermore, we found reduced strength of excitatory synapses to parvalbumin (PV)-expression inhibitory interneurons. These data suggest an increase in the ratio of excitation to inhibition. However, the strength of inhibitory synapses from PV interneurons to excitatory neurons was enhanced, which may rebalance this ratio. Indeed, Arid1b haploinsufficiency in projection neurons was insufficient to cause social deficits and seizure phenotypes observed in a preclinical germline haploinsufficient mouse model. Our data suggest that while excitatory projection neurons likely contribute to autistic phenotypes, pathology in these cells is not the primary cause.
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Kolokotronis K, Suter AA, Ivanovski I, Frey T, Bahr A, Rauch A, Steindl K. DPF2-related Coffin-Siris syndrome type 7 in two generations. Eur J Med Genet 2024; 69:104945. [PMID: 38697389 DOI: 10.1016/j.ejmg.2024.104945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 04/21/2024] [Accepted: 04/29/2024] [Indexed: 05/05/2024]
Abstract
To date 11 patients with Coffin-Siris syndrome type 7 (OMIM 618027) have been described since the first literature report. All reported patients carried de novo variants with presumed dominant negative effect, which localized in the PHD1/PHD2 domains of DPF2. Here we report on the first familial case of Coffin-Siris syndrome type 7. The index patient presented during the 1st year of life with failure to thrive and ectodermal anomalies. The genetic analysis using whole exome sequencing showed a likely pathogenic missense variant in the PHD1 region. The family analysis showed that the mother as well as the older brother of the index patient also carried the detected DPF2 variant in heterozygous state. The mother had a history of school difficulties but no history of failure to thrive and was overall mildly affected. The brother showed developmental delay with autistic features, ectodermal anomalies and overlapping morphologic features but did not have a history of growth failure problems. To our knowledge this is the first report of an inherited likely pathogenic variant in DPF2, underlining the variability of the associated phenotype as well as the importance of considering inherited DPF2 variants during the variant filtering strategy of whole exome data.
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Affiliation(s)
| | | | - Ivan Ivanovski
- Institute of Medical Genetics, University of Zurich, Switzerland
| | - Tanja Frey
- Institute of Medical Genetics, University of Zurich, Switzerland
| | - Angela Bahr
- Institute of Medical Genetics, University of Zurich, Switzerland
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Switzerland; Pediatric Hospital, University of Zurich, Switzerland
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7
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Huang X, Li H, Yang S, Ma M, Lian Y, Wu X, Qi X, Wang X, Rong W, Sheng X. De novo variation in ARID1B gene causes Coffin-Siris syndrome 1 in a Chinese family with excessive early-onset high myopia. BMC Med Genomics 2024; 17:142. [PMID: 38790056 PMCID: PMC11127418 DOI: 10.1186/s12920-024-01904-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Coffin-Siris syndrome (CSS) is a rare autosomal dominant inheritance disorder characterized by distinctive facial features, hypoplasia of the distal phalanx or nail of the fifth and additional digits, developmental or cognitive delay of varying degree, hypotonia, hirsutism/hypertrichosis, sparse scalp hair and varying kind of congenital anomalies. CSS can easily be misdiagnosed as other syndromes or disorders with a similar clinical picture because of their genetic and phenotypic heterogeneity. We describde the genotype-phenotype correlation of one patient from a healthy Chinese family with a novel genotype underlying CSS, who was first diagnosed in the ophthalmology department as early-onset high myopia (eoHM). Comprehensive ophthalmic tests as well as other systemic examinations were performed on participants to confirm the phenotype. The genotype was identified using whole exome sequencing, and further verified the results among other family members by Sanger sequencing. Real-time quantitative PCR (RT-qPCR) technology was used to detect the relative mRNA expression levels of candidate genes between proband and normal family members. The pathogenicity of the identified variant was determined by The American College of Medical Genetics and Genomics (ACMG) guidelines. STRING protein-protein interactions (PPIs) network analysis was used to detect the interaction of candidate gene-related proteins with high myopia gene-related proteins. The patient had excessive eoHM, cone-rod dystrophy, coarse face, excessive hair growth on the face, sparse scalp hair, developmental delay, intellectual disability, moderate hearing loss, dental hypoplasia, patent foramen ovale, chronic non-atrophic gastritis, bilateral renal cysts, cisterna magna, and emotional outbursts with aggression. The genetic assessment revealed that the patient carries a de novo heterozygous frameshift insertion variant in the ARID1B c.3981dup (p.Glu1328ArgfsTer5), which are strongly associated with the typical clinical features of CSS patients. The test results of RT-qPCR showed that mRNA expression of the ARID1B gene in the proband was approximately 30% lower than that of the normal control in the family, suggesting that the variant had an impact on the gene function at the level of mRNA expression. The variant was pathogenic as assessed by ACMG guidelines. Analysis of protein interactions in the STRING online database revealed that the ARID1A protein interacts with the high myopia gene-related proteins FGFR3, ASXL1, ERBB3, and SOX4, whereas the ARID1A protein antagonizes the ARID1B protein. Therefore, in this paper, we are the first to report a de novo heterozygous frameshift insertion variant in the ARID1B gene causing CSS with excessive eoHM. Our study extends the genotypic and phenotypic spectrums for ARID1B-CSS and supplies evidence of significant association of eoHM with variant in ARID1B gene. As CSS has high genetic and phenotypic heterogeneity, our findings highlight the importance of molecular genetic testing and an interdisciplinary clinical diagnostic workup to avoid misdiagnosis as some disorders with similar manifestations of CSS.
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Affiliation(s)
- Xiaoyu Huang
- Ningxia Eye Hospital, People's Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | - Huiping Li
- Ningxia Eye Hospital, People's Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | | | - Meijiao Ma
- Gansu Aier Ophthalmology and Optometry Hospital, Lanzhou, China
| | - Yuanyuan Lian
- Gansu Aier Ophthalmology and Optometry Hospital, Lanzhou, China
| | - Xueli Wu
- Gansu Aier Ophthalmology and Optometry Hospital, Lanzhou, China
| | - Xiaolong Qi
- Ningxia Eye Hospital, People's Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | - Xuhui Wang
- Ningxia Eye Hospital, People's Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | - Weining Rong
- Ningxia Eye Hospital, People's Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China.
| | - Xunlun Sheng
- Gansu Aier Ophthalmology and Optometry Hospital, Lanzhou, China.
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8
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Trajkova S, Kerkhof J, Rossi Sebastiano M, Pavinato L, Ferrero E, Giovenino C, Carli D, Di Gregorio E, Marinoni R, Mandrile G, Palermo F, Carestiato S, Cardaropoli S, Pullano V, Rinninella A, Giorgio E, Pippucci T, Dimartino P, Rzasa J, Rooney K, McConkey H, Petlichkovski A, Pasini B, Sukarova-Angelovska E, Campbell CM, Metcalfe K, Jenkinson S, Banka S, Mussa A, Ferrero GB, Sadikovic B, Brusco A. DNA methylation analysis in patients with neurodevelopmental disorders improves variant interpretation and reveals complexity. HGG ADVANCES 2024; 5:100309. [PMID: 38751117 PMCID: PMC11216013 DOI: 10.1016/j.xhgg.2024.100309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 05/09/2024] [Accepted: 05/07/2024] [Indexed: 06/07/2024] Open
Abstract
Analysis of genomic DNA methylation by generating epigenetic signature profiles (episignatures) is increasingly being implemented in genetic diagnosis. Here we report our experience using episignature analysis to resolve both uncomplicated and complex cases of neurodevelopmental disorders (NDDs). We analyzed 97 NDDs divided into (1) a validation cohort of 59 patients with likely pathogenic/pathogenic variants characterized by a known episignature and (2) a test cohort of 38 patients harboring variants of unknown significance or unidentified variants. The expected episignature was obtained in most cases with likely pathogenic/pathogenic variants (53/59 [90%]), a revealing exception being the overlapping profile of two SMARCB1 pathogenic variants with ARID1A/B:c.6200, confirmed by the overlapping clinical features. In the test cohort, five cases showed the expected episignature, including (1) novel pathogenic variants in ARID1B and BRWD3; (2) a deletion in ATRX causing MRXFH1 X-linked mental retardation; and (3) confirmed the clinical diagnosis of Cornelia de Lange (CdL) syndrome in mutation-negative CdL patients. Episignatures analysis of the in BAF complex components revealed novel functional protein interactions and common episignatures affecting homologous residues in highly conserved paralogous proteins (SMARCA2 M856V and SMARCA4 M866V). Finally, we also found sex-dependent episignatures in X-linked disorders. Implementation of episignature profiling is still in its early days, but with increasing utilization comes increasing awareness of the capacity of this methodology to help resolve the complex challenges of genetic diagnoses.
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Affiliation(s)
- Slavica Trajkova
- Department of Neurosciences Rita Levi-Montalcini, University of Turin, Turin 10126, Italy
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A5W9, Canada
| | - Matteo Rossi Sebastiano
- Molecular Biotechnology Center "Guido Tarone" University of Turin, 10126 Turin, Italy; Department of Molecular Biotechnology and Health Sciences, University of Turin, CASSMedChem, 10126 Turin, Italy
| | - Lisa Pavinato
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy
| | - Enza Ferrero
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy
| | - Chiara Giovenino
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy
| | - Diana Carli
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy
| | - Eleonora Di Gregorio
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126 Turin, Italy
| | - Roberta Marinoni
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126 Turin, Italy
| | - Giorgia Mandrile
- Medical Genetics Unit and Thalassemia Center, San Luigi University Hospital, Orbassano, TO 10049, Italy
| | - Flavia Palermo
- Medical Genetics Unit and Thalassemia Center, San Luigi University Hospital, Orbassano, TO 10049, Italy
| | - Silvia Carestiato
- Department of Neurosciences Rita Levi-Montalcini, University of Turin, Turin 10126, Italy
| | - Simona Cardaropoli
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy
| | - Verdiana Pullano
- Department of Neurosciences Rita Levi-Montalcini, University of Turin, Turin 10126, Italy
| | - Antonina Rinninella
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126 Turin, Italy; Department of Biomedical and Biotechnological Sciences, Medical Genetics, University of Catania, 94124 Catania, Italy
| | - Elisa Giorgio
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy; Neurogenetics Research Center, IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Tommaso Pippucci
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
| | - Paola Dimartino
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
| | - Jessica Rzasa
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A5W9, Canada
| | - Kathleen Rooney
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A5W9, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON N6A3K7, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A5W9, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON N6A3K7, Canada
| | - Aleksandar Petlichkovski
- Department of Immunology and Human Genetics, Faculty of Medicine, University "Sv. Kiril I Metodij", Skopje 1000, Republic of Macedonia
| | - Barbara Pasini
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126 Turin, Italy
| | - Elena Sukarova-Angelovska
- Department of Endocrinology and Genetics, Faculty of Medicine, University "Sv. Kiril I Metodij", Skopje 1000, Republic of Macedonia
| | - Christopher M Campbell
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Kay Metcalfe
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Sarah Jenkinson
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK; Division of Evolution, Infection & Genomics, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9WL, UK
| | - Alessandro Mussa
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy; Pediatric Clinical Genetics Unit, Regina Margherita Childrens' Hospital, 10126 Turin, Italy
| | | | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A5W9, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON N6A3K7, Canada
| | - Alfredo Brusco
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126 Turin, Italy; Department of Neurosciences Rita Levi-Montalcini, University of Turin, Turin 10126, Italy.
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9
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Jahnke‐Majorkovits A, Fauth C, Gander M, Sevecke K. Treatment of psychiatric comorbidities and interaction patterns in Coffin-Siris syndrome: A case report of a 4-year-old girl. Clin Case Rep 2024; 12:e8230. [PMID: 38314187 PMCID: PMC10837036 DOI: 10.1002/ccr3.8230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/03/2023] [Accepted: 11/06/2023] [Indexed: 02/06/2024] Open
Abstract
Coffin-Siris syndrome (CSS) is a rare genetic disorder and often co-occurs with attention-deficit hyperactivity disorder (ADHD) and autism spectrum (ASD). The present case study illustrates possible therapeutic interventions of these common psychiatric comorbidities taking into account the family interaction patterns. This can contribute to improve holistic management and overall level of functionality.
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Affiliation(s)
- Ann‐Christin Jahnke‐Majorkovits
- A.ö. Landeskrankenhaus Hall, Kinder‐ und JugendpsychiatriePsychotherapie und PsychosomatikHall in TirolAustria
- Universitätsklinik für Kinder‐ und JugendpsychiatrieMedizinische Universität InnsbruckInnsbruckAustria
| | - Christine Fauth
- Institut für HumangenetikMed. Univ. InnsbruckInnsbruckAustria
| | - Manuela Gander
- A.ö. Landeskrankenhaus Hall, Kinder‐ und JugendpsychiatriePsychotherapie und PsychosomatikHall in TirolAustria
- Institute of PsychologyUniversity of InnsbruckInnsbruckAustria
| | - Kathrin Sevecke
- A.ö. Landeskrankenhaus Hall, Kinder‐ und JugendpsychiatriePsychotherapie und PsychosomatikHall in TirolAustria
- Universitätsklinik für Kinder‐ und JugendpsychiatrieMedizinische Universität InnsbruckInnsbruckAustria
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10
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Liu H, Zhao Y, Zhao G, Deng Y, Chen YE, Zhang J. SWI/SNF Complex in Vascular Smooth Muscle Cells and Its Implications in Cardiovascular Pathologies. Cells 2024; 13:168. [PMID: 38247859 PMCID: PMC10814623 DOI: 10.3390/cells13020168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
Mature vascular smooth muscle cells (VSMC) exhibit a remarkable degree of plasticity, a characteristic that has intrigued cardiovascular researchers for decades. Recently, it has become increasingly evident that the chromatin remodeler SWItch/Sucrose Non-Fermentable (SWI/SNF) complex plays a pivotal role in orchestrating chromatin conformation, which is critical for gene regulation. In this review, we provide a summary of research related to the involvement of the SWI/SNF complexes in VSMC and cardiovascular diseases (CVD), integrating these discoveries into the current landscape of epigenetic and transcriptional regulation in VSMC. These novel discoveries shed light on our understanding of VSMC biology and pave the way for developing innovative therapeutic strategies in CVD treatment.
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Affiliation(s)
- Hongyu Liu
- Department of Internal Medicine, Cardiovascular Center, University of Michigan Medical Center, 2800 Plymouth Road, Ann Arbor, MI 48109, USA; (H.L.); (Y.Z.)
- Department of Molecular & Integrative Physiology, University of Michigan Medical Center, Ann Arbor, MI 48109, USA
- Department of Vascular Surgery, The Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Yang Zhao
- Department of Internal Medicine, Cardiovascular Center, University of Michigan Medical Center, 2800 Plymouth Road, Ann Arbor, MI 48109, USA; (H.L.); (Y.Z.)
| | - Guizhen Zhao
- Department of Internal Medicine, Cardiovascular Center, University of Michigan Medical Center, 2800 Plymouth Road, Ann Arbor, MI 48109, USA; (H.L.); (Y.Z.)
| | - Yongjie Deng
- Department of Internal Medicine, Cardiovascular Center, University of Michigan Medical Center, 2800 Plymouth Road, Ann Arbor, MI 48109, USA; (H.L.); (Y.Z.)
| | - Y. Eugene Chen
- Department of Internal Medicine, Cardiovascular Center, University of Michigan Medical Center, 2800 Plymouth Road, Ann Arbor, MI 48109, USA; (H.L.); (Y.Z.)
- Department of Cardiac Surgery, University of Michigan Medical Center, Ann Arbor, MI 48109, USA
| | - Jifeng Zhang
- Department of Internal Medicine, Cardiovascular Center, University of Michigan Medical Center, 2800 Plymouth Road, Ann Arbor, MI 48109, USA; (H.L.); (Y.Z.)
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11
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Schmetz A, Lüdecke HJ, Surowy H, Sivalingam S, Bruel AL, Caumes R, Charles P, Chatron N, Chrzanowska K, Codina-Solà M, Colson C, Cuscó I, Denommé-Pichon AS, Edery P, Faivre L, Green A, Heide S, Hsieh TC, Hustinx A, Kleinendorst L, Knopp C, Kraft F, Krawitz PM, Lasa-Aranzasti A, Lesca G, López-González V, Maraval J, Mignot C, Neuhann T, Netzer C, Oehl-Jaschkowitz B, Petit F, Philippe C, Posmyk R, Putoux A, Reis A, Sánchez-Soler MJ, Suh J, Tkemaladze T, Tran Mau Them F, Travessa A, Trujillano L, Valenzuela I, van Haelst MM, Vasileiou G, Vincent-Delorme C, Walther M, Verde P, Bramswig NC, Wieczorek D. Delineation of the adult phenotype of Coffin-Siris syndrome in 35 individuals. Hum Genet 2024; 143:71-84. [PMID: 38117302 DOI: 10.1007/s00439-023-02622-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 11/20/2023] [Indexed: 12/21/2023]
Abstract
Coffin-Siris syndrome (CSS) is a rare multisystemic autosomal dominant disorder. Since 2012, alterations in genes of the SWI/SNF complex were identified as the molecular basis of CSS, studying largely pediatric cohorts. Therefore, there is a lack of information on the phenotype in adulthood, particularly on the clinical outcome in adulthood and associated risks. In an international collaborative effort, data from 35 individuals ≥ 18 years with a molecularly ascertained CSS diagnosis (variants in ARID1B, ARID2, SMARCA4, SMARCB1, SMARCC2, SMARCE1, SOX11, BICRA) using a comprehensive questionnaire was collected. Our results indicate that overweight and obesity are frequent in adults with CSS. Visual impairment, scoliosis, and behavioral anomalies are more prevalent than in published pediatric or mixed cohorts. Cognitive outcomes range from profound intellectual disability (ID) to low normal IQ, with most individuals having moderate ID. The present study describes the first exclusively adult cohort of CSS individuals. We were able to delineate some features of CSS that develop over time and have therefore been underrepresented in previously reported largely pediatric cohorts, and provide recommendations for follow-up.
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Affiliation(s)
- Ariane Schmetz
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Moorenstraße 5, 40225, Düsseldorf, Germany.
| | - Hermann-Josef Lüdecke
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Moorenstraße 5, 40225, Düsseldorf, Germany
| | - Harald Surowy
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Moorenstraße 5, 40225, Düsseldorf, Germany
| | - Sugirtahn Sivalingam
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Moorenstraße 5, 40225, Düsseldorf, Germany
| | - Ange-Line Bruel
- Inserm UMR1231 Team GAD, University of Burgundy and Franche-Comté, 21000, Dijon, France
- Functional Unit of Innovative Diagnosis for Rare Diseases, Dijon Bourgogne University Hospital, 21000, Dijon, France
| | | | - Perrine Charles
- Assistance Publique-Hôpitaux de Paris, Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Nicolas Chatron
- Service de Génétique, Hospices Civils de Lyon, Bron, France
- Institute NeuroMyoGène, Laboratoire Physiopathologie et Génétique du Neurone et du Muscle, CNRS UMR 5261-INSERM U1315, Université de Lyon-Université Claude Bernard Lyon 1, Lyon, France
| | - Krystyna Chrzanowska
- Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Marta Codina-Solà
- Area of Clinical and Molecular Genetics, Vall d'Hebron University Hospital, 08035, Barcelona, Spain
| | - Cindy Colson
- CHU Lille, Clinique de Génétique, 59000, Lille, France
| | - Ivon Cuscó
- Area of Clinical and Molecular Genetics, Vall d'Hebron University Hospital, 08035, Barcelona, Spain
| | - Anne-Sophie Denommé-Pichon
- Inserm UMR1231 Team GAD, University of Burgundy and Franche-Comté, 21000, Dijon, France
- Functional Unit of Innovative Diagnosis for Rare Diseases, Dijon Bourgogne University Hospital, 21000, Dijon, France
| | - Patrick Edery
- Service de Génétique, Hospices Civils de Lyon, Bron, France
- Centre de Recherche en Neurosciences de Lyon, Equipe GENDEV, INSERM U1028, UMR CNRS 5292, Université Claude Bernard Lyon 1, Lyon, France
| | - Laurence Faivre
- Inserm UMR1231 Team GAD, University of Burgundy and Franche-Comté, 21000, Dijon, France
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Fédération Hospitalo-Universitaire TRANSLAD et Institut GIMI, Dijon Bourgogne University Hospital, 21000, Dijon, France
| | - Andrew Green
- Department of Clinical Genetics, Children's Health Ireland at Crumlin, and University College Dublin School of Medicine and Medical Science, Dublin, Ireland
| | - Solveig Heide
- Assistance Publique-Hôpitaux de Paris, Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Tzung-Chien Hsieh
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Alexander Hustinx
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Lotte Kleinendorst
- Department of Clinical Genetics, Amsterdam UMC, Amsterdam, The Netherlands
| | - Cordula Knopp
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University Hospital, 52074, Aachen, Germany
| | - Florian Kraft
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University Hospital, 52074, Aachen, Germany
| | - Peter M Krawitz
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Amaia Lasa-Aranzasti
- Area of Clinical and Molecular Genetics, Vall d'Hebron University Hospital, 08035, Barcelona, Spain
| | - Gaetan Lesca
- Service de Génétique, Hospices Civils de Lyon, Bron, France
- Institute NeuroMyoGène, Laboratoire Physiopathologie et Génétique du Neurone et du Muscle, CNRS UMR 5261-INSERM U1315, Université de Lyon-Université Claude Bernard Lyon 1, Lyon, France
| | - Vanesa López-González
- Sección Genética Médica, Servicio de Pediatría, Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), IMIB-Arrixaca, El Palmar, Murcia, Spain
| | - Julien Maraval
- Inserm UMR1231 Team GAD, University of Burgundy and Franche-Comté, 21000, Dijon, France
- Centre de Référence Déficiences Intellectuelles de Causes Rares, Dijon Bourgogne University Hospital, 21000, Dijon, France
| | - Cyril Mignot
- Assistance Publique-Hôpitaux de Paris, Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | | | - Christian Netzer
- Institute of Human Genetics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Rare Diseases, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | | | | | - Christophe Philippe
- Inserm UMR1231 Team GAD, University of Burgundy and Franche-Comté, 21000, Dijon, France
- Functional Unit of Innovative Diagnosis for Rare Diseases, Dijon Bourgogne University Hospital, 21000, Dijon, France
- Laboratory of Human Genetics, CHR Metz Thionville, Hôpital Mercy, Metz, France
| | - Renata Posmyk
- Department of Clinical Genetics, Medical University in Bialystok, Bialystok, Poland
| | - Audrey Putoux
- Service de Génétique, Hospices Civils de Lyon, Bron, France
- Centre de Recherche en Neurosciences de Lyon, Equipe GENDEV, INSERM U1028, UMR CNRS 5292, Université Claude Bernard Lyon 1, Lyon, France
| | - André Reis
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
- Centre for Rare Diseases Erlangen (ZSEER), 91054, Erlangen, Germany
| | - María José Sánchez-Soler
- Sección Genética Médica, Servicio de Pediatría, Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), IMIB-Arrixaca, El Palmar, Murcia, Spain
| | - Julia Suh
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University Hospital, 52074, Aachen, Germany
- Centre for Rare Diseases Aachen (ZSEA), 52076, Aachen, Germany
| | - Tinatin Tkemaladze
- Department of Molecular and Medical Genetics, Tbilisi State Medical University, Tbilisi, Georgia
| | - Frédéric Tran Mau Them
- Inserm UMR1231 Team GAD, University of Burgundy and Franche-Comté, 21000, Dijon, France
- Functional Unit of Innovative Diagnosis for Rare Diseases, Dijon Bourgogne University Hospital, 21000, Dijon, France
| | - André Travessa
- Medical Genetics Department, Centro Hospitalar Universitário Lisboa Norte, Lisbon, Portugal
| | - Laura Trujillano
- Area of Clinical and Molecular Genetics, Vall d'Hebron University Hospital, 08035, Barcelona, Spain
| | - Irene Valenzuela
- Area of Clinical and Molecular Genetics, Vall d'Hebron University Hospital, 08035, Barcelona, Spain
| | - Mieke M van Haelst
- Department of Clinical Genetics, Amsterdam UMC, Amsterdam, The Netherlands
| | - Georgia Vasileiou
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
- Centre for Rare Diseases Erlangen (ZSEER), 91054, Erlangen, Germany
| | | | - Mona Walther
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Pablo Verde
- Coordination Centre for Clinical Trials, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Nuria C Bramswig
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Moorenstraße 5, 40225, Düsseldorf, Germany
| | - Dagmar Wieczorek
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Moorenstraße 5, 40225, Düsseldorf, Germany
- Center for Rare Diseases, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
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12
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Venger K, Elbracht M, Carlens J, Deutz P, Zeppernick F, Lassay L, Kratz C, Zenker M, Kim J, Stewart DR, Wieland I, Schultz KAP, Schwerk N, Kurth I, Kontny U. Unusual phenotypes in patients with a pathogenic germline variant in DICER1. Fam Cancer 2023; 22:475-480. [PMID: 34331184 PMCID: PMC9743360 DOI: 10.1007/s10689-021-00271-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 07/20/2021] [Indexed: 02/02/2023]
Abstract
Pathogenic germline DICER1 variants are associated with pleuropulmonary blastoma, multinodular goiter, embryonal rhabdomyosarcoma and other tumour types, while mosaic missense DICER1 variants in the RNase IIIb domain are linked to cause GLOW (global developmental delay, lung cysts, overgrowth, and Wilms' tumor) syndrome. Here, we report four families with germline DICER1 pathogenic variants in which one member in each family had a more complex phenotype, including skeletal findings, facial dysmorphism and developmental abnormalities. The developmental features occur with a variable expressivity and incomplete penetrance as also described for the neoplastic and dysplastic lesions associated with DICER1 variants. Whole exome sequencing (WES) was performed on all four cases and revealed no further pathogenic or likely pathogenic dominant, homozygous or compound heterozygous variants in three of them. Notably, a frameshift variant in ARID1B was detected in one patient explaining part of her phenotype. This series of patients shows that pathogenic DICER1 variants may be associated with a broader phenotypic spectrum than initially assumed, including predisposition to different tumours, skeletal findings, dysmorphism and developmental abnormalities, but genetic work up in syndromic patients should be comprehensive in order not to miss additional underlying /modifying causes.
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Affiliation(s)
- Kateryna Venger
- Division of Pediatric Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Miriam Elbracht
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Julia Carlens
- Clinic for Pediatric Pulmonology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Peter Deutz
- Division of Pediatric Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Felix Zeppernick
- Department of Gynecology and Obstetrics, Medical Faculty, RWTH Aachen University, Aachen, Germany
- Department of Obstetrics and Gynecology, University Hospital Giessen, Giessen, Germany
| | - Lisa Lassay
- Division of Pediatric Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Christian Kratz
- Clinic for Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Martin Zenker
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
| | - Jung Kim
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, USA
| | - Douglas R Stewart
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, USA
| | - Ilse Wieland
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
| | - Kris Ann P Schultz
- International PPB/DICER1 Registry, Minneapolis, MN, USA
- Cancer and Blood Disorders, Children's Minnesota, Minneapolis, MN, USA
| | - Nicolaus Schwerk
- Clinic for Pediatric Pulmonology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Ingo Kurth
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Udo Kontny
- Division of Pediatric Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, Medical Faculty, RWTH Aachen University, Aachen, Germany.
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13
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Uctepe E, Erguner B, Sonmez FM. Recurrence of ARID1B -related Coffin-Siris Syndrome by possible gonadal mosaicism. Clin Dysmorphol 2023; 32:180-183. [PMID: 37646735 DOI: 10.1097/mcd.0000000000000473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Affiliation(s)
- Eyyup Uctepe
- Acibadem Ankara Tissue Typing Laboratory, Ankara
| | - Bekir Erguner
- Department of Molecular Biology, Genetics and Bioengineering, Sabanci University, Tuzla, Istanbul
| | - Fatma Mujgan Sonmez
- Department of Child Neurology, Karadeniz Technical University Faculty of Medicine, Retired Lecturer, Trabzon, Turkey
- Private office, Child Neurology, Trabzon, Turkey
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14
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Wu C, Maegawa GHB, Zhang H. Integrating whole-genome sequencing and transcriptomic findings in the diagnosis and management of Coffin-Siris syndrome. Brain Dev 2023; 45:495-504. [PMID: 37302973 DOI: 10.1016/j.braindev.2023.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 05/15/2023] [Accepted: 05/28/2023] [Indexed: 06/13/2023]
Abstract
INTRODUCTION Although the whole-exome sequencing (WES) approach has been widely used in clinic, many rare diseases with syndromic and nonsyndromic neurological manifestations remain undiagnosed. Coffin-Siris syndrome (CSS) is a rare autosomal dominant genetic disease characterized by neurodevelopmental delay. A suspected diagnosis can be made based on the typical CSS clinical features; however, molecular genetic testing is necessary for a confirmed diagnosis. OBJECTIVES Three CSS-like patients with negative results in the WES and chromosomal microarray analysis (CMA) were recruited in this study. METHODS We used whole-genome sequencing (WGS) technology to sequence the peripheral blood of the three families. To further explore the possible pathogenesis of CSS, we performed RNA-sequencing (RNA-seq). RESULTS WGS identified the three CSS patients were carrying de novo copy number variants of the ARID1B gene, which have not been reported before. RNA-seq identified 184 differentially expressed genes (DEGs), with 116 up-regulated and 68 down-regulated. Functional annotation of DEGs showed that two biological processes (immune response, chemokine activity) and two signaling pathways (cytokine-cytokine receptor interaction, chemokine activity) were highlighted. We speculated that ARID1B deficiency might trigger abnormal immune responses, which may be involved in the pathophysiologic mechanisms of CSS. CONCLUSION Our research provided further support for WGS application in CSS diagnosis and made an investigational approach for the underlying mechanisms of CSS.
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Affiliation(s)
- Chenchen Wu
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Gustavo H B Maegawa
- Department of Pediatrics Columbia, University Irving Medical Center, New York-Presbyterian Morgan Stanley Children's Hospital, 622 West 168th Street, PH 17W/PH 11W, New York, NY 10032, United States
| | - Huiwen Zhang
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China.
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15
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Forwood C, Ashton K, Zhu Y, Zhang F, Dias K, Standen K, Evans C, Carey L, Cardamone M, Shalhoub C, Katf H, Riveros C, Hsieh T, Krawitz P, Robinson PN, Dudding‐Byth T, Sadikovic B, Pinner J, Buckley MF, Roscioli T. Integration of EpiSign, facial phenotyping, and likelihood ratio interpretation of clinical abnormalities in the re-classification of an ARID1B missense variant. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2023; 193:e32056. [PMID: 37654076 PMCID: PMC10952833 DOI: 10.1002/ajmg.c.32056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 09/02/2023]
Abstract
Heterozygous ARID1B variants result in Coffin-Siris syndrome. Features may include hypoplastic nails, slow growth, characteristic facial features, hypotonia, hypertrichosis, and sparse scalp hair. Most reported cases are due to ARID1B loss of function variants. We report a boy with developmental delay, feeding difficulties, aspiration, recurrent respiratory infections, slow growth, and hypotonia without a clinical diagnosis, where a previously unreported ARID1B missense variant was classified as a variant of uncertain significance. The pathogenicity of this variant was refined through combined methodologies including genome-wide methylation signature analysis (EpiSign), Machine Learning (ML) facial phenotyping, and LIRICAL. Trio exome sequencing and EpiSign were performed. ML facial phenotyping compared facial images using FaceMatch and GestaltMatcher to syndrome-specific libraries to prioritize the trio exome bioinformatic pipeline gene list output. Phenotype-driven variant prioritization was performed with LIRICAL. A de novo heterozygous missense variant, ARID1B p.(Tyr1268His), was reported as a variant of uncertain significance. The ACMG classification was refined to likely pathogenic by a supportive methylation signature, ML facial phenotyping, and prioritization through LIRICAL. The ARID1B genotype-phenotype has been expanded through an extended analysis of missense variation through genome-wide methylation signatures, ML facial phenotyping, and likelihood-ratio gene prioritization.
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Affiliation(s)
- Caitlin Forwood
- NSW Health Pathology Randwick GenomicsPrince of Wales HospitalSydneyAustralia
- Centre for Clinical GeneticsSydney Children's HospitalRandwickAustralia
- Neuroscience Research Australia (NeuRA)University of New South WalesSydneyAustralia
| | - Katie Ashton
- NSW Health Pathology Randwick GenomicsPrince of Wales HospitalSydneyAustralia
| | - Ying Zhu
- NSW Health Pathology Randwick GenomicsPrince of Wales HospitalSydneyAustralia
| | - Futao Zhang
- NSW Health Pathology Randwick GenomicsPrince of Wales HospitalSydneyAustralia
| | - Kerith‐Rae Dias
- Neuroscience Research Australia (NeuRA)University of New South WalesSydneyAustralia
| | - Krystle Standen
- NSW Health Pathology Randwick GenomicsPrince of Wales HospitalSydneyAustralia
| | - Carey‐Anne Evans
- Neuroscience Research Australia (NeuRA)University of New South WalesSydneyAustralia
| | - Louise Carey
- NSW Health Pathology Randwick GenomicsPrince of Wales HospitalSydneyAustralia
| | - Michael Cardamone
- Sydney Children's HospitalRandwickAustralia
- School of Women's and Children's HealthUNSWSydneyAustralia
| | - Carolyn Shalhoub
- Centre for Clinical GeneticsSydney Children's HospitalRandwickAustralia
| | - Hala Katf
- Sydney Children's HospitalRandwickAustralia
| | - Carlos Riveros
- Bioinformatics, Hunter Medical Research InstituteNewcastleAustralia
| | - Tzung‐Chien Hsieh
- Institute for Genomic Statistics and BioinformaticsUniversity Hospital BonnBonnGermany
| | - Peter Krawitz
- Institute for Genomic Statistics and BioinformaticsUniversity Hospital BonnBonnGermany
| | - Peter N Robinson
- JAX Center for Precision GeneticsThe JAX Cancer CenterFarmingtonConnecticutUSA
| | | | - Bekim Sadikovic
- London Health Sciences Centre, Verspeeten Clinical Genome CentreWestern UniversityLondonCanada
| | - Jason Pinner
- Centre for Clinical GeneticsSydney Children's HospitalRandwickAustralia
- School of Women's and Children's HealthUNSWSydneyAustralia
| | - Michael F. Buckley
- NSW Health Pathology Randwick GenomicsPrince of Wales HospitalSydneyAustralia
| | - Tony Roscioli
- NSW Health Pathology Randwick GenomicsPrince of Wales HospitalSydneyAustralia
- Neuroscience Research Australia (NeuRA)University of New South WalesSydneyAustralia
- School of Clinical MedicineUNSWSydneyAustralia
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16
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Rojananuangnit K, Rojnueangnit K. Microspherophakic Angle Closure Glaucoma in a Patient with Coffin-Siris Syndrome: Case Report. Appl Clin Genet 2023; 16:165-170. [PMID: 37663124 PMCID: PMC10474847 DOI: 10.2147/tacg.s422312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 08/24/2023] [Indexed: 09/05/2023] Open
Abstract
Background Bilateral secondary angle closure glaucoma is a presenting symptom of microspherophakia and ectopia lentis. Characterizing the associated syndrome and confirmation by genetic testing can identify associated systemic abnormalities and provide appropriate genetic counseling. Case Presentation A 42-year-old woman with severe intellectual disability presented with light perception visual acuity and glaucoma, with intraocular pressure (IOP) in her right and left eyes of 69 and 70 mmHg, respectively. She underwent two sessions of 270-degree laser diode transscleral cytophotocoagulation treatment at a 6-month interval and was prescribed topical anti-glaucoma medication. Her family noticed a progressive decrease in her vision while on treatment for 2 years. She was diagnosed with apparent Weill-Marchesani syndrome, accompanied by angle closure glaucoma and microspherophakia. Cataract surgery and intraocular lens implantation were successful in both eyes and post-operative IOP was controlled with anti-glaucoma medication but her vision did not improve from severe glaucomatous optic neuropathy. Her underlying syndrome was investigated genetically by whole exome sequencing. Results Sequencing showed a pathogenic variant in ARID1B, c.3955dupC (p.Gln1319Profs*14), diagnostic of Coffin-Siris syndrome. This is the first report of Coffin-Siris syndrome associated with microspherophakia and angle closure glaucoma. Conclusion Bilateral angle closure glaucoma from ectopia lentis in patients with genetic syndromes could be an indicator of microspherophakia in adulthood. Ophthalmological surveillance is important in patients with Coffin-Siris syndrome.
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Affiliation(s)
- Kulawan Rojananuangnit
- Glaucoma Unit, Department of Ophthalmology, Mettapracharak (Wat Rai Khing) Hospital, Nakhon Pathom, Thailand
| | - Kitiwan Rojnueangnit
- Division of Genetics, Department of Pediatrics, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
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17
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Milutinovic L, Grujicic R, Mandic Maravic V, Joksic I, Ljubomirovic N, Pejovic Milovancevic M. Autism spectrum disorder and Coffin-Siris syndrome-Case report. Front Psychiatry 2023; 14:1199710. [PMID: 37692302 PMCID: PMC10483805 DOI: 10.3389/fpsyt.2023.1199710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/28/2023] [Indexed: 09/12/2023] Open
Abstract
Introduction Autism spectrum disorders (ASDs) are a group of developmental disorders characterized by deficits in social communicative skills and the occurrence of repetitive and/or stereotyped behaviors. Coffin-Siris syndrome (CSS) is classically characterized by aplasia or hypoplasia of the distal phalanx or nail of the fifth and additional digits, developmental or cognitive delay of varying degrees, distinctive facial features, hypotonia, hirsutism/hypertrichosis, and sparse scalp hair. In this study, we present a detailed description of autistic traits in a boy diagnosed with CSS and further discuss their genetic backgrounds. Case description An 8-year-old boy with ASD, congenital anomalies, and neurological problems had been diagnosed with Coffin-Siris syndrome after genetic testing. Genetic testing revealed a heterozygous de novo pathogenic variant (class 5) c.1638_1647del in the ARID1B gene that is causative of Coffin-Siris syndrome but also other intellectual disability (ID)-related disorders, including autism. Tests that preceded the diagnoses, as well as congenital anomalies and developmental issues, were further described in an attempt to better present his phenotype. Conclusion Both autism and ARID1B-related disorders are on a spectrum. This report points out the importance and necessity of further research regarding the genetic backgrounds of these disorders to understand their complex etiology.
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Affiliation(s)
- Luka Milutinovic
- Clinical Department for Children and Adolescents, Institute of Mental Health, Belgrade, Serbia
| | - Roberto Grujicic
- Clinical Department for Children and Adolescents, Institute of Mental Health, Belgrade, Serbia
| | - Vanja Mandic Maravic
- Day Hospital for Psychotic Disorders, Institute of Mental Health, Belgrade, Serbia
| | - Ivana Joksic
- Clinic for Gynecology and Obstetrics “Narodni Front”, Belgrade, Serbia
| | - Natasa Ljubomirovic
- Clinical Department for Children and Adolescents, Institute of Mental Health, Belgrade, Serbia
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18
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MacPherson RA, Shankar V, Anholt RRH, Mackay TFC. Genetic and genomic analyses of Drosophila melanogaster models of chromatin modification disorders. Genetics 2023; 224:iyad061. [PMID: 37036413 PMCID: PMC10411607 DOI: 10.1093/genetics/iyad061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 11/10/2022] [Accepted: 03/30/2023] [Indexed: 04/11/2023] Open
Abstract
Switch/sucrose nonfermentable (SWI/SNF)-related intellectual disability disorders (SSRIDDs) and Cornelia de Lange syndrome are rare syndromic neurodevelopmental disorders with overlapping clinical phenotypes. SSRIDDs are associated with the BAF (Brahma-Related Gene-1 associated factor) complex, whereas CdLS is a disorder of chromatin modification associated with the cohesin complex. Here, we used RNA interference in Drosophila melanogaster to reduce the expression of six genes (brm, osa, Snr1, SMC1, SMC3, vtd) orthologous to human genes associated with SSRIDDs and CdLS. These fly models exhibit changes in sleep, activity, startle behavior (a proxy for sensorimotor integration), and brain morphology. Whole genome RNA sequencing identified 9,657 differentially expressed genes (FDR < 0.05), 156 of which are differentially expressed in both sexes in SSRIDD- and CdLS-specific analyses, including Bap60, which is orthologous to SMARCD1, an SSRIDD-associated BAF component. k-means clustering reveals genes co-regulated within and across SSRIDD and CdLS fly models. RNAi-mediated reduction of expression of six genes co-regulated with focal genes brm, osa, and/or Snr1 recapitulated changes in the behavior of the focal genes. Based on the assumption that fundamental biological processes are evolutionarily conserved, Drosophila models can be used to understand underlying molecular effects of variants in chromatin-modification pathways and may aid in the discovery of drugs that ameliorate deleterious phenotypic effects.
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Affiliation(s)
- Rebecca A MacPherson
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Vijay Shankar
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Robert R H Anholt
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Trudy F C Mackay
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
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19
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Valencia AM, Sankar A, van der Sluijs PJ, Satterstrom FK, Fu J, Talkowski ME, Vergano SAS, Santen GWE, Kadoch C. Landscape of mSWI/SNF chromatin remodeling complex perturbations in neurodevelopmental disorders. Nat Genet 2023; 55:1400-1412. [PMID: 37500730 PMCID: PMC10412456 DOI: 10.1038/s41588-023-01451-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 06/20/2023] [Indexed: 07/29/2023]
Abstract
DNA sequencing-based studies of neurodevelopmental disorders (NDDs) have identified a wide range of genetic determinants. However, a comprehensive analysis of these data, in aggregate, has not to date been performed. Here, we find that genes encoding the mammalian SWI/SNF (mSWI/SNF or BAF) family of ATP-dependent chromatin remodeling protein complexes harbor the greatest number of de novo missense and protein-truncating variants among nuclear protein complexes. Non-truncating NDD-associated protein variants predominantly disrupt the cBAF subcomplex and cluster in four key structural regions associated with high disease severity, including mSWI/SNF-nucleosome interfaces, the ATPase-core ARID-armadillo repeat (ARM) module insertion site, the Arp module and DNA-binding domains. Although over 70% of the residues perturbed in NDDs overlap with those mutated in cancer, ~60% of amino acid changes are NDD-specific. These findings provide a foundation to functionally group variants and link complex aberrancies to phenotypic severity, serving as a resource for the chromatin, clinical genetics and neurodevelopment communities.
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Affiliation(s)
- Alfredo M Valencia
- Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Chemical Biology Program, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Akshay Sankar
- Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - F Kyle Satterstrom
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital, Boston, MA, USA
| | - Jack Fu
- Massachusetts General Hospital, Boston, MA, USA
| | - Michael E Talkowski
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital, Boston, MA, USA
| | - Samantha A Schrier Vergano
- Children's Hospital of the King's Daughters, Norfolk, Virginia, USA
- Department of Pediatrics, Eastern Virginia Medical School, Norfolk, Virginia, USA
| | - Gijs W E Santen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Cigall Kadoch
- Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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20
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Doldur-Balli F, Zimmerman AJ, Keenan BT, Shetty ZY, Grant SF, Seiler C, Veatch OJ, Pack AI. Pleiotropic effects of a high confidence Autism Spectrum Disorder gene, arid1b, on zebrafish sleep. Neurobiol Sleep Circadian Rhythms 2023; 14:100096. [PMID: 37287661 PMCID: PMC10241967 DOI: 10.1016/j.nbscr.2023.100096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/25/2023] [Accepted: 04/29/2023] [Indexed: 06/09/2023] Open
Abstract
Sleep fulfills critical functions in neurodevelopment, such as promoting synaptic plasticity, neuronal wiring, and brain connectivity which are critical phenomena in Autism Spectrum Disorder (ASD) pathophysiology. Sleep disturbance, specifically insomnia, accompanies ASD and is associated with more severe core symptoms (e.g., social impairment). It is possible that focusing on identifying effective ways to treat sleep problems can help alleviate other ASD-related symptoms. A body of evidence indicates shared mechanisms and neurobiological substrates between sleep and ASD and investigation of these may inform therapeutic effects of improving sleep at both behavioral and molecular levels. In this study, we tested if sleep and social behavior were different in a zebrafish model with the arid1b gene mutated compared to controls. This gene was selected for study as expert curations conducted for the Simons Foundation for Autism Research Institute (SFARI) Gene database define it is as a 'high confidence' ASD gene (i.e., clearly implicated) encoding a chromatin remodeling protein. Homozygous arid1b mutants displayed increased arousability and light sleep compared to their heterozygous and wild type counterparts, based on testing a mechano-acoustic stimulus presenting different vibration frequencies of increasing intensity to detect sleep depth. In addition, decreased social preference was observed in arid1b heterozygous and homozygous mutant zebrafish. The behavioral phenotypes reported in our study are in line with findings from mouse models and human studies and demonstrate the utility of zebrafish as a vertebrate model system with high throughput phenotyping in the investigation of changes in sleep in models relevant to ASD. Furthermore, we demonstrate the importance of including assessments of arousal threshold when studying sleep using in vivo models.
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Affiliation(s)
- Fusun Doldur-Balli
- Division of Sleep Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Amber J. Zimmerman
- Division of Sleep Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Brendan T. Keenan
- Division of Sleep Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Zoe Y. Shetty
- Division of Sleep Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Struan F.A. Grant
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pediatrics, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Divisions of Human Genetics and Endocrinology & Diabetes, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Christoph Seiler
- Aquatics Core Facility, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Olivia J. Veatch
- Department of Psychiatry and Behavioral Sciences, University of Kansas Medical Center, Kansas City, KS, USA
| | - Allan I. Pack
- Division of Sleep Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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21
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Henriquez-Lopez CJ, McLean S. Hashitoxicosis in a patient with Nicolaides-Baraitser Syndrome: a case report. Clin Dysmorphol 2023; 32:77-79. [PMID: 36779796 DOI: 10.1097/mcd.0000000000000446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Affiliation(s)
- Claudia Jessy Henriquez-Lopez
- Department of Pediatrics, Children's Hospital of San Antonio
- Department of Pediatrics, Baylor College of Medicine, San Antonio, Texas, USA
| | - Scott McLean
- Department of Pediatrics, Children's Hospital of San Antonio
- Department of Pediatrics, Baylor College of Medicine, San Antonio, Texas, USA
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22
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MacPherson RA, Shankar V, Anholt RRH, Mackay TFC. Genetic and Genomic Analyses of Drosophila melanogaster Models of Chromatin Modification Disorders. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.30.534923. [PMID: 37034595 PMCID: PMC10081333 DOI: 10.1101/2023.03.30.534923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
Switch/Sucrose Non-Fermentable (SWI/SNF)-related intellectual disability disorders (SSRIDDs) and Cornelia de Lange syndrome are rare syndromic neurodevelopmental disorders with overlapping clinical phenotypes. SSRIDDs are associated with the BAF (Brahma-Related Gene-1 Associated Factor) complex, whereas CdLS is a disorder of chromatin modification associated with the cohesin complex. Here, we used RNA interference in Drosophila melanogaster to reduce expression of six genes (brm, osa, Snr1, SMC1, SMC3, vtd) orthologous to human genes associated with SSRIDDs and CdLS. These fly models exhibit changes in sleep, activity, startle behavior (a proxy for sensorimotor integration) and brain morphology. Whole genome RNA sequencing identified 9,657 differentially expressed genes (FDR < 0.05), 156 of which are differentially expressed in both sexes in SSRIDD- and CdLS-specific analyses, including Bap60, which is orthologous to SMARCD1, a SSRIDD-associated BAF component, k-means clustering reveals genes co-regulated within and across SSRIDD and CdLS fly models. RNAi-mediated reduction of expression of six genes co-regulated with focal genes brm, osa, and/or Snr1 recapitulated changes in behavior of the focal genes. Based on the assumption that fundamental biological processes are evolutionarily conserved, Drosophila models can be used to understand underlying molecular effects of variants in chromatin-modification pathways and may aid in discovery of drugs that ameliorate deleterious phenotypic effects.
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Affiliation(s)
- Rebecca A. MacPherson
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Vijay Shankar
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Robert R. H. Anholt
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Trudy F. C. Mackay
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
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23
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Rimoldi M, Rinaldi B, Villa R, Cerasani J, Beltrami B, Iascone M, Silipigni R, Boito S, Gangi S, Colombo L, Porro M, Cesaretti C, Bedeschi MF. Congenital diaphragmatic hernia in Coffin Siris syndrome: Further evidence from two cases. Am J Med Genet A 2023; 191:605-611. [PMID: 36416235 DOI: 10.1002/ajmg.a.63054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/08/2022] [Accepted: 11/08/2022] [Indexed: 11/24/2022]
Abstract
Coffin-Siris Syndrome (CSS) is a rare multi-system dominant condition with a variable clinical presentation mainly characterized by hypoplasia/aplasia of the nail and/or distal phalanx of the fifth digit, coarse facies, hirsutism/hypertrichosis, developmental delay and intellectual disability of variable degree and growth impairment. Congenital anomalies may include cardiac, genitourinary and central nervous system malformations whereas congenital diaphragmatic hernia (CDH) is rarely reported. The genes usually involved in CSS pathogenesis are ARID1B (most frequently), SMARCA4, SMARCB1, ARID1A, SMARCE1, DPF2, and PHF6. Here, we present two cases of CSS presenting with CDH, for whom Whole Exome Sequencing (WES) identified two distinct de novo heterozygous causative variants, one in ARID1B (case 1) and one in SMARCA4 (case 2). Due to the rarity of CDH in CSS, in both cases the occurrence of CDH did not represent a predictive sign of CSS but, on the other hand, prompted genetic testing before (case 1) or independently (case 2) from the clinical hypothesis of CSS. We provide further evidence of the association between CSS and CDH, reviewed previous cases from literature and discuss possible functional links to related conditions.
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Affiliation(s)
- Martina Rimoldi
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Medical Genetics Unit, Milan, Italy
| | - Berardo Rinaldi
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Medical Genetics Unit, Milan, Italy
| | - Roberta Villa
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Medical Genetics Unit, Milan, Italy
| | - Jacopo Cerasani
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neonatal Intensive Care Unit (NICU), Department of Clinical Science and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Benedetta Beltrami
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Medical Genetics Unit, Milan, Italy
| | - Maria Iascone
- Ospedale Papa Giovanni XXIII, Laboratory of Medical Genetics, Bergamo, Italy
| | - Rosamaria Silipigni
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Laboratory of Medical Genetics, Milan, Italy
| | - Simona Boito
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Fetal Medicine and Surgery Service, Milan, Italy
| | - Silvana Gangi
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neonatal Intensive Care Unit (NICU), Department of Clinical Science and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Lorenzo Colombo
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neonatal Intensive Care Unit (NICU), Department of Clinical Science and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Matteo Porro
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Pediatric Physical Medicine and Rehabilitation Unit, Milan, Italy
| | - Claudia Cesaretti
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Medical Genetics Unit, Milan, Italy
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24
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Ciliberto M, Skjei K, Vasko A, Schrier Vergano S. Epilepsy in Coffin-Siris syndrome: A report from the international CSS registry and review of the literature. Am J Med Genet A 2023; 191:22-28. [PMID: 36177969 DOI: 10.1002/ajmg.a.62979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 09/02/2022] [Accepted: 09/10/2022] [Indexed: 12/14/2022]
Abstract
Coffin-Siris syndrome (CSS, MIM135900) is a rare multiple congenital anomaly syndrome caused by pathogenic variants in the BAF complex; up to 28% of patients have previously been reported to have seizures, however, a comprehensive review of epilepsy has not been undertaken in this population. The International CSS Patient Report Database was queried for patients with self-reported seizures, epilepsy, and EEG results. Data gathered included demographic data, pathogenic gene variants, seizure characteristics and treatments, and EEG findings. In addition, a PubMed search was performed using keywords "Coffin-Siris syndrome" and "epilepsy," "seizures," or "EEG." Results from relevant papers are reported. Twenty-four (7.2%) of 334 patients in the database reported having seizures, EEG abnormalities, and/or epilepsy. Median age of seizure onset was 2. 7 years. Fifteen of the 23 patients with seizures or epilepsy had an ARID1B causative variant. Seventeen patients (5.1%) reported EEG abnormalities, the majority of which were described as focal or multifocal (87.5%). In all but one patient, seizures were controlled on antiseizure medications (ASMs). The literature review yielded 311 unique CSS patients, 82 of which (26.4%) carried diagnoses of seizures or epilepsy. Details on seizure type(s), EEG findings, and response to treatment were limited.
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Affiliation(s)
- Michael Ciliberto
- Stead Family Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - Karen Skjei
- The El Paso Center for Seizures and Epilepsy, El Paso, Texas, USA
| | - Ashley Vasko
- Children's Hospital of the King's Daughters, Norfolk, Virginia, USA
| | - Samantha Schrier Vergano
- Children's Hospital of the King's Daughters, Norfolk, Virginia, USA.,Eastern Virginia Medical School, Norfolk, Virginia, USA
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25
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Gillentine MA, Wang T, Eichler EE. Estimating the Prevalence of De Novo Monogenic Neurodevelopmental Disorders from Large Cohort Studies. Biomedicines 2022; 10:2865. [PMID: 36359385 PMCID: PMC9687899 DOI: 10.3390/biomedicines10112865] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/27/2022] [Accepted: 10/28/2022] [Indexed: 11/26/2023] Open
Abstract
Rare diseases impact up to 400 million individuals globally. Of the thousands of known rare diseases, many are rare neurodevelopmental disorders (RNDDs) impacting children. RNDDs have proven to be difficult to assess epidemiologically for several reasons. The rarity of them makes it difficult to observe them in the population, there is clinical overlap among many disorders, making it difficult to assess the prevalence without genetic testing, and data have yet to be available to have accurate counts of cases. Here, we utilized large sequencing cohorts of individuals with rare, de novo monogenic disorders to estimate the prevalence of variation in over 11,000 genes among cohorts with developmental delay, autism spectrum disorder, and/or epilepsy. We found that the prevalence of many RNDDs is positively correlated to the previously estimated incidence. We identified the most often mutated genes among neurodevelopmental disorders broadly, as well as developmental delay and autism spectrum disorder independently. Finally, we assessed if social media group member numbers may be a valuable way to estimate prevalence. These data are critical for individuals and families impacted by these RNDDs, clinicians and geneticists in their understanding of how common diseases are, and for researchers to potentially prioritize research into particular genes or gene sets.
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Affiliation(s)
| | - Tianyun Wang
- Department of Medical Genetics, Center for Medical Genetics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
- Key Laboratory for Neuroscience, Neuroscience Research Institute, Peking University, Ministry of Education of China & National Health Commission of China, Beijing 100191, China
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98105, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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26
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Bilha SC, Teodoriu L, Velicescu C, Caba L. Pituitary hypoplasia and growth hormone deficiency in a patient with Coffin-Siris syndrome and severe short stature: case report and literature review. Arch Clin Cases 2022; 9:121-125. [PMID: 36176497 PMCID: PMC9512126 DOI: 10.22551/2022.36.0903.10216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Coffin-Siris syndrome (CSS) is a rare genetic disorder caused by the haploinsufficiency of one of the various genes that are part of the Brahma/BRG1-associated factor (BAF) complex. The BAF complex is one of the chromatin remodeling complexes, involved in embryonic and neural development, and various gene mutations are associated with cognitive impairment. CSS has a highly variable genotype and phenotype expression, thus lacking standardized criteria for diagnosis. It is generally accepted to associate 5th digit/nail hypoplasia, intellectual disability (ID)/developmental delay and specific coarse facial features. CSS patients usually display miscellaneous cardiac, genitourinary and central nervous system (CNS) anomalies. Many patients also associate intrauterine growth restriction, failure to thrive and short stature, with several cases demonstrating growth hormone deficiency (GHD). We report the case of a 4-year-old girl with severe short stature (-3.2 standard deviations) due to pituitary hypoplasia and GHD that associated hypoplastic distal phalanx of the 5th digit in the hands and feet, severe ID, coarse facial features (bushy eyebrows, bulbous nose, flat nasal bridge, dental anomalies, thick lips, dental anomalies, bilateral epicanthal fold) and CNS anomalies (agenesis of the corpus callosum and bilateral hippocampal atrophy), thus meeting clinical criteria for the diagnosis of CSS. Karyotype was 46,XX. The patient was started on GH replacement therapy, with favorable outcomes. Current practical knowledge regarding CSS diagnosis and management from the endocrinological point of view is also reviewed.
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Affiliation(s)
- Stefana Catalina Bilha
- Endocrinology Department, Grigore T. Popa University of Medicine and Pharmacy Iasi, Romania
| | - Laura Teodoriu
- Endocrinology Department, Grigore T. Popa University of Medicine and Pharmacy Iasi, Romania
| | - Cristian Velicescu
- Surgery Department, Grigore T. Popa University of Medicine and Pharmacy Iasi, Romania.,
Corresponding author: Cristian Velicescu, Surgery Department, Grigore T. Popa University of Medicine and Pharmacy, 16 Universitatii str. Iasi 700115, Romania.
| | - Lavinia Caba
- Department of Medical Genetics, Grigore T. Popa University of Medicine and Pharmacy Iasi, Romania
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27
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Freitas LF, Ribeiro LS, Duarte ML, Silva MOD, Ferreira PM. Coffin–Siris Syndrome in a Patient with Hirschsprung's Disease—Expanding the Phenotype by Mutation ARID1B: Case Report and Literature Review. JOURNAL OF PEDIATRIC NEUROLOGY 2022. [DOI: 10.1055/s-0042-1756453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
AbstractCoffin–Siris syndrome (CSS) is a rare syndrome with autosomal dominant inheritance, and it is characterized by intellectual disability, hypotonia, aplasia/hypoplasia of the distal phalanx of fifth fingernail, feeding difficulties, growth restriction, short stature, speech delay, hirsutism/hypertrichosis, and thinning hair on the scalp. Hearing impairment has also been described in some patients. In this article, we describe the case of a male patient diagnosed with CSS who, at 15 days of life, underwent surgery for megacolon correction and a later intestinal biopsy revealed the affected segment compatible with Hirschsprung's disease (HSCR). This patient was found to have a variant in ARID1B (p. [Pro934Glnfs*5]) in a component of the BAF complex which plays an important role in regulating the expression and differentiation. In addition, it mediates responses to environmental signals resulting from an ATP-dependent chromatin remodeling complex. This case added a unique clinical characteristics and a rare genetic variant in the repertoire of CSS.
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Affiliation(s)
- Leonardo F. Freitas
- Department of Radiology, Universidade Federal de São Paulo, São Paulo-SP, Brazil
| | - Lays S. Ribeiro
- Department of Radiology, Universidade Federal de São Paulo, São Paulo-SP, Brazil
| | - Márcio L. Duarte
- Department of Evidence-based Health, Universidade Federal de São Paulo, São Paulo-SP, Brazil
| | | | - Paula M. Ferreira
- Department of Pediatric neurology, Clínica FORT, Varginha-MG, Brazil
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Fu JM, Satterstrom FK, Peng M, Brand H, Collins RL, Dong S, Wamsley B, Klei L, Wang L, Hao SP, Stevens CR, Cusick C, Babadi M, Banks E, Collins B, Dodge S, Gabriel SB, Gauthier L, Lee SK, Liang L, Ljungdahl A, Mahjani B, Sloofman L, Smirnov AN, Barbosa M, Betancur C, Brusco A, Chung BHY, Cook EH, Cuccaro ML, Domenici E, Ferrero GB, Gargus JJ, Herman GE, Hertz-Picciotto I, Maciel P, Manoach DS, Passos-Bueno MR, Persico AM, Renieri A, Sutcliffe JS, Tassone F, Trabetti E, Campos G, Cardaropoli S, Carli D, Chan MCY, Fallerini C, Giorgio E, Girardi AC, Hansen-Kiss E, Lee SL, Lintas C, Ludena Y, Nguyen R, Pavinato L, Pericak-Vance M, Pessah IN, Schmidt RJ, Smith M, Costa CIS, Trajkova S, Wang JYT, Yu MHC, Cutler DJ, De Rubeis S, Buxbaum JD, Daly MJ, Devlin B, Roeder K, Sanders SJ, Talkowski ME. Rare coding variation provides insight into the genetic architecture and phenotypic context of autism. Nat Genet 2022; 54:1320-1331. [PMID: 35982160 PMCID: PMC9653013 DOI: 10.1038/s41588-022-01104-0] [Citation(s) in RCA: 166] [Impact Index Per Article: 83.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 05/24/2022] [Indexed: 01/11/2023]
Abstract
Some individuals with autism spectrum disorder (ASD) carry functional mutations rarely observed in the general population. We explored the genes disrupted by these variants from joint analysis of protein-truncating variants (PTVs), missense variants and copy number variants (CNVs) in a cohort of 63,237 individuals. We discovered 72 genes associated with ASD at false discovery rate (FDR) ≤ 0.001 (185 at FDR ≤ 0.05). De novo PTVs, damaging missense variants and CNVs represented 57.5%, 21.1% and 8.44% of association evidence, while CNVs conferred greatest relative risk. Meta-analysis with cohorts ascertained for developmental delay (DD) (n = 91,605) yielded 373 genes associated with ASD/DD at FDR ≤ 0.001 (664 at FDR ≤ 0.05), some of which differed in relative frequency of mutation between ASD and DD cohorts. The DD-associated genes were enriched in transcriptomes of progenitor and immature neuronal cells, whereas genes showing stronger evidence in ASD were more enriched in maturing neurons and overlapped with schizophrenia-associated genes, emphasizing that these neuropsychiatric disorders may share common pathways to risk.
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Affiliation(s)
- Jack M Fu
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - F Kyle Satterstrom
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Minshi Peng
- Department of Statistics and Data Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Harrison Brand
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Pediatric Surgical Research Laboratories, Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Ryan L Collins
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA, USA
| | - Shan Dong
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Brie Wamsley
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Lambertus Klei
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Lily Wang
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA, USA
| | - Stephanie P Hao
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Pediatric Surgical Research Laboratories, Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Christine R Stevens
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Caroline Cusick
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mehrtash Babadi
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eric Banks
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Brett Collins
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sheila Dodge
- Genomics Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stacey B Gabriel
- Genomics Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Laura Gauthier
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Samuel K Lee
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lindsay Liang
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Alicia Ljungdahl
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Behrang Mahjani
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Laura Sloofman
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andrey N Smirnov
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mafalda Barbosa
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Catalina Betancur
- Sorbonne Université, INSERM, CNRS, Neuroscience Paris Seine, Institut de Biologie Paris Seine, Paris, France
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Turin, Italy
- Medical Genetics Unit, 'Città della Salute e della Scienza' University Hospital, Turin, Italy
| | - Brian H Y Chung
- Department of Pediatrics and Adolescent Medicine, Duchess of Kent Children's Hospital, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Edwin H Cook
- Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA
| | - Michael L Cuccaro
- The John P Hussman Institute for Human Genomics, The University of Miami Miller School of Medicine, Miami, FL, USA
| | - Enrico Domenici
- Department of Cellular, Computational and Integrative Biology, , University of Trento, Trento, Italy
| | | | - J Jay Gargus
- Center for Autism Research and Translation, University of California Irvine, Irvine, CA, USA
| | - Gail E Herman
- The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Irva Hertz-Picciotto
- MIND (Medical Investigation of Neurodevelopmental Disorders) Institute, University of California Davis, Davis, CA, USA
| | - Patricia Maciel
- Life and Health Sciences Research Institute, School of Medicine, University of Minho, Braga, Portugal
| | - Dara S Manoach
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Maria Rita Passos-Bueno
- Centro de Pesquisas sobre o Genoma Humano e Células tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Antonio M Persico
- Interdepartmental Program 'Autism 0-90', 'Gaetano Martino' University Hospital, University of Messina, Messina, Italy
| | - Alessandra Renieri
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
- Medical Genetics, , University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - James S Sutcliffe
- Department of Molecular Physiology & Biophysics and Psychiatry, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Flora Tassone
- MIND (Medical Investigation of Neurodevelopmental Disorders) Institute, University of California Davis, Davis, CA, USA
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, Sacramento, CA, USA
| | - Elisabetta Trabetti
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biology and Genetics, University of Verona, Verona, Italy
| | - Gabriele Campos
- Centro de Pesquisas sobre o Genoma Humano e Células tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Simona Cardaropoli
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
| | - Diana Carli
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
| | - Marcus C Y Chan
- Department of Pediatrics and Adolescent Medicine, Duchess of Kent Children's Hospital, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Chiara Fallerini
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
- Medical Genetics, , University of Siena, Siena, Italy
| | - Elisa Giorgio
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - Ana Cristina Girardi
- Centro de Pesquisas sobre o Genoma Humano e Células tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Emily Hansen-Kiss
- Department of Diagnostic and Biomedical Sciences, University of Texas Health Science Center at Houston, School of Dentistry, Houston, TX, USA
| | - So Lun Lee
- Department of Pediatrics and Adolescent Medicine, Duchess of Kent Children's Hospital, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Carla Lintas
- Service for Neurodevelopmental Disorders, University Campus Bio-medico of Rome, Rome, Italy
| | - Yunin Ludena
- MIND (Medical Investigation of Neurodevelopmental Disorders) Institute, University of California Davis, Davis, CA, USA
| | - Rachel Nguyen
- Center for Autism Research and Translation, University of California Irvine, Irvine, CA, USA
| | - Lisa Pavinato
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - Margaret Pericak-Vance
- The John P Hussman Institute for Human Genomics, The University of Miami Miller School of Medicine, Miami, FL, USA
| | - Isaac N Pessah
- MIND (Medical Investigation of Neurodevelopmental Disorders) Institute, University of California Davis, Davis, CA, USA
- Department of Molecular Biosciences, University of California Davis, School of Veterinary Medicine, Davis, CA, USA
| | - Rebecca J Schmidt
- MIND (Medical Investigation of Neurodevelopmental Disorders) Institute, University of California Davis, Davis, CA, USA
| | - Moyra Smith
- Center for Autism Research and Translation, University of California Irvine, Irvine, CA, USA
| | - Claudia I S Costa
- Centro de Pesquisas sobre o Genoma Humano e Células tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Slavica Trajkova
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - Jaqueline Y T Wang
- Centro de Pesquisas sobre o Genoma Humano e Células tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Mullin H C Yu
- Department of Pediatrics and Adolescent Medicine, Duchess of Kent Children's Hospital, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - David J Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Mark J Daly
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Kathryn Roeder
- Department of Statistics and Data Science, Carnegie Mellon University, Pittsburgh, PA, USA.
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA.
| | - Stephan J Sanders
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA.
| | - Michael E Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA, USA.
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Early postnatal serotonin modulation prevents adult-stage deficits in Arid1b-deficient mice through synaptic transcriptional reprogramming. Nat Commun 2022; 13:5051. [PMID: 36030255 PMCID: PMC9420115 DOI: 10.1038/s41467-022-32748-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 08/12/2022] [Indexed: 11/19/2022] Open
Abstract
Autism spectrum disorder is characterized by early postnatal symptoms, although little is known about the mechanistic deviations that produce them and whether correcting them has long-lasting preventive effects on adult-stage deficits. ARID1B, a chromatin remodeler implicated in neurodevelopmental disorders, including autism spectrum disorder, exhibits strong embryonic- and early postnatal-stage expression. We report here that Arid1b-happloinsufficient (Arid1b+/–) mice display autistic-like behaviors at juvenile and adult stages accompanied by persistent decreases in excitatory synaptic density and transmission. Chronic treatment of Arid1b+/– mice with fluoxetine, a selective serotonin-reuptake inhibitor, during the first three postnatal weeks prevents synaptic and behavioral deficits in adults. Mechanistically, these rescues accompany transcriptomic changes, including upregulation of FMRP targets and normalization of HDAC4/MEF2A-related transcriptional regulation of the synaptic proteins, SynGAP1 and Arc. These results suggest that chronic modulation of serotonergic receptors during critical early postnatal periods prevents synaptic and behavioral deficits in adult Arid1b+/– mice through transcriptional reprogramming. ARID1B is a chromatin remodeler associated with autism spectrum disorders. Here the authors demonstrate that early postnatal serotonin modulation prevents adult stage deficits in Arid1b-deficient mice through synaptic transcriptional reprogramming.
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30
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Tao DY, Niu HH, Zhang JJ, Zhang HQ, Zeng MH, Cheng SQ. Short stature and melanocytic nevi in a girl with ARID1B-related Coffin-Siris syndrome: a case report. BMC Pediatr 2022; 22:486. [PMID: 35964110 PMCID: PMC9375425 DOI: 10.1186/s12887-022-03535-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 08/02/2022] [Indexed: 11/12/2022] Open
Abstract
Background Coffin-Siris syndrome (CSS) is a rare autosomal dominant disorder characterized by intellectual disability, developmental delay, and characteristic facial features. Few patients with cutaneous phenotype in this rare syndrome have been reported. Case presentation Herein, we describe a 12-year-old Chinese girl diagnosed with CSS, who was referred to our hospital because of intellectual disability and short stature. Prominent characteristics of the cutaneous system were observed: (1) A congenital giant nevus from the left frontal and temporal regions to the entire left scalp; and (2) multiple melanocytic nevi on the face and trunk. Whole exome sequencing revealed a novel heterozygous variant in the ARID1B gene. Recombinant human growth hormone (rhGH) was given for short stature, and resulted in significantly improved height. No enlargement or malignant transformation of nevi occurred within 4 years of follow-up. Conclusion The symptoms in cutaneous system is noteworthy,which may be a neglected phenotype in CSS.The therapeutic response of growth hormone is effective in this patient and no tumor related signs were found. Supplementary Information The online version contains supplementary material available at 10.1186/s12887-022-03535-4.
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Affiliation(s)
- Dong-Ying Tao
- Department of Pediatrics, Xijing Hospital, Fourth Military Medical University, No. 127 Changle West Road, Xincheng District, Xi'an, 710032, Shaanxi Province, China
| | - Huan-Hong Niu
- Department of Pediatrics, Xijing Hospital, Fourth Military Medical University, No. 127 Changle West Road, Xincheng District, Xi'an, 710032, Shaanxi Province, China
| | - Jing-Jing Zhang
- Department of Pediatrics, Xijing Hospital, Fourth Military Medical University, No. 127 Changle West Road, Xincheng District, Xi'an, 710032, Shaanxi Province, China
| | - Hui-Qin Zhang
- Department of Pediatrics, Xijing Hospital, Fourth Military Medical University, No. 127 Changle West Road, Xincheng District, Xi'an, 710032, Shaanxi Province, China
| | - Ming-Hua Zeng
- Medical Experiment and Training Center, Hanzhong Vocational and Technical College, Hanzhong, 723002, Shaanxi Province, China
| | - Sheng-Quan Cheng
- Department of Pediatrics, Xijing Hospital, Fourth Military Medical University, No. 127 Changle West Road, Xincheng District, Xi'an, 710032, Shaanxi Province, China.
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31
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Sofronova V, Fukushima Y, Masuno M, Naka M, Nagata M, Ishihara Y, Miyashita Y, Asano Y, Moriwaki T, Iwata R, Terawaki S, Yamanouchi Y, Otomo T. A novel nonsense variant in ARID1B causing simultaneous RNA decay and exon skipping is associated with Coffin-Siris syndrome. Hum Genome Var 2022; 9:26. [PMID: 35879281 PMCID: PMC9314373 DOI: 10.1038/s41439-022-00203-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/08/2022] [Accepted: 06/27/2022] [Indexed: 01/12/2023] Open
Abstract
Coffin-Siris syndrome (CSS) is a congenital disorder that is characterized by an absent/hypoplastic fifth distal phalanx, psychomotor developmental delay, and coarse facial features. One of the causative genes, ARID1B (AT-rich interactive domain-containing protein 1B), encodes components of the BAF chromatin remodeling complexes. Here, we report a case of a 3-year 8-month-old male with a novel nonsense variant (NM_001374820.1:c.4282C > T, p.(Gln1428*)) in the ARID1B gene, which was identified with whole-exome sequencing. He showed clinical symptoms of cleft soft palate, distinctive facial features (flat nasal bridge, thick eyebrows, and long eyelashes), right cryptorchidism, and hypertrichosis that partially overlapped with CSS. One of the most characteristic features of CSS is absent/hypoplastic fifth distal phalanx. He showed no obvious clinical finding in the lengths of his fingers or in the formation of his fingernails. However, radiographic analyses of the metacarpophalangeal bones revealed shortening of all the distal phalanges and fifth middle phalanges, suggesting brachydactyly. We performed mRNA analyses and revealed that both nonsense-mediated decay and nonsense-associated altered splicing were simultaneously caused by the c.4282C > T nonsense variant. The proband's clinical manifestations fit the previously reported criteria of disease for CSS or intellectual disability with ARID1B variant. Altogether, we suggest that c.4282C > T is a pathogenic variant that causes this clinical phenotype.
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Affiliation(s)
- Viktoriia Sofronova
- grid.415086.e0000 0001 1014 2000Department of Molecular and Genetic Medicine, Kawasaki Medical School, Kurashiki, Japan ,grid.440700.70000 0004 0556 741XLaboratory of Molecular Medicine and Human Genetics, North-Eastern Federal University, Yakutsk, Russia
| | - Yu Fukushima
- grid.415664.40000 0004 0641 4765Division of Neonatology, National Hospital Organization Okayama Medical Center, Okayama, Japan
| | - Mitsuo Masuno
- grid.415106.70000 0004 0641 4861Department of Medical Genetics, Kawasaki Medical School Hospital, Kurashiki, Japan ,grid.412082.d0000 0004 0371 4682Genetic Counseling Program, Graduate School of Health and Welfare, Kawasaki University of Medical Welfare, Kurashiki, Japan
| | - Mami Naka
- grid.412082.d0000 0004 0371 4682Genetic Counseling Program, Graduate School of Health and Welfare, Kawasaki University of Medical Welfare, Kurashiki, Japan
| | - Miho Nagata
- grid.136593.b0000 0004 0373 3971Department of Cardiovascular Medicine (IRUD Analysis Center), Osaka University Graduate School of Medicine, Suita, Japan
| | - Yasuki Ishihara
- grid.136593.b0000 0004 0373 3971Department of Cardiovascular Medicine (IRUD Analysis Center), Osaka University Graduate School of Medicine, Suita, Japan
| | - Yohei Miyashita
- grid.136593.b0000 0004 0373 3971Department of Cardiovascular Medicine (IRUD Analysis Center), Osaka University Graduate School of Medicine, Suita, Japan
| | - Yoshihiro Asano
- grid.136593.b0000 0004 0373 3971Department of Cardiovascular Medicine (IRUD Analysis Center), Osaka University Graduate School of Medicine, Suita, Japan
| | - Takahito Moriwaki
- grid.415086.e0000 0001 1014 2000Department of Molecular and Genetic Medicine, Kawasaki Medical School, Kurashiki, Japan
| | - Rina Iwata
- grid.415086.e0000 0001 1014 2000Department of Molecular and Genetic Medicine, Kawasaki Medical School, Kurashiki, Japan
| | - Seigo Terawaki
- grid.415086.e0000 0001 1014 2000Department of Molecular and Genetic Medicine, Kawasaki Medical School, Kurashiki, Japan
| | - Yasuko Yamanouchi
- grid.415106.70000 0004 0641 4861Department of Medical Genetics, Kawasaki Medical School Hospital, Kurashiki, Japan ,grid.412082.d0000 0004 0371 4682Genetic Counseling Program, Graduate School of Health and Welfare, Kawasaki University of Medical Welfare, Kurashiki, Japan
| | - Takanobu Otomo
- grid.415086.e0000 0001 1014 2000Department of Molecular and Genetic Medicine, Kawasaki Medical School, Kurashiki, Japan ,grid.415106.70000 0004 0641 4861Department of Medical Genetics, Kawasaki Medical School Hospital, Kurashiki, Japan
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Complex Diagnostics of Non-Specific Intellectual Developmental Disorder. Int J Mol Sci 2022; 23:ijms23147764. [PMID: 35887114 PMCID: PMC9323143 DOI: 10.3390/ijms23147764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/11/2022] [Accepted: 07/12/2022] [Indexed: 11/17/2022] Open
Abstract
Intellectual development disorder (IDD) is characterized by a general deficit in intellectual and adaptive functioning. In recent years, there has been a growing interest in studying the genetic structure of IDD. Of particular difficulty are patients with non-specific IDD, for whom it is impossible to establish a clinical diagnosis without complex genetic diagnostics. We examined 198 patients with non-specific IDD from 171 families using whole-exome sequencing and chromosome microarray analysis. Hereditary forms of IDD account for at least 35.7% of non-specific IDD, of which 26.9% are monogenic forms. Variants in the genes associated with the BAF (SWI/SNF) complex were the most frequently identified. We were unable to identify phenotypic features that would allow differential diagnosis of monogenic and microstructural chromosomal rearrangements in non-specific IDD at the stage of clinical examination, but due to its higher efficiency, exome sequencing should be the diagnostic method of the highest priority study after the standard examination of patients with NIDD in Russia.
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Al-Jawahiri R, Foroutan A, Kerkhof J, McConkey H, Levy M, Haghshenas S, Rooney K, Turner J, Shears D, Holder M, Lefroy H, Castle B, Reis LM, Semina EV, Lachlan K, Chandler K, Wright T, Clayton-Smith J, Hug FP, Pitteloud N, Bartoloni L, Hoffjan S, Park SM, Thankamony A, Lees M, Wakeling E, Naik S, Hanker B, Girisha KM, Agolini E, Giuseppe Z, Alban Z, Tessarech M, Keren B, Afenjar A, Zweier C, Reis A, Smol T, Tsurusaki Y, Nobuhiko O, Sekiguchi F, Tsuchida N, Matsumoto N, Kou I, Yonezawa Y, Ikegawa S, Callewaert B, Freeth M, Kleinendorst L, Donaldson A, Alders M, De Paepe A, Sadikovic B, McNeill A. SOX11 variants cause a neurodevelopmental disorder with infrequent ocular malformations and hypogonadotropic hypogonadism and with distinct DNA methylation profile. Genet Med 2022; 24:1261-1273. [PMID: 35341651 PMCID: PMC9245088 DOI: 10.1016/j.gim.2022.02.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 12/28/2022] Open
Abstract
PURPOSE This study aimed to undertake a multidisciplinary characterization of the phenotype associated with SOX11 variants. METHODS Individuals with protein altering variants in SOX11 were identified through exome and genome sequencing and international data sharing. Deep clinical phenotyping was undertaken by referring clinicians. Blood DNA methylation was assessed using Infinium MethylationEPIC array. The expression pattern of SOX11 in developing human brain was defined using RNAscope. RESULTS We reported 38 new patients with SOX11 variants. Idiopathic hypogonadotropic hypogonadism was confirmed as a feature of SOX11 syndrome. A distinctive pattern of blood DNA methylation was identified in SOX11 syndrome, separating SOX11 syndrome from other BAFopathies. CONCLUSION SOX11 syndrome is a distinct clinical entity with characteristic clinical features and episignature differentiating it from BAFopathies.
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Affiliation(s)
- Reem Al-Jawahiri
- Department of Psychology, The University of Sheffield, Sheffield, United Kingdom
| | - Aidin Foroutan
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; The Archie and Irene Verspeeten Clinical Genome Centre, London Health Sciences Foundation, London Health Sciences Centre, London, Ontario, Canada
| | - Jennifer Kerkhof
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; The Archie and Irene Verspeeten Clinical Genome Centre, London Health Sciences Foundation, London Health Sciences Centre, London, Ontario, Canada
| | - Haley McConkey
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; The Archie and Irene Verspeeten Clinical Genome Centre, London Health Sciences Foundation, London Health Sciences Centre, London, Ontario, Canada
| | - Michael Levy
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; The Archie and Irene Verspeeten Clinical Genome Centre, London Health Sciences Foundation, London Health Sciences Centre, London, Ontario, Canada
| | - Sadegheh Haghshenas
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; The Archie and Irene Verspeeten Clinical Genome Centre, London Health Sciences Foundation, London Health Sciences Centre, London, Ontario, Canada
| | - Kathleen Rooney
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; The Archie and Irene Verspeeten Clinical Genome Centre, London Health Sciences Foundation, London Health Sciences Centre, London, Ontario, Canada
| | - Jasmin Turner
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - Debbie Shears
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Muriel Holder
- Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom
| | - Henrietta Lefroy
- Peninsula Clinical Genetics Service, RD&E Heavitree Hospital, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Bruce Castle
- Peninsula Clinical Genetics Service, RD&E Heavitree Hospital, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Linda M Reis
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin, Children's Wisconsin, Milwaukee, WI
| | - Elena V Semina
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin, Children's Wisconsin, Milwaukee, WI
| | - Katherine Lachlan
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Kate Chandler
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Thomas Wright
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Jill Clayton-Smith
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Franziska Phan Hug
- Service of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, Lausanne, Switzerland
| | - Nelly Pitteloud
- Service of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, Lausanne, Switzerland
| | - Lucia Bartoloni
- Service of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, Lausanne, Switzerland
| | - Sabine Hoffjan
- Ruhr-Universitat Bochum, Abteilung für Humangenetik, Bochum, Germany
| | - Soo-Mi Park
- Clinical Genetics, Addenbrooke's Treatment Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Ajay Thankamony
- Clinical Genetics, Addenbrooke's Treatment Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Melissa Lees
- Clinical Genetics, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Emma Wakeling
- Clinical Genetics, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Swati Naik
- West Midlands Regional Clinical Genetics Centre and Department of Clinical Genetics, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, United Kingdom
| | - Britta Hanker
- Ambulanzzentrum UKSH, Institut für Humangenetik, Universitätsklinikum Schleswig-Holstein, Lübeck, Germany
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Emanuele Agolini
- Medical Genetics Laboratory, Bambino Gesu Children's Hospital, Rome, Italy
| | - Zampino Giuseppe
- Paediatric Department, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | | | | | - Boris Keren
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Alexandra Afenjar
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Christiane Zweier
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Andre Reis
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Thomas Smol
- EA7364 RADEME, Institute of Medical Genetics, Lille University Hospital, Lille University, Lille, France
| | - Yoshinori Tsurusaki
- Faculty of Nutritional Science, Sagami Women's University, Sagamihara, Japan
| | - Okamoto Nobuhiko
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Futoshi Sekiguchi
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Ikuyo Kou
- Laboratory for Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo, Japan
| | - Yoshiro Yonezawa
- Laboratory for Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo, Japan; Department of Orthopedic Surgery, Keio University School of Medicine, Keio University, Tokyo, Japan
| | - Shiro Ikegawa
- Laboratory for Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo, Japan
| | - Bert Callewaert
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Megan Freeth
- Department of Psychology, The University of Sheffield, Sheffield, United Kingdom
| | - Lotte Kleinendorst
- Centrum voor Medische Genetica - UZ Gent, Ghent University Hospital, Gent, Belgium
| | - Alan Donaldson
- Department of Clinical Genetics Service, University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom
| | - Marielle Alders
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Anne De Paepe
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada.
| | - Alisdair McNeill
- Department of Neuroscience, The Medical School, The University of Sheffield, Sheffield, United Kingdom; Department of Clinical Genetics, Sheffield Children's Hospital NHS Foundation Trust, Sheffield, United Kingdom.
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Liu M, Wan L, Wang C, Yuan H, Peng Y, Wan N, Tang Z, Yuan X, Chen D, Long Z, Shi Y, Qiu R, Tang B, Jiang H, Chen Z. Coffin-Siris syndrome in two chinese patients with novel pathogenic variants of ARID1A and SMARCA4. Genes Genomics 2022; 44:1061-1070. [PMID: 35353340 DOI: 10.1007/s13258-022-01231-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 02/05/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND Coffin-Siris syndrome (CSS) is a rare congenital syndrome characterized by developmental delay, intellectual disability, microcephaly, coarse face and hypoplastic nail of the fifth digits. Heterozygous variants of different BAF complex-related genes were reported to cause CSS, including ARID1A and SMARCA4. So far, no CSS patients with ARID1A and SMARCA4 variants have been reported in China. OBJECTIVE The aim of the current study was to identify the causes of two Chinese patients with congenital growth deficiency and intellectual disability. METHODS Genomic DNA was extracted from the peripheral venous blood of patients and their family members. Genetic analysis included whole-exome and Sanger sequencing. Pathogenicity assessments of variants were performed according to the guideline of the American College of Medical Genetics and Genomics. The phenotypic characteristics of all CSS subtypes were summarized through literature review. RESULTS We identified two Chinese CSS patients carrying novel variants of ARID1A and SMARCA4 respectively. The cases presented most core symptoms of CSS except for the digits involvement. Additionally, we performed a review of the phenotypic characteristics in CSS, highlighting phenotypic varieties and related potential causes. CONCLUSIONS We reported the first Chinese CSS2 and CSS4 patients with novel variants of ARID1A and SMARCA4. Our study expanded the genetic and phenotypic spectrum of CSS, providing a comprehensive overview of genotype-phenotype correlations of CSS.
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Affiliation(s)
- Mingjie Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Linlin Wan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Chunrong Wang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hongyu Yuan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yun Peng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Na Wan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhichao Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xinrong Yuan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Daji Chen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhe Long
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yuting Shi
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China
| | - Rong Qiu
- School of Computer Science and Engineering, Central South University, Changsha, Hunan, China
| | - Beisha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Diseases, Central South University, Changsha, Hunan, China
- Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China
- Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China
| | - Hong Jiang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Diseases, Central South University, Changsha, Hunan, China
- Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China
- Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China
- National International Collaborative Research Center for Medical Metabolomics, Central South University, Changsha, Hunan, China
| | - Zhao Chen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China.
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, China.
- National Clinical Research Center for Geriatric Diseases, Central South University, Changsha, Hunan, China.
- Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China.
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Wilson KD, Porter EG, Garcia BA. Reprogramming of the epigenome in neurodevelopmental disorders. Crit Rev Biochem Mol Biol 2022; 57:73-112. [PMID: 34601997 PMCID: PMC9462920 DOI: 10.1080/10409238.2021.1979457] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The etiology of neurodevelopmental disorders (NDDs) remains a challenge for researchers. Human brain development is tightly regulated and sensitive to cellular alterations caused by endogenous or exogenous factors. Intriguingly, the surge of clinical sequencing studies has revealed that many of these disorders are monogenic and monoallelic. Notably, chromatin regulation has emerged as highly dysregulated in NDDs, with many syndromes demonstrating phenotypic overlap, such as intellectual disabilities, with one another. Here we discuss epigenetic writers, erasers, readers, remodelers, and even histones mutated in NDD patients, predicted to affect gene regulation. Moreover, this review focuses on disorders associated with mutations in enzymes involved in histone acetylation and methylation, and it highlights syndromes involving chromatin remodeling complexes. Finally, we explore recently discovered histone germline mutations and their pathogenic outcome on neurological function. Epigenetic regulators are mutated at every level of chromatin organization. Throughout this review, we discuss mechanistic investigations, as well as various animal and iPSC models of these disorders and their usefulness in determining pathomechanism and potential therapeutics. Understanding the mechanism of these mutations will illuminate common pathways between disorders. Ultimately, classifying these disorders based on their effects on the epigenome will not only aid in prognosis in patients but will aid in understanding the role of epigenetic machinery throughout neurodevelopment.
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Affiliation(s)
- Khadija D. Wilson
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Elizabeth G. Porter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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Slavotinek A, Lefebvre M, Brehin AC, Thauvin C, Patrier S, Sparks TN, Norton M, Yu J, Huang E. Prenatal presentation of multiple anomalies associated with haploinsufficiency for ARID1A. Eur J Med Genet 2022; 65:104407. [PMID: 34942405 PMCID: PMC9162882 DOI: 10.1016/j.ejmg.2021.104407] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 11/04/2021] [Accepted: 12/14/2021] [Indexed: 02/03/2023]
Abstract
The ARID1A gene is an infrequent cause of Coffin-Siris syndrome (CSS) and has been associated with severe to profound developmental delays and hypotonia in addition to characteristic craniofacial and digital findings. We present three fetuses and a male neonate with ventriculomegaly/hydrocephalus, absence of the corpus callosum (ACC), cerebellar hypoplasia, retinal dysplasia, lung lobulation defects, renal dysplasia, imperforate or anteriorly placed anus, thymus hypoplasia and a single umbilical artery. Facial anomalies included downslanting palpebral fissures, wide-spaced eyes, low-set and posteriorly rotated ears, a small jaw, widely spaced nipples and hypoplastic nails. All fetuses had heterozygous variants predicting premature protein truncation in ARID1A (c.4886dup:p.Val1630Cysfs*18; c.4860dup:p.Pro1621Thrfs*27; and c.175G>T:p.Glu59*) and the baby's microarray demonstrated mosaicism for a deletion at chromosome 1p36.11 (arr[GRCh37] 1p36.11(26,797,508_27,052,080)×1∼2), that contained the first exon of ARID1A. Although malformations, in particular ACC, have been described with CSS caused by pathogenic variants in ARID1A, prenatal presentations associated with this gene are rare. Retinal dysplasia, lung lobulation defects and absent thymus were novel findings in association with ARID1A variants. Studies in cancer have demonstrated that pathogenic ARID1A variants hamper nuclear import of the protein and/or affect interaction with the subunits of SWI/SNF complex, resulting in dysregulation of the PI3K/AKT pathway and perturbed PTEN and PIKC3A signaling. As haploinsufficiency for PTEN and PIKC3A can be associated with ventriculomegaly/hydrocephalus, aberrant expression of these genes is a putative mechanism for the brain malformations demonstrated in patients with ARID1A variants.
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Affiliation(s)
- Anne Slavotinek
- Dept. Pediatrics, University of California San Francisco, San Francisco, CA, 94143, USA, Corresponding author. (A. Slavotinek)
| | - Mathilde Lefebvre
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231, Génétique des Anomalies du Développement, Dijon, France
| | | | - Christel Thauvin
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231, Génétique des Anomalies du Développement, Dijon, France
| | - Sophie Patrier
- Department of Pathology, CHU Rouen, F-76000, Rouen, France
| | - Teresa N. Sparks
- Department of Obstetrics, Gynecology, & Reproductive Sciences, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Mary Norton
- Department of Obstetrics, Gynecology, & Reproductive Sciences, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Jingwei Yu
- Dept. Cytogenetics, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Eric Huang
- Dept. Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
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Chen CA, Lattier J, Zhu W, Rosenfeld J, Wang L, Scott TM, Du H, Patel V, Dang A, Magoulas P, Streff H, Sebastian J, Svihovec S, Curry K, Delgado MR, Hanchard N, Lalani S, Marom R, Madan-Khetarpal S, Saenz M, Dai H, Meng L, Xia F, Bi W, Liu P, Posey JE, Scott DA, Lupski JR, Eng CM, Xiao R, Yuan B. Retrospective analysis of a clinical exome sequencing cohort reveals the mutational spectrum and identifies candidate disease-associated loci for BAFopathies. Genet Med 2022; 24:364-373. [PMID: 34906496 PMCID: PMC8957292 DOI: 10.1016/j.gim.2021.09.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/19/2021] [Accepted: 06/19/2021] [Indexed: 02/03/2023] Open
Abstract
PURPOSE BRG1/BRM-associated factor (BAF) complex is a chromatin remodeling complex that plays a critical role in gene regulation. Defects in the genes encoding BAF subunits lead to BAFopathies, a group of neurodevelopmental disorders with extensive locus and phenotypic heterogeneity. METHODS We retrospectively analyzed data from 16,243 patients referred for clinical exome sequencing (ES) with a focus on the BAF complex. We applied a genotype-first approach, combining predicted genic constraints to propose candidate BAFopathy genes. RESULTS We identified 127 patients carrying pathogenic variants, likely pathogenic variants, or de novo variants of unknown clinical significance in 11 known BAFopathy genes. Those include 34 patients molecularly diagnosed using ES reanalysis with new gene-disease evidence (n = 21) or variant reclassifications in known BAFopathy genes (n = 13). We also identified de novo or predicted loss-of-function variants in 4 candidate BAFopathy genes, including ACTL6A, BICRA (implicated in Coffin-Siris syndrome during this study), PBRM1, and SMARCC1. CONCLUSION We report the mutational spectrum of BAFopathies in an ES cohort. A genotype-driven and pathway-based reanalysis of ES data identified new evidence for candidate genes involved in BAFopathies. Further mechanistic and phenotypic characterization of additional patients are warranted to confirm their roles in human disease and to delineate their associated phenotypic spectrums.
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Affiliation(s)
- Chun-An Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | | | | | - Jill Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Lei Wang
- Baylor Genetics Laboratory, Houston, TX
| | - Tiana M. Scott
- Texas Children’s Hospital, Houston, TX, Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | | | - Anh Dang
- Baylor Genetics Laboratory, Houston, TX
| | - Pilar Magoulas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Texas Children’s Hospital, Houston, TX
| | - Haley Streff
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Texas Children’s Hospital, Houston, TX
| | | | - Shayna Svihovec
- University of Colorado Anschutz Medical Campus; Children’s Hospital Colorado, Aurora, CO
| | - Kathryn Curry
- Genetics and Metabolic Department, St. Luke’s Health System
| | - Mauricio R. Delgado
- Texas Scottish Rite Hospital for Children, Dallas, TX, USA, Neurology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Neil Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Texas Children’s Hospital, Houston, TX
| | - Seema Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Texas Children’s Hospital, Houston, TX
| | - Ronit Marom
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Texas Children’s Hospital, Houston, TX
| | | | - Margarita Saenz
- University of Colorado Anschutz Medical Campus; Children’s Hospital Colorado, Aurora, CO
| | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Baylor Genetics Laboratory, Houston, TX
| | - Linyan Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Baylor Genetics Laboratory, Houston, TX
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Baylor Genetics Laboratory, Houston, TX
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Baylor Genetics Laboratory, Houston, TX
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Baylor Genetics Laboratory, Houston, TX
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Daryl A. Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Texas Children’s Hospital, Houston, TX, Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Texas Children’s Hospital, Houston, TX, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - Christine M. Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Baylor Genetics Laboratory, Houston, TX
| | - Rui Xiao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Baylor Genetics Laboratory, Houston, TX
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Baylor Genetics Laboratory, Houston, TX, Current address: Department of Laboratories, Seattle Children’s Hospital, Seattle, WA
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Neurobiology of ARID1B haploinsufficiency related to neurodevelopmental and psychiatric disorders. Mol Psychiatry 2022; 27:476-489. [PMID: 33686214 PMCID: PMC8423853 DOI: 10.1038/s41380-021-01060-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 02/04/2021] [Accepted: 02/18/2021] [Indexed: 01/31/2023]
Abstract
ARID1B haploinsufficiency is a frequent cause of intellectual disability (ID) and autism spectrum disorder (ASD), and also leads to emotional disturbances. In this review, we examine past and present clinical and preclinical research into the neurobiological function of ARID1B. The presentation of ARID1B-related disorders (ARID1B-RD) is highly heterogeneous, including varying degrees of ID, ASD, and physical features. Recent research includes the development of suitable clinical readiness assessments for the treatment of ARID1B-RD, as well as similar neurodevelopmental disorders. Recently developed mouse models of Arid1b haploinsufficiency successfully mirror many of the behavioral phenotypes of ASD and ID. These animal models have helped to solidify the molecular mechanisms by which ARID1B regulates brain development and function, including epigenetic regulation of the Pvalb gene and promotion of Wnt/β-catenin signaling in neural progenitors in the ventral telencephalon. Finally, preclinical studies have identified the use of a positive allosteric modulator of the GABAA receptor as an effective treatment for some Arid1b haploinsufficiency-related behavioral phenotypes, and there is potential for the refinement of this therapy in order to translate it into clinical use.
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Hutchison DM, Duffens A, Yale K, Park A, Cardenas K, Mesinkovska NA. Eyelash trichomegaly: a systematic review of acquired and congenital aetiologies of lengthened lashes. J Eur Acad Dermatol Venereol 2021; 36:536-546. [PMID: 34919300 DOI: 10.1111/jdv.17877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 10/05/2021] [Accepted: 11/10/2021] [Indexed: 02/01/2023]
Abstract
Long eyelashes have been popularized and many commercially available products exist to achieve eyelash growth as a desired cosmetic effect. Eyelash trichomegaly may be induced by medications, procedures, or be related to medical conditions; however, the exact mechanisms that govern eyelash growth are not well elucidated. This study aims to identify and summarize aetiologies associated with eyelash trichomegaly. We report a systematic review of 148 clinical trials, prospective and retrospective studies, and case reports describing all evidence-based potential aetiologies of eyelash trichomegaly obtained from the Medline/PubMed and Cochrane Library through January 2021. Inclusion criteria were defined as (i) human studies involving congenital and acquired diseases in which eyelash trichomegaly is a characteristic or (ii) assessment of trichomegaly as an adverse or desired effect of a medication or procedure. Exclusion criteria included: animal studies, articles not available in English, outcomes unrelated to eyelash trichomegaly, and secondary review articles. Pharmacologic agents associated with eyelash trichomegaly included prostaglandin analogues (15-keto fluprostenol isopropyl ester, bimatoprost, latanoprost, and travoprost), epidermal growth factor receptor inhibitors (cetuximab, erlotinib, and panitumumab), interferon-alpha, and calcineurin inhibitors (tacrolimus and cyclosporine). Surgical procedures of the eyelid, as well as allergic rhinitis, atopic dermatitis, HIV, ichthyosis vulgaris (IV), uveitis, and vernal keratoconjunctivitis were also associated with increased eyelash growth. Congenital disorders associated with lengthened eyelashes included Cantú syndrome, CHOPS syndrome, Coffin-Siris syndrome, congenital heart disease, Cornelia de Lange syndrome, Costello syndrome, familial trichomegaly, Floating Harbor syndrome, Hermansky-Pudlak syndrome, Kabuki-Makeup syndrome, KBG syndrome, Oliver-McFarlane syndrome, Rubinstein-Taybi syndrome, and Smith-Magenis syndrome. While the most common cause of eyelash trichomegaly is topical bimatoprost use, better understanding of pathways implicated in eyelash trichomegaly may lead to the discovery of additional medications to stimulate eyelash growth and create avenues for future therapeutic interventions.
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Affiliation(s)
- D M Hutchison
- Department of Dermatology, University of California Irvine, Irvine, CA, USA.,Beckman Laser Institute, University of California Irvine, Irvine, CA, USA
| | - A Duffens
- Department of Dermatology, University of California Irvine, Irvine, CA, USA
| | - K Yale
- Department of Dermatology, University of California Irvine, Irvine, CA, USA
| | - A Park
- Beckman Laser Institute, University of California Irvine, Irvine, CA, USA
| | - K Cardenas
- Department of Dermatology, University of California Irvine, Irvine, CA, USA
| | - N A Mesinkovska
- Department of Dermatology, University of California Irvine, Irvine, CA, USA.,Beckman Laser Institute, University of California Irvine, Irvine, CA, USA
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40
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Linke AC, Slušná D, Kohli JS, Álvarez-Linera Prado J, Müller RA, Hinzen W. Morphometry and functional connectivity of auditory cortex in school-age children with profound language disabilities: Five comparative case studies. Brain Cogn 2021; 155:105822. [PMID: 34837801 DOI: 10.1016/j.bandc.2021.105822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 10/27/2021] [Accepted: 11/02/2021] [Indexed: 10/19/2022]
Abstract
Many neurodevelopmental conditions imply absent or severely reduced language capacities at school age. Evidence from functional magnetic resonance imaging is highly limited. We selected a series of five cases scanned with the same fMRI paradigm and the aim of relating individual language profiles onto underlying patterns of functional connectivity (FC) across auditory language cortex: three with neurogenetic syndromes (Coffin-Siris, Landau-Kleffner, and Fragile-X), one with idiopathic intellectual disability, one with autism spectrum disorder (ASD). Compared to both a group with typical development (TD) and a verbal ASD group (total N = 110), they all showed interhemispheric FC below two standard deviations of the TD mean. Children with higher language scores showed higher intrahemispheric FC between Heschl's gyrus and other auditory language regions, as well as an increase of FC during language stimulation compared to rest. An increase of FC in forward vs. reversed speech in the posterior and middle temporal gyri was seen across all cases. The Coffin-Siris case, the most severe, also had the most anomalous FC patterns and showed reduced myelin content, while the Landau-Kleffner case showed reduced cortical thickness. These results suggest potential for neural markers and mechanisms of severe language processing deficits under highly heterogeneous etiological conditions.
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Affiliation(s)
- Annika Carola Linke
- Brain Development Imaging Laboratories, Department of Psychology, San Diego State University, San Diego, CA, USA.
| | - Dominika Slušná
- Department of Translation and Language Sciences, Campus Poblenou, Pompeu Fabra University, Barcelona 08018, Barcelona, Spain
| | - Jiwandeep Singh Kohli
- Brain Development Imaging Laboratories, Department of Psychology, San Diego State University, San Diego, CA, USA
| | | | - Ralph-Axel Müller
- Brain Development Imaging Laboratories, Department of Psychology, San Diego State University, San Diego, CA, USA; San Diego State University/University of California San Diego Joint Doctoral Program in Clinical Psychology, San Diego, CA, USA
| | - Wolfram Hinzen
- Department of Translation and Language Sciences, Campus Poblenou, Pompeu Fabra University, Barcelona 08018, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats, ICREA, 08010 Barcelona, Spain
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Lu G, Peng Q, Wu L, Zhang J, Ma L. Identification of de novo mutations for ARID1B haploinsufficiency associated with Coffin-Siris syndrome 1 in three Chinese families via array-CGH and whole exome sequencing. BMC Med Genomics 2021; 14:270. [PMID: 34775996 PMCID: PMC8591803 DOI: 10.1186/s12920-021-01119-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/05/2021] [Indexed: 11/25/2022] Open
Abstract
Background Coffin–Siris syndrome (CSS) is a multiple malformation syndrome characterized by intellectual disability associated with coarse facial features, hirsutism, sparse scalp hair, and hypoplastic or absent fifth fingernails or toenails. CSS represents a small group of intellectual disability, and could be caused by at least twelve genes. The genetic background is quite heterogenous, making it difficult for clinicians and genetic consultors to pinpoint the exact disease types. Methods Array-Comparative Genomic Hybridization (array-CGH) and whole exome sequencing (WES) were applied for three trios affected with intellectual disability and clinical features similar with those of Coffin–Siris syndrome. Sanger sequencing was used to verify the detected single-nucleotide variants (SNVs). Results All of the three cases were female with normal karyotypes of 46, XX, born of healthy, non-consanguineous parents. A 6q25 microdeletion (arr[hg19]6q25.3(155,966,487–158,803,979) × 1) (2.84 Mb) (case 1) and two loss-of-function (LoF) mutations of ARID1B [c.2332 + 1G > A in case 2 and c.4741C > T (p.Q1581X) in case 3] were identified. All of the three pathogenic abnormalities were de novo, not inherited from their parents. After comparison of publicly available microdeletions containing ARID1B, four types of microdeletions leading to insufficient production of ARID1B were identified, namely deletions covering the whole region of ARID1B, deletions covering the promoter region, deletions covering the termination region or deletions covering enhancer regions. Conclusion Here we identified de novo ARID1B mutations in three Chinese trios. Four types of microdeletions covering ARID1B were identified. This study broadens current knowledge of ARID1B mutations for clinicians and genetic consultors.
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Affiliation(s)
- Guanting Lu
- Department of Pathology, Laboratory of Translational Medicine Research, Deyang Key Laboratory of Tumor Molecular Research, Deyang People's Hospital, No. 173 First Section of TaishanBei Road, Jiangyang District, Deyang, 618000, China.
| | - Qiongling Peng
- Department of Child Healthcare, Shenzhen Baoan Women's and Children's Hospital, Jinan University, 56 Yulyu Road, Baoan District, Shenzhen, 518000, China
| | - Lianying Wu
- Department of Pathology, Laboratory of Translational Medicine Research, Deyang Key Laboratory of Tumor Molecular Research, Deyang People's Hospital, No. 173 First Section of TaishanBei Road, Jiangyang District, Deyang, 618000, China
| | - Jian Zhang
- Department of Pathology, Laboratory of Translational Medicine Research, Deyang Key Laboratory of Tumor Molecular Research, Deyang People's Hospital, No. 173 First Section of TaishanBei Road, Jiangyang District, Deyang, 618000, China
| | - Liya Ma
- Department of Child Healthcare, Shenzhen Baoan Women's and Children's Hospital, Jinan University, 56 Yulyu Road, Baoan District, Shenzhen, 518000, China.
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Caracci MO, Avila ME, Espinoza-Cavieres FA, López HR, Ugarte GD, De Ferrari GV. Wnt/β-Catenin-Dependent Transcription in Autism Spectrum Disorders. Front Mol Neurosci 2021; 14:764756. [PMID: 34858139 PMCID: PMC8632544 DOI: 10.3389/fnmol.2021.764756] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/12/2021] [Indexed: 12/20/2022] Open
Abstract
Autism spectrum disorders (ASD) is a heterogeneous group of neurodevelopmental disorders characterized by synaptic dysfunction and defects in dendritic spine morphology. In the past decade, an extensive list of genes associated with ASD has been identified by genome-wide sequencing initiatives. Several of these genes functionally converge in the regulation of the Wnt/β-catenin signaling pathway, a conserved cascade essential for stem cell pluripotency and cell fate decisions during development. Here, we review current information regarding the transcriptional program of Wnt/β-catenin signaling in ASD. First, we discuss that Wnt/β-catenin gain and loss of function studies recapitulate brain developmental abnormalities associated with ASD. Second, transcriptomic approaches using patient-derived induced pluripotent stem cells (iPSC) cells, featuring mutations in high confidence ASD genes, reveal a significant dysregulation in the expression of Wnt signaling components. Finally, we focus on the activity of chromatin-remodeling proteins and transcription factors considered high confidence ASD genes, including CHD8, ARID1B, ADNP, and TBR1, that regulate Wnt/β-catenin-dependent transcriptional activity in multiple cell types, including pyramidal neurons, interneurons and oligodendrocytes, cells which are becoming increasingly relevant in the study of ASD. We conclude that the level of Wnt/β-catenin signaling activation could explain the high phenotypical heterogeneity of ASD and be instrumental in the development of new diagnostics tools and therapies.
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Affiliation(s)
- Mario O. Caracci
- Faculty of Medicine, Institute of Biomedical Sciences, Universidad Andres Bello, Santiago, Chile
- Faculty of Life Sciences, Institute of Biomedical Sciences, Universidad Andres Bello, Santiago, Chile
| | - Miguel E. Avila
- Faculty of Veterinary Medicine and Agronomy, Nucleus of Applied Research in Veterinary and Agronomic Sciences (NIAVA), Institute of Natural Sciences, Universidad de Las Américas, Santiago, Chile
| | - Francisca A. Espinoza-Cavieres
- Faculty of Medicine, Institute of Biomedical Sciences, Universidad Andres Bello, Santiago, Chile
- Faculty of Life Sciences, Institute of Biomedical Sciences, Universidad Andres Bello, Santiago, Chile
| | - Héctor R. López
- Faculty of Medicine, Institute of Biomedical Sciences, Universidad Andres Bello, Santiago, Chile
- Faculty of Life Sciences, Institute of Biomedical Sciences, Universidad Andres Bello, Santiago, Chile
| | - Giorgia D. Ugarte
- Faculty of Medicine, Institute of Biomedical Sciences, Universidad Andres Bello, Santiago, Chile
- Faculty of Life Sciences, Institute of Biomedical Sciences, Universidad Andres Bello, Santiago, Chile
| | - Giancarlo V. De Ferrari
- Faculty of Medicine, Institute of Biomedical Sciences, Universidad Andres Bello, Santiago, Chile
- Faculty of Life Sciences, Institute of Biomedical Sciences, Universidad Andres Bello, Santiago, Chile
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Inability to switch from ARID1A-BAF to ARID1B-BAF impairs exit from pluripotency and commitment towards neural crest formation in ARID1B-related neurodevelopmental disorders. Nat Commun 2021; 12:6469. [PMID: 34753942 PMCID: PMC8578637 DOI: 10.1038/s41467-021-26810-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 10/21/2021] [Indexed: 01/06/2023] Open
Abstract
Subunit switches in the BAF chromatin remodeler are essential during development. ARID1B and its paralog ARID1A encode for mutually exclusive BAF subunits. De novo ARID1B haploinsufficient mutations cause neurodevelopmental disorders, including Coffin-Siris syndrome, which is characterized by neurological and craniofacial features. Here, we leveraged ARID1B+/− Coffin-Siris patient-derived iPSCs and modeled cranial neural crest cell (CNCC) formation. We discovered that ARID1B is active only during the first stage of this process, coinciding with neuroectoderm specification, where it is part of a lineage-specific BAF configuration (ARID1B-BAF). ARID1B-BAF regulates exit from pluripotency and lineage commitment by attenuating thousands of enhancers and genes of the NANOG and SOX2 networks. In iPSCs, these enhancers are maintained active by ARID1A-containing BAF. At the onset of differentiation, cells transition from ARID1A- to ARID1B-BAF, eliciting attenuation of the NANOG/SOX2 networks and triggering pluripotency exit. Coffin-Siris patient cells fail to perform the ARID1A/ARID1B switch, and maintain ARID1A-BAF at the pluripotency enhancers throughout all stages of CNCC formation. This leads to persistent NANOG/SOX2 activity which impairs CNCC formation. Despite showing the typical neural crest signature (TFAP2A/SOX9-positive), ARID1B-haploinsufficient CNCCs are also aberrantly NANOG-positive. These findings suggest a connection between ARID1B mutations, neuroectoderm specification and a pathogenic mechanism for Coffin-Siris syndrome. Mutations in the ARID1B subunit of the BAF chromatin remodeling complex are associated with the neurodevelopmental Coffin-Siris syndrome. Here the authors reveal that there is a transition from ARID1A-containing complexes to ARID1B during cranial neural crest cell differentiation that is impaired in Coffin-Siris patient-derived cells, which is important for exit from pluripotency.
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Lee Y, Choi Y, Seo GH, Kim GH, Keum C, Kim YM, Do HS, Choi J, Choi IH, Yoo HW, Lee BH. Phenotypic and molecular spectra of patients with switch/sucrose nonfermenting complex-related intellectual disability disorders in Korea. BMC Med Genomics 2021; 14:254. [PMID: 34706719 PMCID: PMC8555129 DOI: 10.1186/s12920-021-01104-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 10/19/2021] [Indexed: 02/04/2023] Open
Abstract
Background The switch/sucrose nonfermenting (SWI/SNF) complex is an adenosine triphosphate-dependent chromatin-remodeling complex associated with the regulation of DNA accessibility. Germline mutations in the components of the SWI/SNF complex are related to human developmental disorders, including the Coffin–Siris syndrome (CSS), Nicolaides–Baraitser syndrome (NCBRS), and nonsyndromic intellectual disability. These disorders are collectively referred to as SWI/SNF complex-related intellectual disability disorders (SSRIDDs). Methods Whole-exome sequencing was performed in 564 Korean patients with neurodevelopmental disorders. Twelve patients with SSRIDDs (2.1%) were identified and their medical records were retrospectively analyzed. Results ARID1B, found in eight patients, was the most frequently altered gene. Four patients harbored pathogenic variants in SMARCA4, SMARCB1, ARID2, and SMARCA2. Ten patients were diagnosed with CSS, and one patient without a typical phenotype was diagnosed with ARID1B-related nonsyndromic intellectual disability. Another patient harboring the SMARCA2 pathogenic variant was diagnosed with NCBRS. All pathogenic variants in ARID1B were truncating, whereas variants in SMARCA2, SMARCB1, and SMARCA4 were nontruncating (missense). Frequently observed phenotypes were thick eyebrows (10/12), hypertrichosis (8/12), coarse face (8/12), thick lips (8/12), and long eyelashes (8/12). Developmental delay was observed in all patients, and profound speech delay was also characteristic. Agenesis or hypoplasia of the corpus callosum was observed in half of the patients (6/12). Conclusions SSRIDDs have a broad disease spectrum, including NCBRS, CSS, and ARID1B-related nonsyndromic intellectual disability. Thus, SSRIDDs should be considered as a small but important cause of human developmental disorders.
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Affiliation(s)
- Yena Lee
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul, 05505, Republic of Korea
| | - Yunha Choi
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul, 05505, Republic of Korea
| | | | - Gu-Hwan Kim
- Medical Genetics Center, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | | | - Yoo-Mi Kim
- Department of Pediatrics, Chungnam National University Sejong Hospital, College of Medicine, Chungnam National University, Sejong, Republic of Korea
| | - Hyo-Sang Do
- Genome Research Center for Birth Defects and Genetic Diseases, Asan Institute for Life Sciences, Asan Medical Center, Seoul, Republic of Korea
| | - Jeongmin Choi
- Genome Research Center for Birth Defects and Genetic Diseases, Asan Institute for Life Sciences, Asan Medical Center, Seoul, Republic of Korea
| | - In Hee Choi
- Department of Genetic Counseling, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Han-Wook Yoo
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul, 05505, Republic of Korea.,Medical Genetics Center, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Beom Hee Lee
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul, 05505, Republic of Korea. .,Medical Genetics Center, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Republic of Korea.
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45
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Valencia AM, Pașca SP. Chromatin dynamics in human brain development and disease. Trends Cell Biol 2021; 32:98-101. [PMID: 34610892 DOI: 10.1016/j.tcb.2021.09.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/03/2021] [Accepted: 09/06/2021] [Indexed: 12/01/2022]
Abstract
Chromatin-related genes are frequently mutated in neurodevelopmental disorders; yet, the mechanisms by which these perturbations disrupt brain assembly and function are not understood. Here, we describe how recent advances in transcriptional and chromatin profiling in combination with cellular models are beginning to inform our understanding of neurodevelopment and chromatinopathies.
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Affiliation(s)
- Alfredo M Valencia
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA 94305, USA
| | - Sergiu P Pașca
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA 94305, USA.
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Gregor A, Meerbrei T, Gerstner T, Toutain A, Lynch SA, Stals K, Maxton C, Lemke JR, Bernat JA, Bombei HM, Foulds N, Hunt D, Kuechler A, Beygo J, Stöbe P, Bouman A, Palomares-Bralo M, Santos-Simarro F, Garcia-Minaur S, Pacio-Miguez M, Popp B, Vasileiou G, Hebebrand M, Reis A, Schuhmann S, Krumbiegel M, Brown NJ, Sparber P, Melikyan L, Bessonova L, Cherevatova T, Sharkov A, Shcherbakova N, Dabir T, Kini U, Schwaibold EMC, Haack TB, Bertoli M, Hoffjan S, Falb R, Shinawi M, Sticht H, Zweier C. De novo missense variants in FBXO11 alter its protein expression and subcellular localization. Hum Mol Genet 2021; 31:440-454. [PMID: 34505148 PMCID: PMC8825234 DOI: 10.1093/hmg/ddab265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/09/2021] [Accepted: 09/05/2021] [Indexed: 12/28/2022] Open
Abstract
Recently, others and we identified de novo FBXO11 (F-Box only protein 11) variants as causative for a variable neurodevelopmental disorder (NDD). We now assembled clinical and mutational information on 23 additional individuals. The phenotypic spectrum remains highly variable, with developmental delay and/or intellectual disability as the core feature and behavioral anomalies, hypotonia and various facial dysmorphism as frequent aspects. The mutational spectrum includes intragenic deletions, likely gene disrupting and missense variants distributed across the protein. To further characterize the functional consequences of FBXO11 missense variants, we analyzed their effects on protein expression and localization by overexpression of 17 different mutant constructs in HEK293 and HeLa cells. We found that the majority of missense variants resulted in subcellular mislocalization and/or reduced FBXO11 protein expression levels. For instance, variants located in the nuclear localization signal and the N-terminal F-Box domain lead to altered subcellular localization with exclusion from the nucleus or the formation of cytoplasmic aggregates and to reduced protein levels in western blot. In contrast, variants localized in the C-terminal Zn-finger UBR domain lead to an accumulation in the cytoplasm without alteration of protein levels. Together with the mutational data, our functional results suggest that most missense variants likely lead to a loss of the original FBXO11 function and thereby highlight haploinsufficiency as the most likely disease mechanism for FBXO11-associated NDDs.
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Affiliation(s)
- Anne Gregor
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany.,Department of Human Genetics, Inselspital Bern, University of Bern, 3010, Bern, Switzerland
| | - Tanja Meerbrei
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | | | - Annick Toutain
- Service de Génétique, CHU de Tours, 37044, Tours, France.,UMR 1253, iBrain, Université de Tours, Inserm, Tours, France
| | - Sally Ann Lynch
- Dept of Clinical Genetics, Temple Street Children's Hospital Dublin 1, D01 YC67, Dublin, Ireland
| | - Karen Stals
- Exeter Genomics Laboratory, Royal Devon & Exeter NHS Foundation Trust, Exeter, EX2 5DW, UK
| | | | - Johannes R Lemke
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, 04103 Leipzig, Germany
| | - John A Bernat
- Division of Medical Genetics & Genomics, Stead Family Department of Pediatrics, University of Iowa Hospital and Clinics, 52242, Iowa City, IA, USA
| | - Hannah M Bombei
- Division of Medical Genetics & Genomics, Stead Family Department of Pediatrics, University of Iowa Hospital and Clinics, 52242, Iowa City, IA, USA
| | - Nicola Foulds
- Wessex Clinical Genetics Services, University Hospital Southampton, Southampton, SO16 5YA, UK
| | - David Hunt
- Wessex Clinical Genetics Services, University Hospital Southampton, Southampton, SO16 5YA, UK.,Department of Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, SO16 5YA, UK
| | - Alma Kuechler
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, 45147, Essen, Germany
| | - Jasmin Beygo
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, 45147, Essen, Germany
| | - Petra Stöbe
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076, Tübingen, Germany
| | - Arjan Bouman
- Department of Clinical Genetics, Erasmus MC University Medical Center Rotterdam, 3015 GD, Rotterdam, The Netherlands
| | - Maria Palomares-Bralo
- Institute of Medical and Molecular Genetics, University Hospital La Paz, 28046 Madrid, Spain
| | - Fernando Santos-Simarro
- Institute of Medical and Molecular Genetics, University Hospital La Paz, 28046 Madrid, Spain
| | - Sixto Garcia-Minaur
- Institute of Medical and Molecular Genetics, University Hospital La Paz, 28046 Madrid, Spain
| | - Marta Pacio-Miguez
- Institute of Medical and Molecular Genetics, University Hospital La Paz, 28046 Madrid, Spain
| | - Bernt Popp
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, 04103 Leipzig, Germany
| | - Georgia Vasileiou
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Moritz Hebebrand
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - André Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Sarah Schuhmann
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Mandy Krumbiegel
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Natasha J Brown
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, VIC 3010, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC 3052, Australia
| | - Peter Sparber
- Research Centre for Medical Genetics, Moscow, 115522, Russia
| | - Lyusya Melikyan
- Research Centre for Medical Genetics, Moscow, 115522, Russia
| | | | | | - Artem Sharkov
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Genomed Ltd., Moscow, 117997, Russia
| | - Natalia Shcherbakova
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Genomed Ltd., Moscow, 117997, Russia.,Independent Clinical Bioinformatics Laboratory, Moscow, 117997, Russia
| | - Tabib Dabir
- Department of Genetic Medicine, Belfast City Hospital, Belfast, BT9 7AB, Northern Ireland, United Kingdom
| | - Usha Kini
- Oxford Centre for Genomic Medicine, Oxford and Spires Cleft Centre, Oxford, OX3 9DU, UK
| | - Eva M C Schwaibold
- Institute of Human Genetics, Heidelberg University, 69120, Heidelberg, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076, Tübingen, Germany
| | - Marta Bertoli
- Northern Genetics Service, Newcastle upon Tyne NHS Foundation Trust, Newcastle upon Tyne, NE1 3BZ, UK
| | - Sabine Hoffjan
- Department of Human Genetics, Ruhr University, 44801, Bochum, Germany
| | - Ruth Falb
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076, Tübingen, Germany
| | - Marwan Shinawi
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Heinrich Sticht
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Christiane Zweier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany.,Department of Human Genetics, Inselspital Bern, University of Bern, 3010, Bern, Switzerland
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van der Sluijs PJ, Alders M, Dingemans AJM, Parbhoo K, van Bon BW, Dempsey JC, Doherty D, den Dunnen JT, Gerkes EH, Milller IM, Moortgat S, Regier DS, Ruivenkamp CAL, Schmalz B, Smol T, Stuurman KE, Vincent-Delorme C, de Vries BBA, Sadikovic B, Hickey SE, Rosenfeld JA, Maystadt I, Santen GWE. A Case Series of Familial ARID1B Variants Illustrating Variable Expression and Suggestions to Update the ACMG Criteria. Genes (Basel) 2021; 12:genes12081275. [PMID: 34440449 PMCID: PMC8393241 DOI: 10.3390/genes12081275] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/13/2021] [Accepted: 08/16/2021] [Indexed: 02/07/2023] Open
Abstract
ARID1B is one of the most frequently mutated genes in intellectual disability (~1%). Most variants are readily classified, since they are de novo and are predicted to lead to loss of function, and therefore classified as pathogenic according to the American College of Medical Genetics and Genomics (ACMG) guidelines for the interpretation of sequence variants. However, familial loss-of-function variants can also occur and can be challenging to interpret. Such variants may be pathogenic with variable expression, causing only a mild phenotype in a parent. Alternatively, since some regions of the ARID1B gene seem to be lacking pathogenic variants, loss-of-function variants in those regions may not lead to ARID1B haploinsufficiency and may therefore be benign. We describe 12 families with potential loss-of-function variants, which were either familial or with unknown inheritance and were in regions where pathogenic variants have not been described or are otherwise challenging to interpret. We performed detailed clinical and DNA methylation studies, which allowed us to confidently classify most variants. In five families we observed transmission of pathogenic variants, confirming their highly variable expression. Our findings provide further evidence for an alternative translational start site and we suggest updates for the ACMG guidelines for the interpretation of sequence variants to incorporate DNA methylation studies and facial analyses.
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Affiliation(s)
- Pleuntje J. van der Sluijs
- Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (P.J.v.d.S.); (C.A.L.R.)
| | - Mariëlle Alders
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
| | - Alexander J. M. Dingemans
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (A.J.M.D.); (B.B.A.d.V.)
| | - Kareesma Parbhoo
- Division of Genetic & Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43205, USA; (K.P.); (B.S.); (S.E.H.)
| | - Bregje W. van Bon
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands;
| | - Jennifer C. Dempsey
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; (J.C.D.); (D.D.)
| | - Dan Doherty
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; (J.C.D.); (D.D.)
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Johan T. den Dunnen
- Human Genetics and Clinical Genetics, Leiden University Medical Centre, 2333 ZA Leiden, The Netherlands;
| | - Erica H. Gerkes
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, The Netherlands;
| | - Ilana M. Milller
- Rare Disease Institute, Children’s National Hospital, Washington, DC 20010, USA; (I.M.M.); (D.S.R.)
| | - Stephanie Moortgat
- Centre de Génétique Humaine, Institut de Pathologie et de Génétique, 6041 Gosselies, Belgium; (S.M.); (I.M.)
| | - Debra S. Regier
- Rare Disease Institute, Children’s National Hospital, Washington, DC 20010, USA; (I.M.M.); (D.S.R.)
| | - Claudia A. L. Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (P.J.v.d.S.); (C.A.L.R.)
| | - Betsy Schmalz
- Division of Genetic & Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43205, USA; (K.P.); (B.S.); (S.E.H.)
| | - Thomas Smol
- EA7364 RADEME, Institut de Génétique Médicale, Université de Lille, CHU de Lille, F-59000 Lille, France;
| | - Kyra E. Stuurman
- Erasmus MC, Department of Clinical Genetics, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands;
| | | | - Bert B. A. de Vries
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (A.J.M.D.); (B.B.A.d.V.)
| | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre and London Health Sciences Centre, Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada;
| | - Scott E. Hickey
- Division of Genetic & Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43205, USA; (K.P.); (B.S.); (S.E.H.)
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA;
- Baylor Genetics Laboratories, Houston, TX 77021, USA
| | - Isabelle Maystadt
- Centre de Génétique Humaine, Institut de Pathologie et de Génétique, 6041 Gosselies, Belgium; (S.M.); (I.M.)
| | - Gijs W. E. Santen
- Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (P.J.v.d.S.); (C.A.L.R.)
- Correspondence:
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48
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Audain E, Wilsdon A, Breckpot J, Izarzugaza JMG, Fitzgerald TW, Kahlert AK, Sifrim A, Wünnemann F, Perez-Riverol Y, Abdul-Khaliq H, Bak M, Bassett AS, Benson WD, Berger F, Daehnert I, Devriendt K, Dittrich S, Daubeney PEF, Garg V, Hackmann K, Hoff K, Hofmann P, Dombrowsky G, Pickardt T, Bauer U, Keavney BD, Klaassen S, Kramer HH, Marshall CR, Milewicz DM, Lemaire S, Coselli JS, Mitchell ME, Tomita-Mitchell A, Prakash SK, Stamm K, Stewart AFR, Silversides CK, Siebert R, Stiller B, Rosenfeld JA, Vater I, Postma AV, Caliebe A, Brook JD, Andelfinger G, Hurles ME, Thienpont B, Larsen LA, Hitz MP. Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease. PLoS Genet 2021; 17:e1009679. [PMID: 34324492 PMCID: PMC8354477 DOI: 10.1371/journal.pgen.1009679] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 08/10/2021] [Accepted: 06/23/2021] [Indexed: 11/18/2022] Open
Abstract
Numerous genetic studies have established a role for rare genomic variants in Congenital Heart Disease (CHD) at the copy number variation (CNV) and de novo variant (DNV) level. To identify novel haploinsufficient CHD disease genes, we performed an integrative analysis of CNVs and DNVs identified in probands with CHD including cases with sporadic thoracic aortic aneurysm. We assembled CNV data from 7,958 cases and 14,082 controls and performed a gene-wise analysis of the burden of rare genomic deletions in cases versus controls. In addition, we performed variation rate testing for DNVs identified in 2,489 parent-offspring trios. Our analysis revealed 21 genes which were significantly affected by rare CNVs and/or DNVs in probands. Fourteen of these genes have previously been associated with CHD while the remaining genes (FEZ1, MYO16, ARID1B, NALCN, WAC, KDM5B and WHSC1) have only been associated in small cases series or show new associations with CHD. In addition, a systems level analysis revealed affected protein-protein interaction networks involved in Notch signaling pathway, heart morphogenesis, DNA repair and cilia/centrosome function. Taken together, this approach highlights the importance of re-analyzing existing datasets to strengthen disease association and identify novel disease genes and pathways.
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Affiliation(s)
- Enrique Audain
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, Kiel, Germany
- German Center for Cardiovascular Research (DZHK), Kiel, Germany
| | - Anna Wilsdon
- School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Jeroen Breckpot
- Centre for Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | | | - Tomas W. Fitzgerald
- European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, United Kingdom
| | - Anne-Karin Kahlert
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, Kiel, Germany
- German Center for Cardiovascular Research (DZHK), Kiel, Germany
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Alejandro Sifrim
- Department of Human Genetics, University of Leuven, KU Leuven, Leuven, Belgium
- Sanger Institute-EBI Single-Cell Genomics Centre, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | | | - Yasset Perez-Riverol
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Hashim Abdul-Khaliq
- Clinic for Pediatric Cardiology—University Hospital of Saarland, Homburg (Saar), Germany
| | - Mads Bak
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Anne S. Bassett
- Toronto Congenital Cardiac Centre for Adults, and Division of Cardiology, Department of Medicine, University Health Network, Toronto, Canada
- Department of Psychiatry, University of Toronto, Toronto, Canada
| | - Woodrow D. Benson
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Felix Berger
- Department of Congenital Heart Disease—Pediatric Cardiology, German Heart Center Berlin, Berlin, Germany
| | - Ingo Daehnert
- Department of Pediatric Cardiology and Congenital Heart Disease, Heart Center, University of Leipzig, Leipzig, Germany
| | - Koenraad Devriendt
- Centre for Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Sven Dittrich
- Department of Pediatric Cardiology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Piers EF Daubeney
- Division of Paediatric Cardiology, Royal Brompton Hospital, London, United Kingdom
| | - Vidu Garg
- The Heart Center, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
- Center for Cardiovascular Research, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, United States of America
| | - Karl Hackmann
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Kirstin Hoff
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, Kiel, Germany
- German Center for Cardiovascular Research (DZHK), Kiel, Germany
| | - Philipp Hofmann
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, Kiel, Germany
- German Center for Cardiovascular Research (DZHK), Kiel, Germany
| | - Gregor Dombrowsky
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, Kiel, Germany
- German Center for Cardiovascular Research (DZHK), Kiel, Germany
| | - Thomas Pickardt
- Competence Network for Congenital Heart Defects, Berlin, Germany
| | - Ulrike Bauer
- Competence Network for Congenital Heart Defects, Berlin, Germany
| | - Bernard D. Keavney
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Sabine Klaassen
- Experimental and Clinical Research Center (ECRC), a joint cooperation between the Charité Medical Faculty and the Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany
- Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Pediatric Cardiology, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
| | - Hans-Heiner Kramer
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, Kiel, Germany
- German Center for Cardiovascular Research (DZHK), Kiel, Germany
| | - Christian R. Marshall
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Dianna M. Milewicz
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Scott Lemaire
- Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas, United States of America
| | - Joseph S. Coselli
- Department of Surgery, Division of Cardiothoracic Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Michael E. Mitchell
- Department of Surgery, Division of Cardiothoracic Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Aoy Tomita-Mitchell
- Department of Surgery, Division of Cardiothoracic Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Siddharth K. Prakash
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Karl Stamm
- Department of Surgery, Division of Cardiothoracic Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Alexandre F. R. Stewart
- Ruddy Canadian Cardiovascular Genetics Centre, University of Ottawa Heart Institute, Ottawa, Canada
| | - Candice K. Silversides
- Toronto Congenital Cardiac Centre for Adults, and Division of Cardiology, Department of Medicine, University Health Network, Toronto, Canada
| | - Reiner Siebert
- Institute of Human Genetics, University Hospital Ulm, Ulm, Germany
- Department of Human Genetics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
| | - Brigitte Stiller
- Department of Congenital Heart Disease and Pediatric Cardiology, University Heart Center Freiburg—Bad Krozingen, Freiburg, Germany
| | - Jill A. Rosenfeld
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Inga Vater
- Department of Human Genetics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
| | - Alex V. Postma
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Almuth Caliebe
- Department of Human Genetics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
| | - J. David Brook
- School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Gregor Andelfinger
- Cardiovascular Genetics, Department of Pediatrics, Centre Hospitalier Universitaire Saint-Justine Research Centre, Université de Montréal, Montreal, Canada
| | - Matthew E. Hurles
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Bernard Thienpont
- Centre for Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Lars Allan Larsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Marc-Phillip Hitz
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, Kiel, Germany
- German Center for Cardiovascular Research (DZHK), Kiel, Germany
- Department of Human Genetics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
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49
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Miyamoto S, Kato M, Hiraide T, Shiohama T, Goto T, Hojo A, Ebata A, Suzuki M, Kobayashi K, Chong PF, Kira R, Matsushita HB, Ikeda H, Hoshino K, Matsufuji M, Moriyama N, Furuyama M, Yamamoto T, Nakashima M, Saitsu H. Comprehensive genetic analysis confers high diagnostic yield in 16 Japanese patients with corpus callosum anomalies. J Hum Genet 2021; 66:1061-1068. [PMID: 33958710 DOI: 10.1038/s10038-021-00932-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 04/12/2021] [Accepted: 04/16/2021] [Indexed: 12/24/2022]
Abstract
Corpus callosum anomalies (CCA) is a common congenital brain anomaly with various etiologies. Although one of the most important etiologies is genetic factors, the genetic background of CCA is heterogenous and diverse types of variants are likely to be causative. In this study, we analyzed 16 Japanese patients with corpus callosum anomalies to delineate clinical features and the genetic background of CCAs. We observed the common phenotypes accompanied by CCAs: intellectual disability (100%), motor developmental delay (93.8%), seizures (60%), and facial dysmorphisms (50%). Brain magnetic resonance imaging showed colpocephaly (enlarged posterior horn of the lateral ventricles, 84.6%) and enlarged supracerebellar cistern (41.7%). Whole exome sequencing revealed genetic alterations in 9 of the 16 patients (56.3%), including 8 de novo alterations (2 copy number variants and variants in ARID1B, CDK8, HIVEP2, and TCF4) and a recessive variant of TBCK. De novo ARID1B variants were identified in three unrelated individuals, suggesting that ARID1B variants are major genetic causes of CCAs. A de novo TCF4 variant and somatic mosaic deletion at 18q21.31-qter encompassing TCF4 suggest an association of TCF4 abnormalities with CCAs. This study, which analyzes CCA patients usung whole exome sequencing, demonstrates that comprehensive genetic analysis would be useful for investigating various causal variants of CCAs.
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Affiliation(s)
- Sachiko Miyamoto
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, Tokyo, Japan
| | - Takuya Hiraide
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Tadashi Shiohama
- Department of Pediatrics, Graduated School of Medicine, Chiba University, Chiba, Japan
| | - Tomohide Goto
- Division of Neurology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Akira Hojo
- Department of Pediatrics, Showa University School of Medicine, Tokyo, Japan
| | - Akio Ebata
- Department of Pediatrics, Showa University School of Medicine, Tokyo, Japan
| | - Manabu Suzuki
- Department of Pediatrics, Showa University School of Medicine, Tokyo, Japan
| | - Kozue Kobayashi
- Department of Pediatrics, Showa University School of Medicine, Tokyo, Japan
| | - Pin Fee Chong
- Department of Pediatric Neurology, Fukuoka Children's Hospital, Fukuoka, Japan
| | - Ryutaro Kira
- Department of Pediatric Neurology, Fukuoka Children's Hospital, Fukuoka, Japan
| | | | - Hiroko Ikeda
- Department of Pediatrics, National Epilepsy Center, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, Shizuoka, Japan
| | - Kyoko Hoshino
- Segawa Memorial Neurological Clinic for Children, Tokyo, Japan
| | - Mayumi Matsufuji
- Department of Pediatrics, Minami Kyushu National Hospital, Aira, Japan
| | - Nobuko Moriyama
- Department of Pediatrics, Hitachi, Ltd., Hitachinaka General Hospital, Hitachinaka, Japan
| | - Masayuki Furuyama
- Department of Pediatrics, Okitama Public General Hospital, Yamagata, Japan
| | - Tatsuya Yamamoto
- Department of Pediatrics, Hirosaki University School of Medicine, Hirosaki, Japan
| | - Mitsuko Nakashima
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan.
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan.
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50
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Min Z, Qian C, Ying D. Novel ARID1B variant inherited from somatogonadal mosaic mother in siblings with Coffin-Siris syndrome 1. Exp Ther Med 2021; 21:614. [PMID: 33936271 PMCID: PMC8082577 DOI: 10.3892/etm.2021.10046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 04/21/2020] [Indexed: 12/20/2022] Open
Abstract
Coffin-Siris syndrome1 (CSS1; Online Mendelian Inheritance in Man no. 135900) is a multiple malformation syndrome characterized by intellectual and/or developmental delay, and hypoplastic or absent fifth fingernails and/or toenails. AT-rich interaction domain-containing protein 1B (ARID1B) is the most frequently mutated gene in CSS1 and the majority of reported cases have been sporadic. Using whole-exome sequencing, the present study identified two siblings with CSS1 with a novel heterozygous co-segregating pathogenic variant in the ARID1B gene (c.3468_3471del). Additionally, the current study confirmed a 4% somatic ARID1B mosaicism in the patient's mother. The results expanded the spectrum of known ARID1B pathogenic variants. To the best of our knowledge, the present study is the first to provide experimental evidence that an ARID1B pathogenic variant can be inherited from a clinically healthy somatogonadal mosaic mother.
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Affiliation(s)
- Zhong Min
- Department of Neurology, Children's Hospital of Chongqing Medical University, Chongqing 400014, P.R. China.,Pediatric Research Institute, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Engineering Research Center of Stem Cell Therapy, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing 400014, P.R. China.,National Clinical Research Center for Child Health and Disorders, Chongqing 400014, P.R. China.,Department of Pediatric, Qianjiang Central Hospital of Chongqing, Chongqing 409000, P.R. China
| | - Cheng Qian
- Pediatric Research Institute, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Engineering Research Center of Stem Cell Therapy, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing 400014, P.R. China.,National Clinical Research Center for Child Health and Disorders, Chongqing 400014, P.R. China.,Department of Primary Child Health Care, Children's Hospital of Chongqing Medical University, Chongqing 400014, P.R. China
| | - Dai Ying
- Pediatric Research Institute, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Engineering Research Center of Stem Cell Therapy, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing 400014, P.R. China.,National Clinical Research Center for Child Health and Disorders, Chongqing 400014, P.R. China.,Department of Primary Child Health Care, Children's Hospital of Chongqing Medical University, Chongqing 400014, P.R. China
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