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Abad C, Robayo MC, Muñiz-Moreno MDM, Bernardi MT, Otero MG, Kosanovic C, Griswold AJ, Pierson TM, Walz K, Young JI. Gatad2b, associated with the neurodevelopmental syndrome GAND, plays a critical role in neurodevelopment and cortical patterning. Transl Psychiatry 2024; 14:33. [PMID: 38238293 PMCID: PMC10796954 DOI: 10.1038/s41398-023-02678-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 11/06/2023] [Accepted: 11/23/2023] [Indexed: 01/22/2024] Open
Abstract
GATAD2B (GATA zinc finger domain containing 2B) variants are associated with the neurodevelopmental syndrome GAND, characterized by intellectual disability (ID), infantile hypotonia, apraxia of speech, epilepsy, macrocephaly and distinct facial features. GATAD2B encodes for a subunit of the Nucleosome Remodeling and Histone Deacetylase (NuRD) complex. NuRD controls transcriptional programs critical for proper neurodevelopment by coupling histone deacetylase with ATP-dependent chromatin remodeling activity. To study mechanisms of pathogenesis for GAND, we characterized a mouse model harboring an inactivating mutation in Gatad2b. Homozygous Gatad2b mutants die perinatally, while haploinsufficient Gatad2b mice exhibit behavioral abnormalities resembling the clinical features of GAND patients. We also observed abnormal cortical patterning, and cellular proportions and cell-specific alterations in the developmental transcriptome in these mice. scRNAseq of embryonic cortex indicated misexpression of genes key for corticogenesis and associated with neurodevelopmental syndromes such as Bcl11b, Nfia and H3f3b and Sox5. These data suggest a crucial role for Gatad2b in brain development.
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Affiliation(s)
- Clemer Abad
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Maria C Robayo
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Maria Del Mar Muñiz-Moreno
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
- KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
| | - Maria T Bernardi
- IQUIBICEN - CONICET, School of Exact and Natural Sciences - University of Buenos Aires, Buenos Aires, Argentina
| | - Maria G Otero
- The Board of Governors Regenerative Medicine Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Christina Kosanovic
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Anthony J Griswold
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Tyler Mark Pierson
- The Board of Governors Regenerative Medicine Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
- Guerin Children's, Departments of Pediatrics, Cedars Sinai Medical Center, Los Angeles, CA, USA
- Department of Neurology, Cedars Sinai Medical Center, Los Angeles, CA, USA
- The Center for the Undiagnosed Patient, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Katherina Walz
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
- IQUIBICEN - CONICET, School of Exact and Natural Sciences - University of Buenos Aires, Buenos Aires, Argentina
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Juan I Young
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA.
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA.
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2
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Bosetti C, Ferrini L, Ferrari AR, Bartolini E, Calderoni S. Children with Autism Spectrum Disorder and Abnormalities of Clinical EEG: A Qualitative Review. J Clin Med 2024; 13:279. [PMID: 38202286 PMCID: PMC10779511 DOI: 10.3390/jcm13010279] [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: 11/20/2023] [Revised: 12/22/2023] [Accepted: 12/31/2023] [Indexed: 01/12/2024] Open
Abstract
Over the last decade, the comorbidity between Autism Spectrum Disorder (ASD) and epilepsy has been widely demonstrated, and many hypotheses regarding the common neurobiological bases of these disorders have been put forward. A variable, but significant, prevalence of abnormalities on electroencephalogram (EEG) has been documented in non-epileptic children with ASD; therefore, several scientific studies have recently tried to demonstrate the role of these abnormalities as a possible biomarker of altered neural connectivity in ASD individuals. This narrative review intends to summarize the main findings of the recent scientific literature regarding abnormalities detected with standard EEG in children/adolescents with idiopathic ASD. Research using three different databases (PubMed, Scopus and Google Scholar) was conducted, resulting in the selection of 10 original articles. Despite an important lack of studies on preschoolers and a deep heterogeneity in results, some authors speculated on a possible association between EEG abnormalities and ASD characteristics, in particular, the severity of symptoms. Although this correlation needs to be more strongly elucidated, these findings may encourage future studies aimed at demonstrating the role of electrical brain abnormalities as an early biomarker of neural circuit alterations in ASD, highlighting the potential diagnostic, prognostic and therapeutic value of EEG in this field.
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Affiliation(s)
- Chiara Bosetti
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, 56128 Pisa, Italy; (C.B.); (L.F.); (A.R.F.); (S.C.)
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy
| | - Luca Ferrini
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, 56128 Pisa, Italy; (C.B.); (L.F.); (A.R.F.); (S.C.)
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, 56126 Pisa, Italy
| | - Anna Rita Ferrari
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, 56128 Pisa, Italy; (C.B.); (L.F.); (A.R.F.); (S.C.)
| | - Emanuele Bartolini
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, 56128 Pisa, Italy; (C.B.); (L.F.); (A.R.F.); (S.C.)
- Tuscany PhD Programme in Neurosciences, 50139 Florence, Italy
| | - Sara Calderoni
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, 56128 Pisa, Italy; (C.B.); (L.F.); (A.R.F.); (S.C.)
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy
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Larrigan S, Joshi SV, Mattar P. Divergent phenotypes in constitutive versus conditional mutant mouse models of Sifrim-Hitz-Weiss syndrome. Hum Mol Genet 2023; 32:3361-3373. [PMID: 37738575 PMCID: PMC10695680 DOI: 10.1093/hmg/ddad157] [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: 02/15/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 09/24/2023] Open
Abstract
Chromatin remodellers are among the most important risk genes associated with neurodevelopmental disorders (NDDs), however, their functions during brain development are not fully understood. Here, we focused on Sifrim-Hitz-Weiss Syndrome (SIHIWES)-an intellectual disability disorder caused by mutations in the CHD4 chromodomain helicase gene. We utilized mouse genetics to excise the Chd4 ATPase/helicase domain-either constitutively, or conditionally in the developing telencephalon. Conditional heterozygotes exhibited no change in cortical size and cellular composition, and had only subtle behavioral phenotypes. Telencephalon-specific conditional knockouts had marked reductions in cortical growth, reduced numbers of upper-layer neurons, and exhibited alterations in anxiety and repetitive behaviors. Despite the fact that whole-body heterozygotes exhibited comparable growth defects, they were unaffected in these behaviors, but instead exhibited female-specific alterations in learning and memory. These data reveal unexpected phenotypic divergence arising from differences in the spatiotemporal deployment of loss-of-function manipulations, underscoring the importance of context in chromatin remodeller function during neurodevelopment.
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Affiliation(s)
- Sarah Larrigan
- Ottawa Hospital Research Institute (OHRI), Ottawa, ON K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Shrilaxmi V Joshi
- Ottawa Hospital Research Institute (OHRI), Ottawa, ON K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Pierre Mattar
- Ottawa Hospital Research Institute (OHRI), Ottawa, ON K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
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Muhammad T, Pastore SF, Good K, Ausió J, Vincent JB. Chromatin gatekeeper and modifier CHD proteins in development, and in autism and other neurological disorders. Psychiatr Genet 2023; 33:213-232. [PMID: 37851134 DOI: 10.1097/ypg.0000000000000353] [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] [Indexed: 10/19/2023]
Abstract
Chromatin, a protein-DNA complex, is a dynamic structure that stores genetic information within the nucleus and responds to molecular/cellular changes in its structure, providing conditional access to the genetic machinery. ATP-dependent chromatin modifiers regulate access of transcription factors and RNA polymerases to DNA by either "opening" or "closing" the structure of chromatin, and its aberrant regulation leads to a variety of neurodevelopmental disorders. The chromodomain helicase DNA-binding (CHD) proteins are ATP-dependent chromatin modifiers involved in the organization of chromatin structure, act as gatekeepers of genomic access, and deposit histone variants required for gene regulation. In this review, we first discuss the structural and functional domains of the CHD proteins, and their binding sites, and phosphorylation, acetylation, and methylation sites. The conservation of important amino acids in SWItch/sucrose non-fermenting (SWI/SNF) domains, and their protein and mRNA tissue expression profiles are discussed. Next, we convey the important binding partners of CHD proteins, their protein complexes and activities, and their involvements in epigenetic regulation. We also show the ChIP-seq binding dynamics for CHD1, CHD2, CHD4, and CHD7 proteins at promoter regions of histone genes, as well as several genes that are critical for neurodevelopment. The role of CHD proteins in development is also discussed. Finally, this review provides information about CHD protein mutations reported in autism and neurodevelopmental disorders, and their pathogenicity. Overall, this review provides information on the progress of research into CHD proteins, their structural and functional domains, epigenetics, and their role in stem cell, development, and neurological disorders.
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Affiliation(s)
- Tahir Muhammad
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health
- Institute of Medical Science, University of Toronto, Toronto, ON
| | - Stephen F Pastore
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health
- Institute of Medical Science, University of Toronto, Toronto, ON
| | - Katrina Good
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC
| | - John B Vincent
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health
- Institute of Medical Science, University of Toronto, Toronto, ON
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
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Wu CS, Tsai TH, Chen WL, Tsai HJ, Chien YL. Ophthalmologic diagnoses in youths with autism spectrum disorder: Prevalence and clinical correlates. Autism Res 2023; 16:2008-2020. [PMID: 37632715 DOI: 10.1002/aur.3019] [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: 06/15/2022] [Accepted: 08/10/2023] [Indexed: 08/28/2023]
Abstract
Autism spectrum disorder (ASD) is associated with a high prevalence of visual dysfunction. This study aimed to investigate the rates of amblyopia, refractive errors, and strabismus, as well as their clinical correlates in ASD. This population-based matched-cohort study used data from the Taiwan National Health Insurance Research Database. A total of 3,551 youths with ASD and 35,510 non-autistic control participants matched by age and sex were included. All the participants were followed-up until they were 18 years old. The prevalence of amblyopia, refractive errors, and strabismus was compared between the ASD and control groups. Effect modifiers, including sex, ASD subgroup, and co-diagnosis of intelligence disability, were examined. Compared to the control group, youths with ASD had a significantly increased risk of amblyopia (adjusted odds ratio [aOR] = 1.75), anisometropia (aOR = 1.66), astigmatism (aOR = 1.51), hypermetropia (aOR = 2.08), exotropia (aOR = 2.86), and esotropia (aOR = 2.63), but a comparable likelihood of myopia according to age. Males with ASD had a significantly lower likelihood of exotropia, but a higher likelihood of myopia than females with ASD. The autism subgroup had a higher OR for hypermetropia, but a lower OR for myopia than the other ASD subgroups. ASD youths with intelligence disabilities demonstrated significantly higher ORs for amblyopia, hypermetropia, and all types of strabismus and lower OR for myopia than those without intelligence disabilities. In conclusion, the rates of amblyopia, refractive errors, and strabismus were higher in youths with ASD. Ocular abnormalities in youths with ASD require a comprehensive assessment and management.
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Affiliation(s)
- Chi-Shin Wu
- National Center for Geriatrics and Welfare Research, National Health Research Institutes, Yunlin, Taiwan
- Department of Psychiatry, National Taiwan University Hospital, Yunlin Branch, Yunlin, Taiwan
| | - Tzu-Hsun Tsai
- Department of Ophthalmology, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
| | - Wei-Li Chen
- Department of Ophthalmology, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
- Advanced Ocular Surface and Corneal Nerve Regeneration Center, National Taiwan University Hospital, Taipei, Taiwan
| | - Hui-Ju Tsai
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Yi-Ling Chien
- Department of Psychiatry, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
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Werren EA, Guxholli A, Jones N, Wagner M, Hannibal I, Granadillo JL, Tyndall AV, Moccia A, Kuehl R, Levandoski KM, Day-Salvatore DL, Wheeler M, Chong JX, Bamshad MJ, Innes AM, Pierson TM, Mackay JP, Bielas SL, Martin DM. De novo variants in GATAD2A in individuals with a neurodevelopmental disorder: GATAD2A-related neurodevelopmental disorder. HGG ADVANCES 2023; 4:100198. [PMID: 37181331 PMCID: PMC10172836 DOI: 10.1016/j.xhgg.2023.100198] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 04/07/2023] [Indexed: 05/16/2023] Open
Abstract
GATA zinc finger domain containing 2A (GATAD2A) is a subunit of the nucleosome remodeling and deacetylase (NuRD) complex. NuRD is known to regulate gene expression during neural development and other processes. The NuRD complex modulates chromatin status through histone deacetylation and ATP-dependent chromatin remodeling activities. Several neurodevelopmental disorders (NDDs) have been previously linked to variants in other components of NuRD's chromatin remodeling subcomplex (NuRDopathies). We identified five individuals with features of an NDD that possessed de novo autosomal dominant variants in GATAD2A. Core features in affected individuals include global developmental delay, structural brain defects, and craniofacial dysmorphology. These GATAD2A variants are predicted to affect protein dosage and/or interactions with other NuRD chromatin remodeling subunits. We provide evidence that a GATAD2A missense variant disrupts interactions of GATAD2A with CHD3, CHD4, and CHD5. Our findings expand the list of NuRDopathies and provide evidence that GATAD2A variants are the genetic basis of a previously uncharacterized developmental disorder.
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Affiliation(s)
- Elizabeth A. Werren
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Alba Guxholli
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Natasha Jones
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Matias Wagner
- Institute of Human Genetics, Technical University of Munich, 80333 Munich, Germany
| | - Iris Hannibal
- Institute of Human Genetics, Technical University of Munich, 80333 Munich, Germany
| | - Jorge L. Granadillo
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Amanda V. Tyndall
- Department of Medical Genetics, Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Amanda Moccia
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Ryan Kuehl
- Saint Peter’s University Hospital, New Brunswick, NJ 08901, USA
| | | | | | - Marsha Wheeler
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - University of Washington Center for Mendelian Genomics
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
- Institute of Human Genetics, Technical University of Munich, 80333 Munich, Germany
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Medical Genetics, Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Saint Peter’s University Hospital, New Brunswick, NJ 08901, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute, Seattle, WA 98195, USA
- Department of Pediatrics, Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Division of Pediatric Neurology, Department of Pediatrics, Guerin Children’s, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Center for the Undiagnosed Patient, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jessica X. Chong
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute, Seattle, WA 98195, USA
| | - Michael J. Bamshad
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute, Seattle, WA 98195, USA
| | - A. Micheil Innes
- Department of Medical Genetics, Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Pediatrics, Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Tyler Mark Pierson
- Division of Pediatric Neurology, Department of Pediatrics, Guerin Children’s, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Center for the Undiagnosed Patient, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Joel P. Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Stephanie L. Bielas
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Donna M. Martin
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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Barili V, Ambrosini E, Uliana V, Bellini M, Vitetta G, Martorana D, Cannizzaro IR, Taiani A, De Sensi E, Caggiati P, Hilton S, Banka S, Percesepe A. Success and Pitfalls of Genetic Testing in Undiagnosed Diseases: Whole Exome Sequencing and Beyond. Genes (Basel) 2023; 14:1241. [PMID: 37372421 DOI: 10.3390/genes14061241] [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: 04/30/2023] [Revised: 06/01/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Novel approaches to uncover the molecular etiology of neurodevelopmental disorders (NDD) are highly needed. Even using a powerful tool such as whole exome sequencing (WES), the diagnostic process may still prove long and arduous due to the high clinical and genetic heterogeneity of these conditions. The main strategies to improve the diagnostic rate are based on family segregation, re-evaluation of the clinical features by reverse-phenotyping, re-analysis of unsolved NGS-based cases and epigenetic functional studies. In this article, we described three selected cases from a cohort of patients with NDD in which trio WES was applied, in order to underline the typical challenges encountered during the diagnostic process: (1) an ultra-rare condition caused by a missense variant in MEIS2, identified through the updated Solve-RD re-analysis; (2) a patient with Noonan-like features in which the NGS analysis revealed a novel variant in NIPBL causing Cornelia de Lange syndrome; and (3) a case with de novo variants in genes involved in the chromatin-remodeling complex, for which the study of the epigenetic signature excluded a pathogenic role. In this perspective, we aimed to (i) provide an example of the relevance of the genetic re-analysis of all unsolved cases through network projects on rare diseases; (ii) point out the role and the uncertainties of the reverse phenotyping in the interpretation of the genetic results; and (iii) describe the use of methylation signatures in neurodevelopmental syndromes for the validation of the variants of uncertain significance.
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Affiliation(s)
- Valeria Barili
- Medical Genetics, Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Enrico Ambrosini
- Medical Genetics, Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Vera Uliana
- Medical Genetics, University Hospital of Parma, 43126 Parma, Italy
| | - Melissa Bellini
- Department of Pediatrics and Neonatology, Guglielmo da Saliceto Hospital, 29121 Piacenza, Italy
| | - Giulia Vitetta
- Medical Genetics, University of Bologna, 40138 Bologna, Italy
| | - Davide Martorana
- Medical Genetics, University Hospital of Parma, 43126 Parma, Italy
| | - Ilenia Rita Cannizzaro
- Medical Genetics, Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Antonietta Taiani
- Medical Genetics, Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Erika De Sensi
- Medical Genetics, Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | | | - Sarah Hilton
- Division of Evolution, Infection & Genomics, School of Biological Sciences, Faculty of Biology, Medicine & Health, The University of Manchester, Manchester M13 9PL, UK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University Foundation NHS Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Siddharth Banka
- Division of Evolution, Infection & Genomics, School of Biological Sciences, Faculty of Biology, Medicine & Health, The University of Manchester, Manchester M13 9PL, UK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University Foundation NHS Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Antonio Percesepe
- Medical Genetics, Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
- Medical Genetics, University Hospital of Parma, 43126 Parma, Italy
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Boulasiki P, Tan XW, Spinelli M, Riccio A. The NuRD Complex in Neurodevelopment and Disease: A Case of Sliding Doors. Cells 2023; 12:cells12081179. [PMID: 37190088 DOI: 10.3390/cells12081179] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/12/2023] [Accepted: 04/14/2023] [Indexed: 05/17/2023] Open
Abstract
The Nucleosome Remodelling and Deacetylase (NuRD) complex represents one of the major chromatin remodelling complexes in mammalian cells, uniquely coupling the ability to "open" the chromatin by inducing nucleosome sliding with histone deacetylase activity. At the core of the NuRD complex are a family of ATPases named CHDs that utilise the energy produced by the hydrolysis of the ATP to induce chromatin structural changes. Recent studies have highlighted the prominent role played by the NuRD in regulating gene expression during brain development and in maintaining neuronal circuitry in the adult cerebellum. Importantly, components of the NuRD complex have been found to carry mutations that profoundly affect neurological and cognitive development in humans. Here, we discuss recent literature concerning the molecular structure of NuRD complexes and how the subunit composition and numerous permutations greatly determine their functions in the nervous system. We will also discuss the role of the CHD family members in an array of neurodevelopmental disorders. Special emphasis will be given to the mechanisms that regulate the NuRD complex composition and assembly in the cortex and how subtle mutations may result in profound defects of brain development and the adult nervous system.
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Affiliation(s)
- Paraskevi Boulasiki
- UCL Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Xiao Wei Tan
- UCL Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Matteo Spinelli
- UCL Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
- Neuroscience Department, Catholic University of the Sacred Heart, 00168 Rome, Italy
| | - Antonella Riccio
- UCL Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
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Pant P, Chitme H, Sircar R, Prasad R, Prasad HO. Genome-wide association study for single nucleotide polymorphism associated with mural and cumulus granulosa cells of PCOS (polycystic ovary syndrome) and non-PCOS patients. FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2023. [DOI: 10.1186/s43094-023-00475-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023] Open
Abstract
Abstract
Background
The genetic make-up of local granulosa cells and their function in the pathophysiology of polycystic ovary syndrome (PCOS) is crucial to a full comprehension of the disorder. The major purpose of this study was to compare the Single Nucleotide Polymorphism (SNP) of cumulus granulosa cells (CGCs) and mural granulosa cells (MGCs) between healthy individuals and women with PCOS using genome-wide association analysis (GWA). A case–control study was conducted in a total of 24 women diagnosed with PCOS and 24 healthy non-PCOS women of reproductive age aggregated into 4 samples of 6 patients each. GWA studies entail several processes, such as cell separation, cellular DNA extraction, library preparation followed by interpretation using bioinformatics databases. SNP locations were identified by reference gene also involves the use of Matrix-assisted laser desorption/ionisation-time of flight (MALDI-TOF) mass spectrometry (MS) (MALDI-TOF-MS) for the first sorting. Hybridization with the gene chip was followed by reading the SNP genotypes according to the publications in the literature. TASSEL (Trait Analysis by aSSociation, Evolution and Linkage) program and methods were used for GWA studies.
Results
An aggregate of 21,039 SNP calls were obtained from our samples. Genes of autoimmune illnesses, obesity, inflammatory illnesses, nervous system diseases such as retinitis pigmentosa, autism, neural tube defects, and Alzheimer's disease; and various malignancies such as lung cancer, colorectal cancer, breast cancer were also identified in these cells. Gene ranking score reveals that granulosa cells carry key genes of neurological system and reproductive systems especially in brain and testis, respectively.
Conclusions
Mural and Cumulus Granulosa cells were shown to have the PCOS directly and indirectly related genes MMP9, PRKAA2, COMT and HP. We found that the expression of ARID4B, MUC5AC, NID2, CREBBP, GNB1, KIF2C, COL18A1, and HNRNPC by these cells may contribute to PCOS.
Graphical abstract
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10
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Shrestha P, Jaganathan A, Huilgol D, Ballon C, Hwangbo Y, Mills AA. Chd5 Regulates the Transcription Factor Six3 to Promote Neuronal Differentiation. Stem Cells 2023; 41:242-251. [PMID: 36636025 PMCID: PMC10020979 DOI: 10.1093/stmcls/sxad002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 12/16/2022] [Indexed: 01/14/2023]
Abstract
Chromodomain helicase DNA-binding protein 5 (Chd5) is an ATP-dependent chromatin remodeler that promotes neuronal differentiation. However, the mechanism behind the action of Chd5 during neurogenesis is not clearly understood. Here we use transcriptional profiling of cells obtained from Chd5 deficient mice at early and late stages of neuronal differentiation to show that Chd5 regulates neurogenesis by directing stepwise transcriptional changes. During early stages of neurogenesis, Chd5 promotes expression of the proneural transcription factor Six3 to repress Wnt5a, a non-canonical Wnt ligand essential for the maturation of neurons. This previously unappreciated ability of Chd5 to transcriptionally repress neuronal maturation factors is critical for both lineage specification and maturation. Thus, Chd5 facilitates early transcriptional changes in neural stem cells, thereby initiating transcriptional programs essential for neuronal fate specification.
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Affiliation(s)
- Padmina Shrestha
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Department of Molecular and Cell Biology, Stony Brook University, Stony Brook, NY, USA
| | | | - Dhananjay Huilgol
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
| | - Carlos Ballon
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Yon Hwangbo
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Alea A Mills
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
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11
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Chow JC, Hormozdiari F. Prediction of Neurodevelopmental Disorders Based on De Novo Coding Variation. J Autism Dev Disord 2023; 53:963-976. [PMID: 35596027 PMCID: PMC9986216 DOI: 10.1007/s10803-022-05586-z] [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] [Accepted: 04/21/2022] [Indexed: 11/27/2022]
Abstract
The early detection of neurodevelopmental disorders (NDDs) can significantly improve patient outcomes. The differential burden of non-synonymous de novo mutation among NDD cases and controls indicates that de novo coding variation can be used to identify a subset of samples that will likely display an NDD phenotype. Thus, we have developed an approach for the accurate prediction of NDDs with very low false positive rate (FPR) using de novo coding variation for a small subset of cases. We use a shallow neural network that integrates de novo likely gene-disruptive and missense variants, measures of gene constraint, and conservation information to predict a small subset of NDD cases at very low FPR and prioritizes NDD risk genes for future clinical study.
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Affiliation(s)
- Julie C Chow
- UC Davis Genome Center, University of California, Davis, CA, 95616, USA.
| | - Fereydoun Hormozdiari
- UC Davis Genome Center, University of California, Davis, CA, 95616, USA.
- MIND Institute, University of California, Davis, 95817, USA.
- Biochemistry and Molecular Medicine, University of California, Davis, 95616, USA.
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12
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Jacquin C, Landais E, Poirsier C, Afenjar A, Akhavi A, Bednarek N, Bénech C, Bonnard A, Bosquet D, Burglen L, Callier P, Chantot-Bastaraud S, Coubes C, Coutton C, Delobel B, Descharmes M, Dupont JM, Gatinois V, Gruchy N, Guterman S, Heddar A, Herissant L, Heron D, Isidor B, Jaeger P, Jouret G, Keren B, Kuentz P, Le Caignec C, Levy J, Lopez N, Manssens Z, Martin-Coignard D, Marey I, Mignot C, Missirian C, Pebrel-Richard C, Pinson L, Puechberty J, Redon S, Sanlaville D, Spodenkiewicz M, Tabet AC, Verloes A, Vieville G, Yardin C, Vialard F, Doco-Fenzy M. 1p36 deletion syndrome: Review and mapping with further characterization of the phenotype, a new cohort of 86 patients. Am J Med Genet A 2023; 191:445-458. [PMID: 36369750 PMCID: PMC10100125 DOI: 10.1002/ajmg.a.63041] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 08/29/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022]
Abstract
Chromosome 1p36 deletion syndrome (1p36DS) is one of the most common terminal deletion syndromes (incidence between 1/5000 and 1/10,000 live births in the American population), due to a heterozygous deletion of part of the short arm of chromosome 1. The 1p36DS is characterized by typical craniofacial features, developmental delay/intellectual disability, hypotonia, epilepsy, cardiomyopathy/congenital heart defect, brain abnormalities, hearing loss, eyes/vision problem, and short stature. The aim of our study was to (1) evaluate the incidence of the 1p36DS in the French population compared to 22q11.2 deletion syndrome and trisomy 21; (2) review the postnatal phenotype related to microarray data, compared to previously publish prenatal data. Thanks to a collaboration with the ACLF (Association des Cytogénéticiens de Langue Française), we have collected data of 86 patients constituting, to the best of our knowledge, the second-largest cohort of 1p36DS patients in the literature. We estimated an average of at least 10 cases per year in France. 1p36DS seems to be much less frequent than 22q11.2 deletion syndrome and trisomy 21. Patients presented mainly dysmorphism, microcephaly, developmental delay/intellectual disability, hypotonia, epilepsy, brain malformations, behavioral disorders, cardiomyopathy, or cardiovascular malformations and, pre and/or postnatal growth retardation. Cardiac abnormalities, brain malformations, and epilepsy were more frequent in distal deletions, whereas microcephaly was more common in proximal deletions. Mapping and genotype-phenotype correlation allowed us to identify four critical regions responsible for intellectual disability. This study highlights some phenotypic variability, according to the deletion position, and helps to refine the phenotype of 1p36DS, allowing improved management and follow-up of patients.
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Affiliation(s)
- Clémence Jacquin
- Service de Génétique, CRMR AnDDI-Rares, CHU Reims, Reims, France
| | - Emilie Landais
- Service de Génétique, CRMR AnDDI-Rares, CHU Reims, Reims, France
| | - Céline Poirsier
- Service de Génétique, CRMR AnDDI-Rares, CHU Reims, Reims, France
| | - Alexandra Afenjar
- Centre de Référence des Malformations et Maladies Congénitales du Cervelet, Département de Génétique et Embryologie Médicale, APHP, Hôpital Trousseau, Paris, France
| | - Ahmad Akhavi
- Cardiologie pédiatrique et congénitale, CHU Reims, Reims, France
| | - Nathalie Bednarek
- Service de pédiatrie, Pôle Femme Parents Enfants, CHU Reims, Reims, France.,CReSTIC/EA 3804, URCA, Reims, France
| | - Caroline Bénech
- University of Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
| | - Adeline Bonnard
- Département de Génétique, Hôpital Robert Debré, Paris, France
| | - Damien Bosquet
- Service de Génétique, Hospices Civils de Lyon, Bron, France
| | - Lydie Burglen
- Centre de Référence des Malformations et Maladies Congénitales du Cervelet, Département de Génétique et Embryologie Médicale, APHP, Hôpital Trousseau, Paris, France
| | | | - Sandra Chantot-Bastaraud
- AP-HP Sorbonne Université, Département de Génétique Médicale, Hôpital Armand Trousseau, Paris, France
| | - Christine Coubes
- Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Génétique clinique, CHU Montpellier, Université Montpellier, Centre de référence anomalies du développement SOOR, Montpellier, France
| | - Charles Coutton
- Département de Génétique et Procréation, Hôpital Couple Enfant, CHU Grenoble-Alpes, Grenoble, France.,Genetic Epigenetic and Therapies of Infertility team, Institute for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, Grenoble, France
| | - Bruno Delobel
- Centre de Génétique Chromosomique, GH de l'Institut Catholique de Lille-Hopital Saint Vincent de Paul, Lille, France
| | - Margaux Descharmes
- Service de pédiatrie, Pôle Femme Parents Enfants, CHU Reims, Reims, France
| | - Jean-Michel Dupont
- Laboratoire de Cytogénétique Constitutionnelle, APHP. Centre-Université Paris Cité site Cochin, Paris, France
| | - Vincent Gatinois
- Plateforme ChromoStem, Unité de génétique chromosomique, Département de génétique moléculaire et cytogénomique, CHU de Montpellier, Université de Montpellier, Montpellier, France
| | - Nicolas Gruchy
- Service de Génétique, CHU Caen, Université Caen Normandie, Caen, France
| | - Sarah Guterman
- Département de Génétique, Centre Hospitalier Intercommunal Poissy-St-Germain-en-Laye, Poissy, France
| | - Abdelkader Heddar
- Laboratoire de Cytogénétique Constitutionnelle, APHP. Centre-Université Paris Cité site Cochin, Paris, France
| | - Lucas Herissant
- Service de Génétique, CRMR AnDDI-Rares, CHU Reims, Reims, France
| | - Delphine Heron
- AP-HP Sorbonne Université, Département de Génétique Médicale, Hôpital Armand Trousseau, Paris, France.,Département de Génétique; Centre de Référence Déficience Intellectuelle de Causes Rares, APHP Sorbonne Université, GH Pitié-Salpêtrière, Paris, France
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU de Nantes, Nantes, France
| | - Pauline Jaeger
- Service de Génétique, Hospices Civils de Lyon, Bron, France
| | - Guillaume Jouret
- National Center of Genetics, Laboratoire National de Santé, Dudelange, Luxembourg
| | - Boris Keren
- Département de Génétique; Centre de Référence Déficience Intellectuelle de Causes Rares, APHP Sorbonne Université, GH Pitié-Salpêtrière, Paris, France
| | - Paul Kuentz
- Oncobiologie Génétique Bioinformatique, CHU de Besançon, Besançon, France
| | | | - Jonathan Levy
- Département de Génétique, Hôpital Robert Debré, Paris, France
| | - Nathalie Lopez
- Service de neuropédiatrie, Hôpital Armand Trousseau, Groupe Hospitalier Universitaire de l'Est Parisien, Paris, France
| | - Zoe Manssens
- Centre de Génétique Chromosomique, GH de l'Institut Catholique de Lille-Hopital Saint Vincent de Paul, Lille, France
| | | | - Isabelle Marey
- Département de Génétique et Procréation, Hôpital Couple Enfant, CHU Grenoble-Alpes, Grenoble, France
| | - Cyril Mignot
- AP-HP Sorbonne Université, Département de Génétique Médicale, Hôpital Armand Trousseau, Paris, France.,Département de Génétique; Centre de Référence Déficience Intellectuelle de Causes Rares, APHP Sorbonne Université, GH Pitié-Salpêtrière, Paris, France
| | - Chantal Missirian
- Laboratoire de Génétique Chromosomique, Département de Génétique Médicale, AP- HM, Marseille, France
| | - Céline Pebrel-Richard
- Service de Cytogénétique Médicale, CHU de Clermont-Ferrand, Clermont-Ferrand, France
| | - Lucile Pinson
- Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Génétique clinique, CHU Montpellier, Université Montpellier, Centre de référence anomalies du développement SOOR, Montpellier, France
| | - Jacques Puechberty
- Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Génétique clinique, CHU Montpellier, Université Montpellier, Centre de référence anomalies du développement SOOR, Montpellier, France
| | - Sylvia Redon
- University of Brest, Inserm, EFS, UMR 1078, GGB, Brest, France.,Service de Génétique Médicale et Biologie de la Reproduction, CHU de Brest, Brest, France
| | | | | | | | - Alain Verloes
- Département de Génétique, Hôpital Robert Debré, Paris, France
| | - Gaelle Vieville
- Département de Génétique et Procréation, Hôpital Couple Enfant, CHU Grenoble-Alpes, Grenoble, France
| | - Catherine Yardin
- Department of Cytogenetics and clinical genetics, Limoges University Hospital, University of Limoges, Limoges, France
| | - François Vialard
- Département de Génétique, Centre Hospitalier Intercommunal Poissy-St-Germain-en-Laye, Poissy, France.,RHuMA, UMR BREED, INRAE-UVSQ-ENVA, Montigny-le-bretonneux, France
| | - Martine Doco-Fenzy
- Service de Génétique, CRMR AnDDI-Rares, CHU Reims, Reims, France.,Service de génétique médicale, CHU de Nantes, Nantes, France.,L'institut du thorax, INSERM, CNRS, UNIV Nantes, CHU de Nantes, Nantes, France
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13
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Tu Z, Zheng Y. Role of ATP-dependent chromatin remodelers in hematopoietic stem and progenitor cell maintenance. Curr Opin Hematol 2022; 29:174-180. [PMID: 35787545 PMCID: PMC9257093 DOI: 10.1097/moh.0000000000000710] [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] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW ATP-dependent chromatin remodeling factors utilize energy from ATP hydrolysis to modulate DNA-histone structures and regulate gene transcription. They are essential during hematopoiesis and for hematopoietic stem and progenitor cell (HSPC) function. This review discusses the recently unveiled roles of these chromatin remodelers in HSPC regulation, with an emphasis on the mechanism of chromodomain helicase DNA-binding (CHD) family members. RECENT FINDINGS Recent studies of ATP-dependent chromatin remodelers have revealed that individual CHD family members engage in distinct mechanisms in regulating HSPC cell fate. For example, CHD8 is required for HSPC survival by restricting both P53 transcriptional activity and protein stability in steady state hematopoiesis while the related CHD7 physically interacts with RUNX family transcription factor 1 (RUNX1) and suppresses RUNX1-induced expansion of HSPCs during blood development. Moreover, other CHD subfamily members such as CHD1/CHD2 and CHD3/CHD4, as well as the switch/sucrose non-fermentable, imitation SWI, and SWI2/SNF2 related (SWR) families of chromatin modulators, have also been found important for HSPC maintenance by distinct mechanisms. SUMMARY The expanding knowledge of ATP-dependent chromatin remodelers in hematopoiesis illustrates their respective critical roles in HSPC maintenance including the regulation of HSPC differentiation, survival, and self-renewal. Further studies are warranted to elucidate how different chromatin remodeling complexes are integrated in various HSPC cell fate decisions during steady-state and stress hematopoiesis.
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Affiliation(s)
- Zhaowei Tu
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Yi Zheng
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
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14
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Analysis of recent shared ancestry in a familial cohort identifies coding and noncoding autism spectrum disorder variants. NPJ Genom Med 2022; 7:13. [PMID: 35190550 PMCID: PMC8861044 DOI: 10.1038/s41525-022-00284-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 01/21/2022] [Indexed: 12/02/2022] Open
Abstract
Autism spectrum disorder (ASD) is a collection of neurodevelopmental disorders characterized by deficits in social communication and restricted, repetitive patterns of behavior or interests. ASD is highly heritable, but genetically and phenotypically heterogeneous, reducing the power to identify causative genes. We performed whole genome sequencing (WGS) in an ASD cohort of 68 individuals from 22 families enriched for recent shared ancestry. We identified an average of 3.07 million variants per genome, of which an average of 112,512 were rare. We mapped runs of homozygosity (ROHs) in affected individuals and found an average genomic homozygosity of 9.65%, consistent with expectations for multiple generations of consanguineous unions. We identified potentially pathogenic rare exonic or splice site variants in 12 known (including KMT2C, SCN1A, SPTBN1, SYNE1, ZNF292) and 12 candidate (including CHD5, GRB10, PPP1R13B) ASD genes. Furthermore, we annotated noncoding variants in ROHs with brain-specific regulatory elements and identified putative disease-causing variants within brain-specific promoters and enhancers for 5 known ASD and neurodevelopmental disease genes (ACTG1, AUTS2, CTNND2, CNTNAP4, SPTBN4). We also identified copy number variants in two known ASD and neurodevelopmental disease loci in two affected individuals. In total we identified potentially etiological variants in known ASD or neurodevelopmental disease genes for ~61% (14/23) of affected individuals. We combined WGS with homozygosity mapping and regulatory element annotations to identify candidate ASD variants. Our analyses add to the growing number of ASD genes and variants and emphasize the importance of leveraging recent shared ancestry to map disease variants in complex neurodevelopmental disorders.
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15
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Abstract
Chromatin is highly dynamic, undergoing continuous global changes in its structure and type of histone and DNA modifications governed by processes such as transcription, repair, replication, and recombination. Members of the chromodomain helicase DNA-binding (CHD) family of enzymes are ATP-dependent chromatin remodelers that are intimately involved in the regulation of chromatin dynamics, altering nucleosomal structure and DNA accessibility. Genetic studies in yeast, fruit flies, zebrafish, and mice underscore essential roles of CHD enzymes in regulating cellular fate and identity, as well as proper embryonic development. With the advent of next-generation sequencing, evidence is emerging that these enzymes are subjected to frequent DNA copy number alterations or mutations and show aberrant expression in malignancies and other human diseases. As such, they might prove to be valuable biomarkers or targets for therapeutic intervention.
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Affiliation(s)
- Andrej Alendar
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands
| | - Anton Berns
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands
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16
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Liu C, Kang N, Guo Y, Gong P. Advances in Chromodomain Helicase DNA-Binding (CHD) Proteins Regulating Stem Cell Differentiation and Human Diseases. Front Cell Dev Biol 2021; 9:710203. [PMID: 34616726 PMCID: PMC8488160 DOI: 10.3389/fcell.2021.710203] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 07/29/2021] [Indexed: 12/15/2022] Open
Abstract
Background: Regulation of gene expression is critical for stem cell differentiation, tissue development, and human health maintenance. Recently, epigenetic modifications of histone and chromatin remodeling have been verified as key controllers of gene expression and human diseases. Objective: In this study, we review the role of chromodomain helicase DNA-binding (CHD) proteins in stem cell differentiation, cell fate decision, and several known human developmental disorders and cancers. Conclusion: CHD proteins play a crucial role in stem cell differentiation and human diseases.
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Affiliation(s)
- Caojie Liu
- State Key Laboratory of Oral Diseases, West China School of Stomatology, Sichuan University, Chengdu, China
| | - Ning Kang
- State Key Laboratory of Oral Diseases, West China School of Stomatology, Sichuan University, Chengdu, China
| | - Yuchen Guo
- State Key Laboratory of Oral Diseases, West China School of Stomatology, Sichuan University, Chengdu, China
| | - Ping Gong
- State Key Laboratory of Oral Diseases, West China School of Stomatology, Sichuan University, Chengdu, China
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