1
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Friedman MJ, Wagner T, Lee H, Rosenfeld MG, Oh S. Enhancer-promoter specificity in gene transcription: molecular mechanisms and disease associations. Exp Mol Med 2024; 56:772-787. [PMID: 38658702 PMCID: PMC11058250 DOI: 10.1038/s12276-024-01233-y] [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: 11/26/2023] [Revised: 02/28/2024] [Accepted: 03/05/2024] [Indexed: 04/26/2024] Open
Abstract
Although often located at a distance from their target gene promoters, enhancers are the primary genomic determinants of temporal and spatial transcriptional specificity in metazoans. Since the discovery of the first enhancer element in simian virus 40, there has been substantial interest in unraveling the mechanism(s) by which enhancers communicate with their partner promoters to ensure proper gene expression. These research efforts have benefited considerably from the application of increasingly sophisticated sequencing- and imaging-based approaches in conjunction with innovative (epi)genome-editing technologies; however, despite various proposed models, the principles of enhancer-promoter interaction have still not been fully elucidated. In this review, we provide an overview of recent progress in the eukaryotic gene transcription field pertaining to enhancer-promoter specificity. A better understanding of the mechanistic basis of lineage- and context-dependent enhancer-promoter engagement, along with the continued identification of functional enhancers, will provide key insights into the spatiotemporal control of gene expression that can reveal therapeutic opportunities for a range of enhancer-related diseases.
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Affiliation(s)
- Meyer J Friedman
- Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Tobias Wagner
- Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Haram Lee
- College of Pharmacy Korea University, 2511 Sejong-ro, Sejong, 30019, Republic of Korea
| | - Michael G Rosenfeld
- Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA.
| | - Soohwan Oh
- College of Pharmacy Korea University, 2511 Sejong-ro, Sejong, 30019, Republic of Korea.
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2
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Karimi K, Mol MO, Haghshenas S, Relator R, Levy MA, Kerkhof J, McConkey H, Brooks A, Zonneveld-Huijssoon E, Gerkes EH, Tedder ML, Vissers L, Salzano E, Piccione M, Asaftei SD, Carli D, Mussa A, Shukarova-Angelovska E, Trajkova S, Brusco A, Merla G, Alders MM, Bouman A, Sadikovic B. Identification of DNA methylation episignature for the intellectual developmental disorder, autosomal dominant 21 syndrome, caused by variants in the CTCF gene. Genet Med 2024; 26:101041. [PMID: 38054406 DOI: 10.1016/j.gim.2023.101041] [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: 06/09/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 12/07/2023] Open
Abstract
PURPOSE The main objective of this study was to assess clinical features and genome-wide DNA methylation profiles in individuals affected by intellectual developmental disorder, autosomal dominant 21 (IDD21) syndrome, caused by variants in the CCCTC-binding factor (CTCF) gene. METHODS DNA samples were extracted from peripheral blood of 16 individuals with clinical features and genetic findings consistent with IDD21. DNA methylation analysis was performed using the Illumina Infinium Methylation EPIC Bead Chip microarrays. The methylation levels were fitted in a multivariate linear regression model to identify the differentially methylated probes. A binary support vector machine classification model was constructed to differentiate IDD21 samples from controls. RESULTS We identified a highly specific, reproducible, and sensitive episignature associated with CTCF variants. Six variants of uncertain significance were tested, of which 2 mapped to the IDD21 episignature and clustered alongside IDD21 cases in both heatmap and multidimensional scaling plots. Comparison of the genomic DNA methylation profile of IDD21 with that of 56 other neurodevelopmental disorders provided insights into the underlying molecular pathophysiology of this disorder. CONCLUSION The robust and specific CTCF/IDD21 episignature expands the growing list of neurodevelopmental disorders with distinct DNA methylation profiles, which can be applied as supporting evidence in variant classification.
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Affiliation(s)
- Karim Karimi
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Canada
| | - Merel O Mol
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Sadegheh Haghshenas
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Canada
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Canada
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Canada
| | - Alice Brooks
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Evelien Zonneveld-Huijssoon
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Erica H Gerkes
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Lisenka Vissers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Emanuela Salzano
- Medical Genetics Unit, AOOR Villa Sofia-Cervello Hospitals, Palermo, Italy
| | - Maria Piccione
- Medical Genetics Unit, AOOR Villa Sofia-Cervello Hospitals, Palermo, Italy; Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Sebastian Dorin Asaftei
- Pediatric Onco-Hematology, Regina Margherita Children's Hospital, Città della Salute e della Scienza di Torino, Torino, Italy
| | - Diana Carli
- Department of Medical Sciences, University of Turin, Turin, Italy; Immunogenetics and Transplant Biology Service, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - Alessandro Mussa
- Department of Public Health and Pediatrics, University of Turin, Turin, Italy
| | - Elena Shukarova-Angelovska
- Department of Endocrinology and Genetics, University Clinic for Children's Diseases, Medical Faculty, University Sv. Kiril i Metodij, Skopje, North Macedonia
| | - Slavica Trajkova
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Turin, Turin, Italy; Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - Giuseppe Merla
- Laboratory of Regulatory and Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (Foggia), Italy; Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Marielle M Alders
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Arjan Bouman
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands.
| | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Canada; Department of Pathology and Laboratory Medicine, Western University, London, Canada.
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3
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Chopra M, Savatt JM, Bingaman TI, Good ME, Morgan A, Cooney C, Rossel AM, VanHoute B, Cordova I, Mahida S, Lanzotti V, Baldridge D, Gurnett CA, Piven J, Hazlett H, Pomeroy SL, Sahin M, Payne PRO, Riggs ER, Constantino JN. Clinical variants paired with phenotype: A rich resource for brain gene curation. Genet Med 2024; 26:101035. [PMID: 38059438 PMCID: PMC10939875 DOI: 10.1016/j.gim.2023.101035] [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: 05/31/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/08/2023] Open
Abstract
PURPOSE Clinically ascertained variants are under-utilized in neurodevelopmental disorder research. We established the Brain Gene Registry (BGR) to coregister clinically identified variants in putative brain genes with participant phenotypes. Here, we report 179 genetic variants in the first 179 BGR registrants and analyze the proportion that were novel to ClinVar at the time of entry and those that were absent in other disease databases. METHODS From 10 academically affiliated institutions, 179 individuals with 179 variants were enrolled into the BGR. Variants were cross-referenced for previous presence in ClinVar and for presence in 6 other genetic databases. RESULTS Of 179 variants in 76 genes, 76 (42.5%) were novel to ClinVar, and 62 (34.6%) were absent from all databases analyzed. Of the 103 variants present in ClinVar, 37 (35.9%) were uncertain (ClinVar aggregate classification of variant of uncertain significance or conflicting classifications). For 5 variants, the aggregate ClinVar classification was inconsistent with the interpretation from the BGR site-provided classification. CONCLUSION A significant proportion of clinical variants that are novel or uncertain are not shared, limiting the evidence base for new gene-disease relationships. Registration of paired clinical genetic test results with phenotype has the potential to advance knowledge of the relationships between genes and neurodevelopmental disorders.
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Affiliation(s)
- Maya Chopra
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital; Boston, MA; Department of Neurology, Boston Children's Hospital Intellectual Disability and Research Center; Harvard Medical School; Boston, MA.
| | - Juliann M Savatt
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA
| | - Taylor I Bingaman
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA
| | - Molly E Good
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA
| | - Alexis Morgan
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA
| | - Caitlin Cooney
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA
| | - Allison M Rossel
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA
| | - Bryanna VanHoute
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA
| | - Ineke Cordova
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA
| | - Sonal Mahida
- Department of Neurology, Boston Children's Hospital Intellectual Disability and Research Center; Harvard Medical School; Boston, MA
| | - Virginia Lanzotti
- Washington University School of Medicine Intellectual and Developmental Disability Research Center, St. Louis, MO
| | - Dustin Baldridge
- Washington University School of Medicine Intellectual and Developmental Disability Research Center, St. Louis, MO
| | - Christina A Gurnett
- Washington University School of Medicine Intellectual and Developmental Disability Research Center, St. Louis, MO
| | - Joseph Piven
- Department of Psychiatry, University of North Carolina Intellectual and Developmental Disability Research Center, Chapel Hill, NC
| | - Heather Hazlett
- Department of Psychiatry, University of North Carolina Intellectual and Developmental Disability Research Center, Chapel Hill, NC
| | - Scott L Pomeroy
- Department of Neurology, Boston Children's Hospital Intellectual Disability and Research Center; Harvard Medical School; Boston, MA
| | - Mustafa Sahin
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital; Boston, MA; Department of Neurology, Boston Children's Hospital Intellectual Disability and Research Center; Harvard Medical School; Boston, MA
| | - Philip R O Payne
- Institute for Informatics Washington University in St. Louis, St. Louis, MO
| | - Erin Rooney Riggs
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA
| | - John N Constantino
- Division of Behavioural and Mental Health, Children's Healthcare of Atlanta, Departments of Psychiatry and Paediatrics, Emory University, Atlanta, GA
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Basson MA. Neurodevelopmental functions of CHD8: new insights and questions. Biochem Soc Trans 2024; 52:15-27. [PMID: 38288845 PMCID: PMC10903457 DOI: 10.1042/bst20220926] [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: 09/11/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 02/29/2024]
Abstract
Heterozygous, de novo, loss-of-function variants of the CHD8 gene are associated with a high penetrance of autism and other neurodevelopmental phenotypes. Identifying the neurodevelopmental functions of high-confidence autism risk genes like CHD8 may improve our understanding of the neurodevelopmental mechanisms that underlie autism spectrum disorders. Over the last decade, a complex picture of pleiotropic CHD8 functions and mechanisms of action has emerged. Multiple brain and non-brain cell types and progenitors appear to be affected by CHD8 haploinsufficiency. Behavioural, cellular and synaptic phenotypes are dependent on the nature of the gene mutation and are modified by sex and genetic background. Here, I review some of the CHD8-interacting proteins and molecular mechanisms identified to date, as well as the impacts of CHD8 deficiency on cellular processes relevant to neurodevelopment. I endeavour to highlight some of the critical questions that still require careful and concerted attention over the next decade to bring us closer to the goal of understanding the salient mechanisms whereby CHD8 deficiency causes neurodevelopmental disorders.
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Affiliation(s)
- M. Albert Basson
- Clinical and Biomedical Sciences, University of Exeter Medical School, Hatherly Laboratories, Exeter EX4 4PS, U.K
- Centre for Craniofacial and Regenerative Biology and MRC Centre for Neurodevelopmental Disorders, King's College London, London SE1 9RT, U.K
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5
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Do C, Jiang G, Cova G, Katsifis CC, Narducci DN, Yang J, Sakellaropoulos T, Vidal R, Lhoumaud P, Fara Regis F, Kakabadze N, Nora EP, Noyes M, Cheng X, Hansen AS, Skok JA. Brain and cancer associated binding domain mutations provide insight into CTCF's relationship with chromatin and its ability to act as a chromatin organizer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.11.575070. [PMID: 38370764 PMCID: PMC10871189 DOI: 10.1101/2024.01.11.575070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Although only a fraction of CTCF motifs are bound in any cell type, and few occupied sites overlap cohesin, the mechanisms underlying cell-type specific attachment and ability to function as a chromatin organizer remain unknown. To investigate the relationship between CTCF and chromatin we applied a combination of imaging, structural and molecular approaches, using a series of brain and cancer associated CTCF mutations that act as CTCF perturbations. We demonstrate that binding and the functional impact of WT and mutant CTCF depend not only on the unique binding properties of each protein, but also on the genomic context of bound sites and enrichment of motifs for expressed TFs abutting these sites. Our studies also highlight the reciprocal relationship between CTCF and chromatin, demonstrating that the unique binding properties of WT and mutant proteins have a distinct impact on accessibility, TF binding, cohesin overlap, chromatin interactivity and gene expression programs, providing insight into their cancer and brain related effects.
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Lomeli C. S, Kristin B. A. Epigenetic regulation of craniofacial development and disease. Birth Defects Res 2024; 116:e2271. [PMID: 37964651 PMCID: PMC10872612 DOI: 10.1002/bdr2.2271] [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: 06/29/2023] [Revised: 10/13/2023] [Accepted: 10/24/2023] [Indexed: 11/16/2023]
Abstract
BACKGROUND The formation of the craniofacial complex relies on proper neural crest development. The gene regulatory networks (GRNs) and signaling pathways orchestrating this process have been extensively studied. These GRNs and signaling cascades are tightly regulated as alterations to any stage of neural crest development can lead to common congenital birth defects, including multiple syndromes affecting facial morphology as well as nonsyndromic facial defects, such as cleft lip with or without cleft palate. Epigenetic factors add a hierarchy to the regulation of transcriptional networks and influence the spatiotemporal activation or repression of specific gene regulatory cascades; however less is known about their exact mechanisms in controlling precise gene regulation. AIMS In this review, we discuss the role of epigenetic factors during neural crest development, specifically during craniofacial development and how compromised activities of these regulators contribute to congenital defects that affect the craniofacial complex.
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Affiliation(s)
- Shull Lomeli C.
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Artinger Kristin B.
- Department of Diagnostic and Biological Sciences, University of Minnesota School of Dentistry, Minneapolis, MN, USA
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7
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Yang J, Horton JR, Liu B, Corces VG, Blumenthal RM, Zhang X, Cheng X. Structures of CTCF-DNA complexes including all 11 zinc fingers. Nucleic Acids Res 2023; 51:8447-8462. [PMID: 37439339 PMCID: PMC10484683 DOI: 10.1093/nar/gkad594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/27/2023] [Accepted: 07/03/2023] [Indexed: 07/14/2023] Open
Abstract
The CCCTC-binding factor (CTCF) binds tens of thousands of enhancers and promoters on mammalian chromosomes by means of its 11 tandem zinc finger (ZF) DNA-binding domain. In addition to the 12-15-bp CORE sequence, some of the CTCF binding sites contain 5' upstream and/or 3' downstream motifs. Here, we describe two structures for overlapping portions of human CTCF, respectively, including ZF1-ZF7 and ZF3-ZF11 in complex with DNA that incorporates the CORE sequence together with either 3' downstream or 5' upstream motifs. Like conventional tandem ZF array proteins, ZF1-ZF7 follow the right-handed twist of the DNA, with each finger occupying and recognizing one triplet of three base pairs in the DNA major groove. ZF8 plays a unique role, acting as a spacer across the DNA minor groove and positioning ZF9-ZF11 to make cross-strand contacts with DNA. We ascribe the difference between the two subgroups of ZF1-ZF7 and ZF8-ZF11 to residues at the two positions -6 and -5 within each finger, with small residues for ZF1-ZF7 and bulkier and polar/charged residues for ZF8-ZF11. ZF8 is also uniquely rich in basic amino acids, which allows salt bridges to DNA phosphates in the minor groove. Highly specific arginine-guanine and glutamine-adenine interactions, used to recognize G:C or A:T base pairs at conventional base-interacting positions of ZFs, also apply to the cross-strand interactions adopted by ZF9-ZF11. The differences between ZF1-ZF7 and ZF8-ZF11 can be rationalized structurally and may contribute to recognition of high-affinity CTCF binding sites.
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Affiliation(s)
- Jie Yang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John R Horton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bin Liu
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Victor G Corces
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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8
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St John M, Tripathi T, Morgan AT, Amor DJ. To speak may draw on epigenetic writing and reading: Unravelling the complexity of speech and language outcomes across chromatin-related neurodevelopmental disorders. Neurosci Biobehav Rev 2023; 152:105293. [PMID: 37353048 DOI: 10.1016/j.neubiorev.2023.105293] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/11/2023] [Accepted: 06/20/2023] [Indexed: 06/25/2023]
Abstract
Speech and language development are complex neurodevelopmental processes that are incompletely understood, yet current evidence suggests that speech and language disorders are prominent in those with disorders of chromatin regulation. This review aimed to unravel what is known about speech and language outcomes for individuals with chromatin-related neurodevelopmental disorders. A systematic literature search following PRISMA guidelines was conducted on 70 chromatin genes, to identify reports of speech/language outcomes across studies, including clinical reports, formal subjective measures, and standardised/objective measures. 3932 studies were identified and screened and 112 were systematically reviewed. Communication impairment was core across chromatin disorders, and specifically, chromatin writers and readers appear to play an important role in motor speech development. Identification of these relationships is important because chromatin disorders show promise as therapeutic targets due to the capacity for epigenetic modification. Further research is required using standardised and formal assessments to understand the nuanced speech/language profiles associated with variants in each gene, and the influence of chromatin dysregulation on the neurobiology of speech and language development.
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Affiliation(s)
- Miya St John
- Speech and Language, Murdoch Children's Research Institute, Parkville, VIC, Australia; Department of Audiology and Speech Pathology, University of Melbourne, VIC, Australia.
| | - Tanya Tripathi
- Neurodisability and Rehabilitation, Murdoch Children's Research Institute, Parkville, VIC, Australia.
| | - Angela T Morgan
- Speech and Language, Murdoch Children's Research Institute, Parkville, VIC, Australia; Department of Audiology and Speech Pathology, University of Melbourne, VIC, Australia; Speech Genomics Clinic, Royal Children's Hospital, Parkville, VIC, Australia.
| | - David J Amor
- Neurodisability and Rehabilitation, Murdoch Children's Research Institute, Parkville, VIC, Australia; Speech Genomics Clinic, Royal Children's Hospital, Parkville, VIC, Australia; Department of Paediatrics, University of Melbourne, VIC, Australia.
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9
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Tan B, Liu S, Feng X, Pan X, Qian G, Liu L, Zhang X, Yao H, Dong X. Expanding the mutational and clinical spectrum of Chinese intellectual disability patients with two novel CTCF variants. Front Pediatr 2023; 11:1195862. [PMID: 37664546 PMCID: PMC10469948 DOI: 10.3389/fped.2023.1195862] [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: 03/29/2023] [Accepted: 08/07/2023] [Indexed: 09/05/2023] Open
Abstract
CCCTC-Binding Factor (CTCF) is a protein-coding gene involved in transcriptional regulation, insulator activity, and regulation of chromatin structure, and is closely associated with intellectual developmental disorders. In this study, we report two unrelated Chinese patients with intellectual disability (ID). According to variant interpretation results from exome sequencing data and RNA-seq data, we present two novel heterozygous CTCF variants, NM_006565.3:c.1519_2184del (p. Glu507_Arg727delins47) and NM_006565.3:c.1838_1852del (p.Glu613_Pro617del), found in two distinct unrelated patients, respectively. Moreover, RNA-seq data of patient 1 indicated the absence of the mutant transcript, while in patient 2, the RNA-seq data revealed a CTCF mRNA transcript with a deletion of 15 nucleotides. Notably, the RNA sequencing data revealed 507 differentially expressed genes shared between these two patients. Specifically, among them, 194 were down-regulated, and 313 were up-regulated, primarily involved in gene regulation and cellular response. Our study expands the genetic and clinical spectrum of CTCF and advances our understanding of the pathogenesis of CTCF in vivo.
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Affiliation(s)
- Bo Tan
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Sihan Liu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, China
| | - Xiaoshu Feng
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, China
| | - Xin Pan
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Guanhua Qian
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Li Liu
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xu Zhang
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hong Yao
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaojing Dong
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Patel PJ, Ren Y, Yan Z. Epigenomic analysis of Alzheimer's disease brains reveals diminished CTCF binding on genes involved in synaptic organization. Neurobiol Dis 2023; 184:106192. [PMID: 37302762 PMCID: PMC10519202 DOI: 10.1016/j.nbd.2023.106192] [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: 02/06/2023] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/13/2023] Open
Abstract
Epigenetic aberrations are suggested to play an important role in transcriptional alterations in Alzheimer's disease (AD). One of the key mechanisms of epigenetic regulation of gene expression is through the dynamic organization of chromatin structure via the master genome architecture protein, CCCTC-binding factor (CTCF). By forming chromatin loops, CTCF can influence gene transcription in a complex manner. To find out whether genome-wide DNA binding sites for CTCF are altered in AD, we compared CTCF chromatin immunoprecipitation sequencing (ChIP-Seq) data from frontal cortex of human AD patients and normal controls (n = 9 pairs, all females). We have revealed that CTCF-binding affinity on many genes is significantly reduced in AD patients, and these genes are enriched in synaptic organization, cell adhesion, and actin cytoskeleton, including synaptic scaffolding molecules and receptors, such as SHANK2, HOMER1, NRXN1, CNTNAP2 and GRIN2A, and protocadherin (PCDH) and cadherin (CDH) family members. By comparing transcriptomic data from AD patients, we have discovered that many of the synaptic and adhesion genes with reduced CTCF binding in AD are significantly reduced in their mRNA expression. Moreover, a significant overlap of genes with the diminished CTCF binding and the reduced H3K27ac is identified in AD, with the common genes enriched in synaptic organization. These data suggest that the CTCF-controlled 3D chromatin organization is perturbed in AD, which may be linked to the diminished expression of target genes, probably through changes in histone modification.
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Affiliation(s)
- Prachetas J Patel
- Department of Physiology and Biophysics, State University of New York at Buffalo, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Yong Ren
- Department of Physiology and Biophysics, State University of New York at Buffalo, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Zhen Yan
- Department of Physiology and Biophysics, State University of New York at Buffalo, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA.
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11
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Zuo Z, Billings T, Walker M, Petkov PM, Fordyce P, Stormo GD. On the dependent recognition of some long zinc finger proteins. Nucleic Acids Res 2023; 51:5364-5376. [PMID: 36951113 PMCID: PMC10287918 DOI: 10.1093/nar/gkad207] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/28/2023] [Accepted: 03/13/2023] [Indexed: 03/24/2023] Open
Abstract
The human genome contains about 800 C2H2 zinc finger proteins (ZFPs), and most of them are composed of long arrays of zinc fingers. Standard ZFP recognition model asserts longer finger arrays should recognize longer DNA-binding sites. However, recent experimental efforts to identify in vivo ZFP binding sites contradict this assumption, with many exhibiting short motifs. Here we use ZFY, CTCF, ZIM3, and ZNF343 as examples to address three closely related questions: What are the reasons that impede current motif discovery methods? What are the functions of those seemingly unused fingers and how can we improve the motif discovery algorithms based on long ZFPs' biophysical properties? Using ZFY, we employed a variety of methods and find evidence for 'dependent recognition' where downstream fingers can recognize some previously undiscovered motifs only in the presence of an intact core site. For CTCF, high-throughput measurements revealed its upstream specificity profile depends on the strength of its core. Moreover, the binding strength of the upstream site modulates CTCF's sensitivity to different epigenetic modifications within the core, providing new insight into how the previously identified intellectual disability-causing and cancer-related mutant R567W disrupts upstream recognition and deregulates the epigenetic control by CTCF. Our results establish that, because of irregular motif structures, variable spacing and dependent recognition between sub-motifs, the specificities of long ZFPs are significantly underestimated, so we developed an algorithm, ModeMap, to infer the motifs and recognition models of ZIM3 and ZNF343, which facilitates high-confidence identification of specific binding sites, including repeats-derived elements. With revised concept, technique, and algorithm, we can discover the overlooked specificities and functions of those 'extra' fingers, and therefore decipher their broader roles in human biology and diseases.
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Affiliation(s)
- Zheng Zuo
- Department of Genetics, Stanford University, CA, USA
- Department of Genetics, Washington University in St. Louis, MO, USA
| | | | | | | | - Polly M Fordyce
- Department of Genetics, Stanford University, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Bioengineering, Stanford University, CA, USA
- Stanford ChEM-H Institute, Stanford University, CA, USA
| | - Gary D Stormo
- Department of Genetics, Washington University in St. Louis, MO, USA
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12
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Price E, Fedida LM, Pugacheva EM, Ji YJ, Loukinov D, Lobanenkov VV. An updated catalog of CTCF variants associated with neurodevelopmental disorder phenotypes. Front Mol Neurosci 2023; 16:1185796. [PMID: 37324587 PMCID: PMC10264798 DOI: 10.3389/fnmol.2023.1185796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 05/02/2023] [Indexed: 06/17/2023] Open
Abstract
Introduction CTCF-related disorder (CRD) is a neurodevelopmental disorder (NDD) caused by monoallelic pathogenic variants in CTCF. The first CTCF variants in CRD cases were documented in 2013. To date, 76 CTCF variants have been further described in the literature. In recent years, due to the increased application of next-generation sequencing (NGS), growing numbers of CTCF variants are being identified, and multiple genotype-phenotype databases cataloging such variants are emerging. Methods In this study, we aimed to expand the genotypic spectrum of CRD, by cataloging NDD phenotypes associated with reported CTCF variants. Here, we systematically reviewed all known CTCF variants reported in case studies and large-scale exome sequencing cohorts. We also conducted a meta-analysis using public variant data from genotype-phenotype databases to identify additional CTCF variants, which we then curated and annotated. Results From this combined approach, we report an additional 86 CTCF variants associated with NDD phenotypes that have not yet been described in the literature. Furthermore, we describe and explain inconsistencies in the quality of reported variants, which impairs the reuse of data for research of NDDs and other pathologies. Discussion From this integrated analysis, we provide a comprehensive and annotated catalog of all currently known CTCF mutations associated with NDD phenotypes, to aid diagnostic applications, as well as translational and basic research.
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13
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Quon S, Yu B, Russ BE, Tsyganov K, Nguyen H, Toma C, Heeg M, Hocker JD, Milner JJ, Crotty S, Pipkin ME, Turner SJ, Goldrath AW. DNA architectural protein CTCF facilitates subset-specific chromatin interactions to limit the formation of memory CD8 + T cells. Immunity 2023; 56:959-978.e10. [PMID: 37040762 PMCID: PMC10265493 DOI: 10.1016/j.immuni.2023.03.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 11/14/2022] [Accepted: 03/20/2023] [Indexed: 04/13/2023]
Abstract
Although the importance of genome organization for transcriptional regulation of cell-fate decisions and function is clear, the changes in chromatin architecture and how these impact effector and memory CD8+ T cell differentiation remain unknown. Using Hi-C, we studied how genome configuration is integrated with CD8+ T cell differentiation during infection and investigated the role of CTCF, a key chromatin remodeler, in modulating CD8+ T cell fates through CTCF knockdown approaches and perturbation of specific CTCF-binding sites. We observed subset-specific changes in chromatin organization and CTCF binding and revealed that weak-affinity CTCF binding promotes terminal differentiation of CD8+ T cells through the regulation of transcriptional programs. Further, patients with de novo CTCF mutations had reduced expression of the terminal-effector genes in peripheral blood lymphocytes. Therefore, in addition to establishing genome architecture, CTCF regulates effector CD8+ T cell heterogeneity through altering interactions that regulate the transcription factor landscape and transcriptome.
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Affiliation(s)
- Sara Quon
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Bingfei Yu
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Brendan E Russ
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Kirill Tsyganov
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Bioinformatics Platform, Biomedical Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Hongtuyet Nguyen
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Clara Toma
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Maximilian Heeg
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - James D Hocker
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - J Justin Milner
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Matthew E Pipkin
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Stephen J Turner
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC 3800, Australia.
| | - Ananda W Goldrath
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA.
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14
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Chen H, Li W, Zhang S, Sun Y, Shen Y, Chen R. CTCF variant begets to short stature by down-regulation of IGF1. J Mol Endocrinol 2023; 70:e220193. [PMID: 36847142 PMCID: PMC10160550 DOI: 10.1530/jme-22-0193] [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: 02/13/2023] [Accepted: 02/27/2023] [Indexed: 03/01/2023]
Abstract
Pathogenic variants in the transcription factor CCCTC-binding factor (CTCF) are associated with mental retardation, autosomal dominant 21 (MRD21, MIM#615502). Current studies supported the strong relationship between CTCF variants and growth, yet the mechanism of CTCF mutation leading to short stature is not known. Clinical information, treatment regimens, and follow-up outcomes of a patient with MRD21 were collected. The possible pathogenic mechanisms of CTCF variants leading to short stature were investigated using immortalized lymphocyte cell lines (LCLs), HEK-293T, and immortalized normal human liver cell lines (LO2). This patient received long-term treatment with recombinant human growth hormone (rhGH) which resulted in an increased height of 1.0 SDS. She had low serum insulin-like growth factor 1 (IGF1) before the treatment and the IGF1 level was not significantly increased during the treatment (-1.38 ± 0.61 SDS). The finding suggested that the CTCF R567W variant could have impaired IGF1 production pathway. We further demonstrated that the mutant CTCF had a reduced ability to bind to the promoter region of IGF1, consequently significantly reducing the transcriptional activation and expression of IGF1. Our novel results demonstrated a direct positive regulation of CTCF on the transcription of the IGF1 promoter. The impaired IGF1 expression due to CTCF mutation may explain the substandard effect of rhGH treatment on MRD21 patients. This study provided novel insights into the molecular basis of CTCF-associated disorder.
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Affiliation(s)
- Hong Chen
- Department of Endocrinology, Genetics and Metabolism, Fuzhou Children’s Hospital of Fujian Medical University, Fuzhou, China
| | - Weiyu Li
- Department of Endocrinology, Genetics and Metabolism, Fuzhou Children’s Hospital of Fujian Medical University, Fuzhou, China
| | - Suping Zhang
- Department of Endocrinology, Genetics and Metabolism, Fuzhou Children’s Hospital of Fujian Medical University, Fuzhou, China
| | - Yunteng Sun
- Department of Endocrinology, Genetics and Metabolism, Fuzhou Children’s Hospital of Fujian Medical University, Fuzhou, China
| | - Yiping Shen
- Department of Genetic and Metabolic Central Laboratory, the Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Guangxi Birth Defects Prevention and Control Institute, Nanning, China
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ruimin Chen
- Department of Endocrinology, Genetics and Metabolism, Fuzhou Children’s Hospital of Fujian Medical University, Fuzhou, China
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15
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Mao A, Chen C, Portillo-Ledesma S, Schlick T. Effect of Single-Residue Mutations on CTCF Binding to DNA: Insights from Molecular Dynamics Simulations. Int J Mol Sci 2023; 24:ijms24076395. [PMID: 37047368 PMCID: PMC10094706 DOI: 10.3390/ijms24076395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 03/31/2023] Open
Abstract
In humans and other eukaryotes, DNA is condensed into chromatin fibers that are further wound into chromosomes. This organization allows regulatory elements in the genome, often distant from each other in the linear DNA, to interact and facilitate gene expression through regions known as topologically associating domains (TADs). CCCTC–binding factor (CTCF) is one of the major components of TAD formation and is responsible for recruiting a partner protein, cohesin, to perform loop extrusion and facilitate proper gene expression within TADs. Because single-residue CTCF mutations have been linked to the development of a variety of cancers in humans, we aim to better understand how these mutations affect the CTCF structure and its interaction with DNA. To this end, we compare all-atom molecular dynamics simulations of a wildtype CTCF–DNA complex to those of eight different cancer-linked CTCF mutant sequences. We find that most mutants have lower binding energies compared to the wildtype protein, leading to the formation of less stable complexes. Depending on the type and position of the mutation, this loss of stability can be attributed to major changes in the electrostatic potential, loss of hydrogen bonds between the CTCF and DNA, and/or destabilization of specific zinc fingers. Interestingly, certain mutations in specific fingers can affect the interaction with the DNA of other fingers, explaining why mere single mutations can impair CTCF function. Overall, these results shed mechanistic insights into experimental observations and further underscore CTCF’s importance in the regulation of chromatin architecture and gene expression.
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Affiliation(s)
- Albert Mao
- Department of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, NY 10003, USA; (A.M.); (C.C.); (S.P.-L.)
| | - Carrie Chen
- Department of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, NY 10003, USA; (A.M.); (C.C.); (S.P.-L.)
| | - Stephanie Portillo-Ledesma
- Department of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, NY 10003, USA; (A.M.); (C.C.); (S.P.-L.)
| | - Tamar Schlick
- Department of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, NY 10003, USA; (A.M.); (C.C.); (S.P.-L.)
- Courant Institute of Mathematical Sciences, New York University, 251 Mercer St., New York, NY 10012, USA
- New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai 200122, China
- Simons Center for Computational Physical Chemistry, New York University, 24 Waverly Place, Silver Building, New York, NY 10003, USA
- Correspondence:
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16
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de Morales HGV, Wang HLV, Garber K, Cheng X, Corces VG, Li H. Expansion of the genotypic and phenotypic spectrum of CTCF-related disorder guides clinical management: 43 new subjects and a comprehensive literature review. Am J Med Genet A 2023; 191:718-729. [PMID: 36454652 PMCID: PMC9928606 DOI: 10.1002/ajmg.a.63065] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 10/22/2022] [Accepted: 11/18/2022] [Indexed: 12/05/2022]
Abstract
Monoallelic variants of CTCF cause an autosomal dominant neurodevelopmental disorder with a wide range of features, including impacts on the brain, growth, and craniofacial development. A growing number of subjects with CTCF-related disorder (CRD) have been identified due to the increased application of exome sequencing, and further delineation of the clinical spectrum of CRD is needed. Here, we examined the clinical features, including facial profiles, and genotypic spectrum of 107 subjects with identified CTCF variants, including 43 new and 64 previously described subjects. Among the 43 new subjects, 23 novel variants were reported. The cardinal clinical features in subjects with CRD included intellectual disability/developmental delay (91%) with speech delay (65%), motor delay (53%), feeding difficulties/failure to thrive (66%), ocular abnormalities (56%), musculoskeletal anomalies (53%), and behavioral problems (52%). Other congenital anomalies were also reported, but none of them were common. Our findings expanded the genotypic and phenotypic spectrum of CRD that will guide genetic counseling, management, and surveillance care for patients with CRD. Additionally, a newly built facial gestalt on the Face2Gene tool will facilitate prompt recognition of CRD by physicians and shorten a patient's diagnostic odyssey.
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Affiliation(s)
| | - Hsiao-Lin V. Wang
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA. 30322
| | - Kathryn Garber
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA. 30322
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX. 77030
| | - Victor G. Corces
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA. 30322
| | - Hong Li
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA. 30322
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA. 30322
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17
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Hirayama T, Kadooka Y, Tarusawa E, Saitoh S, Nakayama H, Hoshino N, Nakama S, Fukuishi T, Kawanishi Y, Umeshima H, Tomita K, Yoshimura Y, Galjart N, Hashimoto K, Ohno N, Yagi T. CTCF loss induces giant lamellar bodies in Purkinje cell dendrites. Acta Neuropathol Commun 2022; 10:172. [PMID: 36447271 PMCID: PMC9706876 DOI: 10.1186/s40478-022-01478-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/14/2022] [Indexed: 12/03/2022] Open
Abstract
CCCTC-binding factor (CTCF) has a key role in higher-order chromatin architecture that is important for establishing and maintaining cell identity by controlling gene expression. In the mature cerebellum, CTCF is highly expressed in Purkinje cells (PCs) as compared with other cerebellar neurons. The cerebellum plays an important role in motor function by regulating PCs, which are the sole output neurons, and defects in PCs cause motor dysfunction. However, the role of CTCF in PCs has not yet been explored. Here we found that the absence of CTCF in mouse PCs led to progressive motor dysfunction and abnormal dendritic morphology in those cells, which included dendritic self-avoidance defects and a proximal shift in the climbing fibre innervation territory on PC dendrites. Furthermore, we found the peculiar lamellar structures known as "giant lamellar bodies" (GLBs), which have been reported in PCs of patients with Werdnig-Hoffman disease, 13q deletion syndrome, and Krabbe disease. GLBs are localized to PC dendrites and are assumed to be associated with neurodegeneration. They have been noted, however, only in case reports following autopsy, and reports of their existence have been very limited. Here we show that GLBs were reproducibly formed in PC dendrites of a mouse model in which CTCF was deleted. GLBs were not noted in PC dendrites at infancy but instead developed over time. In conjunction with GLB development in PC dendrites, the endoplasmic reticulum was almost absent around the nuclei, the mitochondria were markedly swollen and their cristae had decreased drastically, and almost all PCs eventually disappeared as severe motor deficits manifested. Our results revealed the important role of CTCF during normal development and in maintaining PCs and provide new insights into the molecular mechanism of GLB formation during neurodegenerative disease.
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Affiliation(s)
- Teruyoshi Hirayama
- grid.136593.b0000 0004 0373 3971KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, 565-0871 Japan ,grid.267335.60000 0001 1092 3579Department of Anatomy and Developmental Neurobiology, Tokushima University Graduate School of Medical Sciences, 3-18-15 Kuramoto-cho, Tokushima, 770-8503 Japan
| | - Yuuki Kadooka
- grid.136593.b0000 0004 0373 3971KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, 565-0871 Japan
| | - Etsuko Tarusawa
- grid.136593.b0000 0004 0373 3971KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, 565-0871 Japan
| | - Sei Saitoh
- grid.467811.d0000 0001 2272 1771Section of Electron Microscopy, Supportive Center for Brain Research, National Institute for Physiological Sciences, Okazaki, 444-8787 Japan ,grid.256115.40000 0004 1761 798XDepartment of Anatomy II and Cell Biology, Fujita Health University School of Medicine, 1-98 Dengakubo, Kutsukake-cho, Toyoake, 470-1192 Japan
| | - Hisako Nakayama
- grid.410818.40000 0001 0720 6587Department of Physiology, Division of Neurophysiology, School of Medicine, Tokyo Women’s Medical University, Tokyo, 162-8666 Japan ,grid.257022.00000 0000 8711 3200Department of Neurophysiology, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551 Japan
| | - Natsumi Hoshino
- grid.136593.b0000 0004 0373 3971KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, 565-0871 Japan
| | - Soichiro Nakama
- grid.267335.60000 0001 1092 3579Department of Anatomy and Developmental Neurobiology, Tokushima University Graduate School of Medical Sciences, 3-18-15 Kuramoto-cho, Tokushima, 770-8503 Japan
| | - Takahiro Fukuishi
- grid.267335.60000 0001 1092 3579Department of Anatomy and Developmental Neurobiology, Tokushima University Graduate School of Medical Sciences, 3-18-15 Kuramoto-cho, Tokushima, 770-8503 Japan
| | - Yudai Kawanishi
- grid.267335.60000 0001 1092 3579Department of Anatomy and Developmental Neurobiology, Tokushima University Graduate School of Medical Sciences, 3-18-15 Kuramoto-cho, Tokushima, 770-8503 Japan
| | - Hiroki Umeshima
- grid.267335.60000 0001 1092 3579Department of Anatomy and Developmental Neurobiology, Tokushima University Graduate School of Medical Sciences, 3-18-15 Kuramoto-cho, Tokushima, 770-8503 Japan
| | - Koichi Tomita
- grid.267335.60000 0001 1092 3579Department of Anatomy and Developmental Neurobiology, Tokushima University Graduate School of Medical Sciences, 3-18-15 Kuramoto-cho, Tokushima, 770-8503 Japan
| | - Yumiko Yoshimura
- grid.467811.d0000 0001 2272 1771Section of Visual Information Processing, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi 444-8585 Japan ,grid.275033.00000 0004 1763 208XDepartment of Physiological Sciences, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585 Japan
| | - Niels Galjart
- grid.5645.2000000040459992XDepartment of Cell Biology, Erasmus University Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Kouichi Hashimoto
- grid.257022.00000 0000 8711 3200Department of Neurophysiology, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551 Japan
| | - Nobuhiko Ohno
- grid.467811.d0000 0001 2272 1771Division of Ultrastructural Research, National Institute for Physiological Sciences, Okazaki, 444-8585 Japan ,grid.410804.90000000123090000Department of Anatomy, Division of Histology and Cell Biology, Jichi Medical University, Shimotsuke, 329-0498 Japan
| | - Takeshi Yagi
- grid.136593.b0000 0004 0373 3971KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, 565-0871 Japan
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18
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Plaza-Jennings A, Valada A, Akbarian S. 3D Genome Plasticity in Normal and Diseased Neurodevelopment. Genes (Basel) 2022; 13:1999. [PMID: 36360237 PMCID: PMC9690570 DOI: 10.3390/genes13111999] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/18/2022] [Accepted: 10/26/2022] [Indexed: 10/17/2023] Open
Abstract
Non-random spatial organization of the chromosomal material inside the nuclei of brain cells emerges as an important regulatory layer of genome organization and function in health and disease. Here, we discuss how integrative approaches assessing chromatin in context of the 3D genome is providing new insights into normal and diseased neurodevelopment. Studies in primate (incl. human) and rodent brain have confirmed that chromosomal organization in neurons and glia undergoes highly dynamic changes during pre- and early postnatal development, with potential for plasticity across a much wider age window. For example, neuronal 3D genomes from juvenile and adult cerebral cortex and hippocampus undergo chromosomal conformation changes at hundreds of loci in the context of learning and environmental enrichment, viral infection, and neuroinflammation. Furthermore, locus-specific structural DNA variations, such as micro-deletions, duplications, repeat expansions, and retroelement insertions carry the potential to disrupt the broader epigenomic and transcriptional landscape far beyond the boundaries of the site-specific variation, highlighting the critical importance of long-range intra- and inter-chromosomal contacts for neuronal and glial function.
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Affiliation(s)
- Amara Plaza-Jennings
- Graduate School of Biomedical Sciences, Medical Scientist Training Program, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Aditi Valada
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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19
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Gargallo P, Oltra S, Tasso M, Balaguer J, Yáñez Y, Dolz S, Calabria I, Martínez F, Segura V, Juan-Ribelles A, Llavador M, Castel V, Cañete A, Font de Mora J. Germline variant in Ctcf links mental retardation to Wilms tumor predisposition. Eur J Hum Genet 2022; 30:1288-1291. [PMID: 35459888 PMCID: PMC9626537 DOI: 10.1038/s41431-022-01105-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 04/05/2022] [Accepted: 04/12/2022] [Indexed: 02/04/2023] Open
Abstract
CTCF germline mutations have been related to MRD21. We report the first bilateral Wilms tumor suffered by a MRD21 patient carrying an unreported CTCF missense variant in a zinc finger domain of CTCF protein. We found that germline heterozygous variant I446K became homozygous in the tumor due to a loss of heterozygosity rearrangement affecting the whole q arm on chromosome 16. Our findings propose CTCF I446K variant as a link between MRD21 and Wilms tumor predisposition.
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Affiliation(s)
- Pablo Gargallo
- Clinical and Translational Research in Cancer, La Fe Health Research Institute, Valencia, Spain.
- Oncology Department - Health in Code Group, Paterna, Valencia, Spain.
| | - Silvestre Oltra
- Genetics Unit, La Fe Hospital, Valencia, Spain
- Genetics Department, Valencia University, Valencia, Spain
| | - María Tasso
- Pediatric Oncology Unit, General University Hospital of Alicante, Alicante, Spain
| | - Julia Balaguer
- Clinical and Translational Research in Cancer, La Fe Health Research Institute, Valencia, Spain
- Pediatric Oncology and Hematology Unit, La Fe University Hospital, Valencia, Spain
| | - Yania Yáñez
- Clinical and Translational Research in Cancer, La Fe Health Research Institute, Valencia, Spain
| | - Sandra Dolz
- Clinical and Translational Research in Cancer, La Fe Health Research Institute, Valencia, Spain
| | - Inés Calabria
- Oncology Department - Health in Code Group, Paterna, Valencia, Spain
| | | | - Vanessa Segura
- Clinical and Translational Research in Cancer, La Fe Health Research Institute, Valencia, Spain
| | - Antonio Juan-Ribelles
- Clinical and Translational Research in Cancer, La Fe Health Research Institute, Valencia, Spain
- Pediatric Oncology and Hematology Unit, La Fe University Hospital, Valencia, Spain
| | | | - Victoria Castel
- Clinical and Translational Research in Cancer, La Fe Health Research Institute, Valencia, Spain
| | - Adela Cañete
- Clinical and Translational Research in Cancer, La Fe Health Research Institute, Valencia, Spain
- Pediatric Oncology and Hematology Unit, La Fe University Hospital, Valencia, Spain
| | - Jaime Font de Mora
- Clinical and Translational Research in Cancer, La Fe Health Research Institute, Valencia, Spain
- Laboratory of Cellular and Molecular Biology, La Fe Health Research Institute, Valencia, Spain
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20
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Dehingia B, Milewska M, Janowski M, Pękowska A. CTCF
shapes chromatin structure and gene expression in health and disease. EMBO Rep 2022; 23:e55146. [PMID: 35993175 PMCID: PMC9442299 DOI: 10.15252/embr.202255146] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/31/2022] [Accepted: 07/14/2022] [Indexed: 11/09/2022] Open
Affiliation(s)
- Bondita Dehingia
- Dioscuri Centre for Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology Polish Academy of Sciences Warsaw Poland
| | - Małgorzata Milewska
- Dioscuri Centre for Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology Polish Academy of Sciences Warsaw Poland
| | - Marcin Janowski
- Dioscuri Centre for Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology Polish Academy of Sciences Warsaw Poland
| | - Aleksandra Pękowska
- Dioscuri Centre for Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology Polish Academy of Sciences Warsaw Poland
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21
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Heseding HM, Jahn K, Eberlein CK, Wieting J, Maier HB, Proskynitopoulos PJ, Glahn A, Bleich S, Frieling H, Deest M. Distinct promoter regions of the oxytocin receptor gene are hypomethylated in Prader-Willi syndrome and in Prader-Willi syndrome associated psychosis. Transl Psychiatry 2022; 12:246. [PMID: 35688807 PMCID: PMC9187685 DOI: 10.1038/s41398-022-02014-9] [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: 01/18/2022] [Revised: 05/23/2022] [Accepted: 05/30/2022] [Indexed: 11/12/2022] Open
Abstract
Prader-Willi syndrome (PWS) is a rare neurodevelopmental disorder caused by a loss of usually paternally expressed, maternally imprinted genes located on chromosome 15q11-q13. Individuals with PWS display a specific behavioral phenotype and have a higher susceptibility than the general population for certain psychiatric conditions, especially psychosis. An impairment of the oxytocin system has been described in Prader-Willi syndrome, but has not yet been investigated in detail on the epigenetic level. Recent studies have pointed out altered methylation patterns of the oxytocin receptor gene (OXTR) in various psychiatric disorders, including psychosis. In this study, we investigated methylation rates of CpG dinucleotides in the promoter region of the oxytocin receptor gene via bisulfite-sequencing using DNA extracted from peripheral blood samples of 31 individuals with PWS and 14 controls matched for age, sex, and BMI. Individuals with PWS show significantly lower methylation in the intron 1 region of the OXTR than neurotypical controls (p = 0.012). Furthermore, male PWS subjects with psychosis show significantly lower methylation of the OXTR exon 1 region than those without psychosis (p = 0.002). Transcription factor binding site analysis revealed E2F1 as a transcription factor potentially binding to the exon 1 region. E2F1 is physiologically regulated by Necdin, an anti-apoptotic protein whose corresponding gene is located within the PWS locus. This study provides evidence of a disruption of the Oxytocin system on an epigenetic level in PWS in general and in individuals with PWS and psychosis.
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Affiliation(s)
- Hannah M. Heseding
- grid.10423.340000 0000 9529 9877Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Hannover, Germany
| | - Kirsten Jahn
- grid.10423.340000 0000 9529 9877Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Hannover, Germany
| | - Christian K. Eberlein
- grid.10423.340000 0000 9529 9877Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Hannover, Germany
| | - Jelte Wieting
- grid.10423.340000 0000 9529 9877Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Hannover, Germany
| | - Hannah B. Maier
- grid.10423.340000 0000 9529 9877Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Hannover, Germany
| | - Phileas J. Proskynitopoulos
- grid.10423.340000 0000 9529 9877Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Hannover, Germany
| | - Alexander Glahn
- grid.10423.340000 0000 9529 9877Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Hannover, Germany
| | - Stefan Bleich
- grid.10423.340000 0000 9529 9877Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Hannover, Germany
| | - Helge Frieling
- grid.10423.340000 0000 9529 9877Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Hannover, Germany
| | - Maximilian Deest
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Hannover, Germany.
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22
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Davis L, Rayi PR, Getselter D, Kaphzan H, Elliott E. CTCF in parvalbumin-expressing neurons regulates motor, anxiety and social behavior and neuronal identity. Mol Brain 2022; 15:30. [PMID: 35379308 PMCID: PMC8981645 DOI: 10.1186/s13041-022-00916-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/23/2022] [Indexed: 11/10/2022] Open
Abstract
CCCTC-binding factor (CTCF) is a regulator of chromatin organization and has direct effects on gene transcription. Mutations in CTCF have been identified in individuals with neurodevelopmental conditions. There are wide range of behaviors associated with these mutations, including intellectual disabilities, changes in temperament, and autism. Previous mice-model studies have identified roles for CTCF in excitatory neurons in specific behaviors, particularly in regards to learning and memory. However, the role of CTCF in inhibitory neurons is less well defined. In the current study, specific knockout of CTCF in parvalbumin-expressing neurons, a subset of inhibitory neurons, induced a specific behavioral phenotype, including locomotor abnormalities, anxiolytic behavior, and a decrease in social behavior. The anxiolytic and social abnormalities are detected before the onset of locomotor abnormalities. Immunohistochemical analysis revealed a disbalance in parvalbumin-expressing and somatostatin-expressing cells in these mice. Single nuclei RNA sequencing identified changes in gene expression in parvalbumin-expressing neurons that are specific to inhibitory neuronal identity and function. Electrophysiology analysis revealed an enhanced inhibitory tone in the hippocampal pyramidal neurons in knockout mice. These findings indicate that CTCF in parvalbumin-expressing neurons has a significant role in the overall phenotype of CTCF-associated neurodevelopmental deficits.
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Affiliation(s)
- Liron Davis
- Bar Ilan University, Azrieli Faculty of Medicine, Hanrietta Sold 8, 13215, Safed, Israel
| | - Prudhvi Raj Rayi
- Sagol Department of Neurobiology, University of Haifa, Haifa, Israel
| | - Dmitriy Getselter
- Bar Ilan University, Azrieli Faculty of Medicine, Hanrietta Sold 8, 13215, Safed, Israel
| | - Hanoch Kaphzan
- Sagol Department of Neurobiology, University of Haifa, Haifa, Israel
| | - Evan Elliott
- Bar Ilan University, Azrieli Faculty of Medicine, Hanrietta Sold 8, 13215, Safed, Israel.
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23
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Cummings CT, Rowley MJ. Implications of Dosage Deficiencies in CTCF and Cohesin on Genome Organization, Gene Expression, and Human Neurodevelopment. Genes (Basel) 2022; 13:583. [PMID: 35456389 PMCID: PMC9030571 DOI: 10.3390/genes13040583] [Citation(s) in RCA: 2] [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: 02/28/2022] [Revised: 03/14/2022] [Accepted: 03/24/2022] [Indexed: 02/07/2023] Open
Abstract
Properly organizing DNA within the nucleus is critical to ensure normal downstream nuclear functions. CTCF and cohesin act as major architectural proteins, working in concert to generate thousands of high-intensity chromatin loops. Due to their central role in loop formation, a massive research effort has been dedicated to investigating the mechanism by which CTCF and cohesin create these loops. Recent results lead to questioning the direct impact of CTCF loops on gene expression. Additionally, results of controlled depletion experiments in cell lines has indicated that genome architecture may be somewhat resistant to incomplete deficiencies in CTCF or cohesin. However, heterozygous human genetic deficiencies in CTCF and cohesin have illustrated the importance of their dosage in genome architecture, cellular processes, animal behavior, and disease phenotypes. Thus, the importance of considering CTCF or cohesin levels is especially made clear by these heterozygous germline variants that characterize genetic syndromes, which are increasingly recognized in clinical practice. Defined primarily by developmental delay and intellectual disability, the phenotypes of CTCF and cohesin deficiency illustrate the importance of architectural proteins particularly in neurodevelopment. We discuss the distinct roles of CTCF and cohesin in forming chromatin loops, highlight the major role that dosage of each protein plays in the amplitude of observed effects on gene expression, and contrast these results to heterozygous mutation phenotypes in murine models and clinical patients. Insights highlighted by this comparison have implications for future research into these newly emerging genetic syndromes.
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Affiliation(s)
- Christopher T. Cummings
- Munroe-Meyer Institute, Department of Genetic Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA;
- Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - M. Jordan Rowley
- Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
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24
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Sun X, Shen W, Li Z, Zhang W. CCCTC-binding factor transcriptionally regulates Galectin-7 and activates the JNK/STAT3 axis to aggravate bronchial epithelial cell injury. Pediatr Pulmonol 2022; 57:90-99. [PMID: 34643340 DOI: 10.1002/ppul.25726] [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: 04/20/2021] [Revised: 09/15/2021] [Accepted: 09/18/2021] [Indexed: 11/07/2022]
Abstract
OBJECTIVE Studies have shown that the expression of CCCTC-binding factor (CTCF) is significantly upregulated in the airway epithelial cells of asthmatic patients, suggesting that CTCF may play an important role in the progression of asthma. MATERIAL/METHODS Human bronchial epithelial cells BEAS-2B were stimulated with transforming growth factor-β1 (TGF-β1) at a concentration of 10 ng/ml, and CTCF overexpression plasmid and CTCF small interfering RNA were transfected into the cells. The proliferation, apoptosis, inflammatory factor secretion, and airway remodeling marker protein expression of injured cells were detected. We bidirectionally regulated Galectin-7 expression in TGF-β1-induced BEAS-2B cells and overexpress CTCF, while interfering with Galectin-7 to further explore the regulatory effect of CTCF on Galectin-7. We introduced SP600125, a c-Jun N-terminal kinase c-Jun (JNK) pathway inhibitor, to investigate whether CTCF affects asthma progression through the JNK pathway. RESULTS The expression of CTCF in BEAS-2B cells induced by TGF-β1 was significantly upregulated, interfering with CTCF expression promoted cell proliferation, inhibited apoptosis, reduced inflammatory factors secretion, and decreased the expression of airway remodeling marker protein. Luciferase reporter gene analysis and chromatin immunoprecipitation verified that CTCF directly bound to Galectin-7 promoter. The effect of Galectin-7 on cells is consistent with the effect of CTCF on cells. The regulatory effect of CTCF on injured cells was indeed mediated by activation of the JNK/STAT3 axis. CONCLUSIONS CTCF transcriptionally regulated Galectin-7 and activated JNK/STAT3 axis to aggravate bronchial epithelial cell injury.
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Affiliation(s)
- Xinrong Sun
- Department of Hematology, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
- Department of Infectious Diseases, Xi'an Children's Hospital, Xi'an, China
| | - Wenna Shen
- Department of Respiration, Xi'an Children's Hospital, Xi'an, China
| | | | - Wanggang Zhang
- Department of Hematology, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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25
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Gargallo P, Oltra S, Yáñez Y, Juan-Ribelles A, Calabria I, Segura V, Lázaro M, Balaguer J, Tormo T, Dolz S, Fernández JM, Fuentes C, Torres B, Andrés M, Tasso M, Castel V, Font de Mora J, Cañete A. Germline Predisposition to Pediatric Cancer, from Next Generation Sequencing to Medical Care. Cancers (Basel) 2021; 13:5339. [PMID: 34771502 PMCID: PMC8582391 DOI: 10.3390/cancers13215339] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/18/2021] [Accepted: 10/21/2021] [Indexed: 11/16/2022] Open
Abstract
Knowledge about genetic predisposition to pediatric cancer is constantly expanding. The categorization and clinical management of the best-known syndromes has been refined over the years. Meanwhile, new genes for pediatric cancer susceptibility are discovered every year. Our current work shares the results of genetically studying the germline of 170 pediatric patients diagnosed with cancer. Patients were prospectively recruited and studied using a custom panel, OncoNano V2. The well-categorized predisposing syndromes incidence was 9.4%. Likely pathogenic variants for predisposition to the patient's tumor were identified in an additional 5.9% of cases. Additionally, a high number of pathogenic variants associated with recessive diseases was detected, which required family genetic counseling as well. The clinical utility of the Jongmans MC tool was evaluated, showing a high sensitivity for detecting the best-known predisposing syndromes. Our study confirms that the Jongmans MC tool is appropriate for a rapid assessment of patients; however, the updated version of Ripperger T criteria would be more accurate. Meaningfully, based on our findings, up to 9.4% of patients would present genetic alterations predisposing to cancer. Notably, up to 20% of all patients carry germline pathogenic or likely pathogenic variants in genes related to cancer and, thereby, they also require expert genetic counseling. The most important consideration is that the detection rate of genetic causality outside Jongmans MC et al. criteria was very low.
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Affiliation(s)
- Pablo Gargallo
- Pediatric Oncology Department, Hospital Universitario y Politécnico La Fe de Valencia, 46026 Valencia, Spain; (Y.Y.); (A.J.-R.); (V.S.); (J.B.); (T.T.); (J.M.F.); (C.F.); (B.T.); (M.A.); (V.C.); (A.C.)
- Imegen–Health in Code Group, Department of Oncology, Paterna, 46980 Valencia, Spain; (I.C.); (M.L.)
| | - Silvestre Oltra
- Genetics Unit, Hospital Universitario y Politécnico La Fe de Valencia, 46026 Valencia, Spain;
- Genetics Department, Universidad de Valencia, 46010 Valencia, Spain
| | - Yania Yáñez
- Pediatric Oncology Department, Hospital Universitario y Politécnico La Fe de Valencia, 46026 Valencia, Spain; (Y.Y.); (A.J.-R.); (V.S.); (J.B.); (T.T.); (J.M.F.); (C.F.); (B.T.); (M.A.); (V.C.); (A.C.)
| | - Antonio Juan-Ribelles
- Pediatric Oncology Department, Hospital Universitario y Politécnico La Fe de Valencia, 46026 Valencia, Spain; (Y.Y.); (A.J.-R.); (V.S.); (J.B.); (T.T.); (J.M.F.); (C.F.); (B.T.); (M.A.); (V.C.); (A.C.)
| | - Inés Calabria
- Imegen–Health in Code Group, Department of Oncology, Paterna, 46980 Valencia, Spain; (I.C.); (M.L.)
| | - Vanessa Segura
- Pediatric Oncology Department, Hospital Universitario y Politécnico La Fe de Valencia, 46026 Valencia, Spain; (Y.Y.); (A.J.-R.); (V.S.); (J.B.); (T.T.); (J.M.F.); (C.F.); (B.T.); (M.A.); (V.C.); (A.C.)
| | - Marián Lázaro
- Imegen–Health in Code Group, Department of Oncology, Paterna, 46980 Valencia, Spain; (I.C.); (M.L.)
| | - Julia Balaguer
- Pediatric Oncology Department, Hospital Universitario y Politécnico La Fe de Valencia, 46026 Valencia, Spain; (Y.Y.); (A.J.-R.); (V.S.); (J.B.); (T.T.); (J.M.F.); (C.F.); (B.T.); (M.A.); (V.C.); (A.C.)
| | - Teresa Tormo
- Pediatric Oncology Department, Hospital Universitario y Politécnico La Fe de Valencia, 46026 Valencia, Spain; (Y.Y.); (A.J.-R.); (V.S.); (J.B.); (T.T.); (J.M.F.); (C.F.); (B.T.); (M.A.); (V.C.); (A.C.)
| | - Sandra Dolz
- Laboratory of Cellular and Molecular Biology, Clinical and Translational Research in Cancer, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (S.D.); (J.F.d.M.)
| | - José María Fernández
- Pediatric Oncology Department, Hospital Universitario y Politécnico La Fe de Valencia, 46026 Valencia, Spain; (Y.Y.); (A.J.-R.); (V.S.); (J.B.); (T.T.); (J.M.F.); (C.F.); (B.T.); (M.A.); (V.C.); (A.C.)
| | - Carolina Fuentes
- Pediatric Oncology Department, Hospital Universitario y Politécnico La Fe de Valencia, 46026 Valencia, Spain; (Y.Y.); (A.J.-R.); (V.S.); (J.B.); (T.T.); (J.M.F.); (C.F.); (B.T.); (M.A.); (V.C.); (A.C.)
| | - Bárbara Torres
- Pediatric Oncology Department, Hospital Universitario y Politécnico La Fe de Valencia, 46026 Valencia, Spain; (Y.Y.); (A.J.-R.); (V.S.); (J.B.); (T.T.); (J.M.F.); (C.F.); (B.T.); (M.A.); (V.C.); (A.C.)
| | - Mara Andrés
- Pediatric Oncology Department, Hospital Universitario y Politécnico La Fe de Valencia, 46026 Valencia, Spain; (Y.Y.); (A.J.-R.); (V.S.); (J.B.); (T.T.); (J.M.F.); (C.F.); (B.T.); (M.A.); (V.C.); (A.C.)
| | - María Tasso
- Pediatric Oncology Department, Hospital General de Alicante, 03010 Alicante, Spain;
| | - Victoria Castel
- Pediatric Oncology Department, Hospital Universitario y Politécnico La Fe de Valencia, 46026 Valencia, Spain; (Y.Y.); (A.J.-R.); (V.S.); (J.B.); (T.T.); (J.M.F.); (C.F.); (B.T.); (M.A.); (V.C.); (A.C.)
| | - Jaime Font de Mora
- Laboratory of Cellular and Molecular Biology, Clinical and Translational Research in Cancer, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (S.D.); (J.F.d.M.)
| | - Adela Cañete
- Pediatric Oncology Department, Hospital Universitario y Politécnico La Fe de Valencia, 46026 Valencia, Spain; (Y.Y.); (A.J.-R.); (V.S.); (J.B.); (T.T.); (J.M.F.); (C.F.); (B.T.); (M.A.); (V.C.); (A.C.)
- Department of Pediatrics, Obstetrics and Gynecology, University of Valencia, 46010 Valencia, Spain
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26
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Wang HLV, Corces VG. Is developmental synchrony enabled by CTCF residence time? Dev Cell 2021; 56:2545-2546. [PMID: 34582771 DOI: 10.1016/j.devcel.2021.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Depletion of CTCF in cultured cells has minor effects on transcription whereas its mutation leads to embryonic lethality and developmental defects. In a recent issue of Nature Cell Biology, Soochit et al. (2021) show that the residence time of CTCF on DNA may explain its critical role in cell differentiation.
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Affiliation(s)
- Hsiao-Lin V Wang
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Victor G Corces
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA.
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27
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Chawla A, Nagy C, Turecki G. Chromatin Profiling Techniques: Exploring the Chromatin Environment and Its Contributions to Complex Traits. Int J Mol Sci 2021; 22:7612. [PMID: 34299232 PMCID: PMC8305586 DOI: 10.3390/ijms22147612] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 07/09/2021] [Accepted: 07/13/2021] [Indexed: 01/04/2023] Open
Abstract
The genetic architecture of complex traits is multifactorial. Genome-wide association studies (GWASs) have identified risk loci for complex traits and diseases that are disproportionately located at the non-coding regions of the genome. On the other hand, we have just begun to understand the regulatory roles of the non-coding genome, making it challenging to precisely interpret the functions of non-coding variants associated with complex diseases. Additionally, the epigenome plays an active role in mediating cellular responses to fluctuations of sensory or environmental stimuli. However, it remains unclear how exactly non-coding elements associate with epigenetic modifications to regulate gene expression changes and mediate phenotypic outcomes. Therefore, finer interrogations of the human epigenomic landscape in associating with non-coding variants are warranted. Recently, chromatin-profiling techniques have vastly improved our understanding of the numerous functions mediated by the epigenome and DNA structure. Here, we review various chromatin-profiling techniques, such as assays of chromatin accessibility, nucleosome distribution, histone modifications, and chromatin topology, and discuss their applications in unraveling the brain epigenome and etiology of complex traits at tissue homogenate and single-cell resolution. These techniques have elucidated compositional and structural organizing principles of the chromatin environment. Taken together, we believe that high-resolution epigenomic and DNA structure profiling will be one of the best ways to elucidate how non-coding genetic variations impact complex diseases, ultimately allowing us to pinpoint cell-type targets with therapeutic potential.
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Affiliation(s)
- Anjali Chawla
- Integrated Program in Neuroscience, McGill University, 845 Sherbrooke St W, Montreal, QC H3A 0G4, Canada;
- McGill Group for Suicide Studies, Department of Psychiatry, Douglas Mental Health University Institute, McGill University, 6875 LaSalle Blvd, Verdun, QC H4H 1R3, Canada;
| | - Corina Nagy
- McGill Group for Suicide Studies, Department of Psychiatry, Douglas Mental Health University Institute, McGill University, 6875 LaSalle Blvd, Verdun, QC H4H 1R3, Canada;
- Genome Quebec Innovation Centre, Department of Human Genetics, McGill University, 845 Sherbrooke St W, Montreal, QC H3A 0G4, Canada
| | - Gustavo Turecki
- Integrated Program in Neuroscience, McGill University, 845 Sherbrooke St W, Montreal, QC H3A 0G4, Canada;
- McGill Group for Suicide Studies, Department of Psychiatry, Douglas Mental Health University Institute, McGill University, 6875 LaSalle Blvd, Verdun, QC H4H 1R3, Canada;
- Genome Quebec Innovation Centre, Department of Human Genetics, McGill University, 845 Sherbrooke St W, Montreal, QC H3A 0G4, Canada
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28
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Manor J, Dinu D, Azamian MS, Bi W, Darilek S, Lalani SR. A rare description of pure partial trisomy of 16q12.2q24.3 and review of the literature. Am J Med Genet A 2021; 185:2903-2912. [PMID: 34061437 DOI: 10.1002/ajmg.a.62368] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/09/2021] [Accepted: 05/11/2021] [Indexed: 11/11/2022]
Abstract
Trisomy 16 is the most common autosomal trisomy in humans, which is almost uniformly embryonic lethal. Partial trisomy 16 including a segment of the long arm of chromosome 16 is occasionally compatible with life and has been associated with severe congenital defects, growth retardation, and early lethality. Segmental trisomy of 16q is usually described concomitantly with partial monosomy of another chromosome, often resulting from a parental balanced translocation. Pure partial chromosome 16q trisomy is exceedingly rare. About nine children with 16q12→qter and 16q13→qter duplication have been reported in the literature, almost all described with monosomy of a second chromosome, and highlighting very few long-term survivors. A single individual with pure partial distal 16q12.1q23.3 duplication has been reported in an infant, underscoring complexities of genetic counseling and management, especially in view of life-limiting congenital anomalies in rare survivors. Here, we present a 12-month-old child with pure 16q12.2q24.3 trisomy, having continued morbidity related to pulmonary hypertension and chronic lung disease. The features of intrauterine growth retardation, facial dysmorphism, hypotonia, congenital heart defect, distal contractures, urogenital abnormalities, and hearing loss support the association with 16q partial trisomy, as in previous studies. This report expands our current understanding related to the survival of infants with large segmental aneusomy of the long arm of chromosome 16.
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Affiliation(s)
- Joshua Manor
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Daniela Dinu
- Department of Pediatrics, Neonatology section, Texas Children's Hospital, Houston, Texas, USA
| | - Mahshid S Azamian
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Baylor Genetics Laboratories, Houston, Texas, USA
| | - Sandra Darilek
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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29
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Xiang JF, Corces VG. Regulation of 3D chromatin organization by CTCF. Curr Opin Genet Dev 2021; 67:33-40. [PMID: 33259986 PMCID: PMC8084898 DOI: 10.1016/j.gde.2020.10.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/18/2020] [Accepted: 10/26/2020] [Indexed: 01/12/2023]
Abstract
Studies of nuclear architecture using chromosome conformation capture methods have provided a detailed view of how chromatin folds in the 3D nuclear space. New variants of this technology now afford unprecedented resolution and allow the identification of ever smaller folding domains that offer new insights into the mechanisms by which this organization is established and maintained. Here we review recent results in this rapidly evolving field with an emphasis on CTCF function, with the goal of gaining a mechanistic understanding of the principles by which chromatin is folded in the eukaryotic nucleus.
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Affiliation(s)
- Jian-Feng Xiang
- Emory University School of Medicine, Department of Human Genetics, 615 Michael Street, Atlanta, GA 30322, USA
| | - Victor G Corces
- Emory University School of Medicine, Department of Human Genetics, 615 Michael Street, Atlanta, GA 30322, USA.
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30
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Mossink B, Negwer M, Schubert D, Nadif Kasri N. The emerging role of chromatin remodelers in neurodevelopmental disorders: a developmental perspective. Cell Mol Life Sci 2021; 78:2517-2563. [PMID: 33263776 PMCID: PMC8004494 DOI: 10.1007/s00018-020-03714-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/04/2020] [Accepted: 11/16/2020] [Indexed: 12/13/2022]
Abstract
Neurodevelopmental disorders (NDDs), including intellectual disability (ID) and autism spectrum disorders (ASD), are a large group of disorders in which early insults during brain development result in a wide and heterogeneous spectrum of clinical diagnoses. Mutations in genes coding for chromatin remodelers are overrepresented in NDD cohorts, pointing towards epigenetics as a convergent pathogenic pathway between these disorders. In this review we detail the role of NDD-associated chromatin remodelers during the developmental continuum of progenitor expansion, differentiation, cell-type specification, migration and maturation. We discuss how defects in chromatin remodelling during these early developmental time points compound over time and result in impaired brain circuit establishment. In particular, we focus on their role in the three largest cell populations: glutamatergic neurons, GABAergic neurons, and glia cells. An in-depth understanding of the spatiotemporal role of chromatin remodelers during neurodevelopment can contribute to the identification of molecular targets for treatment strategies.
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Affiliation(s)
- Britt Mossink
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB, Nijmegen, The Netherlands
| | - Moritz Negwer
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB, Nijmegen, The Netherlands
| | - Dirk Schubert
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB, Nijmegen, The Netherlands
| | - Nael Nadif Kasri
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB, Nijmegen, The Netherlands.
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Klee EW, Cousin MA, Pinto E Vairo F, Morales-Rosado JA, Macke EL, Jenkinson WG, Ferrer A, Schultz-Rogers LE, Olson RJ, Oliver GR, Sigafoos AN, Schwab TL, Zimmermann MT, Urrutia RA, Kaiwar C, Gupta A, Blackburn PR, Boczek NJ, Prochnow CA, Lowy RJ, Mulvihill LA, McAllister TM, Aoudia SL, Kruisselbrink TM, Gunderson LB, Kemppainen JL, Fisher LJ, Tarnowski JM, Hager MM, Kroc SA, Bertsch NL, Agre KE, Jackson JL, Macklin-Mantia SK, Murphree MI, Rust LM, Summer Bolster JM, Beck SA, Atwal PS, Ellingson MS, Barnett SS, Rasmussen KJ, Lahner CA, Niu Z, Hasadsri L, Ferber MJ, Marcou CA, Clark KJ, Pichurin PN, Deyle DR, Morava-Kozicz E, Gavrilova RH, Dhamija R, Wierenga KJ, Lanpher BC, Babovic-Vuksanovic D, Farrugia G, Schimmenti LA, Stewart AK, Lazaridis KN. Impact of integrated translational research on clinical exome sequencing. Genet Med 2021; 23:498-507. [PMID: 33144682 DOI: 10.1038/s41436-020-01005-9] [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: 07/01/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 02/07/2023] Open
Abstract
PURPOSE Exome sequencing often identifies pathogenic genetic variants in patients with undiagnosed diseases. Nevertheless, frequent findings of variants of uncertain significance necessitate additional efforts to establish causality before reaching a conclusive diagnosis. To provide comprehensive genomic testing to patients with undiagnosed disease, we established an Individualized Medicine Clinic, which offered clinical exome testing and included a Translational Omics Program (TOP) that provided variant curation, research activities, or research exome sequencing. METHODS From 2012 to 2018, 1101 unselected patients with undiagnosed diseases received exome testing. Outcomes were reviewed to assess impact of the TOP and patient characteristics on diagnostic rates through descriptive and multivariate analyses. RESULTS The overall diagnostic yield was 24.9% (274 of 1101 patients), with 174 (15.8% of 1101) diagnosed on the basis of clinical exome sequencing alone. Four hundred twenty-three patients with nondiagnostic or without access to clinical exome sequencing were evaluated by the TOP, with 100 (9% of 1101) patients receiving a diagnosis, accounting for 36.5% of the diagnostic yield. The identification of a genetic diagnosis was influenced by the age at time of testing and the disease phenotype of the patient. CONCLUSION Integration of translational research activities into clinical practice of a tertiary medical center can significantly increase the diagnostic yield of patients with undiagnosed disease.
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Affiliation(s)
- Eric W Klee
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA. .,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA. .,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA.
| | - Margot A Cousin
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Filippo Pinto E Vairo
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Joel A Morales-Rosado
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Erica L Macke
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - W Garrett Jenkinson
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Alejandro Ferrer
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Laura E Schultz-Rogers
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Rory J Olson
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Gavin R Oliver
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Ashley N Sigafoos
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Tanya L Schwab
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Michael T Zimmermann
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Raul A Urrutia
- Division of Research, Department of Surgery and the Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Charu Kaiwar
- Center for Individualized Medicine, Mayo Clinic, Scottsdale, AZ, USA
| | - Aditi Gupta
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Patrick R Blackburn
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Nicole J Boczek
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Carri A Prochnow
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Rebecca J Lowy
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Lindsay A Mulvihill
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Tammy M McAllister
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Stacy L Aoudia
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Teresa M Kruisselbrink
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Jennifer L Kemppainen
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Laura J Fisher
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | | | - Megan M Hager
- Department of Clinical Genomics, Mayo Clinic, Scottsdale, AZ, USA
| | - Sarah A Kroc
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Nicole L Bertsch
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Katherine E Agre
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | | | | | | | - Laura M Rust
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | | | - Scott A Beck
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Paldeep S Atwal
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL, USA.,Center for Individualized Medicine, Mayo Clinic, Jacksonville, FL, USA
| | - Marissa S Ellingson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Sarah S Barnett
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Kristen J Rasmussen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Carrie A Lahner
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Zhiyv Niu
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Linda Hasadsri
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Matthew J Ferber
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Cherisse A Marcou
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Karl J Clark
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Pavel N Pichurin
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - David R Deyle
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Eva Morava-Kozicz
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Ralitza H Gavrilova
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Radhika Dhamija
- Center for Individualized Medicine, Mayo Clinic, Scottsdale, AZ, USA.,Department of Clinical Genomics, Mayo Clinic, Scottsdale, AZ, USA
| | - Klaas J Wierenga
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL, USA.,Center for Individualized Medicine, Mayo Clinic, Jacksonville, FL, USA
| | - Brendan C Lanpher
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Dusica Babovic-Vuksanovic
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Gianrico Farrugia
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Division of Gastroenterology and Hepatology, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Lisa A Schimmenti
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | | | - Konstantinos N Lazaridis
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA. .,Division of Gastroenterology and Hepatology, College of Medicine, Mayo Clinic, Rochester, MN, USA.
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陈 兰, 赫 纹, 刘 玲. [Autosomal dominant intellectual disability type 21 in a neonate]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2021; 23:306-309. [PMID: 33691927 PMCID: PMC7969196 DOI: 10.7499/j.issn.1008-8830.2010095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 01/03/2021] [Indexed: 06/12/2023]
Abstract
This is a case report on a 1-day-old male neonate admitted due to a weak cry for 1 day and recurrent circumoral cyanosis for 2 hours. He had unusual facial features at birth, with a single transverse palmar crease on both hands, flat feet, weak cry, feeding difficulties, congenital heart disease, and abnormality on cerebral MRI. Whole exome sequencing showed a de novo mutation, c.778_781delAAAG(p.Lys260ValfsTer2), in exon 3 of the CTCF gene, which was considered a pathogenic mutation by protein function prediction and might damage the function of CTCF protein. He was diagnosed with autosomal dominant intellectual disability type 21 based on the clinical manifestations and genetic analysis results. This case suggests that genetic analysis should be performed as early as possible for neonates with feeding difficulties which cannot be explained by infection or hypoxia, so as to help with early diagnosis and genetic counselling.
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Affiliation(s)
- 兰 陈
- />贵阳市妇幼保健院新生儿科, 贵州贵阳 550003Guiyang Maternity and Child Health Care Hospital, Guiyang 550003, China
| | - 纹 赫
- />贵阳市妇幼保健院新生儿科, 贵州贵阳 550003Guiyang Maternity and Child Health Care Hospital, Guiyang 550003, China
| | - 玲 刘
- />贵阳市妇幼保健院新生儿科, 贵州贵阳 550003Guiyang Maternity and Child Health Care Hospital, Guiyang 550003, China
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Novel exon-skipping variant disrupting the basic domain of HCFC1 causes intellectual disability without metabolic abnormalities in both male and female patients. J Hum Genet 2021; 66:717-724. [PMID: 33517344 DOI: 10.1038/s10038-020-00892-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 11/05/2020] [Accepted: 11/09/2020] [Indexed: 11/09/2022]
Abstract
HCFC1, a global transcriptional regulator, has been shown to associate with MMACHC expression. Pathogenic variants in HCFC1 cause X-linked combined methylmalonic acidemia and hyperhomocysteinemia, CblX type (MIM# 309541). Recent studies showed that certain variants in HCFC1 are associated with X-linked intellectual disability with mild or absent metabolic abnormalities. Here, we report five subjects (three males, two females) from the same family with a novel predicted loss of function HCFC1 variant. All five patients exhibit developmental delay or intellectual disability/learning difficulty and some dysmorphic features; findings were milder in the female as compared to male subjects. Biochemical studies in all patients did not show methylmalonic acidemia or hyperhomocysteinemia but revealed elevated vitamin B12 levels. Trio exome sequencing of the proband and his parents revealed a maternally inherited novel variant in HCFC1 designated as c.1781_1803 + 3del26insCA (NM_005334). Targeted testing confirmed the presence of the same variant in two half-siblings and maternal great uncle. In silico analysis showed that the variant is expected to reduce the quality of the splice donor site in intron 10 and causes abnormal splicing. Sequencing of proband's cDNA revealed exon 10 skipping. Further molecular studies in the two manifesting females revealed moderate and high skewing of X inactivation. Our results support previous observation that HCFC1 variants located outside the Kelch domain exhibit dissociation of the clinical and biochemical phenotype and cause milder or no metabolic changes. We also show that this novel variant can be associated with a phenotype in females, although with milder severity, but further studies are needed to understand the role of skewed X inactivation among females in this rare disorder. Our work expands the genotypes and phenotypes associated with HCFC1-related disorder.
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Jia Z, Wu Q. Clustered Protocadherins Emerge as Novel Susceptibility Loci for Mental Disorders. Front Neurosci 2020; 14:587819. [PMID: 33262685 PMCID: PMC7688460 DOI: 10.3389/fnins.2020.587819] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/26/2020] [Indexed: 12/24/2022] Open
Abstract
The clustered protocadherins (cPcdhs) are a subfamily of type I single-pass transmembrane cell adhesion molecules predominantly expressed in the brain. Their stochastic and combinatorial expression patterns encode highly diverse neural identity codes which are central for neuronal self-avoidance and non-self discrimination in brain circuit formation. In this review, we first briefly outline mechanisms for generating a tremendous diversity of cPcdh cell-surface assemblies. We then summarize the biological functions of cPcdhs in a wide variety of neurodevelopmental processes, such as neuronal migration and survival, dendritic arborization and self-avoidance, axonal tiling and even spacing, and synaptogenesis. We focus on genetic, epigenetic, and 3D genomic dysregulations of cPcdhs that are associated with various neuropsychiatric and neurodevelopmental diseases. A deeper understanding of regulatory mechanisms and physiological functions of cPcdhs should provide significant insights into the pathogenesis of mental disorders and facilitate development of novel diagnostic and therapeutic strategies.
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Affiliation(s)
| | - Qiang Wu
- Center for Comparative Biomedicine, MOE Key Laboratory of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
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35
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Fliedner A, Kirchner P, Wiesener A, van de Beek I, Waisfisz Q, van Haelst M, Scott DA, Lalani SR, Rosenfeld JA, Azamian MS, Xia F, Dutra-Clarke M, Martinez-Agosto JA, Lee H, Noh GJ, Lippa N, Alkelai A, Aggarwal V, Agre KE, Gavrilova R, Mirzaa GM, Straussberg R, Cohen R, Horist B, Krishnamurthy V, McWalter K, Juusola J, Davis-Keppen L, Ohden L, van Slegtenhorst M, de Man SA, Ekici AB, Gregor A, van de Laar I, Zweier C, Nelson SF, Grody WW, Lee H, Deignan JL, Kang SH, Arboleda VA, Senaratne TN, Dorrani N, Dutra-Clarke MS, Kianmahd J, Hinkamp FL, Neustadt AM, Martinez-Agosto JA, Fogel BL, Quintero-Rivera F. Variants in SCAF4 Cause a Neurodevelopmental Disorder and Are Associated with Impaired mRNA Processing. Am J Hum Genet 2020; 107:544-554. [PMID: 32730804 DOI: 10.1016/j.ajhg.2020.06.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/25/2020] [Indexed: 01/14/2023] Open
Abstract
RNA polymerase II interacts with various other complexes and factors to ensure correct initiation, elongation, and termination of mRNA transcription. One of these proteins is SR-related CTD-associated factor 4 (SCAF4), which is important for correct usage of polyA sites for mRNA termination. Using exome sequencing and international matchmaking, we identified nine likely pathogenic germline variants in SCAF4 including two splice-site and seven truncating variants, all residing in the N-terminal two thirds of the protein. Eight of these variants occurred de novo, and one was inherited. Affected individuals demonstrated a variable neurodevelopmental disorder characterized by mild intellectual disability, seizures, behavioral abnormalities, and various skeletal and structural anomalies. Paired-end RNA sequencing on blood lymphocytes of SCAF4-deficient individuals revealed a broad deregulation of more than 9,000 genes and significant differential splicing of more than 2,900 genes, indicating an important role of SCAF4 in mRNA processing. Knockdown of the SCAF4 ortholog CG4266 in the model organism Drosophila melanogaster resulted in impaired locomotor function, learning, and short-term memory. Furthermore, we observed an increased number of active zones in larval neuromuscular junctions, representing large glutamatergic synapses. These observations indicate a role of CG4266 in nervous system development and function and support the implication of SCAF4 in neurodevelopmental phenotypes. In summary, our data show that heterozygous, likely gene-disrupting variants in SCAF4 are causative for a variable neurodevelopmental disorder associated with impaired mRNA processing.
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36
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Luppino JM, Joyce EF. Single cell analysis pushes the boundaries of TAD formation and function. Curr Opin Genet Dev 2020; 61:25-31. [PMID: 32302920 DOI: 10.1016/j.gde.2020.03.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/16/2020] [Accepted: 03/17/2020] [Indexed: 11/30/2022]
Abstract
Eukaryotic genomes encode genetic information in their linear sequence, but appropriate expression of their genes requires chromosomes to fold into complex three-dimensional structures. Fueled by a growing collection of sequencing and imaging-based technologies, studies have uncovered a hierarchy of DNA interactions, from small chromatin loops that connect genes and enhancers to larger topologically associated domains (TADs) and compartments. However, despite the remarkable conservation of these organizational features, we have a very limited understanding of how this organization influences gene expression. This issue is further complicated in the context of single-cell heterogeneity, as has recently been revealed at both the level of gene activation and chromatin topology. Here, we provide a perspective on recent studies that address cell-to-cell variability and the relationship between structural heterogeneity and gene expression. We propose that transcription is regulated by variable 3D structures driven by at least two independent and partially redundant mechanisms. Collectively, this may provide flexibility to transcriptional regulation at the level of individual cells as well as reproducibility across whole tissues.
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Affiliation(s)
- Jennifer M Luppino
- Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Eric F Joyce
- Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States.
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37
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Squeo GM, Augello B, Massa V, Milani D, Colombo EA, Mazza T, Castellana S, Piccione M, Maitz S, Petracca A, Prontera P, Accadia M, Della Monica M, Di Giacomo MC, Melis D, Selicorni A, Giglio S, Fischetto R, Di Fede E, Malerba N, Russo M, Castori M, Gervasini C, Merla G. Customised next-generation sequencing multigene panel to screen a large cohort of individuals with chromatin-related disorder. J Med Genet 2020; 57:760-768. [PMID: 32170002 DOI: 10.1136/jmedgenet-2019-106724] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/11/2020] [Accepted: 02/19/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND The regulation of the chromatin state by epigenetic mechanisms plays a central role in gene expression, cell function, and maintenance of cell identity. Hereditary disorders of chromatin regulation are a group of conditions caused by abnormalities of the various components of the epigenetic machinery, namely writers, erasers, readers, and chromatin remodelers. Although neurological dysfunction is almost ubiquitous in these disorders, the constellation of additional features characterizing many of these genes and the emerging clinical overlap among them indicate the existence of a community of syndromes. The introduction of high-throughput next generation sequencing (NGS) methods for testing multiple genes simultaneously is a logical step for the implementation of diagnostics of these disorders. METHODS We screened a heterogeneous cohort of 263 index patients by an NGS-targeted panel, containing 68 genes associated with more than 40 OMIM entries affecting chromatin function. RESULTS This strategy allowed us to identify clinically relevant variants in 87 patients (32%), including 30 for which an alternative clinical diagnosis was proposed after sequencing analysis and clinical re-evaluation. CONCLUSION Our findings indicate that this approach is effective not only in disorders with locus heterogeneity, but also in order to anticipate unexpected misdiagnoses due to clinical overlap among cognate disorders. Finally, this work highlights the utility of a prompt diagnosis in such a clinically and genetically heterogeneous group of disorders that we propose to group under the umbrella term of chromatinopathies.
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Affiliation(s)
- Gabriella Maria Squeo
- Division of Medical Genetics, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Bartolomeo Augello
- Division of Medical Genetics, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Valentina Massa
- Dipartimento di Scienze della Salute, Universita degli Studi di Milano Dipartimento di Scienze della Salute, Milano, Italy
| | - Donatella Milani
- UOSD Pediatria ad alta intensità di cura, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Elisa Adele Colombo
- Dipartimento di Scienze della Salute, Universita degli Studi di Milano Dipartimento di Scienze della Salute, Milano, Italy
| | - Tommaso Mazza
- Bioinformatics Unit, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Stefano Castellana
- Bioinformatics Unit, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Maria Piccione
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Silvia Maitz
- Clinical Pediatric Genetics Unit, Pediatrics Clinics, MBBM Foundation, Hospital San Gerardo, Monza, Italy
| | - Antonio Petracca
- Division of Medical Genetics, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Paolo Prontera
- Medical Genetics Unit, University of Perugia Hospital SM della Misericordia, Perugia, Italy
| | - Maria Accadia
- Medical Genetics Service, Hospital "Cardinale G. Panico", Tricase, Italy
| | - Matteo Della Monica
- Medical Genetics Unit, Cardarelli Hospital, Largo A Cardarelli, Napoli, Italy
| | | | - Daniela Melis
- Department of Translational Medical Science, Section of Pediatrics, University of Naples Federico II, Napoli, Italy
| | - Angelo Selicorni
- Pediatric Department, ASST Lariana, Sant'Anna General Hospital, Como, Italy
| | - Sabrina Giglio
- Department of Biomedical, Experimental and Clinical Sciences 'Mario Serio', Medical Genetics Unit, University Hospital Meyer, Firenze, Italy
| | - Rita Fischetto
- Metabolic Diseases, Clinical Genetics and Diabetology Unit, Paediatric Hospital Giovanni XXIII, Bari, Italy
| | - Elisabetta Di Fede
- Dipartimento di Scienze della Salute, Universita degli Studi di Milano Dipartimento di Scienze della Salute, Milano, Italy
| | - Natascia Malerba
- Division of Medical Genetics, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Matteo Russo
- Division of Medical Genetics, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Marco Castori
- Division of Medical Genetics, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Cristina Gervasini
- Dipartimento di Scienze della Salute, Universita degli Studi di Milano Dipartimento di Scienze della Salute, Milano, Italy
| | - Giuseppe Merla
- Division of Medical Genetics, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
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