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Morlino S, Vaccaro L, Leone MP, Nardella G, Bisceglia L, Ortore RP, Verzicco G, Cassano L, Castori M, Cacchiarelli D, Micale L. Combined exome and whole transcriptome sequencing identifies a de novo intronic SRCAP variant causing DEHMBA syndrome with severe sleep disorder. J Hum Genet 2024; 69:287-290. [PMID: 38448605 DOI: 10.1038/s10038-024-01240-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 02/09/2024] [Accepted: 02/27/2024] [Indexed: 03/08/2024]
Abstract
Rare heterozygous variants in exons 33-34 of the SRCAP gene are associated with Floating-Harbor syndrome and have a dominant-negative mechanism of action. At variance, heterozygous null alleles falling in other parts of the same gene cause developmental delay, hypotonia, musculoskeletal defects, and behavioral abnormalities (DEHMBA) syndrome. We report an 18-year-old man with DEHMBA syndrome and obstructive sleep apnea, who underwent exome sequencing (ES) and whole transcriptome sequencing (WTS) on peripheral blood. Trio analysis prioritized the de novo heterozygous c.5658+5 G > A variant. WTS promptly demostrated four different abnormal transcripts affecting >40% of the reads, three of which leading to a frameshift. This study demonstrated the efficacy of a combined ES-WTS approach in solving undiagnosed cases. We also speculated that sleep respiratory disorder may be an underdiagnosed complication of DEHMBA syndrome.
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Affiliation(s)
- Silvia Morlino
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, Viale Cappuccini snc, 71013, San Giovanni Rotondo, Foggia, Italy
| | - Lorenzo Vaccaro
- Armenise/Harvard Laboratory of Integrative Genomics, Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
- Department of Translational Medicine, University of Naples "Federico II", Naples, Italy
| | - Maria Pia Leone
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, Viale Cappuccini snc, 71013, San Giovanni Rotondo, Foggia, Italy
| | - Grazia Nardella
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, Viale Cappuccini snc, 71013, San Giovanni Rotondo, Foggia, Italy
| | - Luigi Bisceglia
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, Viale Cappuccini snc, 71013, San Giovanni Rotondo, Foggia, Italy
| | - Rocco Pio Ortore
- Division of Maxillofacial Surgery and Otolaryngology, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013, Foggia, Italy
| | - Giannandrea Verzicco
- Division of Maxillofacial Surgery and Otolaryngology, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013, Foggia, Italy
| | - Lazzaro Cassano
- Division of Maxillofacial Surgery and Otolaryngology, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013, Foggia, Italy
| | - Marco Castori
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, Viale Cappuccini snc, 71013, San Giovanni Rotondo, Foggia, Italy.
| | - Davide Cacchiarelli
- Armenise/Harvard Laboratory of Integrative Genomics, Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
- Department of Translational Medicine, University of Naples "Federico II", Naples, Italy
- Genomics and Experimental Medicine Program, Scuola Superiore Meridionale, Naples, Italy
| | - Lucia Micale
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, Viale Cappuccini snc, 71013, San Giovanni Rotondo, Foggia, Italy
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Jostes S, Vardabasso C, Dong J, Carcamo S, Singh R, Phelps R, Meadows A, Grossi E, Hasson D, Bernstein E. H2A.Z chaperones converge on E2F target genes for melanoma cell proliferation. Genes Dev 2024; 38:336-353. [PMID: 38744503 PMCID: PMC11146596 DOI: 10.1101/gad.351318.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 04/29/2024] [Indexed: 05/16/2024]
Abstract
High levels of H2A.Z promote melanoma cell proliferation and correlate with poor prognosis. However, the role of the two distinct H2A.Z histone chaperone complexes SRCAP and P400-TIP60 in melanoma remains unclear. Here, we show that individual subunit depletion of SRCAP, P400, and VPS72 (YL1) results in not only the loss of H2A.Z deposition into chromatin but also a reduction of H4 acetylation in melanoma cells. This loss of H4 acetylation is particularly found at the promoters of cell cycle genes directly bound by H2A.Z and its chaperones, suggesting a coordinated regulation between H2A.Z deposition and H4 acetylation to promote their expression. Knockdown of each of the three subunits downregulates E2F1 and its targets, resulting in a cell cycle arrest akin to H2A.Z depletion. However, unlike H2A.Z deficiency, loss of the shared H2A.Z chaperone subunit YL1 induces apoptosis. Furthermore, YL1 is overexpressed in melanoma tissues, and its upregulation is associated with poor patient outcome. Together, these findings provide a rationale for future targeting of H2A.Z chaperones as an epigenetic strategy for melanoma treatment.
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Affiliation(s)
- Sina Jostes
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Chiara Vardabasso
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Joanna Dong
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Saul Carcamo
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Bioinformatics for Next-Generation Sequencing Facility, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Rajendra Singh
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Robert Phelps
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Austin Meadows
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Elena Grossi
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Dan Hasson
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Bioinformatics for Next-Generation Sequencing Facility, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Emily Bernstein
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA;
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
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Alanis S, Blair MP, Kaufman LM, Bhat G, Shapiro MJ. Floating-Harbor syndrome with chorioretinal colobomas. Ophthalmic Genet 2024; 45:207-209. [PMID: 37722826 DOI: 10.1080/13816810.2023.2255895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/30/2023] [Indexed: 09/20/2023]
Abstract
BACKGROUND We present a case of a child with Floating-Harbor Syndrome (FHS) with bilateral chorioretinal coloboma (CC). To the best of our knowledge, this is the first case report of this association. Floating- Harbor syndrome is an extremely rare autosomal dominant genetic disorder with approximately 100 cases reported. It is characterized by a series of atypical features that include short stature with delayed bone age, low birth weight, skeletal anomalies, delayed speech development, and dysmorphic facial characteristics that typically portray a triangular face, deep-set eyes, long eyelashes, and prominent nose. MATERIALS AND METHODS Our patient was examined by a pediatric ophthalmologist for the time at age of 7. Visual acuity, optical coherence tomography (OCT) and Optos imaging were collected on every visit. The patient had whole genome sequencing ordered by a pediatric geneticist to confirm Floating-Harbor syndrome. RESULTS We present the patient's OCT and Optos images that illustrate the location of the patient's inferior chorioretinal coloboma in both eyes. The whole genome sequencing report collected revealed a heterozygous de novo pathogenic variant in the SRCAP gene, consistent with a Floating-Harbor syndrome diagnosis in the literature. DISCUSSION Both genetic and systemic findings are consistent with the diagnosis of Floating-Harbor syndrome in our patient. Rubenstein-Taybi and Floating-Harbor syndrome share a similarity in molecular and physical manifestations, but because of the prevalence in Rubenstein-Taybi diagnoses, it is a syndromic condition that includes coloboma and frequently associated with each other. Therefore, a retinal exam should become part of the standard protocol for those with FHS, as proper diagnosis, examination and treatment can prevent irreversible retinal damage.
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Affiliation(s)
| | - M P Blair
- Retina Consultants, Ltd, Des Plaines, Illinois, USA
| | - L M Kaufman
- Department of Ophthalmology & Visual Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - G Bhat
- University of Illinois Hospital Health & Science Center, Chicago, Illinois, USA
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Rhode J, Hagenau L, Beimdiek J, Ullmann R, Hossain F, Tzvetkova A, Jensen LR, Kuss AW. Generation of two iPSC lines (MHHi001-A-12 and MHHi001-A-13) carrying biallelic truncating mutations at the 3'-end of SRCAP using CRISPR/Cas9. Stem Cell Res 2023; 73:103249. [PMID: 38006676 DOI: 10.1016/j.scr.2023.103249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 11/09/2023] [Indexed: 11/27/2023] Open
Abstract
Non-Floating Harbour Syndrome (FLHS) neurodevelopmental disorder (NDD) is a recently described disorder caused by mutations in certain regions of the SRCAP gene. We generated two iPSC lines that contain truncating mutation on both alleles at the 3'-end of SRCAP using CRISPR/Cas9 technology. Both cell lines are pluripotent, differentiate into the 3 germ layers and contain no genomic aberrations or off-target modifications. The cell lines form part of a human disease model to investigate the effects of truncating mutations in different regions of SRCAP.
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Affiliation(s)
- J Rhode
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - L Hagenau
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - J Beimdiek
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - R Ullmann
- Bundeswehr Institute of Radiobiology Affiliated to the University of Ulm, Munich, Germany
| | - F Hossain
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - A Tzvetkova
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany; Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - L R Jensen
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - A W Kuss
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
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Jostes S, Vardabasso C, Dong J, Carcamo S, Singh R, Phelps R, Meadows A, Hasson D, Bernstein E. H2A.Z chaperones converge on histone H4 acetylation for melanoma cell proliferation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.26.568747. [PMID: 38076914 PMCID: PMC10705243 DOI: 10.1101/2023.11.26.568747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
High levels of H2A.Z promote melanoma cell proliferation and correlate with poor prognosis. However, the role of the two distinct H2A.Z histone chaperone complexes, SRCAP and P400-TIP60, in melanoma remains unclear. Here, we show that individual depletion of SRCAP, P400, and VPS72 (YL1) not only results in loss of H2A.Z deposition into chromatin, but also a striking reduction of H4 acetylation in melanoma cells. This loss of H4 acetylation is found at the promoters of cell cycle genes directly bound by H2A.Z and its chaperones, suggesting a highly coordinated regulation between H2A.Z deposition and H4 acetylation to promote their expression. Knockdown of each of the three subunits downregulates E2F1 and its targets, resulting in a cell cycle arrest akin to H2A.Z depletion. However, unlike H2A.Z deficiency, loss of the shared H2A.Z chaperone subunit YL1 induces apoptosis. Furthermore, YL1 is overexpressed in melanoma tissues, and its upregulation is associated with poor patient outcome. Together, these findings provide a rationale for future targeting of H2A.Z chaperones as an epigenetic strategy for melanoma treatment.
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Affiliation(s)
- Sina Jostes
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Chiara Vardabasso
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joanna Dong
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Saul Carcamo
- Bioinformatics for Next Generation Sequencing Facility, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rajendra Singh
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert Phelps
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Austin Meadows
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dan Hasson
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Bioinformatics for Next Generation Sequencing Facility, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Emily Bernstein
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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Prozzillo Y, Santopietro MV, Messina G, Dimitri P. Unconventional roles of chromatin remodelers and long non-coding RNAs in cell division. Cell Mol Life Sci 2023; 80:365. [PMID: 37982870 PMCID: PMC10661750 DOI: 10.1007/s00018-023-04949-8] [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: 05/17/2023] [Revised: 08/31/2023] [Accepted: 09/02/2023] [Indexed: 11/21/2023]
Abstract
The aim of this review article is to focus on the unconventional roles of epigenetic players (chromatin remodelers and long non-coding RNAs) in cell division, beyond their well-characterized functions in chromatin regulation during cell differentiation and development. In the last two decades, diverse experimental evidence has shown that subunits of SRCAP and p400/TIP60 chromatin remodeling complexes in humans relocate from interphase nuclei to centrosomes, spindle or midbody, with their depletion yielding an array of aberrant outcomes of mitosis and cytokinesis. Remarkably, this behavior is shared by orthologous subunits of the Drosophila melanogaster DOM/TIP60 complex, despite fruit flies and humans diverged over 700 million years ago. In short, the available data support the view that subunits of these complexes are a new class of moonlighting proteins, in that they lead a "double life": during the interphase, they function in chromatin regulation within the nucleus, but as the cell progresses through mitosis, they interact with established mitotic factors, thus becoming integral components of the cell division apparatus. By doing so, they contribute to ensuring the correct distribution of chromosomes in the two daughter cells and, when dysfunctional, can cause genomic instability, a condition that can trigger tumorigenesis and developmental diseases. Research over the past few years has unveiled a major contribution of long non-coding RNAs (lncRNAs) in the epigenetics regulation of gene expression which also impacts on cell division control. Here, we focus on possible structural roles of lncRNAs in the execution of cytokinesis: in particular, we suggest that specific classes of lncRNAs relocate to the midbody to form an architectural scaffold ensuring its proper assembly and function during abscission. Drawing attention to experimental evidence for non-canonical extranuclear roles of chromatin factors and lncRNAs has direct implications on important and novel aspects concerning both the epigenetic regulation and the evolutionary dynamics of cell division with a significant impact on differentiation, development, and diseases.
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Affiliation(s)
- Yuri Prozzillo
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy
| | | | - Giovanni Messina
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy.
- Universita degli Studi di Milano-Bicocca, Piazza dell' Ateneo Nuovo, 1, 20126, Milano, Italy.
| | - Patrizio Dimitri
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy.
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White-Brown A, Choufani S, Weksberg R, Dyment D. Missense variant in SRCAP with distinct DNA methylation signature associated with non-FLHS SRCAP-related neurodevelopmental disorder. Am J Med Genet A 2023; 191:2640-2646. [PMID: 37340855 DOI: 10.1002/ajmg.a.63329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/18/2023] [Accepted: 05/26/2023] [Indexed: 06/22/2023]
Abstract
Floating-Harbor syndrome (FLHS) is a neurodevelopmental disorder (NDD) caused by truncating variants in exons 33 and 34 of the SNF2-related CREBBP activator protein gene (SRCAP). Truncating variants proximal to this location in SRCAP result in a non-FLHS SRCAP-associated NDD; an overlapping but distinct NDD characterized by developmental delay with or without intellectual disability (ID), hypotonia, normal stature, and behavioral and psychiatric issues. Here, we report a young woman who initially presented in childhood with significant delays in speech and mild ID. In young adulthood, she developed schizophrenia. On physical examination, she had facial features suggestive of 22q11 deletion syndrome. After non-diagnostic chromosomal microarray and trio exome sequencing (ES), a re-analysis of trio ES data identified a de novo missense variant in SRCAP that was proximal to the FLHS critical region. Subsequent DNA methylation studies showed the unique methylation signature associated with pathogenic sequence variants in non-FLHS SRCAP-related NDD. This clinical report describes an individual with non-FLHS SRCAP-related NDD caused by an SRCAP missense variant, and it also demonstrates the clinical utility of ES re-analysis and DNA methylation analysis for undiagnosed patients, in particular, those with variants of uncertain significance.
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Affiliation(s)
- Alexandre White-Brown
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Sanaa Choufani
- Genetics and Genome Biology Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Rosanna Weksberg
- Genetics and Genome Biology Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - David Dyment
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
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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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Wang S, Yan S, Xiao J, Chen Y, Chen A, Deng A, Wang T, He J, Peng X. A de novo mutation of ADAMTS8 in a patient with Wiedemann-Steiner syndrome. Mol Cytogenet 2023; 16:21. [PMID: 37649104 PMCID: PMC10469774 DOI: 10.1186/s13039-023-00654-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/18/2023] [Indexed: 09/01/2023] Open
Abstract
BACKGROUND Wiedemann-Steiner syndrome (WDSTS) is a rare autosomal dominant disorder caused by mutations in the KMT2A gene and is usually characterized by hairy elbows, short stature, developmental delay, intellectual disability and obvious facial dysmorphism. CASE PRESENTATION Here, we report a 5-year-old girl with clinical features similar to WDSTS, including postnatal growth delay, retarded intellectual development, and ocular hypertelorism. Through whole-exome sequencing (WES), a frameshift variant of KMT2A was found in the patient but not in her parents' genomic DNA. By bioinformatics analysis, the KMT2A variant was demonstrated to be the top candidate pathogenic variant for the clinical phenotype consistent with WDSTS. Moreover, a duplication of exon 1 in ADAMTS8 (belonging to the zinc metalloproteinase family) was found in the genomic DNA of this patient, which may be responsible for the characteristics that are different from those of WDSTS, including early teething, rapid tooth replacement, and dysplastic enamel. CONCLUSIONS From the above results, we propose that in our patient, the frameshift variant in KMT2A is the main reason for the WDSTS phenotype, and the unreported mutation in ADAMTS8 may be the candidate reason for other characteristics that are different from those of WDSTS. Therefore, this study not only provides a new KMT2A variant associated with WDSTS but is also a reminder that combined mutations may be present in a case with more characteristics than those seen in WDSTS.
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Affiliation(s)
- Sifeng Wang
- Hunan Provincial Key Laboratory of Regional Hereditary Birth Defects Prevention and Control, Changsha Hospital for Maternal and Child Health Care Affiliated to Hunan Normal University, Changsha, China
| | - Shuyuan Yan
- Hunan Provincial Key Laboratory of Regional Hereditary Birth Defects Prevention and Control, Changsha Hospital for Maternal and Child Health Care Affiliated to Hunan Normal University, Changsha, China
| | - Jingjun Xiao
- Hunan Provincial Key Laboratory of Regional Hereditary Birth Defects Prevention and Control, Changsha Hospital for Maternal and Child Health Care Affiliated to Hunan Normal University, Changsha, China
| | - Ying Chen
- Hunan Provincial Key Laboratory of Regional Hereditary Birth Defects Prevention and Control, Changsha Hospital for Maternal and Child Health Care Affiliated to Hunan Normal University, Changsha, China
| | - Anji Chen
- Hunan Provincial Key Laboratory of Regional Hereditary Birth Defects Prevention and Control, Changsha Hospital for Maternal and Child Health Care Affiliated to Hunan Normal University, Changsha, China
| | - Aimin Deng
- Hunan Provincial Key Laboratory of Regional Hereditary Birth Defects Prevention and Control, Changsha Hospital for Maternal and Child Health Care Affiliated to Hunan Normal University, Changsha, China
| | - Tuanmei Wang
- Hunan Provincial Key Laboratory of Regional Hereditary Birth Defects Prevention and Control, Changsha Hospital for Maternal and Child Health Care Affiliated to Hunan Normal University, Changsha, China
| | - Jun He
- Hunan Provincial Key Laboratory of Regional Hereditary Birth Defects Prevention and Control, Changsha Hospital for Maternal and Child Health Care Affiliated to Hunan Normal University, Changsha, China
| | - Xiangwen Peng
- Hunan Provincial Key Laboratory of Regional Hereditary Birth Defects Prevention and Control, Changsha Hospital for Maternal and Child Health Care Affiliated to Hunan Normal University, Changsha, China.
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Hara T, Owada Y, Takata A. Genetics of bipolar disorder: insights into its complex architecture and biology from common and rare variants. J Hum Genet 2023; 68:183-191. [PMID: 35614313 DOI: 10.1038/s10038-022-01046-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/28/2022] [Accepted: 05/11/2022] [Indexed: 11/09/2022]
Abstract
Bipolar disorder (BD) is a common mental disorder characterized by recurrent mood episodes, which causes major socioeconomic burdens globally. Though its disease pathogenesis is largely unknown, the high heritability of BD indicates strong contributions from genetic factors. In this review, we summarize the recent achievements in the genetics of BD, particularly those from genome-wide association study (GWAS) of common variants and next-generation sequencing analysis of rare variants. These include the identification of dozens of robust disease-associated loci, deepening of our understanding of the biology of BD, objective description of correlations with other psychiatric disorders and behavioral traits, formulation of methods for predicting disease risk and drug response, and the discovery of a single gene associated with bipolar disorder and schizophrenia spectrum with a large effect size. On the other hand, the findings to date have not yet made a clear contribution to the improvement of clinical psychiatry of BD. We overview the remaining challenges as well as possible paths to resolve them, referring to studies of other major neuropsychiatric disorders.
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Affiliation(s)
- Tomonori Hara
- Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, Wako, Saitama, 351-0198, Japan.,Department of Organ Anatomy, Tohoku University Graduate School of Medicine, Sendai, Miyagi, 980-8575, Japan
| | - Yuji Owada
- Department of Organ Anatomy, Tohoku University Graduate School of Medicine, Sendai, Miyagi, 980-8575, Japan
| | - Atsushi Takata
- Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, Wako, Saitama, 351-0198, Japan.
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11
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Chohra I, Chung K, Giri S, Malgrange B. ATP-Dependent Chromatin Remodellers in Inner Ear Development. Cells 2023; 12:cells12040532. [PMID: 36831199 PMCID: PMC9954591 DOI: 10.3390/cells12040532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/11/2023] Open
Abstract
During transcription, DNA replication and repair, chromatin structure is constantly modified to reveal specific genetic regions and allow access to DNA-interacting enzymes. ATP-dependent chromatin remodelling complexes use the energy of ATP hydrolysis to modify chromatin architecture by repositioning and rearranging nucleosomes. These complexes are defined by a conserved SNF2-like, catalytic ATPase subunit and are divided into four families: CHD, SWI/SNF, ISWI and INO80. ATP-dependent chromatin remodellers are crucial in regulating development and stem cell biology in numerous organs, including the inner ear. In addition, mutations in genes coding for proteins that are part of chromatin remodellers have been implicated in numerous cases of neurosensory deafness. In this review, we describe the composition, structure and functional activity of these complexes and discuss how they contribute to hearing and neurosensory deafness.
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12
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Fu MP, Merrill SM, Sharma M, Gibson WT, Turvey SE, Kobor MS. Rare diseases of epigenetic origin: Challenges and opportunities. Front Genet 2023; 14:1113086. [PMID: 36814905 PMCID: PMC9939656 DOI: 10.3389/fgene.2023.1113086] [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: 12/01/2022] [Accepted: 01/24/2023] [Indexed: 02/09/2023] Open
Abstract
Rare diseases (RDs), more than 80% of which have a genetic origin, collectively affect approximately 350 million people worldwide. Progress in next-generation sequencing technology has both greatly accelerated the pace of discovery of novel RDs and provided more accurate means for their diagnosis. RDs that are driven by altered epigenetic regulation with an underlying genetic basis are referred to as rare diseases of epigenetic origin (RDEOs). These diseases pose unique challenges in research, as they often show complex genetic and clinical heterogeneity arising from unknown gene-disease mechanisms. Furthermore, multiple other factors, including cell type and developmental time point, can confound attempts to deconvolute the pathophysiology of these disorders. These challenges are further exacerbated by factors that contribute to epigenetic variability and the difficulty of collecting sufficient participant numbers in human studies. However, new molecular and bioinformatics techniques will provide insight into how these disorders manifest over time. This review highlights recent studies addressing these challenges with innovative solutions. Further research will elucidate the mechanisms of action underlying unique RDEOs and facilitate the discovery of treatments and diagnostic biomarkers for screening, thereby improving health trajectories and clinical outcomes of affected patients.
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Affiliation(s)
- Maggie P. Fu
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada,BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Sarah M. Merrill
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada,BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Mehul Sharma
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada,Department of Pediatrics, Faculty of Medicine, BC Children’s Hospital, University of British Columbia, Vancouver, BC, Canada
| | - William T. Gibson
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Stuart E. Turvey
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada,Department of Pediatrics, Faculty of Medicine, BC Children’s Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Michael S. Kobor
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada,BC Children’s Hospital Research Institute, Vancouver, BC, Canada,*Correspondence: Michael S. Kobor,
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13
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Connally NJ, Nazeen S, Lee D, Shi H, Stamatoyannopoulos J, Chun S, Cotsapas C, Cassa CA, Sunyaev SR. The missing link between genetic association and regulatory function. eLife 2022; 11:74970. [PMID: 36515579 PMCID: PMC9842386 DOI: 10.7554/elife.74970] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/02/2022] [Indexed: 12/15/2022] Open
Abstract
The genetic basis of most traits is highly polygenic and dominated by non-coding alleles. It is widely assumed that such alleles exert small regulatory effects on the expression of cis-linked genes. However, despite the availability of gene expression and epigenomic datasets, few variant-to-gene links have emerged. It is unclear whether these sparse results are due to limitations in available data and methods, or to deficiencies in the underlying assumed model. To better distinguish between these possibilities, we identified 220 gene-trait pairs in which protein-coding variants influence a complex trait or its Mendelian cognate. Despite the presence of expression quantitative trait loci near most GWAS associations, by applying a gene-based approach we found limited evidence that the baseline expression of trait-related genes explains GWAS associations, whether using colocalization methods (8% of genes implicated), transcription-wide association (2% of genes implicated), or a combination of regulatory annotations and distance (4% of genes implicated). These results contradict the hypothesis that most complex trait-associated variants coincide with homeostatic expression QTLs, suggesting that better models are needed. The field must confront this deficit and pursue this 'missing regulation.'
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Affiliation(s)
- Noah J Connally
- Department of Biomedical Informatics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
| | - Sumaiya Nazeen
- Department of Biomedical Informatics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Department of Neurology, Harvard Medical SchoolBostonUnited States
| | - Daniel Lee
- Department of Biomedical Informatics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
| | - Huwenbo Shi
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
- Department of Epidemiology, Harvard T.H. Chan School of Public HealthBostonUnited States
| | | | - Sung Chun
- Division of Pulmonary Medicine, Boston Children’s HospitalBostonUnited States
| | - Chris Cotsapas
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
- Department of Neurology, Yale Medical SchoolNew HavenUnited States
- Department of Genetics, Yale Medical SchoolNew HavenUnited States
| | - Christopher A Cassa
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
| | - Shamil R Sunyaev
- Department of Biomedical Informatics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
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14
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Fan J, Moreno AT, Baier AS, Loparo JJ, Peterson CL. H2A.Z deposition by SWR1C involves multiple ATP-dependent steps. Nat Commun 2022; 13:7052. [PMID: 36396651 PMCID: PMC9672302 DOI: 10.1038/s41467-022-34861-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 11/09/2022] [Indexed: 11/18/2022] Open
Abstract
Histone variant H2A.Z is a conserved feature of nucleosomes flanking protein-coding genes. Deposition of H2A.Z requires ATP-dependent replacement of nucleosomal H2A by a chromatin remodeler related to the multi-subunit enzyme, yeast SWR1C. How these enzymes use ATP to promote this nucleosome editing reaction remains unclear. Here we use single-molecule and ensemble methodologies to identify three ATP-dependent phases in the H2A.Z deposition reaction. Real-time analysis of single nucleosome remodeling events reveals an initial priming step that occurs after ATP addition that involves a combination of both transient DNA unwrapping from the nucleosome and histone octamer deformations. Priming is followed by rapid loss of histone H2A, which is subsequently released from the H2A.Z nucleosomal product. Surprisingly, rates of both priming and the release of the H2A/H2B dimer are sensitive to ATP concentration. This complex reaction pathway provides multiple opportunities to regulate timely and accurate deposition of H2A.Z at key genomic locations.
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Affiliation(s)
- Jiayi Fan
- grid.168645.80000 0001 0742 0364Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605 USA ,grid.168645.80000 0001 0742 0364Interdisciplinary Graduate Program, University of Massachusetts Chan Medical School, Worcester, MA 01605 USA
| | - Andrew T. Moreno
- grid.38142.3c000000041936754XDepartment of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Alexander S. Baier
- grid.168645.80000 0001 0742 0364Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605 USA ,grid.168645.80000 0001 0742 0364Medical Scientist Training Program, University of Massachusetts Chan Medical School, Worcester, MA 01605 USA
| | - Joseph J. Loparo
- grid.38142.3c000000041936754XDepartment of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Craig L. Peterson
- grid.168645.80000 0001 0742 0364Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605 USA
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15
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Boycott KM, Hartley T, Kernohan KD, Dyment DA, Howley H, Innes AM, Bernier FP, Brudno M. Care4Rare Canada: Outcomes from a decade of network science for rare disease gene discovery. Am J Hum Genet 2022; 109:1947-1959. [PMID: 36332610 PMCID: PMC9674964 DOI: 10.1016/j.ajhg.2022.10.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 10/04/2022] [Indexed: 11/06/2022] Open
Abstract
The past decade has witnessed a rapid evolution in rare disease (RD) research, fueled by the availability of genome-wide (exome and genome) sequencing. In 2011, as this transformative technology was introduced to the research community, the Care4Rare Canada Consortium was launched: initially as FORGE, followed by Care4Rare, and Care4Rare SOLVE. Over what amounted to three eras of diagnosis and discovery, the Care4Rare Consortium used exome sequencing and, more recently, genome and other 'omic technologies to identify the molecular cause of unsolved RDs. We achieved a diagnostic yield of 34% (623/1,806 of participating families), including the discovery of deleterious variants in 121 genes not previously associated with disease, and we continue to study candidate variants in novel genes for 145 families. The Consortium has made significant contributions to RD research, including development of platforms for data collection and sharing and instigating a Canadian network to catalyze functional characterization research of novel genes. The Consortium was instrumental to implementing genome-wide sequencing as a publicly funded test for RD diagnosis in Canada. Despite the successes of the past decade, the challenge of solving all RDs remains enormous, and the work is far from over. We must leverage clinical and 'omic data for secondary use, develop tools and policies to support safe data sharing, continue to explore the utility of new and emerging technologies, and optimize research protocols to delineate complex disease mechanisms. Successful approaches in each of these realms is required to offer diagnostic clarity to all families with RDs.
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Affiliation(s)
- Kym M. Boycott
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada,Corresponding author
| | - Taila Hartley
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Kristin D. Kernohan
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - David A. Dyment
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Heather Howley
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - A. Micheil Innes
- Department of Medical Genetics and Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Francois P. Bernier
- Department of Medical Genetics and Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada
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16
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Wang G, Xu Y, Wang Q, Chai Y, Sun X, Yang F, Zhang J, Wu M, Liao X, Yu X, Sheng X, Liu Z, Zhang J. Rare and undiagnosed diseases: From disease-causing gene identification to mechanism elucidation. FUNDAMENTAL RESEARCH 2022. [DOI: 10.1016/j.fmre.2022.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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17
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Zhao B, Madden JA, Lin J, Berry GT, Wojcik MH, Zhao X, Brand H, Talkowski M, Lee EA, Agrawal PB. A neurodevelopmental disorder caused by a novel de novo SVA insertion in exon 13 of the SRCAP gene. Eur J Hum Genet 2022; 30:1083-1087. [PMID: 35768521 PMCID: PMC9437004 DOI: 10.1038/s41431-022-01137-3] [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: 01/18/2022] [Revised: 04/24/2022] [Accepted: 06/14/2022] [Indexed: 12/24/2022] Open
Abstract
Pathogenic variants in the SRCAP (SNF2-related CREBBP activator protein) gene, which encodes a chromatin-remodeling ATPase, cause neurodevelopmental disorders including Floating Harbor syndrome (FLHS). Here, we report the discovery of a de novo transposon insertion in SRCAP exon 13 from trio genome sequencing in a 28-year-old female with failure to thrive, developmental delay, mood disorder and seizure disorder. The insertion was a full-length (~2.8 kb), antisense-oriented SVA insertion relative to the SRCAP transcript, bearing a 5' transduction and hallmarks of target-primed reverse transcription. The 20-bp 5' transduction allowed us to trace the source SVA element to an intron of a long non-coding RNA on chromosome 12, which is highly expressed in testis. RNA sequencing and qRT-PCR confirmed significant depletion of SRCAP expression and low-level exon skipping in the proband. This case highlights a novel disease-causing structural variant and the importance of transposon analysis in a clinical diagnostic setting.
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Affiliation(s)
- Boxun Zhao
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jill A Madden
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Jasmine Lin
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
- Division of Newborn Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Gerard T Berry
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Monica H Wojcik
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Division of Newborn Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Xuefang Zhao
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Harrison Brand
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Michael Talkowski
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Eunjung Alice Lee
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA.
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA.
| | - Pankaj B Agrawal
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA.
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Division of Newborn Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
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18
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Allen DZ, Roy S. Otologic manifestations of Floating Harbor Syndrome (FHS): A case series and a review of the literature. OTOLARYNGOLOGY CASE REPORTS 2022. [DOI: 10.1016/j.xocr.2022.100406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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19
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Turkunova ME, Barbitoff YA, Serebryakova EA, Polev DE, Berseneva OS, Bashnina EB, Baranov VS, Glotov OS, Glotov AS. Molecular Genetics and Pathogenesis of the Floating Harbor Syndrome: Case Report of Long-Term Growth Hormone Treatment and a Literature Review. Front Genet 2022; 13:846101. [PMID: 35664296 PMCID: PMC9157637 DOI: 10.3389/fgene.2022.846101] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 04/11/2022] [Indexed: 11/16/2022] Open
Abstract
Introduction: Floating Harbor syndrome (FHS) is an extremely rare disorder, with slightly more than a hundred cases reported worldwide. FHS is caused by heterozygous mutations in the SRCAP gene; however, little is known about the pathogenesis of FHS or the effectiveness of its treatment. Methods: Whole-exome sequencing (WES) was performed for the definitive molecular diagnosis of the disease. Identified variants were validated using Sanger sequencing. In addition, systematic literature and public data on genetic variation in SRCAP and the effects of growth hormone (GH) treatment was conducted. Results: We herein report the first case of FHS in the Russian Federation. The male proband presented with most of the typical phenotypic features of FHS, including short stature, skeletal and facial features, delayed growth and bone age, high pitched voice, and intellectual impairment. The proband also had partial growth hormone deficiency. We report the history of treatment of the proband with GH, which resulted in modest improvement in growth prior to puberty. WES revealed a pathogenic c.7466C>G (p.Ser2489*) mutation in the last exon of the FHS-linked SRCAP gene. A systematic literature review and analysis of available genetic variation datasets highlighted an unusual distribution of pathogenic variants in SRCAP and confirmed the lack of pathogenicity for variants outside of exons 33 and 34. Finally, we suggested a new model of FHS pathogenesis which provides possible basis for the dominant negative nature of FHS-causing mutations and explains limited effects of GH treatment in FHS. Conclusion: Our findings expand the number of reported FHS cases and provide new insights into disease genetics and the efficiency of GH therapy for FHS patients.
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Affiliation(s)
- Mariia E. Turkunova
- Federal State Budget Institution of Higher Education “North-Western State Medical University Named After I.I Mechnikov” Under the Ministry of Public Health of the Russian Federation, Saint-Petersburg, Russia
| | - Yury A. Barbitoff
- Department of Genomic Medicine, D.O.Ott Research Institute of Obstetrics, Gynaecology and Reproductology, St. Petersburg, Russia
- Bioinformatics Institute, St. Petersburg, Russia
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - Elena A. Serebryakova
- Department of Genomic Medicine, D.O.Ott Research Institute of Obstetrics, Gynaecology and Reproductology, St. Petersburg, Russia
- City Center for Medical Genetics, St. Petersburg, Russia
| | - Dmitrii E. Polev
- Department of Genomic Medicine, D.O.Ott Research Institute of Obstetrics, Gynaecology and Reproductology, St. Petersburg, Russia
| | - Olga S. Berseneva
- Federal State Budget Institution of Higher Education “North-Western State Medical University Named After I.I Mechnikov” Under the Ministry of Public Health of the Russian Federation, Saint-Petersburg, Russia
| | - Elena B. Bashnina
- Federal State Budget Institution of Higher Education “North-Western State Medical University Named After I.I Mechnikov” Under the Ministry of Public Health of the Russian Federation, Saint-Petersburg, Russia
| | - Vladislav S. Baranov
- Department of Genomic Medicine, D.O.Ott Research Institute of Obstetrics, Gynaecology and Reproductology, St. Petersburg, Russia
| | - Oleg S. Glotov
- Department of Genomic Medicine, D.O.Ott Research Institute of Obstetrics, Gynaecology and Reproductology, St. Petersburg, Russia
- Children’s Scientific and Clinical Center for Infectious Diseases of the Federal Medical and Biological Agency, St. Petersburg, Russia
| | - Andrey S. Glotov
- Department of Genomic Medicine, D.O.Ott Research Institute of Obstetrics, Gynaecology and Reproductology, St. Petersburg, Russia
- Laboratory of Biobanking and Genomic Medicine of Institute of Translation Biomedicine, St. Petersburg State University, Saint-Petersburg, Russia
- *Correspondence: Andrey S. Glotov,
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20
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Sun S, Jiang Y, Zhang Q, Pan H, Li X, Yang L, Huang M, Wei W, Wang X, Qiu M, Cao L, He H, Yu M, Liu H, Zhao B, Jiang N, Li R, Lin X. Znhit1 controls meiotic initiation in male germ cells by coordinating with Stra8 to activate meiotic gene expression. Dev Cell 2022; 57:901-913.e4. [PMID: 35413238 DOI: 10.1016/j.devcel.2022.03.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 01/25/2022] [Accepted: 03/10/2022] [Indexed: 11/25/2022]
Abstract
The switch from mitosis to meiosis ensures the successive formation of gametes. However, it remains unclear how meiotic initiation occurs within the context of chromatin. Recent studies have shown that zinc finger HIT-type containing 1 (Znhit1), a subunit of the SRCAP chromatin remodeling complex, plays essential roles in modulating the chromatin structure. Herein, we report that the germline-conditional deletion of Znhit1 in male mice specifically blocks meiotic initiation. We show that Znhit1 is required for meiotic prophase events, including synapsis, DNA double-strand break formation, and meiotic DNA replication. Mechanistically, Znhit1 controls the histone variant H2A.Z deposition, which facilitates the expression of meiotic genes, such as Meiosin, but not the expression of Stra8. Interestingly, Znhit1 deficiency disrupts the transcription bubbles of meiotic genes. Thus, our findings identify the essential role of Znhit1-dependent H2A.Z deposition in allowing activation of meiotic gene expression, thereby controlling the initiation of meiosis.
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Affiliation(s)
- Shenfei Sun
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Yamei Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Qiaoli Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai 200438, China; State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Hongjie Pan
- National Health Commission (NHC) Key Laboratory of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai 200032, China
| | - Xinyang Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Li Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Meina Huang
- National Health Commission (NHC) Key Laboratory of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai 200032, China
| | - Wei Wei
- The Joint Laboratory for Lung Development and Related Diseases of West China Second University Hospital, Sichuan University and School of Life Sciences of Fudan University, Chengdu 610041, China
| | - Xiaoye Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Mengdi Qiu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Lihuan Cao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Hua He
- The Joint Laboratory for Lung Development and Related Diseases of West China Second University Hospital, Sichuan University and School of Life Sciences of Fudan University, Chengdu 610041, China
| | - Miao Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Hanmin Liu
- The Joint Laboratory for Lung Development and Related Diseases of West China Second University Hospital, Sichuan University and School of Life Sciences of Fudan University, Chengdu 610041, China
| | - Bing Zhao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai 200438, China.
| | - Ning Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai 200438, China.
| | - Runsheng Li
- National Health Commission (NHC) Key Laboratory of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai 200032, China.
| | - Xinhua Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai 200438, China; The Joint Laboratory for Lung Development and Related Diseases of West China Second University Hospital, Sichuan University and School of Life Sciences of Fudan University, Chengdu 610041, China.
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21
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Granata P, Cocciadiferro D, Zito A, Pessina C, Bassani A, Zambonin F, Novelli A, Fasano M, Casalone R. Whole Exome Sequencing in 16p13.11 Microdeletion Patients Reveals New Variants Through Deductive and Systems Medicine Approaches. Front Genet 2022; 13:798607. [PMID: 35368691 PMCID: PMC8965081 DOI: 10.3389/fgene.2022.798607] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/23/2022] [Indexed: 12/20/2022] Open
Abstract
The 16p13.11 microdeletion, whose prevalence in the general population is about 0.04%, is known in literature as a predisposition factor to neurodevelopmental disorders, being found in about 0.13% of patients with schizophrenia, in 0.5–0.6% of patient with epilepsy, cognitive impairment, autism spectrum disorder (ASD) and aggressiveness. The goal of this study was to identify a specific gene set pattern unique for the affected patients in comparison with other familial components. Due to the incomplete penetrance of this copy number variant (CNV), we studied by whole exome sequencing (WES), with particular regard of 850 SFARI genes, three families with an affected member carrier of inherited 16p13.11 and 16p13.11p12.3 microdeletion and one family with an affected member with a de novo 16p13.11 microdeletion. By combining a deductive approach together with personalized network models, we identified gene signatures potentially capable of explaining the clinical phenotype. Candidate variants in genes of interest were identified as possibly involved in determining the neurological phenotype of the four patients, such as compound heterozygosity in CECR2, variants in MTOR and RICTOR genes, compound heterozygous single nucleotide variants in the LRRK2 gene. Moreover, genes present in the microdeletion region were partially present as central nodes, with a focus on NDE1. No additional pathogenetic or uncertain CNVs were found in all four patients. No significant variants were detected in genes included in the microdeletion in patients 1, 2 and 3, excluding the finding of unmasked recessive variants. In conclusion, WES is a fundamental tool in the genetic investigation of patients having a predisposing variant, which is not sufficient to define the clinical phenotype. Moreover, the analysis of WES data using Systems medicine tools, such as personalized network models, led to the prioritization of genes on a high throughput scale and to discover variants in genes that were not prioritized at first.
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Affiliation(s)
- Paola Granata
- Cytogenetics and Medical Genetics Unit, Department of Services, ASST dei Sette Laghi, Varese, Italy
| | - Dario Cocciadiferro
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Ospedale Pediatrico Bambino Gesù, Roma, Italy
| | - Alessandra Zito
- Cytogenetics and Medical Genetics Unit, Department of Services, ASST dei Sette Laghi, Varese, Italy
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Chiara Pessina
- Cytogenetics and Medical Genetics Unit, Department of Services, ASST dei Sette Laghi, Varese, Italy
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Alessandro Bassani
- Cytogenetics and Medical Genetics Unit, Department of Services, ASST dei Sette Laghi, Varese, Italy
| | - Fabio Zambonin
- Child Neuropsychiatry Unit, Department of Maternal and Child Health, ASST dei Sette Laghi, Varese, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Ospedale Pediatrico Bambino Gesù, Roma, Italy
| | - Mauro Fasano
- Department of Science and High Technology and Center of Bioinformatics, University of Insubria, Busto Arsizio, Italy
- *Correspondence: Mauro Fasano, ; Rosario Casalone,
| | - Rosario Casalone
- Cytogenetics and Medical Genetics Unit, Department of Services, ASST dei Sette Laghi, Varese, Italy
- *Correspondence: Mauro Fasano, ; Rosario Casalone,
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22
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NISHIOKA MASAKI. The Current Progress of Psychiatric Genomics. JUNTENDO IJI ZASSHI = JUNTENDO MEDICAL JOURNAL 2022; 68:2-11. [PMID: 38911007 PMCID: PMC11189800 DOI: 10.14789/jmj.jmj21-0038-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 11/24/2021] [Indexed: 06/25/2024]
Abstract
Psychiatric disorders such as bipolar disorder and schizophrenia are highly heritable. While the genetic contribution to psychiatric disorders is quite sure, specific genetic factors contributing to particular conditions have long been a mystery. Empowered by the initial report of the Human Genome Project, the analysis of the comprehensive set of the human genome, called "genomics," became possible. Subsequent development of large-scale genomic technologies enabled us to elucidate various disease-related genetic information, accelerating our understanding of various diseases. Genomic research on psychiatric disorders is not an exception. In this Review, I introduce significant advancements in psychiatric genomics with a special focus on our investigation of bipolar disorder. International consortiums and advocacy groups accelerate psychiatric genomics, increasing the sample size and statistical power for robust findings. The genetic architecture of schizophrenia has been elucidated in both common and rare variant studies. The genetic architecture of autism spectrum disorder (ASD) has been elucidated mainly by rare variant analysis. As to bipolar disorder, common variant analysis precedes rare variant analysis, but we are struggling to elucidate relevant rare variants. While the genomic approach has explained specific genetic factors for particular disorders, overlapping risk genes or pleiotropy has been observed more than expected. The boundary in the current nosology of psychiatric disorders is more or less challenged. To understand the genotype-phenotype relation more deeply, an attempt to understand phenotypes based on genotypes, called the "genotype first" approach, has started. I discuss this new approach for better understanding and treatment of psychiatric disorders.
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Affiliation(s)
- MASAKI NISHIOKA
- Corresponding author: Masaki Nishioka, Department of Psychiatry, Faculty of Medicine, Juntendo University, Department of Molecular Pathology of Mood Disorders, Faculty of Medicine, Juntendo University, Hongo 2-1-1, Bunkyo-ku, Tokyo, 113-8421, Japan, TEL&FAX: +81-3-5802-1070 E-mail:
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23
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Cao W, Liu X, Su W, Liang H, Tang H, Zhang W, Huang S, Dang N, Qiao A. LINC00665 sponges miR-641 to promote the progression of breast cancer by targeting the SNF2-related CREBBP activator protein (SRCAP). Bioengineered 2022; 13:4573-4586. [PMID: 35152838 PMCID: PMC8974044 DOI: 10.1080/21655979.2022.2031402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The regulatory network of competing endogenous RNAs (ceRNA) exists widely in tumors and affects the expression of cancer-related genes, thus playing an important role in the development and prognosis of human tumors. In this research, we explored the role and mechanism of LINC00665 as a ceRNA in breast cancer. We analyzed the expression and targets of LINC00665 in breast cancer using bioinformatics, and detected their effects on breast cancer cells by CCK8, transwell, colony formation and flow cytometry assays. From our results, LINC00665 knockdown suppressed the proliferation, migration and invasion and induced the apoptosis through inactivating the AKT/mTOR signaling pathway in MCF7 and MDA-MB-231 cells. LINC00665 had five potential downstream target miRNAs (miR-542-3p, miR-624-5p, miR-641, miR-425-5p, and miR-30-3p). In dual-luciferase report gene assay, the fluorescence activity of cells transfected with miR-641 mimics decreased, and the expression of miR-641 decreased significantly after knocking down LINC00665. miR-641 mimics significantly inhibited cell proliferation and invasion in MCF7 and MDA-MB-231 cells. We detected five potential direct targets of miR-641 using qPCR (SRCAP, SIKE1, NADK, KHDC4, and HSPG2). SRCAP expression decreased significantly in miR-641 overexpression cells and the binding of SRCAP’s 3ʹUTR and miR-641 was further confirmed by dual-luciferase report gene assay. SRCAP blocked the proliferation and invasion inhibition induced by miR-641 or si-LINC00665 in MCF7 and MDA-MB-231 cells. In conclusion, LINC00665 could promote the survival and metastasis of breast cancer cells through sponging miR-641 and targeting SRCAP. This research provided new potential targets for targeted therapy in human breast cancer.
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Affiliation(s)
- Wen Cao
- Health College, Yantai Nanshan University, Yantai, Shandong, China
| | - Xiaojing Liu
- Department of Clinical Laboratory Medicine, Shandong University Qilu Hospital, Jinan, China
| | - Weijia Su
- Institute of Basic Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Hao Liang
- Institute of Basic Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Huiru Tang
- Institute of Basic Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Weiliang Zhang
- Institute of Basic Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Shuhong Huang
- Institute of Basic Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Ningning Dang
- Department of Dermatology, Shandong Provincial Hospital Affiliated to Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Aiguo Qiao
- Health College, Yantai Nanshan University, Yantai, Shandong, China
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24
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Histone variant H2A.Z regulates zygotic genome activation. Nat Commun 2021; 12:7002. [PMID: 34853314 PMCID: PMC8636486 DOI: 10.1038/s41467-021-27125-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/28/2021] [Indexed: 12/13/2022] Open
Abstract
During embryogenesis, the genome shifts from transcriptionally quiescent to extensively active in a process known as Zygotic Genome Activation (ZGA). In Drosophila, the pioneer factor Zelda is known to be essential for the progression of development; still, it regulates the activation of only a small subset of genes at ZGA. However, thousands of genes do not require Zelda, suggesting that other mechanisms exist. By conducting GRO-seq, HiC and ChIP-seq in Drosophila embryos, we demonstrate that up to 65% of zygotically activated genes are enriched for the histone variant H2A.Z. H2A.Z enrichment precedes ZGA and RNA Polymerase II loading onto chromatin. In vivo knockdown of maternally contributed Domino, a histone chaperone and ATPase, reduces H2A.Z deposition at transcription start sites, causes global downregulation of housekeeping genes at ZGA, and compromises the establishment of the 3D chromatin structure. We infer that H2A.Z is essential for the de novo establishment of transcriptional programs during ZGA via chromatin reorganization. During embryogenesis, the genome becomes transcriptionally active in a process known as zygotic genome activation (ZGA); how ZGA is initiated is still an open question. Here the authors show histone variant H2A.Z deposition precedes RNA polymerase II binding on chromatin, before ZGA. H2A.Z loss causes transcriptional downregulation of ZGA genes and leads to changes in the 3D genome organization.
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25
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Messina G, Prozzillo Y, Delle Monache F, Santopietro MV, Atterrato MT, Dimitri P. The ATPase SRCAP is associated with the mitotic apparatus, uncovering novel molecular aspects of Floating-Harbor syndrome. BMC Biol 2021; 19:184. [PMID: 34474679 PMCID: PMC8414691 DOI: 10.1186/s12915-021-01109-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 07/22/2021] [Indexed: 11/10/2022] Open
Abstract
Background A variety of human genetic diseases is known to be caused by mutations in genes encoding chromatin factors and epigenetic regulators, such as DNA or histone modifying enzymes and members of ATP-dependent chromatin remodeling complexes. Floating-Harbor syndrome is a rare genetic disease affecting human development caused by dominant truncating mutations in the SRCAP gene, which encodes the ATPase SRCAP, the core catalytic subunit of the homonymous chromatin-remodeling complex. The main function of the SRCAP complex is to promote the exchange of histone H2A with the H2A.Z variant. According to the canonical role played by the SRCAP protein in epigenetic regulation, the Floating-Harbor syndrome is thought to be a consequence of chromatin perturbations. However, additional potential physiological functions of SRCAP have not been sufficiently explored. Results We combined cell biology, reverse genetics, and biochemical approaches to study the subcellular localization of the SRCAP protein and assess its involvement in cell cycle progression in HeLa cells. Surprisingly, we found that SRCAP associates with components of the mitotic apparatus (centrosomes, spindle, midbody), interacts with a plethora of cytokinesis regulators, and positively regulates their recruitment to the midbody. Remarkably, SRCAP depletion perturbs both mitosis and cytokinesis. Similarly, DOM-A, the functional SRCAP orthologue in Drosophila melanogaster, is found at centrosomes and the midbody in Drosophila cells, and its depletion similarly affects both mitosis and cytokinesis. Conclusions Our findings provide first evidence suggesting that SRCAP plays previously undetected and evolutionarily conserved roles in cell division, independent of its functions in chromatin regulation. SRCAP may participate in two different steps of cell division: by ensuring proper chromosome segregation during mitosis and midbody function during cytokinesis. Moreover, our findings emphasize a surprising scenario whereby alterations in cell division produced by SRCAP mutations may contribute to the onset of Floating-Harbor syndrome. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01109-x.
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Affiliation(s)
- Giovanni Messina
- Dipartimento di Biologia e Biotecnologie "Charles Darwin" Sapienza Università di Roma, Via dei Sardi, 70, Roma, Italy. .,Istituto Pasteur Italia Fondazione Cenci-Bolognetti, Viale Regina Elena, 291, 00161, Roma, Italy.
| | - Yuri Prozzillo
- Dipartimento di Biologia e Biotecnologie "Charles Darwin" Sapienza Università di Roma, Via dei Sardi, 70, Roma, Italy
| | - Francesca Delle Monache
- Dipartimento di Biologia e Biotecnologie "Charles Darwin" Sapienza Università di Roma, Via dei Sardi, 70, Roma, Italy
| | - Maria Virginia Santopietro
- Dipartimento di Biologia e Biotecnologie "Charles Darwin" Sapienza Università di Roma, Via dei Sardi, 70, Roma, Italy
| | - Maria Teresa Atterrato
- Dipartimento di Biologia e Biotecnologie "Charles Darwin" Sapienza Università di Roma, Via dei Sardi, 70, Roma, Italy
| | - Patrizio Dimitri
- Dipartimento di Biologia e Biotecnologie "Charles Darwin" Sapienza Università di Roma, Via dei Sardi, 70, Roma, Italy.
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26
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Janowski M, Milewska M, Zare P, Pękowska A. Chromatin Alterations in Neurological Disorders and Strategies of (Epi)Genome Rescue. Pharmaceuticals (Basel) 2021; 14:765. [PMID: 34451862 PMCID: PMC8399958 DOI: 10.3390/ph14080765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/23/2021] [Accepted: 07/24/2021] [Indexed: 12/26/2022] Open
Abstract
Neurological disorders (NDs) comprise a heterogeneous group of conditions that affect the function of the nervous system. Often incurable, NDs have profound and detrimental consequences on the affected individuals' lives. NDs have complex etiologies but commonly feature altered gene expression and dysfunctions of the essential chromatin-modifying factors. Hence, compounds that target DNA and histone modification pathways, the so-called epidrugs, constitute promising tools to treat NDs. Yet, targeting the entire epigenome might reveal insufficient to modify a chosen gene expression or even unnecessary and detrimental to the patients' health. New technologies hold a promise to expand the clinical toolkit in the fight against NDs. (Epi)genome engineering using designer nucleases, including CRISPR-Cas9 and TALENs, can potentially help restore the correct gene expression patterns by targeting a defined gene or pathway, both genetically and epigenetically, with minimal off-target activity. Here, we review the implication of epigenetic machinery in NDs. We outline syndromes caused by mutations in chromatin-modifying enzymes and discuss the functional consequences of mutations in regulatory DNA in NDs. We review the approaches that allow modifying the (epi)genome, including tools based on TALENs and CRISPR-Cas9 technologies, and we highlight how these new strategies could potentially change clinical practices in the treatment of NDs.
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Affiliation(s)
| | | | | | - Aleksandra Pękowska
- Dioscuri Centre for Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteur Street, 02-093 Warsaw, Poland; (M.J.); (M.M.); (P.Z.)
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27
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Montero-Bullón JF, González-Velasco Ó, Isidoro-García M, Lacal J. Integrated in silico MS-based phosphoproteomics and network enrichment analysis of RASopathy proteins. Orphanet J Rare Dis 2021; 16:303. [PMID: 34229750 PMCID: PMC8258961 DOI: 10.1186/s13023-021-01934-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 06/27/2021] [Indexed: 11/30/2022] Open
Abstract
Background RASopathies are a group of syndromes showing clinical overlap caused by mutations in genes affecting the RAS-MAPK pathway. Consequent disruption on cellular signaling leads and is driven by phosphoproteome remodeling. However, we still lack a comprehensive picture of the different key players and altered downstream effectors. Methods An in silico interactome of RASopathy proteins was generated using pathway enrichment analysis/STRING tool, including identification of main hub proteins. We also integrated phosphoproteomic and immunoblotting studies using previous published information on RASopathy proteins and their neighbors in the context of RASopathy syndromes. Data from Phosphosite database (www.phosphosite.org) was collected in order to obtain the potential phosphosites subjected to regulation in the 27 causative RASopathy proteins. We compiled a dataset of dysregulated phosphosites in RASopathies, searched for commonalities between syndromes in harmonized data, and analyzed the role of phosphorylation in the syndromes by the identification of key players between the causative RASopathy proteins and the associated interactome. Results In this study, we provide a curated data set of 27 causative RASopathy genes, identify up to 511 protein–protein associations using pathway enrichment analysis/STRING tool, and identify 12 nodes as main hub proteins. We found that a large group of proteins contain tyrosine residues and their biological processes include but are not limited to the nervous system. Harmonizing published RASopathy phosphoproteomic and immunoblotting studies we identified a total of 147 phosphosites with increased phosphorylation, whereas 47 have reduced phosphorylation. The PKB signaling pathway is the most represented among the dysregulated phosphoproteins within the RASopathy proteins and their neighbors, followed by phosphoproteins implicated in the regulation of cell proliferation and the MAPK pathway. Conclusions This work illustrates the complex network underlying the RASopathies and the potential of phosphoproteomics for dissecting the molecular mechanisms in these syndromes. A combined study of associated genes, their interactome and phosphorylation events in RASopathies, elucidates key players and mechanisms to direct future research, diagnosis and therapeutic windows. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-021-01934-x.
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Affiliation(s)
- Javier-Fernando Montero-Bullón
- Metabolic Engineering Group, Department of Microbiology and Genetics, Faculty of Biology, University of Salamanca, 37007, Salamanca, Spain
| | - Óscar González-Velasco
- Bioinformatics and Functional Genomics Group, IBMCC Cancer Research Center, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - María Isidoro-García
- Institute for Biomedical Research of Salamanca (IBSAL), 37007, Salamanca, Spain.,Network for Cooperative Research in Health-RETICS ARADyAL, 37007, Salamanca, Spain.,Department of Clinical Biochemistry, University Hospital of Salamanca, 37007, Salamanca, Spain.,Department of Medicine, University of Salamanca, 37007, Salamanca, Spain
| | - Jesus Lacal
- Institute for Biomedical Research of Salamanca (IBSAL), 37007, Salamanca, Spain. .,Molecular Genetics of Human Diseases Group, Department of Microbiology and Genetics, Faculty of Biology, University of Salamanca, 37007, Salamanca, Spain.
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28
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Nogueira E, Garma C, Lobo C, Del Olmo B, Arroyo JM, Gómez I. Severe developmental expressive language disorder due to a frameshift mutation in exon 18 of SRCAP gene, far away from the mutational hotspot in exons 33 and 34 associated to the Floating-Harbor syndrome. Neurol Sci 2021; 42:4349-4352. [PMID: 34213696 DOI: 10.1007/s10072-021-05423-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 06/17/2021] [Indexed: 01/13/2023]
Affiliation(s)
- Enrique Nogueira
- Eurofins-Megalab Molecular Diagnostics Laboratory, Madrid, Spain. .,Genetics Service of the Hospital La Zarzuela, Madrid, Spain. .,Genetics Service of the Hospital San Rafael, Madrid, Spain.
| | - Carmen Garma
- Eurofins-Megalab Molecular Diagnostics Laboratory, Madrid, Spain.,Genetics Service of the Hospital La Zarzuela, Madrid, Spain.,Genetics Service of the Hospital San Rafael, Madrid, Spain
| | - Concepción Lobo
- Eurofins-Megalab Molecular Diagnostics Laboratory, Madrid, Spain
| | - Beatriz Del Olmo
- Eurofins-Megalab Molecular Diagnostics Laboratory, Madrid, Spain
| | | | - Iván Gómez
- Eurofins-Megalab Molecular Diagnostics Laboratory, Madrid, Spain.,Genetics Service of the Hospital La Zarzuela, Madrid, Spain
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29
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Systematic analysis of exonic germline and postzygotic de novo mutations in bipolar disorder. Nat Commun 2021; 12:3750. [PMID: 34145229 PMCID: PMC8213845 DOI: 10.1038/s41467-021-23453-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 04/29/2021] [Indexed: 12/30/2022] Open
Abstract
Bipolar disorder is a severe mental illness characterized by recurrent manic and depressive episodes. To better understand its genetic architecture, we analyze ultra-rare de novo mutations in 354 trios with bipolar disorder. For germline de novo mutations, we find significant enrichment of loss-of-function mutations in constrained genes (corrected-P = 0.0410) and deleterious mutations in presynaptic active zone genes (FDR = 0.0415). An analysis integrating single-cell RNA-sequencing data identifies a subset of excitatory neurons preferentially expressing the genes hit by deleterious mutations, which are also characterized by high expression of developmental disorder genes. In the analysis of postzygotic mutations, we observe significant enrichment of deleterious ones in developmental disorder genes (P = 0.00135), including the SRCAP gene mutated in two unrelated probands. These data collectively indicate the contributions of both germline and postzygotic mutations to the risk of bipolar disorder, supporting the hypothesis that postzygotic mutations of developmental disorder genes may contribute to bipolar disorder. The significance of rare and de novo variants in bipolar disorder is not well understood. Here, the authors have analyzed whole exome/genome data from trios to identify deleterious de novo variants associated with bipolar disorder.
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30
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Truncating SRCAP variants outside the Floating-Harbor syndrome locus cause a distinct neurodevelopmental disorder with a specific DNA methylation signature. Am J Hum Genet 2021; 108:1053-1068. [PMID: 33909990 PMCID: PMC8206150 DOI: 10.1016/j.ajhg.2021.04.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 03/31/2021] [Indexed: 02/08/2023] Open
Abstract
Truncating variants in exons 33 and 34 of the SNF2-related CREBBP activator protein (SRCAP) gene cause the neurodevelopmental disorder (NDD) Floating-Harbor syndrome (FLHS), characterized by short stature, speech delay, and facial dysmorphism. Here, we present a cohort of 33 individuals with clinical features distinct from FLHS and truncating (mostly de novo) SRCAP variants either proximal (n = 28) or distal (n = 5) to the FLHS locus. Detailed clinical characterization of the proximal SRCAP individuals identified shared characteristics: developmental delay with or without intellectual disability, behavioral and psychiatric problems, non-specific facial features, musculoskeletal issues, and hypotonia. Because FLHS is known to be associated with a unique set of DNA methylation (DNAm) changes in blood, a DNAm signature, we investigated whether there was a distinct signature associated with our affected individuals. A machine-learning model, based on the FLHS DNAm signature, negatively classified all our tested subjects. Comparing proximal variants with typically developing controls, we identified a DNAm signature distinct from the FLHS signature. Based on the DNAm and clinical data, we refer to the condition as “non-FLHS SRCAP-related NDD.” All five distal variants classified negatively using the FLHS DNAm model while two classified positively using the proximal model. This suggests divergent pathogenicity of these variants, though clinically the distal group presented with NDD, similar to the proximal SRCAP group. In summary, for SRCAP, there is a clear relationship between variant location, DNAm profile, and clinical phenotype. These results highlight the power of combined epigenetic, molecular, and clinical studies to identify and characterize genotype-epigenotype-phenotype correlations.
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31
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Dilshat R, Vu HN, Steingrímsson E. Epigenetic regulation during melanocyte development and homeostasis. Exp Dermatol 2021; 30:1033-1050. [PMID: 34003523 DOI: 10.1111/exd.14391] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 04/09/2021] [Accepted: 05/09/2021] [Indexed: 12/26/2022]
Abstract
Melanocytes originate in the neural crest as precursor cells which then migrate and proliferate to reach their destination where they differentiate into pigment-producing cells. Melanocytes not only determine the colour of hair, skin and eyes but also protect against the harmful effects of UV irradiation. The establishment of the melanocyte lineage is regulated by a defined set of transcription factors and signalling pathways that direct the specific gene expression programmes underpinning melanoblast specification, survival, migration, proliferation and differentiation. In addition, epigenetic modifiers and replacement histones play key roles in regulating gene expression and its timing during the different steps of this process. Here, we discuss the evidence for the role of epigenetic regulators in melanocyte development and function and how they interact with transcription factors and signalling pathways to establish and maintain this important cell lineage.
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Affiliation(s)
- Ramile Dilshat
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, BioMedical Center, University of Iceland, Reykjavik, Iceland
| | - Hong Nhung Vu
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, BioMedical Center, University of Iceland, Reykjavik, Iceland
| | - Eiríkur Steingrímsson
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, BioMedical Center, University of Iceland, Reykjavik, Iceland
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32
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Beaumont RN, Mayne IK, Freathy RM, Wright CF. Common genetic variants with fetal effects on birth weight are enriched for proximity to genes implicated in rare developmental disorders. Hum Mol Genet 2021; 30:1057-1066. [PMID: 33682876 PMCID: PMC8355446 DOI: 10.1093/hmg/ddab060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/11/2021] [Accepted: 02/15/2021] [Indexed: 11/14/2022] Open
Abstract
Birth weight is an important factor in newborn survival; both low and high birth weights are associated with adverse later-life health outcomes. Genome-wide association studies (GWAS) have identified 190 loci associated with maternal or fetal effects on birth weight. Knowledge of the underlying causal genes is crucial to understand how these loci influence birth weight and the links between infant and adult morbidity. Numerous monogenic developmental syndromes are associated with birth weights at the extreme ends of the distribution. Genes implicated in those syndromes may provide valuable information to prioritize candidate genes at the GWAS loci. We examined the proximity of genes implicated in developmental disorders (DDs) to birth weight GWAS loci using simulations to test whether they fall disproportionately close to the GWAS loci. We found birth weight GWAS single nucleotide polymorphisms (SNPs) fall closer to such genes than expected both when the DD gene is the nearest gene to the birth weight SNP and also when examining all genes within 258 kb of the SNP. This enrichment was driven by genes causing monogenic DDs with dominant modes of inheritance. We found examples of SNPs in the intron of one gene marking plausible effects via different nearby genes, highlighting the closest gene to the SNP not necessarily being the functionally relevant gene. This is the first application of this approach to birth weight, which has helped identify GWAS loci likely to have direct fetal effects on birth weight, which could not previously be classified as fetal or maternal owing to insufficient statistical power.
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Affiliation(s)
| | | | - Rachel M Freathy
- To whom correspondence should be addressed at: Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, RILD Building Barrack Road, Exeter EX2 5DW, UK. Tel: +44 (0) 1392 408238;
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Agrawal S, Gupta S, Neupane S, Das D. Floating harbour syndrome with medial entropion: a rare association and brief review. BMJ Case Rep 2021; 14:14/5/e242125. [PMID: 33962930 PMCID: PMC8108651 DOI: 10.1136/bcr-2021-242125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Affiliation(s)
- Sahil Agrawal
- Ophthalmology, Dr. Rajendra Prasad Centre for Ophthalmic Sciences, AIIMS, Delhi, New Delhi, India
| | - Saloni Gupta
- Ophthalmology, Northern Railway Central Hospital New Delhi, New Delhi, Delhi, India
| | - Swechya Neupane
- Ophthalmology, Dr. Rajendra Prasad Centre for Ophthalmic Sciences, AIIMS, Delhi, New Delhi, India
| | - Deepsekhar Das
- Ophthalmology, Dr. Rajendra Prasad Centre for Ophthalmic Sciences, AIIMS, Delhi, New Delhi, India
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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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Dyment DA, O'Donnell-Luria A, Agrawal PB, Coban Akdemir Z, Aleck KA, Antaki D, Al Sharhan H, Au PYB, Aydin H, Beggs AH, Bilguvar K, Boerwinkle E, Brand H, Brownstein CA, Buyske S, Chodirker B, Choi J, Chudley AE, Clericuzio CL, Cox GF, Curry C, de Boer E, de Vries BBA, Dunn K, Dutmer CM, England EM, Fahrner JA, Geckinli BB, Genetti CA, Gezdirici A, Gibson WT, Gleeson JG, Greenberg CR, Hall A, Hamosh A, Hartley T, Jhangiani SN, Karaca E, Kernohan K, Lauzon JL, Lewis MES, Lowry RB, López-Giráldez F, Matise TC, McEvoy-Venneri J, McInnes B, Mhanni A, Garcia Minaur S, Moilanen J, Nguyen A, Nowaczyk MJM, Posey JE, Õunap K, Pehlivan D, Pajusalu S, Penney LS, Poterba T, Prontera P, Doriqui MJR, Sawyer SL, Sobreira N, Stanley V, Torun D, Wargowski D, Witmer PD, Wong I, Xing J, Zaki MS, Zhang Y, Boycott KM, Bamshad MJ, Nickerson DA, Blue EE, Innes AM. Alternative genomic diagnoses for individuals with a clinical diagnosis of Dubowitz syndrome. Am J Med Genet A 2021; 185:119-133. [PMID: 33098347 PMCID: PMC8197629 DOI: 10.1002/ajmg.a.61926] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 08/09/2020] [Accepted: 09/19/2020] [Indexed: 01/19/2023]
Abstract
Dubowitz syndrome (DubS) is considered a recognizable syndrome characterized by a distinctive facial appearance and deficits in growth and development. There have been over 200 individuals reported with Dubowitz or a "Dubowitz-like" condition, although no single gene has been implicated as responsible for its cause. We have performed exome (ES) or genome sequencing (GS) for 31 individuals clinically diagnosed with DubS. After genome-wide sequencing, rare variant filtering and computational and Mendelian genomic analyses, a presumptive molecular diagnosis was made in 13/27 (48%) families. The molecular diagnoses included biallelic variants in SKIV2L, SLC35C1, BRCA1, NSUN2; de novo variants in ARID1B, ARID1A, CREBBP, POGZ, TAF1, HDAC8, and copy-number variation at1p36.11(ARID1A), 8q22.2(VPS13B), Xp22, and Xq13(HDAC8). Variants of unknown significance in known disease genes, and also in genes of uncertain significance, were observed in 7/27 (26%) additional families. Only one gene, HDAC8, could explain the phenotype in more than one family (N = 2). All but two of the genomic diagnoses were for genes discovered, or for conditions recognized, since the introduction of next-generation sequencing. Overall, the DubS-like clinical phenotype is associated with extensive locus heterogeneity and the molecular diagnoses made are for emerging clinical conditions sharing characteristic features that overlap the DubS phenotype.
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Affiliation(s)
- David A Dyment
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Anne O'Donnell-Luria
- Broad Institute of MIT and Harvard, Broad Center for Mendelian Genomics, Cambridge, Massachusetts, USA
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Pankaj B Agrawal
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Kyrieckos A Aleck
- Department of Genetics and Metabolism, Phoenix Children's Medical Group, Phoenix, Arizona, USA
| | - Danny Antaki
- Laboratory for Pediatric Brain Disease, Howard Hughes Medical Institute, University of California, San Diego, California, USA
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | - Hind Al Sharhan
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Pediatrics, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | - Ping-Yee B Au
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Hatip Aydin
- Centre of Genetics Diagnosis, Zeynep Kamil Maternity and Children's Training and Research Hospital, Istanbul, Turkey
| | - Alan H Beggs
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Kaya Bilguvar
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, USA
- Yale Center for Genome Analysis, Yale School of Medicine, New Haven, Connecticut, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Waco, Texas, USA
| | - Harrison Brand
- Broad Institute of MIT and Harvard, Broad Center for Mendelian Genomics, Cambridge, Massachusetts, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Catherine A Brownstein
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Steve Buyske
- Department of Statistics and Biostatistics, Rutgers University, Piscataway, New Jersey, USA
| | - Bernard Chodirker
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Jungmin Choi
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, USA
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, South Korea
| | - Albert E Chudley
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Carol L Clericuzio
- Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
| | - Gerald F Cox
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Cynthia Curry
- University of California, San Francisco, California, USA
- Genetic Medicine, University Pediatric Specialists, Fresno, California, USA
| | - Elke de Boer
- Department of Human Genetics, Raboud University Medical Centre, Nijmegen, Netherlands
| | - Bert B A de Vries
- Department of Human Genetics, Raboud University Medical Centre, Nijmegen, Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Raboud University Medical Centre, Nijmegen, Netherlands
| | - Kathryn Dunn
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Cullen M Dutmer
- Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Eleina M England
- Broad Institute of MIT and Harvard, Broad Center for Mendelian Genomics, Cambridge, Massachusetts, USA
| | - Jill A Fahrner
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Bilgen B Geckinli
- Department of Medical Genetics, School of Medicine, Marmara University, Istanbul, Turkey
| | - Casie A Genetti
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Alper Gezdirici
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul, Turkey
| | - William T Gibson
- Department of Medical Genetics and British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Joseph G Gleeson
- Laboratory for Pediatric Brain Disease, Howard Hughes Medical Institute, University of California, San Diego, California, USA
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | - Cheryl R Greenberg
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - April Hall
- Waisman Center Clinical Genetics, University of Wisconsin, Madison, Wisconsin, USA
| | - Ada Hamosh
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Shalini N Jhangiani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Ender Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Kristin Kernohan
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Julie L Lauzon
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - M E Suzanne Lewis
- Department of Medical Genetics and British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - R Brian Lowry
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Francesc López-Giráldez
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, USA
- Yale Center for Genome Analysis, Yale School of Medicine, New Haven, Connecticut, USA
| | - Tara C Matise
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, New Jersey, USA
| | - Jennifer McEvoy-Venneri
- Laboratory for Pediatric Brain Disease, Howard Hughes Medical Institute, University of California, San Diego, California, USA
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | - Brenda McInnes
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Aziz Mhanni
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sixto Garcia Minaur
- Sección de Genética Clínica, INGEMM (Instituto de Genética Médica y Molecular), Madrid, Spain
| | - Jukka Moilanen
- Department of Clinical Genetics, Oulu University Hospital, Medical Research Center Oulu and PEDEGO Research Unit, University of Oulu, Oulu, Finland
| | - An Nguyen
- Laboratory for Pediatric Brain Disease, Howard Hughes Medical Institute, University of California, San Diego, California, USA
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | - Malgorzata J M Nowaczyk
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Katrin Õunap
- United Laboratories, Department of Clinical Genetics, Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, Department of Clinical Genetics, Tartu University Hospital, Tartu, Estonia
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Sander Pajusalu
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, USA
- United Laboratories, Department of Clinical Genetics, Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, Department of Clinical Genetics, Tartu University Hospital, Tartu, Estonia
| | - Lynette S Penney
- Department of Pediatrics, IWK Health Centre, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Timothy Poterba
- Broad Institute of MIT and Harvard, Broad Center for Mendelian Genomics, Cambridge, Massachusetts, USA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Paolo Prontera
- Medical Genetics Unit, Hospital Santa Maria della Misericordia and University of Perugia, Perugia, Italy
| | | | - Sarah L Sawyer
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Nara Sobreira
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Valentina Stanley
- Laboratory for Pediatric Brain Disease, Howard Hughes Medical Institute, University of California, San Diego, California, USA
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | - Deniz Torun
- Department of Medical Genetics, Gulhane Military Medical Academy, Ankara, Turkey
| | - David Wargowski
- Division of Genetics, Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - P Dane Witmer
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Isaac Wong
- Broad Institute of MIT and Harvard, Broad Center for Mendelian Genomics, Cambridge, Massachusetts, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Jinchuan Xing
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, New Jersey, USA
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Yeting Zhang
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, New Jersey, USA
| | - Kym M Boycott
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Michael J Bamshad
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Brotman-Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Deborah A Nickerson
- Brotman-Baty Institute for Precision Medicine, Seattle, Washington, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Elizabeth E Blue
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - A Micheil Innes
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
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Haghshenas S, Bhai P, Aref-Eshghi E, Sadikovic B. Diagnostic Utility of Genome-Wide DNA Methylation Analysis in Mendelian Neurodevelopmental Disorders. Int J Mol Sci 2020; 21:ijms21239303. [PMID: 33291301 PMCID: PMC7730976 DOI: 10.3390/ijms21239303] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 12/14/2022] Open
Abstract
Mendelian neurodevelopmental disorders customarily present with complex and overlapping symptoms, complicating the clinical diagnosis. Individuals with a growing number of the so-called rare disorders exhibit unique, disorder-specific DNA methylation patterns, consequent to the underlying gene defects. Besides providing insights to the pathophysiology and molecular biology of these disorders, we can use these epigenetic patterns as functional biomarkers for the screening and diagnosis of these conditions. This review summarizes our current understanding of DNA methylation episignatures in rare disorders and describes the underlying technology and analytical approaches. We discuss the computational parameters, including statistical and machine learning methods, used for the screening and classification of genetic variants of uncertain clinical significance. Describing the rationale and principles applied to the specific computational models that are used to develop and adapt the DNA methylation episignatures for the diagnosis of rare disorders, we highlight the opportunities and challenges in this emerging branch of diagnostic medicine.
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Affiliation(s)
- Sadegheh Haghshenas
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada;
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A 5W9, Canada;
| | - Pratibha Bhai
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A 5W9, Canada;
| | - Erfan Aref-Eshghi
- Division of Genomic Diagnostics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA;
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada;
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A 5W9, Canada;
- Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
- Correspondence:
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Ercoskun P, Yuce-Kahraman C. Novel Findings in Floating-Harbor Syndrome and a Mini-Review of the Literature. Mol Syndromol 2020; 12:52-56. [PMID: 33776628 DOI: 10.1159/000512050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 10/03/2020] [Indexed: 11/19/2022] Open
Abstract
Floating-Harbor syndrome (FHS) is a rare autosomal dominant genetic disorder characterized by proportionate short stature with delayed bone maturation, lack of expressive language, and distinctive facial features including a large nose, long eyelashes, deeply set eyes, and triangular face. Mutations in the SRCAP gene cause truncated SNF2-related CREBBP activator protein (SRCAP) and lead to FHS. SRCAP is one of several proteins that act as coactivator for the CREB-binding protein which is associated with Rubinstein-Taybi syndrome (RSTS). This condition likely explains the phenotypic overlap between FHS and RSTS. Herein, we report on a patient with FHS who also had dystrophic toenails, preauricular skin tag, and nasolacrimal duct obstruction which is also defined in patients with RSTS. In summary, the fact that especially nasolacrimal duct obstruction has also been observed in RSTS reinforces the idea that this finding is one of the features of FHS. Assessment of the lacrimal system and examination of skin and nails should be suggested in patients with FHS.
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Affiliation(s)
- Pelin Ercoskun
- Department of Medical Genetics, Faculty of Medicine, Ataturk University, Erzurum, Turkey
| | - Cigdem Yuce-Kahraman
- Department of Medical Genetics, Faculty of Medicine, Ataturk University, Erzurum, Turkey
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Franz M, Hagenau L, Koch R, Neubauer S, Nowack B, Tzvetkova A, Jensen LR, Kuss AW. Generation of an iPSC line (UMGWi001-B) from a patient with Floating-Harbor Syndrome (FLHS) carrying a heterozygous SRCAP mutation (p.Arg2444). Stem Cell Res 2020; 49:102028. [PMID: 33099107 DOI: 10.1016/j.scr.2020.102028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/28/2020] [Accepted: 10/04/2020] [Indexed: 10/23/2022] Open
Abstract
Floating-Harbor syndrome (FLHS) is a rare genetic disease caused by mutations in the SRCAP gene. Here, we generated an induced pluripotent stem cell line from gingival fibroblasts of a male patient with a heterozygous mutation in exon 34 of the SRCAP gene (c.7330C > T, p.Arg2444*). The iPSC colonies have an atypical morphology with diffuse borders and disintegrate quickly upon touch. Still, the cell line expresses pluripotency markers and differentiates into three germ layers. The cell line can be used as patient-specific disease model and help elucidate the molecular mechanisms involving SRCAP in the context of FLHS.
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Affiliation(s)
- M Franz
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - L Hagenau
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - R Koch
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | | | | | - A Tzvetkova
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany; Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - L R Jensen
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - A W Kuss
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.
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Mohammadian Khonsari N, Mohammad Poor Nami S, Hakak-Zargar B, Voth T. Mutations of uncertain significance in heterozygous variants as a possible cause of severe short stature: a case report. Mol Cell Pediatr 2020; 7:11. [PMID: 32935225 PMCID: PMC7492327 DOI: 10.1186/s40348-020-00104-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 08/25/2020] [Indexed: 11/13/2022] Open
Abstract
Background Linear bone growth is achieved by the division of chondrocytes at the growth plate and is regulated by endocrine and paracrine factors such as growth hormone. Mutations that negatively affect chondrogenesis can be a contributor to short stature. One such mutation can occur in the ACAN gene, causing short stature and advanced bone age. Similarly, mutations in growth hormone receptors (GHR) can lead to Laron syndrome (LS), one of the several disorders that are collectively called growth hormone insensitivity syndrome (GHI). Another example is Floating-Harbor syndrome (FHS), a rare autosomal dominant due to mutations in the SRCAP gene that can also result in short stature. Case presentation We report the case of a 6-year-old female with concomitant mutations in the three genes mentioned above. The mutations reported here were found on genetic studies and are usually benign, causing a variant of undetermined significance. However, our patient’s phenotype could only be explained by the compounded effects of pathogenic mutations of these genes. Some of the same mutations were also found in the patient’s father and her paternal grandfather. Both also presented with short stature, though not to the same degree as our patient. While these mutations are often reported to be insignificant, they gave rise to severe short stature and a specific phenotype in the patient when presented together. We think that even though the GHI spectrum is inherited through an autosomal recessive pattern, the sum of these heterozygous mutations resulted in severe short stature despite the limited GHI seen in our patient, the father, and the grandfather, through a rare ACAN and SRCAP mutation that, to our knowledge, has not been previously reported as a pathogenic mutation in the literature. Conclusion We investigated the possible synergistic effects of these variations on exacerbation or masking of the signs and symptoms of GHI with the hope of providing a better understanding of these genes and their function through our rare case.
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Affiliation(s)
| | | | - Benyamin Hakak-Zargar
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Tessa Voth
- Department of Biomedical Physiology and Kinesiology, Faculty of Science, Simon Fraser University, Burnaby, British Columbia, Canada
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Timpano S, Picketts DJ. Neurodevelopmental Disorders Caused by Defective Chromatin Remodeling: Phenotypic Complexity Is Highlighted by a Review of ATRX Function. Front Genet 2020; 11:885. [PMID: 32849845 PMCID: PMC7432156 DOI: 10.3389/fgene.2020.00885] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 07/20/2020] [Indexed: 12/15/2022] Open
Abstract
The ability to determine the genetic etiology of intellectual disability (ID) and neurodevelopmental disorders (NDD) has improved immensely over the last decade. One prevailing metric from these studies is the large percentage of genes encoding epigenetic regulators, including many members of the ATP-dependent chromatin remodeling enzyme family. Chromatin remodeling proteins can be subdivided into five classes that include SWI/SNF, ISWI, CHD, INO80, and ATRX. These proteins utilize the energy from ATP hydrolysis to alter nucleosome positioning and are implicated in many cellular processes. As such, defining their precise roles and contributions to brain development and disease pathogenesis has proven to be complex. In this review, we illustrate that complexity by reviewing the roles of ATRX on genome stability, replication, and transcriptional regulation and how these mechanisms provide key insight into the phenotype of ATR-X patients.
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Affiliation(s)
- Sara Timpano
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - David J Picketts
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada.,Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, ON, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.,Department of Medicine, University of Ottawa, Ottawa, ON, Canada.,University of Ottawa Brain and Mind Research Institute, Ottawa, ON, Canada
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41
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Greenberg RS, Long HK, Swigut T, Wysocka J. Single Amino Acid Change Underlies Distinct Roles of H2A.Z Subtypes in Human Syndrome. Cell 2020; 178:1421-1436.e24. [PMID: 31491386 DOI: 10.1016/j.cell.2019.08.002] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 03/27/2019] [Accepted: 08/01/2019] [Indexed: 12/31/2022]
Abstract
The developmental disorder Floating-Harbor syndrome (FHS) is caused by heterozygous truncating mutations in SRCAP, a gene encoding a chromatin remodeler mediating incorporation of histone variant H2A.Z. Here, we demonstrate that FHS-associated mutations result in loss of SRCAP nuclear localization, alter neural crest gene programs in human in vitro models and Xenopus embryos, and cause craniofacial defects. These defects are mediated by one of two H2A.Z subtypes, H2A.Z.2, whose knockdown mimics and whose overexpression rescues the FHS phenotype. Selective rescue by H2A.Z.2 is conferred by one of the three amino acid differences between the H2A.Z subtypes, S38/T38. We further show that H2A.Z.1 and H2A.Z.2 genomic occupancy patterns are qualitatively similar, but quantitatively distinct, and H2A.Z.2 incorporation at AT-rich enhancers and expression of their associated genes are both sensitized to SRCAP truncations. Altogether, our results illuminate the mechanism underlying a human syndrome and uncover selective functions of H2A.Z subtypes during development.
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Affiliation(s)
- Rachel S Greenberg
- Department of Chemical and Systems Biology and Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hannah K Long
- Department of Chemical and Systems Biology and Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tomek Swigut
- Department of Chemical and Systems Biology and Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joanna Wysocka
- Department of Chemical and Systems Biology and Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
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42
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Son HW, Lee JE, Oh SH, Keum C, Chung WY. Effects of long-term growth hormone therapy in a girl with Floating-Harbor syndrome. Ann Pediatr Endocrinol Metab 2020; 25:126-131. [PMID: 32615693 PMCID: PMC7336260 DOI: 10.6065/apem.1938144.072] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 05/31/2019] [Indexed: 12/12/2022] Open
Abstract
Floating-Harbor syndrome is a rare autosomal dominant disorder that presents with short stature, facial dysmorphism, significantly delayed bone age, skeletal abnormalities, speech and language problems, and intellectual disabilities. Although short stature is one of the main clinical manifestations, use of growth hormone therapy in Floating-Harbor syndrome patients has been limited. Only a few reports have investigated the response to growth hormone therapy with regard to final adult height. We report the case of a 7-year-old girl with FloatingHarbor syndrome and a heterozygous mutation, c.7330C > T (p.Arg2444*), in the SRCAP gene. The patient exhibited dysmorphic facial features, severe intellectual disabilities, obsessive-compulsive and aggressive behaviors, and short stature without growth hormone deficiency. Her height standard deviation score improved after 55 months of growth hormone therapy.
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Affiliation(s)
- Hyun Woo Son
- Department of Pediatrics, Inje University Busan Paik Hospital, Busan, Korea
| | - Jeong Eun Lee
- Department of Pediatrics, Inje University Busan Paik Hospital, Busan, Korea
| | - Seung Hwan Oh
- Department of Diagnostic Laboratory Medicine, Inje University Busan Paik Hospital, Busan, Korea
| | - Changwon Keum
- Rare Genetic Disease Research Center, 3 Billion, Seoul, Korea
| | - Woo Yeong Chung
- Department of Pediatrics, Inje University Busan Paik Hospital, Busan, Korea,Address for correspondence: Woo Yeong Chung, MD, PhD Department of Pediatrics, Inje University Busan Paik Hospital, Inje University College of Medicine, 75 BokJi-ro, Busanjin-gu, Busan 47392, Korea Tel: +82-51-890-6280 Fax: +82-51-895-7785 E-mail:
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43
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Ye B, Yang L, Qian G, Liu B, Zhu X, Zhu P, Ma J, Xie W, Li H, Lu T, Wang Y, Wang S, Du Y, Wang Z, Jiang J, Li J, Fan D, Meng S, Wu J, Tian Y, Fan Z. The chromatin remodeler SRCAP promotes self-renewal of intestinal stem cells. EMBO J 2020; 39:e103786. [PMID: 32449550 DOI: 10.15252/embj.2019103786] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 04/15/2020] [Accepted: 04/20/2020] [Indexed: 12/19/2022] Open
Abstract
Lgr5+ intestinal stem cells (ISCs) exhibit self-renewal and differentiation features under homeostatic conditions, but the mechanisms controlling Lgr5 + ISC self-renewal remain elusive. Here, we show that the chromatin remodeler SRCAP is highly expressed in mouse intestinal epithelium and ISCs. Srcap deletion impairs both self-renewal of ISCs and intestinal epithelial regeneration. Mechanistically, SRCAP recruits the transcriptional regulator REST to the Prdm16 promoter and induces expression of this transcription factor. By activating PPARδ expression, Prdm16 in turn initiates PPARδ signaling, which sustains ISC stemness. Rest or Prdm16 deficiency abrogates the self-renewal capacity of ISCs as well as intestinal epithelial regeneration. Collectively, these data show that the SRCAP-REST-Prdm16-PPARδ axis is required for self-renewal maintenance of Lgr5 + ISCs.
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Affiliation(s)
- Buqing Ye
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Liuliu Yang
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Guomin Qian
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Benyu Liu
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoxiao Zhu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Pingping Zhu
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jing Ma
- MOE Key Laboratory of Bioinformatics, Center for Stem Cell Biology and Regenerative Medicine, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Wei Xie
- MOE Key Laboratory of Bioinformatics, Center for Stem Cell Biology and Regenerative Medicine, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Huimu Li
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Tianku Lu
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yanying Wang
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Shuo Wang
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Ying Du
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Zhimin Wang
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jing Jiang
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Genome Tagging Project (GTP) Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Jinsong Li
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Genome Tagging Project (GTP) Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Dongdong Fan
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Shu Meng
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jiayi Wu
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yong Tian
- University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Zusen Fan
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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Homma TK, Freire BL, Honjo R, Dauber A, Funari MFA, Lerario AM, Albuquerque EVA, Vasques GA, Bertola DR, Kim CA, Malaquias AC, Jorge AAL. Growth and Clinical Characteristics of Children with Floating-Harbor Syndrome: Analysis of Current Original Data and a Review of the Literature. Horm Res Paediatr 2020; 92:115-123. [PMID: 31715605 DOI: 10.1159/000503782] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 09/28/2019] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Floating-Harbor syndrome (FHS) is a rare condition characterized by dysmorphic facial features, short stature, and expressive language delay. OBJECTIVE The aim of this study was to describe a cohort of patients with FHS and review the literature about the response to recombinant human growth hormone (rhGH) therapy. METHODS Anthropometric and laboratory data from 7 patients with FHS were described. The molecular diagnosis was established by multigene analysis. Moreover, we reviewed the literature concerning patients with FHS treated with rhGH. RESULTS All 7 patients were born small for gestational age. At first evaluation, 6 patients had a height standard deviation score (SDS) ≤-2 and 1 had short stature in relation to their target height. Bone age was usually delayed, which rapidly advanced during puberty. Nonspecific skeletal abnormalities were frequently noticed, and normal to elevated plasma IGF-I levels were observed in all except 1 patient with growth hormone deficiency. Information about 20 patients with FHS treated with rhGH was analyzed (4 from our cohort and 16 from the literature). The median height changes during the treatment period (approx. 2.9 years) were 1.1 SDS (range from -0.4 to 3.1). Nontreated patients had an adult height SDS of -4.1 ± 1.2 (n = 10) versus -2.6 ± 0.8 SDS (n = 7, p 0.012) for treated patients. CONCLUSION We observed a laboratory profile compatible with IGF-1 insensitivity in some patients with FHS. Nevertheless, our study suggests that children with FHS may be considered as candidates for rhGH therapy. Further studies are necessary to establish the real benefit and safety of rhGH therapy in these patients.
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Affiliation(s)
- Thais K Homma
- Unidade de Endocrinologia Genetica, Laboratorio de Endocrinologia Celular e Molecular LIM25, Disciplina de Endocrinologia da Faculdade de Medicina da Universidade de Sao Paulo (FMUSP), Sao Paulo, Brazil.,Unidade de Endocrinologia do Desenvolvimento, Laboratorio de Hormonios e Genetica Molecular LIM42, Hospital das Clínicas da Faculdade de Medicina da Universidade de Sao Paulo (FMUSP), Sao Paulo, Brazil
| | - Bruna L Freire
- Unidade de Endocrinologia Genetica, Laboratorio de Endocrinologia Celular e Molecular LIM25, Disciplina de Endocrinologia da Faculdade de Medicina da Universidade de Sao Paulo (FMUSP), Sao Paulo, Brazil.,Unidade de Endocrinologia do Desenvolvimento, Laboratorio de Hormonios e Genetica Molecular LIM42, Hospital das Clínicas da Faculdade de Medicina da Universidade de Sao Paulo (FMUSP), Sao Paulo, Brazil
| | - Rachel Honjo
- Unidade de Genetica do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Andrew Dauber
- Division of Endocrinology, Children's National Health System, Washington, District of Columbia, USA
| | - Mariana F A Funari
- Unidade de Endocrinologia do Desenvolvimento, Laboratorio de Hormonios e Genetica Molecular LIM42, Hospital das Clínicas da Faculdade de Medicina da Universidade de Sao Paulo (FMUSP), Sao Paulo, Brazil
| | - Antonio M Lerario
- Department of Internal Medicine, Division of Metabolism, Endocrinology and Diabetes, University of Michigan, Ann Arbor, Michigan, USA
| | - Edoarda V A Albuquerque
- Unidade de Endocrinologia Genetica, Laboratorio de Endocrinologia Celular e Molecular LIM25, Disciplina de Endocrinologia da Faculdade de Medicina da Universidade de Sao Paulo (FMUSP), Sao Paulo, Brazil
| | - Gabriela A Vasques
- Unidade de Endocrinologia Genetica, Laboratorio de Endocrinologia Celular e Molecular LIM25, Disciplina de Endocrinologia da Faculdade de Medicina da Universidade de Sao Paulo (FMUSP), Sao Paulo, Brazil
| | - Debora R Bertola
- Unidade de Genetica do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Chong A Kim
- Unidade de Genetica do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Alexsandra C Malaquias
- Unidade de Endocrinologia Genetica, Laboratorio de Endocrinologia Celular e Molecular LIM25, Disciplina de Endocrinologia da Faculdade de Medicina da Universidade de Sao Paulo (FMUSP), Sao Paulo, Brazil.,Unidade de Endocrinologia Pediatrica, Departamento de Pediatria, Irmandade da Santa Casa de Misericórdia de São Paulo, Faculdade de Ciências Médicas da Santa Casa de São Paulo, Sao Paulo, Brazil
| | - Alexander A L Jorge
- Unidade de Endocrinologia Genetica, Laboratorio de Endocrinologia Celular e Molecular LIM25, Disciplina de Endocrinologia da Faculdade de Medicina da Universidade de Sao Paulo (FMUSP), Sao Paulo, Brazil, .,Unidade de Endocrinologia do Desenvolvimento, Laboratorio de Hormonios e Genetica Molecular LIM42, Hospital das Clínicas da Faculdade de Medicina da Universidade de Sao Paulo (FMUSP), Sao Paulo, Brazil,
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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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Razmara E, Azimi H, Bitaraf A, Daneshmand MA, Galehdari M, Dokhanchi M, Esmaeilzadeh‐Gharehdaghi E, Garshasbi M. Whole-exome sequencing identified a novel variant in an Iranian patient affected by pycnodysostosis. Mol Genet Genomic Med 2020; 8:e1118. [PMID: 31944631 PMCID: PMC7057126 DOI: 10.1002/mgg3.1118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 11/15/2019] [Accepted: 12/23/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Whole-exome sequencing (WES) has emerged as a successful diagnostic tool in molecular genetics laboratories worldwide. In this study, we aimed to find the potential genetic cause of skeletal disease, a heterogeneous disease, revealing the obvious short stature phenotype. In an Iranian family, we used solo-WES in a suspected patient to decipher the potential genetic cause(s). METHODS A comprehensive clinical and genotyping examination was applied to suspect the disease of the patient. The solo clinical WES was exploited, and the derived data were filtered according to the standard pipelines. In order to validate the WES finding, the region harboring the candidate variant in the CTSK gene was amplified from genomic DNA and sequenced directly by Sanger sequencing. RESULTS Sequence analysis revealed a rare novel nonsense variant, p.(Trp320*); c.905G>A, in the CTSK gene (NM_000396.3). In silico analysis shed light on the contribution of the variant to the pathogenicity of pycnodysostosis. This variant was confirmed by Sanger sequencing and further clinical examinations of the patient confirmed the disease. CONCLUSION The present study shows a rare variant of the CTSK gene, which inherited as autosomal recessive, in an Iranian male patient with pycnodysostosis. Taken together, the novel nonsense CTSK variant meets the criteria of being likely pathogenic according to the American College of Medical Genetics and Genomics-the Association for Molecular Pathology (ACMG-AMP) variant interpretation guidelines.
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Affiliation(s)
- Ehsan Razmara
- Australian Regenerative Medicine InstituteMonash UniversityClaytonVICAustralia
| | | | - Amirreza Bitaraf
- Department of Molecular GeneticsFaculty of Biological SciencesTarbiat Modares UniversityTehranIran
| | | | - Mohammad Galehdari
- Department of BiologyFaculty of SciencesNorth Tehran BranchIslamic Azad UniversityTehranIran
| | - Maryam Dokhanchi
- Department of Biology, Science and Research BranchIslamic Azad UniversityTehranIran
| | | | - Masoud Garshasbi
- Department of Medical GeneticsFaculty of Medical SciencesTarbiat Modares UniversityTehranIran
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47
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Abstract
Aim and objective To report a case with Floating–Harbor syndrome (FHS), emphasizing the general features and dental abnormalities and the treatment procedures and its outcome. Background FHS is an extremely rare genetic disorder, characterized by a triad: short stature, speech delay, and characteristic facies like triangular shape, bulbous nose, wide columella, deep-set eyes, long eyelashes, thin lips, short philtrum, and broad mouth. Approximately 50 cases have been described in the medical literature till date. Diagnosis is often delayed because the characteristic features of this syndrome are nonfamiliar. Case description A male child aged 5 years was referred to the dental OPD with the chief complaint of decayed upper and lower front and back teeth. On examination, the patient was found to have FHS along with the dental caries. Conclusion FHS is a rare genetic dysmorphic/mental retardation syndrome affecting both sexes but more among the female sex. There is no known cure for the disease and the treatment is symptomatic and supportive. Clinical significance An early diagnosis of FHS is important, as it enables with adequate information. These multiple malformations identification by an early diagnosis is crucial, as it requires a multidisciplinary approach in the initial evaluation, treatment, and follow-up. How to cite this article Singana T, Suma NK, Sankriti AM. Floating–Harbor Syndrome: A Rare Case Report. Int J Clin Pediatr Dent 2020;13(5):569–571.
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Affiliation(s)
- Tejaswi Singana
- Department of Pediatric Dentistry, Vokkaligara Sangha Dental College and Hospital, Bengaluru, Karnataka, India
| | | | - Anantha Murthy Sankriti
- Department of Pediatric Dentistry, Vokkaligara Sangha Dental College and Hospital, Bengaluru, Karnataka, India
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48
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Wang H, Zhu H, Zhu W, Xu Y, Wang N, Han B, Song H, Qiao J. Bioinformatic Analysis Identifies Potential Key Genes in the Pathogenesis of Turner Syndrome. Front Endocrinol (Lausanne) 2020; 11:104. [PMID: 32210915 PMCID: PMC7069359 DOI: 10.3389/fendo.2020.00104] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 02/18/2020] [Indexed: 12/29/2022] Open
Abstract
Background: Turner syndrome (TS) is a sex chromosome aneuploidy with a variable spectrum of symptoms including short stature, ovarian failure and skeletal abnormalities. The etiology of TS is complex, and the mechanisms driving its pathogenesis remain unclear. Methods: In our study, we used the online Gene Expression Omnibus (GEO) microarray expression profiling dataset GSE46687 to identify differentially expressed genes (DEGs) between monosomy X TS patients and normal female individuals. The relevant data on 26 subjects with TS (45,XO) and 10 subjects with the normal karyotype (46,XX) was investigated. Then, tissue-specific gene expression, functional enrichment, and protein-protein interaction (PPI) network analyses were performed, and the key modules were identified. Results: In total, 25 upregulated and 60 downregulated genes were identified in the differential expression analysis. The tissue-specific gene expression analysis of the DEGs revealed that the system with the most highly enriched tissue-specific gene expression was the hematologic/immune system, followed by the skin/skeletal muscle and neurologic systems. The PPI network analysis, construction of key modules and manual screening of tissue-specific gene expression resulted in the identification of the following five genes of interest: CD99, CSF2RA, MYL9, MYLPF, and IGFBP2. CD99 and CSF2RA are involved in the hematologic/immune system, MYL9 and MYLPF are related to the circulatory system, and IGFBP2 is related to skeletal abnormalities. In addition, several genes of interest with possible roles in the pathogenesis of TS were identified as being associated with the hematologic/immune system or metabolism. Conclusion: This discovery-driven analysis may be a useful method for elucidating novel mechanisms underlying TS. However, more experiments are needed to further explore the relationships between these genes and TS in the future.
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Affiliation(s)
- Hao Wang
- Department of Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hui Zhu
- Department of Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenjiao Zhu
- Department of Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yue Xu
- Department of Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Nan Wang
- Department of Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bing Han
- Department of Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huaidong Song
- Research Centre for Clinical Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jie Qiao
- Department of Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Li RM, Lu YC, Li Z, Wang JY, Chang J, Lei SQ, Zeng Q, Sang YM. [Floating-Harbor syndrome: a case report and literature review]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2019; 21:1208-1211. [PMID: 31874661 PMCID: PMC7389003 DOI: 10.7499/j.issn.1008-8830.2019.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 09/06/2019] [Indexed: 06/10/2023]
Abstract
Floating-Harbor syndrome (FHS) is an autosomal dominant genetic disease caused by SRCAP mutation. This article reports the clinical features of a boy with FHS. The boy, aged 11 years and 7 months, attended the hospital due to short stature for more than 8 years and had the clinical manifestations of unusual facial features (triangularly shaped face, thin lips and long eyelashes), skeletal dysplasia (curvature finger), expressive language disorder, and retardation of bone age. Genetic detection revealed a novel heterozygous mutation, c.7330 C>T(p.R2444X), in the SRCAP gene. The boy was diagnosed with FHS based on these clinical manifestations and gene detection results. FHS is rare in clinical practice, which may lead to missed diagnosis and misdiagnosis, and gene detection may help with the clinical diagnosis of FHS in children.
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Affiliation(s)
- Rong-Min Li
- Baoding Key Laboratory of Clinical Research on Children's Respiratory and Digestive Diseases/Baoding Children's Hospital, Baoding, Hebei 071000.
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Schmidt J, Wollnik B. Hallermann-Streiff syndrome: A missing molecular link for a highly recognizable syndrome. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2019; 178:398-406. [PMID: 30580479 DOI: 10.1002/ajmg.c.31668] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 10/23/2018] [Accepted: 10/29/2018] [Indexed: 12/31/2022]
Abstract
The use of modern next-generation sequencing-based approaches for gene identification has tremendously improved our understanding of the molecular pathogenesis of the great majority of well-known syndromes, whereas only a few remain to be elucidated. Hallermann-Streiff syndrome is such a disorder for which the molecular basis is still unknown although it represents a highly recognizable phenotype. Clinically, patients with Hallermann-Streiff syndrome show typical craniofacial dysmorphism, eye malformations, a distinctive facial appearance, abnormalities of hair and skin, short stature, and, interestingly, they might also present with aspects of premature aging. The clinical diagnosis is mainly given by the very typical facial gestalt of patients. In this review, we (a) summarize the current knowledge on the phenotypic traits, focusing on described classic cases, (b) discuss the missing molecular link, and (c) present innovative future strategies for gene identification.
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Affiliation(s)
- Julia Schmidt
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Bernd Wollnik
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
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