1
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Bukowska-Olech E, Majchrzak-Celińska A, Przyborska M, Jamsheer A. Chromatinopathies: insight in clinical aspects and underlying epigenetic changes. J Appl Genet 2024; 65:287-301. [PMID: 38180712 PMCID: PMC11003913 DOI: 10.1007/s13353-023-00824-1] [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: 09/07/2023] [Revised: 12/17/2023] [Accepted: 12/18/2023] [Indexed: 01/06/2024]
Abstract
Chromatinopathies (CPs), a group of rare inborn defects characterized by chromatin state imbalance, have evolved from initially resembling Cornelia de Lange syndrome to encompass a wide array of genetic diseases with diverse clinical presentations. The CPs classification now includes human developmental disorders caused by germline mutations in epigenes, genes that regulate the epigenome. Recent advances in next-generation sequencing have enabled the association of 154 epigenes with CPs, revealing distinctive DNA methylation patterns known as episignatures.It has been shown that episignatures are unique for a particular CP or share similarities among specific CP subgroup. Consequently, these episignatures have emerged as promising biomarkers for diagnosing and treating CPs, differentiating subtypes, evaluating variants of unknown significance, and facilitating targeted therapies tailored to the underlying epigenetic dysregulation.The following review was conducted to collect, summarize, and analyze data regarding CPs in such aspects as clinical evaluation encompassing long-term patient care, underlying epigenetic changes, and innovative molecular and bioinformatic methodologies that have been devised for the assessment of CPs. We have also shed light on promising novel treatment options that have surfaced in recent research and presented a synthesis of ongoing clinical trials, contributing to the current understanding of the dynamic and evolving nature of CPs investigation.
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Affiliation(s)
| | | | | | - Aleksander Jamsheer
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
- Centers for Medical Genetics GENESIS, Poznan, Poland
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2
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Nava AA, Arboleda VA. The omics era: a nexus of untapped potential for Mendelian chromatinopathies. Hum Genet 2024; 143:475-495. [PMID: 37115317 PMCID: PMC11078811 DOI: 10.1007/s00439-023-02560-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 04/10/2023] [Indexed: 04/29/2023]
Abstract
The OMICs cascade describes the hierarchical flow of information through biological systems. The epigenome sits at the apex of the cascade, thereby regulating the RNA and protein expression of the human genome and governs cellular identity and function. Genes that regulate the epigenome, termed epigenes, orchestrate complex biological signaling programs that drive human development. The broad expression patterns of epigenes during human development mean that pathogenic germline mutations in epigenes can lead to clinically significant multi-system malformations, developmental delay, intellectual disabilities, and stem cell dysfunction. In this review, we refer to germline developmental disorders caused by epigene mutation as "chromatinopathies". We curated the largest number of human chromatinopathies to date and our expanded approach more than doubled the number of established chromatinopathies to 179 disorders caused by 148 epigenes. Our study revealed that 20.6% (148/720) of epigenes cause at least one chromatinopathy. In this review, we highlight key examples in which OMICs approaches have been applied to chromatinopathy patient biospecimens to identify underlying disease pathogenesis. The rapidly evolving OMICs technologies that couple molecular biology with high-throughput sequencing or proteomics allow us to dissect out the causal mechanisms driving temporal-, cellular-, and tissue-specific expression. Using the full repertoire of data generated by the OMICs cascade to study chromatinopathies will provide invaluable insight into the developmental impact of these epigenes and point toward future precision targets for these rare disorders.
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Affiliation(s)
- Aileen A Nava
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Broad Stem Cell Research Center, University of California, Los Angeles, CA, USA
| | - Valerie A Arboleda
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
- Broad Stem Cell Research Center, University of California, Los Angeles, CA, USA.
- Molecular Biology Institute, University of California, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA.
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3
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Awamleh Z, Choufani S, Wu W, Rots D, Dingemans AJM, Nadif Kasri N, Boronat S, Ibañez-Mico S, Cuesta Herraiz L, Ferrer I, Martínez Carrascal A, Pérez-Jurado LA, Aznar Lain G, Ortigoza-Escobar JD, de Vries BBA, Koolen DA, Weksberg R. A new blood DNA methylation signature for Koolen-de Vries syndrome: Classification of missense KANSL1 variants and comparison to fibroblast cells. Eur J Hum Genet 2024; 32:324-332. [PMID: 38282074 PMCID: PMC10923882 DOI: 10.1038/s41431-024-01538-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 12/27/2023] [Accepted: 01/09/2024] [Indexed: 01/30/2024] Open
Abstract
Pathogenic variants in KANSL1 and 17q21.31 microdeletions are causative of Koolen-de Vries syndrome (KdVS), a neurodevelopmental syndrome with characteristic facial dysmorphia. Our previous work has shown that syndromic conditions caused by pathogenic variants in epigenetic regulatory genes have identifiable patterns of DNA methylation (DNAm) change: DNAm signatures or episignatures. Given the role of KANSL1 in histone acetylation, we tested whether variants underlying KdVS are associated with a DNAm signature. We profiled whole-blood DNAm for 13 individuals with KANSL1 variants, four individuals with 17q21.31 microdeletions, and 21 typically developing individuals, using Illumina's Infinium EPIC array. In this study, we identified a robust DNAm signature of 456 significant CpG sites in 8 individuals with KdVS, a pattern independently validated in an additional 7 individuals with KdVS. We also demonstrate the diagnostic utility of the signature and classify two KANSL1 VUS as well as four variants in individuals with atypical clinical presentation. Lastly, we investigated tissue-specific DNAm changes in fibroblast cells from individuals with KdVS. Collectively, our findings contribute to the understanding of the epigenetic landscape related to KdVS and aid in the diagnosis and classification of variants in this structurally complex genomic region.
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Affiliation(s)
- Zain Awamleh
- Genetics and Genome Biology Program, Research Institute, the Hospital for Sick Children, Toronto, ON, M5G 1×8, Canada
| | - Sanaa Choufani
- Genetics and Genome Biology Program, Research Institute, the Hospital for Sick Children, Toronto, ON, M5G 1×8, Canada
| | - Wendy Wu
- Genetics and Genome Biology Program, Research Institute, the Hospital for Sick Children, Toronto, ON, M5G 1×8, Canada
| | - Dmitrijs Rots
- Department of Human Genetics, Radboud university medical center, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, The Netherlands
| | - Alexander J M Dingemans
- Department of Human Genetics, Radboud university medical center, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, The Netherlands
| | - Nael Nadif Kasri
- Department of Human Genetics, Radboud university medical center, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, The Netherlands
| | - Susana Boronat
- Department of Pediatrics, Hospital del Santa Creu y Sant Pau, Barcelona, Spain
| | - Salvador Ibañez-Mico
- Department of Pediatric Neurology, Hospital Virgen de la Arrixaca, Murcia, Madrid, Spain
| | | | - Irene Ferrer
- Department of Genetics, Consorcio Hospital General de Valencia, Valencia, Spain
| | | | - Luis A Pérez-Jurado
- Genetics Unit, Universitat Pompeu Fabra, Hospital del Mar Research Institute (IMIM) and CIBERER, Barcelona, Spain
| | - Gemma Aznar Lain
- Genetics Unit, Universitat Pompeu Fabra, Hospital del Mar Research Institute (IMIM) and CIBERER, Barcelona, Spain
| | - Juan Dario Ortigoza-Escobar
- Movement Disorders Unit, Institut de Recerca Sant Joan de Déu, CIBERER-ISCIII and European Reference Network for Rare Neurological Diseases (ERN-RND), Barcelona, Spain
| | - Bert B A de Vries
- Department of Human Genetics, Radboud university medical center, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, The Netherlands
| | - David A Koolen
- Department of Human Genetics, Radboud university medical center, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, The Netherlands.
| | - Rosanna Weksberg
- Genetics and Genome Biology Program, Research Institute, the Hospital for Sick Children, Toronto, ON, M5G 1×8, Canada.
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, the Hospital for Sick Children, University of Toronto, Toronto, ON, M5G 1×8, Canada.
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4
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Singh M, Spendlove SJ, Wei A, Bondhus LM, Nava AA, de L Vitorino FN, Amano S, Lee J, Echeverria G, Gomez D, Garcia BA, Arboleda VA. KAT6A mutations in Arboleda-Tham syndrome drive epigenetic regulation of posterior HOXC cluster. Hum Genet 2023; 142:1705-1720. [PMID: 37861717 PMCID: PMC10676314 DOI: 10.1007/s00439-023-02608-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/28/2023] [Indexed: 10/21/2023]
Abstract
Arboleda-Tham Syndrome (ARTHS) is a rare genetic disorder caused by heterozygous, de novo mutations in Lysine(K) acetyltransferase 6A (KAT6A). ARTHS is clinically heterogeneous and characterized by several common features, including intellectual disability, developmental and speech delay, and hypotonia, and affects multiple organ systems. KAT6A is the enzymatic core of a histone-acetylation protein complex; however, the direct histone targets and gene regulatory effects remain unknown. In this study, we use ARTHS patient (n = 8) and control (n = 14) dermal fibroblasts and perform comprehensive profiling of the epigenome and transcriptome caused by KAT6A mutations. We identified differential chromatin accessibility within the promoter or gene body of 23% (14/60) of genes that were differentially expressed between ARTHS and controls. Within fibroblasts, we show a distinct set of genes from the posterior HOXC gene cluster (HOXC10, HOXC11, HOXC-AS3, HOXC-AS2, and HOTAIR) that are overexpressed in ARTHS and are transcription factors critical for early development body segment patterning. The genomic loci harboring HOXC genes are epigenetically regulated with increased chromatin accessibility, high levels of H3K23ac, and increased gene-body DNA methylation compared to controls, all of which are consistent with transcriptomic overexpression. Finally, we used unbiased proteomic mass spectrometry and identified two new histone post-translational modifications (PTMs) that are disrupted in ARTHS: H2A and H3K56 acetylation. Our multi-omics assays have identified novel histone and gene regulatory roles of KAT6A in a large group of ARTHS patients harboring diverse pathogenic mutations. This work provides insight into the role of KAT6A on the epigenomic regulation in somatic cell types.
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Affiliation(s)
- Meghna Singh
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Sarah J Spendlove
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Interdepartmental BioInformatics Program, UCLA, Los Angeles, CA, USA
| | - Angela Wei
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Interdepartmental BioInformatics Program, UCLA, Los Angeles, CA, USA
| | - Leroy M Bondhus
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Aileen A Nava
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Francisca N de L Vitorino
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO, USA
| | - Seth Amano
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Jacob Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Gesenia Echeverria
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Dianne Gomez
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO, USA
| | - Valerie A Arboleda
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA, 90095, USA.
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
- Interdepartmental BioInformatics Program, UCLA, Los Angeles, CA, USA.
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5
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Singh M, Spendlove S, Wei A, Bondhus L, Nava A, de L. Vitorino FN, Amano S, Lee J, Echeverria G, Gomez D, Garcia BA, Arboleda VA. KAT6A mutations in Arboleda-Tham syndrome drive epigenetic regulation of posterior HOXC cluster. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.03.550595. [PMID: 37577627 PMCID: PMC10418288 DOI: 10.1101/2023.08.03.550595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Arboleda-Tham Syndrome (ARTHS) is a rare genetic disorder caused by heterozygous, de novo truncating mutations in Lysine(K) acetyltransferase 6A (KAT6A). ARTHS is clinically heterogeneous and characterized by several common features including intellectual disability, developmental and speech delay, hypotonia and affects multiple organ systems. KAT6A is highly expressed in early development and plays a key role in cell-type specific differentiation. KAT6A is the enzymatic core of a histone-acetylation protein complex, however the direct histone targets and gene regulatory effects remain unknown. In this study, we use ARTHS patient (n=8) and control (n=14) dermal fibroblasts and perform comprehensive profiling of the epigenome and transcriptome caused by KAT6A mutations. We identified differential chromatin accessibility within the promoter or gene body of 23%(14/60) of genes that were differentially expressed between ARTHS and controls. Within fibroblasts, we show a distinct set of genes from the posterior HOXC gene cluster (HOXC10, HOXC11, HOXC-AS3, HOXC-AS2, HOTAIR) that are overexpressed in ARTHS and are transcription factors critical for early development body segment patterning. The genomic loci harboring HOXC genes are epigenetically regulated with increased chromatin accessibility, high levels of H3K23ac, and increased gene-body DNA methylation compared to controls, all of which are consistent with transcriptomic overexpression. Finally, we used unbiased proteomic mass spectrometry and identified two new histone post-translational modifications (PTMs) that are disrupted in ARTHS: H2A and H3K56 acetylation. Our multi-omics assays have identified novel histone and gene regulatory roles of KAT6A in a large group of ARTHS patients harboring diverse pathogenic mutations. This work provides insight into the role of KAT6A on the epigenomic regulation in somatic cell types.
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Affiliation(s)
- Meghna Singh
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Sarah Spendlove
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Interdepartmental BioInformatics Program, UCLA
| | - Angela Wei
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Interdepartmental BioInformatics Program, UCLA
| | - Leroy Bondhus
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Aileen Nava
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | | | - Seth Amano
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Jacob Lee
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Gesenia Echeverria
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Dianne Gomez
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Benjamin A. Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis
| | - Valerie A. Arboleda
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Interdepartmental BioInformatics Program, UCLA
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6
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Ho SKL, Cheng SSW, Cheng THT, Leung LT, Lam EKY, Mok MTS, Lo IFM, Luk HM. Extending the phenotype of Shashi-Pena syndrome: a case report and review of literature. Clin Dysmorphol 2023; 32:139-146. [PMID: 37195319 DOI: 10.1097/mcd.0000000000000462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Affiliation(s)
| | | | | | | | - Emily Kai Yee Lam
- Department of Pathology, Hong Kong Children's Hospital, HKSAR, Hong Kong
| | | | | | - Ho-Ming Luk
- Clinical Genetics Service Unit, Hong Kong Children's Hospital
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7
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Lin I, Wei A, Awamleh Z, Singh M, Ning A, Herrera A, Russell BE, Weksberg R, Arboleda VA. Multiomics of Bohring-Opitz syndrome truncating ASXL1 mutations identify canonical and noncanonical Wnt signaling dysregulation. JCI Insight 2023; 8:e167744. [PMID: 37053013 PMCID: PMC10322691 DOI: 10.1172/jci.insight.167744] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 04/07/2023] [Indexed: 04/14/2023] Open
Abstract
ASXL1 (additional sex combs-like 1) plays key roles in epigenetic regulation of early developmental gene expression. De novo protein-truncating mutations in ASXL1 cause Bohring-Opitz syndrome (BOS; OMIM #605039), a rare neurodevelopmental condition characterized by severe intellectual disabilities, distinctive facial features, hypertrichosis, increased risk of Wilms tumor, and variable congenital anomalies, including heart defects and severe skeletal defects giving rise to a typical BOS posture. These BOS-causing ASXL1 variants are also high-prevalence somatic driver mutations in acute myeloid leukemia. We used primary cells from individuals with BOS (n = 18) and controls (n = 49) to dissect gene regulatory changes caused by ASXL1 mutations using comprehensive multiomics assays for chromatin accessibility (ATAC-seq), DNA methylation, histone methylation binding, and transcriptome in peripheral blood and skin fibroblasts. Our data show that regardless of cell type, ASXL1 mutations drive strong cross-tissue effects that disrupt multiple layers of the epigenome. The data showed a broad activation of canonical Wnt signaling at the transcriptional and protein levels and upregulation of VANGL2, which encodes a planar cell polarity pathway protein that acts through noncanonical Wnt signaling to direct tissue patterning and cell migration. This multiomics approach identifies the core impact of ASXL1 mutations and therapeutic targets for BOS and myeloid leukemias.
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Affiliation(s)
- Isabella Lin
- Department of Human Genetics
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
- Department of Computational Medicine, UCLA, Los Angeles, California, USA
| | - Angela Wei
- Department of Human Genetics
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
- Department of Computational Medicine, UCLA, Los Angeles, California, USA
- Interdepartmental BioInformatics Program, UCLA, Los Angeles, California, USA
| | - Zain Awamleh
- Department of Genetics and Genome Biology Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Meghna Singh
- Department of Human Genetics
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
- Department of Computational Medicine, UCLA, Los Angeles, California, USA
| | - Aileen Ning
- Department of Human Genetics
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
- Department of Computational Medicine, UCLA, Los Angeles, California, USA
| | - Analeyla Herrera
- Department of Human Genetics
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
- Department of Computational Medicine, UCLA, Los Angeles, California, USA
| | | | - Bianca E. Russell
- Division of Genetics, Department of Pediatrics, UCLA, Los Angeles, California, USA
| | - Rosanna Weksberg
- Department of Genetics and Genome Biology Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Clinical & Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Institute of Medical Sciences and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Valerie A. Arboleda
- Department of Human Genetics
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
- Department of Computational Medicine, UCLA, Los Angeles, California, USA
- Interdepartmental BioInformatics Program, UCLA, Los Angeles, California, USA
- Molecular Biology Institute, UCLA, Los Angeles, California, USA
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, California, USA
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8
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McNeill A. 2022: the year that was in the European Journal of Human Genetics. Eur J Hum Genet 2023; 31:131-133. [PMID: 36750730 PMCID: PMC9905485 DOI: 10.1038/s41431-023-01283-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Affiliation(s)
- Alisdair McNeill
- Department of Neuroscience, The University of Sheffield, Sheffield, UK.
- Sheffield Clinical Genetics Department, Sheffield Children's Hospital NHS Foundation Trust, Sheffield, UK.
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9
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van der Laan L, Rooney K, Trooster TM, Mannens MM, Sadikovic B, Henneman P. DNA methylation episignatures: insight into copy number variation. Epigenomics 2022; 14:1373-1388. [PMID: 36537268 DOI: 10.2217/epi-2022-0287] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In this review we discuss epigenetic disorders that result from aberrations in genes linked to epigenetic regulation. We describe current testing methods for the detection of copy number variants (CNVs) in Mendelian disorders, dosage sensitivity, reciprocal phenotypes and the challenges of test selection and overlapping clinical features in genetic diagnosis. We discuss aberrations of DNA methylation and propose a role for episignatures as a novel clinical testing method in CNV disorders. Finally, we postulate that episignature mapping in CNV disorders may provide novel insights into the molecular mechanisms of disease and unlock key findings of the genome-wide impact on disease gene networks.
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Affiliation(s)
- Liselot van der Laan
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Amsterdam, 1105 AZ, The Netherlands
| | - Kathleen Rooney
- Department of Pathology & Laboratory Medicine, Western University, London, Ontario, N5A 3K7, Canada.,Verspeeten Clinical Genome Centre, London Health Science Centre, London, Ontario, N6A 5W9, Canada
| | - Tessa Ma Trooster
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Amsterdam, 1105 AZ, The Netherlands
| | - Marcel Mam Mannens
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Amsterdam, 1105 AZ, The Netherlands
| | - Bekim Sadikovic
- Department of Pathology & Laboratory Medicine, Western University, London, Ontario, N5A 3K7, Canada.,Verspeeten Clinical Genome Centre, London Health Science Centre, London, Ontario, N6A 5W9, Canada
| | - Peter Henneman
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Amsterdam, 1105 AZ, The Netherlands
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10
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Mannens MMAM, Lombardi MP, Alders M, Henneman P, Bliek J. Further Introduction of DNA Methylation (DNAm) Arrays in Regular Diagnostics. Front Genet 2022; 13:831452. [PMID: 35860466 PMCID: PMC9289263 DOI: 10.3389/fgene.2022.831452] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 06/08/2022] [Indexed: 12/01/2022] Open
Abstract
Methylation tests have been used for decades in regular DNA diagnostics focusing primarily on Imprinting disorders or specific loci annotated to specific disease associated gene promotors. With the introduction of DNA methylation (DNAm) arrays such as the Illumina Infinium HumanMethylation450 Beadchip array or the Illumina Infinium Methylation EPIC Beadchip array (850 k), it has become feasible to study the epigenome in a timely and cost-effective way. This has led to new insights regarding the complexity of well-studied imprinting disorders such as the Beckwith Wiedemann syndrome, but it has also led to the introduction of tests such as EpiSign, implemented as a diagnostic test in which a single array experiment can be compared to databases with known episignatures of multiple genetic disorders, especially neurodevelopmental disorders. The successful use of such DNAm tests is rapidly expanding. More and more disorders are found to be associated with discrete episignatures which enables fast and definite diagnoses, as we have shown. The first examples of environmentally induced clinical disorders characterized by discrete aberrant DNAm are discussed underlining the broad application of DNAm testing in regular diagnostics. Here we discuss exemplary findings in our laboratory covering this broad range of applications and we discuss further use of DNAm tests in the near future.
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McNeill A. What's new in genetics in June 2022? Eur J Hum Genet 2022; 30:633-634. [PMID: 35676534 DOI: 10.1038/s41431-022-01122-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Alisdair McNeill
- Department of Neuroscience, The University of Sheffield, Sheffield, UK. .,Sheffield Clinical Genetics Department, Sheffield Children's Hospital NHS Foundation Trust, Sheffield, UK.
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