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Boukas L, Luperchio TR, Razi A, Hansen KD, Bjornsson HT. Neuron-specific chromatin disruption at CpG islands and aging-related regions in Kabuki syndrome mice. Genome Res 2024; 34:696-710. [PMID: 38702196 PMCID: PMC11216309 DOI: 10.1101/gr.278416.123] [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: 08/17/2023] [Accepted: 04/15/2024] [Indexed: 05/06/2024]
Abstract
Many Mendelian developmental disorders caused by coding variants in epigenetic regulators have now been discovered. Epigenetic regulators are broadly expressed, and each of these disorders typically shows phenotypic manifestations from many different organ systems. An open question is whether the chromatin disruption-the root of the pathogenesis-is similar in the different disease-relevant cell types. This is possible in principle, because all these cell types are subject to effects from the same causative gene, which has the same kind of function (e.g., methylates histones) and is disrupted by the same germline variant. We focus on mouse models for Kabuki syndrome types 1 and 2 and find that the chromatin accessibility changes in neurons are mostly distinct from changes in B or T cells. This is not because the neuronal accessibility changes occur at regulatory elements that are only active in neurons. Neurons, but not B or T cells, show preferential chromatin disruption at CpG islands and at regulatory elements linked to aging. A sensitive analysis reveals that regulatory elements disrupted in B/T cells do show chromatin accessibility changes in neurons, but these are very subtle and of uncertain functional significance. Finally, we are able to identify a small set of regulatory elements disrupted in all three cell types. Our findings reveal the cellular-context-specific effect of variants in epigenetic regulators and suggest that blood-derived episignatures, although useful diagnostically, may not be well suited for understanding the mechanistic basis of neurodevelopment in Mendelian disorders of the epigenetic machinery.
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Affiliation(s)
- Leandros Boukas
- Department of Pediatrics, Children's National Hospital, Washington, DC 20010, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
| | - Teresa Romeo Luperchio
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Afrooz Razi
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Kasper D Hansen
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA;
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland 21218, USA
| | - Hans T Bjornsson
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA;
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Faculty of Medicine, University of Iceland, 101 Reykjavík, Iceland
- Landspitali University Hospital, 101 Reykjavík, Iceland
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Rossini L, Ricci S, Montin D, Azzari C, Gambineri E, Tellini M, Conti F, Pession A, Saettini F, Naviglio S, Valencic E, Magnolato A, Baselli L, Azzolini S, Consolini R, Leonardi L, D'Alba I, Carraro E, Romano R, Melis D, Stagi S, Cirillo E, Giardino G, Biffi A, Pignata C, Putti MC, Marzollo A. Immunological Aspects of Kabuki Syndrome: A Retrospective Multicenter Study of the Italian Primary Immunodeficiency Network (IPINet). J Clin Immunol 2024; 44:105. [PMID: 38676773 DOI: 10.1007/s10875-024-01676-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 02/23/2024] [Indexed: 04/29/2024]
Abstract
Kabuki Syndrome (KS) is a multisystemic genetic disorder. A portion of patients has immunological manifestations characterized by increased susceptibility to infections and autoimmunity. Aiming to describe the clinical and laboratory immunological aspects of KS, we conducted a retrospective multicenter observational study on patients with KS treated in centers affiliated to the Italian Primary Immunodeficiency Network.Thirty-nine patients were enrolled, with a median age at evaluation of 10 years (range: 3 m-21y). All individuals had organ malformations of variable severity. Congenital heart defect (CHD) was present in 19/39 patients (49%) and required surgical correction in 9/39 (23%), with associated thymectomy in 7/39 (18%). Autoimmune cytopenia occurred in 6/39 patients (15%) and was significantly correlated with thymectomy (p < 0.002), but not CHD. Individuals with cytopenia treated with mycophenolate as long-term immunomodulatory treatment (n = 4) showed complete response. Increased susceptibility to infections was observed in 22/32 patients (69%). IgG, IgA, and IgM were low in 13/29 (45%), 13/30 (43%) and 4/29 (14%) patients, respectively. Immunoglobulin substitution was required in three patients. Lymphocyte subsets were normal in all patients except for reduced naïve T-cells in 3/15 patients (20%) and reduced memory switched B-cells in 3/17 patients (18%). Elevated CD3 + TCRαβ + CD4-CD8-T-cells were present in 5/17 individuals (23%) and were correlated with hematological and overall autoimmunity (p < 0.05).In conclusion, immunological manifestations of KS in our cohort include susceptibility to infections, antibody deficiency, and autoimmunity. Autoimmune cytopenia is correlated with thymectomy and elevated CD3 + TCRαβ + CD4-CD8-T-cells, and benefits from treatment with mycophenolate.
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Affiliation(s)
- Linda Rossini
- Pediatric Hematology, Oncology and Stem Cell Transplant Division, Padua University Hospital, Via Giustiniani 3, Padua, 35128, Italy
- Maternal and Child Health Department, Padua University, Via Giustiniani, 3, Padua, 35128, Italy
| | - Silvia Ricci
- Immunology, Pediatric Unit, IRCCS Meyer Children's Hospital, viale G.Pieraccini 24, Florence, 50139, Italy
- Department of Health Sciences, University of Florence, Florence, Italy
| | - Davide Montin
- Immunology and Rheumatology Unit, Regina Margherita Children Hospital, Turin, Italy
| | - Chiara Azzari
- Immunology, Pediatric Unit, IRCCS Meyer Children's Hospital, viale G.Pieraccini 24, Florence, 50139, Italy
- Department of Health Sciences, University of Florence, Florence, Italy
| | - Eleonora Gambineri
- Centre of Excellence, Department of Pediatric Hematology-Oncology, IRCCS Meyer Children's Hospital, Florence, Italy
- Department of "NEUROFARBA", Section of Child's Health, University of Florence, Florence, Italy
| | - Marco Tellini
- Centre of Excellence, Department of Pediatric Hematology-Oncology, IRCCS Meyer Children's Hospital, Florence, Italy
| | - Francesca Conti
- Pediatric Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, 40138, Italy
- Dept. of Medical and Surgical Sciences, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Andrea Pession
- Pediatric Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, 40138, Italy
- Dept. of Medical and Surgical Sciences, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Francesco Saettini
- Tettamanti Research Center, University of Milano-Bicocca, University of Milano Bicocca, Monza, Italy
| | - Samuele Naviglio
- Institute for Maternal and Child Health IRCCS "Burlo Garofolo", Trieste, Italy
| | - Erica Valencic
- Institute for Maternal and Child Health IRCCS "Burlo Garofolo", Trieste, Italy
| | - Andrea Magnolato
- Institute for Maternal and Child Health IRCCS "Burlo Garofolo", Trieste, Italy
| | - Lucia Baselli
- Department of Pediatrics, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Rita Consolini
- Section of Clinical and Laboratory Immunology, Division of Pediatrics, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Lucia Leonardi
- Maternal, Infantile and Urological Sciences Department, Sapienza University of Rome, Rome, Italy
| | - Irene D'Alba
- Paediatric Haematology-Oncology, Maternal Infant Hospital "G. Salesi", Ancona, Italy
| | - Elisa Carraro
- Pediatric Hematology, Oncology and Stem Cell Transplant Division, Padua University Hospital, Via Giustiniani 3, Padua, 35128, Italy
| | - Roberta Romano
- Department of Translational Medical Sciences, Section of Pediatrics, Federico II University, Naples, Italy
| | - Daniela Melis
- Department of Medicine, Surgery and Dentistry, University of Salerno, Via Salvador Allende Baronissi, Campania, 84081, Italy
| | - Stefano Stagi
- Department of Health Sciences, University of Florence, Florence, Italy
- Auxoendocrinology Division, Meyer Children's Hospital, IRCCS, viale G.Pieraccini 24, Florence, 50139, Italy
| | - Emilia Cirillo
- Department of Translational Medical Sciences, Section of Pediatrics, Federico II University, Naples, Italy
| | - Giuliana Giardino
- Department of Translational Medical Sciences, Section of Pediatrics, Federico II University, Naples, Italy
| | - Alessandra Biffi
- Pediatric Hematology, Oncology and Stem Cell Transplant Division, Padua University Hospital, Via Giustiniani 3, Padua, 35128, Italy
- Maternal and Child Health Department, Padua University, Via Giustiniani, 3, Padua, 35128, Italy
| | - Claudio Pignata
- Department of Translational Medical Sciences, Section of Pediatrics, Federico II University, Naples, Italy
| | - Maria Caterina Putti
- Pediatric Hematology, Oncology and Stem Cell Transplant Division, Padua University Hospital, Via Giustiniani 3, Padua, 35128, Italy
| | - Antonio Marzollo
- Pediatric Hematology, Oncology and Stem Cell Transplant Division, Padua University Hospital, Via Giustiniani 3, Padua, 35128, Italy.
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Wu P, Xiong C, Rao J, Ouyang M, Zhang H, Wu Y, Liu G. Newly recognized orbital malformations in kabuki syndrome: A case report. Eur J Ophthalmol 2024:11206721241249224. [PMID: 38656196 DOI: 10.1177/11206721241249224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Kabuki syndrome (KS) is a rare congenital disorder with distinctive characteristics. Herein, we describe a KS patient carrying a novel mutation in the KMT2D gene, c.11785C > T (p.Gln3929*). The patient presented with typical eyelid deformities, including eversion of the lateral lower eyelids, long palpebral fissures, hypertelorism, and medial epicanthus. Orbital computed tomography revealed orbital bone malformation with temporally and inferiorly displaced zygomatic bone. The bilateral orbits were shallow with an enlarged angle between the lateral walls. Zygomatic and maxillary bone dysplasia were also observed. Orbital bone anomalies are thought to be one of the characteristics of KS.
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Affiliation(s)
- Pengsen Wu
- Department of Ocular Oncology and Orbital Disease, Shenzhen Eye Hospital, Jinan University, Shenzhen Eye Institute, Shenzhen, China
| | - Cheng Xiong
- Department of Ocular Oncology and Orbital Disease, Shenzhen Eye Hospital, Jinan University, Shenzhen Eye Institute, Shenzhen, China
| | - Jing Rao
- Department of Ocular Oncology and Orbital Disease, Shenzhen Eye Hospital, Jinan University, Shenzhen Eye Institute, Shenzhen, China
| | - Ming Ouyang
- Department of Ocular Oncology and Orbital Disease, Shenzhen Eye Hospital, Jinan University, Shenzhen Eye Institute, Shenzhen, China
| | - Hua Zhang
- Department of Radiology, Shenzhen OCT Hospital, Shenzhen, China
| | - Yuqing Wu
- Department of Ocular Oncology and Orbital Disease, Shenzhen Eye Hospital, Jinan University, Shenzhen Eye Institute, Shenzhen, China
| | - Guiqin Liu
- Department of Ocular Oncology and Orbital Disease, Shenzhen Eye Hospital, Jinan University, Shenzhen Eye Institute, Shenzhen, China
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Tibben BM, Rothbart SB. Mechanisms of DNA Methylation Regulatory Function and Crosstalk with Histone Lysine Methylation. J Mol Biol 2024; 436:168394. [PMID: 38092287 PMCID: PMC10957332 DOI: 10.1016/j.jmb.2023.168394] [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: 09/28/2023] [Revised: 12/06/2023] [Accepted: 12/06/2023] [Indexed: 12/20/2023]
Abstract
DNA methylation is a well-studied epigenetic modification that has key roles in regulating gene expression, maintaining genome integrity, and determining cell fate. Precisely how DNA methylation patterns are established and maintained in specific cell types at key developmental stages is still being elucidated. However, research over the last two decades has contributed to our understanding of DNA methylation regulation by other epigenetic processes. Specifically, lysine methylation on key residues of histone proteins has been shown to contribute to the allosteric regulation of DNA methyltransferase (DNMT) activities. In this review, we discuss the dynamic interplay between DNA methylation and histone lysine methylation as epigenetic regulators of genome function by synthesizing key recent studies in the field. With a focus on DNMT3 enzymes, we discuss mechanisms of DNA methylation and histone lysine methylation crosstalk in the regulation of gene expression and the maintenance of genome integrity. Further, we discuss how alterations to the balance of various sites of histone lysine methylation and DNA methylation contribute to human developmental disorders and cancers. Finally, we provide perspectives on the current direction of the field and highlight areas for continued research and development.
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Affiliation(s)
- Bailey M Tibben
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Scott B Rothbart
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA.
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Kaur A, Chaudhry C, Kaur P, Daniel R, Srivastava P. Pattern Recognition of Common Multiple Congenital Malformation Syndromes with Underlying Chromatinopathy. J Pediatr Genet 2024; 13:6-14. [PMID: 38567171 PMCID: PMC10984715 DOI: 10.1055/s-0042-1748019] [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: 08/17/2021] [Accepted: 03/07/2022] [Indexed: 10/17/2022]
Abstract
Chromatinopathy is an emerging category of multiple malformation syndromes caused by disruption in global transcriptional regulation with imbalances in the chromatin states (i.e., open or closed chromatin). These syndromes are caused by pathogenic variants in genes coding for the writers, erasers, readers, and remodelers of the epigenetic machinery. Majority of these disorders (93%) show neurological dysfunction in the form of intellectual disability. Other overlapping features are growth abnormalities, limb deformities, and immune dysfunction. In this study, we describe a series of children with six common chromatinopathy syndromes with an aim to develop pattern recognition of this emerging category of multiple malformation syndromes.
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Affiliation(s)
- Anupriya Kaur
- Department of Paediatrics, Genetic Metabolic Unit, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Chakshu Chaudhry
- Department of Paediatrics, Genetic Metabolic Unit, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Parminder Kaur
- Department of Paediatrics, Genetic Metabolic Unit, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Roshan Daniel
- Department of Paediatrics, Genetic Metabolic Unit, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Priyanka Srivastava
- Department of Paediatrics, Genetic Metabolic Unit, Post Graduate Institute of Medical Education and Research, Chandigarh, India
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Golden CS, Williams S, Serrano MA. Molecular insights of KMT2D and clinical aspects of Kabuki syndrome type 1. Birth Defects Res 2023; 115:1809-1824. [PMID: 37158694 PMCID: PMC10845236 DOI: 10.1002/bdr2.2183] [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: 01/25/2023] [Revised: 04/03/2023] [Accepted: 04/14/2023] [Indexed: 05/10/2023]
Abstract
BACKGROUND Kabuki syndrome type 1 (KS1), a rare multisystem congenital disorder, presents with characteristic facial features, intellectual disability, persistent fetal fingertip pads, skeletal abnormalities, and postnatal growth delays. KS1 results from pathogenic variants in the KMT2D gene, which encodes a histone methyltransferase protein involved in chromatin remodeling, promoter and enhancer regulation, and scaffold formation during early development. KMT2D also mediates cell signaling pathways, responding to external stimuli and organizing effector protein assembly. Research on KMT2D's molecular mechanisms in KS1 has primarily focused on its histone methyltransferase activity, leaving a gap in understanding the methyltransferase-independent roles in KS1 clinical manifestations. METHODS This scoping review examines KMT2D's role in gene expression regulation across various species, cell types, and contexts. We analyzed human pathogenic KMT2D variants using publicly available databases and compared them to research organism models of KS1. We also conducted a systematic search of healthcare and governmental databases for clinical trials, studies, and therapeutic approaches. RESULTS Our review highlights KMT2D's critical roles beyond methyltransferase activity in diverse cellular contexts and conditions. We identified six distinct groups of KMT2D as a cell signaling mediator, including evidence of methyltransferase-dependent and -independent activity. A comprehensive search of the literature, clinical databases, and public registries emphasizes the need for basic research on KMT2D's functional complexity and longitudinal studies of KS1 patients to establish objective outcome measurements for therapeutic development. CONCLUSION We discuss how KMT2D's role in translating external cellular communication can partly explain the clinical heterogeneity observed in KS1 patients. Additionally, we summarize the current molecular diagnostic approaches and clinical trials targeting KS1. This review is a resource for patient advocacy groups, researchers, and physicians to support KS1 diagnosis and therapeutic development.
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Affiliation(s)
- Carly S Golden
- Center for Regenerative Medicine, Section of Vascular Biology, Department of Medicine, Boston University, Boston, Massachusetts, USA
| | - Saylor Williams
- Center for Regenerative Medicine, Section of Vascular Biology, Department of Medicine, Boston University, Boston, Massachusetts, USA
| | - Maria A Serrano
- Center for Regenerative Medicine, Section of Vascular Biology, Department of Medicine, Boston University, Boston, Massachusetts, USA
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Goodman SJ, Luperchio TR, Ellegood J, Chater-Diehl E, Lerch JP, Bjornsson HT, Weksberg R. Peripheral blood DNA methylation and neuroanatomical responses to HDACi treatment that rescues neurological deficits in a Kabuki syndrome mouse model. Clin Epigenetics 2023; 15:172. [PMID: 37884963 PMCID: PMC10605417 DOI: 10.1186/s13148-023-01582-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/08/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND Recent findings from studies of mouse models of Mendelian disorders of epigenetic machinery strongly support the potential for postnatal therapies to improve neurobehavioral and cognitive deficits. As several of these therapies move into human clinical trials, the search for biomarkers of treatment efficacy is a priority. A potential postnatal treatment of Kabuki syndrome type 1 (KS1), caused by pathogenic variants in KMT2D encoding a histone-lysine methyltransferase, has emerged using a mouse model of KS1 (Kmt2d+/βGeo). In this mouse model, hippocampal memory deficits are ameliorated following treatment with the histone deacetylase inhibitor (HDACi), AR-42. Here, we investigate the effect of both Kmt2d+/βGeo genotype and AR-42 treatment on neuroanatomy and on DNA methylation (DNAm) in peripheral blood. While peripheral blood may not be considered a "primary tissue" with respect to understanding the pathophysiology of neurodevelopmental disorders, it has the potential to serve as an accessible biomarker of disease- and treatment-related changes in the brain. METHODS Half of the KS1 and wildtype mice were treated with 14 days of AR-42. Following treatment, fixed brain samples were imaged using MRI to calculate regional volumes. Blood was assayed for genome-wide DNAm at over 285,000 CpG sites using the Illumina Infinium Mouse Methylation array. DNAm patterns and brain volumes were analyzed in the four groups of animals: wildtype untreated, wildtype AR-42 treated, KS1 untreated and KS1 AR-42 treated. RESULTS We defined a DNAm signature in the blood of KS1 mice, that overlapped with the human KS1 DNAm signature. We also found a striking 10% decrease in total brain volume in untreated KS1 mice compared to untreated wildtype, which correlated with DNAm levels in a subset KS1 signature sites, suggesting that disease severity may be reflected in blood DNAm. Treatment with AR-42 ameliorated DNAm aberrations in KS1 mice at a small number of signature sites. CONCLUSIONS As this treatment impacts both neurological deficits and blood DNAm in mice, future KS clinical trials in humans could be used to assess blood DNAm as an early biomarker of therapeutic efficacy.
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Affiliation(s)
| | - Teresa Romeo Luperchio
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Jacob Ellegood
- Mouse Imaging Centre (MICe), Hospital for Sick Children, Toronto, Canada
| | - Eric Chater-Diehl
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, Canada
| | - Jason P Lerch
- Mouse Imaging Centre (MICe), Hospital for Sick Children, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Wellcome Centre for Integrative Neuroimaging, The University of Oxford, Oxford, UK
- Nuffield Department of Clinical Neuroscience, The University of Oxford, Oxford, UK
| | - Hans Tomas Bjornsson
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, USA
- Faculty of Medicine, University of Iceland, Reykjavík, Iceland
- Landspitali University Hospital, Reykjavík, Iceland
| | - Rosanna Weksberg
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, Canada.
- Division of Clinical and Metabolic Genetics, Hospital for Sick Children, Toronto, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, Canada.
- Institute of Medical Science, University of Toronto, Toronto, Canada.
- Department of Paediatrics, University of Toronto, Toronto, ON, Canada.
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8
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Boukas L, Luperchio TR, Razi A, Hansen KD, Bjornsson HT. Neuron-specific chromatin disruption at CpG islands and aging-related regions in Kabuki syndrome mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.01.551456. [PMID: 37577516 PMCID: PMC10418197 DOI: 10.1101/2023.08.01.551456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Many Mendelian developmental disorders caused by coding variants in epigenetic regulators have now been discovered. Epigenetic regulators are broadly expressed, and each of these disorders typically exhibits phenotypic manifestations from many different organ systems. An open question is whether the chromatin disruption - the root of the pathogenesis - is similar in the different disease-relevant cell types. This is possible in principle, since all these cell-types are subject to effects from the same causative gene, that has the same kind of function (e.g. methylates histones) and is disrupted by the same germline variant. We focus on mouse models for Kabuki syndrome types 1 and 2, and find that the chromatin accessibility abnormalities in neurons are mostly distinct from those in B or T cells. This is not because the neuronal abnormalities occur at regulatory elements that are only active in neurons. Neurons, but not B or T cells, show preferential chromatin disruption at CpG islands and at regulatory elements linked to aging. A sensitive analysis reveals that the regions disrupted in B/T cells do exhibit chromatin accessibility changes in neurons, but these are very subtle and of uncertain functional significance. Finally, we are able to identify a small set of regulatory elements disrupted in all three cell types. Our findings reveal the cellular-context-specific effect of variants in epigenetic regulators, and suggest that blood-derived "episignatures" may not be well-suited for understanding the mechanistic basis of neurodevelopment in Mendelian disorders of the epigenetic machinery.
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Affiliation(s)
- Leandros Boukas
- Department of Pediatrics, Children’s National Hospital
- Department of Genetic Medicine, Johns Hopkins University School of Medicine
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health
| | | | - Afrooz Razi
- Department of Genetic Medicine, Johns Hopkins University School of Medicine
| | - Kasper D. Hansen
- Department of Genetic Medicine, Johns Hopkins University School of Medicine
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health
- Department of Biomedical Engineering, Johns Hopkins School of Medicine
| | - Hans T. Bjornsson
- Department of Genetic Medicine, Johns Hopkins University School of Medicine
- Department of Pediatrics, Johns Hopkins University School of Medicine
- Faculty of Medicine, University of Iceland
- Landspitali University Hospital
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9
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Ritchie FD, Lizarraga SB. The role of histone methyltransferases in neurocognitive disorders associated with brain size abnormalities. Front Neurosci 2023; 17:989109. [PMID: 36845425 PMCID: PMC9950662 DOI: 10.3389/fnins.2023.989109] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 01/17/2023] [Indexed: 02/12/2023] Open
Abstract
Brain size is controlled by several factors during neuronal development, including neural progenitor proliferation, neuronal arborization, gliogenesis, cell death, and synaptogenesis. Multiple neurodevelopmental disorders have co-morbid brain size abnormalities, such as microcephaly and macrocephaly. Mutations in histone methyltransferases that modify histone H3 on Lysine 36 and Lysine 4 (H3K36 and H3K4) have been identified in neurodevelopmental disorders involving both microcephaly and macrocephaly. H3K36 and H3K4 methylation are both associated with transcriptional activation and are proposed to sterically hinder the repressive activity of the Polycomb Repressor Complex 2 (PRC2). During neuronal development, tri-methylation of H3K27 (H3K27me3) by PRC2 leads to genome wide transcriptional repression of genes that regulate cell fate transitions and neuronal arborization. Here we provide a review of neurodevelopmental processes and disorders associated with H3K36 and H3K4 histone methyltransferases, with emphasis on processes that contribute to brain size abnormalities. Additionally, we discuss how the counteracting activities of H3K36 and H3K4 modifying enzymes vs. PRC2 could contribute to brain size abnormalities which is an underexplored mechanism in relation to brain size control.
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Petrin AL, Zeng E, Thomas MA, Moretti-Ferreira D, Marazita ML, Xie XJ, Murray JC, Moreno-Uribe LM. DNA methylation differences in monozygotic twins with Van der Woude syndrome. FRONTIERS IN DENTAL MEDICINE 2023; 4:1120948. [PMID: 36936396 PMCID: PMC10019782 DOI: 10.3389/fdmed.2023.1120948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023] Open
Abstract
Introduction Van der Woude Syndrome (VWS) is an autosomal dominant disorder responsible for 2% of all syndromic orofacial clefts (OFCs) with IRF6 being the primary causal gene (70%). Cases may present with lip pits and either cleft lip, cleft lip with cleft palate, or cleft palate, with marked phenotypic discordance even among individuals carrying the same mutation. This suggests that genetic or epigenetic modifiers may play additional roles in the syndrome's etiology and variability in expression. We report the first DNA methylation profiling of 2 pairs of monozygotic twins with VWS. Our goal is to explore epigenetic contributions to VWS etiology and variable phenotypic expressivity by comparing DNAm profiles in both twin pairs. While the mutations that cause VWS in these twins are known, the additional mechanism behind their phenotypic risk and variability in expression remains unclear. Methods We generated whole genome DNAm data for both twin pairs. Differentially methylated positions (DMPs) were selected based on: (1) a coefficient of variation in DNAm levels in unaffected individuals < 20%, and (2) intra-twin pair absolute difference in DNAm levels >5% (delta beta > | 0.05|). We then divided the DMPs in two subgroups for each twin pair for further analysis: (1) higher methylation levels in twin A (Twin A > Twin B); and (2) higher methylation levels in twin B (Twin B >Twin A). Results and Discussion Gene ontology analysis revealed a list of enriched genes that showed significant differential DNAm, including clef-associated genes. Among the cleft-associated genes, TP63 was the most significant hit (p=7.82E-12). Both twin pairs presented differential DNAm levels in CpG sites in/near TP63 (Twin 1A > Twin 1B and Twin 2A < Twin 2B). The genes TP63 and IRF6 function in a biological regulatory loop to coordinate epithelial proliferation and differentiation in a process that is critical for palatal fusion. The effects of the causal mutations in IRF6 can be further impacted by epigenetic dysregulation of IRF6 itself, or genes in its pathway. Our data shows evidence that changes in DNAm is a plausible mechanism that can lead to markedly distinct phenotypes, even among individuals carrying the same mutation.
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Affiliation(s)
- A. L. Petrin
- College of Dentistry and Dental Clinics, University of Iowa, Iowa, IA, United States
- CORRESPONDENCE A. L. Petrin
| | - E. Zeng
- College of Dentistry and Dental Clinics, University of Iowa, Iowa, IA, United States
| | - M. A. Thomas
- Departments of Medical Genetics and Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - D. Moretti-Ferreira
- Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - M. L. Marazita
- Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, United States
| | - X. J. Xie
- College of Dentistry and Dental Clinics, University of Iowa, Iowa, IA, United States
| | - J. C. Murray
- Carver College of Medicine, University of Iowa, Iowa, IA, United States
| | - L. M. Moreno-Uribe
- College of Dentistry and Dental Clinics, University of Iowa, Iowa, IA, United States
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11
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Usluer E, Sayın GY, Güneş N, Kasap B, Tüysüz B. Investigation of genetic and phenotypic heterogeneity in 37 Turkish patients with Kabuki and Kabuki-like phenotype. Am J Med Genet A 2022; 188:2976-2987. [PMID: 36097644 DOI: 10.1002/ajmg.a.62944] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 06/16/2022] [Accepted: 07/20/2022] [Indexed: 01/31/2023]
Abstract
Kabuki syndrome (KS) is a rare disorder characterized by distinct face, persistent fingertip pads, and intellectual disability (ID) caused by mutation in KMT2D (56%-76%) or KDM6A (5%-8%). Thirty-seven children aged 1-16 years who followed for median of 6.8 years were included in this study, which aimed to investigate the genetic and clinical characteristics of KS patients. KMT2D and KDM6A were evaluated by sequencing and multiplex-ligation-dependent probe amplification in 32 patients. Twenty-one pathogenic variants in KMT2D, of which 17 were truncated and nine were novel, one frame-shift novel variant in KDM6A were identified. The molecular diagnosis rate was 68.7% (22/32). In the whole-exome sequencing analysis performed in the remaining patients, no pathogenic variant that could cause any disease was detected. All patients had ID; 43.2% were severe and moderate. We observed that facial features that became more prominent with age were enough for a possible diagnosis of KS in infancy. The frequencies of facial features, cardiac and renal anomalies, short stature, microcephaly, and epilepsy did not differ depending on whether they had truncating or nontruncating variants or were in variant-negative KS-like group. This study has expanded clinical features of the disease, as well as identified new variants in genes causing KS.
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Affiliation(s)
- Esra Usluer
- Department of Pediatric Genetics, Istanbul University-Cerrahpasa, Cerrahpasa Faculty of Medicine, Istanbul, Turkey
| | - Gözde Yeşil Sayın
- Department of Medical Genetics, Bezmialem University, Medical School, Istanbul, Turkey
| | - Nilay Güneş
- Department of Pediatric Genetics, Istanbul University-Cerrahpasa, Cerrahpasa Faculty of Medicine, Istanbul, Turkey
| | - Buşra Kasap
- Department of Pediatric Genetics, Istanbul University-Cerrahpasa, Cerrahpasa Faculty of Medicine, Istanbul, Turkey
| | - Beyhan Tüysüz
- Department of Pediatric Genetics, Istanbul University-Cerrahpasa, Cerrahpasa Faculty of Medicine, Istanbul, Turkey
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12
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Identification of unique DNA methylation sites in Kabuki syndrome using whole genome bisulfite sequencing and targeted hybridization capture followed by enzymatic methylation sequencing. J Hum Genet 2022; 67:711-720. [PMID: 36167771 DOI: 10.1038/s10038-022-01083-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 09/01/2022] [Accepted: 09/11/2022] [Indexed: 11/08/2022]
Abstract
BACKGROUND Kabuki syndrome (KS) is a congenital malformation syndrome caused by mutations in the KMT2D and KDM6A genes that encode histone modification enzymes. Although KS is considered a single gene disorder, its symptoms vary widely. Recently, disease-specific DNA methylation patterns, or episignatures, have been recognized and used as a diagnostic tool for KS. Because of various crosstalk mechanisms between histone modifications and DNA methylation, DNA methylation analysis may have high potential for investigations into the pathogenesis of KS. RESULTS In this study, we investigated altered CpG-methylation sites that were specific to KS to find important genes associated with the various phenotypes or pathogenesis of KS. Whole genome bisulfite sequencing (WGBS) was performed to select target CpG islands, and enzymatic conversion technology was applied after hybridization capture to confirm KS-specific episignatures of 130 selected differently methylated target regions (DMTRs) in DNA samples from the 65 participants, 31 patients with KS and 34 unaffected individuals, in this study. We identified 26 candidate genes in 22 DMTRs that may be associated with KS. Our results indicate that disease-specific methylation sites can be identified from a small number of WGBS samples, and hybridization capture followed by enzymatic methylation sequencing can simultaneously test the sites. CONCLUSIONS Although DNA methylation can be tissue-specific, our results suggest that methylation profiling of DNA extracted from peripheral blood may be a powerful approach to study the pathogenesis of diseases.
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13
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Montano C, Britton JF, Harris JR, Kerkhof J, Barnes BT, Lee JA, Sadikovic B, Sobreira N, Fahrner JA. Genome-wide DNA methylation profiling confirms a case of low-level mosaic Kabuki syndrome 1. Am J Med Genet A 2022; 188:2217-2225. [PMID: 35384273 PMCID: PMC9321966 DOI: 10.1002/ajmg.a.62754] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/22/2022] [Accepted: 03/18/2022] [Indexed: 12/27/2022]
Abstract
Kabuki syndrome is a Mendelian disorder of the epigenetic machinery characterized by typical dysmorphic features, intellectual disability, and postnatal growth deficiency. Pathogenic variants in the genes encoding the chromatin modifiers KMT2D and KDM6A are responsible for Kabuki syndrome 1 (KS1) and Kabuki syndrome 2 (KS2), respectively. In addition, 11 cases of KS1 caused by mosaic variants in KMT2D have been reported in the literature. Some of these individuals display milder craniofacial and growth phenotypes, and most do not have congenital heart defects. We report the case of an infant with severe hypoplastic left heart syndrome with mitral atresia and aortic atresia (HLHS MA-AA), pulmonary vein stenosis, and atypical facies with a somatic mosaic de novo nonsense variant in KMT2D (c.8200C>T, p.R2734*) identified on trio exome sequencing of peripheral blood and present in 11.2% of sequencing reads. KS was confirmed with EpiSign, a diagnostic genome-wide DNA methylation platform used to identify epigenetic signatures. This case suggests that use of this newly available clinical test can guide the interpretation of low-level mosaic variants identified through sequencing and suggests a new lower limit of mosaicism in whole blood required for a diagnosis of KS.
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Affiliation(s)
- Carolina Montano
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jacquelyn F Britton
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jacqueline R Harris
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, Maryland, USA
| | - Jennifer Kerkhof
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada
| | - Benjamin T Barnes
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jennifer A Lee
- Greenwood Genetic Center, Greenwood, South Carolina, USA
| | - Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Nara Sobreira
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jill A Fahrner
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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14
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Lee S, Ochoa E, Barwick K, Cif L, Rodger F, Docquier F, Pérez-Dueñas B, Clark G, Martin E, Banka S, Kurian MA, Maher ER. Comparison of methylation episignatures in KMT2B- and KMT2D-related human disorders. Epigenomics 2022; 14:537-547. [PMID: 35506254 DOI: 10.2217/epi-2021-0521] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim & methods: To investigate peripheral blood methylation episignatures in KMT2B-related dystonia (DYT-KMT2B), the authors undertook genome-wide methylation profiling of ∼2 M CpGs using a next-generation sequencing-based assay and compared the findings with those in controls and patients with KMT2D-related Kabuki syndrome type 1 (KS1). Results: A total of 1812 significantly differentially methylated CpG positions (false discovery rate < 0.05) were detected in DYT-KMT2B samples compared with controls. Multi-dimensional scaling analysis showed that the 10 DYT-KMT2B samples clustered together and separately from 29 controls and 10 with pathogenic variants in KMT2D. The authors found that most differentially methylated CpG positions were specific to one disorder and that all (DYT-KMT2B) and most (Kabuki syndrome type 1) methylation alterations in CpG islands were gain of methylation events. Conclusion: Using sensitive methylation profiling methodology, the authors replicated recent reports of a methylation episignature for DYT-KMT2B. These findings will facilitate the development of episignature-based assays to improve diagnostic accuracy.
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Affiliation(s)
- Sunwoo Lee
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Eguzkine Ochoa
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Katy Barwick
- Developmental Neurosciences, UCL Great Ormond Street Institute of Child Health, Zayed Centre for Research into Rare Disease in Children, London, WC1N 1DZ, UK
| | - Laura Cif
- Departement de Neurochirurgie, Unite des Pathologies Cerebrales Resistantes, Unite de Recherche sur les Comportements et Mouvements Anormaux, Hopital Gui de Chauliac, Centre Hospitalier Régional Montpellier, Montpellier, France, & Faculte de Medecine, Universite de Montpellier, France
| | - Fay Rodger
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK.,Stratified Medicine Core Laboratory NGS Hub, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - France Docquier
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK.,Stratified Medicine Core Laboratory NGS Hub, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Belén Pérez-Dueñas
- Developmental Neurosciences, UCL Great Ormond Street Institute of Child Health, Zayed Centre for Research into Rare Disease in Children, London, WC1N 1DZ, UK
| | - Graeme Clark
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK.,Stratified Medicine Core Laboratory NGS Hub, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Ezequiel Martin
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK.,Stratified Medicine Core Laboratory NGS Hub, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Siddharth Banka
- Division of Evolution, Infection & Genomics, School of Biological Sciences, Faculty of Biology, Medicine & Health, The University of Manchester, Manchester, UK, & Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University Foundation NHS Trust, Health Innovation Manchester, Manchester, M13 9WL, UK
| | - Manju A Kurian
- Developmental Neurosciences, UCL Great Ormond Street Institute of Child Health, Zayed Centre for Research into Rare Disease in Children, London, WC1N 1DZ, UK
| | - Eamonn R Maher
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
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15
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Castiglioni S, Di Fede E, Bernardelli C, Lettieri A, Parodi C, Grazioli P, Colombo EA, Ancona S, Milani D, Ottaviano E, Borghi E, Massa V, Ghelma F, Vignoli A, Lesma E, Gervasini C. KMT2A: Umbrella Gene for Multiple Diseases. Genes (Basel) 2022; 13:genes13030514. [PMID: 35328068 PMCID: PMC8949091 DOI: 10.3390/genes13030514] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 03/10/2022] [Accepted: 03/12/2022] [Indexed: 02/05/2023] Open
Abstract
KMT2A (Lysine methyltransferase 2A) is a member of the epigenetic machinery, encoding a lysine methyltransferase responsible for the transcriptional activation through lysine 4 of histone 3 (H3K4) methylation. KMT2A has a crucial role in gene expression, thus it is associated to pathological conditions when found mutated. KMT2A germinal mutations are associated to Wiedemann–Steiner syndrome and also in patients with initial clinical diagnosis of several other chromatinopathies (i.e., Coffin–Siris syndromes, Kabuki syndrome, Cornelia De Lange syndrome, Rubinstein–Taybi syndrome), sharing an overlapping phenotype. On the other hand, KMT2A somatic mutations have been reported in several tumors, mainly blood malignancies. Due to its evolutionary conservation, the role of KMT2A in embryonic development, hematopoiesis and neurodevelopment has been explored in different animal models, and in recent decades, epigenetic treatments for disorders linked to KMT2A dysfunction have been extensively investigated. To note, pharmaceutical compounds acting on tumors characterized by KMT2A mutations have been formulated, and even nutritional interventions for chromatinopathies have become the object of study due to the role of microbiota in epigenetic regulation.
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Affiliation(s)
- Silvia Castiglioni
- Department of Health Sciences, Università Degli Studi di Milano, 20142 Milan, Italy; (S.C.); (E.D.F.); (C.B.); (A.L.); (C.P.); (P.G.); (E.A.C.); (S.A.); (E.O.); (E.B.); (V.M.); (F.G.); (A.V.); (E.L.)
| | - Elisabetta Di Fede
- Department of Health Sciences, Università Degli Studi di Milano, 20142 Milan, Italy; (S.C.); (E.D.F.); (C.B.); (A.L.); (C.P.); (P.G.); (E.A.C.); (S.A.); (E.O.); (E.B.); (V.M.); (F.G.); (A.V.); (E.L.)
| | - Clara Bernardelli
- Department of Health Sciences, Università Degli Studi di Milano, 20142 Milan, Italy; (S.C.); (E.D.F.); (C.B.); (A.L.); (C.P.); (P.G.); (E.A.C.); (S.A.); (E.O.); (E.B.); (V.M.); (F.G.); (A.V.); (E.L.)
| | - Antonella Lettieri
- Department of Health Sciences, Università Degli Studi di Milano, 20142 Milan, Italy; (S.C.); (E.D.F.); (C.B.); (A.L.); (C.P.); (P.G.); (E.A.C.); (S.A.); (E.O.); (E.B.); (V.M.); (F.G.); (A.V.); (E.L.)
- “Aldo Ravelli” Center for Neurotechnology and Experimental Brain Therapeutics, Università Degli Studi di Milano, 20142 Milan, Italy
| | - Chiara Parodi
- Department of Health Sciences, Università Degli Studi di Milano, 20142 Milan, Italy; (S.C.); (E.D.F.); (C.B.); (A.L.); (C.P.); (P.G.); (E.A.C.); (S.A.); (E.O.); (E.B.); (V.M.); (F.G.); (A.V.); (E.L.)
| | - Paolo Grazioli
- Department of Health Sciences, Università Degli Studi di Milano, 20142 Milan, Italy; (S.C.); (E.D.F.); (C.B.); (A.L.); (C.P.); (P.G.); (E.A.C.); (S.A.); (E.O.); (E.B.); (V.M.); (F.G.); (A.V.); (E.L.)
| | - Elisa Adele Colombo
- Department of Health Sciences, Università Degli Studi di Milano, 20142 Milan, Italy; (S.C.); (E.D.F.); (C.B.); (A.L.); (C.P.); (P.G.); (E.A.C.); (S.A.); (E.O.); (E.B.); (V.M.); (F.G.); (A.V.); (E.L.)
| | - Silvia Ancona
- Department of Health Sciences, Università Degli Studi di Milano, 20142 Milan, Italy; (S.C.); (E.D.F.); (C.B.); (A.L.); (C.P.); (P.G.); (E.A.C.); (S.A.); (E.O.); (E.B.); (V.M.); (F.G.); (A.V.); (E.L.)
| | - Donatella Milani
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università Degli Studi di Milano, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy;
| | - Emerenziana Ottaviano
- Department of Health Sciences, Università Degli Studi di Milano, 20142 Milan, Italy; (S.C.); (E.D.F.); (C.B.); (A.L.); (C.P.); (P.G.); (E.A.C.); (S.A.); (E.O.); (E.B.); (V.M.); (F.G.); (A.V.); (E.L.)
| | - Elisa Borghi
- Department of Health Sciences, Università Degli Studi di Milano, 20142 Milan, Italy; (S.C.); (E.D.F.); (C.B.); (A.L.); (C.P.); (P.G.); (E.A.C.); (S.A.); (E.O.); (E.B.); (V.M.); (F.G.); (A.V.); (E.L.)
| | - Valentina Massa
- Department of Health Sciences, Università Degli Studi di Milano, 20142 Milan, Italy; (S.C.); (E.D.F.); (C.B.); (A.L.); (C.P.); (P.G.); (E.A.C.); (S.A.); (E.O.); (E.B.); (V.M.); (F.G.); (A.V.); (E.L.)
- “Aldo Ravelli” Center for Neurotechnology and Experimental Brain Therapeutics, Università Degli Studi di Milano, 20142 Milan, Italy
| | - Filippo Ghelma
- Department of Health Sciences, Università Degli Studi di Milano, 20142 Milan, Italy; (S.C.); (E.D.F.); (C.B.); (A.L.); (C.P.); (P.G.); (E.A.C.); (S.A.); (E.O.); (E.B.); (V.M.); (F.G.); (A.V.); (E.L.)
| | - Aglaia Vignoli
- Department of Health Sciences, Università Degli Studi di Milano, 20142 Milan, Italy; (S.C.); (E.D.F.); (C.B.); (A.L.); (C.P.); (P.G.); (E.A.C.); (S.A.); (E.O.); (E.B.); (V.M.); (F.G.); (A.V.); (E.L.)
- Child NeuroPsychiatry Unit, ASST Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy
| | - Elena Lesma
- Department of Health Sciences, Università Degli Studi di Milano, 20142 Milan, Italy; (S.C.); (E.D.F.); (C.B.); (A.L.); (C.P.); (P.G.); (E.A.C.); (S.A.); (E.O.); (E.B.); (V.M.); (F.G.); (A.V.); (E.L.)
| | - Cristina Gervasini
- Department of Health Sciences, Università Degli Studi di Milano, 20142 Milan, Italy; (S.C.); (E.D.F.); (C.B.); (A.L.); (C.P.); (P.G.); (E.A.C.); (S.A.); (E.O.); (E.B.); (V.M.); (F.G.); (A.V.); (E.L.)
- “Aldo Ravelli” Center for Neurotechnology and Experimental Brain Therapeutics, Università Degli Studi di Milano, 20142 Milan, Italy
- Correspondence: ; Tel.: +39-0250-3230-28
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16
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Janssen SM, Lorincz MC. Interplay between chromatin marks in development and disease. Nat Rev Genet 2022; 23:137-153. [PMID: 34608297 DOI: 10.1038/s41576-021-00416-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2021] [Indexed: 02/07/2023]
Abstract
DNA methylation (DNAme) and histone post-translational modifications (PTMs) have important roles in transcriptional regulation. Although many reports have characterized the functions of such chromatin marks in isolation, recent genome-wide studies reveal surprisingly complex interactions between them. Here, we focus on the interplay between DNAme and methylation of specific lysine residues on the histone H3 tail. We describe the impact of genetic perturbation of the relevant methyltransferases in the mouse on the landscape of chromatin marks as well as the transcriptome. In addition, we discuss the specific neurodevelopmental growth syndromes and cancers resulting from pathogenic mutations in the human orthologues of these genes. Integrating these observations underscores the fundamental importance of crosstalk between DNA and histone H3 methylation in development and disease.
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Affiliation(s)
- Sanne M Janssen
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Matthew C Lorincz
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada.
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17
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Foroutan A, Haghshenas S, Bhai P, Levy MA, Kerkhof J, McConkey H, Niceta M, Ciolfi A, Pedace L, Miele E, Genevieve D, Heide S, Alders M, Zampino G, Merla G, Fradin M, Bieth E, Bonneau D, Dieterich K, Fergelot P, Schaefer E, Faivre L, Vitobello A, Maitz S, Fischetto R, Gervasini C, Piccione M, van de Laar I, Tartaglia M, Sadikovic B, Lebre AS. Clinical Utility of a Unique Genome-Wide DNA Methylation Signature for KMT2A-Related Syndrome. Int J Mol Sci 2022; 23:ijms23031815. [PMID: 35163737 PMCID: PMC8836705 DOI: 10.3390/ijms23031815] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/26/2022] [Accepted: 01/31/2022] [Indexed: 12/28/2022] Open
Abstract
Wiedemann–Steiner syndrome (WDSTS) is a Mendelian syndromic intellectual disability (ID) condition associated with hypertrichosis cubiti, short stature, and characteristic facies caused by pathogenic variants in the KMT2A gene. Clinical features can be inconclusive in mild and unusual WDSTS presentations with variable ID (mild to severe), facies (typical or not) and other associated malformations (bone, cerebral, renal, cardiac and ophthalmological anomalies). Interpretation and classification of rare KMT2A variants can be challenging. A genome-wide DNA methylation episignature for KMT2A-related syndrome could allow functional classification of variants and provide insights into the pathophysiology of WDSTS. Therefore, we assessed genome-wide DNA methylation profiles in a cohort of 60 patients with clinical diagnosis for WDSTS or Kabuki and identified a unique highly sensitive and specific DNA methylation episignature as a molecular biomarker of WDSTS. WDSTS episignature enabled classification of variants of uncertain significance in the KMT2A gene as well as confirmation of diagnosis in patients with clinical presentation of WDSTS without known genetic variants. The changes in the methylation profile resulting from KMT2A mutations involve global reduction in methylation in various genes, including homeobox gene promoters. These findings provide novel insights into the molecular etiology of WDSTS and explain the broad phenotypic spectrum of the disease.
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Affiliation(s)
- Aidin Foroutan
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada; (A.F.); (S.H.)
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada; (P.B.); (M.A.L.); (J.K.); (H.M.)
| | - Sadegheh Haghshenas
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada; (A.F.); (S.H.)
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada; (P.B.); (M.A.L.); (J.K.); (H.M.)
| | - Pratibha Bhai
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada; (P.B.); (M.A.L.); (J.K.); (H.M.)
| | - Michael A. Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada; (P.B.); (M.A.L.); (J.K.); (H.M.)
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada; (P.B.); (M.A.L.); (J.K.); (H.M.)
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada; (P.B.); (M.A.L.); (J.K.); (H.M.)
| | - Marcello Niceta
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (M.N.); (A.C.); (M.T.)
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (M.N.); (A.C.); (M.T.)
| | - Lucia Pedace
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (L.P.); (E.M.)
| | - Evelina Miele
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (L.P.); (E.M.)
| | - David Genevieve
- Medical Genetic Department for Rare Diseases and Personalized Medicine, Reference Center AD SOOR, AnDDI-RARE, Groupe DI, Inserm U1183—Institute for Regenerative Medicine and Biotherapy, Montpellier University, Centre Hospitalier Universitaire de Montpellier, 34090 Montpellier, France;
| | - Solveig Heide
- Department of Genetics, Referral Center for Intellectual Disabilities, APHP Sorbonne University, Pitié Salpêtrière Hospital, 75013 Paris, France;
| | - Mariëlle Alders
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
| | - Giuseppe Zampino
- Center for Rare Diseases and Congenital Defects, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168 Rome, Italy;
- Facoltà di Medicina e Chirurgia, Università Cattolica del S. Cuore, 20123 Roma, Italy
| | - Giuseppe Merla
- Department of Molecular Medicine and Medical Biotechnology, Università di Napoli “Federico II”, 80131 Naples, Italy;
- Laboratory of Regulatory and Functional Genomics, Fondazione Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy
| | - Mélanie Fradin
- Service de Génétique, CHU de Rennes, 35203 Rennes, France;
| | - Eric Bieth
- Medical Genetics Department, University of Angers, CHU Angers, 49000 Angers, France;
| | - Dominique Bonneau
- Department of genetics, CHU d’Angers, 49000 Angers, France and MitoVasc, UMR CNRS 6015-INSERM 1083, University of Angers, 49055 Angers, France;
| | - Klaus Dieterich
- CHU Grenoble Alpes, Inserm, U1209, Institute of Advanced Biosciences, Université Grenoble Alpes, 38000 Grenoble, France;
| | - Patricia Fergelot
- Medical Genetics Department, Inserm U1211, Reference Center AD SOOR, AnDDI-RARE, Bordeaux University, Centre Hospitalier Universitaire de Bordeaux, 33076 Bordeaux, France;
| | - Elise Schaefer
- Service de Génétique Médicale—Institut de Génétique Médicale d’Alsace—Hôpitaux Universitaires de Strasbourg, 67091 Strasbourg, France;
| | - Laurence Faivre
- Inserm, UMR1231, Equipe GAD, Bâtiment B3, Université de Bourgogne Franche Comté, 15 boulevard du Maréchal de Lattre de Tassigny, 21000 Dijon, France; (L.F.); (A.V.)
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, Department of Medical Genetics, Dijon University Hospital, 21000 Dijon, France
| | - Antonio Vitobello
- Inserm, UMR1231, Equipe GAD, Bâtiment B3, Université de Bourgogne Franche Comté, 15 boulevard du Maréchal de Lattre de Tassigny, 21000 Dijon, France; (L.F.); (A.V.)
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, Department of Medical Genetics, Dijon University Hospital, 21000 Dijon, France
| | - Silvia Maitz
- Clinical Pediatric Genetics Unit, Pediatrics Clinics, MBBM Foundation, S. Gerardo Hospital, 20900 Monza, Italy;
| | - Rita Fischetto
- Clinical Genetics Unit, Department of Pediatric Medicine, Giovanni XXIII Children’s Hospital, 02115 Bari, Italy;
| | - Cristina Gervasini
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milan, Italy;
| | - Maria Piccione
- Department of Sciences for Health Promotion and Mother and Child Care “G. D’Alessandro”, University of Palermo, 90127 Palermo, Italy;
| | - Ingrid van de Laar
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands;
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (M.N.); (A.C.); (M.T.)
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada; (A.F.); (S.H.)
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada; (P.B.); (M.A.L.); (J.K.); (H.M.)
- Correspondence: (B.S.); (A.-S.L.)
| | - Anne-Sophie Lebre
- Team Physiopathologie des Maladies Psychiatriques, GDR3557-Institut de Psychiatrie, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Université de Paris, 75006 Paris, France
- Centre Hospitalier Universitaire de Reims, Pôle de Biologie Médicale et Pathologie, Service de GénéTique, 51100 Reims, France
- Correspondence: (B.S.); (A.-S.L.)
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18
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Shinko Y, Okazaki S, Otsuka I, Horai T, Kim S, Tanifuji T, Hishimoto A. Accelerated epigenetic age and shortened telomere length based on DNA methylation in Nicolaides-Baraitser syndrome. Mol Genet Genomic Med 2022; 10:e1876. [PMID: 35092358 PMCID: PMC8922957 DOI: 10.1002/mgg3.1876] [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: 04/07/2021] [Revised: 07/06/2021] [Accepted: 01/06/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Nicolaides-Baraitser syndrome (NCBRS) is a rare disorder characterized by neurodevelopmental delays, seizures, and diverse physical characteristics. The DNA methylation (DNAm) profile in NCBRS is significantly different. DNAm is linked to the biological aging of cells and the health risks associated with biological aging. In this study, we examined changes in biological ages in NCBRS to provide insights into the prognosis and health risks of NCBRS. METHODS We used a publicly available dataset to examine biological aging in NCBRS using DNAm-based epigenetic ages, such as PhenoAge and GrimAge, as well as DNAm-based estimator of telomere length (DNAmTL). We investigated 12 cases, clinically diagnosed as NCBRS, and 27 controls. RESULTS Compared to controls, NCBRS cases exhibited significantly accelerated PhenoAge and GrimAge as well as significantly shortened DNAmTL. CONCLUSION These results suggest an acceleration of biological aging in NCBRS and provide insights into the prognosis and health risks of NCBRS.
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Affiliation(s)
- Yutaka Shinko
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Satoshi Okazaki
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Ikuo Otsuka
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Tadasu Horai
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Saehyeon Kim
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Takaki Tanifuji
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Akitoyo Hishimoto
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan.,Department of Psychiatry, Yokohama City University Graduate School of Medicine, Yokohama, Japan
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19
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Hutchison DM, Duffens A, Yale K, Park A, Cardenas K, Mesinkovska NA. Eyelash trichomegaly: a systematic review of acquired and congenital aetiologies of lengthened lashes. J Eur Acad Dermatol Venereol 2021; 36:536-546. [PMID: 34919300 DOI: 10.1111/jdv.17877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 10/05/2021] [Accepted: 11/10/2021] [Indexed: 02/01/2023]
Abstract
Long eyelashes have been popularized and many commercially available products exist to achieve eyelash growth as a desired cosmetic effect. Eyelash trichomegaly may be induced by medications, procedures, or be related to medical conditions; however, the exact mechanisms that govern eyelash growth are not well elucidated. This study aims to identify and summarize aetiologies associated with eyelash trichomegaly. We report a systematic review of 148 clinical trials, prospective and retrospective studies, and case reports describing all evidence-based potential aetiologies of eyelash trichomegaly obtained from the Medline/PubMed and Cochrane Library through January 2021. Inclusion criteria were defined as (i) human studies involving congenital and acquired diseases in which eyelash trichomegaly is a characteristic or (ii) assessment of trichomegaly as an adverse or desired effect of a medication or procedure. Exclusion criteria included: animal studies, articles not available in English, outcomes unrelated to eyelash trichomegaly, and secondary review articles. Pharmacologic agents associated with eyelash trichomegaly included prostaglandin analogues (15-keto fluprostenol isopropyl ester, bimatoprost, latanoprost, and travoprost), epidermal growth factor receptor inhibitors (cetuximab, erlotinib, and panitumumab), interferon-alpha, and calcineurin inhibitors (tacrolimus and cyclosporine). Surgical procedures of the eyelid, as well as allergic rhinitis, atopic dermatitis, HIV, ichthyosis vulgaris (IV), uveitis, and vernal keratoconjunctivitis were also associated with increased eyelash growth. Congenital disorders associated with lengthened eyelashes included Cantú syndrome, CHOPS syndrome, Coffin-Siris syndrome, congenital heart disease, Cornelia de Lange syndrome, Costello syndrome, familial trichomegaly, Floating Harbor syndrome, Hermansky-Pudlak syndrome, Kabuki-Makeup syndrome, KBG syndrome, Oliver-McFarlane syndrome, Rubinstein-Taybi syndrome, and Smith-Magenis syndrome. While the most common cause of eyelash trichomegaly is topical bimatoprost use, better understanding of pathways implicated in eyelash trichomegaly may lead to the discovery of additional medications to stimulate eyelash growth and create avenues for future therapeutic interventions.
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Affiliation(s)
- D M Hutchison
- Department of Dermatology, University of California Irvine, Irvine, CA, USA.,Beckman Laser Institute, University of California Irvine, Irvine, CA, USA
| | - A Duffens
- Department of Dermatology, University of California Irvine, Irvine, CA, USA
| | - K Yale
- Department of Dermatology, University of California Irvine, Irvine, CA, USA
| | - A Park
- Beckman Laser Institute, University of California Irvine, Irvine, CA, USA
| | - K Cardenas
- Department of Dermatology, University of California Irvine, Irvine, CA, USA
| | - N A Mesinkovska
- Department of Dermatology, University of California Irvine, Irvine, CA, USA.,Beckman Laser Institute, University of California Irvine, Irvine, CA, USA
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20
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Sakaria RP, Zaveri PG, Holtrop S, Zhang J, Brown CW, Pivnick EK. Case Report: An Infant With Kabuki Syndrome, Alobar Holoprosencephaly and Truncus Arteriosus: A Case for Whole Exome Sequencing in Neonates With Congenital Anomalies. Front Genet 2021; 12:766316. [PMID: 34899850 PMCID: PMC8660850 DOI: 10.3389/fgene.2021.766316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/29/2021] [Indexed: 11/13/2022] Open
Abstract
Kabuki syndrome is a rare multiple anomalies syndrome associated with mutations in KMT2D or KDM6A. It is characterized by infantile hypotonia, developmental delay and/or intellectual disability, long palpebral fissures with everted lateral third of the lower eyelids and typical facial features. Intracranial anomalies occur infrequently in patients with KS and holoprosencephaly has only been recently described. Additionally, though congenital heart diseases are common in patients with KS, to our knowledge truncus arteriosus has never been reported in a patient with KS. We present an unusual case of KS in an infant with holoprosencephaly and truncus arteriosus with partial anomalous pulmonary venous return. Duo whole exome sequencing in our patient identified a pathogenic nonsense variant in exon 10 of KMT2D (c.2782C > T; p. Gln928*) establishing the diagnosis. This report further expands the phenotypic spectrum of patients with Kabuki syndrome and emphasizes the utility of performing large scale sequencing in neonates with multiple congenital anomalies.
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Affiliation(s)
- Rishika P Sakaria
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN, United States.,Le Bonheur Children's Hospital, Memphis, TN, United States
| | - Parul G Zaveri
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN, United States.,Le Bonheur Children's Hospital, Memphis, TN, United States
| | | | - Jie Zhang
- Le Bonheur Children's Hospital, Memphis, TN, United States.,Department of Pathology and Laboratory Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Chester W Brown
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN, United States.,Le Bonheur Children's Hospital, Memphis, TN, United States
| | - Eniko K Pivnick
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN, United States.,Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, TN, United States
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21
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Komaki S, Ohmomo H, Hachiya T, Sutoh Y, Ono K, Furukawa R, Umekage S, Otsuka-Yamasaki Y, Tanno K, Sasaki M, Shimizu A. Longitudinal DNA methylation dynamics as a practical indicator in clinical epigenetics. Clin Epigenetics 2021; 13:219. [PMID: 34903243 PMCID: PMC8670275 DOI: 10.1186/s13148-021-01202-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 11/24/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND One of the fundamental assumptions of DNA methylation in clinical epigenetics is that DNA methylation status can change over time with or without interplay with environmental and clinical conditions. However, little is known about how DNA methylation status changes over time under ordinary environmental and clinical conditions. In this study, we revisited the high frequency longitudinal DNA methylation data of two Japanese males (24 time-points within three months) and characterized the longitudinal dynamics. RESULTS The results showed that the majority of CpGs on Illumina HumanMethylation450 BeadChip probe set were longitudinally stable over the time period of three months. Focusing on dynamic and stable CpGs extracted from datasets, dynamic CpGs were more likely to be reported as epigenome-wide association study (EWAS) markers of various traits, especially those of immune- and inflammatory-related traits; meanwhile, the stable CpGs were enriched in metabolism-related genes and were less likely to be EWAS markers, indicating that the stable CpGs are stable both in the short-term within individuals and under various environmental and clinical conditions. CONCLUSIONS This study indicates that CpGs with different stabilities are involved in different functions and traits, and thus, they are potential indicators that can be applied for clinical epigenetic studies to outline underlying mechanisms.
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Affiliation(s)
- Shohei Komaki
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 1-1-1, Idaidori, Yahaba, Iwate, 028-3694, Japan
| | - Hideki Ohmomo
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 1-1-1, Idaidori, Yahaba, Iwate, 028-3694, Japan
| | - Tsuyoshi Hachiya
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 1-1-1, Idaidori, Yahaba, Iwate, 028-3694, Japan
| | - Yoichi Sutoh
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 1-1-1, Idaidori, Yahaba, Iwate, 028-3694, Japan
| | - Kanako Ono
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 1-1-1, Idaidori, Yahaba, Iwate, 028-3694, Japan
| | - Ryohei Furukawa
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 1-1-1, Idaidori, Yahaba, Iwate, 028-3694, Japan.,Department of Biology, Research and Education Center for Natural Sciences, Keio University, 4-1-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8521, Japan
| | - So Umekage
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 1-1-1, Idaidori, Yahaba, Iwate, 028-3694, Japan
| | - Yayoi Otsuka-Yamasaki
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 1-1-1, Idaidori, Yahaba, Iwate, 028-3694, Japan
| | - Kozo Tanno
- Division of Clinical Research and Epidemiology, Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Iwate, Japan.,Department of Hygiene and Preventive Medicine, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Shiwa, Iwate, 028-3694, Japan
| | - Makoto Sasaki
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Iwate, Japan.,Division of Ultrahigh Field MRI, Institute for Biomedical Sciences, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Shiwa, Iwate, 028-3694, Japan
| | - Atsushi Shimizu
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 1-1-1, Idaidori, Yahaba, Iwate, 028-3694, Japan. .,Division of Biomedical Information Analysis, Institute for Biomedical Sciences, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Shiwa, Iwate, 028-3694, Japan.
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22
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Wang S, Bleeck A, Nadif Kasri N, Kleefstra T, van Rhijn JR, Schubert D. SETD1A Mediated H3K4 Methylation and Its Role in Neurodevelopmental and Neuropsychiatric Disorders. Front Mol Neurosci 2021; 14:772000. [PMID: 34803610 PMCID: PMC8595121 DOI: 10.3389/fnmol.2021.772000] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/12/2021] [Indexed: 01/07/2023] Open
Abstract
Posttranslational modification of histones and related gene regulation are shown to be affected in an increasing number of neurological disorders. SETD1A is a chromatin remodeler that influences gene expression through the modulation of mono- di- and trimethylation marks on Histone-H3-Lysine-4 (H3K4me1/2/3). H3K4 methylation is predominantly described to result in transcriptional activation, with its mono- di- and trimethylated forms differentially enriched at promoters or enhancers. Recently, dominant mostly de novo variants in SETD1A have clinically been linked to developmental delay, intellectual disability (DD/ID), and schizophrenia (SCZ). Affected individuals often display both developmental and neuropsychiatric abnormalities. The primary diagnoses are mainly dependent on the age at which the individual is assessed. Investigations in mouse models of SETD1A dysfunction have been able to recapitulate key behavioral features associated with ID and SCZ. Furthermore, functional investigations suggest disrupted synaptic and neuronal network function in these mouse models. In this review, we provide an overview of pre-clinical studies on the role of SETD1A in neuronal development. A better understanding of the pathobiology underlying these disorders may provide novel opportunities for therapeutic intervention. As such, we will discuss possible strategies to move forward in elucidating the genotype-phenotype correlation in SETD1A associated disorders.
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Affiliation(s)
- Shan Wang
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, Netherlands
| | - Anna Bleeck
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, Netherlands
| | - Nael Nadif Kasri
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, Netherlands.,Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands.,Centre of Excellence for Neuropsychiatry, Vincent van Gogh Institute for Psychiatry, Venray, Netherlands
| | - Jon-Ruben van Rhijn
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, Netherlands
| | - Dirk Schubert
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, Netherlands
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23
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Wright A, Hall A, Daly T, Fontelonga T, Potter S, Schafer C, Lindsley A, Hung C, Bodamer O, Gussoni E. Lysine methyltransferase 2D regulates muscle fiber size and muscle cell differentiation. FASEB J 2021; 35:e21955. [PMID: 34613626 PMCID: PMC8500524 DOI: 10.1096/fj.202100823r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/27/2021] [Accepted: 09/13/2021] [Indexed: 11/16/2022]
Abstract
Kabuki syndrome (KS) is a rare genetic disorder caused primarily by mutations in the histone modifier genes KMT2D and KDM6A. The genes have broad temporal and spatial expression in many organs, resulting in complex phenotypes observed in KS patients. Hypotonia is one of the clinical presentations associated with KS, yet detailed examination of skeletal muscle samples from KS patients has not been reported. We studied the consequences of loss of KMT2D function in both mouse and human muscles. In mice, heterozygous loss of Kmt2d resulted in reduced neuromuscular junction (NMJ) perimeter, decreased muscle cell differentiation in vitro and impaired myofiber regeneration in vivo. Muscle samples from KS patients of different ages showed presence of increased fibrotic tissue interspersed between myofiber fascicles, which was not seen in mouse muscles. Importantly, when Kmt2d‐deficient muscle stem cells were transplanted in vivo in a physiologic non‐Kabuki environment, their differentiation potential is restored to levels undistinguishable from control cells. Thus, the epigenetic changes due to loss of function of KMT2D appear reversible through a change in milieu, opening a potential therapeutic avenue.
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Affiliation(s)
- Alec Wright
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Arielle Hall
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Tara Daly
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA.,The Roya Kabuki Program, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Tatiana Fontelonga
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Sarah Potter
- Division of Allergy and Immunology, Cincinnati Children's Hospital, Cincinnati, Ohio, USA
| | - Caitlin Schafer
- Division of Allergy and Immunology, Cincinnati Children's Hospital, Cincinnati, Ohio, USA
| | - Andrew Lindsley
- Division of Allergy and Immunology, Cincinnati Children's Hospital, Cincinnati, Ohio, USA.,Amgen, Thousand Oaks, California, USA
| | - Christina Hung
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA.,The Roya Kabuki Program, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Olaf Bodamer
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA.,The Roya Kabuki Program, Boston Children's Hospital, Boston, Massachusetts, USA.,Division of Genetics and Genomics, Broad Institute of MIT and Harvard University, Cambridge, Massachusetts, USA
| | - Emanuela Gussoni
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA.,The Roya Kabuki Program, Boston Children's Hospital, Boston, Massachusetts, USA.,The Stem Cell Program, Boston Children's Hospital, Boston, Massachusetts, USA
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24
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Luperchio TR, Boukas L, Zhang L, Pilarowski G, Jiang J, Kalinousky A, Hansen KD, Bjornsson HT. Leveraging the Mendelian disorders of the epigenetic machinery to systematically map functional epigenetic variation. eLife 2021; 10:65884. [PMID: 34463256 PMCID: PMC8443249 DOI: 10.7554/elife.65884] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 08/27/2021] [Indexed: 12/12/2022] Open
Abstract
Although each Mendelian Disorder of the Epigenetic Machinery (MDEM) has a different causative gene, there are shared disease manifestations. We hypothesize that this phenotypic convergence is a consequence of shared epigenetic alterations. To identify such shared alterations, we interrogate chromatin (ATAC-seq) and expression (RNA-seq) states in B cells from three MDEM mouse models (Kabuki [KS] type 1 and 2 and Rubinstein-Taybi type 1 [RT1] syndromes). We develop a new approach for the overlap analysis and find extensive overlap primarily localized in gene promoters. We show that disruption of chromatin accessibility at promoters often disrupts downstream gene expression, and identify 587 loci and 264 genes with shared disruption across all three MDEMs. Subtle expression alterations of multiple, IgA-relevant genes, collectively contribute to IgA deficiency in KS1 and RT1, but not in KS2. We propose that the joint study of MDEMs offers a principled approach for systematically mapping functional epigenetic variation in mammals.
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Affiliation(s)
- Teresa Romeo Luperchio
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Leandros Boukas
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, United States
| | - Li Zhang
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Genay Pilarowski
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Jenny Jiang
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Allison Kalinousky
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Kasper D Hansen
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, United States
| | - Hans T Bjornsson
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.,Landspitali University Hospital, Reykjavik, Iceland
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25
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Anatomy of DNA methylation signatures: Emerging insights and applications. Am J Hum Genet 2021; 108:1359-1366. [PMID: 34297908 DOI: 10.1016/j.ajhg.2021.06.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 06/16/2021] [Indexed: 01/05/2023] Open
Abstract
DNA methylation (DNAm) signatures are unique patterns of DNAm alterations defined for rare disorders caused by pathogenic variants in epigenetic regulatory genes. The potential of DNAm signatures (also known as "episignatures") is just beginning to emerge as there are >300 known epigenetic regulatory genes, ∼100 of which are linked to neurodevelopmental disorders. To date, approximately 50 signatures have been identified, which have proven unexpectedly successful as predictive tools for classifying variants of uncertain significance as pathogenic or benign. The molecular basis of these signatures is poorly understood. Furthermore, their relationships to primary disease pathophysiology have yet to be adequately investigated, despite clear demonstrations of potential connections. There are currently no published guidelines for signature development. As signatures are highly dependent on the samples and methods used to derive them, we propose a framework for consideration in signature development including sample size, statistical parameters, cell type of origin, and the value of detailed clinical and molecular information. We illustrate the relationship between signature output/efficacy and sample size by generating and testing 837 DNAm signatures of Kleefstra syndrome using downsampling analysis. Our findings highlight that no single DNAm signature encompasses all DNAm alterations present in a rare disorder, and that a substandard study design can generate a DNAm signature that misclassifies variants. Finally, we discuss the importance of further investigating DNAm signatures to inform disease pathophysiology and broaden their scope as a functional assay.
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26
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Li Y, Chen X, Lu C. The interplay between DNA and histone methylation: molecular mechanisms and disease implications. EMBO Rep 2021; 22:e51803. [PMID: 33844406 PMCID: PMC8097341 DOI: 10.15252/embr.202051803] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 02/16/2021] [Accepted: 03/15/2021] [Indexed: 12/21/2022] Open
Abstract
Methylation of cytosine in CpG dinucleotides and histone lysine and arginine residues is a chromatin modification that critically contributes to the regulation of genome integrity, replication, and accessibility. A strong correlation exists between the genome-wide distribution of DNA and histone methylation, suggesting an intimate relationship between these epigenetic marks. Indeed, accumulating literature reveals complex mechanisms underlying the molecular crosstalk between DNA and histone methylation. These in vitro and in vivo discoveries are further supported by the finding that genes encoding DNA- and histone-modifying enzymes are often mutated in overlapping human diseases. Here, we summarize recent advances in understanding how DNA and histone methylation cooperate to maintain the cellular epigenomic landscape. We will also discuss the potential implication of these insights for understanding the etiology of, and developing biomarkers and therapies for, human congenital disorders and cancers that are driven by chromatin abnormalities.
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Affiliation(s)
- Yinglu Li
- Department of Genetics and Development and Herbert Irving Comprehensive Cancer CenterColumbia University Irving Medical CenterNew YorkNYUSA
| | - Xiao Chen
- Department of Genetics and Development and Herbert Irving Comprehensive Cancer CenterColumbia University Irving Medical CenterNew YorkNYUSA
| | - Chao Lu
- Department of Genetics and Development and Herbert Irving Comprehensive Cancer CenterColumbia University Irving Medical CenterNew YorkNYUSA
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27
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Vidaki A, Montiel González D, Planterose Jiménez B, Kayser M. Male-specific age estimation based on Y-chromosomal DNA methylation. Aging (Albany NY) 2021; 13:6442-6458. [PMID: 33744870 PMCID: PMC7993701 DOI: 10.18632/aging.202775] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 02/25/2021] [Indexed: 11/29/2022]
Abstract
Although DNA methylation variation of autosomal CpGs provides robust age predictive biomarkers, no male-specific age predictor exists based on Y-CpGs yet. Since sex chromosomes play an important role in aging, a Y-chromosome-based age predictor would allow studying male-specific aging effects and would also be useful in forensics. Here, we used blood-based DNA methylation microarray data of 1,057 males from six cohorts aged 15-87 and identified 75 Y-CpGs with an interquartile range of ≥0.1. Of these, 22 and six were significantly hyper- and hypomethylated with age (p(cor)<0.05, Bonferroni), respectively. Amongst several machine learning algorithms, a model based on support vector machines with radial kernel performed best in male-specific age prediction. We achieved a mean absolute deviation (MAD) between true and predicted age of 7.54 years (cor=0.81, validation) when using all 75 Y-CpGs, and a MAD of 8.46 years (cor=0.73, validation) based on the most predictive 19 Y-CpGs. The accuracies of both age predictors did not worsen with increased age, in contrast to autosomal CpG-based age predictors that are known to predict age with reduced accuracy in the elderly. Overall, we introduce the first-of-its-kind male-specific epigenetic age predictor for future applications in aging research and forensics.
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Affiliation(s)
- Athina Vidaki
- Department of Genetic Identification, Erasmus University Medical Center Rotterdam, Rotterdam 3000, CA, The Netherlands
| | - Diego Montiel González
- Department of Genetic Identification, Erasmus University Medical Center Rotterdam, Rotterdam 3000, CA, The Netherlands
| | - Benjamin Planterose Jiménez
- Department of Genetic Identification, Erasmus University Medical Center Rotterdam, Rotterdam 3000, CA, The Netherlands
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus University Medical Center Rotterdam, Rotterdam 3000, CA, The Netherlands
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Faundes V, Goh S, Akilapa R, Bezuidenhout H, Bjornsson HT, Bradley L, Brady AF, Brischoux-Boucher E, Brunner H, Bulk S, Canham N, Cody D, Dentici ML, Digilio MC, Elmslie F, Fry AE, Gill H, Hurst J, Johnson D, Julia S, Lachlan K, Lebel RR, Byler M, Gershon E, Lemire E, Gnazzo M, Lepri FR, Marchese A, McEntagart M, McGaughran J, Mizuno S, Okamoto N, Rieubland C, Rodgers J, Sasaki E, Scalais E, Scurr I, Suri M, van der Burgt I, Matsumoto N, Miyake N, Benoit V, Lederer D, Banka S. Clinical delineation, sex differences, and genotype-phenotype correlation in pathogenic KDM6A variants causing X-linked Kabuki syndrome type 2. Genet Med 2021; 23:1202-1210. [PMID: 33674768 PMCID: PMC8257478 DOI: 10.1038/s41436-021-01119-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 02/03/2021] [Accepted: 02/03/2021] [Indexed: 12/17/2022] Open
Abstract
Purpose The variant spectrum and the phenotype of X-linked Kabuki syndrome type 2 (KS2) are poorly understood. Methods Genetic and clinical details of new and published individuals with pathogenic KDM6A variants were compiled and analyzed. Results Sixty-one distinct pathogenic KDM6A variants (50 truncating, 11 missense) from 80 patients (34 males, 46 females) were identified. Missense variants clustered in the TRP 2, 3, 7 and Jmj-C domains. Truncating variants were significantly more likely to be de novo. Thirteen individuals had maternally inherited variants and one had a paternally inherited variant. Neonatal feeding difficulties, hypoglycemia, postnatal growth retardation, poor weight gain, motor delay, intellectual disability (ID), microcephaly, congenital heart anomalies, palate defects, renal malformations, strabismus, hearing loss, recurrent infections, hyperinsulinism, seizures, joint hypermobility, and gastroesophageal reflux were frequent clinical findings. Facial features of over a third of patients were not typical for KS. Males were significantly more likely to be born prematurely, have shorter stature, and severe developmental delay/ID. Conclusion We expand the KDM6A variant spectrum and delineate the KS2 phenotype. We demonstrate that the variability of the KS2 phenotypic depends on sex and the variant type. We also highlight the overlaps and differences between the phenotypes of KS2 and KS1.
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Affiliation(s)
- Víctor Faundes
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.,Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile
| | - Stephanie Goh
- School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Rhoda Akilapa
- NW Thames Regional Genetics Service, Northwick Park Hospital, Harrow, UK
| | - Heidre Bezuidenhout
- Clinical Unit of Medical Genetics and Genetic Counselling, Tygerberg Academic Hospital, Cape Town, South Africa.,Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Hans T Bjornsson
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Lisa Bradley
- Department of Clinical Genetics, Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Angela F Brady
- NW Thames Regional Genetics Service, Northwick Park Hospital, Harrow, UK
| | - Elise Brischoux-Boucher
- Centre de Génétique Humaine, Centre Hospitalier et Universitaire, Université de Franche-Comté, Besançon, France
| | - Han Brunner
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Saskia Bulk
- Centre de Génétique Humaine, CHU de Liège, Liège, Belgium
| | - Natalie Canham
- NW Thames Regional Genetics Service, Northwick Park Hospital, Harrow, UK.,Liverpool Centre for Genomic Medicine, Liverpool Women's Hospital, Crown Street, Liverpool, UK
| | - Declan Cody
- Department of Clinical Genetics, Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Maria Lisa Dentici
- Medical Genetics Unit, Academic Department of Pediatrics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Maria Cristina Digilio
- Medical Genetics Unit, Academic Department of Pediatrics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Frances Elmslie
- SW Thames Regional Genetics Service, St George's, University of London, London, UK
| | - Andrew E Fry
- Institute of Medical Genetics, University Hospital of Wales, Heath Park, Cardiff, UK
| | - Harinder Gill
- Department of Clinical Genetics, Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Jane Hurst
- NE Thames Genetics Service, Great Ormond Street Hospital, London, UK
| | - Diana Johnson
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Northern General Hospital, Sheffield, UK
| | - Sophie Julia
- Departments of Pathology, Neurosurgery, Oncopediatry, Genetics and Molecular Biology, Toulouse University Hospital, Toulouse, France
| | - Katherine Lachlan
- Wessex Clinical Genetics Service and Division of Human Genetics, Princess Anne Hospital, Southampton, UK
| | - Robert Roger Lebel
- Department of Pediatrics, Section of Medical Genetics, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Melissa Byler
- Department of Pediatrics, Section of Medical Genetics, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Eric Gershon
- Department of Pediatrics, Yale New Haven Health, New Haven, CT, USA
| | - Edmond Lemire
- Department of Pediatrics, Royal University Hospital, University of Saskatchewan, Saskatoon, SK, Canada
| | - Maria Gnazzo
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Antonia Marchese
- Service de Pédiatrie, Centre Hospitalier Régional de Namur, Namur, Belgium
| | - Meriel McEntagart
- SW Thames Regional Genetics Service, St George's, University of London, London, UK
| | - Julie McGaughran
- Genetic Health Queensland c/-Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Seiji Mizuno
- Department of Clinical Genetics, Central Hospital, Aichi Developmental Disability Center, Aichi, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan.,Department of Molecular Medicine, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Claudine Rieubland
- Division of Human Genetics, Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Jonathan Rodgers
- Genetic Health Queensland c/-Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Erina Sasaki
- Department of Clinical Genetics, Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Emmanuel Scalais
- Department of Pediatric Neurology, National Hospital, Luxembourg City, Luxembourg
| | - Ingrid Scurr
- Clinical Genetics, University Hospitals Bristol, Bristol, UK
| | - Mohnish Suri
- Nottingham Clinical Genetics Service, City Hospital Campus, Nottingham, UK
| | - Ineke van der Burgt
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Valérie Benoit
- Centre de Génétique Humaine, Institut de Pathologie et de Génétique, Gosselies, Belgium
| | - Damien Lederer
- Centre de Génétique Humaine, Institut de Pathologie et de Génétique, Gosselies, Belgium
| | - Siddharth Banka
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK. .,Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK.
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Khodaeian M, Jafarinia E, Bitarafan F, Shafeii S, Almadani N, Daneshmand MA, Garshasbi M. Kabuki Syndrome: Identification of Two Novel Variants in KMT2D and KDM6A. Mol Syndromol 2021; 12:118-126. [PMID: 34012382 DOI: 10.1159/000513199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 11/19/2020] [Indexed: 01/05/2023] Open
Abstract
Kabuki syndrome (KS) is a rare genetic disorder characterized by the following 5 crucial symptoms: dysmorphic facial features, growth retardation, skeletal abnormalities, intellectual disability, and dermatoglyphic malformations. Studies show that most of the KS cases are caused by mutations or large deletions in the KMT2D gene, while the other cases show mutations in KDM6A. We studied 2 patients with suspected KS in 2 unrelated families by whole-exome sequencing to identify the possible genetic cause(s) and by Sanger sequencing to validate the identified variants and check the segregation in other members of the families. Finally, the potential effects of the variants on the structure and function of respective proteins were tested using in silico predictions. Both affected members of the families showed typical manifestations of KS including intellectual disability, developmental delay, and abnormal facial characteristics. A novel heterozygous frameshift variant in the KMT2D gene, c.4981del; p.(Glu1661Serfs*61), and a novel hemizygote missense variant in the KDM6A gene, c.3301G>A; p.(Glu1101Lys), were detected in patients 1 and 2, respectively. The frameshift variant identified in the first family was de novo, while in the second family, the mother was also heterozygous for the missense variant. The frameshift variant in KMT2D is predicted to lead to a truncated protein which is functionally impaired. The Glu1101 residue of KDM6A (UTX) affected in the second patient is located in a conserved region on the surface of the Jumonji domain and predicted to be causative. Our findings provide evidence on the possible pathogenicity of these 2 variants; however, additional functional studies are necessary to confirm their impacts.
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Affiliation(s)
| | - Ehsan Jafarinia
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Teheran, Iran
| | | | | | - Navid Almadani
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | | | - Masoud Garshasbi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Teheran, Iran
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30
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da Costa LT, dos Anjos LG, Kagohara LT, Torrezan GT, De Paula CAA, Baracat EC, Carraro DM, Carvalho KC. The mutational repertoire of uterine sarcomas and carcinosarcomas in a Brazilian cohort: A preliminary study. Clinics (Sao Paulo) 2021; 76:e2324. [PMID: 33503190 PMCID: PMC7798418 DOI: 10.6061/clinics/2021/e2324] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/15/2020] [Indexed: 01/21/2023] Open
Abstract
OBJECTIVES The present study aimed to contribute to the catalog of genetic mutations involved in the carcinogenic processes of uterine sarcomas (USs) and carcinosarcomas (UCSs), which may assist in the accurate diagnosis of, and selection of treatment regimens for, these conditions. METHODS We performed gene-targeted next-generation sequencing (NGS) of 409 cancer-related genes in 15 US (7 uterine leiomyosarcoma [ULMS], 7 endometrial stromal sarcoma [ESS], 1 adenosarcoma [ADS]), 5 UCS, and 3 uterine leiomyoma (ULM) samples. Quality, frequency, and functional filters were applied to select putative somatic variants. RESULTS Among the 23 samples evaluated in this study, 42 loss-of-function (LOF) mutations and 111 missense mutations were detected, with a total of 153 mutations. Among them, 66 mutations were observed in the Catalogue of Somatic Mutations in Cancer (COSMIC) database. TP53 (48%), ATM (22%), and PIK3CA (17%) were the most frequently mutated genes. With respect to specific tumor subtypes, ESS showed mutations in the PDE4DIP, IGTA10, and DST genes, UCS exhibited mutations in ERBB4, and ULMS showed exclusive alterations in NOTCH2 and HER2. Mutations in the KMT2A gene were observed exclusively in ULM and ULMS. In silico pathway analyses demonstrated that many genes mutated in ULMS and ESS have functions associated with the cellular response to hypoxia and cellular response to peptide hormone stimulus. In UCS and ADS, genes with most alterations have functions associated with phosphatidylinositol kinase activity and glycerophospholipid metabolic process. CONCLUSION This preliminary study observed pathogenic mutations in US and UCS samples. Further studies with a larger cohort and functional analyses will foster the development of a precision medicine-based approach for the treatment of US and UCS.
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Affiliation(s)
- Leonardo Tomiatti da Costa
- Laboratorio de Ginecologia Estrutural e Molecular, Disciplina de Ginecologia, Hospital das Clinicas (HCFMUSP), Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Laura Gonzalez dos Anjos
- Laboratorio de Ginecologia Estrutural e Molecular, Disciplina de Ginecologia, Hospital das Clinicas (HCFMUSP), Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Luciane Tsukamoto Kagohara
- School of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | | | | | - Edmund Chada Baracat
- Laboratorio de Ginecologia Estrutural e Molecular, Disciplina de Ginecologia, Hospital das Clinicas (HCFMUSP), Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Dirce Maria Carraro
- Grupo de Biologia Molecular e Genomica, Centro A.C.Camargo, Sao Paulo, SP, BR
| | - Katia Candido Carvalho
- Laboratorio de Ginecologia Estrutural e Molecular, Disciplina de Ginecologia, Hospital das Clinicas (HCFMUSP), Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, BR
- *Corresponding author. E-mail:
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31
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Turinsky AL, Choufani S, Lu K, Liu D, Mashouri P, Min D, Weksberg R, Brudno M. EpigenCentral: Portal for DNA methylation data analysis and classification in rare diseases. Hum Mutat 2020; 41:1722-1733. [PMID: 32623772 DOI: 10.1002/humu.24076] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 06/12/2020] [Accepted: 07/02/2020] [Indexed: 01/09/2023]
Abstract
Epigenetic processes play a key role in regulating gene expression. Genetic variants that disrupt chromatin-modifying proteins are associated with a broad range of diseases, some of which have specific epigenetic patterns, such as aberrant DNA methylation (DNAm), which may be used as disease biomarkers. While much of the epigenetic research has focused on cancer, there is a paucity of resources devoted to neurodevelopmental disorders (NDDs), which include autism spectrum disorder and many rare, clinically overlapping syndromes. To address this challenge, we created EpigenCentral, a free web resource for biomedical researchers, molecular diagnostic laboratories, and clinical practitioners to perform the interactive classification and analysis of DNAm data related to NDDs. It allows users to search for known disease-associated patterns in their DNAm data, classify genetic variants as pathogenic or benign to assist in molecular diagnostics, or analyze patterns of differential methylation in their data through a simple web form. EpigenCentral is freely available at http://epigen.ccm.sickkids.ca/.
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Affiliation(s)
- Andrei L Turinsky
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Sanaa Choufani
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Kevin Lu
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Da Liu
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Pouria Mashouri
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Daniel Min
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Rosanna Weksberg
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada.,Institute of Medical Science, School of Graduate Studies, University of Toronto, Toronto, Ontario, Canada
| | - Michael Brudno
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.,Techna Institute, University Health Network, Toronto, Ontario, Canada
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32
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Di Fede E, Massa V, Augello B, Squeo G, Scarano E, Perri AM, Fischetto R, Causio FA, Zampino G, Piccione M, Curridori E, Mazza T, Castellana S, Larizza L, Ghelma F, Colombo EA, Gandini MC, Castori M, Merla G, Milani D, Gervasini C. Expanding the phenotype associated to KMT2A variants: overlapping clinical signs between Wiedemann-Steiner and Rubinstein-Taybi syndromes. Eur J Hum Genet 2020; 29:88-98. [PMID: 32641752 PMCID: PMC7852672 DOI: 10.1038/s41431-020-0679-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/03/2020] [Accepted: 06/23/2020] [Indexed: 12/16/2022] Open
Abstract
Lysine-specific methyltransferase 2A (KMT2A) is responsible for methylation of histone H3 (K4H3me) and contributes to chromatin remodeling, acting as "writer" of the epigenetic machinery. Mutations in KMT2A were first reported in Wiedemann-Steiner syndrome (WDSTS). More recently, KMT2A variants have been described in probands with a specific clinical diagnosis comprised in the so-called chromatinopathies. Such conditions, including WDSTS, are a group of overlapping disorders caused by mutations in genes coding for the epigenetic machinery. Among them, Rubinstein-Taybi syndrome (RSTS) is mainly caused by heterozygous pathogenic variants in CREBBP or EP300. In this work, we used next generation sequencing (either by custom-made panel or by whole exome) to identify alternative causative genes in individuals with a RSTS-like phenotype negative to CREBBP and EP300 mutational screening. In six patients we identified different novel unreported variants in KMT2A gene. The identified variants are de novo in at least four out of six tested individuals and all of them display some typical RSTS phenotypic features but also WDSTS specific signs. This study reinforces the concept that germline variants affecting the epigenetic machinery lead to a shared molecular effect (alteration of the chromatin state) determining superimposable clinical conditions.
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Affiliation(s)
- Elisabetta Di Fede
- Genetica Medica e Biologia Applicata, Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milano, Italy
| | - Valentina Massa
- Genetica Medica e Biologia Applicata, Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milano, Italy.,"Aldo Ravelli" Center for Neurotechnology and Experimental Brain Therapeutics, Università degli Studi di Milano, Milano, Italy
| | - Bartolomeo Augello
- Unità di Genetica Medica, IRCSS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Gabriella Squeo
- Unità di Genetica Medica, IRCSS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Emanuela Scarano
- Ambulatorio di Malattie Rare, Sindromologia ed Auxologia U.O. Pediatria AOU S.Orsola-Malpighi, Bologna, Italy
| | - Anna Maria Perri
- Ambulatorio di Malattie Rare, Sindromologia ed Auxologia U.O. Pediatria AOU S.Orsola-Malpighi, Bologna, Italy
| | - Rita Fischetto
- U.O.C. Malattie Metaboliche Genetica Medica, PO Giovanni XXIII, AOU Policlinico Consorziale, Bari, Italy
| | - Francesco Andrea Causio
- U.O.C. Malattie Metaboliche Genetica Medica, PO Giovanni XXIII, AOU Policlinico Consorziale, Bari, Italy
| | - Giuseppe Zampino
- Centro Malattie Rare e Difetti Congeniti, Fondazione Policlinico Universitario A. Gemelli, Università Cattolica, Roma, Italy
| | - Maria Piccione
- Dipartimento di scienze per la promozione della salute e la cura della madre e del bambino "G. D'Alessandro", Università di Palermo, Palermo, Italy
| | - Elena Curridori
- Dipartimento di clinica pediatrica e malattie rare, Ospedale pediatrico Antonio Cao, Cagliari, Italy
| | - Tommaso Mazza
- Unit of Bioinformatics IRCSS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Stefano Castellana
- Unit of Bioinformatics IRCSS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Lidia Larizza
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Filippo Ghelma
- Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milano, Italy
| | - Elisa Adele Colombo
- Genetica Medica e Biologia Applicata, Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milano, Italy
| | - Maria Chiara Gandini
- Genetica Medica e Biologia Applicata, Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milano, Italy
| | - Marco Castori
- Unità di Genetica Medica, IRCSS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Giuseppe Merla
- Unità di Genetica Medica, IRCSS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Donatella Milani
- UOSD Pediatria ad alta intensità di cura, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico Milano, Milano, Italy
| | - Cristina Gervasini
- Genetica Medica e Biologia Applicata, Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milano, Italy. .,"Aldo Ravelli" Center for Neurotechnology and Experimental Brain Therapeutics, Università degli Studi di Milano, Milano, Italy.
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33
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Fahrner JA, Bjornsson HT. Mendelian disorders of the epigenetic machinery: postnatal malleability and therapeutic prospects. Hum Mol Genet 2020; 28:R254-R264. [PMID: 31595951 DOI: 10.1093/hmg/ddz174] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 07/10/2019] [Accepted: 07/11/2019] [Indexed: 12/14/2022] Open
Abstract
The epigenetic machinery in conjunction with the transcriptional machinery is responsible for maintaining genome-wide chromatin states and dynamically regulating gene expression. Mendelian disorders of the epigenetic machinery (MDEMs) are genetic disorders resulting from mutations in components of the epigenetic apparatus. Though individually rare, MDEMs have emerged as a collectively common etiology for intellectual disability (ID) and growth disruption. Studies in model organisms and humans have demonstrated dosage sensitivity of this gene group with haploinsufficiency as a predominant disease mechanism. The epigenetic machinery consists of three enzymatic components (writers, erasers and chromatin remodelers) as well as one non-enzymatic group (readers). A tally of the entire census of such factors revealed that although multiple enzymatic activities never coexist within a single component, individual enzymatic activities often coexist with a reader domain. This group of disorders disrupts both the chromatin and transcription states of target genes downstream of the given component but also DNA methylation on a global scale. Elucidation of these global epigenetic changes may inform our understanding of disease pathogenesis and have diagnostic utility. Moreover, many therapies targeting epigenetic marks already exist, and some have proven successful in treating cancer. This, along with the recent observation that neurological dysfunction in these disorders may in fact be treatable in postnatal life, suggests that the scientific community should prioritize this group as a potentially treatable cause of ID. Here we summarize the recent expansion and major characteristics of MDEMs, as well as the unique therapeutic prospects for this group of disorders.
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Affiliation(s)
- Jill A Fahrner
- McKusick-Nathans Institute of Genetic Medicine, 21205.,Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hans T Bjornsson
- McKusick-Nathans Institute of Genetic Medicine, 21205.,Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Landspitali University Hospital, Reykjavik 101, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik 101, Iceland
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34
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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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Baldridge D, Spillmann RC, Wegner DJ, Wambach JA, White FV, Sisco K, Toler TL, Dickson PI, Cole FS, Shashi V, Grange DK. Phenotypic expansion of KMT2D-related disorder: Beyond Kabuki syndrome. Am J Med Genet A 2020; 182:1053-1065. [PMID: 32083401 DOI: 10.1002/ajmg.a.61518] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 01/29/2020] [Accepted: 01/29/2020] [Indexed: 12/13/2022]
Abstract
Pathogenic variants in KMT2D, which encodes lysine specific methyltransferase 2D, cause autosomal dominant Kabuki syndrome, associated with distinctive dysmorphic features including arched eyebrows, long palpebral fissures with eversion of the lower lid, large protuberant ears, and fetal finger pads. Most disease-causing variants identified to date are putative loss-of-function alleles, although 15-20% of cases are attributed to missense variants. We describe here four patients (including one previously published patient) with de novo KMT2D missense variants and with shared but unusual clinical findings not typically seen in Kabuki syndrome, including athelia (absent nipples), choanal atresia, hypoparathyroidism, delayed or absent pubertal development, and extreme short stature. These individuals also lack the typical dysmorphic facial features found in Kabuki syndrome. Two of the four patients had severe interstitial lung disease. All of these variants cluster within a 40-amino-acid region of the protein that is located just N-terminal of an annotated coiled coil domain. These findings significantly expand the phenotypic spectrum of features associated with variants in KMT2D beyond those seen in Kabuki syndrome and suggest a possible new underlying disease mechanism for these patients.
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Affiliation(s)
- Dustin Baldridge
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Rebecca C Spillmann
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina, USA
| | - Daniel J Wegner
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jennifer A Wambach
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Frances V White
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Kathleen Sisco
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Tomi L Toler
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Patricia I Dickson
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - F Sessions Cole
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Vandana Shashi
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina, USA
| | - Dorothy K Grange
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
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36
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Aygun D, Bjornsson HT. Clinical epigenetics: a primer for the practitioner. Dev Med Child Neurol 2020; 62:192-200. [PMID: 31749156 DOI: 10.1111/dmcn.14398] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/01/2019] [Indexed: 12/12/2022]
Abstract
Disruption of epigenetic modifications and the factors that maintain these modifications is rapidly emerging as a cause of developmental disorders. Here we summarize some of the major principles of epigenetics including how epigenetic modifications are: (1) normally reset in the germ line, (2) form an additional layer of interindividual variation, (3) are environmentally sensitive, and (4) change over time in humans. We also briefly discuss the disruption of growth and intellect associated with the Mendelian disorders of the epigenetic machinery and the classical imprinting disorders (such as Beckwith-Wiedemann syndrome, Silver-Russell syndrome, Prader-Willi syndrome, and Angelman syndrome), as well as suggesting some diagnostic considerations for the clinicians taking care of these patients. Finally, we discuss novel therapeutic strategies targeting epigenetic modifications, which may offer a safe alternative to up and coming genome editing strategies for the treatment of genetic diseases. This review provides a starting point for clinicians interested in epigenetics and the role epigenetic disruption plays in human disease. WHAT THIS PAPER ADDS: Clinicians are introduced to four main principles of epigenetics. Clinical features of imprinting disorders and Mendelian disorders of epigenetic machinery are presented.
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Affiliation(s)
- Deniz Aygun
- School of Arts and Sciences, Tufts University, Medford, MA, USA
| | - Hans T Bjornsson
- McKusick-Nathans Institute of Genetic Medicine, Baltimore, MD, USA.,Department of Pediatrics, Johns Hopkins University, Baltimore, MD, USA.,Department of Genetics and Molecular Medicine, Landspitali University Hospital, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
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37
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Krzyzewska IM, Maas SM, Henneman P, Lip KVD, Venema A, Baranano K, Chassevent A, Aref-Eshghi E, van Essen AJ, Fukuda T, Ikeda H, Jacquemont M, Kim HG, Labalme A, Lewis SME, Lesca G, Madrigal I, Mahida S, Matsumoto N, Rabionet R, Rajcan-Separovic E, Qiao Y, Sadikovic B, Saitsu H, Sweetser DA, Alders M, Mannens MMAM. A genome-wide DNA methylation signature for SETD1B-related syndrome. Clin Epigenetics 2019; 11:156. [PMID: 31685013 PMCID: PMC6830011 DOI: 10.1186/s13148-019-0749-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 09/22/2019] [Indexed: 01/02/2023] Open
Abstract
SETD1B is a component of a histone methyltransferase complex that specifically methylates Lys-4 of histone H3 (H3K4) and is responsible for the epigenetic control of chromatin structure and gene expression. De novo microdeletions encompassing this gene as well as de novo missense mutations were previously linked to syndromic intellectual disability (ID). Here, we identify a specific hypermethylation signature associated with loss of function mutations in the SETD1B gene which may be used as an epigenetic marker supporting the diagnosis of syndromic SETD1B-related diseases. We demonstrate the clinical utility of this unique epi-signature by reclassifying previously identified SETD1B VUS (variant of uncertain significance) in two patients.
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Affiliation(s)
- I M Krzyzewska
- Amsterdam UMC, Department of Clinical Genetics, Genome Diagnostics laboratory Amsterdam, Reproduction & Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - S M Maas
- Amsterdam UMC, Department of Pediatrics, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - P Henneman
- Amsterdam UMC, Department of Clinical Genetics, Genome Diagnostics laboratory Amsterdam, Reproduction & Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - K V D Lip
- Amsterdam UMC, Department of Clinical Genetics, Genome Diagnostics laboratory Amsterdam, Reproduction & Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - A Venema
- Amsterdam UMC, Department of Clinical Genetics, Genome Diagnostics laboratory Amsterdam, Reproduction & Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - K Baranano
- Kennedy Krieger Institute, Department of Neurogenetics, 801 N. Broadway, Rm 564, Baltimore, MD, 21205, USA
| | - A Chassevent
- Kennedy Krieger Institute, Department of Neurogenetics, 801 N. Broadway, Rm 564, Baltimore, MD, 21205, USA
| | - E Aref-Eshghi
- Department of Pathology and Laboratory Medicine, Western University, 800 Commissioner's Road E, London, ON, N6A 5W9, Canada
| | - A J van Essen
- University Medical Centre Groningen, University of Groningen, Department of Medical Genetics, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - T Fukuda
- Department of Pediatrics, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - H Ikeda
- National Epilepsy Centre, NHO, Shizuoka Institute of Epilepsy and Neurological Disorders, 886 Urushiyama, Aoi-ku, Shizuoka, 420-8688, Japan
| | - M Jacquemont
- Department of medical genetics, CHU La Reunion-Groupe Hospitalier Sud Reunion, La Reunion, France
| | - H-G Kim
- Neurological Disorder Center Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - A Labalme
- Department of medical genetics, Hospices Civils de Lyon, Bron, France
| | - S M E Lewis
- Department of Medical Genetics, Children's & Women's Health Centre of British Columbia University of British Columbia, C234-4500 Oak Street, Vancouver, British Columbia, V6H 3N1, Canada
| | - G Lesca
- Department of medical genetics, Hospices Civils de Lyon, Bron, France
| | - I Madrigal
- Biochemistry and Molecular Genetics Service, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Center for Biomedical Network Research on Rare Diseases (CIBERER), Barcelona, Spain
| | - S Mahida
- Kennedy Krieger Institute, Department of Neurogenetics, 801 N. Broadway, Rm 564, Baltimore, MD, 21205, USA
| | - N Matsumoto
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - R Rabionet
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, av diagonal 643, 08028, Barcelona, Spain
| | - E Rajcan-Separovic
- Department of Medical Genetics, Children's & Women's Health Centre of British Columbia University of British Columbia, C234-4500 Oak Street, Vancouver, British Columbia, V6H 3N1, Canada
| | - Y Qiao
- Department of Medical Genetics, Children's & Women's Health Centre of British Columbia University of British Columbia, C234-4500 Oak Street, Vancouver, British Columbia, V6H 3N1, Canada
| | - B Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, 800 Commissioner's Road E, London, ON, N6A 5W9, Canada
| | - H Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - D A Sweetser
- MassGeneral Hospital, Division of Medical Genetics and Metabolism, 175 Cambridge St, Suite 500, Boston, Massachusetts, 02114, USA
| | - M Alders
- Amsterdam UMC, Department of Clinical Genetics, Genome Diagnostics laboratory Amsterdam, Reproduction & Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands.
| | - M M A M Mannens
- Amsterdam UMC, Department of Clinical Genetics, Genome Diagnostics laboratory Amsterdam, Reproduction & Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
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Martin-Herranz DE, Aref-Eshghi E, Bonder MJ, Stubbs TM, Choufani S, Weksberg R, Stegle O, Sadikovic B, Reik W, Thornton JM. Screening for genes that accelerate the epigenetic aging clock in humans reveals a role for the H3K36 methyltransferase NSD1. Genome Biol 2019; 20:146. [PMID: 31409373 PMCID: PMC6693144 DOI: 10.1186/s13059-019-1753-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 07/03/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Epigenetic clocks are mathematical models that predict the biological age of an individual using DNA methylation data and have emerged in the last few years as the most accurate biomarkers of the aging process. However, little is known about the molecular mechanisms that control the rate of such clocks. Here, we have examined the human epigenetic clock in patients with a variety of developmental disorders, harboring mutations in proteins of the epigenetic machinery. RESULTS Using the Horvath epigenetic clock, we perform an unbiased screen for epigenetic age acceleration in the blood of these patients. We demonstrate that loss-of-function mutations in the H3K36 histone methyltransferase NSD1, which cause Sotos syndrome, substantially accelerate epigenetic aging. Furthermore, we show that the normal aging process and Sotos syndrome share methylation changes and the genomic context in which they occur. Finally, we found that the Horvath clock CpG sites are characterized by a higher Shannon methylation entropy when compared with the rest of the genome, which is dramatically decreased in Sotos syndrome patients. CONCLUSIONS These results suggest that the H3K36 methylation machinery is a key component of the epigenetic maintenance system in humans, which controls the rate of epigenetic aging, and this role seems to be conserved in model organisms. Our observations provide novel insights into the mechanisms behind the epigenetic aging clock and we expect will shed light on the different processes that erode the human epigenetic landscape during aging.
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Affiliation(s)
- Daniel E. Martin-Herranz
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Chronomics Ltd., Cambridge, UK
| | - Erfan Aref-Eshghi
- Department of Pathology and Laboratory Medicine, Western University, London, Canada
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Canada
| | - Marc Jan Bonder
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | | | - Sanaa Choufani
- Genetics and Genome Biology Program, Research Institute, The Hospital for Sick Children, Toronto, Canada
| | - Rosanna Weksberg
- Genetics and Genome Biology Program, Research Institute, The Hospital for Sick Children, Toronto, Canada
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, Canada
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Canada
| | - Wolf Reik
- Epigenetics Programme, The Babraham Institute, Cambridge, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Janet M. Thornton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
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Chater-Diehl E, Ejaz R, Cytrynbaum C, Siu MT, Turinsky A, Choufani S, Goodman SJ, Abdul-Rahman O, Bedford M, Dorrani N, Engleman K, Flores-Daboub J, Genevieve D, Mendoza-Londono R, Meschino W, Perrin L, Safina N, Townshend S, Scherer SW, Anagnostou E, Piton A, Deardorff M, Brudno M, Chitayat D, Weksberg R. New insights into DNA methylation signatures: SMARCA2 variants in Nicolaides-Baraitser syndrome. BMC Med Genomics 2019; 12:105. [PMID: 31288860 PMCID: PMC6617651 DOI: 10.1186/s12920-019-0555-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 06/30/2019] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Nicolaides-Baraitser syndrome (NCBRS) is a neurodevelopmental disorder caused by pathogenic sequence variants in SMARCA2 which encodes the catalytic component of the chromatin remodeling BAF complex. Pathogenic variants in genes that encode epigenetic regulators have been associated with genome-wide changes in DNA methylation (DNAm) in affected individuals termed DNAm signatures. METHODS Genome-wide DNAm was assessed in whole-blood samples from the individuals with pathogenic SMARCA2 variants and NCBRS diagnosis (n = 8) compared to neurotypical controls (n = 23) using the Illumina MethylationEPIC array. Differential methylated CpGs between groups (DNAm signature) were identified and used to generate a model enabling classification variants of uncertain significance (VUS; n = 9) in SMARCA2 as "pathogenic" or "benign". A validation cohort of NCBRS cases (n = 8) and controls (n = 96) demonstrated 100% model sensitivity and specificity. RESULTS We identified a DNAm signature of 429 differentially methylated CpG sites in individuals with NCBRS. The genes to which these CpG sites map are involved in cell differentiation, calcium signaling, and neuronal function consistent with NCBRS pathophysiology. DNAm model classifications of VUS were concordant with the clinical phenotype; those within the SMARCA2 ATPase/helicase domain classified as "pathogenic". A patient with a mild neurodevelopmental NCBRS phenotype and a VUS distal to the ATPase/helicase domain did not score as pathogenic, clustering away from cases and controls. She demonstrated an intermediate DNAm profile consisting of one subset of signature CpGs with methylation levels characteristic of controls and another characteristic of NCBRS cases; each mapped to genes with ontologies consistent with the patient's unique clinical presentation. CONCLUSIONS Here we find that a DNAm signature of SMARCA2 pathogenic variants in NCBRS maps to CpGs relevant to disorder pathophysiology, classifies VUS, and is sensitive to the position of the variant in SMARCA2. The patient with an intermediate model score demonstrating a unique genotype-epigenotype-phenotype correlation underscores the potential utility of this signature as a functionally relevant VUS classification system scalable beyond binary "benign" versus "pathogenic" scoring. This is a novel feature of DNAm signatures that could enable phenotypic predictions from genotype data. Our findings also demonstrate that DNAm signatures can be domain-specific, highlighting the precision with which they can reflect genotypic variation.
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Affiliation(s)
- Eric Chater-Diehl
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
| | - Resham Ejaz
- Division of Genetics, Department of Pediatrics, McMaster University, Hamilton, Ontario L8S 4L8 Canada
| | - Cheryl Cytrynbaum
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A1 Canada
| | - Michelle T. Siu
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
| | - Andrei Turinsky
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
| | - Sanaa Choufani
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
| | - Sarah J. Goodman
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
| | - Omar Abdul-Rahman
- Department of Genetic Medicine, Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, NE USA
| | - Melanie Bedford
- Genetics Program, North York General Hospital, Toronto, Ontario M2K 1E1 Canada
- Department of Paediatrics, University of Toronto, Toronto, Ontario M5S 3H7 Canada
| | | | - Kendra Engleman
- Division of Clinical Genetics, Children’s Mercy Hospital, Kansas City, MO 66111 USA
| | - Josue Flores-Daboub
- Division of Pediatric Clinical Genetics, University of Utah School of Medicine, Salt Lake City, UT 84132 USA
| | - David Genevieve
- Service de génétique clinique, Département de génétique médicale, maladies rares, médecine personnalisée, Unité INSERM U1183, Université Montpellier, CHU Montpellier, 34000 Montpellier, France
| | - Roberto Mendoza-Londono
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
- Department of Pediatrics, University of Toronto, Toronto, Ontario M5S 1A1 Canada
| | - Wendy Meschino
- Genetics Program, North York General Hospital, Toronto, Ontario M2K 1E1 Canada
| | - Laurence Perrin
- AP-HP, Department of Genetics, Hôpital Robert Debré, 75019 Paris, France
| | - Nicole Safina
- University of Missouri Kansas City, School of Medicine, Kansas City, MO 64108 USA
- Division of Clinical Genetics, Children’s Mercy Hospital, Kansas City, MO 64108 USA
- Department of Pediatrics, Children’s Mercy Hospital, Kansas City, MO 64108 USA
| | - Sharron Townshend
- Department of Health, Government of Western Australia, Genetic Services of Western Australia, Perth, WA Australia
| | - Stephen W. Scherer
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A1 Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
- McLaughlin Centre, University of Toronto, Toronto, Ontario M5S 1A1 Canada
| | - Evdokia Anagnostou
- Holland Bloorview Kids Rehabilitation Hospital Toronto, Toronto, Ontario M4G 1R8 Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario M5S 1A1 Canada
| | - Amelie Piton
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France
- Laboratoire de Diagnostic Génétique, Nouvel Hôpital Civil, Hôpitaux Universitaires de Strasbourg, 67000 Strasbourg, France
| | - Matthew Deardorff
- Division of Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- The Department of Pediatrics, The Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Michael Brudno
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario M5S 1A1 Canada
| | - David Chitayat
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A1 Canada
- Prenatal Diagnosis and Medical Genetics Program, Mount Sinai Hospital, Toronto, Ontario M5G 1X5 Canada
| | - Rosanna Weksberg
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A1 Canada
- Institute of Medical Sciences, University of Toronto, Toronto, Ontario M5S 1A8 Canada
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40
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Bend EG, Aref-Eshghi E, Everman DB, Rogers RC, Cathey SS, Prijoles EJ, Lyons MJ, Davis H, Clarkson K, Gripp KW, Li D, Bhoj E, Zackai E, Mark P, Hakonarson H, Demmer LA, Levy MA, Kerkhof J, Stuart A, Rodenhiser D, Friez MJ, Stevenson RE, Schwartz CE, Sadikovic B. Gene domain-specific DNA methylation episignatures highlight distinct molecular entities of ADNP syndrome. Clin Epigenetics 2019; 11:64. [PMID: 31029150 PMCID: PMC6487024 DOI: 10.1186/s13148-019-0658-5] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 03/27/2019] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND ADNP syndrome is a rare Mendelian disorder characterized by global developmental delay, intellectual disability, and autism. It is caused by truncating mutations in ADNP, which is involved in chromatin regulation. We hypothesized that the disruption of chromatin regulation might result in specific DNA methylation patterns that could be used in the molecular diagnosis of ADNP syndrome. RESULTS We identified two distinct and partially opposing genomic DNA methylation episignatures in the peripheral blood samples from 22 patients with ADNP syndrome. The "epi-ADNP-1" episignature included ~ 6000 mostly hypomethylated CpGs, and the "epi-ADNP-2" episignature included ~ 1000 predominantly hypermethylated CpGs. The two signatures correlated with the locations of the ADNP mutations. Epi-ADNP-1 mutations occupy the N- and C-terminus, and epi-ADNP-2 mutations are centered on the nuclear localization signal. The episignatures were enriched for genes involved in neuronal system development and function. A classifier trained on these profiles yielded full sensitivity and specificity in detecting patients with either of the two episignatures. Applying this model to seven patients with uncertain clinical diagnosis enabled reclassification of genetic variants of uncertain significance and assigned new diagnosis when the primary clinical suspicion was not correct. When applied to a large cohort of unresolved patients with developmental delay (N = 1150), the model predicted three additional previously undiagnosed patients to have ADNP syndrome. DNA sequencing of these subjects, wherever available, identified pathogenic mutations within the gene domains predicted by the model. CONCLUSIONS We describe the first Mendelian condition with two distinct episignatures caused by mutations in a single gene. These highly sensitive and specific DNA methylation episignatures enable diagnosis, screening, and genetic variant classifications in ADNP syndrome.
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Affiliation(s)
- Eric G. Bend
- Greenwood Genetic Center, 106 Gregor Mendel Cir, Greenwood, SC 29646 USA
- PreventionGenetics, Marshfield, WI USA
| | - Erfan Aref-Eshghi
- Department of Pathology and Laboratory Medicine, Western University, 800 Commissioner’s Road E, London, ON N6A 5W9 Canada
- Molecular Genetics Laboratory, Victoria Hospital, London Health Sciences Centre, London, ON Canada
| | - David B. Everman
- Greenwood Genetic Center, 106 Gregor Mendel Cir, Greenwood, SC 29646 USA
| | - R. Curtis Rogers
- Greenwood Genetic Center, 106 Gregor Mendel Cir, Greenwood, SC 29646 USA
| | - Sara S. Cathey
- Greenwood Genetic Center, 106 Gregor Mendel Cir, Greenwood, SC 29646 USA
| | - Eloise J. Prijoles
- Greenwood Genetic Center, 106 Gregor Mendel Cir, Greenwood, SC 29646 USA
| | - Michael J. Lyons
- Greenwood Genetic Center, 106 Gregor Mendel Cir, Greenwood, SC 29646 USA
| | - Heather Davis
- Greenwood Genetic Center, 106 Gregor Mendel Cir, Greenwood, SC 29646 USA
| | - Katie Clarkson
- Greenwood Genetic Center, 106 Gregor Mendel Cir, Greenwood, SC 29646 USA
| | | | - Dong Li
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Elizabeth Bhoj
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Elaine Zackai
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Paul Mark
- Spectrum Health, Grand Rapids, MI USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Laurie A. Demmer
- Levine Children’s Hospital, Carolinas Medical Center, Charlotte, NC USA
| | - Michael A. Levy
- Department of Pathology and Laboratory Medicine, Western University, 800 Commissioner’s Road E, London, ON N6A 5W9 Canada
- Molecular Genetics Laboratory, Victoria Hospital, London Health Sciences Centre, London, ON Canada
| | - Jennifer Kerkhof
- Department of Pathology and Laboratory Medicine, Western University, 800 Commissioner’s Road E, London, ON N6A 5W9 Canada
- Molecular Genetics Laboratory, Victoria Hospital, London Health Sciences Centre, London, ON Canada
| | - Alan Stuart
- Department of Pathology and Laboratory Medicine, Western University, 800 Commissioner’s Road E, London, ON N6A 5W9 Canada
- Molecular Genetics Laboratory, Victoria Hospital, London Health Sciences Centre, London, ON Canada
| | - David Rodenhiser
- Department of Pediatrics, Biochemistry and Oncology, Western University, London, ON Canada
| | - Michael J. Friez
- Greenwood Genetic Center, 106 Gregor Mendel Cir, Greenwood, SC 29646 USA
| | - Roger E. Stevenson
- Greenwood Genetic Center, 106 Gregor Mendel Cir, Greenwood, SC 29646 USA
| | | | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, 800 Commissioner’s Road E, London, ON N6A 5W9 Canada
- Molecular Genetics Laboratory, Victoria Hospital, London Health Sciences Centre, London, ON Canada
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Aref-Eshghi E, Bend EG, Colaiacovo S, Caudle M, Chakrabarti R, Napier M, Brick L, Brady L, Carere DA, Levy MA, Kerkhof J, Stuart A, Saleh M, Beaudet AL, Li C, Kozenko M, Karp N, Prasad C, Siu VM, Tarnopolsky MA, Ainsworth PJ, Lin H, Rodenhiser DI, Krantz ID, Deardorff MA, Schwartz CE, Sadikovic B. Diagnostic Utility of Genome-wide DNA Methylation Testing in Genetically Unsolved Individuals with Suspected Hereditary Conditions. Am J Hum Genet 2019; 104:685-700. [PMID: 30929737 DOI: 10.1016/j.ajhg.2019.03.008] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 03/05/2019] [Indexed: 12/13/2022] Open
Abstract
Conventional genetic testing of individuals with neurodevelopmental presentations and congenital anomalies (ND/CAs), i.e., the analysis of sequence and copy number variants, leaves a substantial proportion of them unexplained. Some of these cases have been shown to result from DNA methylation defects at a single locus (epi-variants), while others can exhibit syndrome-specific DNA methylation changes across multiple loci (epi-signatures). Here, we investigate the clinical diagnostic utility of genome-wide DNA methylation analysis of peripheral blood in unresolved ND/CAs. We generate a computational model enabling concurrent detection of 14 syndromes using DNA methylation data with full accuracy. We demonstrate the ability of this model in resolving 67 individuals with uncertain clinical diagnoses, some of whom had variants of unknown clinical significance (VUS) in the related genes. We show that the provisional diagnoses can be ruled out in many of the case subjects, some of whom are shown by our model to have other diseases initially not considered. By applying this model to a cohort of 965 ND/CA-affected subjects without a previous diagnostic assumption and a separate assessment of rare epi-variants in this cohort, we identify 15 case subjects with syndromic Mendelian disorders, 12 case subjects with imprinting and trinucleotide repeat expansion disorders, as well as 106 case subjects with rare epi-variants, a portion of which involved genes clinically or functionally linked to the subjects' phenotypes. This study demonstrates that genomic DNA methylation analysis can facilitate the molecular diagnosis of unresolved clinical cases and highlights the potential value of epigenomic testing in the routine clinical assessment of ND/CAs.
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Exploring by whole exome sequencing patients with initial diagnosis of Rubinstein-Taybi syndrome: the interconnections of epigenetic machinery disorders. Hum Genet 2019; 138:257-269. [PMID: 30806792 DOI: 10.1007/s00439-019-01985-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 02/17/2019] [Indexed: 12/29/2022]
Abstract
Rubinstein-Taybi syndrome (RSTS) is an autosomal-dominant neurodevelopmental disease affecting 1:125,000 newborns characterized by intellectual disability, growth retardation, facial dysmorphisms and skeletal abnormalities. RSTS is caused by mutations in genes encoding for writers of the epigenetic machinery: CREBBP (~ 60%) or its homologous EP300 (~ 10%). No causative mutation is identified in up to 30% of patients. We performed whole-exome sequencing (WES) on eight RSTS-like individuals who had normal high-resolution array CGH testing and were CREBBP- and EP300-mutation -negative, to identify the molecular cause. In four cases, we identified putatively causal variants in three genes (ASXL1, KMT2D and KMT2A) encoding members of the epigenetic machinery known to be associated with the Bohring-Opitz, Kabuki and Wiedemann-Steiner syndromes. Each variant is novel, de novo, fulfills the ACMG criteria and is predicted to result in loss-of-function leading to haploinsufficiency of the epi-gene. In two of the remaining cases, homozygous/compound heterozygous variants in XYLT2 and PLCB4 genes, respectively, associated with spondyloocular and auriculocondylar 2 syndromes and in the latter an additional candidate variant in XRN2, a gene yet unrelated to any disease, were detected, but their pathogenicity remains uncertain. These results underscore the broad clinical spectrum of Mendelian disorders of the epigenetic apparatus and the high rate of WES disclosure of the genetic basis in cases which may pose a challenge for phenotype encompassing distinct syndromes. The overlapping features of distinct intellectual disability syndromes reflect common pathogenic molecular mechanisms affecting the complex regulation of balance between open and closed chromatin.
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43
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Velasco G, Francastel C. Genetics meets DNA methylation in rare diseases. Clin Genet 2018; 95:210-220. [DOI: 10.1111/cge.13480] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 11/14/2018] [Accepted: 11/14/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Guillaume Velasco
- Sorbonne Paris Cité, Epigenetics and Cell Fate; UMR 7216 CNRS, Université Paris Diderot; Paris France
| | - Claire Francastel
- Sorbonne Paris Cité, Epigenetics and Cell Fate; UMR 7216 CNRS, Université Paris Diderot; Paris France
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Adam MP, Banka S, Bjornsson HT, Bodamer O, Chudley AE, Harris J, Kawame H, Lanpher BC, Lindsley AW, Merla G, Miyake N, Okamoto N, Stumpel CT, Niikawa N. Kabuki syndrome: international consensus diagnostic criteria. J Med Genet 2018; 56:89-95. [PMID: 30514738 DOI: 10.1136/jmedgenet-2018-105625] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 11/09/2018] [Accepted: 11/15/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND Kabuki syndrome (KS) is a clinically recognisable syndrome in which 70% of patients have a pathogenic variant in KMT2D or KDM6A. Understanding the function of these genes opens the door to targeted therapies. The purpose of this report is to propose diagnostic criteria for KS, particularly when molecular genetic testing is equivocal. METHODS An international group of experts created consensus diagnostic criteria for KS. Systematic PubMed searches returned 70 peer-reviewed publications in which at least one individual with molecularly confirmed KS was reported. The clinical features of individuals with known mutations were reviewed. RESULTS The authors propose that a definitive diagnosis can be made in an individual of any age with a history of infantile hypotonia, developmental delay and/or intellectual disability, and one or both of the following major criteria: (1) a pathogenic or likely pathogenic variant in KMT2D or KDM6A; and (2) typical dysmorphic features (defined below) at some point of life. Typical dysmorphic features include long palpebral fissures with eversion of the lateral third of the lower eyelid and two or more of the following: (1) arched and broad eyebrows with the lateral third displaying notching or sparseness; (2) short columella with depressed nasal tip; (3) large, prominent or cupped ears; and (4) persistent fingertip pads. Further criteria for a probable and possible diagnosis, including a table of suggestive clinical features, are presented. CONCLUSION As targeted therapies for KS are being developed, it is important to be able to make the correct diagnosis, either with or without molecular genetic confirmation.
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Affiliation(s)
- Margaret P Adam
- Division of Genetic Medicine, Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.,Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Hans T Bjornsson
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland.,Department of Genetics and Molecular Medicine, Landspitali University Hospital, Reykjavik, Iceland
| | - Olaf Bodamer
- Division of Genetics and Genomics, Department of Medicine, Boston Children's Hospital/Harvard Medical School, Boston, Massachusetts, USA.,Division of Genetics and Genomics, Broad Institute of MIT and Harvard University, Cambridge, Massachusetts, USA
| | - Albert E Chudley
- Department of Pediatrics and Child Health, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada.,Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Jaqueline Harris
- Departments of Neurology and Pediatrics, Kennedy Krieger Institute, Baltimore, Maryland, USA
| | - Hiroshi Kawame
- Department of Education and Training, Tohoku University School of Medicine, Sendai, Japan
| | - Brendan C Lanpher
- Center for Individualized Medicine, Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Andrew W Lindsley
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, USA
| | - Giuseppe Merla
- Division of Medical Genetics, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Italy
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Izumi, Japan
| | - Constanze T Stumpel
- Department of Clinical Genetics and GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Norio Niikawa
- President, the Research Institute of Personalized Health Sciences, Health Sciences University of Hokkaido, Hokkaido, Japan
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Campos-Sanchez E, Martínez-Cano J, Del Pino Molina L, López-Granados E, Cobaleda C. Epigenetic Deregulation in Human Primary Immunodeficiencies. Trends Immunol 2018; 40:49-65. [PMID: 30509895 DOI: 10.1016/j.it.2018.11.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/02/2018] [Accepted: 11/07/2018] [Indexed: 12/20/2022]
Abstract
Primary immunodeficiencies (PIDs) are immune disorders resulting from defects in genes involved in immune regulation, and manifesting as an increased susceptibility to infections, autoimmunity, and cancer. However, the molecular basis of some prevalent entities remains poorly understood. Epigenetic control is essential for immune functions, and epigenetic alterations have been identified in different PIDs, including syndromes such as immunodeficiency-centromeric-instability-facial-anomalies, Kabuki, or Wolf-Hirschhorn, among others. Although the epigenetic changes may differ among these PIDs, the reversibility of epigenetic modifications suggests that they might become potential therapeutic targets. Here, we review recent mechanistic advances in our understanding of epigenetic alterations associated with certain PIDs, propose that a fully epigenetically driven mechanism might underlie some PIDs, and discuss the possible prophylactic and therapeutic implications.
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Affiliation(s)
- Elena Campos-Sanchez
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC/UAM, Madrid 28049, Spain; These authors contributed equally to this work
| | - Jorge Martínez-Cano
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC/UAM, Madrid 28049, Spain; These authors contributed equally to this work
| | - Lucía Del Pino Molina
- Clinical Immunology Department, Hospital Universitario, La Paz Institute of Biomedical Research, 28046, Madrid, Spain; Lymphocyte Pathophysiology Group, La Paz Institute of Biomedical Research, 28046 Madrid, Spain
| | - Eduardo López-Granados
- Clinical Immunology Department, Hospital Universitario, La Paz Institute of Biomedical Research, 28046, Madrid, Spain; Lymphocyte Pathophysiology Group, La Paz Institute of Biomedical Research, 28046 Madrid, Spain.
| | - Cesar Cobaleda
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC/UAM, Madrid 28049, Spain.
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46
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A comparative analysis of KMT2D missense variants in Kabuki syndrome, cancers and the general population. J Hum Genet 2018; 64:161-170. [PMID: 30459467 DOI: 10.1038/s10038-018-0536-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 10/10/2018] [Accepted: 10/19/2018] [Indexed: 12/21/2022]
Abstract
Determining the clinical significance of germline and somatic KMT2D missense variants (MVs) in Kabuki syndrome (KS) and cancers can be challenging. We analysed 1920 distinct KMT2D MVs that included 1535 germline MVs in controls (Control-MVs), 584 somatic MVs in cancers (Cancer-MVs) and 201 MV in individuals with KS (KS-MVs). The proportion of MVs likely to affect splicing was significantly higher for Cancer-MVs and KS-MVs than in Control-MVs (p = 0.000018). Our analysis identified significant clustering of Cancer-MVs and KS-MVs in the PHD#3 and #4, RING#4 and SET domains. Areas of enrichment restricted to just Cancer-MVs (FYR-C and between amino acids 3043-3248) or KS-MVs (coiled-coil#5, FYR-N and between amino acids 4995-5090) were also found. Cancer-MVs and KS-MVs tended to affect more conserved residues (lower BLOSUM scores, p < 0.001 and p = 0.007). KS-MVs are more likely to increase the energy for protein folding (higher ELASPIC ∆∆G scores, p = 0.03). Cancer-MVs are more likely to disrupt protein interactions (higher StructMAn scores, p = 0.019). We reclassify several presumed pathogenic MVs as benign or as variants of uncertain significance. We raise the possibility of as yet unrecognised 'non-KS' phenotype(s) associated with some germline pathogenic KMT2D MVs. Overall, this work provides insights into the disease mechanism of KMT2D variants and can be extended to other genes, mutations in which also cause developmental syndromes and cancer.
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Cocciadiferro D, Augello B, De Nittis P, Zhang J, Mandriani B, Malerba N, Squeo GM, Romano A, Piccinni B, Verri T, Micale L, Pasqualucci L, Merla G. Dissecting KMT2D missense mutations in Kabuki syndrome patients. Hum Mol Genet 2018; 27:3651-3668. [PMID: 30107592 PMCID: PMC6488975 DOI: 10.1093/hmg/ddy241] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 05/30/2018] [Accepted: 06/21/2018] [Indexed: 02/07/2023] Open
Abstract
Kabuki syndrome is a rare autosomal dominant condition characterized by facial features, various organs malformations, postnatal growth deficiency and intellectual disability. The discovery of frequent germline mutations in the histone methyltransferase KMT2D and the demethylase KDM6A revealed a causative role for histone modifiers in this disease. However, the role of missense mutations has remained unexplored. Here, we expanded the mutation spectrum of KMT2D and KDM6A in KS by identifying 37 new KMT2D sequence variants. Moreover, we functionally dissected 14 KMT2D missense variants, by investigating their impact on the protein enzymatic activity and the binding to members of the WRAD complex. We demonstrate impaired H3K4 methyltransferase activity in 9 of the 14 mutant alleles and show that this reduced activity is due in part to disruption of protein complex formation. These findings have relevant implications for diagnostic and counseling purposes in this disease.
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Affiliation(s)
- Dario Cocciadiferro
- Division of Medical Genetics, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Italy
- PhD Program in Experimental and Regenerative Medicine, Faculty of Medicine, University of Foggia, Italy
| | - Bartolomeo Augello
- Division of Medical Genetics, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Italy
| | | | - Jiyuan Zhang
- Department of Pathology and Cell Biology, Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | - Barbara Mandriani
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli, Naples, Italy
| | - Natascia Malerba
- Division of Medical Genetics, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Italy
- PhD Program in Experimental and Regenerative Medicine, Faculty of Medicine, University of Foggia, Italy
| | - Gabriella M Squeo
- Division of Medical Genetics, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Italy
| | - Alessandro Romano
- Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Barbara Piccinni
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Tiziano Verri
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Lucia Micale
- Division of Medical Genetics, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Italy
| | - Laura Pasqualucci
- Department of Pathology and Cell Biology, Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | - Giuseppe Merla
- Division of Medical Genetics, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Italy
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Li N, Wang Y, Yang Y, Wang P, Huang H, Xiong S, Sun L, Cheng M, Song C, Cheng X, Ding Y, Chang G, Chen Y, Xu Y, Yu T, Yao RE, Shen Y, Wang X, Wang J. Description of the molecular and phenotypic spectrum of Wiedemann-Steiner syndrome in Chinese patients. Orphanet J Rare Dis 2018; 13:178. [PMID: 30305169 PMCID: PMC6180513 DOI: 10.1186/s13023-018-0909-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Accepted: 09/12/2018] [Indexed: 01/16/2023] Open
Abstract
Background Wiedemann–Steiner syndrome (WDSTS) is a rare genetic disorder characterized by facial gestalt, neurodevelopmental delay, skeletal anomalies and growth retardation, which is caused by variation of KMT2A gene. To date, only 2 Chinese WDSTS patients have been reported. Here, we report the phenotypes and KMT2A gene variations in 14 unrelated Chinese WDSTS patients and investigate the phenotypic differences between the Chinese and French cohorts. Methods Next generation sequencing was performed for each patient, and the variants in the KMT2A gene were validated by Sanger sequencing. The phenotypes of 16 Chinese WDSTS patients were summarized and compared to 33 French patients. Results Genetic sequencing identified 13 deleterious de novo KMT2A variants in 14 patients, including 10 truncating, 2 missenses and 1 splicing variants. Of the 13 variants, 11 are novel and two have been reported previously. One of the patients is mosaic in the KMT2A gene. The variation spectra and phenotypic profiles of the Chinese WDSTS patients showed no difference with patients of other ethnicities; however, differ in the frequencies of several clinical features. We demonstrated that variations in the KMT2A gene can lead to both advanced and delayed bone age. We identified 6 novel phenotypes, which include microcephaly, deep palmar crease, external ear deformity, carpal epiphyseal growth retardation, dyslipidemia, and glossoptosis. In addition, patients harbored missense variants in the CXXC zinc finger domain of KMT2A showed more severe neurophenotypes. Conclusion Our study consists of the largest cohort of Chinese WDSTS patients that continues to expand the WDSTS phenotypic and variation spectrum. Our results support the notion that the CXXC zinc finger domain of KMT2A gene is a hotspot for missense variants associated with more severe neurophenotypes. Electronic supplementary material The online version of this article (10.1186/s13023-018-0909-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Niu Li
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, 200127, China.,Institute of Pediatric Translational Medicine, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Yirou Wang
- Department of Endocrinology and Metabolism, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, 200127, China
| | - Yu Yang
- Department of Endocrinology, Metabolism, and Genetics, Jiangxi Provincial Children's Hospital, Nanchang, 330029, Jiangxi, China
| | | | - Hui Huang
- Central laboratory, Jiangxi Provincial Children's Hospital, Nanchang, 330029, Jiangxi, China
| | - Shiyi Xiong
- Fetal Medicine Unit & Prenatal diagnosis center, Shanghai First Maternity and Infant hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Luming Sun
- Fetal Medicine Unit & Prenatal diagnosis center, Shanghai First Maternity and Infant hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Min Cheng
- Department of Neurology, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Cui Song
- Department of Endocrinology and Genetic Metabolic Diseases, Ministry of Education Key Laboratory of Child Development and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders. Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Xinran Cheng
- Department of Endocrinology and Metabolism, Chengdu Women's and Children's Central Hospital, Sichuan Province, Chengdu, 610091, China
| | - Yu Ding
- Department of Endocrinology and Metabolism, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, 200127, China
| | - Guoying Chang
- Department of Endocrinology and Metabolism, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, 200127, China
| | - Yao Chen
- Department of Endocrinology and Metabolism, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, 200127, China
| | - Yufei Xu
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, 200127, China
| | - Tingting Yu
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, 200127, China.,Institute of Pediatric Translational Medicine, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Ru-En Yao
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, 200127, China.,Institute of Pediatric Translational Medicine, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Yiping Shen
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, 200127, China.,Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Xiumin Wang
- Department of Endocrinology and Metabolism, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, 200127, China. .,Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, 1678 Dongfang Road, Shanghai, 200127, People's Republic of China.
| | - Jian Wang
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, 200127, China. .,Institute of Pediatric Translational Medicine, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China. .,Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, 1678 Dongfang Road, Shanghai, 200127, People's Republic of China.
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Struzik M, Gawlik M. The role of the nursing team in the care of patients with Kabuki syndrome. MEDICAL SCIENCE PULSE 2018. [DOI: 10.5604/01.3001.0012.5180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background: Kabuki syndrome is a rare genetic condition characterised by pathological changes within all the systems of the body, but with variable gene expression. All the patients described in the literature so far have specific facial features resembling the masks of actors from the Japanese Kabuki Theatre and mild to moderate mental impairment. Diagnosis is made based by genetic testing for mutations of the KMT2D and KDM6A genes. Therapy is mainly based on symptomatic alleviation of the effects of mutation, rehabilitation and improvement of the quality of patients’ life. Then prognosis of patients with Kabuki syndrome is closely related to the severity of symptoms, which is very variable. Aim of the study: The purpose of the study is to present the nursing problems based on the case report and to present complications caused by the disease entity. Material and methods: The criterion for including the patient in the study was the legal guardian’s (parent’s) consent for the child to participate in the study. Qualitative research was conducted using analysis of medical records, interview with the child and the child’s legal guardian, direct and indirect observation of the child for psycho-social changes related to the disease and interpretation of the data in the context of the theoretical knowledge and our own observations. Case report: The report is based on the case of a 16-year-old girl, diagnosed (at the age of fourteen) with rare genetic disorder – Kabuki syndrome. The patient experiences some characteristic symptoms – big, red lips, lowset and sticky-out ears, drooping eyelids and short fingers and toes. One of the first symptoms suggesting Kabuki syndrome were: spitting up during breastfeeding, problems with swallowing, motor clumsiness and epilepsy. The role of the nursing team during hospitalization was to take care because of habitual dislocation of patella, and to provide psychological suport. At present time the girl uses a wheelchair or she moves on her knees Results: The manifestations of chronic disease contribute to the feeling of excessive stress, regardless of the patient’s age. An adequate diet enriched with proteins contributes to the prevention of bedsores among individuals with Kabuki syndrome, immobilised to various degrees. Regular consultations with specialists, such as cardiologist, neurologist, gastroenterologist, orthopaedist, ophthalmologist, psychologist, orthodontist, speech therapist, immunologist, endocrinologist and dietician reduce the risk of complications associated with the disease in the patient with Kabuki syndrome. Early implementation of rehabilitation, focused to increase muscle tension, contributes to maintaining autonomy and self-care in patients with Kabuki syndrome.
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