51
|
Roles and regulation of histone methylation in animal development. Nat Rev Mol Cell Biol 2019; 20:625-641. [PMID: 31267065 DOI: 10.1038/s41580-019-0151-1] [Citation(s) in RCA: 290] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2019] [Indexed: 12/26/2022]
Abstract
Histone methylation can occur at various sites in histone proteins, primarily on lysine and arginine residues, and it can be governed by multiple positive and negative regulators, even at a single site, to either activate or repress transcription. It is now apparent that histone methylation is critical for almost all stages of development, and its proper regulation is essential for ensuring the coordinated expression of gene networks that govern pluripotency, body patterning and differentiation along appropriate lineages and organogenesis. Notably, developmental histone methylation is highly dynamic. Early embryonic systems display unique histone methylation patterns, prominently including the presence of bivalent (both gene-activating and gene-repressive) marks at lineage-specific genes that resolve to monovalent marks during differentiation, which ensures that appropriate genes are expressed in each tissue type. Studies of the effects of methylation on embryonic stem cell pluripotency and differentiation have helped to elucidate the developmental roles of histone methylation. It has been revealed that methylation and demethylation of both activating and repressive marks are essential for establishing embryonic and extra-embryonic lineages, for ensuring gene dosage compensation via genomic imprinting and for establishing body patterning via HOX gene regulation. Not surprisingly, aberrant methylation during embryogenesis can lead to defects in body patterning and in the development of specific organs. Human genetic disorders arising from mutations in histone methylation regulators have revealed their important roles in the developing skeletal and nervous systems, and they highlight the overlapping and unique roles of different patterns of methylation in ensuring proper development.
Collapse
|
52
|
Harris J, Mahone EM, Bjornsson HT. Molecularly confirmed Kabuki (Niikawa-Kuroki) syndrome patients demonstrate a specific cognitive profile with extensive visuospatial abnormalities. JOURNAL OF INTELLECTUAL DISABILITY RESEARCH : JIDR 2019; 63:489-497. [PMID: 30767315 PMCID: PMC6499655 DOI: 10.1111/jir.12596] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 12/13/2018] [Accepted: 01/07/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND Kabuki (Niikawa-Kuroki) syndrome (KS) is caused by disease-causing variants in either of two components (KMT2D and KDM6A) of the histone methylation machinery. Nearly all individuals with KS have cognitive difficulties, and most have intellectual disability. Recent studies on a mouse model of KS suggest disruption of normal adult neurogenesis in the granule cell layer of the dentate gyrus of the hippocampus. These mutant mice also demonstrate hippocampal memory defects compared with littermates, but this phenotype is rescued postnatally with agents that target the epigenetic machinery. If these findings are relevant to humans with KS, we would expect significant and disproportionate disruption of visuospatial functioning in these individuals. METHODS To test this hypothesis, we have compiled a battery to robustly explore visuospatial function. We prospectively recruited 22 patients with molecularly confirmed KS and 22 IQ-matched patients with intellectual disability. RESULTS We observed significant deficiencies in visual motor, visual perception and visual motor memory in the KS group compared with the IQ-matched group on several measures. In contrast, language function appeared to be marginally better in the KS group compared with the IQ-matched group in a sentence comprehension task. CONCLUSIONS Together, our data suggest specific disruption of visuospatial function, likely linked to the dentate gyrus, in individuals with KS and provide the groundwork for a novel and specific outcome measure for a clinical trial in a KS population.
Collapse
Affiliation(s)
- J Harris
- Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD, USA
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - E M Mahone
- Department of Neuropsychology, Kennedy Krieger Institute, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - H T Bjornsson
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- Department of Genetics and Molecular Medicine, Landspitali University Hospital, Reykjavik, Iceland
| |
Collapse
|
53
|
Martins A, Oliveira MA, Rosa A, Murta J. Salzmann nodular degeneration features in a case of Kabuki make-up syndrome. BMJ Case Rep 2019; 12:e228010. [PMID: 31151969 PMCID: PMC6557394 DOI: 10.1136/bcr-2018-228010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2019] [Indexed: 12/11/2022] Open
Abstract
Kabuki syndrome (KS) is a multiple congenital anomaly syndrome with diversified ophthalmological manifestations. We report a case of a boy with bilateral features of Salzmann nodular degeneration (SND) associated with KS. An 18-year-old Caucasian man with KS presented for a second opinion regarding incapacitating photophobia in his right eye, refractory to medical therapy. Biomicroscopy revealed bilateral subepithelial nodules in the midperiphery of the cornea, less extensive in the left eye, consistent with SND. Symptomatic improvement was achieved after superficial keratectomy, manually performed with a blade and adjuvant application of mitomycin C. We report a rare case of a KS patient with SND. Since KS manifestations may vary widely, it is important to perform an early ophthalmological examination for prompt detection and treatment of ocular abnormalities and thus improve life quality in these patients.
Collapse
Affiliation(s)
- Amélia Martins
- Ophthalmology Department, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | | | - Andreia Rosa
- Ophthalmology Department, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
- Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Joaquim Murta
- Ophthalmology Department, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
- Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| |
Collapse
|
54
|
Abstract
Epigenetic mechanisms, including DNA and histone modifications, are pivotal for normal brain development and functions by modulating spatial and temporal gene expression. Dysregulation of the epigenetic machinery can serve as a causal role in numerous brain disorders. Proper mammalian brain development and functions depend on the precise expression of neuronal-specific genes, transcription factors and epigenetic modifications. Antagonistic polycomb and trithorax proteins form multimeric complexes and play important roles in these processes by epigenetically controlling gene repression or activation through various molecular mechanisms. Aberrant expression or disruption of either protein group can contribute to neurodegenerative diseases. This review focus on the current progress of Polycomb and Trithorax complexes in brain development and disease, and provides a future outlook of the field.
Collapse
|
55
|
de Billy E, Strocchio L, Cacchione A, Agolini E, Gnazzo M, Novelli A, De Vito R, Capolino R, Digilio MC, Caruso R, Mastronuzzi A, Locatelli F. Burkitt lymphoma in a patient with Kabuki syndrome carrying a novel KMT2D mutation. Am J Med Genet A 2018; 179:113-117. [PMID: 30569626 DOI: 10.1002/ajmg.a.60674] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 10/09/2018] [Accepted: 10/16/2018] [Indexed: 12/12/2022]
Abstract
Kabuki syndrome (KS) is an extremely rare genetic disorder, mainly caused by germline mutations at specific epigenetic modifier genes, including KMT2D. Because the tumor suppressor gene KMT2D is also frequently altered in many cancer types, it has been suggested that KS may predispose to the development of cancer. However, KS being a rare disorder, few data are available on the incidence of cancer in KS patients. Here, we report the case of a 5-year-old boy affected by KS who developed Burkitt lymphoma (BL). Genetic analysis revealed the presence of a novel heterozygous mutation in the splice site of the intron 4 of KMT2D gene in both peripheral blood-extracted DNA and tumour cells. In addition, the tumour sample of the patient was positive for the classical somatic chromosomal translocation t(8;14) involving the c-MYC gene frequently identified in BL. We propose that the mutated KMT2D gene contributes to the development of both KS and BL observed in our patient and we suggest that strict surveillance must be performed in KS patients.
Collapse
Affiliation(s)
- Emmanuel de Billy
- Department of Pediatric Hematology/Oncology and Cellular and Gene Therapy, Bambino Gesù Children's Hospital, Rome, Italy
| | - Luisa Strocchio
- Department of Pediatric Hematology/Oncology and Cellular and Gene Therapy, Bambino Gesù Children's Hospital, Rome, Italy
| | - Antonella Cacchione
- Department of Pediatric Hematology/Oncology and Cellular and Gene Therapy, Bambino Gesù Children's Hospital, Rome, Italy
| | - Emanuele Agolini
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, Rome, Italy
| | - Maria Gnazzo
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, Rome, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, Rome, Italy
| | - Rita De Vito
- Pathology Unit, Department of Pathology and Molecular Histopathology, Bambino Gesù Children's Hospital, Rome, Italy
| | - Rossella Capolino
- Medical Genetics Unit, Bambino Gesù Children's Hospital, Rome, Italy
| | | | - Roberta Caruso
- Department of Pediatric Hematology/Oncology and Cellular and Gene Therapy, Bambino Gesù Children's Hospital, Rome, Italy
| | - Angela Mastronuzzi
- Department of Pediatric Hematology/Oncology and Cellular and Gene Therapy, Bambino Gesù Children's Hospital, Rome, Italy
| | - Franco Locatelli
- Department of Pediatric Hematology/Oncology and Cellular and Gene Therapy, Bambino Gesù Children's Hospital, Rome, Italy.,Department of Pediatric Sciences, University of Pavia, Pavia, Italy
| |
Collapse
|
56
|
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: 114] [Impact Index Per Article: 19.0] [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.
Collapse
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
| | | |
Collapse
|
57
|
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.
Collapse
|
58
|
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.
Collapse
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
| |
Collapse
|
59
|
Abstract
A 3-year-old Japanese girl treated for hypoplastic left heart syndrome and Dandy-Walker syndrome was diagnosed with Kabuki syndrome (KS) with a mutation of KMT2D; c.13285C>T:p.Q4429*. Concurrently, macrohematuria portended the diagnosis of Wilms tumor. Postoperative chemotherapy has achieved complete remission despite a prolonged and reduced regimen due to liver dysfunction and convulsions. Cancer predisposition has been suggested for KS due to oncogenic mutations in KMT2D or KDM6A. The first case of nephroblastoma exemplified the treatability of malignancies in KS patients, as shown in the 9 cases reviewed. Active screening and intervention are recommended for the cure of malignancy in KS children.
Collapse
|
60
|
Porntaveetus T, Abid MF, Theerapanon T, Srichomthong C, Ohazama A, Kawasaki K, Kawasaki M, Suphapeetiporn K, Sharpe PT, Shotelersuk V. Expanding the Oro-Dental and Mutational Spectra of Kabuki Syndrome and Expression of KMT2D and KDM6A in Human Tooth Germs. Int J Biol Sci 2018; 14:381-389. [PMID: 29725259 PMCID: PMC5930470 DOI: 10.7150/ijbs.23517] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 02/26/2018] [Indexed: 12/12/2022] Open
Abstract
Kabuki syndrome is a rare genetic disorder characterized by distinct dysmorphic facial features, intellectual disability, and multiple developmental abnormalities. Despite more than 350 documented cases, the oro-dental spectrum associated with kabuki syndrome and expression of KMT2D (histone-lysine N-methyltransferase 2D) or KDM6A (lysine-specific demethylase 6A) genes in tooth development have not been well defined. Here, we report seven unrelated Thai patients with Kabuki syndrome having congenital absence of teeth, malocclusion, high-arched palate, micrognathia, and deviated tooth shape and size. Exome sequencing successfully identified that six patients were heterozygous for mutations in KMT2D, and one in KDM6A. Six were novel mutations, of which five were in KMT2D and one in KDM6A. They were truncating mutations including four frameshift deletions and two nonsense mutations. The predicted non-functional KMT2D and KDM6A proteins are expected to cause disease by haploinsufficiency. Our study expands oro-dental, medical, and mutational spectra associated with Kabuki syndrome. We also demonstrate for the first time that KMT2D and KDM6A are expressed in the dental epithelium of human tooth germs.
Collapse
Affiliation(s)
- Thantrira Porntaveetus
- Craniofacial Genetics and Stem Cells Research Group, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok 10330, Thailand
| | - Mushriq F Abid
- Centre for Craniofacial and Regenerative Biology, Dental Institute, King's College London, London, SE1 9RT, UK
| | - Thanakorn Theerapanon
- Excellence Center in Regenerative Dentistry, Faculty of Dentistry, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Chalurmpon Srichomthong
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.,Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok 10330, Thailand
| | - Atsushi Ohazama
- Division of Oral Anatomy, Niigata University, Niigata 951-8514, Japan
| | | | - Maiko Kawasaki
- Division of Oral Anatomy, Niigata University, Niigata 951-8514, Japan
| | - Kanya Suphapeetiporn
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.,Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok 10330, Thailand
| | - Paul T Sharpe
- Centre for Craniofacial and Regenerative Biology, Dental Institute, King's College London, London, SE1 9RT, UK
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.,Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok 10330, Thailand
| |
Collapse
|
61
|
Sakata S, Okada S, Aoyama K, Hara K, Tani C, Kagawa R, Utsunomiya-Nakamura A, Miyagawa S, Ogata T, Mizuno H, Kobayashi M. Individual Clinically Diagnosed with CHARGE Syndrome but with a Mutation in KMT2D, a Gene Associated with Kabuki Syndrome: A Case Report. Front Genet 2017; 8:210. [PMID: 29321794 PMCID: PMC5732153 DOI: 10.3389/fgene.2017.00210] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 11/28/2017] [Indexed: 11/13/2022] Open
Abstract
We report a Japanese female patient presenting with classic features of CHARGE syndrome, including choanal atresia, growth and development retardation, ear malformations, genital anomalies, multiple endocrine deficiency, and unilateral facial nerve palsy. She was clinically diagnosed with typical CHARGE syndrome, but genetic analysis using the TruSight One Sequence Panel revealed a germline heterozygous mutation in KMT2D with no pathogenic CHD7 alterations associated with CHARGE syndrome. Kabuki syndrome is a rare multisystem disorder characterized by five cardinal manifestations including typical facial features, skeletal anomalies, dermatoglyphic abnormalities, mild to moderate intellectual disability, and postnatal growth deficiency. Germline mutations in KMT2D underlie the molecular pathogenesis of 52–76% of patients with Kabuki syndrome. This is an instructive case that clearly represents a phenotypic overlap between Kabuki syndrome and CHARGE syndrome. It suggests the importance of considering the possibility of a diagnosis of Kabuki syndrome even if patients present with typical symptoms and meet diagnostic criteria of CHARGE syndrome. The case also emphasizes the impact of non-biased exhaustive genetic analysis by next-generation sequencing in the genetic diagnosis of rare congenital disorders with atypical manifestations.
Collapse
Affiliation(s)
- Sonoko Sakata
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Satoshi Okada
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Kohei Aoyama
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Keiichi Hara
- Department of Pediatrics, National Hospital Organization Kure Medical Center, Kure, Japan
| | - Chihiro Tani
- Department of Diagnostic Radiology, Hiroshima University Graduate School of Biomedical and Health Science, Hiroshima, Japan
| | - Reiko Kagawa
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Akari Utsunomiya-Nakamura
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Shinichiro Miyagawa
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan.,Miyagawa Kid's Clinic, Hiroshima, Japan
| | - Tsutomu Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Haruo Mizuno
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan.,Department of Pediatrics, International University of Health and Welfare School of Medicine, Chiba, Japan
| | - Masao Kobayashi
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| |
Collapse
|
62
|
Digilio MC, Gnazzo M, Lepri F, Dentici ML, Pisaneschi E, Baban A, Passarelli C, Capolino R, Angioni A, Novelli A, Marino B, Dallapiccola B. Congenital heart defects in molecularly proven Kabuki syndrome patients. Am J Med Genet A 2017; 173:2912-2922. [DOI: 10.1002/ajmg.a.38417] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Revised: 07/17/2017] [Accepted: 07/24/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Maria Cristina Digilio
- Medical Genetics Unit; Medical Genetics Laboratory; Pediatric Cardiology; Bambino Gesù Pediatric Hospital; IRCCS; Rome Italy
| | - Maria Gnazzo
- Medical Genetics Unit; Medical Genetics Laboratory; Pediatric Cardiology; Bambino Gesù Pediatric Hospital; IRCCS; Rome Italy
| | - Francesca Lepri
- Medical Genetics Unit; Medical Genetics Laboratory; Pediatric Cardiology; Bambino Gesù Pediatric Hospital; IRCCS; Rome Italy
| | - Maria Lisa Dentici
- Medical Genetics Unit; Medical Genetics Laboratory; Pediatric Cardiology; Bambino Gesù Pediatric Hospital; IRCCS; Rome Italy
| | - Elisa Pisaneschi
- Medical Genetics Unit; Medical Genetics Laboratory; Pediatric Cardiology; Bambino Gesù Pediatric Hospital; IRCCS; Rome Italy
| | - Anwar Baban
- Medical Genetics Unit; Medical Genetics Laboratory; Pediatric Cardiology; Bambino Gesù Pediatric Hospital; IRCCS; Rome Italy
| | - Chiara Passarelli
- Medical Genetics Unit; Medical Genetics Laboratory; Pediatric Cardiology; Bambino Gesù Pediatric Hospital; IRCCS; Rome Italy
| | - Rossella Capolino
- Medical Genetics Unit; Medical Genetics Laboratory; Pediatric Cardiology; Bambino Gesù Pediatric Hospital; IRCCS; Rome Italy
| | - Adriano Angioni
- Medical Genetics Unit; Medical Genetics Laboratory; Pediatric Cardiology; Bambino Gesù Pediatric Hospital; IRCCS; Rome Italy
| | - Antonio Novelli
- Medical Genetics Unit; Medical Genetics Laboratory; Pediatric Cardiology; Bambino Gesù Pediatric Hospital; IRCCS; Rome Italy
| | - Bruno Marino
- Department of Pediatrics; Pediatric Cardiology; Sapienza University; Rome Italy
| | - Bruno Dallapiccola
- Medical Genetics Unit; Medical Genetics Laboratory; Pediatric Cardiology; Bambino Gesù Pediatric Hospital; IRCCS; Rome Italy
| |
Collapse
|
63
|
Kurahashi N, Miyake N, Mizuno S, Koshimizu E, Kurahashi H, Yamada K, Natsume J, Aoki Y, Nakamura M, Taniai H, Maki Y, Abe-Hatano C, Matsumoto N, Maruyama K. Characteristics of epilepsy in patients with Kabuki syndrome with KMT2D mutations. Brain Dev 2017; 39:672-677. [PMID: 28404210 DOI: 10.1016/j.braindev.2017.03.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 03/21/2017] [Accepted: 03/23/2017] [Indexed: 11/30/2022]
Abstract
BACKGROUND The characteristics of epilepsy in patients with Kabuki syndrome with KMT2D mutations (KABUK1) have not yet been well documented. This is the first review to explore this. MATERIALS & METHODS We enrolled 14 patients with KABUK1, whose median age was 13.6years (range=4.1-21.3years). Their medical records from October 1981 to May 2016 were retrospectively analyzed. RESULTS Epilepsy was present in 5 (36%) patients. Four of these patients presented with nonsense mutations and one with missense mutations. None presented with brain abnormalities. Four patients presented with annual or monthly focal seizures, of which three evolved to bilateral convulsive seizures. Median onset age of focal epilepsy was 11.8years (range=9.5-12.8years). One presented with monthly myoclonic seizures from age 11.2, whose mother with no other KABUK1 features, had focal epilepsy. The cumulative incidence of epilepsy related to KABUK1 up until age 13 was 45%. Interictal electroencephalogram revealed focal paroxysmal epileptiform discharges (in frontal, central, and parietal regions) in three patients, diffuse high-voltage spike-and-waves in one patient, and normal sleep record in one patient. Myoclonic seizures were rapidly controlled by levetiracetam. In contrast, focal seizures were not controlled in the early period of antiepileptic therapy. CONCLUSION This long-term follow-up of patients with KABUK1 revealed a higher prevalence of epilepsy than previously reported. The age of epilepsy onset and rate of focal seizures evolving to bilateral convulsive seizures in KABUK1 were also higher than previously reported in patients with clinically diagnosed Kabuki syndrome. Although seizure outcome is reported to be favorable in Kabuki syndrome, focal seizures in patients with KABUK1 were not immediately responsive to medication.
Collapse
Affiliation(s)
- Naoko Kurahashi
- Department of Pediatric Neurology, Aichi Prefectural Colony Central Hospital, Japan.
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Japan
| | - Seiji Mizuno
- Department of Pediatrics, Aichi Prefectural Colony Central Hospital, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Japan
| | - Hirokazu Kurahashi
- Department of Pediatric Neurology, Aichi Prefectural Colony Central Hospital, Japan; Department of Pediatrics, Aichi Medical University, Japan
| | - Keitaro Yamada
- Department of Pediatric Neurology, Aichi Prefectural Colony Central Hospital, Japan
| | - Jun Natsume
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Japan
| | - Yusuke Aoki
- Department of Neurology, Aichi Children's Health and Medical Center, Japan
| | - Miho Nakamura
- Department of Functioning Science, Institute for Developmental Research, Aichi Human Service Center, Japan
| | - Hiroko Taniai
- Department of Pediatrics, Aichi Prefectural Colony Central Hospital, Japan; Department of Pediatrics, Nagoya Central Care Center for Disabled Children, Japan
| | - Yuki Maki
- Department of Pediatric Neurology, Aichi Prefectural Colony Central Hospital, Japan
| | - Chihiro Abe-Hatano
- Department of Pediatric Neurology, Aichi Prefectural Colony Central Hospital, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Japan
| | - Koichi Maruyama
- Department of Pediatric Neurology, Aichi Prefectural Colony Central Hospital, Japan
| |
Collapse
|
64
|
Meeks JJ, Shilatifard A. Multiple Roles for the MLL/COMPASS Family in the Epigenetic Regulation of Gene Expression and in Cancer. ANNUAL REVIEW OF CANCER BIOLOGY-SERIES 2017. [DOI: 10.1146/annurev-cancerbio-050216-034333] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Joshua J. Meeks
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
| |
Collapse
|
65
|
Mastrototaro G, Zaghi M, Sessa A. Epigenetic Mistakes in Neurodevelopmental Disorders. J Mol Neurosci 2017; 61:590-602. [DOI: 10.1007/s12031-017-0900-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 02/15/2017] [Indexed: 12/28/2022]
|
66
|
Lintas C, Persico AM. Unraveling molecular pathways shared by Kabuki and Kabuki-like syndromes. Clin Genet 2017; 94:283-295. [PMID: 28139835 DOI: 10.1111/cge.12983] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 01/19/2017] [Indexed: 12/12/2022]
Abstract
Kabuki syndrome (KS) is a rare genetic syndrome characterized by a typical facial gestalt, variable degrees of intellectual disability, organ malformations, postnatal growth retardation and skeletal abnormalities. So far, KMT2D or KDM6A mutation has been identified as the main cause of KS, accounting for 56%-75% and 3%-8% of cases, respectively. Patients without mutations in 1 of the 2 causative KS genes are often referred to as affected by Kabuki-like syndrome. Overall, they represent approximately 30% of KS cases, pointing toward substantial genetic heterogeneity for this condition. Here, we review all currently available literature describing KS-like phenotypes (or phenocopies) associated with genetic variants located in loci different from KMT2D and KDM6A . We also report on a new KS phenocopy harboring a 5 Mb de novo deletion in chr10p11.22-11.21. An enrichment analysis aimed at identifying functional Gene Ontology classes shared by the 2 known KS causative genes and by new candidate genes currently associated with KS-like phenotypes primarily converges upon abnormal chromatin remodeling and transcriptional dysregulation as pivotal to the pathophysiology of KS phenotypic hallmarks. The identification of mutations in genes belonging to the same functional pathways of KMT2D and KDM6A can help design molecular screenings targeted to KS-like phenotypes.
Collapse
Affiliation(s)
- C Lintas
- Unit of Child and Adolescent NeuroPsychiatry, University Campus Bio-Medico, Rome, Italy.,Laboratory of Molecular Psychiatry and Neurogenetics, Department of Medicine, University Campus Bio-Medico, Rome, Italy
| | - A M Persico
- Unit of Child and Adolescent NeuroPsychiatry, "G. Martino" University Hospital, University of Messina, Messina, Italy.,Mafalda Luce Center for Pervasive Developmental Disorders, Milan, Italy
| |
Collapse
|
67
|
Stagi S, Gulino AV, Lapi E, Rigante D. Epigenetic control of the immune system: a lesson from Kabuki syndrome. Immunol Res 2016; 64:345-59. [PMID: 26411453 DOI: 10.1007/s12026-015-8707-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Kabuki syndrome (KS) is a rare multi-systemic disorder characterized by a distinct face, postnatal growth deficiency, mild-to-moderate intellectual disability, skeletal and visceral (mainly cardiovascular, renal, and skeletal) malformations, dermatoglyphic abnormalities. Its cause is related to mutations of two genes: KMT2D (histone-lysine N-methyltransferase 2D) and KDM6A (lysine-specific demethylase 6A), both functioning as epigenetic modulators through histone modifications in the course of embryogenesis and in several biological processes. Epigenetic regulation is defined as the complex of hereditable modifications to DNA and histone proteins that modulates gene expression in the absence of DNA nucleotide sequence changes. Different human disorders are caused by mutations of genes involved in the epigenetic regulation, and not surprisingly, all these share developmental defects, disturbed growth (in excess or defect), multiple congenital organ malformations, and also hematological and immunological defects. In particular, most KS patients show increased susceptibility to infections and have reduced serum immunoglobulin levels, while some suffer also from autoimmune manifestations, such as idiopathic thrombocytopenic purpura, hemolytic anemia, autoimmune thyroiditis, and vitiligo. Herein we review the immunological aspects of KS and propose a novel model to account for the immune dysfunction observed in this condition.
Collapse
Affiliation(s)
- Stefano Stagi
- Health Sciences Department, University of Florence, Anna Meyer Children's University Hospital, Florence, Italy.
| | | | - Elisabetta Lapi
- Health Sciences Department, University of Florence, Anna Meyer Children's University Hospital, Florence, Italy
| | - Donato Rigante
- Institute of Pediatrics, Fondazione Policlinico Universitario Agostino Gemelli, Università Cattolica Sacro Cuore, Rome, Italy
| |
Collapse
|
68
|
Array comparative genomic hybridization and genomic sequencing in the diagnostics of the causes of congenital anomalies. J Appl Genet 2016; 58:185-198. [PMID: 27858254 DOI: 10.1007/s13353-016-0376-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 10/19/2016] [Accepted: 11/03/2016] [Indexed: 12/17/2022]
Abstract
The aim of this review is to provide the current state of knowledge about the usefulness of modern genetic technologies in uncovering the causality of isolated and multiple congenital anomalies. Array comparative genomic hybridization and next-generation sequencing have revolutionized the clinical approach to patients with these phenotypes. Both technologies enable early diagnosis, especially in clinically challenging newborn populations, and help to uncover genetic defects associated with various phenotypes. The application of both complementary methods could assist in identifying many variants that may simultaneously be involved in the development of a number of isolated or multiple congenital anomalies. Both technologies carry serious variant misinterpretation risks as well. Therefore, the methods of variant classification and accessible variant databases are mentioned. A useful strategy of clinical genetic testing with the application of both methodologies is presented. Finally, future directions and challenges are briefly commented on in this review.
Collapse
|
69
|
Badalato L, Farhan SMK, Dilliott AA, Bulman DE, Hegele RA, Goobie SL. KMT2D p.Gln3575His segregating in a family with autosomal dominant choanal atresia strengthens the Kabuki/CHARGE connection. Am J Med Genet A 2016; 173:183-189. [PMID: 27991736 DOI: 10.1002/ajmg.a.38010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 09/21/2016] [Indexed: 11/10/2022]
Abstract
Choanal atresia is rarely reported in Kabuki syndrome, but is a common feature of CHARGE syndrome. Otherwise, the two conditions have a number of overlapping features, and the molecular links between them have recently been elucidated. Here, we report a case of a mother and her two children who presented with congenital choanal atresia. We performed whole exome sequencing on DNA from the mother and her two unaffected parents, and identified a de novo, novel variant in KMT2D. KMT2D p.Gln3575His segregated with disease status in the family, and is associated with a unique and conserved phenotype in the affected family members, with features overlapping with Kabuki and CHARGE syndromes. Our findings further support the potential etiological link between these two classically distinct conditions. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Lauren Badalato
- Faculty of Medicine, Department of Genetics, Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Sali M K Farhan
- Department of Biochemistry and Medicine, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Allison A Dilliott
- Department of Biochemistry and Medicine, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | | | - Dennis E Bulman
- Faculty of Medicine, Departments of Pediatrics, Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Robert A Hegele
- Department of Biochemistry and Medicine, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Sharan L Goobie
- Division of Medical Genetics, Department of Pediatrics, London Health Sciences Centre, Western University, London, Ontario, Canada.,Medical Genetics, Department of Pediatrics, IWK Health Centre, Dalhousie University, Halifax, Nova Scotia, Canada
| |
Collapse
|
70
|
Lu J, Mo G, Ling Y, Ji L. A novel KMT2D mutation resulting in Kabuki syndrome: A case report. Mol Med Rep 2016; 14:3641-5. [PMID: 27573763 PMCID: PMC5042757 DOI: 10.3892/mmr.2016.5683] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 07/18/2016] [Indexed: 01/08/2023] Open
Abstract
Kabuki syndrome (KS) is a rare genetic syndrome characterized by multiple congenital anomalies and varying degrees of mental retardation. Patients with KS often present with facial, skeletal, visceral and dermatoglyphic abnormalities, cardiac anomalies and immunological defects. Mutation of the lysine methyltransferase 2D (KMT2D) gene (formerly known as MLL2) is the primary cause of KS. The present study reported the case of a 4-year-old Chinese girl who presented with atypical KS, including atypical facial features, unclear speech and suspected mental retardation. A diagnosis of KS was confirmed by genetic testing, which revealed a nonsense mutation in exon 16 of KMT2D (c.4485C>A, Tyr1495Ter). To the best of our knowledge, this is a novel mutation that has not been reported previously. The present case underscores the importance of genetic testing in KS diagnosis.
Collapse
Affiliation(s)
- Jun Lu
- Pediatric Department, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou, Hainan 570208, P.R. China
| | - Guiling Mo
- Department of Molecular Genetics, Guangzhou Kingmed Center for Clinical Laboratory Co., Ltd., Guangzhou, Guangdong 510330, P.R. China
| | - Yaojun Ling
- Pediatric Department, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou, Hainan 570208, P.R. China
| | - Lijuan Ji
- Pediatric Department, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou, Hainan 570208, P.R. China
| |
Collapse
|
71
|
Schott DA, Blok MJ, Gerver WJM, Devriendt K, Zimmermann LJI, Stumpel CTRM. Growth pattern in Kabuki syndrome with aKMT2Dmutation. Am J Med Genet A 2016; 170:3172-3179. [DOI: 10.1002/ajmg.a.37930] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 07/04/2016] [Indexed: 11/12/2022]
Affiliation(s)
- Dina A. Schott
- Department of Paediatrics Endocrinology; Zuyderland Medical Centre; Heerlen The Netherlands
| | - Marinus J. Blok
- Department of Clinical Genetics and School for Oncology and Developmental Biology (GROW); Maastricht UMC+; Maastricht The Netherlands
| | - Willem J. M. Gerver
- Department of Paediatrics Endocrinology; Maastricht UMC+; Maastricht The Netherlands
| | | | - Luc J. I. Zimmermann
- Department of Paediatrics Neonatology; Maastricht UMC+; Maastricht The Netherlands
| | - Constance T. R. M. Stumpel
- Department of Clinical Genetics and School for Oncology and Developmental Biology (GROW); Maastricht UMC+; Maastricht The Netherlands
| |
Collapse
|
72
|
Bögershausen N, Gatinois V, Riehmer V, Kayserili H, Becker J, Thoenes M, Simsek-Kiper PÖ, Barat-Houari M, Elcioglu NH, Wieczorek D, Tinschert S, Sarrabay G, Strom TM, Fabre A, Baynam G, Sanchez E, Nürnberg G, Altunoglu U, Capri Y, Isidor B, Lacombe D, Corsini C, Cormier-Daire V, Sanlaville D, Giuliano F, Le Quan Sang KH, Kayirangwa H, Nürnberg P, Meitinger T, Boduroglu K, Zoll B, Lyonnet S, Tzschach A, Verloes A, Di Donato N, Touitou I, Netzer C, Li Y, Geneviève D, Yigit G, Wollnik B. Mutation Update for Kabuki Syndrome GenesKMT2DandKDM6Aand Further Delineation of X-Linked Kabuki Syndrome Subtype 2. Hum Mutat 2016; 37:847-64. [DOI: 10.1002/humu.23026] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 05/26/2016] [Indexed: 12/29/2022]
|
73
|
Priest JR, Osoegawa K, Mohammed N, Nanda V, Kundu R, Schultz K, Lammer EJ, Girirajan S, Scheetz T, Waggott D, Haddad F, Reddy S, Bernstein D, Burns T, Steimle JD, Yang XH, Moskowitz IP, Hurles M, Lifton RP, Nickerson D, Bamshad M, Eichler EE, Mital S, Sheffield V, Quertermous T, Gelb BD, Portman M, Ashley EA. De Novo and Rare Variants at Multiple Loci Support the Oligogenic Origins of Atrioventricular Septal Heart Defects. PLoS Genet 2016; 12:e1005963. [PMID: 27058611 PMCID: PMC4825975 DOI: 10.1371/journal.pgen.1005963] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 03/07/2016] [Indexed: 12/15/2022] Open
Abstract
Congenital heart disease (CHD) has a complex genetic etiology, and recent studies suggest that high penetrance de novo mutations may account for only a small fraction of disease. In a multi-institutional cohort surveyed by exome sequencing, combining analysis of 987 individuals (discovery cohort of 59 affected trios and 59 control trios, and a replication cohort of 100 affected singletons and 533 unaffected singletons) we observe variation at novel and known loci related to a specific cardiac malformation the atrioventricular septal defect (AVSD). In a primary analysis, by combining developmental coexpression networks with inheritance modeling, we identify a de novo mutation in the DNA binding domain of NR1D2 (p.R175W). We show that p.R175W changes the transcriptional activity of Nr1d2 using an in vitro transactivation model in HUVEC cells. Finally, we demonstrate previously unrecognized cardiovascular malformations in the Nr1d2tm1-Dgen knockout mouse. In secondary analyses we map genetic variation to protein-interaction networks suggesting a role for two collagen genes in AVSD, which we corroborate by burden testing in a second replication cohort of 100 AVSDs and 533 controls (p = 8.37e-08). Finally, we apply a rare-disease inheritance model to identify variation in genes previously associated with CHD (ZFPM2, NSD1, NOTCH1, VCAN, and MYH6), cardiac malformations in mouse models (ADAM17, CHRD, IFT140, PTPRJ, RYR1 and ATE1), and hypomorphic alleles of genes causing syndromic CHD (EHMT1, SRCAP, BBS2, NOTCH2, and KMT2D) in 14 of 59 trios, greatly exceeding variation in control trios without CHD (p = 9.60e-06). In total, 32% of trios carried at least one putatively disease-associated variant across 19 loci,suggesting that inherited and de novo variation across a heterogeneous group of loci may contribute to disease risk.
Collapse
Affiliation(s)
- James R. Priest
- Division of Pediatric Cardiology, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
- Cardiovascular Institute, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
| | - Kazutoyo Osoegawa
- Department of Pathology, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
| | - Nebil Mohammed
- University of California San Francisco Benioff Children’s Hospital Oakland, University of California San Francisco, San Francisco, California, United States of America
| | - Vivek Nanda
- Department of Vascular Surgery, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
| | - Ramendra Kundu
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
| | - Kathleen Schultz
- University of California San Francisco Benioff Children’s Hospital Oakland, University of California San Francisco, San Francisco, California, United States of America
| | - Edward J. Lammer
- University of California San Francisco Benioff Children’s Hospital Oakland, University of California San Francisco, San Francisco, California, United States of America
| | - Santhosh Girirajan
- Departments of Biochemistry, Molecular Biology, and Anthropology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Todd Scheetz
- College of Engineering, University of Iowa, Iowa City, Iowa, United States of America
| | - Daryl Waggott
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
| | - Francois Haddad
- Cardiovascular Institute, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
| | - Sushma Reddy
- Division of Pediatric Cardiology, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
- Cardiovascular Institute, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
| | - Daniel Bernstein
- Division of Pediatric Cardiology, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
- Cardiovascular Institute, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
| | - Trudy Burns
- College of Public Health, University of Iowa, Iowa City, Iowa, United States of America
| | - Jeffrey D. Steimle
- Department of Pathology, University of Chicago, Chicago, Illinois, United States of America
| | - Xinan H. Yang
- Department of Pathology, University of Chicago, Chicago, Illinois, United States of America
| | - Ivan P. Moskowitz
- Department of Pathology, University of Chicago, Chicago, Illinois, United States of America
| | - Matthew Hurles
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Richard P. Lifton
- Department of Genetics, Yale University, New Haven, Connecticut, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Debbie Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Michael Bamshad
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Department of Pediatrics, University of Washington, Seattle, Washington, United States of America
| | - Evan E. Eichler
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Seema Mital
- Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Val Sheffield
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
- Division of Medical Genetics, University of Iowa Carver College of Medicine, Iowa City, Iowa, United States of America
| | - Thomas Quertermous
- Cardiovascular Institute, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
| | - Bruce D. Gelb
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mt. Sinai, New York, New York, United States of America
| | - Michael Portman
- Department of Pediatrics, University of Washington, Seattle, Washington, United States of America
| | - Euan A. Ashley
- Cardiovascular Institute, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
| |
Collapse
|
74
|
Yang P, Tan H, Xia Y, Yu Q, Wei X, Guo R, Peng Y, Chen C, Li H, Mei L, Huang Y, Liang D, Wu L. De novo exonic deletion of KDM6A in a Chinese girl with Kabuki syndrome: A case report and brief literature review. Am J Med Genet A 2016; 170:1613-21. [PMID: 27028180 DOI: 10.1002/ajmg.a.37634] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 03/07/2016] [Indexed: 12/15/2022]
Abstract
Kabuki syndrome (KS) is a rare condition with multiple congenital anomalies and mental retardation. Exonic deletions, disrupting the lysine (K)-specific demethylase 6A (KDM6A) gene have been demonstrated as rare cause of KS. Here, we report a de novo 227-kb deletion in chromosome Xp11.3 of a 7-year-old Chinese girl with KS. Besides the symptoms of KS, the patient also presented with skin allergic manifestations, which were considered to be a new, rare feature of the phenotypic spectrum. The deletion includes the upstream region and exons 1-2 of KDM6A and potentially causes haploinsuffiency of the gene. We also discuss the mutation spectrum of KDM6A and clinical variability of patients with KDM6A deletion through a literature review. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Pu Yang
- State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, P.R. China
| | - Hu Tan
- State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, P.R. China
| | - Yan Xia
- State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, P.R. China
| | - Qian Yu
- Department of Haematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, P.R. China
| | - Xianda Wei
- State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, P.R. China
| | - Ruolan Guo
- State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, P.R. China
| | - Ying Peng
- State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, P.R. China
| | - Chen Chen
- State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, P.R. China.,Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, Hunan, P.R. China
| | - Haoxian Li
- State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, P.R. China
| | - Libin Mei
- State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, P.R. China
| | - Yanru Huang
- State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, P.R. China
| | - Desheng Liang
- State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, P.R. China
| | - Lingqian Wu
- State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, P.R. China
| |
Collapse
|
75
|
Paděrová J, Holubová A, Simandlová M, Puchmajerová A, Vlčková M, Malíková M, Pourová R, Vejvalková S, Havlovicová M, Šenkeříková M, Ptáková N, Drábová J, Geryk J, Maver A, Křepelová A, Macek M. Molecular genetic analysis in 14 Czech Kabuki syndrome patients is confirming the utility of phenotypic scoring. Clin Genet 2016; 90:230-7. [DOI: 10.1111/cge.12754] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 01/30/2016] [Accepted: 02/01/2016] [Indexed: 01/17/2023]
Affiliation(s)
- J. Paděrová
- Department of Biology and Medical Genetics; Charles University Prague-2 Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | - A. Holubová
- Department of Biology and Medical Genetics; Charles University Prague-2 Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | - M. Simandlová
- Department of Biology and Medical Genetics; Charles University Prague-2 Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | - A. Puchmajerová
- Department of Biology and Medical Genetics; Charles University Prague-2 Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | - M. Vlčková
- Department of Biology and Medical Genetics; Charles University Prague-2 Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | - M. Malíková
- Department of Biology and Medical Genetics; Charles University Prague-2 Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | - R. Pourová
- Department of Biology and Medical Genetics; Charles University Prague-2 Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | - S. Vejvalková
- Department of Biology and Medical Genetics; Charles University Prague-2 Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | - M. Havlovicová
- Department of Biology and Medical Genetics; Charles University Prague-2 Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | - M. Šenkeříková
- Department of Medical Genetics; Charles University Prague-Faculty of Medicine and University Hospital Hradec Králové; Hradec Králové Czech Republic
| | - N. Ptáková
- Department of Biology and Medical Genetics; Charles University Prague-2 Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | - J. Drábová
- Department of Biology and Medical Genetics; Charles University Prague-2 Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | - J. Geryk
- Department of Biology and Medical Genetics; Charles University Prague-2 Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | - A. Maver
- Department of Obstetrics & Gynecology, Centre for Mendelian Genomics, Clinical Institute of Medical Genetics; University Medical Centre Ljubljana; Ljubljana Slovenia
| | - A. Křepelová
- Department of Biology and Medical Genetics; Charles University Prague-2 Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | - M. Macek
- Department of Biology and Medical Genetics; Charles University Prague-2 Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| |
Collapse
|
76
|
Karagianni P, Lambropoulos V, Stergidou D, Fryssira H, Chatziioannidis I, Spyridakis I. Recurrent giant cell fibroblastoma: Malignancy predisposition in Kabuki syndrome revisited. Am J Med Genet A 2016; 170A:1333-8. [PMID: 26898171 DOI: 10.1002/ajmg.a.37584] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 01/25/2016] [Indexed: 11/07/2022]
Abstract
Kabuki syndrome is a genetic condition characterized by distinctive facial phenotype, mental retardation, and internal organ malformations. Mutations of the epigenetic genes KMT2D and KDM6A cause dysregulation of certain developmental genes and account for the multiple congenital anomalies of the syndrome. Eight cases of malignancies have been reported in young patients with Kabuki syndrome although a causative association to the syndrome has not been established. We report a case of a 12-year-old girl with Kabuki syndrome who developed a tumor on the right side of her neck. A relapsing tumor 19 months after initial excision, proved to be giant cell fibroblastoma. Τhis is the first report of giant cell fibroblastoma -a rare tumor of childhood- in a patient with Kabuki syndrome.
Collapse
Affiliation(s)
- Paraskevi Karagianni
- Department of Neonatology and B' NICU (Neonatal Intensive Care Unit), Aristotle University of Thessaloniki, General Hospital Papageorgiou, Thessaloniki, Greece
| | - Vassilios Lambropoulos
- Second Department of Pediatric Surgery, Aristotle University of Thessaloniki, General Hospital Papageorgiou, Thessaloniki, Greece
| | - Dorothea Stergidou
- Department of Neonatology and B' NICU (Neonatal Intensive Care Unit), Aristotle University of Thessaloniki, General Hospital Papageorgiou, Thessaloniki, Greece
| | - Helena Fryssira
- Department of Medical Genetics, University of Athens School of Medicine, "Aghia Sophia" Children's Hospital, Goudi, Athens, Greece
| | - Ilias Chatziioannidis
- Department of Neonatology and B' NICU (Neonatal Intensive Care Unit), Aristotle University of Thessaloniki, General Hospital Papageorgiou, Thessaloniki, Greece
| | - Ioannis Spyridakis
- Second Department of Pediatric Surgery, Aristotle University of Thessaloniki, General Hospital Papageorgiou, Thessaloniki, Greece
| |
Collapse
|
77
|
Abstract
Genetic causes for human disorders are being discovered at an unprecedented pace. A growing subclass of disease-causing mutations involves changes in the epigenome or in the abundance and activity of proteins that regulate chromatin structure. This article focuses on research that has uncovered human diseases that stem from such epigenetic deregulation. Disease may be caused by direct changes in epigenetic marks, such as DNA methylation, commonly found to affect imprinted gene regulation. Also described are disease-causing genetic mutations in epigenetic modifiers that either affect chromatin in trans or have a cis effect in altering chromatin configuration.
Collapse
Affiliation(s)
- Huda Y Zoghbi
- Howard Hughes Medical Institute, Baylor College of Medicine, and Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
| |
Collapse
|
78
|
|
79
|
Cheon CK, Ko JM. Kabuki syndrome: clinical and molecular characteristics. KOREAN JOURNAL OF PEDIATRICS 2015; 58:317-24. [PMID: 26512256 PMCID: PMC4623449 DOI: 10.3345/kjp.2015.58.9.317] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 06/22/2015] [Indexed: 12/13/2022]
Abstract
Kabuki syndrome (KS) is a rare syndrome characterized by multiple congenital anomalies and mental retardation. Other characteristics include a peculiar facial gestalt, short stature, skeletal and visceral abnormalities, cardiac anomalies, and immunological defects. Whole exome sequencing has uncovered the genetic basis of KS. Prior to 2013, there was no molecular genetic information about KS in Korean patients. More recently, direct Sanger sequencing and exome sequencing revealed KMT2D variants in 11 Korean patients and a KDM6A variant in one Korean patient. The high detection rate of KMT2D and KDM6A mutations (92.3%) is expected owing to the strict criteria used to establish a clinical diagnosis. Increased awareness and understanding of KS among clinicians is important for diagnosis and management of KS and for primary care of KS patients. Because mutation detection rates rely on the accuracy of the clinical diagnosis and the inclusion or exclusion of atypical cases, recognition of KS will facilitate the identification of novel mutations. A brief review of KS is provided, highlighting the clinical and genetic characteristics of patients with KS.
Collapse
Affiliation(s)
- Chong-Kun Cheon
- Department of Pediatrics, Pusan National University Children's Hospital, Pusan National University School of Medicine, Yangsan, Korea
| | - Jung Min Ko
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Korea
| |
Collapse
|
80
|
Vallianatos CN, Iwase S. Disrupted intricacy of histone H3K4 methylation in neurodevelopmental disorders. Epigenomics 2015; 7:503-19. [PMID: 26077434 DOI: 10.2217/epi.15.1] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Methylation of histone H3 lysine 4 (H3K4me) is an intricately regulated posttranslational modification, which is broadly associated with enhancers and promoters of actively transcribed genomic loci. Recent advances in next-generation sequencing have identified a number of H3K4me regulators mutated in neurodevelopmental disorders including intellectual disabilities, autism spectrum disorders, and schizophrenia. Here, we aim to summarize the molecular function of H3K4me-regulating enzymes in brain development and function. We describe four H3K4me methyltransferases (KMT2A, KMT2C, KMT2D, KMT2F), four demethylases (KDM1A, KDM5A, KDM5B, KDM5C), and two reader proteins (PHF21A, PHF8) mutated in neurodevelopmental disorders. Understanding the role of these chromatin regulators in the development and maintenance of neural connections will advance therapeutic opportunities for prevention and treatment of these lifelong neurodevelopmental disorders.
Collapse
Affiliation(s)
- Christina N Vallianatos
- Department of Human Genetics, University of Michigan, 5815 Medical Science II, Ann Arbor, MI 48109, USA.,Predoctoral Training Program in Genetics, University of Michigan, 5815 Medical Science II, Ann Arbor, MI 48109, USA
| | - Shigeki Iwase
- Department of Human Genetics, University of Michigan, 5815 Medical Science II, Ann Arbor, MI 48109, USA
| |
Collapse
|
81
|
|
82
|
Karageorgos I, Mizzi C, Giannopoulou E, Pavlidis C, Peters BA, Zagoriti Z, Stenson PD, Mitropoulos K, Borg J, Kalofonos HP, Drmanac R, Stubbs A, van der Spek P, Cooper DN, Katsila T, Patrinos GP. Identification of cancer predisposition variants in apparently healthy individuals using a next-generation sequencing-based family genomics approach. Hum Genomics 2015; 9:12. [PMID: 26092435 PMCID: PMC4499216 DOI: 10.1186/s40246-015-0034-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Accepted: 06/11/2015] [Indexed: 11/29/2022] Open
Abstract
Cancer, like many common disorders, has a complex etiology, often with a strong genetic component and with multiple environmental factors contributing to susceptibility. A considerable number of genomic variants have been previously reported to be causative of, or associated with, an increased risk for various types of cancer. Here, we adopted a next-generation sequencing approach in 11 members of two families of Greek descent to identify all genomic variants with the potential to predispose family members to cancer. Cross-comparison with data from the Human Gene Mutation Database identified a total of 571 variants, from which 47 % were disease-associated polymorphisms, 26 % disease-associated polymorphisms with additional supporting functional evidence, 19 % functional polymorphisms with in vitro/laboratory or in vivo supporting evidence but no known disease association, 4 % putative disease-causing mutations but with some residual doubt as to their pathological significance, and 3 % disease-causing mutations. Subsequent analysis, focused on the latter variant class most likely to be involved in cancer predisposition, revealed two variants of prime interest, namely MSH2 c.2732T>A (p.L911R) and BRCA1 c.2955delC, the first of which is novel. KMT2D c.13895delC and c.1940C>A variants are additionally reported as incidental findings. The next-generation sequencing-based family genomics approach described herein has the potential to be applied to other types of complex genetic disorder in order to identify variants of potential pathological significance.
Collapse
Affiliation(s)
- Ioannis Karageorgos
- Department of Pharmacy, University of Patras, School of Health Sciences, University Campus, Rion GR-26504, Patras, Greece
| | - Clint Mizzi
- Department of Physiology and Biochemistry, Faculty of Health Sciences, University of Malta, Msida, Malta.,Department of Bioinformatics, School of Medicine and Health Sciences, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Efstathia Giannopoulou
- Clinical Oncology Laboratory, Division of Oncology, Department of Medicine, University of Patras, Patras, Greece
| | - Cristiana Pavlidis
- Department of Pharmacy, University of Patras, School of Health Sciences, University Campus, Rion GR-26504, Patras, Greece
| | - Brock A Peters
- Complete Genomics Inc., Mountain View, CA, USA.,BGI-Shenzhen, Shenzhen, 51803, China
| | - Zoi Zagoriti
- Department of Pharmacy, University of Patras, School of Health Sciences, University Campus, Rion GR-26504, Patras, Greece
| | - Peter D Stenson
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | | | - Joseph Borg
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida, Malta.,Department of Cell Biology and Genetics, School of Medicine and Health Sciences, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Haralabos P Kalofonos
- Clinical Oncology Laboratory, Division of Oncology, Department of Medicine, University of Patras, Patras, Greece
| | - Radoje Drmanac
- Complete Genomics Inc., Mountain View, CA, USA.,BGI-Shenzhen, Shenzhen, 51803, China
| | - Andrew Stubbs
- Department of Bioinformatics, School of Medicine and Health Sciences, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Peter van der Spek
- Department of Bioinformatics, School of Medicine and Health Sciences, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Theodora Katsila
- Department of Pharmacy, University of Patras, School of Health Sciences, University Campus, Rion GR-26504, Patras, Greece
| | - George P Patrinos
- Department of Pharmacy, University of Patras, School of Health Sciences, University Campus, Rion GR-26504, Patras, Greece. .,Department of Bioinformatics, School of Medicine and Health Sciences, Erasmus University Medical Center, Rotterdam, The Netherlands.
| |
Collapse
|
83
|
Le syndrome Kabuki : mise au point et revue de la littérature. Arch Pediatr 2015; 22:653-60. [DOI: 10.1016/j.arcped.2015.03.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 01/02/2015] [Accepted: 03/10/2015] [Indexed: 12/12/2022]
|
84
|
Van Laarhoven PM, Neitzel LR, Quintana AM, Geiger EA, Zackai EH, Clouthier DE, Artinger KB, Ming JE, Shaikh TH. Kabuki syndrome genes KMT2D and KDM6A: functional analyses demonstrate critical roles in craniofacial, heart and brain development. Hum Mol Genet 2015; 24:4443-53. [PMID: 25972376 DOI: 10.1093/hmg/ddv180] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 05/11/2015] [Indexed: 12/16/2022] Open
Abstract
Kabuki syndrome (KS) is a rare multiple congenital anomaly syndrome characterized by distinctive facial features, global developmental delay, intellectual disability and cardiovascular and musculoskeletal abnormalities. While mutations in KMT2D have been identified in a majority of KS patients, a few patients have mutations in KDM6A. We analyzed 40 individuals clinically diagnosed with KS for mutations in KMT2D and KDM6A. Mutations were detected in KMT2D in 12 and KDM6A in 4 cases, respectively. Observed mutations included single-nucleotide variations and indels leading to frame shifts, nonsense, missense or splice-site alterations. In two cases, we discovered overlapping chromosome X microdeletions containing KDM6A. To further elucidate the functional roles of KMT2D and KDM6A, we knocked down the expression of their orthologs in zebrafish. Following knockdown of kmt2d and the two zebrafish paralogs kdm6a and kdm6al, we analyzed morphants for developmental abnormalities in tissues that are affected in individuals with KS, including craniofacial structures, heart and brain. The kmt2d morphants exhibited severe abnormalities in all tissues examined. Although the kdm6a and kdm6al morphants had similar brain abnormalities, kdm6a morphants exhibited craniofacial phenotypes, whereas kdm6al morphants had prominent defects in heart development. Our results provide further support for the similar roles of KMT2D and KDM6A in the etiology of KS by using a vertebrate model organism to provide direct evidence of their roles in the development of organs and tissues affected in KS patients.
Collapse
Affiliation(s)
| | - Leif R Neitzel
- Department of Pediatrics, Section of Clinical Genetics and Metabolism and
| | - Anita M Quintana
- Department of Pediatrics, Section of Clinical Genetics and Metabolism and
| | - Elizabeth A Geiger
- Department of Pediatrics, Section of Clinical Genetics and Metabolism and
| | - Elaine H Zackai
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, the University of Pennsylvania School of Medicine, Philadelphia, PA, USA and
| | - David E Clouthier
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Kristin B Artinger
- Intellectual and Developmental Disabilities Research Center, University of Colorado School of Medicine, Aurora, CO, USA, Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jeffrey E Ming
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, the University of Pennsylvania School of Medicine, Philadelphia, PA, USA and
| | - Tamim H Shaikh
- Department of Pediatrics, Section of Clinical Genetics and Metabolism and, Intellectual and Developmental Disabilities Research Center, University of Colorado School of Medicine, Aurora, CO, USA,
| |
Collapse
|
85
|
Shen E, Shulha H, Weng Z, Akbarian S. Regulation of histone H3K4 methylation in brain development and disease. Philos Trans R Soc Lond B Biol Sci 2015; 369:rstb.2013.0514. [PMID: 25135975 DOI: 10.1098/rstb.2013.0514] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The growing list of mutations implicated in monogenic disorders of the developing brain includes at least seven genes (ARX, CUL4B, KDM5A, KDM5C, KMT2A, KMT2C, KMT2D) with loss-of-function mutations affecting proper regulation of histone H3 lysine 4 methylation, a chromatin mark which on a genome-wide scale is broadly associated with active gene expression, with its mono-, di- and trimethylated forms differentially enriched at promoter and enhancer and other regulatory sequences. In addition to these rare genetic syndromes, dysregulated H3K4 methylation could also play a role in the pathophysiology of some cases diagnosed with autism or schizophrenia, two conditions which on a genome-wide scale are associated with H3K4 methylation changes at hundreds of loci in a subject-specific manner. Importantly, the reported alterations for some of the diseased brain specimens included a widespread broadening of H3K4 methylation profiles at gene promoters, a process that could be regulated by the UpSET(KMT2E/MLL5)-histone deacetylase complex. Furthermore, preclinical studies identified maternal immune activation, parental care and monoaminergic drugs as environmental determinants for brain-specific H3K4 methylation. These novel insights into the epigenetic risk architectures of neurodevelopmental disease will be highly relevant for efforts aimed at improved prevention and treatment of autism and psychosis spectrum disorders.
Collapse
Affiliation(s)
- Erica Shen
- Department of Psychiatry, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hennady Shulha
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Schahram Akbarian
- Department of Psychiatry, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| |
Collapse
|
86
|
Liu S, Hong X, Shen C, Shi Q, Wang J, Xiong F, Qiu Z. Kabuki syndrome: a Chinese case series and systematic review of the spectrum of mutations. BMC MEDICAL GENETICS 2015; 16:26. [PMID: 25896430 PMCID: PMC4630853 DOI: 10.1186/s12881-015-0171-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Accepted: 03/30/2015] [Indexed: 11/17/2022]
Abstract
Background Kabuki syndrome is a rare hereditary disease affecting multiple organs. The causative genes identified to date are KMT2D and KDMA6. The aim of this study is to evaluate the clinical manifestations and the spectrum of mutations of KMT2D. Methods We retrospectively retrieved a series of eight patients from two hospitals in China and conducted Sanger sequencing for all of the patients and their parents if available. We also reviewed the literature and plotted the mutation spectrum of KMT2D. Results The patients generally presented with typical clinical manifestations as previously reported in other countries. Uncommon symptoms included spinal bifida and Dandy-Walker malformation. With respect to the mutations, five mutations were found in five patients, including two frameshift indels, one nonsense mutation and two missense mutations. Conclusions This is the first case series on Kabuki syndrome in Mainland China. Unusual symptoms, such as spinal bifida and Dandy-Walker syndrome, suggested that neurological developmental defects may accompany Kabuki syndrome. This case series helps broaden the mutation spectrum of Kabuki syndrome and adds information regarding the manifestations of Kabuki syndrome.
Collapse
Affiliation(s)
- Shuang Liu
- Department of Pediatrics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Xiafei Hong
- Peking Union Medical College, Beijing, China.
| | - Cheng Shen
- Peking Union Medical College, Beijing, China.
| | | | - Jian Wang
- Peking Union Medical College, Beijing, China.
| | - Feng Xiong
- Endocrinology Department, Children's hospital of ChongQing Medical University, ChongQing, China.
| | - Zhengqing Qiu
- Department of Pediatrics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| |
Collapse
|
87
|
Dentici ML, Di Pede A, Lepri FR, Gnazzo M, Lombardi MH, Auriti C, Petrocchi S, Pisaneschi E, Bellacchio E, Capolino R, Braguglia A, Angioni A, Dotta A, Digilio MC, Dallapiccola B. Kabuki syndrome: clinical and molecular diagnosis in the first year of life. Arch Dis Child 2015; 100:158-64. [PMID: 25281733 DOI: 10.1136/archdischild-2013-305858] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
OBJECTIVE To review the clinical and molecular genetic characteristics of 16 patients presenting a suspected diagnosis of Kabuki syndrome (KS) in the first year of life, to evaluate the clinical handles leading to a prompt diagnosis of KS in newborns. Clinical diagnosis of KS can be challenging during the first year of life, as many diagnostic features become evident only in subsequent years. METHODS All patients were clinically investigated by trained clinical geneticists. A literature review was performed using the Pubmed online database and diagnostic criteria suggested by DYSCERNE-Kabuki Syndrome Guidelines (2010) were used (a European Network of Centres of Expertise for Dysmorphology, funded by the European Commission Executive Agency for Health and Consumers (DG Sanco), Project 2006122). Molecular analysis of the known causative genes of KS, KMT2D/MLL2 and KDM6A, was performed through MiSeq-targeted sequencing platform. All mutations identified were validated by Sanger sequencing protocols. RESULTS Mutations in KMT2D gene were identified in 10/16 (62%) of the patients, whereas none of the patients had KDM6A mutations. Facial dysmorphisms (94%), feeding difficulties (100%) and hypotonia (100%) suggested the clinical diagnosis of KS. No significative differences in terms of facial features were noticed between mutation positive and negative patients of the cohort. Brachydactyly, joint laxity and nail dysplasia were present in about 80% of the patients. Other congenital anomalies were most commonly present in the mutated group of patients, including left-sided cardiac abnormalities, skeletal, renal and anorectal malformations and hypertricosis. CONCLUSIONS We present an overview of patients with KS diagnosed during the first year of life. Early diagnosis is serviceable in terms of clinical management and for targeted genetic counselling.
Collapse
Affiliation(s)
- Maria Lisa Dentici
- Medical Genetics Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Alessandra Di Pede
- Neonatal Intensive Care Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Francesca Romana Lepri
- Cytogenetics and Molecular Genetics Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Maria Gnazzo
- Cytogenetics and Molecular Genetics Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Cinzia Auriti
- Neonatal Intensive Care Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Stefano Petrocchi
- Cytogenetics and Molecular Genetics Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Elisa Pisaneschi
- Cytogenetics and Molecular Genetics Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Rossella Capolino
- Medical Genetics Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Annabella Braguglia
- Neonatal Intensive Care Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Adriano Angioni
- Cytogenetics and Molecular Genetics Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Andrea Dotta
- Neonatal Intensive Care Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Bruno Dallapiccola
- Scientific Directory, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| |
Collapse
|
88
|
Keith BP, Robertson DL, Hentges KE. Locus heterogeneity disease genes encode proteins with high interconnectivity in the human protein interaction network. Front Genet 2014; 5:434. [PMID: 25538735 PMCID: PMC4260505 DOI: 10.3389/fgene.2014.00434] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 11/24/2014] [Indexed: 01/20/2023] Open
Abstract
Mutations in genes potentially lead to a number of genetic diseases with differing severity. These disease genes have been the focus of research in recent years showing that the disease gene population as a whole is not homogeneous, and can be categorized according to their interactions. Locus heterogeneity describes a single disorder caused by mutations in different genes each acting individually to cause the same disease. Using datasets of experimentally derived human disease genes and protein interactions, we created a protein interaction network to investigate the relationships between the products of genes associated with a disease displaying locus heterogeneity, and use network parameters to suggest properties that distinguish these disease genes from the overall disease gene population. Through the manual curation of known causative genes of 100 diseases displaying locus heterogeneity and 397 single-gene Mendelian disorders, we use network parameters to show that our locus heterogeneity network displays distinct properties from the global disease network and a Mendelian network. Using the global human proteome, through random simulation of the network we show that heterogeneous genes display significant interconnectivity. Further topological analysis of this network revealed clustering of locus heterogeneity genes that cause identical disorders, indicating that these disease genes are involved in similar biological processes. We then use this information to suggest additional genes that may contribute to diseases with locus heterogeneity.
Collapse
Affiliation(s)
- Benjamin P Keith
- Faculty of Life Sciences, University of Manchester Manchester, UK
| | | | | |
Collapse
|
89
|
Van Rechem C, Whetstine JR. Examining the impact of gene variants on histone lysine methylation. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1839:1463-76. [PMID: 24859469 PMCID: PMC4752941 DOI: 10.1016/j.bbagrm.2014.05.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 05/14/2014] [Accepted: 05/15/2014] [Indexed: 02/09/2023]
Abstract
In recent years, there has been a boom in the amount of genome-wide sequencing data that has uncovered important and unappreciated links between certain genes, families of genes and enzymatic processes and diseases such as cancer. Such studies have highlighted the impact that chromatin modifying enzymes could have in cancer and other genetic diseases. In this review, we summarize characterized mutations and single nucleotide polymorphisms (SNPs) in histone lysine methyltransferases (KMTs), histone lysine demethylases (KDMs) and histones. We primarily focus on variants with strong disease correlations and discuss how they could impact histone lysine methylation dynamics and gene regulation.
Collapse
Affiliation(s)
- Capucine Van Rechem
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, 13th Street, Charlestown, MA 02129, USA
| | - Johnathan R Whetstine
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, 13th Street, Charlestown, MA 02129, USA.
| |
Collapse
|
90
|
Takagi M, Ishii T, Torii C, Kosaki K, Hasegawa T. A novel mutation in SOX3 polyalanine tract: a case of Kabuki syndrome with combined pituitary hormone deficiency harboring double mutations in MLL2 and SOX3. Pituitary 2014; 17:569-74. [PMID: 24346842 DOI: 10.1007/s11102-013-0546-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
INTRODUCTION Both duplications encompassing SOX3 and loss-of function mutations in SOX3 have been reported in a minor portion of X-linked isolated growth hormone deficiency (GHD) or combined pituitary hormone deficiency (CPHD) patients with or without mental retardation. PATIENTS AND METHODS We report a Japanese male patient with molecularly confirmed Kabuki syndrome who was found to have CPHD. We analyzed all coding exons and flanking introns of currently known nine genes responsible for CPHD by PCR-based sequencing. RESULTS In this CPHD patient, we identified a novel hemizygous 21-base pair deletion, resulting in the loss of 7 alanine residues from polyalanine (PA) tracts of SOX3. The clinically and endocrinologically normal mother of the patient carried the same deletion in a heterozygous manner. In vitro experiments showed that the del 7A SOX3 had increased transactivation of the HESX1 promoter. CONCLUSION Our study provides additional evidence that deletion in PA tracts of SOX3 is associated with hypopituitarism. Female carriers of SOX3 PA tract deletions will show a broad phenotypic spectrum, ranging from clinically normal to CPHD.
Collapse
Affiliation(s)
- Masaki Takagi
- Department of Pediatrics, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | | | | | | | | |
Collapse
|
91
|
Chen YH, Sun MH, Hsia SH, Lai CC, Wu WC. Rare ocular features in a case of Kabuki syndrome (Niikawa-Kuroki syndrome). BMC Ophthalmol 2014; 14:143. [PMID: 25421742 PMCID: PMC4251844 DOI: 10.1186/1471-2415-14-143] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 11/18/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Kabuki syndrome is a multi-system disorder with peculiar facial features, and ophthalmic abnormalities are frequently involved. This case report of a child with Kabuki syndrome describes two new previously unreported ophthalmic conditions. CASE PRESENTATION A 3-year-old Taiwanese boy with Kabuki syndrome had a short stature, spinal dysraphism, intellectual disability and typical facial features. Ophthalmic findings which have been previously reported in the literature and in this patient, included ptosis, esotropia, coloboma of the iris, retina, choroid and optic disc, and microcornea. The newly identified ophthalmic features in this patient included colobomatous microphthalmos and a dysplastic and elevated disc without central cupping. The genetic analysis identified an MLL2 gene mutation. CONCLUSION The presentations of a dysplastic disc and colobomatous microphthalmia are rarely reported in patients with Kabuki syndrome, but these ophthalmic abnormalities may affect vision. Detailed ophthalmic evaluations in children with Kabuki syndrome are advised.
Collapse
Affiliation(s)
| | | | | | | | - Wei-Chi Wu
- Department of Ophthalmology, Chang Gung Memorial Hospital, No, 5, Fu-Hsing Street, Kweishan, Taoyuan 333, Taiwan.
| |
Collapse
|
92
|
Patel N, Alkuraya FS. Overlap between CHARGE and Kabuki syndromes: More than an interesting clinical observation? Am J Med Genet A 2014; 167A:259-60. [DOI: 10.1002/ajmg.a.36804] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 09/08/2014] [Indexed: 10/24/2022]
Affiliation(s)
- Nisha Patel
- Department of Genetics; King Faisal Specialist Hospital and Research Center; Riyadh Saudi Arabia
| | - Fowzan S. Alkuraya
- Department of Genetics; King Faisal Specialist Hospital and Research Center; Riyadh Saudi Arabia
- Department of Anatomy and Cell Biology; College of Medicine; Alfaisal University; Riyadh Saudi Arabia
| |
Collapse
|
93
|
Lin JL, Lee WI, Huang JL, Chen PKT, Chan KC, Lo LJ, You YJ, Shih YF, Tseng TY, Wu MC. Immunologic assessment and KMT2D mutation detection in Kabuki syndrome. Clin Genet 2014; 88:255-60. [PMID: 25142838 DOI: 10.1111/cge.12484] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 08/14/2014] [Accepted: 08/16/2014] [Indexed: 12/31/2022]
Abstract
Kabuki or Niikawa-Kuroki syndrome (KS) is a rare disorder with multiple malformations and recurrent infections, especially otitis media. This study aimed to investigate the genetic defects in Kabuki syndrome and determine if immune status is related to recurrent otitis media. Fourteen patients from 12 unrelated families were enrolled in the 9-year study period (2005-2013). All had Kabuki faces, cleft palate, developmental delay, mental retardation, and the short fifth finger. Recurrent otitis media (12/14) and hearing impairment (8/14) were also more common features. Immunologic analysis revealed lower memory CD19+ cells (11/13), lower memory CD4+ cells (8/13), undetectable anti-HBs antibodies (7/13), and antibody deficiency (7/13), including lower IgA (4), IgG (2), and IgG2 (1). Naïve emigrant lymphocytes, lymphocyte proliferation function, complement activity, and superoxide production in polymorphonuclear cells were all normal. All the patients had KMT2D mutations and 10 novel mutations of R1252X, R1757X,Y1998C, P2550R fs2604X, Q4013X, G5379X, E5425K, R5432X, R5432W, and R5500W. Resembling the phenotype of common variable immunodeficiency, KS patients with antibody deficiency, decreased memory cells, and poor vaccine response increased susceptibility to recurrent otitis media. Large-scale prospective studies are warranted to determine if regular immunoglobulin supplementation decreases the frequency of otitis media and severity of hearing impairment.
Collapse
Affiliation(s)
- J-L Lin
- Division of Genetics and Endocrinology
| | - W-I Lee
- Primary Immunodeficiency Care and Research (PICAR) Institute.,Division of Allergy, Asthma and Rheumatology, Department of Pediatrics
| | - J-L Huang
- Primary Immunodeficiency Care and Research (PICAR) Institute.,Division of Allergy, Asthma and Rheumatology, Department of Pediatrics
| | - P K-T Chen
- Division of Plasty, Department of Surgery
| | - K-C Chan
- Division of Ear, Nose and Throat, Department of Surgery, Chang Gung University College of Medicine and Chang Gung Children's and Memorial Hospital, Taoyuan, Taiwan
| | - L-J Lo
- Division of Plasty, Department of Surgery
| | - Y-J You
- Division of Genetics and Endocrinology
| | - Y-F Shih
- Primary Immunodeficiency Care and Research (PICAR) Institute
| | - T-Y Tseng
- Primary Immunodeficiency Care and Research (PICAR) Institute
| | - M-C Wu
- Division of Genetics and Endocrinology
| |
Collapse
|
94
|
Tunovic S, Barkovich J, Sherr EH, Slavotinek AM. De novo ANKRD11 and KDM1A gene mutations in a male with features of KBG syndrome and Kabuki syndrome. Am J Med Genet A 2014; 164A:1744-9. [PMID: 24838796 DOI: 10.1002/ajmg.a.36450] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 12/31/2013] [Indexed: 11/07/2022]
Abstract
KBG syndrome is a rare, autosomal dominant disorder caused by mutations or deletions leading to haploinsufficiency for the Ankrin Repeating Domain-Containing protein 11 (ANKRD11) at chromosome 16q24.3. Kabuki syndrome is caused by mutations or deletions of lysine (K)-specific methyltransferase 2D (KMT2D) and lysine-specific methylase 6A (KDM6A). We report on a male with developmental delays, cleft palate, craniofacial dysmorphism, hypotonia, and central nervous system anomalies including diminished white matter with thinning of the corpus callosum. Exome sequencing revealed a de novo mutation in ANKRD11, c.2606_2608delAGA, predicting p.Lys869del and an additional, de novo mutation, c.2353T>C, predicting p.Tyr785His in KDM1A, a gene not previously associated with a human phenotype. We describe this child as the first report of a deleterious sequence variant in KDM1A and hypothesize that his phenotype resulted from the combined effect of both mutations.
Collapse
Affiliation(s)
- Sanjin Tunovic
- Department of Pediatrics and Institute for Human Genetics, University of California, San Francisco, San Francisco, California
| | | | | | | |
Collapse
|
95
|
Cheon CK, Sohn YB, Ko JM, Lee YJ, Song JS, Moon JW, Yang BK, Ha IS, Bae EJ, Jin HS, Jeong SY. Identification of KMT2D and KDM6A mutations by exome sequencing in Korean patients with Kabuki syndrome. J Hum Genet 2014; 59:321-5. [PMID: 24739679 DOI: 10.1038/jhg.2014.25] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 03/24/2014] [Accepted: 03/26/2014] [Indexed: 01/13/2023]
Abstract
Kabuki syndrome (KS) (OMIM#147920) is a multiple congenital anomaly/mental retardation syndrome. Recently, pathogenic variants in KMT2D and KDM6A were identified as the causes of KS in 55.8-80.0% of patients. To elucidate further the molecular characteristics of Korean patients with KS, we screened a cohort of patients with clinically defined KS for mutations in KMT2D and KDM6A. Whole-exome sequencing and direct sequencing for validation were performed in 12 patients with a clinical suspicion of KS. KMT2D and KDM6A mutations were identified in 11 (91.7%) patients. No recurrent mutation was observed, and 10 out of the 11 mutations found were novel. KMT2D mutations were detected in 10 patients, including four small deletions or insertions and four nonsense and two missense mutations. One girl had a novel splice-site mutation in KDM6A. Each patient had a unique individual mutation. This is the first report of mutational analysis via exome sequencing in Korean patients with KS. Because the mutation-detection rate was high in this study, rigorous mutation analysis of KMT2D and KDM6A may be an important tool for the early diagnosis and genetic counseling of Korean patients with KS.
Collapse
Affiliation(s)
- Chong Kun Cheon
- 1] Department of Pediatrics, Pediatric Genetics and Metabolism, Pusan National University Children's Hospital, Pusan National University School of Medicine, Yangsan, South Korea [2] Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, South Korea
| | - Young Bae Sohn
- Department of Medical Genetics, Ajou University School of Medicine, Suwon, South Korea
| | - Jung Min Ko
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, South Korea
| | - Yeoun Joo Lee
- Department of Pediatrics, Pediatric Genetics and Metabolism, Pusan National University Children's Hospital, Pusan National University School of Medicine, Yangsan, South Korea
| | - Ji Sun Song
- 1] Department of Pediatrics, Pediatric Genetics and Metabolism, Pusan National University Children's Hospital, Pusan National University School of Medicine, Yangsan, South Korea [2] Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, South Korea
| | - Jea Woo Moon
- Theragen BiO Institute (TBI), Suwon, South Korea
| | | | - Il Soo Ha
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, South Korea
| | - Eun Jung Bae
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, South Korea
| | - Hyun-Seok Jin
- Department of Medical Genetics, Ajou University School of Medicine, Suwon, South Korea
| | - Seon-Yong Jeong
- Department of Medical Genetics, Ajou University School of Medicine, Suwon, South Korea
| |
Collapse
|
96
|
Micale L, Augello B, Maffeo C, Selicorni A, Zucchetti F, Fusco C, De Nittis P, Pellico MT, Mandriani B, Fischetto R, Boccone L, Silengo M, Biamino E, Perria C, Sotgiu S, Serra G, Lapi E, Neri M, Ferlini A, Cavaliere ML, Chiurazzi P, Monica MD, Scarano G, Faravelli F, Ferrari P, Mazzanti L, Pilotta A, Patricelli MG, Bedeschi MF, Benedicenti F, Prontera P, Toschi B, Salviati L, Melis D, Di Battista E, Vancini A, Garavelli L, Zelante L, Merla G. Molecular analysis, pathogenic mechanisms, and readthrough therapy on a large cohort of Kabuki syndrome patients. Hum Mutat 2014; 35:841-50. [PMID: 24633898 PMCID: PMC4234006 DOI: 10.1002/humu.22547] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 03/05/2014] [Indexed: 12/04/2022]
Abstract
Kabuki syndrome (KS) is a multiple congenital anomalies syndrome characterized by characteristic facial features and varying degrees of mental retardation, caused by mutations in KMT2D/MLL2 and KDM6A/UTX genes. In this study, we performed a mutational screening on 303 Kabuki patients by direct sequencing, MLPA, and quantitative PCR identifying 133 KMT2D, 62 never described before, and four KDM6A mutations, three of them are novel. We found that a number of KMT2D truncating mutations result in mRNA degradation through the nonsense-mediated mRNA decay, contributing to protein haploinsufficiency. Furthermore, we demonstrated that the reduction of KMT2D protein level in patients’ lymphoblastoid and skin fibroblast cell lines carrying KMT2D-truncating mutations affects the expression levels of known KMT2D target genes. Finally, we hypothesized that the KS patients may benefit from a readthrough therapy to restore physiological levels of KMT2D and KDM6A proteins. To assess this, we performed a proof-of-principle study on 14 KMT2D and two KDM6A nonsense mutations using specific compounds that mediate translational readthrough and thereby stimulate the re-expression of full-length functional proteins. Our experimental data showed that both KMT2D and KDM6A nonsense mutations displayed high levels of readthrough in response to gentamicin treatment, paving the way to further studies aimed at eventually treating some Kabuki patients with readthrough inducers.
Collapse
Affiliation(s)
- Lucia Micale
- Medical Genetics Unit, IRCCS Casa Sollievo Della Sofferenza Hospital, San Giovanni Rotondo, Italy
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
97
|
Grozeva D, Carss K, Spasic-Boskovic O, Parker MJ, Archer H, Firth HV, Park SM, Canham N, Holder SE, Wilson M, Hackett A, Field M, Floyd JAB, Hurles M, Raymond FL. De novo loss-of-function mutations in SETD5, encoding a methyltransferase in a 3p25 microdeletion syndrome critical region, cause intellectual disability. Am J Hum Genet 2014; 94:618-24. [PMID: 24680889 PMCID: PMC3980521 DOI: 10.1016/j.ajhg.2014.03.006] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 03/11/2014] [Indexed: 11/21/2022] Open
Abstract
To identify further Mendelian causes of intellectual disability (ID), we screened a cohort of 996 individuals with ID for variants in 565 known or candidate genes by using a targeted next-generation sequencing approach. Seven loss-of-function (LoF) mutations-four nonsense (c.1195A>T [p.Lys399(∗)], c.1333C>T [p.Arg445(∗)], c.1866C>G [p.Tyr622(∗)], and c.3001C>T [p.Arg1001(∗)]) and three frameshift (c.2177_2178del [p.Thr726Asnfs(∗)39], c.3771dup [p.Ser1258Glufs(∗)65], and c.3856del [p.Ser1286Leufs(∗)84])-were identified in SETD5, a gene predicted to encode a methyltransferase. All mutations were compatible with de novo dominant inheritance. The affected individuals had moderate to severe ID with additional variable features of brachycephaly; a prominent high forehead with synophrys or striking full and broad eyebrows; a long, thin, and tubular nose; long, narrow upslanting palpebral fissures; and large, fleshy low-set ears. Skeletal anomalies, including significant leg-length discrepancy, were a frequent finding in two individuals. Congenital heart defects, inguinal hernia, or hypospadias were also reported. Behavioral problems, including obsessive-compulsive disorder, hand flapping with ritualized behavior, and autism, were prominent features. SETD5 lies within the critical interval for 3p25 microdeletion syndrome. The individuals with SETD5 mutations showed phenotypic similarity to those previously reported with a deletion in 3p25, and thus loss of SETD5 might be sufficient to account for many of the clinical features observed in this condition. Our findings add to the growing evidence that mutations in genes encoding methyltransferases regulating histone modification are important causes of ID. This analysis provides sufficient evidence that rare de novo LoF mutations in SETD5 are a relatively frequent (0.7%) cause of ID.
Collapse
Affiliation(s)
- Detelina Grozeva
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Keren Carss
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Olivera Spasic-Boskovic
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Michael J Parker
- Sheffield Clinical Genetics Service, Sheffield Children's Hospital, Western Bank, Sheffield S10 2TH, UK
| | - Hayley Archer
- Institute of Medical Genetics, University Hospital of Wales, Heath Park, Cardiff CF14 4XW, UK
| | - Helen V Firth
- Clinical Genetics, Addenbrooke's Treatment Centre, Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge CB2 0QQ, UK
| | - Soo-Mi Park
- Clinical Genetics, Addenbrooke's Treatment Centre, Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge CB2 0QQ, UK
| | - Natalie Canham
- North West Thames Regional Genetics Service (Kennedy Galton Centre), North West London Hospitals NHS Trust, Harrow, Middlesex HA1 3UJ, UK
| | - Susan E Holder
- North West Thames Regional Genetics Service (Kennedy Galton Centre), North West London Hospitals NHS Trust, Harrow, Middlesex HA1 3UJ, UK
| | - Meredith Wilson
- Department of Clinical Genetics, Children's Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Anna Hackett
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW 2298, Australia
| | - Michael Field
- Department of Medical Genetics, Royal North Shore Hospital, St. Leonards, NSW 2298, Australia
| | - James A B Floyd
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK; The Genome Centre, John Vane Science Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Matthew Hurles
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - F Lucy Raymond
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK.
| |
Collapse
|
98
|
Banka S, Lederer D, Benoit V, Jenkins E, Howard E, Bunstone S, Kerr B, McKee S, Lloyd IC, Shears D, Stewart H, White SM, Savarirayan R, Mancini GMS, Beysen D, Cohn RD, Grisart B, Maystadt I, Donnai D. Novel KDM6A (UTX) mutations and a clinical and molecular review of the X-linked Kabuki syndrome (KS2). Clin Genet 2014; 87:252-8. [PMID: 24527667 DOI: 10.1111/cge.12363] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 02/09/2014] [Accepted: 02/12/2014] [Indexed: 01/08/2023]
Abstract
We describe seven patients with KDM6A (located on Xp11.3 and encodes UTX) mutations, a rare cause of Kabuki syndrome (KS2, MIM 300867) and report, for the first time, germ-line missense and splice-site mutations in the gene. We demonstrate that less than 5% cases of Kabuki syndrome are due to KDM6A mutations. Our work shows that similar to the commoner Type 1 Kabuki syndrome (KS1, MIM 147920) caused by KMT2D (previously called MLL2) mutations, KS2 patients are characterized by hypotonia and feeding difficulties during infancy and poor postnatal growth and short stature. Unlike KS1, developmental delay and learning disability are generally moderate-severe in boys but mild-moderate in girls with KS2. Some girls may have a normal developmental profile. Speech and cognition tend to be more severely affected than motor development. Increased susceptibility to infections, join laxity, heart, dental and ophthalmological anomalies are common. Hypoglycaemia is more common in KS2 than in KS1. Facial dysmorphism with KDM6A mutations is variable and diagnosis on facial gestalt alone may be difficult in some patients. Hypertrichosis, long halluces and large central incisors may be useful clues to an underlying KDM6A mutation in some patients.
Collapse
Affiliation(s)
- S Banka
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester Academic Health Science Centre (MAHSC), Manchester, UK; Manchester Centre for Genomic Medicine, Institute of Human Development, University of Manchester, Manchester, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
99
|
Shinsky SA, Hu M, Vought VE, Ng SB, Bamshad MJ, Shendure J, Cosgrove MS. A non-active-site SET domain surface crucial for the interaction of MLL1 and the RbBP5/Ash2L heterodimer within MLL family core complexes. J Mol Biol 2014; 426:2283-99. [PMID: 24680668 DOI: 10.1016/j.jmb.2014.03.011] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 03/14/2014] [Accepted: 03/20/2014] [Indexed: 11/17/2022]
Abstract
The mixed lineage leukemia-1 (MLL1) enzyme is a histone H3 lysine 4 (H3K4) monomethyltransferase and has served as a paradigm for understanding the mechanism of action of the human SET1 family of enzymes that include MLL1-MLL4 and SETd1a,b. Dimethylation of H3K4 requires a sub-complex including WRAD (WDR5, RbBP5, Ash2L, and DPY-30), which binds to each SET1 family member forming a minimal core complex that is required for multiple lysine methylation. We recently demonstrated that WRAD is a novel histone methyltransferase that preferentially catalyzes H3K4 dimethylation in a manner that is dependent on an unknown non-active-site surface from the MLL1 SET domain. Recent genome sequencing studies have identified a number of human disease-associated missense mutations that localize to the SET domains of several MLL family members. In this investigation, we mapped many of these mutations onto the three-dimensional structure of the SET domain and noticed that a subset of MLL2 (KMT2D, ALR, MLL4)-associated Kabuki syndrome missense mutations map to a common solvent-exposed surface that is not expected to alter enzymatic activity. We introduced these mutations into the MLL1 SET domain and observed that all are defective for H3K4 dimethylation by the MLL1 core complex, which is associated with a loss of the ability of MLL1 to interact with WRAD or with the RbBP5/Ash2L heterodimer. Our results suggest that amino acids from this surface, which we term the Kabuki interaction surface or KIS, are required for formation of a second active site within SET1 family core complexes.
Collapse
Affiliation(s)
- Stephen A Shinsky
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Michael Hu
- Department of Biology, Syracuse University, Syracuse, NY 13210, USA
| | - Valarie E Vought
- Department of Biology, Syracuse University, Syracuse, NY 13210, USA
| | - Sarah B Ng
- Department of Genome Sciences, University of Washington Seattle, Seattle, WA 98105, USA
| | - Michael J Bamshad
- Department of Genome Sciences, University of Washington Seattle, Seattle, WA 98105, USA; Department of Pediatrics, University of Washington Seattle, Seattle, WA 98195, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington Seattle, Seattle, WA 98105, USA
| | - Michael S Cosgrove
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA.
| |
Collapse
|
100
|
Lederer D, Shears D, Benoit V, Verellen-Dumoulin C, Maystadt I. A three generation X-linked family with Kabuki syndrome phenotype and a frameshift mutation in KDM6A. Am J Med Genet A 2014; 164A:1289-92. [PMID: 24664873 DOI: 10.1002/ajmg.a.36442] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 12/16/2013] [Indexed: 01/03/2023]
Abstract
Kabuki syndrome is a rare malformation syndrome characterized by a typical facial appearance, skeletal anomalies, cardiac malformation, and mild to moderate intellectual disability. In 55-80% of patients with Kabuki syndrome, a mutation in MLL2 is identified. Recently, eight patients with Kabuki syndrome and a mutation in KDM6A were described. In this report, we describe two brothers with a mutation in KDM6A inherited from their mother and maternal grandmother. The two boys have Kabuki-like phenotypes whereas the mother and grandmother present with attenuated phenotypes. This family represents the first instance of hereditary X-linked Kabuki syndrome. We present a short literature review of the patients described with a mutation in KDM6A.
Collapse
Affiliation(s)
- Damien Lederer
- Center for Human Genetics, IPG, Charleroi, (Gosselies), Belgium
| | | | | | | | | |
Collapse
|