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Yoon JH, Hwang S, Bae H, Kim D, Seo GH, Koh JY, Ju YS, Do HS, Kim S, Kim GH, Kim JH, Choi JH, Lee BH. Clinical and molecular characteristics of Korean patients with Kabuki syndrome. J Hum Genet 2024:10.1038/s10038-024-01258-1. [PMID: 38824232 DOI: 10.1038/s10038-024-01258-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/11/2024] [Accepted: 05/16/2024] [Indexed: 06/03/2024]
Abstract
INTRODUCTION Kabuki syndrome (KS) is a rare disorder characterized by typical facial features, skeletal anomalies, fetal fingertip pad persistence, postnatal growth retardation, and intellectual disabilities. Heterozygous variants of the KMT2D and KDM6A genes are major genetic causes of KS. This study aimed to report the clinical and genetic characteristics of KS. METHODS This study included 28 Korean patients (14 boys and 14 girls) with KS through molecular genetic testing, including direct Sanger sequencing, whole-exome sequencing, or whole-genome sequencing. RESULTS The median age at clinical diagnosis was 18.5 months (IQR 7-58 months), and the median follow-up duration was 80.5 months (IQR 48-112 months). Molecular genetic testing identified different pathogenic variants of the KMT2D (n = 23) and KDM6A (n = 3) genes, including 15 novel variants. Patients showed typical facial features (100%), such as long palpebral fissure and eversion of the lower eyelid; intellectual disability/developmental delay (96%); short stature (79%); and congenital cardiac anomalies (75%). Although 71% experienced failure to thrive in infancy, 54% of patients showed a tendency toward overweight/obesity in early childhood. Patients with KDM6A variants demonstrated severe genotype-phenotype correlation. CONCLUSION This study enhances the understanding of the clinical and genetic characteristics of KS.
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Affiliation(s)
- Ji-Hee Yoon
- Department of Pediatrics, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
- Medical Genetics Center, Asan Medical Center, Seoul, Republic of Korea
- Department of Pediatrics, Kangbuk Samsung Hospital, Sungkyunkwan University of School of Medicine, Seoul, Republic of Korea
| | - Soojin Hwang
- Department of Pediatrics, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
- Medical Genetics Center, Asan Medical Center, Seoul, Republic of Korea
| | - Hyunwoo Bae
- Department of Pediatrics, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
- Medical Genetics Center, Asan Medical Center, Seoul, Republic of Korea
| | - Dohyung Kim
- Department of Pediatrics, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
- Medical Genetics Center, Asan Medical Center, Seoul, Republic of Korea
| | - Go Hun Seo
- Division of Medical genetics, 3billion Inc., Seoul, Republic of Korea
| | | | | | - Hyo-Sang Do
- Asan Institute for Life Sciences, Asan Medical Center, Seoul, Republic of Korea
| | - Soyoung Kim
- Asan Institute for Life Sciences, Asan Medical Center, Seoul, Republic of Korea
| | - Gu-Hwan Kim
- Medical Genetics Center, Asan Medical Center, Seoul, Republic of Korea
| | - Ja Hye Kim
- Department of Pediatrics, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
- Medical Genetics Center, Asan Medical Center, Seoul, Republic of Korea
| | - Jin-Ho Choi
- Department of Pediatrics, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
- Medical Genetics Center, Asan Medical Center, Seoul, Republic of Korea
| | - Beom Hee Lee
- Department of Pediatrics, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
- Medical Genetics Center, Asan Medical Center, Seoul, Republic of Korea.
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Tibben BM, Rothbart SB. Mechanisms of DNA Methylation Regulatory Function and Crosstalk with Histone Lysine Methylation. J Mol Biol 2024; 436:168394. [PMID: 38092287 PMCID: PMC10957332 DOI: 10.1016/j.jmb.2023.168394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/06/2023] [Accepted: 12/06/2023] [Indexed: 12/20/2023]
Abstract
DNA methylation is a well-studied epigenetic modification that has key roles in regulating gene expression, maintaining genome integrity, and determining cell fate. Precisely how DNA methylation patterns are established and maintained in specific cell types at key developmental stages is still being elucidated. However, research over the last two decades has contributed to our understanding of DNA methylation regulation by other epigenetic processes. Specifically, lysine methylation on key residues of histone proteins has been shown to contribute to the allosteric regulation of DNA methyltransferase (DNMT) activities. In this review, we discuss the dynamic interplay between DNA methylation and histone lysine methylation as epigenetic regulators of genome function by synthesizing key recent studies in the field. With a focus on DNMT3 enzymes, we discuss mechanisms of DNA methylation and histone lysine methylation crosstalk in the regulation of gene expression and the maintenance of genome integrity. Further, we discuss how alterations to the balance of various sites of histone lysine methylation and DNA methylation contribute to human developmental disorders and cancers. Finally, we provide perspectives on the current direction of the field and highlight areas for continued research and development.
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Affiliation(s)
- Bailey M Tibben
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Scott B Rothbart
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA.
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Li Z, Ning Z. Neonatal Kabuki syndrome caused by KMT2D mutation: A case report. Medicine (Baltimore) 2023; 102:e36681. [PMID: 38115267 PMCID: PMC10727567 DOI: 10.1097/md.0000000000036681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/20/2023] [Accepted: 11/27/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND Kabuki syndrome (KS) is an autosomal dominant inherited syndrome that involves multiple organs and systems. Gene mutation is the main cause of KS. The reported mutations in X-linked histone H3 lysine 4 methylase (KMT2D) and KDM6A genes are 2 relatively clear pathogenic pathways. In this paper, we report a case of KS with neonatal hypoglycemia and special features caused by KMT2D gene mutation confirmed by whole exome sequencing, it enriched the clinical phenotype spectrum and gene mutation spectrum of KS, which helps to improve the understanding of the disease. CASE REPORT Through whole exome sequencing, we performed gene diagnosis of a newborn child with special facial features and multiple malformations, which revealed heterozygous mutation of NM_003482.3:c.755dupA(p.His252Glnfs*21) in KMT2D gene. It is consistent with the pathogenesis of KS, an autosomal dominat genetic disease caused by KMT2D gene mutation. This pathogenic mutation has not been prebiously reported. DISCUSSION KS has strong clinical characteristics and biological heterogeneity. Genetic diagnosis can help identify mutant gene types. However, the relationship between genotype and phenotype has not been fully clarified. The molecular etiological mechanism still needs to be further explored and elucidated.
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Affiliation(s)
- Zhang Li
- The Second Affiliated Hospital of Dalian Medical University, Dalian City, Liaoning Province, China
| | - Zou Ning
- The Second Affiliated Hospital of Dalian Medical University, Dalian City, Liaoning Province, China
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Golden CS, Williams S, Serrano MA. Molecular insights of KMT2D and clinical aspects of Kabuki syndrome type 1. Birth Defects Res 2023; 115:1809-1824. [PMID: 37158694 PMCID: PMC10845236 DOI: 10.1002/bdr2.2183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 04/03/2023] [Accepted: 04/14/2023] [Indexed: 05/10/2023]
Abstract
BACKGROUND Kabuki syndrome type 1 (KS1), a rare multisystem congenital disorder, presents with characteristic facial features, intellectual disability, persistent fetal fingertip pads, skeletal abnormalities, and postnatal growth delays. KS1 results from pathogenic variants in the KMT2D gene, which encodes a histone methyltransferase protein involved in chromatin remodeling, promoter and enhancer regulation, and scaffold formation during early development. KMT2D also mediates cell signaling pathways, responding to external stimuli and organizing effector protein assembly. Research on KMT2D's molecular mechanisms in KS1 has primarily focused on its histone methyltransferase activity, leaving a gap in understanding the methyltransferase-independent roles in KS1 clinical manifestations. METHODS This scoping review examines KMT2D's role in gene expression regulation across various species, cell types, and contexts. We analyzed human pathogenic KMT2D variants using publicly available databases and compared them to research organism models of KS1. We also conducted a systematic search of healthcare and governmental databases for clinical trials, studies, and therapeutic approaches. RESULTS Our review highlights KMT2D's critical roles beyond methyltransferase activity in diverse cellular contexts and conditions. We identified six distinct groups of KMT2D as a cell signaling mediator, including evidence of methyltransferase-dependent and -independent activity. A comprehensive search of the literature, clinical databases, and public registries emphasizes the need for basic research on KMT2D's functional complexity and longitudinal studies of KS1 patients to establish objective outcome measurements for therapeutic development. CONCLUSION We discuss how KMT2D's role in translating external cellular communication can partly explain the clinical heterogeneity observed in KS1 patients. Additionally, we summarize the current molecular diagnostic approaches and clinical trials targeting KS1. This review is a resource for patient advocacy groups, researchers, and physicians to support KS1 diagnosis and therapeutic development.
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Affiliation(s)
- Carly S Golden
- Center for Regenerative Medicine, Section of Vascular Biology, Department of Medicine, Boston University, Boston, Massachusetts, USA
| | - Saylor Williams
- Center for Regenerative Medicine, Section of Vascular Biology, Department of Medicine, Boston University, Boston, Massachusetts, USA
| | - Maria A Serrano
- Center for Regenerative Medicine, Section of Vascular Biology, Department of Medicine, Boston University, Boston, Massachusetts, USA
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Yi S, Zhang X, Yang Q, Huang J, Zhou X, Qian J, Pan P, Yi S, Zhang S, Zhang Q, Tang X, Huang L, Zhang Q, Qin Z, Luo J. Clinical and molecular analysis of Guangxi patients with Kabuki syndrome and KMT2D mutations. Heliyon 2023; 9:e20223. [PMID: 37810849 PMCID: PMC10550629 DOI: 10.1016/j.heliyon.2023.e20223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 08/10/2023] [Accepted: 09/14/2023] [Indexed: 10/10/2023] Open
Abstract
Kabuki syndrome (KS) is a multiple congenital anomaly syndrome that is characterized by postnatal growth deficiency, hypotonia, short stature, mild-to-moderate intellectual disability, skeletal abnormalities, persistence of fetal fingertip pads, and distinct facial appearance. It is mainly caused by pathogenic/likely pathogenic variants in the KMT2D or KDM6A genes. Here, we described the clinical features of nine sporadic KS patients with considerable phenotypic heterogeneity. In addition to intellectual disability and short stature, our patients presented with a high prevalence of motor retardation and recurrent otitis media. We recommended that KS should be strongly considered in patients with motor delay, short stature, intellectual disability, language disorder and facial deformities. Nine KMT2D variants, four of which were novel, were identified by whole-exome sequencing. The variants included five nonsense variants, two frameshift variants, one missense variant, and one non-canonical splice site variant. In addition, we reviewed the mutation types of the pathogenic KMT2D variants in the ClinVar database. We also indicated that effective mRNA analysis, using biological materials from patients, is helpful in classifying the pathogenicity of atypical splice site variants. Pedigree segregation analysis may also provide valuable information for pathogenicity classification of novel missense variants. These findings extended the mutation spectrum of KMT2D and provided new insights into the understanding of genotype-phenotype correlations, which are helpful for accurate genetic counseling and treatment optimization.
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Affiliation(s)
- Sheng Yi
- Genetic and Metabolic Central Laboratory, Guangxi Birth Defects Research and Prevention Institute, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Clinical Research Center for Pediatric Diseases, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Guangxi Key Laboratory of Birth Defects and Stem Cell Biobank, Guangxi Key Laboratory of Birth Defects Research and Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Xiaofei Zhang
- Genetic and Metabolic Central Laboratory, Guangxi Birth Defects Research and Prevention Institute, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Pediatrics Department, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Qi Yang
- Genetic and Metabolic Central Laboratory, Guangxi Birth Defects Research and Prevention Institute, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Clinical Research Center for Pediatric Diseases, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Guangxi Key Laboratory of Birth Defects and Stem Cell Biobank, Guangxi Key Laboratory of Birth Defects Research and Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Jingjing Huang
- Department of Surgery, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Xunzhao Zhou
- Genetic and Metabolic Central Laboratory, Guangxi Birth Defects Research and Prevention Institute, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Clinical Research Center for Pediatric Diseases, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Guangxi Key Laboratory of Birth Defects and Stem Cell Biobank, Guangxi Key Laboratory of Birth Defects Research and Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Jiale Qian
- Genetic and Metabolic Central Laboratory, Guangxi Birth Defects Research and Prevention Institute, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Pediatrics Department, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Pingshan Pan
- Department of Obstetrics, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Shang Yi
- Genetic and Metabolic Central Laboratory, Guangxi Birth Defects Research and Prevention Institute, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Clinical Research Center for Pediatric Diseases, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Guangxi Key Laboratory of Birth Defects and Stem Cell Biobank, Guangxi Key Laboratory of Birth Defects Research and Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Shujie Zhang
- Genetic and Metabolic Central Laboratory, Guangxi Birth Defects Research and Prevention Institute, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Clinical Research Center for Pediatric Diseases, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Guangxi Key Laboratory of Birth Defects and Stem Cell Biobank, Guangxi Key Laboratory of Birth Defects Research and Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Qiang Zhang
- Genetic and Metabolic Central Laboratory, Guangxi Birth Defects Research and Prevention Institute, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Clinical Research Center for Pediatric Diseases, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Guangxi Key Laboratory of Birth Defects and Stem Cell Biobank, Guangxi Key Laboratory of Birth Defects Research and Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Xianglian Tang
- Genetic and Metabolic Central Laboratory, Guangxi Birth Defects Research and Prevention Institute, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Clinical Research Center for Pediatric Diseases, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Guangxi Key Laboratory of Birth Defects and Stem Cell Biobank, Guangxi Key Laboratory of Birth Defects Research and Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Limei Huang
- Genetic and Metabolic Central Laboratory, Guangxi Birth Defects Research and Prevention Institute, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Clinical Research Center for Pediatric Diseases, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Guangxi Key Laboratory of Birth Defects and Stem Cell Biobank, Guangxi Key Laboratory of Birth Defects Research and Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Qinle Zhang
- Genetic and Metabolic Central Laboratory, Guangxi Birth Defects Research and Prevention Institute, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Clinical Research Center for Pediatric Diseases, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Guangxi Key Laboratory of Birth Defects and Stem Cell Biobank, Guangxi Key Laboratory of Birth Defects Research and Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Zailong Qin
- Genetic and Metabolic Central Laboratory, Guangxi Birth Defects Research and Prevention Institute, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Clinical Research Center for Pediatric Diseases, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Guangxi Key Laboratory of Birth Defects and Stem Cell Biobank, Guangxi Key Laboratory of Birth Defects Research and Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Jingsi Luo
- Genetic and Metabolic Central Laboratory, Guangxi Birth Defects Research and Prevention Institute, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Clinical Research Center for Pediatric Diseases, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Guangxi Key Laboratory of Birth Defects and Stem Cell Biobank, Guangxi Key Laboratory of Birth Defects Research and Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
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Souabni SA, Harvengt A, Legat C, Lysy PA. Congenital hyperinsulinemic hypoglycemia (HH) requiring treatment as the presenting feature of Kabuki syndrome. Clin Case Rep 2023; 11:e7336. [PMID: 37257167 PMCID: PMC10220455 DOI: 10.1002/ccr3.7336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 04/13/2023] [Accepted: 04/20/2023] [Indexed: 06/02/2023] Open
Abstract
Kabuki syndrome is a congenital condition characterized by a set of facial dysmorphic features that often help the clinician to suspect the diagnosis. However, more insidious symptoms can rarely occur, such as manifestations of hypoglycemia in newborns with congenital hyperinsulinism hypoglycemia, especially when a variant of the KDM6A gene is found. In those cases, a treatment with diazoxide can be started and can be replaced with lanreotide if a satisfying glycemic control is not achieved. We report the case of a female patient born at 37 weeks of gestational age, without any obvious facial dysmorphic features, after a non-complicated pregnancy, that presented with feeding difficulties, drowsiness, and irritability revealing a hyperinsulinemic hypoglycemia. Further testing at 6 months old found a KDM6A mutation. The patient was initially treated by diazoxide alone, but its dosage had to be lowered because of the occurrence of treatment side effects, and lanreotide had been added to maintain acceptable blood sugar levels. A congenital hyperinsulinemia hypoglycemia revealed heterozygous truncating variant in the KDM6A gene, also known as X-linked Kabuki syndrome in a newborn. In cases of neonatal hypoglycemia, the first-line therapy is diazoxide. Our report shows that analogues of somatostatin such as lanreotide should be considered if the diazoxide regimen is not tolerated.
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Affiliation(s)
- Saloua Ait Souabni
- Pediatric Endocrinology, Specialized Pediatrics Service Cliniques Universitaires Saint Luc, UCLouvain Brussels Belgium
| | - Antoine Harvengt
- Pediatric Endocrinology, Specialized Pediatrics Service Cliniques Universitaires Saint Luc, UCLouvain Brussels Belgium
| | - Camille Legat
- Pediatric Endocrinology, Specialized Pediatrics Service Cliniques Universitaires Saint Luc, UCLouvain Brussels Belgium
| | - Philippe A Lysy
- Pediatric Endocrinology, Specialized Pediatrics Service Cliniques Universitaires Saint Luc, UCLouvain Brussels Belgium
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7
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Sheppard SE, Bryant L, Wickramasekara RN, Vaccaro C, Robertson B, Hallgren J, Hulen J, Watson CJ, Faundes V, Duffourd Y, Lee P, Simon MC, de la Cruz X, Padilla N, Flores-Mendez M, Akizu N, Smiler J, Pellegrino Da Silva R, Li D, March M, Diaz-Rosado A, Peixoto de Barcelos I, Choa ZX, Lim CY, Dubourg C, Journel H, Demurger F, Mulhern M, Akman C, Lippa N, Andrews M, Baldridge D, Constantino J, van Haeringen A, Snoeck-Streef I, Chow P, Hing A, Graham JM, Au M, Faivre L, Shen W, Mao R, Palumbos J, Viskochil D, Gahl W, Tifft C, Macnamara E, Hauser N, Miller R, Maffeo J, Afenjar A, Doummar D, Keren B, Arn P, Macklin-Mantia S, Meerschaut I, Callewaert B, Reis A, Zweier C, Brewer C, Saggar A, Smeland MF, Kumar A, Elmslie F, Deshpande C, Nizon M, Cogne B, van Ierland Y, Wilke M, van Slegtenhorst M, Koudijs S, Chen JY, Dredge D, Pier D, Wortmann S, Kamsteeg EJ, Koch J, Haynes D, Pollack L, Titheradge H, Ranguin K, Denommé-Pichon AS, Weber S, Pérez de la Fuente R, Sánchez del Pozo J, Lezana Rosales JM, Joset P, Steindl K, Rauch A, Mei D, Mari F, Guerrini R, Lespinasse J, Tran Mau-Them F, Philippe C, Dauriat B, Raymond L, Moutton S, Cueto-González AM, Tan TY, Mignot C, Grotto S, Renaldo F, Drivas TG, Hennessy L, Raper A, Parenti I, Kaiser FJ, Kuechler A, Busk ØL, Islam L, Siedlik JA, Henderson LB, Juusola J, Person R, Schnur RE, Vitobello A, Banka S, Bhoj EJ, Stessman HA. Mechanism of KMT5B haploinsufficiency in neurodevelopment in humans and mice. SCIENCE ADVANCES 2023; 9:eade1463. [PMID: 36897941 PMCID: PMC10005179 DOI: 10.1126/sciadv.ade1463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
Pathogenic variants in KMT5B, a lysine methyltransferase, are associated with global developmental delay, macrocephaly, autism, and congenital anomalies (OMIM# 617788). Given the relatively recent discovery of this disorder, it has not been fully characterized. Deep phenotyping of the largest (n = 43) patient cohort to date identified that hypotonia and congenital heart defects are prominent features that were previously not associated with this syndrome. Both missense variants and putative loss-of-function variants resulted in slow growth in patient-derived cell lines. KMT5B homozygous knockout mice were smaller in size than their wild-type littermates but did not have significantly smaller brains, suggesting relative macrocephaly, also noted as a prominent clinical feature. RNA sequencing of patient lymphoblasts and Kmt5b haploinsufficient mouse brains identified differentially expressed pathways associated with nervous system development and function including axon guidance signaling. Overall, we identified additional pathogenic variants and clinical features in KMT5B-related neurodevelopmental disorder and provide insights into the molecular mechanisms of the disorder using multiple model systems.
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Affiliation(s)
- Sarah E. Sheppard
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Unit on Vascular Malformations, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Laura Bryant
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Rochelle N. Wickramasekara
- Stessman Laboratory, Department of Pharmacology and Neuroscience, Creighton University Medical School, Omaha, NE, USA
- Molecular Diagnostic Laboratory, Boys Town National Research Hospital, Omaha, NE, USA
| | - Courtney Vaccaro
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Brynn Robertson
- Stessman Laboratory, Department of Pharmacology and Neuroscience, Creighton University Medical School, Omaha, NE, USA
| | - Jodi Hallgren
- Stessman Laboratory, Department of Pharmacology and Neuroscience, Creighton University Medical School, Omaha, NE, USA
| | - Jason Hulen
- Stessman Laboratory, Department of Pharmacology and Neuroscience, Creighton University Medical School, Omaha, NE, USA
| | - Cynthia J. Watson
- Stessman Laboratory, Department of Pharmacology and Neuroscience, Creighton University Medical School, Omaha, NE, USA
| | - Victor Faundes
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile
| | - Yannis Duffourd
- Unité Fonctionnelle d’Innovation diagnostique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Pearl Lee
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - M. Celeste Simon
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Xavier de la Cruz
- Vall d’Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca I Estudis Avançats (ICREA), Barcelona, Spain
| | - Natália Padilla
- Vall d’Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Marco Flores-Mendez
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Naiara Akizu
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jacqueline Smiler
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- 10x Genomics, Pleasanton, CA, USA
| | | | - Dong Li
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Michael March
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Abdias Diaz-Rosado
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Zhao Xiang Choa
- Epithelial Epigenetics and Development Laboratory, A*STAR Skin Research Labs, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Chin Yan Lim
- Epithelial Epigenetics and Development Laboratory, A*STAR Skin Research Labs, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Christèle Dubourg
- Laboratoire de Génétique Moléculaire et Génomique, Centre Hospitalier Universitaire de Rennes, Rennes 35033, France
| | - Hubert Journel
- Service de Génétique Médicale, Hopital Chubert, Vannes, Bretagne, France
| | - Florence Demurger
- Department of Clinical Genetics, Service de Génétique Clinique, Centre de Référence Maladies Rares Centre Labellisé Anomalies du Développement-Ouest, Centre Hospitalier Universitaire de Rennes, Rennes 35033, France
| | - Maureen Mulhern
- Department of Pathology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Cigdem Akman
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Natalie Lippa
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Marisa Andrews
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Dustin Baldridge
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - John Constantino
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Arie van Haeringen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Irina Snoeck-Streef
- Department of Child Neurology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Penny Chow
- Department of Pediatrics, Division of Craniofacial Medicine, University of Washington, Seattle, WA, USA
| | - Anne Hing
- Department of Pediatrics, Division of Craniofacial Medicine, University of Washington, Seattle, WA, USA
| | - John M. Graham
- Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, UCLA School of Medicine, Los Angeles, CA, USA
| | - Margaret Au
- Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, UCLA School of Medicine, Los Angeles, CA, USA
| | - Laurence Faivre
- UFR Des Sciences de Santé, INSERM–Université de Bourgogne UMR1231 GAD “Génétique des Anomalies du Développement,” FHU-TRANSLAD, Dijon, France
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, CHU Dijon, Bourgogne, France
| | - Wei Shen
- University of Utah, Salt Lake City, UT, USA
- Mayo Clinic, Rochester, MN, USA
| | - Rong Mao
- University of Utah, Salt Lake City, UT, USA
| | | | | | - William Gahl
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Cynthia Tifft
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ellen Macnamara
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Natalie Hauser
- Medical Genetics, Inova Fairfax Hospital, Falls Church, VA, USA
| | - Rebecca Miller
- Medical Genetics, Inova Fairfax Hospital, Falls Church, VA, USA
| | - Jessica Maffeo
- Medical Genetics, Inova Fairfax Hospital, Falls Church, VA, USA
| | - Alexandra Afenjar
- AP-HP, Sorbonne Université, Département de neuropediatrie, Hospital Armand Trousseau, Paris, France
| | - Diane Doummar
- AP-HP, Sorbonne Université, Département de neuropediatrie, Hospital Armand Trousseau, Paris, France
| | - Boris Keren
- Genetic Department, Pitié-Salpêtrière Hospital, AP-HP, Sorbonne Université, Paris, France
| | - Pamela Arn
- Department of Pediatrics, Nemours Children’s Specialty Care, Jacksonville, FL, USA
| | | | - Ilse Meerschaut
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Bert Callewaert
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - André Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Christiane Zweier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland
| | - Carole Brewer
- Clinical Genetics Department, Royal Devon and Exeter Hospital (Heavitree), Exeter EX1 2ED, UK
| | - Anand Saggar
- Clinical Genetics Department, St George’s Hospital, St George’s Healthcare NHS Trust, London SW17 0QT, UK
| | - Marie F. Smeland
- Department of Medical Genetics, University Hospital of North Norway, Tromsø, Norway
- Department of Pediatric Rehabilitation, University Hospital of North Norway, Norway
| | - Ajith Kumar
- Northeast Thames Regional Genetics Service, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Frances Elmslie
- South West Thames Centre for Genomics, St George’s University Hospitals NHS Foundation Trust, London SW17 0QT, UK
| | - Charu Deshpande
- Department of Medical Genetics, Guy’s Hospital, London SE1 9RT, UK
| | - Mathilde Nizon
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes CEDEX 1, France
| | - Benjamin Cogne
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes CEDEX 1, France
- Nantes Université, CNRS, INSERM, L’institut du thorax, F-44000 Nantes, France
| | - Yvette van Ierland
- Department of Clinical Genetics, Erasmus University Medical Center, P.O. Box 2040, 3000 CA Rotterdam, Netherlands
| | - Martina Wilke
- Department of Clinical Genetics, Erasmus University Medical Center, P.O. Box 2040, 3000 CA Rotterdam, Netherlands
| | - Marjon van Slegtenhorst
- Department of Clinical Genetics, Erasmus University Medical Center, P.O. Box 2040, 3000 CA Rotterdam, Netherlands
| | - Suzanne Koudijs
- Department of Neurology, Erasmus University Medical Center–Sophia Children’s Hospital, P.O. Box 2040, 3000 CA Rotterdam, Netherlands
| | - Jin Yun Chen
- Neurology Department, Massachusetts General Hospital, Boston, MA, USA
| | - David Dredge
- University Children’s Hospital Salzburg, Paracelsus Medical University (PMU), Salzburg, Austria
| | - Danielle Pier
- Neurology Department, Massachusetts General Hospital, Boston, MA, USA
| | - Saskia Wortmann
- University Children’s Hospital Salzburg, Paracelsus Medical University (PMU), Salzburg, Austria
- Amalia Children’s Hospital, RadboudUMC Nijmegen, Nijmegen, Netherlands
| | - Erik-Jan Kamsteeg
- University Children’s Hospital Salzburg, Paracelsus Medical University (PMU), Salzburg, Austria
| | - Johannes Koch
- University Children’s Hospital Salzburg, Paracelsus Medical University (PMU), Salzburg, Austria
| | - Devon Haynes
- Division of Genetics, Arnold Palmer Hospital for Children–Orlando Health, Orlando, FL, USA
| | - Lynda Pollack
- Division of Genetics, Arnold Palmer Hospital for Children–Orlando Health, Orlando, FL, USA
| | - Hannah Titheradge
- West Midlands Regional Genetics Service and Birmingham Health Partners, Birmingham Women’s and Children’s NHS Trust, Birmingham B15 2TG, UK
| | - Kara Ranguin
- Department of Genetics, Reference Centre for Rare Diseases and Developmental Anomalies, Caen Hospital, Caen, France
| | - Anne-Sophie Denommé-Pichon
- Unité Fonctionnelle d’Innovation diagnostique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
- UFR Des Sciences de Santé, INSERM–Université de Bourgogne UMR1231 GAD “Génétique des Anomalies du Développement,” FHU-TRANSLAD, Dijon, France
| | - Sacha Weber
- Department of Genetics, Reference Centre for Rare Diseases and Developmental Anomalies, Caen Hospital, Caen, France
| | | | - Jaime Sánchez del Pozo
- UDISGEN (Unidad de Dismorfología y Genética) 12 de Octubre University Hospital, Madrid, Spain
| | | | - Pascal Joset
- University of Zurich, Institute of Medical Genetics, 8952 Schlieren-Zurich, Switzerland
| | - Katharina Steindl
- University of Zurich, Institute of Medical Genetics, 8952 Schlieren-Zurich, Switzerland
| | - Anita Rauch
- University of Zurich, Institute of Medical Genetics, 8952 Schlieren-Zurich, Switzerland
- University of Zurich, University Children’s Hospital Zurich, 8032 Zurich, Switzerland
- University of Zurich, URPP Adaptive Brain Circuits in Development and Learning (AdaBD), Zurich, Switzerland
- University of Zurich Research Priority Program (URPP) AdaBD: Adaptive Brain Circuits in Development and Learning, Zurich 8006, Switzerland
- University of Zurich Research Priority Program (URPP) ITINERARE: Innovative Therapies in Rare Diseases, Zurich 8006, Switzerland
| | - Davide Mei
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Meyer Children’s Hospital, Member of ERN Epicare, University of Florence, Florence, Italy
| | - Francesco Mari
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Meyer Children’s Hospital, Member of ERN Epicare, University of Florence, Florence, Italy
| | - Renzo Guerrini
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Meyer Children’s Hospital, Member of ERN Epicare, University of Florence, Florence, Italy
| | - James Lespinasse
- UF de Génétique Chromosomique, Centre Hospitalier de Chambéry, Hôtel-dieu, France
| | - Frédéric Tran Mau-Them
- Unité Fonctionnelle d’Innovation diagnostique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
- UFR Des Sciences de Santé, INSERM–Université de Bourgogne UMR1231 GAD “Génétique des Anomalies du Développement,” FHU-TRANSLAD, Dijon, France
| | - Christophe Philippe
- Unité Fonctionnelle d’Innovation diagnostique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
- UFR Des Sciences de Santé, INSERM–Université de Bourgogne UMR1231 GAD “Génétique des Anomalies du Développement,” FHU-TRANSLAD, Dijon, France
| | - Benjamin Dauriat
- Service de cytogénétique et génétique médicale, Centre Hospitalier Universitaire de Limoges, France
| | - Laure Raymond
- Service de génétique, Laboratoire Eurofins Biomnis, Lyon, France
| | | | - Anna M. Cueto-González
- Hospital Vall d'Hebron, Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Tiong Yang Tan
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Cyril Mignot
- AP-HP, Sorbonne Université, Département de Génétique, Paris, France
| | - Sarah Grotto
- AP-HP, Sorbonne Université, Département de Génétique, Paris, France
| | - Florence Renaldo
- AP-HP, Sorbonne Université, Département de neuropediatrie, Centre de référence neurogénétique, Hôpital Armand Trousseau, Paris, France
| | - Theodore G. Drivas
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Laura Hennessy
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Anna Raper
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Ilaria Parenti
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Frank J. Kaiser
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
- Essener Zentrum für Seltene Erkrankungen (EZSE), Universitätsklinikum Essen, Essen, Germany
| | - Alma Kuechler
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Øyvind L. Busk
- Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway
| | - Lily Islam
- West Midlands Regional Genetics Service and Birmingham Health Partners, Birmingham Women’s and Children’s NHS Trust, Birmingham B15 2TG, UK
| | - Jacob A. Siedlik
- Department of Exercise Science and Pre-Health Professions, Creighton University, Omaha, NE, USA
| | | | | | | | - Rhonda E. Schnur
- GeneDx, Gaithersburg, MD, USA
- Department of Pediatrics, Division of Genetics Cooper Medical School of Rowan University Cooper University Health Care 3, Cooper Plaza, Camden, NJ, USA
| | - Antonio Vitobello
- Unité Fonctionnelle d’Innovation diagnostique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
- UFR Des Sciences de Santé, INSERM–Université de Bourgogne UMR1231 GAD “Génétique des Anomalies du Développement,” FHU-TRANSLAD, Dijon, France
| | - Siddharth Banka
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Elizabeth J. Bhoj
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Holly A. F. Stessman
- Stessman Laboratory, Department of Pharmacology and Neuroscience, Creighton University Medical School, Omaha, NE, USA
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8
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Shah SS, Fulton A, Jabroun M, Brightman D, Simpson BN, Bodamer OA. Insights into the genotype-phenotype relationship of ocular manifestations in Kabuki syndrome. Am J Med Genet A 2023; 191:1325-1338. [PMID: 36891680 DOI: 10.1002/ajmg.a.63155] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 03/10/2023]
Abstract
We aim to assess if genotype-phenotype correlations are present within ocular manifestations of Kabuki syndrome (KS) among a large multicenter cohort. We conducted a retrospective, medical record review including clinical history and comprehensive ophthalmological examinations of a total of 47 individuals with molecularly confirmed KS and ocular manifestations at Boston Children's Hospital and Cincinnati Children's Hospital Medical Center. We assessed information regarding ocular structural, functional, and adnexal elements as well as pertinent associated phenotypic features associated with KS. For both type 1 KS (KS1) and type 2 KS (KS2), we observed more severe eye pathology in nonsense variants towards the C-terminus of each gene, KMT2D and KDM6A, respectively. Furthermore, frameshift variants appeared to be not associated with structural ocular elements. Between both types of KS, ocular structural elements were more frequently identified in KS1 compared with KS2, which only involved the optic disc in our cohort. These results reinforce the need for a comprehensive ophthalmologic exam upon diagnosis of KS and regular follow-up exams. The specific genotype may allow risk stratification of the severity of the ophthalmologic manifestation. However, additional studies involving larger cohorts are needed to replicate our observations and conduct powered analyses to more formally risk-stratify based on genotype, highlighting the importance of multicenter collaborations in rare disease research.
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Affiliation(s)
- Suraj S Shah
- Tufts University School of Medicine, Boston, Massachusetts, USA.,Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Anne Fulton
- Department of Ophthalmology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Mireille Jabroun
- Department of Ophthalmology, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Ophthalmology and Vision Science, University of Arizona, Tucson, Arizona, USA
| | - Diana Brightman
- Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati School of Medicine, Cincinnati, Ohio, USA
| | - Brittany N Simpson
- Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati School of Medicine, Cincinnati, Ohio, USA
| | - Olaf A Bodamer
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA.,The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
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9
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Roth C, Kilpinen H, Kurian MA, Barral S. Histone lysine methyltransferase-related neurodevelopmental disorders: current knowledge and saRNA future therapies. Front Cell Dev Biol 2023; 11:1090046. [PMID: 36923252 PMCID: PMC10009263 DOI: 10.3389/fcell.2023.1090046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/06/2023] [Indexed: 03/02/2023] Open
Abstract
Neurodevelopmental disorders encompass a group of debilitating diseases presenting with motor and cognitive dysfunction, with variable age of onset and disease severity. Advances in genetic diagnostic tools have facilitated the identification of several monogenic chromatin remodeling diseases that cause Neurodevelopmental disorders. Chromatin remodelers play a key role in the neuro-epigenetic landscape and regulation of brain development; it is therefore not surprising that mutations, leading to loss of protein function, result in aberrant neurodevelopment. Heterozygous, usually de novo mutations in histone lysine methyltransferases have been described in patients leading to haploinsufficiency, dysregulated protein levels and impaired protein function. Studies in animal models and patient-derived cell lines, have highlighted the role of histone lysine methyltransferases in the regulation of cell self-renewal, cell fate specification and apoptosis. To date, in depth studies of histone lysine methyltransferases in oncology have provided strong evidence of histone lysine methyltransferase dysregulation as a determinant of cancer progression and drug resistance. As a result, histone lysine methyltransferases have become an important therapeutic target for the treatment of different cancer forms. Despite recent advances, we still lack knowledge about the role of histone lysine methyltransferases in neuronal development. This has hampered both the study and development of precision therapies for histone lysine methyltransferases-related Neurodevelopmental disorders. In this review, we will discuss the current knowledge of the role of histone lysine methyltransferases in neuronal development and disease progression. We will also discuss how RNA-based technologies using small-activating RNAs could potentially provide a novel therapeutic approach for the future treatment of histone lysine methyltransferase haploinsufficiency in these Neurodevelopmental disorders, and how they could be first tested in state-of-the-art patient-derived neuronal models.
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Affiliation(s)
- Charlotte Roth
- Molecular Neurosciences, Developmental Neurosciences Programme, Zayed Centre for Research into Rare Disease in Children, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Helena Kilpinen
- Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.,Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Manju A Kurian
- Molecular Neurosciences, Developmental Neurosciences Programme, Zayed Centre for Research into Rare Disease in Children, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom.,Department of Neurology, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Serena Barral
- Molecular Neurosciences, Developmental Neurosciences Programme, Zayed Centre for Research into Rare Disease in Children, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
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10
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Zhong G, Shen Y. Statistical models of the genetic etiology of congenital heart disease. Curr Opin Genet Dev 2022; 76:101967. [PMID: 35939966 PMCID: PMC10586490 DOI: 10.1016/j.gde.2022.101967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 06/29/2022] [Accepted: 07/08/2022] [Indexed: 11/03/2022]
Abstract
Congenital heart disease (CHD) is a collection of anatomically and clinically heterogeneous structure anomalies of heart at birth. Finding genetic causes of CHD can not only shed light on developmental biology of heart, but also provide basis for improving clinical care and interventions. The optimal study design and analytical approaches to identify genetic causes depend on the underlying genetic architecture. A few well-known syndromes with CHD as core conditions, such as Noonan and CHARGE, have known monogenic causes. The genetic causes of most of CHD patients, however, are unknown and likely to be complex. In this review, we highlight recent studies that assume a complex genetic architecture of CHD with two main approaches. One is genomic sequencing studies aiming for identifying rare or de novo risk variants with large genetic effect. The other is genome-wide association studies optimized for common variants with moderate genetic effect.
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Affiliation(s)
- Guojie Zhong
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA; Integrated Program in Cellular, Molecular, and Biological Studies, Columbia University Irving Medical Center, New York, NY, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA; Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA; JP Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY, USA.
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11
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Identification of unique DNA methylation sites in Kabuki syndrome using whole genome bisulfite sequencing and targeted hybridization capture followed by enzymatic methylation sequencing. J Hum Genet 2022; 67:711-720. [PMID: 36167771 DOI: 10.1038/s10038-022-01083-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 09/01/2022] [Accepted: 09/11/2022] [Indexed: 11/08/2022]
Abstract
BACKGROUND Kabuki syndrome (KS) is a congenital malformation syndrome caused by mutations in the KMT2D and KDM6A genes that encode histone modification enzymes. Although KS is considered a single gene disorder, its symptoms vary widely. Recently, disease-specific DNA methylation patterns, or episignatures, have been recognized and used as a diagnostic tool for KS. Because of various crosstalk mechanisms between histone modifications and DNA methylation, DNA methylation analysis may have high potential for investigations into the pathogenesis of KS. RESULTS In this study, we investigated altered CpG-methylation sites that were specific to KS to find important genes associated with the various phenotypes or pathogenesis of KS. Whole genome bisulfite sequencing (WGBS) was performed to select target CpG islands, and enzymatic conversion technology was applied after hybridization capture to confirm KS-specific episignatures of 130 selected differently methylated target regions (DMTRs) in DNA samples from the 65 participants, 31 patients with KS and 34 unaffected individuals, in this study. We identified 26 candidate genes in 22 DMTRs that may be associated with KS. Our results indicate that disease-specific methylation sites can be identified from a small number of WGBS samples, and hybridization capture followed by enzymatic methylation sequencing can simultaneously test the sites. CONCLUSIONS Although DNA methylation can be tissue-specific, our results suggest that methylation profiling of DNA extracted from peripheral blood may be a powerful approach to study the pathogenesis of diseases.
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12
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Jefri M, Zhang X, Stumpf PS, Zhang L, Peng H, Hettige N, Theroux JF, Aouabed Z, Wilson K, Deshmukh S, Antonyan L, Ni A, Alsuwaidi S, Zhang Y, Jabado N, Garcia BA, Schuppert A, Bjornsson HT, Ernst C. Kabuki syndrome stem cell models reveal locus specificity of histone methyltransferase 2D (KMT2D/MLL4). Hum Mol Genet 2022; 31:3715-3728. [PMID: 35640156 PMCID: PMC9616574 DOI: 10.1093/hmg/ddac121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/07/2022] [Accepted: 05/18/2022] [Indexed: 11/14/2022] Open
Abstract
Kabuki syndrome is frequently caused by loss-of-function mutations in one allele of histone 3 lysine 4 (H3K4) methyltransferase KMT2D and is associated with problems in neurological, immunological and skeletal system development. We generated heterozygous KMT2D knockout and Kabuki patient-derived cell models to investigate the role of reduced dosage of KMT2D in stem cells. We discovered chromosomal locus-specific alterations in gene expression, specifically a 110 Kb region containing Synaptotagmin 3 (SYT3), C-Type Lectin Domain Containing 11A (CLEC11A), Chromosome 19 Open Reading Frame 81 (C19ORF81) and SH3 And Multiple Ankyrin Repeat Domains 1 (SHANK1), suggesting locus-specific targeting of KMT2D. Using whole genome histone methylation mapping, we confirmed locus-specific changes in H3K4 methylation patterning coincident with regional decreases in gene expression in Kabuki cell models. Significantly reduced H3K4 peaks aligned with regions of stem cell maps of H3K27 and H3K4 methylation suggesting KMT2D haploinsufficiency impact bivalent enhancers in stem cells. Preparing the genome for subsequent differentiation cues may be of significant importance for Kabuki-related genes. This work provides a new insight into the mechanism of action of an important gene in bone and brain development and may increase our understanding of a specific function of a human disease-relevant H3K4 methyltransferase family member.
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Affiliation(s)
- Malvin Jefri
- Psychiatric Genetics Group, McGill University, 6875 LaSalle Boulevard, Frank Common Building, Room 2101.2, Verdun, Montreal, QC H4H 1R3, Canada,Department of Psychiatry, McGill University and Douglas Hospital Research Institute, Montreal, QC H4H 1R3, Canada
| | - Xin Zhang
- Psychiatric Genetics Group, McGill University, 6875 LaSalle Boulevard, Frank Common Building, Room 2101.2, Verdun, Montreal, QC H4H 1R3, Canada,Department of Psychiatry, McGill University and Douglas Hospital Research Institute, Montreal, QC H4H 1R3, Canada
| | - Patrick S Stumpf
- Institute for Computational Biomedicine, RWTH Aachen University, Aachen 52056, Germany
| | - Li Zhang
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Huashan Peng
- Psychiatric Genetics Group, McGill University, 6875 LaSalle Boulevard, Frank Common Building, Room 2101.2, Verdun, Montreal, QC H4H 1R3, Canada,Department of Psychiatry, McGill University and Douglas Hospital Research Institute, Montreal, QC H4H 1R3, Canada
| | - Nuwan Hettige
- Psychiatric Genetics Group, McGill University, 6875 LaSalle Boulevard, Frank Common Building, Room 2101.2, Verdun, Montreal, QC H4H 1R3, Canada,Department of Psychiatry, McGill University and Douglas Hospital Research Institute, Montreal, QC H4H 1R3, Canada
| | - Jean-Francois Theroux
- Psychiatric Genetics Group, McGill University, 6875 LaSalle Boulevard, Frank Common Building, Room 2101.2, Verdun, Montreal, QC H4H 1R3, Canada,Department of Psychiatry, McGill University and Douglas Hospital Research Institute, Montreal, QC H4H 1R3, Canada
| | - Zahia Aouabed
- Psychiatric Genetics Group, McGill University, 6875 LaSalle Boulevard, Frank Common Building, Room 2101.2, Verdun, Montreal, QC H4H 1R3, Canada,Department of Psychiatry, McGill University and Douglas Hospital Research Institute, Montreal, QC H4H 1R3, Canada
| | - Khadija Wilson
- Department of Biochemistry and Molecular, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Shriya Deshmukh
- Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada
| | - Lilit Antonyan
- Psychiatric Genetics Group, McGill University, 6875 LaSalle Boulevard, Frank Common Building, Room 2101.2, Verdun, Montreal, QC H4H 1R3, Canada,Department of Psychiatry, McGill University and Douglas Hospital Research Institute, Montreal, QC H4H 1R3, Canada
| | - Anjie Ni
- Psychiatric Genetics Group, McGill University, 6875 LaSalle Boulevard, Frank Common Building, Room 2101.2, Verdun, Montreal, QC H4H 1R3, Canada,Department of Psychiatry, McGill University and Douglas Hospital Research Institute, Montreal, QC H4H 1R3, Canada
| | - Shaima Alsuwaidi
- Psychiatric Genetics Group, McGill University, 6875 LaSalle Boulevard, Frank Common Building, Room 2101.2, Verdun, Montreal, QC H4H 1R3, Canada,Department of Psychiatry, McGill University and Douglas Hospital Research Institute, Montreal, QC H4H 1R3, Canada
| | - Ying Zhang
- Psychiatric Genetics Group, McGill University, 6875 LaSalle Boulevard, Frank Common Building, Room 2101.2, Verdun, Montreal, QC H4H 1R3, Canada,Department of Psychiatry, McGill University and Douglas Hospital Research Institute, Montreal, QC H4H 1R3, Canada
| | - Nada Jabado
- Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada,Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada,Department of Pediatrics, McGill University and The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Andreas Schuppert
- Institute for Computational Biomedicine, RWTH Aachen University, Aachen 52056, Germany
| | - Hans T Bjornsson
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA,Faculty of Medicine, University of Iceland, Reykjavik, Iceland,Department of Genetics and Molecular Medicine, Landspitali University Hospital, 101 Reykjavik, Iceland
| | - Carl Ernst
- To whom correspondence should be addressed at: Department of Psychiatry, McGill University and Douglas Hospital Research Institute, 6875 LaSalle boulevard, Frank Common building, Room 2101.2 Verdun, QC H4H 1R3, Canada. Tel: +1 514-761-6131 ext 3382; Fax: +1 514-762-3023;
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13
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Salguero MV, Chan K, Greeley SAW, Dyamenahalli U, Waggoner D, del Gaudio D, Rajiyah T, Lemelman M. Novel KDM6A Kabuki Syndrome Mutation with Hyperinsulinemic Hypoglycemia and Pulmonary Hypertension requiring ECMO. J Endocr Soc 2022; 6:bvac015. [PMID: 35237736 PMCID: PMC8884118 DOI: 10.1210/jendso/bvac015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Indexed: 11/30/2022] Open
Abstract
Kabuki syndrome (KS) is a multisystem disorder estimated to occur in 1:32 000 newborns. Pathogenic mutations cause the majority but not all cases of KS in either KMT2D or KDM6A. KS can be suspected by phenotypic features, including infantile hypotonia, developmental delay, dysmorphic features, congenital heart defects, and others. Still, many of these features are not readily apparent in a newborn. Although neonatal hypoglycemia has been reported in 8% to 10% of patients with KS, the incidence and severity of hyperinsulinemic hypoglycemia (HH) is not well-studied. We present a full-term female infant with HH who was responsive to low-dose diazoxide. At 3 months of age, she was admitted for septic shock, worsening respiratory status, and severe pulmonary hypertension, requiring extracorporeal membrane oxygenation support. Her neonatal history was notable for hypotonia, dysphagia with aspiration requiring gastrostomy tube placement, and a cardiac defect—hypoplastic aortic arch requiring aortic arch repair. She has characteristic facial features, including prominent eyelashes, long palpebral fissures, and a short nasal columella. Next-generation sequencing for HH revealed a de novo likely pathogenic missense variant in KDM6A gene: c.3479G > T, p.Gly1160Val that was absent from population databases. Genetic testing for causes of HH should include testing of the KS genes KMT2D and KDM6A. Early detection of the underlying genetic defect will help guide management as all reported HH cases associated with KS have been responsive to diazoxide. Affected infants with underlying cardiac conditions may be at higher risk of serious respiratory complications such as pulmonary hypertension.
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Affiliation(s)
- Maria V Salguero
- Department of Pediatrics, Section of Adult and Pediatric Endocrinology, University of Chicago
| | - Karen Chan
- Department of Pediatrics, University of Chicago
| | - Siri Atma W Greeley
- Department of Pediatrics, Section of Adult and Pediatric Endocrinology, University of Chicago
| | - Umesh Dyamenahalli
- Department of Pediatrics, Section of Pediatric Cardiology, University of Chicago
| | | | | | - Tara Rajiyah
- Department of Pediatrics, Section of Adult and Pediatric Endocrinology, University of Chicago
| | - Michelle Lemelman
- Department of Pediatrics, Section of Adult and Pediatric Endocrinology, University of Chicago
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14
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Di Candia F, Fontana P, Paglia P, Falco M, Rosano C, Piscopo C, Cappuccio G, Siano MA, De Brasi D, Mandato C, De Maggio I, Squeo GM, Monica MD, Scarano G, Lonardo F, Strisciuglio P, Merla G, Melis D. Clinical heterogeneity of Kabuki syndrome in a cohort of Italian patients and review of the literature. Eur J Pediatr 2022; 181:171-187. [PMID: 34232366 PMCID: PMC8760211 DOI: 10.1007/s00431-021-04108-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 05/02/2021] [Accepted: 05/06/2021] [Indexed: 12/31/2022]
Abstract
Kabuki syndrome (KS) is a well-recognized disorder characterized by postnatal growth deficiency, dysmorphic facial features, skeletal anomalies, and intellectual disability. The syndrome is caused by KMT2D gene mutations or less frequently KDM6A gene mutations or deletions. We report a systematic evaluation of KS patients from Campania region of Italy; data were also compared with literature ones. We collected data of 15 subjects (8 males and 7 females with age range 10-26 years; mean age 16.9 years) with confirmed diagnosis of KS, representing the entire cohort of patients from Campania Region. Each patient performed biochemical testing and instrumental investigation. Neuro-intellectual development, cranio-facial dysmorphisms, and multisystem involvement data were collected retrospectively. For each category, type of defects and frequency of the anomalies were analyzed. Our observation shows that KS patients from Campania region have some particular and previously underscored, neurological and immunological findings. We found high prevalence of EEG's abnormalities (43%) and MRI brain abnormalities (60%). Microcephaly resulted more common in our series (33%), if compared with major cohorts described in literature. Biochemical features of immunodeficiency and autoimmune diseases including thyroid autoimmunity, polyserositis, and vitiligo were observed with high prevalence (54.5%). Low immunoglobulins levels were a frequent finding. Lymphocyte class investigation showed significantly reduced CD8 levels in one patient.Conclusions: These data confirm great heterogeneity of clinical manifestations in KS and suggest to introduce further clinical diagnostic criteria in order to perform a correct and precocious diagnosis. What is Known • Kabuki syndrome is characterized by growth deficiency, dysmorphic facial features, skeletal anomalies, and intellectual disability • Immune dysfunction is a common finding but autoimmune diseases are rarely seen • Neurological features are common What is New • Some particular facial features could help gestalt diagnosis (hypertelorism, broad nasal bridge, micrognathia, tooth agenesis, cutaneous haemangiomas and strabismus) • Higher prevalence of autoimmune disorders than previously reported • Particular neurological features are present in this cohort (EEG and MRI brain abnormalities).
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Affiliation(s)
- Francesca Di Candia
- grid.411293.c0000 0004 1754 9702Pediatric Unit, Translational Medicine Department, Federico II University Hospital, Naples, Italy
| | - Paolo Fontana
- Medical Genetics Unit, San Pio Hospital, Benevento, Italy
| | - Pamela Paglia
- Pediatric Unit, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, (Salerno), Baronissi, Italy
| | - Mariateresa Falco
- Pediatric Unit, San Giovanni di Dio e Ruggi d’Aragona University Hospital, Via San Leonardo, 1 – 84131 Salerno, Italy
| | - Carmen Rosano
- grid.411293.c0000 0004 1754 9702Pediatric Unit, Translational Medicine Department, Federico II University Hospital, Naples, Italy
| | - Carmelo Piscopo
- grid.413172.2Medical Genetics Unit, Cardarelli Hospital, Napoli, Italy
| | - Gerarda Cappuccio
- grid.411293.c0000 0004 1754 9702Pediatric Unit, Translational Medicine Department, Federico II University Hospital, Naples, Italy
| | - Maria Anna Siano
- Pediatric Unit, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, (Salerno), Baronissi, Italy
| | - Daniele De Brasi
- Department of Pediatrics, AORN Santobono-Pausilipon, Napoli, Italy
| | - Claudia Mandato
- Department of Pediatrics, AORN Santobono-Pausilipon, Napoli, Italy
| | - Ilaria De Maggio
- grid.413172.2Medical Genetics Unit, Cardarelli Hospital, Napoli, Italy
| | - Gabriella Maria Squeo
- grid.413503.00000 0004 1757 9135Division of Medical Genetics, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
| | | | | | | | - Pietro Strisciuglio
- grid.411293.c0000 0004 1754 9702Pediatric Unit, Translational Medicine Department, Federico II University Hospital, Naples, Italy
| | - Giuseppe Merla
- grid.413503.00000 0004 1757 9135Division of Medical Genetics, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
| | - Daniela Melis
- Pediatric Unit, Translational Medicine Department, Federico II University Hospital, Naples, Italy. .,Pediatric Unit, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", (Salerno), Baronissi, Italy. .,Pediatric Unit, San Giovanni di Dio e Ruggi d'Aragona University Hospital, Via San Leonardo, 1 - 84131, Salerno, Italy.
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15
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A novel complex genomic rearrangement affecting the KCNJ2 regulatory region causes a variant of Cooks syndrome. Hum Genet 2021; 141:217-227. [PMID: 34821995 DOI: 10.1007/s00439-021-02403-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 11/09/2021] [Indexed: 10/19/2022]
Abstract
Cooks syndrome (CS) is an ultrarare limb malformation due to in tandem microduplications involving KCNJ2 and extending to the 5' regulatory element of SOX9. To date, six CS families were resolved at the molecular level. Subsequent studies explored the evolutionary and pathological complexities of the SOX9-KCNJ2/Sox9-Kcnj2 locus, and suggested a key role for the formation of novel topologically associating domain (TAD) by inter-TAD duplications in causing CS. Here, we report a unique case of CS associated with a de novo 1;17 translocation affecting the KCNJ2 locus. On chromosome 17, the breakpoint mapped between KCNJ16 and KCNJ2, and combined with a ~ 5 kb deletion in the 5' of KCNJ2. Based on available capture Hi-C data, the breakpoint on chromosome 17 separated KCNJ2 from a putative enhancer. Gene expression analysis demonstrated downregulation of KCNJ2 in both patient's blood cells and cultured skin fibroblasts. Our findings suggest that a complex rearrangement falling in the 5' of KCNJ2 may mimic the developmental consequences of in tandem duplications affecting the SOX9-KCNJ2/Sox9-Kcnj2 locus. This finding adds weight to the notion of an intricate role of gene regulatory regions and, presumably, the related three-dimensional chromatin structure in normal and abnormal human morphology.
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16
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Alhendi ASN, Lim D, McKee S, McEntagart M, Tatton-Brown K, Temple IK, Davies JH, Mackay DJG. Whole-genome analysis as a diagnostic tool for patients referred for diagnosis of Silver-Russell syndrome: a real-world study. J Med Genet 2021; 59:613-622. [PMID: 34135092 DOI: 10.1136/jmedgenet-2021-107699] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 05/06/2021] [Indexed: 02/01/2023]
Abstract
BACKGROUND Silver-Russell syndrome (SRS) is an imprinting disorder characterised by prenatal and postnatal growth restriction, but its clinical features are non-specific and its differential diagnosis is broad. Known molecular causes of SRS include imprinting disturbance, single nucleotide variant (SNV), CNV or UPD affecting several genes; however, up to 40% of individuals with a clinical diagnosis of SRS currently receive no positive molecular diagnosis. METHODS To determine whether whole-genome sequencing (WGS) could uncover pathogenic variants missed by current molecular testing, we analysed data of 72 participants recruited to the 100,000 Genomes Project within the clinical category of SRS. RESULTS In 20 participants (27% of the cohort) we identified genetic variants plausibly accounting for SRS. Coding SNVs were identified in genes including CDKN1C, IGF2, IGF1R and ORC1. Maternal-effect variants were found in mothers of five participants, including two participants with imprinting disturbance and one with multilocus imprinting disorder. Two regions of homozygosity were suggestive of UPD involving imprinted regions implicated in SRS and Temple syndrome, and three plausibly pathogenic CNVs were found, including a paternal deletion of PLAGL1. In 48 participants with no plausible pathogenic variant, unbiased analysis of SNVs detected a potential association with STX4. CONCLUSION WGS analysis can detect UPD, CNV and SNV and is potentially a valuable addition to diagnosis of SRS and related growth-restricting disorders.
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Affiliation(s)
- Ahmed S N Alhendi
- Human Genetics and Genomic Medicine, Faculty of Medicine, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Derek Lim
- Department of Clinical Genetics, Birmingham Women's and Children's Hospital, Birmingham, UK
| | - Shane McKee
- Department of Genetic Medicine, Belfast City Hospital, Belfast, UK
| | - Meriel McEntagart
- Department of Clinical Genetics, St George's Healthcare NHS Trust, London, UK
| | | | - I Karen Temple
- Human Genetics and Genomic Medicine, Faculty of Medicine, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Justin H Davies
- Human Genetics and Genomic Medicine, Faculty of Medicine, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Deborah J G Mackay
- Human Genetics and Genomic Medicine, Faculty of Medicine, University Hospital Southampton NHS Foundation Trust, Southampton, UK .,Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK
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17
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Yan S, Lu J, Jiao K. Epigenetic Regulation of Cardiac Neural Crest Cells. Front Cell Dev Biol 2021; 9:678954. [PMID: 33968946 PMCID: PMC8097001 DOI: 10.3389/fcell.2021.678954] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 03/29/2021] [Indexed: 01/02/2023] Open
Abstract
The cardiac neural crest cells (cNCCs) is a transient, migratory cell population that contribute to the formation of major arteries and the septa and valves of the heart. Abnormal development of cNCCs leads to a spectrum of congenital heart defects that mainly affect the outflow region of the hearts. Signaling molecules and transcription factors are the best studied regulatory events controlling cNCC development. In recent years, however, accumulated evidence supports that epigenetic regulation also plays an important role in cNCC development. Here, we summarize the functions of epigenetic regulators during cNCC development as well as cNCC related cardiovascular defects. These factors include ATP-dependent chromatin remodeling factors, histone modifiers and DNA methylation modulators. In many cases, mutations in the genes encoding these factors are known to cause inborn heart diseases. A better understanding of epigenetic regulators, their activities and their roles during heart development will ultimately contribute to the development of new clinical applications for patients with congenital heart disease.
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Affiliation(s)
| | | | - Kai Jiao
- Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL, United States
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18
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Khodaeian M, Jafarinia E, Bitarafan F, Shafeii S, Almadani N, Daneshmand MA, Garshasbi M. Kabuki Syndrome: Identification of Two Novel Variants in KMT2D and KDM6A. Mol Syndromol 2021; 12:118-126. [PMID: 34012382 DOI: 10.1159/000513199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 11/19/2020] [Indexed: 01/05/2023] Open
Abstract
Kabuki syndrome (KS) is a rare genetic disorder characterized by the following 5 crucial symptoms: dysmorphic facial features, growth retardation, skeletal abnormalities, intellectual disability, and dermatoglyphic malformations. Studies show that most of the KS cases are caused by mutations or large deletions in the KMT2D gene, while the other cases show mutations in KDM6A. We studied 2 patients with suspected KS in 2 unrelated families by whole-exome sequencing to identify the possible genetic cause(s) and by Sanger sequencing to validate the identified variants and check the segregation in other members of the families. Finally, the potential effects of the variants on the structure and function of respective proteins were tested using in silico predictions. Both affected members of the families showed typical manifestations of KS including intellectual disability, developmental delay, and abnormal facial characteristics. A novel heterozygous frameshift variant in the KMT2D gene, c.4981del; p.(Glu1661Serfs*61), and a novel hemizygote missense variant in the KDM6A gene, c.3301G>A; p.(Glu1101Lys), were detected in patients 1 and 2, respectively. The frameshift variant identified in the first family was de novo, while in the second family, the mother was also heterozygous for the missense variant. The frameshift variant in KMT2D is predicted to lead to a truncated protein which is functionally impaired. The Glu1101 residue of KDM6A (UTX) affected in the second patient is located in a conserved region on the surface of the Jumonji domain and predicted to be causative. Our findings provide evidence on the possible pathogenicity of these 2 variants; however, additional functional studies are necessary to confirm their impacts.
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Affiliation(s)
| | - Ehsan Jafarinia
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Teheran, Iran
| | | | | | - Navid Almadani
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | | | - Masoud Garshasbi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Teheran, Iran
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19
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Bruni V, Scozzafava C, Gnazzo M, Parisi F, Sestito S, Pensabene L, Novelli A, Concolino D. Facial Dysmorphisms, Macrodontia, Focal Epilepsy, and Thinning of the Corpus Callosum: A Rare Mild Form of Kabuki Syndrome. J Pediatr Genet 2021; 10:49-52. [PMID: 33552639 DOI: 10.1055/s-0040-1701645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/10/2020] [Indexed: 10/25/2022]
Abstract
Kabuki syndrome (KS) is a rare genetic condition with multiple congenital abnormalities and developmental delay. The cardinal manifestations of KS include characteristic facial features, intellectual disability, skeletal defects, dermatoglyphic abnormalities, and postnatal growth deficiencies. Cardiac and urological malformations are commonly present in patient with KS, as well as language deficits and immunological abnormalities. Here, we reported a case of a child with an atypical form of KS, associated with macrodontia, corpus callosum dysmorphism, focal epilepsy responsive to antiepileptic treatment, and a novel KMT2D gene missense variant, c.2413C > T, never reported to date.
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Affiliation(s)
- Valentina Bruni
- Pediatric Unit, Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy
| | - Cristina Scozzafava
- Pediatric Unit, Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy
| | - Maria Gnazzo
- Laboratory of Medical Genetics, IRCCS, Bambino Gesù Children's Hospital, Rome, Italy
| | - Francesca Parisi
- Pediatric Unit, Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy
| | - Simona Sestito
- Pediatric Unit, Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy
| | - Licia Pensabene
- Pediatric Unit, Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, IRCCS, Bambino Gesù Children's Hospital, Rome, Italy
| | - Daniela Concolino
- Pediatric Unit, Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy
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20
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Roles of HIF and 2-Oxoglutarate-Dependent Dioxygenases in Controlling Gene Expression in Hypoxia. Cancers (Basel) 2021; 13:cancers13020350. [PMID: 33477877 PMCID: PMC7832865 DOI: 10.3390/cancers13020350] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/12/2021] [Accepted: 01/15/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Hypoxia—reduction in oxygen availability—plays key roles in both physiological and pathological processes. Given the importance of oxygen for cell and organism viability, mechanisms to sense and respond to hypoxia are in place. A variety of enzymes utilise molecular oxygen, but of particular importance to oxygen sensing are the 2-oxoglutarate (2-OG) dependent dioxygenases (2-OGDs). Of these, Prolyl-hydroxylases have long been recognised to control the levels and function of Hypoxia Inducible Factor (HIF), a master transcriptional regulator in hypoxia, via their hydroxylase activity. However, recent studies are revealing that such dioxygenases are involved in almost all aspects of gene regulation, including chromatin organisation, transcription and translation. Abstract Hypoxia—reduction in oxygen availability—plays key roles in both physiological and pathological processes. Given the importance of oxygen for cell and organism viability, mechanisms to sense and respond to hypoxia are in place. A variety of enzymes utilise molecular oxygen, but of particular importance to oxygen sensing are the 2-oxoglutarate (2-OG) dependent dioxygenases (2-OGDs). Of these, Prolyl-hydroxylases have long been recognised to control the levels and function of Hypoxia Inducible Factor (HIF), a master transcriptional regulator in hypoxia, via their hydroxylase activity. However, recent studies are revealing that dioxygenases are involved in almost all aspects of gene regulation, including chromatin organisation, transcription and translation. We highlight the relevance of HIF and 2-OGDs in the control of gene expression in response to hypoxia and their relevance to human biology and health.
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21
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Fallah MS, Szarics D, Robson CM, Eubanks JH. Impaired Regulation of Histone Methylation and Acetylation Underlies Specific Neurodevelopmental Disorders. Front Genet 2021; 11:613098. [PMID: 33488679 PMCID: PMC7820808 DOI: 10.3389/fgene.2020.613098] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 12/09/2020] [Indexed: 12/19/2022] Open
Abstract
Epigenetic processes are critical for governing the complex spatiotemporal patterns of gene expression in neurodevelopment. One such mechanism is the dynamic network of post-translational histone modifications that facilitate recruitment of transcription factors or even directly alter chromatin structure to modulate gene expression. This is a tightly regulated system, and mutations affecting the function of a single histone-modifying enzyme can shift the normal epigenetic balance and cause detrimental developmental consequences. In this review, we will examine select neurodevelopmental conditions that arise from mutations in genes encoding enzymes that regulate histone methylation and acetylation. The methylation-related conditions discussed include Wiedemann-Steiner, Kabuki, and Sotos syndromes, and the acetylation-related conditions include Rubinstein-Taybi, KAT6A, genitopatellar/Say-Barber-Biesecker-Young-Simpson, and brachydactyly mental retardation syndromes. In particular, we will discuss the clinical/phenotypic and genetic basis of these conditions and the model systems that have been developed to better elucidate cellular and systemic pathological mechanisms.
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Affiliation(s)
- Merrick S Fallah
- Division of Experimental and Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, ON, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Dora Szarics
- Division of Experimental and Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, ON, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Clara M Robson
- Division of Experimental and Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, ON, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - James H Eubanks
- Division of Experimental and Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, ON, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada.,Department of Surgery (Neurosurgery), University of Toronto, Toronto, ON, Canada.,Institute of Medical Science, University of Toronto, Toronto, ON, Canada.,Department of Physiology, University of Toronto, Toronto, ON, Canada
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22
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Schwenty-Lara J, Pauli S, Borchers A. Using Xenopus to analyze neurocristopathies like Kabuki syndrome. Genesis 2020; 59:e23404. [PMID: 33351273 DOI: 10.1002/dvg.23404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/09/2020] [Accepted: 12/09/2020] [Indexed: 11/08/2022]
Abstract
Neurocristopathies are human congenital syndromes that arise from defects in neural crest (NC) development and are typically associated with malformations of the craniofacial skeleton. Genetic analyses have been very successful in identifying pathogenic mutations, however, model organisms are required to characterize how these mutations affect embryonic development thereby leading to complex clinical conditions. The African clawed frog Xenopus laevis provides a broad range of in vivo and in vitro tools allowing for a detailed characterization of NC development. Due to the conserved nature of craniofacial morphogenesis in vertebrates, Xenopus is an efficient and versatile system to dissect the morphological and cellular phenotypes as well as the signaling events leading to NC defects. Here, we review a set of techniques and resources how Xenopus can be used as a disease model to investigate the pathogenesis of Kabuki syndrome and neurocristopathies in a wider sense.
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Affiliation(s)
- Janina Schwenty-Lara
- Department of Biology, Molecular Embryology, Philipps-University Marburg, Marburg, Germany
| | - Silke Pauli
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Annette Borchers
- Department of Biology, Molecular Embryology, Philipps-University Marburg, Marburg, Germany.,DFG Research Training Group, Membrane Plasticity in Tissue Development and Remodeling, GRK 2213, Philipps-University Marburg, Marburg, Germany
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23
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So PL, Luk HM, Yu KPT, Cheng SSW, Hau EWL, Ho SKL, Lam STS, Lo IFM. Clinical and molecular characterization study of Chinese Kabuki syndrome in Hong Kong. Am J Med Genet A 2020; 185:675-686. [PMID: 33314698 DOI: 10.1002/ajmg.a.62003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 10/15/2020] [Accepted: 11/14/2020] [Indexed: 01/21/2023]
Abstract
Kabuki syndrome (OMIM #147920 and 300867) is a rare genetic disorder characterized by a distinctive facial gestalt, intellectual disability and multiple congenital anomalies. We summarized the clinical features and molecular findings of the Kabuki syndrome (KS) patients diagnosed in Hong Kong between January 1991 and December 2019. There were 21 molecularly confirmed KS. Twenty of them were due to pathogenic KMT2D variants and one patient had KDM6A deletion. Nine KMT2D variants were novel. The clinical phenotype of our Chinese KS patients was largely comparable with that reported in patients of other ethnicities. This study expands the mutation spectrum but also provide important natural history information of Chinese KS in literature.
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Affiliation(s)
- Po L So
- Department of Obstetrics and Gynecology, Tuen Mun Hospital, Hong Kong SAR, China
| | - Ho M Luk
- Clinical Genetic Service, Department of Health, Hong Kong Children's Hospital, Hong Kong SAR, China
| | - Kris P T Yu
- Clinical Genetic Service, Department of Health, Hong Kong Children's Hospital, Hong Kong SAR, China
| | - Shirley S W Cheng
- Clinical Genetic Service, Department of Health, Hong Kong Children's Hospital, Hong Kong SAR, China
| | - Edgar W L Hau
- Clinical Genetic Service, Department of Health, Hong Kong Children's Hospital, Hong Kong SAR, China
| | - Stephanie K L Ho
- Clinical Genetic Service, Department of Health, Hong Kong Children's Hospital, Hong Kong SAR, China
| | - Stephen T S Lam
- Clinical Genetics Service, Hong Kong Sanatorium and Hospital, Hong Kong SAR, China
| | - Ivan F M Lo
- Clinical Genetic Service, Department of Health, Hong Kong Children's Hospital, Hong Kong SAR, China
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24
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MLL4-associated condensates counterbalance Polycomb-mediated nuclear mechanical stress in Kabuki syndrome. Nat Genet 2020; 52:1397-1411. [PMID: 33169020 PMCID: PMC7610431 DOI: 10.1038/s41588-020-00724-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 09/22/2020] [Indexed: 12/21/2022]
Abstract
The genetic elements required to tune gene expression are partitioned in active and repressive nuclear condensates. Chromatin compartments include transcriptional clusters whose dynamic establishment and functioning depend on multivalent interactions occurring among transcription factors, cofactors and basal transcriptional machinery. However, how chromatin players contribute to the assembly of transcriptional condensates is poorly understood. By interrogating the effect of KMT2D (also known as MLL4) haploinsufficiency in Kabuki syndrome, we found that mixed lineage leukemia 4 (MLL4) contributes to the assembly of transcriptional condensates through liquid-liquid phase separation. MLL4 loss of function impaired Polycomb-dependent chromatin compartmentalization, altering the nuclear architecture. By releasing the nuclear mechanical stress through inhibition of the mechanosensor ATR, we re-established the mechanosignaling of mesenchymal stem cells and their commitment towards chondrocytes both in vitro and in vivo. This study supports the notion that, in Kabuki syndrome, the haploinsufficiency of MLL4 causes an altered functional partitioning of chromatin, which determines the architecture and mechanical properties of the nucleus.
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25
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Guo W, Zhao Y, Li S, Wang J, Liu X. Hypoglycemia and Dandy-Walker variant in a Kabuki syndrome patient: a case report. BMC MEDICAL GENETICS 2020; 21:193. [PMID: 33008324 PMCID: PMC7531129 DOI: 10.1186/s12881-020-01117-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 09/01/2020] [Indexed: 12/11/2022]
Abstract
Background Kabuki syndrome (KS) is a rare congenital condition with cardinal manifestations of typical facial features, developmental delays, skeletal anomalies, abnormal dermatoglyphic presentations, and mild to moderate intellectual disability. Pathogenic variants in two epigenetic modifier genes, KMT2D and KDM6A, are responsible for KS1 and KS2, respectively. Case presentation A Chinese girl had persistent neonatal hypoglycemia and Dandy-Walker variant. Whole-exome sequencing identified a novel single nucleotide deletion in KMT2D (NM_003482.3 c.12165del p.(Glu4056Serfs*10)) that caused frameshift and premature termination. The mutation was de novo. According to the American College of Medical Genetics and Genomics (ACMG) guidelines, this variant is considered pathogenic. The patient was diagnosed with KS by molecular testing. Conclusion A single novel mutation in KMT2D was identified in a KS patients with hypoglycemia and Dandy-Walker variant in the neonatal stage. A molecular test was conducted to diagnose KS at an early stage.
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Affiliation(s)
- Wei Guo
- Department of Neonatology, Xingtai People's Hospital, Xingtai, 054031, Hebei, China.
| | - Yanguo Zhao
- Department of Neonatology, Xingtai People's Hospital, Xingtai, 054031, Hebei, China
| | - Shuwei Li
- Department of Neonatology, Xingtai People's Hospital, Xingtai, 054031, Hebei, China
| | - Jingqun Wang
- Department of Neonatology, Xingtai People's Hospital, Xingtai, 054031, Hebei, China
| | - Xiang Liu
- Department of Neonatology, Xingtai People's Hospital, Xingtai, 054031, Hebei, China
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Petrizzelli F, Biagini T, Barbieri A, Parca L, Panzironi N, Castellana S, Caputo V, Vescovi AL, Carella M, Mazza T. Mechanisms of pathogenesis of missense mutations on the KDM6A-H3 interaction in type 2 Kabuki Syndrome. Comput Struct Biotechnol J 2020; 18:2033-2042. [PMID: 32802275 PMCID: PMC7412721 DOI: 10.1016/j.csbj.2020.07.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 07/15/2020] [Accepted: 07/16/2020] [Indexed: 02/08/2023] Open
Abstract
Mutations in genes encoding for histone methylation proteins are associated with several developmental disorders. Among them, KDM6A is the disease causative gene of type 2 Kabuki Syndrome, a rare multisystem disease. While nonsense mutations and short insertions/deletions are known to trigger pathogenic mechanisms, the functional effects of missense mutations are still uncharacterized. In this study, we demonstrate that a selected set of missense mutations significantly hamper the interaction between KDM6A and the histone H3, by modifying the dynamics of the linker domain, and then causing a loss of function effect.
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Affiliation(s)
- Francesco Petrizzelli
- Bioinformatics Unit, IRCCS Casa Sollievo della Sofferenza, S. Giovanni Rotondo, Italy
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Tommaso Biagini
- Bioinformatics Unit, IRCCS Casa Sollievo della Sofferenza, S. Giovanni Rotondo, Italy
| | - Alessandro Barbieri
- School of Biology, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- Bioinformatics Institute (BII), Agency for Science, Technology, and Research (A*STAR), Singapore
| | - Luca Parca
- Bioinformatics Unit, IRCCS Casa Sollievo della Sofferenza, S. Giovanni Rotondo, Italy
| | - Noemi Panzironi
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Stefano Castellana
- Bioinformatics Unit, IRCCS Casa Sollievo della Sofferenza, S. Giovanni Rotondo, Italy
| | - Viviana Caputo
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Angelo Luigi Vescovi
- IRCSS Casa Sollievo della Sofferenza, ISBReMIT Institute for Stem Cell Biology, Regenerative Medicine and Innovative Therapies, San Giovanni Rotondo FG, Italy
| | - Massimo Carella
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, S. Giovanni Rotondo, Italy
| | - Tommaso Mazza
- Bioinformatics Unit, IRCCS Casa Sollievo della Sofferenza, S. Giovanni Rotondo, Italy
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27
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Li M, Zhang W, Zhou X. Identification of genes involved in the evolution of human intelligence through combination of inter-species and intra-species genetic variations. PeerJ 2020; 8:e8912. [PMID: 32337102 PMCID: PMC7167246 DOI: 10.7717/peerj.8912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 03/15/2020] [Indexed: 11/20/2022] Open
Abstract
Understanding the evolution of human intelligence is an important undertaking in the science of human genetics. A great deal of biological research has been conducted to search for genes which are related to the significant increase in human brain volume and cerebral cortex complexity during hominid evolution. However, genetic changes affecting intelligence in hominid evolution have remained elusive. We supposed that a subset of intelligence-related genes, which harbored intra-species variations in human populations, may also be evolution-related genes which harbored inter-species variations between humans (Homo sapiens) and great apes (including Pan troglodytes and Pongo abelii). Here we combined inter-species and intra-species genetic variations to discover genes involved in the evolution of human intelligence. Information was collected from published GWAS works on intelligence and a total of 549 genes located within the intelligence-associated loci were identified. The intelligence-related genes containing human-specific variations were detected based on the latest high-quality genome assemblies of three human's closest species. Finally, we identified 40 strong candidates involved in human intelligence evolution. Expression analysis using RNA-Seq data revealed that most of the genes displayed a relatively high expression in the cerebral cortex. For these genes, there is a distinct expression pattern between humans and other species, especially in neocortex tissues. Our work provided a list of strong candidates for the evolution of human intelligence, and also implied that some intelligence-related genes may undergo inter-species evolution and contain intra-species variation.
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Affiliation(s)
- Mengjie Li
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Wenting Zhang
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Xiaoyi Zhou
- College of Life Sciences, Shanghai Normal University, Shanghai, China
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28
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Squeo GM, Augello B, Massa V, Milani D, Colombo EA, Mazza T, Castellana S, Piccione M, Maitz S, Petracca A, Prontera P, Accadia M, Della Monica M, Di Giacomo MC, Melis D, Selicorni A, Giglio S, Fischetto R, Di Fede E, Malerba N, Russo M, Castori M, Gervasini C, Merla G. Customised next-generation sequencing multigene panel to screen a large cohort of individuals with chromatin-related disorder. J Med Genet 2020; 57:760-768. [PMID: 32170002 DOI: 10.1136/jmedgenet-2019-106724] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/11/2020] [Accepted: 02/19/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND The regulation of the chromatin state by epigenetic mechanisms plays a central role in gene expression, cell function, and maintenance of cell identity. Hereditary disorders of chromatin regulation are a group of conditions caused by abnormalities of the various components of the epigenetic machinery, namely writers, erasers, readers, and chromatin remodelers. Although neurological dysfunction is almost ubiquitous in these disorders, the constellation of additional features characterizing many of these genes and the emerging clinical overlap among them indicate the existence of a community of syndromes. The introduction of high-throughput next generation sequencing (NGS) methods for testing multiple genes simultaneously is a logical step for the implementation of diagnostics of these disorders. METHODS We screened a heterogeneous cohort of 263 index patients by an NGS-targeted panel, containing 68 genes associated with more than 40 OMIM entries affecting chromatin function. RESULTS This strategy allowed us to identify clinically relevant variants in 87 patients (32%), including 30 for which an alternative clinical diagnosis was proposed after sequencing analysis and clinical re-evaluation. CONCLUSION Our findings indicate that this approach is effective not only in disorders with locus heterogeneity, but also in order to anticipate unexpected misdiagnoses due to clinical overlap among cognate disorders. Finally, this work highlights the utility of a prompt diagnosis in such a clinically and genetically heterogeneous group of disorders that we propose to group under the umbrella term of chromatinopathies.
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Affiliation(s)
- Gabriella Maria Squeo
- Division of Medical Genetics, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Bartolomeo Augello
- Division of Medical Genetics, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Valentina Massa
- Dipartimento di Scienze della Salute, Universita degli Studi di Milano Dipartimento di Scienze della Salute, Milano, Italy
| | - Donatella Milani
- UOSD Pediatria ad alta intensità di cura, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Elisa Adele Colombo
- Dipartimento di Scienze della Salute, Universita degli Studi di Milano Dipartimento di Scienze della Salute, Milano, Italy
| | - Tommaso Mazza
- Bioinformatics Unit, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Stefano Castellana
- Bioinformatics Unit, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Maria Piccione
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Silvia Maitz
- Clinical Pediatric Genetics Unit, Pediatrics Clinics, MBBM Foundation, Hospital San Gerardo, Monza, Italy
| | - Antonio Petracca
- Division of Medical Genetics, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Paolo Prontera
- Medical Genetics Unit, University of Perugia Hospital SM della Misericordia, Perugia, Italy
| | - Maria Accadia
- Medical Genetics Service, Hospital "Cardinale G. Panico", Tricase, Italy
| | - Matteo Della Monica
- Medical Genetics Unit, Cardarelli Hospital, Largo A Cardarelli, Napoli, Italy
| | | | - Daniela Melis
- Department of Translational Medical Science, Section of Pediatrics, University of Naples Federico II, Napoli, Italy
| | - Angelo Selicorni
- Pediatric Department, ASST Lariana, Sant'Anna General Hospital, Como, Italy
| | - Sabrina Giglio
- Department of Biomedical, Experimental and Clinical Sciences 'Mario Serio', Medical Genetics Unit, University Hospital Meyer, Firenze, Italy
| | - Rita Fischetto
- Metabolic Diseases, Clinical Genetics and Diabetology Unit, Paediatric Hospital Giovanni XXIII, Bari, Italy
| | - Elisabetta Di Fede
- Dipartimento di Scienze della Salute, Universita degli Studi di Milano Dipartimento di Scienze della Salute, Milano, Italy
| | - Natascia Malerba
- Division of Medical Genetics, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Matteo Russo
- Division of Medical Genetics, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Marco Castori
- Division of Medical Genetics, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Cristina Gervasini
- Dipartimento di Scienze della Salute, Universita degli Studi di Milano Dipartimento di Scienze della Salute, Milano, Italy
| | - Giuseppe Merla
- Division of Medical Genetics, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
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TRIM8 interacts with KIF11 and KIFC1 and controls bipolar spindle formation and chromosomal stability. Cancer Lett 2020; 473:98-106. [DOI: 10.1016/j.canlet.2019.12.042] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/20/2019] [Accepted: 12/20/2019] [Indexed: 11/29/2022]
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Cancer-derived UTX TPR mutations G137V and D336G impair interaction with MLL3/4 complexes and affect UTX subcellular localization. Oncogene 2020; 39:3322-3335. [PMID: 32071397 DOI: 10.1038/s41388-020-1218-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 02/02/2020] [Accepted: 02/07/2020] [Indexed: 12/25/2022]
Abstract
The ubiquitously transcribed tetratricopeptide repeat on X chromosome (UTX) is a major histone H3 lysine 27 (H3K27) demethylase and the mixed-lineage leukemia (MLL) proteins are the H3K4 methyltransferases. UTX is one of the major components of MLL3- and MLL4-containing (MlLL3/4) complexes and likely has functions within the complexes. Although UTX is frequently mutated in various types of cancer and is thought to play a crucial role as a tumor suppressor, the importance of UTX interaction with MLL3/4 complexes in cancer formation is poorly understood. Here, we analyzed the ability of cancer-derived UTX mutant proteins to interact with ASH2L, which is a common core component of all the MLL complexes, and MLL3/4-specific components PTIP and PA1, and found that several single-amino acid substitution mutations in the tetratricopeptide repeat (TPR) affect UTX interaction with these components. Interaction-compromised mutants G137V and D336G and a TPR-deleted mutant Δ80-397 were preferentially localized to the cytoplasm, suggesting that UTX is retained in the nucleus by MLL3/4 complexes through their interaction with the TPR. Intriguingly, WT UTX suppressed colony formation in soft agar, whereas G137V failed. This suggests that interaction of UTX with MLL3/4 complex plays a crucial role in their tumor suppressor function. Preferential cytoplasmic localization was also observed for endogenous proteins of G137V and another mutant G137VΔ138 in HCT116 created by CRISPR-Cas9 gene editing. Interestingly, expression levels of these mutants were low and MG312 stabilized both endogenous as well as exogenous G137V proteins. These results reveal a novel mechanism of UTX regulation and reinforce the importance of UTX interaction with MLL3/4 complexes in cancer formation.
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31
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Schwenty-Lara J, Nehl D, Borchers A. The histone methyltransferase KMT2D, mutated in Kabuki syndrome patients, is required for neural crest cell formation and migration. Hum Mol Genet 2020; 29:305-319. [PMID: 31813957 PMCID: PMC7003132 DOI: 10.1093/hmg/ddz284] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 11/18/2019] [Accepted: 11/19/2019] [Indexed: 12/30/2022] Open
Abstract
Kabuki syndrome is an autosomal dominant developmental disorder with high similarities to CHARGE syndrome. It is characterized by a typical facial gestalt in combination with short stature, intellectual disability, skeletal findings and additional features like cardiac and urogenital malformations, cleft palate, hearing loss and ophthalmological anomalies. The major cause of Kabuki syndrome are mutations in KMT2D, a gene encoding a histone H3 lysine 4 (H3K4) methyltransferase belonging to the group of chromatin modifiers. Here we provide evidence that Kabuki syndrome is a neurocrestopathy, by showing that Kmt2d loss-of-function inhibits specific steps of neural crest (NC) development. Using the Xenopus model system, we find that Kmt2d loss-of-function recapitulates major features of Kabuki syndrome including severe craniofacial malformations. A detailed marker analysis revealed defects in NC formation as well as migration. Transplantation experiments confirm that Kmt2d function is required in NC cells. Furthermore, analyzing in vivo and in vitro NC migration behavior demonstrates that Kmt2d is necessary for cell dispersion but not protrusion formation of migrating NC cells. Importantly, Kmt2d knockdown correlates with a decrease in H3K4 monomethylation and H3K27 acetylation supporting a role of Kmt2d in the transcriptional activation of target genes. Consistently, using a candidate approach, we find that Kmt2d loss-of-function inhibits Xenopus Sema3F expression, and overexpression of Sema3F can partially rescue Kmt2d loss-of-function defects. Taken together, our data reveal novel functions of Kmt2d in multiple steps of NC development and support the hypothesis that major features of Kabuki syndrome are caused by defects in NC development.
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Affiliation(s)
- Janina Schwenty-Lara
- Department of Biology, Molecular Embryology, Philipps-Universität Marburg, Marburg 35043, Germany
| | - Denise Nehl
- Department of Biology, Molecular Embryology, Philipps-Universität Marburg, Marburg 35043, Germany
| | - Annette Borchers
- Department of Biology, Molecular Embryology, Philipps-Universität Marburg, Marburg 35043, Germany
- DFG Research Training Group, Membrane Plasticity in Tissue Development and Remodeling, GRK 2213, Philipps-Universität Marburg, Marburg 35043, Germany
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32
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Lavery WJ, Barski A, Wiley S, Schorry EK, Lindsley AW. KMT2C/D COMPASS complex-associated diseases [K CDCOM-ADs]: an emerging class of congenital regulopathies. Clin Epigenetics 2020; 12:10. [PMID: 31924266 PMCID: PMC6954584 DOI: 10.1186/s13148-019-0802-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 12/23/2019] [Indexed: 12/15/2022] Open
Abstract
The type 2 lysine methyltransferases KMT2C and KMT2D are large, enzymatically active scaffold proteins that form the core of nuclear regulatory structures known as KMT2C/D COMPASS complexes (complex of proteins associating with Set1). These evolutionarily conserved proteins regulate DNA promoter and enhancer elements, modulating the activity of diverse cell types critical for embryonic morphogenesis, central nervous system development, and post-natal survival. KMT2C/D COMPASS complexes and their binding partners enhance active gene expression of specific loci via the targeted modification of histone-3 tail residues, in general promoting active euchromatic conformations. Over the last 20 years, mutations in five key COMPASS complex genes have been linked to three human congenital syndromes: Kabuki syndrome (type 1 [KMT2D] and 2 [KDM6A]), Rubinstein-Taybi syndrome (type 1 [CBP] and 2 [EP300]), and Kleefstra syndrome type 2 (KMT2C). Here, we review the composition and biochemical function of the KMT2 complexes. The specific cellular and embryonic roles of the KMT2C/D COMPASS complex are highlight with a focus on clinically relevant mechanisms sensitive to haploinsufficiency. The phenotypic similarities and differences between the members of this new family of disorders are outlined and emerging therapeutic strategies are detailed.
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Affiliation(s)
- William J Lavery
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center (CCHMC), 3333 Burnet Avenue, Cincinnati, OH, 45229-3026, USA
| | - Artem Barski
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center (CCHMC), 3333 Burnet Avenue, Cincinnati, OH, 45229-3026, USA
- Division of Human Genetics, CCHMC, Cincinnati, OH, USA
| | - Susan Wiley
- Division of Developmental and Behavioral Pediatrics, CCHMC, Cincinnati, OH, USA
| | | | - Andrew W Lindsley
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center (CCHMC), 3333 Burnet Avenue, Cincinnati, OH, 45229-3026, USA.
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Wang YR, Xu NX, Wang J, Wang XM. Kabuki syndrome: review of the clinical features, diagnosis and epigenetic mechanisms. World J Pediatr 2019; 15:528-535. [PMID: 31587141 DOI: 10.1007/s12519-019-00309-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 08/07/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND Kabuki syndrome (KS), is a infrequent inherited malformation syndrome caused by mutations in a H3 lysine 4 methylase (KMT2D) or an X-linked histone H3 lysine 27 demethylase (UTX/KDM6A). The characteristics in patients with KS have not yet been well recognized. DATA SOURCES We used databases including PubMed and Google Scholar to search for publications about the clinical features and the etiology of Kabuki syndrome. The most relevant articles to the scope of this review were chosen for analysis. RESULTS Clinical diagnosis of KS is challenging in initial period, because many clinical characteristics become apparent only in subsequent years. Recently, the genetic and functional interaction between KS-associated genes and their products have been elucidated. New clinical findings were reported including nervous system and intellectual performance, endocrine-related disorders and immune deficiency and autoimmune disease. Cancer risks of Kabuki syndrome was reviewed. Meanwhile, we discussed the Kabuki-like syndrome. Digital clinical genetic service, such as dysmorphology database can improve availability and provide high-quality diagnostic services. Given the significant clinical relevance of KS-associated genes and epigenetic modifications crosstalk, efforts in the research for new mechanisms are thus of maximum interest. CONCLUSIONS Kabuki syndrome has a strong clinical and biological heterogeneity. The main pathogenesis of Kabuki syndrome is the imbalance between switch-on and -off of the chromatin. The direction of drug research may be to regulate the normal opening of chromatin. Small molecule inhibitors of histone deacetylases maybe helpful in treatment of mental retardation and reduce cancer risk in KS.
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Affiliation(s)
- Yi-Rou Wang
- Department of Endocrinology and Metabolism, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Nai-Xin Xu
- Huaxi Medical College School of Sichuan University, Sichuan, China
| | - Jian Wang
- Department of Endocrinology and Metabolism, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Department of Genetics, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiu-Min Wang
- Department of Endocrinology and Metabolism, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China. .,Department of Genetics, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China.
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Abstract
PURPOSE Kabuki syndrome (KS) is a rare congenital disorder characterized by multiple systemic anomalies and unique facial characteristics. Here, we present the first case, to the best of our knowledge, of bilateral congenital corneal opacities as an early-onset ocular manifestation of KS associated with a KMT2D gene mutation. METHODS The proband is a girl. At birth, bilateral corneal opacities, short fifth fingers, patent ductus arteriosus, absence of the uvula, and an ectopic kidney on the right side were noted. Ophthalmic examinations revealed vascularized, nonhomogeneous opacities in both corneas; to prevent deprivation amblyopia, bilateral corneal transplantations were performed. RESULTS At 1 year and 10 months of age, she was referred by a general practitioner to our pediatric endocrinologist for failure to thrive. Genetic analysis at that age revealed the presence of a KMT2D gene mutation, and the patient was diagnosed with KS. CONCLUSIONS The clinical diagnosis of KS is challenging because the most remarkable facial features are not evident until early childhood. In this case, bilateral congenital corneal opacities were identified as an early-onset ocular manifestation of KS. KS should be considered as a differential diagnosis in patients with bilateral congenital corneal opacities.
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Morlino S, Carbone A, Ritelli M, Fusco C, Giambra V, Nardella G, Notarangelo A, Panelli P, Mazzoccoli G, Zoppi N, Grammatico P, Wade EM, Colombi M, Castori M, Micale L. TAB2 c.1398dup variant leads to haploinsufficiency and impairs extracellular matrix homeostasis. Hum Mutat 2019; 40:1886-1898. [PMID: 31250519 DOI: 10.1002/humu.23834] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/28/2019] [Accepted: 05/31/2019] [Indexed: 12/16/2022]
Abstract
Transforming growth factor β-activated kinase 1 (TAK1) mediates multiple biological processes through the nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB) and the mitogen-activated protein kinase (MAPK) signaling pathways. TAK1 activation is tightly regulated by its binding partners (TABs). In particular, binding with TAB2 is crucial for cardiovascular development and extracellular matrix (ECM) homeostasis. In our previous work, we reported a novel multisystem disorder associated with the heterozygous TAB2 c.1398dup variant. Here, we dissect the functional effects of this variant in order to understand its molecular pathogenesis. We demonstrate that TAB2 c.1398dup considerably undergoes to nonsense-mediated messenger RNA decay and encodes a truncated protein that loses its ability to bind TAK1. We also show an alteration of the TAK1 autophosphorylation status and of selected downstream signaling pathways in patients' fibroblasts. Immunofluorescence analyses and ECM-related polymerase chain reaction-array panels highlight that patient fibroblasts display ECM disorganization and altered expression of selected ECM components and collagen-related pathways. In conclusion, we deeply dissect the molecular pathogenesis of the TAB2 c.1398dup variant and show that the resulting phenotype is well explained by TAB2 loss-of-function. Our data also offer initial insights on the ECM homeostasis impairment as a molecular mechanism probably underlying a multisystem disorder linked to TAB2.
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Affiliation(s)
- Silvia Morlino
- Laboratory of Medical Genetics, Department of Molecular Medicine, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
| | - Annalucia Carbone
- Division of Internal Medicine and Unit of Chronobiology, Fondazione IRCCS Casa Sollievo della Sofferenza, Foggia, Italy
| | - Marco Ritelli
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, Universityinflammatory disorders and cancer of Brescia, Brescia, Italy
| | - Carmela Fusco
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, Foggia, Italy
| | - Vincenzo Giambra
- Institute for Stem Cell Biology, Regenerative Medicine and Innovative Therapies (ISBReMIT), Fondazione IRCCS Casa Sollievo della Sofferenza, Foggia, Italy
| | - Grazia Nardella
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, Foggia, Italy.,Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | | | - Patrizio Panelli
- Institute for Stem Cell Biology, Regenerative Medicine and Innovative Therapies (ISBReMIT), Fondazione IRCCS Casa Sollievo della Sofferenza, Foggia, Italy
| | - Gianluigi Mazzoccoli
- Division of Internal Medicine and Unit of Chronobiology, Fondazione IRCCS Casa Sollievo della Sofferenza, Foggia, Italy
| | - Nicoletta Zoppi
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, Universityinflammatory disorders and cancer of Brescia, Brescia, Italy
| | - Paola Grammatico
- Laboratory of Medical Genetics, Department of Molecular Medicine, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
| | - Emma M Wade
- Department of Women's and Children's Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Marina Colombi
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, Universityinflammatory disorders and cancer of Brescia, Brescia, Italy
| | - Marco Castori
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, Foggia, Italy
| | - Lucia Micale
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, Foggia, Italy
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Geers NC, Thio HB, de Kort WJ. Capillary malformations in a child with Kabuki syndrome: A case report. JAAD Case Rep 2019; 5:560-562. [PMID: 31245521 PMCID: PMC6581967 DOI: 10.1016/j.jdcr.2019.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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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.
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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
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Venuto S, Castellana S, Monti M, Appolloni I, Fusilli C, Fusco C, Pucci P, Malatesta P, Mazza T, Merla G, Micale L. TRIM8-driven transcriptomic profile of neural stem cells identified glioma-related nodal genes and pathways. Biochim Biophys Acta Gen Subj 2018; 1863:491-501. [PMID: 30528352 DOI: 10.1016/j.bbagen.2018.12.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 11/26/2018] [Accepted: 12/03/2018] [Indexed: 12/25/2022]
Abstract
BACKGROUND We recently reported TRIM8, encoding an E3 ubiquitin ligase, as a gene aberrantly expressed in glioblastoma whose expression suppresses cell growth and induces a significant reduction of clonogenic potential in glioblastoma cell lines. METHODS we provided novel insights on TRIM8 functions by profiling the transcriptome of TRIM8-expressing primary mouse embryonal neural stem cells by RNA-sequencing and bioinformatic analysis. Functional analysis including luciferase assay, western blot, PCR arrays, Real time quantitative PCR were performed to validate the transcriptomic data. RESULTS Our study identified enriched pathways related to the neurotransmission and to the central nervous system (CNS) functions, including axonal guidance, GABA receptor, Ephrin B, synaptic long-term potentiation/depression, and glutamate receptor signalling pathways. Finally, we provided additional evidence about the existence of a functional interactive crosstalk between TRIM8 and STAT3. CONCLUSIONS Our results substantiate the role of TRIM8 in the brain functions through the dysregulation of genes involved in different CNS-related pathways, including JAK-STAT. GENERAL SIGNIFICANCE This study provides novel insights on the physiological TRIM8 function by profiling for the first time the primary Neural Stem Cell over-expressing TRIM8 by using RNA-Sequencing methodology.
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Affiliation(s)
- Santina Venuto
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, Viale Padre Pio, 71013, San Giovanni Rotondo, Foggia, Italy; Experimental and Regenerative Medicine, University of Foggia, Via A. Gramsci, 89/91, 71122, Foggia, Italy.
| | - Stefano Castellana
- Bioinformatics Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, Viale Padre Pio, 71013, San Giovanni Rotondo, Foggia, Italy.
| | - Maria Monti
- CEINGE Advanced Biotechnology, Department of Chemical Sciences, Federico II University, Via Gaetano Salvatore, 486, 80145, Napoli, Italy.
| | - Irene Appolloni
- U.O. Medicina Rigenerativa Ospedale Policlinico San Martino, Largo R. Benzi 10, 16132 Genova, Italy
| | - Caterina Fusilli
- Bioinformatics Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, Viale Padre Pio, 71013, San Giovanni Rotondo, Foggia, Italy.
| | - Carmela Fusco
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, Viale Padre Pio, 71013, San Giovanni Rotondo, Foggia, Italy.
| | - Piero Pucci
- CEINGE Advanced Biotechnology, Department of Chemical Sciences, Federico II University, Via Gaetano Salvatore, 486, 80145, Napoli, Italy.
| | - Paolo Malatesta
- U.O. Medicina Rigenerativa Ospedale Policlinico San Martino, Largo R. Benzi 10, 16132 Genova, Italy; Department of Experimental Medicine (DiMES), University of Genova, Via Leon Battista Alberti, 2, 16132 Genova, Italy.
| | - Tommaso Mazza
- Bioinformatics Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, Viale Padre Pio, 71013, San Giovanni Rotondo, Foggia, Italy.
| | - Giuseppe Merla
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, Viale Padre Pio, 71013, San Giovanni Rotondo, Foggia, Italy.
| | - Lucia Micale
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, Viale Padre Pio, 71013, San Giovanni Rotondo, Foggia, Italy.
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Guo Z, Liu F, Li HJ. Novel KDM6A splice-site mutation in kabuki syndrome with congenital hydrocephalus: a case report. BMC MEDICAL GENETICS 2018; 19:206. [PMID: 30509212 PMCID: PMC6276138 DOI: 10.1186/s12881-018-0724-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 11/21/2018] [Indexed: 01/29/2023]
Abstract
Background Kabuki syndrome (KS) is a rare congenital anomaly syndrome affecting multiple organs. Two genes have been shown to be mutated in patients with KS: lysine (K)-specific demethylase 6A (KDM6A) and lysine (K)-specific methyltransferase 2D (KMT2D, formerly MLL2). Although the congenital clinical characteristic is helpful in diagnosis of the KS, there are no reports of specific findings in fetuses that might suggest the syndrome prenatally. Case presentation In this study, we described a male patient with a novel KDM6A splicing in exon(exon4) and flanking intron(intron3)-exon boundaries characterized by congenital hydrocephalus which had never been reported before. The male patient had inherited the c.335-1G > T splice site mutation from his mother who had fewer dysmorphic features than the patient who displayed a more severe phenotype with multiple organ involvement. Our research suggests that congenital hydrocephalus may accompany KS type 2, which improve the knowledge on KS further more. Conclusions Based on genetic and clinical features, suggest that the c.335-1G > T splicing mutation in KDM6A causing KS-2 disease. At least for this case, we suggest that congenital hydrocephalus is closely associated with KS type 2. Electronic supplementary material The online version of this article (10.1186/s12881-018-0724-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhimei Guo
- Neonatology Department
- , Bethune International Peace Hospital, Shijiazhuang, 050082, China.
| | - Fang Liu
- Neonatology Department
- , Bethune International Peace Hospital, Shijiazhuang, 050082, China
| | - Hai Jun Li
- Liver Disease Diagnosis and Treatment Center of PLA, Bethune International Peace Hospital, Shijiazhuang, 050082, China
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Abstract
PURPOSE OF REVIEW Primary immunodeficiency diseases (PIDs) are genetic disorders classically characterized by impaired host defense and an increased susceptibility to infections. It is now appreciated that these conditions broadly include variations in the genetic code that cause dysregulated immune function. This review highlights the newly defined PIDs in the 2017 International Union of Immunologic Societies (IUIS) report, current approaches to diagnosing PIDs, and the implications for the future management of PIDs. RECENT FINDINGS With the advances in and increased commercial availability of genetic testing and the adoption of the TREC assay into the US Newborn Screening program, the number of identified PIDs has exponentially risen in the past few decades, reaching over 350 disorders. The IUIS Inborn Errors of Immunity committee acknowledged at least 50 new disorders between 2015 and 2017. Furthermore, given the greater recognition of disorders with primarily immune dysregulation, the committee proposed a more inclusive term of 'inborn errors of immunity' to encompass primary immunodeficiencies and immune dysregulation disorders. SUMMARY This latest IUIS report underscores the rapid expansion in the PID field with technologic advancements in immunogenetics and clinical screening discovering new genetic diseases, and therefore, paving the way to novel therapeutics and precision medicine.
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Integrated facial analysis and targeted sequencing identifies a novel KDM6A pathogenic variant resulting in Kabuki syndrome. JOURNAL OF BIO-X RESEARCH 2018. [DOI: 10.1097/jbr.0000000000000022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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A comparative analysis of KMT2D missense variants in Kabuki syndrome, cancers and the general population. J Hum Genet 2018; 64:161-170. [PMID: 30459467 DOI: 10.1038/s10038-018-0536-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 10/10/2018] [Accepted: 10/19/2018] [Indexed: 12/21/2022]
Abstract
Determining the clinical significance of germline and somatic KMT2D missense variants (MVs) in Kabuki syndrome (KS) and cancers can be challenging. We analysed 1920 distinct KMT2D MVs that included 1535 germline MVs in controls (Control-MVs), 584 somatic MVs in cancers (Cancer-MVs) and 201 MV in individuals with KS (KS-MVs). The proportion of MVs likely to affect splicing was significantly higher for Cancer-MVs and KS-MVs than in Control-MVs (p = 0.000018). Our analysis identified significant clustering of Cancer-MVs and KS-MVs in the PHD#3 and #4, RING#4 and SET domains. Areas of enrichment restricted to just Cancer-MVs (FYR-C and between amino acids 3043-3248) or KS-MVs (coiled-coil#5, FYR-N and between amino acids 4995-5090) were also found. Cancer-MVs and KS-MVs tended to affect more conserved residues (lower BLOSUM scores, p < 0.001 and p = 0.007). KS-MVs are more likely to increase the energy for protein folding (higher ELASPIC ∆∆G scores, p = 0.03). Cancer-MVs are more likely to disrupt protein interactions (higher StructMAn scores, p = 0.019). We reclassify several presumed pathogenic MVs as benign or as variants of uncertain significance. We raise the possibility of as yet unrecognised 'non-KS' phenotype(s) associated with some germline pathogenic KMT2D MVs. Overall, this work provides insights into the disease mechanism of KMT2D variants and can be extended to other genes, mutations in which also cause developmental syndromes and cancer.
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Cocciadiferro D, Augello B, De Nittis P, Zhang J, Mandriani B, Malerba N, Squeo GM, Romano A, Piccinni B, Verri T, Micale L, Pasqualucci L, Merla G. Dissecting KMT2D missense mutations in Kabuki syndrome patients. Hum Mol Genet 2018; 27:3651-3668. [PMID: 30107592 PMCID: PMC6488975 DOI: 10.1093/hmg/ddy241] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 05/30/2018] [Accepted: 06/21/2018] [Indexed: 02/07/2023] Open
Abstract
Kabuki syndrome is a rare autosomal dominant condition characterized by facial features, various organs malformations, postnatal growth deficiency and intellectual disability. The discovery of frequent germline mutations in the histone methyltransferase KMT2D and the demethylase KDM6A revealed a causative role for histone modifiers in this disease. However, the role of missense mutations has remained unexplored. Here, we expanded the mutation spectrum of KMT2D and KDM6A in KS by identifying 37 new KMT2D sequence variants. Moreover, we functionally dissected 14 KMT2D missense variants, by investigating their impact on the protein enzymatic activity and the binding to members of the WRAD complex. We demonstrate impaired H3K4 methyltransferase activity in 9 of the 14 mutant alleles and show that this reduced activity is due in part to disruption of protein complex formation. These findings have relevant implications for diagnostic and counseling purposes in this disease.
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Affiliation(s)
- Dario Cocciadiferro
- Division of Medical Genetics, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Italy
- PhD Program in Experimental and Regenerative Medicine, Faculty of Medicine, University of Foggia, Italy
| | - Bartolomeo Augello
- Division of Medical Genetics, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Italy
| | | | - Jiyuan Zhang
- Department of Pathology and Cell Biology, Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | - Barbara Mandriani
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli, Naples, Italy
| | - Natascia Malerba
- Division of Medical Genetics, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Italy
- PhD Program in Experimental and Regenerative Medicine, Faculty of Medicine, University of Foggia, Italy
| | - Gabriella M Squeo
- Division of Medical Genetics, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Italy
| | - Alessandro Romano
- Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Barbara Piccinni
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Tiziano Verri
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Lucia Micale
- Division of Medical Genetics, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Italy
| | - Laura Pasqualucci
- Department of Pathology and Cell Biology, Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | - Giuseppe Merla
- Division of Medical Genetics, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Italy
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Normand EA, Braxton A, Nassef S, Ward PA, Vetrini F, He W, Patel V, Qu C, Westerfield LE, Stover S, Dharmadhikari AV, Muzny DM, Gibbs RA, Dai H, Meng L, Wang X, Xiao R, Liu P, Bi W, Xia F, Walkiewicz M, Van den Veyver IB, Eng CM, Yang Y. Clinical exome sequencing for fetuses with ultrasound abnormalities and a suspected Mendelian disorder. Genome Med 2018; 10:74. [PMID: 30266093 PMCID: PMC6162951 DOI: 10.1186/s13073-018-0582-x] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 09/12/2018] [Indexed: 12/11/2022] Open
Abstract
Background Exome sequencing is now being incorporated into clinical care for pediatric and adult populations, but its integration into prenatal diagnosis has been more limited. One reason for this is the paucity of information about the clinical utility of exome sequencing in the prenatal setting. Methods We retrospectively reviewed indications, results, time to results (turnaround time, TAT), and impact of exome results for 146 consecutive “fetal exomes” performed in a clinical diagnostic laboratory between March 2012 and November 2017. We define a fetal exome as one performed on a sample obtained from a fetus or a product of conception with at least one structural anomaly detected by prenatal imaging or autopsy. Statistical comparisons were performed using Fisher’s exact test. Results Prenatal exome yielded an overall molecular diagnostic rate of 32% (n = 46/146). Of the 46 molecular diagnoses, 50% were autosomal dominant disorders (n = 23/46), 41% were autosomal recessive disorders (n = 19/46), and 9% were X-linked disorders (n = 4/46). The molecular diagnostic rate was highest for fetuses with anomalies affecting multiple organ systems and for fetuses with craniofacial anomalies. Out of 146 cases, a prenatal trio exome option designed for ongoing pregnancies was performed on 62 fetal specimens, resulting in a diagnostic yield of 35% with an average TAT of 14 days for initial reporting (excluding tissue culture time). The molecular diagnoses led to refined recurrence risk estimates, altered medical management, and informed reproductive planning for families. Conclusion Exome sequencing is a useful diagnostic tool when fetal structural anomalies suggest a genetic etiology, but other standard prenatal genetic tests did not provide a diagnosis. Electronic supplementary material The online version of this article (10.1186/s13073-018-0582-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elizabeth A Normand
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Alicia Braxton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Salma Nassef
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Patricia A Ward
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | | | | | | | | | - Lauren E Westerfield
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Samantha Stover
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Donna M Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Linyan Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Xia Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Rui Xiao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Magdalena Walkiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA.,Present address: The National Institute of Allergy and Infectious Disease, NIH, Bethesda, MD, USA
| | - Ignatia B Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. .,Baylor Genetics, Houston, TX, USA.
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45
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Andrade AC, Jee YH, Nilsson O. New Genetic Diagnoses of Short Stature Provide Insights into Local Regulation of Childhood Growth
. Horm Res Paediatr 2018; 88:22-37. [PMID: 28334714 DOI: 10.1159/000455850] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 01/03/2017] [Indexed: 12/12/2022] Open
Abstract
Idiopathic short stature is a common condition with a heterogeneous etiology. Advances in genetic methods, including genome sequencing techniques and bioinformatics approaches, have emerged as important tools to identify the genetic defects in families with monogenic short stature. These findings have contributed to the understanding of growth regulation and indicate that growth plate chondrogenesis, and therefore linear growth, is governed by a large number of genes important for different signaling pathways and cellular functions, including genetic defects in hormonal regulation, paracrine signaling, cartilage matrix, and fundamental cellular processes. In addition, mutations in the same gene can cause a wide phenotypic spectrum depending on the severity and mode of inheritance of the mutation.
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Affiliation(s)
- Anenisia C Andrade
- Division of Pediatric Endocrinology, Department of Women's and Children's Health, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Youn Hee Jee
- Section of Growth and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Ola Nilsson
- Division of Pediatric Endocrinology, Department of Women's and Children's Health, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden.,Department of Medical Sciences, Örebro University and University Hospital, Örebro, Sweden
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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.
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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
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47
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Schenkel LC, Aref-Eshghi E, Skinner C, Ainsworth P, Lin H, Paré G, Rodenhiser DI, Schwartz C, Sadikovic B. Peripheral blood epi-signature of Claes-Jensen syndrome enables sensitive and specific identification of patients and healthy carriers with pathogenic mutations in KDM5C. Clin Epigenetics 2018; 10:21. [PMID: 29456765 PMCID: PMC5813334 DOI: 10.1186/s13148-018-0453-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 02/02/2018] [Indexed: 12/02/2022] Open
Abstract
Background Claes-Jensen syndrome is an X-linked inherited intellectual disability caused by mutations in the KDM5C gene. Kdm5c is a histone lysine demethylase involved in histone modifications and chromatin remodeling. Males with hemizygous mutations in KDM5C present with intellectual disability and facial dysmorphism, while most heterozygous female carriers are asymptomatic. We hypothesized that loss of Kdm5c function may influence other components of the epigenomic machinery including DNA methylation in affected patients. Results Genome-wide DNA methylation analysis of 7 male patients affected with Claes-Jensen syndrome and 56 age- and sex-matched controls identified a specific DNA methylation defect (epi-signature) in the peripheral blood of these patients, including 1769 individual CpGs and 9 genomic regions. Six healthy female carriers showed less pronounced but distinctive changes in the same regions enabling their differentiation from both patients and controls. Highly specific computational model using the most significant methylation changes demonstrated 100% accuracy in differentiating patients, carriers, and controls in the training cohort, which was confirmed on a separate cohort of patients and carriers. The 100% specificity of this unique epi-signature was further confirmed on additional 500 unaffected controls and 600 patients with intellectual disability and developmental delay, including other patient cohorts with previously described epi-signatures. Conclusion Peripheral blood epi-signature in Claes-Jensen syndrome can be used for molecular diagnosis and carrier identification and assist with interpretation of genetic variants of unknown clinical significance in the KDM5C gene. Electronic supplementary material The online version of this article (10.1186/s13148-018-0453-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Laila C Schenkel
- 1Department of Pathology and Laboratory Medicine, Western University, London, Ontario Canada.,2Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario Canada
| | - Erfan Aref-Eshghi
- 1Department of Pathology and Laboratory Medicine, Western University, London, Ontario Canada.,2Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario Canada
| | | | - Peter Ainsworth
- 1Department of Pathology and Laboratory Medicine, Western University, London, Ontario Canada.,2Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario Canada
| | - Hanxin Lin
- 1Department of Pathology and Laboratory Medicine, Western University, London, Ontario Canada.,2Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario Canada
| | - Guillaume Paré
- 4Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario Canada
| | - David I Rodenhiser
- 5Departments of Pediatrics, Biochemistry and Oncology, Western University, London, Ontario Canada
| | | | - Bekim Sadikovic
- 1Department of Pathology and Laboratory Medicine, Western University, London, Ontario Canada.,2Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario Canada.,6Department of Pathology and Laboratory Medicine, Victoria Hospital, London Health Sciences Centre, 800 Commissioner's Road E, B10-104, London, Ontario N6A 5W9 Canada
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Histone Lysine Methylases and Demethylases in the Landscape of Human Developmental Disorders. Am J Hum Genet 2018; 102:175-187. [PMID: 29276005 DOI: 10.1016/j.ajhg.2017.11.013] [Citation(s) in RCA: 161] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 11/17/2017] [Indexed: 11/23/2022] Open
Abstract
Histone lysine methyltransferases (KMTs) and demethylases (KDMs) underpin gene regulation. Here we demonstrate that variants causing haploinsufficiency of KMTs and KDMs are frequently encountered in individuals with developmental disorders. Using a combination of human variation databases and existing animal models, we determine 22 KMTs and KDMs as additional candidates for dominantly inherited developmental disorders. We show that KMTs and KDMs that are associated with, or are candidates for, dominant developmental disorders tend to have a higher level of transcription, longer canonical transcripts, more interactors, and a higher number and more types of post-translational modifications than other KMT and KDMs. We provide evidence to firmly associate KMT2C, ASH1L, and KMT5B haploinsufficiency with dominant developmental disorders. Whereas KMT2C or ASH1L haploinsufficiency results in a predominantly neurodevelopmental phenotype with occasional physical anomalies, KMT5B mutations cause an overgrowth syndrome with intellectual disability. We further expand the phenotypic spectrum of KMT2B-related disorders and show that some individuals can have severe developmental delay without dystonia at least until mid-childhood. Additionally, we describe a recessive histone lysine-methylation defect caused by homozygous or compound heterozygous KDM5B variants and resulting in a recognizable syndrome with developmental delay, facial dysmorphism, and camptodactyly. Collectively, these results emphasize the significance of histone lysine methylation in normal human development and the importance of this process in human developmental disorders. Our results demonstrate that systematic clinically oriented pathway-based analysis of genomic data can accelerate the discovery of rare genetic disorders.
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49
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Aref-Eshghi E, Schenkel LC, Lin H, Skinner C, Ainsworth P, Paré G, Rodenhiser D, Schwartz C, Sadikovic B. The defining DNA methylation signature of Kabuki syndrome enables functional assessment of genetic variants of unknown clinical significance. Epigenetics 2017; 12:923-933. [PMID: 28933623 DOI: 10.1080/15592294.2017.1381807] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Kabuki syndrome (KS) is caused by mutations in KMT2D, which is a histone methyltransferase involved in methylation of H3K4, a histone marker associated with DNA methylation. Analysis of >450,000 CpGs in 24 KS patients with pathogenic mutations in KMT2D and 216 controls, identified 24 genomic regions, along with 1,504 CpG sites with significant DNA methylation changes including a number of Hox genes and the MYO1F gene. Using the most differentiating and significant probes and regions we developed a "methylation variant pathogenicity (MVP) score," which enables 100% sensitive and specific identification of individuals with KS, which was confirmed using multiple public and internal patient DNA methylation databases. We also demonstrated the ability of the MVP score to accurately reclassify variants of unknown significance in subjects with apparent clinical features of KS, enabling its potential use in molecular diagnostics. These findings provide novel insights into the molecular etiology of KS and illustrate that DNA methylation patterns can be interpreted as 'epigenetic echoes' in certain clinical disorders.
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Affiliation(s)
- Erfan Aref-Eshghi
- a Department of Pathology and Laboratory Medicine , Western University , London , ON , Canada
| | - Laila C Schenkel
- a Department of Pathology and Laboratory Medicine , Western University , London , ON , Canada
| | - Hanxin Lin
- b Molecular Genetics Laboratory, Molecular Diagnostics Division , London Health Sciences Centre , London , ON , Canada . Children's Health Research Institute , London , ON , Canada
| | | | - Peter Ainsworth
- b Molecular Genetics Laboratory, Molecular Diagnostics Division , London Health Sciences Centre , London , ON , Canada . Children's Health Research Institute , London , ON , Canada
| | - Guillaume Paré
- d Department of Pathology and Molecular Medicine , McMaster University , Hamilton , ON , Canada
| | - David Rodenhiser
- e Departments of Paediatrics, Biochemistry and Oncology , Western University , London , ON , Canada
| | | | - Bekim Sadikovic
- a Department of Pathology and Laboratory Medicine , Western University , London , ON , Canada.,b Molecular Genetics Laboratory, Molecular Diagnostics Division , London Health Sciences Centre , London , ON , Canada . Children's Health Research Institute , London , ON , Canada
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50
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Shpargel KB, Starmer J, Wang C, Ge K, Magnuson T. UTX-guided neural crest function underlies craniofacial features of Kabuki syndrome. Proc Natl Acad Sci U S A 2017; 114:E9046-E9055. [PMID: 29073101 PMCID: PMC5664495 DOI: 10.1073/pnas.1705011114] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Kabuki syndrome, a congenital craniofacial disorder, manifests from mutations in an X-linked histone H3 lysine 27 demethylase (UTX/KDM6A) or a H3 lysine 4 methylase (KMT2D). However, the cellular and molecular etiology of histone-modifying enzymes in craniofacial disorders is unknown. We now establish Kabuki syndrome as a neurocristopathy, whereby the majority of clinical features are modeled in mice carrying neural crest (NC) deletion of UTX, including craniofacial dysmorphism, cardiac defects, and postnatal growth retardation. Female UTX NC knockout (FKO) demonstrates enhanced phenotypic severity over males (MKOs), due to partial redundancy with UTY, a Y-chromosome demethylase-dead homolog. Thus, NC cells may require demethylase-independent UTX activity. Consistently, Kabuki causative point mutations upstream of the JmjC domain do not disrupt UTX demethylation. We have isolated primary NC cells at a phenocritical postmigratory timepoint in both FKO and MKO mice, and genome-wide expression and histone profiling have revealed UTX molecular function in establishing appropriate chromatin structure to regulate crucial NC stem-cell signaling pathways. However, the majority of UTX regulated genes do not experience aberrations in H3K27me3 or H3K4me3, implicating alternative roles for UTX in transcriptional control. These findings are substantiated through demethylase-dead knockin mutation of UTX, which supports appropriate facial development.
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Affiliation(s)
- Karl B Shpargel
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599-7264
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599-7264
| | - Joshua Starmer
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599-7264
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599-7264
| | - Chaochen Wang
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Kai Ge
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Terry Magnuson
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599-7264;
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599-7264
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