1
|
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.
Collapse
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
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Poreba E, Lesniewicz K, Durzynska J. Histone-lysine N-methyltransferase 2 (KMT2) complexes - a new perspective. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 790:108443. [PMID: 36154872 DOI: 10.1016/j.mrrev.2022.108443] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 06/25/2022] [Accepted: 09/19/2022] [Indexed: 01/01/2023]
Abstract
Histone H3 Lys4 (H3K4) methylation is catalyzed by the Histone-Lysine N-Methyltransferase 2 (KMT2) protein family, and its members are required for gene expression control. In vertebrates, the KMT2s function in large multisubunit complexes known as COMPASS or COMPASS-like complexes (COMplex of Proteins ASsociated with Set1). The activity of these complexes is critical for proper development, and mutation-induced defects in their functioning have frequently been found in human cancers. Moreover, inherited or de novo mutations in KMT2 genes are among the etiological factors in neurodevelopmental disorders such as Kabuki and Kleefstra syndromes. The canonical role of KMT2s is to catalyze H3K4 methylation, which results in a permissive chromatin environment that drives gene expression. However, current findings described in this review demonstrate that these enzymes can regulate processes that are not dependent on methylation: noncatalytic functions of KMT2s include DNA damage response, cell division, and metabolic activities. Moreover, these enzymes may also methylate non-histone substrates and play a methylation-dependent function in the DNA damage response. In this review, we present an overview of the new, noncanonical activities of KMT2 complexes in a variety of cellular processes. These discoveries may have crucial implications for understanding the functions of these methyltransferases in developmental processes, disease, and epigenome-targeting therapeutic strategies in the future.
Collapse
Affiliation(s)
- Elzbieta Poreba
- Department of Genetics, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland.
| | - Krzysztof Lesniewicz
- Department of Molecular and Cellular Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Julia Durzynska
- Department of Genetics, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland.
| |
Collapse
|
4
|
Tang CSM, Mononen M, Lam WY, Jin SC, Zhuang X, Garcia-Barcelo MM, Lin Q, Yang Y, Sahara M, Eroglu E, Chien KR, Hong H, Tam PK, Gruber PJ. Sequencing of a Chinese tetralogy of fallot cohort reveals clustering mutations in myogenic heart progenitors. JCI Insight 2021; 7:152198. [PMID: 34905512 PMCID: PMC8855809 DOI: 10.1172/jci.insight.152198] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 12/08/2021] [Indexed: 11/17/2022] Open
Abstract
Tetralogy of Fallot (TOF) is the most common cyanotic heart defect, yet the underlying genetic mechanisms remain poorly understood. Here, we performed whole-genome sequencing analysis on 146 nonsyndromic TOF parent-offspring trios of Chinese ethnicity. Comparison of de novo variants and recessive genotypes of this data set with data from a European cohort identified both overlapping and potentially novel gene loci and revealed differential functional enrichment between cohorts. To assess the impact of these mutations on early cardiac development, we integrated single-cell and spatial transcriptomics of early human heart development with our genetic findings. We discovered that the candidate gene expression was enriched in the myogenic progenitors of the cardiac outflow tract. Moreover, subsets of the candidate genes were found in specific gene coexpression modules along the cardiomyocyte differentiation trajectory. These integrative functional analyses help dissect the pathogenesis of TOF, revealing cellular hotspots in early heart development resulting in cardiac malformations.
Collapse
Affiliation(s)
- Clara Sze Man Tang
- Department of Surgery, The University of Hong Kong, Hong Kong, Hong Kong
| | - Mimmi Mononen
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Wai-Yee Lam
- Department of Surgery, The University of Hong Kong, Hong Kong, Hong Kong
| | - Sheng Chih Jin
- Department of Genetics, Washington University School of Medicine, St. Louis, United States of America
| | - Xuehan Zhuang
- Department of Surgery, The University of Hong Kong, Hong Kong, Hong Kong
| | | | - Qiongfen Lin
- Department of Surgery, The University of Hong Kong, Hong Kong, Hong Kong
| | - Yujia Yang
- Department of Surgery, Yale University School of Medicine, New Haven, United States of America
| | - Makoto Sahara
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Elif Eroglu
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Kenneth R Chien
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Haifa Hong
- Department of Cardiovascular Surgery, Shanghai Children's Medical Center, Shanghai, China
| | - Paul Kh Tam
- Department of Surgery, The University of Hong Kong, Hong Kong, Hong Kong
| | - Peter J Gruber
- Yale University School of Medicine, New Haven, United States of America
| |
Collapse
|
5
|
Barcelona-Cabeza R, Sanseverino W, Aiese Cigliano R. isoCNV: in silico optimization of copy number variant detection from targeted or exome sequencing data. BMC Bioinformatics 2021; 22:530. [PMID: 34715772 PMCID: PMC8555218 DOI: 10.1186/s12859-021-04452-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 10/19/2021] [Indexed: 01/02/2023] Open
Abstract
Background Accurate copy number variant (CNV) detection is especially challenging for both targeted sequencing (TS) and whole‐exome sequencing (WES) data. To maximize the performance, the parameters of the CNV calling algorithms should be optimized for each specific dataset. This requires obtaining validated CNV information using either multiplex ligation-dependent probe amplification (MLPA) or array comparative genomic hybridization (aCGH). They are gold standard but time-consuming and costly approaches. Results We present isoCNV which optimizes the parameters of DECoN algorithm using only NGS data. The parameter optimization process is performed using an in silico CNV validated dataset obtained from the overlapping calls of three algorithms: CNVkit, panelcn.MOPS and DECoN. We evaluated the performance of our tool and showed that increases the sensitivity in both TS and WES real datasets. Conclusions isoCNV provides an easy-to-use pipeline to optimize DECoN that allows the detection of analysis-ready CNV from a set of DNA alignments obtained under the same conditions. It increases the sensitivity of DECoN without the need for orthogonal methods. isoCNV is available at https://gitlab.com/sequentiateampublic/isocnv.
Collapse
Affiliation(s)
- Rosa Barcelona-Cabeza
- Sequentia Biotech, Carrer de Valencia, Barcelona, Spain.,Departamento de Matemáticas, Escuela Técnica Superior de Ingeniería Industrial de Barcelona (ETSEIB), Universitat Politècnica de Catalunya (UPC), Diagonal 647, Barcelona, Spain
| | | | | |
Collapse
|
6
|
So PL, Luk HM, Cheung KW, Hui W, Chung MY, Mak ASL, Lok WY, Yu KPT, Cheng SSW, Hau EWL, Ho S, Lam STS, Lo IFM. Prenatal phenotype of Kabuki syndrome: A case series and literature review. Prenat Diagn 2021; 41:1089-1100. [PMID: 34185329 DOI: 10.1002/pd.5998] [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: 01/17/2021] [Revised: 05/30/2021] [Accepted: 05/31/2021] [Indexed: 12/11/2022]
Abstract
OBJECTIVES Kabuki syndrome (KS) is a genetic disorder characterized by intellectual disability, facial dysmorphism and congenital anomalies. We aim to investigate the prenatal features of fetuses with KS and to provide a comprehensive review of the literature on prenatal sonographic abnormalities associated with KS. METHODS We retrospectively reviewed the prenatal ultrasound findings of all mothers of children with molecularly confirmed KS in Hong Kong, between 1991 and 2019. We also performed systematic review of the literature to identify studies on the prenatal findings in KS. RESULTS We identified 11 cases with KS with detectable fetal ultrasound findings ranging from no detectable abnormalities to a variety of non-specific findings including increased nuchal translucency, pleural effusion, cardiac anomalies, renal anomalies, intrauterine growth restriction, polyhydramnios, oligohydramnios and single umbilical artery. In combining our cases with the 77 cases published, 42 (50.6%) of them had more than one abnormal antenatal ultrasound finding. The most frequent ultrasound features observed were cardiac anomalies (49.4%), followed by polyhydramnios (28.9%), genitourinary anomalies (26.5%), single umbilical artery (15.7%), intrauterine growth restriction (14.5%) and hydrops fetalis/pleural effusion/ascites (12.0%). CONCLUSIONS These cases demonstrate the prenatal phenotypic heterogeneity associated with KS. Although the ultrasound abnormalities are non-specific, KS should be considered in the differential diagnosis when these fetal findings following normal microarray analysis/karyotyping.
Collapse
Affiliation(s)
- Po Lam So
- Department of Obstetrics and Gynecology, Tuen Mun Hospital, Hong Kong SAR
| | - Ho Ming Luk
- Clinical Genetic Service, Department of Health, Hong Kong SAR
| | - Ka Wang Cheung
- Department of Obstetrics and Gynecology, Queen Mary Hospital, Hong Kong SAR
| | - Winnie Hui
- Department of Obstetrics & Gynecology, Pamela Youde Nethersole Eastern Hospital, Hong Kong SAR
| | - Man Yan Chung
- Department of Obstetrics and Gynecology, Prince of Wales Hospital, Hong Kong SAR
| | - Annisa S L Mak
- Department of Obstetrics and Gynecology, Queen Elizabeth Hospital, Hong Kong SAR
| | - Wing Yi Lok
- Department of Obstetrics and Gynecology, United Christian Hospital, Hong Kong SAR
| | - Kris Pui Tak Yu
- Clinical Genetic Service, Department of Health, Hong Kong SAR
| | | | - Edgar W L Hau
- Clinical Genetic Service, Department of Health, Hong Kong SAR
| | - Stephanie Ho
- Clinical Genetic Service, Department of Health, Hong Kong SAR
| | - Stephen T S Lam
- Clinical Genetics Service, Hong Kong Sanatorium & Hospital, Hong Kong SAR
| | - Ivan F M Lo
- Clinical Genetic Service, Department of Health, Hong Kong SAR
| |
Collapse
|
7
|
Boniel S, Szymańska K, Śmigiel R, Szczałuba K. Kabuki Syndrome-Clinical Review with Molecular Aspects. Genes (Basel) 2021; 12:468. [PMID: 33805950 PMCID: PMC8064399 DOI: 10.3390/genes12040468] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/14/2021] [Accepted: 03/16/2021] [Indexed: 12/13/2022] Open
Abstract
Kabuki syndrome (KS) is a rare developmental disorder principally comprised of developmental delay, hypotonia and a clearly defined dysmorphism: elongation of the structures surrounding the eyes, a shortened and depressed nose, thinning of the upper lip and thickening of the lower lip, large and prominent ears, hypertrichosis and scoliosis. Other characteristics include poor physical growth, cardiac, gastrointestinal and renal anomalies as well as variable behavioral issues, including autistic features. De novo or inherited pathogenic/likely pathogenic variants in the KMT2D gene are the most common cause of KS and account for up to 75% of patients. Variants in KDM6A cause up to 5% of cases (X-linked dominant inheritance), while the etiology of about 20% of cases remains unknown. Current KS diagnostic criteria include hypotonia during infancy, developmental delay and/or intellectual disability, typical dysmorphism and confirmed pathogenic/likely pathogenic variant in KMT2D or KDM6A. Care for KS patients includes the control of physical and psychomotor development during childhood, rehabilitation and multi-specialist care. This paper reviews the current clinical knowledge, provides molecular and scientific links and sheds light on the treatment of Kabuki syndrome individuals.
Collapse
Affiliation(s)
- Snir Boniel
- Department of Medical Genetics, Medical University, Pawinskiego 3c, 02-106 Warsaw, Poland;
| | - Krystyna Szymańska
- Mossakowski Medical Research Center, Department of Experimental and Clinical Neuropathology, Polish Academy of Sciences, 02-106 Warsaw, Poland;
| | - Robert Śmigiel
- Department of Paediatrics, Division of Propaedeutic of Paediatrics and Rare Disorders, Medical University, 51-618 Wroclaw, Poland;
| | - Krzysztof Szczałuba
- Department of Medical Genetics, Medical University, Pawinskiego 3c, 02-106 Warsaw, Poland;
| |
Collapse
|