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Seehawer M, Li Z, Nishida J, Foidart P, Reiter AH, Rojas-Jimenez E, Goyette MA, Yan P, Raval S, Munoz Gomez M, Cejas P, Long HW, Papanastasiou M, Polyak K. Loss of Kmt2c or Kmt2d drives brain metastasis via KDM6A-dependent upregulation of MMP3. Nat Cell Biol 2024:10.1038/s41556-024-01446-3. [PMID: 38926506 DOI: 10.1038/s41556-024-01446-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 05/29/2024] [Indexed: 06/28/2024]
Abstract
KMT2C and KMT2D, encoding histone H3 lysine 4 methyltransferases, are among the most commonly mutated genes in triple-negative breast cancer (TNBC). However, how these mutations may shape epigenomic and transcriptomic landscapes to promote tumorigenesis is largely unknown. Here we describe that deletion of Kmt2c or Kmt2d in non-metastatic murine models of TNBC drives metastasis, especially to the brain. Global chromatin profiling and chromatin immunoprecipitation followed by sequencing revealed altered H3K4me1, H3K27ac and H3K27me3 chromatin marks in knockout cells and demonstrated enhanced binding of the H3K27me3 lysine demethylase KDM6A, which significantly correlated with gene expression. We identified Mmp3 as being commonly upregulated via epigenetic mechanisms in both knockout models. Consistent with these findings, samples from patients with KMT2C-mutant TNBC have higher MMP3 levels. Downregulation or pharmacological inhibition of KDM6A diminished Mmp3 upregulation induced by the loss of histone-lysine N-methyltransferase 2 (KMT2) and prevented brain metastasis similar to direct downregulation of Mmp3. Taken together, we identified the KDM6A-matrix metalloproteinase 3 axis as a key mediator of KMT2C/D loss-driven metastasis in TNBC.
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Affiliation(s)
- Marco Seehawer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Zheqi Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Jun Nishida
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Pierre Foidart
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | | | - Ernesto Rojas-Jimenez
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Marie-Anne Goyette
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Pengze Yan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Shaunak Raval
- The Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Miguel Munoz Gomez
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Paloma Cejas
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Henry W Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
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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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3
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Lee CL, Chuang CK, Chen MR, Lin JL, Chiu HC, Chang YH, Tu YR, Lo YT, Lin HY, Lin SP. Illuminating the Genetic Basis of Congenital Heart Disease in Patients with Kabuki Syndrome. Diagnostics (Basel) 2024; 14:846. [PMID: 38667491 PMCID: PMC11049448 DOI: 10.3390/diagnostics14080846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 04/13/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Congenital heart defects (CHDs) affect a substantial proportion of patients with Kabuki syndrome. However, the prevalence and type of CHD and the genotype-phenotype correlations in Asian populations are not fully elucidated. This study performed a retrospective analysis of 23 Taiwanese patients with molecularly confirmed Kabuki syndrome. Twenty-two patients presented with pathogenic variants in the KMT2D gene. Comprehensive clinical assessments were performed. A literature review was conducted to summarize the spectrum of CHDs in patients with Kabuki syndrome. In total, 16 (73.9%) of 22 patients with pathogenic KMT2D variants had CHDs. The most common types of CHD were atrial septal defects (37.5%), ventricular septal defects (18.8%), coarctation of the aorta (18.8%), bicuspid aortic valve (12.5%), persistent left superior vena cava (12.5%), mitral valve prolapse (12.5%), mitral regurgitation (12.5%), and patent ductus arteriosus (12.5%). Other cardiac abnormalities were less common. Further, there were no clear genotype-phenotype correlations found. A literature review revealed similar patterns of CHDs, with a predominance of left-sided obstructive lesions and septal defects. In conclusion, the most common types of CHDs in Taiwanese patients with Kabuki syndrome who presented with KMT2D mutations are left-sided obstructive lesions and septal defects.
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Grants
- MMH-E-113-13, MMH-MM-112-14, MMH-E-112-13, and MMH-E-111-13 Mackay Memorial Hospital
- NSTC-112-2314-B-195-014-MY3, NSTC-112-2811-B-195-001, NSTC-112-2314-B-195-003, NSTC-111-2314-B-195-017, NSTC-111-2811-B-195-002, NSTC-111-2811-B-195-001, NSTC-110-2314-B-195-014, NSTC-110-2314-B-195-010-MY3, and NSTC-110-2314-B-195-029 Ministry of Science and Technology, Executive Yuan, Taiwan
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Affiliation(s)
- Chung-Lin Lee
- Department of Pediatrics, MacKay Memorial Hospital, Taipei 10449, Taiwan; (C.-L.L.); (M.-R.C.); (H.-C.C.); (Y.-H.C.)
- Institute of Clinical Medicine, National Yang-Ming Chiao-Tung University, Taipei 112304, Taiwan
- Department of Rare Disease Center, MacKay Memorial Hospital, Taipei 10449, Taiwan;
- Department of Medicine, Mackay Medical College, New Taipei City 25245, Taiwan
- Department of Nursing, Mackay Junior College of Medicine, Nursing and Management, Taipei 112021, Taiwan
| | - Chih-Kuang Chuang
- Division of Genetics and Metabolism, Department of Medical Research, MacKay Memorial Hospital, Taipei 10449, Taiwan; (C.-K.C.); (Y.-R.T.)
- College of Medicine, Fu-Jen Catholic University, Taipei 24205, Taiwan
| | - Ming-Ren Chen
- Department of Pediatrics, MacKay Memorial Hospital, Taipei 10449, Taiwan; (C.-L.L.); (M.-R.C.); (H.-C.C.); (Y.-H.C.)
| | - Ju-Li Lin
- Division of Endocrine & Medical Genetics, Department of Pediatrics, Chang Gung Children’s Medical Center, Chang Gung Memorial Hospital, Taoyuan 33378, Taiwan;
| | - Huei-Ching Chiu
- Department of Pediatrics, MacKay Memorial Hospital, Taipei 10449, Taiwan; (C.-L.L.); (M.-R.C.); (H.-C.C.); (Y.-H.C.)
| | - Ya-Hui Chang
- Department of Pediatrics, MacKay Memorial Hospital, Taipei 10449, Taiwan; (C.-L.L.); (M.-R.C.); (H.-C.C.); (Y.-H.C.)
- Department of Rare Disease Center, MacKay Memorial Hospital, Taipei 10449, Taiwan;
| | - Yuan-Rong Tu
- Division of Genetics and Metabolism, Department of Medical Research, MacKay Memorial Hospital, Taipei 10449, Taiwan; (C.-K.C.); (Y.-R.T.)
| | - Yun-Ting Lo
- Department of Rare Disease Center, MacKay Memorial Hospital, Taipei 10449, Taiwan;
| | - Hsiang-Yu Lin
- Department of Pediatrics, MacKay Memorial Hospital, Taipei 10449, Taiwan; (C.-L.L.); (M.-R.C.); (H.-C.C.); (Y.-H.C.)
- Department of Rare Disease Center, MacKay Memorial Hospital, Taipei 10449, Taiwan;
- Department of Medicine, Mackay Medical College, New Taipei City 25245, Taiwan
- Department of Nursing, Mackay Junior College of Medicine, Nursing and Management, Taipei 112021, Taiwan
- Division of Genetics and Metabolism, Department of Medical Research, MacKay Memorial Hospital, Taipei 10449, Taiwan; (C.-K.C.); (Y.-R.T.)
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung 40402, Taiwan
| | - Shuan-Pei Lin
- Department of Pediatrics, MacKay Memorial Hospital, Taipei 10449, Taiwan; (C.-L.L.); (M.-R.C.); (H.-C.C.); (Y.-H.C.)
- Department of Rare Disease Center, MacKay Memorial Hospital, Taipei 10449, Taiwan;
- Department of Medicine, Mackay Medical College, New Taipei City 25245, Taiwan
- Division of Genetics and Metabolism, Department of Medical Research, MacKay Memorial Hospital, Taipei 10449, Taiwan; (C.-K.C.); (Y.-R.T.)
- Department of Infant and Child Care, National Taipei University of Nursing and Health Sciences, Taipei 11219, Taiwan
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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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5
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Niceta M, Ciolfi A, Ferilli M, Pedace L, Cappelletti C, Nardini C, Hildonen M, Chiriatti L, Miele E, Dentici ML, Gnazzo M, Cesario C, Pisaneschi E, Baban A, Novelli A, Maitz S, Selicorni A, Squeo GM, Merla G, Dallapiccola B, Tumer Z, Digilio MC, Priolo M, Tartaglia M. DNA methylation profiling in Kabuki syndrome: reclassification of germline KMT2D VUS and sensitivity in validating postzygotic mosaicism. Eur J Hum Genet 2024:10.1038/s41431-024-01597-9. [PMID: 38528056 DOI: 10.1038/s41431-024-01597-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 03/05/2024] [Accepted: 03/13/2024] [Indexed: 03/27/2024] Open
Abstract
Autosomal dominant Kabuki syndrome (KS) is a rare multiple congenital anomalies/neurodevelopmental disorder caused by heterozygous inactivating variants or structural rearrangements of the lysine-specific methyltransferase 2D (KMT2D) gene. While it is often recognizable due to a distinctive gestalt, the disorder is clinically variable, and a phenotypic scoring system has been introduced to help clinicians to reach a clinical diagnosis. The phenotype, however, can be less pronounced in some patients, including those carrying postzygotic mutations. The full spectrum of pathogenic variation in KMT2D has not fully been characterized, which may hamper the clinical classification of a portion of these variants. DNA methylation (DNAm) profiling has successfully been used as a tool to classify variants in genes associated with several neurodevelopmental disorders, including KS. In this work, we applied a KS-specific DNAm signature in a cohort of 13 individuals with KMT2D VUS and clinical features suggestive or overlapping with KS. We succeeded in correctly classifying all the tested individuals, confirming diagnosis for three subjects and rejecting the pathogenic role of 10 VUS in the context of KS. In the latter group, exome sequencing allowed to identify the genetic cause underlying the disorder in three subjects. By testing five individuals with postzygotic pathogenic KMT2D variants, we also provide evidence that DNAm profiling has power to recognize pathogenic variants at different levels of mosaicism, identifying 15% as the minimum threshold for which DNAm profiling can be applied as an informative diagnostic tool in KS mosaics.
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Affiliation(s)
- Marcello Niceta
- Molecular Genetics and Functional Genomics, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
| | - Andrea Ciolfi
- Molecular Genetics and Functional Genomics, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
| | - Marco Ferilli
- Molecular Genetics and Functional Genomics, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
- Department of Computer, Control and Management Engineering, Sapienza University, 00185, Rome, Italy
| | - Lucia Pedace
- Department of Pediatric Hematology/Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, 00165, Rome, Italy
| | - Camilla Cappelletti
- Molecular Genetics and Functional Genomics, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
| | - Claudia Nardini
- Department of Pediatric Hematology/Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, 00165, Rome, Italy
| | - Mathis Hildonen
- Department of Clinical Genetics, Kennedy Center, Copenhagen University Hospital, Rigshopsitalet, 2600, Glostrup, Denmark
| | - Luigi Chiriatti
- Molecular Genetics and Functional Genomics, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
| | - Evelina Miele
- Department of Pediatric Hematology/Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, 00165, Rome, Italy
| | - Maria Lisa Dentici
- Medical Genetics Unit, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
| | - Maria Gnazzo
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
| | - Claudia Cesario
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
| | - Elisa Pisaneschi
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
| | - Anwar Baban
- Pediatric Cardiology and Cardiac Arrhythmias Unit, Department of Pediatric Cardiology and Cardiac Surgery, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
| | - Silvia Maitz
- Genetica Clinica Pediatrica, Fondazione MBBM, ASST Monza Ospedale San Gerardo, 20900, Monza, Italy
| | | | - Gabriella Maria Squeo
- Laboratory of Regulatory and Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013, Foggia, Italy
| | - Giuseppe Merla
- Laboratory of Regulatory and Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013, Foggia, Italy
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131, Naples, Italy
| | - Bruno Dallapiccola
- Molecular Genetics and Functional Genomics, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
| | - Zeynep Tumer
- Department of Clinical Genetics, Kennedy Center, Copenhagen University Hospital, Rigshopsitalet, 2600, Glostrup, Denmark
- Department of Clinical Medicine, Faculty of Medicine and Health Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | | | - Manuela Priolo
- Medical and Laboratory Genetics, Antonio Cardarelli Hospital, 80131, Naples, Italy
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy.
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6
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Aponte JD, Bannister JJ, Hoskens H, Matthews H, Katsura K, Da Silva C, Cruz T, Pilz JHM, Spritz RA, Forkert ND, Claes P, Bernier FP, Klein OD, Katz DC, Hallgrímsson B. An interactive atlas of three-dimensional syndromic facial morphology. Am J Hum Genet 2024; 111:39-47. [PMID: 38181734 PMCID: PMC10806736 DOI: 10.1016/j.ajhg.2023.11.011] [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: 06/03/2023] [Revised: 11/26/2023] [Accepted: 11/29/2023] [Indexed: 01/07/2024] Open
Abstract
Craniofacial phenotyping is critical for both syndrome delineation and diagnosis because craniofacial abnormalities occur in 30% of characterized genetic syndromes. Clinical reports, textbooks, and available software tools typically provide two-dimensional, static images and illustrations of the characteristic phenotypes of genetic syndromes. In this work, we provide an interactive web application that provides three-dimensional, dynamic visualizations for the characteristic craniofacial effects of 95 syndromes. Users can visualize syndrome facial appearance estimates quantified from data and easily compare craniofacial phenotypes of different syndromes. Our application also provides a map of morphological similarity between a target syndrome and other syndromes. Finally, users can upload 3D facial scans of individuals and compare them to our syndrome atlas estimates. In summary, we provide an interactive reference for the craniofacial phenotypes of syndromes that allows for precise, individual-specific comparisons of dysmorphology.
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Affiliation(s)
- J David Aponte
- Department of Cell Biology & Anatomy, Alberta Children's Hospital Research Institute and McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; DeepSurface AI Inc., Calgary, AB, Canada
| | | | - Hanne Hoskens
- Department of Cell Biology & Anatomy, Alberta Children's Hospital Research Institute and McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | | | - Kaitlin Katsura
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA, USA
| | - Cassidy Da Silva
- Department of Cell Biology & Anatomy, Alberta Children's Hospital Research Institute and McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Tim Cruz
- DeepSurface AI Inc., Calgary, AB, Canada
| | | | - Richard A Spritz
- Department of Pediatrics and the Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, CO, USA
| | - Nils D Forkert
- Department of Radiology and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Peter Claes
- Department of Human Genetics, KU Leuven, Leuven, Belgium; Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
| | - Francois P Bernier
- Department of Medical Genetics and the Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Ophir D Klein
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA, USA; Department of Pediatrics, Cedars-Sinai Guerin Children's, Los Angeles, CA, USA
| | - David C Katz
- Department of Cell Biology & Anatomy, Alberta Children's Hospital Research Institute and McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; DeepSurface AI Inc., Calgary, AB, Canada
| | - Benedikt Hallgrímsson
- Department of Cell Biology & Anatomy, Alberta Children's Hospital Research Institute and McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
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7
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Zhao Z, Aoi Y, Philips CN, Meghani KA, Gold SR, Yu Y, John LS, Qian J, Zeidner JM, Meeks JJ, Shilatifard A. Somatic mutations of MLL4/COMPASS induce cytoplasmic localization providing molecular insight into cancer prognosis and treatment. Proc Natl Acad Sci U S A 2023; 120:e2310063120. [PMID: 38113256 PMCID: PMC10756272 DOI: 10.1073/pnas.2310063120] [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: 06/14/2023] [Accepted: 11/17/2023] [Indexed: 12/21/2023] Open
Abstract
Cancer genome sequencing consortiums have recently catalogued an abundance of somatic mutations, across a wide range of human cancers, in the chromatin-modifying enzymes that regulate gene expression. Defining the molecular mechanisms underlying the potentially oncogenic functions of these epigenetic mutations could serve as the basis for precision medicine approaches to cancer therapy. MLL4 encoded by the KMT2D gene highly mutated in a large number of human cancers, is a key histone lysine monomethyltransferase within the Complex of Proteins Associated with Set1 (COMPASS) family that regulates gene expression through enhancer function, potentially functioning as a tumor suppressor. We report that the KMT2D mutations which cause MLL4 protein truncation also alter MLL4's subcellular localization, resulting in loss-of-function in the nucleus and gain-of-function in the cytoplasm. We demonstrate that isogenic correction of KMT2D truncation mutation rescues the aberrant localization phenotype and restores multiple regulatory functions of MLL4, including COMPASS integrity/stabilization, histone H3K4 mono-methylation, enhancer activation, and therefore transcriptional regulation. Moreover, isogenic correction diminishes the sensitivity of KMT2D-mutated cancer cells to targeted metabolic inhibition. Using immunohistochemistry, we identified that cytoplasmic MLL4 is unique to the tissue of bladder cancer patients with KMT2D truncation mutations. Using a preclinical carcinogen model of bladder cancer in mouse, we demonstrate that truncated cytoplasmic MLL4 predicts response to targeted metabolic inhibition therapy for bladder cancer and could be developed as a biomarker for KMT2D-mutated cancers. We also highlight the broader potential for prognosis, patient stratification and treatment decision-making based on KMT2D mutation status in MLL4 truncation-relevant diseases, including human cancers and Kabuki Syndrome.
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Affiliation(s)
- Zibo Zhao
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
| | - Yuki Aoi
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
| | - Cassandra N. Philips
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
| | - Khyati A. Meghani
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL60611
| | - Sarah R. Gold
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
| | - Yanni Yu
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL60611
| | - Luke St John
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
| | - Jun Qian
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL60611
| | - Jacob M. Zeidner
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
| | - Joshua J. Meeks
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL60611
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
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8
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Shpargel KB, Quickstad G. SETting up the genome: KMT2D and KDM6A genomic function in the Kabuki syndrome craniofacial developmental disorder. Birth Defects Res 2023; 115:1885-1898. [PMID: 37800171 PMCID: PMC11190966 DOI: 10.1002/bdr2.2253] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/04/2023] [Accepted: 09/14/2023] [Indexed: 10/07/2023]
Abstract
BACKGROUND Kabuki syndrome is a congenital developmental disorder that is characterized by distinctive facial gestalt and skeletal abnormalities. Although rare, the disorder shares clinical features with several related craniofacial syndromes that manifest from mutations in chromatin-modifying enzymes. Collectively, these clinical studies underscore the crucial, concerted functions of chromatin factors in shaping developmental genome structure and driving cellular transcriptional states. Kabuki syndrome predominantly results from mutations in KMT2D, a histone H3 lysine 4 methylase, or KDM6A, a histone H3 lysine 27 demethylase. AIMS In this review, we summarize the research efforts to model Kabuki syndrome in vivo to understand the cellular and molecular mechanisms that lead to the craniofacial and skeletal pathogenesis that defines the disorder. DISCUSSION As several studies have indicated the importance of KMT2D and KDM6A function through catalytic-independent mechanisms, we highlight noncanonical roles for these enzymes as recruitment centers for alternative chromatin and transcriptional machinery.
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Affiliation(s)
- Karl B. Shpargel
- Department of GeneticsUniversity of North CarolinaChapel HillNorth CarolinaUSA
| | - Gabrielle Quickstad
- Department of GeneticsUniversity of North CarolinaChapel HillNorth CarolinaUSA
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9
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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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10
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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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11
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Zhang S, Pei G, Li B, Li P, Lin Y. Abnormal phase separation of biomacromolecules in human diseases. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1133-1152. [PMID: 37475546 PMCID: PMC10423695 DOI: 10.3724/abbs.2023139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 07/07/2023] [Indexed: 07/22/2023] Open
Abstract
Membrane-less organelles (MLOs) formed through liquid-liquid phase separation (LLPS) are associated with numerous important biological functions, but the abnormal phase separation will also dysregulate the physiological processes. Emerging evidence points to the importance of LLPS in human health and diseases. Nevertheless, despite recent advancements, our knowledge of the molecular relationship between LLPS and diseases is frequently incomplete. In this review, we outline our current understanding about how aberrant LLPS affects developmental disorders, tandem repeat disorders, cancers and viral infection. We also examine disease mechanisms driven by aberrant condensates, and highlight potential treatment approaches. This study seeks to expand our understanding of LLPS by providing a valuable new paradigm for understanding phase separation and human disorders, as well as to further translate our current knowledge regarding LLPS into therapeutic discoveries.
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Affiliation(s)
- Songhao Zhang
- State Key Laboratory of Membrane BiologyTsinghua University-Peking University Joint Centre for Life SciencesSchool of Life SciencesTsinghua UniversityBeijing100084China
- IDG/McGovern Institute for Brain Research at Tsinghua UniversityBeijing100084China
| | - Gaofeng Pei
- State Key Laboratory of Membrane BiologyTsinghua University-Peking University Joint Centre for Life SciencesSchool of Life SciencesTsinghua UniversityBeijing100084China
- Frontier Research Center for Biological StructureTsinghua UniversityBeijing100084China
| | - Boya Li
- State Key Laboratory of Membrane BiologyTsinghua University-Peking University Joint Centre for Life SciencesSchool of Life SciencesTsinghua UniversityBeijing100084China
- IDG/McGovern Institute for Brain Research at Tsinghua UniversityBeijing100084China
| | - Pilong Li
- State Key Laboratory of Membrane BiologyTsinghua University-Peking University Joint Centre for Life SciencesSchool of Life SciencesTsinghua UniversityBeijing100084China
- Frontier Research Center for Biological StructureTsinghua UniversityBeijing100084China
| | - Yi Lin
- State Key Laboratory of Membrane BiologyTsinghua University-Peking University Joint Centre for Life SciencesSchool of Life SciencesTsinghua UniversityBeijing100084China
- IDG/McGovern Institute for Brain Research at Tsinghua UniversityBeijing100084China
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12
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Zhao Z, Cao K, Watanabe J, Philips CN, Zeidner JM, Ishi Y, Wang Q, Gold SR, Junkins K, Bartom ET, Yue F, Chandel NS, Hashizume R, Ben-Sahra I, Shilatifard A. Therapeutic targeting of metabolic vulnerabilities in cancers with MLL3/4-COMPASS epigenetic regulator mutations. J Clin Invest 2023; 133:e169993. [PMID: 37252797 PMCID: PMC10313365 DOI: 10.1172/jci169993] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/09/2023] [Indexed: 06/01/2023] Open
Abstract
Epigenetic status-altering mutations in chromatin-modifying enzymes are a feature of human diseases, including many cancers. However, the functional outcomes and cellular dependencies arising from these mutations remain unresolved. In this study, we investigated cellular dependencies, or vulnerabilities, that arise when enhancer function is compromised by loss of the frequently mutated COMPASS family members MLL3 and MLL4. CRISPR dropout screens in MLL3/4-depleted mouse embryonic stem cells (mESCs) revealed synthetic lethality upon suppression of purine and pyrimidine nucleotide synthesis pathways. Consistently, we observed a shift in metabolic activity toward increased purine synthesis in MLL3/4-KO mESCs. These cells also exhibited enhanced sensitivity to the purine synthesis inhibitor lometrexol, which induced a unique gene expression signature. RNA-Seq identified the top MLL3/4 target genes coinciding with suppression of purine metabolism, and tandem mass tag proteomic profiling further confirmed upregulation of purine synthesis in MLL3/4-KO cells. Mechanistically, we demonstrated that compensation by MLL1/COMPASS was underlying these effects. Finally, we demonstrated that tumors with MLL3 and/or MLL4 mutations were highly sensitive to lometrexol in vitro and in vivo, both in culture and in animal models of cancer. Our results depicted a targetable metabolic dependency arising from epigenetic factor deficiency, providing molecular insight to inform therapy for cancers with epigenetic alterations secondary to MLL3/4 COMPASS dysfunction.
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Affiliation(s)
- Zibo Zhao
- Department of Biochemistry and Molecular Genetics
- Simpson Querrey Center for Epigenetics
| | - Kaixiang Cao
- Department of Biochemistry and Molecular Genetics
- Simpson Querrey Center for Epigenetics
| | - Jun Watanabe
- Department of Biochemistry and Molecular Genetics
- Robert H. Lurie NCI Comprehensive Cancer Center, and
| | - Cassandra N. Philips
- Department of Biochemistry and Molecular Genetics
- Simpson Querrey Center for Epigenetics
| | - Jacob M. Zeidner
- Department of Biochemistry and Molecular Genetics
- Simpson Querrey Center for Epigenetics
| | - Yukitomo Ishi
- Department of Biochemistry and Molecular Genetics
- Robert H. Lurie NCI Comprehensive Cancer Center, and
| | - Qixuan Wang
- Department of Biochemistry and Molecular Genetics
- Simpson Querrey Center for Epigenetics
| | - Sarah R. Gold
- Department of Biochemistry and Molecular Genetics
- Simpson Querrey Center for Epigenetics
| | - Katherine Junkins
- Department of Biochemistry and Molecular Genetics
- Simpson Querrey Center for Epigenetics
| | - Elizabeth T. Bartom
- Department of Biochemistry and Molecular Genetics
- Simpson Querrey Center for Epigenetics
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics
- Simpson Querrey Center for Epigenetics
| | - Navdeep S. Chandel
- Department of Biochemistry and Molecular Genetics
- Simpson Querrey Center for Epigenetics
- Robert H. Lurie NCI Comprehensive Cancer Center, and
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Rintaro Hashizume
- Department of Biochemistry and Molecular Genetics
- Robert H. Lurie NCI Comprehensive Cancer Center, and
| | - Issam Ben-Sahra
- Department of Biochemistry and Molecular Genetics
- Simpson Querrey Center for Epigenetics
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics
- Simpson Querrey Center for Epigenetics
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13
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Priestley JRC, Rippert AL, Condit C, Izumi K, Kallish S, Drivas TG. Unmasking the challenges of Kabuki syndrome in adulthood: A case series. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2023. [PMID: 37296540 DOI: 10.1002/ajmg.c.32054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/24/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023]
Abstract
Kabuki syndrome is a recognizable Mendelian disorder characterized by the clinical constellation of childhood hypotonia, developmental delay or intellectual impairment, and characteristic dysmorphism resulting from monoallelic pathogenic variants in KMT2D or KDM6A. In the medical literature, most reported patients are children, and data is lacking on the natural history of the condition across the lifespan, with little known about adult-specific presentations and symptoms. Here, we report the results of a retrospective chart review of eight adult patients with Kabuki syndrome, seven of whom are molecularly confirmed. We use their trajectories to highlight the diagnostic challenges unique to an adult population, expand on neurodevelopmental/psychiatric phenotypes across the lifespan, and describe adult-onset medical complications, including a potential cancer risk and unusual and striking premature/accelerated aging phenotype.
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Affiliation(s)
- Jessica R C Priestley
- Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Alyssa L Rippert
- Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Roberts Individualized Medical Genetics Center, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Courtney Condit
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Kaiser Permanente, Tysons Corners Medical Center, Virginia, USA
| | - Kosuke Izumi
- Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Roberts Individualized Medical Genetics Center, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Staci Kallish
- Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Theodore G Drivas
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
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14
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Li S, Li H, Liu D, Xing Q, Chen X, Zhang H, Wen J, Zhu H, Liang D, Li Z, Wu L. Identification of novel mendelian disorders of the epigenetic machinery (MDEMs) associated functional mutations and neurodevelopmental disorders. QJM 2023; 116:355-364. [PMID: 36625521 DOI: 10.1093/qjmed/hcad005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/01/2023] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Mendelian disorders of the epigenetic machinery (MDEMs) are a newly identified group of neurodevelopmental disorders (NDDs) and multiple congenital anoMalies caused by mutations in genes encoding components of the epigenetic machinery. Many studies have shown that MDEM-associated mutations may disrupt the balance between chromatin states and trigger dysplasia. AIM To help eight Chinese families with neurodevelopmental disorders acquire a definitive diagnosis. METHODS In this study, we used whole-exome sequencing (WES) to diagnose eight unrelated Chinese families with NDDs. We also verified the potential pathogenic variants by Sanger sequencing and analyzed the changes in gene expression along with histone methylation modifications. RESULTS Eight variants of six epigenetic machinery genes were identified, six of which were novel. Six variants were pathogenic (P) or likely pathogenic (LP), while two novel missense variants (c.5113T>C in CHD1 and c.10444C>T in KMT2D) were classified to be variants of uncertain significance (VUS). Further functional studies verified that c.5113T>C in CHD1 results in decreased protein levels and increased chromatin modifications (H3K27me3). In addition, c.10444C>T in KMT2D led to a significant decrease in mRNA transcription and chromatin modifications (H3K4me1). Based on experimental evidence, these two VUS variants could be classified as LP. CONCLUSION This study provided a definitive diagnosis of eight families with NDDs and expanded the mutation spectrum of MDEMs, enriching the pathogenesis study of variants in epigenetic machinery genes.
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Affiliation(s)
- Shun Li
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics & Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, 410078, China
| | - Huijuan Li
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics & Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, 410078, China
| | - Dihua Liu
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics & Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, 410078, China
| | - Qin Xing
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics & Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, 410078, China
| | - Xin Chen
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics & Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, 410078, China
| | - Hongyun Zhang
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics & Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, 410078, China
| | - Juan Wen
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics & Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, 410078, China
| | - Huimin Zhu
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics & Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, 410078, China
| | - Desheng Liang
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics & Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, 410078, China
- Laboratory of Molecular Genetics, Hunan Jiahui Genetics Hospital, Changsha, 410078, China
| | - Zhuo Li
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics & Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, 410078, China
| | - Lingqian Wu
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics & Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, 410078, China
- Laboratory of Molecular Genetics, Hunan Jiahui Genetics Hospital, Changsha, 410078, China
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15
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Aukema SM, Glaser S, van den Hout MFCM, Dahlum S, Blok MJ, Hillmer M, Kolarova J, Sciot R, Schott DA, Siebert R, Stumpel CTRM. Molecular characterization of an embryonal rhabdomyosarcoma occurring in a patient with Kabuki syndrome: report and literature review in the light of tumor predisposition syndromes. Fam Cancer 2023; 22:103-118. [PMID: 35856126 PMCID: PMC9829644 DOI: 10.1007/s10689-022-00306-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 07/05/2022] [Indexed: 01/13/2023]
Abstract
Kabuki syndrome is a well-recognized syndrome characterized by facial dysmorphism and developmental delay/intellectual disability and in the majority of patients a germline variant in KMT2D is found. As somatic KMT2D variants can be found in 5-10% of tumors a tumor predisposition in Kabuki syndrome is discussed. So far less than 20 patients with Kabuki syndrome and a concomitant malignancy have been published. Here we report on a female patient with Kabuki syndrome and a c.2558_2559delCT germline variant in KMT2D who developed an embryonal rhabdomyosarcoma (ERMS) at 10 years. On tumor tissue we performed DNA-methylation profiling and exome sequencing (ES). Copy number analyses revealed aneuploidies typical for ERMS including (partial) gains of chromosomes 2, 3, 7, 8, 12, 15, and 20 and 3 focal deletions of chromosome 11p. DNA methylation profiling mapped the case to ERMS by a DNA methylation-based sarcoma classifier. Sequencing suggested gain of the wild-type KMT2D allele in the trisomy 12. Including our patient literature review identified 18 patients with Kabuki syndrome and a malignancy. Overall, the landscape of malignancies in patients with Kabuki syndrome was reminiscent of that of the pediatric population in general. Histopathological and molecular data were only infrequently reported and no report included next generation sequencing and/or DNA-methylation profiling. Although we found no strong arguments pointing towards KS as a tumor predisposition syndrome, based on the small numbers any relation cannot be fully excluded. Further planned studies including profiling of additional tumors and long term follow-up of KS-patients into adulthood could provide further insights.
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Affiliation(s)
- Sietse M Aukema
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), PO Box 5800, 6202 AZ, Maastricht, The Netherlands.
| | - Selina Glaser
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Mari F C M van den Hout
- Department of Pathology, Research Institute GROW, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Sonja Dahlum
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Marinus J Blok
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), PO Box 5800, 6202 AZ, Maastricht, The Netherlands
| | - Morten Hillmer
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Julia Kolarova
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Raf Sciot
- Department of Pathology, University Hospital, University of Leuven, 3000, Louvain, Belgium
| | - Dina A Schott
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), PO Box 5800, 6202 AZ, Maastricht, The Netherlands
- Department of Pediatrics, Zuyderland Medical Center, Heerlen, The Netherlands
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Constance T R M Stumpel
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), PO Box 5800, 6202 AZ, Maastricht, The Netherlands.
- Department of Clinical Genetics and GROW-School for Oncology & Developmental Biology, Maastricht University Medical Center+, Maastricht, The Netherlands.
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16
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Luo H, Liu D, Liu W, Jin J, Bi X, Zhang P, Gu J, Zheng M, Xiao M, Liu X, Zhou J, Wang QF. Clinical and genetic characterization of Epstein-Barr virus-associated T/NK-cell lymphoproliferative diseases. J Allergy Clin Immunol 2022; 151:1096-1109. [PMID: 36423698 DOI: 10.1016/j.jaci.2022.11.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 11/10/2022] [Accepted: 11/16/2022] [Indexed: 11/23/2022]
Abstract
BACKGROUND Epstein-Barr virus (EBV)-associated T-/natural killer (T/NK)-cell lymphoproliferative diseases clinically take on various forms, ranging from an indolent course to an aggressive condition. OBJECTIVE Clinically, failure to establish precise diagnosis and provide proper treatment makes it difficult to help patients. We sought to better understand the underlying pathogenesis and to identify genetic prognostic factors to achieve better treatment efficacy. METHODS In this study, 119 cases of EBV-associated lymphoproliferative diseases, including EBV-associated hemophagocytic lymphohistiocytosis (n = 46) and chronic active EBV disease of T/NK cell type (n = 73), were retrospectively examined. RESULTS Adults aged >20 years at onset accounted for 71.4% of our cohort. About 54.6% patients with unfavorable overall survival developed hemophagocytic lymphohistiocytosis and had higher plasma EBV load. Allogenic hematopoietic stem-cell transplantation was the sole independent favorable factor. We systematically screened germline and somatic aberrations by whole-exome and targeted sequencing. Among 372 antiviral immunity genes, germline variants of 8 genes were significantly enriched. From a panel of 24 driver genes, somatic mutations were frequently identified in dominant EBV-infected T/NK cells. Patients carrying any germline/somatic aberrations in epigenetic modifiers and RIG-I-like receptor (RLR) pathway had worse overall survival than those without 2 type aberrations. Importantly, patients with IFIH1 and/or DDX3X aberrations in the RLR pathway had higher plasma and NK-cell EBV load. Knockdown of DDX3X in NKYS cells downregulated RLR signaling activities and elevated the expression of EBV-encoded oncogenes such as LMP1 and EBNA1. CONCLUSION Genetic defects were prevalent in adult EBV-associated hemophagocytic lymphohistiocytosis patients and patients with chronic active EBV disease of T/NK cell type; these defects were associated with unfavorable prognosis. These findings can help clinicians work out more precise staging of the condition and provide new insights into these EBV-associated diseases.
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Affiliation(s)
- Hui Luo
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan, China
| | - Dan Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Wenbing Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Jin Jin
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan, China
| | - Xiaoman Bi
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Peiling Zhang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan, China
| | - Jia Gu
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan, China
| | - Miao Zheng
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan, China
| | - Min Xiao
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan, China
| | - Xin Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Jianfeng Zhou
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan, China
| | - Qian-Fei Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China; University of Chinese Academy of Sciences, Beijing, China.
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17
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Parallel functional annotation of cancer-associated missense mutations in histone methyltransferases. Sci Rep 2022; 12:18487. [PMID: 36323913 PMCID: PMC9630446 DOI: 10.1038/s41598-022-23229-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 10/27/2022] [Indexed: 12/03/2022] Open
Abstract
Using exome sequencing for biomarker discovery and precision medicine requires connecting nucleotide-level variation with functional changes in encoded proteins. However, for functionally annotating the thousands of cancer-associated missense mutations, or variants of uncertain significance (VUS), purifying variant proteins for biochemical and functional analysis is cost-prohibitive and inefficient. We describe parallel functional annotation (PFA) of large numbers of VUS using small cultures and crude extracts in 96-well plates. Using members of a histone methyltransferase family, we demonstrate high-throughput structural and functional annotation of cancer-associated mutations. By combining functional annotation of paralogs, we discovered two phylogenetic and clustering parameters that improve the accuracy of sequence-based functional predictions to over 90%. Our results demonstrate the value of PFA for defining oncogenic/tumor suppressor functions of histone methyltransferases as well as enhancing the accuracy of sequence-based algorithms in predicting the effects of cancer-associated mutations.
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18
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Genome-wide DNA methylation profiling and exome sequencing resolved a long-time misdiagnosed case. J Hum Genet 2022; 67:547-551. [PMID: 35581385 DOI: 10.1038/s10038-022-01043-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/01/2022] [Accepted: 05/05/2022] [Indexed: 11/08/2022]
Abstract
The search for aetiology of Mendelian disorders is traditionally based on the observation of clinical phenotypes and molecular screening of associated genes. However, a disease-specific diagnosis can be challenging. In this study we detail how the combinatorial genomic and epigenomic assessment allowed to find the underlying molecular event of a clinical case that remained misdiagnosed for years. The individual was referred as affected by an atypical form of Kabuki syndrome with a variant of uncertain significance in the KMT2D gene. However, significant inconsistencies with this diagnosis emerged upon familial segregation of the variant and after the clinical re-evaluation. Therefore, we applied an epigenomic strategy by studying the DNA methylation profile which resulted not consistent with the Kabuki syndrome episignature or with any other disorder-specific episignature described so far, providing strong evidence that the Kabuki syndrome diagnosis does not apply. This result led us to further investigate for epigenetic machinery diseases by using a multigene panel for chromatinopathies. Since this analysis yielded negative results, we applied a whole exome sequencing and identified a de novo pathogenic variant in the CTNNB1 gene associated to NEDSDV syndrome, a neurodevelopmental disorder characterized by intellectual disability and craniofacial anomalies. Based on molecular results and the updated clinical features, we confirmed the NEDSDV diagnosis. Our findings show that the combination of genomic and epigenomics strategies, along with a deeper analysis of clinical phenotype, may provide a significant improvement in the diagnostic protocols for rare genetic disorders and help resolve long-time misdiagnosed and unsolved case.
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19
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Guo L, Zhang M, Gao Y, Qin L, Xia H, Liu L, Wang H. A gonadal mosaicism novel KMT2D mutation identified by haplotype construction and clone sequencing strategy. Clin Chim Acta 2022; 531:197-203. [PMID: 35421397 DOI: 10.1016/j.cca.2022.04.008] [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: 03/18/2022] [Revised: 04/08/2022] [Accepted: 04/08/2022] [Indexed: 11/03/2022]
Abstract
Here we reported a pedigree that gave birth to two characteristic clinical signs of Kabuki syndrome daughters. They had an intellectual disability with special facial features. Their eyebrows were relatively wide and the rear 1/3 of the eyebrows was light and sparse. Their eyes were long, narrow, valgus and strabismus. Their noses were broad at the root and flat at the tip. They also had skeletal dysplasia, mainly manifested in the short second knuckle of the little fingers of both hands. Genetic studies showed a novel de novo KMT2D variant (c.16343G>C; p.R5448P) as a cause of Kabuki syndrome. It was very unlikely that the same de novo mutation occurred in two members of a family. Gonadal mosaicism in one of the parents was suspected. Haplotype construction and clone sequencing was used for mutation source analysis. Finally, we inferred that the haplotype from the mother (Gdel-G-C-T-A) contained the pathogenic mutation. A gonadal mosaicism novel KMT2D mutation was identified in their mother.
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Affiliation(s)
- Liangjie Guo
- Medical Genetics Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou 450003, China
| | - Mengting Zhang
- Medical Genetics Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou 450003, China
| | - Yue Gao
- Medical Genetics Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou 450003, China
| | - Litao Qin
- Medical Genetics Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou 450003, China
| | - Hailan Xia
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Zhengzhou 450002, China
| | - Lin Liu
- Department of Ultrasound, Fuwai Central China Cardiovascular Hospital, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou 450003, China.
| | - Hongdan Wang
- Medical Genetics Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou 450003, China; National Health Commission Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Zhengzhou 450002, China; Henan Provincial People's Hospital, School of Medicine, Henan University, Zhengzhou 450003, China.
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20
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Zhang ZL, Yu PF, Ling ZQ. The role of KMT2 gene in human tumors. Histol Histopathol 2022; 37:323-334. [PMID: 35233758 DOI: 10.14670/hh-18-447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Histone methylation plays a crucial role in the regulation of gene transcriptional expression, and aberration of methylation-modifying enzyme genes can lead to a variety of genetic diseases, including human cancers. The histone modified protein KMT2 (lysin methyltransferase) family are involved in cell proliferation, growth, development and differentiation through regulating gene expression, and are closely related with many blood cancers and solid tumors. In recent years, several studies have shown that mutations in the KMT2 gene occur frequently in a variety of human cancers and the mutation status of the KMT2 gene may be correlated with the occurrence, development and prognosis of some tumors. Research uncovering the clinical characteristics and molecular mechanisms of KMT2 mutation in human tumors will be helpful for early diagnosis and prognosis of tumors as well as drug development for targeted therapies.
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Affiliation(s)
- Zhi-Long Zhang
- Zhejiang Cancer Institute (Experimental Research Center), Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, PR China.,The Second Clinical Medical College of Zhejiang Chinese Medicine University, Hangzhou, PR China
| | - Peng-Fei Yu
- Department of Gastric Surgery, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, PR China.
| | - Zhi-Qiang Ling
- Zhejiang Cancer Institute (Experimental Research Center), Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, PR China.
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21
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Gooch C, Souder JP, Tedder ML, Kerkhof J, Lee JA, Louie RJ, Sadikovic B, Fletcher RS, Robin NH. Near complete deletion of KMT2D in a college student. Am J Med Genet A 2022; 188:1550-1555. [PMID: 35040536 PMCID: PMC8995339 DOI: 10.1002/ajmg.a.62652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 12/22/2021] [Accepted: 12/27/2021] [Indexed: 11/09/2022]
Abstract
Pathogenic variants in KMT2D are typically associated with Kabuki syndrome (KS), a rare multisystem disorder. KS is characterized by facial dysmorphisms, intellectual disability, skeletal and dermatoglyphic differences, and poor growth. Seventy percent of individuals with clinically diagnosed KS have a confirmed pathogenic variant in KMT2D or less commonly KDM6A. The majority of mutations found in KMT2D are de novo nonsense or frameshift, with deletions and duplications rarely reported in the literature. Here, we present the case of near complete deletion of KMT2D in a college student with normal intelligence discovered via exome sequencing and EpiSign methylation testing. This case provides evidence that large deletions in KMT2D are compatible with normal intelligence and presents EpiSign as a method for discovering molecular causes of KS not identified by traditional molecular testing.
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Affiliation(s)
- Catherine Gooch
- Departments of Genetics and Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jaclyn Paige Souder
- Medical Scientist Training Program, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | | | - Jennifer Kerkhof
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada
| | - Jennifer A Lee
- Greenwood Genetic Center, Greenwood, South Carolina, USA
| | | | - Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | | | - Nathaniel H Robin
- Departments of Genetics and Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
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22
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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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23
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Guo HX, Li BW, Hu M, Si SY, Feng K. Novel KDM6A mutation in a Chinese infant with Kabuki syndrome: A case report. World J Clin Cases 2021; 9:10257-10264. [PMID: 34904097 PMCID: PMC8638061 DOI: 10.12998/wjcc.v9.i33.10257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 08/09/2021] [Accepted: 09/19/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Kabuki syndrome (KS) is a rare syndrome characterized by multisystem congenital anomalies and developmental disorder. KMT2D and KDM6A mutations were identified as the main causative genes in KS patients. There are few case reports and genetic analyses, especially of KDM6A gene mutation, in China.
CASE SUMMARY This study reports a de novo KDM6A mutation in a Chinese infant with KS. A 2-month-old Chinese baby was diagnosed with KS, which manifested as hypoglycemia, congenital anal atresia at birth, feeding difficulties, hypotonia, and serious postnatal growth retardation. He died of recurrent respiratory infections at age 13 mo. DNA sequencing of his blood DNA revealed a novel KDM6A frameshift mutation (c.704_705delAG, p. N236Sfs*26) (GRCh37/hg19).
CONCLUSION We present a Chinese KS patient with a novel KDM6A frameshift mutation (c.704_705delAG, p. N236Sfs*26) (GRCh37/hg19), broadening the mutation spectrum.
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Affiliation(s)
- Hong-Xian Guo
- Department of Paediatrics, Strategic Support Force Medical Center of PLA, Beijing 100101, China
| | - Bao-Wei Li
- Department of ENT, Strategic Support Force Medical Center of PLA, Beijing 100101, China
| | - Mei Hu
- ICU, Strategic Support Force Medical Center of PLA, Beijing 100101, China
| | - Shao-Yan Si
- Special Medical Center, Strategic Support Force Medical Center of PLA, Beijing 100101, China
| | - Kai Feng
- Special Medical Center, Strategic Support Force Medical Center of PLA, Beijing 100101, China
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24
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Kerkhof J, Squeo GM, McConkey H, Levy MA, Piemontese MR, Castori M, Accadia M, Biamino E, Della Monica M, Di Giacomo MC, Gervasini C, Maitz S, Melis D, Milani D, Piccione M, Prontera P, Selicorni A, Sadikovic B, Merla G. DNA methylation episignature testing improves molecular diagnosis of Mendelian chromatinopathies. Genet Med 2021; 24:51-60. [PMID: 34906459 DOI: 10.1016/j.gim.2021.08.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/06/2021] [Accepted: 08/12/2021] [Indexed: 12/19/2022] Open
Abstract
PURPOSE Chromatinopathies include more than 50 disorders caused by disease-causing variants of various components of chromatin structure and function. Many of these disorders exhibit unique genome-wide DNA methylation profiles, known as episignatures. In this study, the methylation profile of a large cohort of individuals with chromatinopathies was analyzed for episignature detection. METHODS DNA methylation data was generated on extracted blood samples from 129 affected individuals with the Illumina Infinium EPIC arrays and analyzed using an established bioinformatic pipeline. RESULTS The DNA methylation profiles matched and confirmed the sequence findings in both the discovery and validation cohorts. Twenty-five affected individuals carrying a variant of uncertain significance, did not show a methylation profile matching any of the known episignatures. Three additional variant of uncertain significance cases with an identified KDM6A variant were re-classified as likely pathogenic (n = 2) or re-assigned as Wolf-Hirschhorn syndrome (n = 1). Thirty of the 33 Next Generation Sequencing negative cases did not match a defined episignature while three matched Kabuki syndrome, Rubinstein-Taybi syndrome and BAFopathy respectively. CONCLUSION With the expanding clinical utility of the EpiSign assay, DNA methylation analysis should be considered part of the testing cascade for individuals presenting with clinical features of Mendelian chromatinopathy disorders.
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Affiliation(s)
- Jennifer Kerkhof
- Molecular Diagnostics Program, and Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Canada
| | - Gabriella Maria Squeo
- Laboratory of Regulatory and Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (Foggia), Italy
| | - Haley McConkey
- Molecular Diagnostics Program, and Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Canada
| | - Michael A Levy
- Molecular Diagnostics Program, and Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Canada
| | - Maria Rosaria Piemontese
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (Foggia), Italy
| | - Marco Castori
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (Foggia), Italy
| | - Maria Accadia
- Medical Genetics Service, Hospital "Cardinale G. Panico", Tricase, Lecce, Italy
| | - Elisa Biamino
- Department of Pediatrics, University of Turin, Italy
| | - Matteo Della Monica
- Medical Genetics Unit, Cardarelli Hospital, Largo A Cardarelli, Napoli, Italy
| | | | - Cristina Gervasini
- Division of Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Silvia Maitz
- Clinical Pediatric Genetics Unit, Pediatrics Clinics, MBBM Foundation, Hospital San Gerardo, Monza, Italy
| | - Daniela Melis
- Medical, Surgical, and Dental Department, Università degli Studi di Salerno, Salerno, Italy
| | - Donatella Milani
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Maria Piccione
- Medical Genetics Unit Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Paolo Prontera
- Medical Genetics Unit, University of Perugia Hospital SM della Misericordia, Perugia, Italy
| | - Angelo Selicorni
- Pediatric Department, ASST Lariana, Sant'Anna General Hospital, Como, Italy
| | - Bekim Sadikovic
- Molecular Diagnostics Program, and Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Canada; Department of Pathology and Laboratory Medicine, Western University, London, Canada.
| | - Giuseppe Merla
- Laboratory of Regulatory and Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (Foggia), Italy; Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy.
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25
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Zheng B, Song Z, Chen Y, Yan W. Genomic Analyses of Metaplastic or Sarcomatoid Carcinomas From Different Organs Revealed Frequent Mutations in KMT2D. Front Mol Biosci 2021; 8:688692. [PMID: 34336928 PMCID: PMC8319738 DOI: 10.3389/fmolb.2021.688692] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/07/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Metaplastic or sarcomatoid carcinomas (MSCs) are rare epithelial malignancies with heterologous histological differentiation that can occur in different organs. The objective of the current study was to identify novel somatically mutated genes in MSCs from different organs. Methods: Whole-exome sequencing was performed in 16 paired MSCs originating from the breast (n = 10), esophagus (n = 3), lung (n = 2), and kidney (n = 1). In addition, we collected data on KMT2D mutations from eight independent cohorts (n = 195) diagnosed with MSCs derived from the breast (n = 83), liver (n = 8), esophagus (n = 15), lung (n = 10), and uterus or ovary (n = 79). The expression of KMT2D and its clinical significance were evaluated in our cohort. Results: The most frequently mutated genes were TP53 (13/16, 81%) and KMT2D (5/16,31%). We identified seven somatic KMT2D mutations in the exploratory cohort (n = 16 tumors), including three nonsense mutations, two frameshift indels, one missense mutation, and one splice site mutation. Interestingly, two patients showed double hits on KMT2D with nonsense mutations and frameshift indels. In the eight validation cohorts (n = 195), the average mutation rates for TP53 and KMT2D were 78% (152/195) and 13% (25/195), respectively. Two or more hits on KMT2D were also present in three validation cohorts. Furthermore, KMT2D mutations were associated with low expression of KMT2D, large tumor size and unfavorable prognosis. Conclusions: These findings provide clues for understanding the genetic basis of MSCs originating from different organs and implicate KMT2D alteration as a frequent pathogenic mutation, allowing provision of appropriate treatment for this rare malignant disease in the future.
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Affiliation(s)
- Biqiang Zheng
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | | | - Yong Chen
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wangjun Yan
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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26
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Zhai X, Brownell JE. Biochemical perspectives on targeting KMT2 methyltransferases in cancer. Trends Pharmacol Sci 2021; 42:688-699. [PMID: 34074527 DOI: 10.1016/j.tips.2021.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 04/20/2021] [Accepted: 05/05/2021] [Indexed: 02/05/2023]
Abstract
KMT2 methyltransferases are important regulators of gene transcription through the methylation of histone H3 lysine 4 at promoter and enhancer regions. They reside in large, multisubunit protein complexes, which not only regulate their catalytic activities but also mediate their interactions with chromatin. The KMT2 family was initially associated with cancer due to the discovery of KMT2A translocations in mixed-lineage leukemia (MLL). However, emerging evidences suggest that the methyltransferase activity of KMT2 enzymes can also be important in cancer, raising the prospect of targeting the catalytic domain of KMT2 as a therapeutic strategy. In this review, we summarize recent advances in our understanding of KMT2 enzyme mechanisms and their regulation on nucleosomes, which will provide mechanistic insights into therapeutic discoveries targeting their methyltransferase activities.
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Affiliation(s)
- Xiang Zhai
- Mechanistic Biology & Profiling, Discovery Sciences, R&D, AstraZeneca, Waltham, MA 02451, USA.
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27
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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.
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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;
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28
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Faundes V, Goh S, Akilapa R, Bezuidenhout H, Bjornsson HT, Bradley L, Brady AF, Brischoux-Boucher E, Brunner H, Bulk S, Canham N, Cody D, Dentici ML, Digilio MC, Elmslie F, Fry AE, Gill H, Hurst J, Johnson D, Julia S, Lachlan K, Lebel RR, Byler M, Gershon E, Lemire E, Gnazzo M, Lepri FR, Marchese A, McEntagart M, McGaughran J, Mizuno S, Okamoto N, Rieubland C, Rodgers J, Sasaki E, Scalais E, Scurr I, Suri M, van der Burgt I, Matsumoto N, Miyake N, Benoit V, Lederer D, Banka S. Clinical delineation, sex differences, and genotype-phenotype correlation in pathogenic KDM6A variants causing X-linked Kabuki syndrome type 2. Genet Med 2021; 23:1202-1210. [PMID: 33674768 PMCID: PMC8257478 DOI: 10.1038/s41436-021-01119-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 02/03/2021] [Accepted: 02/03/2021] [Indexed: 12/17/2022] Open
Abstract
Purpose The variant spectrum and the phenotype of X-linked Kabuki syndrome type 2 (KS2) are poorly understood. Methods Genetic and clinical details of new and published individuals with pathogenic KDM6A variants were compiled and analyzed. Results Sixty-one distinct pathogenic KDM6A variants (50 truncating, 11 missense) from 80 patients (34 males, 46 females) were identified. Missense variants clustered in the TRP 2, 3, 7 and Jmj-C domains. Truncating variants were significantly more likely to be de novo. Thirteen individuals had maternally inherited variants and one had a paternally inherited variant. Neonatal feeding difficulties, hypoglycemia, postnatal growth retardation, poor weight gain, motor delay, intellectual disability (ID), microcephaly, congenital heart anomalies, palate defects, renal malformations, strabismus, hearing loss, recurrent infections, hyperinsulinism, seizures, joint hypermobility, and gastroesophageal reflux were frequent clinical findings. Facial features of over a third of patients were not typical for KS. Males were significantly more likely to be born prematurely, have shorter stature, and severe developmental delay/ID. Conclusion We expand the KDM6A variant spectrum and delineate the KS2 phenotype. We demonstrate that the variability of the KS2 phenotypic depends on sex and the variant type. We also highlight the overlaps and differences between the phenotypes of KS2 and KS1.
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Affiliation(s)
- Víctor Faundes
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.,Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile
| | - Stephanie Goh
- School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Rhoda Akilapa
- NW Thames Regional Genetics Service, Northwick Park Hospital, Harrow, UK
| | - Heidre Bezuidenhout
- Clinical Unit of Medical Genetics and Genetic Counselling, Tygerberg Academic Hospital, Cape Town, South Africa.,Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Hans T Bjornsson
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Lisa Bradley
- Department of Clinical Genetics, Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Angela F Brady
- NW Thames Regional Genetics Service, Northwick Park Hospital, Harrow, UK
| | - Elise Brischoux-Boucher
- Centre de Génétique Humaine, Centre Hospitalier et Universitaire, Université de Franche-Comté, Besançon, France
| | - Han Brunner
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Saskia Bulk
- Centre de Génétique Humaine, CHU de Liège, Liège, Belgium
| | - Natalie Canham
- NW Thames Regional Genetics Service, Northwick Park Hospital, Harrow, UK.,Liverpool Centre for Genomic Medicine, Liverpool Women's Hospital, Crown Street, Liverpool, UK
| | - Declan Cody
- Department of Clinical Genetics, Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Maria Lisa Dentici
- Medical Genetics Unit, Academic Department of Pediatrics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Maria Cristina Digilio
- Medical Genetics Unit, Academic Department of Pediatrics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Frances Elmslie
- SW Thames Regional Genetics Service, St George's, University of London, London, UK
| | - Andrew E Fry
- Institute of Medical Genetics, University Hospital of Wales, Heath Park, Cardiff, UK
| | - Harinder Gill
- Department of Clinical Genetics, Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Jane Hurst
- NE Thames Genetics Service, Great Ormond Street Hospital, London, UK
| | - Diana Johnson
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Northern General Hospital, Sheffield, UK
| | - Sophie Julia
- Departments of Pathology, Neurosurgery, Oncopediatry, Genetics and Molecular Biology, Toulouse University Hospital, Toulouse, France
| | - Katherine Lachlan
- Wessex Clinical Genetics Service and Division of Human Genetics, Princess Anne Hospital, Southampton, UK
| | - Robert Roger Lebel
- Department of Pediatrics, Section of Medical Genetics, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Melissa Byler
- Department of Pediatrics, Section of Medical Genetics, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Eric Gershon
- Department of Pediatrics, Yale New Haven Health, New Haven, CT, USA
| | - Edmond Lemire
- Department of Pediatrics, Royal University Hospital, University of Saskatchewan, Saskatoon, SK, Canada
| | - Maria Gnazzo
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Antonia Marchese
- Service de Pédiatrie, Centre Hospitalier Régional de Namur, Namur, Belgium
| | - Meriel McEntagart
- SW Thames Regional Genetics Service, St George's, University of London, London, UK
| | - Julie McGaughran
- Genetic Health Queensland c/-Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Seiji Mizuno
- Department of Clinical Genetics, Central Hospital, Aichi Developmental Disability Center, Aichi, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan.,Department of Molecular Medicine, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Claudine Rieubland
- Division of Human Genetics, Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Jonathan Rodgers
- Genetic Health Queensland c/-Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Erina Sasaki
- Department of Clinical Genetics, Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Emmanuel Scalais
- Department of Pediatric Neurology, National Hospital, Luxembourg City, Luxembourg
| | - Ingrid Scurr
- Clinical Genetics, University Hospitals Bristol, Bristol, UK
| | - Mohnish Suri
- Nottingham Clinical Genetics Service, City Hospital Campus, Nottingham, UK
| | - Ineke van der Burgt
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Valérie Benoit
- Centre de Génétique Humaine, Institut de Pathologie et de Génétique, Gosselies, Belgium
| | - Damien Lederer
- Centre de Génétique Humaine, Institut de Pathologie et de Génétique, Gosselies, Belgium
| | - Siddharth Banka
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK. .,Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK.
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Kilby MD. The role of next-generation sequencing in the investigation of ultrasound-identified fetal structural anomalies. BJOG 2021; 128:420-429. [PMID: 32975887 PMCID: PMC8607475 DOI: 10.1111/1471-0528.16533] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/24/2020] [Indexed: 12/14/2022]
Abstract
Fetal structural anomalies have an impact on fetal mortality and morbidity. Next-generation sequencing (NGS) may be incorporated into clinical pathways for investigation of paediatric morbidity but can also be used to delineate the prognosis of fetal anomalies. This paper reviews the role of NGS in the investigation of fetal malformations, the literature defining the clinical utility, the technique most commonly used and potential promise and challenges for implementation into clinical practice. Prospective case selection with informative pre-test counselling by multidisciplinary teams is imperative. Regulated laboratory sequencing, bioinformatic pathways with potential variant identification and conservative matching with the phenotype is important. TWEETABLE ABSTRACT: Prenatal exome sequencing in fetal structural anomalies yields diagnostic information in up to 20% of cases.
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Affiliation(s)
- M D Kilby
- Fetal Medicine Centre, Birmingham Women's and Children's Foundation Trust, Birmingham, UK.,Institute of Metabolism and Systems Research, College of Medical & Dental Sciences, University of Birmingham, Birmingham, UK
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30
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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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31
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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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32
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Chi YI, Stodola TJ, De Assuncao TM, Leverence EN, Tripathi S, Dsouza NR, Mathison AJ, Basel DG, Volkman BF, Smith BC, Lomberk G, Zimmermann MT, Urrutia R. Molecular mechanics and dynamic simulations of well-known Kabuki syndrome-associated KDM6A variants reveal putative mechanisms of dysfunction. Orphanet J Rare Dis 2021; 16:66. [PMID: 33546721 PMCID: PMC7866879 DOI: 10.1186/s13023-021-01692-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/15/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Kabuki syndrome is a genetic disorder that affects several body systems and presents with variations in symptoms and severity. The syndrome is named for a common phenotype of faces resembling stage makeup used in a Japanese traditional theatrical art named kabuki. The most frequent cause of this syndrome is mutations in the H3K4 family of histone methyltransferases while a smaller percentage results from genetic alterations affecting the histone demethylase, KDM6A. Because of the rare presentation of the latter form of the disease, little is known about how missense changes in the KDM6A protein sequence impact protein function. RESULTS In this study, we use molecular mechanic and molecular dynamic simulations to enhance the annotation and mechanistic interpretation of the potential impact of eleven KDM6A missense variants found in Kabuki syndrome patients. These variants (N910S, D980V, S1025G, C1153R, C1153Y, P1195L, L1200F, Q1212R, Q1248R, R1255W, and R1351Q) are predicted to be pathogenic, likely pathogenic or of uncertain significance by sequence-based analysis. Here, we demonstrate, for the first time, that although Kabuki syndrome missense variants are found outside the functionally critical regions, they could affect overall function by significantly disrupting global and local conformation (C1153R, C1153Y, P1195L, L1200F, Q1212R, Q1248R, R1255W and R1351Q), chemical environment (C1153R, C1153Y, P1195L, L1200F, Q1212R, Q1248R, R1255W and R1351Q), and/or molecular dynamics of the catalytic domain (all variants). In addition, our approaches predict that many mutations, in particular C1153R, could allosterically disrupt the key enzymatic interactions of KDM6A. CONCLUSIONS Our study demonstrates that the KDM6A Kabuki syndrome variants may impair histone demethylase function through various mechanisms that include altered protein integrity, local environment, molecular interactions and protein dynamics. Molecular dynamics simulations of the wild type and the variants are critical to gain a better understanding of molecular dysfunction. This type of comprehensive structure- and MD-based analyses should help develop improved impact scoring systems to interpret the damaging effects of variants in this protein and other related proteins as well as provide detailed mechanistic insight that is not currently predictable from sequence alone.
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Affiliation(s)
- Young-In Chi
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, WI, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Timothy J Stodola
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Thiago M De Assuncao
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Elise N Leverence
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA
| | - Swarnendu Tripathi
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Nikita R Dsouza
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Angela J Mathison
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, WI, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Donald G Basel
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Division of Pediatric Genetics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Brian C Smith
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Gwen Lomberk
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA.,Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Michael T Zimmermann
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, WI, USA.,Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Raul Urrutia
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA. .,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, WI, USA. .,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA. .,Division of Pediatric Genetics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA.
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Weigele J, Bohnsack BL. Genetics Underlying the Interactions between Neural Crest Cells and Eye Development. J Dev Biol 2020; 8:jdb8040026. [PMID: 33182738 PMCID: PMC7712190 DOI: 10.3390/jdb8040026] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/03/2020] [Accepted: 11/07/2020] [Indexed: 12/14/2022] Open
Abstract
The neural crest is a unique, transient stem cell population that is critical for craniofacial and ocular development. Understanding the genetics underlying the steps of neural crest development is essential for gaining insight into the pathogenesis of congenital eye diseases. The neural crest cells play an under-appreciated key role in patterning the neural epithelial-derived optic cup. These interactions between neural crest cells within the periocular mesenchyme and the optic cup, while not well-studied, are critical for optic cup morphogenesis and ocular fissure closure. As a result, microphthalmia and coloboma are common phenotypes in human disease and animal models in which neural crest cell specification and early migration are disrupted. In addition, neural crest cells directly contribute to numerous ocular structures including the cornea, iris, sclera, ciliary body, trabecular meshwork, and aqueous outflow tracts. Defects in later neural crest cell migration and differentiation cause a constellation of well-recognized ocular anterior segment anomalies such as Axenfeld–Rieger Syndrome and Peters Anomaly. This review will focus on the genetics of the neural crest cells within the context of how these complex processes specifically affect overall ocular development and can lead to congenital eye diseases.
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Affiliation(s)
- Jochen Weigele
- Division of Ophthalmology, Ann & Robert H. Lurie Children’s Hospital of Chicago, 225 E. Chicago Ave, Chicago, IL 60611, USA;
- Department of Ophthalmology, Northwestern University Feinberg School of Medicine, 645 N. Michigan Ave, Chicago, IL 60611, USA
| | - Brenda L. Bohnsack
- Division of Ophthalmology, Ann & Robert H. Lurie Children’s Hospital of Chicago, 225 E. Chicago Ave, Chicago, IL 60611, USA;
- Department of Ophthalmology, Northwestern University Feinberg School of Medicine, 645 N. Michigan Ave, Chicago, IL 60611, USA
- Correspondence: ; Tel.: +1-312-227-6180; Fax: +1-312-227-9411
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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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Abstract
The Trithorax group (TrxG) of proteins is a large family of epigenetic regulators that form multiprotein complexes to counteract repressive developmental gene expression programmes established by the Polycomb group of proteins and to promote and maintain an active state of gene expression. Recent studies are providing new insights into how two crucial families of the TrxG - the COMPASS family of histone H3 lysine 4 methyltransferases and the SWI/SNF family of chromatin remodelling complexes - regulate gene expression and developmental programmes, and how misregulation of their activities through genetic abnormalities leads to pathologies such as developmental disorders and malignancies.
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36
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Murakami H, Tsurusaki Y, Enomoto K, Kuroda Y, Yokoi T, Furuya N, Yoshihashi H, Minatogawa M, Abe-Hatano C, Ohashi I, Nishimura N, Kumaki T, Enomoto Y, Naruto T, Iwasaki F, Harada N, Ishikawa A, Kawame H, Sameshima K, Yamaguchi Y, Kobayashi M, Tominaga M, Ishikiriyama S, Tanaka T, Suzumura H, Ninomiya S, Kondo A, Kaname T, Kosaki K, Masuno M, Kuroki Y, Kurosawa K. Update of the genotype and phenotype of KMT2D and KDM6A by genetic screening of 100 patients with clinically suspected Kabuki syndrome. Am J Med Genet A 2020; 182:2333-2344. [PMID: 32803813 DOI: 10.1002/ajmg.a.61793] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/05/2020] [Accepted: 06/23/2020] [Indexed: 12/15/2022]
Abstract
Kabuki syndrome is characterized by a variable degree of intellectual disability, characteristic facial features, and complications in various organs. Many variants have been identified in two causative genes, that is, lysine methyltransferase 2D (KMT2D) and lysine demethylase 6A (KDM6A). In this study, we present the results of genetic screening of 100 patients with a suspected diagnosis of Kabuki syndrome in our center from July 2010 to June 2018. We identified 76 variants (43 novel) in KMT2D and 4 variants (3 novel) in KDM6A as pathogenic or likely pathogenic. Rare variants included a deep splicing variant (c.14000-8C>G) confirmed by RNA sequencing and an 18% mosaicism level for a KMT2D mutation. We also characterized a case with a blended phenotype consisting of Kabuki syndrome, osteogenesis imperfecta, and 16p13.11 microdeletion. We summarized the clinical phenotypes of 44 patients including a patient who developed cervical cancer of unknown origin at 16 years of age. This study presents important details of patients with Kabuki syndrome including rare clinical cases and expands our genetic understanding of this syndrome, which will help clinicians and researchers better manage and understand patients with Kabuki syndrome they may encounter.
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Affiliation(s)
- Hiroaki Murakami
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Yoshinori Tsurusaki
- Clinical Research Institute, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Keisuke Enomoto
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Yukiko Kuroda
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Takayuki Yokoi
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Noritaka Furuya
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Hiroshi Yoshihashi
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Mari Minatogawa
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Chihiro Abe-Hatano
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Ikuko Ohashi
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Naoto Nishimura
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Tatsuro Kumaki
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Yumi Enomoto
- Clinical Research Institute, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Takuya Naruto
- Clinical Research Institute, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Fuminori Iwasaki
- Division of Hematology/Oncology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Noriaki Harada
- Department of Clinical Laboratory, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Aki Ishikawa
- Department of Medical Genetics and Genomics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hiroshi Kawame
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Kiyoko Sameshima
- Division of Medical Genetics, Gunma Children's Medical Center, Gunma, Japan
| | - Yu Yamaguchi
- Division of Medical Genetics, Gunma Children's Medical Center, Gunma, Japan
| | - Masahisa Kobayashi
- Department of Pediatrics, Jikei University School of Medicine, Tokyo, Japan
| | - Makiko Tominaga
- Children's Medical Center, Northern Yokohama Hospital, Showa University, Yokohama, Japan
| | - Satoshi Ishikiriyama
- Division of Clinical Genetics and Cytogenetics, Shizuoka Children's Hospital, Shizuoka, Japan
| | | | - Hiroshi Suzumura
- Department of Pediatrics, Dokkyo Medical University, Tochigi, Japan
| | - Shinsuke Ninomiya
- Department of Clinical Genetics, Kurashiki Central Hospital, Kurashiki, Japan
| | - Akane Kondo
- Department of Gynecology, Shikoku Medical Center for Children and Adults, Kagawa, Japan
| | - Tadashi Kaname
- Department of Genome Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Mitsuo Masuno
- Genetic Counseling Program, Graduate School of Health and Welfare, Kawasaki University of Medical Welfare, Kurashiki, Japan
| | - Yoshikazu Kuroki
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Kenji Kurosawa
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
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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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38
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Shpargel KB, Mangini CL, Xie G, Ge K, Magnuson T. The KMT2D Kabuki syndrome histone methylase controls neural crest cell differentiation and facial morphology. Development 2020; 147:dev.187997. [PMID: 32541010 DOI: 10.1242/dev.187997] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 06/02/2020] [Indexed: 12/13/2022]
Abstract
Kabuki syndrome (KS) is a congenital craniofacial disorder resulting from mutations in the KMT2D histone methylase (KS1) or the UTX histone demethylase (KS2). With small cohorts of KS2 patients, it is not clear whether differences exist in clinical manifestations relative to KS1. We mutated KMT2D in neural crest cells (NCCs) to study cellular and molecular functions in craniofacial development with respect to UTX. Similar to UTX, KMT2D NCC knockout mice demonstrate hypoplasia with reductions in frontonasal bone lengths. We have traced the onset of KMT2D and UTX mutant NCC frontal dysfunction to a stage of altered osteochondral progenitor differentiation. KMT2D NCC loss-of-function does exhibit unique phenotypes distinct from UTX mutation, including fully penetrant cleft palate, mandible hypoplasia and deficits in cranial base ossification. KMT2D mutant NCCs lead to defective secondary palatal shelf elevation with reduced expression of extracellular matrix components. KMT2D mutant chondrocytes in the cranial base fail to properly differentiate, leading to defective endochondral ossification. We conclude that KMT2D is required for appropriate cranial NCC differentiation and KMT2D-specific phenotypes may underlie differences between Kabuki syndrome subtypes.
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Affiliation(s)
- Karl B Shpargel
- Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599-7264, USA
| | - Cassidy L Mangini
- Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599-7264, USA
| | - Guojia Xie
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kai Ge
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Terry Magnuson
- Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599-7264, USA
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Abstract
Although outcomes for follicular lymphoma (FL) continue to improve, it remains incurable for the majority of patients. Through next generation sequencing (NGS) studies, we now recognize that the genomic landscape of FL is skewed toward highly recurrent mutations in genes that encode epigenetic regulators co-occurring with the pathognomonic t(14;18) translocation. Adopting these technologies to study longitudinal and spatially-derived lymphomas has provided unique insights into the tumoral heterogeneity, clonal evolution of the disease and supports the existence of a tumor-repopulating population, considered the Achilles' heel of this lymphoma. An in-depth understanding of the genomics and its contribution to the disease pathogenesis is identifying new biomarkers and therapeutic targets that can be translated into clinical practice and, in the not too distant future, enable us to start considering precision-based approaches to the management of FL.
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Affiliation(s)
- Lucy Pickard
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Giuseppe Palladino
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Jessica Okosun
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
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40
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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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Yap CS, Jamuar SS, Lai AH, Tan ES, Ng I, Ting TW, Tan EC. Identification of KMT2D and KDM6A variants by targeted sequencing from patients with Kabuki syndrome and other congenital disorders. Gene 2020; 731:144360. [DOI: 10.1016/j.gene.2020.144360] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 12/11/2019] [Accepted: 01/08/2020] [Indexed: 01/01/2023]
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Baldridge D, Spillmann RC, Wegner DJ, Wambach JA, White FV, Sisco K, Toler TL, Dickson PI, Cole FS, Shashi V, Grange DK. Phenotypic expansion of KMT2D-related disorder: Beyond Kabuki syndrome. Am J Med Genet A 2020; 182:1053-1065. [PMID: 32083401 DOI: 10.1002/ajmg.a.61518] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 01/29/2020] [Accepted: 01/29/2020] [Indexed: 12/13/2022]
Abstract
Pathogenic variants in KMT2D, which encodes lysine specific methyltransferase 2D, cause autosomal dominant Kabuki syndrome, associated with distinctive dysmorphic features including arched eyebrows, long palpebral fissures with eversion of the lower lid, large protuberant ears, and fetal finger pads. Most disease-causing variants identified to date are putative loss-of-function alleles, although 15-20% of cases are attributed to missense variants. We describe here four patients (including one previously published patient) with de novo KMT2D missense variants and with shared but unusual clinical findings not typically seen in Kabuki syndrome, including athelia (absent nipples), choanal atresia, hypoparathyroidism, delayed or absent pubertal development, and extreme short stature. These individuals also lack the typical dysmorphic facial features found in Kabuki syndrome. Two of the four patients had severe interstitial lung disease. All of these variants cluster within a 40-amino-acid region of the protein that is located just N-terminal of an annotated coiled coil domain. These findings significantly expand the phenotypic spectrum of features associated with variants in KMT2D beyond those seen in Kabuki syndrome and suggest a possible new underlying disease mechanism for these patients.
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Affiliation(s)
- Dustin Baldridge
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Rebecca C Spillmann
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina, USA
| | - Daniel J Wegner
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jennifer A Wambach
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Frances V White
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Kathleen Sisco
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Tomi L Toler
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Patricia I Dickson
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - F Sessions Cole
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Vandana Shashi
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina, USA
| | - Dorothy K Grange
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
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43
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Cuvertino S, Hartill V, Colyer A, Garner T, Nair N, Al-Gazali L, Canham N, Faundes V, Flinter F, Hertecant J, Holder-Espinasse M, Jackson B, Lynch SA, Nadat F, Narasimhan VM, Peckham M, Sellers R, Seri M, Montanari F, Southgate L, Squeo GM, Trembath R, van Heel D, Venuto S, Weisberg D, Stals K, Ellard S, Barton A, Kimber SJ, Sheridan E, Merla G, Stevens A, Johnson CA, Banka S. A restricted spectrum of missense KMT2D variants cause a multiple malformations disorder distinct from Kabuki syndrome. Genet Med 2020; 22:867-877. [PMID: 31949313 PMCID: PMC7200597 DOI: 10.1038/s41436-019-0743-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 12/24/2019] [Indexed: 12/19/2022] Open
Abstract
Purpose To investigate if specific exon 38 or 39 KMT2D missense variants (MVs) cause a condition distinct from
Kabuki syndrome type 1 (KS1). Methods Multiple individuals, with MVs in exons 38 or 39 of KMT2D that encode a highly conserved region of 54
amino acids flanked by Val3527 and Lys3583, were identified and phenotyped.
Functional tests were performed to study their pathogenicity and understand the
disease mechanism. Results The consistent clinical features of the affected individuals, from
seven unrelated families, included choanal atresia, athelia or hypoplastic
nipples, branchial sinus abnormalities, neck pits, lacrimal duct anomalies,
hearing loss, external ear malformations, and thyroid abnormalities. None of the
individuals had intellectual disability. The frequency of clinical features,
objective software-based facial analysis metrics, and genome-wide peripheral
blood DNA methylation patterns in these patients were significantly different
from that of KS1. Circular dichroism spectroscopy indicated that these MVs
perturb KMT2D secondary structure through an increased disordered to ɑ-helical
transition. Conclusion KMT2D MVs located in a specific
region spanning exons 38 and 39 and affecting highly conserved residues cause a
novel multiple malformations syndrome distinct from KS1. Unlike KMT2D haploinsufficiency in KS1, these MVs likely
result in disease through a dominant negative mechanism.
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Affiliation(s)
- Sara Cuvertino
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK.,Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Verity Hartill
- Leeds Institute of Medical Research, Faculty of Medicine and Health, The University of Leeds, Leeds, UK.,Department of Clinical Genetics, Chapel Allerton Hospital, Leeds Teaching Hospitals Trust, Leeds, UK
| | - Alice Colyer
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, The University of Leeds, Leeds, UK
| | - Terence Garner
- Division of Developmental Biology & Medicine, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Nisha Nair
- Centre of Genetics & Genomics Versus Arthritis, Manchester Academic Health Sciences Centre, The University of Manchester, Manchester, UK
| | - Lihadh Al-Gazali
- Department of Paediatrics, College of Medicine & Health Sciences, United Arab University, Al-Ain, UAE
| | - Natalie Canham
- Liverpool Centre for Genomic Medicine, Liverpool Women's NHS Foundation Trust, Liverpool, UK.,North West Thames Regional Genetics Service, Northwick Park Hospital, Harrow, UK
| | - Victor Faundes
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK.,Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Frances Flinter
- Department of Clinical Genetics, Guy's & St Thomas NHS Foundation Trust, London, UK
| | | | | | - Brian Jackson
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, The University of Leeds, Leeds, UK
| | - Sally Ann Lynch
- Temple street Children's University Hospital, Dublin, Ireland
| | - Fatima Nadat
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, The University of Leeds, Leeds, UK
| | | | - Michelle Peckham
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, The University of Leeds, Leeds, UK
| | - Robert Sellers
- Division of Developmental Biology & Medicine, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Marco Seri
- Medical Genetics Unit, St. Orsola-Malpighi, University of Bologna, Bologna, Italy
| | - Francesca Montanari
- Medical Genetics Unit, St. Orsola-Malpighi, University of Bologna, Bologna, Italy
| | - Laura Southgate
- Molecular and Clinical Sciences Research Institute, St George's University of London, London, UK.,Department of Medical & Molecular Genetics, King's College London, London, UK
| | - Gabriella Maria Squeo
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
| | - Richard Trembath
- Department of Medical & Molecular Genetics, King's College London, London, UK
| | | | - Santina Venuto
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
| | - Daniel Weisberg
- Clinical Psychology Department, Royal Manchester Children's Hospital, Manchester University Foundation NHS Trust, Health Innovation Manchester, Manchester, UK
| | - Karen Stals
- Molecular Genetics Department, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Sian Ellard
- Molecular Genetics Department, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK.,Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | | | - Anne Barton
- Centre of Genetics & Genomics Versus Arthritis, Manchester Academic Health Sciences Centre, The University of Manchester, Manchester, UK
| | - Susan J Kimber
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Eamonn Sheridan
- Leeds Institute of Medical Research, Faculty of Medicine and Health, The University of Leeds, Leeds, UK.,Department of Clinical Genetics, Chapel Allerton Hospital, Leeds Teaching Hospitals Trust, Leeds, UK
| | - Giuseppe Merla
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
| | - Adam Stevens
- Division of Developmental Biology & Medicine, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Colin A Johnson
- Leeds Institute of Medical Research, Faculty of Medicine and Health, The University of Leeds, Leeds, UK
| | - Siddharth Banka
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK. .,Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University Foundation NHS Trust, Health Innovation Manchester, Manchester, UK.
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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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45
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De Backer J, Bondue A, Budts W, Evangelista A, Gallego P, Jondeau G, Loeys B, Peña ML, Teixido-Tura G, van de Laar I, Verstraeten A, Roos Hesselink J. Genetic counselling and testing in adults with congenital heart disease: A consensus document of the ESC Working Group of Grown-Up Congenital Heart Disease, the ESC Working Group on Aorta and Peripheral Vascular Disease and the European Society of Human Genetics. Eur J Prev Cardiol 2019; 27:1423-1435. [DOI: 10.1177/2047487319854552] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Thanks to a better knowledge of the genetic causes of many diseases and an improvement in genetic testing techniques, genetics has gained an important role in the multidisciplinary approach to diagnosis and management of congenital heart disease and aortic pathology. With the introduction of strategies for precision medicine, it is expected that this will only increase further in the future. Because basic knowledge of the indications, the opportunities as well as the limitations of genetic testing is essential for correct application in clinical practice, this consensus document aims to give guidance to care-providers involved in the follow-up of adults with congenital heart defects and/or with hereditary aortic disease. This paper is the result of a collaboration between the ESC Working Group of Grown-Up Congenital Heart Disease, the ESC Working Group on Aorta and Peripheral Vascular Disease and the European Society of Human Genetics. Throughout the document, the importance of correct counseling in the process of genetic testing is emphasized, indications and timing for genetic studies are discussed as well as the technical modalities of genetic testing. Finally, the most important genetic diseases in adult congenital heart disease and aortic pathology are also discussed.
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Affiliation(s)
- Julie De Backer
- Department of Cardiology and Center for Medical Genetics, Ghent University Hospital, Belgium
- European Reference Network for Rare Multisystemic Vascular Disease (VASCERN), HTAD Rare Disease Working Group
| | - Antoine Bondue
- Department of Cardiology, Université Libre de Bruxelles, Belgium
| | - Werner Budts
- Congenital and Structural Cardiology, University Hospitals Leuven, Belgium
- Department of Cardiovascular Sciences, KU Leuven, Belgium
| | - Arturo Evangelista
- European Reference Network for Rare Multisystemic Vascular Disease (VASCERN), HTAD Rare Disease Working Group
- Servei de Cardiologia, Hospital Universitari Vall d'Hebron, VHIR. CIBER-CV, Barcelona, Spain
| | - Pastora Gallego
- Department of Cardiology, Hospital Universitario Virgen del Rocio, Spain
| | - Guillaume Jondeau
- European Reference Network for Rare Multisystemic Vascular Disease (VASCERN), HTAD Rare Disease Working Group
- Centre National Maladie Rare pour le Syndrome de Marfan et Apparentés, Hôpital Bichat, France
| | - Bart Loeys
- European Reference Network for Rare Multisystemic Vascular Disease (VASCERN), HTAD Rare Disease Working Group
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Belgium
- Department of Human Genetics, Radboud University Medical Center, the Netherlands
| | - Maria L Peña
- Department of Cardiology, Hospital Universitario Virgen del Rocio, Spain
| | - Gisela Teixido-Tura
- European Reference Network for Rare Multisystemic Vascular Disease (VASCERN), HTAD Rare Disease Working Group
- Servei de Cardiologia, Hospital Universitari Vall d'Hebron, VHIR. CIBER-CV, Barcelona, Spain
| | - Ingrid van de Laar
- European Reference Network for Rare Multisystemic Vascular Disease (VASCERN), HTAD Rare Disease Working Group
- Department of Clinical Genetics, Erasmus MC, the Netherlands
| | - Aline Verstraeten
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Belgium
- Department of Human Genetics, Radboud University Medical Center, the Netherlands
| | - Jolien Roos Hesselink
- European Reference Network for Rare Multisystemic Vascular Disease (VASCERN), HTAD Rare Disease Working Group
- Department of Cardiology, Erasmus MC, the Netherlands
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46
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Sun P, Wu T, Sun X, Cui Z, Zhang H, Xia Q, Zhang D. KMT2D inhibits the growth and metastasis of bladder Cancer cells by maintaining the tumor suppressor genes. Biomed Pharmacother 2019; 115:108924. [PMID: 31100540 DOI: 10.1016/j.biopha.2019.108924] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 04/24/2019] [Accepted: 04/24/2019] [Indexed: 01/06/2023] Open
Abstract
KMT2D, a kind of histone H3 lysine 4 (H3K4) methyltransferase, its abnormal expression confirmed to be associated with diverse tumors, but is lack of defined role in bladder cancer (BC). KMT2D mutation was analyzed using several databases. Immunohistochemistry and clinicopathological analysis of KMT2D in 51 paired of BC tissues and corresponding normal tissues were used to evaluate the relationship between KMT2D and BC. The effects of silencing or over-expressing KMT2D on HTB-9 and T24 cell viability, migration and invasion were performed using MTT, wound scratch and Transwell, respectively. Also, bladder cancer mouse model was established by hypodermic injection of the BC cells. Associated expressions of methylation genes, oncogenes and tumor suppressors were assessed by western blot and quantitative real-time PCR. KMT2D was frequent mutation in various tumors, including BC. It was negative expression in BC tissues and cells, also implicated with tumor stages and lymph node metastasis. In silencing KMT2D HTB-9 and T24 cells, cell viability, migration and invasion were notably promoted. Meanwhile, knockdown of KMT2D benefited to solid tumor formation in vivo. However, over-expressing KMT2D represented contrary results. Especially, KMT2D over-expression induced the activity of H3K4 monomethylation (me1), and effectively enhanced PTEN and p53 expressions as well as repressed STAG2 expression. Meanwhile, KMT2D had no obvious effect on Survivin. This work suggested an anti-tumor role for KMT2D in vitro and in vivo, as well as provided a possible tumor inhibition mechanism in which KMT2D enhanced H3K4me1 activity to support the expressions of tumor suppressors.
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Affiliation(s)
- Peng Sun
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong University, China
| | - Tong Wu
- Department of Chinese Medicine, Shandong Provincial Western Hospital, China
| | - Xiaoliang Sun
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong University, China
| | - Zilian Cui
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong University, China
| | - Haiyang Zhang
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong University, China
| | - Qinghua Xia
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong University, China
| | - Dong Zhang
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong University, China.
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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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