Mechanism of KMT5B haploinsufficiency in neurodevelopment in humans and mice

Author:

Sheppard Sarah E.12ORCID,Bryant Laura1ORCID,Wickramasekara Rochelle N.34ORCID,Vaccaro Courtney1,Robertson Brynn3,Hallgren Jodi3ORCID,Hulen Jason3,Watson Cynthia J.3,Faundes Victor56ORCID,Duffourd Yannis7,Lee Pearl8ORCID,Simon M. Celeste8ORCID,de la Cruz Xavier910ORCID,Padilla Natália9ORCID,Flores-Mendez Marco11ORCID,Akizu Naiara1112ORCID,Smiler Jacqueline113ORCID,Pellegrino Da Silva Renata1,Li Dong1ORCID,March Michael1ORCID,Diaz-Rosado Abdias1,Peixoto de Barcelos Isabella1ORCID,Choa Zhao Xiang1415ORCID,Lim Chin Yan1415ORCID,Dubourg Christèle16ORCID,Journel Hubert17,Demurger Florence18,Mulhern Maureen1920ORCID,Akman Cigdem20,Lippa Natalie21ORCID,Andrews Marisa22ORCID,Baldridge Dustin22ORCID,Constantino John23ORCID,van Haeringen Arie24,Snoeck-Streef Irina25,Chow Penny26ORCID,Hing Anne26,Graham John M.27,Au Margaret27,Faivre Laurence2829ORCID,Shen Wei3031ORCID,Mao Rong30,Palumbos Janice30ORCID,Viskochil David30,Gahl William32ORCID,Tifft Cynthia32ORCID,Macnamara Ellen32ORCID,Hauser Natalie33,Miller Rebecca33,Maffeo Jessica33,Afenjar Alexandra34,Doummar Diane34,Keren Boris35ORCID,Arn Pamela36,Macklin-Mantia Sarah37ORCID,Meerschaut Ilse38ORCID,Callewaert Bert3839ORCID,Reis André40ORCID,Zweier Christiane4041,Brewer Carole42,Saggar Anand43,Smeland Marie F.4445ORCID,Kumar Ajith46ORCID,Elmslie Frances47ORCID,Deshpande Charu48ORCID,Nizon Mathilde49,Cogne Benjamin4950,van Ierland Yvette51ORCID,Wilke Martina51ORCID,van Slegtenhorst Marjon51,Koudijs Suzanne52ORCID,Chen Jin Yun53,Dredge David54,Pier Danielle53ORCID,Wortmann Saskia5455ORCID,Kamsteeg Erik-Jan54ORCID,Koch Johannes54,Haynes Devon56ORCID,Pollack Lynda56,Titheradge Hannah57ORCID,Ranguin Kara58ORCID,Denommé-Pichon Anne-Sophie728ORCID,Weber Sacha58ORCID,Pérez de la Fuente Rubén59ORCID,Sánchez del Pozo Jaime59,Lezana Rosales Jose Miguel59ORCID,Joset Pascal60,Steindl Katharina60ORCID,Rauch Anita6061626364ORCID,Mei Davide65ORCID,Mari Francesco65ORCID,Guerrini Renzo65ORCID,Lespinasse James66,Tran Mau-Them Frédéric728ORCID,Philippe Christophe728,Dauriat Benjamin67,Raymond Laure68,Moutton Sébastien68ORCID,Cueto-González Anna M.6970ORCID,Tan Tiong Yang7172,Mignot Cyril73,Grotto Sarah73,Renaldo Florence74,Drivas Theodore G.7576ORCID,Hennessy Laura76,Raper Anna76,Parenti Ilaria77ORCID,Kaiser Frank J.7778,Kuechler Alma77,Busk Øyvind L.79ORCID,Islam Lily57,Siedlik Jacob A.80ORCID,Henderson Lindsay B.81,Juusola Jane81,Person Richard81,Schnur Rhonda E.8182,Vitobello Antonio728ORCID,Banka Siddharth5ORCID,Bhoj Elizabeth J.1ORCID,Stessman Holly A. F.3ORCID

Affiliation:

1. Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA.

2. Unit on Vascular Malformations, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA.

3. Stessman Laboratory, Department of Pharmacology and Neuroscience, Creighton University Medical School, Omaha, NE, USA.

4. Molecular Diagnostic Laboratory, Boys Town National Research Hospital, Omaha, NE, USA.

5. Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.

6. Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile.

7. Unité Fonctionnelle d’Innovation diagnostique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.

8. Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.

9. Vall d’Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.

10. Institució Catalana de Recerca I Estudis Avançats (ICREA), Barcelona, Spain.

11. Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA.

12. Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA.

13. 10x Genomics, Pleasanton, CA, USA.

14. Epithelial Epigenetics and Development Laboratory, A*STAR Skin Research Labs, Singapore, Singapore.

15. Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.

16. Laboratoire de Génétique Moléculaire et Génomique, Centre Hospitalier Universitaire de Rennes, Rennes 35033, France.

17. Service de Génétique Médicale, Hopital Chubert, Vannes, Bretagne, France.

18. Department of Clinical Genetics, Service de Génétique Clinique, Centre de Référence Maladies Rares Centre Labellisé Anomalies du Développement-Ouest, Centre Hospitalier Universitaire de Rennes, Rennes 35033, France.

19. Department of Pathology, Columbia University Irving Medical Center, New York, NY, USA.

20. Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA.

21. Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA.

22. Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA.

23. Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA.

24. Department of Clinical Genetics, Leiden University Medical Center, Leiden, Netherlands.

25. Department of Child Neurology, University Medical Center Utrecht, Utrecht, Netherlands.

26. Department of Pediatrics, Division of Craniofacial Medicine, University of Washington, Seattle, WA, USA.

27. Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, UCLA School of Medicine, Los Angeles, CA, USA.

28. UFR Des Sciences de Santé, INSERM–Université de Bourgogne UMR1231 GAD “Génétique des Anomalies du Développement,” FHU-TRANSLAD, Dijon, France.

29. Centre de Référence Anomalies du Développement et Syndromes Malformatifs, CHU Dijon, Bourgogne, France.

30. University of Utah, Salt Lake City, UT, USA.

31. Mayo Clinic, Rochester, MN, USA.

32. NIH Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.

33. Medical Genetics, Inova Fairfax Hospital, Falls Church, VA, USA.

34. AP-HP, Sorbonne Université, Département de neuropediatrie, Hospital Armand Trousseau, Paris, France.

35. Genetic Department, Pitié-Salpêtrière Hospital, AP-HP, Sorbonne Université, Paris, France.

36. Department of Pediatrics, Nemours Children’s Specialty Care, Jacksonville, FL, USA.

37. Department of Clinical Genomics, Mayo Clinic Florida, Jacksonville, FL, USA.

38. Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.

39. Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.

40. Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany.

41. Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland.

42. Clinical Genetics Department, Royal Devon and Exeter Hospital (Heavitree), Exeter EX1 2ED, UK.

43. Clinical Genetics Department, St George’s Hospital, St George’s Healthcare NHS Trust, London SW17 0QT, UK.

44. Department of Medical Genetics, University Hospital of North Norway, Tromsø, Norway.

45. Department of Pediatric Rehabilitation, University Hospital of North Norway, Norway.

46. Northeast Thames Regional Genetics Service, Great Ormond Street Hospital, London WC1N 3JH, UK.

47. South West Thames Centre for Genomics, St George’s University Hospitals NHS Foundation Trust, London SW17 0QT, UK.

48. Department of Medical Genetics, Guy’s Hospital, London SE1 9RT, UK.

49. CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes CEDEX 1, France.

50. Nantes Université, CNRS, INSERM, L’institut du thorax, F-44000 Nantes, France.

51. Department of Clinical Genetics, Erasmus University Medical Center, P.O. Box 2040, 3000 CA Rotterdam, Netherlands.

52. Department of Neurology, Erasmus University Medical Center–Sophia Children’s Hospital, P.O. Box 2040, 3000 CA Rotterdam, Netherlands.

53. Neurology Department, Massachusetts General Hospital, Boston, MA, USA.

54. University Children’s Hospital Salzburg, Paracelsus Medical University (PMU), Salzburg, Austria.

55. Amalia Children’s Hospital, RadboudUMC Nijmegen, Nijmegen, Netherlands.

56. Division of Genetics, Arnold Palmer Hospital for Children–Orlando Health, Orlando, FL, USA.

57. West Midlands Regional Genetics Service and Birmingham Health Partners, Birmingham Women’s and Children’s NHS Trust, Birmingham B15 2TG, UK.

58. Department of Genetics, Reference Centre for Rare Diseases and Developmental Anomalies, Caen Hospital, Caen, France.

59. UDISGEN (Unidad de Dismorfología y Genética) 12 de Octubre University Hospital, Madrid, Spain.

60. University of Zurich, Institute of Medical Genetics, 8952 Schlieren-Zurich, Switzerland.

61. University of Zurich, University Children’s Hospital Zurich, 8032 Zurich, Switzerland.

62. University of Zurich, URPP Adaptive Brain Circuits in Development and Learning (AdaBD), Zurich, Switzerland.

63. University of Zurich Research Priority Program (URPP) AdaBD: Adaptive Brain Circuits in Development and Learning, Zurich 8006, Switzerland.

64. University of Zurich Research Priority Program (URPP) ITINERARE: Innovative Therapies in Rare Diseases, Zurich 8006, Switzerland.

65. Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Meyer Children’s Hospital, Member of ERN Epicare, University of Florence, Florence, Italy.

66. UF de Génétique Chromosomique, Centre Hospitalier de Chambéry, Hôtel-dieu, France.

67. Service de cytogénétique et génétique médicale, Centre Hospitalier Universitaire de Limoges, France.

68. Service de génétique, Laboratoire Eurofins Biomnis, Lyon, France.

69. Hospital Vall d'Hebron, Barcelona, Spain.

70. Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain.

71. Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC, Australia.

72. Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia.

73. AP-HP, Sorbonne Université, Département de Génétique, Paris, France.

74. AP-HP, Sorbonne Université, Département de neuropediatrie, Centre de référence neurogénétique, Hôpital Armand Trousseau, Paris, France.

75. Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.

76. Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.

77. Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany.

78. Essener Zentrum für Seltene Erkrankungen (EZSE), Universitätsklinikum Essen, Essen, Germany.

79. Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway.

80. Department of Exercise Science and Pre-Health Professions, Creighton University, Omaha, NE, USA.

81. GeneDx, Gaithersburg, MD, USA.

82. Department of Pediatrics, Division of Genetics Cooper Medical School of Rowan University Cooper University Health Care 3, Cooper Plaza, Camden, NJ, USA.

Abstract

Pathogenic variants in KMT5B , a lysine methyltransferase, are associated with global developmental delay, macrocephaly, autism, and congenital anomalies (OMIM # 617788). Given the relatively recent discovery of this disorder, it has not been fully characterized. Deep phenotyping of the largest ( n  = 43) patient cohort to date identified that hypotonia and congenital heart defects are prominent features that were previously not associated with this syndrome. Both missense variants and putative loss-of-function variants resulted in slow growth in patient-derived cell lines. KMT5B homozygous knockout mice were smaller in size than their wild-type littermates but did not have significantly smaller brains, suggesting relative macrocephaly, also noted as a prominent clinical feature. RNA sequencing of patient lymphoblasts and Kmt5b haploinsufficient mouse brains identified differentially expressed pathways associated with nervous system development and function including axon guidance signaling. Overall, we identified additional pathogenic variants and clinical features in KMT5B -related neurodevelopmental disorder and provide insights into the molecular mechanisms of the disorder using multiple model systems.

Publisher

American Association for the Advancement of Science (AAAS)

Subject

Multidisciplinary

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