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Yoon JG, Lim SK, Seo H, Lee S, Cho J, Kim SY, Koh HY, Poduri AH, Ramakumaran V, Vasudevan P, de Groot MJ, Ko JM, Han D, Chae JH, Lee CH. De novo missense variants in HDAC3 leading to epigenetic machinery dysfunction are associated with a variable neurodevelopmental disorder. Am J Hum Genet 2024:S0002-9297(24)00217-9. [PMID: 39047730 DOI: 10.1016/j.ajhg.2024.06.015] [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: 01/27/2024] [Revised: 06/22/2024] [Accepted: 06/24/2024] [Indexed: 07/27/2024] Open
Abstract
Histone deacetylase 3 (HDAC3) is a crucial epigenetic modulator essential for various developmental and physiological functions. Although its dysfunction is increasingly recognized in abnormal phenotypes, to our knowledge, there have been no established reports of human diseases directly linked to HDAC3 dysfunction. Using trio exome sequencing and extensive phenotypic analysis, we correlated heterozygous de novo variants in HDAC3 with a neurodevelopmental disorder having variable clinical presentations, frequently associated with intellectual disability, developmental delay, epilepsy, and musculoskeletal abnormalities. In a cohort of six individuals, we identified missense variants in HDAC3 (c.277G>A [p.Asp93Asn], c.328G>A [p.Ala110Thr], c.601C>T [p.Pro201Ser], c. 797T>C [p.Leu266Ser], c.799G>A [p.Gly267Ser], and c.1075C>T [p.Arg359Cys]), all located in evolutionarily conserved sites and confirmed as de novo. Experimental studies identified defective deacetylation activity in the p.Asp93Asn, p.Pro201Ser, p.Leu266Ser, and p.Gly267Ser variants, positioned near the enzymatic pocket. In addition, proteomic analysis employing co-immunoprecipitation revealed that the disrupted interactions with molecules involved in the CoREST and NCoR complexes, particularly in the p.Ala110Thr variant, consist of a central pathogenic mechanism. Moreover, immunofluorescence analysis showed diminished nuclear to cytoplasmic fluorescence ratio in the p.Ala110Thr, p.Gly267Ser, and p.Arg359Cys variants, indicating impaired nuclear localization. Taken together, our study highlights that de novo missense variants in HDAC3 are associated with a broad spectrum of neurodevelopmental disorders, which emphasizes the complex role of HDAC3 in histone deacetylase activity, multi-protein complex interactions, and nuclear localization for proper physiological functions. These insights open new avenues for understanding the molecular mechanisms of HDAC3-related disorders and may inform future therapeutic strategies.
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Affiliation(s)
- Jihoon G Yoon
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea; Department of Laboratory Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seong-Kyun Lim
- Department of Pharmacology, Seoul National University College of Medicine, Seoul, Republic of Korea; Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hoseok Seo
- Department of Transdisciplinary Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Seungbok Lee
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea; Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - Jaeso Cho
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea; Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - Soo Yeon Kim
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea; Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - Hyun Yong Koh
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Annapurna H Poduri
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Pradeep Vasudevan
- LNR Genomic Medicine Service, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Martijn J de Groot
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Jung Min Ko
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea; Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - Dohyun Han
- Department of Transdisciplinary Medicine, Seoul National University Hospital, Seoul, Republic of Korea; Department of Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Jong-Hee Chae
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea; Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Republic of Korea.
| | - Chul-Hwan Lee
- Department of Pharmacology, Seoul National University College of Medicine, Seoul, Republic of Korea; Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea; Ischemic/hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Republic of Korea; Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea; Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea; Wide River Institute of Immunology, Seoul National University, Hongcheon, Republic of Korea; The Institute of Molecular Biology & Genetics, Seoul National University, Seoul, Republic of Korea.
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Drackley A, De Simone L, Kuntz N, Rahmani S, Ing A, Rao VK, Rathbun P, Yap KL. Expansion of the phenotypic spectrum associated with pathogenic missense variation in DHX16. Am J Med Genet A 2024; 194:53-58. [PMID: 37664979 DOI: 10.1002/ajmg.a.63392] [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: 04/17/2023] [Revised: 08/15/2023] [Accepted: 08/23/2023] [Indexed: 09/05/2023]
Abstract
Pathogenic heterozygous variants in DHX16 have been recently identified in association with a variety of clinical features, including neuromuscular disease, sensorineural hearing loss, ocular anomalies, and other phenotypes. All DHX16 disease-causing variants previously reported in affected individuals are missense in nature, nearly all of which were found to be de novo. Here we report on a patient with neuromuscular disease, hearing loss, retinal degeneration, and previously unreported phenotypic features including mitochondrial deficiency and primary ovarian insufficiency, in whom a novel de novo likely pathogenic variant in DHX16 NM_003587.4:c.2033A > G (p.Glu678Gly) was identified. Furthermore, we conducted an in-depth literature review of DHX16's role in disease and utilized high-performing in silico prediction algorithms to compare and contrast the predicted effects of all reported disease-associated DHX16 variants on protein structure and function.
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Affiliation(s)
- Andy Drackley
- Department of Pathology & Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
- Division of Genetics, Genomics, and Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Lenika De Simone
- Division of Genetics, Genomics, and Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
- Division of Neurology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Nancy Kuntz
- Division of Neurology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Safa Rahmani
- Division of Ophthalmology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
- Department of Ophthalmology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Alexander Ing
- Department of Pathology & Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
- Division of Genetics, Genomics, and Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Vamshi K Rao
- Division of Neurology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Pamela Rathbun
- Department of Pathology & Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Kai Lee Yap
- Department of Pathology & Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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Cho J, Kim H, Lee S, Yoon JG, Kim H, Kim M, Jang S, Kim W, Kim SY, Chae JH. Expanding association between BICD2 variants and brain malformations and associated lissencephaly. Clin Exp Pediatr 2024; 67:54-56. [PMID: 38129099 PMCID: PMC10764667 DOI: 10.3345/cep.2023.01095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 12/23/2023] Open
Affiliation(s)
- Jaeso Cho
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Korea
| | - Haeryung Kim
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Korea
| | - Seoungbok Lee
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Korea
| | - Jihoon G Yoon
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Korea
| | - HyeJin Kim
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Korea
| | - Minhye Kim
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Korea
| | - Seoyun Jang
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Korea
| | - Woojoong Kim
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Korea
| | - Soo Yeon Kim
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Korea
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Korea
| | - Jong Hee Chae
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Korea
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Korea
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Cho J, Yoon JG, Lee S, Kim S, Kim SY, Kim MJ, Moon J, Chae JH. Expansion of clinico-genetic spectrum of PRDX3 disease: a literature review with two additional cases. Brain Commun 2023; 5:fcad233. [PMID: 37731903 PMCID: PMC10507740 DOI: 10.1093/braincomms/fcad233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/19/2023] [Accepted: 08/25/2023] [Indexed: 09/22/2023] Open
Abstract
Graphical Abstract.
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Affiliation(s)
- Jaeso Cho
- Department of Genomic Medicine, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Jihoon G Yoon
- Department of Genomic Medicine, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Seungbok Lee
- Department of Genomic Medicine, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Sheehyun Kim
- Department of Genomic Medicine, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Soo Yeon Kim
- Department of Genomic Medicine, Seoul National University Hospital, Seoul 03080, Republic of Korea
- Department of Pediatrics, Seoul National University College of Medicine, Seoul03080, Republic of Korea
| | - Man Jin Kim
- Department of Genomic Medicine, Seoul National University Hospital, Seoul 03080, Republic of Korea
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Jangsup Moon
- Department of Genomic Medicine, Seoul National University Hospital, Seoul 03080, Republic of Korea
- Department of Neurology, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Jong-Hee Chae
- Department of Genomic Medicine, Seoul National University Hospital, Seoul 03080, Republic of Korea
- Department of Pediatrics, Seoul National University College of Medicine, Seoul03080, Republic of Korea
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Genome-Wide Sequencing Modalities for Children with Unexplained Global Developmental Delay and Intellectual Disabilities—A Narrative Review. CHILDREN 2023; 10:children10030501. [PMID: 36980059 PMCID: PMC10047410 DOI: 10.3390/children10030501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/25/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023]
Abstract
Unexplained global developmental delay (GDD) and intellectual disabilities (ID) together affect nearly 2% of the pediatric population. Establishing an etiologic diagnosis is crucial for disease management, prognostic evaluation, and provision of physical and psychological support for both the patient and the family. Advancements in genome sequencing have allowed rapid accumulation of gene–disorder associations and have accelerated the search for an etiologic diagnosis for unexplained GDD/ID. We reviewed recent studies that utilized genome-wide analysis technologies, and we discussed their diagnostic yield, strengths, and limitations. Overall, exome sequencing (ES) and genome sequencing (GS) outperformed chromosomal microarrays and targeted panel sequencing. GS provides coverage for both ES and chromosomal microarray regions, providing the maximal diagnostic potential, and the cost of ES and reanalysis of ES-negative results is currently still lower than that of GS alone. Therefore, singleton or trio ES is the more cost-effective option for the initial investigation of individuals with GDD/ID in clinical practice compared to a staged approach or GS alone. Based on these updated evidence, we proposed an evaluation algorithm with ES as the first-tier evaluation for unexplained GDD/ID.
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