Strategic validation of variants of uncertain significance in ECHS1 genetic testing.

Autor:	Kishita Y; Department of Life Science, Faculty of Science and Engineering, Kindai University, Higashiosaka, Osaka, Japan.; Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Bunkyo-ku, Tokyo, Japan., Sugiura A; Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Bunkyo-ku, Tokyo, Japan., Onuki T; Department of Metabolism, Chiba Children's Hospital, Midori-ku, Chiba, Japan., Ebihara T; Department of Neonatology, Chiba Children's Hospital, Midori-ku, Chiba, Japan., Matsuhashi T; Department of Metabolism, Chiba Children's Hospital, Midori-ku, Chiba, Japan., Shimura M; Department of Metabolism, Chiba Children's Hospital, Midori-ku, Chiba, Japan., Fushimi T; Department of Metabolism, Chiba Children's Hospital, Midori-ku, Chiba, Japan., Ichino N; Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Bunkyo-ku, Tokyo, Japan., Nagatakidani Y; Department of Life Science, Faculty of Science and Engineering, Kindai University, Higashiosaka, Osaka, Japan., Nishihata H; Department of Life Science, Faculty of Science and Engineering, Kindai University, Higashiosaka, Osaka, Japan., Nitta KR; Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Bunkyo-ku, Tokyo, Japan., Yatsuka Y; Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Bunkyo-ku, Tokyo, Japan., Imai-Okazaki A; Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Bunkyo-ku, Tokyo, Japan., Wu Y; Chemical Biology Mass Spectrometry Platform (CHEMBIOMS), Faculty of Sciences, University of Geneva, Geneve, Switzerland.; YCI Laboratory for Next-Generation Proteomics, RIKEN Center of Integrative Medical Sciences, Yokohama, Kanagawa, Japan., Osaka H; Department of Pediatrics, Jichi Medical University, Shimotsuke, Tochigi, Japan., Ohtake A; Department of Pediatrics & Clinical Genomics, Faculty of Medicine, Saitama Medical University, Moroyama, Saitama, Japan.; Center for Intractable Diseases, Saitama Medical University Hospital, Moroyama, Saitama, Japan., Murayama K; Department of Metabolism, Chiba Children's Hospital, Midori-ku, Chiba, Japan.; Center for Medical Genetics, Chiba Children's Hospital, Midori-ku, Chiba, Japan., Okazaki Y; Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Bunkyo-ku, Tokyo, Japan ya-okazaki@juntendo.ac.jp.; Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan.
Jazyk:	angličtina
Zdroj:	Journal of medical genetics [J Med Genet] 2023 Oct; Vol. 60 (10), pp. 1006-1015. Date of Electronic Publication: 2023 Apr 13.
DOI:	10.1136/jmg-2022-109027
Abstrakt:	Background: Enoyl-CoA hydratase short-chain 1 (ECHS1) is an enzyme involved in the metabolism of branched chain amino acids and fatty acids. Mutations in the ECHS1 gene lead to mitochondrial short-chain enoyl-CoA hydratase 1 deficiency, resulting in the accumulation of intermediates of valine. This is one of the most common causative genes in mitochondrial diseases. While genetic analysis studies have diagnosed numerous cases with ECHS1 variants, the increasing number of variants of uncertain significance (VUS) in genetic diagnosis is a major problem. Methods: Here, we constructed an assay system to verify VUS function for ECHS1 gene. A high-throughput assay using ECHS1 knockout cells was performed to index these phenotypes by expressing cDNAs containing VUS. In parallel with the VUS validation system, a genetic analysis of samples from patients with mitochondrial disease was performed. The effect on gene expression in cases was verified by RNA-seq and proteome analysis. Results: The functional validation of VUS identified novel variants causing loss of ECHS1 function. The VUS validation system also revealed the effect of the VUS in the compound heterozygous state and provided a new methodology for variant interpretation. Moreover, we performed multiomics analysis and identified a synonymous substitution p.P163= that results in splicing abnormality. The multiomics analysis complemented the diagnosis of some cases that could not be diagnosed by the VUS validation system. Conclusions: In summary, this study uncovered new ECHS1 cases based on VUS validation and omics analysis; these analyses are applicable to the functional evaluation of other genes associated with mitochondrial disease. Competing Interests: Competing interests: None declared. (© Author(s) (or their employer(s)) 2023. No commercial re-use. See rights and permissions. Published by BMJ.)
Databáze:	MEDLINE
Externí odkaz:	Zobrazit plný text záznamu