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Olie CS, O'Brien DP, Jones HB, Liang Z, Damianou A, Sur-Erdem I, Pinto-Fernández A, Raz V, Kessler BM. Deubiquitinases in muscle physiology and disorders. Biochem Soc Trans 2024; 52:1085-1098. [PMID: 38716888 PMCID: PMC11346448 DOI: 10.1042/bst20230562] [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: 11/14/2023] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 06/27/2024]
Abstract
In vivo, muscle and neuronal cells are post-mitotic, and their function is predominantly regulated by proteostasis, a multilayer molecular process that maintains a delicate balance of protein homeostasis. The ubiquitin-proteasome system (UPS) is a key regulator of proteostasis. A dysfunctional UPS is a hallmark of muscle ageing and is often impacted in neuromuscular disorders (NMDs). Malfunction of the UPS often results in aberrant protein accumulation which can lead to protein aggregation and/or mis-localization affecting its function. Deubiquitinating enzymes (DUBs) are key players in the UPS, controlling protein turnover and maintaining the free ubiquitin pool. Several mutations in DUB encoding genes are linked to human NMDs, such as ATXN3, OTUD7A, UCHL1 and USP14, whilst other NMDs are associated with dysregulation of DUB expression. USP5, USP9X and USP14 are implicated in synaptic transmission and remodeling at the neuromuscular junction. Mice lacking USP19 show increased maintenance of lean muscle mass. In this review, we highlight the involvement of DUBs in muscle physiology and NMDs, particularly in processes affecting muscle regeneration, degeneration and inflammation following muscle injury. DUBs have recently garnered much respect as promising drug targets, and their roles in muscle maturation, regeneration and degeneration may provide the framework for novel therapeutics to treat muscular disorders including NMDs, sarcopenia and cachexia.
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Affiliation(s)
- Cyriel S. Olie
- Department of Human Genetics, Leiden University Medical Centre, 2333ZC Leiden, The Netherlands
| | - Darragh P. O'Brien
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K
| | - Hannah B.L. Jones
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K
| | - Zhu Liang
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Andreas Damianou
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Ilknur Sur-Erdem
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Women's Centre, John Radcliffe Hospital, Oxford OX3 9DU, U.K
| | - Adán Pinto-Fernández
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Vered Raz
- Department of Human Genetics, Leiden University Medical Centre, 2333ZC Leiden, The Netherlands
| | - Benedikt M. Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, U.K
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Yang S, Kim SH, Kang M, Joo JY. Harnessing deep learning into hidden mutations of neurological disorders for therapeutic challenges. Arch Pharm Res 2023:10.1007/s12272-023-01450-5. [PMID: 37261600 DOI: 10.1007/s12272-023-01450-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 05/26/2023] [Indexed: 06/02/2023]
Abstract
The relevant study of transcriptome-wide variations and neurological disorders in the evolved field of genomic data science is on the rise. Deep learning has been highlighted utilizing algorithms on massive amounts of data in a human-like manner, and is expected to predict the dependency or druggability of hidden mutations within the genome. Enormous mutational variants in coding and noncoding transcripts have been discovered along the genome by far, despite of the fine-tuned genetic proofreading machinery. These variants could be capable of inducing various pathological conditions, including neurological disorders, which require lifelong care. Several limitations and questions emerge, including the use of conventional processes via limited patient-driven sequence acquisitions and decoding-based inferences as well as how rare variants can be deduced as a population-specific etiology. These puzzles require harnessing of advanced systems for precise disease prediction, drug development and drug applications. In this review, we summarize the pathophysiological discoveries of pathogenic variants in both coding and noncoding transcripts in neurological disorders, and the current advantage of deep learning applications. In addition, we discuss the challenges encountered and how to outperform them with advancing interpretation.
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Affiliation(s)
- Sumin Yang
- Department of Pharmacy, College of Pharmacy, Hanyang University, Rm 407, Bldg.42, 55 Hanyangdaehak-Ro, Sangnok-Gu Ansan, Ansan, Gyeonggi-Do, 15588, Republic of Korea
| | - Sung-Hyun Kim
- Department of Pharmacy, College of Pharmacy, Hanyang University, Rm 407, Bldg.42, 55 Hanyangdaehak-Ro, Sangnok-Gu Ansan, Ansan, Gyeonggi-Do, 15588, Republic of Korea
| | - Mingon Kang
- Department of Computer Science, University of Nevada, Las Vegas, NV, 89154, USA
| | - Jae-Yeol Joo
- Department of Pharmacy, College of Pharmacy, Hanyang University, Rm 407, Bldg.42, 55 Hanyangdaehak-Ro, Sangnok-Gu Ansan, Ansan, Gyeonggi-Do, 15588, Republic of Korea.
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Xiao X, Xu T, Liu H, Liu X, Liao X, Zhou Y, Zhou L, Wang X, Zhu Y, Yang Q, Hao X, Liu Y, Jiang H, Guo J, Wang J, Tang B, Li J, Shen L, Jiao B. CYLD variants identified in Alzheimer's disease and frontotemporal dementia patients. Ann Clin Transl Neurol 2022; 9:1596-1601. [PMID: 36000313 PMCID: PMC9539372 DOI: 10.1002/acn3.51655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 11/25/2022] Open
Abstract
Objectives CYLD was a novel causative gene for frontotemporal dementia (FTD) and amyotrophic lateral sclerosis. Given the clinical and pathological overlap of FTD and Alzheimer's disease (AD), it is necessary to screen CYLD in AD patients and FTD patients in the Chinese population. Methods In our study, using a targeted sequencing panel, we sequenced the CYLD gene in a large cohort of 2485 participants in the Chinese population, including 1008 AD patients, 105 FTD patients, and 1372 controls. Results In the present study, the average onset age of AD and FTD patients was 66.84 ± 30.42 years old and 60 ± 10.00 years old, respectively. Our study reported three novel CYLD variants: p.Phe288Leu (patient No. 1, AD), p.Tyr485Phe (patients No. 6–9, all AD) and p.Thr951Ala (patient No. 10, AD), plus a previously reported variant: p.Arg397Ser (patient No. 2–5, AD and No. 11, FTD). These variants were absent in our in‐house controls and predicted to be deleterious according to the MutationTaster. The variant carriers were composed of 10 AD patients and one FTD patient, and the average onset age was 61.2 ± 10.9 years. The frequency of CYLD variants in AD was similar to that in FTD, which was 0.99% (10/1008) and 0.95% (1/105), respectively. Interpretation Our finding extended the genotype and phenotype of the CYLD gene and demonstrated that CYLD rare damaging variants may be implicated in AD and FTD pathogenesis.
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Affiliation(s)
- Xuewen Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Tianyan Xu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Hui Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Xixi Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Xinxin Liao
- Bioinformatics Center and National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China.,Engineering Research Center of Hunan Province in Cognitive Impairment Disorders, Central South University, Changsha, China.,Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China.,Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Yafang Zhou
- Bioinformatics Center and National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China.,Engineering Research Center of Hunan Province in Cognitive Impairment Disorders, Central South University, Changsha, China.,Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China.,Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Lu Zhou
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Xin Wang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yuan Zhu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Qijie Yang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Xiaoli Hao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yingzi Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Hong Jiang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,Bioinformatics Center and National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China.,Engineering Research Center of Hunan Province in Cognitive Impairment Disorders, Central South University, Changsha, China.,Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
| | - Jifeng Guo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,Bioinformatics Center and National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China.,Engineering Research Center of Hunan Province in Cognitive Impairment Disorders, Central South University, Changsha, China.,Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
| | - Junling Wang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,Bioinformatics Center and National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China.,Engineering Research Center of Hunan Province in Cognitive Impairment Disorders, Central South University, Changsha, China.,Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
| | - Beisha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,Bioinformatics Center and National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China.,Engineering Research Center of Hunan Province in Cognitive Impairment Disorders, Central South University, Changsha, China.,Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
| | - Jinchen Li
- Bioinformatics Center and National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China.,Engineering Research Center of Hunan Province in Cognitive Impairment Disorders, Central South University, Changsha, China.,Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
| | - Lu Shen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,Bioinformatics Center and National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China.,Engineering Research Center of Hunan Province in Cognitive Impairment Disorders, Central South University, Changsha, China.,Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China.,Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, Changsha, China
| | - Bin Jiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,Bioinformatics Center and National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China.,Engineering Research Center of Hunan Province in Cognitive Impairment Disorders, Central South University, Changsha, China.,Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
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