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Lee S, Yoon JG, Hong J, Kim T, Kim N, Vandrovcova J, Yau WY, Cho J, Kim S, Kim MJ, Kim SY, Lee ST, Chu K, Lee SK, Kim HJ, Choi J, Moon J, Chae JH. Prevalence and Characterization of NOTCH2NLC GGC Repeat Expansions in Koreans: From a Hospital Cohort Analysis to a Population-Wide Study. Neurol Genet 2024; 10:e200147. [PMID: 38779172 PMCID: PMC11110025 DOI: 10.1212/nxg.0000000000200147] [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: 10/31/2023] [Accepted: 02/16/2024] [Indexed: 05/25/2024]
Abstract
Background and Objectives GGC repeat expansions in the NOTCH2NLC gene are associated with a broad spectrum of progressive neurologic disorders, notably, neuronal intranuclear inclusion disease (NIID). We aimed to investigate the population-wide prevalence and clinical manifestations of NOTCH2NLC-related disorders in Koreans. Methods We conducted a study using 2 different cohorts from the Korean population. Patients with available brain MRI scans from Seoul National University Hospital (SNUH) were thoroughly reviewed, and NIID-suspected patients presenting the zigzag edging signs underwent genetic evaluation for NOTCH2NLC repeats by Cas9-mediated nanopore sequencing. In addition, we analyzed whole-genome sequencing data from 3,887 individuals in the Korea Biobank cohort to estimate the distribution of the repeat counts in Koreans and to identify putative patients with expanded alleles and neurologic phenotypes. Results In the SNUH cohort, among 90 adult-onset leukoencephalopathy patients with unknown etiologies, we found 20 patients with zigzag edging signs. Except for 2 diagnosed with fragile X-associated tremor/ataxia syndrome and 2 with unavailable samples, all 16 patients (17.8%) were diagnosed with NIID (repeat range: 87-217). By analyzing the Korea Biobank cohort, we estimated the distribution of repeat counts and threshold (>64) for Koreans, identifying 6 potential patients with NIID. Furthermore, long-read sequencing enabled the elucidation of transmission and epigenetic patterns of NOTCH2NLC repeats within a family affected by pediatric-onset NIID. Discussion This study presents the population-wide distribution of NOTCH2NLC repeats and the estimated prevalence of NIID in Koreans, providing valuable insights into the association between repeat counts and disease manifestations in diverse neurologic disorders.
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Affiliation(s)
| | | | | | - Taekeun Kim
- From the Department of Genomic Medicine (S.L., J.G.Y., Jaeso Cho, S.K., M.J.K., S.Y.K., J.M., J.-H.C.), Seoul National University Hospital; Department of Pediatrics (S.L., Jaeso Cho, S.Y.K., J.-H.C.), Seoul National University College of Medicine, Seoul National University Children's Hospital; Department of Biomedical Sciences (J.H., T.K., Jungmin Choi), Korea University College of Medicine; Department of Neurology (N.K., S.-T.L., K.C., S.K.L., H.-J.K., J.M.), Seoul National University Hospital, Korea; Department of Neuromuscular Diseases (J.V.), Institute of Neurology, University College London, United Kingdom; Perron Institute for Neurological and Translational Science (W.Y.Y.), the University of Western Australia, Nedlands, Australia; and Department of Laboratory Medicine (M.J.K.), Seoul National University Hospital, Korea
| | - Narae Kim
- From the Department of Genomic Medicine (S.L., J.G.Y., Jaeso Cho, S.K., M.J.K., S.Y.K., J.M., J.-H.C.), Seoul National University Hospital; Department of Pediatrics (S.L., Jaeso Cho, S.Y.K., J.-H.C.), Seoul National University College of Medicine, Seoul National University Children's Hospital; Department of Biomedical Sciences (J.H., T.K., Jungmin Choi), Korea University College of Medicine; Department of Neurology (N.K., S.-T.L., K.C., S.K.L., H.-J.K., J.M.), Seoul National University Hospital, Korea; Department of Neuromuscular Diseases (J.V.), Institute of Neurology, University College London, United Kingdom; Perron Institute for Neurological and Translational Science (W.Y.Y.), the University of Western Australia, Nedlands, Australia; and Department of Laboratory Medicine (M.J.K.), Seoul National University Hospital, Korea
| | - Jana Vandrovcova
- From the Department of Genomic Medicine (S.L., J.G.Y., Jaeso Cho, S.K., M.J.K., S.Y.K., J.M., J.-H.C.), Seoul National University Hospital; Department of Pediatrics (S.L., Jaeso Cho, S.Y.K., J.-H.C.), Seoul National University College of Medicine, Seoul National University Children's Hospital; Department of Biomedical Sciences (J.H., T.K., Jungmin Choi), Korea University College of Medicine; Department of Neurology (N.K., S.-T.L., K.C., S.K.L., H.-J.K., J.M.), Seoul National University Hospital, Korea; Department of Neuromuscular Diseases (J.V.), Institute of Neurology, University College London, United Kingdom; Perron Institute for Neurological and Translational Science (W.Y.Y.), the University of Western Australia, Nedlands, Australia; and Department of Laboratory Medicine (M.J.K.), Seoul National University Hospital, Korea
| | - Wai Yan Yau
- From the Department of Genomic Medicine (S.L., J.G.Y., Jaeso Cho, S.K., M.J.K., S.Y.K., J.M., J.-H.C.), Seoul National University Hospital; Department of Pediatrics (S.L., Jaeso Cho, S.Y.K., J.-H.C.), Seoul National University College of Medicine, Seoul National University Children's Hospital; Department of Biomedical Sciences (J.H., T.K., Jungmin Choi), Korea University College of Medicine; Department of Neurology (N.K., S.-T.L., K.C., S.K.L., H.-J.K., J.M.), Seoul National University Hospital, Korea; Department of Neuromuscular Diseases (J.V.), Institute of Neurology, University College London, United Kingdom; Perron Institute for Neurological and Translational Science (W.Y.Y.), the University of Western Australia, Nedlands, Australia; and Department of Laboratory Medicine (M.J.K.), Seoul National University Hospital, Korea
| | - Jaeso Cho
- From the Department of Genomic Medicine (S.L., J.G.Y., Jaeso Cho, S.K., M.J.K., S.Y.K., J.M., J.-H.C.), Seoul National University Hospital; Department of Pediatrics (S.L., Jaeso Cho, S.Y.K., J.-H.C.), Seoul National University College of Medicine, Seoul National University Children's Hospital; Department of Biomedical Sciences (J.H., T.K., Jungmin Choi), Korea University College of Medicine; Department of Neurology (N.K., S.-T.L., K.C., S.K.L., H.-J.K., J.M.), Seoul National University Hospital, Korea; Department of Neuromuscular Diseases (J.V.), Institute of Neurology, University College London, United Kingdom; Perron Institute for Neurological and Translational Science (W.Y.Y.), the University of Western Australia, Nedlands, Australia; and Department of Laboratory Medicine (M.J.K.), Seoul National University Hospital, Korea
| | - Sheehyun Kim
- From the Department of Genomic Medicine (S.L., J.G.Y., Jaeso Cho, S.K., M.J.K., S.Y.K., J.M., J.-H.C.), Seoul National University Hospital; Department of Pediatrics (S.L., Jaeso Cho, S.Y.K., J.-H.C.), Seoul National University College of Medicine, Seoul National University Children's Hospital; Department of Biomedical Sciences (J.H., T.K., Jungmin Choi), Korea University College of Medicine; Department of Neurology (N.K., S.-T.L., K.C., S.K.L., H.-J.K., J.M.), Seoul National University Hospital, Korea; Department of Neuromuscular Diseases (J.V.), Institute of Neurology, University College London, United Kingdom; Perron Institute for Neurological and Translational Science (W.Y.Y.), the University of Western Australia, Nedlands, Australia; and Department of Laboratory Medicine (M.J.K.), Seoul National University Hospital, Korea
| | - Man Jin Kim
- From the Department of Genomic Medicine (S.L., J.G.Y., Jaeso Cho, S.K., M.J.K., S.Y.K., J.M., J.-H.C.), Seoul National University Hospital; Department of Pediatrics (S.L., Jaeso Cho, S.Y.K., J.-H.C.), Seoul National University College of Medicine, Seoul National University Children's Hospital; Department of Biomedical Sciences (J.H., T.K., Jungmin Choi), Korea University College of Medicine; Department of Neurology (N.K., S.-T.L., K.C., S.K.L., H.-J.K., J.M.), Seoul National University Hospital, Korea; Department of Neuromuscular Diseases (J.V.), Institute of Neurology, University College London, United Kingdom; Perron Institute for Neurological and Translational Science (W.Y.Y.), the University of Western Australia, Nedlands, Australia; and Department of Laboratory Medicine (M.J.K.), Seoul National University Hospital, Korea
| | - Soo Yeon Kim
- From the Department of Genomic Medicine (S.L., J.G.Y., Jaeso Cho, S.K., M.J.K., S.Y.K., J.M., J.-H.C.), Seoul National University Hospital; Department of Pediatrics (S.L., Jaeso Cho, S.Y.K., J.-H.C.), Seoul National University College of Medicine, Seoul National University Children's Hospital; Department of Biomedical Sciences (J.H., T.K., Jungmin Choi), Korea University College of Medicine; Department of Neurology (N.K., S.-T.L., K.C., S.K.L., H.-J.K., J.M.), Seoul National University Hospital, Korea; Department of Neuromuscular Diseases (J.V.), Institute of Neurology, University College London, United Kingdom; Perron Institute for Neurological and Translational Science (W.Y.Y.), the University of Western Australia, Nedlands, Australia; and Department of Laboratory Medicine (M.J.K.), Seoul National University Hospital, Korea
| | - Soon-Tae Lee
- From the Department of Genomic Medicine (S.L., J.G.Y., Jaeso Cho, S.K., M.J.K., S.Y.K., J.M., J.-H.C.), Seoul National University Hospital; Department of Pediatrics (S.L., Jaeso Cho, S.Y.K., J.-H.C.), Seoul National University College of Medicine, Seoul National University Children's Hospital; Department of Biomedical Sciences (J.H., T.K., Jungmin Choi), Korea University College of Medicine; Department of Neurology (N.K., S.-T.L., K.C., S.K.L., H.-J.K., J.M.), Seoul National University Hospital, Korea; Department of Neuromuscular Diseases (J.V.), Institute of Neurology, University College London, United Kingdom; Perron Institute for Neurological and Translational Science (W.Y.Y.), the University of Western Australia, Nedlands, Australia; and Department of Laboratory Medicine (M.J.K.), Seoul National University Hospital, Korea
| | - Kon Chu
- From the Department of Genomic Medicine (S.L., J.G.Y., Jaeso Cho, S.K., M.J.K., S.Y.K., J.M., J.-H.C.), Seoul National University Hospital; Department of Pediatrics (S.L., Jaeso Cho, S.Y.K., J.-H.C.), Seoul National University College of Medicine, Seoul National University Children's Hospital; Department of Biomedical Sciences (J.H., T.K., Jungmin Choi), Korea University College of Medicine; Department of Neurology (N.K., S.-T.L., K.C., S.K.L., H.-J.K., J.M.), Seoul National University Hospital, Korea; Department of Neuromuscular Diseases (J.V.), Institute of Neurology, University College London, United Kingdom; Perron Institute for Neurological and Translational Science (W.Y.Y.), the University of Western Australia, Nedlands, Australia; and Department of Laboratory Medicine (M.J.K.), Seoul National University Hospital, Korea
| | - Sang Kun Lee
- From the Department of Genomic Medicine (S.L., J.G.Y., Jaeso Cho, S.K., M.J.K., S.Y.K., J.M., J.-H.C.), Seoul National University Hospital; Department of Pediatrics (S.L., Jaeso Cho, S.Y.K., J.-H.C.), Seoul National University College of Medicine, Seoul National University Children's Hospital; Department of Biomedical Sciences (J.H., T.K., Jungmin Choi), Korea University College of Medicine; Department of Neurology (N.K., S.-T.L., K.C., S.K.L., H.-J.K., J.M.), Seoul National University Hospital, Korea; Department of Neuromuscular Diseases (J.V.), Institute of Neurology, University College London, United Kingdom; Perron Institute for Neurological and Translational Science (W.Y.Y.), the University of Western Australia, Nedlands, Australia; and Department of Laboratory Medicine (M.J.K.), Seoul National University Hospital, Korea
| | - Han-Joon Kim
- From the Department of Genomic Medicine (S.L., J.G.Y., Jaeso Cho, S.K., M.J.K., S.Y.K., J.M., J.-H.C.), Seoul National University Hospital; Department of Pediatrics (S.L., Jaeso Cho, S.Y.K., J.-H.C.), Seoul National University College of Medicine, Seoul National University Children's Hospital; Department of Biomedical Sciences (J.H., T.K., Jungmin Choi), Korea University College of Medicine; Department of Neurology (N.K., S.-T.L., K.C., S.K.L., H.-J.K., J.M.), Seoul National University Hospital, Korea; Department of Neuromuscular Diseases (J.V.), Institute of Neurology, University College London, United Kingdom; Perron Institute for Neurological and Translational Science (W.Y.Y.), the University of Western Australia, Nedlands, Australia; and Department of Laboratory Medicine (M.J.K.), Seoul National University Hospital, Korea
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Rajan-Babu IS, Dolzhenko E, Eberle MA, Friedman JM. Sequence composition changes in short tandem repeats: heterogeneity, detection, mechanisms and clinical implications. Nat Rev Genet 2024:10.1038/s41576-024-00696-z. [PMID: 38467784 DOI: 10.1038/s41576-024-00696-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2024] [Indexed: 03/13/2024]
Abstract
Short tandem repeats (STRs) are a class of repetitive elements, composed of tandem arrays of 1-6 base pair sequence motifs, that comprise a substantial fraction of the human genome. STR expansions can cause a wide range of neurological and neuromuscular conditions, known as repeat expansion disorders, whose age of onset, severity, penetrance and/or clinical phenotype are influenced by the length of the repeats and their sequence composition. The presence of non-canonical motifs, depending on the type, frequency and position within the repeat tract, can alter clinical outcomes by modifying somatic and intergenerational repeat stability, gene expression and mutant transcript-mediated and/or protein-mediated toxicities. Here, we review the diverse structural conformations of repeat expansions, technological advances for the characterization of changes in sequence composition, their clinical correlations and the impact on disease mechanisms.
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Affiliation(s)
- Indhu-Shree Rajan-Babu
- Department of Medical Genetics, The University of British Columbia, and Children's & Women's Hospital, Vancouver, British Columbia, Canada.
| | | | | | - Jan M Friedman
- Department of Medical Genetics, The University of British Columbia, and Children's & Women's Hospital, Vancouver, British Columbia, Canada
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
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Yu SY, Xi YL, Xu FQ, Zhang J, Liu YS. Application of long read sequencing in rare diseases: The longer, the better? Eur J Med Genet 2023; 66:104871. [PMID: 38832911 DOI: 10.1016/j.ejmg.2023.104871] [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: 08/18/2023] [Revised: 10/11/2023] [Accepted: 10/22/2023] [Indexed: 06/06/2024]
Abstract
Rare diseases encompass a diverse group of genetic disorders that affect a small proportion of the population. Identifying the underlying genetic causes of these conditions presents significant challenges due to their genetic heterogeneity and complexity. Conventional short-read sequencing (SRS) techniques have been widely used in diagnosing and investigating of rare diseases, with limitations due to the nature of short-read lengths. In recent years, long read sequencing (LRS) technologies have emerged as a valuable tool in overcoming these limitations. This minireview provides a concise overview of the applications of LRS in rare disease research and diagnosis, including the identification of disease-causing tandem repeat expansions, structural variations, and comprehensive analysis of pathogenic variants with LRS.
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Affiliation(s)
- Si-Yan Yu
- Department of Pediatric Laboratory, Affiliated Children's Hospital of Jiangnan University (Wuxi Children's Hospital), Wuxi, Jiangsu, China; The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yu-Lin Xi
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Fu-Qiang Xu
- Department of Gynecology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Jian Zhang
- Department of Medical Laboratory, Affiliated Children's Hospital of Jiangnan University (Wuxi Children's Hospital), Wuxi, Jiangsu, China.
| | - Yan-Shan Liu
- Department of Pediatric Laboratory, Affiliated Children's Hospital of Jiangnan University (Wuxi Children's Hospital), Wuxi, Jiangsu, China; Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China.
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4
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Vollger MR, Korlach J, Eldred KC, Swanson E, Underwood JG, Cheng YHH, Ranchalis J, Mao Y, Blue EE, Schwarze U, Munson KM, Saunders CT, Wenger AM, Allworth A, Chanprasert S, Duerden BL, Glass I, Horike-Pyne M, Kim M, Leppig KA, McLaughlin IJ, Ogawa J, Rosenthal EA, Sheppeard S, Sherman SM, Strohbehn S, Yuen AL, Reh TA, Byers PH, Bamshad MJ, Hisama FM, Jarvik GP, Sancak Y, Dipple KM, Stergachis AB. Synchronized long-read genome, methylome, epigenome, and transcriptome for resolving a Mendelian condition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.26.559521. [PMID: 37808736 PMCID: PMC10557686 DOI: 10.1101/2023.09.26.559521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Resolving the molecular basis of a Mendelian condition (MC) remains challenging owing to the diverse mechanisms by which genetic variants cause disease. To address this, we developed a synchronized long-read genome, methylome, epigenome, and transcriptome sequencing approach, which enables accurate single-nucleotide, insertion-deletion, and structural variant calling and diploid de novo genome assembly, and permits the simultaneous elucidation of haplotype-resolved CpG methylation, chromatin accessibility, and full-length transcript information in a single long-read sequencing run. Application of this approach to an Undiagnosed Diseases Network (UDN) participant with a chromosome X;13 balanced translocation of uncertain significance revealed that this translocation disrupted the functioning of four separate genes (NBEA, PDK3, MAB21L1, and RB1) previously associated with single-gene MCs. Notably, the function of each gene was disrupted via a distinct mechanism that required integration of the four 'omes' to resolve. These included nonsense-mediated decay, fusion transcript formation, enhancer adoption, transcriptional readthrough silencing, and inappropriate X chromosome inactivation of autosomal genes. Overall, this highlights the utility of synchronized long-read multi-omic profiling for mechanistically resolving complex phenotypes.
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Affiliation(s)
- Mitchell R. Vollger
- University of Washington School of Medicine, Department of Genome Sciences, Seattle, WA, USA
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | | | - Kiara C. Eldred
- University of Washington School of Medicine, Department of Biological Structure, Seattle, WA, USA
| | - Elliott Swanson
- University of Washington School of Medicine, Department of Genome Sciences, Seattle, WA, USA
| | | | - Yong-Han H. Cheng
- University of Washington School of Medicine, Department of Genome Sciences, Seattle, WA, USA
| | - Jane Ranchalis
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Yizi Mao
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Elizabeth E. Blue
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
- Institute for Public Health Genetics, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Ulrike Schwarze
- University of Washington School of Medicine, Department of Laboratory Medicine and Pathology, Seattle, WA, USA
| | - Katherine M. Munson
- University of Washington School of Medicine, Department of Genome Sciences, Seattle, WA, USA
| | | | | | - Aimee Allworth
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Sirisak Chanprasert
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | | | - Ian Glass
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- University of Washington, Department of Pediatrics, Seattle, WA, USA
| | - Martha Horike-Pyne
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | | | - Kathleen A. Leppig
- Genetic Services, Kaiser Permanente Washington, Seattle, Washington, USA
| | | | | | | | - Sam Sheppeard
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Stephanie M. Sherman
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Samuel Strohbehn
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Amy L. Yuen
- Genetic Services, Kaiser Permanente Washington, Seattle, Washington, USA
| | | | - Thomas A. Reh
- University of Washington School of Medicine, Department of Biological Structure, Seattle, WA, USA
| | - Peter H. Byers
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
- University of Washington School of Medicine, Department of Laboratory Medicine and Pathology, Seattle, WA, USA
| | - Michael J. Bamshad
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- University of Washington, Department of Pediatrics, Seattle, WA, USA
| | - Fuki M. Hisama
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Gail P. Jarvik
- University of Washington School of Medicine, Department of Genome Sciences, Seattle, WA, USA
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Yasemin Sancak
- University of Washington School of Medicine, Department of Pharmacology, Seattle, WA, USA
| | - Katrina M. Dipple
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- University of Washington, Department of Pediatrics, Seattle, WA, USA
| | - Andrew B. Stergachis
- University of Washington School of Medicine, Department of Genome Sciences, Seattle, WA, USA
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
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Gu X, Jiao K, Yue D, Wang X, Qiao K, Gao M, Lin J, Sun C, Zhao C, Zhu W, Xi J. Intrafamilial phenotypic heterogeneity in GIPC1-related oculopharyngodistal myopathy type 2: a case report. Neuromuscul Disord 2023; 33:93-97. [PMID: 37550168 DOI: 10.1016/j.nmd.2023.07.002] [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: 04/06/2023] [Revised: 05/25/2023] [Accepted: 07/05/2023] [Indexed: 08/09/2023]
Abstract
Oculopharyngodistal myopathy (OPDM) is a rare adult-onset neuromuscular disease characterized by ocular, facial, bulbar and distal limb muscle weakness. Here, we presented a pair of siblings with OPDM2 displaying marked intrafamilial phenotypic heterogeneity. In addition to muscle weakness, the proband also demonstrated tremor and visual disturbance that have not been reported previously in OPDM2. Electrophysiological and pathological studies further suggested the presence of neurogenic impairment in the proband. Repeat-primed polymerase chain reaction (RP-PCR) and fluorescence amplicon length analysis polymerase chain reaction (AL-PCR) confirmed the molecular diagnosis of OPDM2 in the siblings. Given the rarity of the case, the association between OPDM2 and tremor, visual disturbance, or neurogenic impairment remained to be explored.
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Affiliation(s)
- Xinyu Gu
- Department of Neurology, Huashan Hospital, Fudan University, 12, Wulumuqi Road, Shanghai, China
| | - Kexin Jiao
- Department of Neurology, Huashan Hospital, Fudan University, 12, Wulumuqi Road, Shanghai, China
| | - Dongyue Yue
- Department of Neurology, Jing' an District Center Hospital of Shanghai, Shanghai, China
| | - Xilu Wang
- Department of Anthropology and Human Genetics, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, China
| | - Kai Qiao
- Department of Neurology, Huashan Hospital, Fudan University, 12, Wulumuqi Road, Shanghai, China
| | - Mingshi Gao
- Department of Pathology, Huashan Hospital, Fudan University, Shanghai, China
| | - Jie Lin
- Department of Neurology, Huashan Hospital, Fudan University, 12, Wulumuqi Road, Shanghai, China
| | - Chong Sun
- Department of Neurology, Huashan Hospital, Fudan University, 12, Wulumuqi Road, Shanghai, China
| | - Chongbo Zhao
- Department of Neurology, Huashan Hospital, Fudan University, 12, Wulumuqi Road, Shanghai, China
| | - Wenhua Zhu
- Department of Neurology, Huashan Hospital, Fudan University, 12, Wulumuqi Road, Shanghai, China
| | - Jianying Xi
- Department of Neurology, Huashan Hospital, Fudan University, 12, Wulumuqi Road, Shanghai, China.
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Fitrah YA, Higuchi Y, Hara N, Tokutake T, Kanazawa M, Sanpei K, Taneda T, Nakajima A, Koide S, Tsuboguchi S, Watanabe M, Fukumoto J, Ando S, Sato T, Iwafuchi Y, Sato A, Hayashi H, Ishiguro T, Takeda H, Takahashi T, Fukuhara N, Kasuga K, Miyashita A, Onodera O, Ikeuchi T. Heterogenous Genetic, Clinical, and Imaging Features in Patients with Neuronal Intranuclear Inclusion Disease Carrying NOTCH2NLC Repeat Expansion. Brain Sci 2023; 13:955. [PMID: 37371433 DOI: 10.3390/brainsci13060955] [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: 05/19/2023] [Revised: 06/09/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Neuronal intranuclear inclusion disease (NIID) is a neurodegenerative disorder that is caused by the abnormal expansion of non-coding trinucleotide GGC repeats in NOTCH2NLC. NIID is clinically characterized by a broad spectrum of clinical presentations. To date, the relationship between expanded repeat lengths and clinical phenotype in patients with NIID remains unclear. Thus, we aimed to clarify the genetic and clinical spectrum and their association in patients with NIID. For this purpose, we genetically analyzed Japanese patients with adult-onset NIID with characteristic clinical and neuroimaging findings. Trinucleotide repeat expansions of NOTCH2NLC were examined by repeat-primed and amplicon-length PCR. In addition, long-read sequencing was performed to determine repeat size and sequence. The expanded GGC repeats ranging from 94 to 361 in NOTCH2NLC were found in all 15 patients. Two patients carried biallelic repeat expansions. There were marked heterogenous clinical and imaging features in NIID patients. Patients presenting with cerebellar ataxia or urinary dysfunction had a significantly larger GGC repeat size than those without. This significant association disappeared when these parameters were compared with the total trinucleotide repeat number. ARWMC score was significantly higher in patients who had a non-glycine-type trinucleotide interruption within expanded poly-glycine motifs than in those with a pure poly-glycine expansion. These results suggested that the repeat length and sequence in NOTCH2NLC may partly modify some clinical and imaging features of NIID.
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Affiliation(s)
- Yusran Ady Fitrah
- Department of Molecular Genetics, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Yo Higuchi
- Department of Molecular Genetics, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
- Department of Neurology, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
- Department of Neurology, Joetsu General Hospital, Joetsu 943-0172, Japan
| | - Norikazu Hara
- Department of Molecular Genetics, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Takayoshi Tokutake
- Department of Neurology, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Masato Kanazawa
- Department of Neurology, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Kazuhiro Sanpei
- Department of Neurology, Sado General Hospital, Sado 952-1209, Japan
| | - Tomone Taneda
- Department of Neurology, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Akihiko Nakajima
- Department of Neurology, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Shin Koide
- Department of Neurology, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Shintaro Tsuboguchi
- Department of Neurology, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Midori Watanabe
- Department of Neurology, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Junki Fukumoto
- Department of Neurology, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Shoichiro Ando
- Department of Neurology, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Tomoe Sato
- Department of Neurology, Tsubame Rosai Hospital, Tsubame 959-1228, Japan
| | - Yohei Iwafuchi
- Department of Neurology, Niigata City General Hospital, Niigata 950-1197, Japan
| | - Aki Sato
- Department of Neurology, Niigata City General Hospital, Niigata 950-1197, Japan
| | - Hideki Hayashi
- Department of Neurology, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
- Department of Neurology, Sado General Hospital, Sado 952-1209, Japan
| | - Takanobu Ishiguro
- Department of Neurology, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
- Department of Neurology, Sado General Hospital, Sado 952-1209, Japan
| | - Hayato Takeda
- Department of Neurology, Tsukuba University, Tsukuba 950-1197, Japan
| | | | - Nobuyoshi Fukuhara
- Department of Neurology, Joetsu General Hospital, Joetsu 943-0172, Japan
| | - Kensaku Kasuga
- Department of Molecular Genetics, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Akinori Miyashita
- Department of Molecular Genetics, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Osamu Onodera
- Department of Neurology, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Takeshi Ikeuchi
- Department of Molecular Genetics, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
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7
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Visconti VV, Macrì E, D'Apice MR, Centofanti F, Massa R, Novelli G, Botta A. In Cis Effect of DMPK Expanded Alleles in Myotonic Dystrophy Type 1 Patients Carrying Variant Repeats at 5' and 3' Ends of the CTG Array. Int J Mol Sci 2023; 24:10129. [PMID: 37373276 DOI: 10.3390/ijms241210129] [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: 04/17/2023] [Revised: 06/07/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Myotonic dystrophy type 1 (DM1) is an autosomal dominant multisystemic disease caused by a CTG repeat expansion in the 3'-untranslated region (UTR) of DMPK gene. DM1 alleles containing non-CTG variant repeats (VRs) have been described, with uncertain molecular and clinical consequences. The expanded trinucleotide array is flanked by two CpG islands, and the presence of VRs could confer an additional level of epigenetic variability. This study aims to investigate the association between VR-containing DMPK alleles, parental inheritance and methylation pattern of the DM1 locus. The DM1 mutation has been characterized in 20 patients using a combination of SR-PCR, TP-PCR, modified TP-PCR and LR-PCR. Non-CTG motifs have been confirmed by Sanger sequencing. The methylation pattern of the DM1 locus was determined by bisulfite pyrosequencing. We characterized 7 patients with VRs within the CTG tract at 5' end and 13 patients carrying non-CTG sequences at 3' end of the DM1 expansion. DMPK alleles with VRs at 5' end or 3' end were invariably unmethylated upstream of the CTG expansion. Interestingly, DM1 patients with VRs at the 3' end showed higher methylation levels in the downstream island of the CTG repeat tract, preferentially when the disease allele was maternally inherited. Our results suggest a potential correlation between VRs, parental origin of the mutation and methylation pattern of the DMPK expanded alleles. A differential CpG methylation status could play a role in the phenotypic variability of DM1 patients, representing a potentially useful diagnostic tool.
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Affiliation(s)
- Virginia Veronica Visconti
- Department of Biomedicine and Prevention, Genetics Unit, University of Rome "Tor Vergata", Via Montpellier 1, 00133 Rome, Italy
| | - Elisa Macrì
- Department of Biomedicine and Prevention, Genetics Unit, University of Rome "Tor Vergata", Via Montpellier 1, 00133 Rome, Italy
| | - Maria Rosaria D'Apice
- Laboratory of Medical Genetics, Tor Vergata Hospital, Viale Oxford 81, 00133 Rome, Italy
| | - Federica Centofanti
- Department of Biomedicine and Prevention, Genetics Unit, University of Rome "Tor Vergata", Via Montpellier 1, 00133 Rome, Italy
| | - Roberto Massa
- Department of Systems Medicine, University of Rome "Tor Vergata", Via Montpellier 1, 00133 Rome, Italy
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, Genetics Unit, University of Rome "Tor Vergata", Via Montpellier 1, 00133 Rome, Italy
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Neuromed, Via Atinense 18, 86077 Pozzilli, Italy
- Department of Pharmacology, School of Medicine, University of Nevada, Reno, NV 89557, USA
| | - Annalisa Botta
- Department of Biomedicine and Prevention, Genetics Unit, University of Rome "Tor Vergata", Via Montpellier 1, 00133 Rome, Italy
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8
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Ishiura H, Tsuji S, Toda T. Recent advances in CGG repeat diseases and a proposal of fragile X-associated tremor/ataxia syndrome, neuronal intranuclear inclusion disease, and oculophryngodistal myopathy (FNOP) spectrum disorder. J Hum Genet 2023; 68:169-174. [PMID: 36670296 PMCID: PMC9968658 DOI: 10.1038/s10038-022-01116-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 12/21/2022] [Accepted: 12/21/2022] [Indexed: 01/22/2023]
Abstract
While whole genome sequencing and long-read sequencing have become widely available, more and more focuses are on noncoding expanded repeats. Indeed, more than half of noncoding repeat expansions related to diseases have been identified in the five years. An exciting aspect of the progress in this field is an identification of a phenomenon called repeat motif-phenotype correlation. Repeat motif-phenotype correlation in noncoding repeat expansion diseases is first found in benign adult familial myoclonus epilepsy. The concept is extended in the research of CGG repeat expansion diseases. In this review, we focus on newly identified CGG repeat expansion diseases, update the concept of repeat motif-phenotype correlation in CGG repeat expansion diseases, and propose a clinical concept of FNOP (fragile X-associated tremor/ataxia syndrome, neuronal intranuclear inclusion disease, and oculopharyngodistal myopathy)-spectrum disorder, which shares clinical features and thus probably share some common disease pathophysiology, to further facilitate discussion and progress in this field.
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Affiliation(s)
- Hiroyuki Ishiura
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
- Department of Neurology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan.
| | - Shoji Tsuji
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Institute of Medical Genomics, International University of Health and Welfare, Narita, Japan
| | - Tatsushi Toda
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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9
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Current advances in neuronal intranuclear inclusion disease. Neurol Sci 2023; 44:1881-1889. [PMID: 36795299 DOI: 10.1007/s10072-023-06677-0] [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: 12/07/2022] [Accepted: 02/10/2023] [Indexed: 02/17/2023]
Abstract
Neuronal intranuclear inclusion disease (NIID) is a rare but probably underdiagnosed neurodegenerative disorder due to pathogenic GGC expansions in the NOTCH2NLC gene. In this review, we summarize recent developments in the inheritance features, pathogenesis, and histopathologic and radiologic features of NIID that subvert the previous perceptions of NIID. GGC repeat sizes determine the age of onset and clinical phenotypes of NIID patients. Anticipation may be absent in NIID but paternal bias is observed in NIID pedigrees. Eosinophilic intranuclear inclusions in skin tissues once considered pathological hallmarks of NIID can also present in other GGC repeat diseases. Diffusion-weighted imaging (DWI) hyperintensity along the corticomedullary junction once considered the imaging hallmark of NIID can frequently be absent in muscle weakness and parkinsonism phenotype of NIID. Besides, DWI abnormalities can appear years after the onset of predominant symptoms and may even disappear completely with disease progression. Moreover, continuous reports of NOTCH2NLC GGC expansions in patients with other neurodegenerative diseases lead to the proposal of a new concept of NOTCH2NLC-related GGC repeat expansion disorders (NRED). However, by reviewing the previous literature, we point out the limitations of these studies and provide evidence that these patients are actually suffering from neurodegenerative phenotypes of NIID.
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10
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Rapid and comprehensive diagnostic method for repeat expansion diseases using nanopore sequencing. NPJ Genom Med 2022; 7:62. [PMID: 36289212 PMCID: PMC9606279 DOI: 10.1038/s41525-022-00331-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 09/30/2022] [Indexed: 11/23/2022] Open
Abstract
We developed a diagnostic method for repeat expansion diseases using a long-read sequencer to improve currently available, low throughput diagnostic methods. We employed the real-time target enrichment system of the nanopore GridION sequencer using the adaptive sampling option, in which software-based target assignment is available without prior sample enrichment, and built an analysis pipeline that prioritized the disease-causing loci. Twenty-two patients with various neurological and neuromuscular diseases, including 12 with genetically diagnosed repeat expansion diseases and 10 manifesting cerebellar ataxia, but without genetic diagnosis, were analyzed. We first sequenced the 12 molecularly diagnosed patients and accurately confirmed expanded repeats in all with uniform depth of coverage across the loci. Next, we applied our method and a conventional method to 10 molecularly undiagnosed patients. Our method corrected inaccurate diagnoses of two patients by the conventional method. Our method is superior to conventional diagnostic methods in terms of speed, accuracy, and comprehensiveness.
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11
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CGG repeat expansion in NOTCH2NLC causes mitochondrial dysfunction and progressive neurodegeneration in Drosophila model. Proc Natl Acad Sci U S A 2022; 119:e2208649119. [PMID: 36191230 PMCID: PMC9565157 DOI: 10.1073/pnas.2208649119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Neuronal intranuclear inclusion disease (NIID) is a neuromuscular/neurodegenerative disease caused by the expansion of CGG repeats in the 5' untranslated region (UTR) of the NOTCH2NLC gene. These repeats can be translated into a polyglycine-containing protein, uN2CpolyG, which forms protein inclusions and is toxic in cell models, albeit through an unknown mechanism. Here, we established a transgenic Drosophila model expressing uN2CpolyG in multiple systems, which resulted in progressive neuronal cell loss, locomotor deficiency, and shortened lifespan. Interestingly, electron microscopy revealed mitochondrial swelling both in transgenic flies and in muscle biopsies of individuals with NIID. Immunofluorescence and immunoelectron microscopy showed colocalization of uN2CpolyG with mitochondria in cell and patient samples, while biochemical analysis revealed that uN2CpolyG interacted with a mitochondrial RNA binding protein, LRPPRC (leucine-rich pentatricopeptide repeat motif-containing protein). Furthermore, RNA sequencing (RNA-seq) analysis and functional assays showed down-regulated mitochondrial oxidative phosphorylation in uN2CpolyG-expressing flies and NIID muscle biopsies. Finally, idebenone treatment restored mitochondrial function and alleviated neurodegenerative phenotypes in transgenic flies. Overall, these results indicate that transgenic flies expressing uN2CpolyG recapitulate key features of NIID and that reversing mitochondrial dysfunction might provide a potential therapeutic approach for this disorder.
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Abstract
PURPOSE OF REVIEW Oculopharyngodistal myopathy (OPDM) is a rare adolescent or adult-onset neuromuscular disease that is characterized by progressive ocular, facial, pharyngeal and distal limb muscle weakness. The rimmed vacuoles and intranuclear inclusions in myofibers constitute the pathological hallmark of OPDM. In this review, the latest findings related to the genetic, molecular and clinical features of OPDM, as well as the diagnosis and management are summarized. RECENT FINDINGS Four gene mutations, CGG repeats in the 5'-untranslated region of LRP12 , GIPC1 , NOTCH2NLC and RILPL1 have been reported to be disease-causing genes in OPDM, namely OPDM1, OPDM2, OPDM3 and OPDM4, accordingly. So far, limited studies have suggested that CGG repeat expansion within the pathogenic range may play a key role in the pathogenesis of OPDM with the gain-of-function mechanism at the RNA and/or protein level, while repeat expansion over a threshold limit may cause hypermethylation, leading to the transcriptional silencing of the CGG repeats in the expanded allele, which results in the existence of mild phenotype or asymptomatic carriers. SUMMARY Novel gene mutations, possible molecular mechanisms and the clinical features related to different causative genes are discussed in this review. More studies on the exact pathogenic mechanism are needed.
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Affiliation(s)
- Jiaxi Yu
- Department of Neurology, Peking University First Hospital
- Beijing Key Laboratory of Neurovascular Disease Discovery, Beijing, China
| | - Jianwen Deng
- Department of Neurology, Peking University First Hospital
- Beijing Key Laboratory of Neurovascular Disease Discovery, Beijing, China
| | - Zhaoxia Wang
- Department of Neurology, Peking University First Hospital
- Beijing Key Laboratory of Neurovascular Disease Discovery, Beijing, China
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13
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Kameyama S, Mizuguchi T, Doi H, Koyano S, Okubo M, Tada M, Shimizu H, Fukuda H, Tsuchida N, Uchiyama Y, Koshimizu E, Hamanaka K, Fujita A, Misawa K, Miyatake S, Kanai K, Tanaka F, Matsumoto N. Patients with biallelic GGC repeat expansions in NOTCH2NLC exhibiting a typical neuronal intranuclear inclusion disease phenotype. Genomics 2022; 114:110469. [PMID: 36041634 DOI: 10.1016/j.ygeno.2022.110469] [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: 06/24/2022] [Revised: 08/16/2022] [Accepted: 08/26/2022] [Indexed: 11/27/2022]
Abstract
We report two patients with autosomal dominant neuronal intranuclear inclusion disease (NIID) harboring the biallelic GGC repeat expansion in NOTCH2NLC to uncover the impact of repeat expansion zygosity on the clinical phenotype. The zygosity of the entire NOTCH2NLC GGC repeat expansion and DNA methylation were comprehensively evaluated using fluorescent amplicon length PCR (AL-PCR), Southern blotting and targeted long-read sequencing, and detailed genetic/epigenetic and clinical features were described. In AL-PCR, we could not recognize the wild-type allele in both patients. Targeted long-read sequencing revealed that one patient harbored a homozygous repeat expansion. The other patient harbored compound heterozygous repeat expansions. The GGC repeats and the nearest CpG island were hypomethylated in all expanded alleles in both patients. Both patients harboring the biallelic GGC repeat expansion showed a typical dementia-dominant NIID phenotype. In conclusion, the biallelic GGC repeat expansion in two typical NIID patients indicated that NOTCH2NLC-related diseases could be completely dominant.
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Affiliation(s)
- Shinichi Kameyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan; Department of Pathology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan.
| | - Hiroshi Doi
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Shigeru Koyano
- Department of Neurology, Yokohama Minami Kyosai Hospital, Yokohama 236-0037, Japan
| | - Masaki Okubo
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Mikiko Tada
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Hiroshi Shimizu
- Department of Pathology, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Hiromi Fukuda
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan; Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan; Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama 236-0004, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan; Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama 236-0004, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Kazuharu Misawa
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan; Clinical Genetics Department, Yokohama City University Hospital, Yokohama 236-0004, Japan
| | - Kazuaki Kanai
- Department of Neurology, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Fumiaki Tanaka
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan.
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14
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Alfano M, De Antoni L, Centofanti F, Visconti VV, Maestri S, Degli Esposti C, Massa R, D'Apice MR, Novelli G, Delledonne M, Botta A, Rossato M. Characterization of full-length CNBP expanded alleles in myotonic dystrophy type 2 patients by Cas9-mediated enrichment and nanopore sequencing. eLife 2022; 11:80229. [PMID: 36018009 PMCID: PMC9462847 DOI: 10.7554/elife.80229] [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] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/25/2022] [Indexed: 11/30/2022] Open
Abstract
Myotonic dystrophy type 2 (DM2) is caused by CCTG repeat expansions in the CNBP gene, comprising 75 to >11,000 units and featuring extensive mosaicism, making it challenging to sequence fully expanded alleles. To overcome these limitations, we used PCR-free Cas9-mediated nanopore sequencing to characterize CNBP repeat expansions at the single-nucleotide level in nine DM2 patients. The length of normal and expanded alleles can be assessed precisely using this strategy, agreeing with traditional methods, and revealing the degree of mosaicism. We also sequenced an entire ~50 kbp expansion, which has not been achieved previously for DM2 or any other repeat-expansion disorders. Our approach precisely counted the repeats and identified the repeat pattern for both short interrupted and uninterrupted alleles. Interestingly, in the expanded alleles, only two DM2 samples featured the expected pure CCTG repeat pattern, while the other seven presented also TCTG blocks at the 3′ end, which have not been reported before in DM2 patients, but confirmed hereby with orthogonal methods. The demonstrated approach simultaneously determines repeat length, structure/motif, and the extent of somatic mosaicism, promising to improve the molecular diagnosis of DM2 and achieve more accurate genotype–phenotype correlations for the better stratification of DM2 patients in clinical trials.
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Affiliation(s)
| | - Luca De Antoni
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Federica Centofanti
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | | | - Simone Maestri
- Department of Biotechnology, University of Verona, Verona, Italy
| | | | - Roberto Massa
- Department of Systems Medicine (Neurology), University of Rome Tor Vergata, Rome, Italy
| | | | - Giuseppe Novelli
- Laboratory of Medical Genetics, University of Rome Tor Vergata, Rome, Italy
| | | | - Annalisa Botta
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Marzia Rossato
- Department of Biotechnology, University of Verona, Verona, Italy
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15
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Cao Y, Tian W, Wu J, Song X, Cao L, Luan X. DNA hypermethylation of NOTCH2NLC in neuronal intranuclear inclusion disease: a case-control study. J Neurol 2022; 269:6049-6057. [PMID: 35857137 DOI: 10.1007/s00415-022-11272-y] [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: 03/31/2022] [Revised: 05/27/2022] [Accepted: 07/04/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND GGC repeat expansions in NOTCH2NLC gene have been recently proposed to cause neuronal intranuclear inclusion disease (NIID) via prevailing gain-of-function mechanism (protein and RNA toxicity). Nevertheless, increasing evidences suggest that epigenetics can also play a role in the pathogenesis of repeat-mediated disorders. METHODS In this study, using MethylTarget sequencing, we performed a quantitative analysis of the methylation status of 68 CpG sites located around the NOTCH2NLC promoter in 25 NIID patients and 25 age- and gender-matched healthy controls. We further explored the correlation of DNA methylation (DNAm) status with disease features and performed receiver operating characteristic (ROC) analysis. RESULTS DNAm levels of GGC repeats and adjacent CpG islands were higher in the NIID patients than in controls, independent of gender and family history. DNAm levels at 4 CpG sites (CpG_207, CpG_421, GpG_473 and CpG_523) were negatively correlated with age at onset, and DNAm levels at 7 CpG sites (CpG_25, CpG_298, CpG_336, CpG_374, CpG_411, CpG_421 and CpG_473) were positively correlated with GGC repeats. NIID patients had concomitant system symptoms besides nervous system symptoms, and negative correlations between NOTCH2NLC DNAm levels and the number of multi-systemic involvement were observed in the study. The area under the ROC curve at NOTCH2NLC DNAm level reached to 0.733 for the best cutoff point of 0.012. CONCLUSIONS Our findings suggested the aberrant DNAm status of the NOTCH2NLC promoter in NIID, and we explored the link between DNAm levels and disease features quantitatively for the first time, which may help to further explore pathogenic mechanism.
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Affiliation(s)
- Yuwen Cao
- Department of Neurology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Wotu Tian
- Department of Neurology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Jingying Wu
- Department of Neurology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Xingwang Song
- Institute of Neuroscience and Department of Neurology, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Li Cao
- Department of Neurology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China.
| | - Xinghua Luan
- Department of Neurology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China.
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16
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Zeng YH, Yang K, Du GQ, Chen YK, Cao CY, Qiu YS, He J, Lv HD, Qu QQ, Chen JN, Xu GR, Chen L, Zheng FZ, Zhao M, Lin MT, Chen WJ, Hu J, Wang ZQ, Wang N. GGC repeat expansion of RILPL1 is associated with oculopharyngodistal myopathy. Ann Neurol 2022; 92:512-526. [PMID: 35700120 DOI: 10.1002/ana.26436] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 05/04/2022] [Accepted: 05/23/2022] [Indexed: 11/11/2022]
Abstract
OBJECTIVE Oculopharyngodistal myopathy (OPDM) is an adult-onset neuromuscular disease characterized by progressive ptosis, dysarthria, ophthalmoplegia, and distal muscle weakness. Recent studies revealed GGC repeat expansions in 5'-UTR of LRP12, GIPC1, and NOTCH2NLC are associated with OPDM. Despite these advances, around 30% of OPDM patients remain genetically undiagnosed. Herein, we aim to investigate genetic basis for undiagnosed OPDM patients in two unrelated Chinese Han families. METHODS Parametric linkage analysis was performed. Long-read sequencing followed by repeat-primed polymerase chain reaction (RP-PCR) and amplicon length polymerase chain reaction (AL-PCR) were used to determine the genetic cause. Targeted methylation sequencing was implemented to detect epigenetic changes. The possible pathogenesis mechanism was investigated by qPCR, immunoblotting, RNA FISH, and immunofluorescence staining of muscle biopsy samples. RESULTS The disease locus was mapped to 12q24.3. Subsequently, GGC repeat expansion in the promoter region of RILPL1 was identified in six OPDM patients from two families, findings consistent with a founder effect, designated as OPDM type 4 (OPDM4). Targeted methylation sequencing revealed hypermethylation at RILPL1 locus in unaffected individuals with ultralong expansion. Analysis of muscle samples showed no significant differences in RILPL1 mRNA or RILPL1 protein levels between patients and controls. Public CAGE-seq data indicated that alternative TSSs exist upstream of the RefSeq-annotated RILPL1 TSS. Strand-specific RNAseq data revealed bidirectional transcription from the RILPL1 locus. Finally, FISH/IF indicated that both sense and antisense transcripts formed RNA foci and were co-localized with hnRNPA2B1 and p62 in the intranuclear inclusions of OPDM4 patients. INTERPRETATION Our findings implicate abnormal GGC repeat expansions in the promoter region of RILPL1 as a novel genetic cause for OPDM, and suggest a methylation mechanism and a potential RNA toxicity mechanism are involved in OPDM4 pathogenesis. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Yi-Heng Zeng
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China
| | - Kang Yang
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China
| | - Gan-Qin Du
- The First Affiliated Hospital, College of Clinical Medicine of Henan University of Science and Technology, Luoyang, 471000, China
| | - Yi-Kun Chen
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China
| | - Chun-Yan Cao
- The First Affiliated Hospital, College of Clinical Medicine of Henan University of Science and Technology, Luoyang, 471000, China
| | - Yu-Sen Qiu
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China
| | - Jin He
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China
| | - Hai-Dong Lv
- Department of Neurology, The People's Hospital of Jiaozuo City, Jiaozuo, 454150, China
| | - Qian-Qian Qu
- Department of Neurology, The People's Hospital of Jiaozuo City, Jiaozuo, 454150, China
| | - Jian-Nan Chen
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China
| | - Guo-Rong Xu
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China
| | - Long Chen
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China
| | - Fu-Ze Zheng
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China
| | - Miao Zhao
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China
| | - Min-Ting Lin
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China
| | - Wan-Jin Chen
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China
| | - Jing Hu
- Department of Neuromuscular Disorders, The Third Hospital of Hebei Medical University, Shijiazhuang, 050000, China
| | - Zhi-Qiang Wang
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China
| | - Ning Wang
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China
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Lei Y, Meng Y, Guo X, Ning K, Bian Y, Li L, Hu Z, Anashkina AA, Jiang Q, Dong Y, Zhu X. Overview of structural variation calling: Simulation, identification, and visualization. Comput Biol Med 2022; 145:105534. [DOI: 10.1016/j.compbiomed.2022.105534] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/09/2022] [Accepted: 04/14/2022] [Indexed: 12/11/2022]
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Yu J, Shan J, Yu M, Di L, Xie Z, Zhang W, Lv H, Meng L, Zheng Y, Zhao Y, Gang Q, Guo X, Wang Y, Xi J, Zhu W, Da Y, Hong D, Yuan Y, Yan C, Wang Z, Deng J. The CGG repeat expansion in RILPL1 is associated with oculopharyngodistal myopathy type 4. Am J Hum Genet 2022; 109:533-541. [PMID: 35148830 DOI: 10.1016/j.ajhg.2022.01.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/20/2022] [Indexed: 12/13/2022] Open
Abstract
Recent studies indicate that CGG repeat expansions in LRP12, GIPC1, and NOTCH2NLC are associated with oculopharyngodistal myopathy (OPDM) types 1, 2, and 3, respectively. However, some clinicopathologically confirmed OPDM cases continue to have unknown genetic causes. Here, through a combination of long-read whole-genome sequencing (LRS), repeat-primed polymerase chain reaction (RP-PCR), and fluorescence amplicon length analysis PCR (AL-PCR), we found that a CGG repeat expansion in the 5' UTR of RILPL1 is associated with familial and simplex OPDM type 4 (OPDM4). The number of repeats ranged from 139 to 197. Methylation analysis indicates that the methylation levels in RILPL1 were unaltered in OPDM4 individuals. Analyses of muscle biopsies suggested that the expanded CGG repeat might be translated into a toxic poly-glycine protein that co-localizes with p62 in intranuclear inclusions. Moreover, analyses suggest that the toxic RNA gain-of-function effects also contributed to the pathogenesis of this disease. Intriguingly, all four types of OPDM have been found to be associated with the CGG repeat expansions located in 5' UTRs. This finding suggests that a common pathogenic mechanism, driven by the CGG repeat expansion, might underlie all cases of OPDM.
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Boivin M, Charlet-Berguerand N. Trinucleotide CGG Repeat Diseases: An Expanding Field of Polyglycine Proteins? Front Genet 2022; 13:843014. [PMID: 35295941 PMCID: PMC8918734 DOI: 10.3389/fgene.2022.843014] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 01/31/2022] [Indexed: 12/30/2022] Open
Abstract
Microsatellites are repeated DNA sequences of 3–6 nucleotides highly variable in length and sequence and that have important roles in genomes regulation and evolution. However, expansion of a subset of these microsatellites over a threshold size is responsible of more than 50 human genetic diseases. Interestingly, some of these disorders are caused by expansions of similar sequences, sizes and localizations and present striking similarities in clinical manifestations and histopathological features, which suggest a common mechanism of disease. Notably, five identical CGG repeat expansions, but located in different genes, are the causes of fragile X-associated tremor/ataxia syndrome (FXTAS), neuronal intranuclear inclusion disease (NIID), oculopharyngodistal myopathy type 1 to 3 (OPDM1-3) and oculopharyngeal myopathy with leukoencephalopathy (OPML), which are neuromuscular and neurodegenerative syndromes with overlapping symptoms and similar histopathological features, notably the presence of characteristic eosinophilic ubiquitin-positive intranuclear inclusions. In this review we summarize recent finding in neuronal intranuclear inclusion disease and FXTAS, where the causing CGG expansions were found to be embedded within small upstream ORFs (uORFs), resulting in their translation into novel proteins containing a stretch of polyglycine (polyG). Importantly, expression of these polyG proteins is toxic in animal models and is sufficient to reproduce the formation of ubiquitin-positive intranuclear inclusions. These data suggest the existence of a novel class of human genetic pathology, the polyG diseases, and question whether a similar mechanism may exist in other diseases, notably in OPDM and OPML.
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