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Xu S, Wang N, Zuccaro MV, Gerhardt J, Iyyappan R, Scatolin GN, Jiang Z, Baslan T, Koren A, Egli D. DNA replication in early mammalian embryos is patterned, predisposing lamina-associated regions to fragility. Nat Commun 2024; 15:5247. [PMID: 38898078 PMCID: PMC11187207 DOI: 10.1038/s41467-024-49565-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 06/10/2024] [Indexed: 06/21/2024] Open
Abstract
DNA replication in differentiated cells follows a defined program, but when and how it is established during mammalian development is not known. Here we show using single-cell sequencing, that late replicating regions are established in association with the B compartment and the nuclear lamina from the first cell cycle after fertilization on both maternal and paternal genomes. Late replicating regions contain a relative paucity of active origins and few but long genes and low G/C content. In both bovine and mouse embryos, replication timing patterns are established prior to embryonic genome activation. Chromosome breaks, which form spontaneously in bovine embryos at sites concordant with human embryos, preferentially locate to late replicating regions. In mice, late replicating regions show enhanced fragility due to a sparsity of dormant origins that can be activated under conditions of replication stress. This pattern predisposes regions with long neuronal genes to fragility and genetic change prior to separation of soma and germ cell lineages. Our studies show that the segregation of early and late replicating regions is among the first layers of genome organization established after fertilization.
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Affiliation(s)
- Shuangyi Xu
- Division of Molecular Genetics, Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University, New York, NY, 10032, USA
| | - Ning Wang
- Division of Molecular Genetics, Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University, New York, NY, 10032, USA
| | - Michael V Zuccaro
- Division of Molecular Genetics, Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University, New York, NY, 10032, USA
- Graduate Program, Department of Cellular Physiology and Biophysics, Columbia University, New York, NY, USA
| | - Jeannine Gerhardt
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medical School, New York, NY, USA
| | - Rajan Iyyappan
- Department of Animal Sciences, Genetics Institute, University of Florida, Gainesville, FL, USA
| | | | - Zongliang Jiang
- Department of Animal Sciences, Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Timour Baslan
- Department of Biomedical Sciences, School of Veterinary Medicine, The University of Pennsylvania, Philadelphia, PA, USA
| | - Amnon Koren
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Dieter Egli
- Division of Molecular Genetics, Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University, New York, NY, 10032, USA.
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Columbia University, New York, NY, USA.
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Hattori N, Funayama M, Imai Y, Hatano T. Pathogenesis of Parkinson's disease: from hints from monogenic familial PD to biomarkers. J Neural Transm (Vienna) 2024; 131:709-719. [PMID: 38478097 DOI: 10.1007/s00702-024-02747-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 01/16/2024] [Indexed: 06/22/2024]
Abstract
Twenty-five years have passed since the causative gene for familial Parkinson's disease (PD), Parkin (now PRKN), was identified in 1998; PRKN is the most common causative gene in young-onset PD. Parkin encodes a ubiquitin-protein ligase, and Parkin is involved in mitophagy, a type of macroautophagy, in concert with PTEN-induced kinase 1 (PINK1). Both gene products are also involved in mitochondrial quality control. Among the many genetic PD-causing genes discovered, discovering PRKN as a cause of juvenile-onset PD has significantly impacted other neurodegenerative disorders. This is because the involvement of proteolytic systems has been suggested as a common mechanism in neurodegenerative diseases in which inclusion body formation is observed. The discovery of the participation of PRKN in PD has brought attention to the involvement of the proteolytic system in neurodegenerative diseases. Our research group has successfully isolated and identified CHCHD2, which is involved in the mitochondrial electron transfer system, and prosaposin (PSAP), which is involved in the lysosomal system, in this Parkin mechanism. Hereditary PD is undoubtedly an essential clue to solitary PD, and at least 25 or so genes and loci have been reported so far. This number of genes indicates that PD is a very diverse group of diseases. Currently, the diagnosis of PD is based on clinical symptoms and imaging studies. Although highly accurate diagnostic criteria have been published, early diagnosis is becoming increasingly important in treatment strategies for neurodegenerative diseases. Here, we also describe biomarkers that our group is working on.
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Affiliation(s)
- Nobutaka Hattori
- Department of Neurology, Faculty of Medicine, Juntendo University, 2-1-1 Hongo, Bunkyo, Tokyo, 113-8421, Japan.
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, 113-8421, Japan.
- Center for Genomic and Regenerative Medicine, Graduate School of Medicine, Juntendo University, Tokyo, 113-8421, Japan.
- Department of Research for Parkinson's Disease, Juntendo University Graduate School of Medicine, Tokyo, 113-8421, Japan.
- Neurodegenerative Disorders Collaborative Laboratory, RIKEN Center for Brain Science, 2-1-Hirosawa, Wako-shi, Saitama, 351-0198, Japan.
| | - Manabu Funayama
- Department of Neurology, Faculty of Medicine, Juntendo University, 2-1-1 Hongo, Bunkyo, Tokyo, 113-8421, Japan
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, 113-8421, Japan
- Center for Genomic and Regenerative Medicine, Graduate School of Medicine, Juntendo University, Tokyo, 113-8421, Japan
| | - Yuzuru Imai
- Department of Neurology, Faculty of Medicine, Juntendo University, 2-1-1 Hongo, Bunkyo, Tokyo, 113-8421, Japan
- Department of Research for Parkinson's Disease, Juntendo University Graduate School of Medicine, Tokyo, 113-8421, Japan
| | - Taku Hatano
- Department of Neurology, Faculty of Medicine, Juntendo University, 2-1-1 Hongo, Bunkyo, Tokyo, 113-8421, Japan
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Cogan G, Daida K, Billingsley KJ, Tesson C, Forlani S, Jornea L, Arnaud L, Tissier L, LeGuern E, Singleton AB, Ferrien M, Gervais Bernard H, Lesage S, Blauwendraat C, Brice A. Long-read sequencing unravels the complexity of structural variants in PRKN in two individuals with early-onset Parkinson's disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.02.24306523. [PMID: 38746197 PMCID: PMC11092742 DOI: 10.1101/2024.05.02.24306523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Background PRKN biallelic pathogenic variants are the most common cause of autosomal recessive early-onset Parkinson's disease (PD). However, the variants responsible for suspected PRKN- PD individuals are not always identified with standard genetic testing. Objectives Identify the genetic cause in two siblings with a PRKN -PD phenotype using long-read sequencing (LRS). Methods The genetic investigation involved standard testing using successively multiple ligation probe amplification (MLPA), Sanger sequencing, targeted sequencing, whole-exome sequencing and LRS. Results MLPA and targeted sequencing identified one copy of exon four in PRKN but no other variants were identified. Subsequently, LRS unveiled a large deletion encompassing exon 3 to 4 on one allele and a duplication of exon 3 on the second allele; explaining the siblings' phenotype. MLPA could not identify the balanced rearrangement of exon 3. Conclusions This study highlights the potential utility of long-read sequencing in the context of unsolved typical PRKN- PD individuals.
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4
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Irony-Tur Sinai M, Kerem B. Insights into common fragile site instability: DNA replication challenges at DNA repeat sequences. Emerg Top Life Sci 2023; 7:277-287. [PMID: 37876349 PMCID: PMC10754330 DOI: 10.1042/etls20230023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/08/2023] [Accepted: 10/12/2023] [Indexed: 10/26/2023]
Abstract
Common fragile sites (CFS) are specific genomic regions prone to chromosomal instability under conditions of DNA replication stress. CFSs manifest as breaks, gaps, and constrictions on metaphase chromosomes under mild replication stress. These replication-sensitive CFS regions are preferentially unstable during cancer development, as reflected by their association with copy number variants (CNVs) frequently arise in most tumor types. Over the years, it became clear that a combination of different characteristics underlies the enhanced sensitivity of CFSs to replication stress. As of today, there is a strong evidence that the core fragility regions along CFSs overlap with actively transcribed large genes with delayed replication timing upon replication stress. Recently, the mechanistic basis for CFS instability was further extended to regions which span topologically associated domain (TAD) boundaries, generating a fragility signature composed of replication, transcription and genome organization. The presence of difficult-to-replicate AT-rich repeats was one of the early features suggested to characterize a subgroup of CFSs. These long stretches of AT-dinucleotide have the potential to fold into stable secondary structures which may impede replication fork progression, leaving the region under-replicated. Here, we focus on the molecular mechanisms underlying repeat instability at CFSs and on the proteins involved in the resolution of secondary structure impediments arising along repetitive sequence elements which are essential for the maintenance of genome stability.
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Affiliation(s)
- Michal Irony-Tur Sinai
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Jerusalem, Israel
| | - Batsheva Kerem
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Jerusalem, Israel
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5
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Daida K, Funayama M, Billingsley KJ, Malik L, Miano-Burkhardt A, Leonard HL, Makarious MB, Iwaki H, Ding J, Gibbs JR, Ishiguro M, Yoshino H, Ogaki K, Oyama G, Nishioka K, Nonaka R, Akamatsu W, Blauwendraat C, Hattori N. Long-Read Sequencing Resolves a Complex Structural Variant in PRKN Parkinson's Disease. Mov Disord 2023; 38:2249-2257. [PMID: 37926948 PMCID: PMC10843047 DOI: 10.1002/mds.29610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/17/2023] [Accepted: 09/11/2023] [Indexed: 11/07/2023] Open
Abstract
BACKGROUND Parkin RBR E3 ubiquitin-protein ligase (PRKN) mutations are the most common cause of young onset and autosomal recessive Parkinson's disease (PD). PRKN is located in FRA6E, which is one of the common fragile sites in the human genome, making this region prone to structural variants. However, complex structural variants such as inversions of PRKN are seldom reported, suggesting that there are potentially unrevealed complex pathogenic PRKN structural variants. OBJECTIVES To identify complex structural variants in PRKN using long-read sequencing. METHODS We investigated the genetic cause of monozygotic twins presenting with a young onset dystonia-parkinsonism using targeted sequencing, whole exome sequencing, multiple ligation probe amplification, and long-read sequencing. We assessed the presence and frequency of complex inversions overlapping PRKN using whole-genome sequencing data of Accelerating Medicines Partnership Parkinson's disease (AMP-PD) and United Kingdom (UK)-Biobank datasets. RESULTS Multiple ligation probe amplification identified a heterozygous exon three deletion in PRKN and long-read sequencing identified a large novel inversion spanning over 7 Mb, including a large part of the coding DNA sequence of PRKN. We could diagnose the affected subjects as compound heterozygous carriers of PRKN. We analyzed whole genome sequencing data of 43,538 participants of the UK-Biobank and 4941 participants of the AMP-PD datasets. Nine inversions in the UK-Biobank and two in AMP PD were identified and were considered potentially damaging and likely to affect PRKN expression. CONCLUSIONS This is the first report describing a large 7 Mb inversion involving breakpoints outside of PRKN. This study highlights the importance of using long-read sequencing for structural variant analysis in unresolved young-onset PD cases. © 2023 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.
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Affiliation(s)
- Kensuke Daida
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Department of Neurology, Faculty of Medicine, Juntendo University, Hongo, Tokyo, Japan
| | - Manabu Funayama
- Department of Neurology, Faculty of Medicine, Juntendo University, Hongo, Tokyo, Japan
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Kimberley J Billingsley
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Laksh Malik
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Abigail Miano-Burkhardt
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Hampton L. Leonard
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International LLC, Washington, DC, USA
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Mary B. Makarious
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK, WC1N 3BG
- UCL Movement Disorders Centre, University College London, London, UK, WC1N 3BG
| | - Hirotaka Iwaki
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International LLC, Washington, DC, USA
| | - Jinhui Ding
- Computational Biology Group, Laboratory of Neurogenetics,National Institute on Aging, NIH, PorterNeuroscience ResearchCenter,Bethesda, MD, USA
| | - J. Raphael Gibbs
- Computational Biology Group, Laboratory of Neurogenetics,National Institute on Aging, NIH, PorterNeuroscience ResearchCenter,Bethesda, MD, USA
| | - Mayu Ishiguro
- Department of Neurology, Faculty of Medicine, Juntendo University, Hongo, Tokyo, Japan
| | - Hiroyo Yoshino
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Kotaro Ogaki
- Department of Neurology, Faculty of Medicine, Juntendo University, Hongo, Tokyo, Japan
| | - Genko Oyama
- Department of Neurology, Faculty of Medicine, Juntendo University, Hongo, Tokyo, Japan
| | - Kenya Nishioka
- Department of Neurology, Juntendo Tokyo Koto Geriatric Medical Center 3-3-20 Shinsuna, Koto-ku, Tokyo 136-0075
| | - Risa Nonaka
- Department of Neurology, Faculty of Medicine, Juntendo University, Hongo, Tokyo, Japan
- Department of Clinical Data of Parkinson’s Disease, Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Center for Genomic and Regenerative Medicine, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Wado Akamatsu
- Center for Genomic and Regenerative Medicine, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Cornelis Blauwendraat
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Nobutaka Hattori
- Department of Neurology, Faculty of Medicine, Juntendo University, Hongo, Tokyo, Japan
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Neurodegenerative Disorders Collaborative Laboratory, RIKEN Center for Brain Science, Wako, Saitama, Japan
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6
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Liang K, Guo Z, Zhang S, Chen D, Zou R, Weng Y, Peng C, Xu Z, Zhang J, Liu X, Pang X, Ji Y, Liao D, Lai M, Peng H, Ke Y, Wang Z, Wang Y. GPR37 expression as a prognostic marker in gliomas: a bioinformatics-based analysis. Aging (Albany NY) 2023; 15:10146-10167. [PMID: 37837549 PMCID: PMC10599758 DOI: 10.18632/aging.205063] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 08/21/2023] [Indexed: 10/16/2023]
Abstract
BACKGROUND Gliomas are the most frequently diagnosed primary brain tumors, and are associated with multiple molecular aberrations during their development and progression. GPR37 is an orphan G protein-coupled receptor (GPCR) that is implicated in different physiological pathways in the brain, and has been linked to various malignancies. The aim of this study was to explore the relationship between GPR37 gene expression and the clinicopathological factors, patient prognosis, tumor-infiltrating immune cell signature GSEA and methylation levels in glioma. METHODS We explored the diagnostic value, clinical relevance, and molecular function of GPR37 in glioma using TCGA, STRING, cBioPortal, Tumor Immunity Estimation Resource (TIMER) database and MethSurv databases. Besides, the "ssGSEA" algorithm was conducted to estimate immune cells infiltration abundance, with 'ggplot2' package visualizing the results. Immunohistochemical staining of clinical samples were used to verify the speculations of bioinformatics analysis. RESULTS GPR37 expression was significantly higher in the glioma tissues compared to the normal brain tissues, and was linked to poor prognosis. Functional annotation of GPR37 showed enrichment of ether lipid metabolism, fat digestion and absorption, and histidine metabolism. In addition, GSEA showed that GPR37 was positively correlated to the positive regulation of macrophage derived foam cell differentiation, negative regulation of T cell receptor signaling pathway, neuroactive ligand receptor interaction, calcium signaling pathway, and negatively associated with immunoglobulin complex, immunoglobulin complex circulating, ribosome and spliceosome mediated by circulating immunoglobulin etc. TIMER2.0 and ssGSEA showed that GPR37 expression was significantly associated with the infiltration of T cells, CD8 T cell, eosinophils, macrophages, neutrophils, NK CD56dim cells, NK cells, plasmacytoid DCs (pDCs), T helper cells and T effector memory (Tem) cells. In addition, high GPR37 expression was positively correlated with increased infiltration of M2 macrophages, which in turn was associated with poor prognosis. Furthermore, GPR37 was positively correlated with various immune checkpoints (ICPs). Finally, hypomethylation of the GPR37 promoter was associated with its high expression levels and poor prognosis in glioma. CONCLUSION GPR37 had diagnostic and prognostic value in glioma. The possible biological mechanisms of GPR37 provide novel insights into the clinical diagnosis and treatment of glioma.
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Affiliation(s)
- Kairong Liang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Zhaoxiong Guo
- Science and Technology Innovation Center, Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Shizhen Zhang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Danmin Chen
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Renheng Zou
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Yuhao Weng
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Chengxiang Peng
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Zhichao Xu
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Jingbai Zhang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Xiaorui Liu
- Department of Pharmacy, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou 510095, China
| | - Xiao Pang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Yunxiang Ji
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Degui Liao
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Miaoling Lai
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Huaidong Peng
- Department of Pharmacy, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Yanbin Ke
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Zhaotao Wang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Yezhong Wang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
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7
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Daida K, Funayama M, Billingsley KJ, Malik L, Miano-Burkhardt A, Leonard HL, Makarious MB, Iwaki H, Ding J, Gibbs JR, Ishiguro M, Yoshino H, Ogaki K, Oyama G, Nishioka K, Nonaka R, Akamatsu W, Blauwendraat C, Hattori N. Long-read sequencing resolves a complex structural variant in PRKN Parkinson's disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.14.23293948. [PMID: 37790330 PMCID: PMC10543050 DOI: 10.1101/2023.08.14.23293948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Background PRKN mutations are the most common cause of young onset and autosomal recessive Parkinson's disease (PD). PRKN is located in FRA6E which is one of the common fragile sites in the human genome, making this region prone to structural variants. However, complex structural variants such as inversions of PRKN are seldom reported, suggesting that there are potentially unrevealed complex pathogenic PRKN structural variants. Objectives To identify complex structural variants in PRKN using long-read sequencing. Methods We investigated the genetic cause of monozygotic twins presenting with a young onset dystonia-parkinsonism using targeted sequencing, whole exome sequencing, multiple ligation probe amplification, and long-read. We assessed the presence and frequency of complex inversions overlapping PRKN using whole-genome sequencing data of AMP-PD and UK-Biobank datasets. Results Multiple ligation probe amplification identified a heterozygous exon 3 deletion in PRKN and long-read sequencing identified a large novel inversion spanning over 7Mb, including a large part of the coding DNA sequence of PRKN. We could diagnose the affected subjects as compound heterozygous carriers of PRKN. We analyzed whole genome sequencing data of 43,538 participants of the UK-Biobank and 4,941 participants of the AMP-PD datasets. Nine inversions in the UK-Biobank and two in AMP PD were identified and were considered potentially damaging and likely to affect PRKN isoforms. Conclusions This is the first report describing a large 7Mb inversion involving breakpoints outside of PRKN. This study highlights the importance of using long-read whole genome sequencing for structural variant analysis in unresolved young-onset PD cases.
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Affiliation(s)
- Kensuke Daida
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
| | - Manabu Funayama
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Kimberley J Billingsley
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Laksh Malik
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Abigail Miano-Burkhardt
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Hampton L. Leonard
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International LLC, Washington, DC, USA
- German Center for Neurodegenerative Diseases (DZNE), Tubingen, Germany
| | - Mary B. Makarious
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK, WC1N 3BG
- UCL Movement Disorders Centre, University College London, London, UK, WC1N 3BG
| | - Hirotaka Iwaki
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International LLC, Washington, DC, USA
| | - Jinhui Ding
- BiocomputationalGroup, Laboratory of Neurogenetics,National Institute on Aging, NIH, PorterNeuroscience ResearchCenter,Bethesda, MD, USA
| | - J. Raphael Gibbs
- BiocomputationalGroup, Laboratory of Neurogenetics,National Institute on Aging, NIH, PorterNeuroscience ResearchCenter,Bethesda, MD, USA
| | - Mayu Ishiguro
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
| | - Hiroyo Yoshino
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Kotaro Ogaki
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
| | - Genko Oyama
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
| | - Kenya Nishioka
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
| | - Risa Nonaka
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
- Department of Clinical Data of Parkinson’s Disease, Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Center for Genomic and Regenerative Medicine, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Wado Akamatsu
- Center for Genomic and Regenerative Medicine, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Cornelis Blauwendraat
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Nobutaka Hattori
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Neurodegenerative Disorders Collaborative Laboratory, RIKEN Center for Brain Science, Wako, Saitama, Japan
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Kislova AV, Zheglo D, Pozhitnova VO, Sviridov PS, Gadzhieva EP, Voronina ES. Replication stress causes delayed mitotic entry and chromosome 12 fragility at the ANKS1B large neuronal gene in human induced pluripotent stem cells. Chromosome Res 2023; 31:23. [PMID: 37597021 DOI: 10.1007/s10577-023-09729-5] [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: 04/05/2023] [Revised: 07/10/2023] [Accepted: 07/19/2023] [Indexed: 08/21/2023]
Abstract
Substantial background level of replication stress is a feature of embryonic and induced pluripotent stem cells (iPSCs), which can predispose to numerical and structural chromosomal instability, including recurrent aberrations of chromosome 12. In differentiated cells, replication stress-sensitive genomic regions, including common fragile sites, are widely mapped through mitotic chromosome break induction by mild aphidicolin treatment, an inhibitor of replicative polymerases. IPSCs exhibit lower apoptotic threshold and higher repair capacity hindering fragile site mapping. Caffeine potentiates genotoxic effects and abrogates G2/M checkpoint delay induced by chemical and physical mutagens. Using 5-ethynyl-2'-deoxyuridine (EdU) for replication labeling, we characterized the mitotic entry dynamics of asynchronous iPSCs exposed to aphidicolin and/or caffeine. Under the adjusted timing of replication stress exposure accounting revealed cell cycle delay, higher metaphase chromosome breakage rate was observed in iPSCs compared to primary lymphocytes. Using differential chromosome staining and subsequent locus-specific fluorescent in situ hybridization, we mapped the FRA12L fragile site spanning the large neuronal ANKS1B gene at 12q23.1, which may contribute to recurrent chromosome 12 missegregation and rearrangements in iPSCs. Publicly available data on the ANKS1B genetic alterations and their possible functional impact are reviewed. Our study provides the first evidence of common fragile site induction in iPSCs and reveals potential somatic instability of a clinically relevant gene during early human development and in vitro cell expansion.
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Affiliation(s)
| | - Diana Zheglo
- Laboratory of Mutagenesis, Research Centre for Medical Genetics, Moscow, Russia.
| | | | - Philipp S Sviridov
- Laboratory of Mutagenesis, Research Centre for Medical Genetics, Moscow, Russia
| | - Elmira P Gadzhieva
- Laboratory of Mutagenesis, Research Centre for Medical Genetics, Moscow, Russia
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9
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Bakhit Y, Tesson C, Ibrahim MO, Eltom K, Eltazi I, Elsayed LE, Lesage S, Seidi O, Corvol J, Wüllner U. PLA2G6-associated late-onset parkinsonism in a Sudanese family. Ann Clin Transl Neurol 2023; 10:983-989. [PMID: 37139542 PMCID: PMC10270271 DOI: 10.1002/acn3.51781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 02/25/2023] [Accepted: 03/27/2023] [Indexed: 05/05/2023] Open
Abstract
INTRODUCTION The phospholipase A2 group VI gene (PLA2G6) encodes an enzyme that catalyzes the hydrolytic release of fatty acids from phospholipids. Four neurological disorders with infantile, juvenile, or early adult-onset are associated with PLA2G6 genetic alterations, namely infantile neuroaxonal dystrophy (INAD), atypical neuroaxonal dystrophy (ANAD), dystonia-parkinsonism (DP), and autosomal recessive early-onset parkinsonism (AREP). Few studies in Africa reported PLA2G6-associated disorders and none with parkinsonism of late adult onset. MATERIAL AND METHODS The patients were clinically assessed following UK Brain Bank diagnostic criteria and International Parkinson and Movement Disorder Society's Unified Parkinson's Disease Rating Scale (MDS-UPDRS). Brain MRI without contrast was performed. Genetic testing was done using a custom-made Twist panel, screening 34 known genes, 27 risk factors, and 8 candidate genes associated with parkinsonism. Filtered variants were PCR-amplified and validated using Sanger sequencing and also tested in additional family members to study their segregation. RESULT Two siblings born to consanguineous parents developed parkinsonism at the age of 58 and 60 years, respectively. MRI showed an enlarged right hippocampus in patient 2, but no overt abnormalities indicative of INAD or iron deposits. We found two heterozygous variants in PLA2G6, an in-frame deletion NM_003560:c.2070_2072del (p.Val691del) and a missense variant NM_003560:c.956C>T (p.Thr319Met). Both variants were classified as pathogenic. CONCLUSION This is the first case in which PLA2G6 is associated with late-onset parkinsonism. Functional analysis is needed to confirm the dual effect of both variants on the structure and function of iPLA2β.
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Affiliation(s)
- Yousuf Bakhit
- Department of NeurologyUniversity Hospital BonnBonnGermany
- Department of Basic Medical Sciences, Faculty of DentistryUniversity of KhartoumKhartoumSudan
- Sudan Neuroscience ProjectsUniversity of KhartoumKhartoumSudan
| | - Christelle Tesson
- Assistance Publique Hôpitaux de Paris, Department of Neurology, Pitié‐Salpêtrière HospitalSorbonne Université, Paris Brain Institute – ICM, Inserm, CNRSParisFrance
| | - Mohamed O. Ibrahim
- Sudan Neuroscience ProjectsUniversity of KhartoumKhartoumSudan
- Department of Biochemistry, Faculty of MedicineSudan University of Science and TechnologyKhartoumSudan
| | - Khalid Eltom
- Sudan Neuroscience ProjectsUniversity of KhartoumKhartoumSudan
- Department of Medical Cell Biology, Uppsala Biomedical CenterUppsala UniversityUppsalaSweden
| | - Isra Eltazi
- Department of Neurology, Soba Teaching Hospital, And Department of Medicine, Faculty of MedicineUniversity of KhartoumKhartoumSudan
| | - Liena E.O. Elsayed
- Department of Basic Sciences, College of MedicinePrincess Nourah bint Abdulrahman UniversityRiyadhSaudi Arabia
| | - Suzanne Lesage
- Assistance Publique Hôpitaux de Paris, Department of Neurology, Pitié‐Salpêtrière HospitalSorbonne Université, Paris Brain Institute – ICM, Inserm, CNRSParisFrance
| | - Osheik Seidi
- Department of Neurology, Soba Teaching Hospital, And Department of Medicine, Faculty of MedicineUniversity of KhartoumKhartoumSudan
| | - Jean‐Christophe Corvol
- Assistance Publique Hôpitaux de Paris, Department of Neurology, Pitié‐Salpêtrière HospitalSorbonne Université, Paris Brain Institute – ICM, Inserm, CNRSParisFrance
| | - Ullrich Wüllner
- Department of NeurologyUniversity Hospital BonnBonnGermany
- German Center for Neurodegenerative Diseases (DZNE)BonnGermany
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10
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Smith J, Barnett E, Rodger EJ, Chatterjee A, Subramaniam RM. Neuroendocrine Neoplasms: Genetics and Epigenetics. PET Clin 2023; 18:169-187. [PMID: 36858744 DOI: 10.1016/j.cpet.2022.11.003] [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] [Indexed: 03/02/2023]
Abstract
Neuroendocrine neoplasms (NENs) are a group of rare, heterogeneous tumors of neuroendocrine cell origin, affecting a range of different organs. The clinical management of NENs poses significant challenges, as tumors are often diagnosed at an advanced stage where overall survival remains poor with current treatment regimens. In addition, a host of complex and often unique molecular changes underpin the pathobiology of each NEN subtype. Exploitation of the unique genetic and epigenetic signatures driving each NEN subtype provides an opportunity to enhance the diagnosis, treatment, and monitoring of NEN in an emerging era of individualized medicine.
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Affiliation(s)
- Jim Smith
- Department of Pathology, Dunedin School of Medicine, University of Otago, PO Box 56, Dunedin 9054, New Zealand; Te Whatu Ora - Southern, Dunedin Public Hospital, 270 Great King Street, PO Box 913, Dunedin, New Zealand.
| | - Edward Barnett
- Department of Pathology, Dunedin School of Medicine, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Euan J Rodger
- Department of Pathology, Dunedin School of Medicine, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Rathan M Subramaniam
- Department of Medicine, Otago Medical School, University of Otago, PO Box 56, Dunedin 9054, New Zealand; Department of Radiology, Duke University, 2301 Erwin Rd, BOX 3808, Durham, NC 27705, USA
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11
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Aksoy Yasar FB, Shingu T, Zamler DB, Zaman MF, Chien DL, Zhang Q, Ren J, Hu J. Quaking but not parkin is the major tumor suppressor in 6q deleted region in glioblastoma. Front Cell Dev Biol 2022; 10:931387. [PMID: 36051438 PMCID: PMC9424994 DOI: 10.3389/fcell.2022.931387] [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: 04/28/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Glioblastoma (GBM) is a high-grade, aggressive brain tumor with dismal median survival time of 15 months. Chromosome 6q (Ch6q) is a hotspot of genomic alterations, which is commonly deleted or hyper-methylated in GBM. Two neighboring genes in this region, QKI and PRKN have been appointed as tumor suppressors in GBM. While a genetically modified mouse model (GEMM) of GBM has been successfully generated with Qk deletion in the central nervous system (CNS), in vivo genetic evidence supporting the tumor suppressor function of Prkn has not been established. In the present study, we generated a mouse model with Prkn-null allele and conditional Trp53 and Pten deletions in the neural stem cells (NSCs) and compared the tumorigenicity of this model to our previous GBM model with Qk deletion within the same system. We find that Qk but not Prkn is the potent tumor suppressor in the frequently altered Ch6q region in GBM.
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Affiliation(s)
- Fatma Betul Aksoy Yasar
- Department of Cancer Biology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
| | - Takashi Shingu
- Department of Cancer Biology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
| | - Daniel B. Zamler
- Department of Cancer Biology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Mohammad Fayyad Zaman
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
| | - Derek Lin Chien
- School of Arts and Sciences, University of Rochester, Rochester, NY, United States
| | - Qiang Zhang
- Department of Cancer Biology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
| | - Jiangong Ren
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Jian Hu
- Department of Cancer Biology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
- *Correspondence: Jian Hu,
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12
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Waldrop MA, Moore SA, Mathews KD, Darbro BW, Medne L, Finkel R, Connolly AM, Crawford TO, Drachman D, Wein N, Habib AA, Krzesniak-Swinarska MA, Zaidman CM, Collins JJ, Jokela M, Udd B, Day JW, Ortiz-Guerrero G, Statland J, Butterfield RJ, Dunn DM, Weiss RB, Flanigan KM. Intron mutations and early transcription termination in Duchenne and Becker muscular dystrophy. Hum Mutat 2022; 43:511-528. [PMID: 35165973 PMCID: PMC9901284 DOI: 10.1002/humu.24343] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 02/05/2022] [Accepted: 02/07/2022] [Indexed: 11/11/2022]
Abstract
DMD pathogenic variants for Duchenne and Becker muscular dystrophy are detectable with high sensitivity by standard clinical exome analyses of genomic DNA. However, up to 7% of DMD mutations are deep intronic and analysis of muscle-derived RNA is an important diagnostic step for patients who have negative genomic testing but abnormal dystrophin expression in muscle. In this study, muscle biopsies were evaluated from 19 patients with clinical features of a dystrophinopathy, but negative clinical DMD mutation analysis. Reverse transcription-polymerase chain reaction or high-throughput RNA sequencing methods identified 19 mutations with one of three pathogenic pseudoexon types: deep intronic point mutations, deletions or insertions, and translocations. In association with point mutations creating intronic splice acceptor sites, we observed the first examples of DMD pseudo 3'-terminal exon mutations causing high efficiency transcription termination within introns. This connection between splicing and premature transcription termination is reminiscent of U1 snRNP-mediating telescripting in sustaining RNA polymerase II elongation across large genes, such as DMD. We propose a novel classification of three distinct types of mutations identifiable by muscle RNA analysis, each of which differ in potential treatment approaches. Recognition and appropriate characterization may lead to therapies directed toward full-length dystrophin expression for some patients.
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Affiliation(s)
- Megan A. Waldrop
- The Center for Gene Therapy, Nationwide Children’s Hospital, Columbus, OH 43205,Department of Neurology, The Ohio State University, Columbus, OH 43205,Department of Pediatrics, The Ohio State University, Columbus, OH 43205
| | - Steven A. Moore
- Department of Pathology, The University of Iowa, Iowa City, IA, 52242
| | | | | | - Livja Medne
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | | | - Anne M. Connolly
- Department of Neurology, Washington University, Saint Louis, MO 63110
| | | | | | - Nicolas Wein
- The Center for Gene Therapy, Nationwide Children’s Hospital, Columbus, OH 43205
| | | | | | - Craig M. Zaidman
- Department of Neurology, Washington University, Saint Louis, MO 63110
| | - James J. Collins
- Department of Pediatric Neurology, Mercy Hospitals, Springfield, MO 65804
| | - Manu Jokela
- Neuromuscular Research Center, Tampere University Hospital and University of Tampere, Tampere, Finland,Division of Clinical Neurosciences, Turku University Hospital and University of Turku, Turku, Finland
| | - Bjarne Udd
- Neuromuscular Research Center, Tampere University Hospital and University of Tampere, Tampere, Finland
| | - John W. Day
- Department of Neurology, University of Minnesota Medical Center, Minneapolis, MN 55454
| | | | - Jeff Statland
- Department of Neurology, University of Kansas, Kansas City, KS
| | - Russell J. Butterfield
- Department of Pediatrics, The University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Diane M. Dunn
- Department of Human Genetics, The University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Robert B. Weiss
- Department of Pediatrics, The University of Utah School of Medicine, Salt Lake City, UT 84112,Department of Human Genetics, The University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Kevin M. Flanigan
- The Center for Gene Therapy, Nationwide Children’s Hospital, Columbus, OH 43205,Department of Neurology, The Ohio State University, Columbus, OH 43205,Department of Pediatrics, The Ohio State University, Columbus, OH 43205
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13
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DMD exon 2 duplication due to a complex genomic rearrangement is associated with a somatic mosaicism. Neuromuscul Disord 2021; 32:263-269. [DOI: 10.1016/j.nmd.2021.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 11/24/2021] [Accepted: 12/13/2021] [Indexed: 12/23/2022]
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14
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Mor-Shaked H, Paz-Ebstein E, Basal A, Ben-Haim S, Grobe H, Heymann S, Israel Z, Namnah M, Nitzan A, Rosenbluh C, Saada A, Tzur T, Yanovsky-Dagan S, Zaidel-Bar R, Harel T, Arkadir D. Levodopa-responsive dystonia caused by biallelic PRKN exon inversion invisible to exome sequencing. Brain Commun 2021; 3:fcab197. [PMID: 34514401 PMCID: PMC8421701 DOI: 10.1093/braincomms/fcab197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/20/2021] [Accepted: 07/05/2021] [Indexed: 11/23/2022] Open
Abstract
Biallelic pathogenic variants in PRKN (PARK2), encoding the E3 ubiquitin ligase parkin, lead to early-onset Parkinson's disease. Structural variants, including duplications or deletions, are common in PRKN due to their location within the fragile site FRA6E. These variants are readily detectable by copy number variation analysis. We studied four siblings with levodopa-responsive dystonia by exome sequencing followed by genome sequencing. Affected individuals developed juvenile levodopa-responsive dystonia with subsequent appearance of parkinsonism and motor fluctuations that improved by subthalamic stimulation. Exome sequencing and copy number variation analysis were not diagnostic, yet revealed a shared homozygous block including PRKN. Genome sequencing revealed an inversion within PRKN, with intronic breakpoints flanking exon 5. Breakpoint junction analysis implicated non-homologous end joining and possibly replicative mechanisms as the repair pathways involved. Analysis of cDNA indicated skipping of exon 5 (84 bp) that was replaced by 93 bp of retained intronic sequence, preserving the reading frame yet altering a significant number of residues. Balanced copy number inversions in PRKN are associated with a severe phenotype. Such structural variants, undetected by exome analysis and by copy number variation analysis, should be considered in the relevant clinical setting. These findings raise the possibility that PRKN structural variants are more common than currently estimated.
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Affiliation(s)
- Hagar Mor-Shaked
- Department of Genetics, Hadassah Medical Organization, Jerusalem 91120, Israel.,Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Emuna Paz-Ebstein
- Department of Genetics, Hadassah Medical Organization, Jerusalem 91120, Israel.,Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Adily Basal
- Department of Genetics, Hadassah Medical Organization, Jerusalem 91120, Israel
| | - Simona Ben-Haim
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel.,Department of Nuclear Medicine, Hadassah Medical Organization, Jerusalem 91120, Israel.,Institute of Nuclear Medicine, University College London and UCL Hospitals, NHS Trust, London NW1 2BU, UK
| | - Hanna Grobe
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo 69978, Israel
| | - Sami Heymann
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel.,Department of Neurosurgery, Hadassah Medical Organization, Jerusalem 91120, Israel
| | - Zvi Israel
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel.,Department of Neurosurgery, Hadassah Medical Organization, Jerusalem 91120, Israel
| | - Montaser Namnah
- Department of Neurology, Hadassah Medical Organization, Jerusalem 91120, Israel
| | - Anat Nitzan
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo 69978, Israel
| | - Chaggai Rosenbluh
- Department of Genetics, Hadassah Medical Organization, Jerusalem 91120, Israel
| | - Ann Saada
- Department of Genetics, Hadassah Medical Organization, Jerusalem 91120, Israel.,Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Tomer Tzur
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel.,Department of Plastic Surgery, Hadassah Medical Organization, Jerusalem 91120, Israel
| | | | - Ronen Zaidel-Bar
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo 69978, Israel
| | - Tamar Harel
- Department of Genetics, Hadassah Medical Organization, Jerusalem 91120, Israel.,Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - David Arkadir
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel.,Department of Neurology, Hadassah Medical Organization, Jerusalem 91120, Israel
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15
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Rasnic R, Linial M. Chromoanagenesis Landscape in 10,000 TCGA Patients. Cancers (Basel) 2021; 13:4197. [PMID: 34439350 PMCID: PMC8392194 DOI: 10.3390/cancers13164197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/14/2021] [Accepted: 08/17/2021] [Indexed: 11/17/2022] Open
Abstract
During the past decade, whole-genome sequencing of tumor biopsies and individuals with congenital disorders highlighted the phenomenon of chromoanagenesis, a single chaotic event of chromosomal rearrangement. Chromoanagenesis was shown to be frequent in many types of cancers, to occur in early stages of cancer development, and significantly impact the tumor's nature. However, an in-depth, cancer-type dependent analysis has been somewhat incomplete due to the shortage in whole genome sequencing of cancerous samples. In this study, we extracted data from The Pan-Cancer Analysis of Whole Genome (PCAWG) and The Cancer Genome Atlas (TCGA) to construct and test a machine learning algorithm that can detect chromoanagenesis with high accuracy (86%). The algorithm was applied to ~10,000 unlabeled TCGA cancer patients. We utilize the chromoanagenesis assignment results, to analyze cancer-type specific chromoanagenesis characteristics in 20 TCGA cancer types. Our results unveil prominent genes affected in either chromoanagenesis or non-chromoanagenesis tumorigenesis. The analysis reveals a mutual exclusivity relationship between the genes impaired in chromoanagenesis versus non-chromoanagenesis cases. We offer the discovered characteristics as possible targets for cancer diagnostic and therapeutic purposes.
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Affiliation(s)
- Roni Rasnic
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Michal Linial
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel;
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16
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van Riet J, van de Werken HJG, Cuppen E, Eskens FALM, Tesselaar M, van Veenendaal LM, Klümpen HJ, Dercksen MW, Valk GD, Lolkema MP, Sleijfer S, Mostert B. The genomic landscape of 85 advanced neuroendocrine neoplasms reveals subtype-heterogeneity and potential therapeutic targets. Nat Commun 2021; 12:4612. [PMID: 34326338 PMCID: PMC8322054 DOI: 10.1038/s41467-021-24812-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 07/01/2021] [Indexed: 02/07/2023] Open
Abstract
Metastatic and locally-advanced neuroendocrine neoplasms (aNEN) form clinically and genetically heterogeneous malignancies, characterized by distinct prognoses based upon primary tumor localization, functionality, grade, proliferation index and diverse outcomes to treatment. Here, we report the mutational landscape of 85 whole-genome sequenced aNEN. This landscape reveals distinct genomic subpopulations of aNEN based on primary localization and differentiation grade; we observe relatively high tumor mutational burdens (TMB) in neuroendocrine carcinoma (average 5.45 somatic mutations per megabase) with TP53, KRAS, RB1, CSMD3, APC, CSMD1, LRATD2, TRRAP and MYC as major drivers versus an overall low TMB in neuroendocrine tumors (1.09). Furthermore, we observe distinct drivers which are enriched in somatic aberrations in pancreatic (MEN1, ATRX, DAXX, DMD and CREBBP) and midgut-derived neuroendocrine tumors (CDKN1B). Finally, 49% of aNEN patients reveal potential therapeutic targets based upon actionable (and responsive) somatic aberrations within their genome; potentially directing improvements in aNEN treatment strategies.
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Affiliation(s)
- Job van Riet
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, the Netherlands
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, the Netherlands
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Harmen J G van de Werken
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, the Netherlands.
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, the Netherlands.
| | - Edwin Cuppen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, the Netherlands
- Hartwig Medical Foundation, Amsterdam, the Netherlands
| | - Ferry A L M Eskens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Margot Tesselaar
- Department of Medical Oncology, Cancer Institute, University of Amsterdam, Amsterdam, The Netherlands
| | - Linde M van Veenendaal
- Department of Medical Oncology, Cancer Institute, University of Amsterdam, Amsterdam, The Netherlands
| | - Heinz-Josef Klümpen
- Department of Medical Oncology, Amsterdam University Medical Centers, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Marcus W Dercksen
- Department of Internal Medicine, Maxima Medisch Centrum, Veldhoven, The Netherlands
| | - Gerlof D Valk
- Department of Endocrine Oncology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Martijn P Lolkema
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
- Center for Personalized Cancer Treatment, Rotterdam, the Netherlands
| | - Stefan Sleijfer
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
- Center for Personalized Cancer Treatment, Rotterdam, the Netherlands
| | - Bianca Mostert
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.
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17
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Artemyeva-Isman OV, Porter ACG. U5 snRNA Interactions With Exons Ensure Splicing Precision. Front Genet 2021; 12:676971. [PMID: 34276781 PMCID: PMC8283771 DOI: 10.3389/fgene.2021.676971] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/12/2021] [Indexed: 11/13/2022] Open
Abstract
Imperfect conservation of human pre-mRNA splice sites is necessary to produce alternative isoforms. This flexibility is combined with the precision of the message reading frame. Apart from intron-termini GU_AG and the branchpoint A, the most conserved are the exon-end guanine and +5G of the intron start. Association between these guanines cannot be explained solely by base-pairing with U1 snRNA in the early spliceosome complex. U6 succeeds U1 and pairs +5G in the pre-catalytic spliceosome, while U5 binds the exon end. Current U5 snRNA reconstructions by CryoEM cannot explain the conservation of the exon-end G. Conversely, human mutation analyses show that guanines of both exon termini can suppress splicing mutations. Our U5 hypothesis explains the mechanism of splicing precision and the role of these conserved guanines in the pre-catalytic spliceosome. We propose: (1) optimal binding register for human exons and U5-the exon junction positioned at U5Loop1 C39|C38; (2) common mechanism for base-pairing of human U5 snRNA with diverse exons and bacterial Ll.LtrB intron with new loci in retrotransposition-guided by base pair geometry; and (3) U5 plays a significant role in specific exon recognition in the pre-catalytic spliceosome. Statistical analyses showed increased U5 Watson-Crick pairs with the 5'exon in the absence of +5G at the intron start. In 5'exon positions -3 and -5, this effect is specific to U5 snRNA rather than U1 snRNA of the early spliceosome. Increased U5 Watson-Crick pairs with 3'exon position +1 coincide with substitutions of the conserved -3C at the intron 3'end. Based on mutation and X-ray evidence, we propose that -3C pairs with U2 G31 juxtaposing the branchpoint and the 3'intron end. The intron-termini pair, formed in the pre-catalytic spliceosome to be ready for transition after branching, and the early involvement of the 3'intron end ensure that the 3'exon contacts U5 in the pre-catalytic complex. We suggest that splicing precision is safeguarded cooperatively by U5, U6, and U2 snRNAs that stabilize the pre-catalytic complex by Watson-Crick base pairing. In addition, our new U5 model explains the splicing effect of exon-start +1G mutations: U5 Watson-Crick pairs with exon +2C/+3G strongly promote exon inclusion. We discuss potential applications for snRNA therapeutics and gene repair by reverse splicing.
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Affiliation(s)
- Olga V Artemyeva-Isman
- Gene Targeting Group, Centre for Haematology, Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Andrew C G Porter
- Gene Targeting Group, Centre for Haematology, Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, United Kingdom
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18
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Paul S, Pickrell AM. Hidden phenotypes of PINK1/Parkin knockout mice. Biochim Biophys Acta Gen Subj 2021; 1865:129871. [PMID: 33571581 DOI: 10.1016/j.bbagen.2021.129871] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/26/2021] [Accepted: 02/05/2021] [Indexed: 12/26/2022]
Abstract
PINK1, a serine/threonine ubiquitin kinase, and Parkin, an E3 ubiquitin ligase, work in coordination to target damaged mitochondria to the lysosome in a process called mitophagy. This review will cover what we have learned from PINK1 and Parkin knockout (KO) mice. Systemic PINK1 and Parkin KO mouse models haven't faithfully recapitulated early onset forms of Parkinson's disease found in humans with recessive mutations in these genes. However, the utilization of these mouse models has given us insight into how PINK1 and Parkin contribute to mitochondrial quality control and function in different tissues beyond the brain such as in heart and adipose tissue. Although PINK1 and Parkin KO mice have been generated over a decade ago, these models are still being used today to creatively elucidate cell-type specific functions. Recently, these mouse models have uncovered that these proteins contribute to innate immunity and cancer phenotypes.
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Affiliation(s)
- Swagatika Paul
- Graduate Studies in Biomedical and Veterinary Sciences, Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA 24601, USA; School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Alicia M Pickrell
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
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19
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Jones L, Naidoo M, Machado LR, Anthony K. The Duchenne muscular dystrophy gene and cancer. Cell Oncol (Dordr) 2021; 44:19-32. [PMID: 33188621 PMCID: PMC7906933 DOI: 10.1007/s13402-020-00572-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Mutation of the Duchenne muscular dystrophy (DMD) gene causes Duchenne and Becker muscular dystrophy, degenerative neuromuscular disorders that primarily affect voluntary muscles. However, increasing evidence implicates DMD in the development of all major cancer types. DMD is a large gene with 79 exons that codes for the essential muscle protein dystrophin. Alternative promotor usage drives the production of several additional dystrophin protein products with roles that extend beyond skeletal muscle. The importance and function(s) of these gene products outside of muscle are not well understood. CONCLUSIONS We highlight a clear role for DMD in the pathogenesis of several cancers, including sarcomas, leukaemia's, lymphomas, nervous system tumours, melanomas and various carcinomas. We note that the normal balance of DMD gene products is often disrupted in cancer. The short dystrophin protein Dp71 is, for example, typically maintained in cancer whilst the full-length Dp427 gene product, a likely tumour suppressor, is frequently inactivated in cancer due to a recurrent loss of 5' exons. Therefore, the ratio of short and long gene products may be important in tumorigenesis. In this review, we summarise the tumours in which DMD is implicated and provide a hypothesis for possible mechanisms of tumorigenesis, although the question of cause or effect may remain. We hope to stimulate further study into the potential role of DMD gene products in cancer and the development of novel therapeutics that target DMD.
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Affiliation(s)
- Leanne Jones
- Centre for Physical Activity and Life Sciences, University of Northampton, University Drive, Northampton, NN1 5PH, UK
| | - Michael Naidoo
- Centre for Physical Activity and Life Sciences, University of Northampton, University Drive, Northampton, NN1 5PH, UK
| | - Lee R Machado
- Centre for Physical Activity and Life Sciences, University of Northampton, University Drive, Northampton, NN1 5PH, UK
- Department of Genetics and Genome Science, University of Leicester, LE1 7RH, Leicester, UK
| | - Karen Anthony
- Centre for Physical Activity and Life Sciences, University of Northampton, University Drive, Northampton, NN1 5PH, UK.
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20
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Sarraf SA, Sideris DP, Giagtzoglou N, Ni L, Kankel MW, Sen A, Bochicchio LE, Huang CH, Nussenzweig SC, Worley SH, Morton PD, Artavanis-Tsakonas S, Youle RJ, Pickrell AM. PINK1/Parkin Influences Cell Cycle by Sequestering TBK1 at Damaged Mitochondria, Inhibiting Mitosis. Cell Rep 2020; 29:225-235.e5. [PMID: 31577952 PMCID: PMC6880866 DOI: 10.1016/j.celrep.2019.08.085] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 05/13/2019] [Accepted: 08/27/2019] [Indexed: 12/21/2022] Open
Abstract
PINK1 and Parkin are established mediators of mitophagy, the selective removal of damaged mitochondria by autophagy. PINK1 and Parkin have been proposed to act as tumor suppressors, as loss-of-function mutations are correlated with enhanced tumorigenesis. However, it is unclear how PINK1 and Parkin act in coordination during mitophagy to influence the cell cycle. Here we show that PINK1 and Parkin genetically interact with proteins involved in cell cycle regulation, and loss of PINK1 and Parkin accelerates cell growth. PINK1- and Parkin-mediated activation of TBK1 at the mitochondria during mitophagy leads to a block in mitosis due to the sequestration of TBK1 from its physiological role at centrosomes during mitosis. Our study supports a diverse role for the far-reaching, regulatory effects of mitochondrial quality control in cellular homeostasis and demonstrates that the PINK1/Parkin pathway genetically interacts with the cell cycle, providing a framework for understanding the molecular basis linking PINK1 and Parkin to mitosis. Sarraf et al. use mouse and fly genetics to discover that PINK1 and Parkin influence cell cycle progression. Mitophagy and mitosis independently activate TBK1 at damaged mitochondria and centrosomes, respectively, influencing whether the cell will address mitochondrial quality control or progress with proliferation.
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Affiliation(s)
- Shireen A Sarraf
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD 20892, USA
| | - Dionisia P Sideris
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD 20892, USA
| | | | - Lina Ni
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Mark W Kankel
- Neuromuscular & Movement Disorders, Biogen, Inc., Cambridge, MA 02142, USA
| | - Anindya Sen
- Pathway Discovery Laboratory, Biogen, Inc., Cambridge, MA 02142, USA
| | - Lauren E Bochicchio
- Translational Biology, Medicine, and Health Graduate Program, Virginia Polytechnic Institute and State University, Roanoke, VA 24016, USA
| | - Chiu-Hui Huang
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD 20892, USA
| | - Samuel C Nussenzweig
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD 20892, USA
| | - Stuart H Worley
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Paul D Morton
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Spyros Artavanis-Tsakonas
- Pathway Discovery Laboratory, Biogen, Inc., Cambridge, MA 02142, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Richard J Youle
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD 20892, USA
| | - Alicia M Pickrell
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD 20892, USA; School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
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21
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Impaired Replication Timing Promotes Tissue-Specific Expression of Common Fragile Sites. Genes (Basel) 2020; 11:genes11030326. [PMID: 32204553 PMCID: PMC7140878 DOI: 10.3390/genes11030326] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 02/27/2020] [Accepted: 03/06/2020] [Indexed: 12/24/2022] Open
Abstract
Common fragile sites (CFSs) are particularly vulnerable regions of the genome that become visible as breaks, gaps, or constrictions on metaphase chromosomes when cells are under replicative stress. Impairment in DNA replication, late replication timing, enrichment of A/T nucleotides that tend to form secondary structures, the paucity of active or inducible replication origins, the generation of R-loops, and the collision between replication and transcription machineries on particularly long genes are some of the reported characteristics of CFSs that may contribute to their tissue-specific fragility. Here, we validated the induction of two CFSs previously found in the human fetal lung fibroblast line, Medical Research Council cell strain 5 (MRC-5), in another cell line derived from the same fetal tissue, Institute for Medical Research-90 cells (IMR-90). After induction of CFSs through aphidicolin, we confirmed the expression of the CFS 1p31.1 on chromosome 1 and CFS 3q13.3 on chromosome 3 in both fetal lines. Interestingly, these sites were found to not be fragile in lymphocytes, suggesting a role for epigenetic or transcriptional programs for this tissue specificity. Both these sites contained late-replicating genes NEGR1 (neuronal growth regulator 1) at 1p31.1 and LSAMP (limbic system-associated membrane protein) at 3q13.3, which are much longer, 0.880 and 1.4 Mb, respectively, than the average gene length. Given the established connection between long genes and CFS, we compiled information from the literature on all previously identified CFSs expressed in fibroblasts and lymphocytes in response to aphidicolin, including the size of the genes contained in each fragile region. Our comprehensive analysis confirmed that the genes found within CFSs are longer than the average human gene; interestingly, the two longest genes in the human genome are found within CFSs: Contactin Associated Protein 2 gene (CNTNAP2) in a lymphocytes’ CFS, and Duchenne muscular dystrophy gene (DMD) in a CFS expressed in both lymphocytes and fibroblasts. This indicates that the presence of very long genes is a unifying feature of all CFSs. We also obtained replication profiles of the 1p31.1 and 3q13.3 sites under both perturbed and unperturbed conditions using a combination of fluorescent in situ hybridization (FISH) and immunofluorescence against bromodeoxyuridine (BrdU) on interphase nuclei. Our analysis of the replication dynamics of these CFSs showed that, compared to lymphocytes where these regions are non-fragile, fibroblasts display incomplete replication of the fragile alleles, even in the absence of exogenous replication stress. Our data point to the existence of intrinsic features, in addition to the presence of long genes, which affect DNA replication of the CFSs in fibroblasts, thus promoting chromosomal instability in a tissue-specific manner.
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22
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Abstract
Common fragile sites (CFSs) are large chromosomal regions that exhibit breakage on metaphase chromosomes upon replication stress. They become preferentially unstable at the early stage of cancer development and are hotspots for chromosomal rearrangements in cancers. Increasing evidence has highlighted the complexity underlying the instability of CFSs, and a combination of multiple mechanisms is believed to cause CFS fragility. We will review recent advancements in our understanding of the molecular mechanisms underlying the maintenance of CFS stability and the relevance of CFSs to cancer-associated genome instability. We will emphasize the contribution of the structure-prone AT-rich sequences to CFS instability, which is in line with the recent genome-wide study showing that structure-forming repeat sequences are principal sites of replication stress.
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Affiliation(s)
- Shibo Li
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, San Diego, CA 92037 USA
| | - Xiaohua Wu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, San Diego, CA 92037 USA
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23
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Ovejero S, Bueno A, Sacristán MP. Working on Genomic Stability: From the S-Phase to Mitosis. Genes (Basel) 2020; 11:E225. [PMID: 32093406 PMCID: PMC7074175 DOI: 10.3390/genes11020225] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/17/2020] [Accepted: 02/18/2020] [Indexed: 12/15/2022] Open
Abstract
Fidelity in chromosome duplication and segregation is indispensable for maintaining genomic stability and the perpetuation of life. Challenges to genome integrity jeopardize cell survival and are at the root of different types of pathologies, such as cancer. The following three main sources of genomic instability exist: DNA damage, replicative stress, and chromosome segregation defects. In response to these challenges, eukaryotic cells have evolved control mechanisms, also known as checkpoint systems, which sense under-replicated or damaged DNA and activate specialized DNA repair machineries. Cells make use of these checkpoints throughout interphase to shield genome integrity before mitosis. Later on, when the cells enter into mitosis, the spindle assembly checkpoint (SAC) is activated and remains active until the chromosomes are properly attached to the spindle apparatus to ensure an equal segregation among daughter cells. All of these processes are tightly interconnected and under strict regulation in the context of the cell division cycle. The chromosomal instability underlying cancer pathogenesis has recently emerged as a major source for understanding the mitotic processes that helps to safeguard genome integrity. Here, we review the special interconnection between the S-phase and mitosis in the presence of under-replicated DNA regions. Furthermore, we discuss what is known about the DNA damage response activated in mitosis that preserves chromosomal integrity.
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Affiliation(s)
- Sara Ovejero
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC), Universidad de Salamanca-CSIC, Campus Miguel de Unamuno, 37007 Salamanca, Spain
- Institute of Human Genetics, CNRS, University of Montpellier, 34000 Montpellier, France
- Department of Biological Hematology, CHU Montpellier, 34295 Montpellier, France
| | - Avelino Bueno
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC), Universidad de Salamanca-CSIC, Campus Miguel de Unamuno, 37007 Salamanca, Spain
- Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - María P. Sacristán
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC), Universidad de Salamanca-CSIC, Campus Miguel de Unamuno, 37007 Salamanca, Spain
- Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain
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24
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Perez-Rodriguez D, Kalyva M, Leija-Salazar M, Lashley T, Tarabichi M, Chelban V, Gentleman S, Schottlaender L, Franklin H, Vasmatzis G, Houlden H, Schapira AHV, Warner TT, Holton JL, Jaunmuktane Z, Proukakis C. Investigation of somatic CNVs in brains of synucleinopathy cases using targeted SNCA analysis and single cell sequencing. Acta Neuropathol Commun 2019; 7:219. [PMID: 31870437 PMCID: PMC6929293 DOI: 10.1186/s40478-019-0873-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 12/17/2019] [Indexed: 12/17/2022] Open
Abstract
Synucleinopathies are mostly sporadic neurodegenerative disorders of partly unexplained aetiology, and include Parkinson's disease (PD) and multiple system atrophy (MSA). We have further investigated our recent finding of somatic SNCA (α-synuclein) copy number variants (CNVs, specifically gains) in synucleinopathies, using Fluorescent in-situ Hybridisation for SNCA, and single-cell whole genome sequencing for the first time in a synucleinopathy. In the cingulate cortex, mosaicism levels for SNCA gains were higher in MSA and PD than controls in neurons (> 2% in both diseases), and for MSA also in non-neurons. In MSA substantia nigra (SN), we noted SNCA gains in > 3% of dopaminergic (DA) neurons (identified by neuromelanin) and neuromelanin-negative cells, including olig2-positive oligodendroglia. Cells with CNVs were more likely to have α-synuclein inclusions, in a pattern corresponding to cell categories mostly relevant to the disease: DA neurons in Lewy-body cases, and other cells in the striatonigral degeneration-dominant MSA variant (MSA-SND). Higher mosaicism levels in SN neuromelanin-negative cells may correlate with younger onset in typical MSA-SND, and in cingulate neurons with younger death in PD. Larger sample sizes will, however, be required to confirm these putative findings. We obtained genome-wide somatic CNV profiles from 169 cells from the substantia nigra of two MSA cases, and pons and putamen of one. These showed somatic CNVs in ~ 30% of cells, with clonality and origins in segmental duplications for some. CNVs had distinct profiles based on cell type, with neurons having a mix of gains and losses, and other cells having almost exclusively gains, although control data sets will be required to determine possible disease relevance. We propose that somatic SNCA CNVs may contribute to the aetiology and pathogenesis of synucleinopathies, and that genome-wide somatic CNVs in MSA brain merit further study.
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Affiliation(s)
- Diego Perez-Rodriguez
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Maria Kalyva
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Melissa Leija-Salazar
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Tammaryn Lashley
- Queen Square Brain Bank for Neurological disorders, UCL Queen Square Institute of Neurology, 1 Wakefield street, London, WC1N 1PJ, UK
| | - Maxime Tarabichi
- The Francis Crick Institute, Midland Road 1, London, NW1 1AT, UK
| | - Viorica Chelban
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | | | - Lucia Schottlaender
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - Hannah Franklin
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - George Vasmatzis
- Center for Individualized Medicine, Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - Anthony H V Schapira
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Thomas T Warner
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- Queen Square Brain Bank for Neurological disorders, UCL Queen Square Institute of Neurology, 1 Wakefield street, London, WC1N 1PJ, UK
- National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - Janice L Holton
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- Queen Square Brain Bank for Neurological disorders, UCL Queen Square Institute of Neurology, 1 Wakefield street, London, WC1N 1PJ, UK
| | - Zane Jaunmuktane
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- Queen Square Brain Bank for Neurological disorders, UCL Queen Square Institute of Neurology, 1 Wakefield street, London, WC1N 1PJ, UK
- National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - Christos Proukakis
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK.
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25
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Ling C, Dai Y, Fang L, Yao F, Liu Z, Qiu Z, Cui L, Xia F, Zhao C, Zhang S, Wang K, Zhang X. Exonic rearrangements in DMD in Chinese Han individuals affected with Duchenne and Becker muscular dystrophies. Hum Mutat 2019; 41:668-677. [PMID: 31705731 PMCID: PMC7028077 DOI: 10.1002/humu.23953] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 10/31/2019] [Accepted: 11/07/2019] [Indexed: 01/12/2023]
Abstract
Exonic deletions and duplications within DMD are the main pathogenic variants in Duchenne and Becker muscular dystrophies (DMD/BMD). However, few studies have profiled the flanking sequences of breakpoints and the potential mechanism underlying the breakpoints in different fragile regions of DMD. In this study, 896 Chinese male probands afflicted with DMD/BMD were selected from unrelated families and analyzed using multiplex ligation‐dependent probe amplification of the DMD gene, in which we identified exon deletions in 784 subjects and duplications in 112 subjects. Deletions occurred most frequently in the genomic region encompassing exons 45–55, accounting for 73% of all deletion patterns. Furthermore, to unravel the potential mechanism that induced breaks, DMD gene capture and sequencing were performed to identify the breakpoints in 37 subjects with deletions encompassing exons 45–55 of DMD; we found that DMD instability did not arise from a single cause; instead, long‐sequence motifs, nonconsensus microhomologies, low‐copy repeats, and microindels were embedded around the breakpoints, which may predispose DMD to instability. In summary, this study highlights the heterogeneous characteristics of the flanking sequences around the breakpoints and helps us to understand the mechanism underlying DMD gene instability.
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Affiliation(s)
- Chao Ling
- The Laboratory of Clinical Genetics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Yi Dai
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Li Fang
- Department of Pathology & Laboratory Medicine, Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Fengxia Yao
- The Laboratory of Clinical Genetics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Zhe Liu
- The Laboratory of Clinical Genetics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Zhengqing Qiu
- Department of Pediatrics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Liying Cui
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Chen Zhao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Shuyang Zhang
- Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Kai Wang
- Department of Pathology & Laboratory Medicine, Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Xue Zhang
- The Laboratory of Clinical Genetics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.,Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, McKusick-Zhang Center for GeneticMedicine, School of Basic Medicine Peking, Union Medical College, Beijing, China
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26
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Duan H, Lei Z, Xu F, Pan T, Lu D, Ding P, Zhu C, Pan C, Zhang S. PARK2 Suppresses Proliferation and Tumorigenicity in Non-small Cell Lung Cancer. Front Oncol 2019; 9:790. [PMID: 31508359 PMCID: PMC6716169 DOI: 10.3389/fonc.2019.00790] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 08/06/2019] [Indexed: 12/26/2022] Open
Abstract
Aims: PARK2 mutation is originally associated with the progression of Parkinson's disease. In recent years, PARK2 has been reported as a tumor suppressor gene in various cancers, including lung cancer. However, the biological functions and potential molecular mechanisms of PARK2 in non-small cell lung cancer (NSCLC) are still unclear. Methods: The level of PARK2 expression in 32 tissue samples of NSCLC and matched non-tumor lung tissues was detected by Western blot, and 64 specimens of NSCLC tissues were detected by immunohistochemistry. H1299 and H460 cell lines were used to PARK2 overexpression models, and H460 cell line was also used to PARK2 knockdown model. Using cell viability, colony formation, cell cycle, apoptosis, migration, and invasion assay, the biological functions of PARK2 were evaluated and the potential molecular mechanism of PARK2 was investigated in vitro. Meanwhile, 22 nude mice were employed for in vivo studies. Results: Western blot analysis revealed a decrease of PARK2 protein expression in human NSCLC samples. Immunohistochemistry also identified a vastly reduced expression of PARK2 in NSCLC (72%) and low PARK2 expression was significantly associated with tumor histological grade, lymph node metastasis and advanced TNM stage. Overexpression of PARK2 suppressed cell proliferation, colony formation, migration, and invasion, arrested cell cycle progression in the G1 phase, and induced apoptosis in human non-small cell lines H1299 and H460 in vitro. Meanwhile, knockdown of PARK2 had the opposite biological functions. In addition, PARK2 significantly decreased the tumor volumes in subcutaneous xenograft model and reduced the incidence of metastatic tumors in the transfer model. Exploration of the molecular mechanism of PARK2 in NSCLC showed that PARK2 negatively regulated the EGFR/AKT/mTOR signaling pathway. Conclusions: PARK2 was an important tumor suppressor in NSCLC, which might inhibit cancer growth and metastases through the down regulation of the EGFR/AKT/mTOR signaling pathway.
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Affiliation(s)
- Huijie Duan
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, The Second Affiliated Hospital, School of Medicine, Cancer Institute, Zhejiang University, Hangzhou, China
| | - Zhong Lei
- Department of Orthopedics Research Institute, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Fei Xu
- Department of Oncology, Municipal Hospital of Qingdao, Qingdao, China
| | - Tao Pan
- Department of Breast Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Demin Lu
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, The Second Affiliated Hospital, School of Medicine, Cancer Institute, Zhejiang University, Hangzhou, China
| | - Peili Ding
- Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, The Second Affiliated Hospital, School of Medicine, Cancer Institute, Zhejiang University, Hangzhou, China
| | - Chunpeng Zhu
- Department of Gastroenterology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chi Pan
- Department of Breast Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Suzhan Zhang
- Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, The Second Affiliated Hospital, School of Medicine, Cancer Institute, Zhejiang University, Hangzhou, China.,Research Center for Air Pollution and Health, School of Medicine, Zhejiang University, Hangzhou, China
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27
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Gardner HL, Sivaprakasam K, Briones N, Zismann V, Perdigones N, Drenner K, Facista S, Richholt R, Liang W, Aldrich J, Trent JM, Shields PG, Robinson N, Johnson J, Lana S, Houghton P, Fenger J, Lorch G, Janeway KA, London CA, Hendricks WPD. Canine osteosarcoma genome sequencing identifies recurrent mutations in DMD and the histone methyltransferase gene SETD2. Commun Biol 2019; 2:266. [PMID: 31341965 PMCID: PMC6642146 DOI: 10.1038/s42003-019-0487-2] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 05/29/2019] [Indexed: 02/08/2023] Open
Abstract
Osteosarcoma (OS) is a rare, metastatic, human adolescent cancer that also occurs in pet dogs. To define the genomic underpinnings of canine OS, we performed multi-platform analysis of OS tumors from 59 dogs, including whole genome sequencing (n = 24) and whole exome sequencing (WES; n = 13) of primary tumors and matched normal tissue, WES (n = 10) of matched primary/metastatic/normal samples and RNA sequencing (n = 54) of primary tumors. We found that canine OS recapitulates features of human OS including low point mutation burden (median 1.98 per Mb) with a trend towards higher burden in metastases, high structural complexity, frequent TP53 (71%), PI3K pathway (37%), and MAPK pathway mutations (17%), and low expression of immune-associated genes. We also identified novel features of canine OS including putatively inactivating somatic SETD2 (42%) and DMD (50%) aberrations. These findings set the stage for understanding OS development in dogs and humans, and establish genomic contexts for future comparative analyses.
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Affiliation(s)
- Heather L. Gardner
- Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, MA 02111 USA
| | | | - Natalia Briones
- Translational Genomics Research Institute, Phoenix, AZ 85004 USA
| | - Victoria Zismann
- Translational Genomics Research Institute, Phoenix, AZ 85004 USA
| | | | - Kevin Drenner
- Translational Genomics Research Institute, Phoenix, AZ 85004 USA
| | | | - Ryan Richholt
- Translational Genomics Research Institute, Phoenix, AZ 85004 USA
| | - Winnie Liang
- Translational Genomics Research Institute, Phoenix, AZ 85004 USA
| | - Jessica Aldrich
- Translational Genomics Research Institute, Phoenix, AZ 85004 USA
| | - Jeffrey M. Trent
- Translational Genomics Research Institute, Phoenix, AZ 85004 USA
| | - Peter G. Shields
- College of Medicine, The Ohio State University, Columbus, OH 43210 USA
| | - Nicholas Robinson
- Cummings School of Veterinary Medicine, Tufts University, Grafton, MA 01536 USA
| | | | - Susan Lana
- Colorado State University, Fort Collins, CO 80525 USA
| | - Peter Houghton
- University of Texas Health Science Center, San Antonio, TX 78229 USA
| | - Joelle Fenger
- Department of Veterinary Clinical Sciences, The Ohio State University, Columbus, OH 43210 USA
| | - Gwendolen Lorch
- Department of Veterinary Clinical Sciences, The Ohio State University, Columbus, OH 43210 USA
| | | | - Cheryl A. London
- Cummings School of Veterinary Medicine, Tufts University, Grafton, MA 01536 USA
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Irony-Tur Sinai M, Kerem B. Genomic instability in fragile sites-still adding the pieces. Genes Chromosomes Cancer 2018; 58:295-304. [PMID: 30525255 DOI: 10.1002/gcc.22715] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 11/28/2018] [Accepted: 11/29/2018] [Indexed: 12/19/2022] Open
Abstract
Common fragile sites (CFSs) are specific genomic regions in normal chromosomes that exhibit genomic instability under DNA replication stress. As replication stress is an early feature of cancer development, CFSs are involved in the signature of genomic instability found in malignant tumors. The landscape of CFSs is tissue-specific and differs under different replication stress inducers. Nevertheless, the features underlying CFS sensitivity to replication stress are shared. Here, we review the events generating replication stress and discuss the unique characteristics of CFS regions and the cellular responses aimed to stabilizing these regions.
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Affiliation(s)
- Michal Irony-Tur Sinai
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Jerusalem, Israel
| | - Batsheva Kerem
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Jerusalem, Israel
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29
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Debatisse M, Rosselli F. A journey with common fragile sites: From S phase to telophase. Genes Chromosomes Cancer 2018; 58:305-316. [PMID: 30387289 DOI: 10.1002/gcc.22704] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 10/25/2018] [Indexed: 12/17/2022] Open
Abstract
Some regions of the genome, notably common fragile sites (CFSs), are hypersensitive to replication stress and often involved in the generation of gross chromosome rearrangements in cancer cells. CFSs nest within very large genes and display cell-type-dependent instability. Fragile or not, large genes tend to replicate late in S-phase. A number of data now show that transcription perturbs replication completion across the body of large genes, particularly upon replication stress. However, the molecular mechanisms by which transcription elicits such under-replication and subsequent instability remain unclear. We present here our view of the mechanisms responsible for CFS under-replication and those allowing the cells to cope with this problem in G2 and mitosis. We notably focus on the major role played by the FANC proteins in the protection of CFSs from S phase up to late mitosis. We finally discuss a possible rationale for the conservation of large genes across vertebrate evolution.
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Affiliation(s)
- Michelle Debatisse
- CNRS UMR 8200, Equipe labellisée "La ligue Contre le Cancer", Villejuif, France.,Sorbonne Universités, UPMC Univ Paris 06, Paris, France.,Gustave Roussy Cancer Center, Villejuif, France
| | - Filippo Rosselli
- CNRS UMR 8200, Equipe labellisée "La ligue Contre le Cancer", Villejuif, France.,Gustave Roussy Cancer Center, Villejuif, France.,Université Paris Saclay - Paris Sud, Orsay, France
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30
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Palumbo E, Russo A. Common fragile site instability in normal cells: Lessons and perspectives. Genes Chromosomes Cancer 2018; 58:260-269. [PMID: 30387295 DOI: 10.1002/gcc.22705] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/25/2018] [Accepted: 10/01/2018] [Indexed: 12/26/2022] Open
Abstract
Mechanisms and events related to common fragile site (CFS) instability are well known in cancer cells. Here, we argue that normal cells remain an important experimental model to address questions related to CFS instability in the absence of alterations in cell cycle and DNA damage repair pathways, which are common features acquired in cancer. Furthermore, a major gap of knowledge concerns the stability of CFSs during gametogenesis. CFS instability in meiotic or postmeiotic stages of the germ cell line could generate chromosome deletions or large rearrangements. This in turn can lead to the functional loss of the several CFS-associated genes with tumor suppressor function. Our hypothesis is that such mutations can potentially result in genetic predisposition to develop cancer. Indirect evidence for CFS instability in human germ cells has been provided by genomic investigations in family pedigrees associated with genetic disease. The issue of CFS instability in the germ cell line should represent one of the future efforts, and may take advantage of the existence of sequence and functional conservation of CFSs between rodents and humans.
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Affiliation(s)
- Elisa Palumbo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Antonella Russo
- Department of Molecular Medicine, University of Padova, Padova, Italy
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31
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Zheglo D, Brueckner LM, Sepman O, Wecht EM, Kuligina E, Suspitsin E, Imyanitov E, Savelyeva L. The FRA14B
common fragile site maps to a region prone to somatic and germline rearrangements within the large GPHN
gene. Genes Chromosomes Cancer 2018; 58:284-294. [DOI: 10.1002/gcc.22706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/31/2018] [Accepted: 11/01/2018] [Indexed: 01/27/2023] Open
Affiliation(s)
- Diana Zheglo
- FSBI Research Centre for Medical Genetics; Moscow Russia
| | - Lena M. Brueckner
- Division of Neuroblastoma Genomics; German Cancer Research Center (DKFZ); Heidelberg Germany
| | - Olga Sepman
- Klinik fuer Allgemein-, Viszeral-, Thorax- und minimal-invasive Chirurgie; Pforzheim Germany
| | - Elisa M. Wecht
- Division of Neuroblastoma Genomics; German Cancer Research Center (DKFZ); Heidelberg Germany
| | | | - Evgenij Suspitsin
- Petrov Institute of Oncology; St Petersburg Russia
- St. Petersburg Pediatric Medical University; Sankt-Peterburg Russia
| | - Evgenij Imyanitov
- Petrov Institute of Oncology; St Petersburg Russia
- Mechnikov North-Western Medical University; Saint Petersburg Russia
| | - Larissa Savelyeva
- Division of Neuroblastoma Genomics; German Cancer Research Center (DKFZ); Heidelberg Germany
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32
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Ma P, Zhang S, Zhang H, Fang S, Dong Y, Zhang Y, Hao W, Wu S, Zhao Y. Comprehensive genetic characteristics of dystrophinopathies in China. Orphanet J Rare Dis 2018; 13:109. [PMID: 29973226 PMCID: PMC6032532 DOI: 10.1186/s13023-018-0853-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 06/20/2018] [Indexed: 11/10/2022] Open
Abstract
Background Dystrophinopathies are a set of severe and incurable X-linked neuromuscular disorders caused by mutations in the dystrophin gene (DMD). These mutations form a complex spectrum. A national registration network is essential not only to provide more information about the prevalence and natural history of the disease, but also to collect genetic data for analyzing the mutational spectrum. This information is extremely beneficial for basic scientific research, genetic diagnosis, trial planning, clinical care, and gene therapy. Methods We collected data from 1400 patients (1042 patients with confirmed unrelated Duchenne muscular dystrophy [DMD] or Becker muscular dystrophy [BMD]) registered in the Chinese Genetic Disease Registry from March 2012 to August 2017 and analyzed the genetic mutational characteristics of these patients. Results Large deletions were the most frequent type of mutation (72.2%), followed by nonsense mutations (11.9%), exon duplications (8.8%), small deletions (3.0%), splice-site mutations (2.1%), small insertions (1.3%), missense mutations (0.6%), and a combination mutation of a deletion and a duplication (0.1%). Exon 45–50 deletion was the most frequent deletion type, while exon 2 duplication was the most common duplication type. Two deletion hotspots were calculated—one located toward the central part (exon 45–52) of the gene and the other toward the 5’end (exon 8–26). We found no significant difference between hereditary and de novo mutations on deletion hotspots. Nonsense mutations accounted for 62.9% of all small mutations (197 patients). Conclusion We built a comprehensive national dystrophinopathy mutation database in China, which is essential for basic and clinical research in this field. The mutational spectrum and characteristics of this DMD/BMD group were largely consistent with those in previous international DMD/BMD studies, with some differences. Based on our results, about 12% of DMD/BMD patients with nonsense mutations may benefit from stop codon read-through therapy. Additionally, the top three targets for exon-skipping therapy are exon 51 (141, 13.5%), exon 53 (115, 11.0%), and exon 45 (84, 8.0%). Electronic supplementary material The online version of this article (10.1186/s13023-018-0853-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Peipei Ma
- Department of Neurology, the General Hospital of Chinese People's Armed Police Force, Beijing, China
| | - Shu Zhang
- Department of Neurology, the General Hospital of Chinese People's Armed Police Force, Beijing, China
| | - Hao Zhang
- Department of Neurology, the General Hospital of Chinese People's Armed Police Force, Beijing, China
| | - Siying Fang
- Department of Neurology, the General Hospital of Chinese People's Armed Police Force, Beijing, China
| | - Yuru Dong
- Department of Magnetic Resonance, the General Hospital of Chinese People's Armed Police Force, Beijing, China
| | - Yan Zhang
- Department of Precision Medicine Laboratory, the General Hospital of Chinese People's Armed Police Force, Beijing, China
| | - Weiwei Hao
- Department of Precision Medicine Laboratory, the General Hospital of Chinese People's Armed Police Force, Beijing, China
| | - Shiwen Wu
- Department of Neurology, the General Hospital of Chinese People's Armed Police Force, Beijing, China.
| | - Yuying Zhao
- Research Institute of Neuromuscular and Neurodegenerative Diseases and Department of Neurology, Qilu Hospital, Shandong University, Jinan, Shandong, China.
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33
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Elhawary NA, Jiffri EH, Jambi S, Mufti AH, Dannoun A, Kordi H, Khogeer A, Jiffri OH, Elhawary AN, Tayeb MT. Molecular characterization of exonic rearrangements and frame shifts in the dystrophin gene in Duchenne muscular dystrophy patients in a Saudi community. Hum Genomics 2018; 12:18. [PMID: 29631625 PMCID: PMC5891934 DOI: 10.1186/s40246-018-0152-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 04/02/2018] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND In individuals with Duchenne muscular dystrophy (DMD), exon skipping treatment to restore a wild-type phenotype or correct the frame shift of the mRNA transcript of the dystrophin (DMD) gene are mutation-specific. To explore the molecular characterization of DMD rearrangements and predict the reading frame, we simultaneously screened all 79 DMD gene exons of 45 unrelated male DMD patients using a multiplex ligation-dependent probe amplification (MLPA) assay for deletion/duplication patterns. Multiplex PCR was used to confirm single deletions detected by the MLPA. RESULTS There was an obvious diagnostic delay, with an extremely statistically significant difference between the age at initial symptoms and the age of clinical evaluation of DMD cases (t value, 10.3; 95% confidence interval 5.95-8.80, P < 0.0001); the mean difference between the two groups was 7.4 years. Overall, we identified 147 intragenic rearrangements: 46.3% deletions and 53.7% duplications. Most of the deletions (92.5%) were between exons 44 and 56, with exon 50 being the most frequently involved (19.1%). Eight new rearrangements, including a mixed deletion/duplication and double duplications, were linked to seven cases with DMD. Of all the cases, 17.8% had duplications with no hot spots. In addition, confirmation of the reading frame hypothesis helped account for new DMD rearrangements in this study. We found that 81% of our Saudi patients would potentially benefit from exon skipping, of which 42.9% had a mutation amenable to skipping of exon 51. CONCLUSIONS Our study could generate considerable data on mutational rearrangements that may promote future experimental therapies in Saudi Arabia.
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Affiliation(s)
- Nasser A Elhawary
- Department of Medical Genetics, Medicine College, Umm Al-Qura University, P.O. Box 57543, Mecca, 21955, Saudi Arabia.
- Department of Molecular Genetics, Faculty of Medicine, Ain Shams University, Cairo, 11566, Egypt.
| | - Essam H Jiffri
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdul-Aziz University, Jeddah, Saudi Arabia
| | - Samira Jambi
- Department of Pediatrics, Al Hada Military Hospital, Al Hada, Saudi Arabia
| | - Ahmad H Mufti
- Department of Medical Genetics, Medicine College, Umm Al-Qura University, P.O. Box 57543, Mecca, 21955, Saudi Arabia
| | - Anas Dannoun
- Department of Medical Genetics, Medicine College, Umm Al-Qura University, P.O. Box 57543, Mecca, 21955, Saudi Arabia
| | - Hassan Kordi
- Department of Medical Genetics, Medicine College, Umm Al-Qura University, P.O. Box 57543, Mecca, 21955, Saudi Arabia
| | - Asim Khogeer
- Department of Plan and Research, General Directorate of Health Affairs, Mecca Region, Ministry of Health, Mecca, Saudi Arabia
| | - Osama H Jiffri
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdul-Aziz University, Jeddah, Saudi Arabia
| | | | - Mohammed T Tayeb
- Department of Medical Genetics, Medicine College, Umm Al-Qura University, P.O. Box 57543, Mecca, 21955, Saudi Arabia
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34
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Molecular characterization of exonic rearrangements and frame shifts in the dystrophin gene in Duchenne muscular dystrophy patients in a Saudi community. Hum Genomics 2018. [PMID: 29631625 DOI: 10.1186/s40246-018-0152-8]] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In individuals with Duchenne muscular dystrophy (DMD), exon skipping treatment to restore a wild-type phenotype or correct the frame shift of the mRNA transcript of the dystrophin (DMD) gene are mutation-specific. To explore the molecular characterization of DMD rearrangements and predict the reading frame, we simultaneously screened all 79 DMD gene exons of 45 unrelated male DMD patients using a multiplex ligation-dependent probe amplification (MLPA) assay for deletion/duplication patterns. Multiplex PCR was used to confirm single deletions detected by the MLPA. RESULTS There was an obvious diagnostic delay, with an extremely statistically significant difference between the age at initial symptoms and the age of clinical evaluation of DMD cases (t value, 10.3; 95% confidence interval 5.95-8.80, P < 0.0001); the mean difference between the two groups was 7.4 years. Overall, we identified 147 intragenic rearrangements: 46.3% deletions and 53.7% duplications. Most of the deletions (92.5%) were between exons 44 and 56, with exon 50 being the most frequently involved (19.1%). Eight new rearrangements, including a mixed deletion/duplication and double duplications, were linked to seven cases with DMD. Of all the cases, 17.8% had duplications with no hot spots. In addition, confirmation of the reading frame hypothesis helped account for new DMD rearrangements in this study. We found that 81% of our Saudi patients would potentially benefit from exon skipping, of which 42.9% had a mutation amenable to skipping of exon 51. CONCLUSIONS Our study could generate considerable data on mutational rearrangements that may promote future experimental therapies in Saudi Arabia.
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35
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Marey I, Ben Yaou R, Deburgrave N, Vasson A, Nectoux J, Leturcq F, Eymard B, Laforet P, Behin A, Stojkovic T, Mayer M, Tiffreau V, Desguerre I, Boyer FC, Nadaj-Pakleza A, Ferrer X, Wahbi K, Becane HM, Claustres M, Chelly J, Cossee M. Non Random Distribution of DMD Deletion Breakpoints and Implication of Double Strand Breaks Repair and Replication Error Repair Mechanisms. J Neuromuscul Dis 2018; 3:227-245. [PMID: 27854212 DOI: 10.3233/jnd-150134] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
BACKGROUND Dystrophinopathies are mostly caused by copy number variations, especially deletions, in the dystrophin gene (DMD). Despite the large size of the gene, deletions do not occur randomly but mainly in two hot spots, the main one involving exons 45 to 55. The underlying mechanisms are complex and implicate two main mechanisms: Non-homologous end joining (NHEJ) and micro-homology mediated replication-dependent recombination (MMRDR). OBJECTIVE Our goals were to assess the distribution of intronic breakpoints (BPs) in the genomic sequence of the main hot spot of deletions within DMD gene and to search for specific sequences at or near to BPs that might promote BP occurrence or be associated with DNA break repair. METHODS Using comparative genomic hybridization microarray, 57 deletions within the intron 44 to 55 region were mapped. Moreover, 21 junction fragments were sequenced to search for specific sequences. RESULTS Non-randomly distributed BPs were found in introns 44, 47, 48, 49 and 53 and 50% of BPs clustered within genomic regions of less than 700bp. Repeated elements (REs), known to promote gene rearrangement via several mechanisms, were present in the vicinity of 90% of clustered BPs and less frequently (72%) close to scattered BPs, illustrating the important role of such elements in the occurrence of DMD deletions. Palindromic and TTTAAA sequences, which also promote DNA instability, were identified at fragment junctions in 20% and 5% of cases, respectively. Micro-homologies (76%) and insertions or deletions of small sequences were frequently found at BP junctions. CONCLUSIONS Our results illustrate, in a large series of patients, the important role of RE and other genomic features in DNA breaks, and the involvement of different mechanisms in DMD gene deletions: Mainly replication error repair mechanisms, but also NHEJ and potentially aberrant firing of replication origins. A combination of these mechanisms may also be possible.
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Affiliation(s)
- Isabelle Marey
- Service de Biochimie et Génétique Moléculaire, HUPC Hôpital Cochin, Paris, France
| | - Rabah Ben Yaou
- UPMC-Paris 6, UM 76, INSERM, U974, CNRS, UMR 7215, Center of Research in Myology, Institut de Myologie, Paris, France.,AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Centre de Référence de Pathologie Neuromusculaire Paris-Est, Paris, France
| | - Nathalie Deburgrave
- Service de Biochimie et Génétique Moléculaire, HUPC Hôpital Cochin, Paris, France
| | - Aurélie Vasson
- Service de Biochimie et Génétique Moléculaire, HUPC Hôpital Cochin, Paris, France
| | - Juliette Nectoux
- Service de Biochimie et Génétique Moléculaire, HUPC Hôpital Cochin, Paris, France.,INSERM, U1016, Institut Cochin, CNRS UMR8104, Université Paris Descartes, Paris, France
| | - France Leturcq
- Service de Biochimie et Génétique Moléculaire, HUPC Hôpital Cochin, Paris, France.,UPMC-Paris 6, UM 76, INSERM, U974, CNRS, UMR 7215, Center of Research in Myology, Institut de Myologie, Paris, France
| | - Bruno Eymard
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Centre de Référence de Pathologie Neuromusculaire Paris-Est, Paris, France
| | - Pascal Laforet
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Centre de Référence de Pathologie Neuromusculaire Paris-Est, Paris, France
| | - Anthony Behin
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Centre de Référence de Pathologie Neuromusculaire Paris-Est, Paris, France
| | - Tanya Stojkovic
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Centre de Référence de Pathologie Neuromusculaire Paris-Est, Paris, France
| | - Michèle Mayer
- AP-HP, Hôpital Armand TROUSSEAU, Centre de référence de pathologie neuromusculaire Paris-Est, Paris, France
| | - Vincent Tiffreau
- Université de Lille 2, EA 4488, Centre de référence des maladies neuromusculaires du CHRU de Lille, Service de médecine physique et réadaptation, Hôpital Swynghedauw, Lille, France
| | - Isabelle Desguerre
- AP-HP, Hôpital Necker-Enfants Malades, Service de Neuropédiatrie, Centre de référence de pathologie neuromusculaires Garches-Necker-Mondor-Hendaye, Paris, France
| | - François Constant Boyer
- Service de Médecine Physique et Réadaptation, Centre de référence de pathologie neuromusculaires, Hôpital Sébastopol, CHU de Reims, Reims, France
| | - Aleksandra Nadaj-Pakleza
- Service de neurologie, Centre de référence de pathologie neuromusculaires Pays de Loire, Hôpital Larrey, CHU d'Angers, Angers, France
| | - Xavier Ferrer
- Service de neurologie, Centre de référence de pathologie neuromusculaires Aquitaine, Hôpital Pellegrin, CHU de Bordeaux, Bordeaux, France
| | - Karim Wahbi
- APHP, service de cardiologie, Hôpital Cochin, Paris, France
| | - Henri-Marc Becane
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Centre de Référence de Pathologie Neuromusculaire Paris-Est, Paris, France
| | - Mireille Claustres
- CHRU Montpellier, Laboratoire de Génétique moléculaire, Montpellier, France.,Université de Montpellier, Laboratoire de Génétique de Maladies rares, EA 7402, Montpellier, France
| | - Jamel Chelly
- Service de Biochimie et Génétique Moléculaire, HUPC Hôpital Cochin, Paris, France.,INSERM, U1016, Institut Cochin, CNRS UMR8104, Université Paris Descartes, Paris, France
| | - Mireille Cossee
- CHRU Montpellier, Laboratoire de Génétique moléculaire, Montpellier, France.,Université de Montpellier, Laboratoire de Génétique de Maladies rares, EA 7402, Montpellier, France
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Abstract
Osteosarcoma (OS) is the most common primary malignant bone tumor mainly occurring in children and adolescents. In past decades, studies revealed that PARK2 was a vital tumor suppressor gene in many malignant solid tumors. However, the role of PARK2 in OS remains largely unclear. Therefore, we assessed PARK2 expression in OS tissue and adjacent non-tumor tissues by immunohistochemical (IHC) analysis, and evaluated PARK2 mRNA expression in OS cell lines by real-time PCR analysis. The HOS and U2OS cell lines were employed to establish a PARK2 overexpression model. Using this model, we investigated the potential role of PARK2 in OS and explored the underlying molecular mechanisms. Our study showed PARK2 was downregulated in OS tissue and cell lines, which was significantly associated with higher tumor stage (P < 0.05). Overexpression of PARK2 arrested the cell cycle, inhibited cell proliferation, migration, and invasion, induced cell apoptosis, and reduced tube formation in vitro. Moreover, overexpression of PARK2 significantly suppressed tumor growth and angiogenesis in vivo. Additionally, PARK2 negatively regulated OS development through the JAK2/STAT3/VEGF pathway. Our findings demonstrate that PARK2 is a tumor suppressor gene that may negatively affect OS growth and angiogenesis via partly inhibiting the JAK2/STAT3/VEGF signaling pathway.
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37
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Leija-Salazar M, Piette C, Proukakis C. Review: Somatic mutations in neurodegeneration. Neuropathol Appl Neurobiol 2018; 44:267-285. [PMID: 29369391 DOI: 10.1111/nan.12465] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/13/2018] [Indexed: 12/22/2022]
Abstract
Somatic mutations are postzygotic mutations which may lead to mosaicism, the presence of cells with genetic differences in an organism. Their role in cancer is well established, but detailed investigation in health and other diseases has only been recently possible. This has been empowered by the improvements of sequencing techniques, including single-cell sequencing, which can still be error-prone but is rapidly improving. Mosaicism appears relatively common in the human body, including the normal brain, probably arising in early development, but also potentially during ageing. In this review, we first discuss theoretical considerations and current evidence relevant to somatic mutations in the brain. We present a framework to explain how they may be integrated with current views on neurodegeneration, focusing mainly on sporadic late-onset neurodegenerative diseases (Parkinson's disease, Alzheimer's disease and amyotrophic lateral sclerosis). We review the relevant studies so far, with the first evidence emerging in Alzheimer's in particular. We also discuss the role of mosaicism in inherited neurodegenerative disorders, particularly somatic instability of tandem repeats. We summarize existing views and data to present a model whereby the time of origin and spatial distribution of relevant somatic mutations, combined with any additional risk factors, may partly determine the development and onset age of sporadic neurodegenerative diseases.
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Affiliation(s)
- M Leija-Salazar
- Department of Clinical Neuroscience, University College London Institute of Neurology, London, UK
| | - C Piette
- Department of Clinical Neuroscience, University College London Institute of Neurology, London, UK
| | - C Proukakis
- Department of Clinical Neuroscience, University College London Institute of Neurology, London, UK
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38
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Bouhouche A, Tesson C, Regragui W, Rahmani M, Drouet V, Tibar H, Souirti Z, Ben El Haj R, Bouslam N, Yahyaoui M, Brice A, Benomar A, Lesage S. Mutation Analysis of Consanguineous Moroccan Patients with Parkinson's Disease Combining Microarray and Gene Panel. Front Neurol 2017; 8:567. [PMID: 29163333 PMCID: PMC5674924 DOI: 10.3389/fneur.2017.00567] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 10/10/2017] [Indexed: 01/20/2023] Open
Abstract
During the last two decades, 15 different genes have been reported to be responsible for the monogenic form of Parkinson’s disease (PD), representing a worldwide frequency of 5–10%. Among them, 10 genes have been associated with autosomal recessive PD, with PRKN and PINK1 being the most frequent. In a cohort of 145 unrelated Moroccan PD patients enrolled since 2013, 19 patients were born from a consanguineous marriage, of which 15 were isolated cases and 4 familial. One patient was homozygous for the common LRRK2 G2019S mutation and the 18 others who did not carry this mutation were screened for exon rearrangements in the PRKN gene using Affymetrix Cytoscan HD microarray. Two patients were determined homozygous for PRKN exon-deletions, while another patient presented with compound heterozygous inheritance (3/18, 17%). Two other patients showed a region of homozygosity covering the 1p36.12 locus and were sequenced for the candidate PINK1 gene, which revealed two homozygous point mutations: the known Q456X mutation in exon 7 and a novel L539F variation in exon 8. The 13 remaining patients were subjected to next-generation sequencing (NGS) that targeted a panel of 22 PD-causing genes and overlapping phenotypes. NGS data showed that two unrelated consanguineous patients with juvenile-onset PD (12 and 13 years) carried the same homozygous stop mutation W258X in the ATP13A2 gene, possibly resulting from a founder effect; and one patient with late onset (76 years) carried a novel heterozygous frameshift mutation in SYNJ1. Clinical analysis showed that patients with the ATP13A2 mutation developed juvenile-onset PD with a severe phenotype, whereas patients having either PRKN or PINK1 mutations displayed early-onset PD with a relatively mild phenotype. By identifying pathogenic mutations in 45% (8/18) of our consanguineous Moroccan PD series, we demonstrate that the combination of chromosomal microarray analysis and NGS is a powerful approach to pinpoint the genetic bases of autosomal recessive PD, particularly in countries with a high rate of consanguinity.
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Affiliation(s)
- Ahmed Bouhouche
- Research Team in Neurology and Neurogenetics, Faculty of Medicine and Pharmacy, Genomics Center of Human Pathologies, University Mohammed V, Rabat, Morocco
| | - Christelle Tesson
- Sorbonne Universités, UPMC Université Paris 6 UMR_S 1127, INSERM U 1127, CNRS UMR 7225, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France
| | - Wafaa Regragui
- Research Team in Neurology and Neurogenetics, Faculty of Medicine and Pharmacy, Genomics Center of Human Pathologies, University Mohammed V, Rabat, Morocco
| | - Mounia Rahmani
- Research Team in Neurology and Neurogenetics, Faculty of Medicine and Pharmacy, Genomics Center of Human Pathologies, University Mohammed V, Rabat, Morocco
| | - Valérie Drouet
- Sorbonne Universités, UPMC Université Paris 6 UMR_S 1127, INSERM U 1127, CNRS UMR 7225, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France
| | - Houyam Tibar
- Research Team in Neurology and Neurogenetics, Faculty of Medicine and Pharmacy, Genomics Center of Human Pathologies, University Mohammed V, Rabat, Morocco
| | - Zouhayr Souirti
- Clinical Neurosciences Laboratory, Faculty of Medicine and Pharmacy, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Rafiqua Ben El Haj
- Research Team in Neurology and Neurogenetics, Faculty of Medicine and Pharmacy, Genomics Center of Human Pathologies, University Mohammed V, Rabat, Morocco
| | - Naima Bouslam
- Research Team in Neurology and Neurogenetics, Faculty of Medicine and Pharmacy, Genomics Center of Human Pathologies, University Mohammed V, Rabat, Morocco
| | - Mohamed Yahyaoui
- Research Team in Neurology and Neurogenetics, Faculty of Medicine and Pharmacy, Genomics Center of Human Pathologies, University Mohammed V, Rabat, Morocco
| | - Alexis Brice
- Sorbonne Universités, UPMC Université Paris 6 UMR_S 1127, INSERM U 1127, CNRS UMR 7225, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France
| | - Ali Benomar
- Research Team in Neurology and Neurogenetics, Faculty of Medicine and Pharmacy, Genomics Center of Human Pathologies, University Mohammed V, Rabat, Morocco
| | - Suzanne Lesage
- Sorbonne Universités, UPMC Université Paris 6 UMR_S 1127, INSERM U 1127, CNRS UMR 7225, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France
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Precise mapping of 17 deletion breakpoints within the central hotspot deletion region (introns 50 and 51) of the DMD gene. J Hum Genet 2017; 62:1057-1063. [PMID: 28878337 DOI: 10.1038/jhg.2017.84] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 07/06/2017] [Accepted: 07/24/2017] [Indexed: 01/04/2023]
Abstract
Exon deletions in the human DMD gene, which encodes the dystrophin protein, are the molecular defect in 50-70% of cases of Duchenne/Becker muscular dystrophies. Deletions are preferentially clustered in the 5' (exons 2-20) and the central (exons 45-53) region of DMD, likely because local DNA structure predisposes to specific breakage or recombination events. Notably, innovative therapeutic strategies may rescue dystrophin function by homology-based specific targeting of sequences within the central DMD hot spot deletion region. To further study molecular mechanisms that generate such frequent genome variations and to identify residual intronic sequences, we sequenced 17 deletion breakpoints within introns 50 and 51 of DMD and analyzed the surrounding genomic architecture. There was no breakpoint clustering within the introns nor extensive homology between sequences adjacent to each junction. However, at or near the breakpoint, we found microhomology, short tandem repeats, interspersed repeat elements and short sequence stretches that predispose to DNA deletion or bending. Identification of such structural elements contributes to elucidate general mechanisms generating deletion within the DMD gene. Moreover, precise mapping of deletion breakpoints and localization of repeated elements are of interest, because residual intronic sequences may be targeted by therapeutic strategies based on genome editing correction.
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Abstract
Nearly 20 years have passed since we identified the causative gene for a familial Parkinson's disease, parkin (now known as PARK2), in 1998. PARK2 is the most common gene responsible for young-onset Parkinson's disease. It codes for the protein Parkin RBR E3 ubiquitin-protein ligase (PARK2), which directly links to the ubiquitin-proteasome as a ubiquitin ligase. PARK2 is involved in mitophagy, which is a type of autophagy, in collaboration with PTEN-induced putative kinase 1 (PINK1). The PINK1 gene (previously known as PARK6) is also a causative gene for young-onset Parkinson's disease. Both gene products may be involved in regulating quality control within the mitochondria. The discovery of PARK2 as a cause of young-onset Parkinson's disease has had a major impact on other neurodegenerative diseases. The involvement of protein degradation systems has been implicated as a common mechanism for neurodegenerative diseases in which inclusion body formation is observed. The discovery of the involvement of PARK2 in Parkinson's disease focused attention on the involvement of protein degradation systems in neurodegenerative diseases. In this review, we focus on the history of the discovery of PARK2, the clinical phenotypes of patients with PARK2 mutations, and its functional roles.
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Affiliation(s)
- Nobutaka Hattori
- Department of Neurology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo, Tokyo, 113-8421, Japan.
| | - Yoshikuni Mizuno
- Department of Neurology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo, Tokyo, 113-8421, Japan
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PMS2 inactivation by a complex rearrangement involving an HERV retroelement and the inverted 100-kb duplicon on 7p22.1. Eur J Hum Genet 2016; 24:1598-1604. [PMID: 27329736 DOI: 10.1038/ejhg.2016.75] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 05/12/2016] [Accepted: 05/26/2016] [Indexed: 11/08/2022] Open
Abstract
Biallelic PMS2 mutations are responsible for more than half of all cases of constitutional mismatch repair deficiency (CMMRD), a recessively inherited childhood cancer predisposition syndrome. The mismatch repair gene PMS2 is partly embedded within one copy of an inverted 100-kb low-copy repeat (LCR) on 7p22.1. In an individual with CMMRD syndrome, PMS2 was found to be homozygously inactivated by a complex chromosomal rearrangement, which separates the 5'-part from the 3'-part of the gene. The rearrangement involves sequences of the inverted 100-kb LCR and a human endogenous retrovirus element and may be associated with an inversion that is indistinguishable from the known inversion polymorphism affecting the ~0.7-Mb sequence intervening the LCR. Its formation is best explained by a replication-based mechanism (RBM) such as fork stalling and template switching/microhomology-mediated break-induced replication (FoSTeS/MMBIR). This finding supports the hypothesis that the inverted LCR can not only facilitate the formation of the non-allelic homologous recombination-mediated inversion polymorphism but it also promotes the occurrence of more complex rearrangements that can be associated with a large inversion, as well, but are mediated by a RBM. This further suggests that among the inversion polymorphism on 7p22.1, more complex rearrangements might be hidden. Furthermore, as the locus is embedded in a common fragile site (CFS) region, this rearrangement also supports the recently raised hypothesis that CFS sequence motifs may facilitate replication-based rearrangement mechanisms.
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Morais S, Bastos-Ferreira R, Sequeiros J, Alonso I. Genomic mechanisms underlying PARK2 large deletions identified in a cohort of patients with PD. NEUROLOGY-GENETICS 2016; 2:e73. [PMID: 27182553 PMCID: PMC4856358 DOI: 10.1212/nxg.0000000000000073] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 03/09/2016] [Indexed: 11/15/2022]
Abstract
OBJECTIVES To identify the genomic mechanisms that result in PARK2 large gene deletions. METHODS We conducted mutation screening using PCR amplification of PARK2-coding regions and exon-intron boundaries, followed by sequencing to evaluate a large series of 244 unrelated Portuguese patients with symptoms of Parkinson disease. For the detection of large gene rearrangements, we performed multiplex ligation-dependent probe amplification, followed by long-range PCR and sequencing to map deletion breakpoints. RESULTS We identified biallelic pathogenic parkin mutations in 40 of the 244 patients. There were 18 different mutations, some of them novel. This study included mapping of 17 deletion breakpoints showing that nonhomologous end joining is the most common mechanism responsible for these gene rearrangements. None of these deletion breakpoints were previously described, and only one was present in 2 unrelated families, indicating that most of the deletions result from independent events. CONCLUSIONS The c.155delA mutation is highly prevalent in the Portuguese population (62.5% of the cases). Large deletions were present in 42.5% of the patients. We present the largest study on the molecular mechanisms that mediate PARK2 deletions in a homogeneous population.
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Affiliation(s)
- Sara Morais
- UnIGENe (S.M., J.S., I.A.), Institute for Molecular and Cell Biology; i3S (S.M., R.B.-F., J.S., I.A.), Instituto de Investigação e Inovação em Saúde; CGPP (R.B.-F., J.S., I.A.), Institute for Molecular and Cell Biology; and Instituto de Ciências Biomédicas Abel Salazar (J.S., I.A.), University of Porto, Portugal
| | - Rita Bastos-Ferreira
- UnIGENe (S.M., J.S., I.A.), Institute for Molecular and Cell Biology; i3S (S.M., R.B.-F., J.S., I.A.), Instituto de Investigação e Inovação em Saúde; CGPP (R.B.-F., J.S., I.A.), Institute for Molecular and Cell Biology; and Instituto de Ciências Biomédicas Abel Salazar (J.S., I.A.), University of Porto, Portugal
| | - Jorge Sequeiros
- UnIGENe (S.M., J.S., I.A.), Institute for Molecular and Cell Biology; i3S (S.M., R.B.-F., J.S., I.A.), Instituto de Investigação e Inovação em Saúde; CGPP (R.B.-F., J.S., I.A.), Institute for Molecular and Cell Biology; and Instituto de Ciências Biomédicas Abel Salazar (J.S., I.A.), University of Porto, Portugal
| | - Isabel Alonso
- UnIGENe (S.M., J.S., I.A.), Institute for Molecular and Cell Biology; i3S (S.M., R.B.-F., J.S., I.A.), Instituto de Investigação e Inovação em Saúde; CGPP (R.B.-F., J.S., I.A.), Institute for Molecular and Cell Biology; and Instituto de Ciências Biomédicas Abel Salazar (J.S., I.A.), University of Porto, Portugal
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Huttenlocher J, Stefansson H, Steinberg S, Helgadottir HT, Sveinbjörnsdóttir S, Riess O, Bauer P, Stefansson K. Heterozygote carriers for CNVs in PARK2 are at increased risk of Parkinson's disease. Hum Mol Genet 2015; 24:5637-43. [PMID: 26188007 DOI: 10.1093/hmg/ddv277] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Accepted: 07/10/2015] [Indexed: 01/26/2023] Open
Abstract
Together with point mutations, homozygous deletions or duplications in PARK2 are responsible for the majority of autosomal recessive juvenile Parkinsonism. It is debated, however, whether heterozygous carriers of these mutations are at increased risk of Parkinson's disease (PD). Our goal was to determine whether heterozygous carriers of copy number variants (CNVs) affecting exons of the PARK2 gene are at risk of PD that is greater than that of non-carriers. We searched for CNVs affecting exons of PARK2 in a sample of 105 749 genotyped Icelanders. In total, 989 carriers, including 24 diagnosed with PD, were identified. The heterozygous carriers were tested for association in a sample of 1415 PD patients and 40 474 controls ≥65 years of age. PD patients were more often heterozygous carriers of PARK2 CNVs than controls [odds ratio (OR) = 1.69, P = 0.03] and compound heterozygous PD patients for a CNV and a missense mutation were not found. Furthermore, we conducted a meta-analysis of studies reporting on case-control samples screened for heterozygous PARK2 CNVs. Ten studies were included in the final analysis, with 4538 cases and 4213 controls. The pooled OR and P-value for the published and Icelandic results showed significant association between PARK2 CNVs and risk of PD (OR = 2.11, P = 2.54 × 10(-6)). Our analysis shows that heterozygous carriers of CNVs affecting exons of PARK2 have greater risk of PD than non-carriers.
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Affiliation(s)
- Johanna Huttenlocher
- deCODE Genetics/AMGEN, Reykjavik 101, Iceland, Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen D-72076, Germany
| | | | | | | | - Sigurlaug Sveinbjörnsdóttir
- Department of Neurology, National University Hospital, Reykjavik 101, Iceland, Department of Neurology, MEHT, Broomfield Hospital, Court Road, Essex CM1 7ET, UK, Neuroscience Department, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK and
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen D-72076, Germany
| | - Peter Bauer
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen D-72076, Germany
| | - Kari Stefansson
- deCODE Genetics/AMGEN, Reykjavik 101, Iceland, Faculty of Medicine, University of Iceland, Reykjavik IS-101, Iceland
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Ambroziak W, Koziorowski D, Duszyc K, Górka-Skoczylas P, Potulska-Chromik A, Sławek J, Hoffman-Zacharska D. Genomic instability in the PARK2 locus is associated with Parkinson's disease. J Appl Genet 2015; 56:451-461. [PMID: 25833766 PMCID: PMC4617850 DOI: 10.1007/s13353-015-0282-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 03/05/2015] [Accepted: 03/05/2015] [Indexed: 12/01/2022]
Abstract
Parkinson’s disease (PD) is a common neurodegenerative disorder affecting mostly elderly people, although there is a group of patients developing so-called early-onset PD (EOPD). Mutations in the PARK2 gene are a common cause of autosomal recessive EOPD. PARK2 belongs to the family of extremely large human genes which are often localised in genomic common fragile sites (CFSs) and exhibit gross instability. PARK2 is located in the centre of FRA6E, the third most mutation-susceptible CFS of the human genome. The gene encompasses a region of 1.3 Mbp and, among its mutations, large rearrangements of single or multiple exons account for around 50 %. We performed an analysis of the PARK2 gene in a group of 344 PD patients with EOPD and classical form of the disease. Copy number changes were first identified using multiplex ligation probe amplification (MLPA), with their ranges characterised by array comparative genomic hybridisation (aCGH). Exact breakpoints were mapped using direct sequencing. Rearrangements were found in eight subjects, including five deletions and three duplications. Rearrangements were mostly non-recurrent and no repetitive sequences or extended homologies were identified in the regions flanking breakpoint junctions. However, in most cases, 1–3 bp microhomologies were present, strongly suggesting that microhomology-mediated mechanisms, specifically non-homologous end joining (NHEJ) and fork stalling and template switching (FoSTeS)/microhomology-mediated break-induced replication (MMBIR), are predominantly involved in the rearrangement processes in this genomic region.
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Affiliation(s)
- Wojciech Ambroziak
- Department of Medical Genetics, Institute of Mother and Child, Kasprzaka 17A, 01-211, Warsaw, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Dariusz Koziorowski
- Department of Neurology, Faculty of Heath Science, Medical University of Warsaw, Kondratowicza 8, 03-242, Warsaw, Poland
| | - Kinga Duszyc
- Department of Medical Genetics, Institute of Mother and Child, Kasprzaka 17A, 01-211, Warsaw, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Paulina Górka-Skoczylas
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Anna Potulska-Chromik
- Department of Neurology, Medical University of Warsaw, Banacha 1, 02-097, Warsaw, Poland
| | - Jarosław Sławek
- Department of Neurological and Psychiatric Nursing, Medical University of Gdańsk, Dębinki 7, 80-952, Gdańsk, Poland
| | - Dorota Hoffman-Zacharska
- Department of Medical Genetics, Institute of Mother and Child, Kasprzaka 17A, 01-211, Warsaw, Poland. .,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawińskiego 5a, 02-106, Warsaw, Poland.
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Ozeri-Galai E, Tur-Sinai M, Bester AC, Kerem B. Interplay between genetic and epigenetic factors governs common fragile site instability in cancer. Cell Mol Life Sci 2014; 71:4495-506. [PMID: 25297918 PMCID: PMC11113459 DOI: 10.1007/s00018-014-1719-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 08/28/2014] [Indexed: 11/28/2022]
Abstract
Common fragile sites (CFSs) are regions within the normal chromosomal structure that were characterized as hotspots for genomic instability in cancer almost 30 years ago. In recent years, many efforts have been made to understand the basis of CFS fragility and their involvement in the genomic signature of instability found in malignant tumors. CFSs are among the first regions to undergo genomic instability during cancer development because of their intrinsic sensitivity to replication stress conditions, which result from oncogene expression. The preferred sensitivity of CFSs to replication stress stems from various mechanisms including: replication fork arrest at AT-rich repeats, origin paucity along large genomic regions, failure in activation of dormant origins, late replication timing, collision between replication and transcription along large genes, all leading to incomplete replication of the CFS region and resulting in chromosomal instability. Here we review shared and unique characteristics of CFSs, their underlying causes and implications, particularly for the development of cancer.
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Affiliation(s)
- Efrat Ozeri-Galai
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Edmond J. Safra Campus, 91904 Jerusalem, Israel
| | - Michal Tur-Sinai
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Edmond J. Safra Campus, 91904 Jerusalem, Israel
| | - Assaf C. Bester
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Edmond J. Safra Campus, 91904 Jerusalem, Israel
| | - Batsheva Kerem
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Edmond J. Safra Campus, 91904 Jerusalem, Israel
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Focal chromosomal copy number aberrations in cancer—Needles in a genome haystack. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:2698-2704. [DOI: 10.1016/j.bbamcr.2014.08.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 07/29/2014] [Accepted: 08/01/2014] [Indexed: 12/22/2022]
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Chen C, Ma H, Zhang F, Chen L, Xing X, Wang S, Zhang X, Luo Y. Screening of Duchenne muscular dystrophy (DMD) mutations and investigating its mutational mechanism in Chinese patients. PLoS One 2014; 9:e108038. [PMID: 25244321 PMCID: PMC4171529 DOI: 10.1371/journal.pone.0108038] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 08/25/2014] [Indexed: 11/18/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is a common X-linked recessive disease of muscle degeneration and death. In order to provide accurate and reliable genetic counseling and prenatal diagnosis, we screened DMD mutations in a cohort of 119 Chinese patients using multiplex ligation-dependent probe amplification (MLPA) and denaturing high performance liquid chromatography (DHPLC) followed by Sanger sequencing. In these unrelated DMD patients, we identified 11 patients with DMD small mutations (9.2%) and 81 patients with DMD deletions/duplications (del/dup) (68.1%), of which 64 (79.0%) were deletions, 16 (19.8%) were duplications, and one (1.2%) was both deletion and duplication. Furthermore, we analyzed the frequency of DMD breakpoint in the 64 deletion cases by calculating exon-deletion events of certain exon interval that revealed a novel mutation hotspot boundary. To explore why DMD rearrangement breakpoints were predisposed to specific regions (hotspot), we precisely characterized junction sequences of breakpoints at the nucleotide level in 21 patients with exon deleted/duplicated in DMD with a high-resolution SNP microarray assay. There were no exactly recurrent breakpoints and there was also no significant difference between single-exon del/dup and multiple-exon del/dup cases. The data from the current study provided a comprehensive strategy to detect DMD mutations for clinical practice, and identified two deletion hotspots at exon 43–55 and exon 10–23 by calculating exon-deletion events of certain exon interval. Furthermore, this is the first study to characterize DMD breakpoint at the nucleotide level in a Chinese population. Our observations provide better understanding of the mechanism for DMD gene rearrangements.
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Affiliation(s)
- Chen Chen
- The Research Center for Medical Genomics, Key Laboratory of Medical Cell Biology, Chinese Ministry of Education, College of Basic Medical Science, China Medical University, Shenyang, China
| | - Hongwei Ma
- Department of Developing Pediatrics, Shengjing Hospital, China Medical University, Shenyang, China
| | - Feng Zhang
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Lu Chen
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Xuesha Xing
- The Research Center for Medical Genomics, Key Laboratory of Medical Cell Biology, Chinese Ministry of Education, College of Basic Medical Science, China Medical University, Shenyang, China
| | - Shusen Wang
- The Research Center for Medical Genomics, Key Laboratory of Medical Cell Biology, Chinese Ministry of Education, College of Basic Medical Science, China Medical University, Shenyang, China
| | - Xue Zhang
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yang Luo
- The Research Center for Medical Genomics, Key Laboratory of Medical Cell Biology, Chinese Ministry of Education, College of Basic Medical Science, China Medical University, Shenyang, China
- * E-mail:
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Guerreiro R, Brás J, Hardy J, Singleton A. Next generation sequencing techniques in neurological diseases: redefining clinical and molecular associations. Hum Mol Genet 2014; 23:R47-53. [PMID: 24794858 PMCID: PMC4170717 DOI: 10.1093/hmg/ddu203] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The development of next-generation sequencing technologies has allowed for the identification of several new genes and genetic factors in human genetics. Common results from the application of these technologies have revealed unexpected presentations for mutations in known disease genes. In this review, we summarize the major contributions of exome sequencing to the study of neurodegenerative disorders and other neurological conditions and discuss the interface between Mendelian and complex neurological diseases with a particular focus on pleiotropic events.
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Affiliation(s)
- Rita Guerreiro
- Department of Molecular Neuroscience and Reta Lila Weston Laboratories, UCL Institute of Neurology, London WC1N 1PJ, UK Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD 20892, USA
| | - José Brás
- Department of Molecular Neuroscience and Reta Lila Weston Laboratories, UCL Institute of Neurology, London WC1N 1PJ, UK
| | - John Hardy
- Department of Molecular Neuroscience and Reta Lila Weston Laboratories, UCL Institute of Neurology, London WC1N 1PJ, UK
| | - Andrew Singleton
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD 20892, USA
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49
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Chai C, Lim KL. Genetic insights into sporadic Parkinson's disease pathogenesis. Curr Genomics 2014; 14:486-501. [PMID: 24532982 PMCID: PMC3924245 DOI: 10.2174/1389202914666131210195808] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 09/09/2013] [Accepted: 10/22/2013] [Indexed: 12/23/2022] Open
Abstract
Intensive research over the last 15 years has led to the identification of several autosomal recessive and dominant
genes that cause familial Parkinson’s disease (PD). Importantly, the functional characterization of these genes has
shed considerable insights into the molecular mechanisms underlying the etiology and pathogenesis of PD. Collectively;
these studies implicate aberrant protein and mitochondrial homeostasis as key contributors to the development of PD, with
oxidative stress likely acting as an important nexus between the two pathogenic events. Interestingly, recent genome-wide
association studies (GWAS) have revealed variations in at least two of the identified familial PD genes (i.e. α-synuclein
and LRRK2) as significant risk factors for the development of sporadic PD. At the same time, the studies also uncovered
variability in novel alleles that is associated with increased risk for the disease. Additionally, in-silico meta-analyses of
GWAS data have allowed major steps into the investigation of the roles of gene-gene and gene-environment interactions
in sporadic PD. The emergent picture from the progress made thus far is that the etiology of sporadic PD is multi-factorial
and presumably involves a complex interplay between a multitude of gene networks and the environment. Nonetheless,
the biochemical pathways underlying familial and sporadic forms of PD are likely to be shared.
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Affiliation(s)
- Chou Chai
- Duke-NUS Graduate Medical School, Singapore
| | - Kah-Leong Lim
- Duke-NUS Graduate Medical School, Singapore ; Department of Physiology, National University of Singapore, Singapore ; Neurodegeneration Research Laboratory, National Neuroscience Institute, Singapore
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50
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Ishiura H, Takahashi Y, Hayashi T, Saito K, Furuya H, Watanabe M, Murata M, Suzuki M, Sugiura A, Sawai S, Shibuya K, Ueda N, Ichikawa Y, Kanazawa I, Goto J, Tsuji S. Molecular epidemiology and clinical spectrum of hereditary spastic paraplegia in the Japanese population based on comprehensive mutational analyses. J Hum Genet 2014; 59:163-72. [PMID: 24451228 DOI: 10.1038/jhg.2013.139] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 11/16/2013] [Accepted: 11/29/2013] [Indexed: 12/12/2022]
Abstract
Hereditary spastic paraplegia (HSP) is one of the most genetically heterogeneous neurodegenerative disorders characterized by progressive spasticity and pyramidal weakness of lower limbs. Because >30 causative genes have been identified, screening of multiple genes is required for establishing molecular diagnosis of individual patients with HSP. To elucidate molecular epidemiology of HSP in the Japanese population, we have conducted mutational analyses of 16 causative genes of HSP (L1CAM, PLP1, ATL1, SPAST, CYP7B1, NIPA1, SPG7, KIAA0196, KIF5A, HSPD1, BSCL2, SPG11, SPG20, SPG21, REEP1 and ZFYVE27) using resequencing microarrays, array-based comparative genomic hybridization and Sanger sequencing. The mutational analysis of 129 Japanese patients revealed 49 mutations in 46 patients, 32 of which were novel. Molecular diagnosis was accomplished for 67.3% (33/49) of autosomal dominant HSP patients. Even among sporadic HSP patients, mutations were identified in 11.1% (7/63) of them. The present study elucidated the molecular epidemiology of HSP in the Japanese population and further broadened the mutational and clinical spectra of HSP.
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Affiliation(s)
- Hiroyuki Ishiura
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yuji Takahashi
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Toshihiro Hayashi
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kayoko Saito
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Hirokazu Furuya
- Department of Neurology, Neuro-Muscular Center, National Omuta Hospital, Fukuoka, Japan
| | - Mitsunori Watanabe
- Department of Neurology, Institute of Brain Science, Hirosaki University Graduate School of Medicine, Aomori, Japan
| | - Miho Murata
- Department of Neurology, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Mikiya Suzuki
- Department of Neurology, Higashisaitama Hospital, National Hospital Organization, Saitama, Japan
| | - Akira Sugiura
- Department of Neurology, Shizuoka Institute of Epilepsy and Neurological Disorders, Shizuoka, Japan
| | - Setsu Sawai
- 1] Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan [2] Division of Laboratory Medicine and Clinical Genetics, Chiba University Hospital, Chiba, Japan
| | - Kazumoto Shibuya
- Department of Neurology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Naohisa Ueda
- 1] Department of Neurology, Chigasaki Municipal Hospital, Kanagawa, Japan [2] Department of Neurology, Yokohama City University School of Medicine, Kanagawa, Japan
| | - Yaeko Ichikawa
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ichiro Kanazawa
- Graduate School, International University of Health and Welfare, Tokyo, Japan
| | - Jun Goto
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shoji Tsuji
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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