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Passchier EMJ, Bisseling Q, Helman G, van Spaendonk RML, Simons C, Olsthoorn RCL, van der Veen H, Abbink TEM, van der Knaap MS, Min R. Megalencephalic leukoencephalopathy with subcortical cysts: a variant update and review of the literature. Front Genet 2024; 15:1352947. [PMID: 38487253 PMCID: PMC10938252 DOI: 10.3389/fgene.2024.1352947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 01/29/2024] [Indexed: 03/17/2024] Open
Abstract
The leukodystrophy megalencephalic leukoencephalopathy with subcortical cysts (MLC) is characterized by infantile-onset macrocephaly and chronic edema of the brain white matter. With delayed onset, patients typically experience motor problems, epilepsy and slow cognitive decline. No treatment is available. Classic MLC is caused by bi-allelic recessive pathogenic variants in MLC1 or GLIALCAM (also called HEPACAM). Heterozygous dominant pathogenic variants in GLIALCAM lead to remitting MLC, where patients show a similar phenotype in early life, followed by normalization of white matter edema and no clinical regression. Rare patients with heterozygous dominant variants in GPRC5B and classic MLC were recently described. In addition, two siblings with bi-allelic recessive variants in AQP4 and remitting MLC have been identified. The last systematic overview of variants linked to MLC dates back to 2006. We provide an updated overview of published and novel variants. We report on genetic variants from 508 patients with MLC as confirmed by MRI diagnosis (258 from our database and 250 extracted from 64 published reports). We describe 151 unique MLC1 variants, 29 GLIALCAM variants, 2 GPRC5B variants and 1 AQP4 variant observed in these MLC patients. We include experiments confirming pathogenicity for some variants, discuss particularly notable variants, and provide an overview of recent scientific and clinical insight in the pathophysiology of MLC.
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Affiliation(s)
- Emma M. J. Passchier
- Department of Child Neurology, Amsterdam Leukodystrophy Center, Emma Children’s Hospital, Amsterdam University Medical Center, Amsterdam Neuroscience, Amsterdam, Netherlands
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Quinty Bisseling
- Department of Child Neurology, Amsterdam Leukodystrophy Center, Emma Children’s Hospital, Amsterdam University Medical Center, Amsterdam Neuroscience, Amsterdam, Netherlands
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Guy Helman
- Translational Bioinformatics, Murdoch Children’s Research Institute, The Royal Children’s Hospital, Parkville, VIC, Australia
| | | | - Cas Simons
- Translational Bioinformatics, Murdoch Children’s Research Institute, The Royal Children’s Hospital, Parkville, VIC, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | | | - Hieke van der Veen
- Department of Child Neurology, Amsterdam Leukodystrophy Center, Emma Children’s Hospital, Amsterdam University Medical Center, Amsterdam Neuroscience, Amsterdam, Netherlands
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Truus E. M. Abbink
- Department of Child Neurology, Amsterdam Leukodystrophy Center, Emma Children’s Hospital, Amsterdam University Medical Center, Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Marjo S. van der Knaap
- Department of Child Neurology, Amsterdam Leukodystrophy Center, Emma Children’s Hospital, Amsterdam University Medical Center, Amsterdam Neuroscience, Amsterdam, Netherlands
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Rogier Min
- Department of Child Neurology, Amsterdam Leukodystrophy Center, Emma Children’s Hospital, Amsterdam University Medical Center, Amsterdam Neuroscience, Amsterdam, Netherlands
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam, Netherlands
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2
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Amin M, Vignal C, Hamed AAA, Mohammed IN, Elseed MA, Drunat S, Babai A, Eltaraifee E, Elbadi I, Abubaker R, Mustafa D, Yahia A, Koko M, Osman M, Bakhit Y, Elshafea A, Alsiddig M, Haroun S, Lelay G, Elsayed LEO, Ahmed AE, Boespflug-Tanguy O, Dorboz I. Novel variants causing megalencephalic leukodystrophy in Sudanese families. J Hum Genet 2021; 67:127-132. [PMID: 34504271 DOI: 10.1038/s10038-021-00945-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 05/12/2021] [Accepted: 05/28/2021] [Indexed: 11/09/2022]
Abstract
Mutations in MLC1 cause megalencephalic leukoencephalopathy with subcortical cysts (MLC), a rare form of leukodystrophy characterized by macrocephaly, epilepsy, spasticity, and slow mental deterioration. Genetic studies of MLC are lacking from many parts of the world, especially in Sub-Saharan Africa. Genomic DNA was extracted for 67 leukodystrophic patients from 43 Sudanese families. Mutations were screened using the NGS panel testing 139 leukodystrophies and leukoencephalopathies causing genes (NextSeq500 Illumina). Five homozygous MLC1 variants were discovered in seven patients from five distinct families, including three consanguineous families from the same region of Sudan. Three variants were missense (c.971 T > G, p.Ile324Ser; c.344 T > C, p.Phe115Ser; and c.881 C > T, p.Pro294Leu), one duplication (c.831_838dupATATCTGT, p.Ser280Tyrfs*8), and one synonymous/splicing-site mutation (c.762 C > T, p.Ser254). The segregation pattern was consistent with autosomal recessive inheritance. The clinical presentation and brain MRI of the seven affected patients were consistent with the diagnosis of MLC1. Due to the high frequency of distinct MLC1 mutations found in our leukodystrophic Sudanese families, we analyzed the coding sequence of MLC1 gene in 124 individuals from the Sudanese genome project in comparison with the 1000-genome project. We found that Sudan has the highest proportion of deleterious variants in MLC1 gene compared with other populations from the 1000-genome project.
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Affiliation(s)
- Mutaz Amin
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan.,Université de Paris, NeuroDiderot, UMR 1141, INSERM, Paris, France
| | - Cedric Vignal
- Unité de Génétique Moleculaire, Departement de Genetique Médicale, APHP, Hopital Robert-Debré, Paris, France
| | - Ahlam A A Hamed
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | | | - Maha A Elseed
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Severine Drunat
- Université de Paris, NeuroDiderot, UMR 1141, INSERM, Paris, France.,Unité de Génétique Moleculaire, Departement de Genetique Médicale, APHP, Hopital Robert-Debré, Paris, France
| | - Arwa Babai
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | | | - Iman Elbadi
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Rayan Abubaker
- Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | - Doaa Mustafa
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Ashraf Yahia
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan.,Institut du Cerveau, INSERM U1127, CNRS UMR7225, Sorbonne Université, Paris, France
| | - Mahmoud Koko
- Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | - Melka Osman
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Yousuf Bakhit
- Faculty of Dentistry, University of Khartoum, Khartoum, Sudan
| | - Azza Elshafea
- Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | | | - Sahwah Haroun
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Gurvan Lelay
- Université de Paris, NeuroDiderot, UMR 1141, INSERM, Paris, France
| | | | - Ammar E Ahmed
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Odile Boespflug-Tanguy
- Université de Paris, NeuroDiderot, UMR 1141, INSERM, Paris, France.,Neuropediatrie, LEUKOFRANCE, APHP, Hopital Robert-Debré, Paris, France
| | - Imen Dorboz
- Université de Paris, NeuroDiderot, UMR 1141, INSERM, Paris, France.
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3
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International consensus recommendations on the diagnostic work-up for malformations of cortical development. Nat Rev Neurol 2020; 16:618-635. [PMID: 32895508 PMCID: PMC7790753 DOI: 10.1038/s41582-020-0395-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2020] [Indexed: 12/22/2022]
Abstract
Malformations of cortical development (MCDs) are neurodevelopmental disorders that result from abnormal development of the cerebral cortex in utero. MCDs place a substantial burden on affected individuals, their families and societies worldwide, as these individuals can experience lifelong drug-resistant epilepsy, cerebral palsy, feeding difficulties, intellectual disability and other neurological and behavioural anomalies. The diagnostic pathway for MCDs is complex owing to wide variations in presentation and aetiology, thereby hampering timely and adequate management. In this article, the international MCD network Neuro-MIG provides consensus recommendations to aid both expert and non-expert clinicians in the diagnostic work-up of MCDs with the aim of improving patient management worldwide. We reviewed the literature on clinical presentation, aetiology and diagnostic approaches for the main MCD subtypes and collected data on current practices and recommendations from clinicians and diagnostic laboratories within Neuro-MIG. We reached consensus by 42 professionals from 20 countries, using expert discussions and a Delphi consensus process. We present a diagnostic workflow that can be applied to any individual with MCD and a comprehensive list of MCD-related genes with their associated phenotypes. The workflow is designed to maximize the diagnostic yield and increase the number of patients receiving personalized care and counselling on prognosis and recurrence risk.
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4
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Understanding human DNA variants affecting pre-mRNA splicing in the NGS era. ADVANCES IN GENETICS 2019; 103:39-90. [PMID: 30904096 DOI: 10.1016/bs.adgen.2018.09.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Pre-mRNA splicing, an essential step in eukaryotic gene expression, relies on recognition of short sequences on the primary transcript intron ends and takes place along transcription by RNA polymerase II. Exonic and intronic auxiliary elements may modify the strength of exon definition and intron recognition. Splicing DNA variants (SV) have been associated with human genetic diseases at canonical intron sites, as well as exonic substitutions putatively classified as nonsense, missense or synonymous variants. Their effects on mRNA may be modulated by cryptic splice sites associated to the SV allele, comprehending exon skipping or shortening, and partial or complete intron retention. As splicing mRNA outputs result from combinatorial effects of both intrinsic and extrinsic factors, in vitro functional assays supported by computational analyses are recommended to assist SV pathogenicity assessment for human Mendelian inheritance diseases. The increasing use of next-generating sequencing (NGS) targeting full genomic gene sequence has raised awareness of the relevance of deep intronic SV in genetic diseases and inclusion of pseudo-exons into mRNA. Finally, we take advantage of recent advances in sequencing and computational technologies to analyze alternative splicing in cancer. We explore the Catalog of Somatic Mutations in Cancer (COSMIC) to describe the proportion of splice-site mutations in cis and trans regulatory elements. Genomic data from large cohorts of different cancer types are increasingly available, in addition to repositories of normal and somatic genetic variations. These are likely to bring new insights to understanding the genetic control of alternative splicing by mapping splicing quantitative trait loci in tumors.
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Dai CL, He WB, Du J, Tan YQ, Lu GX, Li W. A case of megalencephalic leukoencephalopathy with subcortical cysts type 1 was identified with a novel compound heterozygous alteration (c.135delC; c.423+2dupT) in China. Clin Case Rep 2017; 5:961-967. [PMID: 28588848 PMCID: PMC5458048 DOI: 10.1002/ccr3.986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 03/14/2017] [Accepted: 03/19/2017] [Indexed: 11/08/2022] Open
Abstract
We report a compound heterozygous mutation (c.135delC; c.423+2dupT) of MLC1 gene in a Chinese patient underlying infantile macrocephaly and neurological deterioration in early childhood. Brain MRI revealed diffusion abnormality in swollen white matter and a subcortical cyst. The cDNA sequencing analysis for the c.423+2dupT variant revealed skipping of exon 5.
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Affiliation(s)
- Cong-Ling Dai
- Institute of Reproductive and Stem Cell Engineering Central South University Hunan 410008 China
| | - Wen-Bin He
- Institute of Reproductive and Stem Cell Engineering Central South University Hunan 410008 China.,Reproductive and Genetic Hospital of Citic-Xiangya Hunan 410008 China
| | - Juan Du
- Institute of Reproductive and Stem Cell Engineering Central South University Hunan 410008 China.,Reproductive and Genetic Hospital of Citic-Xiangya Hunan 410008 China
| | - Yue-Qiu Tan
- Institute of Reproductive and Stem Cell Engineering Central South University Hunan 410008 China.,Reproductive and Genetic Hospital of Citic-Xiangya Hunan 410008 China
| | - Guang-Xiu Lu
- Institute of Reproductive and Stem Cell Engineering Central South University Hunan 410008 China.,Reproductive and Genetic Hospital of Citic-Xiangya Hunan 410008 China.,National Engineering and Research Center of Human Stem Cells Changsha Hunan 410000 China
| | - Wen Li
- Institute of Reproductive and Stem Cell Engineering Central South University Hunan 410008 China.,Reproductive and Genetic Hospital of Citic-Xiangya Hunan 410008 China
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6
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Lokki AI, Kaartokallio T, Holmberg V, Onkamo P, Koskinen LLE, Saavalainen P, Heinonen S, Kajantie E, Kere J, Kivinen K, Pouta A, Villa PM, Hiltunen L, Laivuori H, Meri S. Analysis of Complement C3 Gene Reveals Susceptibility to Severe Preeclampsia. Front Immunol 2017; 8:589. [PMID: 28611769 PMCID: PMC5446983 DOI: 10.3389/fimmu.2017.00589] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 05/03/2017] [Indexed: 11/29/2022] Open
Abstract
Preeclampsia (PE) is a common vascular disease of pregnancy with genetic predisposition. Dysregulation of the complement system has been implicated, but molecular mechanisms are incompletely understood. In this study, we determined the potential linkage of severe PE to the most central complement gene, C3. Three cohorts of Finnish patients and controls were recruited for a genetic case-control study. Participants were genotyped using Sequenom genotyping and Sanger sequencing. Initially, we studied 259 Finnish patients with severe PE and 426 controls from the Southern Finland PE and the Finnish population-based PE cohorts. We used a custom-made single nucleotide polymorphism (SNP) genotyping assay consisting of 98 SNPs in 18 genes that encode components of the complement system. Following the primary screening, C3 was selected as the candidate gene and consequently Sanger sequenced. Fourteen SNPs from C3 were also genotyped by a Sequenom panel in 960 patients with severe PE and 705 controls, including already sequenced individuals. Three of the 43 SNPs observed within C3 were associated with severe PE: rs2287845 (p = 0.038, OR = 1.158), rs366510 (p = 0.039, OR = 1.158), and rs2287848 (p = 0.041, OR = 1.155). We also discovered 16 SNP haplotypes with extreme linkage disequilibrium in the middle of the gene with a protective (p = 0.044, OR = 0.628) or a predisposing (p = 0.011, OR = 2.110) effect to severe PE depending on the allele combination. Genetic variants associated with PE are located in key domains of C3 and could thereby influence the function of C3. This is, as far as we are aware, the first candidate gene in the complement system with an association to a clinically relevant PE subphenotype, severe PE. The result highlights a potential role for the complement system in the pathogenesis of PE and may help in defining prognostic and therapeutic subgroups of preeclamptic women.
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Affiliation(s)
- A Inkeri Lokki
- Immunobiology, Research Programs Unit, University of Helsinki, Helsinki, Finland.,Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Bacteriology and Immunology, University of Helsinki, Helsinki, Finland
| | - Tea Kaartokallio
- Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Ville Holmberg
- Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Clinic of Infectious Diseases, HYKS Inflammation Center, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Päivi Onkamo
- Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Lotta L E Koskinen
- Immunobiology, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Päivi Saavalainen
- Immunobiology, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Seppo Heinonen
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Eero Kajantie
- Chronic Disease Prevention Unit, Department of Health, National Institute for Health and Welfare, Helsinki, Finland.,Children's Hospital, Helsinki University Hospital, University of Helsinki, Helsinki, Finland.,PEDEGO Research Unit, MRC Oulu, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Folkhälsan Institute of Genetics, Helsinki, Finland.,Molecular Neurology, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Katja Kivinen
- Division of Cardiovascular Medicine, University of Cambridge, Cambridge, UK
| | - Anneli Pouta
- PEDEGO Research Unit, MRC Oulu, Oulu University Hospital, University of Oulu, Oulu, Finland.,Department of Government Services, National Institute for Health and Welfare, Helsinki, Finland
| | - Pia M Villa
- Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | | | - Hannele Laivuori
- Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland.,Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Seppo Meri
- Immunobiology, Research Programs Unit, University of Helsinki, Helsinki, Finland.,Bacteriology and Immunology, University of Helsinki, Helsinki, Finland
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7
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Deep intronic mutations and human disease. Hum Genet 2017; 136:1093-1111. [DOI: 10.1007/s00439-017-1809-4] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 05/05/2017] [Indexed: 12/22/2022]
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8
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Cao B, Yan H, Guo M, Xie H, Wu Y, Gu Q, Xiao J, Shang J, Yang Y, Xiong H, Niu Z, Wu X, Jiang Y, Wang J. Ten Novel Mutations in Chinese Patients with Megalencephalic Leukoencephalopathy with Subcortical Cysts and a Long-Term Follow-Up Research. PLoS One 2016; 11:e0157258. [PMID: 27322623 PMCID: PMC4913951 DOI: 10.1371/journal.pone.0157258] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 05/26/2016] [Indexed: 11/21/2022] Open
Abstract
Objective Megalencephalic leukoencephalopathy with subcortical cysts (MLC, OMIM 604004) is a rare neurological deterioration disease. We aimed to clarify clinical and genetic features of Chinese MLC patients. Methods Clinical information and peripheral venous blood of 20 patients and their families were collected, Sanger-sequencing and Multiple Ligation-dependent Probe Amplification were performed to make genetic analysis. Splicing-site mutation was confirmed with RT-PCR. UPD was detected by haplotype analysis. Follow-up study was performed through telephone for 27 patients. Results Out of 20 patients, macrocephaly, classic MRI features, motor development delay and cognitive impairment were detected in 20(100%), 20(100%), 17(85%) and 4(20%) patients, respectively. 20(100%) were clinically diagnosed with MLC. 19(95%) were genetically diagnosed with 10 novel mutations in MLC1, MLC1 and GlialCAM mutations were identified in 15 and 4 patients, respectively. Deletion mutation from exon4 to exon9 and a homozygous point mutation due to maternal UPD of chromosome22 in MLC1 were found firstly. c.598-2A>C in MLC1 leads to the skip of exon8. c.772-1G>C in MLC1 accounting for 15.5%(9/58) alleles in Chinese patients might be a founder or a hot-spot mutation. Out of 27 patients in the follow-up study, head circumference was ranged from 56cm to 61cm in patients older than 5yeas old, with a median of 57cm. Motor development delay and cognitive impairment were detected in 22(81.5%) and 5(18.5%) patients, respectively. Motor and cognitive deterioration was found in 5 (18.5%) and 2 patients (7.4%), respectively. Improvements and MRI recovery were first found in Chinese patients. Rate of seizures (45.5%), transient motor retrogress (45.5%) and unconsciousness (13.6%) after head trauma was much higher than that after fever (18.2%, 9.1%, 0%, respectively). Significance It’s a clinical and genetic analysis and a follow-up study for largest sample of Chinese MLC patients, identifying 10 novel mutations, expanding mutation spectrums and discovering clinical features of Chinese MLC patients.
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Affiliation(s)
- Binbin Cao
- Department of Pediatrics, Peking University First Hospital, Beijing 100034, China
| | - Huifang Yan
- Department of Pediatrics, Peking University First Hospital, Beijing 100034, China
| | - Mangmang Guo
- Department of Pediatrics, Peking University First Hospital, Beijing 100034, China
- Department of Pediatrics, Beijing Tian Tan Hospital, Capital Medical University Beijing 100050, China
| | - Han Xie
- Department of Pediatrics, Peking University First Hospital, Beijing 100034, China
| | - Ye Wu
- Department of Pediatrics, Peking University First Hospital, Beijing 100034, China
| | - Qiang Gu
- Department of Pediatrics, Peking University First Hospital, Beijing 100034, China
| | - Jiangxi Xiao
- Department of Radiology, Peking University First Hospital, Beijing 100034, China
| | - Jing Shang
- Department of Pediatrics, Peking University First Hospital, Beijing 100034, China
- Department of Neurology, Shanxi Dayi Hospital, Taiyuan 030000, Shanxi Province, China
| | - Yanling Yang
- Department of Pediatrics, Peking University First Hospital, Beijing 100034, China
| | - Hui Xiong
- Department of Pediatrics, Peking University First Hospital, Beijing 100034, China
| | - Zhengping Niu
- Department of Neurology, First Hospital of Shanxi Medical University, Taiyuan 030001, Shanxi Province, China
| | - Xiru Wu
- Department of Pediatrics, Peking University First Hospital, Beijing 100034, China
| | - Yuwu Jiang
- Department of Pediatrics, Peking University First Hospital, Beijing 100034, China
- * E-mail: (YWJ); (JMW)
| | - Jingmin Wang
- Department of Pediatrics, Peking University First Hospital, Beijing 100034, China
- * E-mail: (YWJ); (JMW)
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9
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Updated genetic testing of Italian patients referred with a clinical diagnosis of primary hyperoxaluria. J Nephrol 2016; 30:219-225. [PMID: 26946417 DOI: 10.1007/s40620-016-0287-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Accepted: 02/13/2016] [Indexed: 12/16/2022]
Abstract
BACKGROUND Primary hyperoxaluria (PH) is a rare autosomal recessive disease commonly arising in childhood and presenting with nephrolithiasis, nephrocalcinosis and/or chronic renal failure. Three genes are currently known as responsible: alanine-glyoxylate aminotransferase (AGXT, PH type 1), glyoxylate reductase/hydroxypyruvate reductase (GRHPR, PH type 2), and 4-hydroxy-2-oxoglutarate aldolase (HOGA1, PH type 3). In our Centre, at the end of 2014 molecular diagnosis of PH1 had been performed in 80 patients, while one patient received a PH2 diagnosis. MATERIALS AND METHODS Fifteen patients referred to our Centre and suspected to have PH on clinical grounds were negative for pathogenic variants in the entire coding sequence and exon-intron boundaries of the AGXT gene. Therefore, we extended the analysis to the AGXT promoter region and the GRHPR and HOGA1 genes. RESULTS Two patients were heterozygous for two novel AGXT-promoter variants (c.-647C > T, c.-424C > T) that were probably non pathogenic. One patient was homozygous for a novel HOGA1 variant of intron 2 (c.341-81delT), whose pathogenicity predicted by in silico splicing tools was not confirmed by a minigene splicing assay in COS-7 and HEK293T cells. CONCLUSION New genetic subtypes of PH can be hypothesized in our patients, that may be caused by mutations in other gene encoding proteins of glyoxylate metabolism. Alternatively, some kind of mutations (e.g., deletions/duplications, deep intronic splicing regulatory variants) could be missed in a few cases, similarly to other genetic diseases.
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10
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Longo MG, Vairo F, Souza CF, Giugliani R, Vedolin LM. Brain imaging and genetic risk in the pediatric population, part 1: inherited metabolic diseases. Neuroimaging Clin N Am 2015; 25:31-51. [PMID: 25476511 DOI: 10.1016/j.nic.2014.09.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
In this article, the genotype-MR phenotype correlation of the most common or clinically important inherited metabolic diseases (IMD) in the pediatric population is reviewed. A nonsystematic search of the PubMed/Medline database of relevant studies about "genotype-phenotype correlation" in IMD was performed. Some MR phenotypes related to specific gene mutations were found, such as bilateral hypertrophy of inferior olives in patients harboring POLG and SURF1 mutations, and central lesions in the cervical spinal cord in patients with nonketotic hyperglycinemia harboring GLRX5 gene mutation.
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Affiliation(s)
- Maria Gabriela Longo
- Radiology Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
| | - Filippo Vairo
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil; Post Graduation Program on Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Carolina Fischinger Souza
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
| | - Roberto Giugliani
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil; Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Leonardo Modesti Vedolin
- Radiology Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil; Post Graduation Program on Medical Sciences: Medicine, Department of Internal Medicine, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil.
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11
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Deep intronic GPR143 mutation in a Japanese family with ocular albinism. Sci Rep 2015; 5:11334. [PMID: 26061757 PMCID: PMC4650666 DOI: 10.1038/srep11334] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 05/21/2015] [Indexed: 11/08/2022] Open
Abstract
Deep intronic mutations are often ignored as possible causes of human disease. Using whole-exome sequencing, we analysed genomic DNAs of a Japanese family with two male siblings affected by ocular albinism and congenital nystagmus. Although mutations or copy number alterations of coding regions were not identified in candidate genes, the novel intronic mutation c.659-131 T > G within GPR143 intron 5 was identified as hemizygous in affected siblings and as heterozygous in the unaffected mother. This mutation was predicted to create a cryptic splice donor site within intron 5 and activate a cryptic acceptor site at 41nt upstream, causing the insertion into the coding sequence of an out-of-frame 41-bp pseudoexon with a premature stop codon in the aberrant transcript, which was confirmed by minigene experiments. This result expands the mutational spectrum of GPR143 and suggests the utility of next-generation sequencing integrated with in silico and experimental analyses for improving the molecular diagnosis of this disease.
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Fuchs-Telem D, Nousbeck J, Singer A, McGrath JA, Sarig O, Sprecher E. New intragenic and promoter region deletion mutations in FERMT1 underscore genetic homogeneity in Kindler syndrome. Clin Exp Dermatol 2015; 39:361-7. [PMID: 24635080 DOI: 10.1111/ced.12222] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2013] [Indexed: 12/17/2022]
Abstract
BACKGROUND Kindler syndrome (KS) is a rare autosomal recessive skin disorder, which was recently reclassified as a subtype of epidermolysis bullosa. Despite the fact that loss-of-function mutations in the FERMT1 gene, encoding kindlin-1, have been shown to cause the syndrome in numerous patients, a small number of typical cases of KS in which FERMT1 mutations could not be identified has raised the possibility that the disorder may be genetically heterogeneous. AIM To assess two highly consanguineous families with clinical characteristics of KS. RESULTS In the first family, a hitherto unreported deletion (c.137-140delTAGT) in FERMT1 was detected, which is predicted to lead to premature termination of translation. However, direct sequencing of the coding region of FERMT1 failed to disclose any pathogenic change in the second family. To confirm the possibility that the disease in this family may be due to a mutation in another gene, we used homozygosity mapping, and found that all affected family members share a segment of homozygosity on 20p12.3, spanning the FERMT1 gene. Accordingly, a large and highly unusual deletion (g.-711-1241del) spanning the putative FERMT1 promoter sequence and the first noncoding exon of the gene was found to cosegregate with the disease phenotype in this family, and to prevent transcription of the gene, as attested by the lack of FERMT1 message in the skin of a patient. CONCLUSION The present data provide evidence in support of genetic homogeneity in KS.
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Affiliation(s)
- D Fuchs-Telem
- Department of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel
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Siva K, Covello G, Denti MA. Exon-skipping antisense oligonucleotides to correct missplicing in neurogenetic diseases. Nucleic Acid Ther 2014; 24:69-86. [PMID: 24506781 DOI: 10.1089/nat.2013.0461] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Alternative splicing is an important regulator of the transcriptome. However, mutations may cause alteration of splicing patterns, which in turn leads to disease. During the past 10 years, exon skipping has been looked upon as a powerful tool for correction of missplicing in disease and progress has been made towards clinical trials. In this review, we discuss the use of antisense oligonucleotides to correct splicing defects through exon skipping, with a special focus on diseases affecting the nervous system, and the latest stage achieved in its progress.
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Affiliation(s)
- Kavitha Siva
- 1 Center for Integrative Biology (CIBIO), University of Trento , Trento, Italy
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Role of pseudoexons and pseudointrons in human cancer. Int J Cell Biol 2013; 2013:810572. [PMID: 24204383 PMCID: PMC3800588 DOI: 10.1155/2013/810572] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 08/09/2013] [Indexed: 11/18/2022] Open
Abstract
In all eukaryotic organisms, pre-mRNA splicing and alternative splicing processes play an essential role in regulating the flow of information required to drive complex developmental and metabolic pathways. As a result, eukaryotic cells have developed a very efficient macromolecular machinery, called the spliceosome, to correctly recognize the pre-mRNA sequences that need to be inserted in a mature mRNA (exons) from those that should be removed (introns). In healthy individuals, alternative and constitutive splicing processes function with a high degree of precision and fidelity in order to ensure the correct working of this machinery. In recent years, however, medical research has shown that alterations at the splicing level play an increasingly important role in many human hereditary diseases, neurodegenerative processes, and especially in cancer origin and progression. In this minireview, we will focus on several genes whose association with cancer has been well established in previous studies, such as ATM, BRCA1/A2, and NF1. In particular, our objective will be to provide an overview of the known mechanisms underlying activation/repression of pseudoexons and pseudointrons; the possible utilization of these events as biomarkers of tumor staging/grading; and finally, the treatment options for reversing pathologic splicing events.
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Blázquez L, Aiastui A, Goicoechea M, Martins de Araujo M, Avril A, Beley C, García L, Valcárcel J, Fortes P, López de Munain A. In vitro correction of a pseudoexon-generating deep intronic mutation in LGMD2A by antisense oligonucleotides and modified small nuclear RNAs. Hum Mutat 2013; 34:1387-95. [PMID: 23864287 DOI: 10.1002/humu.22379] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 07/08/2013] [Indexed: 12/25/2022]
Abstract
Limb-girdle muscular dystrophy type 2A (LGMD2A) is the most frequent autosomal recessive muscular dystrophy. It is caused by mutations in the calpain-3 (CAPN3) gene. The majority of the mutations described to date are located in the coding sequence of the gene. However, it is estimated that 25% of the mutations are present at exon-intron boundaries and modify the pre-mRNA splicing of the CAPN3 transcript. We have previously described the first deep intronic mutation in the CAPN3 gene: c.1782+1072G>C mutation. This mutation causes the pseudoexonization of an intronic sequence of the CAPN3 gene in the mature mRNA. In the present work, we show that the point mutation generates the inclusion of the pseudoexon in the mRNA using a minigene assay. In search of a treatment that restores normal splicing, splicing modulation was induced by RNA-based strategies, which included antisense oligonucleotides and modified small-nuclear RNAs. The best effect was observed with antisense sequences, which induced pseudoexon skipping in both HeLa cells cotransfected with mutant minigene and in fibroblasts from patients. Finally, transfection of antisense sequences and siRNA downregulation of serine/arginine-rich splicing factor 1 (SRSF1) indicate that binding of this factor to splicing enhancer sequences is involved in pseudoexon activation.
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Affiliation(s)
- Lorea Blázquez
- Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain; Neuroscience Area, Health Research Institute Biodonostia, San Sebastian, Spain
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Havens MA, Duelli DM, Hastings ML. Targeting RNA splicing for disease therapy. WILEY INTERDISCIPLINARY REVIEWS. RNA 2013; 4:247-66. [PMID: 23512601 PMCID: PMC3631270 DOI: 10.1002/wrna.1158] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Splicing of pre-messenger RNA into mature messenger RNA is an essential step for the expression of most genes in higher eukaryotes. Defects in this process typically affect cellular function and can have pathological consequences. Many human genetic diseases are caused by mutations that cause splicing defects. Furthermore, a number of diseases are associated with splicing defects that are not attributed to overt mutations. Targeting splicing directly to correct disease-associated aberrant splicing is a logical approach to therapy. Splicing is a favorable intervention point for disease therapeutics, because it is an early step in gene expression and does not alter the genome. Significant advances have been made in the development of approaches to manipulate splicing for therapy. Splicing can be manipulated with a number of tools including antisense oligonucleotides, modified small nuclear RNAs (snRNAs), trans-splicing, and small molecule compounds, all of which have been used to increase specific alternatively spliced isoforms or to correct aberrant gene expression resulting from gene mutations that alter splicing. Here we describe clinically relevant splicing defects in disease states, the current tools used to target and alter splicing, specific mutations and diseases that are being targeted using splice-modulating approaches, and emerging therapeutics.
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Affiliation(s)
- Mallory A. Havens
- Department of Cell Biology and Anatomy, Chicago Medical School, Rosalind Franklin University of Medicine and Science. North Chicago, IL, 60064, USA. No conflicts of interest
| | - Dominik M. Duelli
- Department of Cellular and Molecular Pharmacology, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, 60064, USA. No conflicts of interest
| | - Michelle L. Hastings
- Department of Cell Biology and Anatomy, Chicago Medical School, Rosalind Franklin University of Medicine and Science. North Chicago, IL, 60064, USA, Phone: 847-578-8517 Fax: 847-578-3253. No conflicts of interest
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Next-generation sequencing reveals deep intronic cryptic ABCC8 and HADH splicing founder mutations causing hyperinsulinism by pseudoexon activation. Am J Hum Genet 2013; 92:131-6. [PMID: 23273570 DOI: 10.1016/j.ajhg.2012.11.017] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 10/30/2012] [Accepted: 11/20/2012] [Indexed: 02/01/2023] Open
Abstract
Next-generation sequencing (NGS) enables analysis of the human genome on a scale previously unachievable by Sanger sequencing. Exome sequencing of the coding regions and conserved splice sites has been very successful in the identification of disease-causing mutations, and targeting of these regions has extended clinical diagnostic testing from analysis of fewer than ten genes per phenotype to more than 100. Noncoding mutations have been less extensively studied despite evidence from mRNA analysis for the existence of deep intronic mutations in >20 genes. We investigated individuals with hyperinsulinaemic hypoglycaemia and biochemical or genetic evidence to suggest noncoding mutations by using NGS to analyze the entire genomic regions of ABCC8 (117 kb) and HADH (94 kb) from overlapping ~10 kb PCR amplicons. Two deep intronic mutations, c.1333-1013A>G in ABCC8 and c.636+471G>T HADH, were identified. Both are predicted to create a cryptic splice donor site and an out-of-frame pseudoexon. Sequence analysis of mRNA from affected individuals' fibroblasts or lymphoblastoid cells confirmed mutant transcripts with pseudoexon inclusion and premature termination codons. Testing of additional individuals showed that these are founder mutations in the Irish and Turkish populations, accounting for 14% of focal hyperinsulinism cases and 32% of subjects with HADH mutations in our cohort. The identification of deep intronic mutations has previously focused on the detection of aberrant mRNA transcripts in a subset of disorders for which RNA is readily obtained from the target tissue or ectopically expressed at sufficient levels. Our approach of using NGS to analyze the entire genomic DNA sequence is applicable to any disease.
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Cavalieri S, Pozzi E, Gatti RA, Brusco A. Deep-intronic ATM mutation detected by genomic resequencing and corrected in vitro by antisense morpholino oligonucleotide (AMO). Eur J Hum Genet 2012; 21:774-8. [PMID: 23211698 DOI: 10.1038/ejhg.2012.266] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Recent development of next-generation DNA sequencing (NGS) techniques is changing the approach to search for mutations in human genetic diseases. We applied NGS to study an A-T patient in which one of the two expected mutations was not found after DHPLC, cDNA sequencing and MLPA screening. The 160-kb ATM genomic region was divided into 31 partially overlapping fragments of 4-6 kb and amplified by long-range PCR in the patient and mother, who carried the same mutation by segregation. We identified six intronic variants that were shared by the two genomes and not reported in the dbSNP(132) database. Among these, c.1236-405C>T located in IVS11 was predicted to be pathogenic because it affected splicing. This mutation creates a cryptic novel donor (5') splice site (score 1.00) 405 bp upstream of the exon 12 acceptor (3') splice site. cDNA analysis showed the inclusion of a 212-bp non-coding 'pseudoexon' with a premature stop codon. We validated the functional effect of the splicing mutation using a minigene assay. Using antisense morpholino oligonucleotides, designed to mask the cryptic donor splice-site created by the c.1236-405C>T mutation, we abrogated the aberrant splicing product to a wild-type ATM transcript, and in vitro reverted the functional ATM kinase impairment of the patients' lymphoblasts. Resequencing is an effective strategy for identifying rare splicing mutations in patients for whom other mutation analyses have failed (DHPLC, MLPA, or cDNA sequencing). This is especially important because many of these patients will carry rare splicing variants that are amenable to antisense-based correction.
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Affiliation(s)
- Simona Cavalieri
- Università di Torino, Department of Medical Sciences & Azienda Ospedaliera Città della Salute e della Scienza, Turin, Italy
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