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Ma Q, Chen G, Li Y, Guo Z, Zhang X. The molecular genetics of PI3K/PTEN/AKT/mTOR pathway in the malformations of cortical development. Genes Dis 2024; 11:101021. [PMID: 39006182 PMCID: PMC11245990 DOI: 10.1016/j.gendis.2023.04.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 04/07/2023] [Accepted: 04/30/2023] [Indexed: 07/16/2024] Open
Abstract
Malformations of cortical development (MCD) are a group of developmental disorders characterized by abnormal cortical structures caused by genetic or harmful environmental factors. Many kinds of MCD are caused by genetic variation. MCD is the common cause of intellectual disability and intractable epilepsy. With rapid advances in imaging and sequencing technologies, the diagnostic rate of MCD has been increasing, and many potential genes causing MCD have been successively identified. However, the high genetic heterogeneity of MCD makes it challenging to understand the molecular pathogenesis of MCD and to identify effective targeted drugs. Thus, in this review, we outline important events of cortical development. Then we illustrate the progress of molecular genetic studies about MCD focusing on the PI3K/PTEN/AKT/mTOR pathway. Finally, we briefly discuss the diagnostic methods, disease models, and therapeutic strategies for MCD. The information will facilitate further research on MCD. Understanding the role of the PI3K/PTEN/AKT/mTOR pathway in MCD could lead to a novel strategy for treating MCD-related diseases.
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Affiliation(s)
- Qing Ma
- NHC and CAMS Key Laboratory of Molecular Probe and Targeted Theranostics, Harbin Medical University, Harbin, Heilongjiang 150000, China
| | - Guang Chen
- Department of Urology, The Fourth Hospital of Harbin Medical University, Harbin, Heilongjiang 150000, China
| | - Ying Li
- NHC and CAMS Key Laboratory of Molecular Probe and Targeted Theranostics, Harbin Medical University, Harbin, Heilongjiang 150000, China
- Department of Child and Adolescent Health, School of Public Health, Harbin Medical University, Harbin, Heilongjiang 150000, China
| | - Zhenming Guo
- Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - Xue Zhang
- NHC and CAMS Key Laboratory of Molecular Probe and Targeted Theranostics, Harbin Medical University, Harbin, Heilongjiang 150000, China
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Wang C, Zhao X, Wu Z, Huang G, Lin R, Chen H, Xu K, Sun K, Zhou H, Shu J. Identification of Differentially Expressed mRNAs and miRNAs and Related Regulatory Networks in Cumulus Oophorus Complexes Associated with Fertilization. Reprod Sci 2024; 31:1408-1419. [PMID: 38216777 DOI: 10.1007/s43032-023-01413-7] [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: 08/21/2023] [Accepted: 11/16/2023] [Indexed: 01/14/2024]
Abstract
Cumulus oophorus complexes (COCs) are the first extracellular barriers that sperm must pass through to fuse with oocytes, which have an important role in oocyte maturation and fertilization. However, little is known about the molecular mechanisms of COCs involved in fertilization. In this study, COCs were collected and then randomly divided into a test group that interacted with sperm and a control group that did not interact with sperm. Then, the total RNA was extracted; RNA transcriptome and small RNA libraries were prepared, sequenced, and analyzed. The results showed that 1283 differentially expressed genes (DEGs), including 560 upregulated and 723 downregulated genes. In addition, 57 differentially expressed miRNAs (DEMIs) with 35 upregulated and 22 downregulated were also detected. After the RNA-seq results were verified by RT-qPCR, 86 effective DEGs and 40 DEMIs were finally screened and a DEMI-DEG regulatory network was constructed. From this, the top ten hub target genes were HNF4A, SPN, WSCD1, TMEM239, SLC2A4, E2F2, SIAH3, ADORA3, PIK3R2, and GDNF, and they were all downregulated. The top ten hub DEMIs were miR-6876-5p, miR-877-3p, miR-6818-5p, miR-4690-3p, miR-6789-3p, miR-6837-5p, miR-6861-5p, miR-4421, miR-6501-5p, and miR-6875-3p, all of which were upregulated. The KEGG signaling pathway enrichment analysis showed that the effective DEGs were significantly enriched in the calcium, AMPK, and phospholipase D signaling pathways. Our study identified several DEGs and DEMIs and potential miRNA-mRNA regulatory pathways in COCs and these may contribute to fertilization. This study may provide novel insights into potential biomarkers for fertilization failure.
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Affiliation(s)
- Caizhu Wang
- Department of Reproductive Medicine, Guangxi Maternal and Child Health Hospital, Nanning, 530003, Guangxi, China
| | - Xin Zhao
- Department of Reproductive Medicine, Guangxi Maternal and Child Health Hospital, Nanning, 530003, Guangxi, China
| | - Zhulian Wu
- Department of Reproductive Medicine, Guangxi Maternal and Child Health Hospital, Nanning, 530003, Guangxi, China
| | - Guiting Huang
- Department of Reproductive Medicine, Guangxi Maternal and Child Health Hospital, Nanning, 530003, Guangxi, China
| | - Ruoyun Lin
- Department of Reproductive Medicine, Guangxi Maternal and Child Health Hospital, Nanning, 530003, Guangxi, China
| | - Huanhua Chen
- Department of Reproductive Medicine, Guangxi Maternal and Child Health Hospital, Nanning, 530003, Guangxi, China
| | - Kongrong Xu
- Department of Reproductive Medicine, Guangxi Maternal and Child Health Hospital, Nanning, 530003, Guangxi, China
| | - Kejian Sun
- Department of Reproductive Medicine, Guangxi Maternal and Child Health Hospital, Nanning, 530003, Guangxi, China
| | - Hong Zhou
- Department of Reproductive Medicine, Guangxi Maternal and Child Health Hospital, Nanning, 530003, Guangxi, China.
| | - Jinhui Shu
- Department of Reproductive Medicine, Guangxi Maternal and Child Health Hospital, Nanning, 530003, Guangxi, China.
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Järvelä I, Paetau R, Rajendran Y, Acharya A, Bharadwaj T, Leal SM, Lehesjoki AE, Palomäki M, Schrauwen I. Heterogeneous genetic patterns in bilateral perisylvian polymicrogyria: insights from a Finnish family cohort. Brain Commun 2024; 6:fcae142. [PMID: 38712318 PMCID: PMC11073749 DOI: 10.1093/braincomms/fcae142] [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: 12/08/2023] [Revised: 02/21/2024] [Accepted: 04/16/2024] [Indexed: 05/08/2024] Open
Abstract
Bilateral perisylvian polymicrogyria is the most common form of regional polymicrogyria within malformations of cortical development, constituting 20% of all malformations of cortical development. Bilateral perisylvian polymicrogyria is characterized by an excessive folding of the cerebral cortex and abnormal cortical layering. Notable clinical features include upper motoneuron dysfunction, dysarthria and asymmetric quadriparesis. Cognitive impairment and epilepsy are frequently observed. To identify genetic variants underlying bilateral perisylvian polymicrogyria in Finland, we examined 21 families using standard exome sequencing, complemented by optical genome mapping and/or deep exome sequencing. Pathogenic or likely pathogenic variants were identified in 5/21 (24%) of families, of which all were confirmed as de novo. These variants were identified in five genes, i.e. DDX23, NUS1, SCN3A, TUBA1A and TUBB2B, with NUS1 and DDX23 being associated with bilateral perisylvian polymicrogyria for the first time. In conclusion, our results confirm the previously reported genetic heterogeneity of bilateral perisylvian polymicrogyria and underscore the necessity of more advanced methods to elucidate the genetic background of bilateral perisylvian polymicrogyria.
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Affiliation(s)
- Irma Järvelä
- Department of Medical Genetics, University of Helsinki, 00251 Helsinki, Finland
| | - Ritva Paetau
- Department of Child Neurology, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
| | - Yasmin Rajendran
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Department of Neurology, Columbia University Medical Center, 10032 New York, NY, USA
| | - Anushree Acharya
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Department of Neurology, Columbia University Medical Center, 10032 New York, NY, USA
| | - Thashi Bharadwaj
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Department of Neurology, Columbia University Medical Center, 10032 New York, NY, USA
| | - Suzanne M Leal
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Department of Neurology, Columbia University Medical Center, 10032 New York, NY, USA
- Taub Institute, Columbia University Medical Center, 10032 New York, NY, USA
| | - Anna-Elina Lehesjoki
- Department of Medical Genetics, University of Helsinki, 00251 Helsinki, Finland
- Folkhälsan Research Center, 00290 Helsinki, Finland
| | - Maarit Palomäki
- Medical Imaging Center, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Department of Neurology, Columbia University Medical Center, 10032 New York, NY, USA
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Gooley S, Perucca P, Tubb C, Hildebrand MS, Berkovic SF. Somatic mosaicism in focal epilepsies. Curr Opin Neurol 2024; 37:105-114. [PMID: 38235675 DOI: 10.1097/wco.0000000000001244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
PURPOSE OF REVIEW Over the past decade, it has become clear that brain somatic mosaicism is an important contributor to many focal epilepsies. The number of cases and the range of underlying pathologies with somatic mosaicism are rapidly increasing. This growth in somatic variant discovery is revealing dysfunction in distinct molecular pathways in different focal epilepsies. RECENT FINDINGS We briefly summarize the current diagnostic yield of pathogenic somatic variants across all types of focal epilepsy where somatic mosaicism has been implicated and outline the specific molecular pathways affected by these variants. We will highlight the recent findings that have increased diagnostic yields such as the discovery of pathogenic somatic variants in novel genes, and new techniques that allow the discovery of somatic variants at much lower variant allele fractions. SUMMARY A major focus will be on the emerging evidence that somatic mosaicism may contribute to some of the more common focal epilepsies such as temporal lobe epilepsy with hippocampal sclerosis, which could lead to it being re-conceptualized as a genetic disorder.
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Affiliation(s)
- Samuel Gooley
- Epilepsy Research Centre, Department of Medicine, University of Melbourne
- Bladin-Berkovic Comprehensive Epilepsy Program, Department of Neurology, Austin Health, Heidelberg
| | - Piero Perucca
- Epilepsy Research Centre, Department of Medicine, University of Melbourne
- Bladin-Berkovic Comprehensive Epilepsy Program, Department of Neurology, Austin Health, Heidelberg
- Department of Neuroscience, Central Clinical School, Monash University
- Department of Neurology, Alfred Health, Melbourne
- Department of Neurology, The Royal Melbourne Hospital
| | - Caitlin Tubb
- Epilepsy Research Centre, Department of Medicine, University of Melbourne
| | - Michael S Hildebrand
- Epilepsy Research Centre, Department of Medicine, University of Melbourne
- Neuroscience Group, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Samuel F Berkovic
- Epilepsy Research Centre, Department of Medicine, University of Melbourne
- Bladin-Berkovic Comprehensive Epilepsy Program, Department of Neurology, Austin Health, Heidelberg
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5
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Hale AT, Boudreau H, Devulapalli R, Duy PQ, Atchley TJ, Dewan MC, Goolam M, Fieggen G, Spader HL, Smith AA, Blount JP, Johnston JM, Rocque BG, Rozzelle CJ, Chong Z, Strahle JM, Schiff SJ, Kahle KT. The genetic basis of hydrocephalus: genes, pathways, mechanisms, and global impact. Fluids Barriers CNS 2024; 21:24. [PMID: 38439105 PMCID: PMC10913327 DOI: 10.1186/s12987-024-00513-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 01/25/2024] [Indexed: 03/06/2024] Open
Abstract
Hydrocephalus (HC) is a heterogenous disease characterized by alterations in cerebrospinal fluid (CSF) dynamics that may cause increased intracranial pressure. HC is a component of a wide array of genetic syndromes as well as a secondary consequence of brain injury (intraventricular hemorrhage (IVH), infection, etc.) that can present across the age spectrum, highlighting the phenotypic heterogeneity of the disease. Surgical treatments include ventricular shunting and endoscopic third ventriculostomy with or without choroid plexus cauterization, both of which are prone to failure, and no effective pharmacologic treatments for HC have been developed. Thus, there is an urgent need to understand the genetic architecture and molecular pathogenesis of HC. Without this knowledge, the development of preventive, diagnostic, and therapeutic measures is impeded. However, the genetics of HC is extraordinarily complex, based on studies of varying size, scope, and rigor. This review serves to provide a comprehensive overview of genes, pathways, mechanisms, and global impact of genetics contributing to all etiologies of HC in humans.
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Affiliation(s)
- Andrew T Hale
- Department of Neurosurgery, University of Alabama at Birmingham, FOT Suite 1060, 1720 2ndAve, Birmingham, AL, 35294, UK.
| | - Hunter Boudreau
- Department of Neurosurgery, University of Alabama at Birmingham, FOT Suite 1060, 1720 2ndAve, Birmingham, AL, 35294, UK
| | - Rishi Devulapalli
- Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, UK
| | - Phan Q Duy
- Department of Neurosurgery, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Travis J Atchley
- Department of Neurosurgery, University of Alabama at Birmingham, FOT Suite 1060, 1720 2ndAve, Birmingham, AL, 35294, UK
| | - Michael C Dewan
- Division of Pediatric Neurosurgery, Monroe Carell Jr. Children's Hospital, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Mubeen Goolam
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Graham Fieggen
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Division of Pediatric Neurosurgery, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, South Africa
| | - Heather L Spader
- Department of Neurosurgery, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Anastasia A Smith
- Division of Pediatric Neurosurgery, Children's of Alabama, University of Alabama at Birmingham, Birmingham, AL, UK
| | - Jeffrey P Blount
- Division of Pediatric Neurosurgery, Children's of Alabama, University of Alabama at Birmingham, Birmingham, AL, UK
| | - James M Johnston
- Division of Pediatric Neurosurgery, Children's of Alabama, University of Alabama at Birmingham, Birmingham, AL, UK
| | - Brandon G Rocque
- Division of Pediatric Neurosurgery, Children's of Alabama, University of Alabama at Birmingham, Birmingham, AL, UK
| | - Curtis J Rozzelle
- Division of Pediatric Neurosurgery, Children's of Alabama, University of Alabama at Birmingham, Birmingham, AL, UK
| | - Zechen Chong
- Heflin Center for Genomics, University of Alabama at Birmingham, Birmingham, AL, UK
| | - Jennifer M Strahle
- Division of Pediatric Neurosurgery, St. Louis Children's Hospital, Washington University in St. Louis, St. Louis, MO, USA
| | - Steven J Schiff
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Kristopher T Kahle
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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6
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Akula SK, Chen AY, Neil JE, Shao DD, Mo A, Hylton NK, DiTroia S, Ganesh VS, Smith RS, O’Kane K, Yeh RC, Marciano JH, Kirkham S, Kenny CJ, Song JHT, Al Saffar M, Millan F, Harris DJ, Murphy AV, Klemp KC, Braddock SR, Brand H, Wong I, Talkowski ME, O’Donnell-Luria A, Lai A, Hill RS, Mochida GH, Doan RN, Barkovich AJ, Yang E, Amrom D, Andermann E, Poduri A, Walsh CA. Exome Sequencing and the Identification of New Genes and Shared Mechanisms in Polymicrogyria. JAMA Neurol 2023; 80:980-988. [PMID: 37486637 PMCID: PMC10366952 DOI: 10.1001/jamaneurol.2023.2363] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 03/23/2023] [Indexed: 07/25/2023]
Abstract
Importance Polymicrogyria is the most commonly diagnosed cortical malformation and is associated with neurodevelopmental sequelae including epilepsy, motor abnormalities, and cognitive deficits. Polymicrogyria frequently co-occurs with other brain malformations or as part of syndromic diseases. Past studies of polymicrogyria have defined heterogeneous genetic and nongenetic causes but have explained only a small fraction of cases. Objective To survey germline genetic causes of polymicrogyria in a large cohort and to consider novel polymicrogyria gene associations. Design, Setting, and Participants This genetic association study analyzed panel sequencing and exome sequencing of accrued DNA samples from a retrospective cohort of families with members with polymicrogyria. Samples were accrued over more than 20 years (1994 to 2020), and sequencing occurred in 2 stages: panel sequencing (June 2015 to January 2016) and whole-exome sequencing (September 2019 to March 2020). Individuals seen at multiple clinical sites for neurological complaints found to have polymicrogyria on neuroimaging, then referred to the research team by evaluating clinicians, were included in the study. Targeted next-generation sequencing and/or exome sequencing were performed on probands (and available parents and siblings) from 284 families with individuals who had isolated polymicrogyria or polymicrogyria as part of a clinical syndrome and no genetic diagnosis at time of referral from clinic, with sequencing from 275 families passing quality control. Main Outcomes and Measures The number of families in whom genetic sequencing yielded a molecular diagnosis that explained the polymicrogyria in the family. Secondarily, the relative frequency of different genetic causes of polymicrogyria and whether specific genetic causes were associated with co-occurring head size changes were also analyzed. Results In 32.7% (90 of 275) of polymicrogyria-affected families, genetic variants were identified that provided satisfactory molecular explanations. Known genes most frequently implicated by polymicrogyria-associated variants in this cohort were PIK3R2, TUBB2B, COL4A1, and SCN3A. Six candidate novel polymicrogyria genes were identified or confirmed: de novo missense variants in PANX1, QRICH1, and SCN2A and compound heterozygous variants in TMEM161B, KIF26A, and MAN2C1, each with consistent genotype-phenotype relationships in multiple families. Conclusions and Relevance This study's findings reveal a higher than previously recognized rate of identifiable genetic causes, specifically of channelopathies, in individuals with polymicrogyria and support the utility of exome sequencing for families affected with polymicrogyria.
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Affiliation(s)
- Shyam K. Akula
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts
- Harvard-MIT MD/PhD Program, Harvard Medical School, Boston, Massachusetts
| | - Allen Y. Chen
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
- Division of Rheumatology, Hospital for Special Surgery, New York, New York
| | - Jennifer E. Neil
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts
| | - Diane D. Shao
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
- Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts
| | - Alisa Mo
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
- Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts
| | - Norma K. Hylton
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts
- Harvard-MIT MD/PhD Program, Harvard Medical School, Boston, Massachusetts
| | - Stephanie DiTroia
- Program in Medical and Population Genetics, Center for Genomic Medicine, Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Vijay S. Ganesh
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts
| | - Richard S. Smith
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Katherine O’Kane
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts
| | - Rebecca C. Yeh
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts
| | - Jack H. Marciano
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts
| | - Samantha Kirkham
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts
| | - Connor J. Kenny
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts
| | - Janet H. T. Song
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts
| | - Muna Al Saffar
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts
- Department of Genetics and Genomics, United Arab Emirates University, United Arab Emirates
| | | | - David J. Harris
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts
| | - Andrea V. Murphy
- Division of Medical Genetics, Our Lady of the Lake Health System, Baton Rouge, Louisiana
| | - Kara C. Klemp
- Division of Medical Genetics, Department of Pediatrics Saint Louis University School of Medicine, St Louis, Missouri
| | - Stephen R. Braddock
- Division of Medical Genetics, Department of Pediatrics Saint Louis University School of Medicine, St Louis, Missouri
| | - Harrison Brand
- Program in Medical and Population Genetics, Center for Genomic Medicine, Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Neurology, Harvard Medical School, Boston, Massachusetts
| | - Isaac Wong
- Program in Medical and Population Genetics, Center for Genomic Medicine, Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Neurology, Harvard Medical School, Boston, Massachusetts
| | - Michael E. Talkowski
- Program in Medical and Population Genetics, Center for Genomic Medicine, Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Neurology, Harvard Medical School, Boston, Massachusetts
| | - Anne O’Donnell-Luria
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
- Program in Medical and Population Genetics, Center for Genomic Medicine, Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Abbe Lai
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
- Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts
| | - Robert Sean Hill
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts
| | - Ganeshwaran H. Mochida
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
- Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts
| | - Ryan N. Doan
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
| | - A. James Barkovich
- Benioff Children’s Hospital, Departments of Radiology, Pediatrics, Neurology, and Neurological Surgery, University of California, San Francisco, San Francisco
| | - Edward Yang
- Department of Radiology, Boston Children’s Hospital, Boston, Massachusetts
| | - Dina Amrom
- Neurogenetics Unit, Montreal Neurological Hospital and Institute, Montreal, Quebec, Canada
- Department of Neurology & Neurosurgery, McGill University, Montreal, Quebec, Canada
- Department of Neurology, Queen Fabiola Children’s University Hospital, Brussels, Belgium
- Pediatric Neurology Unit, Centre Hospitalier de Luxembourg, Grand-Duchy of Luxembourg
| | - Eva Andermann
- Department of Neurology & Neurosurgery, McGill University, Montreal, Quebec, Canada
- Pediatric Neurology Unit, Centre Hospitalier de Luxembourg, Grand-Duchy of Luxembourg
- Epilepsy Research Group, Montreal Neurological Hospital and Institute, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Annapurna Poduri
- Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts
| | - Christopher A. Walsh
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts
- Harvard-MIT MD/PhD Program, Harvard Medical School, Boston, Massachusetts
- Program in Medical and Population Genetics, Center for Genomic Medicine, Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
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7
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Morleo M, Venditti R, Theodorou E, Briere LC, Rosello M, Tirozzi A, Tammaro R, Al-Badri N, High FA, Shi J, Putti E, Ferrante L, Cetrangolo V, Torella A, Walker MA, Tenconi R, Iascone M, Mei D, Guerrini R, van der Smagt J, Kroes HY, van Gassen KLI, Bilal M, Umair M, Pingault V, Attie-Bitach T, Amiel J, Ejaz R, Rodan L, Zollino M, Agrawal PB, Del Bene F, Nigro V, Sweetser DA, Franco B. De novo missense variants in phosphatidylinositol kinase PIP5KIγ underlie a neurodevelopmental syndrome associated with altered phosphoinositide signaling. Am J Hum Genet 2023; 110:1377-1393. [PMID: 37451268 PMCID: PMC10432144 DOI: 10.1016/j.ajhg.2023.06.012] [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: 01/24/2023] [Revised: 06/22/2023] [Accepted: 06/22/2023] [Indexed: 07/18/2023] Open
Abstract
Phosphoinositides (PIs) are membrane phospholipids produced through the local activity of PI kinases and phosphatases that selectively add or remove phosphate groups from the inositol head group. PIs control membrane composition and play key roles in many cellular processes including actin dynamics, endosomal trafficking, autophagy, and nuclear functions. Mutations in phosphatidylinositol 4,5 bisphosphate [PI(4,5)P2] phosphatases cause a broad spectrum of neurodevelopmental disorders such as Lowe and Joubert syndromes and congenital muscular dystrophy with cataracts and intellectual disability, which are thus associated with increased levels of PI(4,5)P2. Here, we describe a neurodevelopmental disorder associated with an increase in the production of PI(4,5)P2 and with PI-signaling dysfunction. We identified three de novo heterozygous missense variants in PIP5K1C, which encodes an isoform of the phosphatidylinositol 4-phosphate 5-kinase (PIP5KIγ), in nine unrelated children exhibiting intellectual disability, developmental delay, acquired microcephaly, seizures, visual abnormalities, and dysmorphic features. We provide evidence that the PIP5K1C variants result in an increase of the endosomal PI(4,5)P2 pool, giving rise to ectopic recruitment of filamentous actin at early endosomes (EEs) that in turn causes dysfunction in EE trafficking. In addition, we generated an in vivo zebrafish model that recapitulates the disorder we describe with developmental defects affecting the forebrain, including the eyes, as well as craniofacial abnormalities, further demonstrating the pathogenic effect of the PIP5K1C variants.
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Affiliation(s)
- Manuela Morleo
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy; Department of Precision Medicine, University of Campania "Luigi Vanvitelli," Naples, Italy.
| | - Rossella Venditti
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy; Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II," Medical School, Naples, Italy
| | - Evangelos Theodorou
- Center for Genomic Medicine, Divisions of Pediatric Hematology/Oncology and Medical Genetics and Metabolism, Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Lauren C Briere
- Center for Genomic Medicine, Divisions of Pediatric Hematology/Oncology and Medical Genetics and Metabolism, Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Marion Rosello
- Sorbonne Université, INSERM U968, CNRS UMR 7210, Institut de la Vision, Paris, France
| | - Alfonsina Tirozzi
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli," Naples, Italy; Department of Epidemiology and Prevention, IRCCS NEUROMED, Pozzilli, Italy
| | - Roberta Tammaro
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy
| | - Nour Al-Badri
- Sorbonne Université, INSERM U968, CNRS UMR 7210, Institut de la Vision, Paris, France
| | - Frances A High
- Division of Medical Genetics & Metabolism, Massachusetts General Hospital for Children, Boston, MA 02114, USA
| | - Jiahai Shi
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Elena Putti
- Sorbonne Université, INSERM U968, CNRS UMR 7210, Institut de la Vision, Paris, France
| | - Luigi Ferrante
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy
| | - Viviana Cetrangolo
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy
| | - Annalaura Torella
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy; Department of Precision Medicine, University of Campania "Luigi Vanvitelli," Naples, Italy
| | - Melissa A Walker
- Department of Neurology, Division of Neurogenetics, Child Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Romano Tenconi
- Clinical Genetics Unit, Department of Women and Children's Health, University of Padova, Padova, Italy
| | - Maria Iascone
- Medical Genetics, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy
| | - Davide Mei
- Meyer Children's Hospital IRCCS, Neuroscience Department, Florence, Italy
| | - Renzo Guerrini
- Meyer Children's Hospital IRCCS, Neuroscience Department, Florence, Italy
| | - Jasper van der Smagt
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Hester Y Kroes
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Koen L I van Gassen
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Muhammad Bilal
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center & King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Veronica Pingault
- Service de Médecine Génomique des Maladies Rares, et Institut Imagine, Hôpital Necker-Enfants Malades, Paris, France
| | - Tania Attie-Bitach
- Service de Médecine Génomique des Maladies Rares, et Institut Imagine, Hôpital Necker-Enfants Malades, Paris, France
| | - Jeannine Amiel
- Service de Médecine Génomique des Maladies Rares, et Institut Imagine, Hôpital Necker-Enfants Malades, Paris, France
| | - Resham Ejaz
- Division of Genetics, Department of Pediatrics, McMaster Children's Hospital, Hamilton, ON, Canada
| | - Lance Rodan
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA; Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Marcella Zollino
- Institute of Medical Genetics, A. Gemelli School of Medicine, Catholic University of the Sacred Heart, Rome, Italy
| | - Pankaj B Agrawal
- Divisions of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA; Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Filippo Del Bene
- Sorbonne Université, INSERM U968, CNRS UMR 7210, Institut de la Vision, Paris, France
| | - Vincenzo Nigro
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy; Department of Precision Medicine, University of Campania "Luigi Vanvitelli," Naples, Italy
| | - David A Sweetser
- Center for Genomic Medicine, Divisions of Pediatric Hematology/Oncology and Medical Genetics and Metabolism, Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Brunella Franco
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy; Scuola Superiore Meridionale (SSM, School of Advanced Studies), Genomics and Experimental Medicine Program, Naples, Italy; Medical Genetics, Department of Translational Medicine, University of Naples "Federico II," Via Sergio Pansini, 80131 Naples, Italy
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8
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Gelot AB, Courtin T, Sileo C, Keren B, Soreze-Smagghue Y, Whalen S, Represa A. Polymicrogyria with Dysmorphic Neurons in a Patient with SNCA2 Mutation. J Neuropathol Exp Neurol 2022; 81:758-761. [PMID: 35788683 DOI: 10.1093/jnen/nlac052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Antoinette-Bernabe Gelot
- INMED, INSERM, Aix-Marseille University, Marseille, France.,Neuropathology, Hôpital Trousseau, Assistance Publique-Hôpitaux Parisiens (AP-HP), Sorbonne Université, Paris, France
| | - Thomas Courtin
- Genetic Department, Centre de Référence des Déficiences Intellectuelles de Causes Rares, GRC UPMC, "Déficiences Intellectuelles et Autisme", Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Chiara Sileo
- Department of Pediatric Imaging, Hôpital Trousseau, Assistance Publique-Hôpitaux Parisiens (AP-HP), Sorbonne Université, Paris, France
| | - Boris Keren
- Genetic Department, Centre de Référence des Déficiences Intellectuelles de Causes Rares, GRC UPMC, "Déficiences Intellectuelles et Autisme", Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Yohan Soreze-Smagghue
- Paediatric and Neonatal Reanimation, Hôpital Trousseau, Assistance Publique-Hôpitaux Parisiens (AP-HP), Sorbonne Université, Paris, France
| | - Sandra Whalen
- Genetic Department, Hôpital Trousseau, Assistance Publique-Hôpitaux Parisiens (AP-HP), Sorbonne Université, Paris, France
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9
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Zhou J, Xu N, Liu B, Wang C, He Z, Lenahan C, Tang W, Zeng H, Guo H. LncRNA XLOC013218 promotes cell proliferation and TMZ resistance by targeting PIK3R2-mediated PI3K/AKT pathway in glioma. Cancer Sci 2022; 113:2681-2692. [PMID: 35637600 PMCID: PMC9357648 DOI: 10.1111/cas.15387] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/11/2022] [Accepted: 04/20/2022] [Indexed: 11/28/2022] Open
Abstract
The discovery of long non-coding RNAs (lncRNAs) has improved the understanding of development and progression in various cancer sub-types. However, the role of lncRNAs in temozolomide (TMZ) resistance in glioblastoma (GBM) remains largely undefined. In this present study, the differential expression of lncRNAs were identified between U87 and U87TR (TMZ-resistant) cells. LncRNA XLOC013218 (XLOC) was drastically upregulated in TMZ-resistant cells and was associated with poor prognosis in glioma. Overexpression of XLOC markedly increased TMZ resistance, promoted proliferation, and inhibited apoptosis in vitro and in vivo. In addition, RNA-seq analysis and gain-of-function or loss-of-function studies revealed that PIK3R2 was the potential target of XLOC. Mechanistically, XLOC recruited Specificity Protein 1 (Sp1) transcription factor and promoted the binding of Sp1 to the promoters of PIK3R2, which elevated the expression of PIK3R2 in both mRNA and protein levels. Finally, PIK3R2-mediated activation of the PI3K/AKT signaling pathway promoted TMZ resistance and cell proliferation, but inhibited cell apoptosis. In conclusion, these data highlight the vital role of XLOC/Sp1/PIK3R2/PI3K/AKT axis in GBM TMZ resistance.
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Affiliation(s)
- Jian Zhou
- Department of Neurosurgery Center, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, China
| | - Ningbo Xu
- Department of Neurosurgery Center, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, China
| | - Boyang Liu
- Department of Neurosurgery Center, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, China
| | - Chenyang Wang
- Department of Neurosurgery Center, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, China
| | - Zhenyan He
- Department of Neurosurgery, The Affiliated Tumor Hospital of Zhengzhou University, Zhengzhou, 450008, China
| | - Cameron Lenahan
- Department of Biomedical Sciences, Burrell College of Osteopathic Medicine, Las Cruces, 88003, NM, USA
| | - Wenhui Tang
- Department of Neurosurgery Center, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, China
| | - Huijun Zeng
- Department of Neurosurgery Center, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, China
| | - Hongbo Guo
- Department of Neurosurgery Center, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, China
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10
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Moloney PB, Dugan P, Widdess-Walsh P, Devinsky O, Delanty N. Genomics in the Presurgical Epilepsy Evaluation. Epilepsy Res 2022; 184:106951. [DOI: 10.1016/j.eplepsyres.2022.106951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/23/2022] [Accepted: 05/25/2022] [Indexed: 11/03/2022]
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11
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Chen WL, Pao E, Owens J, Glass I, Pritchard C, Shirts BH, Lockwood C, Mirzaa GM. The utility of cerebrospinal fluid-derived cell-free DNA in molecular diagnostics for the PIK3CA-related megalencephaly-capillary malformation (MCAP) syndrome: a case report. Cold Spring Harb Mol Case Stud 2022; 8:mcs.a006188. [PMID: 35483878 PMCID: PMC9059787 DOI: 10.1101/mcs.a006188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 03/18/2022] [Indexed: 11/24/2022] Open
Abstract
The megalencephaly-capillary malformation (MCAP) syndrome is an overgrowth disorder caused by mosaic gain-of-function variants in PIK3CA It is characterized by megalencephaly or hemimegalencephaly, vascular malformations, somatic overgrowth, among other features. Epilepsy is commonly associated with MCAP, and a subset of individuals have cortical malformations requiring resective epilepsy surgery. Like other mosaic disorders, establishing a molecular diagnosis is largely achieved by screening lesional tissues (such as brain or skin), with a low diagnostic yield from peripheral tissues (such as blood). Therefore, in individuals with MCAP in whom lesional tissues are scarce or unavailable or those ineligible for epilepsy surgery, establishing a molecular diagnosis can be challenging. Here we report on the utility of cerebrospinal fluid (CSF)-derived cfDNA for the molecular diagnosis of an individual with MCAP syndrome harboring a mosaic PIK3CA variant (c.3139C > T, p.His1047Tyr). The proband presented with asymmetric megalencephaly without significant dysgyria. He did not have refractory epilepsy and was therefore not a candidate for epilepsy surgery. However, he developed diffuse large B-cell lymphoma (DLBCL) in late childhood, with four CSF samples obtained via lumbar puncture for cancer staging during which one sample was collected for cfDNA extraction and sequencing. PIK3CA variant allele fractions in CSF cell-free DNA (cfDNA), skin fibroblasts, and peripheral blood were 3.08%, 37.31%, and 2.04%, respectively. This report illustrates the utility of CSF-derived cfDNA in MCAP syndrome. Minimally invasive-based molecular diagnostic approaches utilizing cfDNA not only facilitate accurate genetic diagnosis but also have important therapeutic implications for individuals with refractory epilepsy as repurposed PI3K-AKT-MTOR pathway-inhibitors become more widely available.
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Affiliation(s)
- Wei-Liang Chen
- School of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA
| | - Emily Pao
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington 98101, USA
| | - James Owens
- Department of Neurology, University of Washington, Seattle, Washington 98195, USA
| | - Ian Glass
- Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA
| | - Colin Pritchard
- Department of Laboratory Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Brain H. Shirts
- Department of Laboratory Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Christina Lockwood
- Department of Laboratory Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Ghayda M. Mirzaa
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington 98101, USA;,Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA;,The Brotman Baty Institute for Precision Medicine, Seattle, Washington 98195, USA
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12
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Morozova E, Morozov D, Belousova M, Utkuzova M, Madiakina A. Uncommon variants of speech disorder in children: congenital bilateral perisylvian syndrome. Zh Nevrol Psikhiatr Im S S Korsakova 2022; 122:21-26. [DOI: 10.17116/jnevro202212209221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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13
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Moloney PB, Cavalleri GL, Delanty N. Epilepsy in the mTORopathies: opportunities for precision medicine. Brain Commun 2021; 3:fcab222. [PMID: 34632383 PMCID: PMC8495134 DOI: 10.1093/braincomms/fcab222] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/23/2021] [Accepted: 08/30/2021] [Indexed: 01/16/2023] Open
Abstract
The mechanistic target of rapamycin signalling pathway serves as a ubiquitous regulator of cell metabolism, growth, proliferation and survival. The main cellular activity of the mechanistic target of rapamycin cascade funnels through mechanistic target of rapamycin complex 1, which is inhibited by rapamycin, a macrolide compound produced by the bacterium Streptomyces hygroscopicus. Pathogenic variants in genes encoding upstream regulators of mechanistic target of rapamycin complex 1 cause epilepsies and neurodevelopmental disorders. Tuberous sclerosis complex is a multisystem disorder caused by mutations in mechanistic target of rapamycin regulators TSC1 or TSC2, with prominent neurological manifestations including epilepsy, focal cortical dysplasia and neuropsychiatric disorders. Focal cortical dysplasia type II results from somatic brain mutations in mechanistic target of rapamycin pathway activators MTOR, AKT3, PIK3CA and RHEB and is a major cause of drug-resistant epilepsy. DEPDC5, NPRL2 and NPRL3 code for subunits of the GTPase-activating protein (GAP) activity towards Rags 1 complex (GATOR1), the principal amino acid-sensing regulator of mechanistic target of rapamycin complex 1. Germline pathogenic variants in GATOR1 genes cause non-lesional focal epilepsies and epilepsies associated with malformations of cortical development. Collectively, the mTORopathies are characterized by excessive mechanistic target of rapamycin pathway activation and drug-resistant epilepsy. In the first large-scale precision medicine trial in a genetically mediated epilepsy, everolimus (a synthetic analogue of rapamycin) was effective at reducing seizure frequency in people with tuberous sclerosis complex. Rapamycin reduced seizures in rodent models of DEPDC5-related epilepsy and focal cortical dysplasia type II. This review outlines a personalized medicine approach to the management of epilepsies in the mTORopathies. We advocate for early diagnostic sequencing of mechanistic target of rapamycin pathway genes in drug-resistant epilepsy, as identification of a pathogenic variant may point to an occult dysplasia in apparently non-lesional epilepsy or may uncover important prognostic information including, an increased risk of sudden unexpected death in epilepsy in the GATORopathies or favourable epilepsy surgery outcomes in focal cortical dysplasia type II due to somatic brain mutations. Lastly, we discuss the potential therapeutic application of mechanistic target of rapamycin inhibitors for drug-resistant seizures in GATOR1-related epilepsies and focal cortical dysplasia type II.
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Affiliation(s)
- Patrick B Moloney
- FutureNeuro, the Science Foundation Ireland Research Centre for Chronic and Rare Neurological Diseases, Royal College of Surgeons in Ireland, Dublin, D02 VN51, Ireland
| | - Gianpiero L Cavalleri
- FutureNeuro, the Science Foundation Ireland Research Centre for Chronic and Rare Neurological Diseases, Royal College of Surgeons in Ireland, Dublin, D02 VN51, Ireland
| | - Norman Delanty
- FutureNeuro, the Science Foundation Ireland Research Centre for Chronic and Rare Neurological Diseases, Royal College of Surgeons in Ireland, Dublin, D02 VN51, Ireland
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14
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Abstract
The human brain is characterized by the large size and intricate folding of its cerebral cortex, which are fundamental for our higher cognitive function and frequently altered in pathological dysfunction. Cortex folding is not unique to humans, nor even to primates, but is common across mammals. Cortical growth and folding are the result of complex developmental processes that involve neural stem and progenitor cells and their cellular lineages, the migration and differentiation of neurons, and the genetic programs that regulate and fine-tune these processes. All these factors combined generate mechanical stress and strain on the developing neural tissue, which ultimately drives orderly cortical deformation and folding. In this review we examine and summarize the current knowledge on the molecular, cellular, histogenic and mechanical mechanisms that are involved in and influence folding of the cerebral cortex, and how they emerged and changed during mammalian evolution. We discuss the main types of pathological malformations of human cortex folding, their specific developmental origin, and how investigating their genetic causes has illuminated our understanding of key events involved. We close our review by presenting the state-of-the-art animal and in vitro models of cortex folding that are currently used to study these devastating developmental brain disorders in children, and what are the main challenges that remain ahead of us to fully understand brain folding.
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Affiliation(s)
- Lucia Del Valle Anton
- Instituto de Neurociencias, Agencia Estatal Consejo Superior de Investigaciones Científicas, San Juan de Alicante, Alicante, Spain
| | - Victor Borrell
- Instituto de Neurociencias, Agencia Estatal Consejo Superior de Investigaciones Científicas, San Juan de Alicante, Alicante, Spain
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15
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The Names of Things: The 2018 Bernard Sachs Lecture. Pediatr Neurol 2021; 122:41-49. [PMID: 34330614 DOI: 10.1016/j.pediatrneurol.2021.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 05/05/2021] [Indexed: 11/22/2022]
Abstract
In 2018, I was honored to receive the Bernard Sachs Award for a lifetime of work expanding knowledge of diverse neurodevelopmental disorders. Summarizing work over more than 30 years is difficult but is an opportunity to chronicle the dramatic changes in the medical and scientific world that have transformed the field of Child Neurology over this time, as reflected in my own work. Here I have chosen to highlight five broad themes of my research beginning with my interest in descriptive terms that drive wider understanding and my choice for the title of this review. From there I will go on to contrast the state of knowledge as I entered the field with the state of knowledge today for four human brain malformations-lissencephaly, megalencephaly, cerebellar malformations, and polymicrogyria. For all, the changes have been dramatic.
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16
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Vetro A, Nielsen HN, Holm R, Hevner RF, Parrini E, Powis Z, Møller RS, Bellan C, Simonati A, Lesca G, Helbig KL, Palmer EE, Mei D, Ballardini E, Van Haeringen A, Syrbe S, Leuzzi V, Cioni G, Curry CJ, Costain G, Santucci M, Chong K, Mancini GMS, Clayton-Smith J, Bigoni S, Scheffer IE, Dobyns WB, Vilsen B, Guerrini R. ATP1A2- and ATP1A3-associated early profound epileptic encephalopathy and polymicrogyria. Brain 2021; 144:1435-1450. [PMID: 33880529 DOI: 10.1093/brain/awab052] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 01/20/2023] Open
Abstract
Constitutional heterozygous mutations of ATP1A2 and ATP1A3, encoding for two distinct isoforms of the Na+/K+-ATPase (NKA) alpha-subunit, have been associated with familial hemiplegic migraine (ATP1A2), alternating hemiplegia of childhood (ATP1A2/A3), rapid-onset dystonia-parkinsonism, cerebellar ataxia-areflexia-progressive optic atrophy, and relapsing encephalopathy with cerebellar ataxia (all ATP1A3). A few reports have described single individuals with heterozygous mutations of ATP1A2/A3 associated with severe childhood epilepsies. Early lethal hydrops fetalis, arthrogryposis, microcephaly, and polymicrogyria have been associated with homozygous truncating mutations in ATP1A2. We investigated the genetic causes of developmental and epileptic encephalopathies variably associated with malformations of cortical development in a large cohort and identified 22 patients with de novo or inherited heterozygous ATP1A2/A3 mutations. We characterized clinical, neuroimaging and neuropathological findings, performed in silico and in vitro assays of the mutations' effects on the NKA-pump function, and studied genotype-phenotype correlations. Twenty-two patients harboured 19 distinct heterozygous mutations of ATP1A2 (six patients, five mutations) and ATP1A3 (16 patients, 14 mutations, including a mosaic individual). Polymicrogyria occurred in 10 (45%) patients, showing a mainly bilateral perisylvian pattern. Most patients manifested early, often neonatal, onset seizures with a multifocal or migrating pattern. A distinctive, 'profound' phenotype, featuring polymicrogyria or progressive brain atrophy and epilepsy, resulted in early lethality in seven patients (32%). In silico evaluation predicted all mutations to be detrimental. We tested 14 mutations in transfected COS-1 cells and demonstrated impaired NKA-pump activity, consistent with severe loss of function. Genotype-phenotype analysis suggested a link between the most severe phenotypes and lack of COS-1 cell survival, and also revealed a wide continuum of severity distributed across mutations that variably impair NKA-pump activity. We performed neuropathological analysis of the whole brain in two individuals with polymicrogyria respectively related to a heterozygous ATP1A3 mutation and a homozygous ATP1A2 mutation and found close similarities with findings suggesting a mainly neural pathogenesis, compounded by vascular and leptomeningeal abnormalities. Combining our report with other studies, we estimate that ∼5% of mutations in ATP1A2 and 12% in ATP1A3 can be associated with the severe and novel phenotypes that we describe here. Notably, a few of these mutations were associated with more than one phenotype. These findings assign novel, 'profound' and early lethal phenotypes of developmental and epileptic encephalopathies and polymicrogyria to the phenotypic spectrum associated with heterozygous ATP1A2/A3 mutations and indicate that severely impaired NKA pump function can disrupt brain morphogenesis.
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Affiliation(s)
- Annalisa Vetro
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Meyer Children's Hospital, University of Florence, Florence, Italy
| | - Hang N Nielsen
- Department of Biomedicine, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Rikke Holm
- Department of Biomedicine, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Robert F Hevner
- Department of Pathology, University of California San Diego, San Diego, CA, USA
| | - Elena Parrini
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Meyer Children's Hospital, University of Florence, Florence, Italy
| | - Zoe Powis
- Ambry Genetics, Aliso Viejo, CA, USA
| | - Rikke S Møller
- Department of Epilepsy Genetics and Personalized Medicine Danish Epilepsy Centre, Filadelfia, Denmark.,Department of Regional Health Services, University of Southern Denmark, Odense, Denmark
| | - Cristina Bellan
- Department of Neonatal Intensive Care Unit, Bolognini Hospital, ASST-Bergamo Est, Seriate, Italy
| | - Alessandro Simonati
- Neurology (Child Neurology and Neuropathology), Department of Neuroscience, Biomedicine and Movement, University of Verona, Verona, Italy
| | - Gaétan Lesca
- Department of Medical Genetics, Member of the ERN EpiCARE, University Hospital of Lyon, Lyon, France
| | - Katherine L Helbig
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elizabeth E Palmer
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, NSW, Australia.,School of Women's and Children's Health, University of New South Wales, Randwick, NSW, Australia
| | - Davide Mei
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Meyer Children's Hospital, University of Florence, Florence, Italy
| | - Elisa Ballardini
- Neonatal Intensive Care Unit, Pediatric Section, Department of Medical Sciences, Ferrara University, Ferrara, Italy
| | - Arie Van Haeringen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Steffen Syrbe
- Division of Pediatric Epileptology, Centre for Paediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Vincenzo Leuzzi
- Department of Human Neuroscience, Unit of Child Neurology and Psychiatry, Sapienza University, Rome, Italy
| | - Giovanni Cioni
- Department of Developmental Neuroscience, IRCCS Fondazione Stella Maris, Pisa, Italy
| | - Cynthia J Curry
- Genetic Medicine, Department of Pediatrics, University of California, San Francisco/Fresno, CA, USA
| | - Gregory Costain
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Margherita Santucci
- Child Neuropsychiatry Unit, IRCCS, Institute of Neurological Sciences, Bellaria Hospital, Bologna, Italy.,DIBINEM, University of Bologna, Bologna, Italy
| | - Karen Chong
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Grazia M S Mancini
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Jill Clayton-Smith
- Manchester Centre for Genomic Medicine, University of Manchester, St Mary's Hospital, Manchester, UK
| | - Stefania Bigoni
- Medical Genetics Unit, Department of Mother and Child, Ferrara University Hospital, Ferrara, Italy
| | - Ingrid E Scheffer
- University of Melbourne, Austin Health and Royal Children's Hospital, Florey and Murdoch Institutes, Melbourne, Australia
| | - William B Dobyns
- Department of Pediatrics (Genetics), University of Minnesota, Minneapolis, MN, USA
| | - Bente Vilsen
- Department of Biomedicine, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Renzo Guerrini
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Meyer Children's Hospital, University of Florence, Florence, Italy
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17
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Wang Y, Peng J, Bai S, Yu H, He H, Fan C, Hao Y, Guan Y. A PIK3R2 Mutation in Familial Temporal Lobe Epilepsy as a Possible Pathogenic Variant. Front Genet 2021; 12:596709. [PMID: 34040629 PMCID: PMC8141861 DOI: 10.3389/fgene.2021.596709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
Temporal lobe epilepsy (TLE), the most common form of medically refractory focal epilepsy in adults, often requires surgery to alleviate seizures. By using next-generation sequencing, we identified a PIK3R2 mutation (NM_005027.4: c.265C > T; NP_005018.2: p.Arg89Cys) in a family with mesial temporal lobe epilepsy. PIK3R2 encodes p85β, the regulatory subunit of Class IA phosphoinositide 3-kinase (PI3K) and the mutation we identified in PIK3R2 seems to function unexpectedly as a possible pathogenic variant. The mutation is predicted to be potentially pathogenic by multiple bioinformatics tools. Through a functional assay, we verified that the mutation enhances the function of PI3K in induced pluripotent stem cells (iPSCs) derived from peripheral blood mononuclear cells (PBMCs) of the proband. Finally, pathological testing of the resected temporal lobe cortex showed that the expression of PIK3R2 was significantly higher in patients with refractory temporal lobe epilepsy than in those of non-epileptic diseases as a control group. It can be inferred that PIK3R2 might play an important role in the development of TLE.
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Affiliation(s)
- Yishu Wang
- Department of Neurology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Peng
- Department of Neurology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuwei Bai
- Department of Neurology, The Second Affiliated Hospital of Xinjiang Medical University, Ürümqi, China
| | - Haojun Yu
- Department of Neurology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hong He
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Chunxiang Fan
- TCM Department, Shanghai Punan Hospital of Pudong New District, Shanghai, China
| | - Yong Hao
- Department of Neurology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Neurology, Ningbo Hangzhou Bay Hospital, Ningbo, China
| | - Yangtai Guan
- Department of Neurology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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18
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Abstract
INTRODUCTION Focal cortical dysplasias (FCDs) represent the most common etiology in pediatric drug-resistant focal epilepsies undergoing surgical treatment. The localization, extent and histopathological features of FCDs are considerably variable. Somatic mosaic mutations of genes that encode proteins in the PI3K-AKTmTOR pathway, which also includes the tuberous sclerosis associated genes TSC1 and TSC2, have been implicated in FCD type II in a substantial subset of patients. Surgery is the principal therapeutic option for FCD-related epilepsy. Advanced neurophysiological and neuroimaging techniques have improved surgical outcome and reduced the risk of postsurgical deficits. Pharmacological MTOR inhibitors are being tested in clinical trials and might represent an example of personalized treatment of epilepsy based on the known mechanisms of disease, used alone or in combination with surgery. AREAS COVERED This review will critically analyze the advances in the diagnosis and treatment of FCDs, with a special focus on the novel therapeutic options prompted by a better understanding of their pathophysiology. EXPERT OPINION Focal cortical dysplasia is a main cause of drug-resistant epilepsy, especially in children. Novel, personalized approaches are needed to more effectively treat FCD-related epilepsy and its cognitive consequences.
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Affiliation(s)
- Renzo Guerrini
- Neuroscience Department, Children's Hospital Meyer-University of Florence, Florence, Italy
| | - Carmen Barba
- Neuroscience Department, Children's Hospital Meyer-University of Florence, Florence, Italy
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19
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Diverse genetic causes of polymicrogyria with epilepsy. Epilepsia 2021; 62:973-983. [PMID: 33818783 PMCID: PMC10838185 DOI: 10.1111/epi.16854] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 12/25/2022]
Abstract
OBJECTIVE We sought to identify novel genes and to establish the contribution of known genes in a large cohort of patients with nonsyndromic sporadic polymicrogyria and epilepsy. METHODS We enrolled participants with polymicrogyria and their parents through the Epilepsy Phenome/Genome Project. We performed phenotyping and whole exome sequencing (WES), trio analysis, and gene-level collapsing analysis to identify de novo or inherited variants, including germline or mosaic (postzygotic) single nucleotide variants, small insertion-deletion (indel) variants, and copy number variants present in leukocyte-derived DNA. RESULTS Across the cohort of 86 individuals with polymicrogyria and epilepsy, we identified seven with pathogenic or likely pathogenic variants in PIK3R2, including four germline and three mosaic variants. PIK3R2 was the only gene harboring more than expected de novo variants across the entire cohort, and likewise the only gene that passed the genome-wide threshold of significance in the gene-level rare variant collapsing analysis. Consistent with previous reports, the PIK3R2 phenotype consisted of bilateral polymicrogyria concentrated in the perisylvian region with macrocephaly. Beyond PIK3R2, we also identified one case each with likely causal de novo variants in CCND2 and DYNC1H1 and biallelic variants in WDR62, all genes previously associated with polymicrogyria. Candidate genetic explanations in this cohort included single nucleotide de novo variants in other epilepsy-associated and neurodevelopmental disease-associated genes (SCN2A in two individuals, GRIA3, CACNA1C) and a 597-kb deletion at 15q25, a neurodevelopmental disease susceptibility locus. SIGNIFICANCE This study confirms germline and postzygotically acquired de novo variants in PIK3R2 as an important cause of bilateral perisylvian polymicrogyria, notably with macrocephaly. In total, trio-based WES identified a genetic diagnosis in 12% and a candidate diagnosis in 6% of our polymicrogyria cohort. Our results suggest possible roles for SCN2A, GRIA3, CACNA1C, and 15q25 deletion in polymicrogyria, each already associated with epilepsy or other neurodevelopmental conditions without brain malformations. The role of these genes in polymicrogyria will be further understood as more patients with polymicrogyria undergo genetic evaluation.
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20
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Excitatory/Inhibitory Synaptic Ratios in Polymicrogyria and Down Syndrome Help Explain Epileptogenesis in Malformations. Pediatr Neurol 2021; 116:41-54. [PMID: 33450624 DOI: 10.1016/j.pediatrneurol.2020.11.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/29/2020] [Accepted: 11/01/2020] [Indexed: 12/25/2022]
Abstract
BACKGROUND The ratio between excitatory (glutamatergic) and inhibitory (GABAergic) inputs into maturing individual cortical neurons influences their epileptic potential. Structural factors during development that alter synaptic inputs can be demonstrated neuropathologically. Increased mitochondrial activity identifies neurons with excessive discharge rates. METHODS This study focuses on the neuropathological examinaion of surgical resections for epilepsy and at autopsy, in fetuses, infants, and children, using immunocytochemical markers, and electron microscopy in selected cases. Polymicrogyria and Down syndrome are highlighted. RESULTS Factors influencing afferent synaptic ratios include the following: (1) synaptic short-circuitry in fused molecular zones of adjacent gyri (polymicrogyria); (2) impaired development of dendritic spines decreasing excitation (Down syndrome); (3) extracellular keratan sulfate proteoglycan binding to somatic membranes but not dendritic spines may be focally diminished (cerebral atrophy, schizencephaly, lissencephaly, polymicrogyria) or augmented, ensheathing individual axons (holoprosencephaly), or acting as a barrier to axonal passage in the U-fiber layer. If keratan is diminished, glutamate receptors on the neuronal soma enable ectopic axosomatic excitatory synapses to form; (4) dysplastic, megalocytic neurons and balloon cells in mammalian target of rapamycin disorders; (5) satellitosis of glial cells displacing axosomatic synapses; (6) peri-neuronal inflammation (tuberous sclerosis) and heat-shock proteins. CONCLUSIONS Synaptic ratio of excitatory/inhibitory afferents is a major fundamental basis of epileptogenesis at the neuronal level. Neuropathology can demonstrate subcellular changes that help explain either epilepsy or lack of seizures in immature brains. Synaptic ratios in malformations influence postnatal epileptogenesis. Single neurons can be hypermetabolic and potentially epileptogenic.
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21
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Klingler E, Francis F, Jabaudon D, Cappello S. Mapping the molecular and cellular complexity of cortical malformations. Science 2021; 371:371/6527/eaba4517. [PMID: 33479124 DOI: 10.1126/science.aba4517] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The cerebral cortex is an intricate structure that controls human features such as language and cognition. Cortical functions rely on specialized neurons that emerge during development from complex molecular and cellular interactions. Neurodevelopmental disorders occur when one or several of these steps is incorrectly executed. Although a number of causal genes and disease phenotypes have been identified, the sequence of events linking molecular disruption to clinical expression mostly remains obscure. Here, focusing on human malformations of cortical development, we illustrate how complex interactions at the genetic, cellular, and circuit levels together contribute to diversity and variability in disease phenotypes. Using specific examples and an online resource, we propose that a multilevel assessment of disease processes is key to identifying points of vulnerability and developing new therapeutic strategies.
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Affiliation(s)
- Esther Klingler
- Department of Basic Neurosciences, University of Geneva, CH-1202 Geneva, Switzerland
| | - Fiona Francis
- INSERM U 1270, F-75005 Paris, France.,Sorbonne University, UMR-S 1270, F-75005 Paris, France.,Institut du Fer à Moulin, F-75005 Paris, France
| | - Denis Jabaudon
- Department of Basic Neurosciences, University of Geneva, CH-1202 Geneva, Switzerland. .,Clinic of Neurology, Geneva University Hospital, 1211 Geneva, Switzerland
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22
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Accogli A, Geraldo AF, Piccolo G, Riva A, Scala M, Balagura G, Salpietro V, Madia F, Maghnie M, Zara F, Striano P, Tortora D, Severino M, Capra V. Diagnostic Approach to Macrocephaly in Children. Front Pediatr 2021; 9:794069. [PMID: 35096710 PMCID: PMC8795981 DOI: 10.3389/fped.2021.794069] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/02/2021] [Indexed: 01/19/2023] Open
Abstract
Macrocephaly affects up to 5% of the pediatric population and is defined as an abnormally large head with an occipitofrontal circumference (OFC) >2 standard deviations (SD) above the mean for a given age and sex. Taking into account that about 2-3% of the healthy population has an OFC between 2 and 3 SD, macrocephaly is considered as "clinically relevant" when OFC is above 3 SD. This implies the urgent need for a diagnostic workflow to use in the clinical setting to dissect the several causes of increased OFC, from the benign form of familial macrocephaly and the Benign enlargement of subarachnoid spaces (BESS) to many pathological conditions, including genetic disorders. Moreover, macrocephaly should be differentiated by megalencephaly (MEG), which refers exclusively to brain overgrowth, exceeding twice the SD (3SD-"clinically relevant" megalencephaly). While macrocephaly can be isolated and benign or may be the first indication of an underlying congenital, genetic, or acquired disorder, megalencephaly is most likely due to a genetic cause. Apart from the head size evaluation, a detailed family and personal history, neuroimaging, and a careful clinical evaluation are crucial to reach the correct diagnosis. In this review, we seek to underline the clinical aspects of macrocephaly and megalencephaly, emphasizing the main differential diagnosis with a major focus on common genetic disorders. We thus provide a clinico-radiological algorithm to guide pediatricians in the assessment of children with macrocephaly.
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Affiliation(s)
- Andrea Accogli
- Division of Medical Genetics, Department of Medicine, McGill University Health Centre, Montreal, QC, Canada
| | - Ana Filipa Geraldo
- Diagnostic Neuroradiology Unit, Imaging Department, Centro Hospitalar Vila Nova de Gaia/Espinho, Vila Nova de Gaia, Portugal
| | - Gianluca Piccolo
- Pediatric Neurology and Neuromuscular Diseases Unit, IRCCS Giannina Gaslini Institute, Genoa, Italy
| | - Antonella Riva
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Genoa, Italy
| | - Marcello Scala
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Genoa, Italy
| | - Ganna Balagura
- Pediatric Neurology and Neuromuscular Diseases Unit, IRCCS Giannina Gaslini Institute, Genoa, Italy
| | - Vincenzo Salpietro
- Pediatric Neurology and Neuromuscular Diseases Unit, IRCCS Giannina Gaslini Institute, Genoa, Italy.,Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Genoa, Italy
| | - Francesca Madia
- Pediatric Clinic and Endocrinology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Mohamad Maghnie
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Genoa, Italy.,Pediatric Clinic and Endocrinology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Federico Zara
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Genoa, Italy.,Medical Genetics Unit, IRCCS Giannina Gaslini Institute, Genoa, Italy
| | - Pasquale Striano
- Pediatric Neurology and Neuromuscular Diseases Unit, IRCCS Giannina Gaslini Institute, Genoa, Italy.,Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Genoa, Italy
| | - Domenico Tortora
- Neuroradiology Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | | | - Valeria Capra
- Medical Genetics Unit, IRCCS Giannina Gaslini Institute, Genoa, Italy
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23
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Abstract
The mammalian cerebral cortex is the pinnacle of brain evolution, reaching its maximum complexity in terms of neuron number, diversity and functional circuitry. The emergence of this outstanding complexity begins during embryonic development, when a limited number of neural stem and progenitor cells manage to generate myriads of neurons in the appropriate numbers, types and proportions, in a process called neurogenesis. Here we review the current knowledge on the regulation of cortical neurogenesis, beginning with a description of the types of progenitor cells and their lineage relationships. This is followed by a review of the determinants of neuron fate, the molecular and genetic regulatory mechanisms, and considerations on the evolution of cortical neurogenesis in vertebrates leading to humans. We finish with an overview on how dysregulation of neurogenesis is a leading cause of human brain malformations and functional disabilities.
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Affiliation(s)
- Ana Villalba
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas & Universidad Miguel Hernández, Sant Joan d'Alacant, Spain
| | - Magdalena Götz
- Institute for Stem Cell Research, Helmholtz Zentrum München & Biomedical Center, Ludwig-Maximilians Universitaet, Planegg-Martinsried, Germany
| | - Víctor Borrell
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas & Universidad Miguel Hernández, Sant Joan d'Alacant, Spain.
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24
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Stutterd CA, Brock S, Stouffs K, Fanjul-Fernandez M, Lockhart PJ, McGillivray G, Mandelstam S, Pope K, Delatycki MB, Jansen A, Leventer RJ. Genetic heterogeneity of polymicrogyria: study of 123 patients using deep sequencing. Brain Commun 2020; 3:fcaa221. [PMID: 33604570 PMCID: PMC7878248 DOI: 10.1093/braincomms/fcaa221] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/23/2020] [Accepted: 10/27/2020] [Indexed: 12/29/2022] Open
Abstract
Polymicrogyria is a malformation of cortical development characterized by overfolding and abnormal lamination of the cerebral cortex. Manifestations include epilepsy, speech disturbance and motor and cognitive disability. Causes include acquired prenatal insults and inherited and de novo genetic variants. The proportion of patients with polymicrogyria and a causative germline or mosaic variant is not known. The aim of this study was to identify the monogenic causes of polymicrogyria in a heterogeneous cohort of patients reflective of specialized referral services. Patients with polymicrogyria were recruited from two clinical centres in Australia and Belgium. Patients with evidence of congenital cytomegalovirus infection or causative chromosomal copy number variants were excluded. One hundred and twenty-three patients were tested using deep sequencing gene panels including known and candidate genes for malformations of cortical development. Causative and potentially causative variants were identified and correlated with phenotypic features. Pathogenic or likely pathogenic variants were identified in 25/123 (20.3%) patients. A candidate variant was identified for an additional patient but could not be confirmed as de novo, and therefore it was classified as being of uncertain significance with high clinical relevance. Of the 22 dominant variants identified, 5 were mosaic with allele fractions less than 0.33 and the lowest allele fraction 0.09. The most common causative genes were TUBA1A and PIK3R2. The other eleven causative genes were PIK3CA, NEDD4L, COL4A1, COL4A2, GPSM2, GRIN2B, WDR62, TUBB3, TUBB2B, ACTG1 and FH. A genetic cause was more likely to be identified in the presence of an abnormal head size or additional brain malformations suggestive of a tubulinopathy, such as dysmorphic basal ganglia. A gene panel test provides greater sequencing depth and sensitivity for mosaic variants than whole exome or genome sequencing but is limited to the genes included, potentially missing variants in newly discovered genes. The diagnostic yield of 20.3% indicates that polymicrogyria may be associated with genes not yet known to be associated with brain malformations, brain-specific somatic mutations or non-genetic causes.
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Affiliation(s)
- Chloe A Stutterd
- Murdoch Children's Research Institute, Melbourne, 3052, Australia.,University of Melbourne Department of Paediatrics, Melbourne, 3052, Australia.,Royal Children's Hospital, Melbourne, 3052, Australia.,Victorian Clinical Genetics Service, Melbourne, 3052, Australia
| | - Stefanie Brock
- Neurogenetics Research group, Vrije Universiteit Brussel, Belgium.,Department of Pathology, UZ Brussel, Belgium
| | - Katrien Stouffs
- Neurogenetics Research group, Vrije Universiteit Brussel, Belgium.,Centre for Medical Genetics, UZ Brussel, Belgium
| | | | - Paul J Lockhart
- Murdoch Children's Research Institute, Melbourne, 3052, Australia.,University of Melbourne Department of Paediatrics, Melbourne, 3052, Australia
| | | | - Simone Mandelstam
- Murdoch Children's Research Institute, Melbourne, 3052, Australia.,University of Melbourne Department of Paediatrics, Melbourne, 3052, Australia.,Royal Children's Hospital, Melbourne, 3052, Australia
| | - Kate Pope
- Murdoch Children's Research Institute, Melbourne, 3052, Australia
| | - Martin B Delatycki
- Murdoch Children's Research Institute, Melbourne, 3052, Australia.,University of Melbourne Department of Paediatrics, Melbourne, 3052, Australia.,Victorian Clinical Genetics Service, Melbourne, 3052, Australia
| | - Anna Jansen
- Neurogenetics Research group, Vrije Universiteit Brussel, Belgium.,Pediatric Neurology Unit, UZ Brussel, Belgium
| | - Richard J Leventer
- Murdoch Children's Research Institute, Melbourne, 3052, Australia.,University of Melbourne Department of Paediatrics, Melbourne, 3052, Australia.,Royal Children's Hospital, Melbourne, 3052, Australia
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25
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Shi X, Lim Y, Myers AK, Stallings BL, Mccoy A, Zeiger J, Scheck J, Cho G, Marsh ED, Mirzaa GM, Tao T, Golden JA. PIK3R2/Pik3r2 Activating Mutations Result in Brain Overgrowth and EEG Changes. Ann Neurol 2020; 88:1077-1094. [PMID: 32856318 PMCID: PMC8176885 DOI: 10.1002/ana.25890] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 08/23/2020] [Accepted: 08/24/2020] [Indexed: 01/23/2023]
Abstract
OBJECTIVE Mutations in phosphatidylinositol-4,5-bisphosphate 3-kinase (PI3K) complex have been associated with a broad spectrum of brain and organ overgrowth syndromes. For example, mutations in phosphatidylinositol-3-kinase regulatory subunit 2 (PIK3R2) have been identified in human patients with megalencephaly polymicrogyria polydactyly hydrocephalus (MPPH) syndrome, which includes brain overgrowth. To better understand the pathogenesis of PIK3R2-related mutations, we have developed and characterized a murine model. METHODS We generated a knock-in mouse model for the most common human PIK3R2 mutation, p.G373R (p.G367R in mice) using CRISPR/Cas9. The mouse phenotypes, including brain size, seizure activity, cortical lamination, cell proliferation/size/density, interneuron migration, and PI3K pathway activation, were analyzed using standard methodologies. For human patients with PIK3R2 mutations, clinical data (occipitofrontal circumference [OFC] and epilepsy) were retrospectively obtained from our clinical records (published / unpublished). RESULTS The PI3K-AKT pathway was hyperactivated in these mice, confirming the p.G367R mutation is an activating mutation in vivo. Similar to human patients with PIK3R2 mutations, these mice have enlarged brains. We found cell size to be increased but not cell numbers. The embryonic brain showed mild defects in cortical lamination, although not observed in the mature brain. Furthermore, electroencephalogram (EEG) recordings from mutant mice showed background slowing and rare seizures, again similar to our observations in human patients. INTERPRETATION We have generated a PIK3R2 mouse model that exhibits megalencephaly and EEG changes, both of which overlap with human patients. Our data provide novel insight into the pathogenesis of the human disease caused by PIK3R2 p.G373R mutation. We anticipate this model will be valuable in testing therapeutic options for human patients with MPPH. ANN NEUROL 2020;88:1077-1094.
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Affiliation(s)
- Xiuyu Shi
- State Key Laboratory of Stress Cell Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361005, China
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Youngshin Lim
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Abigail K. Myers
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Brenna L. Stallings
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Almedia Mccoy
- Departments of Neurology and Pediatrics, Division of Child Neurology, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jordan Zeiger
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Joshua Scheck
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Ginam Cho
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Eric D. Marsh
- Departments of Neurology and Pediatrics, Division of Child Neurology, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Ghayda M. Mirzaa
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Tao Tao
- State Key Laboratory of Stress Cell Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361005, China
| | - Jeffrey A. Golden
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
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26
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Kalman ZE, Mészáros B, Gáspári Z, Dobson L. Distribution of disease-causing germline mutations in coiled-coils implies an important role of their N-terminal region. Sci Rep 2020; 10:17333. [PMID: 33060664 PMCID: PMC7562717 DOI: 10.1038/s41598-020-74354-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 09/21/2020] [Indexed: 11/08/2022] Open
Abstract
Next-generation sequencing resulted in the identification of a huge number of naturally occurring variations in human proteins. The correct interpretation of the functional effects of these variations necessitates the understanding of how they modulate protein structure. Coiled-coils are α-helical structures responsible for a diverse range of functions, but most importantly, they facilitate the structural organization of macromolecular scaffolds via oligomerization. In this study, we analyzed a comprehensive set of disease-associated germline mutations in coiled-coil structures. Our results suggest an important role of residues near the N-terminal part of coiled-coil regions, possibly critical for superhelix assembly and folding in some cases. We also show that coiled-coils of different oligomerization states exhibit characteristically distinct patterns of disease-causing mutations. Our study provides structural and functional explanations on how disease emerges through the mutation of these structural motifs.
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Affiliation(s)
- Zsofia E Kalman
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50/A, 1083, Budapest, Hungary
- 3in-PPCU Research Group, 2500, Esztergom, Hungary
| | - Bálint Mészáros
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Zoltán Gáspári
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50/A, 1083, Budapest, Hungary.
| | - Laszlo Dobson
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50/A, 1083, Budapest, Hungary.
- Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, 1117, Budapest, Hungary.
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27
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Miller CR, Lee K, Pfau RB, Reshmi SC, Corsmeier DJ, Hashimoto S, Dave-Wala A, Jayaraman V, Koboldt D, Matthews T, Mouhlas D, Stein M, McKinney A, Grossman T, Kelly BJ, White P, Magrini V, Wilson RK, Mardis ER, Cottrell CE. Disease-associated mosaic variation in clinical exome sequencing: a two-year pediatric tertiary care experience. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a005231. [PMID: 32371413 PMCID: PMC7304353 DOI: 10.1101/mcs.a005231] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 04/29/2020] [Indexed: 11/25/2022] Open
Abstract
Exome sequencing (ES) has become an important tool in pediatric genomic medicine, improving identification of disease-associated variation due to assay breadth. Depth is also afforded by ES, enabling detection of lower-frequency mosaic variation compared to Sanger sequencing in the studied tissue, thus enhancing diagnostic yield. Within a pediatric tertiary-care hospital, we report two years of clinical ES data from probands evaluated for genetic disease to assess diagnostic yield, characteristics of causal variants, and prevalence of mosaicism among disease-causing variants. Exome-derived, phenotype-driven variant data from 357 probands was analyzed concurrent with parental ES data, when available. Blood was the source of nucleic acid. Sequence read alignments were manually reviewed for all assessed variants. Sanger sequencing was used for suspected de novo or mosaic variation. Clinical provider notes were reviewed to determine concordance between laboratory-reported data and the ordering provider's interpretation of variant-associated disease causality. Laboratory-derived diagnostic yield and provider-substantiated diagnoses had 91.4% concordance. The cohort returned 117 provider-substantiated diagnoses among 115 probands for a diagnostic yield of 32.2%. De novo variants represented 64.9% of disease-associated variation within trio analyses. Among the 115 probands, five harbored disease-associated somatic mosaic variation. Two additional probands were observed to inherit a disease-associated variant from an unaffected mosaic parent. Among inheritance patterns, de novo variation was the most frequent disease etiology. Somatic mosaicism is increasingly recognized as a significant contributor to genetic disease, particularly with increased sequence depth attainable from ES. This report highlights the potential and importance of detecting mosaicism in ES.
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Affiliation(s)
- Cecelia R Miller
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pathology
| | - Kristy Lee
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pathology
| | - Ruthann B Pfau
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pathology.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Shalini C Reshmi
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pathology.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Donald J Corsmeier
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Sayaka Hashimoto
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Ashita Dave-Wala
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Vijayakumar Jayaraman
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Daniel Koboldt
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Theodora Matthews
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Danielle Mouhlas
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Maggie Stein
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Aimee McKinney
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Tom Grossman
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Benjamin J Kelly
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Peter White
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Vincent Magrini
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Richard K Wilson
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Elaine R Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Catherine E Cottrell
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pathology.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
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28
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Lodato MA, Walsh CA. Genome aging: somatic mutation in the brain links age-related decline with disease and nominates pathogenic mechanisms. Hum Mol Genet 2020; 28:R197-R206. [PMID: 31578549 DOI: 10.1093/hmg/ddz191] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 07/25/2019] [Accepted: 07/26/2019] [Indexed: 12/19/2022] Open
Abstract
Aging is a mysterious process, not only controlled genetically but also subject to random damage that can accumulate over time. While DNA damage and subsequent mutation in somatic cells were first proposed as drivers of aging more than 60 years ago, whether and to what degree these processes shape the neuronal genome in the human brain could not be tested until recent technological breakthroughs related to single-cell whole-genome sequencing. Indeed, somatic single-nucleotide variants (SNVs) increase with age in the human brain, in a somewhat stochastic process that may nonetheless be controlled by underlying genetic programs. Evidence from the literature suggests that in addition to demonstrated increases in somatic SNVs during aging in normal brains, somatic mutation may also play a role in late-onset, sporadic neurodegenerative diseases, such as Alzheimer's disease and Parkinson's disease. In this review, we will discuss somatic mutation in the human brain, mechanisms by which somatic mutations occur and can be controlled, and how this process can impact human health.
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Affiliation(s)
- Michael A Lodato
- Division of Genetics and Genomics, Manton Center for Orphan Disease, Boston Children's Hospital, Boston, MA, USA.,Howard Hughes Medical Institute, Boston, MA, USA.,Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease, Boston Children's Hospital, Boston, MA, USA.,Howard Hughes Medical Institute, Boston, MA, USA.,Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
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29
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Fu R, Tong JS. miR-126 reduces trastuzumab resistance by targeting PIK3R2 and regulating AKT/mTOR pathway in breast cancer cells. J Cell Mol Med 2020; 24:7600-7608. [PMID: 32410348 PMCID: PMC7339158 DOI: 10.1111/jcmm.15396] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/18/2020] [Accepted: 04/27/2020] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) have been found to play a key role in drug resistance. In the current study, we aimed to explore the potential role of miR‐126 in trastuzumab resistance in breast cancer cells. We found that the trastuzumab‐resistant cell lines SKBR3/TR and BT474/TR had low expression of miR‐126 and increased ability to migrate and invade. The resistance, invasion and mobilization abilities of the cells resistant to trastuzumab were reduced by ectopic expression of miR‐126 mimics. In comparison, inhibition of miR‐126 in SKBR3 parental cells had the opposite effect of an increased resistance to trastuzumab as well as invasion and migration. It was also found that miR‐126 directly targets PIK3R2 in breast cancer cells. PIK3R2‐knockdown cells showed decreased resistance to trastuzumab, while overexpression of PIK3R2 increased trastuzumab resistance. In addition, our finding showed that overexpression of miR‐126 reduced resistance to trastuzumab in the trastuzumab‐resistant cells and that inhibition of the PIK3R2/PI3K/AKT/mTOR signalling pathway was involved in this effect. SKBR3/TR cells also showed increased sensitivity to trastuzumab mediated by miR‐126 in vivo. In conclusion, the above findings demonstrated that overexpression of miR‐126 or down‐regulation of its target gene may be a potential approach to overcome trastuzumab resistance in breast cancer cells.
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Affiliation(s)
- Rao Fu
- College of Chemical Engineering, Northeast Electric Power University, Jilin city, China
| | - Jing-Shan Tong
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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30
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Lee S, Kim SH, Kim B, Lee ST, Choi JR, Kim HD, Lee JS, Kang HC. Clinical Implementation of Targeted Gene Sequencing for Malformation of Cortical Development. Pediatr Neurol 2020; 103:27-34. [PMID: 31481326 DOI: 10.1016/j.pediatrneurol.2019.07.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 07/16/2019] [Accepted: 07/21/2019] [Indexed: 11/29/2022]
Abstract
BACKGROUND Malformations of cortical development comprise phenotypically heterogeneous conditions, and the diagnostic value of genetic testing in blood still remains to be elucidated. We used targeted gene sequencing to identify malformations of cortical development caused by germline mutations and characteristics associated with pathogenic mutations. METHODS A total of 81 patients with malformations of cortical development were included. Genomic DNA was isolated from peripheral blood. Ninety-six genes were assessed using a targeted next-generation sequencing panel. Single-nucleotide variants and exonic and chromosomal copy number variations were examined with our customized pipeline. RESULTS Genetic causes were identified from blood in 19 (23.5%) patients with malformations of cortical development; 14 patients had pathogenic or likely pathogenic single-nucleotide variants in seven genes, including DCX (n = 5), DEPDC5 (n = 2), PAFAH1B1 (n = 3), TUBA1A (n = 1), TUBA8 (n = 1), TUBB2B (n = 1), and TUBB3 (n = 1). Five patients had pathogenic copy number variations. Multifocal involvement of the lesion (tangential distribution, P < 0.001) and concurrent involvement of multiple structures such as the cortex, white matter, and ventricle (radial distribution, P = 0.003) were more commonly found in patients with identified genetic causes. Intellectual disability was also more commonly associated with pathogenic mutations (P = 0.048). In a multivariable regression analysis, both tangential and radial radiological distribution of malformations of cortical development were independently associated with positive germline test results. CONCLUSION We identified germline mutations in almost one-fourth of our patients with malformations of cortical development by using targeted gene sequencing. Germline abnormalities were more likely found in patients who had multifocal malformations of cortical development.
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Affiliation(s)
- Sangbo Lee
- Division of Pediatric Neurology, Epilepsy Research Institute, Severance Children's Hospital, Department of Pediatrics, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Se Hee Kim
- Division of Pediatric Neurology, Epilepsy Research Institute, Severance Children's Hospital, Department of Pediatrics, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Borahm Kim
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Heung Dong Kim
- Division of Pediatric Neurology, Epilepsy Research Institute, Severance Children's Hospital, Department of Pediatrics, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Joon Soo Lee
- Division of Pediatric Neurology, Epilepsy Research Institute, Severance Children's Hospital, Department of Pediatrics, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hoon-Chul Kang
- Division of Pediatric Neurology, Epilepsy Research Institute, Severance Children's Hospital, Department of Pediatrics, Yonsei University College of Medicine, Seoul, Republic of Korea.
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31
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Guerrini R, Parrini E, Esposito A, Fassio A, Conti V. Lesional and non-lesional epilepsies: A blurring genetic boundary. Eur J Paediatr Neurol 2020; 24:24-29. [PMID: 31875834 DOI: 10.1016/j.ejpn.2019.12.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 12/05/2019] [Accepted: 12/06/2019] [Indexed: 01/02/2023]
Abstract
There has been a traditional conceptual partition between the so-called non-lesional genetic epilepsies and the genetically determined interposed epileptogenic structural abnormalities. In this review, we summarise how growing evidence acquired through neuroimaging and neurobiology modelling is demonstrating that a distinction between lesional and functional (or non-lesional) epileptogenesis is less obvious than previously thought, particularly for epileptogenic neurodevelopmental disorders, but also for most genetically determined epilepsies.
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Affiliation(s)
- Renzo Guerrini
- Paediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Children's Hospital Anna Meyer-University of Florence, 50139, Florence, Italy.
| | - Elena Parrini
- Paediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Children's Hospital Anna Meyer-University of Florence, 50139, Florence, Italy
| | - Alessandro Esposito
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, 16100, Genoa, Italy; Department of Experimental Medicine, University of Genoa, 16100, Genoa, Italy
| | - Anna Fassio
- Department of Experimental Medicine, University of Genoa, 16100, Genoa, Italy; IRCCS Ospedale Policlinico San Martino, 16100, Genoa, Italy
| | - Valerio Conti
- Paediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Children's Hospital Anna Meyer-University of Florence, 50139, Florence, Italy
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32
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Polymicrogyria associated with 17p13.3p13.2 duplication: Case report and review of the literature. Eur J Med Genet 2019; 63:103774. [PMID: 31585183 DOI: 10.1016/j.ejmg.2019.103774] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/26/2019] [Accepted: 09/22/2019] [Indexed: 11/20/2022]
Abstract
We present the case of a male infant with bilateral perisylvian polymicrogyria associated with a de novo duplication of chromosome region 17p13.3p13.2. To our knowledge, this is the first report of polymicrogyria associated with the 17p13.3 contiguous gene duplication syndrome. Testing for known monogenic causes of polymicrogyria was negative and there was no clinical evidence of an acquired prenatal cause. Given the critical, dose-sensitive role that the 17p13.3 region plays in brain development, we suggest that the chromosome duplication is the most likely explanation for the polymicrogyria. Clinical and functional studies have demonstrated deleterious effects of increased LIS1 expression on the developing brain and the contribution of YWHAE to the brain phenotype of the 17p13 duplication syndrome. There is also evidence that CRK, the other candidate gene in this region, via interaction with LIS1, plays a critical role in cortical development. In addition to LIS1, YWHAE and CRK, our patient's chromosome duplication involves at least 100 other genes, less than half of which are annotated at the time of writing. It is expected that the ongoing use of chromosome microarray and next-generation sequencing to investigate the genetic causes of brain malformations will continue to extend our understanding of the 17p13 region and of the contributions of the genes in this region to cortical development.
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33
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Braden RO, Leventer RJ, Jansen A, Scheffer IE, Morgan AT. Speech and language in bilateral perisylvian polymicrogyria: a systematic review. Dev Med Child Neurol 2019; 61:1145-1152. [PMID: 30680716 DOI: 10.1111/dmcn.14153] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/24/2018] [Indexed: 01/23/2023]
Abstract
AIM We aimed to systematically review the speech production, language, and oral function phenotype of bilateral perisylvian polymicrogyria (BPP), and examine the correlation between the topography of polymicrogyria and the severity of speech, language, and oral functional impairment. METHOD A systematic search of MEDLINE, Embase, and PubMed databases was completed on 26th October 2017 using Medical Subject Heading terms synonymous with BPP and speech, language, or oral motor impairment. In total, 2411 papers were identified and 48 met inclusion criteria. RESULTS Expressive and receptive language impairment and oral structural and functional deficits are frequent in BPP. Expressive deficits are frequently more severe than receptive. Only one study used formal assessments to demonstrate the presence of speech disorder, namely dysarthria. Seven studies reported an association between diffuse BPP and more severe language impairment. INTERPRETATION Findings confirmed that language deficits are common in BPP, though assessment of the specific speech phenotype is limited. The paucity of high quality studies detailing the specific communication phenotype of BPP highlights the need for further investigation. Improving understanding of this phenotype will inform the development of targeted therapies and lead to better long-term outcomes. WHAT THIS PAPER ADDS Speech, language, and oral functional impairments are common in individuals with bilateral perisylvian polymicrogyria. Posterior polymicrogyria is associated with a less severe language impairment than anterior polymicrogyria. Deeper investigation of speech is needed to understand implicated networks in this malformation.
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Affiliation(s)
- Ruth O Braden
- Murdoch Children's Research Institute, Parkville, Melbourne, Victoria, Australia.,Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Melbourne, Victoria, Australia
| | - Richard J Leventer
- Murdoch Children's Research Institute, Parkville, Melbourne, Victoria, Australia.,Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Melbourne, Victoria, Australia.,Royal Children's Hospital, Parkville, Melbourne, Victoria, Australia
| | - Anna Jansen
- Neurogenetics Research Group, Reproduction Genetics and Regenerative Medicine Research Cluster, Vrije Universiteit Brussel, Brussels, Belgium.,Pediatric Neurology Unit, Department of Pediatrics, University Hospital Brussels, Brussels, Belgium
| | - Ingrid E Scheffer
- Murdoch Children's Research Institute, Parkville, Melbourne, Victoria, Australia.,Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Melbourne, Victoria, Australia.,Royal Children's Hospital, Parkville, Melbourne, Victoria, Australia.,Austin Health, Heidelberg, Melbourne, Victoria, Australia.,The Florey Institute of Neuroscience and Mental Health, Melbourne, Victoria, Australia
| | - Angela T Morgan
- Murdoch Children's Research Institute, Parkville, Melbourne, Victoria, Australia.,Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Melbourne, Victoria, Australia.,Royal Children's Hospital, Parkville, Melbourne, Victoria, Australia
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34
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Dobyns WB, Mirzaa GM. Megalencephaly syndromes associated with mutations of core components of the PI3K-AKT-MTOR pathway: PIK3CA, PIK3R2, AKT3, and MTOR. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2019; 181:582-590. [PMID: 31441589 DOI: 10.1002/ajmg.c.31736] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 07/15/2019] [Accepted: 07/16/2019] [Indexed: 11/09/2022]
Abstract
Megalencephaly (MEG) is a developmental abnormality of brain growth characterized by early onset, often progressive, brain overgrowth. Focal forms of megalencephaly associated with cortical dysplasia, such as hemimegalencephaly and focal cortical dysplasia, are common causes of focal intractable epilepsy in children. The increasing use of high throughput sequencing methods, including high depth sequencing to more accurately detect and quantify mosaic mutations, has allowed us to identify the molecular etiologies of many MEG syndromes, including most notably the PI3K-AKT-MTOR related MEG disorders. Thorough molecular and clinical characterization of affected individuals further allow us to derive preliminary genotype-phenotype correlations depending on the gene, mutation, level of mosaicism, and tissue distribution. Our review of published data on these disorders so far shows that mildly activating variants (that are typically constitutional or germline) are associated with diffuse megalencephaly with intellectual disability and/or autism spectrum disorder; moderately activating variants (that are typically high-level mosaic) are associated with megalencephaly with pigmentary abnormalities of the skin; and strongly activating variants (that are usually very low-level mosaic) are associated with focal brain malformations including hemimegalencephaly and focal cortical dysplasia. Accurate molecular diagnosis of these disorders is undoubtedly crucial to more optimally treat children with these disorders using PI3K-AKT-MTOR pathway inhibitors.
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Affiliation(s)
- William B Dobyns
- University of Washington School of Medicine, Seattle, Washington.,Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington
| | - Ghayda M Mirzaa
- University of Washington School of Medicine, Seattle, Washington.,Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington
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35
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Xu Q, Uliel-Sibony S, Dunham C, Sarnat H, Flores-Sarnat L, Brunga L, Davidson S, Lo W, Shlien A, Connolly M, Boelman C, Datta A. mTOR Inhibitors as a New Therapeutic Strategy in Treatment Resistant Epilepsy in Hemimegalencephaly: A Case Report. J Child Neurol 2019; 34:132-138. [PMID: 30514132 DOI: 10.1177/0883073818813238] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Hemimegalencephaly is a hamartomatous malformation of one hemisphere. Functional hemispherectomy, the definitive treatment, is associated with significant morbidity and mortality in early infancy. Dysregulation of the mTOR pathway can result in malformations of cortical development, and mTOR inhibitors can effectively reduce seizures in tuberous sclerosis complex. We report a 6-day-old female with hemimegalencephaly and frequent seizures despite 9 antiseizure medications. At 3 months of age, while awaiting hemispherectomy, an mTOR inhibitor, rapamycin, was initiated by the neurologist. After 1 week of treatment, there was >50% reduction in seizures and total seizure burden, and after 2 weeks, development improved, resulting in deferral of surgery by 2.5 months with an increased body weight. Pathology demonstrated cortical dysplasia with upregulation of the mTOR pathway. Deep-sequencing of brain tissue demonstrated 16% mosaicism for a pathogenic de novo MTOR gene mutation. This case exemplifies how mTOR inhibitors could be considered for seizure reduction in patients with hemimegalencephaly while awaiting surgery.
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Affiliation(s)
- Qi Xu
- 1 Division of Neurology, University of British Columbia, BC Children's Hospital, Vancouver, BC, Canada
| | - Shimrit Uliel-Sibony
- 1 Division of Neurology, University of British Columbia, BC Children's Hospital, Vancouver, BC, Canada
| | - Christopher Dunham
- 2 Department of Pathology, University of British Columbia, BC Children's Hospital, Vancouver, BC, Canada
| | - Harvey Sarnat
- 3 Division of Pediatric Neurology, University of Calgary, Alberta Children's Hospital, Calgary, AB, Canada
| | - Laura Flores-Sarnat
- 3 Division of Pediatric Neurology, University of Calgary, Alberta Children's Hospital, Calgary, AB, Canada
| | - Ledia Brunga
- 4 University of Toronto, Program in Genetics and Genome Biology, the Hospital for Sick Children, Toronto, ON, Canada
| | - Scott Davidson
- 4 University of Toronto, Program in Genetics and Genome Biology, the Hospital for Sick Children, Toronto, ON, Canada
| | - Winnie Lo
- 4 University of Toronto, Program in Genetics and Genome Biology, the Hospital for Sick Children, Toronto, ON, Canada
| | - Adam Shlien
- 4 University of Toronto, Program in Genetics and Genome Biology, the Hospital for Sick Children, Toronto, ON, Canada
| | - Mary Connolly
- 1 Division of Neurology, University of British Columbia, BC Children's Hospital, Vancouver, BC, Canada
| | - Cyrus Boelman
- 1 Division of Neurology, University of British Columbia, BC Children's Hospital, Vancouver, BC, Canada
| | - Anita Datta
- 1 Division of Neurology, University of British Columbia, BC Children's Hospital, Vancouver, BC, Canada
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36
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Juric-Sekhar G, Hevner RF. Malformations of Cerebral Cortex Development: Molecules and Mechanisms. ANNUAL REVIEW OF PATHOLOGY 2019; 14:293-318. [PMID: 30677308 PMCID: PMC6938687 DOI: 10.1146/annurev-pathmechdis-012418-012927] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Malformations of cortical development encompass heterogeneous groups of structural brain anomalies associated with complex neurodevelopmental disorders and diverse genetic and nongenetic etiologies. Recent progress in understanding the genetic basis of brain malformations has been driven by extraordinary advances in DNA sequencing technologies. For example, somatic mosaic mutations that activate mammalian target of rapamycin signaling in cortical progenitor cells during development are now recognized as the cause of hemimegalencephaly and some types of focal cortical dysplasia. In addition, research on brain development has begun to reveal the cellular and molecular bases of cortical gyrification and axon pathway formation, providing better understanding of disorders involving these processes. New neuroimaging techniques with improved resolution have enhanced our ability to characterize subtle malformations, such as those associated with intellectual disability and autism. In this review, we broadly discuss cortical malformations and focus on several for which genetic etiologies have elucidated pathogenesis.
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Affiliation(s)
- Gordana Juric-Sekhar
- Department of Pathology, University of Washington School of Medicine, Seattle, Washington 98195, USA; ,
- Department of Neurological Surgery, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Robert F Hevner
- Department of Pathology, University of Washington School of Medicine, Seattle, Washington 98195, USA; ,
- Department of Neurological Surgery, University of Washington School of Medicine, Seattle, Washington 98195, USA
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington 98105, USA
- Current affiliation: Department of Pathology, University of California, San Diego, California 92093, USA
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37
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Abstract
Genetic variation contributes significantly to brain function and dysfunction, and studying the genetic factors responsible for neurological phenotypes is tremendously valuable for understanding brain development, physiology, and pathophysiology, as well as for advancements in disease diagnostics and therapeutics. Many genetic determinants of neurobiology are inherited from parents through the germline and are present in all cells of an individual, but others, known as somatic or mosaic mutations, may be acquired post-conception and are therefore present in only a subset of an individual’s cells. While the relationship between somatic mutation and cancer is clear, recent studies have also established a role for somatic mutations in several non-malignant neurological diseases of childhood, including cerebral cortical malformations and epilepsy disorders, autism spectrum disorder, and other neuropsychiatric diseases.
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Affiliation(s)
- Rachel E Rodin
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts; Departments of Neurology and Pediatrics, Harvard Medical School, Boston, Massachusetts; Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts; Departments of Neurology and Pediatrics, Harvard Medical School, Boston, Massachusetts; Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
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38
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Mirzaa G, Timms AE, Conti V, Boyle EA, Girisha KM, Martin B, Kircher M, Olds C, Juusola J, Collins S, Park K, Carter M, Glass I, Krägeloh-Mann I, Chitayat D, Parikh AS, Bradshaw R, Torti E, Braddock S, Burke L, Ghedia S, Stephan M, Stewart F, Prasad C, Napier M, Saitta S, Straussberg R, Gabbett M, O'Connor BC, Keegan CE, Yin LJ, Lai AHM, Martin N, McKinnon M, Addor MC, Boccuto L, Schwartz CE, Lanoel A, Conway RL, Devriendt K, Tatton-Brown K, Pierpont ME, Painter M, Worgan L, Reggin J, Hennekam R, Tsuchiya K, Pritchard CC, Aracena M, Gripp KW, Cordisco M, Van Esch H, Garavelli L, Curry C, Goriely A, Kayserilli H, Shendure J, Graham J, Guerrini R, Dobyns WB. PIK3CA-associated developmental disorders exhibit distinct classes of mutations with variable expression and tissue distribution. JCI Insight 2018; 1:87623. [PMID: 27631024 PMCID: PMC5019182 DOI: 10.1172/jci.insight.87623] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Mosaicism is increasingly recognized as a cause of developmental disorders with the advent of next-generation sequencing (NGS). Mosaic mutations of PIK3CA have been associated with the widest spectrum of phenotypes associated with overgrowth and vascular malformations. We performed targeted NGS using 2 independent deep-coverage methods that utilize molecular inversion probes and amplicon sequencing in a cohort of 241 samples from 181 individuals with brain and/or body overgrowth. We identified PIK3CA mutations in 60 individuals. Several other individuals (n = 12) were identified separately to have mutations in PIK3CA by clinical targeted-panel testing (n = 6), whole-exome sequencing (n = 5), or Sanger sequencing (n = 1). Based on the clinical and molecular features, this cohort segregated into three distinct groups: (a) severe focal overgrowth due to low-level but highly activating (hotspot) mutations, (b) predominantly brain overgrowth and less severe somatic overgrowth due to less-activating mutations, and (c) intermediate phenotypes (capillary malformations with overgrowth) with intermediately activating mutations. Sixteen of 29 PIK3CA mutations were novel. We also identified constitutional PIK3CA mutations in 10 patients. Our molecular data, combined with review of the literature, show that PIK3CA-related overgrowth disorders comprise a discontinuous spectrum of disorders that correlate with the severity and distribution of mutations. The clinical and molecular spectrum of PIK3CA-related developmental disorders are correlated with types of mutations, tissue distributions, and levels of mosaicism with the clinical phenotype.
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Affiliation(s)
- Ghayda Mirzaa
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington, USA.,Center for Integrative Brain Research and
| | - Andrew E Timms
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Valerio Conti
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Neuroscience Department, A. Meyer Children's Hospital, University of Florence, Florence, Italy
| | - Evan August Boyle
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, Karnataka, India
| | - Beth Martin
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Martin Kircher
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | | | - Jane Juusola
- Whole Exome Sequencing Program, GeneDx, Gaithersburg, Maryland, USA
| | | | | | - Melissa Carter
- Regional Genetics Program, The Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Ian Glass
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington, USA.,Center for Integrative Brain Research and
| | - Inge Krägeloh-Mann
- Department of Pediatrics, and Pediatric Neurology and Developmental Medicine, University Children's Hospital, Tübingen, Germany
| | - David Chitayat
- Mount Sinai Hospital, The Prenatal Diagnosis and Medical Genetics Division, Department of Obstetrics and Gynecology, and.,Department of Pediatrics, Division of Clinical and Metabolic Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Aditi Shah Parikh
- Center for Human Genetics, University Hospitals Case Medical Center, Cleveland, Ohio, USA
| | - Rachael Bradshaw
- Department of Pediatrics, Division of Medical Genetics, Saint Louis University, St. Louis, Missouri, USA
| | - Erin Torti
- Department of Pediatrics, Division of Medical Genetics, Saint Louis University, St. Louis, Missouri, USA
| | - Stephen Braddock
- Department of Pediatrics, Division of Medical Genetics, Saint Louis University, St. Louis, Missouri, USA
| | - Leah Burke
- Department of Pediatrics, University of Vermont College of Medicine, Burlington, Vermont, USA
| | - Sondhya Ghedia
- Department of Clinical Genetics, Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Mark Stephan
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Fiona Stewart
- Belfast Health and Social Care Trust, Belfast, United Kingdom
| | - Chitra Prasad
- Genetics, Metabolism and Pediatrics, London, Ontario, Canada
| | - Melanie Napier
- Genetics, Metabolism and Pediatrics, London, Ontario, Canada
| | - Sulagna Saitta
- Clinical Genetics, Center for Personalized Medicine, Children's Hospital Los Angeles, Keck School of Medicine at University of Southern California, Los Angeles, California, USA
| | - Rachel Straussberg
- Neurology Unit, Schneider Children's Medical Center of Israel, Petach Tikva, and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Michael Gabbett
- School of Medicine, Griffith University, Brisbane, Queensland, Australia
| | - Bridget C O'Connor
- Division of Genetics, Department of Pediatrics, and.,Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Catherine E Keegan
- Division of Genetics, Department of Pediatrics, and.,Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Lim Jiin Yin
- Genetics Service, Department of Pediatric Medicine, KK Women's and Children's Hospital, Singapore
| | - Angeline Hwei Meeng Lai
- Genetics Service, Department of Pediatric Medicine, KK Women's and Children's Hospital, Singapore
| | - Nicole Martin
- Department of Pediatrics, Division of Clinical and Metabolic Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Margaret McKinnon
- British Columbia Medical Genetics Provincial Program, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marie-Claude Addor
- Service de génétique médicale, Centre Hospitalier Universitaire Vaudois CHUV, Switzerland
| | - Luigi Boccuto
- Greenwood Genetic Center, Greenwood, South Carolina, USA
| | | | - Agustina Lanoel
- Department of Dermatology, Children Hospital Prof. Dr. J. P. Garrahan, Buenos Aires, Argentina
| | - Robert L Conway
- Children's Hospital of Michigan, Wayne State University, Detroit, Michigan, USA
| | - Koenraad Devriendt
- Center for Human Genetics, University Hospitals Leuven and KU Leuven, Leuven, Belgium
| | - Katrina Tatton-Brown
- South West Thames Regional Genetics Service, St George's University NHS Foundation Trust, London, and Section of Cancer Genetics, Institute of Cancer Research, Sutton, United Kingdom
| | - Mary Ella Pierpont
- Department of Pediatrics and Ophthalmology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Michael Painter
- Department of Child Neurology, University of Florida, Jacksonville, Florida, USA
| | - Lisa Worgan
- Department of Genetics, Liverpool Hospital, Liverpool, New South Wales, Australia
| | - James Reggin
- Department of Neurology, University of Washington, Seattle, Washington, USA.,Providence Child Neurology, Providence Sacred Heart Medical Center and Children's Hospital, Spokane, Washington, USA
| | - Raoul Hennekam
- Department of Pediatrics and Translational Genetics, Department of Pediatrics, Academic Medical Center, University of Amsterdam Medical Center, Amsterdam, The Netherlands
| | - Karen Tsuchiya
- Department of Laboratories, Seattle Children's Hospital and.,Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Colin C Pritchard
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Mariana Aracena
- División de Pediatría, Pontificia Universidad Católica de Chile, Pediatra-Genetista, Unidad de Genética, Hospital Dr. Luis Calvo Mackenna, Santiago, Chile
| | - Karen W Gripp
- Department of Pediatrics, Sidney Kimmel Medical School at T. Jefferson University, Chief of Division of Medical Genetics, A.I. duPont Hospital for Children, Wilmington, Delaware, USA
| | - Maria Cordisco
- Departments of Dermatology and Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Hilde Van Esch
- Center for Human Genetics, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Livia Garavelli
- Clinical Genetics Unit, IRCCS Santa Maria Nuova Hospital, Reggio Emilia, Italy
| | - Cynthia Curry
- University of California, San Francisco, San Francisco/Genetic Medicine Central California, San Francisco, California, USA
| | - Anne Goriely
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Hulya Kayserilli
- Koç University, School of Medicine, Medical Genetics Department, Koç University Hospital, Istanbul, Turkey
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA.,Howard Hughes Medical Institute, Seattle, Washington, USA
| | - John Graham
- Department of Pediatrics, Cedars-Sinai Medical Center, Harbor-UCLA Medical Center, David Geffen School of Medicine Los Angeles, California, USA
| | - Renzo Guerrini
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Neuroscience Department, A. Meyer Children's Hospital, University of Florence, Florence, Italy
| | - William B Dobyns
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington, USA.,Center for Integrative Brain Research and.,Department of Neurology, University of Washington, Seattle, Washington, USA
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Challenges in managing epilepsy associated with focal cortical dysplasia in children. Epilepsy Res 2018; 145:1-17. [DOI: 10.1016/j.eplepsyres.2018.05.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 04/30/2018] [Accepted: 05/12/2018] [Indexed: 12/15/2022]
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Abstract
PURPOSE OF REVIEW This article provides an overview of the most common nervous system malformations and serves as a reference for the latest advances in diagnosis and treatment. RECENT FINDINGS Major advances have occurred in recognizing the genetic basis of nervous system malformations. Environmental causes of nervous system malformations, such as perinatal infections including Zika virus, are also reviewed. Treatment for nervous system malformations begins prior to birth with prevention. Folic acid supplementation reduces the risk of neural tube defects and is an important part of health maintenance for pregnant women. Fetal surgery is now available for prenatal repair of myelomeningocele and has been demonstrated to improve outcomes. SUMMARY Each type of nervous system malformation is relatively uncommon, but, collectively, they constitute a large population of neurologic patients. The diagnosis of nervous system malformations begins with radiographic characterization. Genetic studies, including chromosomal microarray, targeted gene sequencing, and next-generation sequencing, are increasingly important aspects of the assessment. A genetic diagnosis may identify an associated medical condition and is necessary for family planning. Treatment consists primarily of supportive therapies for developmental delays and epilepsy, but prenatal surgery for myelomeningocele offers a glimpse of future possibilities. Prognosis depends on multiple clinical factors, including the examination findings, imaging characteristics, and genetic results. Treatment is best conducted in a multidisciplinary setting with neurology, neurosurgery, developmental pediatrics, and genetics working together as a comprehensive team.
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Tubulinopathies continued: refining the phenotypic spectrum associated with variants in TUBG1. Eur J Hum Genet 2018; 26:1132-1142. [PMID: 29706637 PMCID: PMC6057922 DOI: 10.1038/s41431-018-0146-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 03/02/2018] [Accepted: 03/13/2018] [Indexed: 12/30/2022] Open
Abstract
Tubulinopathies are a heterogeneous group of conditions with a wide spectrum of clinical severity resulting from variants in genes of the tubulin superfamily. Variants in TUBG1 have been described in three patients with posterior predominant pachygyria and microcephaly. We here report eight additional patients with four novel heterozygous variants in TUBG1 identified by next-generation sequencing (NGS) analysis. All had severe motor and cognitive impairment and all except one developed seizures in early life. The core imaging features included a pachygyric cortex with posterior to anterior gradient, enlarged lateral ventricles most pronounced over the posterior horns, and variable degrees of reduced white matter volume. Basal ganglia, corpus callosum, brainstem, and cerebellum were often normal, in contrast to patients with variants in other tubulin genes where these structures are frequently malformed. The imaging phenotype associated with variants in TUBG1 is therefore more in line with the phenotype resulting from variants in LIS1 (a.k.a. PAFAH1B1). This difference may, at least in part, be explained by gamma-tubulin’s physiological function in microtubule nucleation, which differs from that of alpha and beta-tubulin.
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42
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Genetics and mechanisms leading to human cortical malformations. Semin Cell Dev Biol 2018; 76:33-75. [DOI: 10.1016/j.semcdb.2017.09.031] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 09/21/2017] [Accepted: 09/21/2017] [Indexed: 02/06/2023]
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Dornan GL, Burke JE. Molecular Mechanisms of Human Disease Mediated by Oncogenic and Primary Immunodeficiency Mutations in Class IA Phosphoinositide 3-Kinases. Front Immunol 2018; 9:575. [PMID: 29616047 PMCID: PMC5868324 DOI: 10.3389/fimmu.2018.00575] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 03/07/2018] [Indexed: 12/13/2022] Open
Abstract
The signaling lipid phosphatidylinositol 3,4,5, trisphosphate (PIP3) is an essential mediator of many vital cellular processes, including growth, survival, and metabolism. PIP3 is generated through the action of the class I phosphoinositide 3-kinases (PI3K), and their activity is tightly controlled through interactions with regulatory proteins and activating stimuli. The class IA PI3Ks are composed of three distinct p110 catalytic subunits (p110α, p110β, and p110δ), and they play different roles in specific tissues due to disparities in both expression and engagement downstream of cell-surface receptors. Disruption of PI3K regulation is a frequent driver of numerous human diseases. Activating mutations in the PIK3CA gene encoding the p110α catalytic subunit of class IA PI3K are frequently mutated in several cancer types, and mutations in the PIK3CD gene encoding the p110δ catalytic subunit have been identified in primary immunodeficiency patients. All class IA p110 subunits interact with p85 regulatory subunits, and mutations/deletions in different p85 regulatory subunits have been identified in both cancer and primary immunodeficiencies. In this review, we will summarize our current understanding for the molecular basis of how class IA PI3K catalytic activity is regulated by p85 regulatory subunits, and how activating mutations in the PI3K catalytic subunits PIK3CA and PIK3CD (p110α, p110δ) and regulatory subunits PIK3R1 (p85α) mediate PI3K activation and human disease.
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Affiliation(s)
- Gillian L Dornan
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
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44
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Gstrein T, Edwards A, Přistoupilová A, Leca I, Breuss M, Pilat-Carotta S, Hansen AH, Tripathy R, Traunbauer AK, Hochstoeger T, Rosoklija G, Repic M, Landler L, Stránecký V, Dürnberger G, Keane TM, Zuber J, Adams DJ, Flint J, Honzik T, Gut M, Beltran S, Mechtler K, Sherr E, Kmoch S, Gut I, Keays DA. Mutations in Vps15 perturb neuronal migration in mice and are associated with neurodevelopmental disease in humans. Nat Neurosci 2018; 21:207-217. [PMID: 29311744 PMCID: PMC5897053 DOI: 10.1038/s41593-017-0053-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 11/22/2017] [Indexed: 01/31/2023]
Abstract
The formation of the vertebrate brain requires the generation, migration, differentiation and survival of neurons. Genetic mutations that perturb these critical cellular events can result in malformations of the telencephalon, providing a molecular window into brain development. Here we report the identification of an N-ethyl-N-nitrosourea-induced mouse mutant characterized by a fractured hippocampal pyramidal cell layer, attributable to defects in neuronal migration. We show that this is caused by a hypomorphic mutation in Vps15 that perturbs endosomal-lysosomal trafficking and autophagy, resulting in an upregulation of Nischarin, which inhibits Pak1 signaling. The complete ablation of Vps15 results in the accumulation of autophagic substrates, the induction of apoptosis and severe cortical atrophy. Finally, we report that mutations in VPS15 are associated with cortical atrophy and epilepsy in humans. These data highlight the importance of the Vps15-Vps34 complex and the Nischarin-Pak1 signaling hub in the development of the telencephalon.
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Affiliation(s)
- Thomas Gstrein
- Institute of Molecular Pathology (IMP), Vienna Biocentre (VBC), Vienna, Austria
| | - Andrew Edwards
- Wellcome Trust Center for Human Genetics (WTCHG), Oxford, UK
| | - Anna Přistoupilová
- Institute of Inherited Metabolic Disorders, Charles University, Prague, Czech Republic
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Ines Leca
- Institute of Molecular Pathology (IMP), Vienna Biocentre (VBC), Vienna, Austria
| | - Martin Breuss
- Institute of Molecular Pathology (IMP), Vienna Biocentre (VBC), Vienna, Austria
| | | | - Andi H Hansen
- Institute of Molecular Pathology (IMP), Vienna Biocentre (VBC), Vienna, Austria
| | - Ratna Tripathy
- Institute of Molecular Pathology (IMP), Vienna Biocentre (VBC), Vienna, Austria
| | - Anna K Traunbauer
- Institute of Molecular Pathology (IMP), Vienna Biocentre (VBC), Vienna, Austria
| | - Tobias Hochstoeger
- Institute of Molecular Pathology (IMP), Vienna Biocentre (VBC), Vienna, Austria
| | - Gavril Rosoklija
- Institute of Molecular Pathology (IMP), Vienna Biocentre (VBC), Vienna, Austria
| | - Marco Repic
- Institute for Molecular Biotechnology (IMBA), Vienna, Austria
| | - Lukas Landler
- Institute of Molecular Pathology (IMP), Vienna Biocentre (VBC), Vienna, Austria
| | - Viktor Stránecký
- Institute of Inherited Metabolic Disorders, Charles University, Prague, Czech Republic
| | - Gerhard Dürnberger
- Institute of Molecular Pathology (IMP), Vienna Biocentre (VBC), Vienna, Austria
| | - Thomas M Keane
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Johannes Zuber
- Institute of Molecular Pathology (IMP), Vienna Biocentre (VBC), Vienna, Austria
| | - David J Adams
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Jonathan Flint
- Wellcome Trust Center for Human Genetics (WTCHG), Oxford, UK
| | - Tomas Honzik
- Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Sergi Beltran
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Karl Mechtler
- Institute of Molecular Pathology (IMP), Vienna Biocentre (VBC), Vienna, Austria
| | - Elliott Sherr
- Institute of Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Stanislav Kmoch
- Institute of Inherited Metabolic Disorders, Charles University, Prague, Czech Republic
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - David A Keays
- Institute of Molecular Pathology (IMP), Vienna Biocentre (VBC), Vienna, Austria.
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Fernández-Marmiesse A, Gouveia S, Couce ML. NGS Technologies as a Turning Point in Rare Disease Research , Diagnosis and Treatment. Curr Med Chem 2018; 25:404-432. [PMID: 28721829 PMCID: PMC5815091 DOI: 10.2174/0929867324666170718101946] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 06/19/2017] [Accepted: 07/14/2017] [Indexed: 01/17/2023]
Abstract
Approximately 25-50 million Americans, 30 million Europeans, and 8% of the Australian population have a rare disease. Rare diseases are thus a common problem for clinicians and account for enormous healthcare costs worldwide due to the difficulty of establishing a specific diagnosis. In this article, we review the milestones achieved in our understanding of rare diseases since the emergence of next-generation sequencing (NGS) technologies and analyze how these advances have influenced research and diagnosis. The first half of this review describes how NGS has changed diagnostic workflows and provided an unprecedented, simple way of discovering novel disease-associated genes. We focus particularly on metabolic and neurodevelopmental disorders. NGS has enabled cheap and rapid genetic diagnosis, highlighted the relevance of mosaic and de novo mutations, brought to light the wide phenotypic spectrum of most genes, detected digenic inheritance or the presence of more than one rare disease in the same patient, and paved the way for promising new therapies. In the second part of the review, we look at the limitations and challenges of NGS, including determination of variant causality, the loss of variants in coding and non-coding regions, and the detection of somatic mosaicism variants and epigenetic mutations, and discuss how these can be overcome in the near future.
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Affiliation(s)
- Ana Fernández-Marmiesse
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Sofía Gouveia
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - María L. Couce
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
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Kurtas N, Arrigoni F, Errichiello E, Zucca C, Maghini C, D'Angelo MG, Beri S, Giorda R, Bertuzzo S, Delledonne M, Xumerle L, Rossato M, Zuffardi O, Bonaglia MC. Chromothripsis and ring chromosome 22: a paradigm of genomic complexity in the Phelan-McDermid syndrome (22q13 deletion syndrome). J Med Genet 2018; 55:269-277. [PMID: 29378768 PMCID: PMC5869459 DOI: 10.1136/jmedgenet-2017-105125] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 12/21/2017] [Accepted: 01/08/2018] [Indexed: 12/14/2022]
Abstract
Introduction Phelan-McDermid syndrome (PMS) is caused by SHANK3 haploinsufficiency. Its wide phenotypic variation is attributed partly to the type and size of 22q13 genomic lesion (deletion, unbalanced translocation, ring chromosome), partly to additional undefined factors. We investigated a child with severe global neurodevelopmental delay (NDD) compatible with her distal 22q13 deletion, complicated by bilateral perisylvian polymicrogyria (BPP) and urticarial rashes, unreported in PMS. Methods Following the cytogenetic and array-comparative genomic hybridization (CGH) detection of a r(22) with SHANK3 deletion and two upstream duplications, whole-genome sequencing (WGS) in blood and whole-exome sequencing (WES) in blood and saliva were performed to highlight potential chromothripsis/chromoanagenesis events and any possible BPP-associated variants, even in low-level mosaicism. Results WGS confirmed the deletion and highlighted inversion and displaced order of eight fragments, three of them duplicated. The microhomology-mediated insertion of partial Alu-elements at one breakpoint junction disrupted the topological associating domain joining NFAM1 to the transcriptional coregulator TCF20. WES failed to detect BPP-associated variants. Conclusions Although we were unable to highlight the molecular basis of BPP, our data suggest that SHANK3 haploinsufficiency and TCF20 misregulation, both associated with intellectual disability, contributed to the patient’s NDD, while NFAM1 interruption likely caused her skin rashes, as previously reported. We provide the first example of chromoanasynthesis in a constitutional ring chromosome and reinforce the growing evidence that chromosomal rearrangements may be more complex than estimated by conventional diagnostic approaches and affect the phenotype by global alteration of the topological chromatin organisation rather than simply by deletion or duplication of dosage-sensitive genes.
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Affiliation(s)
- Nehir Kurtas
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Filippo Arrigoni
- Neuroimaging Laboratory, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, Italy
| | | | - Claudio Zucca
- Clinical Neurophysiology Unit, Scientific Institute IRCCS Eugenio Medea, Bosisio Parini, Italy
| | - Cristina Maghini
- Neuromuscular Disorders Unit, Scientific Institute IRCCS Eugenio Medea, Bosisio Parini, Italy
| | - Maria Grazia D'Angelo
- Neuromuscular Disorders Unit, Scientific Institute IRCCS Eugenio Medea, Bosisio Parini, Italy
| | - Silvana Beri
- Molecular Biology Laboratory, Scientific Institute IRCCS Eugenio Medea, Bosisio Parini, Italy
| | - Roberto Giorda
- Molecular Biology Laboratory, Scientific Institute IRCCS Eugenio Medea, Bosisio Parini, Italy
| | - Sara Bertuzzo
- Cytogenetics Laboratory, Scientific Institute IRCCS Eugenio Medea, Bosisio Parini, Italy
| | | | - Luciano Xumerle
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Marzia Rossato
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Orsetta Zuffardi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Maria Clara Bonaglia
- Cytogenetics Laboratory, Scientific Institute IRCCS Eugenio Medea, Bosisio Parini, Italy
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47
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Genetik der kortikalen Fehlbildungen. MED GENET-BERLIN 2018. [DOI: 10.1007/s11825-017-0165-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Zusammenfassung
Kortikale Malformationen sind vielfältig und stellen eine wichtige Ursache der geistigen Entwicklungsstörung und der Epilepsie dar. Die Ätiologie der kortikalen Fehlbildungen ist sehr heterogen und beinhaltet sowohl rein exogene Ursachen als auch chromosomale und monogene Erkrankungen. Eine effiziente genetische Diagnostik bedarf der akkuraten Interpretation des Magnetresonanztomographie(MRT)-Musters. Bei einigen klinischen Formen kann eine zielgerichtete Einzelgendiagnostik erfolgen, die anderen klinischen Entitäten erfordern dagegen eine komplexe Stufendiagnostik und können nur mittels Hochdurchsatzsequenzierung aufgeklärt werden. In diesem Beitrag werden die 4 häufigsten kortikalen Fehlbildungen im Hinblick auf die typischen klinischen Symptome, MRT-Merkmale und den Algorithmus der genetischen Abklärung vorgestellt.
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48
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D'Gama AM, Woodworth MB, Hossain AA, Bizzotto S, Hatem NE, LaCoursiere CM, Najm I, Ying Z, Yang E, Barkovich AJ, Kwiatkowski DJ, Vinters HV, Madsen JR, Mathern GW, Blümcke I, Poduri A, Walsh CA. Somatic Mutations Activating the mTOR Pathway in Dorsal Telencephalic Progenitors Cause a Continuum of Cortical Dysplasias. Cell Rep 2017; 21:3754-3766. [PMID: 29281825 PMCID: PMC5752134 DOI: 10.1016/j.celrep.2017.11.106] [Citation(s) in RCA: 207] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 10/02/2017] [Accepted: 11/29/2017] [Indexed: 01/16/2023] Open
Abstract
Focal cortical dysplasia (FCD) and hemimegalencephaly (HME) are epileptogenic neurodevelopmental malformations caused by mutations in mTOR pathway genes. Deep sequencing of these genes in FCD/HME brain tissue identified an etiology in 27 of 66 cases (41%). Radiographically indistinguishable lesions are caused by somatic activating mutations in AKT3, MTOR, and PIK3CA and germline loss-of-function mutations in DEPDC5, NPRL2, and TSC1/2, including TSC2 mutations in isolated HME demonstrating a "two-hit" model. Mutations in the same gene cause a disease continuum from FCD to HME to bilateral brain overgrowth, reflecting the progenitor cell and developmental time when the mutation occurred. Single-cell sequencing demonstrated mTOR activation in neurons in all lesions. Conditional Pik3ca activation in the mouse cortex showed that mTOR activation in excitatory neurons and glia, but not interneurons, is sufficient for abnormal cortical overgrowth. These data suggest that mTOR activation in dorsal telencephalic progenitors, in some cases specifically the excitatory neuron lineage, causes cortical dysplasia.
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Affiliation(s)
- Alissa M D'Gama
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Mollie B Woodworth
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Amer A Hossain
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Sara Bizzotto
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Nicole E Hatem
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | | | - Imad Najm
- Epilepsy Center, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Zhong Ying
- Epilepsy Center, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Edward Yang
- Department of Radiology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Radiology, Harvard Medical School, Boston, MA 02115, USA
| | - A James Barkovich
- Departments of Radiology and Diagnostic Imaging, Neurology, Pediatrics, and Neurosurgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Harry V Vinters
- Departments of Pathology and Laboratory Medicine (Neuropathology) and Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Joseph R Madsen
- Department of Neurosurgery, Boston Children's Hospital, Boston, MA, USA
| | - Gary W Mathern
- Departments of Neurosurgery and Psychiatry and Biobehavioral Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ingmar Blümcke
- Epilepsy Center, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Neuropathology, University Hospital Erlangen, Schwabachanlage 6, 91054 Erlangen, Germany
| | - Annapurna Poduri
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Epilepsy Genetics Program, Division of Epilepsy and Clinical Neurophysiology, Department of Neurology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
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Chang F, Liu L, Fang E, Zhang G, Chen T, Cao K, Li Y, Li MM. Molecular Diagnosis of Mosaic Overgrowth Syndromes Using a Custom-Designed Next-Generation Sequencing Panel. J Mol Diagn 2017; 19:613-624. [DOI: 10.1016/j.jmoldx.2017.04.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 03/27/2017] [Accepted: 04/18/2017] [Indexed: 12/19/2022] Open
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Hong SJ, Bernhardt BC, Gill RS, Bernasconi N, Bernasconi A. The spectrum of structural and functional network alterations in malformations of cortical development. Brain 2017; 140:2133-2143. [DOI: 10.1093/brain/awx145] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 05/07/2017] [Indexed: 12/28/2022] Open
Affiliation(s)
- Seok-Jun Hong
- Neuroimaging of Epilepsy Laboratory, Department of Neurology and McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
| | - Boris C Bernhardt
- Neuroimaging of Epilepsy Laboratory, Department of Neurology and McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
| | - Ravnoor S Gill
- Neuroimaging of Epilepsy Laboratory, Department of Neurology and McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
| | - Neda Bernasconi
- Neuroimaging of Epilepsy Laboratory, Department of Neurology and McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
| | - Andrea Bernasconi
- Neuroimaging of Epilepsy Laboratory, Department of Neurology and McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
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