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Scheffer IE, Zuberi S, Mefford HC, Guerrini R, McTague A. Developmental and epileptic encephalopathies. Nat Rev Dis Primers 2024; 10:61. [PMID: 39237642 DOI: 10.1038/s41572-024-00546-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/29/2024] [Indexed: 09/07/2024]
Abstract
Developmental and epileptic encephalopathies, the most severe group of epilepsies, are characterized by seizures and frequent epileptiform activity associated with developmental slowing or regression. Onset typically occurs in infancy or childhood and includes many well-defined epilepsy syndromes. Patients have wide-ranging comorbidities including intellectual disability, psychiatric features, such as autism spectrum disorder and behavioural problems, movement and musculoskeletal disorders, gastrointestinal and sleep problems, together with an increased mortality rate. Problems change with age and patients require substantial support throughout life, placing a high psychosocial burden on parents, carers and the community. In many patients, the aetiology can be identified, and a genetic cause is found in >50% of patients using next-generation sequencing technologies. More than 900 genes have been identified as monogenic causes of developmental and epileptic encephalopathies and many cell components and processes have been implicated in their pathophysiology, including ion channels and transporters, synaptic proteins, cell signalling and metabolism and epigenetic regulation. Polygenic risk score analyses have shown that common variants also contribute to phenotypic variability. Holistic management, which encompasses antiseizure therapies and care for multimorbidities, is determined both by epilepsy syndrome and aetiology. Identification of the underlying aetiology enables the development of precision medicines to improve the long-term outcome of patients with these devastating diseases.
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Affiliation(s)
- Ingrid E Scheffer
- Epilepsy Research Centre, The University of Melbourne, Austin Health, Heidelberg, Victoria, Australia.
- Florey and Murdoch Children's Research Institutes, Melbourne, Victoria, Australia.
- Department of Paediatrics, The University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia.
| | - Sameer Zuberi
- Paediatric Neurosciences Research Group, School of Health & Wellbeing, University of Glasgow, Glasgow, UK
- Paediatric Neurosciences, Royal Hospital for Children, Glasgow, UK
| | - Heather C Mefford
- Center for Paediatric Neurological Disease Research, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Renzo Guerrini
- Neuroscience Department, Children's Hospital Meyer IRCCS, Florence, Italy
- University of Florence, Florence, Italy
| | - Amy McTague
- Developmental Neurosciences, UCL Great Ormond Street Institute of Child Health, London, UK
- Department of Neurology, Great Ormond Street Hospital, London, UK
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2
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Mangum R, Lin FY, Parsons DW. Recent Advancements and Innovations in Pediatric Precision Oncology. J Pediatr Hematol Oncol 2024; 46:262-271. [PMID: 38857189 DOI: 10.1097/mph.0000000000002871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 03/29/2024] [Indexed: 06/12/2024]
Abstract
Precision oncology incorporates comprehensive genomic profiling into the individualized clinical care of pediatric cancer patients. In recent years, comprehensive pan-cancer analyses have led to the successful implementation of genomics-based pediatric trials and accelerated approval of novel targeted agents. In addition, disease-specific studies have resulted in molecular subclassification of myriad cancer types with subsequent tailoring of treatment intensity based on the patient's prognostic factors. This review discusses the progress of the field and highlights developments that are leading to more personalized cancer care and improved patient outcomes. Increased understanding of the evolution of precision oncology over recent decades emphasizes the tremendous impact of improved genomic applications. New technologies and improved diagnostic modalities offer further promise for future advancements within the field.
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Affiliation(s)
- Ross Mangum
- Center for Cancer and Blood Disorders, Phoenix Children's Hospital, Phoenix, AZ
| | - Frank Y Lin
- Department of Pediatrics, Texas Children's Cancer Center
- The Dan L. Duncan Cancer Center
| | - D Williams Parsons
- Department of Pediatrics, Texas Children's Cancer Center
- The Dan L. Duncan Cancer Center
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
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3
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Macdonald-Laurs E, Dzau W, Warren AEL, Coleman M, Mignone C, Stephenson SEM, Howell KB. Identification and treatment of surgically-remediable causes of infantile epileptic spasms syndrome. Expert Rev Neurother 2024; 24:661-680. [PMID: 38814860 DOI: 10.1080/14737175.2024.2360117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 05/22/2024] [Indexed: 06/01/2024]
Abstract
INTRODUCTION Infantile epileptic spasms syndrome (IESS) is a common developmental and epileptic encephalopathy with poor long-term outcomes. A substantial proportion of patients with IESS have a potentially surgically remediable etiology. Despite this, epilepsy surgery is underutilized in this patient group. Some surgically remediable etiologies, such as focal cortical dysplasia and malformation of cortical development with oligodendroglial hyperplasia in epilepsy (MOGHE), are under-diagnosed in infants and young children. Even when a surgically remediable etiology is recognised, for example, tuberous sclerosis or focal encephalomalacia, epilepsy surgery may be delayed or not considered due to diffuse EEG changes, unclear surgical boundaries, or concerns about operating in this age group. AREAS COVERED In this review, the authors discuss the common surgically remediable etiologies of IESS, their clinical and EEG features, and the imaging techniques that can aid in their diagnosis. They then describe the surgical approaches used in this patient group, and the beneficial impact that early epilepsy surgery can have on developing brain networks. EXPERT OPINION Epilepsy surgery remains underutilized even when a potentially surgically remediable cause is recognized. Overcoming the barriers that result in under-recognition of surgical candidates and underutilization of epilepsy surgery in IESS will improve long-term seizure and developmental outcomes.
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Affiliation(s)
- Emma Macdonald-Laurs
- Department of Neurology, The Royal Children's Hospital, Parkville, VIC, Australia
- Neurosciences Group, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
| | - Winston Dzau
- Neurosciences Group, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
| | - Aaron E L Warren
- Department of Medicine (Austin Health), The University of Melbourne, Melbourne, VIC, Australia
- Brigham and Women's Hospital, Harvard Medical School, Massachusetts, USA
| | - Matthew Coleman
- Neurosciences Group, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
| | - Cristina Mignone
- Department of Medical Imaging, The Royal Children's Hospital, Parkville, VIC, Australia
| | - Sarah E M Stephenson
- Neurosciences Group, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
| | - Katherine B Howell
- Department of Neurology, The Royal Children's Hospital, Parkville, VIC, Australia
- Neurosciences Group, Murdoch Children's Research Institute, Parkville, VIC, Australia
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Silver BB, Brooks A, Gerrish K, Tokar EJ. Isolation and Characterization of Cell-Free DNA from Cerebral Organoids. Int J Mol Sci 2024; 25:5522. [PMID: 38791569 PMCID: PMC11121789 DOI: 10.3390/ijms25105522] [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: 04/23/2024] [Revised: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
Early detection of neurological conditions is critical for timely diagnosis and treatment. Identifying cellular-level changes is essential for implementing therapeutic interventions prior to symptomatic disease onset. However, monitoring brain tissue directly through biopsies is invasive and poses a high risk. Bodily fluids such as blood or cerebrospinal fluid contain information in many forms, including proteins and nucleic acids. In particular, cell-free DNA (cfDNA) has potential as a versatile neurological biomarker. Yet, our knowledge of cfDNA released by brain tissue and how cfDNA changes in response to deleterious events within the brain is incomplete. Mapping changes in cfDNA to specific cellular events is difficult in vivo, wherein many tissues contribute to circulating cfDNA. Organoids are tractable systems for examining specific changes consistently in a human background. However, few studies have investigated cfDNA released from organoids. Here, we examined cfDNA isolated from cerebral organoids. We found that cerebral organoids release quantities of cfDNA sufficient for downstream analysis with droplet-digital PCR and whole-genome sequencing. Further, gene ontology analysis of genes aligning with sequenced cfDNA fragments revealed associations with terms related to neurodevelopment and autism spectrum disorder. We conclude that cerebral organoids hold promise as tools for the discovery of cfDNA biomarkers related to neurodevelopmental and neurological disorders.
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Affiliation(s)
- Brian B. Silver
- Mechanistic Toxicology Branch, Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC 27709, USA
- Molecular Genomics Core, Division of Intramural Research, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC 27709, USA;
| | - Ashley Brooks
- Biostatistics and Computational Biology Branch, Division of Intramural Research, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC 27709, USA;
| | - Kevin Gerrish
- Molecular Genomics Core, Division of Intramural Research, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC 27709, USA;
| | - Erik J. Tokar
- Mechanistic Toxicology Branch, Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC 27709, 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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Man A, Di Scipio M, Grewal S, Suk Y, Trinari E, Ejaz R, Whitney R. The Genetics of Tuberous Sclerosis Complex and Related mTORopathies: Current Understanding and Future Directions. Genes (Basel) 2024; 15:332. [PMID: 38540392 PMCID: PMC10970281 DOI: 10.3390/genes15030332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 03/02/2024] [Accepted: 03/02/2024] [Indexed: 06/14/2024] Open
Abstract
The mechanistic target of rapamycin (mTOR) pathway serves as a master regulator of cell growth, proliferation, and survival. Upregulation of the mTOR pathway has been shown to cause malformations of cortical development, medically refractory epilepsies, and neurodevelopmental disorders, collectively described as mTORopathies. Tuberous sclerosis complex (TSC) serves as the prototypical mTORopathy. Characterized by the development of benign tumors in multiple organs, pathogenic variants in TSC1 or TSC2 disrupt the TSC protein complex, a negative regulator of the mTOR pathway. Variants in critical domains of the TSC complex, especially in the catalytic TSC2 subunit, correlate with increased disease severity. Variants in less crucial exons and non-coding regions, as well as those undetectable with conventional testing, may lead to milder phenotypes. Despite the assumption of complete penetrance, expressivity varies within families, and certain variants delay disease onset with milder neurological effects. Understanding these genotype-phenotype correlations is crucial for effective clinical management. Notably, 15% of patients have no mutation identified by conventional genetic testing, with the majority of cases postulated to be caused by somatic TSC1/TSC2 variants which present complex diagnostic challenges. Advancements in genetic testing, prenatal screening, and precision medicine hold promise for changing the diagnostic and treatment paradigm for TSC and related mTORopathies. Herein, we explore the genetic and molecular mechanisms of TSC and other mTORopathies, emphasizing contemporary genetic methods in understanding and diagnosing the condition.
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Affiliation(s)
- Alice Man
- Michael G. DeGroote School of Medicine, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Matteo Di Scipio
- Michael G. DeGroote School of Medicine, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Shan Grewal
- Michael G. DeGroote School of Medicine, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Yujin Suk
- Michael G. DeGroote School of Medicine, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Elisabetta Trinari
- Division of Developmental Pediatrics, Department of Pediatrics, McMaster Children’s Hospital, Hamilton, ON L8N 3Z5, Canada
| | - Resham Ejaz
- Division of Genetics, Department of Pediatrics, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Robyn Whitney
- Division of Neurology, Department of Pediatrics, McMaster University, Hamilton, ON L8S 4L8, Canada
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Hallermayr A, Keßler T, Steinke-Lange V, Heitzer E, Holinski-Feder E, Speicher M. The utility of liquid biopsy in clinical genetic diagnosis of cancer and monogenic mosaic disorders. MED GENET-BERLIN 2023; 35:275-284. [PMID: 38835734 PMCID: PMC11006364 DOI: 10.1515/medgen-2023-2066] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Liquid biopsy for minimally invasive diagnosis and monitoring of cancer patients is progressing toward routine clinical practice. With the implementation of highly sensitive next-generation sequencing (NGS) based assays for the analysis of cfDNA, however, consideration of the utility of liquid biopsy for clinical genetic testing is critical. While the focus of liquid biopsy for cancer diagnosis is the detection of circulating tumor DNA (ctDNA) as a fraction of total cell-free DNA (cfDNA), cfDNA analysis reveals both somatic mosaic tumor and germline variants and clonal hematopoiesis. Here we outline advantages and limitations of mosaic and germline variant detection as well as the impact of clonal hematopoiesis on liquid biopsy in cancer diagnosis. We also evaluate the potential of cfDNA analysis for the molecular diagnosis of monogenic mosaic disorders.
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Affiliation(s)
| | - Thomas Keßler
- MGZ - Medizinisch Genetisches Zentrum München Germany
| | | | - Ellen Heitzer
- Medical University of Graz Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine (Austria) Graz Austria
| | | | - Michael Speicher
- Medical University of Graz Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine (Austria), Neue Stiftingtalstraße 2 Graz Austria
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Johannesen KM, Tümer Z, Weckhuysen S, Barakat TS, Bayat A. Solving the unsolved genetic epilepsies: Current and future perspectives. Epilepsia 2023; 64:3143-3154. [PMID: 37750451 DOI: 10.1111/epi.17780] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 09/27/2023]
Abstract
Many patients with epilepsy undergo exome or genome sequencing as part of a diagnostic workup; however, many remain genetically unsolved. There are various factors that account for negative results in exome/genome sequencing for patients with epilepsy: (1) the underlying cause is not genetic; (2) there is a complex polygenic explanation; (3) the illness is monogenic but the causative gene remains to be linked to a human disorder; (4) family segregation with reduced penetrance; (5) somatic mosaicism or the complexity of, for example, a structural rearrangement; or (6) limited knowledge or diagnostic tools that hinder the proper classification of a variant, resulting in its designation as a variant of unknown significance. The objective of this review is to outline some of the diagnostic options that lie beyond the exome/genome, and that might become clinically relevant within the foreseeable future. These options include: (1) re-analysis of older exome/genome data as knowledge increases or symptoms change; (2) looking for somatic mosaicism or long-read sequencing to detect low-complexity repeat variants or specific structural variants missed by traditional exome/genome sequencing; (3) exploration of the non-coding genome including disruption of topologically associated domains, long range non-coding RNA, or other regulatory elements; and finally (4) transcriptomics, DNA methylation signatures, and metabolomics as complementary diagnostic methods that may be used in the assessment of variants of unknown significance. Some of these tools are currently not integrated into standard diagnostic workup. However, it is reasonable to expect that they will become increasingly available and improve current diagnostic capabilities, thereby enabling precision diagnosis in patients who are currently undiagnosed.
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Affiliation(s)
- Katrine M Johannesen
- Department of Genetics, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Epilepsy Genetics and Personalized Medicine, The Danish Epilepsy Center, Dianalund, Denmark
| | - Zeynep Tümer
- Department of Genetics, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sarah Weckhuysen
- Applied and Translational Neurogenomics Group, VIB Centre for Molecular Neurology, Antwerp, Belgium
- Translational Neurosciences, Faculty of Medicine and Health Science, University of Antwerp, Antwerp, Belgium
- Department of Neurology, University Hospital Antwerp, Antwerp, Belgium
- μNEURO Research Centre of Excellence, University of Antwerp, Antwerp, Belgium
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
- Discovery Unit, Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
- ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Allan Bayat
- Department of Epilepsy Genetics and Personalized Medicine, The Danish Epilepsy Center, Dianalund, Denmark
- Department of Regional Health Research, University of Southern Denmark, Odense, Denmark
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
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Straka B, Splitkova B, Vlckova M, Tesner P, Rezacova H, Krskova L, Koblizek M, Kyncl M, Maulisova A, Bukacova K, Uhrova-Meszarosova A, Musilova A, Kudr M, Ebel M, Belohlavkova A, Jahodova A, Liby P, Tichy M, Jezdik P, Zamecnik J, Aronica E, Krsek P. Genetic testing in children enrolled in epilepsy surgery program. A real-life study. Eur J Paediatr Neurol 2023; 47:80-87. [PMID: 37812946 DOI: 10.1016/j.ejpn.2023.09.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 09/22/2023] [Accepted: 09/27/2023] [Indexed: 10/11/2023]
Abstract
OBJECTIVE Although genetic causes of drug-resistant focal epilepsy and selected focal malformations of cortical development (MCD) have been described, a limited number of studies comprehensively analysed genetic diagnoses in patients undergoing pre-surgical evaluation, their outcomes and the effect of genetic diagnosis on surgical strategy. METHODS We analysed a prospective cohort of children enrolled in epilepsy surgery program over January 2018-July 2022. The majority of patients underwent germline and/or somatic genetic testing. We searched for predictors of surgical outcome and positive result of germline genetic testing. RESULTS Ninety-five patients were enrolled in epilepsy surgery program and 64 underwent resective epilepsy surgery. We ascertained germline genetic diagnosis in 13/74 patients having underwent germline gene testing (pathogenic or likely pathogenic variants in CHRNA4, NPRL3, DEPDC5, FGF12, GRIA2, SZT2, STXBP1) and identified three copy number variants. Thirty-five patients underwent somatic gene testing; we detected 10 pathogenic or likely pathogenic variants in genes SLC35A2, PTEN, MTOR, DEPDC5, NPRL3. Germline genetic diagnosis was significantly associated with the diagnosis of focal epilepsy with unknown seizure onset. SIGNIFICANCE Germline and somatic gene testing can ascertain a definite genetic diagnosis in a significant subgroup of patients in epilepsy surgery programs. Diagnosis of focal genetic epilepsy may tip the scales against the decision to proceed with invasive EEG study or surgical resection; however, selected patients with genetic focal epilepsies associated with MCD may benefit from resective epilepsy surgery and therefore, a genetic diagnosis does not disqualify patients from presurgical evaluation and epilepsy surgery.
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Affiliation(s)
- Barbora Straka
- Department of Paediatric Neurology, Motol Epilepsy Center, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Full Member of the ERN EpiCARE, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Barbora Splitkova
- Department of Paediatric Neurology, Motol Epilepsy Center, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Full Member of the ERN EpiCARE, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Marketa Vlckova
- Department of Biology and Medical Genetics, Motol Epilepsy Center, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Motol University Hospital, Full Member of the ERN EpiCARE, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Pavel Tesner
- Department of Biology and Medical Genetics, Motol Epilepsy Center, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Motol University Hospital, Full Member of the ERN EpiCARE, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Hana Rezacova
- Department of Biology and Medical Genetics, Motol Epilepsy Center, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Motol University Hospital, Full Member of the ERN EpiCARE, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Lenka Krskova
- Department of Pathology and Molecular Medicine, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Full Member of the ERN EpiCARE, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Miroslav Koblizek
- Department of Pathology and Molecular Medicine, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Full Member of the ERN EpiCARE, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Martin Kyncl
- Department of Radiology, Motol Epilepsy Center, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Full Member of the ERN EpiCARE, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Alice Maulisova
- Department of Clinical Psychology, Motol University Hospital, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Katerina Bukacova
- Department of Clinical Psychology, Motol University Hospital, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Anna Uhrova-Meszarosova
- Department of Paediatric Neurology, Motol Epilepsy Center, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Full Member of the ERN EpiCARE, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Alena Musilova
- Department of Paediatric Neurology, Motol Epilepsy Center, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Full Member of the ERN EpiCARE, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Martin Kudr
- Department of Paediatric Neurology, Motol Epilepsy Center, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Full Member of the ERN EpiCARE, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Matyas Ebel
- Department of Paediatric Neurology, Motol Epilepsy Center, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Full Member of the ERN EpiCARE, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Anezka Belohlavkova
- Department of Paediatric Neurology, Motol Epilepsy Center, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Full Member of the ERN EpiCARE, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Alena Jahodova
- Department of Paediatric Neurology, Motol Epilepsy Center, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Full Member of the ERN EpiCARE, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Petr Liby
- Department of Neurosurgery, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Full Member of the ERN EpiCARE, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Michal Tichy
- Department of Neurosurgery, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Full Member of the ERN EpiCARE, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Petr Jezdik
- Faculty of Electrical Engineering, Department of Circuit Theory, Czech Technical University in Prague, Technicka 2, Praha 6, 166 27, Czech Republic.
| | - Josef Zamecnik
- Department of Pathology and Molecular Medicine, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Full Member of the ERN EpiCARE, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Eleonora Aronica
- Amsterdam UMC Location University of Amsterdam, Department of Neuropathology, Amsterdam Neuroscience, the Netherlands; Stichting Epilepsie Instellingen Nederland (SEIN), Heemstede, the Netherlands.
| | - Pavel Krsek
- Department of Paediatric Neurology, Motol Epilepsy Center, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Full Member of the ERN EpiCARE, V Uvalu 84, 15006, Prague, Czech Republic.
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10
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Khoshkhoo S, Wang Y, Chahine Y, Erson-Omay EZ, Robert SM, Kiziltug E, Damisah EC, Nelson-Williams C, Zhu G, Kong W, Huang AY, Stronge E, Phillips HW, Chhouk BH, Bizzotto S, Chen MH, Adikari TN, Ye Z, Witkowski T, Lai D, Lee N, Lokan J, Scheffer IE, Berkovic SF, Haider S, Hildebrand MS, Yang E, Gunel M, Lifton RP, Richardson RM, Blümcke I, Alexandrescu S, Huttner A, Heinzen EL, Zhu J, Poduri A, DeLanerolle N, Spencer DD, Lee EA, Walsh CA, Kahle KT. Contribution of Somatic Ras/Raf/Mitogen-Activated Protein Kinase Variants in the Hippocampus in Drug-Resistant Mesial Temporal Lobe Epilepsy. JAMA Neurol 2023; 80:578-587. [PMID: 37126322 PMCID: PMC10152377 DOI: 10.1001/jamaneurol.2023.0473] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/31/2022] [Indexed: 05/02/2023]
Abstract
Importance Mesial temporal lobe epilepsy (MTLE) is the most common focal epilepsy subtype and is often refractory to antiseizure medications. While most patients with MTLE do not have pathogenic germline genetic variants, the contribution of postzygotic (ie, somatic) variants in the brain is unknown. Objective To test the association between pathogenic somatic variants in the hippocampus and MTLE. Design, Setting, and Participants This case-control genetic association study analyzed the DNA derived from hippocampal tissue of neurosurgically treated patients with MTLE and age-matched and sex-matched neurotypical controls. Participants treated at level 4 epilepsy centers were enrolled from 1988 through 2019, and clinical data were collected retrospectively. Whole-exome and gene-panel sequencing (each genomic region sequenced more than 500 times on average) were used to identify candidate pathogenic somatic variants. A subset of novel variants was functionally evaluated using cellular and molecular assays. Patients with nonlesional and lesional (mesial temporal sclerosis, focal cortical dysplasia, and low-grade epilepsy-associated tumors) drug-resistant MTLE who underwent anterior medial temporal lobectomy were eligible. All patients with available frozen tissue and appropriate consents were included. Control brain tissue was obtained from neurotypical donors at brain banks. Data were analyzed from June 2020 to August 2022. Exposures Drug-resistant MTLE. Main Outcomes and Measures Presence and abundance of pathogenic somatic variants in the hippocampus vs the unaffected temporal neocortex. Results Of 105 included patients with MTLE, 53 (50.5%) were female, and the median (IQR) age was 32 (26-44) years; of 30 neurotypical controls, 11 (36.7%) were female, and the median (IQR) age was 37 (18-53) years. Eleven pathogenic somatic variants enriched in the hippocampus relative to the unaffected temporal neocortex (median [IQR] variant allele frequency, 1.92 [1.5-2.7] vs 0.3 [0-0.9]; P = .01) were detected in patients with MTLE but not in controls. Ten of these variants were in PTPN11, SOS1, KRAS, BRAF, and NF1, all predicted to constitutively activate Ras/Raf/mitogen-activated protein kinase (MAPK) signaling. Immunohistochemical studies of variant-positive hippocampal tissue demonstrated increased Erk1/2 phosphorylation, indicative of Ras/Raf/MAPK activation, predominantly in glial cells. Molecular assays showed abnormal liquid-liquid phase separation for the PTPN11 variants as a possible dominant gain-of-function mechanism. Conclusions and Relevance Hippocampal somatic variants, particularly those activating Ras/Raf/MAPK signaling, may contribute to the pathogenesis of sporadic, drug-resistant MTLE. These findings may provide a novel genetic mechanism and highlight new therapeutic targets for this common indication for epilepsy surgery.
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Affiliation(s)
- Sattar Khoshkhoo
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Yilan Wang
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts
| | - Yasmine Chahine
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts
| | - E. Zeynep Erson-Omay
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut
| | - Stephanie M. Robert
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut
| | - Emre Kiziltug
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut
| | - Eyiyemisi C. Damisah
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut
| | | | - Guangya Zhu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Wenna Kong
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - August Yue Huang
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
| | - Edward Stronge
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - H. Westley Phillips
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Neurosurgery, David Geffen School of Medicine, University of California, Los Angeles
| | - Brian H. Chhouk
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts
| | - Sara Bizzotto
- Sorbonne University, Paris Brain Institute (ICM), National Institute of Health and Medical Research (INSERM), National Center for Scientific Research (CNRS), Paris, France
| | - Ming Hui Chen
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts
| | - Thiuni N. Adikari
- Department of Medicine (Austin Health), University of Melbourne, Heidelberg, Australia
| | - Zimeng Ye
- Department of Medicine (Austin Health), University of Melbourne, Heidelberg, Australia
| | - Tom Witkowski
- Department of Medicine (Austin Health), University of Melbourne, Heidelberg, Australia
| | - Dulcie Lai
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill
| | - Nadine Lee
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts
| | - Julie Lokan
- Department of Anatomical Pathology, Austin Health, Heidelberg, Australia
| | - Ingrid E. Scheffer
- Department of Medicine (Austin Health), University of Melbourne, Heidelberg, Australia
- Murdoch Children’s Research Institute, Parkville, Australia
- Florey Institute of Neuroscience and Mental Health, Heidelberg, Australia
- Department of Pediatrics, University of Melbourne, Royal Children’s Hospital, Parkville, Australia
- Bladin-Berkovic Comprehensive Epilepsy Program, Department of Neurology, Austin Health, Heidelberg, Australia
| | - Samuel F. Berkovic
- Department of Medicine (Austin Health), University of Melbourne, Heidelberg, Australia
- Bladin-Berkovic Comprehensive Epilepsy Program, Department of Neurology, Austin Health, Heidelberg, Australia
| | - Shozeb Haider
- Department of Pharmaceutical and Biological Chemistry, University College London School of Pharmacy, London, United Kingdom
| | - Michael S. Hildebrand
- Department of Medicine (Austin Health), University of Melbourne, Heidelberg, Australia
- Murdoch Children’s Research Institute, Parkville, Australia
| | - Edward Yang
- Department of Radiology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Murat Gunel
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut
| | - Richard P. Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, New York
| | | | - Ingmar Blümcke
- Department of Neuropathology, University Hospitals Erlangen, Erlangen, Germany
- Epilepsy Center, Cleveland Clinic, Cleveland, Ohio
| | - Sanda Alexandrescu
- Department of Pathology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Anita Huttner
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut
| | - Erin L. Heinzen
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill
| | - Jidong Zhu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Annapurna Poduri
- Epilepsy Genetics Program, Division of Epilepsy and Neurophysiology, Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Nihal DeLanerolle
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut
| | - Dennis D. Spencer
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut
| | - Eunjung Alice Lee
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
| | - Christopher A. Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Neurology and Pediatrics, Harvard Medical School, Boston, Massachusetts
- Allen Discovery Center for Human Brain Evolution, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
- Howard Hughes Medical Institute, Boston, Massachusetts
| | - Kristopher T. Kahle
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, New York
- Department of Neurosurgery, Boston Children’s Hospital, Boston, Massachusetts
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11
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Checri R, Chipaux M, Ferrand-Sorbets S, Raffo E, Bulteau C, Rosenberg SD, Doladilhe M, Dorfmüller G, Adle-Biassette H, Baldassari S, Baulac S. Detection of brain somatic mutations in focal cortical dysplasia during epilepsy presurgical workup. Brain Commun 2023; 5:fcad174. [PMID: 37324239 PMCID: PMC10261848 DOI: 10.1093/braincomms/fcad174] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 04/01/2023] [Accepted: 05/31/2023] [Indexed: 06/17/2023] Open
Abstract
Brain-restricted somatic variants in genes of the mechanistic target of rapamycin signalling pathway cause focal epilepsies associated with focal cortical dysplasia type II. We hypothesized that somatic variants could be identified from trace tissue adherent to explanted stereoelectroencephalography electrodes used in the presurgical epilepsy workup to localize the epileptogenic zone. We investigated three paediatric patients with drug-resistant focal epilepsy subjected to neurosurgery. In the resected brain tissue, we identified low-level mosaic somatic mutations in AKT3 and DEPDC5 genes. We collected stereoelectroencephalography depth electrodes in the context of a second presurgical evaluation and identified 4/33 mutation-positive electrodes that were either located in the epileptogenic zone or at the border of the dysplasia. We provide the proof-of-concept that somatic mutations with low levels of mosaicism can be detected from individual stereoelectroencephalography electrodes and support a link between the mutation load and the epileptic activity. Our findings emphasize future opportunities for integrating genetic testing from stereoelectroencephalography electrodes into the presurgical evaluation of refractory epilepsy patients with focal cortical dysplasia type II to improve the patients' diagnostic journey and guide towards precision medicine.
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Affiliation(s)
| | | | - Sarah Ferrand-Sorbets
- Department of Pediatric Neurosurgery, Rothschild Foundation Hospital EpiCARE, 75019, Paris, France
| | - Emmanuel Raffo
- Department of Pediatric Neurosurgery, Rothschild Foundation Hospital EpiCARE, 75019, Paris, France
- Unité de recherche 3450 DevAH, Développement, Adaptation et Handicap, Campus Brabois-Santé, Université de Lorraine, 54505, Vandoeuvre-lès-Nancy, France
| | - Christine Bulteau
- Department of Pediatric Neurosurgery, Rothschild Foundation Hospital EpiCARE, 75019, Paris, France
- Université de Paris Cité, MC2Lab, Institut de Psychologie, F-92100 Boulogne-Billancourt, France
| | | | - Marion Doladilhe
- Sorbonne Université, Institut du Cerveau—Paris Brain Institute—ICM, Inserm, CNRS, Hôpital de la Pitié Salpêtrière, 75013, Paris, France
| | - Georg Dorfmüller
- Department of Pediatric Neurosurgery, Rothschild Foundation Hospital EpiCARE, 75019, Paris, France
| | - Homa Adle-Biassette
- Université de Paris Cité, service d’Anatomie Pathologique, APHP, Hôpital Lariboisière, DMU DREAM, UMR 1141, INSERM, 75010, Paris, France
| | | | - Stéphanie Baulac
- Correspondence to: Stéphanie Baulac Institut du Cerveau, 47 bd de l’hôpital, 75013, Paris, France E-mail:
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12
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Gaitsch H, Franklin RJM, Reich DS. Cell-free DNA-based liquid biopsies in neurology. Brain 2023; 146:1758-1774. [PMID: 36408894 PMCID: PMC10151188 DOI: 10.1093/brain/awac438] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/26/2022] [Accepted: 11/10/2022] [Indexed: 11/22/2022] Open
Abstract
This article reviews recent developments in the application of cell-free DNA-based liquid biopsies to neurological diseases. Over the past few decades, an explosion of interest in the use of accessible biofluids to identify and track molecular disease has revolutionized the fields of oncology, prenatal medicine and others. More recently, technological advances in signal detection have allowed for informative analysis of biofluids that are typically sparse in cells and other circulating components, such as CSF. In parallel, advancements in epigenetic profiling have allowed for novel applications of liquid biopsies to diseases without characteristic mutational profiles, including many degenerative, autoimmune, inflammatory, ischaemic and infectious disorders. These events have paved the way for a wide array of neurological conditions to benefit from enhanced diagnostic, prognostic, and treatment abilities through the use of liquid biomarkers: a 'liquid biopsy' approach. This review includes an overview of types of liquid biopsy targets with a focus on circulating cell-free DNA, methods used to identify and probe potential liquid biomarkers, and recent applications of such biomarkers to a variety of complex neurological conditions including CNS tumours, stroke, traumatic brain injury, Alzheimer's disease, epilepsy, multiple sclerosis and neuroinfectious disease. Finally, the challenges of translating liquid biopsies to use in clinical neurology settings-and the opportunities for improvement in disease management that such translation may provide-are discussed.
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Affiliation(s)
- Hallie Gaitsch
- NIH-Oxford-Cambridge Scholars Program, Wellcome-MRC Cambridge Stem Cell Institute and Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 1TN, UK
| | | | - Daniel S Reich
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
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13
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Susgun S, Demirel M, Yalcin Cakmakli G, Salman B, K Oguz K, Elibol B, Ugur Iseri SA, Yapıcı Z. Targeted resequencing reveals high-level mosaicism for a novel frameshift variant in WDR45 associated with beta-propeller protein-associated neurodegeneration. Int J Neurosci 2023:1-6. [PMID: 37099669 DOI: 10.1080/00207454.2023.2208279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
OBJECTIVES Beta-propeller protein-associated neurodegeneration (BPAN) is a rare X-linked dominant neurodegenerative disease, which is characterized by iron accumulation in the basal ganglia. BPAN is associated with pathogenic variation in WDR45, which has been reported almost exclusively in females most probably due to male lethality in the hemizygous state. METHODS Whole exome sequencing (WES) and targeted deep sequencing were performed for a male with a clinical diagnosis of BPAN at the age of 37. RESULTS The novel frameshift variant in WDR45 detected by WES was further analyzed with targeted resequencing to detect a mosaicism level of 85.5% in the blood sample of the proband. DISCUSSION Although the main role of WDR45 remains elusive, recent studies show that WDR45 may contribute to neurodegeneration through defects in autophagy, iron storage and ferritin metabolism, mitochondria organization, and endoplasmic reticulum homeostasis. The extend of spatiotemporal haploinsufficiency of WDR45 frameshifting variants caused by mosaicism in males may lead to variable clinical severity, which may be hard to elaborate clinically. Promising genetic analysis strategies using targeted deep sequencing may help determine the clinical outcome of somatic mosaicism in neurological disorders including BPAN. Additionally, we suggest that deep sequencing should be conducted in cerebrospinal fluid samples to provide more reliable results in terms of reflecting the mosaicism level in the brain for future studies.
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Affiliation(s)
- Seda Susgun
- Department of Genetics, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
- Institute of Graduate Studies in Health Sciences, Istanbul University, Istanbul, Turkey
- Department of Medical Biology, Faculty of Medicine, Bezmialem Vakif University, Istanbul, Turkey
| | - Mert Demirel
- Department of Neurology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Gul Yalcin Cakmakli
- Department of Neurology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Baris Salman
- Department of Genetics, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
- Institute of Graduate Studies in Health Sciences, Istanbul University, Istanbul, Turkey
| | - Kader K Oguz
- Department of Radiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Bulent Elibol
- Department of Neurology, Institute of Neurological Sciences and Psychiatry, Hacettepe University School of Medicine, Ankara, Turkey
| | - Sibel Aylin Ugur Iseri
- Department of Genetics, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Zuhal Yapıcı
- Department of Neurology, Faculty of Medicine, Istanbul University, Istanbul, Turkey
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14
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Kim SH, Kwon SS, Park MR, Lee HA, Kim JH, Cha J, Kim S, Baek ST, Kim SH, Lee JS, Kim HD, Choi JR, Lee ST, Kang HC. Detecting low-variant allele frequency mosaic pathogenic variants of NF1, TSC2, and AKT3 genes from blood in patients with neurodevelopmental disorders. J Mol Diagn 2023:S1525-1578(23)00080-6. [PMID: 37088138 DOI: 10.1016/j.jmoldx.2023.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 04/05/2023] [Accepted: 04/10/2023] [Indexed: 04/25/2023] Open
Abstract
Growing evidence indicates that early, and late postzygotic mosaicism can cause neurodevelopmental disorders (NDD), but detection of low variant allele frequency (VAF) mosaic variants from blood remains a challenge. We reviewed data of 2,162 patients with NDDs who underwent conventional genetic tests and performed a deep sequencing using specifically designed mosaic NGS panel in the patients with negative genetic test results. Forty-four patents with neurocutaneous syndrome, malformation of cortical development or nonlesional epileptic encephalopathies were included. In total, mosaic variants were detected from blood in 1.2% (25/2,162) of the patients. Using conventional NGS panels, 22 mosaic variants (VAF 8.8-29.8%) were identified in 18 different genes including TSC2, DCX, SLC2A1, PCDH19, DNM1, STXBP1, SCN2A, SCN1A, PURA, POGZ, PAFAH1B1, NF1, KIF21A, KCNQ2, GABRA1, EEF1A2, CDKL5, and ARID1B. Using a specifically designed mosaicism NGS panel, three mosaic variants of the NF1, TSC2, and AKT3 genes were identified (VAF 2.0-11.2%). Mosaic variants were found frequently in the patients who had neurocutaneous syndrome (2/7, 28.6%) whereas only one or no mosaic variant was detected for patients who had malformations of cortical development (1/20, 5%) or nonlesional epileptic encephalopathies (0%, 0/17). In summary, mosaic variants contribute to spectrum of NDDs can be detected from blood via the conventional NGS and specifically designed mosaicism NGS panels, and detection of mosaic variants using blood will increase diagnostic yield.
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Affiliation(s)
- Se Hee Kim
- Pediatric Neurology, Department of Pediatrics, Yonsei University College of Medicine, Severance Children's Hospital, Seoul, Republic of Korea
| | - Soon Sung Kwon
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Mi Ri Park
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hyeon Ah Lee
- Department of Laboratory Medicine, Graduate School of Medical Science, Brain Korea 21 PLUS Project, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ji Hun Kim
- Pediatric Neurology, Department of Pediatrics, Yonsei University College of Medicine, Severance Children's Hospital, Seoul, Republic of Korea
| | - JiHoon Cha
- Department of Radiology and Center for Imaging Science, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Sangwoo Kim
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Republic of Korea; Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seung Tae Baek
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Se Hoon Kim
- Department of Pathology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Joon Soo Lee
- Pediatric Neurology, Department of Pediatrics, Yonsei University College of Medicine, Severance Children's Hospital, Seoul, Republic of Korea
| | - Heung Dong Kim
- Pediatric Neurology, Department of Pediatrics, Yonsei University College of Medicine, Severance Children's Hospital, Seoul, Republic of Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea; Dxome, Seoul, Republic of Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea; Dxome, Seoul, Republic of Korea.
| | - Hoon-Chul Kang
- Pediatric Neurology, Department of Pediatrics, Yonsei University College of Medicine, Severance Children's Hospital, Seoul, Republic of Korea.
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15
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Verebi C, Nectoux J, Gorwood P, Le Strat Y, Duriez P, Ramoz N, Bienvenu T. A systematic literature review and meta-analysis of circulating nucleic acids as biomarkers in psychiatry. Prog Neuropsychopharmacol Biol Psychiatry 2023; 125:110770. [PMID: 37068545 DOI: 10.1016/j.pnpbp.2023.110770] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 04/14/2023] [Accepted: 04/14/2023] [Indexed: 04/19/2023]
Abstract
Common mental disorders (CMDs) such as depression, anxiety and post-traumatic stress disorders account for 40% of the global burden of disease. In most psychiatric disorders, both diagnosis and monitoring can be challenging, frequently requiring long-term investigation and follow-up. The discovery of better methods to facilitate accurate and fast diagnosis and monitoring of psychiatric disorders is therefore crucial. Circulating nucleic acids (CNAs) are among these new tools. CNAs (DNA or RNA) can be found circulating in body biofluids, and can be isolated from biological samples such as plasma. They can serve as biomarkers for diagnosis and prognoses. They appear to be promising for disorders (such as psychiatric disorders) that involve organs or structures that are difficult to assess. This review presents an accurate assessment of the current literature about the use of plasma and serum cell-free DNA (cfDNA) as biomarkers for several aspects of psychiatric disorders: diagnosis, prognosis, treatment response, and monitor disease progression. For each psychiatric disorder, we examine the effect sizes to give insights on the efficacy of CNAs as biomarkers. The global effect size for plasma nuclear and mitochondrial cfDNA studies was generally moderate for psychiatric disorders. In addition, we discuss future applications of CNAs and particularly cfDNA as non-invasive biomarkers for these diseases.
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Affiliation(s)
- Camille Verebi
- Service de Médecine Génomique des Maladies de Système et d'Organe, Hôpital Cochin, AP.HP.CUP, Paris, France; INSERM U1266, Institut de Psychiatrie et de Neurosciences de Paris, Paris, France
| | - Juliette Nectoux
- Service de Médecine Génomique des Maladies de Système et d'Organe, Hôpital Cochin, AP.HP.CUP, Paris, France
| | - Philip Gorwood
- INSERM U1266, Institut de Psychiatrie et de Neurosciences de Paris, Paris, France; Université Paris Cité, GHU Paris Psychiatrie et Neurosciences (CMME), Paris, France
| | - Yann Le Strat
- AP-HP, Department of Psychiatry, Louis Mourier Hospital, Université Paris Cité, Faculté de Médecine, Colombes, France
| | - Philibert Duriez
- INSERM U1266, Institut de Psychiatrie et de Neurosciences de Paris, Paris, France; Université Paris Cité, GHU Paris Psychiatrie et Neurosciences (CMME), Paris, France
| | - Nicolas Ramoz
- INSERM U1266, Institut de Psychiatrie et de Neurosciences de Paris, Paris, France
| | - Thierry Bienvenu
- Service de Médecine Génomique des Maladies de Système et d'Organe, Hôpital Cochin, AP.HP.CUP, Paris, France; INSERM U1266, Institut de Psychiatrie et de Neurosciences de Paris, Paris, France.
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16
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D'Gama AM, Poduri A. Brain somatic mosaicism in epilepsy: Bringing results Back to the clinic. Neurobiol Dis 2023; 181:106104. [PMID: 36972791 DOI: 10.1016/j.nbd.2023.106104] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 03/28/2023] Open
Abstract
Over the past decade, there has been tremendous progress in understanding brain somatic mosaicism in epilepsy in the research setting. Access to resected brain tissue samples from patients with medically refractory epilepsy undergoing epilepsy surgery has been key to making these discoveries. In this review, we discuss the gap between making discoveries in the research setting and bringing results back to the clinical setting. Current clinical genetic testing mainly uses clinically accessible tissue samples, like blood and saliva, and can detect inherited and de novo germline variants and potentially non-brain-limited mosaic variants that have resulted from post-zygotic mutation (also called "somatic mutations"). Methods developed in the research setting to detect brain-limited mosaic variants using brain tissue samples need to be further translated and validated in the clinical setting, which will allow post-resection brain tissue genetic diagnoses. However, obtaining a genetic diagnosis after surgery for refractory focal epilepsy, when brain tissue samples are available, is arguably "too late" to guide precision management. Emerging methods using cerebrospinal fluid (CSF) and subdural electroencephalogram (SEEG) depth electrodes hold promise for establishing genetic diagnoses pre-resection without the need for actual brain tissue. In parallel, development of curation rules for interpreting the pathogenicity of mosaic variants, which have unique considerations compared to germline variants, will assist clinically accredited laboratories and epilepsy geneticists in making genetic diagnoses. Returning results of brain-limited mosaic variants to patients and their families will end their diagnostic odyssey and advance epilepsy precision management.
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17
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Wang Y, Yu T, Blümcke I, Cai Y, Sun K, Gao R, Wang Y, Fu Y, Wang W, Wang Y, Zhang G, Piao Y. The clinico-pathological characterisation of focal cortical dysplasia type IIb genetically defined by MTOR mosaicism. Neuropathol Appl Neurobiol 2023; 49:e12874. [PMID: 36544434 DOI: 10.1111/nan.12874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 08/18/2022] [Accepted: 10/11/2022] [Indexed: 12/24/2022]
Abstract
AIMS Focal cortical dysplasia (FCD) is a major cause of drug-resistant paediatric epilepsy and is amenable to successful neurosurgical resection. FCD ILAE Type IIb is the most common FCD subtype, and brain somatic mutations affecting the mTOR pathway play a major pathogenic role. The aim of this study was to comprehensively describe the genotype-phenotype association of 20 patients with histopathologically confirmed FCDIIb using next generation sequencing (NGS) of paired blood-brain samples. METHODS Clinical and neuropathological data were retrospectively reviewed from the hospital archive. The NGS panel included 11 mTOR-pathway-related genes with maximum coverage of 2000×. The detected variants were validated by digital droplet PCR. RESULTS Pathogenic MTOR variants were identified in 10 patients (50%). Further comparison with MTOR-wildtype FCDIIb suggested a profound genotype-phenotype association characterised by (1) a non-temporal lobe lesion on MRI, (2) a larger lesion volume occupying grey and white matter (3.032 ± 1.859 cm3 vs 1.110 ± 0.856 cm3 , p = 0.014), (3) more balloon cells (50.20 ± 14.40 BC/mm2 vs 31.64 ± 30.56 BC/mm2 , p = 0.099) and dysmorphic neurons (48.72 ± 19.47DN/mm2 vs 15.28 ± 13.95DN/mm2 , p = 0.000) and (4) a positive correlation between VAF and the lesion volume (r = 0.802, p = 0.017). CONCLUSIONS Our study identified frequent MTOR mutations in the cell-rich FCDIIb phenotype, clinically characterised by a non-temporal location and large lesion volume. Comprehensive genotype-phenotype associations will help us further explore and define the broad spectrum of FCD lesions to make more targeted therapies available in the realm of epileptology.
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Affiliation(s)
- Yajie Wang
- Department of Pathology, Xuanwu Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Epilepsy, Capital Medical University, Beijing, China.,National Center for Neurological Disorders, Beijing, China
| | - Tao Yu
- Clinical Research Center for Epilepsy, Capital Medical University, Beijing, China.,National Center for Neurological Disorders, Beijing, China.,Beijing Institute of Functional Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing, China.,Department of Functional Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Ingmar Blümcke
- Department of Neuropathology, University Hospital Erlangen, Erlangen, Germany
| | - Yanning Cai
- Clinical Research Center for Epilepsy, Capital Medical University, Beijing, China.,National Center for Neurological Disorders, Beijing, China.,Department of Neurobiology and Clinical Biobank, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Ke Sun
- Clinical Research Center for Epilepsy, Capital Medical University, Beijing, China.,National Center for Neurological Disorders, Beijing, China.,Beijing Institute of Functional Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing, China.,Department of Functional Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Runshi Gao
- Clinical Research Center for Epilepsy, Capital Medical University, Beijing, China.,National Center for Neurological Disorders, Beijing, China.,Beijing Institute of Functional Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing, China.,Department of Functional Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Yujiao Wang
- Department of Pathology, Xuanwu Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Epilepsy, Capital Medical University, Beijing, China.,National Center for Neurological Disorders, Beijing, China
| | - Yongjuan Fu
- Department of Pathology, Xuanwu Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Epilepsy, Capital Medical University, Beijing, China.,National Center for Neurological Disorders, Beijing, China
| | - Wei Wang
- Clinical Research Center for Epilepsy, Capital Medical University, Beijing, China.,National Center for Neurological Disorders, Beijing, China.,Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Yuping Wang
- Clinical Research Center for Epilepsy, Capital Medical University, Beijing, China.,National Center for Neurological Disorders, Beijing, China.,Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Neuromodulation, Beijing, China.,Center of Epilepsy, Institute of Sleep and Consciousness Disorders, Beijing Institute for Brain Disorders, Capital Medical University, Beijing, China
| | - Guojun Zhang
- Clinical Research Center for Epilepsy, Capital Medical University, Beijing, China.,National Center for Neurological Disorders, Beijing, China.,Beijing Institute of Functional Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing, China.,Department of Functional Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Yueshan Piao
- Department of Pathology, Xuanwu Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Epilepsy, Capital Medical University, Beijing, China.,National Center for Neurological Disorders, Beijing, China
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18
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The methylome and cell-free DNA: current applications in medicine and pediatric disease. Pediatr Res 2023:10.1038/s41390-022-02448-3. [PMID: 36646885 PMCID: PMC9842217 DOI: 10.1038/s41390-022-02448-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 11/21/2022] [Accepted: 12/18/2022] [Indexed: 01/18/2023]
Abstract
DNA methylation is an epigenetic mechanism that contributes to cell regulation and development, and different methylation patterns allow for the identification of cell and tissue type. Cell-free DNA (cfDNA) is composed of small circulating fragments of DNA found in plasma and urine. Total cfDNA levels correlate with the presence of inflammation and tissue injury in a variety of disease states. Unfortunately, the utility of cfDNA is limited by its lack of tissue or cell-type specificity. However, methylome analysis of cfDNA allows the identification of the tissue or cell type from which cfDNA originated. Thus, methylation patterns in cfDNA from tissues isolated from direct study may provide windows into health and disease states, thereby serving as a "liquid biopsy". This review will discuss methylation and its role in establishing cellular identity, cfDNA as a biomarker and its pathophysiologic role in the inflammatory process, and the ways cfDNA and methylomics can be jointly applied in medicine. IMPACT: Cell-free DNA (cfDNA) is increasingly being used as a noninvasive diagnostic and disease-monitoring tool in pediatric medicine. However, the lack of specificity of cfDNA limits its utility. Identification of cell type-specific methylation signatures can help overcome the limited specificity of cfDNA. As knowledge of the cfDNA methylome improves, cfDNA will be more broadly applied in medicine, such that clinicians will need to understand the methods and applications of its use.
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19
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Ye Z, Bennett MF, Neal A, Laing JA, Hunn MK, Wittayacharoenpong T, Todaro M, Patel SK, Bahlo M, Kwan P, O'Brien TJ, Scheffer IE, Berkovic SF, Perucca P, Hildebrand MS. Somatic Mosaic Pathogenic Variant Gradient Detected in Trace Brain Tissue From Stereo-EEG Depth Electrodes. Neurology 2022; 99:1036-1041. [PMID: 36192176 DOI: 10.1212/wnl.0000000000201469] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 09/09/2022] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND AND OBJECTIVES Mosaic pathogenic variants restricted to the brain are increasingly recognized as a cause of focal epilepsies. We aimed to identify a mosaic pathogenic variant and its anatomical gradient in brain DNA derived from trace tissue on explanted stereoelectroencephalography (SEEG) electrodes. METHODS We studied a patient with nonlesional multifocal epilepsy undergoing presurgical evaluation with SEEG. After explantation, the electrodes were divided into 3 pools based on their brain location (right posterior quadrant, left posterior quadrant, hippocampus/temporal neocortex). Tissue from each pool was processed for trace DNA that was whole genome amplified prior to high-depth exome sequencing. Droplet digital PCR was performed to quantify mosaicism. A brain-specific glial fibrillary acidic protein (GFAP) assay enabled cell-of-origin analysis. RESULTS We demonstrated a mosaic gradient for a novel pathogenic KCNT1 loss-of-function variant (c.530G>A, p.W177X) predicted to lead to nonsense-mediated decay. Strikingly, the mosaic gradient correlated strongly with the SEEG findings because the highest variant allele frequency was in the right posterior quadrant, reflecting the most epileptogenic region on EEG studies. An elevated GFAP level indicated enrichment of brain-derived cells in SEEG cell suspension. DISCUSSION This study demonstrates a proof of concept that mosaic gradients of pathogenic variants can be established using trace tissue from explanted SEEG electrodes.
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Affiliation(s)
- Zimeng Ye
- From the Department of Medicine (Austin Health) (Z.Y., M.F.B., S.K.P., I.E.S., S.F.B., P.P., M.S.H.), University of Melbourne, Heidelberg; Population Health and Immunity Division (M.F.B., M.B.), The Walter and Eliza Hall Institute of Medical Research, Parkville; Department of Medical Biology (M.F.B., M.B.), The University of Melbourne, Parkville; Department of Neurology (A.N., P.K., T.J.O.B., P.P.), Royal Melbourne Hospital, Parkville; Department of Neurology (A.N., J.A.L., T.W., M.T., P.K., T.J.O.B., P.P.), Alfred Hospital, Melbourne; Department of Medicine (A.N., P.K., T.J.O.B.), Royal Melbourne Hospital, University of Melbourne, Parkville; Department of Neurosciences (A.N., J.A.L., T.W., M.T., P.K., T.J.O.B., P.P.), The Central Clinical School, Monash University, Melbourne; Department of Neurology (A.N.), St Vincent's Hospital, Fitzroy; Department of Neurosurgery (M.K.H.), The Alfred Hospital, Melbourne; Florey Institute of Neuroscience and Mental Health (S.K.P., I.E.S.), Heidelberg; Murdoch Children's Research Institute (I.E.S., M.S.H.), Parkville; Department of Paediatrics (I.E.S.), University of Melbourne, Royal Children's Hospital, Parkville; and Bladin-Berkovic Comprehensive Epilepsy Program (S.F.B., P.P.), Department of Neurology, Austin Health, Heidelberg, Australia
| | - Mark F Bennett
- From the Department of Medicine (Austin Health) (Z.Y., M.F.B., S.K.P., I.E.S., S.F.B., P.P., M.S.H.), University of Melbourne, Heidelberg; Population Health and Immunity Division (M.F.B., M.B.), The Walter and Eliza Hall Institute of Medical Research, Parkville; Department of Medical Biology (M.F.B., M.B.), The University of Melbourne, Parkville; Department of Neurology (A.N., P.K., T.J.O.B., P.P.), Royal Melbourne Hospital, Parkville; Department of Neurology (A.N., J.A.L., T.W., M.T., P.K., T.J.O.B., P.P.), Alfred Hospital, Melbourne; Department of Medicine (A.N., P.K., T.J.O.B.), Royal Melbourne Hospital, University of Melbourne, Parkville; Department of Neurosciences (A.N., J.A.L., T.W., M.T., P.K., T.J.O.B., P.P.), The Central Clinical School, Monash University, Melbourne; Department of Neurology (A.N.), St Vincent's Hospital, Fitzroy; Department of Neurosurgery (M.K.H.), The Alfred Hospital, Melbourne; Florey Institute of Neuroscience and Mental Health (S.K.P., I.E.S.), Heidelberg; Murdoch Children's Research Institute (I.E.S., M.S.H.), Parkville; Department of Paediatrics (I.E.S.), University of Melbourne, Royal Children's Hospital, Parkville; and Bladin-Berkovic Comprehensive Epilepsy Program (S.F.B., P.P.), Department of Neurology, Austin Health, Heidelberg, Australia
| | - Andrew Neal
- From the Department of Medicine (Austin Health) (Z.Y., M.F.B., S.K.P., I.E.S., S.F.B., P.P., M.S.H.), University of Melbourne, Heidelberg; Population Health and Immunity Division (M.F.B., M.B.), The Walter and Eliza Hall Institute of Medical Research, Parkville; Department of Medical Biology (M.F.B., M.B.), The University of Melbourne, Parkville; Department of Neurology (A.N., P.K., T.J.O.B., P.P.), Royal Melbourne Hospital, Parkville; Department of Neurology (A.N., J.A.L., T.W., M.T., P.K., T.J.O.B., P.P.), Alfred Hospital, Melbourne; Department of Medicine (A.N., P.K., T.J.O.B.), Royal Melbourne Hospital, University of Melbourne, Parkville; Department of Neurosciences (A.N., J.A.L., T.W., M.T., P.K., T.J.O.B., P.P.), The Central Clinical School, Monash University, Melbourne; Department of Neurology (A.N.), St Vincent's Hospital, Fitzroy; Department of Neurosurgery (M.K.H.), The Alfred Hospital, Melbourne; Florey Institute of Neuroscience and Mental Health (S.K.P., I.E.S.), Heidelberg; Murdoch Children's Research Institute (I.E.S., M.S.H.), Parkville; Department of Paediatrics (I.E.S.), University of Melbourne, Royal Children's Hospital, Parkville; and Bladin-Berkovic Comprehensive Epilepsy Program (S.F.B., P.P.), Department of Neurology, Austin Health, Heidelberg, Australia
| | - Joshua A Laing
- From the Department of Medicine (Austin Health) (Z.Y., M.F.B., S.K.P., I.E.S., S.F.B., P.P., M.S.H.), University of Melbourne, Heidelberg; Population Health and Immunity Division (M.F.B., M.B.), The Walter and Eliza Hall Institute of Medical Research, Parkville; Department of Medical Biology (M.F.B., M.B.), The University of Melbourne, Parkville; Department of Neurology (A.N., P.K., T.J.O.B., P.P.), Royal Melbourne Hospital, Parkville; Department of Neurology (A.N., J.A.L., T.W., M.T., P.K., T.J.O.B., P.P.), Alfred Hospital, Melbourne; Department of Medicine (A.N., P.K., T.J.O.B.), Royal Melbourne Hospital, University of Melbourne, Parkville; Department of Neurosciences (A.N., J.A.L., T.W., M.T., P.K., T.J.O.B., P.P.), The Central Clinical School, Monash University, Melbourne; Department of Neurology (A.N.), St Vincent's Hospital, Fitzroy; Department of Neurosurgery (M.K.H.), The Alfred Hospital, Melbourne; Florey Institute of Neuroscience and Mental Health (S.K.P., I.E.S.), Heidelberg; Murdoch Children's Research Institute (I.E.S., M.S.H.), Parkville; Department of Paediatrics (I.E.S.), University of Melbourne, Royal Children's Hospital, Parkville; and Bladin-Berkovic Comprehensive Epilepsy Program (S.F.B., P.P.), Department of Neurology, Austin Health, Heidelberg, Australia
| | - Martin K Hunn
- From the Department of Medicine (Austin Health) (Z.Y., M.F.B., S.K.P., I.E.S., S.F.B., P.P., M.S.H.), University of Melbourne, Heidelberg; Population Health and Immunity Division (M.F.B., M.B.), The Walter and Eliza Hall Institute of Medical Research, Parkville; Department of Medical Biology (M.F.B., M.B.), The University of Melbourne, Parkville; Department of Neurology (A.N., P.K., T.J.O.B., P.P.), Royal Melbourne Hospital, Parkville; Department of Neurology (A.N., J.A.L., T.W., M.T., P.K., T.J.O.B., P.P.), Alfred Hospital, Melbourne; Department of Medicine (A.N., P.K., T.J.O.B.), Royal Melbourne Hospital, University of Melbourne, Parkville; Department of Neurosciences (A.N., J.A.L., T.W., M.T., P.K., T.J.O.B., P.P.), The Central Clinical School, Monash University, Melbourne; Department of Neurology (A.N.), St Vincent's Hospital, Fitzroy; Department of Neurosurgery (M.K.H.), The Alfred Hospital, Melbourne; Florey Institute of Neuroscience and Mental Health (S.K.P., I.E.S.), Heidelberg; Murdoch Children's Research Institute (I.E.S., M.S.H.), Parkville; Department of Paediatrics (I.E.S.), University of Melbourne, Royal Children's Hospital, Parkville; and Bladin-Berkovic Comprehensive Epilepsy Program (S.F.B., P.P.), Department of Neurology, Austin Health, Heidelberg, Australia
| | - Thanomporn Wittayacharoenpong
- From the Department of Medicine (Austin Health) (Z.Y., M.F.B., S.K.P., I.E.S., S.F.B., P.P., M.S.H.), University of Melbourne, Heidelberg; Population Health and Immunity Division (M.F.B., M.B.), The Walter and Eliza Hall Institute of Medical Research, Parkville; Department of Medical Biology (M.F.B., M.B.), The University of Melbourne, Parkville; Department of Neurology (A.N., P.K., T.J.O.B., P.P.), Royal Melbourne Hospital, Parkville; Department of Neurology (A.N., J.A.L., T.W., M.T., P.K., T.J.O.B., P.P.), Alfred Hospital, Melbourne; Department of Medicine (A.N., P.K., T.J.O.B.), Royal Melbourne Hospital, University of Melbourne, Parkville; Department of Neurosciences (A.N., J.A.L., T.W., M.T., P.K., T.J.O.B., P.P.), The Central Clinical School, Monash University, Melbourne; Department of Neurology (A.N.), St Vincent's Hospital, Fitzroy; Department of Neurosurgery (M.K.H.), The Alfred Hospital, Melbourne; Florey Institute of Neuroscience and Mental Health (S.K.P., I.E.S.), Heidelberg; Murdoch Children's Research Institute (I.E.S., M.S.H.), Parkville; Department of Paediatrics (I.E.S.), University of Melbourne, Royal Children's Hospital, Parkville; and Bladin-Berkovic Comprehensive Epilepsy Program (S.F.B., P.P.), Department of Neurology, Austin Health, Heidelberg, Australia
| | - Marian Todaro
- From the Department of Medicine (Austin Health) (Z.Y., M.F.B., S.K.P., I.E.S., S.F.B., P.P., M.S.H.), University of Melbourne, Heidelberg; Population Health and Immunity Division (M.F.B., M.B.), The Walter and Eliza Hall Institute of Medical Research, Parkville; Department of Medical Biology (M.F.B., M.B.), The University of Melbourne, Parkville; Department of Neurology (A.N., P.K., T.J.O.B., P.P.), Royal Melbourne Hospital, Parkville; Department of Neurology (A.N., J.A.L., T.W., M.T., P.K., T.J.O.B., P.P.), Alfred Hospital, Melbourne; Department of Medicine (A.N., P.K., T.J.O.B.), Royal Melbourne Hospital, University of Melbourne, Parkville; Department of Neurosciences (A.N., J.A.L., T.W., M.T., P.K., T.J.O.B., P.P.), The Central Clinical School, Monash University, Melbourne; Department of Neurology (A.N.), St Vincent's Hospital, Fitzroy; Department of Neurosurgery (M.K.H.), The Alfred Hospital, Melbourne; Florey Institute of Neuroscience and Mental Health (S.K.P., I.E.S.), Heidelberg; Murdoch Children's Research Institute (I.E.S., M.S.H.), Parkville; Department of Paediatrics (I.E.S.), University of Melbourne, Royal Children's Hospital, Parkville; and Bladin-Berkovic Comprehensive Epilepsy Program (S.F.B., P.P.), Department of Neurology, Austin Health, Heidelberg, Australia
| | - Sheila K Patel
- From the Department of Medicine (Austin Health) (Z.Y., M.F.B., S.K.P., I.E.S., S.F.B., P.P., M.S.H.), University of Melbourne, Heidelberg; Population Health and Immunity Division (M.F.B., M.B.), The Walter and Eliza Hall Institute of Medical Research, Parkville; Department of Medical Biology (M.F.B., M.B.), The University of Melbourne, Parkville; Department of Neurology (A.N., P.K., T.J.O.B., P.P.), Royal Melbourne Hospital, Parkville; Department of Neurology (A.N., J.A.L., T.W., M.T., P.K., T.J.O.B., P.P.), Alfred Hospital, Melbourne; Department of Medicine (A.N., P.K., T.J.O.B.), Royal Melbourne Hospital, University of Melbourne, Parkville; Department of Neurosciences (A.N., J.A.L., T.W., M.T., P.K., T.J.O.B., P.P.), The Central Clinical School, Monash University, Melbourne; Department of Neurology (A.N.), St Vincent's Hospital, Fitzroy; Department of Neurosurgery (M.K.H.), The Alfred Hospital, Melbourne; Florey Institute of Neuroscience and Mental Health (S.K.P., I.E.S.), Heidelberg; Murdoch Children's Research Institute (I.E.S., M.S.H.), Parkville; Department of Paediatrics (I.E.S.), University of Melbourne, Royal Children's Hospital, Parkville; and Bladin-Berkovic Comprehensive Epilepsy Program (S.F.B., P.P.), Department of Neurology, Austin Health, Heidelberg, Australia
| | - Melanie Bahlo
- From the Department of Medicine (Austin Health) (Z.Y., M.F.B., S.K.P., I.E.S., S.F.B., P.P., M.S.H.), University of Melbourne, Heidelberg; Population Health and Immunity Division (M.F.B., M.B.), The Walter and Eliza Hall Institute of Medical Research, Parkville; Department of Medical Biology (M.F.B., M.B.), The University of Melbourne, Parkville; Department of Neurology (A.N., P.K., T.J.O.B., P.P.), Royal Melbourne Hospital, Parkville; Department of Neurology (A.N., J.A.L., T.W., M.T., P.K., T.J.O.B., P.P.), Alfred Hospital, Melbourne; Department of Medicine (A.N., P.K., T.J.O.B.), Royal Melbourne Hospital, University of Melbourne, Parkville; Department of Neurosciences (A.N., J.A.L., T.W., M.T., P.K., T.J.O.B., P.P.), The Central Clinical School, Monash University, Melbourne; Department of Neurology (A.N.), St Vincent's Hospital, Fitzroy; Department of Neurosurgery (M.K.H.), The Alfred Hospital, Melbourne; Florey Institute of Neuroscience and Mental Health (S.K.P., I.E.S.), Heidelberg; Murdoch Children's Research Institute (I.E.S., M.S.H.), Parkville; Department of Paediatrics (I.E.S.), University of Melbourne, Royal Children's Hospital, Parkville; and Bladin-Berkovic Comprehensive Epilepsy Program (S.F.B., P.P.), Department of Neurology, Austin Health, Heidelberg, Australia
| | - Patrick Kwan
- From the Department of Medicine (Austin Health) (Z.Y., M.F.B., S.K.P., I.E.S., S.F.B., P.P., M.S.H.), University of Melbourne, Heidelberg; Population Health and Immunity Division (M.F.B., M.B.), The Walter and Eliza Hall Institute of Medical Research, Parkville; Department of Medical Biology (M.F.B., M.B.), The University of Melbourne, Parkville; Department of Neurology (A.N., P.K., T.J.O.B., P.P.), Royal Melbourne Hospital, Parkville; Department of Neurology (A.N., J.A.L., T.W., M.T., P.K., T.J.O.B., P.P.), Alfred Hospital, Melbourne; Department of Medicine (A.N., P.K., T.J.O.B.), Royal Melbourne Hospital, University of Melbourne, Parkville; Department of Neurosciences (A.N., J.A.L., T.W., M.T., P.K., T.J.O.B., P.P.), The Central Clinical School, Monash University, Melbourne; Department of Neurology (A.N.), St Vincent's Hospital, Fitzroy; Department of Neurosurgery (M.K.H.), The Alfred Hospital, Melbourne; Florey Institute of Neuroscience and Mental Health (S.K.P., I.E.S.), Heidelberg; Murdoch Children's Research Institute (I.E.S., M.S.H.), Parkville; Department of Paediatrics (I.E.S.), University of Melbourne, Royal Children's Hospital, Parkville; and Bladin-Berkovic Comprehensive Epilepsy Program (S.F.B., P.P.), Department of Neurology, Austin Health, Heidelberg, Australia
| | - Terence J O'Brien
- From the Department of Medicine (Austin Health) (Z.Y., M.F.B., S.K.P., I.E.S., S.F.B., P.P., M.S.H.), University of Melbourne, Heidelberg; Population Health and Immunity Division (M.F.B., M.B.), The Walter and Eliza Hall Institute of Medical Research, Parkville; Department of Medical Biology (M.F.B., M.B.), The University of Melbourne, Parkville; Department of Neurology (A.N., P.K., T.J.O.B., P.P.), Royal Melbourne Hospital, Parkville; Department of Neurology (A.N., J.A.L., T.W., M.T., P.K., T.J.O.B., P.P.), Alfred Hospital, Melbourne; Department of Medicine (A.N., P.K., T.J.O.B.), Royal Melbourne Hospital, University of Melbourne, Parkville; Department of Neurosciences (A.N., J.A.L., T.W., M.T., P.K., T.J.O.B., P.P.), The Central Clinical School, Monash University, Melbourne; Department of Neurology (A.N.), St Vincent's Hospital, Fitzroy; Department of Neurosurgery (M.K.H.), The Alfred Hospital, Melbourne; Florey Institute of Neuroscience and Mental Health (S.K.P., I.E.S.), Heidelberg; Murdoch Children's Research Institute (I.E.S., M.S.H.), Parkville; Department of Paediatrics (I.E.S.), University of Melbourne, Royal Children's Hospital, Parkville; and Bladin-Berkovic Comprehensive Epilepsy Program (S.F.B., P.P.), Department of Neurology, Austin Health, Heidelberg, Australia
| | - Ingrid E Scheffer
- From the Department of Medicine (Austin Health) (Z.Y., M.F.B., S.K.P., I.E.S., S.F.B., P.P., M.S.H.), University of Melbourne, Heidelberg; Population Health and Immunity Division (M.F.B., M.B.), The Walter and Eliza Hall Institute of Medical Research, Parkville; Department of Medical Biology (M.F.B., M.B.), The University of Melbourne, Parkville; Department of Neurology (A.N., P.K., T.J.O.B., P.P.), Royal Melbourne Hospital, Parkville; Department of Neurology (A.N., J.A.L., T.W., M.T., P.K., T.J.O.B., P.P.), Alfred Hospital, Melbourne; Department of Medicine (A.N., P.K., T.J.O.B.), Royal Melbourne Hospital, University of Melbourne, Parkville; Department of Neurosciences (A.N., J.A.L., T.W., M.T., P.K., T.J.O.B., P.P.), The Central Clinical School, Monash University, Melbourne; Department of Neurology (A.N.), St Vincent's Hospital, Fitzroy; Department of Neurosurgery (M.K.H.), The Alfred Hospital, Melbourne; Florey Institute of Neuroscience and Mental Health (S.K.P., I.E.S.), Heidelberg; Murdoch Children's Research Institute (I.E.S., M.S.H.), Parkville; Department of Paediatrics (I.E.S.), University of Melbourne, Royal Children's Hospital, Parkville; and Bladin-Berkovic Comprehensive Epilepsy Program (S.F.B., P.P.), Department of Neurology, Austin Health, Heidelberg, Australia
| | - Samuel F Berkovic
- From the Department of Medicine (Austin Health) (Z.Y., M.F.B., S.K.P., I.E.S., S.F.B., P.P., M.S.H.), University of Melbourne, Heidelberg; Population Health and Immunity Division (M.F.B., M.B.), The Walter and Eliza Hall Institute of Medical Research, Parkville; Department of Medical Biology (M.F.B., M.B.), The University of Melbourne, Parkville; Department of Neurology (A.N., P.K., T.J.O.B., P.P.), Royal Melbourne Hospital, Parkville; Department of Neurology (A.N., J.A.L., T.W., M.T., P.K., T.J.O.B., P.P.), Alfred Hospital, Melbourne; Department of Medicine (A.N., P.K., T.J.O.B.), Royal Melbourne Hospital, University of Melbourne, Parkville; Department of Neurosciences (A.N., J.A.L., T.W., M.T., P.K., T.J.O.B., P.P.), The Central Clinical School, Monash University, Melbourne; Department of Neurology (A.N.), St Vincent's Hospital, Fitzroy; Department of Neurosurgery (M.K.H.), The Alfred Hospital, Melbourne; Florey Institute of Neuroscience and Mental Health (S.K.P., I.E.S.), Heidelberg; Murdoch Children's Research Institute (I.E.S., M.S.H.), Parkville; Department of Paediatrics (I.E.S.), University of Melbourne, Royal Children's Hospital, Parkville; and Bladin-Berkovic Comprehensive Epilepsy Program (S.F.B., P.P.), Department of Neurology, Austin Health, Heidelberg, Australia
| | - Piero Perucca
- From the Department of Medicine (Austin Health) (Z.Y., M.F.B., S.K.P., I.E.S., S.F.B., P.P., M.S.H.), University of Melbourne, Heidelberg; Population Health and Immunity Division (M.F.B., M.B.), The Walter and Eliza Hall Institute of Medical Research, Parkville; Department of Medical Biology (M.F.B., M.B.), The University of Melbourne, Parkville; Department of Neurology (A.N., P.K., T.J.O.B., P.P.), Royal Melbourne Hospital, Parkville; Department of Neurology (A.N., J.A.L., T.W., M.T., P.K., T.J.O.B., P.P.), Alfred Hospital, Melbourne; Department of Medicine (A.N., P.K., T.J.O.B.), Royal Melbourne Hospital, University of Melbourne, Parkville; Department of Neurosciences (A.N., J.A.L., T.W., M.T., P.K., T.J.O.B., P.P.), The Central Clinical School, Monash University, Melbourne; Department of Neurology (A.N.), St Vincent's Hospital, Fitzroy; Department of Neurosurgery (M.K.H.), The Alfred Hospital, Melbourne; Florey Institute of Neuroscience and Mental Health (S.K.P., I.E.S.), Heidelberg; Murdoch Children's Research Institute (I.E.S., M.S.H.), Parkville; Department of Paediatrics (I.E.S.), University of Melbourne, Royal Children's Hospital, Parkville; and Bladin-Berkovic Comprehensive Epilepsy Program (S.F.B., P.P.), Department of Neurology, Austin Health, Heidelberg, Australia
| | - Michael S Hildebrand
- From the Department of Medicine (Austin Health) (Z.Y., M.F.B., S.K.P., I.E.S., S.F.B., P.P., M.S.H.), University of Melbourne, Heidelberg; Population Health and Immunity Division (M.F.B., M.B.), The Walter and Eliza Hall Institute of Medical Research, Parkville; Department of Medical Biology (M.F.B., M.B.), The University of Melbourne, Parkville; Department of Neurology (A.N., P.K., T.J.O.B., P.P.), Royal Melbourne Hospital, Parkville; Department of Neurology (A.N., J.A.L., T.W., M.T., P.K., T.J.O.B., P.P.), Alfred Hospital, Melbourne; Department of Medicine (A.N., P.K., T.J.O.B.), Royal Melbourne Hospital, University of Melbourne, Parkville; Department of Neurosciences (A.N., J.A.L., T.W., M.T., P.K., T.J.O.B., P.P.), The Central Clinical School, Monash University, Melbourne; Department of Neurology (A.N.), St Vincent's Hospital, Fitzroy; Department of Neurosurgery (M.K.H.), The Alfred Hospital, Melbourne; Florey Institute of Neuroscience and Mental Health (S.K.P., I.E.S.), Heidelberg; Murdoch Children's Research Institute (I.E.S., M.S.H.), Parkville; Department of Paediatrics (I.E.S.), University of Melbourne, Royal Children's Hospital, Parkville; and Bladin-Berkovic Comprehensive Epilepsy Program (S.F.B., P.P.), Department of Neurology, Austin Health, Heidelberg, Australia.
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20
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Southwood D, Singh S, Chatterton Z. Brain-derived cell-free DNA. Neural Regen Res 2022; 17:2213-2214. [PMID: 35259835 PMCID: PMC9083148 DOI: 10.4103/1673-5374.335794] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/30/2021] [Accepted: 11/09/2021] [Indexed: 11/29/2022] Open
Affiliation(s)
- Dean Southwood
- Brain and Mind Center, School of Medical Sciences, Department of Neuroscience, The University of Sydney, Camperdown, NSW, Australia
| | - Sanyukta Singh
- Brain and Mind Center, School of Medical Sciences, Department of Neuroscience, The University of Sydney, Camperdown, NSW, Australia
| | - Zac Chatterton
- Brain and Mind Center, School of Medical Sciences, Department of Neuroscience, The University of Sydney, Camperdown, NSW, Australia
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21
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Krey I, Platzer K, Esterhuizen A, Berkovic SF, Helbig I, Hildebrand MS, Lerche H, Lowenstein D, Møller RS, Poduri A, Sadleir L, Sisodiya SM, Weckhuysen S, Wilmshurst JM, Weber Y, Lemke JR. Current practice in diagnostic genetic testing of the epilepsies. Epileptic Disord 2022; 24:765-786. [PMID: 35830287 PMCID: PMC10752379 DOI: 10.1684/epd.2022.1448] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/10/2022] [Indexed: 01/19/2023]
Abstract
Epilepsy genetics is a rapidly developing field, in which novel disease-associated genes, novel mechanisms associated with epilepsy, and precision medicine approaches are continuously being identified. In the past decade, advances in genomic knowledge and analysis platforms have begun to make clinical genetic testing accessible for, in principle, people of all ages with epilepsy. For this reason, the Genetics Commission of the International League Against Epilepsy (ILAE) presents this update on clinical genetic testing practice, including current techniques, indications, yield of genetic testing, recommendations for pre- and post-test counseling, and follow-up after genetic testing is completed. We acknowledge that the resources vary across different settings but highlight that genetic diagnostic testing for epilepsy should be prioritized when the likelihood of an informative finding is high. Results of genetic testing, in particular the identification of causative genetic variants, are likely to improve individual care. We emphasize the importance of genetic testing for individuals with epilepsy as we enter the era of precision therapy.
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Affiliation(s)
- Ilona Krey
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Alina Esterhuizen
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa
| | - Samuel F. Berkovic
- Epilepsy Research Centre, Department of Medicine, University of Melbourne (Austin Health), Heidelberg, VIC, Australia
| | - Ingo Helbig
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein, Christian-Albrechts-University, Building C, Arnold-Heller-Straße 3, 24105 Kiel, Germany
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA 19104, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children’s Hospital of Philadelphia, Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA 19104, USA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA, 19104 USA
- Department of Neurology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19104 USA
| | - Michael S. Hildebrand
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, Heidelberg and Murdoch Children’s Research Institute, Royal Children’s Hospital, Victoria, Australia
| | - Holger Lerche
- Department of Epileptology and Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Germany
| | - Daniel Lowenstein
- Department of Neurology, University of California, San Francisco, USA
| | - Rikke S. Møller
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre, Dianalund, Denmark
- Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark
| | - Annapurna Poduri
- Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Lynette Sadleir
- Department of Paediatrics and Child Health, University of Otago, Wellington, New Zealand
| | - Sanjay M. Sisodiya
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology London, UK and Chalfont Centre for Epilepsy, Buckinghamshire, UK
| | - Sarah Weckhuysen
- Center for Molecular Neurology, VIB-University of Antwerp, VIB, Antwerp, Belgium; Department of Neurology, University Hospital Antwerp, Antwerp, Belgium
| | - Jo M. Wilmshurst
- Department of Paediatric Neurology, Paediatric and Child Health, Red Cross War Memorial Children’s Hospital, Neuroscience Institute, University of Cape Town, South Africa
| | - Yvonne Weber
- Department of Epileptology and Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Germany
- Department of Epileptology and Neurology, University of Aachen, Germany
| | - Johannes R. Lemke
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
- Center for Rare Diseases, University of Leipzig Medical Center, Leipzig, Germany
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22
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Najm I, Lal D, Alonso Vanegas M, Cendes F, Lopes-Cendes I, Palmini A, Paglioli E, Sarnat HB, Walsh CA, Wiebe S, Aronica E, Baulac S, Coras R, Kobow K, Cross JH, Garbelli R, Holthausen H, Rössler K, Thom M, El-Osta A, Lee JH, Miyata H, Guerrini R, Piao YS, Zhou D, Blümcke I. The ILAE consensus classification of focal cortical dysplasia: An update proposed by an ad hoc task force of the ILAE diagnostic methods commission. Epilepsia 2022; 63:1899-1919. [PMID: 35706131 PMCID: PMC9545778 DOI: 10.1111/epi.17301] [Citation(s) in RCA: 113] [Impact Index Per Article: 56.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/24/2022] [Accepted: 05/13/2022] [Indexed: 02/05/2023]
Abstract
Ongoing challenges in diagnosing focal cortical dysplasia (FCD) mandate continuous research and consensus agreement to improve disease definition and classification. An International League Against Epilepsy (ILAE) Task Force (TF) reviewed the FCD classification of 2011 to identify existing gaps and provide a timely update. The following methodology was applied to achieve this goal: a survey of published literature indexed with ((Focal Cortical Dysplasia) AND (epilepsy)) between 01/01/2012 and 06/30/2021 (n = 1349) in PubMed identified the knowledge gained since 2012 and new developments in the field. An online survey consulted the ILAE community about the current use of the FCD classification scheme with 367 people answering. The TF performed an iterative clinico-pathological and genetic agreement study to objectively measure the diagnostic gap in blood/brain samples from 22 patients suspicious for FCD and submitted to epilepsy surgery. The literature confirmed new molecular-genetic characterizations involving the mechanistic Target Of Rapamycin (mTOR) pathway in FCD type II (FCDII), and SLC35A2 in mild malformations of cortical development (mMCDs) with oligodendroglial hyperplasia (MOGHE). The electro-clinical-imaging phenotypes and surgical outcomes were better defined and validated for FCDII. Little new information was acquired on clinical, histopathological, or genetic characteristics of FCD type I (FCDI) and FCD type III (FCDIII). The survey identified mMCDs, FCDI, and genetic characterization as fields for improvement in an updated classification. Our iterative clinico-pathological and genetic agreement study confirmed the importance of immunohistochemical staining, neuroimaging, and genetic tests to improve the diagnostic yield. The TF proposes to include mMCDs, MOGHE, and "no definite FCD on histopathology" as new categories in the updated FCD classification. The histopathological classification can be further augmented by advanced neuroimaging and genetic studies to comprehensively diagnose FCD subtypes; these different levels should then be integrated into a multi-layered diagnostic scheme. This update may help to foster multidisciplinary efforts toward a better understanding of FCD and the development of novel targeted treatment options.
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Affiliation(s)
- Imad Najm
- Charles Shor Epilepsy Center, Neurological Institute, Cleveland, Ohio, USA
| | - Dennis Lal
- Charles Shor Epilepsy Center, Neurological Institute, Cleveland, Ohio, USA.,Genomic Medicine Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | | | - Fernando Cendes
- Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), University of Campinas - UNICAMP, Campinas, Sao Paulo, Brazil.,Department of Neurology, University of Campinas - UNICAMP, Campinas, Sao Paulo, Brazil
| | - Iscia Lopes-Cendes
- Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), University of Campinas - UNICAMP, Campinas, Sao Paulo, Brazil.,Department of Translational Medicine, University of Campinas - UNICAMP, Campinas, Sao Paulo, Brazil
| | - Andre Palmini
- Department of Clinical Neurosciences, School of Medicine, Pontificia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil.,Porto Alegre Epilepsy Surgery Program, Hospital São Lucas PUCRS, Porto Alegre, Brazil
| | - Eliseu Paglioli
- Department of Surgery, School of Medicine, Pontificia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Harvey B Sarnat
- Department of Paediatrics, Department of Pathology (Neuropathology) and Department of Clinical Neurosciences, University of Calgary Faculty of Medicine, Alberta Children's Hospital Research Institute, Calgary, Alberta, Canada
| | - Christopher A Walsh
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA.,Departments of Pediatrics and Neurology, Harvard Medical School, Boston, Massachusetts, USA
| | - Samuel Wiebe
- Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Eleonora Aronica
- Department of (Neuro) Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Stichting Epilepsie Instellingen Nederland (SEIN), Heemstede, the Netherlands
| | - Stéphanie Baulac
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Roland Coras
- Department of Neuropathology, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Katja Kobow
- Developmental Neurosciences Programme, UCL NIHR BRC Great Ormond Street Institute of Child Health and Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - J Helen Cross
- Developmental Neurosciences Programme, UCL NIHR BRC Great Ormond Street Institute of Child Health and Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Rita Garbelli
- Epilepsy Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Hans Holthausen
- Center for Pediatric Neurology, Neurorehabilitation and Epileptology, Schoen-Clinic, Vogtareuth, Germany
| | - Karl Rössler
- Department of Neurosurgery, Allgemeines Krankenhaus Wien, Vienna Medical University, Wien, Austria
| | - Maria Thom
- Department of Neuropathology, Institute of Neurology, University College London, UK
| | - Assam El-Osta
- Epigenetics in Human Health and Disease Laboratory, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Jeong Ho Lee
- Graduate School of Medical Science and Engineering, KAIST and SoVarGen, Daejeon, South Korea
| | - Hajime Miyata
- Department of Neuropathology, Research Institute for Brain and Blood Vessels, Akita Cerebrospinal and Cardiovascular Center, Akita, Japan
| | - Renzo Guerrini
- Neuroscience Department, Children's Hospital Anna Meyer- University of Florence, Florence, Italy
| | - Yue-Shan Piao
- National Center for Neurological Disorders, Department of Pathology, Xuanwu Hospital, Capital Medical University, and Clinical Research Center for Epilepsy, Capital Medical University, Beijing, China
| | - Dong Zhou
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China
| | - Ingmar Blümcke
- Charles Shor Epilepsy Center, Neurological Institute, Cleveland, Ohio, USA.,Department of Neuropathology, Universitätsklinikum Erlangen, Erlangen, Germany
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23
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Wasilewska K, Gambin T, Rydzanicz M, Szczałuba K, Płoski R. Postzygotic mutations and where to find them - Recent advances and future implications in the field of non-neoplastic somatic mosaicism. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 790:108426. [PMID: 35690331 DOI: 10.1016/j.mrrev.2022.108426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 05/05/2022] [Accepted: 06/03/2022] [Indexed: 01/01/2023]
Abstract
The technological progress of massively parallel sequencing (MPS) has triggered a remarkable development in the research on postzygotic mutations. Although the overwhelming majority of studies in the field focus on oncogenesis, non-neoplastic diseases are attracting more and more attention. The aim of this review was to summarize some of the most recent findings in the field of somatic mosaicism in diseases other than neoplastic events. We discuss the abundance and role of postzygotic mutations, with a special emphasis on disorders which occur only in a mosaic form (obligatory mosaic diseases; OMDs). Based on the list of OMDs compiled from the published literature and three databases (OMIM, Orphanet and MosaicBase), we demonstrate the prevalence of cancer-related genes across OMDs and suggest other sources to further explore OMDs and OMD-related genes. Additionally, we comment on some practical aspects related to mosaic diseases, such as approaches to tissue sampling, the MPS coverage required to detect variants at a very low frequency, as well as on bioinformatic and molecular tools dedicated to detect somatic mutations in MPS data.
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Affiliation(s)
- Krystyna Wasilewska
- Department of Medical Genetics, Medical University of Warsaw, ul. Pawińskiego 3c, 02-106 Warsaw, Poland
| | - Tomasz Gambin
- Institute of Computer Science, Warsaw University of Technology, Nowowiejska 15/19, 00-665 Warsaw, Poland
| | - Małgorzata Rydzanicz
- Department of Medical Genetics, Medical University of Warsaw, ul. Pawińskiego 3c, 02-106 Warsaw, Poland
| | - Krzysztof Szczałuba
- Department of Medical Genetics, Medical University of Warsaw, ul. Pawińskiego 3c, 02-106 Warsaw, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, ul. Pawińskiego 3c, 02-106 Warsaw, Poland.
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24
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Lee S, Lee JH. Brain somatic mutations as RNA therapeutic targets in neurological disorders. Ann N Y Acad Sci 2022; 1514:11-20. [PMID: 35527236 DOI: 10.1111/nyas.14786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Research into the genetic etiology of a neurological disorder can provide directions for genetic diagnosis and targeted therapy. In the past, germline mutations, which are transmitted from parents or newly arise from parental germ cells, were considered as major genetic causes of neurological disorders. However, recent evidence has shown that somatic mutations in the brain, which can arise from neural stem cells during development or over aging, account for a significant number of brain disorders, ranging from neurodevelopmental, neurodegenerative, and neuropsychiatric to neoplastic disease. Moreover, the identification of disease-causing somatic mutations or mutated genes has provided new insights into molecular pathogenesis and unveiled potential therapeutic targets for treating neurological disorders that have few, or no, therapeutic options. RNA therapeutics, including antisense oligonucleotide (ASO) and small interfering RNA (siRNA), are emerging as promising therapeutic tools for treating genetic neurological disorders. As the number of approved and investigational ASO and siRNA drugs for neurological disorders associated with germline mutations increases, they may also prove to be attractive modalities for treating neurologic disorders resulting from somatic mutations. In this perspective, we highlight several neurological diseases caused by brain somatic mutations and discuss the potential role of RNA therapeutics in these conditions.
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Affiliation(s)
- Sungyul Lee
- SoVarGen Co., Ltd., Daejeon, Republic of Korea
| | - Jeong Ho Lee
- SoVarGen Co., Ltd., Daejeon, Republic of Korea.,Graduate School of Medical Science and Engineering, Korea Advanced Institute Science and Technology (KAIST), KAIST BioMedical Research Center, Daejeon, Republic of Korea
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25
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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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26
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CfDNA Measurement as a Diagnostic Tool for the Detection of Brain Somatic Mutations in Refractory Epilepsy. Int J Mol Sci 2022; 23:ijms23094879. [PMID: 35563270 PMCID: PMC9102996 DOI: 10.3390/ijms23094879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/21/2022] [Accepted: 04/26/2022] [Indexed: 02/04/2023] Open
Abstract
Epilepsy is a neurological disorder that affects more than 50 million people. Its etiology is unknown in approximately 60% of cases, although the existence of a genetic factor is estimated in about 75% of these individuals. Hundreds of genes involved in epilepsy are known, and their number is increasing progressively, especially with next-generation sequencing techniques. However, there are still many cases in which the results of these molecular studies do not fully explain the phenotype of the patients. Somatic mutations specific to brain tissue could contribute to the phenotypic spectrum of epilepsy. Undetectable in the genomic DNA of blood cells, these alterations can be identified in cell-free DNA (cfDNA). We aim to review the current literature regarding the detection of somatic variants in cfDNA to diagnose refractory epilepsy, highlighting novel research directions and suggesting further studies.
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27
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Wadden J, Ravi K, John V, Babila CM, Koschmann C. Cell-Free Tumor DNA (cf-tDNA) Liquid Biopsy: Current Methods and Use in Brain Tumor Immunotherapy. Front Immunol 2022; 13:882452. [PMID: 35464472 PMCID: PMC9018987 DOI: 10.3389/fimmu.2022.882452] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 03/14/2022] [Indexed: 11/27/2022] Open
Abstract
Gliomas are tumors derived from mutations in glial brain cells. Gliomas cause significant morbidity and mortality and development of precision diagnostics and novel targeted immunotherapies are critically important. Radiographic imaging is the most common technique to diagnose and track response to treatment, but is an imperfect tool. Imaging does not provide molecular information, which is becoming critically important for identifying targeted immunotherapies and monitoring tumor evolution. Furthermore, immunotherapy induced inflammation can masquerade as tumor progression in images (pseudoprogression) and confound clinical decision making. More recently, circulating cell free tumor DNA (cf-tDNA) has been investigated as a promising biomarker for minimally invasive glioma diagnosis and disease monitoring. cf-tDNA is shed by gliomas into surrounding biofluids (e.g. cerebrospinal fluid and plasma) and, if precisely quantified, might provide a quantitative measure of tumor burden to help resolve pseudoprogression. cf-tDNA can also identify tumor genetic mutations to help guide targeted therapies. However, due to low concentrations of cf-tDNA, recovery and analysis remains challenging. Plasma cf-tDNA typically represents <1% of total cf-DNA due to the blood-brain barrier, limiting their usefulness in practice and motivating the development and use of highly sensitive and specific detection methods. This mini review summarizes the current and future trends of various approaches for cf-tDNA detection and analysis, including new methods that promise more rapid, lower-cost, and accessible diagnostics. We also review the most recent clinical case studies for longitudinal disease monitoring and highlight focus areas, such as novel accurate detection methodologies, as critical research priorities to enable translation to clinic.
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Affiliation(s)
- Jack Wadden
- Department of Pediatric Hematology and Oncology, Michigan Medicine, Ann Arbor, MI, United States
| | | | | | | | - Carl Koschmann
- Department of Pediatric Hematology and Oncology, Michigan Medicine, Ann Arbor, MI, United States
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28
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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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29
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Hoffmann L, Blümcke I. Neuropathology and epilepsy surgery. Curr Opin Neurol 2022; 35:202-207. [PMID: 35067500 DOI: 10.1097/wco.0000000000001030] [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: 11/26/2022]
Abstract
PURPOSE OF REVIEW Neurosurgical treatment of patients suffering from drug-resistant focal epilepsy is recognized as a successful, yet underutilized medical treatment option. By searching PubMed for articles published between January 2020 and September 2021 with the broad search terms 'neuropathology' AND 'epilepsy surgery', this review highlights the active field of etiology-based epilepsy research in human tissue. RECENT FINDINGS All papers addressing the most common epileptogenic human brain disease entities, i.e. focal cortical dysplasia (FCD), brain tumors or hippocampal sclerosis, and written in English language were eligible for our review. We can conclude from this review that etiology-based studies are of foremost interest for (1) the development of prediction models for postsurgical seizure outcome; (2) decipher genetic and molecular alterations to better define disease entities and underlying molecular pathomechanisms, and (3) the translation of human tissue-derived biomarker into clinically useful diagnostics or novel therapeutic targets in the near future. SUMMARY Highlighting FCD brain somatic gain-of-function variants in mammalian target of Rapamycin are a leading pathway to better classify FCD. An integrated genotype-phenotype analysis enables to classify the broad spectrum of low-grade and epilepsy-associated brain tumors. Further DNA-methylation-based disease classification will increase the mechanistic understanding and diagnostic precision of difficult to classify pathologies in the future.
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Affiliation(s)
- Lucas Hoffmann
- Department of Neuropathology, University Hospital Erlangen, Erlangen, Germany
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30
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Fischer J, Di Donato N. Diagnostic pitfalls in patients with malformations of cortical development. Eur J Paediatr Neurol 2022; 37:123-128. [PMID: 35228169 DOI: 10.1016/j.ejpn.2022.01.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 11/27/2022]
Abstract
Malformations of cortical development (MCDs) are a major source of morbidity and mortality in the pediatric patient cohort. Correct diagnosis of the cause is essential for symptom management, disease prognosis and family counselling but is frequently hampered due to numerous potential pitfalls in the diagnostic process. This review highlights potential problems that either prevent the establishment of a diagnosis or are the sources of diagnostic errors. The focus is placed on hereditary causes of MCDs and strategies will be proposed to circumvent potential diagnostic pitfalls. Errors may occur during variant detection, filtering, or interpretation in relation to patient's phenotype. Based on detailed clinical assessment suitable targeted and untargeted methods to identify pathogenic variants with context-dependent filtering and evaluation approaches will be discussed.
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Affiliation(s)
- Jan Fischer
- Institute for Clinical Genetics, University Hospital, TU Dresden, Dresden, Germany
| | - Nataliya Di Donato
- Institute for Clinical Genetics, University Hospital, TU Dresden, Dresden, Germany.
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31
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Scheffer IE. Lightning progress in child neurology in the past 20 years. Lancet Neurol 2022; 21:111-113. [DOI: 10.1016/s1474-4422(22)00002-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 11/29/2022]
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Lee WS, Baldassari S, Stephenson SEM, Lockhart PJ, Baulac S, Leventer RJ. Cortical Dysplasia and the mTOR Pathway: How the Study of Human Brain Tissue Has Led to Insights into Epileptogenesis. Int J Mol Sci 2022; 23:1344. [PMID: 35163267 PMCID: PMC8835853 DOI: 10.3390/ijms23031344] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/14/2022] [Accepted: 01/16/2022] [Indexed: 02/01/2023] Open
Abstract
Type II focal cortical dysplasia (FCD) is a neuropathological entity characterised by cortical dyslamination with the presence of dysmorphic neurons only (FCDIIA) or the presence of both dysmorphic neurons and balloon cells (FCDIIB). The year 2021 marks the 50th anniversary of the recognition of FCD as a cause of drug resistant epilepsy, and it is now the most common reason for epilepsy surgery. The causes of FCD remained unknown until relatively recently. The study of resected human FCD tissue using novel genomic technologies has led to remarkable advances in understanding the genetic basis of FCD. Mechanistic parallels have emerged between these non-neoplastic lesions and neoplastic disorders of cell growth and differentiation, especially through perturbations of the mammalian target of rapamycin (mTOR) signalling pathway. This narrative review presents the advances through which the aetiology of FCDII has been elucidated in chronological order, from recognition of an association between FCD and the mTOR pathway to the identification of somatic mosaicism within FCD tissue. We discuss the role of a two-hit mechanism, highlight current challenges and future directions in detecting somatic mosaicism in brain and discuss how knowledge of FCD may inform novel precision treatments of these focal epileptogenic malformations of human cortical development.
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Affiliation(s)
- Wei Shern Lee
- Bruce Lefroy Centre, Murdoch Children’s Research Institute, Parkville 3052, Australia; (W.S.L.); (S.E.M.S.); (P.J.L.)
- Department of Paediatrics, The University of Melbourne, Parkville 3052, Australia
| | - Sara Baldassari
- Institut du Cerveau-Paris Brain Institute-ICM, Sorbonne Université, Inserm, CNRS, Hôpital de la Pitié Salpêtrière, F-75013 Paris, France;
| | - Sarah E. M. Stephenson
- Bruce Lefroy Centre, Murdoch Children’s Research Institute, Parkville 3052, Australia; (W.S.L.); (S.E.M.S.); (P.J.L.)
- Department of Paediatrics, The University of Melbourne, Parkville 3052, Australia
| | - Paul J. Lockhart
- Bruce Lefroy Centre, Murdoch Children’s Research Institute, Parkville 3052, Australia; (W.S.L.); (S.E.M.S.); (P.J.L.)
- Department of Paediatrics, The University of Melbourne, Parkville 3052, Australia
| | - Stéphanie Baulac
- Institut du Cerveau-Paris Brain Institute-ICM, Sorbonne Université, Inserm, CNRS, Hôpital de la Pitié Salpêtrière, F-75013 Paris, France;
| | - Richard J. Leventer
- Department of Paediatrics, The University of Melbourne, Parkville 3052, Australia
- Murdoch Children’s Research Institute, Parkville 3052, Australia
- Department of Neurology, The Royal Children’s Hospital, Parkville 3052, Australia
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Whitlock JH, Soelter TM, Williams AS, Hardigan AA, Lasseigne BN. Liquid biopsies in epilepsy: biomarkers for etiology, diagnosis, prognosis, and therapeutics. Hum Cell 2022; 35:15-22. [PMID: 34694568 PMCID: PMC8732818 DOI: 10.1007/s13577-021-00624-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 09/29/2021] [Indexed: 01/19/2023]
Abstract
Epilepsy is one of the most common diseases of the central nervous system, impacting nearly 50 million people around the world. Heterogeneous in nature, epilepsy presents in children and adults alike. Currently, surgery is one treatment approach that can completely cure epilepsy. However, not all individuals are eligible for surgical procedures or have successful outcomes. In addition to surgical approaches, antiepileptic drugs (AEDs) have also allowed individuals with epilepsy to achieve freedom from seizures. Others have found treatment through nonpharmacologic approaches such as vagus nerve stimulation, or responsive neurostimulation. Difficulty in accessing samples of human brain tissue along with advances in sequencing technology have driven researchers to investigate sampling liquid biopsies in blood, serum, plasma, and cerebrospinal fluid within the context of epilepsy. Liquid biopsies provide minimal or non-invasive sample collection approaches and can be assayed relatively easily across multiple time points, unlike tissue-based sampling. Various efforts have investigated circulating nucleic acids from these samples including microRNAs, cell-free DNA, transfer RNAs, and long non-coding RNAs. Here, we review nucleic acid-based liquid biopsies in epilepsy to improve understanding of etiology, diagnosis, prediction, and therapeutic monitoring.
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Affiliation(s)
- Jordan H Whitlock
- Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Tabea M Soelter
- Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Avery S Williams
- Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Andrew A Hardigan
- Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Brittany N Lasseigne
- Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL, USA.
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34
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Guerrini R, Balestrini S, Wirrell EC, Walker MC. Monogenic Epilepsies: Disease Mechanisms, Clinical Phenotypes, and Targeted Therapies. Neurology 2021; 97:817-831. [PMID: 34493617 PMCID: PMC10336826 DOI: 10.1212/wnl.0000000000012744] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 08/18/2021] [Indexed: 02/05/2023] Open
Abstract
A monogenic etiology can be identified in up to 40% of people with severe epilepsy. To address earlier and more appropriate treatment strategies, clinicians are required to know the implications that specific genetic causes might have on pathophysiology, natural history, comorbidities, and treatment choices. In this narrative review, we summarize concepts on the genetic epilepsies based on the underlying pathophysiologic mechanisms and present the current knowledge on treatment options based on evidence provided by controlled trials or studies with lower classification of evidence. Overall, evidence robust enough to guide antiseizure medication (ASM) choices in genetic epilepsies remains limited to the more frequent conditions for which controlled trials and observational studies have been possible. Most monogenic disorders are very rare and ASM choices for them are still based on inferences drawn from observational studies and early, often anecdotal, experiences with precision therapies. Precision medicine remains applicable to only a narrow number of patients with monogenic epilepsies and may target only part of the actual functional defects. Phenotypic heterogeneity is remarkable, and some genetic mutations activate epileptogenesis through their developmental effects, which may not be reversed postnatally. Other genes seem to have pure functional consequences on excitability, acting through either loss- or gain-of-function effects, and these may have opposite treatment implications. In addition, the functional consequences of missense mutations may be difficult to predict, making precision treatment approaches considerably more complex than estimated by deterministic interpretations. Knowledge of genetic etiologies can influence the approach to surgical treatment of focal epilepsies. Identification of germline mutations in specific genes contraindicates surgery while mutations in other genes do not. Identification, quantification, and functional characterization of specific somatic mutations before surgery using CSF liquid biopsy or after surgery in brain specimens will likely be integrated in planning surgical strategies and reintervention after a first unsuccessful surgery as initial evidence suggests that mutational load may correlate with the epileptogenic zone. Promising future directions include gene manipulation by DNA or mRNA targeting; although most are still far from clinical use, some are in early phase clinical development.
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Affiliation(s)
- Renzo Guerrini
- From the Neuroscience Department (R.G., S.B.), Meyer Children's Hospital-University of Florence, Italy; Department of Clinical and Experimental Epilepsy (S.B., M.C.W.), UCL Queen Square Institute of Neurology, London; Chalfont Centre for Epilepsy (S.B.), Buckinghamshire, UK; and Divisions of Child and Adolescent Neurology and Epilepsy (E.C.W.), Department of Neurology, Mayo Clinic, Rochester, MN.
| | - Simona Balestrini
- From the Neuroscience Department (R.G., S.B.), Meyer Children's Hospital-University of Florence, Italy; Department of Clinical and Experimental Epilepsy (S.B., M.C.W.), UCL Queen Square Institute of Neurology, London; Chalfont Centre for Epilepsy (S.B.), Buckinghamshire, UK; and Divisions of Child and Adolescent Neurology and Epilepsy (E.C.W.), Department of Neurology, Mayo Clinic, Rochester, MN
| | - Elaine C Wirrell
- From the Neuroscience Department (R.G., S.B.), Meyer Children's Hospital-University of Florence, Italy; Department of Clinical and Experimental Epilepsy (S.B., M.C.W.), UCL Queen Square Institute of Neurology, London; Chalfont Centre for Epilepsy (S.B.), Buckinghamshire, UK; and Divisions of Child and Adolescent Neurology and Epilepsy (E.C.W.), Department of Neurology, Mayo Clinic, Rochester, MN
| | - Matthew C Walker
- From the Neuroscience Department (R.G., S.B.), Meyer Children's Hospital-University of Florence, Italy; Department of Clinical and Experimental Epilepsy (S.B., M.C.W.), UCL Queen Square Institute of Neurology, London; Chalfont Centre for Epilepsy (S.B.), Buckinghamshire, UK; and Divisions of Child and Adolescent Neurology and Epilepsy (E.C.W.), Department of Neurology, Mayo Clinic, Rochester, MN
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35
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Neocortical development and epilepsy: insights from focal cortical dysplasia and brain tumours. Lancet Neurol 2021; 20:943-955. [PMID: 34687638 DOI: 10.1016/s1474-4422(21)00265-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 07/14/2021] [Accepted: 08/05/2021] [Indexed: 01/16/2023]
Abstract
During the past decade, there have been considerable advances in understanding of the genetic and morphogenic processes underlying cortical malformations and developmental brain tumours. Focal malformations are caused by somatic (postzygotic) variants in genes related to cell growth (ie, in the mTOR pathway in focal cortical dysplasia type 2), which are acquired in neuronal progenitors during neurodevelopment. In comparison, developmental brain tumours result from somatic variants in genes related to cell proliferation (eg, in the MAP-kinase pathway in ganglioglioma), which affect proliferating glioneuronal precursors. The timing of the genetic event and the specific gene involved during neurodevelopment will drive the nature and size of the lesion, whether it is a developmental malformation or a brain tumour. There is also emerging evidence that epigenetic processes underlie a molecular memory in epileptogenesis. This knowledge will together facilitate understanding of why and how patients with these lesions have epilepsy, and could form a basis for a move towards precision medicine for this challenging cohort of patients.
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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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37
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Ye Z, Bennett MF, Bahlo M, Scheffer IE, Berkovic SF, Perucca P, Hildebrand MS. Cutting edge approaches to detecting brain mosaicism associated with common focal epilepsies: implications for diagnosis and potential therapies. Expert Rev Neurother 2021; 21:1309-1316. [PMID: 34519595 DOI: 10.1080/14737175.2021.1981288] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Mosaic variants arising in brain tissue are increasingly being recognized as a hidden cause of focal epilepsy. This knowledge gain has been driven by new, highly sensitive genetic technologies and genome-wide analysis of brain tissue from surgical resection or autopsy in a small proportion of patients with focal epilepsy. Recently reported novel strategies to detect mosaic variants limited to brain have exploited trace brain DNA obtained from cerebrospinal fluid liquid biopsies or stereo-electroencephalography electrodes. AREAS COVERED The authors review the data on these innovative approaches published in PubMed before 12 June 2021, discuss the challenges associated with their application, and describe how they are likely to improve detection of mosaic variants to provide new molecular diagnoses and therapeutic targets for focal epilepsy, with potential utility in other nonmalignant neurological disorders. EXPERT OPINION These cutting-edge approaches may reveal the hidden genetic etiology of focal epilepsies and provide guidance for precision medicine.
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Affiliation(s)
- Zimeng Ye
- Department of Medicine (Austin Health), Epilepsy Research Centre, University of Melbourne, Heidelberg, Australia
| | - Mark F Bennett
- Department of Medicine (Austin Health), Epilepsy Research Centre, University of Melbourne, Heidelberg, Australia.,Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Ingrid E Scheffer
- Department of Medicine (Austin Health), Epilepsy Research Centre, University of Melbourne, Heidelberg, Australia.,Neuroscience Research Group, Murdoch Children's Research Institute, Parkville, Australia.,Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Australia.,Department of Neurology, Comprehensive Epilepsy Program, Austin Health, Heidelberg, Australia
| | - Samuel F Berkovic
- Department of Medicine (Austin Health), Epilepsy Research Centre, University of Melbourne, Heidelberg, Australia.,Department of Neurology, Comprehensive Epilepsy Program, Austin Health, Heidelberg, Australia
| | - Piero Perucca
- Department of Medicine (Austin Health), Epilepsy Research Centre, University of Melbourne, Heidelberg, Australia.,Department of Neurology, Comprehensive Epilepsy Program, Austin Health, Heidelberg, Australia.,Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia.,Department of Neurology, Alfred Health, Melbourne, Australia.,Department of Neurology, The Royal Melbourne Hospital, Parkville, Australia
| | - Michael S Hildebrand
- Department of Medicine (Austin Health), Epilepsy Research Centre, University of Melbourne, Heidelberg, Australia.,Neuroscience Research Group, Murdoch Children's Research Institute, Parkville, Australia
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Ye Z, Scheffer IE, Berkovic SF, Hildebrand MS. Improving Specificity of Cerebrospinal Fluid Liquid Biopsy for Genetic Testing. Ann Neurol 2021; 90:693-694. [PMID: 34374121 DOI: 10.1002/ana.26191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 06/09/2021] [Indexed: 02/01/2023]
Affiliation(s)
- Zimeng Ye
- Department of Medicine (Austin Health), University of Melbourne, Melbourne, Victoria, Australia
| | - Ingrid E Scheffer
- Department of Medicine (Austin Health), University of Melbourne, Melbourne, Victoria, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, Victoria, Australia.,Department of Neurology, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Samuel F Berkovic
- Department of Medicine (Austin Health), University of Melbourne, Melbourne, Victoria, Australia
| | - Michael S Hildebrand
- Department of Medicine (Austin Health), University of Melbourne, Melbourne, Victoria, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria, Australia
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Kim S, Baldassari S, Baulac S, Lee JH. Reply to "Improving Specificity of CSF Liquid Biopsy for Genetic Testing". Ann Neurol 2021; 90:694-695. [PMID: 34368987 DOI: 10.1002/ana.26188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/03/2021] [Accepted: 08/06/2021] [Indexed: 11/07/2022]
Affiliation(s)
- Seyeon Kim
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, South Korea
| | - Sara Baldassari
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
| | - Stéphanie Baulac
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
| | - Jeong Ho Lee
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, South Korea.,SoVarGen, Inc., Daejeon, South Korea
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40
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Chatterton Z, Mendelev N, Chen S, Carr W, Kamimori GH, Ge Y, Dwork AJ, Haghighi F. Bisulfite Amplicon Sequencing Can Detect Glia and Neuron Cell-Free DNA in Blood Plasma. Front Mol Neurosci 2021; 14:672614. [PMID: 34276305 PMCID: PMC8283182 DOI: 10.3389/fnmol.2021.672614] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 06/14/2021] [Indexed: 11/13/2022] Open
Abstract
Sampling the live brain is difficult and dangerous, and withdrawing cerebrospinal fluid is uncomfortable and frightening to the subject, so new sources of real-time analysis are constantly sought. Cell-free DNA (cfDNA) derived from glia and neurons offers the potential for wide-ranging neurological disease diagnosis and monitoring. However, new laboratory and bioinformatic strategies are needed. DNA methylation patterns on individual cfDNA fragments can be used to ascribe their cell-of-origin. Here we describe bisulfite sequencing assays and bioinformatic processing methods to identify cfDNA derived from glia and neurons. In proof-of-concept experiments, we describe the presence of both glia- and neuron-cfDNA in the blood plasma of human subjects following mild trauma. This detection of glia- and neuron-cfDNA represents a significant step forward in the translation of liquid biopsies for neurological diseases.
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Affiliation(s)
- Zac Chatterton
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Medical Epigenetics, James J. Peters VA Medical Center, New York, NY, United States
- Brain and Mind Centre, School of Medical Science, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Natalia Mendelev
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Medical Epigenetics, James J. Peters VA Medical Center, New York, NY, United States
| | - Sean Chen
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Medical Epigenetics, James J. Peters VA Medical Center, New York, NY, United States
| | - Walter Carr
- Walter Reed Army Institute of Research, Silver Spring, MD, United States
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, United States
| | - Gary H. Kamimori
- Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Yongchao Ge
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Andrew J. Dwork
- Department of Pathology and Cell Biology, Columbia University, New York, NY, United States
- Department of Psychiatry, Columbia University, New York, NY, United States
- Molecular Imaging and Neuropathology Division, New York State Psychiatric Institute, New York, NY, United States
| | - Fatemeh Haghighi
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Medical Epigenetics, James J. Peters VA Medical Center, New York, NY, United States
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Kobow K, Baulac S, von Deimling A, Lee JH. Molecular diagnostics in drug-resistant focal epilepsy define new disease entities. Brain Pathol 2021; 31:e12963. [PMID: 34196984 PMCID: PMC8412082 DOI: 10.1111/bpa.12963] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 03/31/2021] [Indexed: 01/16/2023] Open
Abstract
Structural brain lesions, including the broad range of malformations of cortical development (MCD) and glioneuronal tumors, are among the most common causes of drug-resistant focal epilepsy. Epilepsy surgery can provide a curative treatment option in respective patients. The currently available pre-surgical multi-modal diagnostic armamentarium includes high- and ultra-high resolution magnetic resonance imaging (MRI) and intracerebral EEG to identify a focal structural brain lesion as epilepsy underlying etiology. However, specificity and accuracy in diagnosing the type of lesion have proven to be limited. Moreover, the diagnostic process does not stop with the decision for surgery. The neuropathological diagnosis remains the gold standard for disease classification and patient stratification, but is particularly complex with high inter-observer variability. Here, the identification of lesion-specific mosaic variants together with epigenetic profiling of lesional brain tissue became new tools to more reliably identify disease entities. In this review, we will discuss how the paradigm shifts from histopathology toward an integrated diagnostic approach in cancer and the more recent development of the DNA methylation-based brain tumor classifier have started to influence epilepsy diagnostics. Some examples will be highlighted showing how the diagnosis and our mechanistic understanding of difficult to classify structural brain lesions associated with focal epilepsy has improved with molecular genetic data being considered in decision making.
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Affiliation(s)
- Katja Kobow
- Department of NeuropathologyUniversitätsklinikum ErlangenFriedrich‐Alexander‐University of Erlangen‐Nürnberg (FAU)ErlangenGermany
| | - Stéphanie Baulac
- Institut du Cerveau—Paris Brain Institute—ICMInsermCNRSSorbonne UniversitéParisFrance
| | - Andreas von Deimling
- Department of NeuropathologyUniversitätsklinikum HeidelbergHeidelbergGermany
- CCU NeuropathologyGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Jeong Ho Lee
- Graduate School of Medical Science and EngineeringKAISTDaejeonKorea
- SoVarGen, IncDaejeonRepublic of Korea
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D'Gama AM, Poduri A. Precision Therapy for Epilepsy Related to Brain Malformations. Neurotherapeutics 2021; 18:1548-1563. [PMID: 34608615 PMCID: PMC8608994 DOI: 10.1007/s13311-021-01122-6] [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] [Accepted: 09/04/2021] [Indexed: 02/04/2023] Open
Abstract
Malformations of cortical development (MCDs) represent a range of neurodevelopmental disorders that are collectively common causes of developmental delay and epilepsy, especially refractory childhood epilepsy. Initial treatment with antiseizure medications is empiric, and consideration of surgery is the standard of care for eligible patients with medically refractory epilepsy. In the past decade, advances in next generation sequencing technologies have accelerated progress in understanding the genetic etiologies of MCDs, and precision therapies for focal MCDs are emerging. Notably, mutations that lead to abnormal activation of the mammalian target of rapamycin (mTOR) pathway, which provides critical control of cell growth and proliferation, have emerged as a common cause of malformations. These include tuberous sclerosis complex (TSC), hemimegalencephaly (HME), and some types of focal cortical dysplasia (FCD). TSC currently represents the best example for the pathway from gene discovery to relatively safe and efficacious targeted therapy for epilepsy related to MCDs. Based on extensive pre-clinical and clinical data, the mTOR inhibitor everolimus is currently approved for the treatment of focal refractory seizures in patients with TSC. Although clinical studies are just emerging for FCD and HME, we believe the next decade will bring significant advancements in precision therapies for epilepsy related to these and other MCDs.
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Affiliation(s)
- Alissa M D'Gama
- Divisions of Newborn Medicine and Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital, Boston, MA, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Annapurna Poduri
- Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital, Boston, MA, USA.
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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Kim S, Baldassari S, Sim NS, Chipaux M, Dorfmüller G, Kim DS, Chang WS, Taly V, Lee JH, Baulac S. Detection of Brain Somatic Mutations in Cerebrospinal Fluid from Refractory Epilepsy Patients. Ann Neurol 2021; 89:1248-1252. [PMID: 33834539 DOI: 10.1002/ana.26080] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/26/2021] [Accepted: 04/04/2021] [Indexed: 01/05/2023]
Abstract
Brain mosaic mutations are a major cause of refractory focal epilepsies with cortical malformations such as focal cortical dysplasia, hemimegalencephaly, malformation of cortical development with oligodendroglial hyperplasia in epilepsy, and ganglioglioma. Here, we collected cerebrospinal fluid (CSF) during epilepsy surgery to search for somatic variants in cell-free DNA (cfDNA) using targeted droplet digital polymerase chain reaction. In 3 of 12 epileptic patients with known somatic mutations previously identified in brain tissue, we here provide evidence that brain mosaicism can be detected in the CSF-derived cfDNA. These findings suggest future opportunities for detecting the mutant allele driving epilepsy in CSF. ANN NEUROL 2021;89:1248-1252.
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Affiliation(s)
- Seyeon Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Sara Baldassari
- Sorbonne University, Paris Brain Institute (ICM), National Institute of Health and Medical Research (INSERM), National Center for Scientific Research (CNRS), Paris, France
| | - Nam Suk Sim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Mathilde Chipaux
- Department of Pediatric Neurosurgery, Rothschild Foundation Hospital, Paris, France
| | - Georg Dorfmüller
- Department of Pediatric Neurosurgery, Rothschild Foundation Hospital, Paris, France
| | - Dong Seok Kim
- Department of Neurosurgery, Pediatric Neurosurgery, Severance Children's Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Won Seok Chang
- Department of Neurosurgery, Brain Research Institute, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Valérie Taly
- Cordeliers Research Center, National Institute of Health and Medical Research UMRS 1138, National Center for Scientific Research SNC 5096, Sorbonne University, USPC, University of Paris, National League Against Cancer Team, Paris, France
| | - Jeong Ho Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea.,SoVarGen, Daejeon, Republic of Korea
| | - Stéphanie Baulac
- Sorbonne University, Paris Brain Institute (ICM), National Institute of Health and Medical Research (INSERM), National Center for Scientific Research (CNRS), Paris, France
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