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Wagstyl K, Kobow K, Casillas-Espinosa PM, Cole AJ, Jiménez-Jiménez D, Nariai H, Baulac S, O'Brien T, Henshall DC, Akman O, Sankar R, Galanopoulou AS, Auvin S. WONOEP 2022: Neurotechnology for the diagnosis of epilepsy. Epilepsia 2024. [PMID: 38829313 DOI: 10.1111/epi.18028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 06/05/2024]
Abstract
Epilepsy's myriad causes and clinical presentations ensure that accurate diagnoses and targeted treatments remain a challenge. Advanced neurotechnologies are needed to better characterize individual patients across multiple modalities and analytical techniques. At the XVIth Workshop on Neurobiology of Epilepsy: Early Onset Epilepsies: Neurobiology and Novel Therapeutic Strategies (WONOEP 2022), the session on "advanced tools" highlighted a range of approaches, from molecular phenotyping of genetic epilepsy models and resected tissue samples to imaging-guided localization of epileptogenic tissue for surgical resection of focal malformations. These tools integrate cutting edge research, clinical data acquisition, and advanced computational methods to leverage the rich information contained within increasingly large datasets. A number of common challenges and opportunities emerged, including the need for multidisciplinary collaboration, multimodal integration, potential ethical challenges, and the multistage path to clinical translation. Despite these challenges, advanced epilepsy neurotechnologies offer the potential to improve our understanding of the underlying causes of epilepsy and our capacity to provide patient-specific treatment.
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Affiliation(s)
- Konrad Wagstyl
- School of Biomedical Engineering & Imaging Science, King's College London, London, UK
- Developmental Neurosciences, UCL Great Ormond Street for Child Health, UCL, London, UK
| | - Katja Kobow
- Institute of Neuropathology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Pablo M Casillas-Espinosa
- Department of Medicine, Royal Melbourne Hospital, University of Melbourne, Parkville, Victoria, Australia
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Department of Neurology, Alfred Hospital, Melbourne, Victoria, Australia
| | - Andrew J Cole
- MGH Epilepsy Service, Division of Clinical Neurophysiology, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Diego Jiménez-Jiménez
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, UK
| | - Hiroki Nariai
- Division of Pediatric Neurology, Department of Pediatrics, UCLA Medical Center, Los Angeles, California, USA
| | - Stéphanie Baulac
- Institut du Cerveau-Paris Brain Institute-ICM, INSERM, CNRS, Sorbonne Université, Paris, France
| | - Terence O'Brien
- Department of Medicine, Royal Melbourne Hospital, University of Melbourne, Parkville, Victoria, Australia
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Department of Neurology, Alfred Hospital, Melbourne, Victoria, Australia
| | - David C Henshall
- FutureNeuro SFI Research Centre, RCSI University of Medicine and Health Sciences, Dublin, Ireland
- Department of Physiology and Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Ozlem Akman
- Department of Physiology, Faculty of Medicine, Demiroglu Bilim University, Istanbul, Turkey
| | - Raman Sankar
- Division of Pediatric Neurology, Department of Pediatrics, UCLA Mattel Children's Hospital, David Geffen School of Medicine, Los Angeles, California, USA
- UCLA Children's Discovery and Innovation Institute, California, Los Angeles, USA
| | - Aristea S Galanopoulou
- Saul R. Korey Department of Neurology, Isabelle Rapin Division of Child Neurology, Laboratory of Developmental Epilepsy, Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Stéphane Auvin
- Université Paris-Cité, INSERM NeuroDiderot, Paris, France
- Pediatric Neurology Department, APHP, Robert Debré University Hospital, CRMR Epilepsies Rares, EpiCARE member, Paris, France
- Institut Universitaire de France, Paris, France
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Waldvogel SM, Posey JE, Goodell MA. Human embryonic genetic mosaicism and its effects on development and disease. Nat Rev Genet 2024:10.1038/s41576-024-00715-z. [PMID: 38605218 DOI: 10.1038/s41576-024-00715-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2024] [Indexed: 04/13/2024]
Abstract
Nearly every mammalian cell division is accompanied by a mutational event that becomes fixed in a daughter cell. When carried forward to additional cell progeny, a clone of variant cells can emerge. As a result, mammals are complex mosaics of clones that are genetically distinct from one another. Recent high-throughput sequencing studies have revealed that mosaicism is common, clone sizes often increase with age and specific variants can affect tissue function and disease development. Variants that are acquired during early embryogenesis are shared by multiple cell types and can affect numerous tissues. Within tissues, variant clones compete, which can result in their expansion or elimination. Embryonic mosaicism has clinical implications for genetic disease severity and transmission but is likely an under-recognized phenomenon. To better understand its implications for mosaic individuals, it is essential to leverage research tools that can elucidate the mechanisms by which expanded embryonic variants influence development and disease.
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Affiliation(s)
- Sarah M Waldvogel
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
- Graduate Program in Cancer and Cell Biology, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Margaret A Goodell
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
- Graduate Program in Cancer and Cell Biology, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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3
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Leng K, Cadwell CR, Devine WP, Tihan T, Qi Z, Singhal NS, Glenn OA, Kamiya S, Wiita AP, Berger AC, Shieh JT, Titus EW, Paredes MF, Upadhyay V. Cell-Type Specificity of Mosaic Chromosome 1q Gain Resolved by snRNA-seq in a Case of Epilepsy With Hyaline Protoplasmic Astrocytopathy. Neurol Genet 2024; 10:e200142. [PMID: 38586598 PMCID: PMC10997208 DOI: 10.1212/nxg.0000000000200142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 01/24/2024] [Indexed: 04/09/2024]
Abstract
Objectives Mosaic gain of chromosome 1q (chr1q) has been associated with malformation of cortical development (MCD) and epilepsy. Hyaline protoplasmic astrocytopathy (HPA) is a rare neuropathologic finding seen in cases of epilepsy with MCD. The cell-type specificity of mosaic chr1q gain in the brain and the molecular signatures of HPA are unknown. Methods We present the case of a child with pharmacoresistant epilepsy who underwent epileptic focus resections at age 3 and 5 years and was found to have mosaic chr1q gain and HPA. We performed single-nuclei RNA sequencing (snRNA-seq) of brain tissue from the second resection. Results snRNA-seq showed increased expression of chr1q genes specifically in subsets of neurons and astrocytes. Differentially expressed genes associated with inferred chr1q gain included AKT3 and genes associated with cell adhesion or migration. A subpopulation of astrocytes demonstrated marked enrichment for synapse-associated transcripts, possibly linked to the astrocytic inclusions observed in HPA. Discussion snRNA-seq may be used to infer the cell-type specificity of mosaic chromosomal copy number changes and identify associated gene expression alterations, which in the case of chr1q gain may involve aberrations in cell migration. Future studies using spatial profiling could yield further insights on the molecular signatures of HPA.
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Affiliation(s)
- Kun Leng
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
| | - Cathryn R Cadwell
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
| | - Walter P Devine
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
| | - Tarik Tihan
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
| | - Zhongxia Qi
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
| | - Nilika S Singhal
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
| | - Orit A Glenn
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
| | - Sherry Kamiya
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
| | - Arun P Wiita
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
| | - Amy C Berger
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
| | - Joseph T Shieh
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
| | - Erron W Titus
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
| | - Mercedes F Paredes
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
| | - Vaibhav Upadhyay
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
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4
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Leng K, Cadwell CR, Patrick Devine W, Tihan T, Qi Z, Singhal N, Glenn O, Kamiya S, Wiita A, Berger A, Shieh JT, Titus EW, Paredes MF, Upadhyay V. Cell type specificity of mosaic chromosome 1q gain resolved by snRNA-seq in a case of epilepsy with hyaline protoplasmic astrocytopathy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.16.562560. [PMID: 38328093 PMCID: PMC10849466 DOI: 10.1101/2023.10.16.562560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Introduction Mosaic gain of chromosome 1q (chr1q) has been associated with malformation of cortical development (MCD) and epilepsy. Hyaline protoplasmic astrocytopathy (HPA) is a rare neuropathological finding seen in cases of epilepsy with MCD. The cell-type specificity of mosaic chr1q gain in the brain and the molecular signatures of HPA are unknown. Methods We present a child with pharmacoresistant epilepsy who underwent epileptic focus resections at age 3 and 5 years and was found to have mosaic chr1q gain and HPA. We performed single-nuclei RNA-sequencing (snRNA-seq) of brain tissue from the second resection. Results snRNA-seq showed increased expression of chr1q genes specifically in subsets of neurons and astrocytes. Differentially expressed genes associated with inferred chr1q gain included AKT3 and genes associated with cell adhesion or migration. A subpopulation of astrocytes demonstrated marked enrichment for synapse-associated transcripts, possibly linked to the astrocytic inclusions observed in HPA. Discussion snRNA-seq may be used to infer the cell type-specificity of mosaic chromosomal copy number changes and identify associated gene expression alterations, which in the case of chr1q gain may involve aberrations in cell migration. Future studies using spatial profiling could yield further insights on the molecular signatures of HPA.
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Affiliation(s)
- Kun Leng
- Medical Scientist Training Program, University of California, San Francisco
| | - Cathryn R. Cadwell
- Department of Pathology, University of California, San Francisco
- Department of Neurological Surgery, University of California San Francisco
- Weill Institute for Neuroscience, University of California, San Francisco
| | | | - Tarik Tihan
- Department of Pathology, University of California, San Francisco
| | - Zhongxia Qi
- Department of Laboratory Medicine, University of California, San Francisco
| | - Nilika Singhal
- Division of Epilepsy, Department of Neurology, University of California, San Francisco
| | - Orit Glenn
- Department of Radiology and Biomedical Imaging, University of California, San Francisco
| | - Sherry Kamiya
- Department of Pathology, University of California, San Francisco
| | - Arun Wiita
- Department of Laboratory Medicine, University of California, San Francisco
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
- Chan Zuckerberg Biohub, San Francisco
| | - Amy Berger
- Department of Medicine, University of California, San Francisco
- Current affiliation: Denali Therapeutics
| | - Joseph T. Shieh
- Medical Genetics, Department of Pediatrics, University of California, San Francisco
| | - Erron W. Titus
- Medical Scientist Training Program, University of California, San Francisco
- Department of Laboratory Medicine, University of California, San Francisco
| | - Mercedes F. Paredes
- Weill Institute for Neuroscience, University of California, San Francisco
- Division of Epilepsy, Department of Neurology, University of California, San Francisco
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5
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Miller KE, Rivaldi AC, Shinagawa N, Sran S, Navarro JB, Westfall JJ, Miller AR, Roberts RD, Akkari Y, Supinger R, Hester ME, Marhabaie M, Gade M, Lu J, Rodziyevska O, Bhattacharjee MB, Von Allmen GK, Yang E, Lidov HGW, Harini C, Shah MN, Leonard J, Pindrik J, Shaikhouni A, Goldman JE, Pierson CR, Thomas DL, Boué DR, Ostendorf AP, Mardis ER, Poduri A, Koboldt DC, Heinzen EL, Bedrosian TA. Post-zygotic rescue of meiotic errors causes brain mosaicism and focal epilepsy. Nat Genet 2023; 55:1920-1928. [PMID: 37872450 PMCID: PMC10714261 DOI: 10.1038/s41588-023-01547-z] [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: 04/12/2023] [Accepted: 09/21/2023] [Indexed: 10/25/2023]
Abstract
Somatic mosaicism is a known cause of neurological disorders, including developmental brain malformations and epilepsy. Brain mosaicism is traditionally attributed to post-zygotic genetic alterations arising in fetal development. Here we describe post-zygotic rescue of meiotic errors as an alternate origin of brain mosaicism in patients with focal epilepsy who have mosaic chromosome 1q copy number gains. Genomic analysis showed evidence of an extra parentally derived chromosome 1q allele in the resected brain tissue from five of six patients. This copy number gain is observed only in patient brain tissue, but not in blood or buccal cells, and is strongly enriched in astrocytes. Astrocytes carrying chromosome 1q gains exhibit distinct gene expression signatures and hyaline inclusions, supporting a novel genetic association for astrocytic inclusions in epilepsy. Further, these data demonstrate an alternate mechanism of brain chromosomal mosaicism, with parentally derived copy number gain isolated to brain, reflecting rescue in other tissues during development.
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Affiliation(s)
- Katherine E Miller
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Adithe C Rivaldi
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Noriyuki Shinagawa
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Sahib Sran
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Jason B Navarro
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Jesse J Westfall
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Anthony R Miller
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Ryan D Roberts
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Yassmine Akkari
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Rachel Supinger
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Mark E Hester
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Mohammad Marhabaie
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Meethila Gade
- Division of Pharmacotherapy and Experimental Therapeutics in the Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jinfeng Lu
- Division of Pharmacotherapy and Experimental Therapeutics in the Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Olga Rodziyevska
- Division of Child Neurology, Department of Pediatrics, McGovern Medical School, Houston, TX, USA
| | | | - Gretchen K Von Allmen
- Division of Child Neurology, Department of Pediatrics, McGovern Medical School, Houston, TX, USA
- Department of Neurology, McGovern Medical School, Houston, TX, USA
| | - Edward Yang
- Department of Radiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Hart G W Lidov
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Chellamani Harini
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Manish N Shah
- Departments of Pediatric Surgery and Neurosurgery, McGovern Medical School, Houston, TX, USA
| | - Jeffrey Leonard
- Department of Neurosurgery, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Neurosurgery, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Jonathan Pindrik
- Department of Neurosurgery, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Neurosurgery, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Ammar Shaikhouni
- Department of Neurosurgery, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Neurosurgery, The Ohio State University College of Medicine, Columbus, OH, USA
| | - James E Goldman
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Christopher R Pierson
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pathology, The Ohio State University College of Medicine, Columbus, OH, USA
- Department of Biomedical Education & Anatomy, Division of Anatomy, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Diana L Thomas
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pathology, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Daniel R Boué
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pathology, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Adam P Ostendorf
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA
- Division of Pediatric Neurology, Nationwide Children's Hospital, Columbus, OH, USA
| | - Elaine R Mardis
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Neurosurgery, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Annapurna Poduri
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Daniel C Koboldt
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Erin L Heinzen
- Division of Pharmacotherapy and Experimental Therapeutics in the Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Genetics in the School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Tracy A Bedrosian
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA.
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA.
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6
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Wang DD, Katoch M, Jabari S, Blumcke I, Blumenthal DB, Lu DH, Coras R, Wang YJ, Shi J, Zhou WJ, Kobow K, Piao YS. The specific DNA methylation landscape in focal cortical dysplasia ILAE type 3D. Acta Neuropathol Commun 2023; 11:129. [PMID: 37559109 PMCID: PMC10410964 DOI: 10.1186/s40478-023-01618-6] [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: 03/30/2023] [Accepted: 07/09/2023] [Indexed: 08/11/2023] Open
Abstract
Focal Cortical Dysplasia (FCD) is a frequent cause of drug-resistant focal epilepsy in children and young adults. The international FCD classifications of 2011 and 2022 have identified several clinico-pathological subtypes, either occurring isolated, i.e., FCD ILAE Type 1 or 2, or in association with a principal cortical lesion, i.e., FCD Type 3. Here, we addressed the DNA methylation signature of a previously described new subtype of FCD 3D occurring in the occipital lobe of very young children and microscopically defined by neuronal cell loss in cortical layer 4. We studied the DNA methylation profile using 850 K BeadChip arrays in a retrospective cohort of 104 patients with FCD 1 A, 2 A, 2B, 3D, TLE without FCD, and 16 postmortem specimens without neurological disorders as controls, operated in China or Germany. DNA was extracted from formalin-fixed paraffin-embedded tissue blocks with microscopically confirmed lesions, and DNA methylation profiles were bioinformatically analyzed with a recently developed deep learning algorithm. Our results revealed a distinct position of FCD 3D in the DNA methylation map of common FCD subtypes, also different from non-FCD epilepsy surgery controls or non-epileptic postmortem controls. Within the FCD 3D cohort, the DNA methylation signature separated three histopathology subtypes, i.e., glial scarring around porencephalic cysts, loss of layer 4, and Rasmussen encephalitis. Differential methylation in FCD 3D with loss of layer 4 mapped explicitly to biological pathways related to neurodegeneration, biogenesis of the extracellular matrix (ECM) components, axon guidance, and regulation of the actin cytoskeleton. Our data suggest that DNA methylation signatures in cortical malformations are not only of diagnostic value but also phenotypically relevant, providing the molecular underpinnings of structural and histopathological features associated with epilepsy. Further studies will be necessary to confirm these results and clarify their functional relevance and epileptogenic potential in these difficult-to-treat children.
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Affiliation(s)
- Dan-Dan Wang
- Department of Pathology, Xuanwu Hospital, Capital Medical University, No. 45, Changchun Street, Xicheng District, Beijing, 100053, China
- Clinical Research Center for Epilepsy, Capital Medical University, Beijing, 100053, China
- National Center for Neurological Disorders, Beijing, 100053, China
| | - Mitali Katoch
- Department of Neuropathology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Samir Jabari
- Department of Neuropathology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Ingmar Blumcke
- Department of Neuropathology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - David B Blumenthal
- Biomedical Network Science Lab, Department of Artificial Intelligence in Biomedical Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - De-Hong Lu
- Department of Pathology, Xuanwu Hospital, Capital Medical University, No. 45, Changchun Street, Xicheng District, Beijing, 100053, China
- Clinical Research Center for Epilepsy, Capital Medical University, Beijing, 100053, China
- National Center for Neurological Disorders, Beijing, 100053, China
| | - Roland Coras
- Department of Neuropathology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Yu-Jiao Wang
- Department of Pathology, Xuanwu Hospital, Capital Medical University, No. 45, Changchun Street, Xicheng District, Beijing, 100053, China
- Clinical Research Center for Epilepsy, Capital Medical University, Beijing, 100053, China
- National Center for Neurological Disorders, Beijing, 100053, China
| | - Jie Shi
- Department of Neurosurgery, Tsinghua University Yuquan Hospital, Beijing, 100049, China
| | - Wen-Jing Zhou
- Department of Neurosurgery, Tsinghua University Yuquan Hospital, Beijing, 100049, China
| | - Katja Kobow
- Department of Neuropathology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.
| | - Yue-Shan Piao
- Department of Pathology, Xuanwu Hospital, Capital Medical University, No. 45, Changchun Street, Xicheng District, Beijing, 100053, China.
- Clinical Research Center for Epilepsy, Capital Medical University, Beijing, 100053, China.
- National Center for Neurological Disorders, Beijing, 100053, China.
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7
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Boßelmann CM, Leu C, Lal D. Technological and computational approaches to detect somatic mosaicism in epilepsy. Neurobiol Dis 2023:106208. [PMID: 37343892 DOI: 10.1016/j.nbd.2023.106208] [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: 03/05/2023] [Revised: 06/03/2023] [Accepted: 06/16/2023] [Indexed: 06/23/2023] Open
Abstract
Lesional epilepsy is a common and severe disease commonly associated with malformations of cortical development, including focal cortical dysplasia and hemimegalencephaly. Recent advances in sequencing and variant calling technologies have identified several genetic causes, including both short/single nucleotide and structural somatic variation. In this review, we aim to provide a comprehensive overview of the methodological advancements in this field while highlighting the unresolved technological and computational challenges that persist, including ultra-low variant allele fractions in bulk tissue, low availability of paired control samples, spatial variability of mutational burden within the lesion, and the issue of false-positive calls and validation procedures. Information from genetic testing in focal epilepsy may be integrated into clinical care to inform histopathological diagnosis, postoperative prognosis, and candidate precision therapies.
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Affiliation(s)
- Christian M Boßelmann
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Costin Leu
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Department of Clinical and Experimental Epilepsy, Institute of Neurology, University College London, London, UK.
| | - Dennis Lal
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and M.I.T., Cambridge, MA, USA; Cologne Center for Genomics (CCG), University of Cologne, Cologne, DE, USA
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8
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Hoffmann L, Coras R, Kobow K, López-Rivera JA, Lal D, Leu C, Najm I, Nürnberg P, Herms J, Harter PN, Bien CG, Kalbhenn T, Müller M, Pieper T, Hartlieb T, Kudernatsch M, Hamer H, Brandner S, Rössler K, Blümcke I, Jabari S. Ganglioglioma with adverse clinical outcome and atypical histopathological features were defined by alterations in PTPN11/KRAS/NF1 and other RAS-/MAP-Kinase pathway genes. Acta Neuropathol 2023; 145:815-827. [PMID: 36973520 PMCID: PMC10175344 DOI: 10.1007/s00401-023-02561-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/27/2023] [Accepted: 03/09/2023] [Indexed: 03/29/2023]
Abstract
Exome-wide sequencing studies recently described PTPN11 as a novel brain somatic epilepsy gene. In contrast, germline mutations of PTPN11 are known to cause Noonan syndrome, a multisystem disorder characterized by abnormal facial features, developmental delay, and sporadically, also brain tumors. Herein, we performed a deep phenotype-genotype analysis of a comprehensive series of ganglioglioma (GG) with brain somatic alterations of the PTPN11/KRAS/NF1 genes compared to GG with common MAP-Kinase signaling pathway alterations, i.e., BRAFV600E. Seventy-two GG were submitted to whole exome sequencing and genotyping and 84 low grade epilepsy associated tumors (LEAT) to DNA-methylation analysis. In 28 tumours, both analyses were available from the same sample. Clinical data were retrieved from hospital files including disease onset, age at surgery, brain localization, and seizure outcome. A comprehensive histopathology staining panel was available in all cases. We identified eight GG with PTPN11 alterations, copy number variant (CNV) gains of chromosome 12, and the commonality of additional CNV gains in NF1, KRAS, FGFR4 and RHEB, as well as BRAFV600E alterations. Histopathology revealed an atypical glio-neuronal phenotype with subarachnoidal tumor spread and large, pleomorphic, and multinuclear cellular features. Only three out of eight patients with GG and PTPN11/KRAS/NF1 alterations were free of disabling-seizures 2 years after surgery (38% had Engel I). This was remarkably different from our series of GG with only BRAFV600E mutations (85% had Engel I). Unsupervised cluster analysis of DNA methylation arrays separated these tumours from well-established LEAT categories. Our data point to a subgroup of GG with cellular atypia in glial and neuronal cell components, adverse postsurgical outcome, and genetically characterized by complex alterations in PTPN11 and other RAS-/MAP-Kinase and/or mTOR signaling pathways. These findings need prospective validation in clinical practice as they argue for an adaptation of the WHO grading system in developmental, glio-neuronal tumors associated with early onset focal epilepsy.
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Affiliation(s)
- Lucas Hoffmann
- Department of Neuropathology, Partner of the European Reference Network (ERN) EpiCARE, Universitätsklinikum Erlangen, FAU Erlangen-Nürnberg, Erlangen, 91054, Germany
| | - Roland Coras
- Department of Neuropathology, Partner of the European Reference Network (ERN) EpiCARE, Universitätsklinikum Erlangen, FAU Erlangen-Nürnberg, Erlangen, 91054, Germany
| | - Katja Kobow
- Department of Neuropathology, Partner of the European Reference Network (ERN) EpiCARE, Universitätsklinikum Erlangen, FAU Erlangen-Nürnberg, Erlangen, 91054, Germany
| | - Javier A López-Rivera
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, USA
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
- Charles Shor Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, USA
| | - Dennis Lal
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
- Charles Shor Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and M.I.T, Cambridge, MA, 02142, USA
- Cologne Center for Genomics (CCG), Medical Faculty of the University of Cologne, University Hospital of Cologne, 50931, Cologne, Germany
| | - Costin Leu
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
- Charles Shor Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and M.I.T, Cambridge, MA, 02142, USA
- Cologne Center for Genomics (CCG), Medical Faculty of the University of Cologne, University Hospital of Cologne, 50931, Cologne, Germany
| | - Imad Najm
- Charles Shor Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, USA
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG), Medical Faculty of the University of Cologne, University Hospital of Cologne, 50931, Cologne, Germany
| | - Jochen Herms
- Center for Neuropathology and Prion Research, LMU Munich, Munich, Germany
| | - Patrick N Harter
- Center for Neuropathology and Prion Research, LMU Munich, Munich, Germany
| | - Christian G Bien
- Department of Epileptology (Krankenhaus Mara), Medical School, Bielefeld University, Bielefeld, 33617, Germany
| | - Thilo Kalbhenn
- Department of Epileptology (Krankenhaus Mara), Medical School, Bielefeld University, Bielefeld, 33617, Germany
- Department of Neurosurgery (Evangelisches Klinikum Bethel), Medical School, Bielefeld University, Bielefeld, 33617, Germany
| | - Markus Müller
- Department of Epileptology (Krankenhaus Mara), Medical School, Bielefeld University, Bielefeld, 33617, Germany
| | - Tom Pieper
- Center for Pediatric Neurology, Neurorehabilitation, and Epileptology, Schoen-Clinic, Vogtareuth, 83569, Rosenheim, Germany
| | - Till Hartlieb
- Center for Pediatric Neurology, Neurorehabilitation, and Epileptology, Schoen-Clinic, Vogtareuth, 83569, Rosenheim, Germany
| | - Manfred Kudernatsch
- Center for Pediatric Neurology, Neurorehabilitation, and Epileptology, Schoen-Clinic, Vogtareuth, 83569, Rosenheim, Germany
| | - Hajo Hamer
- Epilepsy Center, EpiCARE Partner, Universitätsklinikum Erlangen, FAU Erlangen-Nürnberg, Erlangen, 91054, Germany
| | - Sebastian Brandner
- Department of Neurosurgery, EpiCARE Partner, Universitätsklinikum Erlangen, FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Karl Rössler
- Department of Neurosurgery, EpiCARE Partner, Universitätsklinikum Erlangen, FAU Erlangen-Nürnberg, Erlangen, Germany
- Department of Neurosurgery, EpiCARE Partner, Medical University of Vienna, Vienna General Hospital, Vienna, Austria
| | - Ingmar Blümcke
- Department of Neuropathology, Partner of the European Reference Network (ERN) EpiCARE, Universitätsklinikum Erlangen, FAU Erlangen-Nürnberg, Erlangen, 91054, Germany
| | - Samir Jabari
- Department of Neuropathology, Partner of the European Reference Network (ERN) EpiCARE, Universitätsklinikum Erlangen, FAU Erlangen-Nürnberg, Erlangen, 91054, Germany.
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9
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Lai D, Gade M, Yang E, Koh HY, Lu J, Walley NM, Buckley AF, Sands TT, Akman CI, Mikati MA, McKhann GM, Goldman JE, Canoll P, Alexander AL, Park KL, Von Allmen GK, Rodziyevska O, Bhattacharjee MB, Lidov HGW, Vogel H, Grant GA, Porter BE, Poduri AH, Crino PB, Heinzen EL. Somatic variants in diverse genes leads to a spectrum of focal cortical malformations. Brain 2022; 145:2704-2720. [PMID: 35441233 PMCID: PMC9612793 DOI: 10.1093/brain/awac117] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/19/2022] [Accepted: 03/13/2022] [Indexed: 11/14/2022] Open
Abstract
Post-zygotically acquired genetic variants, or somatic variants, that arise during cortical development have emerged as important causes of focal epilepsies, particularly those due to malformations of cortical development. Pathogenic somatic variants have been identified in many genes within the PI3K-AKT-mTOR-signalling pathway in individuals with hemimegalencephaly and focal cortical dysplasia (type II), and more recently in SLC35A2 in individuals with focal cortical dysplasia (type I) or non-dysplastic epileptic cortex. Given the expanding role of somatic variants across different brain malformations, we sought to delineate the landscape of somatic variants in a large cohort of patients who underwent epilepsy surgery with hemimegalencephaly or focal cortical dysplasia. We evaluated samples from 123 children with hemimegalencephaly (n = 16), focal cortical dysplasia type I and related phenotypes (n = 48), focal cortical dysplasia type II (n = 44), or focal cortical dysplasia type III (n = 15). We performed high-depth exome sequencing in brain tissue-derived DNA from each case and identified somatic single nucleotide, indel and large copy number variants. In 75% of individuals with hemimegalencephaly and 29% with focal cortical dysplasia type II, we identified pathogenic variants in PI3K-AKT-mTOR pathway genes. Four of 48 cases with focal cortical dysplasia type I (8%) had a likely pathogenic variant in SLC35A2. While no other gene had multiple disease-causing somatic variants across the focal cortical dysplasia type I cohort, four individuals in this group had a single pathogenic or likely pathogenic somatic variant in CASK, KRAS, NF1 and NIPBL, genes previously associated with neurodevelopmental disorders. No rare pathogenic or likely pathogenic somatic variants in any neurological disease genes like those identified in the focal cortical dysplasia type I cohort were found in 63 neurologically normal controls (P = 0.017), suggesting a role for these novel variants. We also identified a somatic loss-of-function variant in the known epilepsy gene, PCDH19, present in a small number of alleles in the dysplastic tissue from a female patient with focal cortical dysplasia IIIa with hippocampal sclerosis. In contrast to focal cortical dysplasia type II, neither focal cortical dysplasia type I nor III had somatic variants in genes that converge on a unifying biological pathway, suggesting greater genetic heterogeneity compared to type II. Importantly, we demonstrate that focal cortical dysplasia types I, II and III are associated with somatic gene variants across a broad range of genes, many associated with epilepsy in clinical syndromes caused by germline variants, as well as including some not previously associated with radiographically evident cortical brain malformations.
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Affiliation(s)
- Dulcie Lai
- Division of Pharmacology and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Meethila Gade
- Division of Pharmacology and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Edward Yang
- Department of Radiology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hyun Yong Koh
- Division of Epilepsy and Clinical Neurophysiology, Department of Neurology, Boston Children's Hospital, Boston, MA 02115, USA.,Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Jinfeng Lu
- Division of Pharmacology and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Nicole M Walley
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Anne F Buckley
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
| | - Tristan T Sands
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, USA.,Department of Neurology, Columbia University Medical Center, New York, NY 10032, USA
| | - Cigdem I Akman
- Department of Neurology, Columbia University Medical Center, New York, NY 10032, USA
| | - Mohamad A Mikati
- Department of Neurobiology, Duke University, Durham, NC 27708, USA.,Division of Pediatric Neurology, Duke University Medical Center, Durham, NC 27710, USA
| | - Guy M McKhann
- Department of Neurosurgery, Columbia University, New York Presbyterian Hospital, New York, NY 10032, USA
| | - James E Goldman
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Peter Canoll
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Allyson L Alexander
- Department of Neurosurgery, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Kristen L Park
- Department of Pediatrics and Neurology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Gretchen K Von Allmen
- Department of Neurology, McGovern Medical School, Houston, TX 77030, USA.,Division of Child Neurology, Department of Pediatrics, McGovern Medical School, Houston, TX 77030, USA
| | - Olga Rodziyevska
- Division of Child Neurology, Department of Pediatrics, McGovern Medical School, Houston, TX 77030, USA
| | | | - Hart G W Lidov
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hannes Vogel
- Department of Pathology, Stanford University, School of Medicine, Stanford, CA 94305, USA
| | - Gerald A Grant
- Department of Neurosurgery, Lucile Packard Children's Hospital at Stanford, School of Medicine, Stanford, CA 94305, USA
| | - Brenda E Porter
- Department of Neurology and Neurological Sciences, Stanford University, School of Medicine, Stanford, CA 94305, USA
| | - Annapurna H Poduri
- Division of Epilepsy and Clinical Neurophysiology, Department of Neurology, Boston Children's Hospital, Boston, MA 02115, USA.,Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Peter B Crino
- Department of Neurology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Erin L Heinzen
- Division of Pharmacology and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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10
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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: 93] [Impact Index Per Article: 46.5] [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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11
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Ruggiero RN, Peixoto-Santos JE, Bueno-Junior LS, Valente KD, Leite JP. Editorial: Psychiatric Comorbidities in the Epilepsies: Extensive Mechanisms and Broad Questions. Front Integr Neurosci 2022; 16:951170. [PMID: 35784497 PMCID: PMC9249385 DOI: 10.3389/fnint.2022.951170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 05/31/2022] [Indexed: 11/20/2022] Open
Affiliation(s)
- Rafael Naime Ruggiero
- Department of Neurosciences and Behavioral Sciences, Ribeirao Preto Medical School, University of São Paulo (USP), Ribeirao Preto, Brazil
- *Correspondence: Rafael Naime Ruggiero
| | - Jose Eduardo Peixoto-Santos
- Neuroscience Sector, Department of Neurology and Neurosurgery, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | | | - Kette D. Valente
- Institute and Department of Psychiatry, Faculty of Medicine of the University of São Paulo (HCFMUSP), São Paulo, Brazil
| | - Joao Pereira Leite
- Department of Neurosciences and Behavioral Sciences, Ribeirao Preto Medical School, University of São Paulo (USP), Ribeirao Preto, Brazil
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12
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Bedrosian TA, Miller KE, Grischow OE, Schieffer KM, LaHaye S, Yoon H, Miller AR, Navarro J, Westfall J, Leraas K, Choi S, Williamson R, Fitch J, Kelly BJ, White P, Lee K, McGrath S, Cottrell CE, Magrini V, Leonard J, Pindrik J, Shaikhouni A, Boué DR, Thomas DL, Pierson CR, Wilson RK, Ostendorf AP, Mardis ER, Koboldt DC. Detection of brain somatic variation in epilepsy-associated developmental lesions. Epilepsia 2022; 63:1981-1997. [PMID: 35687047 DOI: 10.1111/epi.17323] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 06/07/2022] [Accepted: 06/07/2022] [Indexed: 12/15/2022]
Abstract
OBJECTIVE Epilepsy-associated developmental lesions, including malformations of cortical development and low-grade developmental tumors, represent a major cause of drug-resistant seizures requiring surgical intervention in children. Brain-restricted somatic mosaicism has been implicated in the genetic etiology of these lesions; however, many contributory genes remain unidentified. METHODS We enrolled 50 children who were undergoing epilepsy surgery into a translational research study. Resected tissue was divided for clinical neuropathologic evaluation and genomic analysis. We performed exome and RNA sequencing to identify somatic variation and we confirmed our findings using high-depth targeted DNA sequencing. RESULTS We uncovered candidate disease-causing somatic variation affecting 28 patients (56%), as well as candidate germline variants affecting 4 patients (8%). In agreement with previous studies, we identified somatic variation affecting solute carrier family 35 member A2 (SLC35A2) and mechanistic target of rapamycin kinase (MTOR) pathway genes in patients with focal cortical dysplasia. Somatic gains of chromosome 1q were detected in 30% (3 of 10) of patients with Type I focal cortical dysplasia (FCD)s. Somatic variation in mitogen-activated protein kinase (MAPK) pathway genes (i.e., fibroblast growth factor receptor 1 [FGFR1], FGFR2, B-raf proto-oncogene, serine/threonine kinase [BRAF], and KRAS proto-oncogene, GTPase [KRAS]) was associated with low-grade epilepsy-associated developmental tumors. RNA sequencing enabled the detection of somatic structural variation that would have otherwise been missed, and which accounted for more than one-half of epilepsy-associated tumor diagnoses. Sampling across multiple anatomic regions revealed that somatic variant allele fractions vary widely within epileptogenic tissue. Finally, we identified putative disease-causing variants in genes not yet associated with focal cortical dysplasia. SIGNIFICANCE These results further elucidate the genetic basis of structural brain abnormalities leading to focal epilepsy in children and point to new candidate disease genes.
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Affiliation(s)
- Tracy A Bedrosian
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Katherine E Miller
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Olivia E Grischow
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Kathleen M Schieffer
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Stephanie LaHaye
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Hyojung Yoon
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Anthony R Miller
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Jason Navarro
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Jesse Westfall
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Kristen Leraas
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Samantha Choi
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Rachel Williamson
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - James Fitch
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Benjamin J Kelly
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Peter White
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Kristy Lee
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA.,Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Sean McGrath
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Catherine E Cottrell
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Vincent Magrini
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Jeffrey Leonard
- Department of Neurosurgery, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Neurosurgery, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Jonathan Pindrik
- Department of Neurosurgery, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Neurosurgery, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Ammar Shaikhouni
- Department of Neurosurgery, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Neurosurgery, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Daniel R Boué
- Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio, USA.,Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Division of Anatomy, Department of Biomedical Education & Anatomy, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Diana L Thomas
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Christopher R Pierson
- Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio, USA.,Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Division of Anatomy, Department of Biomedical Education & Anatomy, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Richard K Wilson
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Adam P Ostendorf
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA.,Division of Pediatric Neurology, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Elaine R Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA.,Department of Neurosurgery, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Daniel C Koboldt
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
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13
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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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14
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Koelsche C, von Deimling A. Methylation classifiers: brain tumors, sarcomas and what's next. Genes Chromosomes Cancer 2022; 61:346-355. [PMID: 35388566 DOI: 10.1002/gcc.23041] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/16/2022] [Accepted: 03/18/2022] [Indexed: 11/09/2022] Open
Abstract
Tumor classification has evolved over the last decades with technical progress contributing much to our current concepts. Among diagnostic hallmark novelties were immunostaining, Fluorescence in situ hybridization, Sanger sequencing followed by massive parallel DNA sequencing and recently, epigenetic analyses have entered the stage. Although each of these techniques was revolutionary and, in some way, also disruptive in certain diagnostic fields, it took years to decades for broad implementation into standard pathological-diagnostic algorithms. In contrast, DNA methylation profiling has been accepted in short time as a game changer with lasting impact on brain tumor classification and with potential for classification of other tumor types. This review provides a brief introduction in DNA methylation-based tumor classification. We present why DNA methylation signatures are attractive diagnostic biomarkers, discuss present achievements and future aims and explain the integration of methylation-based classifiers in diagnostic procedure. Finally, we provide an outlook on the challenges and opportunities associated with DNA methylation-based tumor profiling. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Christian Koelsche
- Department of General Pathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
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15
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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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16
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Genetic mosaicism in the human brain: from lineage tracing to neuropsychiatric disorders. Nat Rev Neurosci 2022; 23:275-286. [PMID: 35322263 DOI: 10.1038/s41583-022-00572-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2022] [Indexed: 12/18/2022]
Abstract
Genetic mosaicism is the result of the accumulation of somatic mutations in the human genome starting from the first postzygotic cell generation and continuing throughout the whole life of an individual. The rapid development of next-generation and single-cell sequencing technologies is now allowing the study of genetic mosaicism in normal tissues, revealing unprecedented insights into their clonal architecture and physiology. The somatic variant repertoire of an adult human neuron is the result of somatic mutations that accumulate in the brain by different mechanisms and at different rates during development and ageing. Non-pathogenic developmental mutations function as natural barcodes that once identified in deep bulk or single-cell sequencing can be used to retrospectively reconstruct human lineages. This approach has revealed novel insights into the clonal structure of the human brain, which is a mosaic of clones traceable to the early embryo that contribute differentially to the brain and distinct areas of the cortex. Some of the mutations happening during development, however, have a pathogenic effect and can contribute to some epileptic malformations of cortical development and autism spectrum disorder. In this Review, we discuss recent findings in the context of genetic mosaicism and their implications for brain development and disease.
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17
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Eukaryotic translation initiation factor 4E binding protein 1 (EIF4EBP1) expression in glioblastoma is driven by ETS1- and MYBL2-dependent transcriptional activation. Cell Death Dis 2022; 8:91. [PMID: 35228525 PMCID: PMC8885828 DOI: 10.1038/s41420-022-00883-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/04/2022] [Accepted: 02/10/2022] [Indexed: 12/13/2022]
Abstract
Eukaryotic translation initiation factor 4E binding protein 1 (EIF4EBP1) encodes the 4EBP1 protein, a negative regulator of mRNA translation and a substrate of the mechanistic target of rapamycin (mTOR), whose function and relevance in cancer is still under debate. Here, we analyzed EIF4EBP1 expression in different glioma patient cohorts and investigated its mode of transcriptional regulation in glioblastoma cells. We verified that EIF4EBP1 mRNA is overexpressed in malignant gliomas, including isocitrate dehydrogenase (IDH)-wildtype glioblastomas, relative to non-neoplastic brain tissue in multiple publically available datasets. Our analyses revealed that EIF4EBP1 overexpression in malignant gliomas is neither due to gene amplification nor to altered DNA methylation, but rather results from aberrant transcriptional activation by distinct transcription factors. We found seven transcription factor candidates co-expressed with EIF4EBP1 in gliomas and bound to the EIF4EBP1 promoter, as revealed by chromatin immunoprecipitation (ChIP)-sequencing data. We investigated the ability of these candidates to activate the EIF4EBP1 promoter using luciferase reporter assays, which supported four transcription factors as candidate EIF4EBP1 regulators, namely MYBL2, ETS1, HIF-1A, and E2F6. Finally, by employing transient knock-down experiments to repress either of these transcription factors, we identified MYBL2 and ETS1 as the relevant transcriptional drivers of enhanced EIF4EBP1 expression in malignant glioma cells. Taken together, our findings confirm enhanced expression of EIF4EBP1 in malignant gliomas relative to non-neoplastic brain tissue and characterize the underlying molecular pathomechanisms.
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18
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Gilani A, Kleinschmidt-DeMasters BK. Histopathologic features of nasal glial heterotopia (nasal glioma). Childs Nerv Syst 2022; 38:63-75. [PMID: 34562130 DOI: 10.1007/s00381-021-05369-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/19/2021] [Indexed: 11/24/2022]
Abstract
PURPOSE Nasal glioneuronal heterotopia (NGH) is an uncommon developmental abnormality of the nasal cavity or paranasal soft tissue. Few detailed histologic studies of NGH exist, and molecular analyses have not been performed to date. METHODS We describe six cases of pediatric NGH and two representative encephaloceles encountered in our practice over the past 20 years. RESULTS Two clinically distinct patient groups were noted, those with 1) intranasal nasal cavity mass (n = 3), or 2) extranasal cutaneous mass on the nose (n = 3, 1 on nasal apex, 2 on nasal bridge). Intranasal cases presented within the first week of life, whereas the extranasal NGH presented at ages of 4, 7, and 8 months. Resection was curative in 5/6 cases, with a single case showing local recurrence. Histologic examination showed a predominantly glial cell composition, with nests of GFAP-immunoreactive neuropil containing large, often multinucleated astrocytes. Neurons, although difficult to identify on H&E-stains, were readily observed in all cases by NeuN-immunostain. At least focal leptomeninges were noted in 2/3 intranasal and 1/3 extranasal NGHs on routine histology, SSTR2A immunohistochemistry further confirmed leptomeninges/ arachnoid cells in 4/6 cases. 1 of 4 NGH (extranasal) cases showed copy number variations in chromosome 16, 17 and 19, which were also present in 1/2 encephalocele cases. The full significance of these alterations remains unknown. CONCLUSION We find evidence of histologic overlap between NGH and encephalocele, and, for the first time, report molecular alterations shared between the two entities, suggesting that these conditions may represent spectrum of the same histopathologic entity.
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Affiliation(s)
- A Gilani
- Department of Pathology, University of Colorado, Children's Hospital Colorado, Aurora, CO, USA.
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19
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Jabari S, Kobow K, Pieper T, Hartlieb T, Kudernatsch M, Polster T, Bien CG, Kalbhenn T, Simon M, Hamer H, Rössler K, Feucht M, Mühlebner A, Najm I, Peixoto-Santos JE, Gil-Nagel A, Delgado RT, Aledo-Serrano A, Hou Y, Coras R, von Deimling A, Blümcke I. DNA methylation-based classification of malformations of cortical development in the human brain. Acta Neuropathol 2022; 143:93-104. [PMID: 34797422 PMCID: PMC8732912 DOI: 10.1007/s00401-021-02386-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/26/2021] [Accepted: 11/15/2021] [Indexed: 12/16/2022]
Abstract
Malformations of cortical development (MCD) comprise a broad spectrum of structural brain lesions frequently associated with epilepsy. Disease definition and diagnosis remain challenging and are often prone to arbitrary judgment. Molecular classification of histopathological entities may help rationalize the diagnostic process. We present a retrospective, multi-center analysis of genome-wide DNA methylation from human brain specimens obtained from epilepsy surgery using EPIC 850 K BeadChip arrays. A total of 308 samples were included in the study. In the reference cohort, 239 formalin-fixed and paraffin-embedded (FFPE) tissue samples were histopathologically classified as MCD, including 12 major subtype pathologies. They were compared to 15 FFPE samples from surgical non-MCD cortices and 11 FFPE samples from post-mortem non-epilepsy controls. We applied three different statistical approaches to decipher the DNA methylation pattern of histopathological MCD entities, i.e., pairwise comparison, machine learning, and deep learning algorithms. Our deep learning model, which represented a shallow neuronal network, achieved the highest level of accuracy. A test cohort of 43 independent surgical samples from different epilepsy centers was used to test the precision of our DNA methylation-based MCD classifier. All samples from the test cohort were accurately assigned to their disease classes by the algorithm. These data demonstrate DNA methylation-based MCD classification suitability across major histopathological entities amenable to epilepsy surgery and age groups and will help establish an integrated diagnostic classification scheme for epilepsy-associated MCD.
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Affiliation(s)
- Samir Jabari
- Department of Neuropathology, Affiliated Partner of the ERN EpiCARE, Universitätsklinikum Erlangen, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Katja Kobow
- Department of Neuropathology, Affiliated Partner of the ERN EpiCARE, Universitätsklinikum Erlangen, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany.
| | - Tom Pieper
- Center for Pediatric Neurology, Neurorehabilitation and Epileptology, Vogtareuth, Germany
| | - Till Hartlieb
- Center for Pediatric Neurology, Neurorehabilitation and Epileptology, Vogtareuth, Germany
- Research Institute, Rehabilitation, Transition, Palliation", PMU Salzburg, Salzburg, Austria
| | - Manfred Kudernatsch
- Center for Neurosurgery and Epilepsy Surgery, Schön Klinik Vogtareuth, Vogtareuth, Germany
- Research Institute, Rehabilitation, Transition, Palliation", PMU Salzburg, Salzburg, Austria
| | - Tilman Polster
- Department of Epileptology (Krankenhaus Mara), Medical School, Bielefeld University, Bielefeld, Germany
| | - Christian G Bien
- Department of Epileptology (Krankenhaus Mara), Medical School, Bielefeld University, Bielefeld, Germany
| | - Thilo Kalbhenn
- Department of Neurosurgery - Epilepsy Surgery, Evangelisches Klinikum Bethel, Universitätsklinikum OWL, Bielefeld University, Bielefeld, Germany
| | - Matthias Simon
- Department of Neurosurgery - Epilepsy Surgery, Evangelisches Klinikum Bethel, Universitätsklinikum OWL, Bielefeld University, Bielefeld, Germany
| | - Hajo Hamer
- Department of Neurology, Epilepsy Center, Universitätsklinikum Erlangen, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Karl Rössler
- Department of Neurosurgery, Universitätsklinikum Erlangen, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
- Department of Neurosurgery, Medical University Vienna, Vienna, Austria
| | - Martha Feucht
- Department of Pediatrics and Adolescent Medicine, Affiliated Partner of the ERN EpiCARE, Medical University Vienna, Vienna, Austria
| | - Angelika Mühlebner
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of (Neuro) Pathology, Amsterdam UMC, Location AMC, Amsterdam, The Netherlands
| | - Imad Najm
- Charles Shor Epilepsy Center, Cleveland Clinic, Cleveland, OH, USA
- Department of Neurology, Cleveland Clinic, Cleveland, OH, USA
| | | | | | | | | | - Yanghao Hou
- Department of Neuropathology, German Cancer Research Center (DKFZ), Universitätsklinikum Heidelberg, and CCU Neuropathology, Heidelberg, Germany
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Roland Coras
- Department of Neuropathology, Affiliated Partner of the ERN EpiCARE, Universitätsklinikum Erlangen, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Andreas von Deimling
- Department of Neuropathology, German Cancer Research Center (DKFZ), Universitätsklinikum Heidelberg, and CCU Neuropathology, Heidelberg, Germany
| | - Ingmar Blümcke
- Department of Neuropathology, Affiliated Partner of the ERN EpiCARE, Universitätsklinikum Erlangen, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
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20
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Holthausen H, Coras R, Tang Y, Bai L, Wang I, Pieper T, Kudernatsch M, Hartlieb T, Staudt M, Winkler P, Hofer W, Jabari S, Kobow K, Blumcke I. Multilobar unilateral hypoplasia with emphasis on the posterior quadrant and severe epilepsy in children with FCD ILAE Type 1A. Epilepsia 2021; 63:42-60. [PMID: 34741301 DOI: 10.1111/epi.17114] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 10/08/2021] [Accepted: 10/18/2021] [Indexed: 02/05/2023]
Abstract
OBJECTIVE Focal cortical dysplasia (FCD) Type 1 and its three subtypes have yet not been fully characterized at the clinical, anatomopathological, and molecular level (International League Against Epilepsy [ILAE] FCD classification from 2011). We aimed to describe the clinical phenotype of patients with histopathologically confirmed FCD1A obtained from a single epilepsy center between 2002 and 2016. METHODS Medical records were retrieved from the hospital's archive. Results from electroencephalography (EEG) video recordings, neuroimaging, and histopathology were reevaluated. Magnetic resonance imaging (MRI) post-processing was retrospectively performed in nine patients. DNA methylation studies were carried out from archival surgical brain tissue in 11 patients. RESULTS Nineteen children with a histopathological diagnosis of FCD1A were included. The average onset of epilepsy was 0.9 years (range 0.2-10 years). All children had severe cognitive impairment and one third had mild motor deficits, yet fine finger movements were preserved in all patients. All patients had daily seizures, being drug resistant from disease onset. Interictal electroencephalography revealed bilateral multi-regional epileptiform discharges. Interictal status epilepticus was observed in 8 and countless subclinical seizures in 11 patients. Regional continuous irregular slow waves were of higher lateralizing and localizing yield than spikes. Posterior background rhythms were normal in 16 of 19 children. Neuroimaging showed unilateral multilobar hypoplasia and increased T2-FLAIR signals of the white matter in 18 of 19 patients. All children underwent tailored multilobar resections, with seizure freedom achieved in 47% (Engel class I). There was no case with frontal involvement without involvement of the posterior quadrant by MRI and histopathology. DNA methylation profiling distinguished FCD1A samples from all other epilepsy specimens and controls. SIGNIFICANCE We identified a cohort of young children with drug resistance from seizure onset, bad EEG with posterior emphasis, lack of any focal neurological deficits but severe cognitive impairment, subtle hypoplasia of the epileptogenic area on MRI, and histopathologically defined and molecularly confirmed by DNA methylation analysis as FCD ILAE Type 1A.
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Affiliation(s)
- Hans Holthausen
- Center for Pediatric Neurology, Neurorehabilitation, and Epileptology, Schoen-Clinic, Vogtareuth, Germany
| | - Roland Coras
- Department of Neuropathology, University Hospitals Erlangen, Erlangen, Germany
| | - Yingying Tang
- Department of Neurology, West China Hospital of Sichuan University, Chengdu, Sichuan, China.,Epilepsy Center, Cleveland Clinic, Cleveland, Ohio, USA
| | - Lily Bai
- Epilepsy Center, Cleveland Clinic, Cleveland, Ohio, USA
| | - Irene Wang
- Epilepsy Center, Cleveland Clinic, Cleveland, Ohio, USA
| | - Tom Pieper
- Center for Pediatric Neurology, Neurorehabilitation, and Epileptology, Schoen-Clinic, Vogtareuth, Germany
| | - Manfred Kudernatsch
- Center for Pediatric Neurology, Neurorehabilitation, and Epileptology, Schoen-Clinic, Vogtareuth, Germany.,Paracelsus Private Medical University, Salzburg, Austria
| | - Till Hartlieb
- Center for Pediatric Neurology, Neurorehabilitation, and Epileptology, Schoen-Clinic, Vogtareuth, Germany.,Paracelsus Private Medical University, Salzburg, Austria
| | - Martin Staudt
- Center for Pediatric Neurology, Neurorehabilitation, and Epileptology, Schoen-Clinic, Vogtareuth, Germany
| | - Peter Winkler
- Center for Pediatric Neurology, Neurorehabilitation, and Epileptology, Schoen-Clinic, Vogtareuth, Germany
| | - Wiebke Hofer
- Center for Pediatric Neurology, Neurorehabilitation, and Epileptology, Schoen-Clinic, Vogtareuth, Germany
| | - Samir Jabari
- Department of Neuropathology, University Hospitals Erlangen, Erlangen, Germany
| | - Katja Kobow
- Department of Neuropathology, University Hospitals Erlangen, Erlangen, Germany
| | - Ingmar Blumcke
- Department of Neuropathology, University Hospitals Erlangen, Erlangen, Germany.,Epilepsy Center, Cleveland Clinic, Cleveland, Ohio, USA
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21
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Jablonski J, Hoffmann L, Blümcke I, Fejtová A, Uebe S, Ekici AB, Gnatkovsky V, Kobow K. Experimental Epileptogenesis in a Cell Culture Model of Primary Neurons from Rat Brain: A Temporal Multi-Scale Study. Cells 2021; 10:cells10113004. [PMID: 34831225 PMCID: PMC8616120 DOI: 10.3390/cells10113004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/27/2021] [Accepted: 11/02/2021] [Indexed: 12/24/2022] Open
Abstract
Understanding seizure development requires an integrated knowledge of different scales of organization of epileptic networks. We developed a model of “epilepsy-in-a-dish” based on dissociated primary neuronal cells from neonatal rat hippocampus. We demonstrate how a single application of glutamate stimulated neurons to generate spontaneous synchronous spiking activity with further progression into spontaneous seizure-like events after a distinct latency period. By computational analysis, we compared the observed neuronal activity in vitro with intracranial electroencephalography (EEG) data recorded from epilepsy patients and identified strong similarities, including a related sequence of events with defined onset, progression, and termination. Next, a link between the neurophysiological changes with network composition and cellular structure down to molecular changes was established. Temporal development of epileptiform network activity correlated with increased neurite outgrowth and altered branching, increased ratio of glutamatergic over GABAergic synapses, and loss of calbindin-positive interneurons, as well as genome-wide alterations in DNA methylation. Differentially methylated genes were engaged in various cellular activities related to cellular structure, intracellular signaling, and regulation of gene expression. Our data provide evidence that a single short-term excess of glutamate is sufficient to induce a cascade of events covering different scales from molecule- to network-level, all of which jointly contribute to seizure development.
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Affiliation(s)
- Janos Jablonski
- Department of Neuropathology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (J.J.); (L.H.); (I.B.)
| | - Lucas Hoffmann
- Department of Neuropathology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (J.J.); (L.H.); (I.B.)
| | - Ingmar Blümcke
- Department of Neuropathology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (J.J.); (L.H.); (I.B.)
| | - Anna Fejtová
- Department of Psychiatry and Psychotherapy, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany;
| | - Steffen Uebe
- NGS Core Unit, Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (S.U.); (A.B.E.)
| | - Arif B. Ekici
- NGS Core Unit, Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (S.U.); (A.B.E.)
| | - Vadym Gnatkovsky
- Department of Epileptology, University Hospital Bonn, 53127 Bonn, Germany;
| | - Katja Kobow
- Department of Neuropathology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (J.J.); (L.H.); (I.B.)
- Correspondence: ; Tel.: +49-9131-8522859
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22
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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: 30] [Impact Index Per Article: 10.0] [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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23
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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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24
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Blumcke I, Cendes F, Miyata H, Thom M, Aronica E, Najm I. Toward a refined genotype-phenotype classification scheme for the international consensus classification of Focal Cortical Dysplasia. Brain Pathol 2021; 31:e12956. [PMID: 34196989 PMCID: PMC8412090 DOI: 10.1111/bpa.12956] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 03/18/2021] [Indexed: 12/28/2022] Open
Abstract
Focal Cortical Dysplasia (FCD) is the most common cause of drug-resistant focal epilepsy in children and young adults. The diagnosis of currently defined FCD subtypes relies on a histopathological assessment of surgical brain tissue. The many ongoing challenges in the diagnosis of FCD and their various subtypes mandate, however, continuous research and consensus agreement to develop a reliable classification scheme. Advanced neuroimaging and genetic studies have proven to augment the diagnosis of FCD subtypes and should be considered for an integrated clinico-pathological and molecular classification. In this review, we will discuss the histopathological foundation of the current FCD classification and potential advancements when using genetic analysis of somatic brain mutations in neurosurgically resected brain specimens and postprocessing of presurgical neuroimaging data. Combining clinical, imaging, histopathology, and molecular studies will help to define the disease spectrum better and finally unveil FCD-specific treatment options.
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Affiliation(s)
- Ingmar Blumcke
- Department of NeuropathologyUniversity Hospital ErlangenFriedrich‐Alexander‐University Erlangen‐NürnbergErlangenGermany
- Epilepsy CenterCleveland Clinic FoundationClevelandOHUSA
| | - Fernando Cendes
- Department of NeurologyUniversity of Campinas—UNICAMPCampinasSPBrazil
| | - Hajime Miyata
- Department of NeuropathologyResearch Institute for Brain and Blood VesselsAkita Cerebrospinal and Cardiovascular CenterAkitaJapan
| | - Maria Thom
- Department of NeuropathologyInstitute of Neurology, University College LondonLondonUK
| | - Eleonora Aronica
- Department of (Neuro)PathologyAmsterdam UMCUniversity of AmsterdamAmsterdam
- Stichting Epilepsie Instellingen Nederland (SEINHeemstedeThe Netherlands
| | - Imad Najm
- Epilepsy CenterCleveland Clinic FoundationClevelandOHUSA
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Maury EA, Walsh CA. Somatic copy number variants in neuropsychiatric disorders. Curr Opin Genet Dev 2021; 68:9-17. [PMID: 33444936 PMCID: PMC8205940 DOI: 10.1016/j.gde.2020.12.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/19/2020] [Accepted: 12/22/2020] [Indexed: 01/11/2023]
Abstract
Copy number variants (CNVs) have been implicated in neuropsychiatric disorders, with rare-inherited and de novo CNVs (dnCNVs) having large effects on disease liability. Recent studies started exploring a class of dnCNVs that occur post-zygotically, and are therefore present in some but not all cells of the body. Analogous to conditional mutations in animal models, the presence of risk mutations in a fraction of cells has the potential to enlighten how damaging mutations affect cell-type/cell-circuit specific pathologies leading to neuropsychiatric manifestations. Although mosaic CNVs appear to contribute to a modest fraction of risk (0.3-0.5%), expanding our insights about them with more sensitive experimental and statistical methods, has the potential to help clarify mechanisms of neuropsychiatric disease.
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Affiliation(s)
- Eduardo A Maury
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA; Bioinformatics & Integrative Genomics Program and Harvard/MIT MD-PHD Program, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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