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Han P, Welsh CT, Smith MT, Schmidt RE, Carroll SL. Complex Patterns of GABAergic Neuronal Deficiency and Type 2 Potassium-Chloride Cotransporter Immaturity in Human Focal Cortical Dysplasia. J Neuropathol Exp Neurol 2020; 78:365-372. [PMID: 30856249 DOI: 10.1093/jnen/nlz009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Focal cortical dysplasia (FCD) is a common histopathologic finding in cortical specimens resected for refractory epilepsy. GABAergic neuronal abnormalities and K-Cl cotransporter type 2 (KCC2) immaturity may be contributing factors for FCD-related epilepsy. We examined surgical specimens from 12 cases diagnosed with FCD, and brain tissues without developmental abnormality obtained from 6 autopsy cases. We found that GABAergic neuronal density was abnormal in FCD with 2 distinct patterns. In 7 of 12 (58%) FCD subjects, the GABAergic neuron density in dysplastic regions and in neighboring nondysplastic regions was equally reduced, hence we call this a "broad pattern." In the remaining cases, GABAergic neuron density was decreased in dysplastic regions but not in the neighboring nondysplastic regions; we designate this "restricted pattern." The different patterns are not associated with pathologic subtypes of FCD. Intracytoplasmic retention of KCC2 is evident in dysmorphic neurons in the majority of FCD type II subjects (5/7) but not in FCD type I. Our study suggests that (1) "broad" GABAergic deficiency may reflect epileptic vulnerability outside the dysplastic area; and (2) abnormal distribution of KCC2 may contribute to seizure generation in patients with FCD type II but not in type I.
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Affiliation(s)
- Pengcheng Han
- Department of Pathology and Laboratory Medicine.,Department of Pathology and Laboratory Medicine Residency Program, Medical University of South Carolina, Charleston, South Carolina
| | | | | | - Robert E Schmidt
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
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Tisza MJ, Pastrana DV, Welch NL, Stewart B, Peretti A, Starrett GJ, Pang YYS, Krishnamurthy SR, Pesavento PA, McDermott DH, Murphy PM, Whited JL, Miller B, Brenchley J, Rosshart SP, Rehermann B, Doorbar J, Ta'ala BA, Pletnikova O, Troncoso JC, Resnick SM, Bolduc B, Sullivan MB, Varsani A, Segall AM, Buck CB. Discovery of several thousand highly diverse circular DNA viruses. eLife 2020; 9:51971. [PMID: 32014111 PMCID: PMC7000223 DOI: 10.7554/elife.51971] [Citation(s) in RCA: 116] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 01/06/2020] [Indexed: 12/18/2022] Open
Abstract
Although millions of distinct virus species likely exist, only approximately 9000 are catalogued in GenBank's RefSeq database. We selectively enriched for the genomes of circular DNA viruses in over 70 animal samples, ranging from nematodes to human tissue specimens. A bioinformatics pipeline, Cenote-Taker, was developed to automatically annotate over 2500 complete genomes in a GenBank-compliant format. The new genomes belong to dozens of established and emerging viral families. Some appear to be the result of previously undescribed recombination events between ssDNA and ssRNA viruses. In addition, hundreds of circular DNA elements that do not encode any discernable similarities to previously characterized sequences were identified. To characterize these ‘dark matter’ sequences, we used an artificial neural network to identify candidate viral capsid proteins, several of which formed virus-like particles when expressed in culture. These data further the understanding of viral sequence diversity and allow for high throughput documentation of the virosphere. When scientists hunt for new DNA sequences, sometimes they get a lot more than they bargained for. Such is the case in metagenomic surveys, which analyze not just DNA of a particular organism, but all the DNA in an environment at large. A vexing problem with these surveys is the overwhelming number of DNA sequences detected that are so different from any known microbe that they cannot be classified using traditional approaches. However, some of these “known unknowns” are undoubtedly viral sequences, because only a fraction of the enormous diversity of viruses has been characterized. This “viral dark matter” is a major obstacle for those studying viruses. This led Tisza et al. to attempt to classify some of the unknown viral sequences in their metagenomic surveys. The search, which specifically focused on viruses with circular DNA genomes, detected over 2,500 circular viral genomes. Intensive analysis revealed that many of these genomes had similar makeup to previously discovered viruses, but hundreds of them were totally different from any known virus, based on typical methods of comparison. Computational analysis of genes that were conserved among some of these brand-new circular sequences often revealed virus-like features. Experiments on a few of these genes showed that they encoded proteins capable of forming particles reminiscent of characteristic viral shells, implying that these new sequences are indeed viruses. Tisza et al. have added the 2,500 newly characterized viral sequences to the publicly accessible GenBank database, and the sequences are being considered for the more authoritative RefSeq database, which currently contains around 9,000 complete viral genomes. The expanded databases will hopefully now better equip scientists to explore the enormous diversity of viruses and help medics and veterinarians to detect disease-causing viruses in humans and other animals.
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Affiliation(s)
- Michael J Tisza
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Diana V Pastrana
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Nicole L Welch
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Brittany Stewart
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Alberto Peretti
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Gabriel J Starrett
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Yuk-Ying S Pang
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Siddharth R Krishnamurthy
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States
| | - Patricia A Pesavento
- Department of Pathology, Microbiology, and Immunology, University of California, Davis, Davis, United States
| | - David H McDermott
- Molecular Signaling Section, Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States
| | - Philip M Murphy
- Molecular Signaling Section, Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States
| | - Jessica L Whited
- Department of Orthopedic Surgery, Harvard Medical School, The Harvard Stem Cell Institute, Brigham and Women's Hospital, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, United States
| | - Bess Miller
- Department of Orthopedic Surgery, Harvard Medical School, The Harvard Stem Cell Institute, Brigham and Women's Hospital, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Jason Brenchley
- Barrier Immunity Section, Lab of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Cambridge, United States
| | - Stephan P Rosshart
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
| | - Barbara Rehermann
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
| | - John Doorbar
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | | | - Olga Pletnikova
- Department of Pathology (Neuropathology), Johns Hopkins University School of Medicine, Baltimore, United States
| | - Juan C Troncoso
- Department of Pathology (Neuropathology), Johns Hopkins University School of Medicine, Baltimore, United States
| | - Susan M Resnick
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, United States
| | - Ben Bolduc
- Department of Microbiology, Ohio State University, Columbus, United States
| | - Matthew B Sullivan
- Department of Microbiology, Ohio State University, Columbus, United States.,Civil Environmental and Geodetic Engineering, Ohio State University, Columbus, United States
| | - Arvind Varsani
- The Biodesign Center of Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, United States.,Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Rondebosch, South Africa
| | - Anca M Segall
- Viral Information Institute and Department of Biology, San Diego State University, San Diego, United States
| | - Christopher B Buck
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
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Iffland PH, Crino PB. Focal Cortical Dysplasia: Gene Mutations, Cell Signaling, and Therapeutic Implications. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2017; 12:547-571. [PMID: 28135561 DOI: 10.1146/annurev-pathol-052016-100138] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Focal cortical dysplasias (FCDs) are malformations of cortical development (MCDs) that are highly associated with medication-resistant epilepsy and are the most common cause of neocortical epilepsy in children. FCDs are a heterogeneous group of developmental disorders caused by germline or somatic mutations that occur in genes regulating the PI3K/Akt/mTOR pathway-a key pathway in neuronal growth and migration. Accordingly, FCDs are characterized by abnormal cortical lamination, cell morphology (e.g., cytomegaly), and cellular polarity. In some FCD subtypes, balloon cells express proteins typically seen in neuroglial progenitor cells. Because recurrent intractable seizures are a common feature of FCDs, epileptogenic electrophysiological properties are also observed in addition to local inflammation. Here, we will summarize the current literature regarding FCDs, addressing the current classification system, histopathology, molecular genetics, electrophysiology, and transcriptome and cell signaling changes.
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Affiliation(s)
- Philip H Iffland
- Shriners Hospitals Pediatric Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania 19140;
| | - Peter B Crino
- Department of Neurology, University of Maryland School of Medicine, Baltimore, Maryland 21201;
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Guerrini R, Duchowny M, Jayakar P, Krsek P, Kahane P, Tassi L, Melani F, Polster T, Andre VM, Cepeda C, Krueger DA, Cross JH, Spreafico R, Cosottini M, Gotman J, Chassoux F, Ryvlin P, Bartolomei F, Bernasconi A, Stefan H, Miller I, Devaux B, Najm I, Giordano F, Vonck K, Barba C, Blumcke I. Diagnostic methods and treatment options for focal cortical dysplasia. Epilepsia 2015; 56:1669-86. [DOI: 10.1111/epi.13200] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/21/2015] [Indexed: 12/16/2022]
Affiliation(s)
- Renzo Guerrini
- Pediatric Neurology and Neurogenetics Unit and Laboratories; Children's Hospital Meyer-University of Florence; Florence Italy
- IRCCS Stella Maris Foundation; Pisa Italy
| | - Michael Duchowny
- Neuroscience Program and the Comprehensive Epilepsy Center; Miami Children's Hospital; Miami Florida U.S.A
| | - Prasanna Jayakar
- Department of Neurology; Miami Children's Hospital; Miami Florida U.S.A
| | - Pavel Krsek
- Department of Pediatric Neurology; 2nd Faculty of Medicine; Motol University Hospital; Charles University; Prague Czech Republic
| | - Philippe Kahane
- INSERM U836; University of Grenoble Alpes, GIN; Grenoble; France
- Epilepsy Unit; Michallon Hospital; Grenoble France
| | - Laura Tassi
- Epilepsy Surgery Center; Niguarda Hospital; Milan Italy
| | - Federico Melani
- Pediatric Neurology and Neurogenetics Unit and Laboratories; Children's Hospital Meyer-University of Florence; Florence Italy
| | - Tilman Polster
- Department of Child Neurology; Bethel Epilepsy Center; Bielefeld Germany
| | | | - Carlos Cepeda
- Intellectual and Developmental Disabilities Research Center; David Geffen School of Medicine; University of California at Los Angeles; Los Angeles California U.S.A
| | - Darcy A. Krueger
- Division of Neurology; Department of Pediatrics; Cincinnati Children's Hospital Medical Center; University of Cincinnati College of Medicine; Cincinnati Ohio U.S.A
| | - J. Helen Cross
- UCL-Institute of Child Health; Great Ormond Street Hospital for Children NHS Foundation Trust; London United Kingdom
- Young Epilepsy; Lingfield United Kingdom
| | - Roberto Spreafico
- Clinical Epileptology and Experimental Neurophysiology Unit; Neurological InstituteC. Besta”; Milan Italy
| | - Mirco Cosottini
- Department of Translational Research and New Technologies in Medicine and Surgery; University of Pisa; Pisa Italy
| | - Jean Gotman
- Montreal Neurological Institute and Hospital; McGill University; Montreal Quebec Canada
| | | | - Philippe Ryvlin
- Department of Clinical Neurosciences; CHUV; Lausanne Switzerland
- Translational and Integrative Group in Epilepsy Research (TIGER) and Institute for Epilepsies (IDEE); Lyon's Neuroscience Center; INSERM U1028; CNRS 5292; UCBL; Le Vinatier Hospital; Bron; Lyon France
| | - Fabrice Bartolomei
- Faculty of Medicine; INSERM, U1106; Institute of Neurosciences of Systems; Marseille France
- Faculty of Medicine; Aix Marseille University; Marseille France
- Clinical Neurophysiology Unit; Department of Clinical Neurosciences; CHU Timone; Marseille France
- Henri-Gastaut Hospital; Saint-Paul Center; Marseille France
| | - Andrea Bernasconi
- Neuroimaging of Epilepsy Laboratory; McConnell Brain Imaging Center; Montreal Neurological Institute and Hospital; McGill University; Montreal Quebec Canada
| | - Hermann Stefan
- Epilepsy Center Erlangen (ZEE); University Erlangen-Nürnberg; Erlangen Germany
| | - Ian Miller
- Department of Neurology and Comprehensive Epilepsy Program; Brain Institute; Miami Children's Hospital; Miami Florida U.S.A
| | | | - Imad Najm
- Epilepsy Center; Neurological Institute; Cleveland Clinic; Cleveland OH U.S.A
| | - Flavio Giordano
- Pediatric Neurosurgery Unit; Children's Hospital Meyer-University of Florence; Florence Italy
| | - Kristl Vonck
- Laboratory for Clinical and Experimental Neurophysiology, Neurobiology and Neuropsychology; Department of Neurology; Ghent University; Ghent Belgium
| | - Carmen Barba
- Pediatric Neurology and Neurogenetics Unit and Laboratories; Children's Hospital Meyer-University of Florence; Florence Italy
| | - Ingmar Blumcke
- Department of Neuropathology; University Hospital Erlangen; Erlangen Germany
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