Maurits W C B Sanders, Bobby P C Koeleman, Eva H Brilstra, Floor E Jansen, Sara Baldassari, Mathilde Chipaux, Nam Suk Sim, Ara Ko, Hoon-Chul Kang, Ingmar Blümcke, Dennis Lal, Stéphanie Baulac, Jeong Ho Lee, Eleonora Aronica, Kees P J Braun
We studied the distribution of germline and somatic variants in epilepsy surgery patients with (suspected) malformations of cortical development (MCD) who underwent surgery between 2015 and 2020 at University Medical Center Utrecht (the Netherlands) and pooled our data with four previously published cohort studies. Tissue analysis yielded a pathogenic variant in 203 of 663 (31%) combined cases. In 126 of 379 (33%) focal cortical dysplasia (FCD) type II cases and 23 of 37 (62%) hemimegalencephaly cases, a pathogenic variant was identified, mostly involving the mTOR signaling pathway. Pathogenic variants in 10 focal epilepsy genes were found in 48 of 178 (27%) FCDI/mild MCD/mMCD with oligodendroglial hyperplasia and epilepsy cases; 36 of these (75%) were SLC35A2 variants. Six of 69 (9%) patients without a histopathological lesion had a pathogenic variant in SLC35A2 (n = 5) or DEPDC5 (n = 1). A germline variant in blood DNA was confirmed in all cases with a pathogenic variant in tissue, with a variant allele frequency (VAF) of ~50%. In seven of 114 patients (6%) with a somatic variant in tissue, mosaicism in blood was detected. More than half of pathogenic somatic variants had a VAF < 5%. Further analysis of the correlation between genetic variants and surgical outcomes will improve patient counseling and may guide postoperative treatment decisions.
{"title":"Somatic variant analysis of resected brain tissue in epilepsy surgery patients.","authors":"Maurits W C B Sanders, Bobby P C Koeleman, Eva H Brilstra, Floor E Jansen, Sara Baldassari, Mathilde Chipaux, Nam Suk Sim, Ara Ko, Hoon-Chul Kang, Ingmar Blümcke, Dennis Lal, Stéphanie Baulac, Jeong Ho Lee, Eleonora Aronica, Kees P J Braun","doi":"10.1111/epi.18148","DOIUrl":"https://doi.org/10.1111/epi.18148","url":null,"abstract":"<p><p>We studied the distribution of germline and somatic variants in epilepsy surgery patients with (suspected) malformations of cortical development (MCD) who underwent surgery between 2015 and 2020 at University Medical Center Utrecht (the Netherlands) and pooled our data with four previously published cohort studies. Tissue analysis yielded a pathogenic variant in 203 of 663 (31%) combined cases. In 126 of 379 (33%) focal cortical dysplasia (FCD) type II cases and 23 of 37 (62%) hemimegalencephaly cases, a pathogenic variant was identified, mostly involving the mTOR signaling pathway. Pathogenic variants in 10 focal epilepsy genes were found in 48 of 178 (27%) FCDI/mild MCD/mMCD with oligodendroglial hyperplasia and epilepsy cases; 36 of these (75%) were SLC35A2 variants. Six of 69 (9%) patients without a histopathological lesion had a pathogenic variant in SLC35A2 (n = 5) or DEPDC5 (n = 1). A germline variant in blood DNA was confirmed in all cases with a pathogenic variant in tissue, with a variant allele frequency (VAF) of ~50%. In seven of 114 patients (6%) with a somatic variant in tissue, mosaicism in blood was detected. More than half of pathogenic somatic variants had a VAF < 5%. Further analysis of the correlation between genetic variants and surgical outcomes will improve patient counseling and may guide postoperative treatment decisions.</p>","PeriodicalId":11768,"journal":{"name":"Epilepsia","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2024-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142497332","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Hyojung Yoon, Amanda Ringland, James J Anderson, Sahibjot Sran, Soad Elziny, Cindy Huynh, Noriyuki Shinagawa, Samantha Badertscher, Rachel R Corrigan, Lauren Mashburn-Warren, Foued Amari, Min Chen, Vincenzo Coppola, Peter B Crino, Tracy A Bedrosian
Objective: Brain somatic variants in SLC35A2 were recently identified as a genetic marker for mild malformations of cortical development with oligodendroglial hyperplasia in epilepsy (MOGHE). The role of SLC35A2 in cortical development and the contributions of abnormal neurons and oligodendrocytes to seizure activity in MOGHE remain largely unexplored.
Methods: Here, we generated a novel Slc35a2 floxed allele, which we used to develop two Slc35a2 conditional knockout mouse lines targeting (1) the Emx1 dorsal telencephalic lineage (excitatory neurons and glia) and (2) the Olig2 lineage (oligodendrocytes). We examined brain structure, behavior, and seizure activity.
Results: Knockout of Slc35a2 from the Emx1 lineage, which targets both cortical neurons and oligodendrocytes, resulted in early lethality and caused abnormal cortical development, increased oligodendroglial cell density, early onset seizures, and developmental delays akin to what is observed in patients with MOGHE. By tracing neuronal development with 5-Ethynyl-2'-deoxyuridine (EdU) birthdating experiments, we found that Slc35a2 deficiency disrupts corticogenesis by delaying radial migration of neurons from the subventricular zone. To discern the contributions of oligodendrocytes to these phenotypes, we knocked out Slc35a2 from the Olig2 lineage. This recapitulated the increased oligodendroglial cell density and resulted in abnormal electroencephalographic activity, but without a clear seizure phenotype, suggesting Slc35a2 deficiency in neurons is required for epileptogenesis.
Significance: This study presents two novel Slc35a2 conditional knockout mouse models and characterizes the effects on brain development, behavior, and epileptogenesis. Together, these results demonstrate a direct causal role for SLC35A2 in MOGHE-like phenotypes, including a critical role in neuronal migration during brain development, and identify neurons as key contributors to SLC35A2-related epileptogenesis.
{"title":"Mouse models of Slc35a2 brain mosaicism reveal mechanisms of mild malformations of cortical development with oligodendroglial hyperplasia in epilepsy.","authors":"Hyojung Yoon, Amanda Ringland, James J Anderson, Sahibjot Sran, Soad Elziny, Cindy Huynh, Noriyuki Shinagawa, Samantha Badertscher, Rachel R Corrigan, Lauren Mashburn-Warren, Foued Amari, Min Chen, Vincenzo Coppola, Peter B Crino, Tracy A Bedrosian","doi":"10.1111/epi.18166","DOIUrl":"https://doi.org/10.1111/epi.18166","url":null,"abstract":"<p><strong>Objective: </strong>Brain somatic variants in SLC35A2 were recently identified as a genetic marker for mild malformations of cortical development with oligodendroglial hyperplasia in epilepsy (MOGHE). The role of SLC35A2 in cortical development and the contributions of abnormal neurons and oligodendrocytes to seizure activity in MOGHE remain largely unexplored.</p><p><strong>Methods: </strong>Here, we generated a novel Slc35a2 floxed allele, which we used to develop two Slc35a2 conditional knockout mouse lines targeting (1) the Emx1 dorsal telencephalic lineage (excitatory neurons and glia) and (2) the Olig2 lineage (oligodendrocytes). We examined brain structure, behavior, and seizure activity.</p><p><strong>Results: </strong>Knockout of Slc35a2 from the Emx1 lineage, which targets both cortical neurons and oligodendrocytes, resulted in early lethality and caused abnormal cortical development, increased oligodendroglial cell density, early onset seizures, and developmental delays akin to what is observed in patients with MOGHE. By tracing neuronal development with 5-Ethynyl-2'-deoxyuridine (EdU) birthdating experiments, we found that Slc35a2 deficiency disrupts corticogenesis by delaying radial migration of neurons from the subventricular zone. To discern the contributions of oligodendrocytes to these phenotypes, we knocked out Slc35a2 from the Olig2 lineage. This recapitulated the increased oligodendroglial cell density and resulted in abnormal electroencephalographic activity, but without a clear seizure phenotype, suggesting Slc35a2 deficiency in neurons is required for epileptogenesis.</p><p><strong>Significance: </strong>This study presents two novel Slc35a2 conditional knockout mouse models and characterizes the effects on brain development, behavior, and epileptogenesis. Together, these results demonstrate a direct causal role for SLC35A2 in MOGHE-like phenotypes, including a critical role in neuronal migration during brain development, and identify neurons as key contributors to SLC35A2-related epileptogenesis.</p>","PeriodicalId":11768,"journal":{"name":"Epilepsia","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2024-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142497330","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Hagar Cohen, Nahawand Bahash, Bruria Raccah, Ilan Matok, Dana Ekstein, Lee Goldstein, Yosef Kalish, Sara Eyal
{"title":"The level is in the details: Why differences between direct-acting oral anticoagulants should be considered in the treatment of patients with epilepsy.","authors":"Hagar Cohen, Nahawand Bahash, Bruria Raccah, Ilan Matok, Dana Ekstein, Lee Goldstein, Yosef Kalish, Sara Eyal","doi":"10.1111/epi.18144","DOIUrl":"https://doi.org/10.1111/epi.18144","url":null,"abstract":"","PeriodicalId":11768,"journal":{"name":"Epilepsia","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2024-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142497333","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Objective: Recently, we developed a first artificial intelligence (AI)-based digital pathology classifier for focal cortical dysplasia (FCD) as defined by the ILAE classification. Herein, we tested the usefulness of the classifier in a retrospective histopathology workup scenario.
Methods: Eighty-six new cases with histopathologically confirmed FCD ILAE type Ia (FCDIa), FCDIIa, FCDIIb, mild malformation of cortical development with oligodendroglial hyperplasia in epilepsy (MOGHE), or mild malformations of cortical development were selected, 20 of which had confirmed gene mosaicism.
Results: The classifier always recognized the correct histopathology diagnosis in four or more 1000 × 1000-μm digital tiles in all cases. Furthermore, the final diagnosis overlapped with the largest batch of tiles assigned by the algorithm to one diagnostic entity in 80.2% of all cases. However, 86.2% of all cases revealed more than one diagnostic category. As an example, FCDIIb was identified in all of the 23 patients with histopathologically assigned FCDIIb, whereas the classifier correctly recognized FCDIIa tiles in 19 of these cases (83%), that is, dysmorphic neurons but no balloon cells. In contrast, the classifier misdiagnosed FCDIIb tiles in seven of 23 cases histopathologically assigned to FCDIIa (33%). This mandates a second look by the signing histopathologist to either confirm balloon cells or differentiate from reactive astrocytes. The algorithm also recognized coexisting architectural dysplasia, for example, vertically oriented microcolumns as in FCDIa, in 22% of cases classified as FCDII and in 62% of cases with MOGHE. Microscopic review confirmed microcolumns in the majority of tiles, suggesting that vertically oriented architectural abnormalities are more common than previously anticipated.
Significance: An AI-based diagnostic classifier will become a helpful tool in our future histopathology laboratory, in particular when large anatomical resections from epilepsy surgery require extensive resources. We also provide an open access web application allowing the histopathologist to virtually review digital tiles obtained from epilepsy surgery to corroborate their final diagnosis.
{"title":"A deep-learning-based histopathology classifier for focal cortical dysplasia (FCD) unravels a complex scenario of comorbid FCD subtypes.","authors":"Jörg Vorndran, Ingmar Blümcke","doi":"10.1111/epi.18161","DOIUrl":"https://doi.org/10.1111/epi.18161","url":null,"abstract":"<p><strong>Objective: </strong>Recently, we developed a first artificial intelligence (AI)-based digital pathology classifier for focal cortical dysplasia (FCD) as defined by the ILAE classification. Herein, we tested the usefulness of the classifier in a retrospective histopathology workup scenario.</p><p><strong>Methods: </strong>Eighty-six new cases with histopathologically confirmed FCD ILAE type Ia (FCDIa), FCDIIa, FCDIIb, mild malformation of cortical development with oligodendroglial hyperplasia in epilepsy (MOGHE), or mild malformations of cortical development were selected, 20 of which had confirmed gene mosaicism.</p><p><strong>Results: </strong>The classifier always recognized the correct histopathology diagnosis in four or more 1000 × 1000-μm digital tiles in all cases. Furthermore, the final diagnosis overlapped with the largest batch of tiles assigned by the algorithm to one diagnostic entity in 80.2% of all cases. However, 86.2% of all cases revealed more than one diagnostic category. As an example, FCDIIb was identified in all of the 23 patients with histopathologically assigned FCDIIb, whereas the classifier correctly recognized FCDIIa tiles in 19 of these cases (83%), that is, dysmorphic neurons but no balloon cells. In contrast, the classifier misdiagnosed FCDIIb tiles in seven of 23 cases histopathologically assigned to FCDIIa (33%). This mandates a second look by the signing histopathologist to either confirm balloon cells or differentiate from reactive astrocytes. The algorithm also recognized coexisting architectural dysplasia, for example, vertically oriented microcolumns as in FCDIa, in 22% of cases classified as FCDII and in 62% of cases with MOGHE. Microscopic review confirmed microcolumns in the majority of tiles, suggesting that vertically oriented architectural abnormalities are more common than previously anticipated.</p><p><strong>Significance: </strong>An AI-based diagnostic classifier will become a helpful tool in our future histopathology laboratory, in particular when large anatomical resections from epilepsy surgery require extensive resources. We also provide an open access web application allowing the histopathologist to virtually review digital tiles obtained from epilepsy surgery to corroborate their final diagnosis.</p>","PeriodicalId":11768,"journal":{"name":"Epilepsia","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142497365","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ludovica Montanucci, Tobias Brünger, Christian M Boßelmann, Alina Ivaniuk, Eduardo Pérez-Palma, Samden Lhatoo, Costin Leu, Dennis Lal
Objective: Determining the pathogenicity of missense variants in clinical genetic tests for individuals with epilepsy is crucial for guiding personalized treatment. However, achieving a definitive pathogenic classification remains challenging, with most missense variants still classified as variants of uncertain significance (VUS) and with the availability of many computational tools which may provide conflicting predictions. Here, we aim to evaluate the performance of state-of-the-art computational tools in pathogenicity prediction of missense variants in epilepsy-associated genes. This will assist in selecting the most appropriate tool and critically assess their use in clinical setting.
Methods: We assessed the performance of nine in silico pathogenicity prediction tools for missense variants in epilepsy-associated genes on three carefully curated data sets. The first two data sets comprise missense variants in epilepsy associated genes that have been uploaded to ClinVar in the last year and were, therefore, not part of the training set of any of the nine considered tools. These two data sets are based on two different lists of epilepsy-associated genes and comprise ~700 and ~ 250 missense variants, respectively. The third data set includes ~400 missense variants within epilepsy-associated genes for which the functional effects have been determined experimentally and are therefore used here to infer pathogenicity. These three data sets represent the best available approximation to blind and independent test sets.
Results: Among the nine assessed tools, AlphaMissense (area under the curve [AUC]: .93, .88, and .95) and REVEL (AUC: .93, .88, and .93) showed the best classification performance, also outperforming other tools in the number of classified variants.
Significance: We show which recently developed prediction tools achieve higher performance in epilepsy-associated genes and should be integrated, therefore, into the American College of Medical Genetics and Genomics/Association of Molecular Pathology (AGMC/AMP) variant classification process. Periodic reevaluation of genetic test results with newly developed or updated tools should be incorporated into standard clinical practice to improve diagnostic yield and better inform precision medicine.
{"title":"Evaluating novel in silico tools for accurate pathogenicity classification in epilepsy-associated genetic missense variants.","authors":"Ludovica Montanucci, Tobias Brünger, Christian M Boßelmann, Alina Ivaniuk, Eduardo Pérez-Palma, Samden Lhatoo, Costin Leu, Dennis Lal","doi":"10.1111/epi.18155","DOIUrl":"https://doi.org/10.1111/epi.18155","url":null,"abstract":"<p><strong>Objective: </strong>Determining the pathogenicity of missense variants in clinical genetic tests for individuals with epilepsy is crucial for guiding personalized treatment. However, achieving a definitive pathogenic classification remains challenging, with most missense variants still classified as variants of uncertain significance (VUS) and with the availability of many computational tools which may provide conflicting predictions. Here, we aim to evaluate the performance of state-of-the-art computational tools in pathogenicity prediction of missense variants in epilepsy-associated genes. This will assist in selecting the most appropriate tool and critically assess their use in clinical setting.</p><p><strong>Methods: </strong>We assessed the performance of nine in silico pathogenicity prediction tools for missense variants in epilepsy-associated genes on three carefully curated data sets. The first two data sets comprise missense variants in epilepsy associated genes that have been uploaded to ClinVar in the last year and were, therefore, not part of the training set of any of the nine considered tools. These two data sets are based on two different lists of epilepsy-associated genes and comprise ~700 and ~ 250 missense variants, respectively. The third data set includes ~400 missense variants within epilepsy-associated genes for which the functional effects have been determined experimentally and are therefore used here to infer pathogenicity. These three data sets represent the best available approximation to blind and independent test sets.</p><p><strong>Results: </strong>Among the nine assessed tools, AlphaMissense (area under the curve [AUC]: .93, .88, and .95) and REVEL (AUC: .93, .88, and .93) showed the best classification performance, also outperforming other tools in the number of classified variants.</p><p><strong>Significance: </strong>We show which recently developed prediction tools achieve higher performance in epilepsy-associated genes and should be integrated, therefore, into the American College of Medical Genetics and Genomics/Association of Molecular Pathology (AGMC/AMP) variant classification process. Periodic reevaluation of genetic test results with newly developed or updated tools should be incorporated into standard clinical practice to improve diagnostic yield and better inform precision medicine.</p>","PeriodicalId":11768,"journal":{"name":"Epilepsia","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142497328","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}