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1. Analysis of 1386 epileptogenic brain lesions reveals association with DYRK1A and EGFR

Author

Boßelmann, Christian M., Leu, Costin, Brünger, Tobias, Hoffmann, Lucas, Baldassari, Sara, Chipaux, Mathilde, Coras, Roland, Kobow, Katja, Hamer, Hajo, Delev, Daniel, Rössler, Karl, Bien, Christian G., Kalbhenn, Thilo, Pieper, Tom, Hartlieb, Till, Becker, Kerstin, Ferguson, Lisa, Busch, Robyn M., Baulac, Stéphanie, Nürnberg, Peter, Najm, Imad, Blümcke, Ingmar, and Lal, Dennis

Published
2024
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2. SLC6A1 variant pathogenicity, molecular function and phenotype: a genetic and clinical analysis.

Author

Stefanski, Arthur, Pérez-Palma, Eduardo, Brünger, Tobias, Montanucci, Ludovica, Gati, Cornelius, Klöckner, Chiara, Johannesen, Katrine, Goodspeed, Kimberly, Macnee, Marie, Deng, Alexander, Aledo-Serrano, Ángel, Borovikov, Artem, Kava, Maina, Bouman, Arjan, Hajianpour, M, Pal, Deb, Engelen, Marc, Hagebeuk, Eveline, Shinawi, Marwan, Heidlebaugh, Alexis, Oetjens, Kathryn, Hoffman, Trevor, Striano, Pasquale, Freed, Amanda, Futtrup, Line, Balslev, Thomas, Abulí, Anna, Danvoye, Leslie, Lederer, Damien, Balci, Tugce, Nouri, Maryam, Butler, Elizabeth, Drewes, Sarah, van Engelen, Kalene, Howell, Katherine, Khoury, Jean, May, Patrick, Trinidad, Marena, Froelich, Steven, Lemke, Johannes, Tiller, Jacob, Freed, Amber, Kang, Jing-Qiong, Wuster, Arthur, Møller, Rikke, and Lal, Dennis

Subjects
SLC6A1, autism, epilepsy, genetics, neurodevelopmental disorder, Humans, GABA Plasma Membrane Transport Proteins, Genetic Association Studies, Mutation, Missense, Phenotype
Abstract

Genetic variants in the SLC6A1 gene can cause a broad phenotypic disease spectrum by altering the protein function. Thus, systematically curated clinically relevant genotype-phenotype associations are needed to understand the disease mechanism and improve therapeutic decision-making. We aggregated genetic and clinical data from 172 individuals with likely pathogenic/pathogenic (lp/p) SLC6A1 variants and functional data for 184 variants (14.1% lp/p). Clinical and functional data were available for a subset of 126 individuals. We explored the potential associations of variant positions on the GAT1 3D structure with variant pathogenicity, altered molecular function and phenotype severity using bioinformatic approaches. The GAT1 transmembrane domains 1, 6 and extracellular loop 4 (EL4) were enriched for patient over population variants. Across functionally tested missense variants (n = 156), the spatial proximity from the ligand was associated with loss-of-function in the GAT1 transporter activity. For variants with complete loss of in vitro GABA uptake, we found a 4.6-fold enrichment in patients having severe disease versus non-severe disease (P = 2.9 × 10-3, 95% confidence interval: 1.5-15.3). In summary, we delineated associations between the 3D structure and variant pathogenicity, variant function and phenotype in SLC6A1-related disorders. This knowledge supports biology-informed variant interpretation and research on GAT1 function. All our data can be interactively explored in the SLC6A1 portal (https://slc6a1-portal.broadinstitute.org/).

Published
2023

3. Genome-wide identification and phenotypic characterization of seizure-associated copy number variations in 741,075 individuals.

Author

Montanucci, Ludovica, Lewis-Smith, David, Collins, Ryan, Niestroj, Lisa-Marie, Parthasarathy, Shridhar, Xian, Julie, Ganesan, Shiva, Macnee, Marie, Brünger, Tobias, Thomas, Rhys, Talkowski, Michael, Helbig, Ingo, Leu, Costin, and Lal, Dennis

Subjects
Humans, DNA Copy Number Variations, Phenotype, Epilepsy, Genome-Wide Association Study, Seizures
Abstract

Copy number variants (CNV) are established risk factors for neurodevelopmental disorders with seizures or epilepsy. With the hypothesis that seizure disorders share genetic risk factors, we pooled CNV data from 10,590 individuals with seizure disorders, 16,109 individuals with clinically validated epilepsy, and 492,324 population controls and identified 25 genome-wide significant loci, 22 of which are novel for seizure disorders, such as deletions at 1p36.33, 1q44, 2p21-p16.3, 3q29, 8p23.3-p23.2, 9p24.3, 10q26.3, 15q11.2, 15q12-q13.1, 16p12.2, 17q21.31, duplications at 2q13, 9q34.3, 16p13.3, 17q12, 19p13.3, 20q13.33, and reciprocal CNVs at 16p11.2, and 22q11.21. Using genetic data from additional 248,751 individuals with 23 neuropsychiatric phenotypes, we explored the pleiotropy of these 25 loci. Finally, in a subset of individuals with epilepsy and detailed clinical data available, we performed phenome-wide association analyses between individual CNVs and clinical annotations categorized through the Human Phenotype Ontology (HPO). For six CNVs, we identified 19 significant associations with specific HPO terms and generated, for all CNVs, phenotype signatures across 17 clinical categories relevant for epileptologists. This is the most comprehensive investigation of CNVs in epilepsy and related seizure disorders, with potential implications for clinical practice.

Published
2023

5. Evaluating novel in silico tools for accurate pathogenicity classification in epilepsy‐associated genetic missense variants.

Author

Montanucci, Ludovica, Brünger, Tobias, Boßelmann, Christian M., Ivaniuk, Alina, Pérez‐Palma, Eduardo, Lhatoo, Samden, Leu, Costin, and Lal, Dennis

Subjects
*MEDICAL genetics, *MISSENSE mutation, *MOLECULAR pathology, *GENETIC variation, *GENETIC testing
Abstract

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. [ABSTRACT FROM AUTHOR]

Published
2024
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6. Molecular dynamics simulations reveal molecular mechanisms for the gain and loss of function effects of fourSCN2Avariants

Author

Bhattarai, Nisha, primary, Montanucci, Ludovica, additional, Brünger, Tobias, additional, Pérez-Palma, Eduardo, additional, Martin, William, additional, Smith, Iris Nira, additional, Eng, Charis, additional, Cheng, Feixiong, additional, Helbig, Ingo, additional, Møller, Rikke S, additional, Brunklaus, Andreas, additional, Schorge, Stephanie, additional, and Lal, Dennis, additional

Published
2024
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7. Severe communication delays are independent of seizure burden and persist despite contemporary treatments in SCN1A+ Dravet syndrome: Insights from the ENVISION natural history study

Author

Perry, M. Scott, primary, Scheffer, Ingrid E., additional, Sullivan, Joseph, additional, Brunklaus, Andreas, additional, Boronat, Susana, additional, Wheless, James W., additional, Laux, Linda, additional, Patel, Anup D., additional, Roberts, Colin M., additional, Dlugos, Dennis, additional, Holder, Deborah, additional, Knupp, Kelly G., additional, Lallas, Matt, additional, Phillips, Steven, additional, Segal, Eric, additional, Smeyers, Patricia, additional, Lal, Dennis, additional, Wirrell, Elaine, additional, Zuberi, Sameer, additional, Brünger, Tobias, additional, Wojnaroski, Mary, additional, Maru, Benit, additional, O'Donnell, Penrose, additional, Morton, Magda, additional, James, Emma, additional, Vila, Maria Candida, additional, Huang, Norman, additional, Gofshteyn, Jacqueline S., additional, and Rico, Salvador, additional

Published
2023
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9. Scanning mutagenesis of the voltage-gated sodium channel NaV1.2 using base editing

Author

Pablo, Juan Lorenzo B., primary, Cornett, Savannah L., additional, Wang, Lei A., additional, Jo, Sooyeon, additional, Brünger, Tobias, additional, Budnik, Nikita, additional, Hegde, Mudra, additional, DeKeyser, Jean-Marc, additional, Thompson, Christopher H., additional, Doench, John G., additional, Lal, Dennis, additional, George, Alfred L., additional, and Pan, Jen Q., additional

Published
2023
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10. Conserved patterns across ion channels correlate with variant pathogenicity and clinical phenotypes

Author

Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Fonds National de la Recherche - FnR [sponsor], Brünger, Tobias, Pérez-Palma, Eduardo, Montanucci, Ludovica, Nothnagel, Michael, Møller, Rikke S., Schorge, Stephanie, Zuberi, Sameer, Symonds, Joseph, Lemke, Johannes R., Brunklaus, Andreas, Traynelis, Stephen F., May, Patrick, Lal, Dennis, Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Fonds National de la Recherche - FnR [sponsor], Brünger, Tobias, Pérez-Palma, Eduardo, Montanucci, Ludovica, Nothnagel, Michael, Møller, Rikke S., Schorge, Stephanie, Zuberi, Sameer, Symonds, Joseph, Lemke, Johannes R., Brunklaus, Andreas, Traynelis, Stephen F., May, Patrick, and Lal, Dennis

Abstract

Clinically identified genetic variants in ion channels can be benign or cause disease by increasing or decreasing the protein function. Consequently, therapeutic decision-making is challenging without molecular testing of each variant. Our biophysical knowledge of ion channel structures and function is just emerging, and it is currently not well understood which amino acid residues cause disease when mutated.We sought to systematically identify biological properties associated with variant pathogenicity across all major voltage and ligand-gated ion channel families. We collected and curated 3,049 pathogenic variants from hundreds of neurodevelopmental and other disorders and 12,546 population variants for 30 ion channel or channel subunits for which a high-quality protein structure was available. Using a wide range of bioinformatics approaches, we computed 163 structural features and tested them for pathogenic variant enrichment. We developed a novel 3D spatial distance scoring approach that enables comparisons of pathogenic and population variant distribution across protein structures.We discovered and independently replicated that several pore residue properties and proximity to the pore axis were most significantly enriched for pathogenic variants compared to population variants. Using our 3D scoring approach, we showed that the strongest pathogenic variant enrichment was observed for pore-lining residues and alpha-helix residues within 5Å distance from the pore axis center and not involved in gating. Within the subset of residues located at the pore, the hydrophobicity of the pore was the feature most strongly associated with variant pathogenicity. We also found an association between the identified properties and both clinical phenotypes and functional in vitro assays for voltage-gated sodium channels (SCN1A, SCN2A, SCN8A) and N-methyl-D-aspartate (NMDA) receptor (GRIN1, GRIN2A, GRIN2B) encoding genes. In an independent expert-curated dataset of 1,422 neurodeve

Published
2023

11. Delineation of functionally essential protein regions for 242 neurodevelopmental genes

Author

Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Fonds National de la Recherche - FnR [sponsor], DFG [sponsor], BMBF [sponsor], Iqbal, Sumaiya, Brünger, Tobias, Pérez-Palma, Eduardo, Macnee, Marie, Brunklaus, Andreas, Daly, Mark J., Campbell, Arthur J., Hoksza, David, May, Patrick, Lal, Dennis, Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Fonds National de la Recherche - FnR [sponsor], DFG [sponsor], BMBF [sponsor], Iqbal, Sumaiya, Brünger, Tobias, Pérez-Palma, Eduardo, Macnee, Marie, Brunklaus, Andreas, Daly, Mark J., Campbell, Arthur J., Hoksza, David, May, Patrick, and Lal, Dennis

Abstract

Neurodevelopmental disorders (NDDs), including severe pediatric epilepsy, autism, and intellectual disabilities are heterogeneous conditions in which clinical genetic testing can often identify a pathogenic variant. For many of them, genetic therapies will be tested in this or the coming years in clinical trials. In contrast to first-generation symptomatic treatments, the new disease-modifying precision medicines require a genetic test-informed diagnosis before a patient can be enrolled in a clinical trial. However, even in 2022, most identified genetic variants in NDD genes are ‘Variants of Uncertain Significance’. To safely enroll patients in precision medicine clinical trials, it is important to increase our knowledge about which regions in NDD-associated proteins can ‘tolerate’ missense variants and which ones are ‘essential’ and will cause a NDD when mutated. In addition, knowledge about functionally indispensable regions in the three-dimensional (3D) structure context of proteins can also provide insights into the molecular mechanisms of disease variants. We developed a novel consensus approach that overlays evolutionary, and population based genomic scores to identify 3D essential sites (Essential3D) on protein structures. After extensive benchmarking of AlphaFold predicted and experimentally solved protein structures, we generated the currently largest expert curated protein structure set for 242 NDDs and identified 14,377 Essential3D sites across 189 gene disorders associated proteins. We demonstrate that the consensus annotation of Essential3D sites improves prioritization of disease mutations over single annotations. The identified Essential3D sites were enriched for functional features such as intermembrane regions or active sites and discovered key inter-molecule interactions in protein complexes that were otherwise not annotated. Using the currently largest autism, developmental disorders, and epilepsies exome sequencing studies including >360,000 NDD

Published
2023

12. CNV-ClinViewer: Enhancing the clinical interpretation of large copy-number variants online

Author

Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Fonds National de la Recherche - FnR [sponsor], DFG [sponsor], BMBF [sponsor], Macnee, Marie, Pérez-Palma, Eduardo, Brünger, Tobias, Klöckner, Chiara, Platzer, Konrad, Stefanski, Arthur, Montanucci, Ludovica, Bayat, Allan, Radtke, Maximilian, Collins, Ryan L., Talkowski, Michael, Blankenberg, Daniel, Møller, Rikke S., Lemke, Johannes R., Nothnagel, Michael, May, Patrick, Lal, Dennis, Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Fonds National de la Recherche - FnR [sponsor], DFG [sponsor], BMBF [sponsor], Macnee, Marie, Pérez-Palma, Eduardo, Brünger, Tobias, Klöckner, Chiara, Platzer, Konrad, Stefanski, Arthur, Montanucci, Ludovica, Bayat, Allan, Radtke, Maximilian, Collins, Ryan L., Talkowski, Michael, Blankenberg, Daniel, Møller, Rikke S., Lemke, Johannes R., Nothnagel, Michael, May, Patrick, and Lal, Dennis

Abstract

Pathogenic copy number variants (CNVs) can cause a heterogeneous spectrum of rare and severe disorders. However, most CNVs are benign and are part of natural variation in human genomes. CNV pathogenicity classification, genotype-phenotype analyses, and therapeutic target identification are challenging and time-consuming tasks that require the integration and analysis of information from multiple scattered sources by experts.Here, we introduce the CNV-ClinViewer, an open-source web-application for clinical evaluation and visual exploration of CNVs. The application enables real-time interactive exploration of large CNV datasets in a user-friendly designed interface and facilitates semi-automated clinical CNV interpretation following the ACMG guidelines by integrating the ClassifCNV tool. In combination with clinical judgment the application enables clinicians and researchers to formulate novel hypotheses and guide their decision-making process. Subsequently, the CNV-ClinViewer enhances for clinical investigators patient care and for basic scientists translational genomic research.The web-application is freely available at https://cnv-ClinViewer.broadinstitute.org and the open-source code can be found at https://github.com/LalResearchGroup/CNV-clinviewer.Supplementary data are available at Bioinformatics online.

Published
2023

13. SLC6A1 variant pathogenicity, molecular function, and phenotype: a genetic and clinical analysis

Author

Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Fonds National de la Recherche - FnR [sponsor], Stefanski, Arthur, Pérez-Palma, Eduardo, Brünger, Tobias, Montanucci, Ludovica, Gati, Cornelius, Klöckner, Chiara, Johannesen, Katrine M., Goodspeed, Kimberly, Macnee, Marie, Deng, Alexander T., Aledo-Serrano, Ángel, Borovikov, Artem, Kava, Maina, Bouman, Arjan M., Hajianpour, M. J., Pal, Deb K., Engelen, Marc, Hagebeuk, Eveline E. O., Shinawi, Marwan, Heidlebaugh, Alexis R., Oetjens, Kathryn, Hoffman, Trevor L., Striano, Pasquale, Freed, Amanda S., Futtrup, Line, Balslev, Thomas, Abulí, Anna, Danvoye, Leslie, Lederer, Damien, Balci, Tugce, Nabavi Nouri, Maryam, Butler, Elizabeth, Drewes, Sarah, van Engelen, Kalene, Howell, Katherine B., Khoury, Jean, May, Patrick, Trinidad, Marena, Froelich, Steven, Lemke, Johannes R., Tiller, Jacob, Freed, Amber N., Kang, Jing-Qiong, Wuster, Arthur, Møller, Rikke S., Lal, Dennis, Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Fonds National de la Recherche - FnR [sponsor], Stefanski, Arthur, Pérez-Palma, Eduardo, Brünger, Tobias, Montanucci, Ludovica, Gati, Cornelius, Klöckner, Chiara, Johannesen, Katrine M., Goodspeed, Kimberly, Macnee, Marie, Deng, Alexander T., Aledo-Serrano, Ángel, Borovikov, Artem, Kava, Maina, Bouman, Arjan M., Hajianpour, M. J., Pal, Deb K., Engelen, Marc, Hagebeuk, Eveline E. O., Shinawi, Marwan, Heidlebaugh, Alexis R., Oetjens, Kathryn, Hoffman, Trevor L., Striano, Pasquale, Freed, Amanda S., Futtrup, Line, Balslev, Thomas, Abulí, Anna, Danvoye, Leslie, Lederer, Damien, Balci, Tugce, Nabavi Nouri, Maryam, Butler, Elizabeth, Drewes, Sarah, van Engelen, Kalene, Howell, Katherine B., Khoury, Jean, May, Patrick, Trinidad, Marena, Froelich, Steven, Lemke, Johannes R., Tiller, Jacob, Freed, Amber N., Kang, Jing-Qiong, Wuster, Arthur, Møller, Rikke S., and Lal, Dennis

Abstract

Genetic variants in the SLC6A1 gene can cause a broad phenotypic disease spectrum by altering the protein function. Thus, systematically curated clinically relevant genotype-phenotype associations are needed to understand the disease mechanism and improve therapeutic decision-making. We aggregated genetic and clinical data from 172 individuals with likely pathogenic/pathogenic (lp/p) SLC6A1 variants and functional data for 184 variants (14.1% lp/p). Clinical and functional data were available for a subset of 126 individuals. We explored the potential associations of variant positions on the GAT1 3D structure with variant pathogenicity, altered molecular function, and phenotype severity using bioinformatic approaches. The GAT1 transmembrane domains 1, 6, and extracellular loop 4 (EL4) were enriched for patient over population variants. Across functionally tested missense variants (n = 156), the spatial proximity from the ligand was associated with loss-of-function in the GAT1 transporter activity. For variants with complete loss of in vitro GABA uptake, we found a 4.6-fold enrichment in patients having severe disease vs. non-severe disease (P = 2.9e-3, 95% CI: 1.5 - 15.3). In summary, we delineated associations between the 3D structure and variant pathogenicity, variant function, and phenotype in SLC6A1-related disorders. This knowledge supports biology-informed variant interpretation and research on GAT1 function. All our data can be interactively explored in the SLC6A1 Portal (https://slc6a1-portal.broadinstitute.org/).

Published
2023

14. Pathogenic paralogous variants can be used to apply the ACMG PS1 and PM5 variant interpretation criteria 2023.08.22.23294353

Author

Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], BMBF [sponsor], Brünger, Tobias, Ivaniuk, Alina, Pérez-Palma, Eduardo, Montanucci, Ludovica, Cohen, Stacey, Smith, Lacey, Parthasarathy, Shridhar, Helbig, Ingo, Nothnagel, Michael, May, Patrick, Lal, Dennis, Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], BMBF [sponsor], Brünger, Tobias, Ivaniuk, Alina, Pérez-Palma, Eduardo, Montanucci, Ludovica, Cohen, Stacey, Smith, Lacey, Parthasarathy, Shridhar, Helbig, Ingo, Nothnagel, Michael, May, Patrick, and Lal, Dennis

Abstract

Purpose The majority of missense variants in clinical genetic tests are classified as variants of uncertain significance. Broadening the evidence of the PS1 and PM5 criteria has the potential to increase conclusive variant interpretation. Methods We hypothesized that incorporation of pathogenic missense variants in conserved residues across paralogous genes can increase the number of variants where ACMG PS1/PM5 criteria can be applied. We mapped over 2.5 million pathogenic and general population variants from ClinVar, HGMD, and gnomAD databases onto 9,990 genes and aligned these by gene families. Subsequently, we developed a novel framework to extend PS1/PM5 by incorporating pathogenic paralogous variants annotations (para-PS1/PM5). Results We demonstrate that para-PS1/PM5 criteria increase the number of classifiable amino acids 3.6-fold compared to PS1 and PM5. Across all gene families with at least two disease-associated genes, the calculated likelihood ratios suggest moderate evidence for pathogenicity. Moreover, for 36 genes, the extended para-PS1/PM5 criteria reach strong evidence level. Conclusion We show that single pathogenic paralogous variants incorporation at paralogous protein positions increases the applicability of the PS1 and PM5 criteria, likely leading to a reduction of variants of uncertain significance across many monogenic disorders. Future iterations of the ACMG guidelines may consider para-PS1 and para-PM5.

Published
2023

15. Bioinformatic approaches to determine pathogenicity and function of clinical genetic variants across ion channels and neurodevelopmental disorder associated genes

Author

Brünger, Tobias and Brünger, Tobias

Abstract

Clinical genetic testing for rare monogenic diseases has the scope of identifying the disease-causing variants. Identification of the molecular etiology of the disease can already today improve clinical care and is essential for the administration of precision medicines that are currently in development for many disorders. However, distinguishing pathogenic variants from benign genetic variants remains a challenge – in particular for missense variants where a single amino acid is substituted. The effects of a pathogenic variant on the protein function, for example, whether it causes a gain (GoF) or a loss (LoF) of the protein function, is most of the time not understood since most genetic variants are ultra-rare and have not been molecularly tested. In particular, for genes associated with severe developmental disorders, first-generation symptomatic treatments offer often only limited relief. Consequently, the development and application of targeted treatments that promise improvement is urgently needed. Identifying the disease-causing pathogenic and predicting their function is crucial as targeted therapies can only be administered to patients with classified pathogenic variants whose functional effects are known to avoid adverse treatment outcomes. In this dissertation, I present bioinformatic approaches to enhance the assessment of variant pathogenicity and understanding of the functional effects of genetic variants. The developed approaches were applied on an exome-wide scale using public datasets and for selected disorders for which I had expert-curated clinical-genetic data available from collaborators. The major focus of this thesis is on genes implicated in neurodevelopmental disorders and diseases associated with ion channel dysfunction for which collaboration with other research groups enabled the aggregation of required genetic, clinical, and functional datasets to develop and test the bioinformatic approaches. In the first study (Bruenger and Ivaniuk et

Published
2023

16. SLC6A1 variant pathogenicity, molecular function and phenotype:a genetic and clinical analysis

Author

Stefanski, Arthur, Pérez-Palma, Eduardo, Brünger, Tobias, Montanucci, Ludovica, Gati, Cornelius, Klöckner, Chiara, Johannesen, Katrine M., Goodspeed, Kimberly, Macnee, Marie, Deng, Alexander T., Aledo-Serrano, Ángel, Borovikov, Artem, Kava, Maina, Bouman, Arjan M., Hajianpour, M. J., Pal, Deb K., Engelen, Marc, Hagebeuk, Eveline E.O., Shinawi, Marwan, Heidlebaugh, Alexis R., Oetjens, Kathryn, Hoffman, Trevor L., Striano, Pasquale, Freed, Amanda S., Futtrup, Line, Balslev, Thomas, Abulí, Anna, Danvoye, Leslie, Lederer, Damien, Balci, Tugce, Nouri, Maryam Nabavi, Butler, Elizabeth, Drewes, Sarah, van Engelen, Kalene, Howell, Katherine B., Khoury, Jean, May, Patrick, Trinidad, Marena, Froelich, Steven, Lemke, Johannes R., Tiller, Jacob, Freed, Amber N., Kang, Jing Qiong, Wuster, Arthur, Møller, Rikke S., Lal, Dennis, Stefanski, Arthur, Pérez-Palma, Eduardo, Brünger, Tobias, Montanucci, Ludovica, Gati, Cornelius, Klöckner, Chiara, Johannesen, Katrine M., Goodspeed, Kimberly, Macnee, Marie, Deng, Alexander T., Aledo-Serrano, Ángel, Borovikov, Artem, Kava, Maina, Bouman, Arjan M., Hajianpour, M. J., Pal, Deb K., Engelen, Marc, Hagebeuk, Eveline E.O., Shinawi, Marwan, Heidlebaugh, Alexis R., Oetjens, Kathryn, Hoffman, Trevor L., Striano, Pasquale, Freed, Amanda S., Futtrup, Line, Balslev, Thomas, Abulí, Anna, Danvoye, Leslie, Lederer, Damien, Balci, Tugce, Nouri, Maryam Nabavi, Butler, Elizabeth, Drewes, Sarah, van Engelen, Kalene, Howell, Katherine B., Khoury, Jean, May, Patrick, Trinidad, Marena, Froelich, Steven, Lemke, Johannes R., Tiller, Jacob, Freed, Amber N., Kang, Jing Qiong, Wuster, Arthur, Møller, Rikke S., and Lal, Dennis

Abstract

Genetic variants in the SLC6A1 gene can cause a broad phenotypic disease spectrum by altering the protein function. Thus, systematically curated clinically relevant genotype-phenotype associations are needed to understand the disease mechanism and improve therapeutic decision-making. We aggregated genetic and clinical data from 172 individuals with likely pathogenic/pathogenic (lp/p) SLC6A1 variants and functional data for 184 variants (14.1% lp/p). Clinical and functional data were available for a subset of 126 individuals. We explored the potential associations of variant positions on the GAT1 3D structure with variant pathogenicity, altered molecular function and phenotype severity using bioinformatic approaches. The GAT1 transmembrane domains 1, 6 and extracellular loop 4 (EL4) were enriched for patient over population variants. Across functionally tested missense variants (n = 156), the spatial proximity from the ligand was associated with loss-of-function in the GAT1 transporter activity. For variants with complete loss of in vitro GABA uptake, we found a 4.6-fold enrichment in patients having severe disease versus non-severe disease (P = 2.9 × 10-3, 95% confidence interval: 1.5-15.3). In summary, we delineated associations between the 3D structure and variant pathogenicity, variant function and phenotype in SLC6A1-related disorders. This knowledge supports biology-informed variant interpretation and research on GAT1 function. All our data can be interactively explored in the SLC6A1 portal (https://slc6a1-portal.broadinstitute.org/).

Published
2023

17. Severe communication delays are independent of seizure burden and persist despite contemporary treatments in SCN1A+ Dravet syndrome: Insights from the ENVISION natural history study.

Author

Perry, M. Scott, Scheffer, Ingrid E., Sullivan, Joseph, Brunklaus, Andreas, Boronat, Susana, Wheless, James W., Laux, Linda, Patel, Anup D., Roberts, Colin M., Dlugos, Dennis, Holder, Deborah, Knupp, Kelly G., Lallas, Matt, Phillips, Steven, Segal, Eric, Smeyers, Patricia, Lal, Dennis, Wirrell, Elaine, Zuberi, Sameer, and Brünger, Tobias

Abstract

Objective: Dravet syndrome (DS) is a developmental and epileptic encephalopathy characterized by high seizure burden, treatment‐resistant epilepsy, and developmental stagnation. Family members rate communication deficits among the most impactful disease manifestations. We evaluated seizure burden and language/communication development in children with DS. Methods: ENVISION was a prospective, observational study evaluating children with DS associated with SCN1A pathogenic variants (SCN1A+ DS) enrolled at age ≤5 years. Seizure burden and antiseizure medications were assessed every 3 months and communication and language every 6 months with the Bayley Scales of Infant and Toddler Development 3rd edition and the parent‐reported Vineland Adaptive Behavior Scales 3rd edition. We report data from the first year of observation, including analyses stratified by age at Baseline: 0:6–2:0 years:months (Y:M; youngest), 2:1–3:6 Y:M (middle), and 3:7–5:0 Y:M (oldest). Results: Between December 2020 and March 2023, 58 children with DS enrolled at 16 sites internationally. Median follow‐up was 17.5 months (range =.0–24.0), with 54 of 58 (93.1%) followed for at least 6 months and 51 of 58 (87.9%) for 12 months. Monthly countable seizure frequency (MCSF) increased with age (median [minimum–maximum] = 1.0 in the youngest [1.0–70.0] and middle [1.0–242.0] age groups and 4.5 [.0–2647.0] in the oldest age group), and remained high, despite use of currently approved antiseizure medications. Language/communication delays were observed early, and developmental stagnation occurred after age 2 years with both instruments. In predictive modeling, chronologic age was the only significant covariate of seizure frequency (effect size =.52, p =.024). MCSF, number of antiseizure medications, age at first seizure, and convulsive status epilepticus were not predictors of language/communication raw scores. Significance: In infants and young children with SCN1A+ DS, language/communication delay and stagnation were independent of seizure burden. Our findings emphasize that the optimal therapeutic window to prevent language/communication delay is before 3 years of age. [ABSTRACT FROM AUTHOR]

Published
2024
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18. CNV-ClinViewer: Enhancing the clinical interpretation of large copy-number variants online

Author

Macnee, Marie, primary, Pérez-Palma, Eduardo, additional, Brünger, Tobias, additional, Klöckner, Chiara, additional, Platzer, Konrad, additional, Stefanski, Arthur, additional, Montanucci, Ludovica, additional, Bayat, Allan, additional, Radtke, Maximilian, additional, Collins, Ryan L, additional, Talkowski, Michael, additional, Blankenberg, Daniel, additional, Møller, Rikke S, additional, Lemke, Johannes R, additional, Nothnagel, Michael, additional, May, Patrick, additional, and Lal, Dennis, additional

Published
2023
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19. Quantitative Phenotype Morbidity Description of SATB2-Associated Syndrome

Author

Zarate, Yuri A., primary, Bosanko, Katherine, additional, Kannan, Amrit, additional, Thomason, Ashlen, additional, Nutt, Beth, additional, Kumar, Nihit, additional, Simmons, Kirt, additional, Hiegert, Aaron, additional, Hartzell, Larry, additional, Johnson, Adam, additional, Prater, Tabitha, additional, Pérez-Palma, Eduardo, additional, Brünger, Tobias, additional, Stefanski, Arthur, additional, Lal, Dennis, additional, and Caffrey, Aisling R., additional

Published
2023
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20. P369: SATB2-associated syndrome severity score: Genotype/phenotype correlations and the SATB2 portal

Author

Zarate, Yuri, primary, Bosanko, Katherine, additional, Kannan, Amrit, additional, Thomason, Ashlen, additional, Nutt, Beth, additional, Kumar, Nihit, additional, Simmons, Kirk, additional, Hiegert, Aaron, additional, Hartzell, Larry, additional, Johnson, Adam, additional, Prater, Tabitha, additional, Kimberlain, Jillian, additional, Caffrey, Aisling, additional, Stefanski, Arthur, additional, Brünger, Tobias, additional, Pérez-Palma, Eduardo, additional, and Lal, Dennis, additional

Published
2023
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22. The gain of function SCN1A disorder spectrum: novel epilepsy phenotypes and therapeutic implications

Author

Brunklaus, Andreas, Brünger, Tobias, Feng, Tony, Fons, Carmen, Lehikoinen, Anni, Panagiotakaki, Eleni, Vintan, Mihaela-Adela, Symonds, Joseph, Andrew, James, Arzimanoglou, Alexis, Gallois, Julie, Delima, Sarah, Hanrahan, Donncha, Lesca, Gaetan, MacLeod, Stewart, Marjanovic, Dragan, McTague, Amy, Nuñez-Enamorado, Noemi, Perez-Palma, Eduardo, Perry, M. Scott, Pysden, Karen, Russ-Hall, Sophie J., Scheffer, Ingrid E., Sully, Krystal, Syrbe, Steffen, Vaher, Ulvi, Velayutham, Murugan, Vogt, Julie, Weiss, Shelly, Wirrell, Elaine, Zuberi, Sameer M., Lal, Dennis, Møller, Rikke S., and Mantegazza, Massimo

Abstract

No abstract available.

Published
2022

23. Conserved patterns across ion channels correlate with variant pathogenicity and clinical phenotypes

Author

Brünger, Tobias, primary, Pérez-Palma, Eduardo, additional, Montanucci, Ludovica, additional, Nothnagel, Michael, additional, Møller, Rikke S, additional, Schorge, Stephanie, additional, Zuberi, Sameer, additional, Symonds, Joseph, additional, Lemke, Johannes R, additional, Brunklaus, Andreas, additional, Traynelis, Stephen F, additional, May, Patrick, additional, and Lal, Dennis, additional

Published
2022
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24. Conserved patterns across ion channels correlate with variant pathogenicity and clinical phenotypes 2022.03.23.485339

Author

Brünger, Tobias, Perez-Palma, Eduardo, Montanucci, Ludovica, Nothnagel, Michael, Moller, Rikke S., Schorge, Stephanie, Zuberi, Sameer, Symonds, Joseph, Lemke, Johannes R., Brunklaus, Andreas, Traynelis, Stephen F., May, Patrick, Lal, Dennis, FNR [sponsor], and Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center]

Subjects
Neurologie [D14] [Sciences de la santé humaine], Neurology [D14] [Human health sciences], Genetics & genetic processes [F10] [Life sciences], Génétique & processus génétiques [F10] [Sciences du vivant]
Abstract

Clinically identified genetic variants in ion channels can be benign or cause disease by increasing or decreasing the protein function. Consequently, therapeutic decision-making is challenging without molecular testing of each variant. Our biophysical knowledge of ion channel structures and function is just emerging, and it is currently not well understood which amino acid residues cause disease when mutated.We sought to systematically identify biological properties associated with variant pathogenicity across all major voltage and ligand-gated ion channel families. We collected and curated 3,049 pathogenic variants from hundreds of neurodevelopmental and other disorders and 12,546 population variants for 30 ion channel or channel subunits for which a high-quality protein structure was available. Using a wide range of bioinformatics approaches, we computed 163 structural features and tested them for pathogenic variant enrichment. We developed a novel 3D spatial distance scoring approach that enables comparisons of pathogenic and population variant distribution across protein structures.We discovered and independently replicated that several pore residue properties and proximity to the pore axis were most significantly enriched for pathogenic variants compared to population variants. Using our novel 3D scoring approach, we showed that the strongest pathogenic variant enrichment was observed for pore-lining residues and alpha-helix residues within 5 A distance from the pore axis center and not involved in gating. Within the subset of residues located at the pore, the hydrophobicity of the pore was the feature most strongly associated with variant pathogenicity. We also found an association between the identified properties and both clinical phenotypes and fucntional in vitro assays for voltage-gated sodium channels (SCN1A, SCN2A, SCN8A) and N-methyl-D-aspartate (NMDA) receptor (GRIN1, GRIN2A, GRIN2B) encoding genes. In an independent expert-curated dataset of 1,422 neurodevelopmental disorder pathogenic patient variants, and 679 electrophysiological experiments that pore axis distance is associated with seizure age of onset and cognitive performance as well as differential gain vs. loss-of-channel function.In summary, we identified biological properties associated with ion-channel malfunction and show that these are correlated with in vitro functional read-outs and clinical phenotypes in patients with neurodevelopmental disorders. Our results suggest that clinical decision support algorithms that predict variant pathogenicity and function are feasible in the future.Competing Interest StatementThe authors have declared no competing interest.DSSPDictionary of Protein Secondary StructuregnomADGenome aggregation DatabaseGoFGain of functionGRIN genesGRIN1, GRIN2A. GRIN2BHGMDHuman Gene Mutation DatabaseNMDA receptorN-methyl-D-aspartate receptorGABA receptorGamma-aminobutyric acid receptorLoFLoss of functionSCN genesSCN1A, SCN2A, SCN8AVCFVariant Call Format

Published
2022

25. Conserved patterns across ion channels correlate with variant pathogenicity and clinical phenotypes 2022.03.23.485339

Author

Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], FNR [sponsor], Brünger, Tobias, Perez-Palma, Eduardo, Montanucci, Ludovica, Nothnagel, Michael, Moller, Rikke S., Schorge, Stephanie, Zuberi, Sameer, Symonds, Joseph, Lemke, Johannes R., Brunklaus, Andreas, Traynelis, Stephen F., May, Patrick, Lal, Dennis, Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], FNR [sponsor], Brünger, Tobias, Perez-Palma, Eduardo, Montanucci, Ludovica, Nothnagel, Michael, Moller, Rikke S., Schorge, Stephanie, Zuberi, Sameer, Symonds, Joseph, Lemke, Johannes R., Brunklaus, Andreas, Traynelis, Stephen F., May, Patrick, and Lal, Dennis

Abstract

Clinically identified genetic variants in ion channels can be benign or cause disease by increasing or decreasing the protein function. Consequently, therapeutic decision-making is challenging without molecular testing of each variant. Our biophysical knowledge of ion channel structures and function is just emerging, and it is currently not well understood which amino acid residues cause disease when mutated.We sought to systematically identify biological properties associated with variant pathogenicity across all major voltage and ligand-gated ion channel families. We collected and curated 3,049 pathogenic variants from hundreds of neurodevelopmental and other disorders and 12,546 population variants for 30 ion channel or channel subunits for which a high-quality protein structure was available. Using a wide range of bioinformatics approaches, we computed 163 structural features and tested them for pathogenic variant enrichment. We developed a novel 3D spatial distance scoring approach that enables comparisons of pathogenic and population variant distribution across protein structures.We discovered and independently replicated that several pore residue properties and proximity to the pore axis were most significantly enriched for pathogenic variants compared to population variants. Using our novel 3D scoring approach, we showed that the strongest pathogenic variant enrichment was observed for pore-lining residues and alpha-helix residues within 5 A distance from the pore axis center and not involved in gating. Within the subset of residues located at the pore, the hydrophobicity of the pore was the feature most strongly associated with variant pathogenicity. We also found an association between the identified properties and both clinical phenotypes and fucntional in vitro assays for voltage-gated sodium channels (SCN1A, SCN2A, SCN8A) and N-methyl-D-aspartate (NMDA) receptor (GRIN1, GRIN2A, GRIN2B) encoding genes. In an independent expert-curated dataset of 1,422 ne

Published
2022

26. CNV-ClinViewer: Enhancing the clinical interpretation of large copy-number variants online

Author

Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Fonds National de la Recherche - FnR; BMBF [sponsor], Macnee, Marie, Perez-Palma, Eduardo, Brünger, Tobias, Klöckner, Chiara, Platzer, Konrad, Stefanski, Arthur, Montanucci, Ludovica, Bayat, Allan, Radtke, Maximilian, Collins, Ryan L., Talkowski, Michael, Blankenberg, Daniel, Møller, Rikke S., Lemke, Johannes R., Nothnagel, Michael, May, Patrick, Lal, Dennis, Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Fonds National de la Recherche - FnR; BMBF [sponsor], Macnee, Marie, Perez-Palma, Eduardo, Brünger, Tobias, Klöckner, Chiara, Platzer, Konrad, Stefanski, Arthur, Montanucci, Ludovica, Bayat, Allan, Radtke, Maximilian, Collins, Ryan L., Talkowski, Michael, Blankenberg, Daniel, Møller, Rikke S., Lemke, Johannes R., Nothnagel, Michael, May, Patrick, and Lal, Dennis

Abstract

Purpose Large copy number variants (CNVs) can cause a heterogeneous spectrum of rare and severe disorders. However, most CNVs are benign and are part of natural variation in human genomes. CNV pathogenicity classification, genotype-phenotype analyses, and therapeutic target identification are challenging and time-consuming tasks that require the integration and analysis of information from multiple scattered sources by experts. Methods We developed a web-application combining >250,000 patient and population CNVs together with a large set of biomedical annotations and provide tools for CNV classification based on ACMG/ClinGen guidelines and gene-set enrichment analyses. Results Here, we introduce the CNV-ClinViewer (https://cnv-ClinViewer.broadinstitute.org), an open-source web-application for clinical evaluation and visual exploration of CNVs. The application enables real-time interactive exploration of large CNV datasets in a user-friendly designed interface. Conclusion Overall, this resource facilitates semi-automated clinical CNV interpretation and genomic loci exploration and, in combination with clinical judgment, enables clinicians and researchers to formulate novel hypotheses and guide their decision-making process. Subsequently, the CNV-ClinViewer enhances for clinical investigators patient care and for basic scientists translational genomic research.

Published
2022

27. Genotype-phenotype correlations in SCN8A-related disorders reveal prognostic and therapeutic implications

Author

Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], BMBF, Treat-ION, 01GM1907 [sponsor], Johannesen, Katrine M., Liu, Yuanyuan, Koko, Mahmoud, Gjerulfsen, Cathrine E., Sonnenberg, Lukas, Schubert, Julian, Fenger, Christina D., Eltokhi, Ahmed, Rannap, Maert, Koch, Nils A., Lauxmann, Stephan, Krüger, Johanna, Kegele, Josua, Canafoglia, Laura, Franceschetti, Silvana, Mayer, Thomas, Rebstock, Johannes, Zacher, Pia, Ruf, Susanne, Alber, Michael, Sterbova, Katalin, Lassuthová, Petra, Vlckova, Marketa, Lemke, Johannes R., Platzer, Konrad, Krey, Ilona, Heine, Constanze, Wieczorek, Dagmar, Kroell-Seger, Judith, Lund, Caroline, Klein, Karl Martin, Billie Au, P. Y., Rho, Jong M., Ho, Alice W., Masnada, Silvia, Veggiotti, Pierangelo, Giordano, Lucio, Accorsi, Patrizia, Hoei-Hansen, Christina E., Striano, Pasquale, Zara, Federico, Verhelst, Helene, Verhoeven, Judith S., van der Zwaag, Bert, Harder, Aster V. E., Brilstra, Eva, Pendziwiat, Manuela, Lebon, Sebastian, Vaccarezza, Maria, Minh Le, Ngoc, Christensen, Jakob, Grønborg, Sabine, Scherer, Stephen W., Howe, Jennifer, Fazeli, Walid, Howell, Katherine B., Leventer, Richard, Stutterd, Chloe, Walsh, Sonja, Gerard, Marion, Gerard, Bénédicte, Matricardi, Sara, Bonardi, Claudia M., Sartori, Stefano, Berger, Andrea, Hoffman-Zacharska, Dorota, Mastrangelo, Massimo, Darra, Francesca, Vøllo, Arve, Motazacker, M. Mahdi, Lakeman, Phillis, Nizon, Mathilde, Betzler, Cornelia, Altuzarra, Cecilia, Caume, Roseline, Roubertie, Agathe, Gélisse, Philippe, Marini, Carla, Guerrini, Renzo, Bilan, Frederic, Tibussek, Daniel, Koch-Hogrebe, Margarete, Perry, M. Scott, Ichikawa, Shoji, Dadali, Elena, Sharkov, Artem, Mishina, Irina, Abramov, Mikhail, Kanivets, Ilya, Korostelev, Sergey, Kutsev, Sergey, Wain, Karen E., Eisenhauer, Nancy, Wagner, Monisa, Savatt, Juliann M., Müller-Schlüter, Karen, Bassan, Haim, Borovikov, Artem, Nassogne, Marie-Cecile, Destrée, Anne, Schoonjans, An-Sofie, Meuwissen, Marije, Buzatu, Marga, Jansen, Anna, Scalais, Emmanuel, Srivastava, Siddharth, Tan, Wen-Hann, Olson, Heather E., Loddenkemper, Tobias, Poduri, Annapurna, Helbig, Katherine L., Helbig, Ingo, Fitzgerald, Mark P., Goldberg, Ethan M., Roser, Timo, Borggraefe, Ingo, Brünger, Tobias, May, Patrick, Lal, Dennis, Lederer, Damien, Rubboli, Guido, Heyne, Henrike O., Lesca, Gaetan, Hedrich, Ulrike B. S., Benda, Jan, Gardella, Elena, Lerche, Holger, Møller, Rikke S., Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], BMBF, Treat-ION, 01GM1907 [sponsor], Johannesen, Katrine M., Liu, Yuanyuan, Koko, Mahmoud, Gjerulfsen, Cathrine E., Sonnenberg, Lukas, Schubert, Julian, Fenger, Christina D., Eltokhi, Ahmed, Rannap, Maert, Koch, Nils A., Lauxmann, Stephan, Krüger, Johanna, Kegele, Josua, Canafoglia, Laura, Franceschetti, Silvana, Mayer, Thomas, Rebstock, Johannes, Zacher, Pia, Ruf, Susanne, Alber, Michael, Sterbova, Katalin, Lassuthová, Petra, Vlckova, Marketa, Lemke, Johannes R., Platzer, Konrad, Krey, Ilona, Heine, Constanze, Wieczorek, Dagmar, Kroell-Seger, Judith, Lund, Caroline, Klein, Karl Martin, Billie Au, P. Y., Rho, Jong M., Ho, Alice W., Masnada, Silvia, Veggiotti, Pierangelo, Giordano, Lucio, Accorsi, Patrizia, Hoei-Hansen, Christina E., Striano, Pasquale, Zara, Federico, Verhelst, Helene, Verhoeven, Judith S., van der Zwaag, Bert, Harder, Aster V. E., Brilstra, Eva, Pendziwiat, Manuela, Lebon, Sebastian, Vaccarezza, Maria, Minh Le, Ngoc, Christensen, Jakob, Grønborg, Sabine, Scherer, Stephen W., Howe, Jennifer, Fazeli, Walid, Howell, Katherine B., Leventer, Richard, Stutterd, Chloe, Walsh, Sonja, Gerard, Marion, Gerard, Bénédicte, Matricardi, Sara, Bonardi, Claudia M., Sartori, Stefano, Berger, Andrea, Hoffman-Zacharska, Dorota, Mastrangelo, Massimo, Darra, Francesca, Vøllo, Arve, Motazacker, M. Mahdi, Lakeman, Phillis, Nizon, Mathilde, Betzler, Cornelia, Altuzarra, Cecilia, Caume, Roseline, Roubertie, Agathe, Gélisse, Philippe, Marini, Carla, Guerrini, Renzo, Bilan, Frederic, Tibussek, Daniel, Koch-Hogrebe, Margarete, Perry, M. Scott, Ichikawa, Shoji, Dadali, Elena, Sharkov, Artem, Mishina, Irina, Abramov, Mikhail, Kanivets, Ilya, Korostelev, Sergey, Kutsev, Sergey, Wain, Karen E., Eisenhauer, Nancy, Wagner, Monisa, Savatt, Juliann M., Müller-Schlüter, Karen, Bassan, Haim, Borovikov, Artem, Nassogne, Marie-Cecile, Destrée, Anne, Schoonjans, An-Sofie, Meuwissen, Marije, Buzatu, Marga, Jansen, Anna, Scalais, Emmanuel, Srivastava, Siddharth, Tan, Wen-Hann, Olson, Heather E., Loddenkemper, Tobias, Poduri, Annapurna, Helbig, Katherine L., Helbig, Ingo, Fitzgerald, Mark P., Goldberg, Ethan M., Roser, Timo, Borggraefe, Ingo, Brünger, Tobias, May, Patrick, Lal, Dennis, Lederer, Damien, Rubboli, Guido, Heyne, Henrike O., Lesca, Gaetan, Hedrich, Ulrike B. S., Benda, Jan, Gardella, Elena, Lerche, Holger, and Møller, Rikke S.

Abstract

We report detailed functional analyses and genotype-phenotype correlations in 392 individuals carrying disease-causing variants in SCN8A, encoding the voltage-gated Na+ channel NaV1.6, with the aim of describing clinical phenotypes related to functional effects. Six different clinical subgroups could be identified: 1) Benign familial infantile epilepsy (BFIE) (n = 15, normal cognition, treatable seizures), 2) intermediate epilepsy (n = 33, mild ID, partially pharmaco-responsive), 3) developmental and epileptic encephalopathy (DEE, n = 177, severe ID, majority pharmaco-resistant), 4) generalized epilepsy (n = 20, mild to moderate ID, frequently with absence seizures), 5) unclassifiable epilepsy (n = 127), and 6) neurodevelopmental disorder without epilepsy (n = 20, mild to moderate ID). Groups 1–3 presented with focal or multifocal seizures (median age of onset: four months) and focal epileptiform discharges, whereas the onset of seizures in group 4 was later (median: 42 months) with generalized epileptiform discharges. We performed functional studies expressing missense variants in ND7/23 neuroblastoma cells and primary neuronal cultures using recombinant tetrodotoxin-insensitive human NaV1.6 channels and whole-cell patch-clamping. Two variants causing DEE showed a strong gain-of-function (GOF, hyperpolarising shift of steady-state activation, strongly increased neuronal firing rate), and one variant causing BFIE or intermediate epilepsy showed a mild GOF (defective fast inactivation, less increased firing). In contrast, all three variants causing generalized epilepsy induced a loss-of-function (LOF, reduced current amplitudes, depolarising shift of steady-state activation, reduced neuronal firing). Including previous studies, functional effects were known for 170 individuals. All 136 individuals carrying a functionally tested GOF variant had either focal (97, groups 1–3), or unclassifiable epilepsy (39), whereas 34 with a LOF variant had either generalized (14), no

Published
2022

28. Genotype-phenotype correlations in SCN8A-related disorders reveal prognostic and therapeutic implications

Author

Johannesen, Katrine M., Liu, Yuanyuan, Koko, Mahmoud, Gjerulfsen, Cathrine E., Sonnenberg, Lukas, Schubert, Julian, Fenger, Christina D., Eltokhi, Ahmed, Rannap, Maert, Koch, Nils A., Lauxmann, Stephan, Krüger, Johanna, Kegele, Josua, Canafoglia, Laura, Franceschetti, Silvana, Mayer, Thomas, Rebstock, Johannes, Zacher, Pia, Ruf, Susanne, Alber, Michael, Sterbova, Katalin, Lassuthová, Petra, Vlckova, Marketa, Lemke, Johannes R., Platzer, Konrad, Krey, Ilona, Heine, Constanze, Wieczorek, Dagmar, Kroell-Seger, Judith, Lund, Caroline, Klein, Karl Martin, Au, P. Y.Billie, Rho, Jong M., Ho, Alice W., Masnada, Silvia, Veggiotti, Pierangelo, Giordano, Lucio, Accorsi, Patrizia, Hoei-Hansen, Christina E., Striano, Pasquale, Zara, Federico, Verhelst, Helene, Verhoeven, Judith S., Braakman, Hilde M.H., van der Zwaag, Bert, Harder, Aster V.E., Brilstra, Eva, Pendziwiat, Manuela, Lebon, Sebastian, Vaccarezza, Maria, Le, Ngoc Minh, Christensen, Jakob, Grønborg, Sabine, Scherer, Stephen W., Howe, Jennifer, Fazeli, Walid, Howell, Katherine B., Leventer, Richard, Stutterd, Chloe, Walsh, Sonja, Gerard, Marion, Gerard, Bénédicte, Matricardi, Sara, Bonardi, Claudia M., Sartori, Stefano, Berger, Andrea, Hoffman-Zacharska, Dorota, Mastrangelo, Massimo, Darra, Francesca, Vøllo, Arve, Motazacker, M. Mahdi, Lakeman, Phillis, Nizon, Mathilde, Betzler, Cornelia, Altuzarra, Cecilia, Caume, Roseline, Roubertie, Agathe, Gélisse, Philippe, Marini, Carla, Guerrini, Renzo, Bilan, Frederic, Tibussek, Daniel, Koch-Hogrebe, Margarete, Perry, M. Scott, Ichikawa, Shoji, Dadali, Elena, Sharkov, Artem, Mishina, Irina, Abramov, Mikhail, Kanivets, Ilya, Korostelev, Sergey, Kutsev, Sergey, Wain, Karen E., Eisenhauer, Nancy, Wagner, Monisa, Savatt, Juliann M., Müller-Schlüter, Karen, Bassan, Haim, Borovikov, Artem, Nassogne, Marie Cecile, Destrée, Anne, Schoonjans, An Sofie, Meuwissen, Marije, Buzatu, Marga, Jansen, Anna, Scalais, Emmanuel, Srivastava, Siddharth, Tan, Wen Hann, Olson, Heather E., Loddenkemper, Tobias, Poduri, Annapurna, Helbig, Katherine L., Helbig, Ingo, Fitzgerald, Mark P., Goldberg, Ethan M., Roser, Timo, Borggraefe, Ingo, Brünger, Tobias, May, Patrick, Lal, Dennis, Lederer, Damien, Rubboli, Guido, Heyne, Henrike O., Lesca, Gaetan, Hedrich, Ulrike B.S., Benda, Jan, Gardella, Elena, Lerche, Holger, Møller, Rikke S., Johannesen, Katrine M., Liu, Yuanyuan, Koko, Mahmoud, Gjerulfsen, Cathrine E., Sonnenberg, Lukas, Schubert, Julian, Fenger, Christina D., Eltokhi, Ahmed, Rannap, Maert, Koch, Nils A., Lauxmann, Stephan, Krüger, Johanna, Kegele, Josua, Canafoglia, Laura, Franceschetti, Silvana, Mayer, Thomas, Rebstock, Johannes, Zacher, Pia, Ruf, Susanne, Alber, Michael, Sterbova, Katalin, Lassuthová, Petra, Vlckova, Marketa, Lemke, Johannes R., Platzer, Konrad, Krey, Ilona, Heine, Constanze, Wieczorek, Dagmar, Kroell-Seger, Judith, Lund, Caroline, Klein, Karl Martin, Au, P. Y.Billie, Rho, Jong M., Ho, Alice W., Masnada, Silvia, Veggiotti, Pierangelo, Giordano, Lucio, Accorsi, Patrizia, Hoei-Hansen, Christina E., Striano, Pasquale, Zara, Federico, Verhelst, Helene, Verhoeven, Judith S., Braakman, Hilde M.H., van der Zwaag, Bert, Harder, Aster V.E., Brilstra, Eva, Pendziwiat, Manuela, Lebon, Sebastian, Vaccarezza, Maria, Le, Ngoc Minh, Christensen, Jakob, Grønborg, Sabine, Scherer, Stephen W., Howe, Jennifer, Fazeli, Walid, Howell, Katherine B., Leventer, Richard, Stutterd, Chloe, Walsh, Sonja, Gerard, Marion, Gerard, Bénédicte, Matricardi, Sara, Bonardi, Claudia M., Sartori, Stefano, Berger, Andrea, Hoffman-Zacharska, Dorota, Mastrangelo, Massimo, Darra, Francesca, Vøllo, Arve, Motazacker, M. Mahdi, Lakeman, Phillis, Nizon, Mathilde, Betzler, Cornelia, Altuzarra, Cecilia, Caume, Roseline, Roubertie, Agathe, Gélisse, Philippe, Marini, Carla, Guerrini, Renzo, Bilan, Frederic, Tibussek, Daniel, Koch-Hogrebe, Margarete, Perry, M. Scott, Ichikawa, Shoji, Dadali, Elena, Sharkov, Artem, Mishina, Irina, Abramov, Mikhail, Kanivets, Ilya, Korostelev, Sergey, Kutsev, Sergey, Wain, Karen E., Eisenhauer, Nancy, Wagner, Monisa, Savatt, Juliann M., Müller-Schlüter, Karen, Bassan, Haim, Borovikov, Artem, Nassogne, Marie Cecile, Destrée, Anne, Schoonjans, An Sofie, Meuwissen, Marije, Buzatu, Marga, Jansen, Anna, Scalais, Emmanuel, Srivastava, Siddharth, Tan, Wen Hann, Olson, Heather E., Loddenkemper, Tobias, Poduri, Annapurna, Helbig, Katherine L., Helbig, Ingo, Fitzgerald, Mark P., Goldberg, Ethan M., Roser, Timo, Borggraefe, Ingo, Brünger, Tobias, May, Patrick, Lal, Dennis, Lederer, Damien, Rubboli, Guido, Heyne, Henrike O., Lesca, Gaetan, Hedrich, Ulrike B.S., Benda, Jan, Gardella, Elena, Lerche, Holger, and Møller, Rikke S.

Abstract

We report detailed functional analyses and genotype-phenotype correlations in 392 individuals carrying disease-causing variants in SCN8A, encoding the voltage-gated Na+ channel Nav1.6, with the aim of describing clinical phenotypes related to functional effects. Six different clinical subgroups were identified: Group 1, benign familial infantile epilepsy (n = 15, normal cognition, treatable seizures); Group 2, intermediate epilepsy (n = 33, mild intellectual disability, partially pharmaco-responsive); Group 3, developmental and epileptic encephalopathy (n = 177, severe intellectual disability, majority pharmaco-resistant); Group 4, generalized epilepsy (n = 20, mild to moderate intellectual disability, frequently with absence seizures); Group 5, unclassifiable epilepsy (n = 127); and Group 6, neurodevelopmental disorder without epilepsy (n = 20, mild to moderate intellectual disability). Those in Groups 1-3 presented with focal or multifocal seizures (median age of onset: 4 months) and focal epileptiform discharges, whereas the onset of seizures in patients with generalized epilepsy was later (median: 42 months) with generalized epileptiform discharges. We performed functional studies expressing missense variants in ND7/23 neuroblastoma cells and primary neuronal cultures using recombinant tetrodotoxin-insensitive human Nav1.6 channels and whole-cell patch-clamping. Two variants causing developmental and epileptic encephalopathy showed a strong gain-of-function (hyperpolarizing shift of steady-state activation, strongly increased neuronal firing rate) and one variant causing benign familial infantile epilepsy or intermediate epilepsy showed a mild gain-of-function (defective fast inactivation, less increased firing). In contrast, all three variants causing generalized epilepsy induced a loss-of-function (reduced current amplitudes, depolarizing shift of steady-state activation, reduced neuronal firing). Functional effects were known for 170 individuals. All 136 i

Published
2022

29. Genotype-phenotype correlations in SCN8A-related disorders reveal prognostic and therapeutic implications

Author

Genetica Sectie Genoomdiagnostiek, Child Health, Genetica Klinische Genetica, Brain, Johannesen, Katrine M, Liu, Yuanyuan, Koko, Mahmoud, Gjerulfsen, Cathrine E, Sonnenberg, Lukas, Schubert, Julian, Fenger, Christina D, Eltokhi, Ahmed, Rannap, Maert, Koch, Nils A, Lauxmann, Stephan, Krüger, Johanna, Kegele, Josua, Canafoglia, Laura, Franceschetti, Silvana, Mayer, Thomas, Rebstock, Johannes, Zacher, Pia, Ruf, Susanne, Alber, Michael, Sterbova, Katalin, Lassuthová, Petra, Vlckova, Marketa, Lemke, Johannes R, Platzer, Konrad, Krey, Ilona, Heine, Constanze, Wieczorek, Dagmar, Kroell-Seger, Judith, Lund, Caroline, Klein, Karl Martin, Billie Au, P Y, Rho, Jong M, Ho, Alice W, Masnada, Silvia, Veggiotti, Pierangelo, Giordano, Lucio, Accorsi, Patrizia, Hoei-Hansen, Christina E, Striano, Pasquale, Zara, Federico, Verhelst, Helene, Verhoeven, Judith S, van der Zwaag, Bert, Harder, Aster V E, Brilstra, Eva, Pendziwiat, Manuela, Lebon, Sebastian, Vaccarezza, Maria, Minh Le, Ngoc, Christensen, Jakob, Grønborg, Sabine, Scherer, Stephen W, Howe, Jennifer, Fazeli, Walid, Howell, Katherine B, Leventer, Richard, Stutterd, Chloe, Walsh, Sonja, Gerard, Marion, Gerard, Bénédicte, Matricardi, Sara, Bonardi, Claudia M, Sartori, Stefano, Berger, Andrea, Hoffman-Zacharska, Dorota, Mastrangelo, Massimo, Darra, Francesca, Vøllo, Arve, Motazacker, M Mahdi, Lakeman, Phillis, Nizon, Mathilde, Betzler, Cornelia, Altuzarra, Cecilia, Caume, Roseline, Roubertie, Agathe, Gélisse, Philippe, Marini, Carla, Guerrini, Renzo, Bilan, Frederic, Tibussek, Daniel, Koch-Hogrebe, Margarete, Perry, M Scott, Ichikawa, Shoji, Dadali, Elena, Sharkov, Artem, Mishina, Irina, Abramov, Mikhail, Kanivets, Ilya, Korostelev, Sergey, Kutsev, Sergey, Wain, Karen E, Eisenhauer, Nancy, Wagner, Monisa, Savatt, Juliann M, Müller-Schlüter, Karen, Bassan, Haim, Borovikov, Artem, Nassogne, Marie-Cecile, Destrée, Anne, Schoonjans, An-Sofie, Meuwissen, Marije, Buzatu, Marga, Jansen, Anna, Scalais, Emmanuel, Srivastava, Siddharth, Tan, Wen-Hann, Olson, Heather E, Loddenkemper, Tobias, Poduri, Annapurna, Helbig, Katherine L, Helbig, Ingo, Fitzgerald, Mark P, Goldberg, Ethan M, Roser, Timo, Borggraefe, Ingo, Brünger, Tobias, May, Patrick, Lal, Dennis, Lederer, Damien, Rubboli, Guido, Heyne, Henrike O, Lesca, Gaetan, Hedrich, Ulrike B S, Benda, Jan, Gardella, Elena, Lerche, Holger, Møller, Rikke S, Genetica Sectie Genoomdiagnostiek, Child Health, Genetica Klinische Genetica, Brain, Johannesen, Katrine M, Liu, Yuanyuan, Koko, Mahmoud, Gjerulfsen, Cathrine E, Sonnenberg, Lukas, Schubert, Julian, Fenger, Christina D, Eltokhi, Ahmed, Rannap, Maert, Koch, Nils A, Lauxmann, Stephan, Krüger, Johanna, Kegele, Josua, Canafoglia, Laura, Franceschetti, Silvana, Mayer, Thomas, Rebstock, Johannes, Zacher, Pia, Ruf, Susanne, Alber, Michael, Sterbova, Katalin, Lassuthová, Petra, Vlckova, Marketa, Lemke, Johannes R, Platzer, Konrad, Krey, Ilona, Heine, Constanze, Wieczorek, Dagmar, Kroell-Seger, Judith, Lund, Caroline, Klein, Karl Martin, Billie Au, P Y, Rho, Jong M, Ho, Alice W, Masnada, Silvia, Veggiotti, Pierangelo, Giordano, Lucio, Accorsi, Patrizia, Hoei-Hansen, Christina E, Striano, Pasquale, Zara, Federico, Verhelst, Helene, Verhoeven, Judith S, van der Zwaag, Bert, Harder, Aster V E, Brilstra, Eva, Pendziwiat, Manuela, Lebon, Sebastian, Vaccarezza, Maria, Minh Le, Ngoc, Christensen, Jakob, Grønborg, Sabine, Scherer, Stephen W, Howe, Jennifer, Fazeli, Walid, Howell, Katherine B, Leventer, Richard, Stutterd, Chloe, Walsh, Sonja, Gerard, Marion, Gerard, Bénédicte, Matricardi, Sara, Bonardi, Claudia M, Sartori, Stefano, Berger, Andrea, Hoffman-Zacharska, Dorota, Mastrangelo, Massimo, Darra, Francesca, Vøllo, Arve, Motazacker, M Mahdi, Lakeman, Phillis, Nizon, Mathilde, Betzler, Cornelia, Altuzarra, Cecilia, Caume, Roseline, Roubertie, Agathe, Gélisse, Philippe, Marini, Carla, Guerrini, Renzo, Bilan, Frederic, Tibussek, Daniel, Koch-Hogrebe, Margarete, Perry, M Scott, Ichikawa, Shoji, Dadali, Elena, Sharkov, Artem, Mishina, Irina, Abramov, Mikhail, Kanivets, Ilya, Korostelev, Sergey, Kutsev, Sergey, Wain, Karen E, Eisenhauer, Nancy, Wagner, Monisa, Savatt, Juliann M, Müller-Schlüter, Karen, Bassan, Haim, Borovikov, Artem, Nassogne, Marie-Cecile, Destrée, Anne, Schoonjans, An-Sofie, Meuwissen, Marije, Buzatu, Marga, Jansen, Anna, Scalais, Emmanuel, Srivastava, Siddharth, Tan, Wen-Hann, Olson, Heather E, Loddenkemper, Tobias, Poduri, Annapurna, Helbig, Katherine L, Helbig, Ingo, Fitzgerald, Mark P, Goldberg, Ethan M, Roser, Timo, Borggraefe, Ingo, Brünger, Tobias, May, Patrick, Lal, Dennis, Lederer, Damien, Rubboli, Guido, Heyne, Henrike O, Lesca, Gaetan, Hedrich, Ulrike B S, Benda, Jan, Gardella, Elena, Lerche, Holger, and Møller, Rikke S

Published
2022

30. Spectrum of Phenotypic, Genetic, and Functional Characteristics in Patients With Epilepsy With KCNC2 Pathogenic Variants

Author

Schwarz, Niklas, primary, Seiffert, Simone, additional, Pendziwiat, Manuela, additional, Rademacher, Annika Verena, additional, Brünger, Tobias, additional, Hedrich, Ulrike B.S., additional, Augustijn, Paul B., additional, Baier, Hartmut, additional, Bayat, Allan, additional, Bisulli, Francesca, additional, Buono, Russell J., additional, Bruria, Ben Zeev, additional, Doyle, Michael G., additional, Guerrini, Renzo, additional, Heimer, Gali, additional, Iacomino, Michele, additional, Kearney, Hugh, additional, Klein, Karl Martin, additional, Kousiappa, Ioanna, additional, Kunz, Wolfram S., additional, Lerche, Holger, additional, Licchetta, Laura, additional, Lohmann, Ebba, additional, Minardi, Raffaella, additional, McDonald, Marie, additional, Montgomery, Sarah, additional, Mulahasanovic, Lejla, additional, Oegema, Renske, additional, Ortal, Barel, additional, Papacostas, Savvas S., additional, Ragona, Francesca, additional, Granata, Tiziana, additional, Reif, Phillip S., additional, Rosenow, Felix, additional, Rothschild, Annick, additional, Scudieri, Paolo, additional, Striano, Pasquale, additional, Tinuper, Paolo, additional, Tanteles, George A., additional, Vetro, Annalisa, additional, Zahnert, Felix, additional, Goldberg, Ethan M., additional, Zara, Federico, additional, Lal, Dennis, additional, May, Patrick, additional, Muhle, Hiltrud, additional, Helbig, Ingo, additional, and Weber, Yvonne, additional

Published
2022
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31. CNV-ClinViewer: Enhancing the clinical interpretation of large copy-number variants online

Author

Macnee, Marie, primary, Pérez-Palma, Eduardo, additional, Brünger, Tobias, additional, Klöckner, Chiara, additional, Platzer, Konrad, additional, Stefanski, Arthur, additional, Montanucci, Ludovica, additional, Bayat, Allan, additional, Radtke, Maximilian, additional, Collins, Ryan L, additional, Talkowski, Michael, additional, Blankenberg, Daniel, additional, Møller, Rikke S, additional, Lemke, Johannes R, additional, Nothnagel, Michael, additional, May, Patrick, additional, and Lal, Dennis, additional

Published
2022
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32. Spectrum of Phenotypic, Genetic, and Functional Characteristics in Patients With Epilepsy With KCNC2 Pathogenic Variants

Author

Schwarz, Niklas, Seiffert, Simone, Pendziwiat, Manuela, Rademacher, Annika Verena, Brünger, Tobias, Hedrich, Ulrike B. S., Augustijn, Paul B., Baier, Hartmut, Bayat, Allan, Bisulli, Francesca, Buono, Russell J., Bruria, Ben Zeev, Doyle, Michael G., Guerrini, Renzo, Heimer, Gali, Iacomino, Michele, Kearney, Hugh, Klein, Karl Martin, Kousiappa, Ioanna, Kunz, Wolfram S., Lerche, Holger, Licchetta, Laura, Lohmann, Ebba, Minardi, Raffaella, McDonald, Marie, Montgomery, Sarah, Mulahasanovic, Lejla, Oegema, Renske, Ortal, Barel, Papacostas, Savvas S., Ragona, Francesca, Granata, Tiziana, Reif, Phillip S., Rosenow, Felix, Rothschild, Annick, Scudieri, Paolo, Striano, Pasquale, Tinuper, Paolo, Tanteles, George A., Vetro, Annalisa, Zahnert, Felix, Goldberg, Ethan M., Zara, Federico, Lal, Dennis, May, Patrick, Muhle, Hiltrud, Helbig, Ingo, Weber, Yvonne, Schwarz N., Seiffert S., Pendziwiat M., Rademacher A.V., Brunger T., Hedrich U.B.S., Augustijn P.B., Baier H., Bayat A., Bisulli F., Buono R.J., Bruria B.Z., Doyle M.G., Guerrini R., Heimer G., Iacomino M., Kearney H., Klein K.M., Kousiappa I., Kunz W.S., Lerche H., Licchetta L., Lohmann E., Minardi R., McDonald M., Montgomery S., Mulahasanovic L., Oegema R., Ortal B., Papacostas S.S., Ragona F., Granata T., Reif P.S., Rosenow F., Rothschild A., Scudieri P., Striano P., Tinuper P., Tanteles G.A., Vetro A., Zahnert F., Goldberg E.M., Zara F., Lal D., May P., Muhle H., Helbig I., and Weber Y.

Subjects
Phenotype, Epilepsy, Shaw Potassium Channel, Epilepsy, Generalized, Seizure, Whole Exome Sequencing, Human
Abstract

Neurology : official journal of the American Academy of Neurology 98(20), e2046-e2059 (2022). doi:10.1212/WNL.0000000000200660, Published by Ovid, [S.l.]

Published
2022
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33. Conserved patterns across ion channels correlate with variant pathogenicity and clinical phenotypes.

Author

Brünger, Tobias, Pérez-Palma, Eduardo, Montanucci, Ludovica, Nothnagel, Michael, Møller, Rikke S, Schorge, Stephanie, Zuberi, Sameer, Symonds, Joseph, Lemke, Johannes R, Brunklaus, Andreas, Traynelis, Stephen F, May, Patrick, and Lal, Dennis

Subjects
*ION channels, *CLINICAL decision support systems, *SODIUM channels, *AMINO acid residues, *PHENOTYPES
Abstract

Clinically identified genetic variants in ion channels can be benign or cause disease by increasing or decreasing the protein function. As a consequence, therapeutic decision-making is challenging without molecular testing of each variant. Our biophysical knowledge of ion-channel structures and function is just emerging, and it is currently not well understood which amino acid residues cause disease when mutated. We sought to systematically identify biological properties associated with variant pathogenicity across all major voltage and ligand-gated ion-channel families. We collected and curated 3049 pathogenic variants from hundreds of neurodevelopmental and other disorders and 12 546 population variants for 30 ion channel or channel subunits for which a high-quality protein structure was available. Using a wide range of bioinformatics approaches, we computed 163 structural features and tested them for pathogenic variant enrichment. We developed a novel 3D spatial distance scoring approach that enables comparisons of pathogenic and population variant distribution across protein structures. We discovered and independently replicated that several pore residue properties and proximity to the pore axis were most significantly enriched for pathogenic variants compared to population variants. Using our 3D scoring approach, we showed that the strongest pathogenic variant enrichment was observed for pore-lining residues and alpha-helix residues within 5Å distance from the pore axis centre and not involved in gating. Within the subset of residues located at the pore, the hydrophobicity of the pore was the feature most strongly associated with variant pathogenicity. We also found an association between the identified properties and both clinical phenotypes and functional in vitro assays for voltage-gated sodium channels (SCN1A, SCN2A, SCN8A) and N -methyl-D-aspartate receptor (GRIN1, GRIN2A, GRIN2B) encoding genes. In an independent expert-curated dataset of 1422 neurodevelopmental disorder pathogenic patient variants and 679 electrophysiological experiments, we show that pore axis distance is associated with seizure age of onset and cognitive performance as well as differential gain versus loss-of-channel function. In summary, we identified biological properties associated with ion-channel malfunction and show that these are correlated with in vitro functional readouts and clinical phenotypes in patients with neurodevelopmental disorders. Our results suggest that clinical decision support algorithms that predict variant pathogenicity and function are feasible in the future. [ABSTRACT FROM AUTHOR]

Published
2023
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36. Delineation of functionally essential protein regions for 242 neurodevelopmental genes.

Author

Iqbal, Sumaiya, Brünger, Tobias, Pérez-Palma, Eduardo, Macnee, Marie, Brunklaus, Andreas, Daly, Mark J, Campbell, Arthur J, Hoksza, David, May, Patrick, and Lal, Dennis

Subjects
*PROTEIN structure, *EPILEPSY, *NEURAL development, *GENETIC testing, *GENETIC variation, *MISSENSE mutation, *PROTEIN-ligand interactions
Abstract

Neurodevelopmental disorders (NDDs), including severe paediatric epilepsy, autism and intellectual disabilities are heterogeneous conditions in which clinical genetic testing can often identify a pathogenic variant. For many of them, genetic therapies will be tested in this or the coming years in clinical trials. In contrast to first-generation symptomatic treatments, the new disease-modifying precision medicines require a genetic test-informed diagnosis before a patient can be enrolled in a clinical trial. However, even in 2022, most identified genetic variants in NDD genes are 'variants of uncertain significance'. To safely enrol patients in precision medicine clinical trials, it is important to increase our knowledge about which regions in NDD-associated proteins can 'tolerate' missense variants and which ones are 'essential' and will cause a NDD when mutated. In addition, knowledge about functionally indispensable regions in the 3D structure context of proteins can also provide insights into the molecular mechanisms of disease variants. We developed a novel consensus approach that overlays evolutionary, and population based genomic scores to identify 3D essential sites (Essential3D) on protein structures. After extensive benchmarking of AlphaFold predicted and experimentally solved protein structures, we generated the currently largest expert curated protein structure set for 242 NDDs and identified 14 377 Essential3D sites across 189 gene disorders associated proteins. We demonstrate that the consensus annotation of Essential3D sites improves prioritization of disease mutations over single annotations. The identified Essential3D sites were enriched for functional features such as intermembrane regions or active sites and discovered key inter-molecule interactions in protein complexes that were otherwise not annotated. Using the currently largest autism, developmental disorders, and epilepsies exome sequencing studies including >360 000 NDD patients and population controls, we found that missense variants at Essential3D sites are 8-fold enriched in patients. In summary, we developed a comprehensive protein structure set for 242 NDDs and identified 14 377 Essential3D sites in these. All data are available at https://es-ndd.broadinstitute.org for interactive visual inspection to enhance variant interpretation and development of mechanistic hypotheses for 242 NDDs genes. The provided resources will enhance clinical variant interpretation and in silico drug target development for NDD-associated genes and encoded proteins. [ABSTRACT FROM AUTHOR]

Published
2023
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37. Heterozygous variants in KCNC2 cause a broad spectrum of epilepsy phenotypes associated with characteristic functional alterations 2021.05.21.21257099

Author

Schwarz, Niklas, Seiffert, Simone, Pendziwiat, Manuela, Rademacher, Annika, Brünger, Tobias, Hedrich, Ulrike B. S., Augustijn, Paul B., Baier, Hartmut, Bayat, Allan, Bisulli, Francesca, Buono, Russell J., Bruria, Ben Zeev, Doyle, Michael G., Guerrini, Renzo, Heimer, Gali, Iacomino, Michele, Kearney, Hugh, Klein, Karl Martin, Kousiappa, Ioanna, Kunz, Wolfram S., Lerche, Holger, Licchetta, Laura, Lohmann, Ebba, Minardi, Raffaella, McDonald, Marie, Montgomery, Sarah, Mulahasanovic, Lejla, Oegema, Renske, Ortal, Barel, Papacostas, Savvas S., Ragona, Francesca, Granata, Tiziana, Reif, Philipp S., Rosenow, Felix, Rothschild, Annick, Scudieri, Paolo, Striano, Pasquale, Tinuper, Paolo, Tanteles, George A., Vetro, Annalisa, Zahnert, Felix, Zara, Federico, Lal, Dennis, May, Patrick, Muhle, Hiltrud, Helbig, Ingo, Weber, Yvonne, BMBF Treat-ION grant (01GM1907). [sponsor], and Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center]

Subjects
KCNC2, Neurologie [D14] [Sciences de la santé humaine], Neurology [D14] [Human health sciences], epilepsy, Genetics & genetic processes [F10] [Life sciences], Génétique & processus génétiques [F10] [Sciences du vivant], potassium channel
Abstract

Background KCNC2 encodes a member of the shaw-related voltage-gated potassium channel family (KV3.2), which are important for sustained high-frequency firing and optimized energy efficiency of action potentials in the brain.Methods Individuals with KCNC2 variants detected by exome sequencing were selected for clinical, further genetic and functional analysis. The cases were referred through clinical and research collaborations in our study. Four de novo variants were examined electrophysiologically in Xenopus laevis oocytes.Results We identified novel KCNC2 variants in 27 patients with various forms of epilepsy. Functional analysis demonstrated gain-of-function in severe and loss-of-function in milder phenotypes as the underlying pathomechanisms with specific response to valproic acid.Conclusion These findings implicate KCNC2 as a novel causative gene for epilepsy emphasizing the critical role of KV3.2 in the regulation of brain excitability with an interesting genotype-phenotype correlation and a potential concept for precision medicine.

Published
2021

38. Genotype-phenotype correlations in SCN8A-related disorders reveal prognostic and therapeutic implications

Author

Johannesen, Katrine M., Liu, Yuanyuan, Gjerulfsen, Cathrine E., Koko, Mahmoud, Sonnenberg, Lukas, Schubert, Julian, Fenger, Christina D., Eltokhi, Ahmed, Rannap, Maert, Koch, Nils A., Lauxmann, Stephan, Krüger, Johanna, Kegele, Josua, Canafoglia, Laura, Franceschetti, Silvana, Mayer, Thomas, Rebstock, Johannes, Zacher, Pia, Ruf, Susanne, Alber, Michael, Sterbova, Katalin, Lassuthová, Petra, Vlckova, Marketa, Lemke, Johannes R., Krey, Ilona, Heine, Constanze, Wieczorek, Dagmar, Kroell-Seger, Judith, Lund, Caroline, Klein, Karl Martin, Au, P. Y. Billie, Rho, Jong M., Ho, Alice W., Masnada, Silvia, Veggiotti, Pierangelo, Giordano, Lucio, Accorsi, Patrizia, Hoei-Hansen, Christina E., Striano, Pasquale, Zara, Federico, Verhelst, Helene, S.Verhoeven, Judith, van der Zwaag, Bert, Harder, Aster V. E., Brilstra, Eva, Pendziwiat, Manuela, Lebon, Sebastian, Vaccarezza, Maria, Le, Ngoc Minh, Christensen, Jakob, Schmidt-Petersen, Mette U., Grønborg, Sabine, Scherer, Stephen W., Howe, Jennifer, Fazeli, Walid, Howell, Katherine B., Leventer, Richard, Stutterd, Chloe, Walsh, Sonja, Gerard, Marion, Gerard, Bénédicte, Matricardi, Sara, Bonardi, Claudia M., Sartori, Stefano, Berger, Andrea, Hoffman-Zacharska, Dorota, Mastrangelo, Massimo, Darra, Francesca, Vøllo, Arve, Motazacker, M. Mahdi, Lakeman, Phillis, Nizon, Mathilde, Betzler, Cornelia, Altuzarra, Cecilia, Caume, Roseline, Roubertie, Agathe, Gélisse, Philippe, Marini, Carla, Guerrini, Renzo, Bilan, Frederic, Tibussek, Daniel, Koch-Hogrebe, Margarete, Perry, M. Scott, Ichikawa, Shoji, Dadali, Elena, Sharkov, Artem, Mishina, Irina, Abramov, Mikhail, Kanivets, Ilya, Korostelev, Sergey, Kutsev, Sergey, Wain, Karen E., Eisenhauer, Nancy, Wagner, Monisa, Savatt, Juliann M., Müller-Schlüter, Karen, Bassan, Haim, Borovikov, Artem, Nassogne, Marie-Cecile, Destrée, Anne, Schoonjans, An-Sofie, Meuwissen, Marije, Buzatu, Marga, Jansen, Anna, Scalais, Emmanuel, Srivastava, Siddharth, Tan, Wen-Hann, Olson, Heather E., Loddenkemper, Tobias, Poduri, Annapurna, Helbig, Katherine L., Helbig, Ingo, Fitzgerald, Mark P., Goldberg, Ethan M., Roser, Timo, Borggraefe, Ingo, Brünger, Tobias, May, Patrick, Lal, Dennis, Lederer, Damien, Rubboli, Guido, Lesca, Gaetan, Hedrich, Ulrike B. S., Benda, Jan, Gardella, Elena, Lerche, Holger, Møller, Rikke S., and Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center]

Subjects
Genetics & genetic processes [F10] [Life sciences], Génétique & processus génétiques [F10] [Sciences du vivant]
Abstract

We report detailed functional analyses and genotype-phenotype correlations in 433 individuals carrying disease-causing variants in SCN8A, encoding the voltage-gated Na+ channel NaV1.6. Five different clinical subgroups could be identified: 1) Benign familial infantile epilepsy (BFIE) (n=17, normal cognition, treatable seizures), 2) intermediate epilepsy (n=36, mild ID, partially pharmacoresponsive), 3) developmental and epileptic encephalopathy (DEE, n=191, severe ID, majority pharmacoresistant), 4) generalized epilepsy (n=21, mild to moderate ID, frequently with absence seizures), and 5) affected individuals without epilepsy (n=25, mild to moderate ID). Groups 1-3 presented with early-onset (median: four months) focal or multifocal seizures and epileptic discharges, whereas the onset of seizures in group 4 was later (median: 39 months) with generalized epileptic discharges. The epilepsy was not classifiable in 143 individuals. We performed functional studies expressing missense variants in ND7/23 neuroblastoma cells and primary neuronal cultures using recombinant tetrodotoxin insensitive human NaV1.6 channels and whole-cell patch clamping. Two variants causing DEE showed a strong gain-of-function (GOF, hyperpolarising shift of steady-state activation, strongly increased neuronal firing rate), and one variant causing BFIE or intermediate epilepsy showed a mild GOF (defective fast inactivation, less increased firing). In contrast, all three variants causing generalized epilepsy induced a loss-of-function (LOF, reduced current amplitudes, depolarising shift of steady-state activation, reduced neuronal firing). Including previous studies, functional effects were known for 165 individuals. All 133 individuals carrying GOF variants had either focal (76, groups 1-3), or unclassifiable epilepsy (37), whereas 32 with LOF variants had either generalized (14), no (11) or unclassifiable (5) epilepsy; only two had DEE. Computational modeling in the GOF group revealed a significant correlation between the severity of the electrophysiological and clinical phenotypes. GOF variant carriers responded significantly better to sodium channel blockers (SCBs) than to other anti-seizure medications, and the same applied for all individuals of groups 1-3.In conclusion, our data reveal clear genotype-phenotype correlations between age at seizure onset, type of epilepsy and gain- or loss-of-function effects of SCN8A variants. Generalized epilepsy with absence seizures is the main epilepsy phenotype of LOF variant carriers and the extent of the electrophysiological dysfunction of the GOF variants is a main determinant of the severity of the clinical phenotype in focal epilepsies. Our pharmacological data indicate that SCBs present a therapeutic treatment option in early onset SCN8A-related focal epilepsy.

Published
2021

39. Genotype-phenotype correlations in SCN8A-related disorders reveal prognostic and therapeutic implications

Author

Johannesen, Katrine M, primary, Liu, Yuanyuan, additional, Koko, Mahmoud, additional, Gjerulfsen, Cathrine E, additional, Sonnenberg, Lukas, additional, Schubert, Julian, additional, Fenger, Christina D, additional, Eltokhi, Ahmed, additional, Rannap, Maert, additional, Koch, Nils A, additional, Lauxmann, Stephan, additional, Krüger, Johanna, additional, Kegele, Josua, additional, Canafoglia, Laura, additional, Franceschetti, Silvana, additional, Mayer, Thomas, additional, Rebstock, Johannes, additional, Zacher, Pia, additional, Ruf, Susanne, additional, Alber, Michael, additional, Sterbova, Katalin, additional, Lassuthová, Petra, additional, Vlckova, Marketa, additional, Lemke, Johannes R, additional, Platzer, Konrad, additional, Krey, Ilona, additional, Heine, Constanze, additional, Wieczorek, Dagmar, additional, Kroell-Seger, Judith, additional, Lund, Caroline, additional, Klein, Karl Martin, additional, Au, P Y Billie, additional, Rho, Jong M, additional, Ho, Alice W, additional, Masnada, Silvia, additional, Veggiotti, Pierangelo, additional, Giordano, Lucio, additional, Accorsi, Patrizia, additional, Hoei-Hansen, Christina E, additional, Striano, Pasquale, additional, Zara, Federico, additional, Verhelst, Helene, additional, Verhoeven, Judith S, additional, Braakman, Hilde M H, additional, van der Zwaag, Bert, additional, Harder, Aster V E, additional, Brilstra, Eva, additional, Pendziwiat, Manuela, additional, Lebon, Sebastian, additional, Vaccarezza, Maria, additional, Le, Ngoc Minh, additional, Christensen, Jakob, additional, Grønborg, Sabine, additional, Scherer, Stephen W, additional, Howe, Jennifer, additional, Fazeli, Walid, additional, Howell, Katherine B, additional, Leventer, Richard, additional, Stutterd, Chloe, additional, Walsh, Sonja, additional, Gerard, Marion, additional, Gerard, Bénédicte, additional, Matricardi, Sara, additional, Bonardi, Claudia M, additional, Sartori, Stefano, additional, Berger, Andrea, additional, Hoffman-Zacharska, Dorota, additional, Mastrangelo, Massimo, additional, Darra, Francesca, additional, Vøllo, Arve, additional, Motazacker, M Mahdi, additional, Lakeman, Phillis, additional, Nizon, Mathilde, additional, Betzler, Cornelia, additional, Altuzarra, Cecilia, additional, Caume, Roseline, additional, Roubertie, Agathe, additional, Gélisse, Philippe, additional, Marini, Carla, additional, Guerrini, Renzo, additional, Bilan, Frederic, additional, Tibussek, Daniel, additional, Koch-Hogrebe, Margarete, additional, Perry, M Scott, additional, Ichikawa, Shoji, additional, Dadali, Elena, additional, Sharkov, Artem, additional, Mishina, Irina, additional, Abramov, Mikhail, additional, Kanivets, Ilya, additional, Korostelev, Sergey, additional, Kutsev, Sergey, additional, Wain, Karen E, additional, Eisenhauer, Nancy, additional, Wagner, Monisa, additional, Savatt, Juliann M, additional, Müller-Schlüter, Karen, additional, Bassan, Haim, additional, Borovikov, Artem, additional, Nassogne, Marie Cecile, additional, Destrée, Anne, additional, Schoonjans, An Sofie, additional, Meuwissen, Marije, additional, Buzatu, Marga, additional, Jansen, Anna, additional, Scalais, Emmanuel, additional, Srivastava, Siddharth, additional, Tan, Wen Hann, additional, Olson, Heather E, additional, Loddenkemper, Tobias, additional, Poduri, Annapurna, additional, Helbig, Katherine L, additional, Helbig, Ingo, additional, Fitzgerald, Mark P, additional, Goldberg, Ethan M, additional, Roser, Timo, additional, Borggraefe, Ingo, additional, Brünger, Tobias, additional, May, Patrick, additional, Lal, Dennis, additional, Lederer, Damien, additional, Rubboli, Guido, additional, Heyne, Henrike O, additional, Lesca, Gaetan, additional, Hedrich, Ulrike B S, additional, Benda, Jan, additional, Gardella, Elena, additional, Lerche, Holger, additional, and Møller, Rikke S, additional

Published
2021
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40. Heterozygous variants in KCNC2 cause a broad spectrum of epilepsy phenotypes associated with characteristic functional alterations 2021.05.21.21257099

Author

Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], BMBF Treat-ION grant (01GM1907). [sponsor], Schwarz, Niklas, Seiffert, Simone, Pendziwiat, Manuela, Rademacher, Annika, Brünger, Tobias, Hedrich, Ulrike B. S., Augustijn, Paul B., Baier, Hartmut, Bayat, Allan, Bisulli, Francesca, Buono, Russell J., Bruria, Ben Zeev, Doyle, Michael G., Guerrini, Renzo, Heimer, Gali, Iacomino, Michele, Kearney, Hugh, Klein, Karl Martin, Kousiappa, Ioanna, Kunz, Wolfram S., Lerche, Holger, Licchetta, Laura, Lohmann, Ebba, Minardi, Raffaella, McDonald, Marie, Montgomery, Sarah, Mulahasanovic, Lejla, Oegema, Renske, Ortal, Barel, Papacostas, Savvas S., Ragona, Francesca, Granata, Tiziana, Reif, Philipp S., Rosenow, Felix, Rothschild, Annick, Scudieri, Paolo, Striano, Pasquale, Tinuper, Paolo, Tanteles, George A., Vetro, Annalisa, Zahnert, Felix, Zara, Federico, Lal, Dennis, May, Patrick, Muhle, Hiltrud, Helbig, Ingo, Weber, Yvonne, Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], BMBF Treat-ION grant (01GM1907). [sponsor], Schwarz, Niklas, Seiffert, Simone, Pendziwiat, Manuela, Rademacher, Annika, Brünger, Tobias, Hedrich, Ulrike B. S., Augustijn, Paul B., Baier, Hartmut, Bayat, Allan, Bisulli, Francesca, Buono, Russell J., Bruria, Ben Zeev, Doyle, Michael G., Guerrini, Renzo, Heimer, Gali, Iacomino, Michele, Kearney, Hugh, Klein, Karl Martin, Kousiappa, Ioanna, Kunz, Wolfram S., Lerche, Holger, Licchetta, Laura, Lohmann, Ebba, Minardi, Raffaella, McDonald, Marie, Montgomery, Sarah, Mulahasanovic, Lejla, Oegema, Renske, Ortal, Barel, Papacostas, Savvas S., Ragona, Francesca, Granata, Tiziana, Reif, Philipp S., Rosenow, Felix, Rothschild, Annick, Scudieri, Paolo, Striano, Pasquale, Tinuper, Paolo, Tanteles, George A., Vetro, Annalisa, Zahnert, Felix, Zara, Federico, Lal, Dennis, May, Patrick, Muhle, Hiltrud, Helbig, Ingo, and Weber, Yvonne

Abstract

Background KCNC2 encodes a member of the shaw-related voltage-gated potassium channel family (KV3.2), which are important for sustained high-frequency firing and optimized energy efficiency of action potentials in the brain.Methods Individuals with KCNC2 variants detected by exome sequencing were selected for clinical, further genetic and functional analysis. The cases were referred through clinical and research collaborations in our study. Four de novo variants were examined electrophysiologically in Xenopus laevis oocytes.Results We identified novel KCNC2 variants in 27 patients with various forms of epilepsy. Functional analysis demonstrated gain-of-function in severe and loss-of-function in milder phenotypes as the underlying pathomechanisms with specific response to valproic acid.Conclusion These findings implicate KCNC2 as a novel causative gene for epilepsy emphasizing the critical role of KV3.2 in the regulation of brain excitability with an interesting genotype-phenotype correlation and a potential concept for precision medicine.

Published
2021

41. Genotype-phenotype correlations in SCN8A-related disorders reveal prognostic and therapeutic implications

Author

Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Johannesen, Katrine M., Liu, Yuanyuan, Gjerulfsen, Cathrine E., Koko, Mahmoud, Sonnenberg, Lukas, Schubert, Julian, Fenger, Christina D., Eltokhi, Ahmed, Rannap, Maert, Koch, Nils A., Lauxmann, Stephan, Krüger, Johanna, Kegele, Josua, Canafoglia, Laura, Franceschetti, Silvana, Mayer, Thomas, Rebstock, Johannes, Zacher, Pia, Ruf, Susanne, Alber, Michael, Sterbova, Katalin, Lassuthová, Petra, Vlckova, Marketa, Lemke, Johannes R., Krey, Ilona, Heine, Constanze, Wieczorek, Dagmar, Kroell-Seger, Judith, Lund, Caroline, Klein, Karl Martin, Au, P. Y. Billie, Rho, Jong M., Ho, Alice W., Masnada, Silvia, Veggiotti, Pierangelo, Giordano, Lucio, Accorsi, Patrizia, Hoei-Hansen, Christina E., Striano, Pasquale, Zara, Federico, Verhelst, Helene, S.Verhoeven, Judith, van der Zwaag, Bert, Harder, Aster V. E., Brilstra, Eva, Pendziwiat, Manuela, Lebon, Sebastian, Vaccarezza, Maria, Le, Ngoc Minh, Christensen, Jakob, Schmidt-Petersen, Mette U., Grønborg, Sabine, Scherer, Stephen W., Howe, Jennifer, Fazeli, Walid, Howell, Katherine B., Leventer, Richard, Stutterd, Chloe, Walsh, Sonja, Gerard, Marion, Gerard, Bénédicte, Matricardi, Sara, Bonardi, Claudia M., Sartori, Stefano, Berger, Andrea, Hoffman-Zacharska, Dorota, Mastrangelo, Massimo, Darra, Francesca, Vøllo, Arve, Motazacker, M. Mahdi, Lakeman, Phillis, Nizon, Mathilde, Betzler, Cornelia, Altuzarra, Cecilia, Caume, Roseline, Roubertie, Agathe, Gélisse, Philippe, Marini, Carla, Guerrini, Renzo, Bilan, Frederic, Tibussek, Daniel, Koch-Hogrebe, Margarete, Perry, M. Scott, Ichikawa, Shoji, Dadali, Elena, Sharkov, Artem, Mishina, Irina, Abramov, Mikhail, Kanivets, Ilya, Korostelev, Sergey, Kutsev, Sergey, Wain, Karen E., Eisenhauer, Nancy, Wagner, Monisa, Savatt, Juliann M., Müller-Schlüter, Karen, Bassan, Haim, Borovikov, Artem, Nassogne, Marie-Cecile, Destrée, Anne, Schoonjans, An-Sofie, Meuwissen, Marije, Buzatu, Marga, Jansen, Anna, Scalais, Emmanuel, Srivastava, Siddharth, Tan, Wen-Hann, Olson, Heather E., Loddenkemper, Tobias, Poduri, Annapurna, Helbig, Katherine L., Helbig, Ingo, Fitzgerald, Mark P., Goldberg, Ethan M., Roser, Timo, Borggraefe, Ingo, Brünger, Tobias, May, Patrick, Lal, Dennis, Lederer, Damien, Rubboli, Guido, Lesca, Gaetan, Hedrich, Ulrike B. S., Benda, Jan, Gardella, Elena, Lerche, Holger, Møller, Rikke S., Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Johannesen, Katrine M., Liu, Yuanyuan, Gjerulfsen, Cathrine E., Koko, Mahmoud, Sonnenberg, Lukas, Schubert, Julian, Fenger, Christina D., Eltokhi, Ahmed, Rannap, Maert, Koch, Nils A., Lauxmann, Stephan, Krüger, Johanna, Kegele, Josua, Canafoglia, Laura, Franceschetti, Silvana, Mayer, Thomas, Rebstock, Johannes, Zacher, Pia, Ruf, Susanne, Alber, Michael, Sterbova, Katalin, Lassuthová, Petra, Vlckova, Marketa, Lemke, Johannes R., Krey, Ilona, Heine, Constanze, Wieczorek, Dagmar, Kroell-Seger, Judith, Lund, Caroline, Klein, Karl Martin, Au, P. Y. Billie, Rho, Jong M., Ho, Alice W., Masnada, Silvia, Veggiotti, Pierangelo, Giordano, Lucio, Accorsi, Patrizia, Hoei-Hansen, Christina E., Striano, Pasquale, Zara, Federico, Verhelst, Helene, S.Verhoeven, Judith, van der Zwaag, Bert, Harder, Aster V. E., Brilstra, Eva, Pendziwiat, Manuela, Lebon, Sebastian, Vaccarezza, Maria, Le, Ngoc Minh, Christensen, Jakob, Schmidt-Petersen, Mette U., Grønborg, Sabine, Scherer, Stephen W., Howe, Jennifer, Fazeli, Walid, Howell, Katherine B., Leventer, Richard, Stutterd, Chloe, Walsh, Sonja, Gerard, Marion, Gerard, Bénédicte, Matricardi, Sara, Bonardi, Claudia M., Sartori, Stefano, Berger, Andrea, Hoffman-Zacharska, Dorota, Mastrangelo, Massimo, Darra, Francesca, Vøllo, Arve, Motazacker, M. Mahdi, Lakeman, Phillis, Nizon, Mathilde, Betzler, Cornelia, Altuzarra, Cecilia, Caume, Roseline, Roubertie, Agathe, Gélisse, Philippe, Marini, Carla, Guerrini, Renzo, Bilan, Frederic, Tibussek, Daniel, Koch-Hogrebe, Margarete, Perry, M. Scott, Ichikawa, Shoji, Dadali, Elena, Sharkov, Artem, Mishina, Irina, Abramov, Mikhail, Kanivets, Ilya, Korostelev, Sergey, Kutsev, Sergey, Wain, Karen E., Eisenhauer, Nancy, Wagner, Monisa, Savatt, Juliann M., Müller-Schlüter, Karen, Bassan, Haim, Borovikov, Artem, Nassogne, Marie-Cecile, Destrée, Anne, Schoonjans, An-Sofie, Meuwissen, Marije, Buzatu, Marga, Jansen, Anna, Scalais, Emmanuel, Srivastava, Siddharth, Tan, Wen-Hann, Olson, Heather E., Loddenkemper, Tobias, Poduri, Annapurna, Helbig, Katherine L., Helbig, Ingo, Fitzgerald, Mark P., Goldberg, Ethan M., Roser, Timo, Borggraefe, Ingo, Brünger, Tobias, May, Patrick, Lal, Dennis, Lederer, Damien, Rubboli, Guido, Lesca, Gaetan, Hedrich, Ulrike B. S., Benda, Jan, Gardella, Elena, Lerche, Holger, and Møller, Rikke S.

Abstract

We report detailed functional analyses and genotype-phenotype correlations in 433 individuals carrying disease-causing variants in SCN8A, encoding the voltage-gated Na+ channel NaV1.6. Five different clinical subgroups could be identified: 1) Benign familial infantile epilepsy (BFIE) (n=17, normal cognition, treatable seizures), 2) intermediate epilepsy (n=36, mild ID, partially pharmacoresponsive), 3) developmental and epileptic encephalopathy (DEE, n=191, severe ID, majority pharmacoresistant), 4) generalized epilepsy (n=21, mild to moderate ID, frequently with absence seizures), and 5) affected individuals without epilepsy (n=25, mild to moderate ID). Groups 1-3 presented with early-onset (median: four months) focal or multifocal seizures and epileptic discharges, whereas the onset of seizures in group 4 was later (median: 39 months) with generalized epileptic discharges. The epilepsy was not classifiable in 143 individuals. We performed functional studies expressing missense variants in ND7/23 neuroblastoma cells and primary neuronal cultures using recombinant tetrodotoxin insensitive human NaV1.6 channels and whole-cell patch clamping. Two variants causing DEE showed a strong gain-of-function (GOF, hyperpolarising shift of steady-state activation, strongly increased neuronal firing rate), and one variant causing BFIE or intermediate epilepsy showed a mild GOF (defective fast inactivation, less increased firing). In contrast, all three variants causing generalized epilepsy induced a loss-of-function (LOF, reduced current amplitudes, depolarising shift of steady-state activation, reduced neuronal firing). Including previous studies, functional effects were known for 165 individuals. All 133 individuals carrying GOF variants had either focal (76, groups 1-3), or unclassifiable epilepsy (37), whereas 32 with LOF variants had either generalized (14), no (11) or unclassifiable (5) epilepsy; only two had DEE. Computational modeling in the GOF group revealed a signific

Published
2021

42. Heterozygous variants in KCNC2 cause a broad spectrum of epilepsy phenotypes associated with characteristic functional alterations

Author

Schwarz, Niklas, primary, Seiffert, Simone, additional, Pendziwiat, Manuela, additional, Rademacher, Annika, additional, Brünger, Tobias, additional, Hedrich, Ulrike B.S., additional, Augustijn, Paul B, additional, Baier, Hartmut, additional, Bayat, Allan, additional, Bisulli, Francesca, additional, Buono, Russell J, additional, Bruria, Ben Zeev, additional, Doyle, Michael G, additional, Guerrini, Renzo, additional, Heimer, Gali, additional, Iacomino, Michele, additional, Kearney, Hugh, additional, Klein, Karl Martin, additional, Kousiappa, Ioanna, additional, Kunz, Wolfram S., additional, Lerche, Holger, additional, Licchetta, Laura, additional, Lohmann, Ebba, additional, Minardi, Raffaella, additional, McDonald, Marie, additional, Montgomery, Sarah, additional, Mulahasanovic, Lejla, additional, Oegema, Renske, additional, Ortal, Barel, additional, Papacostas, Savvas S., additional, Ragona, Francesca, additional, Granata, Tiziana, additional, Reif, Philipp S., additional, Rosenow, Felix, additional, Rothschild, Annick, additional, Scudieri, Paolo, additional, Striano, Pasquale, additional, Tinuper, Paolo, additional, Tanteles, George A., additional, Vetro, Annalisa, additional, Zahnert, Felix, additional, Zara, Federico, additional, Lal, Dennis, additional, May, Patrick, additional, Muhle, Hiltrud, additional, Helbig, Ingo, additional, and Weber, Yvonne, additional

Published
2021
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44. Lessons learned from 40 novel PIGA patients and a review of the literature

Author

Bayat, Allan, primary, Knaus, Alexej, additional, Pendziwiat, Manuela, additional, Afenjar, Alexandra, additional, Barakat, Tahsin Stefan, additional, Bosch, Friedrich, additional, Callewaert, Bert, additional, Calvas, Patrick, additional, Ceulemans, Berten, additional, Chassaing, Nicolas, additional, Depienne, Christel, additional, Endziniene, Milda, additional, Ferreira, Carlos R., additional, Moura de Souza, Carolina Fischinger, additional, Freihuber, Cécile, additional, Ganesan, Shiva, additional, Gataullina, Svetlana, additional, Guerrini, Renzo, additional, Guerrot, Anne‐Marie, additional, Hansen, Lars, additional, Jezela‐Stanek, Aleksandra, additional, Karsenty, Caroline, additional, Kievit, Anneke, additional, Kooy, Frank R., additional, Korff, Christian M., additional, Kragh Hansen, Johanne, additional, Larsen, Martin, additional, Layet, Valérie, additional, Lesca, Gaetan, additional, McBride, Kim L., additional, Meuwissen, Marije, additional, Mignot, Cyril, additional, Montomoli, Martino, additional, Moore, Hannah, additional, Naudion, Sophie, additional, Nava, Caroline, additional, Nougues, Marie‐Christine, additional, Parrini, Elena, additional, Pastore, Matthew, additional, Schelhaas, Jurgen H., additional, Skinner, Steven, additional, Szczałuba, Krzysztoł, additional, Thomas, Ashley, additional, Thomassen, Mads, additional, Tranebjærg, Lisbeth, additional, van Slegtenhorst, Marjon, additional, Wolfe, Lynne A., additional, Lal, Dennis, additional, Gardella, Elena, additional, Bomme Ousager, Lilian, additional, Brünger, Tobias, additional, Helbig, Ingo, additional, Krawitz, Peter, additional, and Møller, Rikke S., additional

Published
2020
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45. Spectrum of Phenotypic, Genetic, and Functional Characteristics in Patients With Epilepsy With Pathogenic Variants.

Author

Schwarz, Niklas, Seiffert, Simone, Pendziwiat, Manuela, Rademacher, Annika Verena, Brünger, Tobias, Hedrich, Ulrike B.S., Augustijn, Paul B., Baier, Hartmut, Bayat, Allan, Bisulli, Francesca, Buono, Russell J., Bruria, Ben Zeev, Doyle, Michael G., Guerrini, Renzo, Heimer, Gali, Iacomino, Michele, Kearney, Hugh, Klein, Karl Martin, Kousiappa, Ioanna, and Kunz, Wolfram S.

Published
2022
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46. Reply: Follow the allosteric transitions to predict variant pathogenicity: a channel-specific approach.

Author

Montanucci, Ludovica, Brünger, Tobias, and Lal, Dennis

Subjects
*PROTEIN structure prediction, *ION channels
Abstract

The article is a response to a comment on a previous study about predicting the pathogenicity of variants in ion channels. The authors of the response acknowledge that their cross-channel approach may not be accurate for all families of ion channels due to their structural and functional differences. They suggest that a protein-specific approach, tailored to the structure and activation mechanism of each ion channel, may be more effective. The response highlights the merits of this approach, including the need for clinical-grade accuracy, consideration of protein dynamics, and the refinement of predictive features. The study by Absalom et al. demonstrates the potential of a protein-specific approach to improve variant classification and deepen our understanding of biological functions. [Extracted from the article]

Published
2024
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47. Lessons learned from 40 novel PIGA patients and a review of the literature

Author

Bayat, Allan, Knaus, Alexej, Pendziwiat, Manuela, Afenjar, Alexandra, Stefan Barakat, Tahsin, Bosch, Friedrich, Callewaert, Bert, Calvas, Patrick, Ceulemans, Berten, Chassaing, Nicolas, Depienne, Christel, Endziniene, Milda, Ferreira, Carlos R., Moura de Souza, Carolina Fischinger, Freihuber, Cécile, Ganesan, Shiva, Gataullina, Svetlana, Guerrini, Renzo, Guerrot, Anne Marie, Hansen, Lars, Jezela-Stanek, Aleksandra, Karsenty, Caroline, Kievit, Anneke, Kooy, Frank R., Korff, Christian M., Kragh Hansen, Johanne, Larsen, Martin, Layet, Valérie, Lesca, Gaetan, McBride, Kim L., Meuwissen, Marije, Mignot, Cyril, Montomoli, Martino, Moore, Hannah, Naudion, Sophie, Nava, Caroline, Nougues, Marie Christine, Parrini, Elena, Pastore, Matthew, Schelhaas, Jurgen H., Skinner, Steven, Szczałuba, Krzysztoł, Thomas, Ashley, Thomassen, Mads, Tranebjærg, Lisbeth, van Slegtenhorst, Marjon, Wolfe, Lynne A., Lal, Dennis, Gardella, Elena, Bomme Ousager, Lilian, Brünger, Tobias, Helbig, Ingo, Krawitz, Peter, Møller, Rikke S., Bayat, Allan, Knaus, Alexej, Pendziwiat, Manuela, Afenjar, Alexandra, Stefan Barakat, Tahsin, Bosch, Friedrich, Callewaert, Bert, Calvas, Patrick, Ceulemans, Berten, Chassaing, Nicolas, Depienne, Christel, Endziniene, Milda, Ferreira, Carlos R., Moura de Souza, Carolina Fischinger, Freihuber, Cécile, Ganesan, Shiva, Gataullina, Svetlana, Guerrini, Renzo, Guerrot, Anne Marie, Hansen, Lars, Jezela-Stanek, Aleksandra, Karsenty, Caroline, Kievit, Anneke, Kooy, Frank R., Korff, Christian M., Kragh Hansen, Johanne, Larsen, Martin, Layet, Valérie, Lesca, Gaetan, McBride, Kim L., Meuwissen, Marije, Mignot, Cyril, Montomoli, Martino, Moore, Hannah, Naudion, Sophie, Nava, Caroline, Nougues, Marie Christine, Parrini, Elena, Pastore, Matthew, Schelhaas, Jurgen H., Skinner, Steven, Szczałuba, Krzysztoł, Thomas, Ashley, Thomassen, Mads, Tranebjærg, Lisbeth, van Slegtenhorst, Marjon, Wolfe, Lynne A., Lal, Dennis, Gardella, Elena, Bomme Ousager, Lilian, Brünger, Tobias, Helbig, Ingo, Krawitz, Peter, and Møller, Rikke S.

Abstract

Objective: To define the phenotypic spectrum of phosphatidylinositol glycan class A protein (PIGA)-related congenital disorder of glycosylation (PIGA-CDG) and evaluate genotype-phenotype correlations. Methods: Our cohort encompasses 40 affected males with a pathogenic PIGA variant. We performed a detailed phenotypic assessment, and in addition, we reviewed the available clinical data of 36 previously published cases and assessed the variant pathogenicity using bioinformatical approaches. Results: Most individuals had hypotonia, moderate to profound global developmental delay, and intractable seizures. We found that PIGA-CDG spans from a pure neurological phenotype at the mild end to a Fryns syndrome–like phenotype. We found a high frequency of cardiac anomalies including structural anomalies and cardiomyopathy, and a high frequency of spontaneous death, especially in childhood. Comparative bioinformatical analysis of common variants, found in the healthy population, and pathogenic variants, identified in affected individuals, revealed a profound physiochemical dissimilarity of the substituted amino acids in variant constrained regions of the protein. Significance: Our comprehensive analysis of the largest cohort of published and novel PIGA patients broadens the spectrum of PIGA-CDG. Our genotype-phenotype correlation facilitates the estimation on pathogenicity of variants with unknown clinical significance and prognosis for individuals with pathogenic variants in PIGA.

Published
2020

49. The spectrum of intermediateSCN 8A‐related epilepsy

Author

Johannesen, Katrine M., primary, Gardella, Elena, additional, Encinas, Alejandra C., additional, Lehesjoki, Anna‐Elina, additional, Linnankivi, Tarja, additional, Petersen, Michael B., additional, Lund, Ida Charlotte Bay, additional, Blichfeldt, Susanne, additional, Miranda, Maria J., additional, Pal, Deb K., additional, Lascelles, Karine, additional, Procopis, Peter, additional, Orsini, Alessandro, additional, Bonuccelli, Alice, additional, Giacomini, Thea, additional, Helbig, Ingo, additional, Fenger, Christina D., additional, Sisodiya, Sanjay M., additional, Hernandez‐Hernandez, Laura, additional, Krithika, Sundararaman, additional, Rumple, Melissa, additional, Masnada, Silvia, additional, Valente, Marialuisa, additional, Cereda, Cristina, additional, Giordano, Lucio, additional, Accorsi, Patrizia, additional, Bürki, Sarah E., additional, Mancardi, Margherita, additional, Korff, Christian, additional, Guerrini, Renzo, additional, Spiczak, Sarah, additional, Hoffman‐Zacharska, Dorota, additional, Mazurczak, Tomasz, additional, Coppola, Antonietta, additional, Buono, Salvatore, additional, Vecchi, Marilena, additional, Hammer, Michael F., additional, Varesio, Costanza, additional, Veggiotti, Pierangelo, additional, Lal, Dennis, additional, Brünger, Tobias, additional, Zara, Federico, additional, Striano, Pasquale, additional, Rubboli, Guido, additional, and Møller, Rikke S., additional

Published
2019
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50. Spectrum of Phenotypic, Genetic, and Functional Characteristics in Patients With Epilepsy With KCNC2Pathogenic Variants

Author

Schwarz, Niklas, Seiffert, Simone, Pendziwiat, Manuela, Rademacher, Annika Verena, Brünger, Tobias, Hedrich, Ulrike B.S., Augustijn, Paul B., Baier, Hartmut, Bayat, Allan, Bisulli, Francesca, Buono, Russell J., Bruria, Ben Zeev, Doyle, Michael G., Guerrini, Renzo, Heimer, Gali, Iacomino, Michele, Kearney, Hugh, Klein, Karl Martin, Kousiappa, Ioanna, Kunz, Wolfram S., Lerche, Holger, Licchetta, Laura, Lohmann, Ebba, Minardi, Raffaella, McDonald, Marie, Montgomery, Sarah, Mulahasanovic, Lejla, Oegema, Renske, Ortal, Barel, Papacostas, Savvas S., Ragona, Francesca, Granata, Tiziana, Reif, Phillip S., Rosenow, Felix, Rothschild, Annick, Scudieri, Paolo, Striano, Pasquale, Tinuper, Paolo, Tanteles, George A., Vetro, Annalisa, Zahnert, Felix, Goldberg, Ethan M., Zara, Federico, Lal, Dennis, May, Patrick, Muhle, Hiltrud, Helbig, Ingo, and Weber, Yvonne

Published
2022
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