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Heins-Marroquin U, Singh RR, Perathoner S, Gavotto F, Merino Ruiz C, Patraskaki M, Gomez-Giro G, Kleine Borgmann F, Meyer M, Carpentier A, Warmoes MO, Jäger C, Mittelbronn M, Schwamborn JC, Cordero-Maldonado ML, Crawford AD, Schymanski EL, Linster CL. CLN3 deficiency leads to neurological and metabolic perturbations during early development. Life Sci Alliance 2024; 7:e202302057. [PMID: 38195117 PMCID: PMC10776888 DOI: 10.26508/lsa.202302057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 01/11/2024] Open
Abstract
Juvenile neuronal ceroid lipofuscinosis (or Batten disease) is an autosomal recessive, rare neurodegenerative disorder that affects mainly children above the age of 5 yr and is most commonly caused by mutations in the highly conserved CLN3 gene. Here, we generated cln3 morphants and stable mutant lines in zebrafish. Although neither morphant nor mutant cln3 larvae showed any obvious developmental or morphological defects, behavioral phenotyping of the mutant larvae revealed hyposensitivity to abrupt light changes and hypersensitivity to pro-convulsive drugs. Importantly, in-depth metabolomics and lipidomics analyses revealed significant accumulation of several glycerophosphodiesters (GPDs) and cholesteryl esters, and a global decrease in bis(monoacylglycero)phosphate species, two of which (GPDs and bis(monoacylglycero)phosphates) were previously proposed as potential biomarkers for CLN3 disease based on independent studies in other organisms. We could also demonstrate GPD accumulation in human-induced pluripotent stem cell-derived cerebral organoids carrying a pathogenic variant for CLN3 Our models revealed that GPDs accumulate at very early stages of life in the absence of functional CLN3 and highlight glycerophosphoinositol and BMP as promising biomarker candidates for pre-symptomatic CLN3 disease.
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Affiliation(s)
- Ursula Heins-Marroquin
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Randolph R Singh
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
- https://ror.org/00hj8s172 Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Simon Perathoner
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Floriane Gavotto
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Carla Merino Ruiz
- Institut d'Investigació Sanitària Pere Virgili, Tarragona, Spain
- Biosfer Teslab SL, Reus, Spain
| | - Myrto Patraskaki
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Gemma Gomez-Giro
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Felix Kleine Borgmann
- National Center of Pathology (NCP), Laboratoire national de santé (LNS), Dudelange, Luxembourg
- Department of Oncology (DONC), Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | - Melanie Meyer
- National Center of Pathology (NCP), Laboratoire national de santé (LNS), Dudelange, Luxembourg
| | - Anaïs Carpentier
- National Center of Pathology (NCP), Laboratoire national de santé (LNS), Dudelange, Luxembourg
| | - Marc O Warmoes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Christian Jäger
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Michel Mittelbronn
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
- National Center of Pathology (NCP), Laboratoire national de santé (LNS), Dudelange, Luxembourg
- Department of Oncology (DONC), Luxembourg Institute of Health (LIH), Strassen, Luxembourg
- Luxembourg Center of Neuropathology (LCNP), Dudelange, Luxembourg
- Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Department of Life Science and Medicine (DLSM), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Jens C Schwamborn
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | | | - Alexander D Crawford
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
- Department of Preclinical Sciences and Pathology, Norwegian University of Life Sciences (NMBU), Ås, Norway
- Institute for Orphan Drug Discovery, Bremerhaven, Germany
| | - Emma L Schymanski
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Carole L Linster
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
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2
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Martins TG, Soliman R, Cordero-Maldonado ML, Donato C, Ameli C, Mombaerts L, Skupin A, Peri F, Crawford AD. Seizure-induced increase in microglial cell population in the developing zebrafish brain. Epilepsy Res 2023; 195:107203. [PMID: 37572541 DOI: 10.1016/j.eplepsyres.2023.107203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 06/21/2023] [Accepted: 07/31/2023] [Indexed: 08/14/2023]
Abstract
Epilepsy is a chronic brain disorder characterized by unprovoked and recurrent seizures, of which 60% are of unknown etiology. Recent studies implicate microglia in the pathophysiology of epilepsy. However, their role in this process, in particular following early-life seizures, remains poorly understood due in part to the lack of suitable experimental models allowing the in vivo imaging of microglial activity. Given the advantage of zebrafish larvae for minimally-invasive imaging approaches, we sought for the first time to describe the microglial responses after acute seizures in two different zebrafish larval models: a chemically-induced epileptic model by the systemic injection of kainate at 3 days post-fertilization, and the didys552 genetic epilepsy model, which carries a mutation in scn1lab that leads to spontaneous epileptiform discharges. Kainate-treated larvae exhibited transient brain damage as shown by increased numbers of apoptotic nuclei as early as one day post-injection, which was followed by an increase in the number of microglia in the brain. A similar microglial phenotype was also observed in didys552-/- mutants, suggesting that microglia numbers change in response to seizure-like activity in the brain. Interestingly, kainate-treated larvae also displayed a decreased seizure threshold towards subsequent pentylenetetrazole-induced seizures, as shown by higher locomotor and encephalographic activity in comparison with vehicle-injected larvae. These results are comparable to kainate-induced rodent seizure models and suggest the suitability of these zebrafish seizure models for future studies, in particular to elucidate the links between epileptogenesis and microglial dynamic changes after seizure induction in the developing brain, and to understand how these modulate seizure susceptibility.
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Affiliation(s)
- Teresa G Martins
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg.
| | - Remon Soliman
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | | | - Cristina Donato
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Corrado Ameli
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Laurent Mombaerts
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Alexander Skupin
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg; University of California, San Diego (UCSD), La Jolla, CA, United States
| | - Francesca Peri
- Developmental Biology Group, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Alexander D Crawford
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg; Institute for Orphan Drug Discovery, Bremerhaven, Germany.
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3
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Mhlongo F, Cordero-Maldonado ML, Crawford AD, Katerere D, Sandasi M, Hattingh AC, Koekemoer TC, van de Venter M, Viljoen AM. Evaluation of the wound healing properties of South African medicinal plants using zebrafish and in vitro bioassays. J Ethnopharmacol 2022; 286:114867. [PMID: 34822956 DOI: 10.1016/j.jep.2021.114867] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 11/02/2021] [Accepted: 11/21/2021] [Indexed: 06/13/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE In South Africa, medicinal plants have a history of traditional use, with many species used for treating wounds. The scientific basis of such uses remains largely unexplored. AIM OF THE STUDY To screen South African plants used ethnomedicinally for wound healing based on their pro-angiogenic and wound healing activity, using transgenic zebrafish larvae and cell culture assays. MATERIALS AND METHODS South African medicinal plants used for wound healing were chosen according to literature. Dried plant material was extracted using six solvents of varying polarities. Pro-angiogenesis was assessed in vivo by observing morphological changes in sub-intestinal vessels after crude extract treatment of transgenic zebrafish larvae with vasculature-specific expression of a green fluorescent protein. Subsequently, the in vitro anti-inflammatory, fibroblast proliferation and collagen production effects of the plant extracts that were active in the zebrafish angiogenesis assay were investigated using murine macrophage (RAW 264.7) and human fibroblast (MRHF) cell lines. RESULTS Fourteen plants were extracted using six different solvents to yield 84 extracts and the non-toxic (n=72) were initially screened for pro-angiogenic activity in the zebrafish assay. Of these plant species, extracts of Lobostemon fruticosus, Scabiosa columbaria and Cotyledon orbiculata exhibited good activity in a concentration-dependent manner. All active extracts showed negligible in vitro toxicity using the MTT assay. Lobostemon fruticosus and Scabiosa columbaria extracts showed noteworthy anti-inflammatory activity in RAW 264.7 macrophages. The acetone extract of Lobostemon fruticosus stimulated the most collagen production at 122% above control values using the MRHF cell line, while all four of the selected extracts significantly stimulated cellular proliferation in vitro in the MRHF cell line. CONCLUSIONS The screening of the selected plant species provided valuable preliminary information validating the use of some of the plants in traditional medicine used for wound healing in South Africa. This study is the first to discover through an evidence-based pharmacology approach the wound healing properties of such plant species using the zebrafish as an in vivo model.
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Affiliation(s)
- Fikile Mhlongo
- Department of Pharmaceutical Sciences, Faculty of Science, Tshwane University of Technology, Private Bag X680, Pretoria, 0001, South Africa
| | | | - Alexander D Crawford
- Luxembourg Centre for Systems Biomedicine, Université du Luxembourg, Belval, Luxembourg; Department of Preclinical Sciences and Pathology, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - David Katerere
- Department of Pharmaceutical Sciences, Faculty of Science, Tshwane University of Technology, Private Bag X680, Pretoria, 0001, South Africa
| | - Maxleene Sandasi
- Department of Pharmaceutical Sciences, Faculty of Science, Tshwane University of Technology, Private Bag X680, Pretoria, 0001, South Africa; SAMRC Herbal Drugs Research Unit, Tshwane University of Technology, Pretoria, South Africa
| | - Anna C Hattingh
- Department of Biochemistry and Microbiology, Nelson Mandela University, Port Elizabeth, South Africa
| | - Trevor C Koekemoer
- Department of Biochemistry and Microbiology, Nelson Mandela University, Port Elizabeth, South Africa
| | - Maryna van de Venter
- Department of Biochemistry and Microbiology, Nelson Mandela University, Port Elizabeth, South Africa
| | - Alvaro M Viljoen
- Department of Pharmaceutical Sciences, Faculty of Science, Tshwane University of Technology, Private Bag X680, Pretoria, 0001, South Africa; SAMRC Herbal Drugs Research Unit, Tshwane University of Technology, Pretoria, South Africa.
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4
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Soliman R, Cordero-Maldonado ML, Martins TG, Moein M, Conrotte JF, Warmack RA, Skupin A, Crawford AD, Clarke SG, Linster CL. l-Isoaspartyl Methyltransferase Deficiency in Zebrafish Leads to Impaired Calcium Signaling in the Brain. Front Genet 2021; 11:612343. [PMID: 33552132 PMCID: PMC7859441 DOI: 10.3389/fgene.2020.612343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/21/2020] [Indexed: 11/13/2022] Open
Abstract
Isomerization of l-aspartyl and l-asparaginyl residues to l-isoaspartyl residues is one type of protein damage that can occur under physiological conditions and leads to conformational changes, loss of function, and enhanced protein degradation. Protein l-isoaspartyl methyltransferase (PCMT) is a repair enzyme whose action initiates the reconversion of abnormal l-isoaspartyl residues to normal l-aspartyl residues in proteins. Many lines of evidence support a crucial role for PCMT in the brain, but the mechanisms involved remain poorly understood. Here, we investigated PCMT activity and function in zebrafish, a vertebrate model that is particularly well-suited to analyze brain function using a variety of techniques. We characterized the expression products of the zebrafish PCMT homologous genes pcmt and pcmtl. Both zebrafish proteins showed a robust l-isoaspartyl methyltransferase activity and highest mRNA transcript levels were found in brain and testes. Zebrafish morphant larvae with a knockdown in both the pcmt and pcmtl genes showed pronounced morphological abnormalities, decreased survival, and increased isoaspartyl levels. Interestingly, we identified a profound perturbation of brain calcium homeostasis in these morphants. An abnormal calcium response upon ATP stimulation was also observed in mouse hippocampal HT22 cells knocked out for Pcmt1. This work shows that zebrafish is a promising model to unravel further facets of PCMT function and demonstrates, for the first time in vivo, that PCMT plays a pivotal role in the regulation of calcium fluxes.
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Affiliation(s)
- Remon Soliman
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | | | - Teresa G Martins
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Mahsa Moein
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Jean-François Conrotte
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Rebeccah A Warmack
- Department of Chemistry and Biochemistry, The Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
| | - Alexander Skupin
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.,University of California, San Diego, La Jolla, CA, United States
| | - Alexander D Crawford
- Department of Preclinical Sciences and Pathology, Norwegian University of Life Sciences, Oslo, Norway.,Institute for Orphan Drug Discovery, Bremer Innovations- und Technologiezentrum, Bremen, Germany
| | - Steven G Clarke
- Department of Chemistry and Biochemistry, The Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
| | - Carole L Linster
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
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5
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Tiraboschi E, Martina S, van der Ent W, Grzyb K, Gawel K, Cordero-Maldonado ML, Poovathingal SK, Heintz S, Satheesh SV, Brattespe J, Xu J, Suster M, Skupin A, Esguerra CV. New insights into the early mechanisms of epileptogenesis in a zebrafish model of Dravet syndrome. Epilepsia 2020; 61:549-560. [PMID: 32096222 DOI: 10.1111/epi.16456] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 02/03/2020] [Accepted: 02/03/2020] [Indexed: 12/17/2022]
Abstract
OBJECTIVE To pinpoint the earliest cellular defects underlying seizure onset (epileptogenic period) during perinatal brain development in a new zebrafish model of Dravet syndrome (DS) and to investigate potential disease-modifying activity of the 5HT2 receptor agonist fenfluramine. METHODS We used CRISPR/Cas9 mutagenesis to introduce a missense mutation, designed to perturb ion transport function in all channel isoforms, into scn1lab, the zebrafish orthologue of SCN1A (encoding voltage-gated sodium channel alpha subunit 1). We performed behavioral analysis and electroencephalographic recordings to measure convulsions and epileptiform discharges, followed by single-cell RNA-Seq, morphometric analysis of transgenic reporter-labeled γ-aminobutyric acidergic (GABAergic) neurons, and pharmacological profiling of mutant larvae. RESULTS Homozygous mutant (scn1labmut/mut ) larvae displayed spontaneous seizures with interictal, preictal, and ictal discharges (mean = 7.5 per 20-minute recording; P < .0001; one-way analysis of variance). Drop-Seq analysis revealed a 2:1 shift in the ratio of glutamatergic to GABAergic neurons in scn1labmut/mut larval brains versus wild type (WT), with dynamic changes in neuronal, glial, and progenitor cell populations. To explore disease pathophysiology further, we quantified dendritic arborization in GABAergic neurons and observed a 40% reduction in arbor number compared to WT (P < .001; n = 15 mutant, n = 16 WT). We postulate that the significant reduction in inhibitory arbors causes an inhibitory to excitatory neurotransmitter imbalance that contributes to seizures and enhanced electrical brain activity in scn1labmut/mut larvae (high-frequency range), with subsequent GABAergic neuronal loss and astrogliosis. Chronic fenfluramine administration completely restored dendritic arbor numbers to normal in scn1labmut/mut larvae, whereas similar treatment with the benzodiazepine diazepam attenuated seizures, but was ineffective in restoring neuronal cytoarchitecture. BrdU labeling revealed cell overproliferation in scn1labmut/mut larval brains that were rescued by fenfluramine but not diazepam. SIGNIFICANCE Our findings provide novel insights into early mechanisms of DS pathogenesis, describe dynamic cell population changes in the scn1labmut/mut brain, and present first-time evidence for potential disease modification by fenfluramine.
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Affiliation(s)
- Ettore Tiraboschi
- Chemical Neuroscience Group, Center for Molecular Medicine Norway, University of Oslo, Oslo, Norway
| | - Silvia Martina
- Integrative Cell Signaling Group, Luxembourg Center for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Wietske van der Ent
- Chemical Neuroscience Group, Center for Molecular Medicine Norway, University of Oslo, Oslo, Norway
| | - Kamil Grzyb
- Integrative Cell Signaling Group, Luxembourg Center for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Kinga Gawel
- Chemical Neuroscience Group, Center for Molecular Medicine Norway, University of Oslo, Oslo, Norway.,Department of Experimental and Clinical Pharmacology, Medical University of Lublin, Lublin, Poland
| | - Maria Lorena Cordero-Maldonado
- Integrative Cell Signaling Group, Luxembourg Center for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Suresh Kumar Poovathingal
- Integrative Cell Signaling Group, Luxembourg Center for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Sarah Heintz
- Chemical Neuroscience Group, Center for Molecular Medicine Norway, University of Oslo, Oslo, Norway
| | | | - Jarle Brattespe
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Ju Xu
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | | | - Alexander Skupin
- Integrative Cell Signaling Group, Luxembourg Center for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Camila V Esguerra
- Chemical Neuroscience Group, Center for Molecular Medicine Norway, University of Oslo, Oslo, Norway.,Department of Pharmacy, University of Oslo, Oslo, Norway
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Heins-Marroquin U, Jung PP, Cordero-Maldonado ML, Crawford AD, Linster CL. Phenotypic assays in yeast and zebrafish reveal drugs that rescue ATP13A2 deficiency. Brain Commun 2019; 1:fcz019. [PMID: 32954262 PMCID: PMC7425419 DOI: 10.1093/braincomms/fcz019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 07/27/2019] [Accepted: 08/16/2019] [Indexed: 12/21/2022] Open
Abstract
Mutations in ATP13A2 (PARK9) are causally linked to the rare neurodegenerative disorders Kufor-Rakeb syndrome, hereditary spastic paraplegia and neuronal ceroid lipofuscinosis. This suggests that ATP13A2, a lysosomal cation-transporting ATPase, plays a crucial role in neuronal cells. The heterogeneity of the clinical spectrum of ATP13A2-associated disorders is not yet well understood and currently, these diseases remain without effective treatment. Interestingly, ATP13A2 is widely conserved among eukaryotes, and the yeast model for ATP13A2 deficiency was the first to indicate a role in heavy metal homeostasis, which was later confirmed in human cells. In this study, we show that the deletion of YPK9 (the yeast orthologue of ATP13A2) in Saccharomyces cerevisiae leads to growth impairment in the presence of Zn2+, Mn2+, Co2+ and Ni2+, with the strongest phenotype being observed in the presence of zinc. Using the ypk9Δ mutant, we developed a high-throughput growth rescue screen based on the Zn2+ sensitivity phenotype. Screening of two libraries of Food and Drug Administration-approved drugs identified 11 compounds that rescued growth. Subsequently, we generated a zebrafish model for ATP13A2 deficiency and found that both partial and complete loss of atp13a2 function led to increased sensitivity to Mn2+. Based on this phenotype, we confirmed two of the drugs found in the yeast screen to also exert a rescue effect in zebrafish-N-acetylcysteine, a potent antioxidant, and furaltadone, a nitrofuran antibiotic. This study further supports that combining the high-throughput screening capacity of yeast with rapid in vivo drug testing in zebrafish can represent an efficient drug repurposing strategy in the context of rare inherited disorders involving conserved genes. This work also deepens the understanding of the role of ATP13A2 in heavy metal detoxification and provides a new in vivo model for investigating ATP13A2 deficiency.
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Affiliation(s)
- Ursula Heins-Marroquin
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux, Luxembourg
| | - Paul P Jung
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux, Luxembourg
| | | | - Alexander D Crawford
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux, Luxembourg
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, 0454 Oslo, Norway
- Institute for Orphan Drug Discovery, Bremer Innovations- und Technologiezentrum, 28359 Bremen, Germany
| | - Carole L Linster
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux, Luxembourg
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7
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Glaab E, Antony P, Köglsberger S, Forster JI, Cordero-Maldonado ML, Crawford A, Garcia P, Buttini M. Transcriptome profiling data reveals ubiquitin-specific peptidase 9 knockdown effects. Data Brief 2019; 25:104130. [PMID: 31294067 PMCID: PMC6595415 DOI: 10.1016/j.dib.2019.104130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 04/26/2019] [Accepted: 06/03/2019] [Indexed: 11/28/2022] Open
Abstract
Ubiquitin specific peptidase 9 (USP9) is a deubiquitinase encoded by a sex-linked gene with a Y-chromosomal form (USP9Y) and an X-chromosomal form (USP9X) that escapes X-inactivation. Since USP9 is a key regulatory gene with sex-linked expression in the human brain, the gene may be of interest for researchers studying molecular gender differences and ubiquitin signaling in the brain. To assess the downstream effects of knocking down USP9X and USP9Y on a transcriptome-wide scale, we have conducted microarray profiling experiments using the human DU145 prostate cancer cell culture model, after confirming the robust expression of both USP9X and USP9Y in this model. By designing shRNA constructs for the specific knockdown of USP9X and the joint knockdown of USP9X and USP9Y, we have compared gene expression changes in both knockdowns to control conditions to infer potential shared and X- or Y-form specific alterations. Here, we provide details of the corresponding microarray profiling data, which has been deposited in the Gene Expression Omnibus database (GEO series accession number GSE79376). A biological interpretation of the data in the context of a potential involvement of USP9 in Alzheimer's disease has previously been presented in Köglsberger et al. (2016). To facilitate the re-use and re-analysis of the data for other applications, e.g. the study of ubiquitin signaling and protein turnover control, and the regulation of molecular gender differences in the human brain and brain-related disorders, we provide a more in-depth discussion of the data properties, specifications and possible use cases.
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Affiliation(s)
- Enrico Glaab
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg
| | - Paul Antony
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg
| | - Sandra Köglsberger
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg
| | - Julia Ilona Forster
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg
| | - Maria Lorena Cordero-Maldonado
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg
| | - Alexander Crawford
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Pierre Garcia
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg
| | - Manuel Buttini
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg
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8
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Cordero-Maldonado ML, Perathoner S, van der Kolk KJ, Boland R, Heins-Marroquin U, Spaink HP, Meijer AH, Crawford AD, de Sonneville J. Deep learning image recognition enables efficient genome editing in zebrafish by automated injections. PLoS One 2019; 14:e0202377. [PMID: 30615627 PMCID: PMC6322765 DOI: 10.1371/journal.pone.0202377] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 12/13/2018] [Indexed: 12/30/2022] Open
Abstract
One of the most popular techniques in zebrafish research is microinjection. This is a rapid and efficient way to genetically manipulate early developing embryos, and to introduce microbes, chemical compounds, nanoparticles or tracers at larval stages. Here we demonstrate the development of a machine learning software that allows for microinjection at a trained target site in zebrafish eggs at unprecedented speed. The software is based on the open-source deep-learning library Inception v3. In a first step, the software distinguishes wells containing embryos at one-cell stage from wells to be skipped with an accuracy of 93%. A second step was developed to pinpoint the injection site. Deep learning allows to predict this location on average within 42 μm to manually annotated sites. Using a Graphics Processing Unit (GPU), both steps together take less than 100 milliseconds. We first tested our system by injecting a morpholino into the middle of the yolk and found that the automated injection efficiency is as efficient as manual injection (~ 80%). Next, we tested both CRISPR/Cas9 and DNA construct injections into the zygote and obtained a comparable efficiency to that of an experienced experimentalist. Combined with a higher throughput, this results in a higher yield. Hence, the automated injection of CRISPR/Cas9 will allow high-throughput applications to knock out and knock in relevant genes to study their mechanisms or pathways of interest in diverse areas of biomedical research.
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Affiliation(s)
| | - Simon Perathoner
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | | | - Ralf Boland
- Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Ursula Heins-Marroquin
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Herman P Spaink
- Institute of Biology, Leiden University, Leiden, the Netherlands
| | | | - Alexander D Crawford
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
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Siverio-Mota D, Andujar I, Marrero-Ponce Y, Giner RM, Diaz-Mendoza C, Paba GM, Vicet-Muro L, Cordero-Maldonado ML, de Witte PAM, Crawford AD, Veitia MSI, Perez-Jimenez F, Aran VJ. Anti-Inflammatory Activity and Cheminformatics Analysis of New Poten t 2-Substituted 1-Methyl-5-Nitroindazolinones. Curr Top Med Chem 2018; 17:3236-3248. [DOI: 10.2174/1568026618666180119125255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 12/29/2017] [Accepted: 01/11/2018] [Indexed: 11/22/2022]
Affiliation(s)
- Dany Siverio-Mota
- Laboratory for Molecular Biodiscovery, Department of Pharmaceutical and Pharmacological Sciences, University of Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Isabel Andujar
- Departamento de Farmacologia, Facultad de Farmacia, Universitat de Valencia, Valencia, Spain
| | - Yovani Marrero-Ponce
- Unidad de Investigacion de Diseno de Farmacos y Conectividad Molecular, Departamento de Quimica Física, Facultad de Farmacia, Universitat de Valencia, Spain
| | - Rosa M. Giner
- Departamento de Farmacologia, Facultad de Farmacia, Universitat de Valencia, Valencia, Spain
| | - Claudia Diaz-Mendoza
- Fundacion Universitaria Tecnologico Comfenalco - Cartagena. Grupo de Investigacion Ambiental (GIA), Facultad de Ingenierias, Cartagena de Indias, Bolivar, Colombia
| | - Ganiveth Manjarrez Paba
- Fundacion Universitaria Tecnologico Comfenalco - Cartagena. Grupo de Investigacion Ambiental (GIA), Facultad de Ingenierias, Cartagena de Indias, Bolivar, Colombia
| | - Liliana Vicet-Muro
- Laboratory for Molecular Biodiscovery, Department of Pharmaceutical and Pharmacological Sciences, University of Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Maria Lorena Cordero-Maldonado
- Laboratory for Molecular Biodiscovery, Department of Pharmaceutical and Pharmacological Sciences, University of Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Peter A. M. de Witte
- Laboratory for Molecular Biodiscovery, Department of Pharmaceutical and Pharmacological Sciences, University of Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Alexander D. Crawford
- Laboratory for Molecular Biodiscovery, Department of Pharmaceutical and Pharmacological Sciences, University of Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Maite Sylla-Iyarreta Veitia
- Equipe de chimie moleculaire, Laboratoire de Chimie moleculaire, genie des procedes chimiques et energetiques, EA7341, Conservatoire national des arts et metiers, 2 rue Conte, 75003 Paris, France
| | - Facundo Perez-Jimenez
- Unidad de Investigacion de Diseno de Farmacos y Conectividad Molecular, Departamento de Quimica Física, Facultad de Farmacia, Universitat de Valencia, Spain
| | - Vicente J. Aran
- Instituto de Quimica Medica, CSIC, c/Juan de la Cierva 3, 28006 Madrid, Spain
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Perathoner S, Cordero-Maldonado ML, Crawford AD. Potential of zebrafish as a model for exploring the role of the amygdala in emotional memory and motivational behavior. J Neurosci Res 2016; 94:445-62. [DOI: 10.1002/jnr.23712] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 12/22/2015] [Accepted: 12/22/2015] [Indexed: 01/18/2023]
Affiliation(s)
- Simon Perathoner
- Luxembourg Centre for Systems Biomedicine (LCSB); University of Luxembourg; Belvaux Luxembourg
| | | | - Alexander D. Crawford
- Luxembourg Centre for Systems Biomedicine (LCSB); University of Luxembourg; Belvaux Luxembourg
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11
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Galizia EC, Myers CT, Leu C, de Kovel CGF, Afrikanova T, Cordero-Maldonado ML, Martins TG, Jacmin M, Drury S, Krishna Chinthapalli V, Muhle H, Pendziwiat M, Sander T, Ruppert AK, Møller RS, Thiele H, Krause R, Schubert J, Lehesjoki AE, Nürnberg P, Lerche H, Palotie A, Coppola A, Striano S, Gaudio LD, Boustred C, Schneider AL, Lench N, Jocic-Jakubi B, Covanis A, Capovilla G, Veggiotti P, Piccioli M, Parisi P, Cantonetti L, Sadleir LG, Mullen SA, Berkovic SF, Stephani U, Helbig I, Crawford AD, Esguerra CV, Kasteleijn-Nolst Trenité DGA, Koeleman BPC, Mefford HC, Scheffer IE, Sisodiya SM. CHD2 variants are a risk factor for photosensitivity in epilepsy. Brain 2015; 138:1198-207. [PMID: 25783594 PMCID: PMC4407192 DOI: 10.1093/brain/awv052] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 01/07/2015] [Indexed: 12/24/2022] Open
Abstract
Photosensitivity in epilepsy is common and has high heritability, but its genetic basis remains uncertain. Galizia et al. reveal an overrepresentation of unique variants of CHD2 — which encodes the transcriptional regulator ‘chromodomain helicase DNA-binding protein 2’ — in photosensitive epilepsies, and show that chd2 knockdown in zebrafish causes photosensitivity. Photosensitivity is a heritable abnormal cortical response to flickering light, manifesting as particular electroencephalographic changes, with or without seizures. Photosensitivity is prominent in a very rare epileptic encephalopathy due to de novo CHD2 mutations, but is also seen in epileptic encephalopathies due to other gene mutations. We determined whether CHD2 variation underlies photosensitivity in common epilepsies, specific photosensitive epilepsies and individuals with photosensitivity without seizures. We studied 580 individuals with epilepsy and either photosensitive seizures or abnormal photoparoxysmal response on electroencephalography, or both, and 55 individuals with photoparoxysmal response but no seizures. We compared CHD2 sequence data to publicly available data from 34 427 individuals, not enriched for epilepsy. We investigated the role of unique variants seen only once in the entire data set. We sought CHD2 variants in 238 exomes from familial genetic generalized epilepsies, and in other public exome data sets. We identified 11 unique variants in the 580 individuals with photosensitive epilepsies and 128 unique variants in the 34 427 controls: unique CHD2 variation is over-represented in cases overall (P = 2·17 × 10−5). Among epilepsy syndromes, there was over-representation of unique CHD2 variants (3/36 cases) in the archetypal photosensitive epilepsy syndrome, eyelid myoclonia with absences (P = 3·50 × 10−4). CHD2 variation was not over-represented in photoparoxysmal response without seizures. Zebrafish larvae with chd2 knockdown were tested for photosensitivity. Chd2 knockdown markedly enhanced mild innate zebrafish larval photosensitivity. CHD2 mutation is the first identified cause of the archetypal generalized photosensitive epilepsy syndrome, eyelid myoclonia with absences. Unique CHD2 variants are also associated with photosensitivity in common epilepsies. CHD2 does not encode an ion channel, opening new avenues for research into human cortical excitability.
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Affiliation(s)
- Elizabeth C Galizia
- 1 NIHR Biomedical Research Centre Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, National Hospital for Neurology and Neurosurgery, Queen Square, London, UK 2 Epilepsy Society, Bucks, UK
| | | | - Costin Leu
- 1 NIHR Biomedical Research Centre Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, National Hospital for Neurology and Neurosurgery, Queen Square, London, UK 2 Epilepsy Society, Bucks, UK
| | - Carolien G F de Kovel
- 4 Department of Medical Genetics Research, University Medical Centre Utrecht, The Netherlands
| | - Tatiana Afrikanova
- 5 Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | | | - Teresa G Martins
- 5 Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Maxime Jacmin
- 5 Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Suzanne Drury
- 6 North East Thames Regional Genetics Laboratories, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - V Krishna Chinthapalli
- 1 NIHR Biomedical Research Centre Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, National Hospital for Neurology and Neurosurgery, Queen Square, London, UK 2 Epilepsy Society, Bucks, UK
| | - Hiltrud Muhle
- 7 Department of Neuropaediatrics, University Medical Centre Schleswig-Holstein and Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Manuela Pendziwiat
- 7 Department of Neuropaediatrics, University Medical Centre Schleswig-Holstein and Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Thomas Sander
- 8 Cologne Centre for Genomics, University of Cologne, Cologne, Germany
| | | | - Rikke S Møller
- 9 Danish Epilepsy Centre, Dianalund, Denmark 10 Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark
| | - Holger Thiele
- 8 Cologne Centre for Genomics, University of Cologne, Cologne, Germany
| | - Roland Krause
- 5 Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Julian Schubert
- 11 Deptartment of Neurology and Epileptology, Hertie Institut for Clinical Brain Research, Tübingen, Germany
| | - Anna-Elina Lehesjoki
- 12 Folkhälsan Institute of Genetics and Neuroscience Centre, University of Helsinki, Helsinki, Finland 13 Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
| | - Peter Nürnberg
- 8 Cologne Centre for Genomics, University of Cologne, Cologne, Germany
| | - Holger Lerche
- 11 Deptartment of Neurology and Epileptology, Hertie Institut for Clinical Brain Research, Tübingen, Germany
| | | | - Aarno Palotie
- 14 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK 15 Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland 16 Program in Medical and Population Genetics and Genetic Analysis Platform, The Broad Institute of MIT and Harvard, Cambridge, USA
| | - Antonietta Coppola
- 1 NIHR Biomedical Research Centre Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, National Hospital for Neurology and Neurosurgery, Queen Square, London, UK 2 Epilepsy Society, Bucks, UK 17 Epilepsy Centre, Neurology Department, Federico II University of Naples, Naples, Italy
| | - Salvatore Striano
- 17 Epilepsy Centre, Neurology Department, Federico II University of Naples, Naples, Italy
| | - Luigi Del Gaudio
- 17 Epilepsy Centre, Neurology Department, Federico II University of Naples, Naples, Italy
| | - Christopher Boustred
- 6 North East Thames Regional Genetics Laboratories, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Amy L Schneider
- 18 Department of Medicine, University of Melbourne, Austin Health, Melbourne, Australia
| | - Nicholas Lench
- 6 North East Thames Regional Genetics Laboratories, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Bosanka Jocic-Jakubi
- 19 Department of Child Neurology, Paediatric Clinic, Clinical Centre Nis, Serbia 20 Department of Paediatric Neurology, Paediatric Clinic, Al Sabah Hospital, Kuwait
| | - Athanasios Covanis
- 21 Neurology Department, The Children's Hospital Agia Sophia, Athens, Greece
| | | | - Pierangelo Veggiotti
- 23 Department of Child Neurology and Psychiatry C. Mondino National Neurological Institute, Via Mondino, 2, 27100, Pavia, Italy 24 Brain and Behaviour Department, University of Pavia, Pavia, Italy
| | - Marta Piccioli
- 25 Neurophysiopathology Unit, San Filippo Neri Hospital, Rome, Italy
| | - Pasquale Parisi
- 26 Child Neurology, NESMOS Department, Faculty of Medicine and Psychology, Sapienza University, Rome, Italy
| | - Laura Cantonetti
- 27 Neurorehabilitation Unit, Department of Neuroscience and Neurorehabilitation, IRCCS, Bambino Gesu' Children's Hospital, Rome, Italy
| | - Lynette G Sadleir
- 28 Department of Paediatrics and Child Health, School of Medicine and Health Sciences, University of Otago, Wellington, New Zealand
| | - Saul A Mullen
- 29 Florey Institute of Neurosciences and Mental Health, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, Australia
| | - Samuel F Berkovic
- 18 Department of Medicine, University of Melbourne, Austin Health, Melbourne, Australia
| | - Ulrich Stephani
- 7 Department of Neuropaediatrics, University Medical Centre Schleswig-Holstein and Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Ingo Helbig
- 7 Department of Neuropaediatrics, University Medical Centre Schleswig-Holstein and Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Alexander D Crawford
- 5 Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Camila V Esguerra
- 30 Chemical Neuroscience Group, Biotechnology Centre of Oslo, University of Oslo, Oslo, Norway 31 Laboratory for Molecular Biodiscovery, University of Leuven, Leuven, Belgium
| | | | - Bobby P C Koeleman
- 4 Department of Medical Genetics Research, University Medical Centre Utrecht, The Netherlands
| | | | - Ingrid E Scheffer
- 18 Department of Medicine, University of Melbourne, Austin Health, Melbourne, Australia 29 Florey Institute of Neurosciences and Mental Health, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, Australia
| | - Sanjay M Sisodiya
- 1 NIHR Biomedical Research Centre Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, National Hospital for Neurology and Neurosurgery, Queen Square, London, UK 2 Epilepsy Society, Bucks, UK
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