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Al-Ali AK, Al-Rubaish AM, Alali RA, Almansori MS, Al-Jumaan MA, Alshehri AM, Al-Madan MS, Vatte C, Cherlin T, Young S, Verma SS, Morahan G, Koeleman BPC, Keating BJ. Uncovering myocardial infarction genetic signatures using GWAS exploration in Saudi and European cohorts. Sci Rep 2023; 13:21866. [PMID: 38072966 PMCID: PMC10711020 DOI: 10.1038/s41598-023-49105-1] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 12/04/2023] [Indexed: 12/18/2023] Open
Abstract
Genome-wide association studies (GWAS) have yielded significant insights into the genetic architecture of myocardial infarction (MI), although studies in non-European populations are still lacking. Saudi Arabian cohorts offer an opportunity to discover novel genetic variants impacting disease risk due to a high rate of consanguinity. Genome-wide genotyping (GWG), imputation and GWAS followed by meta-analysis were performed based on two independent Saudi Arabian studies comprising 3950 MI patients and 2324 non-MI controls. Meta-analyses were then performed with these two Saudi MI studies and the CardioGRAMplusC4D and UK BioBank GWAS as controls. Meta-analyses of the two Saudi MI studies resulted in 17 SNPs with genome-wide significance. Meta-analyses of all 4 studies revealed 66 loci with genome-wide significance levels of p < 5 × 10-8. All of these variants, except rs2764203, have previously been reported as MI-associated loci or to have high linkage disequilibrium with known loci. One SNP association in Shisa family member 5 (SHISA5) (rs11707229) was evident at a much higher frequency in the Saudi MI populations (> 12% MAF). In conclusion, our results replicated many MI associations, whereas in Saudi-only GWAS (meta-analyses), several new loci were implicated that require future validation and functional analyses.
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Affiliation(s)
- Amein K Al-Ali
- Department of Clinical Biochemistry, College of Medicine, Imam Abdulrahman bin Faisal University, 3144, Dammam, Saudi Arabia.
| | - Abdullah M Al-Rubaish
- Department of Internal Medicine, King Fahd Hospital of the University, 34445, Al-Khobar, Saudi Arabia
- College of Medicine, Imam Abdulrahman bin Faisal University, 31441, Dammam, Saudi Arabia
| | - Rudaynah A Alali
- Department of Internal Medicine, King Fahd Hospital of the University, 34445, Al-Khobar, Saudi Arabia
- College of Medicine, Imam Abdulrahman bin Faisal University, 31441, Dammam, Saudi Arabia
| | - Mohammed S Almansori
- Department of Internal Medicine, King Fahd Hospital of the University, 34445, Al-Khobar, Saudi Arabia
- College of Medicine, Imam Abdulrahman bin Faisal University, 31441, Dammam, Saudi Arabia
| | - Mohammed A Al-Jumaan
- College of Medicine, Imam Abdulrahman bin Faisal University, 31441, Dammam, Saudi Arabia
- Department of Emergency Medicine, King Fahd Hospital of the University, 34445, Al-Khobar, Saudi Arabia
| | - Abdullah M Alshehri
- Department of Internal Medicine, King Fahd Hospital of the University, 34445, Al-Khobar, Saudi Arabia
- College of Medicine, Imam Abdulrahman bin Faisal University, 31441, Dammam, Saudi Arabia
| | - Mohammed S Al-Madan
- College of Medicine, Imam Abdulrahman bin Faisal University, 31441, Dammam, Saudi Arabia
- Department of Pediatrics, King Fahd Hospital of the University, 34445, Al-Khobar, Saudi Arabia
| | - ChittiBabu Vatte
- Department of Clinical Biochemistry, College of Medicine, Imam Abdulrahman bin Faisal University, 3144, Dammam, Saudi Arabia
| | - Tess Cherlin
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sylvia Young
- Centre for Diabetes Research, Harry Perkins Institute of Medical Research, University of Western Australia, Nedlands, 6009, Australia
| | - Shefali S Verma
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Grant Morahan
- Centre for Diabetes Research, Harry Perkins Institute of Medical Research, University of Western Australia, Nedlands, 6009, Australia
| | - Bobby P C Koeleman
- Department of Genetics, University Medical Center Utrecht, Utrecht, 85500/3508 GA, The Netherlands
| | - Brendan J Keating
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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2
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Nijboer TCW, Hessel EVS, van Haaften GW, van Zandvoort MJ, van der Spek PJ, Troelstra C, de Kovel CGF, Koeleman BPC, van der Zwaag B, Brilstra EH, Burbach JPH. Identification of candidate genes for developmental colour agnosia in a single unique family. PLoS One 2023; 18:e0290013. [PMID: 37672513 PMCID: PMC10482254 DOI: 10.1371/journal.pone.0290013] [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: 06/30/2023] [Accepted: 07/31/2023] [Indexed: 09/08/2023] Open
Abstract
Colour agnosia is a disorder that impairs colour knowledge (naming, recognition) despite intact colour perception. Previously, we have identified the first and only-known family with hereditary developmental colour agnosia. The aim of the current study was to explore genomic regions and candidate genes that potentially cause this trait in this family. For three family members with developmental colour agnosia and three unaffected family members CGH-array analysis and exome sequencing was performed, and linkage analysis was carried out using DominantMapper, resulting in the identification of 19 cosegregating chromosomal regions. Whole exome sequencing resulted in 11 rare coding variants present in all affected family members with developmental colour agnosia and absent in unaffected members. These variants affected genes that have been implicated in neural processes and functions (CACNA2D4, DDX25, GRINA, MYO15A) or that have an indirect link to brain function, development or disease (MAML2, STAU1, TMED3, RABEPK), and a remaining group lacking brain expression or involved in non-neural traits (DEPDC7, OR1J1, OR8D4). Although this is an explorative study, the small set of candidate genes that could serve as a starting point for unravelling mechanisms of higher level cognitive functions and cortical specialization, and disorders therein such as developmental colour agnosia.
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Affiliation(s)
- Tanja C. W. Nijboer
- UMCU Brain Center and Center of Excellence for Rehabilitation Medicine, University Medical Center Utrecht and De Hoogstraat Rehabilitation, Utrecht, The Netherlands
- Department of Experimental Psychology and Helmholtz Institute, Utrecht University, Utrecht, The Netherlands
| | - Ellen V. S. Hessel
- UMCU Brain Center and Center of Excellence for Rehabilitation Medicine, University Medical Center Utrecht and De Hoogstraat Rehabilitation, Utrecht, The Netherlands
- Department of Biomedical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Gijs W. van Haaften
- Department of Biomedical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Martine J. van Zandvoort
- Department of Experimental Psychology and Helmholtz Institute, Utrecht University, Utrecht, The Netherlands
| | - Peter J. van der Spek
- Department of Pathology, Erasmus Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Christine Troelstra
- Department of Pathology, Erasmus Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Carolien G. F. de Kovel
- Department of Biomedical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bobby P. C. Koeleman
- Department of Biomedical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bert van der Zwaag
- Department of Biomedical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Eva H. Brilstra
- Department of Biomedical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - J. Peter H. Burbach
- UMCU Brain Center, Department of Translational Neuroscience, University Medical Center Utrecht, Utrecht, the Netherlands
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Stevelink R, Campbell C, Chen S, Abou-Khalil B, Adesoji OM, Afawi Z, Amadori E, Anderson A, Anderson J, Andrade DM, Annesi G, Auce P, Avbersek A, Bahlo M, Baker MD, Balagura G, Balestrini S, Barba C, Barboza K, Bartolomei F, Bast T, Baum L, Baumgartner T, Baykan B, Bebek N, Becker AJ, Becker F, Bennett CA, Berghuis B, Berkovic SF, Beydoun A, Bianchini C, Bisulli F, Blatt I, Bobbili DR, Borggraefe I, Bosselmann C, Braatz V, Bradfield JP, Brockmann K, Brody LC, Buono RJ, Busch RM, Caglayan H, Campbell E, Canafoglia L, Canavati C, Cascino GD, Castellotti B, Catarino CB, Cavalleri GL, Cerrato F, Chassoux F, Cherny SS, Cheung CL, Chinthapalli K, Chou IJ, Chung SK, Churchhouse C, Clark PO, Cole AJ, Compston A, Coppola A, Cosico M, Cossette P, Craig JJ, Cusick C, Daly MJ, Davis LK, de Haan GJ, Delanty N, Depondt C, Derambure P, Devinsky O, Di Vito L, Dlugos DJ, Doccini V, Doherty CP, El-Naggar H, Elger CE, Ellis CA, Eriksson JG, Faucon A, Feng YCA, Ferguson L, Ferraro TN, Ferri L, Feucht M, Fitzgerald M, Fonferko-Shadrach B, Fortunato F, Franceschetti S, Franke A, French JA, Freri E, Gagliardi M, Gambardella A, Geller EB, Giangregorio T, Gjerstad L, Glauser T, Goldberg E, Goldman A, Granata T, Greenberg DA, Guerrini R, Gupta N, Haas KF, Hakonarson H, Hallmann K, Hassanin E, Hegde M, Heinzen EL, Helbig I, Hengsbach C, Heyne HO, Hirose S, Hirsch E, Hjalgrim H, Howrigan DP, Hucks D, Hung PC, Iacomino M, Imbach LL, Inoue Y, Ishii A, Jamnadas-Khoda J, Jehi L, Johnson MR, Kälviäinen R, Kamatani Y, Kanaan M, Kanai M, Kantanen AM, Kara B, Kariuki SM, Kasperavičiūte D, Kasteleijn-Nolst Trenite D, Kato M, Kegele J, Kesim Y, Khoueiry-Zgheib N, King C, Kirsch HE, Klein KM, Kluger G, Knake S, Knowlton RC, Koeleman BPC, Korczyn AD, Koupparis A, Kousiappa I, Krause R, Krenn M, Krestel H, Krey I, Kunz WS, Kurki MI, Kurlemann G, Kuzniecky R, Kwan P, Labate A, Lacey A, Lal D, Landoulsi Z, Lau YL, Lauxmann S, Leech SL, Lehesjoki AE, Lemke JR, Lerche H, Lesca G, Leu C, Lewin N, Lewis-Smith D, Li GHY, Li QS, Licchetta L, Lin KL, Lindhout D, Linnankivi T, Lopes-Cendes I, Lowenstein DH, Lui CHT, Madia F, Magnusson S, Marson AG, May P, McGraw CM, Mei D, Mills JL, Minardi R, Mirza N, Møller RS, Molloy AM, Montomoli M, Mostacci B, Muccioli L, Muhle H, Müller-Schlüter K, Najm IM, Nasreddine W, Neale BM, Neubauer B, Newton CRJC, Nöthen MM, Nothnagel M, Nürnberg P, O’Brien TJ, Okada Y, Ólafsson E, Oliver KL, Özkara C, Palotie A, Pangilinan F, Papacostas SS, Parrini E, Pato CN, Pato MT, Pendziwiat M, Petrovski S, Pickrell WO, Pinsky R, Pippucci T, Poduri A, Pondrelli F, Powell RHW, Privitera M, Rademacher A, Radtke R, Ragona F, Rau S, Rees MI, Regan BM, Reif PS, Rhelms S, Riva A, Rosenow F, Ryvlin P, Saarela A, Sadleir LG, Sander JW, Sander T, Scala M, Scattergood T, Schachter SC, Schankin CJ, Scheffer IE, Schmitz B, Schoch S, Schubert-Bast S, Schulze-Bonhage A, Scudieri P, Sham P, Sheidley BR, Shih JJ, Sills GJ, Sisodiya SM, Smith MC, Smith PE, Sonsma ACM, Speed D, Sperling MR, Stefansson H, Stefansson K, Steinhoff BJ, Stephani U, Stewart WC, Stipa C, Striano P, Stroink H, Strzelczyk A, Surges R, Suzuki T, Tan KM, Taneja RS, Tanteles GA, Taubøll E, Thio LL, Thomas GN, Thomas RH, Timonen O, Tinuper P, Todaro M, Topaloğlu P, Tozzi R, Tsai MH, Tumiene B, Turkdogan D, Unnsteinsdóttir U, Utkus A, Vaidiswaran P, Valton L, van Baalen A, Vetro A, Vining EPG, Visscher F, von Brauchitsch S, von Wrede R, Wagner RG, Weber YG, Weckhuysen S, Weisenberg J, Weller M, Widdess-Walsh P, Wolff M, Wolking S, Wu D, Yamakawa K, Yang W, Yapıcı Z, Yücesan E, Zagaglia S, Zahnert F, Zara F, Zhou W, Zimprich F, Zsurka G, Zulfiqar Ali Q. GWAS meta-analysis of over 29,000 people with epilepsy identifies 26 risk loci and subtype-specific genetic architecture. Nat Genet 2023; 55:1471-1482. [PMID: 37653029 PMCID: PMC10484785 DOI: 10.1038/s41588-023-01485-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 07/21/2023] [Indexed: 09/02/2023]
Abstract
Epilepsy is a highly heritable disorder affecting over 50 million people worldwide, of which about one-third are resistant to current treatments. Here we report a multi-ancestry genome-wide association study including 29,944 cases, stratified into three broad categories and seven subtypes of epilepsy, and 52,538 controls. We identify 26 genome-wide significant loci, 19 of which are specific to genetic generalized epilepsy (GGE). We implicate 29 likely causal genes underlying these 26 loci. SNP-based heritability analyses show that common variants explain between 39.6% and 90% of genetic risk for GGE and its subtypes. Subtype analysis revealed markedly different genetic architectures between focal and generalized epilepsies. Gene-set analyses of GGE signals implicate synaptic processes in both excitatory and inhibitory neurons in the brain. Prioritized candidate genes overlap with monogenic epilepsy genes and with targets of current antiseizure medications. Finally, we leverage our results to identify alternate drugs with predicted efficacy if repurposed for epilepsy treatment.
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Martins Custodio H, Clayton LM, Bellampalli R, Pagni S, Silvennoinen K, Caswell R, Brunklaus A, Guerrini R, Koeleman BPC, Lemke JR, Møller RS, Scheffer IE, Weckhuysen S, Zara F, Zuberi S, Kuchenbaecker K, Balestrini S, Mills JD, Sisodiya SM. Widespread genomic influences on phenotype in Dravet syndrome, a 'monogenic' condition. Brain 2023; 146:3885-3897. [PMID: 37006128 PMCID: PMC10473570 DOI: 10.1093/brain/awad111] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 02/01/2023] [Accepted: 03/12/2023] [Indexed: 04/04/2023] Open
Abstract
Dravet syndrome is an archetypal rare severe epilepsy, considered 'monogenic', typically caused by loss-of-function SCN1A variants. Despite a recognizable core phenotype, its marked phenotypic heterogeneity is incompletely explained by differences in the causal SCN1A variant or clinical factors. In 34 adults with SCN1A-related Dravet syndrome, we show additional genomic variation beyond SCN1A contributes to phenotype and its diversity, with an excess of rare variants in epilepsy-related genes as a set and examples of blended phenotypes, including one individual with an ultra-rare DEPDC5 variant and focal cortical dysplasia. The polygenic risk score for intelligence was lower, and for longevity, higher, in Dravet syndrome than in epilepsy controls. The causal, major-effect, SCN1A variant may need to act against a broadly compromised genomic background to generate the full Dravet syndrome phenotype, whilst genomic resilience may help to ameliorate the risk of premature mortality in adult Dravet syndrome survivors.
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Affiliation(s)
- Helena Martins Custodio
- University College London Queen Square Institute of Neurology, Department of Clinical and Experimental Epilepsy, London, WC1N 3BG, UK
- Chalfont Centre for Epilepsy, Chalfont St Peter SL9 0RJ, UK
| | - Lisa M Clayton
- University College London Queen Square Institute of Neurology, Department of Clinical and Experimental Epilepsy, London, WC1N 3BG, UK
- Chalfont Centre for Epilepsy, Chalfont St Peter SL9 0RJ, UK
| | - Ravishankara Bellampalli
- University College London Queen Square Institute of Neurology, Department of Clinical and Experimental Epilepsy, London, WC1N 3BG, UK
- Chalfont Centre for Epilepsy, Chalfont St Peter SL9 0RJ, UK
| | - Susanna Pagni
- University College London Queen Square Institute of Neurology, Department of Clinical and Experimental Epilepsy, London, WC1N 3BG, UK
- Chalfont Centre for Epilepsy, Chalfont St Peter SL9 0RJ, UK
| | - Katri Silvennoinen
- University College London Queen Square Institute of Neurology, Department of Clinical and Experimental Epilepsy, London, WC1N 3BG, UK
- Chalfont Centre for Epilepsy, Chalfont St Peter SL9 0RJ, UK
- Kuopio Epilepsy Center, Neurocenter, Kuopio University Hospital, Kuopio 70210, Finland
| | - Richard Caswell
- Exeter Genomics Laboratory, Royal Devon University Healthcare NHS Foundation Trust, Exeter EX2 5DW, UK
| | - Andreas Brunklaus
- Paediatric Neuroscience Research Group, Royal Hospital for Children, Glasgow G51 4TF, UK
- Institute of Health and Wellbeing, University of Glasgow, Glasgow G12 8TB, UK
| | - Renzo Guerrini
- Neuroscience Department, Meyer Children’s Hospital IRCSS, University of Florence, 50139 Florence, Italy
| | - Bobby P C Koeleman
- Department of Genetics, University Medical Centre Utrecht, 3584CX Utrecht, The Netherlands
| | - Johannes R Lemke
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig 04103, Germany
- Center for Rare Diseases, University of Leipzig Medical Center, Leipzig 04103, Germany
| | - Rikke S Møller
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre, DK-4293 Dianalund, Denmark
- Department of Regional Health Research, University of Southern Denmark, DK-5230 Odense, Denmark
| | - Ingrid E Scheffer
- Epilepsy Research Centre, Florey Institute, University of Melbourne, Austin Health and Royal Children's Hospital, Melbourne, VIC 3084, Australia
- Murdoch Children's Research Institute, Parkville, VIC 3052, Australia
| | - Sarah Weckhuysen
- Applied and Translational Neurogenomics Group, VIB Centre for Molecular Neurology, VIB, Antwerp 2610, Belgium
- Translational Neurosciences, Faculty of Medicine and Health Science, University of Antwerp, Antwerp 2650, Belgium
- Department of Neurology, University Hospital Antwerp, Antwerp 2650, Belgium
- µNEURO Research Centre of Excellence, University of Antwerp, Antwerp 2610, Belgium
| | - Federico Zara
- Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
- Department of Neurosciences Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, 16132 Genoa, Italy
| | - Sameer Zuberi
- Paediatric Neuroscience Research Group, Royal Hospital for Children, Glasgow G51 4TF, UK
- Institute of Health and Wellbeing, University of Glasgow, Glasgow G12 8TB, UK
| | | | - Simona Balestrini
- University College London Queen Square Institute of Neurology, Department of Clinical and Experimental Epilepsy, London, WC1N 3BG, UK
- Chalfont Centre for Epilepsy, Chalfont St Peter SL9 0RJ, UK
- Neuroscience Department, Meyer Children’s Hospital IRCSS, University of Florence, 50139 Florence, Italy
| | - James D Mills
- University College London Queen Square Institute of Neurology, Department of Clinical and Experimental Epilepsy, London, WC1N 3BG, UK
- Chalfont Centre for Epilepsy, Chalfont St Peter SL9 0RJ, UK
- Amsterdam UMC, University of Amsterdam, Department of (Neuro)Pathology, Amsterdam Neuroscience, 1105 AZ Amsterdam, The Netherlands
| | - Sanjay M Sisodiya
- University College London Queen Square Institute of Neurology, Department of Clinical and Experimental Epilepsy, London, WC1N 3BG, UK
- Chalfont Centre for Epilepsy, Chalfont St Peter SL9 0RJ, UK
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5
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Dirkx N, Weuring WJ, De Vriendt E, Smal N, van de Vondervoort J, van 't Slot R, Koetsier M, Zonnekein N, De Pooter T, Weckhuysen S, Koeleman BPC. Increased prime edit rates in KCNQ2 and SCN1A via single nicking all-in-one plasmids. BMC Biol 2023; 21:156. [PMID: 37443005 PMCID: PMC10347817 DOI: 10.1186/s12915-023-01646-7] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 06/07/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND Prime editing (PE) is the most recent gene editing technology able to introduce targeted alterations to the genome, including single base pair changes, small insertions, and deletions. Several improvements to the PE machinery have been made in the past few years, and these have been tested in a range of model systems including immortalized cell lines, stem cells, and animal models. While double nicking RNA (dncRNA) PE systems PE3 and PE5 currently show the highest editing rates, they come with reduced accuracy as undesired indels or SNVs arise at edited loci. Here, we aimed to improve single ncRNA (sncRNA) systems PE2 and PE4max by generating novel all-in-one (pAIO) plasmids driven by an EF-1α promoter, which is especially suitable for human-induced pluripotent stem cell (hiPSC) models. RESULTS pAIO-EF1α-PE2 and pAIO-EF1α-PE4max were used to edit the voltage gated potassium channel gene KCNQ2 and voltage gated sodium channel gene SCN1A. Two clinically relevant mutations were corrected using pAIO-EF1α-PE2 including the homozygous truncating SCN1A R612* variant in HEK293T cells and the heterozygous gain-of-function KCNQ2 R201C variant in patient-derived hiPSC. We show that sncRNA PE yielded detectable editing rates in hiPSC ranging between 6.4% and 9.8%, which was further increased to 41% after a GFP-based fluorescence-activated cell sorting (FACS) cell sorting step. Furthermore, we show that selecting the high GFP expressing population improved editing efficiencies up to 3.2-fold compared to the low GFP expressing population, demonstrating that not only delivery but also the number of copies of the PE enzyme and/or pegRNA per cell are important for efficient editing. Edit rates were not improved when an additional silent protospacer-adjacent motif (PAM)-removing alteration was introduced in hiPSC at the target locus. Finally, there were no genome-wide off-target effects using pAIO-EF1α-PE2 and no off-target editing activity near the edit locus highlighting the accuracy of snc prime editors. CONCLUSION Taken together, our study shows an improved efficacy of EF-1α driven sncRNA pAIO-PE plasmids in hiPSC reaching high editing rates, especially after FACS sorting. Optimizing these sncRNA PE systems is of high value when considering future therapeutic in vivo use, where accuracy will be extremely important.
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Affiliation(s)
- N Dirkx
- Applied & Translational Neurogenomics Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium.
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
| | - Wout J Weuring
- Department of Genetics, University Medical Center Utrecht, Utrecht, 3584 CX, The Netherlands.
| | - E De Vriendt
- Applied & Translational Neurogenomics Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
| | - N Smal
- Applied & Translational Neurogenomics Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - J van de Vondervoort
- Department of Genetics, University Medical Center Utrecht, Utrecht, 3584 CX, The Netherlands
| | - Ruben van 't Slot
- Department of Genetics, University Medical Center Utrecht, Utrecht, 3584 CX, The Netherlands
| | - M Koetsier
- Department of Genetics, University Medical Center Utrecht, Utrecht, 3584 CX, The Netherlands
| | - N Zonnekein
- Applied & Translational Neurogenomics Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Tim De Pooter
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
| | - S Weckhuysen
- Applied & Translational Neurogenomics Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Translational Neurosciences, Faculty of Medicine and Health Science, University of Antwerp, Antwerp, Belgium
- Department of Neurology, Antwerp University Hospital, Antwerp, Belgium
| | - B P C Koeleman
- Department of Genetics, University Medical Center Utrecht, Utrecht, 3584 CX, The Netherlands
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6
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Alyousef YM, Alonaizan FA, Alsulaiman AA, Abukabbos H, Aldarwish MI, Alali AA, Almasood NN, Vatte C, Cyrus C, Habara AH, Koeleman BPC. Corrigendum to 'Oral microbiota analyses of Saudi sickle cell anemics with dental caries' International Dental Journal, 73/1, February 2023, Pages 144-150. Int Dent J 2023; 73:470. [PMID: 37201962 DOI: 10.1016/j.identj.2023.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023] Open
Affiliation(s)
- Yousef M Alyousef
- College of Dentistry, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Faisal A Alonaizan
- College of Dentistry, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Ahmed A Alsulaiman
- College of Dentistry, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Halima Abukabbos
- Department of Pediatric Dentistry, School of Dentistry, University of Detroit Mercy, Michigan, USA
| | | | - Ali A Alali
- College of Dentistry, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Naif N Almasood
- College of Dentistry, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Chittibabu Vatte
- Department of Clinical Biochemistry, College of Medicine, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Cyril Cyrus
- Department of Clinical Biochemistry, College of Medicine, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Alawi H Habara
- Department of Clinical Biochemistry, College of Medicine, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia.
| | - Bobby P C Koeleman
- Department of Genetics, University Medical Center Utrecht, the Netherlands
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7
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Stevelink R, Koeleman BPC, Sisodiya SM. Distinct genetic basis of common epilepsies and structural magnetic resonance imaging measures. Epilepsia 2023; 64:e82-e86. [PMID: 36799507 DOI: 10.1111/epi.17529] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 02/01/2023] [Accepted: 02/01/2023] [Indexed: 02/18/2023]
Abstract
Focal and generalized epilepsies are associated with robust differences in magnetic resonance imaging (MRI) measures of subcortical structures, gray matter, and white matter. However, it is unknown whether such structural brain differences reflect the cause or consequence of epilepsy or its treatment. Analyses of common genetic variants underlying both common epilepsy risk and variability in structural brain measures can give further insights, as such inherited variants are not influenced by disease or treatment. Here, we performed genetic correlation analyses using data from the largest genome-wide association study (GWAS) on common epilepsy (n = 27 559 cases and 42 436 controls) and GWASs on MRI measures of white (n = 33 292) or gray matter (n = 51 665). We did not detect any significant genetic correlation between any type of common epilepsy and any of 280 measures of gray matter, white matter, or subcortical structures. These results suggest that there are distinct genetic bases underlying risk of common epilepsy and for structural brain measures. This would imply that the genetic basis of normal structural brain variation is unrelated to that of common epilepsy. Structural changes in epilepsy could rather be the consequence of epilepsy, its comorbidities, or its treatment, offering a cumulative record of disease.
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Affiliation(s)
- Remi Stevelink
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands.,Department of Child Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Bobby P C Koeleman
- Department of Child Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Sanjay M Sisodiya
- Department of Clinical and Experimental Epilepsy, University College London Queen Square Institute of Neurology, London, UK.,Chalfont Centre for Epilepsy, Bucks, UK.,Chalfont Centre for Epilepsy, Chalfont St. Peter, UK
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Abumadini MS, Al Ghamdi KS, Alqahtani AH, Almedallah DK, Callans L, Jarad JA, Cyrus C, Koeleman BPC, Keating BJ, Pankratz N, Al-Ali AK. Genome-wide copy number variant screening of Saudi schizophrenia patients reveals larger deletions in cases versus controls. Front Mol Neurosci 2023; 16:1069375. [PMID: 36846569 PMCID: PMC9950097 DOI: 10.3389/fnmol.2023.1069375] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 01/20/2023] [Indexed: 02/12/2023] Open
Abstract
Introduction Genome-wide association studies have discovered common polymorphisms in regions associated with schizophrenia. No genome-wide analyses have been performed in Saudi schizophrenia subjects. Methods Genome-wide genotyping data from 136 Saudi schizophrenia cases and 97 Saudi controls in addition to 4,625 American were examined for copy number variants (CNVs). A hidden Markov model approach was used to call CNVs. Results CNVs in schizophrenia cases were twice as large on average than CNVs in controls (p = 0.04). The analyses focused on extremely large >250 kilobases CNVs or homozygous deletions of any size. One extremely large deletion was noted in a single case (16.5 megabases on chromosome 10). Two cases had an 814 kb duplication of chromosome 7 spanning a cluster of genes, including circadian-related loci, and two other cases had 277 kb deletions of chromosome 9 encompassing an olfactory receptors gene family. CNVs were also seen in loci previously associated with schizophrenia, namely a 16p11 proximal duplication and two 22q11.2 deletions. Discussion Runs of homozygosity (ROHs) were analyzed across the genome to investigate correlation with schizophrenia risk. While rates and sizes of these ROHs were similar in cases and controls, we identified 10 regions where multiple cases had ROHs and controls did not.
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Affiliation(s)
- Mahdi S. Abumadini
- Department of Psychiatry, King Fahd Hospital of the University, Al-Khobar and College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Kholoud S. Al Ghamdi
- Department of Physiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Abdullah H. Alqahtani
- Department of Psychiatry, King Fahd Hospital of the University, Al-Khobar and College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Dana K. Almedallah
- Department of Psychiatry, King Fahd Hospital of the University, Al-Khobar and College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Lauren Callans
- Department of Surgery, University of Pennsylvania School of Medicine, Philadelphia, PA, United States
| | - Jumanah A. Jarad
- Department of Psychiatry, King Fahd Hospital of the University, Al-Khobar and College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Cyril Cyrus
- Department of Clinical Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Bobby P. C. Koeleman
- Department of Genetics, Division Lab, University Medical Center Utrecht, Utrecht, Netherlands
| | - Brendan J. Keating
- Department of Surgery, University of Pennsylvania School of Medicine, Philadelphia, PA, United States
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, United States
| | - Amein K. Al-Ali
- Department of Clinical Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia,*Correspondence: Amein K. Al-Ali, ✉
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Mirza N, Stevelink R, Taweel B, Koeleman BPC, Marson AG. Using common genetic variants to find drugs for common epilepsies. Brain Commun 2021; 3:fcab287. [PMID: 34988442 PMCID: PMC8710935 DOI: 10.1093/braincomms/fcab287] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/17/2021] [Accepted: 10/20/2021] [Indexed: 12/18/2022] Open
Abstract
Better drugs are needed for common epilepsies. Drug repurposing offers the potential of significant savings in the time and cost of developing new treatments. In order to select the best candidate drug(s) to repurpose for a disease, it is desirable to predict the relative clinical efficacy that drugs will have against the disease. Common epilepsy can be divided into different types and syndromes. Different antiseizure medications are most effective for different types and syndromes of common epilepsy. For predictions of antiepileptic efficacy to be clinically translatable, it is essential that the predictions are specific to each form of common epilepsy, and reflect the patterns of drug efficacy observed in clinical studies and practice. These requirements are not fulfilled by previously published drug predictions for epilepsy. We developed a novel method for predicting the relative efficacy of drugs against any common epilepsy, by using its Genome-Wide Association Study summary statistics and drugs' activity data. The methodological advancement in our technique is that the drug predictions for a disease are based upon drugs' effects on the function and abundance of proteins, and the magnitude and direction of those effects, relative to the importance, degree and direction of the proteins' dysregulation in the disease. We used this method to predict the relative efficacy of all drugs, licensed for any condition, against each of the major types and syndromes of common epilepsy. Our predictions are concordant with findings from real-world experience and randomized clinical trials. Our method predicts the efficacy of existing antiseizure medications against common epilepsies; in this prediction, our method outperforms the best alternative existing method: area under receiver operating characteristic curve (mean ± standard deviation) 0.83 ± 0.03 and 0.63 ± 0.04, respectively. Importantly, our method predicts which antiseizure medications are amongst the more efficacious in clinical practice, and which antiseizure medications are amongst the less efficacious in clinical practice, for each of the main syndromes of common epilepsy, and it predicts the distinct order of efficacy of individual antiseizure medications in clinical trials of different common epilepsies. We identify promising candidate drugs for each of the major syndromes of common epilepsy. We screen five promising predicted drugs in an animal model: each exerts a significant dose-dependent effect upon seizures. Our predictions are a novel resource for selecting suitable candidate drugs that could potentially be repurposed for each of the major syndromes of common epilepsy. Our method is potentially generalizable to other complex diseases.
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Affiliation(s)
- Nasir Mirza
- Department of Pharmacology & Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3GE, UK
| | - Remi Stevelink
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht 3584 CX, the Netherlands; member of the ERN EpiCARE
- Department of Child Neurology, University Medical Center Utrecht Brain Center, Utrecht 3584 CX, the Netherlands
| | - Basel Taweel
- School of Medicine, University of Liverpool, Liverpool L69 3GE, UK
| | - Bobby P C Koeleman
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht 3584 CX, the Netherlands; member of the ERN EpiCARE
| | - Anthony G Marson
- Department of Pharmacology & Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3GE, UK
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Weuring W, Geerligs J, Koeleman BPC. Gene Therapies for Monogenic Autism Spectrum Disorders. Genes (Basel) 2021; 12:genes12111667. [PMID: 34828273 PMCID: PMC8617899 DOI: 10.3390/genes12111667] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 12/26/2022] Open
Abstract
Novel genome editing and transient gene therapies have been developed the past ten years, resulting in the first in-human clinical trials for monogenic disorders. Syndromic autism spectrum disorders can be caused by mutations in a single gene. Given the monogenic aspect and severity of syndromic ASD, it is an ideal candidate for gene therapies. Here, we selected 11 monogenic ASD syndromes, validated by animal models, and reviewed current gene therapies for each syndrome. Given the wide variety and novelty of some forms of gene therapy, the best possible option must be decided based on the gene and mutation.
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11
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Weuring WJ, Dilevska I, Hoekman J, van de Vondervoort J, Koetsier M, van 't Slot RH, Braun KPJ, Koeleman BPC. CRISPRa-Mediated Upregulation of scn1laa During Early Development Causes Epileptiform Activity and dCas9-Associated Toxicity. CRISPR J 2021; 4:575-582. [PMID: 34406040 DOI: 10.1089/crispr.2021.0013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Dravet syndrome (DS) is a monogenic epileptic encephalopathy caused by loss-of-function mutations in the voltage-gated sodium channel (VGSC) gene SCN1A. DS has an age of onset within the first year of life and severe disease prognosis. In the past years, it has been shown that upregulation of endogenous SCN1A can be beneficial in animal models for DS, but a complete rescue was not observed. We hypothesized that upregulation during early development that precedes onset of first symptoms might improve disease outcome. To test this hypothesis, we first evaluated the CRISPR activating method for early upregulation of voltage gated sodium channels during early development. We injected CRISPRa components, which target the proximal or distal promoter region of the VGSC gene scn1Laa in the yolk of one-cell stage zebrafish embryos. The effect of both dCas9-VPR and dCas9-VP64 was evaluated. Both CRISPRa fusions showed toxicity in the majority of embryos, with or without guide RNAs. The few embryos that survived developed normally, and dCas9-VPR induces an upregulation of scn1Laa mRNA until 24 hours after fertilization. At 5 days post fertilization, CRISPRa-injected embryos showed an epileptic phenotype, including locomotor burst movements, hyperactivity, and epileptiform activity originating from the brain. In addition to previously published scn1Laa and scn1Lab loss-of-function models, we conclude that gain of scn1Laa function can have an equally severe phenotype. Upregulation of scn1Laa in the current zebrafish model for DS, scn1Lab-KO, aggravated the disease phenotype, highlighting that early-stage upregulation using CRISPRa can lead to both toxicity and a worsening of the disease phenotype.
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Affiliation(s)
- Wout J Weuring
- Department of Genetics, University Medical Center Utrecht Brain Center, University Medical Centre Utrecht, Utrecht, The Netherlands; and University Medical Centre Utrecht, Utrecht, The Netherlands; member of the ERN EpiCARE
| | - Ivana Dilevska
- Department of Genetics, University Medical Center Utrecht Brain Center, University Medical Centre Utrecht, Utrecht, The Netherlands; and University Medical Centre Utrecht, Utrecht, The Netherlands; member of the ERN EpiCARE
| | - Jos Hoekman
- Department of Genetics, University Medical Center Utrecht Brain Center, University Medical Centre Utrecht, Utrecht, The Netherlands; and University Medical Centre Utrecht, Utrecht, The Netherlands; member of the ERN EpiCARE
| | - Joep van de Vondervoort
- Department of Genetics, University Medical Center Utrecht Brain Center, University Medical Centre Utrecht, Utrecht, The Netherlands; and University Medical Centre Utrecht, Utrecht, The Netherlands; member of the ERN EpiCARE
| | - Martijn Koetsier
- Department of Genetics, University Medical Center Utrecht Brain Center, University Medical Centre Utrecht, Utrecht, The Netherlands; and University Medical Centre Utrecht, Utrecht, The Netherlands; member of the ERN EpiCARE
| | - Ruben H van 't Slot
- Department of Genetics, University Medical Center Utrecht Brain Center, University Medical Centre Utrecht, Utrecht, The Netherlands; and University Medical Centre Utrecht, Utrecht, The Netherlands; member of the ERN EpiCARE
| | - Kees P J Braun
- Department of Neurology and Neurosurgery, University Medical Centre Utrecht, Utrecht, The Netherlands; member of the ERN EpiCARE
| | - Bobby P C Koeleman
- Department of Genetics, University Medical Center Utrecht Brain Center, University Medical Centre Utrecht, Utrecht, The Netherlands; and University Medical Centre Utrecht, Utrecht, The Netherlands; member of the ERN EpiCARE
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12
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Wolking S, Moreau C, McCormack M, Krause R, Krenn M, Berkovic S, Cavalleri GL, Delanty N, Depondt C, Johnson MR, Koeleman BPC, Kunz WS, Lerche H, Marson AG, O’Brien TJ, Petrovski S, Sander JW, Sills GJ, Striano P, Zara F, Zimprich F, Sisodiya SM, Girard SL, Cossette P. Assessing the role of rare genetic variants in drug-resistant, non-lesional focal epilepsy. Ann Clin Transl Neurol 2021; 8:1376-1387. [PMID: 34018700 PMCID: PMC8283173 DOI: 10.1002/acn3.51374] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 03/08/2021] [Accepted: 04/14/2021] [Indexed: 12/29/2022] Open
Abstract
OBJECTIVE Resistance to antiseizure medications (ASMs) is one of the major concerns in the treatment of epilepsy. Despite the increasing number of ASMs available, the proportion of individuals with drug-resistant epilepsy remains unchanged. In this study, we aimed to investigate the role of rare genetic variants in ASM resistance. METHODS We performed exome sequencing of 1,128 individuals with non-familial non-acquired focal epilepsy (NAFE) (762 non-responders, 366 responders) and were provided with 1,734 healthy controls. We undertook replication in a cohort of 350 individuals with NAFE (165 non-responders, 185 responders). We performed gene-based and gene-set-based kernel association tests to investigate potential enrichment of rare variants in relation to drug response status and to risk for NAFE. RESULTS We found no gene or gene set that reached genome-wide significance. Yet, we identified several prospective candidate genes - among them DEPDC5, which showed a potential association with resistance to ASMs. We found some evidence for an enrichment of truncating variants in dominant familial NAFE genes in our cohort of non-familial NAFE and in association with drug-resistant NAFE. INTERPRETATION Our study identifies potential candidate genes for ASM resistance. Our results corroborate the role of rare variants for non-familial NAFE and imply their involvement in drug-resistant epilepsy. Future large-scale genetic research studies are needed to substantiate these findings.
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Affiliation(s)
- Stefan Wolking
- Université de MontréalMontrealCanada
- Neurology and EpileptologyHertie Institute for Clinical Brain ResearchUniversity of TübingenTübingenGermany
- Department of Epileptology and NeurologyUniversity of AachenAachenGermany
| | - Claudia Moreau
- Centre Intersectoriel en Santé DurableUniversité du Québec à ChicoutimiSaguenayCanada
| | - Mark McCormack
- Molecular and Cellular TherapeuticsRoyal College of Surgeons in IrelandDublinIreland
| | - Roland Krause
- Luxembourg Centre for Systems BiomedicineUniversity of LuxembourgEsch‐sur‐AlzetteLuxembourg
| | - Martin Krenn
- Department of NeurologyMedical University of ViennaViennaAustria
| | | | - Samuel Berkovic
- Department of MedicineEpilepsy Research Centre, Austin HealthUniversity of MelbourneMelbourneAustralia
- Department of NeurologyAustin HealthHeidelbergAustralia
| | - Gianpiero L. Cavalleri
- Department of Molecular and Cellular TherapeuticsRoyal College of Surgeons in IrelandDublinIreland
- FutureNeuro Research CentreScience Foundation IrelandDublinIreland
- Division of Brain SciencesImperial College Faculty of MedicineLondonUK
| | - Norman Delanty
- Department of Molecular and Cellular TherapeuticsRoyal College of Surgeons in IrelandDublinIreland
- FutureNeuro Research CentreScience Foundation IrelandDublinIreland
- Division of NeurologyBeaumont HospitalDublinIreland
| | - Chantal Depondt
- Department of NeurologyHôpital ErasmeUniversité Libre de BruxellesBrusselsBelgium
| | | | | | - Wolfram S. Kunz
- Institute of Experimental Epileptology and Cognition Research and Department of EpileptologyUniversity of BonnBonnGermany
| | - Holger Lerche
- Neurology and EpileptologyHertie Institute for Clinical Brain ResearchUniversity of TübingenTübingenGermany
| | - Anthony G. Marson
- Department of Molecular and Clinical PharmacologyInstitute of Translational MedicineUniversity of LiverpoolLiverpoolUK
- The Walton Centre NHS Foundation TrustLiverpoolUK
- Liverpool Health PartnersLiverpoolUK
| | - Terence J. O’Brien
- Departments of Medicine and NeurologyRoyal Melbourne HospitalUniversity of MelbourneParkvilleAustralia
- Departments of Neuroscience and NeurologyThe Central Clinical SchoolMonash University and The Alfred HospitalMelbourneAustralia
| | - Slave Petrovski
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&DAstraZenecaCambridgeUK
| | - Josemir W. Sander
- Department of Clinical and Experimental EpilepsyUCL Queen Square Institute of NeurologyLondonUK
- Chalfont Centre for EpilepsyChalfont‐St‐PeterUK
- Stichting Epilepsie Instellingen Nederland (SEIN)HeemstedeNetherlands
| | | | - Pasquale Striano
- Pediatric Neurology and Muscular Diseases UnitIRCCS "G. Gaslini" InstituteGenovaItaly
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child HealthUniversity of GenoaGenovaItaly
| | - Federico Zara
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child HealthUniversity of GenoaGenovaItaly
- Laboratory of Neurogenetics and NeuroscienceIRCCS "G. Gaslini" InstituteGenovaItaly
| | - Fritz Zimprich
- Department of NeurologyMedical University of ViennaViennaAustria
| | - Sanjay M. Sisodiya
- Department of Clinical and Experimental EpilepsyUCL Queen Square Institute of NeurologyLondonUK
- Chalfont Centre for EpilepsyChalfont‐St‐PeterUK
| | - Simon L. Girard
- Centre Intersectoriel en Santé DurableUniversité du Québec à ChicoutimiSaguenayCanada
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Wolking S, Campbell C, Stapleton C, McCormack M, Delanty N, Depondt C, Johnson MR, Koeleman BPC, Krause R, Kunz WS, Marson AG, Sander JW, Sills GJ, Striano P, Zara F, Sisodiya SM, Cavalleri GL, Lerche H. Role of Common Genetic Variants for Drug-Resistance to Specific Anti-Seizure Medications. Front Pharmacol 2021; 12:688386. [PMID: 34177598 PMCID: PMC8220970 DOI: 10.3389/fphar.2021.688386] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/10/2021] [Indexed: 12/20/2022] Open
Abstract
Objective: Resistance to anti-seizure medications (ASMs) presents a significant hurdle in the treatment of people with epilepsy. Genetic markers for resistance to individual ASMs could support clinicians to make better-informed choices for their patients. In this study, we aimed to elucidate whether the response to individual ASMs was associated with common genetic variation. Methods: A cohort of 3,649 individuals of European descent with epilepsy was deeply phenotyped and underwent single nucleotide polymorphism (SNP)-genotyping. We conducted genome-wide association analyses (GWASs) on responders to specific ASMs or groups of functionally related ASMs, using non-responders as controls. We performed a polygenic risk score (PRS) analyses based on risk variants for epilepsy and neuropsychiatric disorders and ASM resistance itself to delineate the polygenic burden of ASM-specific drug resistance. Results: We identified several potential regions of interest but did not detect genome-wide significant loci for ASM-specific response. We did not find polygenic risk for epilepsy, neuropsychiatric disorders, and drug-resistance associated with drug response to specific ASMs or mechanistically related groups of ASMs. Significance: This study could not ascertain the predictive value of common genetic variants for ASM responder status. The identified suggestive loci will need replication in future studies of a larger scale.
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Affiliation(s)
- Stefan Wolking
- Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- Department of Epileptology and Neurology, University of Aachen, Aachen, Germany
| | - Ciarán Campbell
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Caragh Stapleton
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Mark McCormack
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Norman Delanty
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
- FutureNeuro Research Centre, Science Foundation Ireland, Dublin, Ireland
- Division of Neurology, Beaumont Hospital, Dublin, Ireland
| | - Chantal Depondt
- Department of Neurology, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Michael R. Johnson
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, United Kingdom
| | | | - Roland Krause
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Wolfram S. Kunz
- Institute of Experimental Epileptology and Cognition Research and Department of Epileptology, University of Bonn, Bonn, Germany
| | - Anthony G. Marson
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
- The Walton Centre NHS Foundation Trust, Liverpool, United Kingdom
- Liverpool Health Partners, Liverpool, United Kingdom
| | - Josemir W. Sander
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, United Kingdom
- Chalfont Centre for Epilepsy, Chalfont-St-Peter, United Kingdom
- Stichting Epilepsie Instellingen Nederland (SEIN), Heemstede, Netherlands
| | - Graeme J. Sills
- School of Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Pasquale Striano
- IRCCS "G. Gaslini" Institute, Genova, Italy
- Department of Neurosciences, University of Genoa, Genova, Italy
| | - Federico Zara
- IRCCS "G. Gaslini" Institute, Genova, Italy
- Department of Neurosciences, University of Genoa, Genova, Italy
| | - Sanjay M. Sisodiya
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, United Kingdom
- Chalfont Centre for Epilepsy, Chalfont-St-Peter, United Kingdom
| | - Gianpiero L. Cavalleri
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
- FutureNeuro Research Centre, Science Foundation Ireland, Dublin, Ireland
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, United Kingdom
| | - Holger Lerche
- Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
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14
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Stevelink R, Luykx JJ, Lin BD, Leu C, Lal D, Smith AW, Schijven D, Carpay JA, Rademaker K, Rodrigues Baldez RA, Devinsky O, Braun KPJ, Jansen FE, Smit DJA, Koeleman BPC. Shared genetic basis between genetic generalized epilepsy and background electroencephalographic oscillations. Epilepsia 2021; 62:1518-1527. [PMID: 34002374 PMCID: PMC8672363 DOI: 10.1111/epi.16922] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 01/22/2021] [Indexed: 11/29/2022]
Abstract
Objective Paroxysmal epileptiform abnormalities on electroencephalography (EEG) are the hallmark of epilepsies, but it is uncertain to what extent epilepsy and background EEG oscillations share neurobiological underpinnings. Here, we aimed to assess the genetic correlation between epilepsy and background EEG oscillations. Methods Confounding factors, including the heterogeneous etiology of epilepsies and medication effects, hamper studies on background brain activity in people with epilepsy. To overcome this limitation, we compared genetic data from a genome‐wide association study (GWAS) on epilepsy (n = 12 803 people with epilepsy and 24 218 controls) with that from a GWAS on background EEG (n = 8425 subjects without epilepsy), in which background EEG oscillation power was quantified in four different frequency bands: alpha, beta, delta, and theta. We replicated our findings in an independent epilepsy replication dataset (n = 4851 people with epilepsy and 20 428 controls). To assess the genetic overlap between these phenotypes, we performed genetic correlation analyses using linkage disequilibrium score regression, polygenic risk scores, and Mendelian randomization analyses. Results Our analyses show strong genetic correlations of genetic generalized epilepsy (GGE) with background EEG oscillations, primarily in the beta frequency band. Furthermore, we show that subjects with higher beta and theta polygenic risk scores have a significantly higher risk of having generalized epilepsy. Mendelian randomization analyses suggest a causal effect of GGE genetic liability on beta oscillations. Significance Our results point to shared biological mechanisms underlying background EEG oscillations and the susceptibility for GGE, opening avenues to investigate the clinical utility of background EEG oscillations in the diagnostic workup of epilepsy.
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Affiliation(s)
- Remi Stevelink
- Department of Genetics, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.,Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Jurjen J Luykx
- Department of Psychiatry, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.,Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.,GGNet Mental Health, Apeldoorn, the Netherlands
| | - Bochao D Lin
- Department of Psychiatry, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.,Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Costin Leu
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachussets, USA
| | - Dennis Lal
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachussets, USA
| | - Alexander W Smith
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachussets, USA
| | - Dick Schijven
- Department of Psychiatry, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.,Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Johannes A Carpay
- Department of Neurology, Tergooi Hospital, Hilversum, the Netherlands
| | - Koen Rademaker
- Department of Psychiatry, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Roiza A Rodrigues Baldez
- Clinical Research Laboratory on Neuroinfectious Diseases, Evandro Chagas Clinical Research Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Orrin Devinsky
- Comprehensive Epilepsy Center, New York University School of Medicine, New York, New York, USA
| | - Kees P J Braun
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Floor E Jansen
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Dirk J A Smit
- Psychiatry Department, Amsterdam Neuroscience, Amsterdam Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Bobby P C Koeleman
- Department of Genetics, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
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15
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Berghuis B, Hulst J, Sonsma A, McCormack M, de Haan GJ, Sander JW, Lindhout D, Koeleman BPC. Symptomatology of carbamazepine- and oxcarbazepine-induced hyponatremia in people with epilepsy. Epilepsia 2021; 62:778-784. [PMID: 33576502 PMCID: PMC8248112 DOI: 10.1111/epi.16828] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 01/08/2021] [Accepted: 01/12/2021] [Indexed: 01/15/2023]
Abstract
OBJECTIVE To ascertain whether adverse effects experienced by people taking carbamazepine or oxcarbazepine could be attributed to carbamazepine- or oxcarbazepine-induced hyponatremia (COIH). METHODS We performed an observational study, collecting data between 2017 and 2019 on serum sodium levels and adverse effects retrospectively in people with epilepsy while receiving treatment with either carbamazepine (CBZ) or oxcarbazepine (OXC). We defined hyponatremia as sodium level ≤134 mEq/L and severe hyponatremia as sodium level ≤128 mEq/L. Adverse effects experienced were compared between groups of individuals with and without hyponatremia. RESULTS A total of 1370 people using CBZ or OXC were identified, of whom 410 had at least one episode of hyponatremia. We checked for symptoms related to the use of CBZ and OXC in 710 people (410 with and 300 without hyponatremia) and found relevant information in 688. Adverse effects occurred in 65% of people with hyponatremia compared to 21% with normal sodium levels (odds ratio [OR] 7.5, P ≤ .001) and in 83% of people with severe hyponatremia compared to 55% in those with mild hyponatremia (P ≤ .001). Significant predictors of adverse effects were the drug (OXC vs CBZ), and the number of concomitant anti-seizure medications. Dizziness (28% vs 6%), tiredness (22% vs 7%), instability (19% vs 3%), and diplopia (16% vs 4%) were reported more often in the hyponatremia group than in patients with normal levels. SIGNIFICANCE People with COIH had a 7-fold increased risk of developing adverse effects during treatment. Clinicians should consider ascertainment of sodium levels in patients taking CBZ and OXC and act upon findings.
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Affiliation(s)
- Bianca Berghuis
- Stichting Epilepsie Instellingen Nederland (SEIN), Zwolle, The Netherlands
| | - Janic Hulst
- Stichting Epilepsie Instellingen Nederland (SEIN), Zwolle, The Netherlands
| | - Anja Sonsma
- Centre of Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Mark McCormack
- Centre of Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Gerrit-Jan de Haan
- Stichting Epilepsie Instellingen Nederland (SEIN), Zwolle, The Netherlands
| | - Josemir W Sander
- Stichting Epilepsie Instellingen Nederland (SEIN), Zwolle, The Netherlands.,NIHR UCL Hospitals Biomedical Research Centre, UCL Institute of Neurology, Queen Square, London WC1N 3BG & Chalfont Centre for Epilepsy, Chalfont, UK
| | - Dick Lindhout
- Stichting Epilepsie Instellingen Nederland (SEIN), Zwolle, The Netherlands.,Department of Human Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bobby P C Koeleman
- Centre of Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
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16
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Benova B, Sanders MWCB, Uhrova-Meszarosova A, Belohlavkova A, Hermanovska B, Novak V, Stanek D, Vlckova M, Zamecnik J, Aronica E, Braun KPJ, Koeleman BPC, Jansen FE, Krsek P. GATOR1-related focal cortical dysplasia in epilepsy surgery patients and their families: A possible gradient in severity? Eur J Paediatr Neurol 2021; 30:88-96. [PMID: 33461085 DOI: 10.1016/j.ejpn.2020.12.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 10/16/2020] [Accepted: 12/04/2020] [Indexed: 12/23/2022]
Abstract
BACKGROUND Variants of GATOR1-genes represent a recognised cause of focal cortical dysplasia (FCD), the most common structural aetiology in paediatric drug-resistant focal epilepsy. Reports on familial cases of GATOR1-associated FCD are limited, especially with respect to epilepsy surgery outcomes. METHODS We present phenotypical manifestations of four unrelated patients with drug-resistant focal epilepsy, FCD and a first-degree relative with epilepsy. All patients underwent targeted gene panel sequencing as a part of the presurgical work up. Literature search was performed to compare our findings to previously published cases. RESULTS The children (probands) had a more severe phenotype than their parents, including drug-resistant epilepsy and developmental delay, and they failed to achieve seizure freedom post-surgically. All patients had histopathologically confirmed FCD (types IIa, IIb, Ia). In Patient 1 and her affected father, we detected a known pathogenic NPRL2 variant. In patients 2 and 3 and their affected parents, we found novel likely pathogenic germline DEPDC5 variants. In family 4, we detected a novel variant in NPRL3. We identified 15 additional cases who underwent epilepsy surgery for GATOR1-associated FCD, with a positive family history of epilepsy in the literature; in 8/13 tested, the variant was inherited from an asymptomatic parent. CONCLUSION The presented cases displayed a severity gradient in phenotype with children more severely affected than the parents. Although patients with GATOR1-associated FCD are considered good surgical candidates, post-surgical seizure outcome was poor in our familial cases, suggesting that accurate identification of the epileptogenic zone may be more challenging in this subgroup of patients.
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Affiliation(s)
- Barbora Benova
- Department of Paediatric Neurology, Motol Epilepsy Center, 2nd Faculty of Medicine, Charles University and Motol University Hospital, V Uvalu 84, 15006, Prague, Czech Republic; Neurogenetics Laboratory of the Department of Paediatric Neurology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, V Uvalu 84, Prague, 15006, Czech Republic.
| | - Maurits W C B Sanders
- Department of Child Neurology, Brain Center University Medical Center Utrecht, the Netherlands.
| | - Anna Uhrova-Meszarosova
- Department of Paediatric Neurology, Motol Epilepsy Center, 2nd Faculty of Medicine, Charles University and Motol University Hospital, V Uvalu 84, 15006, Prague, Czech Republic; Neurogenetics Laboratory of the Department of Paediatric Neurology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, V Uvalu 84, Prague, 15006, Czech Republic.
| | - Anezka Belohlavkova
- Department of Paediatric Neurology, Motol Epilepsy Center, 2nd Faculty of Medicine, Charles University and Motol University Hospital, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Barbora Hermanovska
- Department of Paediatric Neurology, Motol Epilepsy Center, 2nd Faculty of Medicine, Charles University and Motol University Hospital, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Vilem Novak
- Department of Paediatric Neurology, Ostrava Faculty Hospital, 17. Listopadu 1790, 708 00, Ostrava-Poruba, Czech Republic.
| | - David Stanek
- Neurogenetics Laboratory of the Department of Paediatric Neurology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, V Uvalu 84, Prague, 15006, Czech Republic.
| | - Marketa Vlckova
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine, Charles University and Motol University Hospital, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Josef Zamecnik
- Department of Pathology and Molecular Medicine, 2nd Faculty of Medicine, Charles University and Motol University Hospital, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Eleonora Aronica
- Amsterdam UMC, University of Amsterdam, Department of (Neuro)Pathology, Amsterdam, Meibergdreef 9, 1105, AZ Amsterdam, the Netherlands; Stichting Epilepsie Instellingen Nederland (SEIN), Achterweg 2, 2103, SW, Heemstede, the Netherlands.
| | - Kees P J Braun
- Department of Child Neurology, Brain Center University Medical Center Utrecht, the Netherlands.
| | - Bobby P C Koeleman
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands.
| | - Floor E Jansen
- Department of Child Neurology, Brain Center University Medical Center Utrecht, the Netherlands.
| | - Pavel Krsek
- Department of Paediatric Neurology, Motol Epilepsy Center, 2nd Faculty of Medicine, Charles University and Motol University Hospital, V Uvalu 84, 15006, Prague, Czech Republic.
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17
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Stamberger H, Hammer TB, Gardella E, Vlaskamp DRM, Bertelsen B, Mandelstam S, de Lange I, Zhang J, Myers CT, Fenger C, Afawi Z, Almanza Fuerte EP, Andrade DM, Balcik Y, Ben Zeev B, Bennett MF, Berkovic SF, Isidor B, Bouman A, Brilstra E, Busk ØL, Cairns A, Caumes R, Chatron N, Dale RC, de Geus C, Edery P, Gill D, Granild-Jensen JB, Gunderson L, Gunning B, Heimer G, Helle JR, Hildebrand MS, Hollingsworth G, Kharytonov V, Klee EW, Koeleman BPC, Koolen DA, Korff C, Küry S, Lesca G, Lev D, Leventer RJ, Mackay MT, Macke EL, McEntagart M, Mohammad SS, Monin P, Montomoli M, Morava E, Moutton S, Muir AM, Parrini E, Procopis P, Ranza E, Reed L, Reif PS, Rosenow F, Rossi M, Sadleir LG, Sadoway T, Schelhaas HJ, Schneider AL, Shah K, Shalev R, Sisodiya SM, Smol T, Stumpel CTRM, Stuurman K, Symonds JD, Mau-Them FT, Verbeek N, Verhoeven JS, Wallace G, Yosovich K, Zarate YA, Zerem A, Zuberi SM, Guerrini R, Mefford HC, Patel C, Zhang YH, Møller RS, Scheffer IE. NEXMIF encephalopathy: an X-linked disorder with male and female phenotypic patterns. Genet Med 2020; 23:363-373. [PMID: 33144681 DOI: 10.1038/s41436-020-00988-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [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: 06/08/2020] [Revised: 09/21/2020] [Accepted: 09/21/2020] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Pathogenic variants in the X-linked gene NEXMIF (previously KIAA2022) are associated with intellectual disability (ID), autism spectrum disorder, and epilepsy. We aimed to delineate the female and male phenotypic spectrum of NEXMIF encephalopathy. METHODS Through an international collaboration, we analyzed the phenotypes and genotypes of 87 patients with NEXMIF encephalopathy. RESULTS Sixty-three females and 24 males (46 new patients) with NEXMIF encephalopathy were studied, with 30 novel variants. Phenotypic features included developmental delay/ID in 86/87 (99%), seizures in 71/86 (83%) and multiple comorbidities. Generalized seizures predominated including myoclonic seizures and absence seizures (both 46/70, 66%), absence with eyelid myoclonia (17/70, 24%), and atonic seizures (30/70, 43%). Males had more severe developmental impairment; females had epilepsy more frequently, and varied from unaffected to severely affected. All NEXMIF pathogenic variants led to a premature stop codon or were deleterious structural variants. Most arose de novo, although X-linked segregation occurred for both sexes. Somatic mosaicism occurred in two males and a family with suspected parental mosaicism. CONCLUSION NEXMIF encephalopathy is an X-linked, generalized developmental and epileptic encephalopathy characterized by myoclonic-atonic epilepsy overlapping with eyelid myoclonia with absence. Some patients have developmental encephalopathy without epilepsy. Males have more severe developmental impairment. NEXMIF encephalopathy arises due to loss-of-function variants.
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Affiliation(s)
- Hannah Stamberger
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbourne, Melbourne, VIC, Australia.,Applied and Translational Neurogenomics group, Center for Molecular Neurology, VIB, and Department of Neurology, University Hospital of Antwerp, University of Antwerp, Antwerpen, Belgium
| | - Trine B Hammer
- Department of Epilepsy Genetics, Danish Epilepsy Centre Filadelfia, Dianalund, Denmark.,Clinical Genetic Department, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Elena Gardella
- Department of Epilepsy Genetics, Danish Epilepsy Centre Filadelfia, Dianalund, Denmark.,Institute for Regional Health Services Research, University of Southern Denmark, Odense, Denmark
| | - Danique R M Vlaskamp
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbourne, Melbourne, VIC, Australia.,University of Groningen, University Medical Center Groningen, Department of Neurology, Groningen, the Netherlands.,University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Birgitte Bertelsen
- Center for Genomic Medicine, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Simone Mandelstam
- Royal Children's Hospital, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Pediatrics, University of Melbourne, Melbourne, VIC, Australia.,Department of Radiology, University of Melbourne, Melbourne, VIC, Australia.,Florey Institute of Neuroscience and Mental Health, Melbourne, VIC, Australia
| | - Iris de Lange
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jing Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Candace T Myers
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Christina Fenger
- Department of Epilepsy Genetics, Danish Epilepsy Centre Filadelfia, Dianalund, Denmark
| | - Zaid Afawi
- Tel Aviv University Medical School, Tel Aviv, Israel
| | - Edith P Almanza Fuerte
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Danielle M Andrade
- Division of Neurology, Toronto Western Hospital, University of Toronto, Toronto, ON, Canada
| | - Yunus Balcik
- Epilepsy Center Frankfurt Rhine-Main, Center of Neurology and Neurosurgery, University Hospital Frankfurt, and Center for Personalized Translational Epilepsy Research (CePTER), Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Bruria Ben Zeev
- Edmond and Lily Safra Children's Hospital, Pediatric Neurology Unit, Tel-Hashomer, Israel.,Tel Aviv University, Sackler School of Medicine, Tel Aviv, Israel
| | - Mark F Bennett
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbourne, Melbourne, VIC, Australia.,The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology University of Melbourne, Melbourne, VIC, Australia
| | - Samuel F Berkovic
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbourne, Melbourne, VIC, Australia
| | | | - Arjan Bouman
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Eva Brilstra
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Øyvind L Busk
- Section for Medical Genetics, Telemark Hospital, Skien, Norway
| | - Anita Cairns
- Department of Neurosciences, Queensland Children's Hospital, Brisbane, QLD, Australia
| | - Roseline Caumes
- Service de Neuropédiatrie, Pôle de Médecine et Spécialités Médicales, CHRU de Lille, Lille, France
| | - Nicolas Chatron
- Lyon University Hospitals, Departments of Genetics, Lyon, France
| | - Russell C Dale
- T.Y. Nelson Department of Neurology and Neurosurgery, The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Christa de Geus
- University Medical Centre Groningen, Department of Genetics, Groningen, The Netherlands
| | - Patrick Edery
- Lyon University Hospitals, Departments of Genetics, Lyon, France.,INSERM U1028, CNRS UMR5292, Centre de Recherche en Neurosciences de Lyon, GENDEV Team, Bron, France
| | - Deepak Gill
- T.Y. Nelson Department of Neurology and Neurosurgery, The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | | | - Lauren Gunderson
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | | | - Gali Heimer
- Edmond and Lily Safra Children's Hospital, Pediatric Neurology Unit, Tel-Hashomer, Israel.,Tel Aviv University, Sackler School of Medicine, Tel Aviv, Israel
| | - Johan R Helle
- Section for Medical Genetics, Telemark Hospital, Skien, Norway
| | - Michael S Hildebrand
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbourne, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Georgie Hollingsworth
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbourne, Melbourne, VIC, Australia
| | | | - Eric W Klee
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Bobby P C Koeleman
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - David A Koolen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Christian Korff
- Pediatric Neurology Unit, University Hospitals, Geneva, Switzerland
| | - Sébastien Küry
- Service de génétique médicale, CHU Nantes, Nantes, France
| | - Gaetan Lesca
- Lyon University Hospitals, Departments of Genetics, Lyon, France
| | - Dorit Lev
- Tel Aviv University, Sackler School of Medicine, Tel Aviv, Israel.,Institute of Medical Genetics, Wolfson Medical Center, Holon, Israel
| | - Richard J Leventer
- Royal Children's Hospital, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Pediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Mark T Mackay
- Royal Children's Hospital, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Pediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Erica L Macke
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Meriel McEntagart
- Medical Genetics, St George's University Hospitals NHS FT, Cranmer Tce, London, United Kingdom
| | - Shekeeb S Mohammad
- T.Y. Nelson Department of Neurology and Neurosurgery, The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Pauline Monin
- Lyon University Hospitals, Departments of Genetics, Lyon, France
| | - Martino Montomoli
- Department of Neuroscience, Pharmacology and Child Health, Children's Hospital A. Meyer and University of Florence, Florence, Italy
| | - Eva Morava
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Sebastien Moutton
- CPDPN, Pôle mère enfant, Maison de Santé Protestante Bordeaux Bagatelle, Talence, France.,INSERM UMR1231 GAD, FHU-TRANSLAD, Université de Bourgogne, Dijon, France
| | - Alison M Muir
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Elena Parrini
- Department of Neuroscience, Pharmacology and Child Health, Children's Hospital A. Meyer and University of Florence, Florence, Italy
| | - Peter Procopis
- T.Y. Nelson Department of Neurology and Neurosurgery, The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, Sydney, Australia.,Discipline of Child and Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Emmanuelle Ranza
- Medigenome, Swiss Institute of Genomic Medicine, Geneva, Switzerland
| | - Laura Reed
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Philipp S Reif
- Epilepsy Center Frankfurt Rhine-Main, Center of Neurology and Neurosurgery, University Hospital Frankfurt, and Center for Personalized Translational Epilepsy Research (CePTER), Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Felix Rosenow
- Epilepsy Center Frankfurt Rhine-Main, Center of Neurology and Neurosurgery, University Hospital Frankfurt, and Center for Personalized Translational Epilepsy Research (CePTER), Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Massimiliano Rossi
- Lyon University Hospitals, Departments of Genetics, Lyon, France.,INSERM U1028, CNRS UMR5292, Centre de Recherche en Neurosciences de Lyon, GENDEV Team, Bron, France
| | - Lynette G Sadleir
- Department of Paediatrics and Child Health, University of Otago Wellington, Wellington, New Zealand
| | - Tara Sadoway
- Division of Neurology, Toronto Western Hospital, University of Toronto, Toronto, ON, Canada
| | | | - Amy L Schneider
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbourne, Melbourne, VIC, Australia
| | | | - Ruth Shalev
- Neuropaediatric Unit, Shaare Zedek Medical Centre, Hebrew University School of Medicine, Jerusalem, Israel
| | - Sanjay M Sisodiya
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, United Kingdom and Chalfont Centre for Epilepsy, Bucks, UK
| | - Thomas Smol
- Institut de Génétique Médicale, Hopital Jeanne de Flandre, Lille University Hospital, Lille, France
| | - Connie T R M Stumpel
- Department of Clinical Genetics and GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Kyra Stuurman
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Joseph D Symonds
- Paediatric Neurosciences Research Group, Royal Hospital for Children, Glasgow, UK.,College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Frederic Tran Mau-Them
- UF Innovation en diagnostic genomique des maladies rares, CHU Dijon Bourgogne, Dijon, France.,INSERM UMR1231 GAD, Dijon, France
| | - Nienke Verbeek
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Judith S Verhoeven
- Academic Center for Epileptology, Kempenhaege, Department of Neurology, Heeze, The Netherlands
| | - Geoffrey Wallace
- Department of Neurosciences, Queensland Children's Hospital, Brisbane, QLD, Australia.,School of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Keren Yosovich
- Molecular Genetics Lab, Wolfson Medical Center, Holon, Israel
| | - Yuri A Zarate
- Section of Genetics and Metabolism, Department of Pediatrics, University of Arkansas for Medical Sciences, Arkansas Children's Hospital, Little Rock, AR, USA
| | - Ayelet Zerem
- Tel Aviv University, Sackler School of Medicine, Tel Aviv, Israel.,White Matter Disease Care, Pediatric Neurology Unit, Dana-Dwak Children's Hospital, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Sameer M Zuberi
- Paediatric Neurosciences Research Group, Royal Hospital for Children, Glasgow, UK.,College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Renzo Guerrini
- Department of Neuroscience, Pharmacology and Child Health, Children's Hospital A. Meyer and University of Florence, Florence, Italy
| | - Heather C Mefford
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Chirag Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Yue-Hua Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Rikke S Møller
- Department of Epilepsy Genetics, Danish Epilepsy Centre Filadelfia, Dianalund, Denmark.,Institute for Regional Health Services Research, University of Southern Denmark, Odense, Denmark
| | - Ingrid E Scheffer
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbourne, Melbourne, VIC, Australia. .,Royal Children's Hospital, Melbourne, VIC, Australia. .,Murdoch Children's Research Institute, Melbourne, VIC, Australia. .,Department of Pediatrics, University of Melbourne, Melbourne, VIC, Australia. .,Florey Institute of Neuroscience and Mental Health, Melbourne, VIC, Australia.
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18
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Schijven D, Stevelink R, McCormack M, van Rheenen W, Luykx JJ, Koeleman BPC, Veldink JH. Analysis of shared common genetic risk between amyotrophic lateral sclerosis and epilepsy. Neurobiol Aging 2020; 92:153.e1-153.e5. [PMID: 32409253 PMCID: PMC7818383 DOI: 10.1016/j.neurobiolaging.2020.04.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 01/31/2020] [Accepted: 04/10/2020] [Indexed: 12/04/2022]
Abstract
Because hyper-excitability has been shown to be a shared pathophysiological mechanism, we used the latest and largest genome-wide studies in amyotrophic lateral sclerosis (n = 36,052) and epilepsy (n = 38,349) to determine genetic overlap between these conditions. First, we showed no significant genetic correlation, also when binned on minor allele frequency. Second, we confirmed the absence of polygenic overlap using genomic risk score analysis. Finally, we did not identify pleiotropic variants in meta-analyses of the 2 diseases. Our findings indicate that amyotrophic lateral sclerosis and epilepsy do not share common genetic risk, showing that hyper-excitability in both disorders has distinct origins.
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Affiliation(s)
- Dick Schijven
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands; Department of Psychiatry, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands; Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Remi Stevelink
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Mark McCormack
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands; Department of Molecular and Cellular Therapeutics, The Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Wouter van Rheenen
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Jurjen J Luykx
- Department of Psychiatry, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Bobby P C Koeleman
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Jan H Veldink
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.
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19
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Perucca P, Anderson A, Jazayeri D, Hitchcock A, Graham J, Todaro M, Tomson T, Battino D, Perucca E, Ferri MM, Rochtus A, Lagae L, Canevini MP, Zambrelli E, Campbell E, Koeleman BPC, Scheffer IE, Berkovic SF, Kwan P, Sisodiya SM, Goldstein DB, Petrovski S, Craig J, Vajda FJE, O'Brien TJ. Antiepileptic Drug Teratogenicity and De Novo Genetic Variation Load. Ann Neurol 2020; 87:897-906. [PMID: 32215971 DOI: 10.1002/ana.25724] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 03/13/2020] [Accepted: 03/20/2020] [Indexed: 12/12/2022]
Abstract
OBJECTIVE The mechanisms by which antiepileptic drugs (AEDs) cause birth defects (BDs) are unknown. Data suggest that AED-induced BDs may result from a genome-wide increase of de novo variants in the embryo, a mechanism that we investigated. METHODS Whole exome sequencing data from child-parent trios were interrogated for de novo single-nucleotide variants/indels (dnSNVs/indels) and de novo copy number variants (dnCNVs). Generalized linear models were applied to assess de novo variant burdens in children exposed prenatally to AEDs (AED-exposed children) versus children without BDs not exposed prenatally to AEDs (AED-unexposed unaffected children), and AED-exposed children with BDs versus those without BDs, adjusting for confounders. Fisher exact test was used to compare categorical data. RESULTS Sixty-seven child-parent trios were included: 10 with AED-exposed children with BDs, 46 with AED-exposed unaffected children, and 11 with AED-unexposed unaffected children. The dnSNV/indel burden did not differ between AED-exposed children and AED-unexposed unaffected children (median dnSNV/indel number/child [range] = 3 [0-7] vs 3 [1-5], p = 0.50). Among AED-exposed children, there were no significant differences between those with BDs and those unaffected. Likely deleterious dnSNVs/indels were detected in 9 of 67 (13%) children, none of whom had BDs. The proportion of cases harboring likely deleterious dnSNVs/indels did not differ significantly between AED-unexposed and AED-exposed children. The dnCNV burden was not associated with AED exposure or birth outcome. INTERPRETATION Our study indicates that prenatal AED exposure does not increase the burden of de novo variants, and that this mechanism is not a major contributor to AED-induced BDs. These results can be incorporated in routine patient counseling. ANN NEUROL 2020;87:897-906.
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Affiliation(s)
- Piero Perucca
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Departments of Medicine and Neurology, University of Melbourne, Royal Melbourne Hospital, Melbourne, Victoria, Australia.,Department of Neurology, Alfred Health, Melbourne, Victoria, Australia
| | - Alison Anderson
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Departments of Medicine and Neurology, University of Melbourne, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Dana Jazayeri
- Departments of Medicine and Neurology, University of Melbourne, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Alison Hitchcock
- Departments of Medicine and Neurology, University of Melbourne, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Janet Graham
- Departments of Medicine and Neurology, University of Melbourne, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Marian Todaro
- Departments of Medicine and Neurology, University of Melbourne, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Torbjörn Tomson
- Department of Clinical Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Dina Battino
- Epilepsy Center, Department of Neurophysiology and Experimental Epileptology, IRCCS Neurological Institute "Carlo Besta" Foundation, Milan, Italy
| | - Emilio Perucca
- Department of Internal Medicine and Therapeutics, University of Pavia, and Clinical Trial Center, IRCCS Mondino Foundation, Pavia, Italy
| | | | - Anne Rochtus
- Department of Development and Regeneration, Section of Pediatric Neurology, University Hospitals Leuven, Leuven, Belgium
| | - Lieven Lagae
- Department of Development and Regeneration, Section of Pediatric Neurology, University Hospitals Leuven, Leuven, Belgium
| | - Maria Paola Canevini
- Child Neuropsychiatry Unit-Epilepsy Center, San Paolo Hospital, Milan, Italy.,Department of Health Sciences, University of Milan, Milan, Italy
| | - Elena Zambrelli
- Child Neuropsychiatry Unit-Epilepsy Center, San Paolo Hospital, Milan, Italy
| | - Ellen Campbell
- Belfast Health and Social Care Trust, Belfast, United Kingdom
| | - Bobby P C Koeleman
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Ingrid E Scheffer
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbourne, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Florey and Murdoch Children's Research Institutes, Melbourne, Victoria, Australia
| | - Samuel F Berkovic
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Patrick Kwan
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Departments of Medicine and Neurology, University of Melbourne, Royal Melbourne Hospital, Melbourne, Victoria, Australia.,Department of Neurology, Alfred Health, Melbourne, Victoria, Australia
| | - Sanjay M Sisodiya
- Department of Clinical and Experimental Epilepsy, University College London Queen Square Institute of Neurology, London, United Kingdom.,Chalfont Centre for Epilepsy, Chalfont-St-Peter, United Kingdom
| | - David B Goldstein
- Institute of Genomic Medicine, Columbia University, New York, NY, USA
| | - Slavé Petrovski
- Departments of Medicine and Neurology, University of Melbourne, Royal Melbourne Hospital, Melbourne, Victoria, Australia.,Centre for Genomic Research, AstraZeneca, Cambridge, United Kingdom
| | - John Craig
- Belfast Health and Social Care Trust, Belfast, United Kingdom
| | - Frank J E Vajda
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Departments of Medicine and Neurology, University of Melbourne, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Terence J O'Brien
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Departments of Medicine and Neurology, University of Melbourne, Royal Melbourne Hospital, Melbourne, Victoria, Australia.,Department of Neurology, Alfred Health, Melbourne, Victoria, Australia
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20
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Lal D, May P, Perez-Palma E, Samocha KE, Kosmicki JA, Robinson EB, Møller RS, Krause R, Nürnberg P, Weckhuysen S, De Jonghe P, Guerrini R, Niestroj LM, Du J, Marini C, Ware JS, Kurki M, Gormley P, Tang S, Wu S, Biskup S, Poduri A, Neubauer BA, Koeleman BPC, Helbig KL, Weber YG, Helbig I, Majithia AR, Palotie A, Daly MJ. Gene family information facilitates variant interpretation and identification of disease-associated genes in neurodevelopmental disorders. Genome Med 2020; 12:28. [PMID: 32183904 PMCID: PMC7079346 DOI: 10.1186/s13073-020-00725-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 02/21/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Classifying pathogenicity of missense variants represents a major challenge in clinical practice during the diagnoses of rare and genetic heterogeneous neurodevelopmental disorders (NDDs). While orthologous gene conservation is commonly employed in variant annotation, approximately 80% of known disease-associated genes belong to gene families. The use of gene family information for disease gene discovery and variant interpretation has not yet been investigated on a genome-wide scale. We empirically evaluate whether paralog-conserved or non-conserved sites in human gene families are important in NDDs. METHODS Gene family information was collected from Ensembl. Paralog-conserved sites were defined based on paralog sequence alignments; 10,068 NDD patients and 2078 controls were statistically evaluated for de novo variant burden in gene families. RESULTS We demonstrate that disease-associated missense variants are enriched at paralog-conserved sites across all disease groups and inheritance models tested. We developed a gene family de novo enrichment framework that identified 43 exome-wide enriched gene families including 98 de novo variant carrying genes in NDD patients of which 28 represent novel candidate genes for NDD which are brain expressed and under evolutionary constraint. CONCLUSION This study represents the first method to incorporate gene family information into a statistical framework to interpret variant data for NDDs and to discover new NDD-associated genes.
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Affiliation(s)
- Dennis Lal
- Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA.
- Stanley Center for Psychiatric Research, The Broad Institute of Harvard and M.I.T, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, USA.
- Cologne Center for Genomics, University of Cologne, Cologne, Germany.
- Genomic Medicine Institute, Lerner Research Institute Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH, 44195, USA.
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6, Avenue du Swing, 4367, Belvaux, Luxembourg.
| | - Eduardo Perez-Palma
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Genomic Medicine Institute, Lerner Research Institute Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH, 44195, USA
| | - Kaitlin E Samocha
- Stanley Center for Psychiatric Research, The Broad Institute of Harvard and M.I.T, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, USA
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Jack A Kosmicki
- Stanley Center for Psychiatric Research, The Broad Institute of Harvard and M.I.T, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, USA
| | - Elise B Robinson
- Stanley Center for Psychiatric Research, The Broad Institute of Harvard and M.I.T, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Rikke S Møller
- The Danish Epilepsy Centre, Dianalund, Denmark
- Institute for Regional Health research, University of Southern Denmark, Odense, Denmark
| | - Roland Krause
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6, Avenue du Swing, 4367, Belvaux, Luxembourg
| | - Peter Nürnberg
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Sarah Weckhuysen
- Division of Neurology, Antwerp University Hospital, Antwerp, Belgium
- Neurogenetics Group, Center for Molecular Neurology, VIB, Antwerp, Belgium
- Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Peter De Jonghe
- Division of Neurology, Antwerp University Hospital, Antwerp, Belgium
| | - Renzo Guerrini
- Pediatric Neurology and Neuroscience Department, Children's Hospital Anna Meyer, University of Florence, Florence, Italy
| | - Lisa M Niestroj
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Juliana Du
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Carla Marini
- Pediatric Neurology and Neuroscience Department, Children's Hospital Anna Meyer, University of Florence, Florence, Italy
| | - James S Ware
- National Heart & Lung Institute and MRC London Institute of Medical Science, Imperial College London, London, UK
| | - Mitja Kurki
- Stanley Center for Psychiatric Research, The Broad Institute of Harvard and M.I.T, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, USA
| | - Padhraig Gormley
- Stanley Center for Psychiatric Research, The Broad Institute of Harvard and M.I.T, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, USA
| | - Sha Tang
- Division of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, USA
| | - Sitao Wu
- Division of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, USA
| | - Saskia Biskup
- CeGat and Practice for Human Genetics, Tübingen, Germany
| | - Annapurna Poduri
- Epilepsy Genetics Program, Boston Children's Hospital, Boston, MA, USA
| | - Bernd A Neubauer
- Department of Neuropediatrics UKGM, University of Giessen, Giessen, Germany
| | - Bobby P C Koeleman
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Katherine L Helbig
- Division of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, USA
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Yvonne G Weber
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- Department of Epileptology and Neurology, University of Aachen, Aachen, Germany
| | - Ingo Helbig
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Neurology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Amit R Majithia
- Division of Endocrinology, Department of Medicine, University of California, San Diego, CA, USA
| | - Aarno Palotie
- Stanley Center for Psychiatric Research, The Broad Institute of Harvard and M.I.T, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, USA
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Mark J Daly
- Stanley Center for Psychiatric Research, The Broad Institute of Harvard and M.I.T, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, USA.
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland.
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21
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Weuring WJ, Singh S, Volkers L, Rook MB, van ‘t Slot RH, Bosma M, Inserra M, Vetter I, Verhoeven-Duif NM, Braun KPJ, Rivara M, Koeleman BPC. NaV1.1 and NaV1.6 selective compounds reduce the behavior phenotype and epileptiform activity in a novel zebrafish model for Dravet Syndrome. PLoS One 2020; 15:e0219106. [PMID: 32134913 PMCID: PMC7058281 DOI: 10.1371/journal.pone.0219106] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 02/04/2020] [Indexed: 12/03/2022] Open
Abstract
Dravet syndrome is caused by dominant loss-of-function mutations in SCN1A which cause reduced activity of Nav1.1 leading to lack of neuronal inhibition. On the other hand, gain-of-function mutations in SCN8A can lead to a severe epileptic encephalopathy subtype by over activating NaV1.6 channels. These observations suggest that Nav1.1 and Nav1.6 represent two opposing sides of the neuronal balance between inhibition and activation. Here, we hypothesize that Dravet syndrome may be treated by either enhancing Nav1.1 or reducing Nav1.6 activity. To test this hypothesis we generated and characterized a novel DS zebrafish model and tested new compounds that selectively activate or inhibit the human NaV1.1 or NaV1.6 channel respectively. We used CRISPR/Cas9 to generate two separate Scn1Lab knockout lines as an alternative to previous zebrafish models generated by random mutagenesis or morpholino oligomers. Using an optimized locomotor assay, spontaneous burst movements were detected that were unique to Scn1Lab knockouts and disappear when introducing human SCN1A mRNA. Besides the behavioral phenotype, Scn1Lab knockouts show sudden, electrical discharges in the brain that indicate epileptic seizures in zebrafish. Scn1Lab knockouts showed increased sensitivity to the GABA antagonist pentylenetetrazole and a reduction in whole organism GABA levels. Drug screenings further validated a Dravet syndrome phenotype. We tested the NaV1.1 activator AA43279 and two novel NaV1.6 inhibitors MV1369 and MV1312 in the Scn1Lab knockouts. Both type of compounds significantly reduced the number of spontaneous burst movements and seizure activity. Our results show that selective inhibition of NaV1.6 could be just as efficient as selective activation of NaV1.1 and these approaches could prove to be novel potential treatment strategies for Dravet syndrome and other (genetic) epilepsies. Compounds tested in zebrafish however, should always be further validated in other model systems for efficacy in mammals and to screen for potential side effects.
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Affiliation(s)
- Wout J. Weuring
- Department of Genetics, Center for Molecular Medicine, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Sakshi Singh
- Department of Genetics, Center for Molecular Medicine, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Linda Volkers
- Department of Cardiology, Laboratory of Experimental Cardiology, University Medical Centre Leiden, Leiden, the Netherlands
| | - Martin B. Rook
- Department of Medical Physiology, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Ruben H. van ‘t Slot
- Department of Genetics, Center for Molecular Medicine, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Marjolein Bosma
- Department of Genetics, Center for Molecular Medicine, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Marco Inserra
- Centre for Pain Research & School of Pharmacy, University of Queensland, Brisbane, Australia
| | - Irina Vetter
- Centre for Pain Research & School of Pharmacy, University of Queensland, Brisbane, Australia
| | - Nanda M. Verhoeven-Duif
- Department of Genetics, Center for Molecular Medicine, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Kees P. J. Braun
- Department of Neurology, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Mirko Rivara
- Food and Drug Department, University of Parma, Parma, Italy
| | - Bobby P. C. Koeleman
- Department of Genetics, Center for Molecular Medicine, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
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22
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de Lange IM, Mulder F, van 't Slot R, Sonsma ACM, van Kempen MJA, Nijman IJ, Ernst RF, Knoers NVAM, Brilstra EH, Koeleman BPC. Modifier genes in SCN1A-related epilepsy syndromes. Mol Genet Genomic Med 2020; 8:e1103. [PMID: 32032478 PMCID: PMC7196470 DOI: 10.1002/mgg3.1103] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 11/19/2018] [Revised: 11/25/2019] [Accepted: 11/26/2019] [Indexed: 12/24/2022] Open
Abstract
Background SCN1A is one of the most important epilepsy‐related genes, with pathogenic variants leading to a range of phenotypes with varying disease severity. Different modifying factors have been hypothesized to influence SCN1A‐related phenotypes. We investigate the presence of rare and more common variants in epilepsy‐related genes as potential modifiers of SCN1A‐related disease severity. Methods 87 patients with SCN1A‐related epilepsy were investigated. Whole‐exome sequencing was performed by the Beijing Genomics Institute (BGI). Functional variants in 422 genes associated with epilepsy and/or neuronal excitability were investigated. Differences in proportions of variants between the epilepsy genes and four control gene sets were calculated, and compared to the proportions of variants in the same genes in the ExAC database. Results Statistically significant excesses of variants in epilepsy genes were observed in the complete cohort and in the combined group of mildly and severely affected patients, particularly for variants with minor allele frequencies of <0.05. Patients with extreme phenotypes showed much greater excesses of epilepsy gene variants than patients with intermediate phenotypes. Conclusion Our results indicate that relatively common variants in epilepsy genes, which would not necessarily be classified as pathogenic, may play a large role in modulating SCN1A phenotypes. They may modify the phenotypes of both severely and mildly affected patients. Our results may be a first step toward meaningful testing of modifier gene variants in regular diagnostics for individual patients, to provide a better estimation of disease severity for newly diagnosed patients.
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Affiliation(s)
- Iris M de Lange
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Flip Mulder
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ruben van 't Slot
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Anja C M Sonsma
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marjan J A van Kempen
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Isaac J Nijman
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Robert F Ernst
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Nine V A M Knoers
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Eva H Brilstra
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bobby P C Koeleman
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
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23
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Claessens LA, Wesselius J, van Lummel M, Laban S, Mulder F, Mul D, Nikolic T, Aanstoot HJ, Koeleman BPC, Roep BO. Clinical and genetic correlates of islet-autoimmune signatures in juvenile-onset type 1 diabetes. Diabetologia 2020; 63:351-361. [PMID: 31754749 PMCID: PMC6946733 DOI: 10.1007/s00125-019-05032-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 09/18/2019] [Indexed: 12/14/2022]
Abstract
AIMS/HYPOTHESIS Heterogeneity in individuals with type 1 diabetes has become more generally appreciated, but has not yet been extensively and systematically characterised. Here, we aimed to characterise type 1 diabetes heterogeneity by creating immunological, genetic and clinical profiles for individuals with juvenile-onset type 1 diabetes in a cross-sectional study. METHODS Participants were HLA-genotyped to determine HLA-DR-DQ risk, and SNP-genotyped to generate a non-HLA genetic risk score (GRS) based on 93 type 1 diabetes-associated SNP variants outside the MHC region. Islet autoimmunity was assessed as T cell proliferation upon stimulation with the beta cell antigens GAD65, islet antigen-2 (IA-2), preproinsulin (PPI) and defective ribosomal product of the insulin gene (INS-DRIP). Clinical parameters were collected retrospectively. RESULTS Of 80 individuals, 67 had proliferation responses to one or more islet antigens, with vast differences in the extent of proliferation. Based on the multitude and amplitude of the proliferation responses, individuals were clustered into non-, intermediate and high responders. High responders could not be characterised entirely by enrichment for the highest risk HLA-DR3-DQ2/DR4-DQ8 genotype. However, high responders did have a significantly higher non-HLA GRS. Clinically, high T cell responses to beta cell antigens did not reflect in worsened glycaemic control, increased complications, development of associated autoimmunity or younger age at disease onset. The number of beta cell antigens that an individual responded to increased with disease duration, pointing to chronic islet autoimmunity and epitope spreading. CONCLUSIONS/INTERPRETATION Collectively, these data provide new insights into type 1 diabetes disease heterogeneity and highlight the importance of stratifying patients on the basis of their genetic and autoimmune signatures for immunotherapy and personalised disease management.
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Affiliation(s)
- Laura A Claessens
- Department of Immunohaematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - Joris Wesselius
- Department of Immunohaematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - Menno van Lummel
- Department of Immunohaematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - Sandra Laban
- Department of Immunohaematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - Flip Mulder
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Dick Mul
- Diabeter, Center for Pediatric and Adolescent Diabetes Care and Research, Rotterdam, the Netherlands
| | - Tanja Nikolic
- Department of Immunohaematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - Henk-Jan Aanstoot
- Diabeter, Center for Pediatric and Adolescent Diabetes Care and Research, Rotterdam, the Netherlands
| | - Bobby P C Koeleman
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Bart O Roep
- Department of Immunohaematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands.
- Department of Diabetes Immunology, Diabetes & Metabolism Research Institute, Beckman Research Institute, National Medical Center, City of Hope, 1500 E Duarte Road, Duarte, CA, 91010, USA.
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24
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Heavin SB, McCormack M, Wolking S, Slattery L, Walley N, Avbersek A, Novy J, Sinha SR, Radtke R, Doherty C, Auce P, Craig J, Johnson MR, Koeleman BPC, Krause R, Kunz WS, Marson AG, O'Brien TJ, Sander JW, Sills GJ, Stefansson H, Striano P, Zara F, Depondt C, Sisodiya S, Goldstein D, Lerche H, Cavalleri GL, Delanty N. Genomic and clinical predictors of lacosamide response in refractory epilepsies. Epilepsia Open 2019; 4:563-571. [PMID: 31819912 PMCID: PMC6885661 DOI: 10.1002/epi4.12360] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 08/21/2019] [Accepted: 08/29/2019] [Indexed: 12/27/2022] Open
Abstract
OBJECTIVE Clinical and genetic predictors of response to antiepileptic drugs (AEDs) are largely unknown. We examined predictors of lacosamide response in a real-world clinical setting. METHODS We tested the association of clinical predictors with treatment response using regression modeling in a cohort of people with refractory epilepsy. Genetic assessment for lacosamide response was conducted via genome-wide association studies and exome studies, comprising 281 candidate genes. RESULTS Most patients (479/483) were treated with LCM in addition to other AEDs. Our results corroborate previous findings that patients with refractory genetic generalized epilepsy (GGE) may respond to treatment with LCM. No clear clinical predictors were identified. We then compared 73 lacosamide responders, defined as those experiencing greater than 75% seizure reduction or seizure freedom, to 495 nonresponders (<25% seizure reduction). No variants reached the genome-wide significance threshold in our case-control analysis. SIGNIFICANCE No genetic predictor of lacosamide response was identified. Patients with refractory GGE might benefit from treatment with lacosamide.
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Affiliation(s)
- Sinéad B. Heavin
- School of Pharmacy and Biomolecular SciencesRoyal College of SurgeonsDublinIreland
| | - Mark McCormack
- School of Pharmacy and Biomolecular SciencesRoyal College of SurgeonsDublinIreland
- Luxembourg Centre for Systems BiomedicineUniversity of LuxembourgEsch‐sur‐AlzetteLuxembourg
| | - Stefan Wolking
- Department of Neurology and EpileptologyHertie Institute for Clinical Brain ResearchUniversity of TübingenTübingenGermany
| | - Lisa Slattery
- School of Pharmacy and Biomolecular SciencesRoyal College of SurgeonsDublinIreland
| | - Nicole Walley
- Centre for Human Genome VariationDuke UniversityDurhamNCUSA
| | - Andreja Avbersek
- Department of Clinical and Experimental EpilepsyUCL Queen Square Institute of NeurologyLondonUK
- Chalfont Centre for EpilepsyBuckinghamshireUK
| | - Jan Novy
- Department of Clinical and Experimental EpilepsyUCL Queen Square Institute of NeurologyLondonUK
- Chalfont Centre for EpilepsyBuckinghamshireUK
| | | | - Rod Radtke
- Centre for Human Genome VariationDuke UniversityDurhamNCUSA
| | - Colin Doherty
- School of MedicineTrinity College DublinDublinIreland
- Department of NeurologySt James's HospitalDublinIreland
| | - Pauls Auce
- Department of Molecular and Clinical PharmacologyInstitute of Translational MedicineUniversity of LiverpoolLiverpoolUK
| | - John Craig
- Department of NeurosciencesBelfast Health and Social Care TrustBelfastUK
| | | | - Bobby P. C. Koeleman
- Center of Molecular MedicineUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Roland Krause
- Luxembourg Centre for Systems BiomedicineUniversity of LuxembourgEsch‐sur‐AlzetteLuxembourg
| | - Wolfram S. Kunz
- Institute of Experimental Epileptology and Cognition Research and Department of EpileptologyUniversity of BonnBonnGermany
| | - Anthony G. Marson
- Department of Molecular and Clinical PharmacologyInstitute of Translational MedicineUniversity of LiverpoolLiverpoolUK
| | - Terence J. O'Brien
- The Departments of Neuroscience and NeurologyThe Alfred HospitalMonash UniversityVictoriaAustralia
| | - Josemir W. Sander
- Department of Clinical and Experimental EpilepsyUCL Queen Square Institute of NeurologyLondonUK
- Chalfont Centre for EpilepsyBuckinghamshireUK
- Stichting Epilepsie Instellingen Nederland (SEIN)HeemstedeThe Netherlands
| | - Graeme J. Sills
- Department of Molecular and Clinical PharmacologyInstitute of Translational MedicineUniversity of LiverpoolLiverpoolUK
| | | | - Pasquale Striano
- Pediatric Neurology and Muscular Diseases UnitDINOGMI‐Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child HealthInstitute "G. Gaslini"University of GenovaGenovaItaly
| | - Federico Zara
- Laboratory of Neurogenetics and NeuroscienceInstitute G. GasliniGenovaItaly
| | | | | | - Chantal Depondt
- Department of NeurologyHôpital ErasmeUniversité Libre de BruxellesBrusselsBelgium
| | - Sanjay Sisodiya
- Department of Clinical and Experimental EpilepsyUCL Queen Square Institute of NeurologyLondonUK
- Chalfont Centre for EpilepsyBuckinghamshireUK
| | - David Goldstein
- Institute for Genomic MedicineColumbia UniversityNew YorkNYUSA
| | - Holger Lerche
- Department of Neurology and EpileptologyHertie Institute for Clinical Brain ResearchUniversity of TübingenTübingenGermany
| | - Gianpiero L. Cavalleri
- School of Pharmacy and Biomolecular SciencesRoyal College of SurgeonsDublinIreland
- Division of Brain SciencesImperial College Faculty of MedicineLondonUK
| | - Norman Delanty
- School of Pharmacy and Biomolecular SciencesRoyal College of SurgeonsDublinIreland
- The FutureNeuro SFI Research CentreRoyal College of Surgeons in IrelandDublinIreland
- Division of NeurologyBeaumont HospitalDublinIreland
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25
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Sanders MWCB, Lemmens CMC, Jansen FE, Brilstra EH, Koeleman BPC, Braun KPJ. Implications of genetic diagnostics in epilepsy surgery candidates: A single-center cohort study. Epilepsia Open 2019; 4:609-617. [PMID: 31819917 PMCID: PMC6885658 DOI: 10.1002/epi4.12366] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [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: 01/14/2019] [Revised: 09/02/2019] [Accepted: 10/12/2019] [Indexed: 01/20/2023] Open
Abstract
OBJECTIVE Genetic causes are increasingly identified in patients with focal epilepsy. These genetic causes may be related to the effectiveness of epilepsy surgery. We aimed to assess the use and yield of genetic testing in a large cohort of patients who were evaluated for epilepsy surgery. METHODS We performed a retrospective single-center consecutive cohort study of patients who were evaluated for surgery between 1990 and 2016. Within this cohort, we assessed the use of genetic testing-either before or after presurgical decision-making. We evaluated genetic results as well as the outcome of presurgical decision-making and surgery, and compared these end points for different subgroups-especially MRI-positive vs MRI-negative patients. Patients with tuberous sclerosis (TSC) and KRIT1 mutations were excluded from analysis. RESULTS Of the 2385 epilepsy patients who were evaluated for surgery, 1280 (54%) received surgical treatment in our center. Of the entire cohort, 325 (14%) underwent genetic testing, comprising 156 of 450 MRI-negative patients (35%) vs 169 of 1935 MRI-positive patients (9%). A genetic cause of epilepsy was found in 40 of the 325 patients (12%, 2% of the entire cohort), mainly consisting of mutations in ion channel function and synaptic transmission genes, and mTOR pathway gene mutations. Three of the seven patients with mTOR pathway gene mutations underwent surgery; two achieved complete seizure freedom. One of the 17 patients with germline mutations in ion channel function and synaptic transmission genes received resective surgery but was not rendered seizure-free; two other patients underwent invasive intracranial EEG-monitoring before being rejected. SIGNIFICANCE This study shows that genetic testing is increasingly applied in focal epilepsy patients who are considered for epilepsy surgery. The diagnostic yield of genetic testing is highest in next generation sequencing techniques, and the outcome of genetic testing assists selecting eligible patients for invasive intracranial monitoring and resective surgery.
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Affiliation(s)
- Maurits W. C. B. Sanders
- Department of Child NeurologyBrain Center Rudolf MagnusUniversity Medical CenterUtrechtThe Netherlands
| | - Cynthia M. C. Lemmens
- Department of Child NeurologyBrain Center Rudolf MagnusUniversity Medical CenterUtrechtThe Netherlands
| | - Floor E. Jansen
- Department of Child NeurologyBrain Center Rudolf MagnusUniversity Medical CenterUtrechtThe Netherlands
| | - Eva H. Brilstra
- Department of GeneticsCenter for Molecular MedicineUniversity Medical CenterUtrechtThe Netherlands
| | - Bobby P. C. Koeleman
- Department of GeneticsCenter for Molecular MedicineUniversity Medical CenterUtrechtThe Netherlands
| | - Kees P. J. Braun
- Department of Child NeurologyBrain Center Rudolf MagnusUniversity Medical CenterUtrechtThe Netherlands
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26
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Leu C, Stevelink R, Smith AW, Goleva SB, Kanai M, Ferguson L, Campbell C, Kamatani Y, Okada Y, Sisodiya SM, Cavalleri GL, Koeleman BPC, Lerche H, Jehi L, Davis LK, Najm IM, Palotie A, Daly MJ, Busch RM, Lal D. Polygenic burden in focal and generalized epilepsies. Brain 2019; 142:3473-3481. [PMID: 31608925 PMCID: PMC6821205 DOI: 10.1093/brain/awz292] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 07/10/2019] [Accepted: 07/29/2019] [Indexed: 01/12/2023] Open
Abstract
Rare genetic variants can cause epilepsy, and genetic testing has been widely adopted for severe, paediatric-onset epilepsies. The phenotypic consequences of common genetic risk burden for epilepsies and their potential future clinical applications have not yet been determined. Using polygenic risk scores (PRS) from a European-ancestry genome-wide association study in generalized and focal epilepsy, we quantified common genetic burden in patients with generalized epilepsy (GE-PRS) or focal epilepsy (FE-PRS) from two independent non-Finnish European cohorts (Epi25 Consortium, n = 5705; Cleveland Clinic Epilepsy Center, n = 620; both compared to 20 435 controls). One Finnish-ancestry population isolate (Finnish-ancestry Epi25, n = 449; compared to 1559 controls), two European-ancestry biobanks (UK Biobank, n = 383 656; Vanderbilt biorepository, n = 49 494), and one Japanese-ancestry biobank (BioBank Japan, n = 168 680) were used for additional replications. Across 8386 patients with epilepsy and 622 212 population controls, we found and replicated significantly higher GE-PRS in patients with generalized epilepsy of European-ancestry compared to patients with focal epilepsy (Epi25: P = 1.64×10-15; Cleveland: P = 2.85×10-4; Finnish-ancestry Epi25: P = 1.80×10-4) or population controls (Epi25: P = 2.35×10-70; Cleveland: P = 1.43×10-7; Finnish-ancestry Epi25: P = 3.11×10-4; UK Biobank and Vanderbilt biorepository meta-analysis: P = 7.99×10-4). FE-PRS were significantly higher in patients with focal epilepsy compared to controls in the non-Finnish, non-biobank cohorts (Epi25: P = 5.74×10-19; Cleveland: P = 1.69×10-6). European ancestry-derived PRS did not predict generalized epilepsy or focal epilepsy in Japanese-ancestry individuals. Finally, we observed a significant 4.6-fold and a 4.5-fold enrichment of patients with generalized epilepsy compared to controls in the top 0.5% highest GE-PRS of the two non-Finnish European cohorts (Epi25: P = 2.60×10-15; Cleveland: P = 1.39×10-2). We conclude that common variant risk associated with epilepsy is significantly enriched in multiple cohorts of patients with epilepsy compared to controls-in particular for generalized epilepsy. As sample sizes and PRS accuracy continue to increase with further common variant discovery, PRS could complement established clinical biomarkers and augment genetic testing for patient classification, comorbidity research, and potentially targeted treatment.
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Affiliation(s)
- Costin Leu
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and M.I.T, Cambridge, MA, USA
- Department of Clinical and Experimental Epilepsy, Institute of Neurology, University College London, Queen Square, London, UK
| | - Remi Stevelink
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Alexander W Smith
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and M.I.T, Cambridge, MA, USA
| | - Slavina B Goleva
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA
| | - Masahiro Kanai
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and M.I.T, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Lisa Ferguson
- Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Psychiatry and Psychology, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Neurology, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ciaran Campbell
- Department of Molecular and Cellular Therapeutics, The Royal College of Surgeons in Ireland, Dublin 2, Ireland
- The FutureNeuro Research Centre, Dublin 2, Ireland
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yukinori Okada
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Sanjay M Sisodiya
- Department of Clinical and Experimental Epilepsy, Institute of Neurology, University College London, Queen Square, London, UK
- Chalfont Centre for Epilepsy, Chalfont-St-Peter, Buckinghamshire, UK
| | - Gianpiero L Cavalleri
- Department of Molecular and Cellular Therapeutics, The Royal College of Surgeons in Ireland, Dublin 2, Ireland
- The FutureNeuro Research Centre, Dublin 2, Ireland
| | - Bobby P C Koeleman
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Holger Lerche
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Lara Jehi
- Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Neurology, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Lea K Davis
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA
| | - Imad M Najm
- Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Neurology, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Aarno Palotie
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and M.I.T, Cambridge, MA, USA
- Institute of Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Mark J Daly
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and M.I.T, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Institute of Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Robyn M Busch
- Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Psychiatry and Psychology, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Neurology, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA
| | | | - Dennis Lal
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and M.I.T, Cambridge, MA, USA
- Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
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27
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López-Isac E, Acosta-Herrera M, Kerick M, Assassi S, Satpathy AT, Granja J, Mumbach MR, Beretta L, Simeón CP, Carreira P, Ortego-Centeno N, Castellvi I, Bossini-Castillo L, Carmona FD, Orozco G, Hunzelmann N, Distler JHW, Franke A, Lunardi C, Moroncini G, Gabrielli A, de Vries-Bouwstra J, Wijmenga C, Koeleman BPC, Nordin A, Padyukov L, Hoffmann-Vold AM, Lie B, Proudman S, Stevens W, Nikpour M, Vyse T, Herrick AL, Worthington J, Denton CP, Allanore Y, Brown MA, Radstake TRDJ, Fonseca C, Chang HY, Mayes MD, Martin J. GWAS for systemic sclerosis identifies multiple risk loci and highlights fibrotic and vasculopathy pathways. Nat Commun 2019; 10:4955. [PMID: 31672989 PMCID: PMC6823490 DOI: 10.1038/s41467-019-12760-y] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 09/30/2019] [Indexed: 12/12/2022] Open
Abstract
Systemic sclerosis (SSc) is an autoimmune disease that shows one of the highest mortality rates among rheumatic diseases. We perform a large genome-wide association study (GWAS), and meta-analysis with previous GWASs, in 26,679 individuals and identify 27 independent genome-wide associated signals, including 13 new risk loci. The novel associations nearly double the number of genome-wide hits reported for SSc thus far. We define 95% credible sets of less than 5 likely causal variants in 12 loci. Additionally, we identify specific SSc subtype-associated signals. Functional analysis of high-priority variants shows the potential function of SSc signals, with the identification of 43 robust target genes through HiChIP. Our results point towards molecular pathways potentially involved in vasculopathy and fibrosis, two main hallmarks in SSc, and highlight the spectrum of critical cell types for the disease. This work supports a better understanding of the genetic basis of SSc and provides directions for future functional experiments.
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Affiliation(s)
- Elena López-Isac
- Institute of Parasitology and Biomedicine López-Neyra, IPBLN-CSIC, Granada, Spain.
| | | | - Martin Kerick
- Institute of Parasitology and Biomedicine López-Neyra, IPBLN-CSIC, Granada, Spain
| | - Shervin Assassi
- The University of Texas Health Science Center-Houston, Houston, USA
| | - Ansuman T Satpathy
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Jeffrey Granja
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Maxwell R Mumbach
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Lorenzo Beretta
- Referral Center for Systemic Autoimmune Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano, Milan, Italy
| | - Carmen P Simeón
- Department of Internal Medicine, Valle de Hebrón Hospital, Barcelona, Spain
| | - Patricia Carreira
- Department of Rheumatology, 12 de Octubre University Hospital, Madrid, Spain
| | | | - Ivan Castellvi
- Department of Rheumatology, Santa Creu i Sant Pau University Hospital, Barcelona, Spain
| | | | - F David Carmona
- Department of Genetics and Institute of Biotechnology, University of Granada, Granada, Spain
| | - Gisela Orozco
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Oxford Road, Manchester, UK
| | | | - Jörg H W Distler
- Department of Internal Medicine 3, Institute for Clinical Immunology, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Claudio Lunardi
- Department of Medicine, Università degli Studi di Verona, Verona, Italy
| | - Gianluca Moroncini
- Clinica Medica, Department of Clinical and Molecular Science, Università Politecnica delle Marche and Ospedali Riuniti, Ancona, Italy
| | - Armando Gabrielli
- Clinica Medica, Department of Clinical and Molecular Science, Università Politecnica delle Marche and Ospedali Riuniti, Ancona, Italy
| | | | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | | | - Annika Nordin
- Division of Rheumatology, Department of Medicine, Karolinska University Hospital, Karolinska Institute, Stockholm, Sweden
| | - Leonid Padyukov
- Division of Rheumatology, Department of Medicine, Karolinska University Hospital, Karolinska Institute, Stockholm, Sweden
| | | | - Benedicte Lie
- Department of Medical Genetics, and the Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Susanna Proudman
- Royal Adelaide Hospital and University of Adelaide, Adelaide, SA, Australia
| | | | - Mandana Nikpour
- The University of Melbourne at St. Vincent's Hospital, Melbourne, VIC, Australia
| | - Timothy Vyse
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Ariane L Herrick
- Centre for Musculoskeletal Research, The University of Manchester, Salford Royal NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester, UK
| | - Jane Worthington
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Oxford Road, Manchester, UK
| | - Christopher P Denton
- Centre for Rheumatology, Royal Free and University College Medical School, London, United Kingdom
| | - Yannick Allanore
- Department of Rheumatology A, Cochin Hospital, INSERM U1016, Paris Descartes University, Paris, France
| | - Matthew A Brown
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Timothy R D J Radstake
- Department of Rheumatology & Clinical Immunology, Laboratory of Translational Immunology, department of Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Carmen Fonseca
- Centre for Rheumatology, Royal Free and University College Medical School, London, United Kingdom
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Maureen D Mayes
- The University of Texas Health Science Center-Houston, Houston, USA
| | - Javier Martin
- Institute of Parasitology and Biomedicine López-Neyra, IPBLN-CSIC, Granada, Spain.
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28
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Stevelink R, Pangilinan F, Jansen FE, Braun KPJ, Molloy AM, Brody LC, Koeleman BPC. Assessing the genetic association between vitamin B6 metabolism and genetic generalized epilepsy. Mol Genet Metab Rep 2019; 21:100518. [PMID: 31641590 PMCID: PMC6796782 DOI: 10.1016/j.ymgmr.2019.100518] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 09/06/2019] [Accepted: 09/07/2019] [Indexed: 01/23/2023] Open
Abstract
Altered vitamin B6 metabolism due to pathogenic variants in the gene PNPO causes early onset epileptic encephalopathy, which can be treated with high doses of vitamin B6. We recently reported that single nucleotide polymorphisms (SNPs) that influence PNPO expression in the brain are associated with genetic generalized epilepsy (GGE). However, it is not known whether any of these GGE-associated SNPs influence vitamin B6 metabolite levels. Such an influence would suggest that vitamin B6 could play a role in GGE therapy. Here, we performed genome-wide association studies (GWAS) to assess the influence of GGE associated genetic variants on measures of vitamin B6 metabolism in blood plasma in 2232 healthy individuals. We also asked if SNPs that influence vitamin B6 were associated with GGE in 3122 affected individuals and 20,244 controls. Our GWAS of vitamin B6 metabolites reproduced a previous association and found a novel genome-wide significant locus. The SNPs in these loci were not associated with GGE. We found that 84 GGE-associated SNPs influence expression levels of PNPO in the brain as well as in blood. However, these SNPs were not associated with vitamin B6 metabolism in plasma. By leveraging polygenic risk scoring (PRS), we found suggestive evidence of higher catabolism and lower levels of the active and transport forms of vitamin B6 in GGE, although these findings require further replication.
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Affiliation(s)
- Remi Stevelink
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands.,Department of Child Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Faith Pangilinan
- National Human Genome Research Institute, National Institutes of Health, Bethesda, USA
| | - Floor E Jansen
- Department of Child Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Kees P J Braun
- Department of Child Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Anne M Molloy
- School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Lawrence C Brody
- National Human Genome Research Institute, National Institutes of Health, Bethesda, USA
| | - Bobby P C Koeleman
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands
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29
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Schellevis RL, van Dijk EHC, Breukink MB, Altay L, Bakker B, Koeleman BPC, Kiemeney LA, Swinkels DW, Keunen JEE, Fauser S, Hoyng CB, den Hollander AI, Boon CJF, de Jong EK. Role of the Complement System in Chronic Central Serous Chorioretinopathy: A Genome-Wide Association Study. JAMA Ophthalmol 2019; 136:1128-1136. [PMID: 30073298 DOI: 10.1001/jamaophthalmol.2018.3190] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Importance To date, several targeted genetic studies on chronic central serous chorioretinopathy (cCSC) have been performed; however, unbiased genome-wide studies into the genetics of cCSC have not been reported. To discover new genetic loci associated with cCSC and to better understand the causative mechanism of this disease, we performed a genome-wide association study (GWAS) on patients with cCSC. Objective To discover new genetic loci and pathways associated with cCSC and to predict the association of genetic variants with gene expression in patients with cCSC. Design, Setting, and Participants This case-control GWAS was completed in the general community, 3 referral university medical centers, and outpatient care on Europeans individuals with cCSC and population-based control participants. Genotype data was collected from May 2013 to August 2017, and data analysis occurred from August 2017 to November 2017. Main Outcomes and Measures Associations of single-nucleotide polymorphisms, haplotypes, genetic pathways, and predicted gene expression with cCSC. Results A total of 521 patients with cCSC (median age, 51 years; interquartile range [IQR], 44-59 years; 420 [80.6%] male) and 3577 European population-based control participants (median age, 52 years; IQR, 37-71 years; 1630 [45.6%] male) were included. One locus on chromosome 1 at the complement factor H (CFH) gene reached genome-wide significance and was associated with an increased risk of cCSC (rs1329428; odds ratio [OR], 1.57 [95% CI, 1.38-1.80]; P = 3.12 × 10-11). The CFH haplotypes H1 and H3 were protective for cCSC (H1: OR, 0.64 [95% CI, 0.53-0.77]; P = 2.18 × 10-6; H3: OR, 0.54 [95% CI, 0.42-0.70]; P = 2.49 × 10-6), whereas haplotypes H2, H4, H5, and the aggregate of rare CFH haplotypes conferred increased risk (H2: OR, 1.57 [95% CI, 1.30-1.89]; P = 2.18 × 10-6; H4: OR, 1.43 [95% CI, 1.13-1.80]; P = 2.49 × 10-3; H5: OR, 1.80 [95% CI, 1.36-2.39]; P = 4.61 × 10-5; rare haplotypes: OR, 1.99 [95% CI, 1.43-2.77]; P = 4.59 × 10-5). Pathway analyses showed involvement of the complement cascade and alternative open reading frame (ARF) pathway in cCSC. Using PrediXcan, we identified changes in predicted expression of complement genes CFH, complement factor H related 1 (CFHR1), complement factor related 4 (CFHR4), and membrane cofactor protein (MCP/CD46). Additionally, the potassium sodium-activated channel subfamily T member 2 (KCNT2) and tumor necrosis factor receptor superfamily member 10a (TNFRSF10A) genes were differentially expressed in patients with cCSC. Conclusions and Relevance In this GWAS on cCSC, we identified a locus on chromosome 1 at the CFH gene that was significantly associated with cCSC, and we report protective and risk-conferring haplotypes in this gene. Pathway analyses were enriched for complement genes, and gene expression analysis suggests a role for CFH, CFHR1, CFHR4, CD46, KCNT2, and TNFRSF10A in the disease. Taken together, these results underscore the potential importance of the complement pathway in the causative mechanisms of cCSC.
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Affiliation(s)
- Rosa L Schellevis
- Department of Ophthalmology, Donders Institute of Brain, Cognition and Behaviour, Radboud university medical centre, Nijmegen, the Netherlands
| | - Elon H C van Dijk
- Department of Ophthalmology, Leiden University Medical Center, Leiden, the Netherlands
| | - Myrte B Breukink
- Department of Ophthalmology, Donders Institute of Brain, Cognition and Behaviour, Radboud university medical centre, Nijmegen, the Netherlands
| | - Lebriz Altay
- Department of Ophthalmology, University Hospital of Cologne, Cologne, Germany
| | - Bjorn Bakker
- Department of Ophthalmology, Donders Institute of Brain, Cognition and Behaviour, Radboud university medical centre, Nijmegen, the Netherlands
| | - Bobby P C Koeleman
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Lambertus A Kiemeney
- Radboud Institute for Health Sciences, Radboud university medical centre, Nijmegen, the Netherlands
| | - Dorine W Swinkels
- Translational Metabolic Laboratory, Radboud Institute for Molecular Life Sciences, Radboud university medical centre, Nijmegen, the Netherlands
| | - Jan E E Keunen
- Department of Ophthalmology, Donders Institute of Brain, Cognition and Behaviour, Radboud university medical centre, Nijmegen, the Netherlands
| | - Sascha Fauser
- Department of Ophthalmology, University Hospital of Cologne, Cologne, Germany.,F. Hoffmann-La Roche, Basel, Switzerland
| | - Carel B Hoyng
- Department of Ophthalmology, Donders Institute of Brain, Cognition and Behaviour, Radboud university medical centre, Nijmegen, the Netherlands
| | - Anneke I den Hollander
- Department of Ophthalmology, Donders Institute of Brain, Cognition and Behaviour, Radboud university medical centre, Nijmegen, the Netherlands.,Department of Human Genetics, Donders Institute of Brain, Cognition and Behaviour, Radboud university medical centre, Nijmegen, the Netherlands
| | - Camiel J F Boon
- Department of Ophthalmology, Leiden University Medical Center, Leiden, the Netherlands.,Department of Ophthalmology, Academic Medical Center, Amsterdam, the Netherlands
| | - Eiko K de Jong
- Department of Ophthalmology, Donders Institute of Brain, Cognition and Behaviour, Radboud university medical centre, Nijmegen, the Netherlands
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Silvennoinen K, de Lange N, Zagaglia S, Balestrini S, Androsova G, Wassenaar M, Auce P, Avbersek A, Becker F, Berghuis B, Campbell E, Coppola A, Francis B, Wolking S, Cavalleri GL, Craig J, Delanty N, Johnson MR, Koeleman BPC, Kunz WS, Lerche H, Marson AG, O’Brien TJ, Sander JW, Sills GJ, Striano P, Zara F, van der Palen J, Krause R, Depondt C, Sisodiya SM. Comparative effectiveness of antiepileptic drugs in juvenile myoclonic epilepsy. Epilepsia Open 2019; 4:420-430. [PMID: 31440723 PMCID: PMC6698679 DOI: 10.1002/epi4.12349] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/11/2019] [Accepted: 06/22/2019] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVE To study the effectiveness and tolerability of antiepileptic drugs (AEDs) commonly used in juvenile myoclonic epilepsy (JME). METHODS People with JME were identified from a large database of individuals with epilepsy, which includes detailed retrospective information on AED use. We assessed secular changes in AED use and calculated rates of response (12-month seizure freedom) and adverse drug reactions (ADRs) for the five most common AEDs. Retention was modeled with a Cox proportional hazards model. We compared valproate use between males and females. RESULTS We included 305 people with 688 AED trials of valproate, lamotrigine, levetiracetam, carbamazepine, and topiramate. Valproate and carbamazepine were most often prescribed as the first AED. The response rate to valproate was highest among the five AEDs (42.7%), and significantly higher than response rates for lamotrigine, carbamazepine, and topiramate; the difference to the response rate to levetiracetam (37.1%) was not significant. The rates of ADRs were highest for topiramate (45.5%) and valproate (37.5%). Commonest ADRs included weight change, lethargy, and tremor. In the Cox proportional hazards model, later start year (1.10 [1.08-1.13], P < 0.001) and female sex (1.41 [1.07-1.85], P = 0.02) were associated with shorter trial duration. Valproate was associated with the longest treatment duration; trials with carbamazepine and topiramate were significantly shorter (HR [CI]: 3.29 [2.15-5.02], P < 0.001 and 1.93 [1.31-2.86], P < 0.001). The relative frequency of valproate trials shows a decreasing trend since 2003 while there is an increasing trend for levetiracetam. Fewer females than males received valproate (76.2% vs 92.6%, P = 0.001). SIGNIFICANCE In people with JME, valproate is an effective AED; levetiracetam emerged as an alternative. Valproate is now contraindicated in women of childbearing potential without special precautions. With appropriate selection and safeguards in place, valproate should remain available as a therapy, including as an alternative for women of childbearing potential whose seizures are resistant to other treatments.
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Affiliation(s)
- Katri Silvennoinen
- Department of Clinical and Experimental EpilepsyUCL Queen Square Institute of NeurologyLondonUK
- Chalfont Centre for EpilepsyChalfont St. PeterUK
| | - Nikola de Lange
- Luxembourg Centre for Systems BiomedicineUniversity of LuxembourgBelvauxLuxembourg
| | - Sara Zagaglia
- Department of Clinical and Experimental EpilepsyUCL Queen Square Institute of NeurologyLondonUK
- Chalfont Centre for EpilepsyChalfont St. PeterUK
- Department of Experimental and Clinical MedicinePolytechnic University of MarcheAnconaItaly
| | - Simona Balestrini
- Department of Clinical and Experimental EpilepsyUCL Queen Square Institute of NeurologyLondonUK
- Chalfont Centre for EpilepsyChalfont St. PeterUK
- Department of Experimental and Clinical MedicinePolytechnic University of MarcheAnconaItaly
| | - Ganna Androsova
- Luxembourg Centre for Systems BiomedicineUniversity of LuxembourgBelvauxLuxembourg
| | - Merel Wassenaar
- Stichting Epilepsie Instellingen Nederland (SEIN)HeemstedeThe Netherlands
| | - Pauls Auce
- Department of Molecular and Clinical Pharmacology, Institute of Translational MedicineUniversity of LiverpoolLiverpoolUK
- The Walton Centre NHS Foundation TrustLiverpoolUK
| | - Andreja Avbersek
- Department of Clinical and Experimental EpilepsyUCL Queen Square Institute of NeurologyLondonUK
| | - Felicitas Becker
- Hertie Institute for Clinical Brain ResearchUniversity of TübingenTübingenGermany
| | - Bianca Berghuis
- Stichting Epilepsie Instellingen Nederland (SEIN)HeemstedeThe Netherlands
| | | | - Antonietta Coppola
- Pediatric Neurology and Muscular Diseases Unit, Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child HealthUniversity of GenoaGenoaItaly
- Department of Neuroscience, Reproductive and Odontostomatological SciencesFederico II UniversityNaplesItaly
| | - Ben Francis
- Department of BiostatisticsUniversity of LiverpoolLiverpoolUK
| | - Stefan Wolking
- Hertie Institute for Clinical Brain ResearchUniversity of TübingenTübingenGermany
| | | | - John Craig
- Belfast Health and Social Care TrustBelfastUK
| | - Norman Delanty
- Molecular and Cellular TherapeuticsRoyal College of Surgeons in IrelandDublinIreland
- Department of NeurologyBeaumont HospitalDublinIreland
| | | | | | | | - Holger Lerche
- Hertie Institute for Clinical Brain ResearchUniversity of TübingenTübingenGermany
| | - Anthony G. Marson
- Department of Molecular and Clinical Pharmacology, Institute of Translational MedicineUniversity of LiverpoolLiverpoolUK
- The Walton Centre NHS Foundation TrustLiverpoolUK
| | - Terence J. O’Brien
- Departments of Neuroscience and Neurology, Central Clinical SchoolMonash University, The Alfred HospitalMelbourneVic.Australia
| | - Josemir W. Sander
- Department of Clinical and Experimental EpilepsyUCL Queen Square Institute of NeurologyLondonUK
- Chalfont Centre for EpilepsyChalfont St. PeterUK
- Stichting Epilepsie Instellingen Nederland (SEIN)HeemstedeThe Netherlands
| | - Graeme J. Sills
- Department of Molecular and Clinical Pharmacology, Institute of Translational MedicineUniversity of LiverpoolLiverpoolUK
| | - Pasquale Striano
- Pediatric Neurology and Muscular Diseases Unit, Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child HealthUniversity of GenoaGenoaItaly
- Pediatric Neurology and Muscular Diseases UnitIRCCS Istituto G. GasliniGenovaItaly
| | - Federico Zara
- Laboratory of Neurogenetics and NeuroscienceIRCCS Istituto G. GasliniGenovaItaly
| | | | - Roland Krause
- Luxembourg Centre for Systems BiomedicineUniversity of LuxembourgBelvauxLuxembourg
| | - Chantal Depondt
- Department of NeurologyHôpital Erasme, Université Libre de BruxellesBrusselsBelgium
| | - Sanjay M. Sisodiya
- Department of Clinical and Experimental EpilepsyUCL Queen Square Institute of NeurologyLondonUK
- Chalfont Centre for EpilepsyChalfont St. PeterUK
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31
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de Lange IM, Weuring W, van 't Slot R, Gunning B, Sonsma ACM, McCormack M, de Kovel C, van Gemert LJJM, Mulder F, van Kempen MJA, Knoers NVAM, Brilstra EH, Koeleman BPC. Influence of common SCN1A promoter variants on the severity of SCN1A-related phenotypes. Mol Genet Genomic Med 2019; 7:e00727. [PMID: 31144463 PMCID: PMC6625088 DOI: 10.1002/mgg3.727] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 11/19/2018] [Revised: 03/22/2019] [Accepted: 04/22/2019] [Indexed: 01/09/2023] Open
Abstract
Background Pathogenic variants in SCN1A cause variable epilepsy disorders with different disease severities. We here investigate whether common variation in the promoter region of the unaffected SCN1A allele could reduce normal expression, leading to a decreased residual function of Nav1.1, and therefore to more severe clinical outcomes in patients affected by pathogenic SCN1A variants. Methods Five different SCN1A promoter‐haplotypes were functionally assessed in SH‐SY5Y cells using Firefly and Renilla luciferase assays. The SCN1A promoter region was analyzed in a cohort of 143 participants with SCN1A pathogenic variants. Differences in clinical features and outcomes between participants with and without common variants in the SCN1A promoter‐region of their unaffected allele were investigated. Results All non‐wildtype haplotypes showed a significant reduction in luciferase expression, compared to the wildtype promoter‐region (65%–80%, p = 0.039–0.0023). No statistically significant differences in clinical outcomes were observed between patients with and without common promoter variants. However, patients with a wildtype promoter‐haplotype on their unaffected SCN1A allele showed a nonsignificant trend for milder phenotypes. Conclusion The nonsignificant observed trends in our study warrant replication studies in larger cohorts to explore the potential modifying role of these common SCN1A promoter‐haplotypes.
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Affiliation(s)
- Iris M de Lange
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Wout Weuring
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ruben van 't Slot
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Anja C M Sonsma
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Mark McCormack
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Carolien de Kovel
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Flip Mulder
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marjan J A van Kempen
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Nine V A M Knoers
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Eva H Brilstra
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bobby P C Koeleman
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
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He Y, de Witte LD, Schubart CD, Van Gastel WA, Koeleman BPC, de Jong S, Ophoff RA, Hol EM, Boks MP. Liprin alfa 2 gene expression is increased by cannabis use and associated with neuropsychological function. Eur Neuropsychopharmacol 2019; 29:643-652. [PMID: 30879928 DOI: 10.1016/j.euroneuro.2019.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 01/13/2019] [Accepted: 03/02/2019] [Indexed: 11/18/2022]
Abstract
The relation of heavy cannabis use with decreased neuropsychological function has frequently been described but the underlying biological mechanisms are still largely unknown. This study investigates the relation of cannabis use with genome wide gene expression and subsequently examines the relations with neuropsychological function. Genome-wide gene expression in whole blood was compared between heavy cannabis users (N = 90) and cannabis naïve participants (N = 100) that were matched for psychotic like experiences. The results were validated using quantitative real-time PCR. Psychotic like experiences were assessed using the Comprehensive Assessment of Psychotic Experiences (CAPE). Neuropsychological function was estimated using four subtasks of the Wechsler Adult Intelligence Scale (WAIS). Subsequent in vitro studies in monocytes and a neuroblastoma cell line investigated expression changes in response to two major psychotropic components of cannabis; tetrahydrocannabinol (THC) and cannabidiol (CBD). mRNA expression of Protein Tyrosine Phosphatase Receptor Type F Polypeptide-Interacting-Protein Alpha-2 (PPFIA2) was significantly higher in cannabis users (LogFold Change 0.17) and confirmed by qPCR analysis. PPFIA2 expression level was negatively correlated with estimated intelligence (B=-22.9, p = 0.002) also in the 100 non-users (B=-28.5, p = 0.037). In vitro exposure of monocytes to CBD led to significant increase in PPFIA2 expression. However, exposure of monocytes to THC and neuroblastoma cells to THC or CBD did not change PPFIA2 expression. Change in PPFIA2 gene expression in response to cannabinoids is a putative mechanism by which cannabis could influence neuropsychological functions. The findings warrant further exploration of the role of PPFIA2 in cannabis induced changes of neuropsychological function, particularly in relation to CBD.
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Affiliation(s)
- Yujie He
- Department of Psychiatry, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, The Netherlands; Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, The Netherlands
| | - Lot D de Witte
- Department of Psychiatry, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, The Netherlands; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Chris D Schubart
- Ter Gooi Hospital, Department of Psychiatry, Blaricum, The Netherlands
| | | | - Bobby P C Koeleman
- Department of Medical Genetics, University Medical Centre Utrecht, Utrecht University, The Netherlands
| | - Simone de Jong
- MRC Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, UK
| | - Roel A Ophoff
- UCLA Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Los Angeles, CA, USA
| | - Elly M Hol
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, The Netherlands; Neuroimmunology, Netherlands Institute for Neuroscience, An institute of the royal academy of arts and sciences, Amsterdam, The Netherlands
| | - Marco P Boks
- Department of Psychiatry, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, The Netherlands.
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Berghuis B, Stapleton C, Sonsma ACM, Hulst J, de Haan G, Lindhout D, Demurtas R, Krause R, Depondt C, Kunz WS, Zara F, Striano P, Craig J, Auce P, Marson AG, Stefansson H, O'Brien TJ, Johnson MR, Sills GJ, Wolking S, Lerche H, Sisodiya SM, Sander JW, Cavalleri GL, Koeleman BPC, McCormack M. A genome-wide association study of sodium levels and drug metabolism in an epilepsy cohort treated with carbamazepine and oxcarbazepine. Epilepsia Open 2019; 4:102-109. [PMID: 30868120 PMCID: PMC6398103 DOI: 10.1002/epi4.12297] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 08/16/2018] [Revised: 12/02/2018] [Accepted: 12/06/2018] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVE To ascertain the clinical and genetic factors contributing to carbamazepine- and oxcarbazepine-induced hyponatremia (COIH), and to carbamazepine (CBZ) metabolism, in a retrospectively collected, cross-sectional cohort of people with epilepsy. METHODS We collected data on serum sodium levels and antiepileptic drug levels in people with epilepsy attending a tertiary epilepsy center while on treatment with CBZ or OXC. We defined hyponatremia as Na+ ≤134 mEq/L. We estimated the CBZ metabolic ratio defined as the log transformation of the ratio of metabolite CBZ-diol to unchanged drug precursor substrate as measured in serum. RESULTS Clinical and genetic data relating to carbamazepine and oxcarbazepine trials were collected in 1141 patients. We did not observe any genome-wide significant associations with sodium level in a linear trend or hyponatremia as a dichotomous trait. Age, sex, number of comedications, phenytoin use, phenobarbital use, and sodium valproate use were significant predictors of CBZ metabolic ratio. No genome-wide significant associations with CBZ metabolic ratio were found. SIGNIFICANCE Although we did not detect a genetic predictor of hyponatremia or CBZ metabolism in our cohort, our findings suggest that the determinants of CBZ metabolism are multifactorial.
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Affiliation(s)
- Bianca Berghuis
- Stichting Epilepsie Instellingen Nederland (SEIN)ZwolleThe Netherlands
| | - Caragh Stapleton
- Molecular and Cellular TherapeuticsRoyal College of Surgeons in IrelandDublinIreland
| | - Anja C. M. Sonsma
- Department of GeneticsUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Janic Hulst
- Stichting Epilepsie Instellingen Nederland (SEIN)ZwolleThe Netherlands
| | | | - Dick Lindhout
- Stichting Epilepsie Instellingen Nederland (SEIN)ZwolleThe Netherlands
- Department of GeneticsUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Rita Demurtas
- Department of Clinical and Experimental EpilepsyInstitute of NeurologyUniversity College LondonLondonUK
| | - Roland Krause
- Luxembourg Centre for Systems BiomedicineUniversity of LuxembourgEsch‐sur‐AlzetteLuxembourg
| | - Chantal Depondt
- Laboratory of Experimental NeurologyHôpital ErasmeUniversité Libre de BruxellesBrusselsBelgium
| | - Wolfram S. Kunz
- Institute of Experimental Epileptology and Cognition Research and Department of EpileptologyUniversity of BonnBonnGermany
| | - Federico Zara
- Laboratory of Neurogenetics and NeuroscienceInstitute G. GasliniGenovaItaly
| | - Pasquale Striano
- Pediatric Neurology and Muscular Diseases UnitDINOGMI‐Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child HealthUniversity of GenovaInstitute “G. Gaslini”GenovaItaly
| | - John Craig
- Department of NeurosciencesBelfast Health and Social Care TrustBelfastUK
| | - Pauls Auce
- Department of Molecular and Clinical PharmacologyInstitute of Translational MedicineUniversity of LiverpoolLiverpoolUK
| | - Anthony G. Marson
- Department of Molecular and Clinical PharmacologyInstitute of Translational MedicineUniversity of LiverpoolLiverpoolUK
| | | | - Terence J. O'Brien
- The Departments of Medicine and NeurologyThe Melbourne Brain CentreThe University of MelbourneThe Royal Melbourne HospitalMelbourneAustralia
| | | | - Graeme J. Sills
- Department of Molecular and Clinical PharmacologyInstitute of Translational MedicineUniversity of LiverpoolLiverpoolUK
| | - Stefan Wolking
- Department of Neurology and EpileptologyUniversity of TübingenHertie Institute for Clinical Brain ResearchTübingenGermany
| | - Holger Lerche
- Department of Neurology and EpileptologyUniversity of TübingenHertie Institute for Clinical Brain ResearchTübingenGermany
| | - Sanjay M. Sisodiya
- Department of Clinical and Experimental EpilepsyInstitute of NeurologyUniversity College LondonLondonUK
- Chalfont Centre for EpilepsyChalfont St. PeterUK
| | - Josemir W. Sander
- Stichting Epilepsie Instellingen Nederland (SEIN)ZwolleThe Netherlands
- Department of Clinical and Experimental EpilepsyInstitute of NeurologyUniversity College LondonLondonUK
- Chalfont Centre for EpilepsyChalfont St. PeterUK
| | - Gianpiero L. Cavalleri
- Molecular and Cellular TherapeuticsRoyal College of Surgeons in IrelandDublinIreland
- The FutureNeuro Research CentreRoyal College of Surgeons in IrelandDublinIreland
| | | | - Mark McCormack
- Molecular and Cellular TherapeuticsRoyal College of Surgeons in IrelandDublinIreland
- Department of GeneticsUniversity Medical Center UtrechtUtrechtThe Netherlands
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de Lange IM, Gunning B, Sonsma ACM, van Gemert L, van Kempen M, Verbeek NE, Sinoo C, Nicolai J, Knoers NVAM, Koeleman BPC, Brilstra EH. Outcomes and comorbidities of SCN1A-related seizure disorders. Epilepsy Behav 2019; 90:252-259. [PMID: 30527252 DOI: 10.1016/j.yebeh.2018.09.041] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 09/25/2018] [Accepted: 09/26/2018] [Indexed: 01/06/2023]
Abstract
PURPOSE Differentiating between Dravet syndrome and non-Dravet SCN1A-related phenotypes is important for prognosis regarding epilepsy severity, cognitive development, and comorbidities. When a child is diagnosed with genetic epilepsy with febrile seizures plus (GEFS+) or febrile seizures (FS), accurate prognostic information is essential as well, but detailed information on seizure course, seizure freedom, medication use, and comorbidities is lacking for this milder patient group. In this cross-sectional study, we explore disease characteristics in milder SCN1A-related phenotypes and the nature, occurrence, and relationships of SCN1A-related comorbidities in both patients with Dravet and non-Dravet syndromes. METHODS A cohort of 164 Dutch participants with SCN1A-related seizures was evaluated, consisting of 116 patients with Dravet syndrome and 48 patients with either GEFS+, febrile seizures plus (FS+), or FS. Clinical data were collected from medical records, semi-structured telephone interviews, and three questionnaires: the Functional Mobility Scale (FMS), the Pediatric Quality of Life Inventory (PedsQL) Measurement Model, and the Child or Adult Behavior Checklists (CBCL/ABCL). RESULTS Walking disabilities and severe behavioral problems affect 71% and 43% of patients with Dravet syndrome respectively and are almost never present in patients with non-Dravet syndromes. These comorbidities are strongly correlated to lower quality-of-life (QoL) scores. Less severe comorbidities occur in patients with non-Dravet syndromes: learning problems and psychological/behavioral problems are reported for 27% and 38% respectively. The average QoL score of the non-Dravet group was comparable with that of the general population. The majority of patients with non-Dravet syndromes becomes seizure-free after 10 years of age (85%). CONCLUSIONS Severe behavioral problems and walking disabilities are common in patients with Dravet syndrome and should receive specific attention during clinical management. Although the epilepsy course of patients with non-Dravet syndromes is much more favorable, milder comorbidities frequently occur in this group as well. Our results may be of great value for clinical care and informing newly diagnosed patients and their parents about prognosis.
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Affiliation(s)
- Iris M de Lange
- Department of Genetics, University Medical Center Utrecht, Utrecht University, the Netherlands.
| | | | - Anja C M Sonsma
- Department of Genetics, University Medical Center Utrecht, Utrecht University, the Netherlands
| | - Lisette van Gemert
- Academical Center of Epileptology, Maastricht and Heeze, the Netherlands
| | - Marjan van Kempen
- Department of Genetics, University Medical Center Utrecht, Utrecht University, the Netherlands
| | - Nienke E Verbeek
- Department of Genetics, University Medical Center Utrecht, Utrecht University, the Netherlands
| | - Claudia Sinoo
- Department of Genetics, University Medical Center Utrecht, Utrecht University, the Netherlands
| | - Joost Nicolai
- Academical Center of Epileptology, Maastricht and Heeze, the Netherlands
| | - Nine V A M Knoers
- Department of Genetics, University Medical Center Utrecht, Utrecht University, the Netherlands; Department of Genetics, University Medical Center Groningen, Groningen, the Netherlands
| | - Bobby P C Koeleman
- Department of Genetics, University Medical Center Utrecht, Utrecht University, the Netherlands
| | - Eva H Brilstra
- Department of Genetics, University Medical Center Utrecht, Utrecht University, the Netherlands
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Kuiper JJW, van Setten J, Devall M, Cretu-Stancu M, Hiddingh S, Ophoff RA, Missotten TOAR, van Velthoven M, Den Hollander AI, Hoyng CB, James E, Reeves E, Cordero-Coma M, Fonollosa A, Adán A, Martín J, Koeleman BPC, de Boer JH, Pulit SL, Márquez A, Radstake TRDJ. Functionally distinct ERAP1 and ERAP2 are a hallmark of HLA-A29-(Birdshot) Uveitis. Hum Mol Genet 2018; 27:4333-4343. [PMID: 30215709 PMCID: PMC6276832 DOI: 10.1093/hmg/ddy319] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [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: 06/25/2018] [Revised: 09/06/2018] [Accepted: 09/07/2018] [Indexed: 12/12/2022] Open
Abstract
Birdshot Uveitis (Birdshot) is a rare eye condition that affects HLA-A29-positive individuals and could be considered a prototypic member of the recently proposed 'MHC-I (major histocompatibility complex class I)-opathy' family. Genetic studies have pinpointed the endoplasmic reticulum aminopeptidase (ERAP1) and (ERAP2) genes as shared associations across MHC-I-opathies, which suggests ERAP dysfunction may be a root cause for MHC-I-opathies. We mapped the ERAP1 and ERAP2 haplotypes in 84 Dutch cases and 890 controls. We identified association at variant rs10044354, which mediated a marked increase in ERAP2 expression. We also identified and cloned an independently associated ERAP1 haplotype (tagged by rs2287987) present in more than half of the cases; this ERAP1 haplotype is also the primary risk and protective haplotype for other MHC-I-opathies. We show that the risk ERAP1 haplotype conferred significantly altered expression of ERAP1 isoforms in transcriptomic data (n = 360), resulting in lowered protein expression and distinct enzymatic activity. Both the association for rs10044354 (meta-analysis: odds ratio (OR) [95% CI]=2.07[1.58-2.71], P = 1.24 × 10(-7)) and rs2287987 (OR[95% CI]: =2.01[1.51-2.67], P = 1.41 × 10(-6)) replicated and showed consistent direction of effect in an independent Spanish cohort of 46 cases and 2103 controls. In both cohorts, the combined rs2287987-rs10044354 haplotype associated with Birdshot more strongly than either variant alone [meta-analysis: P=3.9 × 10(-9)]. Finally, we observed that ERAP2 protein expression is dependent on the ERAP1 background across three European populations (n = 3353). In conclusion, a functionally distinct combination of ERAP1 and ERAP2 are a hallmark of Birdshot and provide rationale for strategies designed to correct ERAP function for treatment of Birdshot and MHC-I-opathies more broadly.
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Affiliation(s)
- Jonas J W Kuiper
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
- Laboratory of Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Jessica van Setten
- Department of Cardiology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Matthew Devall
- Laboratory of Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Mircea Cretu-Stancu
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Sanne Hiddingh
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
- Laboratory of Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Roel A Ophoff
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, Netherlands
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | | | | | - Anneke I Den Hollander
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, Nijmegen, Netherlands
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Carel B Hoyng
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Edward James
- Centre for Cancer Immunology, Faculty of Medicine, University Hospital Southampton, Southampton, UK
| | - Emma Reeves
- Centre for Cancer Immunology, Faculty of Medicine, University Hospital Southampton, Southampton, UK
| | - Miguel Cordero-Coma
- Ophthalmology Department, Hospital de León, IBIOMED, Universidad de León, León, Spain
| | - Alejandro Fonollosa
- Ophthalmology Department, BioCruces Health Research Institute, Hospital Universitario Cruces, Barakaldo, Spain
| | - Alfredo Adán
- Ophthalmology Department, Hospital Clinic, Barcelona, Spain
| | - Javier Martín
- Instituto de Parasitología y Biomedicina ‘López-Neyra’, CSIC, PTS Granada, Granada Spain
| | - Bobby P C Koeleman
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Joke H de Boer
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Sara L Pulit
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- Centre for Health Information and Discovery, Big Data Institute, Oxford University, Oxford, UK
| | - Ana Márquez
- Systemic Autoimmune Disease Unit, Hospital Universitario San Cecilio, Instituto de Investigación Biosanitaria de Granada, Granada Spain
| | - Timothy R D J Radstake
- Laboratory of Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht, Netherlands
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36
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de Lange IM, Koudijs MJ, van ‘t Slot R, Sonsma ACM, Mulder F, Carbo EC, van Kempen MJA, Nijman IJ, Ernst RF, Savelberg SMC, Knoers NVAM, Brilstra EH, Koeleman BPC. Assessment of parental mosaicism in SCN1A-related epilepsy by single-molecule molecular inversion probes and next-generation sequencing. J Med Genet 2018; 56:75-80. [DOI: 10.1136/jmedgenet-2018-105672] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 09/24/2018] [Accepted: 09/30/2018] [Indexed: 01/08/2023]
Abstract
BackgroundDravet syndrome is a severe genetic encephalopathy, caused by pathogenic variants in SCN1A. Low-grade parental mosaicism occurs in a substantial proportion of families (7%–13%) and has important implications for recurrence risks. However, parental mosaicism can remain undetected by methods regularly used in diagnostics. In this study, we use single-molecule molecular inversion probes (smMIP), a technique with high sensitivity for detecting low-grade mosaic variants and high cost-effectiveness, to investigate the incidence of parental mosaicism of SCN1A variants in a cohort of 90 families and assess the feasibility of this technique.MethodsDeep sequencing of SCN1A was performed using smMIPs. False positive rates for each of the proband’s pathogenic variants were determined in 145 unrelated samples. If parents showed corresponding variant alleles at a significantly higher rate than the established noise ratio, mosaicism was confirmed by droplet digital PCR (ddPCR).ResultsSequence coverage of at least 100× at the location of the corresponding pathogenic variant was reached for 80 parent couples. The variant ratio was significantly higher than the established noise ratio in eight parent couples, of which four (5%) were regarded as true mosaics, based on ddPCR results. The false positive rate of smMIP analysis without ddPCR was therefore 50%. Three of these variants had previously been considered de novo in the proband by Sanger sequencing.ConclusionsmMIP technology combined withnext generation sequencing (NGS) performs better than Sanger sequencing in the detection of parental mosaicism. Because parental mosaicism has important implications for genetic counselling and recurrence risks, we stress the importance of implementing high-sensitivity NGS-based assays in standard diagnostics.
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Stevelink R, Koeleman BPC, Sander JW, Jansen FE, Braun KPJ. Refractory juvenile myoclonic epilepsy: a meta-analysis of prevalence and risk factors. Eur J Neurol 2018; 26:856-864. [PMID: 30223294 PMCID: PMC6586162 DOI: 10.1111/ene.13811] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [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: 06/09/2018] [Accepted: 09/12/2018] [Indexed: 01/12/2023]
Abstract
Background and purpose Juvenile myoclonic epilepsy (JME) is a common epilepsy syndrome for which treatment response is generally assumed to be good. We aimed to determine the prevalence and prognostic risk factors for refractoriness of JME. Methods We systematically searched PubMed and EMBASE and included 43 eligible studies, reporting seizure outcome after antiepileptic drug (AED) treatment in JME cohorts. We defined refractory JME as persistence of any seizure despite AED treatment and performed a random‐effects meta‐analysis to assess the prevalence of refractory JME and of seizure recurrence after AED withdrawal in individuals with well‐controlled seizures. Studies reporting potential prognostic risk factors in relation to seizure outcome were included for subsequent meta‐analysis of risk factors for refractoriness. Results Overall, 35% (95% confidence interval, 29–41%) of individuals (n = 3311) were refractory. There was marked heterogeneity between studies. Seizures recurred in 78% (95% confidence interval, 52–94%) of individuals who attempted to withdraw from treatment after a period of seizure freedom (n = 246). Seizure outcome by publication year suggested that prognosis did not improve over time. Meta‐analysis suggested six variables as prognostic factors for refractoriness, i.e. having three seizure types, absence seizures, psychiatric comorbidities, earlier age at seizure onset, history of childhood absence epilepsy and praxis‐induced seizures. Conclusion One‐third of people with JME were refractory, which is a higher prevalence than expected. Risk factors were identified and can be used to guide treatment and counselling of people with JME.
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Affiliation(s)
- R Stevelink
- Department of Child Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht.,Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht
| | - B P C Koeleman
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht
| | - J W Sander
- Stichting Epilepsie Instellingen Nederland (SEIN), Heemstede, The Netherlands.,UCL Institute of Neurology, NIHR University College London Hospitals Biomedical Research Centre, London.,Chalfont Centre for Epilepsy, Chalfont St Peter, UK
| | - F E Jansen
- Department of Child Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht
| | - K P J Braun
- Department of Child Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht
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Abstract
SummarySeveral human genetic linkage maps have been constructed as part of the Human Genome Project. These maps show the positional order of closely linked, highly informative AC-repeat polymorphisms on each human chromosome, and are extremely useful in genetic linkage analysis of inheritable diseases. For a candidate gene approach the current linkage maps are less useful, since they consist mainly of anonymous markers rather than of specific genes. This situation also applies for inheritable disorders of blood coagulation. Numerous genes are involved in the blood coagulation cascade and its regulation, and can be considered as candidate genes for unexplained haemophilia and thrombophilia. We have selected 29 candidate genes that seem to be the ones most likely to be involved in thrombophilia. For 19 genes genotype data were already present in the CEPH database (version 7.0). We typed 7 additional genes in the CEPH reference families, i.e. the factor V, factor XII, protein C, protein S, prothrombin, thrombomodulin, and heparin cofactor II gene. The genotype data were used to integrate these 26 genes in the current genetic linkage map, and to identify closely linked AC-repeat polymorphisms. This information will benefit the investigation of inheritable disorders of blood coagulation, especially thrombophilia.
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Affiliation(s)
- Bobby P C Koeleman
- The Haemostasis and Thrombosis Research Center, University Hospital Leiden, Leiden
| | | | - Egbert Bakker
- The Department of Human Genetics, State University Leiden, Leiden, The Netherlands
| | - Rogier M Bertina
- The Haemostasis and Thrombosis Research Center, University Hospital Leiden, Leiden
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Koeleman BPC, Rumpt DV, Hamulyák K, Reitsma PH, Bertina RM. Factor V Leiden: An Additional Risk Factor for Thrombosis in Protein S Deficient Families? Thromb Haemost 2018. [DOI: 10.1055/s-0038-1649778] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
SummaryWe recently reported a high prevalence of the FV Leiden mutation (R506Q, responsible for Activated Protein C resistance) among symptomatic protein C deficient probands (19%), and the involvement of the FV Leiden mutation in the expression of thrombophilia in six protein C deficient families. Here, we report the results of a similar study in protein S deficient probands and families. Among 16 symptomatic protein S deficient probands the prevalence of the FV Leiden mutation was high (38%). This high prevalence is significantly different from that in the normal population, and is probably caused by the selection of probands for familial thrombosis and protein S deficiency. In 4 families, the segregation of the FV Leiden mutation and the protein S deficiency could be studied. In sibships where both abnormalities were segregating, the percentage of symptomatic individuals with both abnormalities was 80%. Three of the seven subjects with only the FV Leiden mutation, and two out of the three subjects with only protein S deficiency had developed thrombosis. These results indicate that in the families presented here the combination of the FV Leiden mutation and the protein S deficiency is associated with a high risk for thrombosis. A reliable estimate of the penetrance of the single defects is not possible, because the number of individuals with a single defect is too low.
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Affiliation(s)
- B P C Koeleman
- The Hemostasis and Thrombosis Research Center, Department of Hematology, University Hospital, Leiden, The Netherlands
| | - D van Rumpt
- Ziekenhuis Velp, University of Limburg, Maastricht, The Netherlands
| | - K Hamulyák
- Department of Biochemistry and Hematology, University of Limburg, Maastricht, The Netherlands
| | - P H Reitsma
- The Hemostasis and Thrombosis Research Center, Department of Hematology, University Hospital, Leiden, The Netherlands
| | - R M Bertina
- The Hemostasis and Thrombosis Research Center, Department of Hematology, University Hospital, Leiden, The Netherlands
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40
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Holm LJ, Krogvold L, Hasselby JP, Kaur S, Claessens LA, Russell MA, Mathews CE, Hanssen KF, Morgan NG, Koeleman BPC, Roep BO, Gerling IC, Pociot F, Dahl-Jørgensen K, Buschard K. Abnormal islet sphingolipid metabolism in type 1 diabetes. Diabetologia 2018; 61:1650-1661. [PMID: 29671030 PMCID: PMC6445476 DOI: 10.1007/s00125-018-4614-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 03/15/2018] [Indexed: 12/17/2022]
Abstract
AIMS/HYPOTHESIS Sphingolipids play important roles in beta cell physiology, by regulating proinsulin folding and insulin secretion and in controlling apoptosis, as studied in animal models and cell cultures. Here we investigate whether sphingolipid metabolism may contribute to the pathogenesis of human type 1 diabetes and whether increasing the levels of the sphingolipid sulfatide would prevent models of diabetes in NOD mice. METHODS We examined the amount and distribution of sulfatide in human pancreatic islets by immunohistochemistry, immunofluorescence and electron microscopy. Transcriptional analysis was used to evaluate expression of sphingolipid-related genes in isolated human islets. Genome-wide association studies (GWAS) and a T cell proliferation assay were used to identify type 1 diabetes related polymorphisms and test how these affect cellular islet autoimmunity. Finally, we treated NOD mice with fenofibrate, a known activator of sulfatide biosynthesis, to evaluate the effect on experimental autoimmune diabetes development. RESULTS We found reduced amounts of sulfatide, 23% of the levels in control participants, in pancreatic islets of individuals with newly diagnosed type 1 diabetes, which were associated with reduced expression of enzymes involved in sphingolipid metabolism. Next, we discovered eight gene polymorphisms (ORMDL3, SPHK2, B4GALNT1, SLC1A5, GALC, PPARD, PPARG and B4GALT1) involved in sphingolipid metabolism that contribute to the genetic predisposition to type 1 diabetes. These gene polymorphisms correlated with the degree of cellular islet autoimmunity in a cohort of individuals with type 1 diabetes. Finally, using fenofibrate, which activates sulfatide biosynthesis, we completely prevented diabetes in NOD mice and even reversed the disease in half of otherwise diabetic animals. CONCLUSIONS/INTERPRETATION These results indicate that islet sphingolipid metabolism is abnormal in type 1 diabetes and suggest that modulation may represent a novel therapeutic approach. DATA AVAILABILITY The RNA expression data is available online at https://www.dropbox.com/s/93mk5tzl5fdyo6b/Abnormal%20islet%20sphingolipid%20metabolism%20in%20type%201%20diabetes%2C%20RNA%20expression.xlsx?dl=0 . A list of SNPs identified is available at https://www.dropbox.com/s/yfojma9xanpp2ju/Abnormal%20islet%20sphingolipid%20metabolism%20in%20type%201%20diabetes%20SNP.xlsx?dl=0 .
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Affiliation(s)
- Laurits J Holm
- The Bartholin Institute, Department of Pathology, Rigshospitalet, Copenhagen Biocenter, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Lars Krogvold
- Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
- Faculty of Odontology, University of Oslo, Oslo, Norway
| | - Jane P Hasselby
- Department of Pathology, Rigshospitalet, Copenhagen, Denmark
| | | | - Laura A Claessens
- Department of Immunohaematology & Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
- Department of Medical Genetics, University Medical Center, Utrecht, the Netherlands
| | - Mark A Russell
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Exeter, UK
| | - Clayton E Mathews
- Department of Pathology, University of Florida, Gainesville, FL, USA
| | - Kristian F Hanssen
- Faculty of Odontology, University of Oslo, Oslo, Norway
- Department of Endocrinology, Oslo University Hospital, Oslo, Norway
| | - Noel G Morgan
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Exeter, UK
| | - Bobby P C Koeleman
- Department of Medical Genetics, University Medical Center, Utrecht, the Netherlands
| | - Bart O Roep
- Department of Immunohaematology & Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
- Department of Diabetes Immunology, Diabetes & Metabolism Research Institute, Beckman Research Institute at the City of Hope, Duarte, CA, USA
| | - Ivan C Gerling
- Department of Medicine, University of Tennessee, Memphis, TN, USA
| | | | - Knut Dahl-Jørgensen
- Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
- Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Karsten Buschard
- The Bartholin Institute, Department of Pathology, Rigshospitalet, Copenhagen Biocenter, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.
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41
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Heyne HO, Singh T, Stamberger H, Abou Jamra R, Caglayan H, Craiu D, De Jonghe P, Guerrini R, Helbig KL, Koeleman BPC, Kosmicki JA, Linnankivi T, May P, Muhle H, Møller RS, Neubauer BA, Palotie A, Pendziwiat M, Striano P, Tang S, Wu S, Poduri A, Weber YG, Weckhuysen S, Sisodiya SM, Daly MJ, Helbig I, Lal D, Lemke JR. De novo variants in neurodevelopmental disorders with epilepsy. Nat Genet 2018; 50:1048-1053. [DOI: 10.1038/s41588-018-0143-7] [Citation(s) in RCA: 168] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 04/09/2018] [Indexed: 12/31/2022]
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42
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de Lange IM, Gunning B, Sonsma ACM, van Gemert L, van Kempen M, Verbeek NE, Nicolai J, Knoers NVAM, Koeleman BPC, Brilstra EH. Influence of contraindicated medication use on cognitive outcome in Dravet syndrome and age at first afebrile seizure as a clinical predictor in SCN1A
-related seizure phenotypes. Epilepsia 2018; 59:1154-1165. [DOI: 10.1111/epi.14191] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Iris M. de Lange
- Department of Medical Genetics; University Medical Center Utrecht; Utrecht University; Utrecht The Netherlands
| | - Boudewijn Gunning
- The Epilepsy Institutes of The Netherlands Foundation (SEIN); Zwolle The Netherlands
| | - Anja C. M. Sonsma
- Department of Medical Genetics; University Medical Center Utrecht; Utrecht University; Utrecht The Netherlands
| | | | - Marjan van Kempen
- Department of Medical Genetics; University Medical Center Utrecht; Utrecht University; Utrecht The Netherlands
| | - Nienke E. Verbeek
- Department of Medical Genetics; University Medical Center Utrecht; Utrecht University; Utrecht The Netherlands
| | - Joost Nicolai
- Academical Center of Epileptology; Maastricht and Heeze The Netherlands
| | - Nine V. A. M. Knoers
- Department of Medical Genetics; University Medical Center Utrecht; Utrecht University; Utrecht The Netherlands
| | - Bobby P. C. Koeleman
- Department of Medical Genetics; University Medical Center Utrecht; Utrecht University; Utrecht The Netherlands
| | - Eva H. Brilstra
- Department of Medical Genetics; University Medical Center Utrecht; Utrecht University; Utrecht The Netherlands
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43
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de Lange IM, Koudijs MJ, van 't Slot R, Gunning B, Sonsma ACM, van Gemert LJJM, Mulder F, Carbo EC, van Kempen MJA, Verbeek NE, Nijman IJ, Ernst RF, Savelberg SMC, Knoers NVAM, Brilstra EH, Koeleman BPC. Mosaicism of de novo pathogenic SCN1A
variants in epilepsy is a frequent phenomenon that correlates with variable phenotypes. Epilepsia 2018; 59:690-703. [DOI: 10.1111/epi.14021] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Iris M. de Lange
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
| | - Marco J. Koudijs
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
| | - Ruben van 't Slot
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
| | | | - Anja C. M. Sonsma
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
| | | | - Flip Mulder
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
| | - Ellen C. Carbo
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
| | - Marjan J. A. van Kempen
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
| | - Nienke E. Verbeek
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
| | - Isaac J. Nijman
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
| | - Robert F. Ernst
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
| | - Sanne M. C. Savelberg
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
| | - Nine V. A. M. Knoers
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
| | - Eva H. Brilstra
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
| | - Bobby P. C. Koeleman
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
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McCormack M, Gui H, Ingason A, Speed D, Wright GEB, Zhang EJ, Secolin R, Yasuda C, Kwok M, Wolking S, Becker F, Rau S, Avbersek A, Heggeli K, Leu C, Depondt C, Sills GJ, Marson AG, Auce P, Brodie MJ, Francis B, Johnson MR, Koeleman BPC, Striano P, Coppola A, Zara F, Kunz WS, Sander JW, Lerche H, Klein KM, Weckhuysen S, Krenn M, Gudmundsson LJ, Stefánsson K, Krause R, Shear N, Ross CJD, Delanty N, Pirmohamed M, Carleton BC, Cendes F, Lopes-Cendes I, Liao WP, O'Brien TJ, Sisodiya SM, Cherny S, Kwan P, Baum L, Cavalleri GL. Genetic variation in CFH predicts phenytoin-induced maculopapular exanthema in European-descent patients. Neurology 2018; 90:e332-e341. [PMID: 29288229 PMCID: PMC5798660 DOI: 10.1212/wnl.0000000000004853] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 10/02/2017] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVE To characterize, among European and Han Chinese populations, the genetic predictors of maculopapular exanthema (MPE), a cutaneous adverse drug reaction common to antiepileptic drugs. METHODS We conducted a case-control genome-wide association study of autosomal genotypes, including Class I and II human leukocyte antigen (HLA) alleles, in 323 cases and 1,321 drug-tolerant controls from epilepsy cohorts of northern European and Han Chinese descent. Results from each cohort were meta-analyzed. RESULTS We report an association between a rare variant in the complement factor H-related 4 (CFHR4) gene and phenytoin-induced MPE in Europeans (p = 4.5 × 10-11; odds ratio [95% confidence interval] 7 [3.2-16]). This variant is in complete linkage disequilibrium with a missense variant (N1050Y) in the complement factor H (CFH) gene. In addition, our results reinforce the association between HLA-A*31:01 and carbamazepine hypersensitivity. We did not identify significant genetic associations with MPE among Han Chinese patients. CONCLUSIONS The identification of genetic predictors of MPE in CFHR4 and CFH, members of the complement factor H-related protein family, suggest a new link between regulation of the complement system alternative pathway and phenytoin-induced hypersensitivity in European-ancestral patients.
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Affiliation(s)
- Mark McCormack
- Author affiliations are provided at the end of the article
| | - Hongsheng Gui
- Author affiliations are provided at the end of the article
| | - Andrés Ingason
- Author affiliations are provided at the end of the article
| | - Doug Speed
- Author affiliations are provided at the end of the article
| | | | - Eunice J Zhang
- Author affiliations are provided at the end of the article
| | | | | | - Maxwell Kwok
- Author affiliations are provided at the end of the article
| | - Stefan Wolking
- Author affiliations are provided at the end of the article
| | | | - Sarah Rau
- Author affiliations are provided at the end of the article
| | | | | | - Costin Leu
- Author affiliations are provided at the end of the article
| | | | - Graeme J Sills
- Author affiliations are provided at the end of the article
| | | | - Pauls Auce
- Author affiliations are provided at the end of the article
| | | | - Ben Francis
- Author affiliations are provided at the end of the article
| | | | | | | | | | - Federico Zara
- Author affiliations are provided at the end of the article
| | - Wolfram S Kunz
- Author affiliations are provided at the end of the article
| | | | - Holger Lerche
- Author affiliations are provided at the end of the article
| | | | | | - Martin Krenn
- Author affiliations are provided at the end of the article
| | | | | | - Roland Krause
- Author affiliations are provided at the end of the article
| | - Neil Shear
- Author affiliations are provided at the end of the article
| | - Colin J D Ross
- Author affiliations are provided at the end of the article
| | - Norman Delanty
- Author affiliations are provided at the end of the article
| | | | | | | | | | - Wei-Ping Liao
- Author affiliations are provided at the end of the article
| | | | | | - Stacey Cherny
- Author affiliations are provided at the end of the article
| | - Patrick Kwan
- Author affiliations are provided at the end of the article
| | - Larry Baum
- Author affiliations are provided at the end of the article
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de Kovel CGF, Syrbe S, Brilstra EH, Verbeek N, Kerr B, Dubbs H, Bayat A, Desai S, Naidu S, Srivastava S, Cagaylan H, Yis U, Saunders C, Rook M, Plugge S, Muhle H, Afawi Z, Klein KM, Jayaraman V, Rajagopalan R, Goldberg E, Marsh E, Kessler S, Bergqvist C, Conlin LK, Krok BL, Thiffault I, Pendziwiat M, Helbig I, Polster T, Borggraefe I, Lemke JR, van den Boogaardt MJ, Møller RS, Koeleman BPC. Neurodevelopmental Disorders Caused by De Novo Variants in KCNB1 Genotypes and Phenotypes. JAMA Neurol 2017; 74:1228-1236. [PMID: 28806457 DOI: 10.1001/jamaneurol.2017.1714] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Importance Knowing the range of symptoms seen in patients with a missense or loss-of-function variant in KCNB1 and how these symptoms correlate with the type of variant will help clinicians with diagnosis and prognosis when treating new patients. Objectives To investigate the clinical spectrum associated with KCNB1 variants and the genotype-phenotype correlations. Design, Setting, and Participants This study summarized the clinical and genetic information of patients with a presumed pathogenic variant in KCNB1. Patients were identified in research projects or during clinical testing. Information on patients from previously published articles was collected and authors contacted if feasible. All patients were seen at a clinic at one of the participating institutes because of presumed genetic disorder. They were tested in a clinical setting or included in a research project. Main Outcomes and Measures The genetic variant and its inheritance and information on the patient's symptoms and characteristics in a predefined format. All variants were identified with massive parallel sequencing and confirmed with Sanger sequencing in the patient. Absence of the variant in the parents could be confirmed with Sanger sequencing in all families except one. Results Of 26 patients (10 female, 15 male, 1 unknown; mean age at inclusion, 9.8 years; age range, 2-32 years) with developmental delay, 20 (77%) carried a missense variant in the ion channel domain of KCNB1, with a concentration of variants in region S5 to S6. Three variants that led to premature stops were located in the C-terminal and 3 in the ion channel domain. Twenty-one of 25 patients (84%) had seizures, with 9 patients (36%) starting with epileptic spasms between 3 and 18 months of age. All patients had developmental delay, with 17 (65%) experiencing severe developmental delay; 14 (82%) with severe delay had behavioral problems. The developmental delay was milder in 4 of 6 patients with stop variants and in a patient with a variant in the S2 transmembrane element rather than the S4 to S6 region. Conclusions and Relevance De novo KCNB1 missense variants in the ion channel domain and loss-of-function variants in this domain and the C-terminal likely cause neurodevelopmental disorders with or without seizures. Patients with presumed pathogenic variants in KCNB1 have a variable phenotype. However, the type and position of the variants in the protein are (imperfectly) correlated with the severity of the disorder.
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Affiliation(s)
- Carolien G F de Kovel
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands.,Department of Language and Genetics, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
| | - Steffen Syrbe
- Division of Child Neurology and Inherited Metabolic Diseases, Department of General Pediatrics, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Eva H Brilstra
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Nienke Verbeek
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Bronwyn Kerr
- Institute of Evolution, Systems and Genomics, Faculty of Medical and Human Sciences, University of Manchester, Manchester, England.,Manchester Centre For Genomic Medicine, Central Manchester University Hospitals National Health Service Foundation Trust, Manchester, England.,Manchester Academic Health Science Centre, Manchester, England
| | - Holly Dubbs
- Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Allan Bayat
- Department of Pediatrics, University Hospital of Hvidovre, Copenhagen, Denmark
| | - Sonal Desai
- Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, Maryland
| | - Sakkubai Naidu
- Department of Neurology and Pediatrics, Johns Hopkins School of Medicine, Baltimore, Maryland.,Hugo Moser Research Institute, Kennedy Krieger Institute, Baltimore, Maryland
| | | | - Hande Cagaylan
- Department of Molecular Biology and Genetics, Bogaziçi University, Istanbul, Turkey
| | - Uluc Yis
- Division of Child Neurology, Department of Pediatrics, School of Medicine, Dokuz Eylül University, İzmir, Turkey
| | - Carol Saunders
- Center for Pediatric Genomic Medicine, Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, Missouri.,Department of Pediatrics, Children's Mercy Hospital, Kansas City, Missouri.,Pediatric Pathology and Laboratory Medicine, University of Missouri-Kansas City School of Medicine, Kansas City
| | - Martin Rook
- Department of Medical Physiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Susanna Plugge
- Department of Biomedical Sciences, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Hiltrud Muhle
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein, Christian Albrechts University, Kiel, Germany
| | - Zaid Afawi
- Department of Physiology and Pharmacology, Tel Aviv University Medical School, Ramat Aviv, Israel
| | - Karl-Martin Klein
- Department of Neurology, Epilepsy Center Frankfurt Rhine-Main, Center of Neurology and Neurosurgery, University Hospital, Goethe-University Frankfurt, Frankfurt, Germany
| | - Vijayakumar Jayaraman
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Ramakrishnan Rajagopalan
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Ethan Goldberg
- Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Eric Marsh
- Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Sudha Kessler
- Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Christina Bergqvist
- Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Laura K Conlin
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Bryan L Krok
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, Missouri.,Department of Pediatrics, Children's Mercy Hospital, Kansas City, Missouri
| | - Manuela Pendziwiat
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein, Christian Albrechts University, Kiel, Germany
| | - Ingo Helbig
- Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,University Medical Center Schleswig-Holstein, Christian Albrechts University, Kiel, Germany
| | - Tilman Polster
- Epilepsiezentrum Bethel, Krankenhaus Mara, Kinderepileptologie, Bielefeld, Germany
| | - Ingo Borggraefe
- Department of Pediatric Neurology, Developmental Medicine and Social Pediatrics Dr. von Hauner's Children's Hospital, University of Munich, Munich, Germany
| | - Johannes R Lemke
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig, Germany
| | | | - Rikke S Møller
- Danish Epilepsy Centre, Dianalund, Denmark.,Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark
| | - Bobby P C Koeleman
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
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Androsova G, Krause R, Borghei M, Wassenaar M, Auce P, Avbersek A, Becker F, Berghuis B, Campbell E, Coppola A, Francis B, Wolking S, Cavalleri GL, Craig J, Delanty N, Koeleman BPC, Kunz WS, Lerche H, Marson AG, Sander JW, Sills GJ, Striano P, Zara F, Sisodiya SM, Depondt C. Comparative effectiveness of antiepileptic drugs in patients with mesial temporal lobe epilepsy with hippocampal sclerosis. Epilepsia 2017; 58:1734-1741. [DOI: 10.1111/epi.13871] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/25/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Ganna Androsova
- Luxembourg Center for Systems Biomedicine; University of Luxembourg; Esch-sur-Alzette Luxembourg
| | - Roland Krause
- Luxembourg Center for Systems Biomedicine; University of Luxembourg; Esch-sur-Alzette Luxembourg
| | - Mojgansadat Borghei
- Laboratory of Experimental Neurology; Université Libre de Bruxelles; Brussels Belgium
| | - Merel Wassenaar
- Stichting Epilepsie Instellingen Nederland (SEIN); Heemstede The Netherlands
| | - Pauls Auce
- Department of Molecular and Clinical Pharmacology; Institute of Translational Medicine; University of Liverpool; Liverpool United Kingdom
- The Walton Centre NHS Foundation Trust; Liverpool United Kingdom
| | - Andreja Avbersek
- Department of Clinical and Experimental Epilepsy; UCL Institute of Neurology; London United Kingdom
| | - Felicitas Becker
- Hertie Institute for Clinical Brain Research; University of Tübingen; Tübingen Germany
| | - Bianca Berghuis
- Stichting Epilepsie Instellingen Nederland (SEIN); Heemstede The Netherlands
| | - Ellen Campbell
- Belfast Health and Social Care Trust; Belfast United Kingdom
| | - Antonietta Coppola
- Pediatric Neurology and Muscular Diseases Unit; Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health; University of Genoa; Genoa Italy
| | - Ben Francis
- Department of Biostatistics; University of Liverpool; Liverpool United Kingdom
| | - Stefan Wolking
- Hertie Institute for Clinical Brain Research; University of Tübingen; Tübingen Germany
| | - Gianpiero L. Cavalleri
- Molecular and Cellular Therapeutics; Royal College of Surgeons in Ireland; Dublin Ireland
| | - John Craig
- Belfast Health and Social Care Trust; Belfast United Kingdom
| | - Norman Delanty
- Molecular and Cellular Therapeutics; Royal College of Surgeons in Ireland; Dublin Ireland
- Department of Neurology; Beaumont Hospital; Dublin Ireland
| | - Bobby P. C. Koeleman
- Department of Genetics; University Medical Center Utrecht; Utrecht The Netherlands
| | - Wolfram S. Kunz
- Department of Epileptology; University of Bonn; Bonn Germany
| | - Holger Lerche
- Hertie Institute for Clinical Brain Research; University of Tübingen; Tübingen Germany
| | - Anthony G. Marson
- Department of Molecular and Clinical Pharmacology; Institute of Translational Medicine; University of Liverpool; Liverpool United Kingdom
- The Walton Centre NHS Foundation Trust; Liverpool United Kingdom
| | - Josemir W. Sander
- Stichting Epilepsie Instellingen Nederland (SEIN); Heemstede The Netherlands
- NIHR University College London Hospitals Biomedical Research Centre; UCL Institute of Neurology; London United Kingdom
- The Chalfont Centre for Epilepsy; Chalfont St. Peters United Kingdom
| | - Graeme J. Sills
- Department of Molecular and Clinical Pharmacology; Institute of Translational Medicine; University of Liverpool; Liverpool United Kingdom
| | - Pasquale Striano
- Pediatric Neurology and Muscular Diseases Unit; Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health; University of Genoa; Genoa Italy
| | - Federico Zara
- Laboratory of Neurogenetics and Neuroscience; Institute G. Gaslini; Genoa Italy
| | - Sanjay M. Sisodiya
- Department of Clinical and Experimental Epilepsy; UCL Institute of Neurology; London United Kingdom
- The Chalfont Centre for Epilepsy; Chalfont St. Peters United Kingdom
| | - Chantal Depondt
- Laboratory of Experimental Neurology; Université Libre de Bruxelles; Brussels Belgium
- Department of Neurology; Hôpital Erasme; Université Libre de Bruxelles; Brussels Belgium
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47
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López-Isac E, Martín JE, Assassi S, Simeón CP, Carreira P, Ortego-Centeno N, Freire M, Beltrán E, Narváez J, Alegre-Sancho JJ, Fernández-Gutiérrez B, Balsa A, Ortiz AM, González-Gay MA, Beretta L, Santaniello A, Bellocchi C, Lunardi C, Moroncini G, Gabrielli A, Witte T, Hunzelmann N, Distler JHW, Riekemasten G, van der Helm-van Mil AH, de Vries-Bouwstra J, Magro-Checa C, Voskuyl AE, Vonk MC, Molberg Ø, Merriman T, Hesselstrand R, Nordin A, Padyukov L, Herrick A, Eyre S, Koeleman BPC, Denton CP, Fonseca C, Radstake TRDJ, Worthington J, Mayes MD, Martín J. Brief Report: IRF4 Newly Identified as a Common Susceptibility Locus for Systemic Sclerosis and Rheumatoid Arthritis in a Cross-Disease Meta-Analysis of Genome-Wide Association Studies. Arthritis Rheumatol 2017; 68:2338-44. [PMID: 27111665 DOI: 10.1002/art.39730] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 04/19/2016] [Indexed: 01/21/2023]
Abstract
OBJECTIVE Systemic sclerosis (SSc) and rheumatoid arthritis (RA) are autoimmune diseases that have similar clinical and immunologic characteristics. To date, several shared SSc-RA genetic loci have been identified independently. The aim of the current study was to systematically search for new common SSc-RA loci through an interdisease meta-genome-wide association (meta-GWAS) strategy. METHODS The study was designed as a meta-analysis combining GWAS data sets of patients with SSc and patients with RA, using a strategy that allowed identification of loci with both same-direction and opposite-direction allelic effects. The top single-nucleotide polymorphisms were followed up in independent SSc and RA case-control cohorts. This allowed an increase in the sample size to a total of 8,830 patients with SSc, 16,870 patients with RA, and 43,393 healthy controls. RESULTS This cross-disease meta-analysis of the GWAS data sets identified several loci with nominal association signals (P < 5 × 10(-6) ) that also showed evidence of association in the disease-specific GWAS scans. These loci included several genomic regions not previously reported as shared loci, as well as several risk factors that were previously found to be associated with both diseases. Follow-up analyses of the putatively new SSc-RA loci identified IRF4 as a shared risk factor for these 2 diseases (Pcombined = 3.29 × 10(-12) ). Analysis of the biologic relevance of the known SSc-RA shared loci identified the type I interferon and interleukin-12 signaling pathways as the main common etiologic factors. CONCLUSION This study identified a novel shared locus, IRF4, for the risk of SSc and RA, and highlighted the usefulness of a cross-disease GWAS meta-analysis strategy in the identification of common risk loci.
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Affiliation(s)
- Elena López-Isac
- Institute of Parasitology and Biomedicine López-Neyra CSIC, Granada, Spain
| | | | | | | | | | | | - Mayka Freire
- Complexo Hospitalario Universitario de Vigo, Vigo, Spain
| | - Emma Beltrán
- Hospital General Universitario de Valencia, Valencia, Spain
| | | | | | | | | | - Alejandro Balsa
- Hospital Universitario La Paz, Instituto de Investigación Sanitaria La Paz, Madrid, Spain
| | - Ana M Ortiz
- Hospital Universitario La Princesa, Instituto de Investigación Sanitaria La Princesa, Madrid, Spain
| | | | - Lorenzo Beretta
- Referral Center for Systemic Autoimmune Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano, Milan, Italy
| | - Alessandro Santaniello
- Referral Center for Systemic Autoimmune Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano, Milan, Italy
| | - Chiara Bellocchi
- Referral Center for Systemic Autoimmune Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano, Milan, Italy
| | | | | | - Armando Gabrielli
- Università Politecnica delle Marche and Ospedali Riuniti, Ancona, Italy
| | | | | | | | | | | | | | | | | | - Madelon C Vonk
- Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Øyvind Molberg
- Oslo University Hospital Rikshospitalet and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | | | - Annika Nordin
- Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Leonid Padyukov
- Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Ariane Herrick
- University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Steve Eyre
- University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | | | - Christopher P Denton
- Centre for Rheumatology, Royal Free and University College Medical School, London, UK
| | - Carmen Fonseca
- Centre for Rheumatology, Royal Free and University College Medical School, London, UK
| | - Timothy R D J Radstake
- University Medical Center Utrecht, Utrecht, The Netherlands. Members of the Spanish Scleroderma Group are shown in Appendix A
| | - Jane Worthington
- University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | | | - Javier Martín
- Institute of Parasitology and Biomedicine López-Neyra CSIC, Granada, Spain
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48
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Berghuis B, van der Palen J, de Haan GJ, Lindhout D, Koeleman BPC, Sander JW. Carbamazepine- and oxcarbazepine-induced hyponatremia in people with epilepsy. Epilepsia 2017; 58:1227-1233. [PMID: 28542738 DOI: 10.1111/epi.13777] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/07/2017] [Indexed: 12/13/2022]
Abstract
OBJECTIVE To ascertain possible determinants of carbamazepine (CBZ)- and oxcarbazepine (OXC)-induced hyponatremia in a large cohort of people with epilepsy. METHODS We collected data on serum sodium levels in people with epilepsy who were attending a tertiary epilepsy center while on treatment with CBZ or OXC. We defined hyponatremia as Na+ ≤134 mEq/L and severe hyponatremia as Na+ ≤128 mEq/L. RESULTS We identified 1,782 people who had used CBZ (n = 1,424) or OXC (n = 358), of whom 50 were treated with both drugs. Data on sodium level measurements were available in 1,132 on CBZ and in 289 on OXC. Hyponatremia occurred in 26% of those taking CBZ and 46% of those taking OXC. This was severe in 7% in the CBZ group and 22% in the OXC group. Hyponatremia was symptomatic in 48% and led to admissions in 3%. Age over 40 years, high serum levels of CBZ and OXC, and concomitant use of other antiepileptic drugs were the main risk factors for hyponatremia in both treatment groups. Female patients on OXC were at a higher risk than male patients of hyponatremia. The risk of hyponatremia on CBZ was significantly associated with the risk of hyponatremia on OXC within a subgroup that used both drugs consecutively. SIGNIFICANCE Hyponatremia is a common problem in people taking CBZ or OXC. Regular ascertainment of sodium levels in those taking either drug is recommended and results should be acted on.
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Affiliation(s)
- Bianca Berghuis
- Stichting Epilepsie Instellingen Nederland (SEIN), Zwolle, The Netherlands
| | - Job van der Palen
- Department of Epidemiology, Medical School Twente, Enschede, The Netherlands.,Department of Research Methodology, Measurement and Data Analysis, University of Twente, Enschede, The Netherlands
| | - Gerrit-Jan de Haan
- Stichting Epilepsie Instellingen Nederland (SEIN), Zwolle, The Netherlands
| | - Dick Lindhout
- Stichting Epilepsie Instellingen Nederland (SEIN), Zwolle, The Netherlands.,Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bobby P C Koeleman
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Josemir W Sander
- Stichting Epilepsie Instellingen Nederland (SEIN), Zwolle, The Netherlands.,NIHR UCL Hospitals Biomedical Research Centre, UCL Institute of Neurology, London, United Kingdom.,Chalfont Centre for Epilepsy, Chalfont St. Peter, United Kingdom
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49
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Vossen CY, van Hylckama Vlieg A, Teruel-Montoya R, Salloum-Asfar S, de Haan H, Corral J, Reitsma P, Koeleman BPC, Martínez C. Identification of coagulation gene 3'UTR variants that are potentially regulated by microRNAs. Br J Haematol 2017; 177:782-790. [PMID: 28444748 DOI: 10.1111/bjh.14629] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [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: 11/02/2016] [Accepted: 12/31/2016] [Indexed: 12/21/2022]
Abstract
MicroRNAs have been recognized as critical regulators of gene expression and might affect the risk of venous thrombosis. We aimed to identify 3' untranslated region (UTR) variants in coagulation genes that influence coagulation factor levels and venous thrombosis risk. The 3'UTR of coagulation genes were sequenced in subjects with extremely high or low plasma levels of these factors in two case-control studies. In total, 28 variants were identified. Five single nucleotide polymorphisms (SNPs) were predominantly present in one extreme level group (F2 rs1799963, F8 rs1050705 and F11 rs4253429, rs4253430 and rs1062547). Additional to F2 rs1799963, F8 rs1050705 (in men) and F11 rs4253430 were associated with an increased risk of venous thrombosis albeit confidence intervals were wide. The three F11 SNPs were in high linkage disequilibrium with functional variants rs2289252 and rs2036914. Rs1062547 and rs4253430 were associated with a significant increase of plasma FXI activity in heterozygotes and homozygotes in wild-type controls. In silico prediction revealed that these SNPs might disturb the binding sites of miR-544 and miR-513a-3p. Only miR-544 provoked a significant decrease of the luciferase activity that was not observed with a rs4253430 mutated vector. In conclusion, these results reinforce that microRNAs are candidates to play a role in haemostasis and complex disorders, such as thrombosis.
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Affiliation(s)
- Carla Y Vossen
- Medical Genetics, University Medical Centre Utrecht, Utrecht, the Netherlands.,Clinical Epidemiology, Leiden University Medical Centre, Leiden, the Netherlands
| | | | | | - Salam Salloum-Asfar
- Servicio de Hematología y Oncología Médica. Hospital Universitario Morales Meseguer y Centro Regional de Hemodonación, IMIB-Arrixaca, Universidad de Murcia, Murcia, Spain
| | - Hugoline de Haan
- Clinical Epidemiology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Javier Corral
- Servicio de Hematología y Oncología Médica. Hospital Universitario Morales Meseguer y Centro Regional de Hemodonación, IMIB-Arrixaca, Universidad de Murcia, Murcia, Spain
| | - Pieter Reitsma
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Centre, Leiden, the Netherlands.,Thrombosis and Haemostasis, Leiden University Medical Centre, Leiden, the Netherlands
| | - Bobby P C Koeleman
- Medical Genetics, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Constantino Martínez
- Servicio de Hematología y Oncología Médica. Hospital Universitario Morales Meseguer y Centro Regional de Hemodonación, IMIB-Arrixaca, Universidad de Murcia, Murcia, Spain
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50
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Weinsheimer S, Bendjilali N, Nelson J, Guo DE, Zaroff JG, Sidney S, McCulloch CE, Al-Shahi Salman R, Berg JN, Koeleman BPC, Simon M, Bostroem A, Fontanella M, Sturiale CL, Pola R, Puca A, Lawton MT, Young WL, Pawlikowska L, Klijn CJM, Kim H. Genome-wide association study of sporadic brain arteriovenous malformations. J Neurol Neurosurg Psychiatry 2016; 87:916-23. [PMID: 26818729 PMCID: PMC4963303 DOI: 10.1136/jnnp-2015-312272] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 12/28/2015] [Indexed: 12/30/2022]
Abstract
BACKGROUND The pathogenesis of sporadic brain arteriovenous malformations (BAVMs) remains unknown, but studies suggest a genetic component. We estimated the heritability of sporadic BAVM and performed a genome-wide association study (GWAS) to investigate association of common single nucleotide polymorphisms (SNPs) with risk of sporadic BAVM in the international, multicentre Genetics of Arteriovenous Malformation (GEN-AVM) consortium. METHODS The Caucasian discovery cohort included 515 BAVM cases and 1191 controls genotyped using Affymetrix genome-wide SNP arrays. Genotype data were imputed to 1000 Genomes Project data, and well-imputed SNPs (>0.01 minor allele frequency) were analysed for association with BAVM. 57 top BAVM-associated SNPs (51 SNPs with p<10(-05) or p<10(-04) in candidate pathway genes, and 6 candidate BAVM SNPs) were tested in a replication cohort including 608 BAVM cases and 744 controls. RESULTS The estimated heritability of BAVM was 17.6% (SE 8.9%, age and sex-adjusted p=0.015). None of the SNPs were significantly associated with BAVM in the replication cohort after correction for multiple testing. 6 SNPs had a nominal p<0.1 in the replication cohort and map to introns in EGFEM1P, SP4 and CDKAL1 or near JAG1 and BNC2. Of the 6 candidate SNPs, 2 in ACVRL1 and MMP3 had a nominal p<0.05 in the replication cohort. CONCLUSIONS We performed the first GWAS of sporadic BAVM in the largest BAVM cohort assembled to date. No GWAS SNPs were replicated, suggesting that common SNPs do not contribute strongly to BAVM susceptibility. However, heritability estimates suggest a modest but significant genetic contribution.
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Affiliation(s)
- Shantel Weinsheimer
- Mental Health Center, Sct. Hans MHS-Capital Region of Denmark, Institute of Biological Psychiatry, Roskilde, Denmark
| | | | - Jeffrey Nelson
- Department of Anesthesia and Perioperative Care, Center for Cerebrovascular Research, University of California, San Francisco, California, USA
| | - Diana E Guo
- Department of Anesthesia and Perioperative Care, Center for Cerebrovascular Research, University of California, San Francisco, California, USA
| | - Jonathan G Zaroff
- Division of Research, Kaiser Permanente of Northern California, Oakland, California, USA
| | - Stephen Sidney
- Division of Research, Kaiser Permanente of Northern California, Oakland, California, USA
| | - Charles E McCulloch
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
| | | | - Jonathan N Berg
- Department of Clinical Genetics, University of Dundee, Dundee, UK
| | - Bobby P C Koeleman
- Department of Medical Genetics, University Medical Center, Utrecht, The Netherlands
| | - Matthias Simon
- Department of Neurosurgery, University of Bonn Medical Center, Bonn, Germany
| | - Azize Bostroem
- Department of Neurosurgery, University of Bonn Medical Center, Bonn, Germany
| | - Marco Fontanella
- Division of Neurosurgery, University of Torino, University of Brescia, Brescia, Italy
| | | | - Roberto Pola
- Institute of Medicine, Catholic University of Rome, Rome, Italy
| | - Alfredo Puca
- Institute of Neurosurgery, Catholic University of Rome, Rome, Italy
| | - Michael T Lawton
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - William L Young
- Department of Anesthesia and Perioperative Care, Center for Cerebrovascular Research, University of California, San Francisco, California, USA
| | - Ludmila Pawlikowska
- Department of Anesthesia and Perioperative Care, Center for Cerebrovascular Research, University of California, San Francisco, California, USA Institute for Human Genetics, University of California, San Francisco, California, USA
| | - Catharina J M Klijn
- Department of Neurology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Helen Kim
- Department of Anesthesia and Perioperative Care, Center for Cerebrovascular Research, University of California, San Francisco, California, USA Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA Institute for Human Genetics, University of California, San Francisco, California, USA
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