2023
Super-enhancer hijacking drives ectopic expression of hedgehog pathway ligands in meningiomas
Youngblood M, Erson-Omay Z, Li C, Najem H, Coșkun S, Tyrtova E, Montejo J, Miyagishima D, Barak T, Nishimura S, Harmancı A, Clark V, Duran D, Huttner A, Avşar T, Bayri Y, Schramm J, Boetto J, Peyre M, Riche M, Goldbrunner R, Amankulor N, Louvi A, Bilgüvar K, Pamir M, Özduman K, Kilic T, Knight J, Simon M, Horbinski C, Kalamarides M, Timmer M, Heimberger A, Mishra-Gorur K, Moliterno J, Yasuno K, Günel M. Super-enhancer hijacking drives ectopic expression of hedgehog pathway ligands in meningiomas. Nature Communications 2023, 14: 6279. PMID: 37805627, PMCID: PMC10560290, DOI: 10.1038/s41467-023-41926-y.Peer-Reviewed Original Research
2020
Mutations disrupting neuritogenesis genes confer risk for cerebral palsy
Jin SC, Lewis SA, Bakhtiari S, Zeng X, Sierant MC, Shetty S, Nordlie SM, Elie A, Corbett MA, Norton BY, van Eyk CL, Haider S, Guida BS, Magee H, Liu J, Pastore S, Vincent JB, Brunstrom-Hernandez J, Papavasileiou A, Fahey MC, Berry JG, Harper K, Zhou C, Zhang J, Li B, Zhao H, Heim J, Webber DL, Frank MSB, Xia L, Xu Y, Zhu D, Zhang B, Sheth AH, Knight JR, Castaldi C, Tikhonova IR, López-Giráldez F, Keren B, Whalen S, Buratti J, Doummar D, Cho M, Retterer K, Millan F, Wang Y, Waugh JL, Rodan L, Cohen JS, Fatemi A, Lin AE, Phillips JP, Feyma T, MacLennan SC, Vaughan S, Crompton KE, Reid SM, Reddihough DS, Shang Q, Gao C, Novak I, Badawi N, Wilson YA, McIntyre SJ, Mane SM, Wang X, Amor DJ, Zarnescu DC, Lu Q, Xing Q, Zhu C, Bilguvar K, Padilla-Lopez S, Lifton RP, Gecz J, MacLennan AH, Kruer MC. Mutations disrupting neuritogenesis genes confer risk for cerebral palsy. Nature Genetics 2020, 52: 1046-1056. PMID: 32989326, PMCID: PMC9148538, DOI: 10.1038/s41588-020-0695-1.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBeta CateninCerebral PalsyCyclin DCytoskeletonDrosophilaExomeExome SequencingExtracellular MatrixF-Box ProteinsFemaleFocal AdhesionsGenetic Predisposition to DiseaseGenome, HumanHumansMaleMutationNeuritesRhoB GTP-Binding ProteinRisk FactorsSequence Analysis, DNASignal TransductionTubulinTumor Suppressor ProteinsConceptsDamaging de novo mutationsCerebral palsyDe novo mutationsCerebral palsy casesRisk genesDamaging de novoNovo mutationsWhole-exome sequencingPalsy casesNeuromotor functionD levelsMonogenic etiologyCyclin D levelsNeuronal connectivityPalsyGene confer riskConfer riskRecessive variantsNeurodevelopmental disorder genesReverse genetic screenDisorder genesParent-offspring triosGenome-wide significanceGenomic factorsCytoskeleton pathway
2019
Mutations in TFAP2B and previously unimplicated genes of the BMP, Wnt, and Hedgehog pathways in syndromic craniosynostosis
Timberlake AT, Jin SC, Nelson-Williams C, Wu R, Furey CG, Islam B, Haider S, Loring E, Galm A, Steinbacher D, Larysz D, Staffenberg D, Flores R, Rodriguez E, Boggon T, Persing J, Lifton R, Lifton RP, Gunel M, Mane S, Bilguvar K, Gerstein M, Loring E, Nelson-Williams C, Lopez F, Knight J. Mutations in TFAP2B and previously unimplicated genes of the BMP, Wnt, and Hedgehog pathways in syndromic craniosynostosis. Proceedings Of The National Academy Of Sciences Of The United States Of America 2019, 116: 15116-15121. PMID: 31292255, PMCID: PMC6660739, DOI: 10.1073/pnas.1902041116.Peer-Reviewed Original ResearchMeSH KeywordsAdolescentAlpha CateninChildChild, PreschoolCraniosynostosesExomeExome SequencingFemaleGene ExpressionGlypicansHistone AcetyltransferasesHumansMaleMutationNuclear ProteinsPedigreeRisk AssessmentSignal TransductionSkullSOXC Transcription FactorsTranscription Factor AP-2Zinc Finger Protein Gli2ConceptsRare damaging mutationsSyndromic craniosynostosisCongenital anomaliesDamaging mutationsSyndromic casesExome sequencingAdditional congenital anomaliesFrequent congenital anomaliesDamaging de novo mutationsNeural crest cell migrationDamaging de novoCrest cell migrationCS patientsMutation burdenChromatin modifiersSubsequent childrenTranscription factorsDe novo mutationsCS casesCS geneHedgehog pathwayDisease locusPremature fusionFunction mutationsCraniosynostosis
2018
Mutations in Chromatin Modifier and Ephrin Signaling Genes in Vein of Galen Malformation
Duran D, Zeng X, Jin SC, Choi J, Nelson-Williams C, Yatsula B, Gaillard J, Furey CG, Lu Q, Timberlake AT, Dong W, Sorscher MA, Loring E, Klein J, Allocco A, Hunt A, Conine S, Karimy JK, Youngblood MW, Zhang J, DiLuna ML, Matouk CC, Mane S, Tikhonova IR, Castaldi C, López-Giráldez F, Knight J, Haider S, Soban M, Alper SL, Komiyama M, Ducruet AF, Zabramski JM, Dardik A, Walcott BP, Stapleton CJ, Aagaard-Kienitz B, Rodesch G, Jackson E, Smith ER, Orbach DB, Berenstein A, Bilguvar K, Vikkula M, Gunel M, Lifton RP, Kahle KT. Mutations in Chromatin Modifier and Ephrin Signaling Genes in Vein of Galen Malformation. Neuron 2018, 101: 429-443.e4. PMID: 30578106, PMCID: PMC10292091, DOI: 10.1016/j.neuron.2018.11.041.Peer-Reviewed Original ResearchConceptsChromatin modifiersVascular developmentSpecification of arteriesDeep venous systemNormal vascular developmentParent-offspring triosSignaling GenesGalen malformationDamaging mutationsGenesMutationsEssential roleArterio-venous malformationsCutaneous vascular abnormalitiesNovo mutationsExome sequencingDisease biologyIncomplete penetranceVariable expressivityVascular abnormalitiesVenous systemMutation carriersArterial bloodMutation burdenClinical implications
2017
GABBR2 mutations determine phenotype in rett syndrome and epileptic encephalopathy
Yoo Y, Jung J, Lee Y, Lee Y, Cho H, Na E, Hong J, Kim E, Lee JS, Lee JS, Hong C, Park S, Wie J, Miller K, Shur N, Clow C, Ebel RS, DeBrosse SD, Henderson LB, Willaert R, Castaldi C, Tikhonova I, Bilgüvar K, Mane S, Kim KJ, Hwang YS, Lee S, So I, Lim BC, Choi H, Seong JY, Shin YB, Jung H, Chae J, Choi M. GABBR2 mutations determine phenotype in rett syndrome and epileptic encephalopathy. Annals Of Neurology 2017, 82: 466-478. PMID: 28856709, DOI: 10.1002/ana.25032.Peer-Reviewed Original ResearchMeSH KeywordsExomeGenotypeHEK293 CellsHumansMethyl-CpG-Binding Protein 2MutationPhenotypeReceptors, GABA-BRett SyndromeSignal TransductionSpasms, InfantileConceptsRett syndromeGenetic factorsAppropriate medical interventionΓ-aminobutyric acid signalingDistinct diagnostic criteriaDevastating neurodevelopmental disorderWhole-exome sequencingAnn NeurolClinical featuresEE patientsEpileptic encephalopathyDe novo variantsNovel genetic factorsDiagnostic criteriaAnimal modelsMedical interventionsAccurate diagnosisReceptor activityReceptor functionSpecific molecular mechanismsPatientsRTT-like patientsNeurodevelopmental disordersNovo variantsMECP2 mutationsDe novo mutations in inhibitors of Wnt, BMP, and Ras/ERK signaling pathways in non-syndromic midline craniosynostosis
Timberlake AT, Furey CG, Choi J, Nelson-Williams C, Loring E, Galm A, Kahle K, Steinbacher D, Larysz D, Persing J, Lifton R, Bilguvar K, Mane S, Tikhonova I, Castaldi C, Knight J. De novo mutations in inhibitors of Wnt, BMP, and Ras/ERK signaling pathways in non-syndromic midline craniosynostosis. Proceedings Of The National Academy Of Sciences Of The United States Of America 2017, 114: e7341-e7347. PMID: 28808027, PMCID: PMC5584457, DOI: 10.1073/pnas.1709255114.Peer-Reviewed Original ResearchConceptsBone morphogenetic proteinRas/ERKDe novo mutationsNovo mutationsRas/ERK pathwayDamaging de novo mutationsHigh locus heterogeneityRare syndromic diseaseCommon risk variantsInhibitor of WntSyndromic craniosynostosesNew genesParent-offspring triosSyndromic diseaseMorphogenetic proteinsNegative regulatorERK pathwayMore cranial suturesGenesMidline craniosynostosisRisk variantsWntLocus heterogeneityMutationsExome sequencingIntegrated genomic analyses of de novo pathways underlying atypical meningiomas
Harmancı AS, Youngblood MW, Clark VE, Coşkun S, Henegariu O, Duran D, Erson-Omay EZ, Kaulen LD, Lee TI, Abraham BJ, Simon M, Krischek B, Timmer M, Goldbrunner R, Omay SB, Baranoski J, Baran B, Carrión-Grant G, Bai H, Mishra-Gorur K, Schramm J, Moliterno J, Vortmeyer AO, Bilgüvar K, Yasuno K, Young RA, Günel M. Integrated genomic analyses of de novo pathways underlying atypical meningiomas. Nature Communications 2017, 8: 14433. PMID: 28195122, PMCID: PMC5316884, DOI: 10.1038/ncomms14433.Peer-Reviewed Original ResearchMeSH KeywordsBinding SitesBrain NeoplasmsCell Transformation, NeoplasticChromosomal InstabilityCluster AnalysisDNA MethylationE2F2 Transcription FactorEnhancer of Zeste Homolog 2 ProteinEpigenomicsExomeForkhead Box Protein M1Gene Expression ProfilingGene Expression Regulation, NeoplasticGene Regulatory NetworksGene SilencingGenes, Neurofibromatosis 2GenomeGenomicsGenotyping TechniquesHuman Embryonic Stem CellsHumansJumonji Domain-Containing Histone DemethylasesMeningeal NeoplasmsMeningiomaMolecular Probe TechniquesMutationPhenotypePolycomb Repressive Complex 2Promoter Regions, GeneticRNA, MessengerSequence AnalysisSignal TransductionSMARCB1 ProteinTranscriptomeConceptsPolycomb repressive complex 2Human embryonic stem cellsRepressive complex 2Integrated genomic analysisEmbryonic stem cellsDe novo pathwayH3K27me3 signalsTranscriptional networksPRC2 complexEpigenomic analysisCellular statesCatalytic subunitGenomic analysisGenomic instabilityHypermethylated phenotypeGenomic landscapeNovo pathwayDisplay lossStem cellsPotential therapeutic targetExhibit upregulationPromoter mutationsTherapeutic targetMutationsComplexes 2
2016
Overlapping 16p13.11 deletion and gain of copies variations associated with childhood onset psychosis include genes with mechanistic implications for autism associated pathways: Two case reports
Brownstein CA, Kleiman RJ, Engle EC, Towne MC, D'Angelo EJ, Yu TW, Beggs AH, Picker J, Fogler JM, Carroll D, Schmitt RC, Wolff RR, Shen Y, Lip V, Bilguvar K, Kim A, Tembulkar S, O'Donnell K, Gonzalez-Heydrich J. Overlapping 16p13.11 deletion and gain of copies variations associated with childhood onset psychosis include genes with mechanistic implications for autism associated pathways: Two case reports. American Journal Of Medical Genetics Part A 2016, 170: 1165-1173. PMID: 26887912, PMCID: PMC4833544, DOI: 10.1002/ajmg.a.37595.Peer-Reviewed Original Research
2015
Functional Synergy between Cholecystokinin Receptors CCKAR and CCKBR in Mammalian Brain Development
Nishimura S, Bilgüvar K, Ishigame K, Sestan N, Günel M, Louvi A. Functional Synergy between Cholecystokinin Receptors CCKAR and CCKBR in Mammalian Brain Development. PLOS ONE 2015, 10: e0124295. PMID: 25875176, PMCID: PMC4398320, DOI: 10.1371/journal.pone.0124295.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAnimals, NewbornBone Morphogenetic Protein 7Cell MovementChemokine CXCL12CholecystokininCorpus CallosumEmbryo, MammalianGene Expression ProfilingGene Expression Regulation, DevelopmentalHomozygoteHumansInterneuronsMiceMice, KnockoutMidline Thalamic NucleiMutationNeocortexNeuropilin-2Receptor, Cholecystokinin AReceptor, Cholecystokinin BReceptors, N-Methyl-D-AspartateSignal TransductionTranscriptomeConceptsCCK receptorsBrain developmentMammalian neocortical developmentCentral nervous systemCortical interneuron migrationHomozygous mutant miceMammalian brain developmentPeripheral organsReceptor lossCorpus callosumCortical developmentPostnatal brainAbundant neuropeptideNervous systemInterneuron migrationMutant miceEmbryonic neocortexNeocortical developmentReceptorsPeptide hormonesG proteinsCholecystokininReciprocal expressionCCKBRBrainVascular Endothelial Growth Factor Receptor 3 Controls Neural Stem Cell Activation in Mice and Humans
Han J, Calvo CF, Kang TH, Baker KL, Park JH, Parras C, Levittas M, Birba U, Pibouin-Fragner L, Fragner P, Bilguvar K, Duman RS, Nurmi H, Alitalo K, Eichmann AC, Thomas JL. Vascular Endothelial Growth Factor Receptor 3 Controls Neural Stem Cell Activation in Mice and Humans. Cell Reports 2015, 10: 1158-1172. PMID: 25704818, PMCID: PMC4685253, DOI: 10.1016/j.celrep.2015.01.049.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell DifferentiationCell ProliferationCells, CulturedEmbryonic Stem CellsExtracellular Signal-Regulated MAP KinasesHippocampusHumansMiceMice, Inbred C57BLNeural Stem CellsNeurogenesisProto-Oncogene Proteins c-aktRecombinant ProteinsSignal TransductionVascular Endothelial Growth Factor CVascular Endothelial Growth Factor Receptor-3ConceptsHuman embryonic stem cellsNeural stem cellsVascular endothelial growth factor receptor 3Growth factor receptor 3NSC activationStem cellsProgenitor cellsAdult hippocampal neural stem cellsEmbryonic stem cellsNeural stem cell activationStem cell activationQuiescent neural stem cellsNeural progenitor cellsCell fateReceptor 3Specific regulatorsAdult mammalian hippocampusMolecular mechanismsCell cycleHippocampal neural stem cellsLigand VEGFERK pathwayConditional deletionNew neuronsVEGFR3
2011
Rare Copy Number Variants in Tourette Syndrome Disrupt Genes in Histaminergic Pathways and Overlap with Autism
Fernandez TV, Sanders SJ, Yurkiewicz IR, Ercan-Sencicek AG, Kim YS, Fishman DO, Raubeson MJ, Song Y, Yasuno K, Ho WS, Bilguvar K, Glessner J, Chu SH, Leckman JF, King RA, Gilbert DL, Heiman GA, Tischfield JA, Hoekstra PJ, Devlin B, Hakonarson H, Mane SM, Günel M, State MW. Rare Copy Number Variants in Tourette Syndrome Disrupt Genes in Histaminergic Pathways and Overlap with Autism. Biological Psychiatry 2011, 71: 392-402. PMID: 22169095, PMCID: PMC3282144, DOI: 10.1016/j.biopsych.2011.09.034.Peer-Reviewed Original ResearchConceptsCopy number variationsRare copy number variationsNovel risk regionsEnrichment of genesGamma-aminobutyric acid receptor genesNervous system developmentEtiology of TSParent-child triosRare copy number variantsCopy number variantsGene mappingPathway analysisDe novo eventsAxon guidanceCell adhesionMolecular pathwaysNumber variationsRelevant pathwaysCNV analysisNumber variantsGenesReceptor geneDe novoNovo eventsPathway