2017
Integrated 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
Mutational landscape of uterine and ovarian carcinosarcomas implicates histone genes in epithelial–mesenchymal transition
Zhao S, Bellone S, Lopez S, Thakral D, Schwab C, English DP, Black J, Cocco E, Choi J, Zammataro L, Predolini F, Bonazzoli E, Bi M, Buza N, Hui P, Wong S, Abu-Khalaf M, Ravaggi A, Bignotti E, Bandiera E, Romani C, Todeschini P, Tassi R, Zanotti L, Odicino F, Pecorelli S, Donzelli C, Ardighieri L, Facchetti F, Falchetti M, Silasi DA, Ratner E, Azodi M, Schwartz PE, Mane S, Angioli R, Terranova C, Quick CM, Edraki B, Bilgüvar K, Lee M, Choi M, Stiegler AL, Boggon TJ, Schlessinger J, Lifton RP, Santin AD. Mutational landscape of uterine and ovarian carcinosarcomas implicates histone genes in epithelial–mesenchymal transition. Proceedings Of The National Academy Of Sciences Of The United States Of America 2016, 113: 12238-12243. PMID: 27791010, PMCID: PMC5087050, DOI: 10.1073/pnas.1614120113.Peer-Reviewed Original ResearchMeSH KeywordsAgedAged, 80 and overCarcinosarcomaClass I Phosphatidylinositol 3-KinasesDNA-Binding ProteinsEpithelial-Mesenchymal TransitionFemaleGene Expression Regulation, NeoplasticHistonesHumansMiddle AgedMutationOvarian NeoplasmsPTEN PhosphohydrolaseTelomeraseTumor Suppressor Protein p53Uterine NeoplasmsConceptsEpithelial-mesenchymal transitionWhole-exome sequencingHistone gene clusterMutational landscapeStable transgenic expressionExcess of mutationsMultiregion whole-exome sequencingHistone genesEvolutionary historyPhylogenetic relationshipsGene clusterHistone H2AChromosome segmentsSeparate lineagesCancer genesGenetic landscapeUterine serous carcinoma cell linesTransgenic expressionGenesCarcinoma cell linesGene TP53Frequent amplificationFrequent deletionsChromosome 6pInvasive propertiesRecurrent somatic mutations in POLR2A define a distinct subset of meningiomas
Clark VE, Harmancı AS, Bai H, Youngblood MW, Lee TI, Baranoski JF, Ercan-Sencicek AG, Abraham BJ, Weintraub AS, Hnisz D, Simon M, Krischek B, Erson-Omay EZ, Henegariu O, Carrión-Grant G, Mishra-Gorur K, Durán D, Goldmann JE, Schramm J, Goldbrunner R, Piepmeier JM, Vortmeyer AO, Günel JM, Bilgüvar K, Yasuno K, Young RA, Günel M. Recurrent somatic mutations in POLR2A define a distinct subset of meningiomas. Nature Genetics 2016, 48: 1253-1259. PMID: 27548314, PMCID: PMC5114141, DOI: 10.1038/ng.3651.Peer-Reviewed Original ResearchCatalytic DomainChromosomes, Human, Pair 22Cohort StudiesDNA Mutational AnalysisEnhancer Elements, GeneticExomeGene Expression Regulation, NeoplasticGenotypeHumansKruppel-Like Factor 4Kruppel-Like Transcription FactorsMeningeal NeoplasmsMeningiomaMutationNeurofibromin 2RNA Polymerase IITumor Necrosis Factor Receptor-Associated Peptides and Proteins
2015
Integrated genomic characterization of IDH1-mutant glioma malignant progression
Bai H, Harmancı AS, Erson-Omay EZ, Li J, Coşkun S, Simon M, Krischek B, Özduman K, Omay SB, Sorensen EA, Turcan Ş, Bakırcığlu M, Carrión-Grant G, Murray PB, Clark VE, Ercan-Sencicek AG, Knight J, Sencar L, Altınok S, Kaulen LD, Gülez B, Timmer M, Schramm J, Mishra-Gorur K, Henegariu O, Moliterno J, Louvi A, Chan TA, Tannheimer SL, Pamir MN, Vortmeyer AO, Bilguvar K, Yasuno K, Günel M. Integrated genomic characterization of IDH1-mutant glioma malignant progression. Nature Genetics 2015, 48: 59-66. PMID: 26618343, PMCID: PMC4829945, DOI: 10.1038/ng.3457.Peer-Reviewed Original ResearchConceptsDevelopmental transcription factorsActivation of MYCMalignant progressionGenomic approachesPI3K pathwayGlioma malignant progressionEpigenetic silencingIDH1 mutant gliomasTranscription factorsIntegrated genomic characterizationGenomic characterizationRTK-RASOncogenic pathwaysK pathwayClonal expansionPathwaySilencingMYCProgressionAbsence of KMT2D/MLL2 mutations in abdominal paraganglioma
Stenman A, Juhlin CC, Haglund F, Brown TC, Clark VE, Svahn F, Bilguvar K, Goh G, Korah R, Lifton RP, Carling T. Absence of KMT2D/MLL2 mutations in abdominal paraganglioma. Clinical Endocrinology 2015, 84: 632-634. PMID: 26303934, DOI: 10.1111/cen.12884.Peer-Reviewed Original ResearchAbdominal NeoplasmsDNA-Binding ProteinsGene Expression Regulation, NeoplasticHumansImmunohistochemistryMutationNeoplasm ProteinsParagangliomaReverse Transcriptase Polymerase Chain ReactionSomatic V600E BRAF Mutation in Linear and Sporadic Syringocystadenoma Papilliferum
Levinsohn JL, Sugarman JL, Bilguvar K, McNiff JM, Choate K, Genomics T. Somatic V600E BRAF Mutation in Linear and Sporadic Syringocystadenoma Papilliferum. Journal Of Investigative Dermatology 2015, 135: 2536-2538. PMID: 25950823, PMCID: PMC4567902, DOI: 10.1038/jid.2015.180.Peer-Reviewed Original ResearchBiopsy, NeedleChildCystadenomaFemaleGene Expression Regulation, NeoplasticHumansImmunohistochemistryMutationProto-Oncogene Proteins B-rafSweat Gland NeoplasmsSyringoma