2024
Genome-Wide Association Studies of 3 Distinct Recovery Phenotypes in Mild Ischemic Stroke
Aldridge C, Braun R, Lohse K, de Havenon A, Cole J, Cramer S, Lindgren A, Keene K, Hsu F, Worrall B. Genome-Wide Association Studies of 3 Distinct Recovery Phenotypes in Mild Ischemic Stroke. Neurology 2024, 102: e208011. PMID: 38181310, PMCID: PMC11023036, DOI: 10.1212/wnl.0000000000208011.Peer-Reviewed Original ResearchAgedATP-Binding Cassette TransportersFemaleGenome-Wide Association StudyHumansIschemic StrokeJumonji Domain-Containing Histone DemethylasesMaleNerve Tissue ProteinsPhenotypeReceptors, ImmunologicStroke
2023
Primary complex motor stereotypies are associated with de novo damaging DNA coding mutations that identify KDM5B as a risk gene
Fernandez T, Williams Z, Kline T, Rajendran S, Augustine F, Wright N, Sullivan C, Olfson E, Abdallah S, Liu W, Hoffman E, Gupta A, Singer H. Primary complex motor stereotypies are associated with de novo damaging DNA coding mutations that identify KDM5B as a risk gene. PLOS ONE 2023, 18: e0291978. PMID: 37788244, PMCID: PMC10547198, DOI: 10.1371/journal.pone.0291978.Peer-Reviewed Original ResearchMeSH KeywordsAutism Spectrum DisorderDNAExome SequencingGenetic Predisposition to DiseaseHumansJumonji Domain-Containing Histone DemethylasesMutationNuclear ProteinsRepressor ProteinsTourette SyndromeConceptsRisk genesDe novo damaging variantsGene expression patternsWhole-exome DNA sequencingMid-fetal developmentAdditional risk genesHigh-confidence risk genesParent-child triosGene OntologyCell signalingExpression patternsCalcium ion transportFunctional convergenceCell cycleDamaging variantsGenesDNA sequencingDe novoASD probandsGenetic etiologyBiological mechanismsSequencingDNANetwork analysisIon transport
2022
Targeting Krebs-cycle-deficient renal cell carcinoma with Poly ADP-ribose polymerase inhibitors and low-dose alkylating chemotherapy
Ueno D, Vasquez JC, Sule A, Liang J, van Doorn J, Sundaram R, Friedman S, Caliliw R, Ohtake S, Bao X, Li J, Ye H, Boyd K, Huang RR, Dodson J, Boutros P, Bindra RS, Shuch B. Targeting Krebs-cycle-deficient renal cell carcinoma with Poly ADP-ribose polymerase inhibitors and low-dose alkylating chemotherapy. Oncotarget 2022, 13: 1054-1067. PMID: 36128328, PMCID: PMC9477221, DOI: 10.18632/oncotarget.28273.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine Diphosphate RiboseAnimalsCarcinoma, Renal CellCitric Acid CycleDioxygenasesDNAFumarate HydrataseFumaratesHumansJumonji Domain-Containing Histone DemethylasesKidney NeoplasmsLysineMicePoly (ADP-Ribose) Polymerase-1Poly(ADP-ribose) Polymerase InhibitorsSuccinate DehydrogenaseSuccinatesTemozolomideConceptsRenal cell carcinomaPoly ADP-ribose polymerase inhibitorsADP-ribose polymerase inhibitorsCell carcinomaSDH-deficient renal cell carcinomaPolymerase inhibitorsLow-dose temozolomideAggressive renal cell carcinomaHereditary cancer syndromesNovel therapeutic strategiesDeficient murine modelStandard dosingTMZ resultsMurine modelTherapeutic strategiesCombination treatmentCancer syndromesTumor growthHomologous recombination DNA repair pathwayAccumulation of fumarateHR deficiencyPARP inhibitionTemozolomideChemotherapyCarcinoma
2021
KDM5B promotes immune evasion by recruiting SETDB1 to silence retroelements
Zhang SM, Cai WL, Liu X, Thakral D, Luo J, Chan LH, McGeary MK, Song E, Blenman KRM, Micevic G, Jessel S, Zhang Y, Yin M, Booth CJ, Jilaveanu LB, Damsky W, Sznol M, Kluger HM, Iwasaki A, Bosenberg MW, Yan Q. KDM5B promotes immune evasion by recruiting SETDB1 to silence retroelements. Nature 2021, 598: 682-687. PMID: 34671158, PMCID: PMC8555464, DOI: 10.1038/s41586-021-03994-2.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell Line, TumorDNA-Binding ProteinsEpigenesis, GeneticGene SilencingHeterochromatinHistone-Lysine N-MethyltransferaseHumansInterferon Type IJumonji Domain-Containing Histone DemethylasesMaleMelanomaMiceMice, Inbred C57BLMice, KnockoutNuclear ProteinsRepressor ProteinsRetroelementsTumor EscapeConceptsImmune checkpoint blockadeImmune evasionCheckpoint blockadeImmune responseAnti-tumor immune responseRobust adaptive immune responseTumor immune evasionAnti-tumor immunityAdaptive immune responsesType I interferon responseDNA-sensing pathwayMouse melanoma modelImmunotherapy resistanceMost patientsCurrent immunotherapiesTumor immunogenicityImmune memoryMelanoma modelCytosolic RNA sensingRole of KDM5BConsiderable efficacyInterferon responseImmunotherapyEpigenetic therapyBlockadeA microProtein repressor complex in the shoot meristem controls the transition to flowering
Rodrigues VL, Dolde U, Sun B, Blaakmeer A, Straub D, Eguen T, Botterweg-Paredes E, Hong S, Graeff M, Li MW, Gendron JM, Wenkel S. A microProtein repressor complex in the shoot meristem controls the transition to flowering. Plant Physiology 2021, 187: 187-202. PMID: 34015131, PMCID: PMC8418433, DOI: 10.1093/plphys/kiab235.Peer-Reviewed Original ResearchMeSH KeywordsArabidopsisArabidopsis ProteinsFlorigenFlowersJumonji Domain-Containing Histone DemethylasesMeristemConceptsShoot apical meristemEarly flowering phenotypeGenetic suppressor screenPost-translational regulatorFloral repressionSuppressor screenChromatin modificationsFloral transitionFloral meristemRepressive complexesShoot meristemRepressor complexGenetic interactionsApical meristemCONSTANSEarly floweringShoot apexUndifferentiated stateJMJ14Sequencing studiesMeristemAdditional roleSum1MicroproteinsPlants
2020
Oncometabolites suppress DNA repair by disrupting local chromatin signalling
Sulkowski PL, Oeck S, Dow J, Economos NG, Mirfakhraie L, Liu Y, Noronha K, Bao X, Li J, Shuch BM, King MC, Bindra RS, Glazer PM. Oncometabolites suppress DNA repair by disrupting local chromatin signalling. Nature 2020, 582: 586-591. PMID: 32494005, PMCID: PMC7319896, DOI: 10.1038/s41586-020-2363-0.Peer-Reviewed Original ResearchMeSH KeywordsAtaxia Telangiectasia Mutated ProteinsCell Line, TumorChromatinDNA BreaksDNA RepairHomologous RecombinationHumansJumonji Domain-Containing Histone DemethylasesLysine Acetyltransferase 5MethylationNeoplasmsPoly(ADP-ribose) Polymerase InhibitorsSignal TransductionConceptsDNA repairDNA breaksFumarate hydrataseDownstream repair factorsHistone 3 lysine 9Homology-dependent repairPoly (ADP-ribose) polymeraseRecruitment of TIP60Deregulation of metabolismChromatin signalingSuccinate dehydrogenase genesGenome integrityLysine 9Repair factorsDehydrogenase geneEnd resectionIsocitrate dehydrogenase 1Aberrant hypermethylationMechanistic basisSomatic mutationsDehydrogenase 1GenesHuman malignanciesProper executionMutations
2019
KDM5B Promotes Drug Resistance by Regulating Melanoma Propagating Cell Subpopulations
Liu X, Zhang SM, McGeary MK, Krykbaeva I, Lai L, Jansen DJ, Kales SC, Simeonov A, Hall MD, Kelly DP, Bosenberg MW, Yan Q. KDM5B Promotes Drug Resistance by Regulating Melanoma Propagating Cell Subpopulations. Molecular Cancer Therapeutics 2019, 18: molcanther.0395.2018. PMID: 30523048, PMCID: PMC6397704, DOI: 10.1158/1535-7163.mct-18-0395.Peer-Reviewed Original Research
2018
KDM5 histone demethylases repress immune response via suppression of STING
Wu L, Cao J, Cai WL, Lang SM, Horton JR, Jansen DJ, Liu ZZ, Chen JF, Zhang M, Mott BT, Pohida K, Rai G, Kales SC, Henderson MJ, Hu X, Jadhav A, Maloney DJ, Simeonov A, Zhu S, Iwasaki A, Hall MD, Cheng X, Shadel GS, Yan Q. KDM5 histone demethylases repress immune response via suppression of STING. PLOS Biology 2018, 16: e2006134. PMID: 30080846, PMCID: PMC6095604, DOI: 10.1371/journal.pbio.2006134.Peer-Reviewed Original ResearchMeSH KeywordsCell LineCytosolDNAHistone DemethylasesHistone MethyltransferasesHistonesHumansImmunity, InnateImmunotherapyInterferonsJumonji Domain-Containing Histone DemethylasesMCF-7 CellsMembrane ProteinsNuclear ProteinsRepressor ProteinsSignal TransductionConceptsImmune responseSTING expressionCyclic GMP-AMP synthase stimulatorSuppression of STINGCancer cellsCancer immunotherapy agentsHuman papilloma virusAdaptive immune responsesMultiple clinical trialsExpression of STINGBreast cancer cellsInnate immune defenseRobust interferon responseMultiple cancer typesIntratumoral CD8Immunotherapy agentsAnticancer immunotherapyPatient survivalNeck cancerPapilloma virusClinical trialsT cellsSTING agonistsKDM5 histonePositive headA Non-canonical BCOR-PRC1.1 Complex Represses Differentiation Programs in Human ESCs
Wang Z, Gearhart MD, Lee YW, Kumar I, Ramazanov B, Zhang Y, Hernandez C, Lu AY, Neuenkirchen N, Deng J, Jin J, Kluger Y, Neubert TA, Bardwell VJ, Ivanova NB. A Non-canonical BCOR-PRC1.1 Complex Represses Differentiation Programs in Human ESCs. Cell Stem Cell 2018, 22: 235-251.e9. PMID: 29337181, PMCID: PMC5797497, DOI: 10.1016/j.stem.2017.12.002.Peer-Reviewed Original ResearchMeSH KeywordsCell DifferentiationChromatinF-Box ProteinsHistonesHuman Embryonic Stem CellsHumansJumonji Domain-Containing Histone DemethylasesLysineMethylationMultiprotein ComplexesPolycomb Repressive Complex 1Polycomb Repressive Complex 2Promoter Regions, GeneticProtein DomainsProto-Oncogene ProteinsRepressor ProteinsConceptsEmbryonic stem cellsHuman embryonic stem cellsPolycomb domainsNon-canonical PRC1 complexesKey developmental lociNon-canonical complexesPolycomb group (PcG) proteinsE3 ubiquitin ligasesStem cell systemInitiation of differentiationDevelopmental lociPRC1 complexesRepressive chromatinRepressor functionPRC1.1 complexMesoderm lineageGroup proteinsCo-repressorAccessory subunitsDifferentiation programCanonical complexDevelopmental systemsC-terminusGene targetsN-terminus
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
KDM5 lysine demethylases are involved in maintenance of 3′UTR length
Blair LP, Liu Z, Labitigan RL, Wu L, Zheng D, Xia Z, Pearson EL, Nazeer FI, Cao J, Lang SM, Rines RJ, Mackintosh SG, Moore CL, Li W, Tian B, Tackett AJ, Yan Q. KDM5 lysine demethylases are involved in maintenance of 3′UTR length. Science Advances 2016, 2: e1501662. PMID: 28138513, PMCID: PMC5262454, DOI: 10.1126/sciadv.1501662.Peer-Reviewed Original ResearchMeSH Keywords3' Untranslated RegionsBreast NeoplasmsCyclin D1DEAD-box RNA HelicasesFemaleHumansJumonji Domain-Containing Histone DemethylasesMCF-7 CellsNeoplasm ProteinsNuclear ProteinsRepressor ProteinsRetinoblastoma-Binding Protein 2Ribonuclease IIISaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsConceptsAlternative mRNA formsLysine demethylasesLysine demethylasePolyadenylation sitesJhd2Novel roleProcessing machineryKDM5B expressionMRNA formsBreast cancer cellsDemethylasesTargetable mechanismHuman breast tumor tissuesKDM5BProtein expressionCancer cellsKDM5AGenesCritical roleBreast tumor tissuesCellsExpressionChromatinSaccharomycesDemethylase
2015
Polymorphisms in genes in the androgen pathway and risk of Barrett's esophagus and esophageal adenocarcinoma
Ek WE, Lagergren K, Cook M, Wu AH, Abnet CC, Levine D, Chow W, Bernstein L, Risch HA, Shaheen NJ, Bird NC, Corley DA, Hardie LJ, Fitzgerald RC, Gammon MD, Romero Y, Liu G, Ye W, Vaughan TL, MacGregor S, Whiteman DC, Westberg L, Lagergren J. Polymorphisms in genes in the androgen pathway and risk of Barrett's esophagus and esophageal adenocarcinoma. International Journal Of Cancer 2015, 138: 1146-1152. PMID: 26414697, PMCID: PMC4715576, DOI: 10.1002/ijc.29863.Peer-Reviewed Original ResearchMeSH KeywordsAdenocarcinomaAdultAgedBarrett EsophagusEsophageal NeoplasmsFemaleGenetic Predisposition to DiseaseHumansJumonji Domain-Containing Histone DemethylasesMaleMiddle AgedOxidoreductases, N-DemethylatingPolymorphism, Single NucleotideRiskSteroid 17-alpha-HydroxylaseConceptsRisk of BEBarrett's esophagusEsophageal adenocarcinomaSingle nucleotide polymorphismsAndrogen pathwayRisk of EACStrong male predominanceBody mass indexMale predominanceTobacco smokingTobacco smokersBE patientsHip ratioEAC patientsSex hormonesReflux statusLarger sample sizeEsophagusInfluence riskGenetic epidemiological analysisPatientsControl participantsAdenocarcinomaRiskGenetic variants
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