2025
Epigenetic therapy sensitizes anti–PD-1 refractory head and neck cancers to immunotherapy rechallenge
Qin T, Mattox A, Campbell J, Park J, Shin K, Li S, Sadow P, Faquin W, Micevic G, Daniels A, Haddad R, Garris C, Pittet M, Mempel T, ONeill A, Sartor M, Pai S. Epigenetic therapy sensitizes anti–PD-1 refractory head and neck cancers to immunotherapy rechallenge. Journal Of Clinical Investigation 2025, 135: e181671. PMID: 40091844, PMCID: PMC11910227, DOI: 10.1172/jci181671.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAntibodies, MonoclonalAntibodies, Monoclonal, HumanizedAntineoplastic Combined Chemotherapy ProtocolsAzacitidineB7-H1 AntigenEpigenesis, GeneticFemaleHead and Neck NeoplasmsHumansImmune Checkpoint InhibitorsImmunotherapyMaleMiddle AgedProgrammed Cell Death 1 ReceptorSquamous Cell Carcinoma of Head and NeckTumor MicroenvironmentConceptsHead and neck squamous cell carcinomaTumor microenvironmentProlonged OSOverall survivalIFN-gCD8+ T cell infiltrationCD4+ T regulatory cellsOn-treatment tumor biopsiesNeck squamous cell carcinomaSystemic host immune responseBackgroundImmune checkpoint blockadeMetastatic (R/MMedian overall survivalPD-L1 expressionT cell infiltrationLocal tumor microenvironmentT regulatory cellsSquamous cell carcinomaBiologically effective dosePhase 1b clinical trialHost immune responseCheckpoint blockadeOS ratesPD-L1Tumor biopsiesEpigenomic pathways from racism to preterm birth: secondary analysis of the Nulliparous Pregnancy Outcomes Study: monitoring Mothers-to-be (nuMoM2b) cohort study in the USA to examine how DNA methylation mediates the relationship between multilevel racism and preterm birth in black women: a study protocol
Barcelona V, Ray M, Zhao Y, Samari G, Wu H, Reho P, McNeil R, Reddy U. Epigenomic pathways from racism to preterm birth: secondary analysis of the Nulliparous Pregnancy Outcomes Study: monitoring Mothers-to-be (nuMoM2b) cohort study in the USA to examine how DNA methylation mediates the relationship between multilevel racism and preterm birth in black women: a study protocol. BMJ Open 2025, 15: e091801. PMID: 40037666, PMCID: PMC11881185, DOI: 10.1136/bmjopen-2024-091801.Peer-Reviewed Original ResearchConceptsNulliparous Pregnancy Outcomes StudyMonitoring Mothers-to-BeMothers-to-beBlack womenPregnancy Outcomes StudyParticipants' electronic health recordsPreterm birthSecondary analysisCohort studyGeocoded participant addressesSecondary analysis of dataStudy protocolElectronic health recordsStructural racism measuresUniversity Institutional Review BoardEffects of individual-Black pregnant womenOutcome studiesRacial residential segregationProspective cohort studyPregnancy-related morbidityParticipant's addressHealth recordsAdverse pregnancy outcomesWhite womenEpigenetic signatures of intergenerational exposure to violence in three generations of Syrian refugees
Mulligan C, Quinn E, Hamadmad D, Dutton C, Nevell L, Binder A, Panter-Brick C, Dajani R. Epigenetic signatures of intergenerational exposure to violence in three generations of Syrian refugees. Scientific Reports 2025, 15: 5945. PMID: 40016245, PMCID: PMC11868390, DOI: 10.1038/s41598-025-89818-z.Peer-Reviewed Original ResearchConceptsSyrian refugeesExposure to violenceWar-related violenceExposed to violenceExposure to warAdult health outcomesViolenceIntergenerational exposureSurvey dataRefugeesHealth outcomesEpigenome-wide association studiesTrauma effectsInfluence infantsImpact future generationsEpigenetic age accelerationFuture generationsMothersAssociated with germlineMaternal traumaFamilyAssociation studiesPregnant mothersWarDNA methylationEpigenetic age acceleration in idiopathic pulmonary fibrosis revealed by DNA methylation clocks
Kurbanov D, Ahangari F, Adams T, De Man R, Tang J, Carlon M, Abu Hussein N, Cortesi E, Zapata M, De Sadelaar L, Wuyts W, Vanaudenaerde B, Kaminski N, McDonough J. Epigenetic age acceleration in idiopathic pulmonary fibrosis revealed by DNA methylation clocks. American Journal Of Physiology - Lung Cellular And Molecular Physiology 2025, 328: l456-l462. PMID: 39970931, DOI: 10.1152/ajplung.00171.2024.Peer-Reviewed Original ResearchMeSH KeywordsAgedAgingDNA MethylationEpigenesis, GeneticFemaleHumansIdiopathic Pulmonary FibrosisLungMaleMiddle AgedConceptsIdiopathic pulmonary fibrosisIdiopathic pulmonary fibrosis tissuePulmonary fibrosisLung tissueEpigenetic clocksPotential of DNA methylationDNA methylation levelsDebilitating lung diseaseIllumina MethylationEPIC arrayHuman lung tissueEpigenetic ageDNA methylation clocksBiological ageAffected lung tissueIPF casesClinical prognosisMethylation patternsDNA methylationLung diseaseHealthy controlsAcceleration of biological agingMethylation levelsMethylationEPIC arrayAge accelerationClinical assessmentBidirectional relationship between epigenetic age and stroke, dementia, and late-life depression
Rivier C, Szejko N, Renedo D, Clocchiatti-Tuozzo S, Huo S, de Havenon A, Zhao H, Gill T, Sheth K, Falcone G. Bidirectional relationship between epigenetic age and stroke, dementia, and late-life depression. Nature Communications 2025, 16: 1261. PMID: 39893209, PMCID: PMC11787333, DOI: 10.1038/s41467-024-54721-0.Peer-Reviewed Original ResearchThis study shows a bidirectional link between accelerated epigenetic aging and brain health events like stroke, dementia, and depression, supporting new prevention strategies for aging-related conditions.Impact of age-related changes in buccal epithelial cells on pediatric epigenetic biomarker research
Merrill S, Konwar C, Fatima F, Dever K, MacIsaac J, Letourneau N, Giesbrecht G, Dewey D, England-Mason G, Lewis C, Wang D, Teh A, Meaney M, Gonzalez A, Noll J, De Weerth C, Bush N, O’Donnell K, Stewart S, Kobor M. Impact of age-related changes in buccal epithelial cells on pediatric epigenetic biomarker research. Nature Communications 2025, 16: 609. PMID: 39800776, PMCID: PMC11725590, DOI: 10.1038/s41467-025-55909-8.Peer-Reviewed Original ResearchConceptsBuccal epithelial cellsAge-related changesObsessive-compulsive disorderEpithelial cellsDiurnal cortisol slopeCheek swabsImpact of age-related changesCortisol slopeAssociated with ageOral cellsDevelopmental rangeAge accelerationDNA methylation studiesHeterogeneous sampleNeutrophil proportionBiomarker researchMethylation studiesAgeSwabsWeak associationEpigenetic age
2024
Epigenome-wide association studies identify novel DNA methylation sites associated with PTSD: a meta-analysis of 23 military and civilian cohorts
Katrinli S, Wani A, Maihofer A, Ratanatharathorn A, Daskalakis N, Montalvo-Ortiz J, Núñez-Ríos D, Zannas A, Zhao X, Aiello A, Ashley-Koch A, Avetyan D, Baker D, Beckham J, Boks M, Brick L, Bromet E, Champagne F, Chen C, Dalvie S, Dennis M, Fatumo S, Fortier C, Galea S, Garrett M, Geuze E, Grant G, Hauser M, Hayes J, Hemmings S, Huber B, Jajoo A, Jansen S, Kessler R, Kimbrel N, King A, Kleinman J, Koen N, Koenen K, Kuan P, Liberzon I, Linnstaedt S, Lori A, Luft B, Luykx J, Marx C, McLean S, Mehta D, Milberg W, Miller M, Mufford M, Musanabaganwa C, Mutabaruka J, Mutesa L, Nemeroff C, Nugent N, Orcutt H, Qin X, Rauch S, Ressler K, Risbrough V, Rutembesa E, Rutten B, Seedat S, Stein D, Stein M, Toikumo S, Ursano R, Uwineza A, Verfaellie M, Vermetten E, Vinkers C, Ware E, Wildman D, Wolf E, Young R, Zhao Y, van den Heuvel L, Uddin M, Nievergelt C, Smith A, Logue M. Epigenome-wide association studies identify novel DNA methylation sites associated with PTSD: a meta-analysis of 23 military and civilian cohorts. Genome Medicine 2024, 16: 147. PMID: 39696436, PMCID: PMC11658418, DOI: 10.1186/s13073-024-01417-1.Peer-Reviewed Original ResearchConceptsEpigenome-wide association studiesDNA methylationPsychiatric Genomics ConsortiumPost-traumatic stress disorderAssociation studiesMeta-analysis of epigenome-wide association studiesMethylation levelsGenome-wide expression dataEpigenetic gene regulationBrain regionsPGC-PTSDAnnotated genesBlood cell proportionsCpG lociGene regulationSusceptibility to post-traumatic stress disorderExpression dataAssociated with post-traumatic stress disorderIllumina HumanMethylation450Genomics ConsortiumOccurrence of post-traumatic stress disorderAssociated with biological differencesCpGMultiple brain regionsPostmortem brain samplesX-linked deletion of Crossfirre, Firre, and Dxz4 in vivo uncovers diverse phenotypes and combinatorial effects on autosomes
Hasenbein T, Hoelzl S, Smith Z, Gerhardinger C, Gonner M, Aguilar-Pimentel A, Amarie O, Becker L, Calzada-Wack J, Dragano N, da Silva-Buttkus P, Garrett L, Hölter S, Kraiger M, Östereicher M, Rathkolb B, Sanz-Moreno A, Spielmann N, Wurst W, Gailus-Durner V, Fuchs H, Hrabě de Angelis M, Meissner A, Engelhardt S, Rinn J, Andergassen D. X-linked deletion of Crossfirre, Firre, and Dxz4 in vivo uncovers diverse phenotypes and combinatorial effects on autosomes. Nature Communications 2024, 15: 10631. PMID: 39638999, PMCID: PMC11621363, DOI: 10.1038/s41467-024-54673-5.Peer-Reviewed Original ResearchConceptsAutosomal gene regulationRegions genome-wideAllele-specific analysisSex-specific lociLoci in vivoX-linked genesRandom X-chromosome inactivationX-chromosome inactivationSex-specific phenotypesFirre locusGenome-wideIn vivo roleChromatin structureGene regulationX chromosomeEpigenetic featuresDXZ4Epigenetic profilesKnockout studiesLociDiverse phenotypesLncRNA FIRREFunctional roleCombinatorial effectsFIRREEpigenetics-targeted drugs: current paradigms and future challenges
Dai W, Qiao X, Fang Y, Guo R, Bai P, Liu S, Li T, Jiang Y, Wei S, Na Z, Xiao X, Li D. Epigenetics-targeted drugs: current paradigms and future challenges. Signal Transduction And Targeted Therapy 2024, 9: 332. PMID: 39592582, PMCID: PMC11627502, DOI: 10.1038/s41392-024-02039-0.Peer-Reviewed Original ResearchConceptsNon-coding RNA regulationDNA base sequenceRNA modificationsRNA regulationChromatin remodelingHistone modificationsEnhancer of zeste homolog 2Epigenetic landscapeGenetic informationOrganismal developmentDNA methyltransferasesEpigenetic enzymesDNA modificationsBase sequenceHomolog 2Zeste homolog 2Histone deacetylasesHuman diseasesIsocitrate dehydrogenaseDNAPathological contextsRegulatory systemChromatinEnzymeHistoneA multi-trait epigenome-wide association study identified DNA methylation signature of inflammation among men with HIV
Chen J, Hui Q, Titanji B, So-Armah K, Freiberg M, Justice A, Xu K, Zhu X, Gwinn M, Marconi V, Sun Y. A multi-trait epigenome-wide association study identified DNA methylation signature of inflammation among men with HIV. Clinical Epigenetics 2024, 16: 152. PMID: 39488703, PMCID: PMC11531128, DOI: 10.1186/s13148-024-01763-2.Peer-Reviewed Original ResearchConceptsEpigenome-wide association studiesDNA methylationAssociation studiesDNAm sitesDNA methylation sitesAssociated with DNA methylationDNA methylation signaturesInflammatory markersResponse to virusesImmune response to virusesVeterans Aging Cohort StudySignatures of inflammationGenesIdentified sitesAging Cohort StudyInflammation-related genesPathwayPersistent inflammationMale PWHCohort studyExcess morbidityPWHStudy populationInflammationStatistical powerMulti-omics profiling of DNA methylation and gene expression alterations in human cocaine use disorder
Zillich E, Belschner H, Avetyan D, Andrade-Brito D, Martínez-Magaña J, Frank J, Mechawar N, Turecki G, Cabana-Domínguez J, Fernàndez-Castillo N, Cormand B, Montalvo-Ortiz J, Nöthen M, Hansson A, Rietschel M, Spanagel R, Witt S, Zillich L. Multi-omics profiling of DNA methylation and gene expression alterations in human cocaine use disorder. Translational Psychiatry 2024, 14: 428. PMID: 39384764, PMCID: PMC11464785, DOI: 10.1038/s41398-024-03139-9.Peer-Reviewed Original ResearchConceptsCocaine use disorderUse disorderAlternative splicingHuman prefrontal cortexProfiling of DNA methylationBrodmann area 9Differential alternative splicingDeregulated biological processesPostmortem brain tissueMulti-omics approachCocaine intakeMulti-omics studiesPrefrontal cortexBrain alterationsMulti-omics profilingGene expression alterationsArea 9Fatty acid metabolismReceptor-targeting drugsSpliced transcriptsEpigenome-wideDNA methylationNeuronal morphogenesisAS changesDrug repositioning analysisHuman genetics and epigenetics of alcohol use disorder
Zhou H, Gelernter J. Human genetics and epigenetics of alcohol use disorder. Journal Of Clinical Investigation 2024, 134: e172885. PMID: 39145449, PMCID: PMC11324314, DOI: 10.1172/jci172885.Peer-Reviewed Original ResearchMeSH KeywordsAlcoholismEpigenesis, GeneticGenetic Predisposition to DiseaseGenome-Wide Association StudyHumansConceptsEpigenome-wide association studiesEWAS studiesPower of GWASTranscriptome-wide associationGenome-wide scanAlcohol use disorderWhole-genome sequencingDrug-gene interactionsSingle-cell sequencingAssociation studiesDownstream analysisHuman geneticsGenetic variantsEpigenetic risk factorsVariant functionEpigenetic changesSpatial transcriptomicsUse disorderEpigeneticsDisease risk predictionGenetic correlationsDiversity of populationGeneticsComplex etiologyEnvironmental factorsMaternal Adverse Childhood Experiences and Biological Aging During Pregnancy and in Newborns
Dye C, Alschuler D, Wu H, Duarte C, Monk C, Belsky D, Lee S, O’Donnell K, Baccarelli A, Scorza P. Maternal Adverse Childhood Experiences and Biological Aging During Pregnancy and in Newborns. JAMA Network Open 2024, 7: e2427063. PMID: 39120899, PMCID: PMC11316241, DOI: 10.1001/jamanetworkopen.2024.27063.Peer-Reviewed Original ResearchConceptsMaternal adverse childhood experiencesAdverse childhood experiencesEdinburgh Postnatal Depression ScaleAccessible Resource for Integrated Epigenomics StudiesEpigenetic age accelerationGestational age accelerationAssociated with epigenetic agingAvon Longitudinal Study of ParentsLongitudinal Study of ParentsPostnatal Depression ScalePrimary outcomeChildhood experiencesAvon Longitudinal StudyEpigenetic ageStudy of ParentsAge accelerationHigher ACE scoresCross-sectional studyEpigenetic clocksMother-offspring dyadsDepression ScaleHealth districtMother-child dyadsDNA methylation–based epigenetic clocksInvestigate depressionDetecting small cell transformation in patients with advanced EGFR mutant lung adenocarcinoma through epigenomic cfDNA profiling
Zarif T, Meador C, Qiu X, Seo J, Davidsohn M, Savignano H, Lakshminarayanan G, McClure H, Canniff J, Fortunato B, Li R, Banwait M, Semaan K, Eid M, Long H, Hung Y, Mahadevan N, Barbie D, Oser M, Piotrowska Z, Choueiri T, Baca S, Hata A, Freedman M, Berchuck J. Detecting small cell transformation in patients with advanced EGFR mutant lung adenocarcinoma through epigenomic cfDNA profiling. Clinical Cancer Research 2024, 30: 3798-3811. PMID: 38912901, PMCID: PMC11369616, DOI: 10.1158/1078-0432.ccr-24-0466.Peer-Reviewed Original ResearchConceptsEGFR mutant lung adenocarcinomaSmall cell lung cancerSmall cell transformationLung cancer patient-derived xenograftPatient-derived xenograftsLung adenocarcinomaEGFR mutantsChIP-seqEpigenomic featuresMeDIP-seqImmunoprecipitation sequencingCell transformationHistological transformation to small cell lung cancerTransformation to small cell lung cancerMethylated DNA immunoprecipitation sequencingTransposase-accessible chromatin sequencingH3K27ac ChIP-seqMechanisms of treatment resistanceChromatin immunoprecipitation sequencingHistone modification H3K27acMutant lung adenocarcinomaCell lung cancerChromatin accessibilityChromatin sequencingEpigenomic landscapeFrom metabolic to epigenetic: Insight into trained macrophages in atherosclerosis (Review)
Li T, Feng W, Yan W, Wang T. From metabolic to epigenetic: Insight into trained macrophages in atherosclerosis (Review). Molecular Medicine Reports 2024, 30: 145. PMID: 38904193, DOI: 10.3892/mmr.2024.13269.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAtherosclerosisEpigenesis, GeneticHumansImmunity, InnateMacrophagesPlaque, AtheroscleroticConceptsTrained immunityTrained macrophagesAbundant immune cellsCharacteristics of innate immunityChronic inflammatory diseaseAtherosclerotic plaquesProgression of ASImmune cellsInflammatory diseasesImmune responseTherapeutic approachesClinical strategiesEpigenetic reprogrammingDeposition of lipoproteinsCardiovascular diseaseInnate immunityMacrophagesAtherosclerosisImmunityDiseasePlaqueCellsComplex mechanismsUsing a comprehensive atlas and predictive models to reveal the complexity and evolution of brain-active regulatory elements
Pratt H, Andrews G, Shedd N, Phalke N, Li T, Pampari A, Jensen M, Wen C, Consortium P, Gandal M, Geschwind D, Gerstein M, Moore J, Kundaje A, Colubri A, Weng Z. Using a comprehensive atlas and predictive models to reveal the complexity and evolution of brain-active regulatory elements. Science Advances 2024, 10: eadj4452. PMID: 38781344, PMCID: PMC11114231, DOI: 10.1126/sciadv.adj4452.Peer-Reviewed Original ResearchConceptsEpigenetic dataCell-type-specific gene regulationCis-regulatory elementsComprehensive atlasGenetic variants associated with psychiatric disordersLineage-specific transcription factorsBrain cell typesMammalian elementsPsychENCODE ConsortiumNoncoding regionsEvolutionary historyGene regulationRegulatory elementsSequence mutationsTranscription factorsSequence syntaxRegulatory informationPrimate-specific sequencesBinding sitesHuman traitsCell typesFunctional implicationsPsychiatric disordersSequenceFetal brain developmentUpdate in genetic and epigenetic causes of hypertension
Mani A. Update in genetic and epigenetic causes of hypertension. Cellular And Molecular Life Sciences 2024, 81: 201. PMID: 38691164, PMCID: PMC11062952, DOI: 10.1007/s00018-024-05220-4.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsEpigenesis, GeneticGenetic Predisposition to DiseaseGenome-Wide Association StudyHumansHypertensionConceptsGenome-wide association studiesProtein-coding sequencesGWAS-identified lociGWAS-identified genesHuman Genome ProjectEpigenetic mechanism of actionActual genesGenome ProjectAssociation studiesGenetic variationPolygenic formsGenetic basisGenetic variantsEpigenetic mechanismsHeritable diseaseEpigenetic causesPolygenic causeGenesLociPotential targetMechanism of actionManagement of blood pressurePRDM6SequenceVariantsZNF397 Deficiency Triggers TET2-driven Lineage Plasticity and AR-Targeted Therapy Resistance in Prostate Cancer
Xu Y, Yang Y, Wang Z, Sjostrom M, Jiang Y, Tang Y, Cheng S, Deng S, Wang C, Gonzalez J, Johnson N, Li X, Li X, Metang L, Mukherji A, Xu Q, Tirado C, Wainwright G, Yu X, Barnes S, Hofstad M, Chen Y, Zhu H, Hanker A, Raj G, Zhu G, He H, Wang Z, Arteaga C, Liang H, Feng F, Wang Y, Wang T, Mu P. ZNF397 Deficiency Triggers TET2-driven Lineage Plasticity and AR-Targeted Therapy Resistance in Prostate Cancer. Cancer Discovery 2024, 14: 1496-1521. PMID: 38591846, PMCID: PMC11285331, DOI: 10.1158/2159-8290.cd-23-0539.Peer-Reviewed Original ResearchConceptsLineage plasticityTherapy resistanceProstate cancerCancer cellsAndrogen receptorResistance to AR-targeted therapiesLuminal lineageAR-targeted therapiesOvercome therapy resistanceTransition of cancer cellsEpigenetic regulatory machineryBona fide coactivatorTherapy responseAR signalingEpigenetic rewiringDrug resistanceTherapeutic strategiesEpigenetic reprogrammingProstateTherapyCancerPhenotypic plasticityRegulatory machineryAndrogenTranscriptional programsThe role of epigenetic mechanisms in the long‐term effects of early‐life adversity and mother–infant relationship on physiology and behavior of offspring in laboratory rats and mice
Burenkova O, Grigorenko E. The role of epigenetic mechanisms in the long‐term effects of early‐life adversity and mother–infant relationship on physiology and behavior of offspring in laboratory rats and mice. Developmental Psychobiology 2024, 66: e22479. PMID: 38470450, PMCID: PMC10959231, DOI: 10.1002/dev.22479.Peer-Reviewed Original ResearchConceptsEarly-life adversityEffects of early-life adversityBehavior of offspringMother-infant relationshipRegulation of hypothalamic-pituitary-adrenal axisHypothalamic-pituitary-adrenal axisBrain-derived neurotrophic factorLaboratory ratsMaternity careBehavioral profileEpigenetic mechanismsNeurotrophic factorExperimental manipulationEarly postnatal periodPharmacological interventionsLong-term effectsAdversityLong-term influenceRatsAdaptation of offspringOffspringEpigenetic editingTranslational potentialNatural variationMiceAn epigenetic timer regulates the transition from cell division to cell expansion during Arabidopsis petal organogenesis
Huang R, Irish V. An epigenetic timer regulates the transition from cell division to cell expansion during Arabidopsis petal organogenesis. PLOS Genetics 2024, 20: e1011203. PMID: 38442104, PMCID: PMC10942257, DOI: 10.1371/journal.pgen.1011203.Peer-Reviewed Original ResearchMeSH KeywordsArabidopsisArabidopsis ProteinsCell DivisionEpigenesis, GeneticFlowersGene Expression Regulation, PlantTranscription FactorsConceptsCell division to cell expansionCell divisionCell expansionRemodeling of chromatin accessibilityResponse to environmental changesRNA polymerase activityPlant developmental timingRegulate developmental eventsMultiple cell divisionsDownstream direct targetsCorepressor TOPLESSArabidopsis petalsChromatin accessibilityHistone modificationsPetal developmentEpigenetic stateTranscriptional repressorPetal organogenesisPolymerase activityEpigenetic memoryPetal primordiaPlant organogenesisCell cycleEpigenetic factorsControl organogenesis
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