2025
Aberrant DNA methylation of genes regulating CD4+ T cell HIV‐1 reservoir in women with HIV
Xu K, Zhang X, Asam K, Quach B, Page G, Konkle‐Parker D, Martinez C, Lahiri C, Topper E, Cohen M, Kassaye S, DeHovitz J, Kuniholm M, Archin N, Valizadeh A, Tien P, Marconi V, Hancock D, Johnson E, Aouizerat B. Aberrant DNA methylation of genes regulating CD4+ T cell HIV‐1 reservoir in women with HIV. Clinical And Translational Medicine 2025, 15: e70267. PMID: 40070009, PMCID: PMC11896887, DOI: 10.1002/ctm2.70267.Peer-Reviewed Original ResearchConceptsCD4+ T cellsHIV-1 reservoirHIV-1 latencyT cellsHIV-1Aberrant DNA methylationMechanisms of HIV-1 latencyViral replicationVirally suppressed womenDNA methylationHIV-1 integration sitesHIV-1 replicationMolecular targetsDifferentially methylated CpG sitesImmune defenceDNA methylation sequencingHost epigenetic landscapeDNA methylation sitesHIV-1 DNA integrationDifferentially methylated sitesHost genome integrityInterferon signaling genesCure HIVHost-virus interactionsCD4Epigenetic 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 ResearchConceptsIdiopathic 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 assessment
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 samplesA Multi‐Omic Analysis of Molecular Risk and Resilience Factors in Late‐Onset Alzheimer’s Disease in APOEe4 Carriers
Markov Y, Priyanka A, Higgins‐Chen A. A Multi‐Omic Analysis of Molecular Risk and Resilience Factors in Late‐Onset Alzheimer’s Disease in APOEe4 Carriers. Alzheimer's & Dementia 2024, 20: e092941. PMCID: PMC11709863, DOI: 10.1002/alz.092941.Peer-Reviewed Original ResearchLate-onset Alzheimer's diseaseMulti-omics analysisApolipoprotein ESusceptible to AD pathologyDisease resilienceDeep whole-exome sequencingMulti-omics datasetsDNA methylation profilesAlzheimer's diseaseWhole-exome sequencingMolecular signaturesLabel-free mass spectrometryIllumina EPIC arrayDNA methylationExome sequencingMethylation profilesEPIC arrayOmics levelsReligious Orders StudyAD pathologyMulti-tissueMutated genesGenesE4 alleleExtracellular matrixTet2 Loss in Hematopoietic Stem Cells Triggers Chromatin Reorganization through DNA Methylation Shifts
Roy R, Pillai M, Boddu P. Tet2 Loss in Hematopoietic Stem Cells Triggers Chromatin Reorganization through DNA Methylation Shifts. Blood 2024, 144: 1812. DOI: 10.1182/blood-2024-211494.Peer-Reviewed Original ResearchTopologically associating domainsDisruption of TAD boundariesTopologically associating domains boundariesTAD boundariesMutant cellsChromatin organizationChromatin compartmentsDNA methylationLT-HSCsKO cellsEnhancer-promoterHigher-order chromatin organizationTet2 lossStudy of chromatin organizationGene expressionMethyl-seq dataHypermethylated differentially methylated regionsPaired-end readsWT cellsGene regulatory networksConversion of 5-methylcytosineDifferentially methylated regionsMyelodysplastic syndromeCompartment shiftsChanges to DNA methylationA 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 analysisThe fetal origins of metabolic health: exploring the association between newborn biological age and metabolism hormones in childhood
Jia Z, Qiu F, He Y, Chen H, Yang C, Liu H, Zheng T, Xu S, Wang S, Li Y. The fetal origins of metabolic health: exploring the association between newborn biological age and metabolism hormones in childhood. BMC Medicine 2024, 22: 429. PMID: 39379967, PMCID: PMC11462715, DOI: 10.1186/s12916-024-03629-z.Peer-Reviewed Original ResearchConceptsRestricted cubic splinesLeptin levelsMetabolic hormonesMetabolic healthDNA methylationRestricted cubic spline analysisProspective birth cohort studyDNA methylation ageMother-child pairsBirth cohort studyDNA copy numberFetal originMitochondrial DNA copy numberResultsThe linear regression analysisReal-time PCRCohort studyHorvath's epigenetic clockInsulin levelsInverse associationLeptinQuantitative real-time PCRInfinium MethylationEPIC BeadChipElectrochemiluminescence assayLinear regression analysisMetabolic statusEpigenetic Changes in Cerebrospinal Fluid and Blood of People With Neurosyphilis
Mostaghimi D, Mehta S, Yoon J, Kosana P, Marra C, Corley M, Farhadian S. Epigenetic Changes in Cerebrospinal Fluid and Blood of People With Neurosyphilis. The Journal Of Infectious Diseases 2024, jiae476. PMID: 39356164, DOI: 10.1093/infdis/jiae476.Peer-Reviewed Original ResearchPeripheral blood mononuclear cellsCerebrospinal fluidRNA expression changesEpigenetic changesExpression changesBlood mononuclear cellsDifferentially methylated sitesDNA methylation profilesInsulin-responsive pathwaysAntibiotic treatmentImmune cellsB cellsMononuclear cellsMethylation changesDNA methylationMethylation profilesMatched controlsBacterial infectionsNon-NENeurosyphilisBlood of peopleInfectionRNANSDNA methylation in mammalian development and disease
Smith Z, Hetzel S, Meissner A. DNA methylation in mammalian development and disease. Nature Reviews Genetics 2024, 26: 7-30. PMID: 39134824, DOI: 10.1038/s41576-024-00760-8.Peer-Reviewed Original ResearchLong-read sequencing technologiesDNA methylation fieldDNA methylation landscapeGenome functionMethylation landscapeSequencing technologiesEpigenetic codeGenomic characterizationRegulatory layerDNA methylationCell physiologyMammalian developmentMammalian lifespanGenetic featuresFunctional understandingSingle-cellDNAMechanistic discoveriesSomatic transitionsPhases of discoveryDevelopmental potentialDiscoveryPhenotypeSenescencePhysiologyGene body DNA hydroxymethylation restricts the magnitude of transcriptional changes during aging
Occean J, Yang N, Sun Y, Dawkins M, Munk R, Belair C, Dar S, Anerillas C, Wang L, Shi C, Dunn C, Bernier M, Price N, Kim J, Cui C, Fan J, Bhattacharyya M, De S, Maragkakis M, de Cabo R, Sidoli S, Sen P. Gene body DNA hydroxymethylation restricts the magnitude of transcriptional changes during aging. Nature Communications 2024, 15: 6357. PMID: 39069555, PMCID: PMC11284234, DOI: 10.1038/s41467-024-50725-y.Peer-Reviewed Original ResearchConceptsTissue-specific functionsDNA hydroxymethylationMagnitude of transcriptional changesAlternative splicing eventsMagnitude of gene expression changesTissue-specific genesGene expression changesGene bodiesSplicing eventsDNA methylationModel organismsTranscriptional changesExpression changesGenesAge-related diseasesFunctional roleMouse liverHuman tissuesProlonged quiescenceRestriction functionSplicingDNAMiceAge-related contextSenescenceAcyl-CoA Synthetase Medium-Chain Family Member 5–Mediated Fatty Acid Metabolism Dysregulation Promotes the Progression of Hepatocellular Carcinoma
Yang L, Pham K, Xi Y, Jiang S, Robertson K, Liu C. Acyl-CoA Synthetase Medium-Chain Family Member 5–Mediated Fatty Acid Metabolism Dysregulation Promotes the Progression of Hepatocellular Carcinoma. American Journal Of Pathology 2024, 194: 1951-1966. PMID: 39069168, PMCID: PMC11423759, DOI: 10.1016/j.ajpath.2024.07.002.Peer-Reviewed Original ResearchConceptsDNA methyltransferase 1Fatty acid metabolismAcyl-CoADown-regulationAcid metabolismDecreased STAT3 phosphorylationCell linesPromoter region methylationHepatocellular carcinoma cell lineHepatocellular carcinoma patient samplesDNA methylationFatty acid accumulationDysregulated fatty acid metabolismSTAT3 phosphorylationDecreased cell proliferationHepatocellular carcinomaHepatocellular carcinoma tumor tissuesMethyltransferase 1Region methylationRegulatory mechanismsACSM5Molecular mechanismsMetabolic dysregulationProgression of hepatocellular carcinomaAcid accumulationEpigenetic heterogeneity hotspots in human liver disease progression
Hlady R, Zhao X, Khoury L, Wagner R, Luna A, Pham K, Pyrosopoulos N, Jain D, Wang L, Liu C, Robertson K. Epigenetic heterogeneity hotspots in human liver disease progression. Hepatology 2024, 81: 1197-1210. PMID: 39028883, PMCID: PMC11742070, DOI: 10.1097/hep.0000000000001023.Peer-Reviewed Original ResearchEpigenetic heterogeneityGenome-wide profiling of DNA methylationProfiling of DNA methylationDNA methylation landscapeGenome-wide profilingGene expression heterogeneityCopy number variationsMethylation landscapeOnset of liver cancerDNA methylationLiver disease developmentPhenotypic effectsNumber variationsGenetic heterogeneityTranscriptional heterogeneityFunctional screeningLiver disease progressionCopy numberExpression heterogeneityGene expressionTumor suppressorHuman diseasesGenesPathological phenotypesKey pathwaysEpigenome-Wide Association Study of Depressive Symptoms in Black Women in the InterGEN Study
Taylor B, Zhao Y, Perez N, Potts-Thompson S, Crusto C, Creber R, Taylor J. Epigenome-Wide Association Study of Depressive Symptoms in Black Women in the InterGEN Study. International Journal Of Molecular Sciences 2024, 25: 7681. PMID: 39062924, PMCID: PMC11277114, DOI: 10.3390/ijms25147681.Peer-Reviewed Original ResearchDepressive symptomsPerceived discriminationSuch as low socioeconomic statusBlack womenIncreased risk of depressionStudies of depressive symptomsSecondary analysis of dataBeck Depression InventoryPrevalence of depressionRisk of depressionLow socioeconomic statusExperiences of discriminationInterGEN StudyDepression InventoryDNA methylation sitesSocioeconomic statusEvent ScalePsychosocial stressorsSecondary analysisDepressionDNA methylationEpigenome-wide association studiesPsychological factorsAnalysis of dataIncreased riskDNA methylation profiles of cancer-related fatigue associated with markers of inflammation and immunometabolism
Xiao C, Peng G, Conneely K, Zhao H, Felger J, Wommack E, Higgins K, Shin D, Saba N, Bruner D, Miller A. DNA methylation profiles of cancer-related fatigue associated with markers of inflammation and immunometabolism. Molecular Psychiatry 2024, 30: 76-83. PMID: 38977918, DOI: 10.1038/s41380-024-02652-z.Peer-Reviewed Original ResearchGene expressionMethylation lociAssociated with gene expressionHead and neck cancerDNA methylation profilesProtein markersLipid metabolismInvolvement of genesIllumina MethylationEPICDNA methylationRelevant gene expressionEpigenetic modificationsExpression pairsInflammatory markersInflammatory responseLociHead and neck cancer patientsAssociated with inflammatory markersGenesDNAMarkers of inflammationAssociated with fatigueExpressionMethylationPost-radiotherapyTranslation of Epigenetics in Cell-Free DNA Liquid Biopsy Technology and Precision Oncology
Tan W, Nagabhyrava S, Ang-Olson O, Das P, Ladel L, Sailo B, He L, Sharma A, Ahuja N. Translation of Epigenetics in Cell-Free DNA Liquid Biopsy Technology and Precision Oncology. Current Issues In Molecular Biology 2024, 46: 6533-6565. PMID: 39057032, PMCID: PMC11276574, DOI: 10.3390/cimb46070390.Peer-Reviewed Original ResearchCell-free DNA liquid biopsyCell-free DNALiquid biopsy technologiesLiquid biopsyBiopsy technologyEarly cancer detectionClinical applicationCfDNA-based liquid biopsyMonitoring residual diseaseEarly detection testsCancer detectionPotential of epigeneticsPersonalized cancer treatmentImprove cancer outcomesTissue of originFragmentation pattern analysisResidual diseaseDNA methylationMulti-cancer early detection testTreatment responseBiopsyCancer outcomesCancer preventionEpigeneticsPrecision oncologyFolate metabolism and risk of childhood acute lymphoblastic leukemia: a genetic pathway analysis from the Childhood Cancer and Leukemia International Consortium
Metayer C, Spector L, Scheurer M, Jeon S, Scott R, Takagi M, Clavel J, Manabe A, Ma X, Hailu E, Lupo P, Urayama K, Bonaventure A, Kato M, Meirhaeghe A, Chiang C, Morimoto L, Wiemels J. Folate metabolism and risk of childhood acute lymphoblastic leukemia: a genetic pathway analysis from the Childhood Cancer and Leukemia International Consortium. Cancer Epidemiology Biomarkers & Prevention 2024, 33: 1248-1252. PMID: 38904462, PMCID: PMC11369612, DOI: 10.1158/1055-9965.epi-24-0189.Peer-Reviewed Original ResearchSingle nucleotide polymorphismsGenome-wide dataAncestry groupsFolate metabolic pathwayGenetic variantsChildhood cancerMetabolic pathwaysGenetic pathway analysisRisk of childhood ALLRisk of childhood acute lymphoblastic leukemiaGene-folate interactionsChildhood ALL riskCase-control studyDNA methylationMETAL softwareGenetic studiesNucleotide polymorphismsPathway analysisMeta-analysis of original dataALL riskGenetic effectsAncestryFolate pathwayMaternal genetic effectsFolate intakeSingle-stranded pre-methylated 5mC adapters uncover the methylation profile of plasma ultrashort Single-stranded cell-free DNA
Cheng J, Swarup N, Morselli M, Huang W, Aziz M, Caggiano C, Kordi M, Patel A, Chia D, Kim Y, Li F, Wei F, Zaitlen N, Krysan K, Dubinett S, Pellegrini M, Wong D. Single-stranded pre-methylated 5mC adapters uncover the methylation profile of plasma ultrashort Single-stranded cell-free DNA. Nucleic Acids Research 2024, 52: e50-e50. PMID: 38797520, PMCID: PMC11194076, DOI: 10.1093/nar/gkae276.Peer-Reviewed Original ResearchTranscription start siteMethylation profilesCell-free DNAWhole-genome bisulfite sequencingCytosine methylation changesLevels of DNA methylationSingle-base resolutionUpstream transcription start siteBS-seqStart siteBisulfite sequencingCpG islandsDNA fragmentationBisulfite conversionMethylation changesDNA methylationBisulfite treatmentLarge DNAsMethylation analysisDNANon-cancer samplesBisulfiteFragmentsHemopoietic cellsMethylationEpigenome-wide association study of lung cancer among never smokers in two prospective cohorts in Shanghai, China
Rahman M, Breeze C, Shu X, Wong J, Blechter B, Cardenas A, Wang X, Ji B, Hu W, Cai Q, Hosgood H, Yang G, Shi J, Long J, Gao Y, Bell D, Zheng W, Rothman N, Lan Q. Epigenome-wide association study of lung cancer among never smokers in two prospective cohorts in Shanghai, China. Thorax 2024, 79: 735-744. PMID: 38702190, PMCID: PMC11251856, DOI: 10.1136/thorax-2023-220352.Peer-Reviewed Original ResearchAssociated with lung cancerLung cancer casesNever smokersHealth StudyOral rinse samplesCancer casesShanghai Men's Health StudyShanghai Women's Health StudyIncident lung cancer casesEpigenome-wide significance levelLung cancerWomen's Health StudyAetiology of lung cancerFixed-effect meta-analysisMen's Health StudyNested case-control studyCase-control studyBlood DNA methylationSmoking remainsStudy of Lung CancerGrimAge accelerationNever-smoking controlsRinse samplesDNA methylationIllumina MethylationEPIC array
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