2024
Examining Methylation at the Intersection of Genetic Risk To Alzheimer’s Disease And Alcohol Use Disorder
Pathak G, Pietrzak R, Levey D, Montalvo‐Ortiz J, Kranzler H, Gelernter J, Polimanti R. Examining Methylation at the Intersection of Genetic Risk To Alzheimer’s Disease And Alcohol Use Disorder. Alzheimer's & Dementia 2024, 20: e086508. PMCID: PMC11710760, DOI: 10.1002/alz.086508.Peer-Reviewed Original ResearchEpigenome-wide association studiesGenetic susceptibility to ADSusceptibility to ADCpG sitesPolygenic scoresAD pathogenesisAlzheimer's diseaseTOPMed reference panelEuropean ancestry participantsIllumina EPIC arrayBrain lipid metabolismCpG associationsAssociation studiesIdentified genesGenotype dataGenetic ancestryImprove statistical powerReference panelAncestry participantsEPIC arrayBonferroni significanceCpGMethylation intensityAlcohol use disorder diagnosisRisk of neurodegenerationExamining Methylation at the Intersection of Genetic Risk To Alzheimer's Disease And Alcohol Use Disorder
Pathak G, Pietrzak R, Levey D, Montalvo‐Ortiz J, Kranzler H, Gelernter J, Polimanti R. Examining Methylation at the Intersection of Genetic Risk To Alzheimer's Disease And Alcohol Use Disorder. Alzheimer's & Dementia 2024, 20: e093693. PMCID: PMC11712840, DOI: 10.1002/alz.093693.Peer-Reviewed Original ResearchEpigenome-wide association studiesGenetic susceptibility to ADSusceptibility to ADCpG sitesPolygenic scoresAD pathogenesisAlzheimer's diseaseTOPMed reference panelEuropean ancestry participantsIllumina EPIC arrayBrain lipid metabolismCpG associationsAssociation studiesIdentified genesGenotype dataGenetic ancestryImprove statistical powerReference panelAncestry participantsEPIC arrayBonferroni significanceCpGMethylation intensityAlcohol use disorder diagnosisRisk of neurodegenerationMediation analysis in longitudinal study with high-dimensional methylation mediators
Cui Y, Lin Q, Yuan X, Jiang F, Ma S, Yu Z. Mediation analysis in longitudinal study with high-dimensional methylation mediators. Briefings In Bioinformatics 2024, 25: bbae496. PMID: 39406521, PMCID: PMC11479716, DOI: 10.1093/bib/bbae496.Peer-Reviewed Original ResearchConceptsBody mass indexMediation analysisPaternal body mass indexGeneralized estimating equationsLinear mixed-effects modelsCohort dataMass indexMixed-effects modelsDNA methylation sitesHigh-dimensional mediation analysisLongitudinal studyBonferroni correctionAccurate parameter estimatesSobel testVariable selectionLongitudinal dataSimulation studyIndependence screeningMethylation sitesCpG sitesIndirect effectsParameter estimationLinearization methodHypothesis testingEpigenetic molecular underpinnings of brain structural-functional connectivity decoupling in patients with major depressive disorder
Tang L, Zhao P, Pan C, Song Y, Zheng J, Zhu R, Wang F, Tang Y. Epigenetic molecular underpinnings of brain structural-functional connectivity decoupling in patients with major depressive disorder. Journal Of Affective Disorders 2024, 363: 249-257. PMID: 39029702, DOI: 10.1016/j.jad.2024.07.110.Peer-Reviewed Original ResearchMajor depressive disorderMajor depressive disorder patientsStructural-functional connectivityHPA axisDepressive disorderIncreased susceptibility to MDDSusceptibility to major depressive disorderMajor depressive disorder treatmentHealthy controlsStress-related disordersBrain network dynamicsMultimodal neuroimaging dataGender-matched healthy controlsSubcortical regionsNeuroimaging dataChronic stressCortical regionsNodal levelMedical statusFunctional networksCRHR1FKBP5CpG sitesDisordersMolecular underpinningsDetection of hepatocellular carcinoma methylation markers in salivary DNA
Mezzacappa C, Wang Z, Lu L, Risch H, Taddei T, Yu H. Detection of hepatocellular carcinoma methylation markers in salivary DNA. Bioscience Reports 2024, 44: bsr20232063. PMID: 38457142, PMCID: PMC10958141, DOI: 10.1042/bsr20232063.Peer-Reviewed Original ResearchHepatocellular carcinoma screeningCase patientsHepatocellular carcinomaControl subjectsDiagnosis of hepatocellular carcinomaAssociated with hepatocellular carcinomaScreening testSalivary DNASaliva-based testCpG sitesStudy of risk factorsSalivary DNA methylationDNA methylationViral hepatitisCirculating DNAAlterations to DNA methylationRisk factorsMethylation markersPatientsRegulation of cell cycle progressionBlood samplesCell cycle progressionAffected individualsAlternative to blood samplingMultiple comparisonsComputationally inferred cell-type specific epigenome-wide DNA methylation analysis unveils distinct methylation patterns among immune cells for HIV infection in three cohorts
Zhang X, Hu Y, Vandenhoudt R, Yan C, Marconi V, Cohen M, Wang Z, Justice A, Aouizerat B, Xu K. Computationally inferred cell-type specific epigenome-wide DNA methylation analysis unveils distinct methylation patterns among immune cells for HIV infection in three cohorts. PLOS Pathogens 2024, 20: e1012063. PMID: 38466776, PMCID: PMC10957090, DOI: 10.1371/journal.ppat.1012063.Peer-Reviewed Original ResearchCD4+ T cellsEpigenome-wide association studiesPeripheral blood mononuclear cellsHIV infectionHIV pathogenesisT cellsCpG sitesNatural killer (NK) cellsCell typesAssociated with HIV infectionCD8+ T cellsMethylation patternsCpG methylationDNA methylationEpigenome-wide DNA methylation analysisBlood mononuclear cellsImmune cell typesDifferentially methylated CpG sitesUnique CpG sitesDifferential CpG methylationDNA methylation analysisSignificant CpG sitesArray-based methodsGene set enrichment analysisComputational deconvolution methodsBlood epigenome-wide association studies of suicide attempt in adults with bipolar disorder
Mirza S, Lima C, Del Favero-Campbell A, Rubinstein A, Topolski N, Cabrera-Mendoza B, Kovács E, Blumberg H, Richards J, Williams A, Wemmie J, Magnotta V, Fiedorowicz J, Gaine M, Walss-Bass C, Quevedo J, Soares J, Fries G. Blood epigenome-wide association studies of suicide attempt in adults with bipolar disorder. Translational Psychiatry 2024, 14: 70. PMID: 38296944, PMCID: PMC10831084, DOI: 10.1038/s41398-024-02760-y.Peer-Reviewed Original ResearchConceptsEpigenome-wide association studiesDifferentially methylated regionsDifferentially methylated positionsAssociation studiesCo-methylation network analysisBipolar disorderDNA methylation patternsSuicide attemptsReplication cohortHistory of SAGene ontology analysisSignificant CpG sitesMethylation patternsDNA methylationCpG sitesOntology analysisImmune-related genesEnrichment analysisNon-psychiatric controlsCalcium signalingGenesDNAClinical interviewSA historyNetwork analysis
2023
Trans-ancestry epigenome-wide association meta-analysis of DNA methylation with lifetime cannabis use
Fang F, Quach B, Lawrence K, van Dongen J, Marks J, Lundgren S, Lin M, Odintsova V, Costeira R, Xu Z, Zhou L, Mandal M, Xia Y, Vink J, Bierut L, Ollikainen M, Taylor J, Bell J, Kaprio J, Boomsma D, Xu K, Sandler D, Hancock D, Johnson E. Trans-ancestry epigenome-wide association meta-analysis of DNA methylation with lifetime cannabis use. Molecular Psychiatry 2023, 29: 124-133. PMID: 37935791, PMCID: PMC11078760, DOI: 10.1038/s41380-023-02310-w.Peer-Reviewed Original ResearchEpigenome-wide association studiesDNA methylationCpG sitesDNA methylation changesEpigenome-wide associationSignificant CpG sitesMethylation changesBlood-based DNA methylationAssociation studiesSignificant CpGsEWAS analysisFalse discovery rateMethylationHealth outcomesLifetime cannabisCigarette smokingDiscovery rateMethylation scoreADGRF1APOBRACTN1SitesADAM12CpGEnvironmental exposuresF71. NETWORK OF CO-METHYLATION ASSOCIATED WITH GREY MATTER MATURATION IN HUMAN ADOLESCENCE
Jensen D, Chen J, Turner J, Stephen J, Wang Y, Wilson T, Calhoun V, Liu J. F71. NETWORK OF CO-METHYLATION ASSOCIATED WITH GREY MATTER MATURATION IN HUMAN ADOLESCENCE. European Neuropsychopharmacology 2023, 75: s258-s259. DOI: 10.1016/j.euroneuro.2023.08.455.Peer-Reviewed Original ResearchStructural MRIBrain maturationNeuronal systemsCo-methylation network analysisPeriod of brain maturationAdolescent brain developmentAdolescent brain maturationPhases of neurodevelopmentIndependent component analysisGray matterHuman brain structureGM maturationDNAm changesCo-methylation modulesPrefrontal cortexExecutive functionFrontal poleGM volumeTime pointsSubjects aged 9Brain structuresCpG sitesSynaptic pruningBrain developmentDNA methylationCpH methylome analysis in human cortical neurons identifies novel gene pathways and drug targets for opioid use disorder
Nagamatsu S, Rompala G, Hurd Y, Núñez-Rios D, Montalvo-Ortiz J, Group T, Alvarez V, Benedek D, Che A, Cruz D, Davis D, Girgenti M, Hoffman E, Holtzheimer P, Huber B, Kaye A, Krystal J, Labadorf A, Keane T, Logue M, McKee A, Marx B, Mash D, Miller M, Noller C, JM-O, Scott W, Schnurr P, Stein T, Ursano R, Williamson D, Wolf E, Young K. CpH methylome analysis in human cortical neurons identifies novel gene pathways and drug targets for opioid use disorder. Frontiers In Psychiatry 2023, 13: 1078894. PMID: 36745154, PMCID: PMC9892724, DOI: 10.3389/fpsyt.2022.1078894.Peer-Reviewed Original ResearchOpioid use disorderOrbital frontal cortexDNA methylationKEGG enrichment analysisUse disordersMCPH lociTreatment of OUDGene OntologyEnrichment analysisOpioid-related drugsCpG sitesDrug targetsOxidative bisulfite sequencingImportant biological pathwaysDrug interaction analysisDrug-gene interaction databaseNervous system developmentSmoking statusBrain BankCortical neuronsFrontal cortexNeuronal nucleiHuman studiesGene regulationMethylome analysis
2022
Nicotine dose-dependent epigenomic-wide DNA methylation changes in the mice with long-term electronic cigarette exposure.
Peng G, Xi Y, Bellini C, Pham K, Zhuang ZW, Yan Q, Jia M, Wang G, Lu L, Tang MS, Zhao H, Wang H. Nicotine dose-dependent epigenomic-wide DNA methylation changes in the mice with long-term electronic cigarette exposure. American Journal Of Cancer Research 2022, 12: 3679-3692. PMID: 36119846, PMCID: PMC9442002.Peer-Reviewed Original ResearchElectronic cigarette exposureCigarette exposureMale ApoE-/- miceApoE-/- miceCytokine mRNA expressionPoor health outcomesWhite blood cellsElectronic cigarette useDose-dependent mannerE-cigarette aerosolAerosol inhalationCigarette smokingActivation of MAPKHigher nicotine concentrationsMAPK pathway activationCell-damaging effectsCpG sitesHealth outcomesCigarette useMRNA expressionNicotine concentrationsPathway activationSignificant CpG sitesBlood cellsSignificant alterationsEpigenome-wide association study of posttraumatic stress disorder identifies novel loci in U.S. military veterans
Montalvo-Ortiz JL, Gelernter J, Cheng Z, Girgenti MJ, Xu K, Zhang X, Gopalan S, Zhou H, Duman RS, Southwick SM, Krystal JH, Pietrzak R. Epigenome-wide association study of posttraumatic stress disorder identifies novel loci in U.S. military veterans. Translational Psychiatry 2022, 12: 65. PMID: 35177594, PMCID: PMC8854688, DOI: 10.1038/s41398-022-01822-3.Peer-Reviewed Original ResearchConceptsEpigenome-wide association studiesAssociation studiesTranscription regulationCpG sitesGenome-wide association studiesCell type proportionsPosttraumatic stress disorderPotential epigenetic biomarkersSignificant CpG sitesEpigenetic mechanismsDNA methylationNovel lociCell signalingEpigenetic biomarkersMethylation analysisAxonal guidanceNovel molecular biomarkersEPIC BeadChipLifetime posttraumatic stress disorderMilitary veteransPostmortem brain tissueMedial orbitofrontal cortexMolecular biomarkersRegulationU.S. military veteransNeighborhood characteristics and breast tumor methylation: using epigenomics to explore cancer outcome disparities
Gohar J, Do W, Miller-Kleinhenz J, Conneely K, Krishnamurti U, D’Angelo O, Gogineni K, Torres M, Gabram-Mendola S, McCullough L. Neighborhood characteristics and breast tumor methylation: using epigenomics to explore cancer outcome disparities. Breast Cancer Research And Treatment 2022, 191: 653-663. PMID: 34978015, DOI: 10.1007/s10549-021-06430-1.Peer-Reviewed Original ResearchConceptsNeighborhood-level factorsCause mortalityMultivariable Cox proportional hazards modelsCox proportional hazards modelCancer outcome disparitiesBreast cancer outcomesTumor methylationProportional hazards modelNon-Hispanic blacksArea-level factorsCancer outcomesFalse discovery rate thresholdBody of evidenceCancer disparitiesBreast cancerOutcome disparitiesCpG sitesTumor progressionTumor tissueWhite womenGuanine dinucleotide sitesRacial disparitiesMortalityTumor epigenomeLinear regression modelsThe Interaction of Trauma Exposure and DNA Methylation on Blood Pressure Among Black Women in the InterGEN Study
Caceres B, Huang Y, Barcelona V, Wang Z, Newhall K, Cerdeña J, Crusto C, Sun Y, Taylor J. The Interaction of Trauma Exposure and DNA Methylation on Blood Pressure Among Black Women in the InterGEN Study. Epigenetics Insights 2022, 15: 25168657221138510. PMID: 36466626, PMCID: PMC9716582, DOI: 10.1177/25168657221138510.Peer-Reviewed Original ResearchDiastolic blood pressureBlood pressureTrauma exposureHypertension riskBody mass indexChildhood traumaEpigenome-wide significance levelBlack mothersBlack womenSeparate linear mixed-effects modelsMass indexCigarette smokingMean ageHigh riskLinear mixed effects modelsBlack adultsTraumaDNA methylationVicarious traumaEpigenetic mechanismsCpG sitesMixed effects models
2021
Brain areas involved with obsessive-compulsive disorder present different DNA methylation modulation
de Oliveira K, Camilo C, Gastaldi V, Sant’Anna Feltrin A, Lisboa B, de Jesus Rodrigues de Paula V, Moretto A, Lafer B, Hoexter M, Miguel E, Maschietto M, Brentani H. Brain areas involved with obsessive-compulsive disorder present different DNA methylation modulation. BMC Genomic Data 2021, 22: 45. PMID: 34717534, PMCID: PMC8557022, DOI: 10.1186/s12863-021-00993-0.Peer-Reviewed Original ResearchConceptsGene modulesMethylation changesBrain areasCpG sitesProtein-protein interaction networkDNA methylation modulationCommon transcriptional factorsDNA methylation changesSpecific signaling pathwaysGene expression dataOCD patientsPost-mortem brain tissueEpigenetic mechanismsInteraction networksMethylation modulationHypomethylation patternTranscriptional factorsEnvironmental risk factorsGene expressionBiological processesBackgroundObsessive–compulsive disorderSignaling pathwaysExpression dataG proteinsRisk factorsGenome-wide association analysis reveals regulation of at-risk loci by DNA methylation in prostate cancer
Liu Q, Liu G, Martin DT, Xing YT, Weiss RM, Qi J, Kang J. Genome-wide association analysis reveals regulation of at-risk loci by DNA methylation in prostate cancer. Asian Journal Of Andrology 2021, 23: 472-478. PMID: 33762478, PMCID: PMC8451484, DOI: 10.4103/aja.aja_20_21.Peer-Reviewed Original ResearchConceptsDNA methylationRisk lociGene expressionGenome-wide association analysisExpression quantitative trait loci (eQTL) analysisQuantitative trait locus (QTL) analysisMethylation-regulated genesEpigenetic association studiesSingle nucleotide polymorphism analysisNucleotide polymorphism analysisTranscript regulationGenomic regionsCancer Genome AtlasEpigenetic changesEpigenetic alterationsLocus analysisAssociation studiesAssociation analysisProgression of tumorsCpG sitesGenesLociMethylationGenome AtlasImportant locusEXT1 methylation promotes proliferation and migration and predicts the clinical outcome of non‐small cell lung carcinoma via WNT signalling pathway
Kong W, Chen Y, Zhao Z, Zhang L, Lin X, Luo X, Wang S, Song Z, Lin X, Lai G, Yu Z. EXT1 methylation promotes proliferation and migration and predicts the clinical outcome of non‐small cell lung carcinoma via WNT signalling pathway. Journal Of Cellular And Molecular Medicine 2021, 25: 2609-2620. PMID: 33565239, PMCID: PMC7933929, DOI: 10.1111/jcmm.16277.Peer-Reviewed Original ResearchMeSH KeywordsBiomarkers, TumorCarcinoma, Non-Small-Cell LungCell Line, TumorCell MovementCell ProliferationCpG IslandsDNA MethylationGene Expression Regulation, NeoplasticHumansLung NeoplasmsN-AcetylglucosaminyltransferasesNeoplasm GradingNeoplasm StagingPrognosisSurvival AnalysisWnt Signaling PathwayConceptsGene expressionGene body methylationDNA methylation levelsPotential downstream targetsDNA methylation sitesDNA methylationMethylation sitesDownstream targetsMethylation levelsWnt pathwayCpG sitesNSCLC cell linesMethylationWntExpression levelsCell linesPathway patternsPotential targetXAV-939EXT1ProliferationMigration ratePathwayExpressionUnderlying mechanism
2020
Obesity-associated methylation in breast tumors: a possible link to disparate outcomes?
Do W, Conneely K, Gabram-Mendola S, Krishnamurti U, D’Angelo O, Miller-Kleinhenz J, Gogineni K, Torres M, McCullough L. Obesity-associated methylation in breast tumors: a possible link to disparate outcomes? Breast Cancer Research And Treatment 2020, 181: 135-144. PMID: 32236829, DOI: 10.1007/s10549-020-05605-6.Peer-Reviewed Original ResearchConceptsCause mortalityER statusMultivariable Cox proportional hazards modelsCox proportional hazards modelBreast cancer tumor tissuesBreast cancer outcomesBreast cancer incidenceEstrogen receptor statusBody mass indexPrimary risk factorNon-Hispanic blacksCancer tumor tissuesReceptor statusMass indexCancer outcomesCpG sitesRisk factorsCancer incidenceBreast cancerHazards modelBreast tumorsTumor tissueWhite womenObesityRace disparities
2019
Identification of bovine CpG SNPs as potential targets for epigenetic regulation via DNA methylation
Maldonado MBC, de Rezende Neto NB, Nagamatsu ST, Carazzolle MF, Hoff JL, Whitacre LK, Schnabel RD, Behura SK, McKay SD, Taylor JF, Lopes FL. Identification of bovine CpG SNPs as potential targets for epigenetic regulation via DNA methylation. PLOS ONE 2019, 14: e0222329. PMID: 31513639, PMCID: PMC6742455, DOI: 10.1371/journal.pone.0222329.Peer-Reviewed Original ResearchConceptsSingle nucleotide polymorphismsCpG islandsDNA methylationReference genome sequence assemblyDatabase of SNPsCpG sitesBull Genomes ProjectGenome sequence assemblyDivergent feed efficiencyBovine phenotypesEpigenetic polymorphismEpigenetic controlEpigenetic regulationIntergenic regionNearby genesMethylation targetsGenomic sequencesMethylation patternsSequence assemblyGenome ProjectMethylation profilesMethylation sitesSNP databaseDifferential expressionVariant annotationEpigenome‐Wide DNA Methylation Association Analysis Identified Novel Loci in Peripheral Cells for Alcohol Consumption Among European American Male Veterans
Xu K, Montalvo‐Ortiz J, Zhang X, Southwick SM, Krystal JH, Pietrzak RH, Gelernter J. Epigenome‐Wide DNA Methylation Association Analysis Identified Novel Loci in Peripheral Cells for Alcohol Consumption Among European American Male Veterans. Alcohol Clinical And Experimental Research 2019, 43: 2111-2121. PMID: 31386212, PMCID: PMC9377208, DOI: 10.1111/acer.14168.Peer-Reviewed Original ResearchConceptsEpigenome-wide association studiesDNA methylationCpG sitesSignificant CpG sitesHigh-density methylation arraysNovel DNA methylation sitesNew CpG sitesDNA methylation sitesEpigenome-wide DNA methylationAmino acid transportIndividual CpG sitesGene lengthPeripheral cellsNovel lociDNA sitesKEGG databaseMethylation sitesEnrichment analysisMethylation arraysAssociation studiesAssociation analysisGenesMethylationAcid transportFalse discovery rate
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