2023
Profiling neuronal methylome and hydroxymethylome of opioid use disorder in the human orbitofrontal cortex
Rompala G, Nagamatsu S, Martínez-Magaña J, Nuñez-Ríos D, Wang J, Girgenti M, Krystal J, Gelernter J, Hurd Y, Montalvo-Ortiz J. Profiling neuronal methylome and hydroxymethylome of opioid use disorder in the human orbitofrontal cortex. Nature Communications 2023, 14: 4544. PMID: 37507366, PMCID: PMC10382503, DOI: 10.1038/s41467-023-40285-y.Peer-Reviewed Original ResearchConceptsOpioid use disorderMulti-omics findingsGene expression patternsCo-methylation analysisGene expression profilesMulti-omics profilingGene networksDNA methylationNeuronal methylomesDNA hydroxymethylationMethylomic analysisExpression patternsExpression profilesEpigenetic disturbancesUse disordersPsychiatric traitsOrbitofrontal cortexOpioid-related drugsPostmortem orbitofrontal cortexEnvironmental factorsDrug interaction analysisOUD treatmentHuman orbitofrontal cortexOpioid signalingInteraction analysis
2022
Epigenome-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 veterans
2019
Epigenome‐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
2017
Genetic–epigenetic interactions in cis: a major focus in the post-GWAS era
Do C, Shearer A, Suzuki M, Terry MB, Gelernter J, Greally JM, Tycko B. Genetic–epigenetic interactions in cis: a major focus in the post-GWAS era. Genome Biology 2017, 18: 120. PMID: 28629478, PMCID: PMC5477265, DOI: 10.1186/s13059-017-1250-y.Peer-Reviewed Original ResearchConceptsMethylation quantitative trait lociCCCTC-binding factorEpigenome-wide association studiesGenetic-epigenetic interactionsAllele-specific DNA methylationSequence variantsPost-GWAS eraQuantitative trait lociRegulatory sequence variantsGWAS signalsTrait lociDNA methylationTranscription factorsTranscriptional pathwaysAssociation studiesNon-genetic effectsStudy eraMajor focusMethylationLociVariantsCommon diseaseSitesNeuropsychiatric disordersPathway
2016
Review: DNA methylation and alcohol use disorders: Progress and challenges
Zhang H, Gelernter J. Review: DNA methylation and alcohol use disorders: Progress and challenges. American Journal On Addictions 2016, 26: 502-515. PMID: 27759945, PMCID: PMC6003819, DOI: 10.1111/ajad.12465.Peer-Reviewed Original ResearchConceptsDNA methylation changesDNA methylationMethylation changesGenome-wide DNA methylation studyGene expressionPromoter regionGlobal DNA methylation levelsDNA methylation profilesDNA methylation studiesDNA methylation levelsWidespread DNA methylationCandidate gene studiesEpigenetic mechanismsGenetic variationConsequences of AUDMethylation profilesMethylation studiesGene studiesMethylation levelsMethylationAUD subjectsGene-environment interactionsEnvironmental factorsInteractive effectsExpression
2014
Identification of methylation quantitative trait loci (mQTLs) influencing promoter DNA methylation of alcohol dependence risk genes
Zhang H, Wang F, Kranzler HR, Yang C, Xu H, Wang Z, Zhao H, Gelernter J. Identification of methylation quantitative trait loci (mQTLs) influencing promoter DNA methylation of alcohol dependence risk genes. Human Genetics 2014, 133: 1093-1104. PMID: 24889829, PMCID: PMC4127343, DOI: 10.1007/s00439-014-1452-2.Peer-Reviewed Original ResearchConceptsMethylation quantitative trait lociQuantitative trait lociDNA methylationTrait lociSignificant methylation quantitative trait lociSequence variantsRisk genesGene expression regulationGenome-wide association studiesGenome-wide genotype dataPromoter DNA methylationAD risk genesGene promoter regionExpression QTLsExpression regulationGenetic variationPromoter CpGsPromoter region
2013
Sex-biased methylome and transcriptome in human prefrontal cortex
Xu H, Wang F, Liu Y, Yu Y, Gelernter J, Zhang H. Sex-biased methylome and transcriptome in human prefrontal cortex. Human Molecular Genetics 2013, 23: 1260-1270. PMID: 24163133, PMCID: PMC3919013, DOI: 10.1093/hmg/ddt516.Peer-Reviewed Original ResearchConceptsDNA methylationGene expressionSex-biased DNA methylationMultiple test correctionGenome-wide DNA methylationGene Ontology annotationsDAVID functional annotation analysisFunctional annotation analysisRibosome structurePhenotypic variationAnnotation analysisGO termsProtein translationRNA bindingOntology annotationsHost genesDifferential methylationExpression correlationTranscriptomic profilesDifferential brain developmentDifferential expressionMethylation levelsGenesMethylationTranscriptome