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 analysisCpH 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
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 rateAccelerated DNA Methylation Aging in U.S. Military Veterans: Results From the National Health and Resilience in Veterans Study
Tamman AJF, Montalvo-Ortiz JL, Southwick SM, Krystal JH, Levy BR, Pietrzak RH. Accelerated DNA Methylation Aging in U.S. Military Veterans: Results From the National Health and Resilience in Veterans Study. American Journal Of Geriatric Psychiatry 2019, 27: 528-532. PMID: 30792041, DOI: 10.1016/j.jagp.2019.01.001.Peer-Reviewed Original ResearchConceptsNational HealthPsychosocial factorsVeterans StudyMale U.S. veteransLifetime trauma burdenAccelerated DNA methylation agingDNA methylation agingU.S. military veteransMethylation agingTrauma burdenU.S. veteransPrevention effortsAdditional correlatesNegative beliefsMilitary veteransSexual traumaVeteransTraumatic stressDNA methylationHealthChild sexual traumaBody massRepresentative sample
2018
Machine learning selected smoking-associated DNA methylation signatures that predict HIV prognosis and mortality
Zhang X, Hu Y, Aouizerat BE, Peng G, Marconi VC, Corley MJ, Hulgan T, Bryant KJ, Zhao H, Krystal JH, Justice AC, Xu K. Machine learning selected smoking-associated DNA methylation signatures that predict HIV prognosis and mortality. Clinical Epigenetics 2018, 10: 155. PMID: 30545403, PMCID: PMC6293604, DOI: 10.1186/s13148-018-0591-z.Peer-Reviewed Original ResearchConceptsWhite blood cellsSmoking-associated DNA methylationHIV prognosisInfection-related clinical outcomesBlood cellsSmoking-associated CpGsHIV-positive individualsImmune-related outcomesEpigenome-wide significant CpGsClinical outcomesTobacco smokingVeteran populationSurvival rateDNA methylation indexMortalityFrailtyHIVMethylation indexPrognosisMethylation signaturesDNA methylationOutcomesCell cycleCpGSignificant CpGsDNA methylation signatures analysis with Illumina Infinitum MethylationEPIC and Infinium Human Methylation 450K BeadChip
Zhang X, Zhang X, Hu Y, Justice A, Li B, Wang Z, Zhao H, Krystal J, Xu K. DNA methylation signatures analysis with Illumina Infinitum MethylationEPIC and Infinium Human Methylation 450K BeadChip. Protocol Exchange 2018 DOI: 10.1038/protex.2018.080.Peer-Reviewed Original Research
2017
DNA methylation signatures analysis with Illumina Infinitum MethylationEPIC and Infinium Human Methylation 450K BeadChip
Zhang X, Zhang X, Hu Y, Justice A, Li B, Wang Z, Zhao H, Krystal J, Xu K. DNA methylation signatures analysis with Illumina Infinitum MethylationEPIC and Infinium Human Methylation 450K BeadChip. Protocol Exchange 2017 DOI: 10.1038/protex.2017.135.Peer-Reviewed Original Research
2016
Epigenome-wide differential DNA methylation between HIV-infected and uninfected individuals
Zhang X, Justice AC, Hu Y, Wang Z, Zhao H, Wang G, Johnson EO, Emu B, Sutton RE, Krystal JH, Xu K. Epigenome-wide differential DNA methylation between HIV-infected and uninfected individuals. Epigenetics 2016, 11: 750-760. PMID: 27672717, PMCID: PMC5094631, DOI: 10.1080/15592294.2016.1221569.Peer-Reviewed Original ResearchDifferential DNA methylationDNA methylationLarge-scale epigenome-wide association studyMajor histocompatibility complex (MHC) class I gene expressionNovel host genesEpigenome-wide association studiesClass I gene expressionVeterans Aging Cohort StudyEpigenome-wide significant CpGsEpigenetic controlHIV-1 infectionHost genesI gene expressionEpigenetic changesHost genomeCARD domainKey regulatorGene expressionAssociation studiesSignificant CpGsGene 5CpG sitesMethylationCell typesLower methylation