2022
Soluble CD14-associated DNA methylation sites predict mortality among men with HIV infection
Titanji BK, Wang Z, Chen J, Hui Q, So-Armah K, Freiberg M, Justice AC, Ke X, Marconi VC, Sun YV. Soluble CD14-associated DNA methylation sites predict mortality among men with HIV infection. AIDS 2022, 36: 1563-1571. PMID: 35979830, PMCID: PMC9394925, DOI: 10.1097/qad.0000000000003279.Peer-Reviewed Original ResearchConceptsVeterans Aging Cohort StudyAging Cohort StudyElevated plasma levelsCox regression modelUnderstanding of prognosisPeripheral blood samplesPotential therapeutic targetEpigenome-wide association studiesMultiple testingCause mortalitySCD14 levelsCohort studyHIV infectionPlasma levelsSoluble CD14Disease progressionImmune functionSurvival timeBlood samplesSCD14Therapeutic targetPWHAntiviral responseSignificant associationDNAm sitesIncorporating local ancestry improves identification of ancestry-associated methylation signatures and meQTLs in African Americans
Li B, Aouizerat BE, Cheng Y, Anastos K, Justice AC, Zhao H, Xu K. Incorporating local ancestry improves identification of ancestry-associated methylation signatures and meQTLs in African Americans. Communications Biology 2022, 5: 401. PMID: 35488087, PMCID: PMC9054854, DOI: 10.1038/s42003-022-03353-5.Peer-Reviewed Original ResearchA new monocyte epigenetic clock reveals nonlinear effects of alcohol consumption on biological aging in three independent cohorts (N = 2242)
Liang X, Sinha R, Justice AC, Cohen MH, Aouizerat BE, Xu K. A new monocyte epigenetic clock reveals nonlinear effects of alcohol consumption on biological aging in three independent cohorts (N = 2242). Alcohol Clinical And Experimental Research 2022, 46: 736-748. PMID: 35257385, PMCID: PMC9117474, DOI: 10.1111/acer.14803.Peer-Reviewed Original Research
2020
DNA methylation biomarker selected by an ensemble machine learning approach predicts mortality risk in an HIV-positive veteran population
Shu C, Justice AC, Zhang X, Marconi VC, Hancock DB, Johnson EO, Xu K. DNA methylation biomarker selected by an ensemble machine learning approach predicts mortality risk in an HIV-positive veteran population. Epigenetics 2020, 16: 741-753. PMID: 33092459, PMCID: PMC8216205, DOI: 10.1080/15592294.2020.1824097.Peer-Reviewed Original ResearchConceptsVeterans Aging Cohort StudyMortality risk groupsAging Cohort StudyHigher mortality riskMortality riskRisk groupsCohort studyHigh mortality risk groupLow-mortality risk groupsInflammation response pathwayHIV-positive participantsHuman immunodeficiency virusLow-risk groupImproved life expectancyVACS IndexHIV populationNatural killerImmunodeficiency virusPredictive biomarkersPLWHDNA methylation biomarkersVeteran populationSurvival analysisEpigenome-wide associationHIVDNA methylation mediates the effect of cocaine use on HIV severity
Shu C, Justice AC, Zhang X, Wang Z, Hancock DB, Johnson EO, Xu K. DNA methylation mediates the effect of cocaine use on HIV severity. Clinical Epigenetics 2020, 12: 140. PMID: 32928285, PMCID: PMC7491141, DOI: 10.1186/s13148-020-00934-1.Peer-Reviewed Original ResearchConceptsHIV-positive participantsHIV severityVACS IndexCocaine useCocaine effectsVeterans Aging Cohort Study Biomarker CohortVeterans Aging Cohort Study (VACS) IndexEpigenome-wide associationHuman immunodeficiency virus (HIV) progressionHigher VACS indexFrequent cocaine useCandidate CpG sitesPersistent cocaine useMendelian randomization analysisHIV outcomesBiomarker cohortHIV progressionVirus progressionVAC indexVeteran populationAntiviral responseCandidate mediatorsStudy indicesMR analysisSeverityDNA methylation signature on phosphatidylethanol, not on self-reported alcohol consumption, predicts hazardous alcohol consumption in two distinct populations
Liang X, Justice AC, So-Armah K, Krystal JH, Sinha R, Xu K. DNA methylation signature on phosphatidylethanol, not on self-reported alcohol consumption, predicts hazardous alcohol consumption in two distinct populations. Molecular Psychiatry 2020, 26: 2238-2253. PMID: 32034291, PMCID: PMC8440221, DOI: 10.1038/s41380-020-0668-x.Peer-Reviewed Original ResearchConceptsHazardous alcohol drinkingSelf-reported alcohol consumptionAlcohol consumptionCohort 2Cohort 1Epigenome-wide association studiesSelf-reported dataHazardous alcohol consumptionAlcohol use disorderDNAm signaturesObjective measuresAlcohol drinkingClinical assessmentUse disordersRobust biomarkersDNA methylation signaturesValidation setDistinct populationsCharacteristic curvePEthEpigenetic biomarkersMethylation signatures
2019
DNA Methylation Markers of Type 2 Diabetes Mellitus Among Male Veterans With or Without Human Immunodeficiency Virus Infection
Mathur R, Hui Q, Huang Y, Gwinn M, So-Armah K, Freiberg MS, Justice AC, Xu K, Marconi VC, Sun YV. DNA Methylation Markers of Type 2 Diabetes Mellitus Among Male Veterans With or Without Human Immunodeficiency Virus Infection. The Journal Of Infectious Diseases 2019, 219: 1959-1962. PMID: 30649532, PMCID: PMC6534194, DOI: 10.1093/infdis/jiz023.Peer-Reviewed Original ResearchConceptsHuman immunodeficiency virus (HIV) infectionHIV infection statusImmunodeficiency virus infectionVirus infectionVeterans Aging Cohort StudyType 2 diabetes mellitusInfection statusPancreatic β-cell functionAging Cohort StudyΒ-cell functionCohort studyDiabetes mellitusT2DM pathogenesisMale veteransType 2DNA methylation markersSuggestive interactionStatistical significanceMale participantsMellitusT2DMMethylation markersNovel associationsInfectionSuggestive statistical significance
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 CpGsUsing DNA methylation to validate an electronic medical record phenotype for smoking
McGinnis KA, Justice AC, Tate JP, Kranzler HR, Tindle HA, Becker WC, Concato J, Gelernter J, Li B, Zhang X, Zhao H, Crothers K, Xu K, Group F. Using DNA methylation to validate an electronic medical record phenotype for smoking. Addiction Biology 2018, 24: 1056-1065. PMID: 30284751, PMCID: PMC6541538, DOI: 10.1111/adb.12670.Peer-Reviewed Original ResearchConceptsVeterans Aging Cohort StudyAging Cohort StudyStrong associationDNA methylation sitesSmoking metricsCohort studyCurrent smokingSmoking statusSpearman correlation coefficientBiomarker cohortBlood samplesSmoking behaviorCriterion standardLogistic regressionSmokingSmoking phenotypesCurve analysisGroup assignmentText notesAssociationDescriptive statisticsPhenotypeCorrelation coefficientGenetic discoveriesPercent
2017
DNA methylation signatures of illicit drug injection and hepatitis C are associated with HIV frailty
Zhang X, Hu Y, Justice AC, Li B, Wang Z, Zhao H, Krystal JH, Xu K. DNA methylation signatures of illicit drug injection and hepatitis C are associated with HIV frailty. Nature Communications 2017, 8: 2243. PMID: 29269866, PMCID: PMC5740109, DOI: 10.1038/s41467-017-02326-1.Peer-Reviewed Original ResearchConceptsIllicit drug injectionHepatitis C infectionWhite blood cellsIllicit drug useCo-occurring conditionsMethylation signaturesDiscovery sampleC infectionHepatitis CEpigenome-wide association analysisLower frailtyDrug injectionHigh frailtyImmune functionHealth outcomesDrug useFrailtyDNA methylation signaturesBlood cellsHIVReplication sampleEpigenetic programmingSignificant CpGsEpigenetic effectsIndividualsIdentification of HIV infection-related DNA methylation sites and advanced epigenetic aging in HIV-positive, treatment-naive U.S. veterans
Nelson KN, Hui Q, Rimland D, Xu K, Freiberg MS, Justice AC, Marconi VC, Sun YV. Identification of HIV infection-related DNA methylation sites and advanced epigenetic aging in HIV-positive, treatment-naive U.S. veterans. AIDS 2017, 31: 571-575. PMID: 27922854, PMCID: PMC5263111, DOI: 10.1097/qad.0000000000001360.Peer-Reviewed Original ResearchConceptsHIV-positive individualsHIV-negative individualsHIV infectionART initiationBlood samplesTreatment-naive HIV-positive individualsVeterans Aging Cohort StudyHIV-negative groupHIV-positive patientsAging Cohort StudyDNAm ageCohort of veteransPeripheral blood samplesNaive HIVAntiretroviral therapyAntiretroviral treatmentCohort studyStudy cohortAge-related diseasesMyocardial infarctionLarge cohortHealthy personsHigh riskHIVU.S. veterans