2025
High MGMT expression identifies aggressive colorectal cancer with distinct genomic features and immune evasion properties
Zhang J, Rajendran B, Desai S, Gibson J, DiPalermo J, LoRusso P, Kong Y, Zhao H, Cecchini M, Schalper K. High MGMT expression identifies aggressive colorectal cancer with distinct genomic features and immune evasion properties. Journal For ImmunoTherapy Of Cancer 2025, 13: e011653. PMID: 40935566, DOI: 10.1136/jitc-2025-011653.Peer-Reviewed Original ResearchThis study shows that high MGMT expression in colorectal cancer is linked to aggressive behavior, distinct genomic features, immune evasion, and shorter survival, highlighting its potential as a biomarker for prognosis and therapeutic targeting.Incorporating local ancestry information to predict genetically associated DNA methylation in admixed populations
Cheng Y, Zhou G, Li H, Zhang X, Justice A, Martinez C, Aouizerat B, Xu K, Zhao H. Incorporating local ancestry information to predict genetically associated DNA methylation in admixed populations. Briefings In Bioinformatics 2025, 26: bbaf325. PMID: 40622482, PMCID: PMC12232425, DOI: 10.1093/bib/bbaf325.Peer-Reviewed Original ResearchConceptsMethylome-wide association studiesAdmixed populationsComplex traitsLocal ancestryAssociation studiesDNA methylationAssociated with complex traitsLocal ancestry informationPopulations of European ancestryCpG methylation levelsNon-European populationsMeasurement of methylationAncestry informationCpG sitesMethylation levelsEuropean ancestryEpigenetic underpinningsCpGAncestryTraitsMethylationAmerican populationAfrican American populationDNAPopulationBidirectional relationship between epigenetic age and stroke, dementia, and late-life depression
Rivier C, Szejko N, Renedo D, Clocchiatti-Tuozzo S, Huo S, de Havenon A, Zhao H, Gill T, Sheth K, Falcone G. Bidirectional relationship between epigenetic age and stroke, dementia, and late-life depression. Nature Communications 2025, 16: 1261. PMID: 39893209, PMCID: PMC11787333, DOI: 10.1038/s41467-024-54721-0.Peer-Reviewed Original ResearchThis study shows a bidirectional link between accelerated epigenetic aging and brain health events like stroke, dementia, and depression, supporting new prevention strategies for aging-related conditions.Hypermethylation of PM20D1 Is Associated With Carotid Bifurcation Intima‐Media Thickness in Dominican Republic Families
Dueker N, Zhao H, Gardener H, Kaur S, Dong C, Cabral D, Sacco R, Blanton S, Rundek T, Wang L. Hypermethylation of PM20D1 Is Associated With Carotid Bifurcation Intima‐Media Thickness in Dominican Republic Families. Journal Of The American Heart Association 2025, 14: e034033. PMID: 39791430, PMCID: PMC12054445, DOI: 10.1161/jaha.123.034033.Peer-Reviewed Original ResearchConceptsDifferentially Methylated RegionsMendelian randomization analysisCytosine nucleotidesCarotid intima-media thicknessExpression quantitative trait loci studiesRandomization analysisExpression quantitative trait lociIntima-media thicknessQuantitative trait loci studiesEpigenome-wide association studiesQuantitative trait lociTraditional vascular risk factorsBifurcation intima-media thicknessBlood-derived DNAGuanine nucleotide siteLinear mixed model analysisNucleotide sitesVascular risk factorsMeasures of atherosclerosisCarotid bifurcation intima-media thicknessTrait lociAssociation studiesNucleotide methylationLoci studiesGenetic variants
2024
HBI: a hierarchical Bayesian interaction model to estimate cell-type-specific methylation quantitative trait loci incorporating priors from cell-sorted bisulfite sequencing data
Cheng Y, Cai B, Li H, Zhang X, D’Souza G, Shrestha S, Edmonds A, Meyers J, Fischl M, Kassaye S, Anastos K, Cohen M, Aouizerat B, Xu K, Zhao H. HBI: a hierarchical Bayesian interaction model to estimate cell-type-specific methylation quantitative trait loci incorporating priors from cell-sorted bisulfite sequencing data. Genome Biology 2024, 25: 273. PMID: 39407252, PMCID: PMC11476968, DOI: 10.1186/s13059-024-03411-7.Peer-Reviewed Original ResearchMeSH KeywordsBayes TheoremDNA MethylationHumansModels, GeneticQuantitative Trait LociSequence Analysis, DNAConceptsMethylation quantitative trait lociQuantitative trait lociTrait lociMethylation dataFunctional annotation of genetic variantsAnnotation of genetic variantsGenetic variantsBisulfite sequencing dataEffects of genetic variantsBiologically relevant cell typesDNA methylation levelsCell typesFunctional annotationSequence dataComplex traitsMethylation datasetsRelevant cell typesMeQTLsMethylation levelsMethylation regulatorsReal data analysesLociVariantsMethylationDNA
2023
Reply to: Genetic differentiation at probe SNPs leads to spurious results in meQTL discovery
Cheng Y, Li B, Zhang X, Aouizerat B, Zhao H, Xu K. Reply to: Genetic differentiation at probe SNPs leads to spurious results in meQTL discovery. Communications Biology 2023, 6: 1296. PMID: 38129596, PMCID: PMC10739901, DOI: 10.1038/s42003-023-05646-9.Peer-Reviewed Original Research
2022
Outcomes Stratification of Head and Neck Cancer Using Pre- and Post-treatment DNA Methylation From Peripheral Blood
Qian D, Ulrich B, Peng G, Zhao H, Conneely K, Miller A, Bruner D, Eldridge R, Wommack E, Higgins K, Shin D, Saba N, Smith A, Burtness B, Park H, Stokes W, Beitler J, Xiao C. Outcomes Stratification of Head and Neck Cancer Using Pre- and Post-treatment DNA Methylation From Peripheral Blood. International Journal Of Radiation Oncology • Biology • Physics 2022, 115: 1217-1228. PMID: 36410685, PMCID: PMC12272450, DOI: 10.1016/j.ijrobp.2022.11.009.Peer-Reviewed Original ResearchConceptsRecurrence-free survivalWorse recurrence-free survivalOverall survivalMethylation risk scoreRadiation therapyValidation cohortPeripheral bloodDiscovery cohortOutcome stratificationShorter recurrence-free survivalNeck squamous cell carcinomaGastrostomy tube insertionHigher neutrophil countOral cavity cancerAforementioned risk factorsSquamous cell carcinomaPeripheral blood samplesNonmetastatic HNSCCNeutrophil countPrognostic factorsCox regressionPrognostic valueCell carcinomaTube insertionImmune modulation
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