2024
Folate metabolism and risk of childhood acute lymphoblastic leukemia: a genetic pathway analysis from the Childhood Cancer and Leukemia International Consortium
Metayer C, Spector L, Scheurer M, Jeon S, Scott R, Takagi M, Clavel J, Manabe A, Ma X, Hailu E, Lupo P, Urayama K, Bonaventure A, Kato M, Meirhaeghe A, Chiang C, Morimoto L, Wiemels J. Folate metabolism and risk of childhood acute lymphoblastic leukemia: a genetic pathway analysis from the Childhood Cancer and Leukemia International Consortium. Cancer Epidemiology Biomarkers & Prevention 2024, 33: 1248-1252. PMID: 38904462, PMCID: PMC11369612, DOI: 10.1158/1055-9965.epi-24-0189.Peer-Reviewed Original ResearchSingle nucleotide polymorphismsGenome-wide dataAncestry groupsFolate metabolic pathwayGenetic variantsChildhood cancerMetabolic pathwaysGenetic pathway analysisRisk of childhood ALLRisk of childhood acute lymphoblastic leukemiaGene-folate interactionsChildhood ALL riskCase-control studyDNA methylationMETAL softwareGenetic studiesNucleotide polymorphismsPathway analysisMeta-analysis of original dataALL riskGenetic effectsAncestryFolate pathwayMaternal genetic effectsFolate intake
2022
Incorporation of DNA methylation quantitative trait loci (mQTLs) in epigenome-wide association analysis: application to birthweight effects in neonatal whole blood
Li S, Mancuso N, Metayer C, Ma X, de Smith A, Wiemels J. Incorporation of DNA methylation quantitative trait loci (mQTLs) in epigenome-wide association analysis: application to birthweight effects in neonatal whole blood. Clinical Epigenetics 2022, 14: 158. PMID: 36457128, PMCID: PMC9714153, DOI: 10.1186/s13148-022-01385-6.Peer-Reviewed Original ResearchConceptsMethylation quantitative trait lociSingle nucleotide polymorphismsDNA methylationGenetic variationDNA methylation quantitative trait lociGenetic effectsDiverse genetic ancestryEPIC arrayCpG island shore regionQuantitative trait lociDNA methylation dataEpigenome-wide association analysisTrait lociDevelopmental traitsEWAS resultsGenetic elementsGene expressionMethylation dataAssociation studiesK arrayAssociation analysisCertain lociMethylation levelsIllumina 450Top hitsInvestigating DNA methylation as a mediator of genetic risk in childhood acute lymphoblastic leukemia
Xu K, Li S, Pandey P, Kang AY, Morimoto LM, Mancuso N, Ma X, Metayer C, Wiemels JL, de Smith AJ. Investigating DNA methylation as a mediator of genetic risk in childhood acute lymphoblastic leukemia. Human Molecular Genetics 2022, 31: 3741-3756. PMID: 35717575, PMCID: PMC9616572, DOI: 10.1093/hmg/ddac137.Peer-Reviewed Original ResearchConceptsEpigenome-wide association studiesSingle nucleotide polymorphismsGenetic risk lociDNA methylationRisk single nucleotide polymorphismsRisk lociAssociation studiesHeritable genetic variationGenome-wide association studiesMost single nucleotide polymorphismsDNA methylation differencesNon-European populationsEpigenetic mechanismsGenetic variationMethylation differencesSignificant DMPsPromoter regionFunctional pathwaysCpG positionsAssociation analysisFunctional roleMethylationNucleotide polymorphismsLociBlood DNA
2021
The genome-wide impact of trisomy 21 on DNA methylation and its implications for hematopoiesis
Muskens IS, Li S, Jackson T, Elliot N, Hansen HM, Myint SS, Pandey P, Schraw JM, Roy R, Anguiano J, Goudevenou K, Siegmund KD, Lupo PJ, de Bruijn MFTR, Walsh KM, Vyas P, Ma X, Roy A, Roberts I, Wiemels JL, de Smith AJ. The genome-wide impact of trisomy 21 on DNA methylation and its implications for hematopoiesis. Nature Communications 2021, 12: 821. PMID: 33547282, PMCID: PMC7865055, DOI: 10.1038/s41467-021-21064-z.Peer-Reviewed Original ResearchMeSH KeywordsCase-Control StudiesCore Binding Factor Alpha 2 SubunitCpG IslandsDNA MethylationDown SyndromeEpigenesis, GeneticFemaleFetusGATA1 Transcription FactorGenome, HumanGenome-Wide Association StudyHematopoiesisHematopoietic Stem CellsHumansInfant, NewbornLiverMalePromoter Regions, GeneticProto-Oncogene Protein c-fli-1ConceptsDNA methylationGenome-wide impactGenome-wide effectsGenome-wide perturbationsPromoter/enhancer regionEpigenome-wide association studiesAssociation study resultsGene expression changesHematopoietic stem/progenitor cellsCell-type heterogeneityStem/progenitor cellsEpigenome-wide significant CpGsHematopoietic developmentDifferential methylationEpigenetic changesGene expressionPromoter regionEnhancer regionExpression changesAssociation studiesSignificant CpGsImportant regulatorSignificant hypermethylationHematopoietic cellsMethylation
2014
PTPRG inhibition by DNA methylation and cooperation with RAS gene activation in childhood acute lymphoblastic leukemia
Xiao J, Lee S, Xiao Y, Ma X, Houseman EA, Hsu L, Roy R, Wrensch M, de Smith A, Chokkalingam A, Buffler P, Wiencke JK, Wiemels JL. PTPRG inhibition by DNA methylation and cooperation with RAS gene activation in childhood acute lymphoblastic leukemia. International Journal Of Cancer 2014, 135: 1101-1109. PMID: 24496747, PMCID: PMC4776754, DOI: 10.1002/ijc.28759.Peer-Reviewed Original ResearchMeSH KeywordsCell Transformation, NeoplasticChildChild, PreschoolDNA MethylationDNA-Binding ProteinsEnzyme ActivationEpigenesis, GeneticExtracellular Signal-Regulated MAP KinasesGene Expression Regulation, LeukemicHEK293 CellsHumansMutationPhosphorylationPrecursor Cell Lymphoblastic Leukemia-LymphomaPromoter Regions, GeneticRas ProteinsReceptor-Like Protein Tyrosine Phosphatases, Class 5Transcription FactorsTranscriptional ActivationConceptsDNA methylationPTPRG expressionDNA methylation profilesDNA methylation statusDephosphorylation of ERKMember genesEpigenetic mechanismsGene activationMutant RASRAS gene activationMethylation profilesGene expressionPtprg geneMethylation statusCell growthAdditional roleMethylationPotential therapeutic targetCell linesGenetic characteristicsGenesLeukemia phenotypeTherapeutic targetMutationsExpression
2012
A global DNA methylation and gene expression analysis of early human B-cell development reveals a demethylation signature and transcription factor network
Lee ST, Xiao Y, Muench MO, Xiao J, Fomin ME, Wiencke JK, Zheng S, Dou X, de Smith A, Chokkalingam A, Buffler P, Ma X, Wiemels JL. A global DNA methylation and gene expression analysis of early human B-cell development reveals a demethylation signature and transcription factor network. Nucleic Acids Research 2012, 40: 11339-11351. PMID: 23074194, PMCID: PMC3526268, DOI: 10.1093/nar/gks957.Peer-Reviewed Original ResearchConceptsB cell developmentDNA methylationMultipotent progenitorsDemethylation eventsEpigenetic changesGene body DNA methylationEarly B cell developmentTranscription factor networkTranscription factor sitesDNA methylation changesHuman B cell developmentB cell-related diseasesFeatures of promotersGene expression analysisGlobal DNA methylationTF occupancyGene bodiesPre-B-cell leukemiaFactor networkCpG islandsMethylation changesFactor sitesExpression analysisFetal bone marrowExpression arrays