2024
Detection of sarcomatoid renal cell carcinoma using plasma cell-free DNA methylation.
Semaan K, El Zarif T, Seo J, Eid M, Canniff J, Fortunato B, Savignano H, Davidsohn M, Lakshminarayanan G, Saad E, Saliby R, Bakouny Z, Matar S, Nuzzo P, Berchuck J, Signoretti S, Braun D, Freedman M, Baca S, Choueiri T. Detection of sarcomatoid renal cell carcinoma using plasma cell-free DNA methylation. Journal Of Clinical Oncology 2024, 42: 449-449. DOI: 10.1200/jco.2024.42.4_suppl.449.Peer-Reviewed Original ResearchDifferentially Methylated RegionsRenal cell carcinomaCell-free DNAMeDIP-seqSarcomatoid differentiationDNA methylation signalsArea under the receiver operating characteristicHigh-throughput sequencingCell carcinomaCell-free DNA methylationFalse discovery rateResponse to immune checkpoint blockadeEpigenomic approachesCfMeDIP-seqSarcomatoid renal cell carcinomaMethylation immunoprecipitationDNA methylationHistological subtypes of cancerAssociated with poor survivalImmune checkpoint blockadeSubtypes of cancerDana-Farber Cancer InstituteSpatial heterogeneityArea under the receiver operating characteristic curveWilcoxon rank sum test
2022
Glucocorticoids unmask silent non-coding genetic risk variants for common diseases
Nguyen T, Gao H, Liu D, Philips T, Ye Z, Lee J, Shi G, Copenhaver K, Zhang L, Wei L, Yu J, Zhang H, Barath A, Luong M, Zhang C, Gaspar-Maia A, Li H, Wang L, Ordog T, Weinshilboum R. Glucocorticoids unmask silent non-coding genetic risk variants for common diseases. Nucleic Acids Research 2022, 50: 11635-11653. PMID: 36399508, PMCID: PMC9723631, DOI: 10.1093/nar/gkac1045.Peer-Reviewed Original ResearchConceptsGene expressionGenomic sequence variantsNon-coding variantsCis-regulatory elementsLigand-dependent associationBreast cancer risk genesInfluence gene expressionCancer risk genesGenetic risk variantsGene-by-environment interactionsEpigenomic approachesSequence variantsAffected genesRisk variantsAssociated with clinical phenotypesRisk genesVariant functionDisease phenotypeDrug responseGenesDisease riskMechanistic frameworkMAST4Clinical phenotypeRisk factorsLoss of PBRM1 alters promoter histone modifications and activates ALDH1A1 to drive renal cell carcinomaPBRM1 loss increases H3K4me3 marks and expression of ALDH1A1
Schoenfeld D, Zhou R, Zairis S, Su W, Steinbach N, Mathur D, Bansal A, Zachem A, Tavarez B, Hasson D, Bernstein E, Rabadan R, Parsons R. Loss of PBRM1 alters promoter histone modifications and activates ALDH1A1 to drive renal cell carcinomaPBRM1 loss increases H3K4me3 marks and expression of ALDH1A1. Molecular Cancer Research 2022, 20: 1193-1207. PMID: 35412614, PMCID: PMC9357026, DOI: 10.1158/1541-7786.mcr-21-1039.Peer-Reviewed Original ResearchConceptsRetinoic acid biosynthesisSuch target genesPromoter histone modificationsAcid biosynthesisHistone modificationsClear cell renal cell carcinomaTarget genesLoss of PBRM1SWI/SNF complexSWI/SNF chromatinSWI/SNF subunitsHistone modification ChIP-seqSWI/SNF componentsATAC-seq dataCcRCC cell linesDe novo gainPBAF subunitsH3K4me3 peaksH3K4me3 marksPBAF complexSNF complexEpigenomic approachesChIP-seqRNA-seqHigh mutation frequency
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