2023
Epigenomic charting and functional annotation of risk loci in renal cell carcinoma
Nassar A, Abou Alaiwi S, Baca S, Adib E, Corona R, Seo J, Fonseca M, Spisak S, El Zarif T, Tisza V, Braun D, Du H, He M, Flaifel A, Alchoueiry M, Denize T, Matar S, Acosta A, Shukla S, Hou Y, Steinharter J, Bouchard G, Berchuck J, O’Connor E, Bell C, Nuzzo P, Mary Lee G, Signoretti S, Hirsch M, Pomerantz M, Henske E, Gusev A, Lawrenson K, Choueiri T, Kwiatkowski D, Freedman M. Epigenomic charting and functional annotation of risk loci in renal cell carcinoma. Nature Communications 2023, 14: 346. PMID: 36681680, PMCID: PMC9867739, DOI: 10.1038/s41467-023-35833-5.Peer-Reviewed Original ResearchMeSH KeywordsCarcinoma, Renal CellEpigenomicsForkhead Transcription FactorsHumansKidney NeoplasmsOncogenesTranscription FactorsConceptsMaster transcription factorChIP-seqATAC-seq dataH3K27ac ChIP-seqCcRCC cell linesEpigenomic atlasATAC-seqFunctional annotationTranscriptional landscapePrimary human samplesTranscription factorsRNA-seqRisk lociTranscriptional upregulationSNP arrayRisk SNPsETS-1EpigenomeCell linesFOXI1Renal cell carcinomaEPAS1RCC histologic subtypesHuman samplesBHLHE41
2020
Interplay of somatic alterations and immune infiltration modulates response to PD-1 blockade in advanced clear cell renal cell carcinoma
Braun DA, Hou Y, Bakouny Z, Ficial M, Sant’ Angelo M, Forman J, Ross-Macdonald P, Berger AC, Jegede OA, Elagina L, Steinharter J, Sun M, Wind-Rotolo M, Pignon JC, Cherniack AD, Lichtenstein L, Neuberg D, Catalano P, Freeman GJ, Sharpe AH, McDermott DF, Van Allen EM, Signoretti S, Wu CJ, Shukla SA, Choueiri TK. Interplay of somatic alterations and immune infiltration modulates response to PD-1 blockade in advanced clear cell renal cell carcinoma. Nature Medicine 2020, 26: 909-918. PMID: 32472114, PMCID: PMC7499153, DOI: 10.1038/s41591-020-0839-y.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAged, 80 and overAntigen PresentationAntineoplastic Agents, ImmunologicalCarcinoma, Renal CellCD8-Positive T-LymphocytesChromosome DeletionChromosomes, Human, Pair 6Chromosomes, Human, Pair 9Class I Phosphatidylinositol 3-KinasesDNA-Binding ProteinsExome SequencingFemaleFluorescent Antibody TechniqueGene DeletionGenomicsHistocompatibility Antigens Class IIHistone DemethylasesHistone-Lysine N-MethyltransferaseHumansKidney NeoplasmsLymphocytes, Tumor-InfiltratingMaleMiddle AgedMutationNivolumabPrognosisProteasome Endopeptidase ComplexPTEN PhosphohydrolaseSequence Analysis, RNATOR Serine-Threonine KinasesTranscription FactorsTuberous Sclerosis Complex 1 ProteinTumor Suppressor ProteinsUbiquitin ThiolesteraseVon Hippel-Lindau Tumor Suppressor ProteinConceptsAdvanced clear cell renal cell carcinomaClear cell renal cell carcinomaPD-1 blockadeCell renal cell carcinomaRenal cell carcinomaCell carcinomaDegree of CD8Numerous chromosomal alterationsProspective clinical trialsSomatic alterationsInfiltrated tumorsClinical responseCell infiltrationTherapeutic responseClinical trialsTherapeutic efficacyBlockadeCcRCC tumorsTumorsPBRM1 mutationsModulates responseCD8Chromosomal alterationsImmunofluorescence analysisCarcinoma