2020
Pan-cancer analysis of somatic mutations and epigenetic alterations in insulated neighbourhood boundaries
Pinoli P, Stamoulakatou E, Nguyen A, Martínez M, Ceri S. Pan-cancer analysis of somatic mutations and epigenetic alterations in insulated neighbourhood boundaries. PLOS ONE 2020, 15: e0227180. PMID: 31945090, PMCID: PMC6964824, DOI: 10.1371/journal.pone.0227180.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid MotifsBinding SitesCCCTC-Binding FactorChromosomes, Human, Pair 11DNA Copy Number VariationsDNA MethylationDNA Mutational AnalysisEpigenesis, GeneticExonsFemaleGene Expression Regulation, NeoplasticGenome, HumanHumansInsulator ElementsMutation RateNeoplasmsPoint MutationPromoter Regions, GeneticConceptsCTCF motifsCopy number alterationsSomatic mutationsAbnormal methylationCTCF binding sitesCopy number alteration eventsAnalysis of somatic mutationsMatched normal samplesCancer typesCTCF bindingOncogene dysregulationMutation enrichmentPan-cancer analysisPositive selectionEpigenetic alterationsIn-boundaryGenomic alterationsMotifMutational signaturesBinding sitesMutationsCTCFPan-cancerCopyNormal samples
2019
A Single-Cell Atlas of the Tumor and Immune Ecosystem of Human Breast Cancer
Wagner J, Rapsomaniki M, Chevrier S, Anzeneder T, Langwieder C, Dykgers A, Rees M, Ramaswamy A, Muenst S, Soysal S, Jacobs A, Windhager J, Silina K, van den Broek M, Dedes K, Martínez M, Weber W, Bodenmiller B. A Single-Cell Atlas of the Tumor and Immune Ecosystem of Human Breast Cancer. Cell 2019, 177: 1330-1345.e18. PMID: 30982598, PMCID: PMC6526772, DOI: 10.1016/j.cell.2019.03.005.Peer-Reviewed Original ResearchConceptsBreast cancerBreast cancer ecosystemsTumor-associated macrophagesResponse to therapyHuman breast tumorsTumor cell compositionHuman breast cancerNon-tumor tissue samplesPrecision medicine approachT cellsBreast tumorsImmune cellsPoor prognosisAntibody panelTumor cellsTumor ecosystemHeterogeneous diseaseClinical dataDisease progressionTumorSingle-cell atlasMass cytometryPhenotypic abnormalitiesMedicine approachImmune ecosystem