2020
Convergent network effects along the axis of gene expression during prostate cancer progression
Charmpi K, Guo T, Zhong Q, Wagner U, Sun R, Toussaint N, Fritz C, Yuan C, Chen H, Rupp N, Christiansen A, Rutishauser D, Rüschoff J, Fankhauser C, Saba K, Poyet C, Hermanns T, Oehl K, Moore A, Beisel C, Calzone L, Martignetti L, Zhang Q, Zhu Y, Martínez M, Manica M, Haffner M, Aebersold R, Wild P, Beyer A. Convergent network effects along the axis of gene expression during prostate cancer progression. Genome Biology 2020, 21: 302. PMID: 33317623, PMCID: PMC7737297, DOI: 10.1186/s13059-020-02188-9.Peer-Reviewed Original ResearchConceptsHigh-throughput genomic measurementsProstate cancer progressionGene expressionMolecular networksCopy number alterationsCancer progressionComplex genomic alterationsTumor phenotypePrediction of recurrence-free survivalGenomic measurementsRecurrence-free survivalProstate cancer patientsProteomic alterationsGenomic aberrationsAggressive tumor phenotypeGenomic alterationsDownstream proteinsGenomic effectsNetwork-based approachProstate samplesTumor siteBiochemical stateMalignant tumorsProtein levelsTumor tissuesInferring clonal composition from multiple tumor biopsies
Manica M, Kim H, Mathis R, Chouvarine P, Rutishauser D, De Vargas Roditi L, Szalai B, Wagner U, Oehl K, Saba K, Pati A, Saez-Rodriguez J, Roy A, Parsons D, Wild P, Martínez M, Sumazin P. Inferring clonal composition from multiple tumor biopsies. Npj Systems Biology And Applications 2020, 6: 27. PMID: 32843649, PMCID: PMC7447821, DOI: 10.1038/s41540-020-00147-5.Peer-Reviewed Original ResearchConceptsCopy number alterationsEffects of copy number alterationsGenetic instabilityClonal evolutionClonal compositionDrug-resistant prostate cancerAcquisition of mutationsDrug-resistant subclonesPhylogeny reconstructionTumor phylogeniesRelative abundanceTumor biopsiesWilms tumorProstate cancerGenetic alterationsGenetic profileMultiple biopsiesTumor profilingHepatocellular carcinomaPhylogenyTumorSubclonesAnalysis of simulated dataMutationsBiopsyPan-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
2016
Depletion of FOXM1 via MET Targeting Underlies Establishment of a DNA Damage–Induced Senescence Program in Gastric Cancer
Francica P, Nisa L, Aebersold D, Langer R, Bladt F, Blaukat A, Stroka D, Martínez M, Zimmer Y, Medová M. Depletion of FOXM1 via MET Targeting Underlies Establishment of a DNA Damage–Induced Senescence Program in Gastric Cancer. Clinical Cancer Research 2016, 22: 5322-5336. PMID: 27185371, DOI: 10.1158/1078-0432.ccr-15-2987.Peer-Reviewed Original ResearchConceptsDNA damage-induced senescenceMET inhibitionMET targetingGastric tumorsNegative regulator of senescenceHuman gastric cancer cell linesGastric cancer cell linesInfliction of DNA damageAberrant MET expressionEctopic expression of FoxM1Tumor tissue microarraysCopy number alterationsRegulation of senescenceMET receptor tyrosine kinaseDepletion of FOXM1Receptor tyrosine kinasesGastric tumor cellsExpression of FoxM1Cancer cell linesCancer Genome AtlasDownregulation of FoxM1Deregulated signalingDownstream effectorsNegative regulatorTumor radiosensitivity