2014
T-RECS: STABLE SELECTION OF DYNAMICALLY FORMED GROUPS OF FEATURES WITH APPLICATION TO PREDICTION OF CLINICAL OUTCOMES
Altman R, Dunker A, Hunter L, Ritchie M, Murray T, Klein T, HUANG G, TSAMARDINOS I, RAGHU V, KAMINSKI N, BENOS P. T-RECS: STABLE SELECTION OF DYNAMICALLY FORMED GROUPS OF FEATURES WITH APPLICATION TO PREDICTION OF CLINICAL OUTCOMES. Biocomputing 2014, 20: 431-42. PMID: 25592602, PMCID: PMC4299881, DOI: 10.1142/9789814644730_0041.Peer-Reviewed Original ResearchConceptsTraditional feature selection methodsFeature selection methodCohort of patientsPersonalized medicine strategiesReal expression dataFeature selectionClassification accuracyCluster selectionBiological datasetsClinical outcomesCluster featuresLung diseaseBreast cancerSelection methodPatient classificationStructured natureMedicine strategiesSurvival dataTarget variablesEfficient selectionCohortStable selectionImportant featuresMatrix Metalloproteinase-19 Promotes Metastatic Behavior In Vitro and Is Associated with Increased Mortality in Non–Small Cell Lung Cancer
Yu G, Herazo-Maya JD, Nukui T, Romkes M, Parwani A, Juan-Guardela BM, Robertson J, Gauldie J, Siegfried JM, Kaminski N, Kass DJ. Matrix Metalloproteinase-19 Promotes Metastatic Behavior In Vitro and Is Associated with Increased Mortality in Non–Small Cell Lung Cancer. American Journal Of Respiratory And Critical Care Medicine 2014, 190: 780-790. PMID: 25250855, PMCID: PMC4299607, DOI: 10.1164/rccm.201310-1903oc.Peer-Reviewed Original ResearchConceptsNon-small cell lung cancerCell lung cancerLung cancerEpithelial-mesenchymal transitionLung tumorsMatrix metalloproteinasesProgression of NSCLCNormal lung tissuesHuman lung cancerNSCLC cell linesMultiple NSCLC cell linesLung cancer tumorsMMP19 expressionPoor prognosisCancer deathControl subjectsIncreased MortalityLung tissueNSCLC cellsMolecular pathogenesisPotential biomarkersDisease severityMetastatic behaviorCancerCancer tumorsMicroRNA mimicry blocks pulmonary fibrosis
Montgomery RL, Yu G, Latimer PA, Stack C, Robinson K, Dalby CM, Kaminski N, van Rooij E. MicroRNA mimicry blocks pulmonary fibrosis. EMBO Molecular Medicine 2014, 6: 1347-1356. PMID: 25239947, PMCID: PMC4287936, DOI: 10.15252/emmm.201303604.Peer-Reviewed Original ResearchNrf2 Amplifies Oxidative Stress via Induction of Klf9
Zucker SN, Fink EE, Bagati A, Mannava S, Bianchi-Smiraglia A, Bogner PN, Wawrzyniak JA, Foley C, Leonova KI, Grimm MJ, Moparthy K, Ionov Y, Wang J, Liu S, Sexton S, Kandel ES, Bakin AV, Zhang Y, Kaminski N, Segal BH, Nikiforov MA. Nrf2 Amplifies Oxidative Stress via Induction of Klf9. Molecular Cell 2014, 53: 916-928. PMID: 24613345, PMCID: PMC4049522, DOI: 10.1016/j.molcel.2014.01.033.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBinding SitesBleomycinCell Line, TumorGene Expression RegulationGenes, ReporterHumansKruppel-Like Transcription FactorsLuciferasesLungMiceNF-E2-Related Factor 2NIH 3T3 CellsOxidative StressPromoter Regions, GeneticProtein BindingPulmonary FibrosisReactive Oxygen SpeciesSignal TransductionConceptsReactive oxygen speciesKey transcriptional regulatorMetabolism of ROSOxidative stressPathogenesis of bleomycinKruppel-like factor 9Thioredoxin reductase 2Subsequent cell deathTranscription factor 2Antioxidant gene expressionUbiquitous regulatorsTranscriptional regulatorsIntracellular reactive oxygen speciesLung injuryFeedforward regulationPulmonary fibrosisGene expressionOxidant injuryROS clearanceCell deathReductase 2Mouse tissuesCultured cellsNF-E2Factor 9
2012
First-in-Human Trial of a STAT3 Decoy Oligonucleotide in Head and Neck Tumors: Implications for Cancer Therapy
Sen M, Thomas SM, Kim S, Yeh JI, Ferris RL, Johnson JT, Duvvuri U, Lee J, Sahu N, Joyce S, Freilino ML, Shi H, Li C, Ly D, Rapireddy S, Etter JP, Li PK, Wang L, Chiosea S, Seethala RR, Gooding WE, Chen X, Kaminski N, Pandit K, Johnson DE, Grandis JR. First-in-Human Trial of a STAT3 Decoy Oligonucleotide in Head and Neck Tumors: Implications for Cancer Therapy. Cancer Discovery 2012, 2: 694-705. PMID: 22719020, PMCID: PMC3668699, DOI: 10.1158/2159-8290.cd-12-0191.Peer-Reviewed Original ResearchConceptsSTAT3 target genesTarget genesSTAT3 target gene expressionSTAT3-selective inhibitorsTarget gene expressionInhibited xenograft growthSelective STAT3 inhibitorSystemic administrationTranscription factor decoyTranscription factorsSTAT3 proteinBroader clinical developmentGene expressionPhase 0 trialsSTAT3 inhibitorHuman cancersSTAT3Expression levelsSTAT3 decoyCancer cellsCellular viabilityNeck cancerSaline controlsNeck tumorsHuman trialsZyxin Is a Transforming Growth Factor-β (TGF-β)/Smad3 Target Gene That Regulates Lung Cancer Cell Motility via Integrin α5β1*
Mise N, Savai R, Yu H, Schwarz J, Kaminski N, Eickelberg O. Zyxin Is a Transforming Growth Factor-β (TGF-β)/Smad3 Target Gene That Regulates Lung Cancer Cell Motility via Integrin α5β1*. Journal Of Biological Chemistry 2012, 287: 31393-31405. PMID: 22778267, PMCID: PMC3438968, DOI: 10.1074/jbc.m112.357624.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell Adhesion MoleculesCell Line, TumorCell MovementFocal AdhesionsGene SilencingHumansIntegrin alpha5beta1Intercellular JunctionsLung NeoplasmsMiceMice, Mutant StrainsMicrofilament ProteinsPhosphoproteinsProto-Oncogene Proteins p21(ras)Signal TransductionSmad3 ProteinTransforming Growth Factor beta1ZyxinConceptsEpithelial-mesenchymal transitionCancer cell motilityCell motilityFocal adhesionsZyxin expressionCell-extracellular matrix adhesionLung cancer cellsFocal adhesion proteinsSingle cell motilityCell-cell junctionsCell adherens junctionsNovel functional targetSingle cell migrationLung cancer cell motilityCancer cellsNovel direct targetZyxin geneTGF-β signalingTumor suppressor effectActin cytoskeletonAdherens junctionsCytoskeletal organizationZyxinTarget genesAdhesion proteins