2012
Integrated analysis of tumor samples sheds light on tumor heterogeneity.
Parisi F, Micsinai M, Strino F, Ariyan S, Narayan D, Bacchiocchi A, Cheng E, Xu F, Li P, Kluger H, Halaban R, Kluger Y. Integrated analysis of tumor samples sheds light on tumor heterogeneity. The Yale Journal Of Biology And Medicine 2012, 85: 347-61. PMID: 23012583, PMCID: PMC3447199.Peer-Reviewed Original ResearchMeSH KeywordsCell Line, TumorChromosome MappingChromosomes, HumanDNA Copy Number VariationsEvolution, MolecularGene Expression ProfilingGene Expression Regulation, NeoplasticGenes, NeoplasmHumansIntercellular Signaling Peptides and ProteinsKaryotypingMelanomaMutationOligonucleotide Array Sequence AnalysisPolymorphism, Single NucleotideProto-Oncogene Proteins B-rafConceptsHigh-throughput profilingGene expression levelsExpression levelsDifferent gene expression levelsGene expression profilingCopy number analysisExpression profilingSNP arrayPathway analysisCopy number statusWnt pathwayTumor samplesNumber alteration profilesTumor heterogeneityTumor evolutionCopy number alteration profilesGenomic aberrationsIntegrated analysisCell linesTumor subclonesNumber analysisNumber statusProfilingDriver mutationsRecurrent association
2006
Expression of Tumor Necrosis Factor–Related Apoptosis-Inducing Ligand Receptors 1 and 2 in Melanoma
McCarthy MM, DiVito KA, Sznol M, Kovacs D, Halaban R, Berger AJ, Flaherty KT, Camp RL, Lazova R, Rimm DL, Kluger HM. Expression of Tumor Necrosis Factor–Related Apoptosis-Inducing Ligand Receptors 1 and 2 in Melanoma. Clinical Cancer Research 2006, 12: 3856-3863. PMID: 16778114, PMCID: PMC1839847, DOI: 10.1158/1078-0432.ccr-06-0190.Peer-Reviewed Original ResearchMeSH KeywordsGene Expression RegulationGene Expression Regulation, NeoplasticHumansMelanomaNeoplasm MetastasisOligonucleotide Array Sequence AnalysisReceptors, TNF-Related Apoptosis-Inducing LigandReceptors, Tumor Necrosis FactorReference ValuesCharacterizing disease states from topological properties of transcriptional regulatory networks
Tuck DP, Kluger HM, Kluger Y. Characterizing disease states from topological properties of transcriptional regulatory networks. BMC Bioinformatics 2006, 7: 236. PMID: 16670008, PMCID: PMC1482723, DOI: 10.1186/1471-2105-7-236.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsBiomarkers, TumorComputer SimulationDiagnosis, Computer-AssistedGene Expression ProfilingGene Expression Regulation, NeoplasticHumansModels, GeneticNeoplasmsOligonucleotide Array Sequence AnalysisSignal TransductionTranscription FactorsConceptsTranscriptional regulatory networksRegulatory networksTranscription factorsTranscriptional networksRegulated genesGene deregulationExpression profilesDiseased statesGene regulatory networksCentrality of genesGene expression experimentsGene expression profilesGene expression studiesGene centralityRegulatory linkExpression experimentsExpression studiesGene linksGenesCell typesExpression datasetsGene subsetsDifferential activityNormal cellsRemarkable degree
2005
Evaluating the Expression and Prognostic Value of TRAIL-R1 and TRAIL-R2 in Breast Cancer
McCarthy MM, Sznol M, DiVito KA, Camp RL, Rimm DL, Kluger HM. Evaluating the Expression and Prognostic Value of TRAIL-R1 and TRAIL-R2 in Breast Cancer. Clinical Cancer Research 2005, 11: 5188-5194. PMID: 16033835, DOI: 10.1158/1078-0432.ccr-05-0158.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAged, 80 and overBreast NeoplasmsCase-Control StudiesFemaleFollow-Up StudiesGene Expression ProfilingHumansMiddle AgedMultivariate AnalysisOligonucleotide Array Sequence AnalysisPrognosisReceptors, TNF-Related Apoptosis-Inducing LigandReceptors, Tumor Necrosis FactorSurvival AnalysisConceptsEarly-stage breast cancerTRAIL-R2 expressionBreast cancerPrognostic valueTRAIL-R2TRAIL-R1Normal breast specimensTumor necrosis factor-related apoptosis-inducing ligand receptor 1Lymph node involvementSubset of patientsBreast cancer patientsIndependent prognostic markerTRAIL-R1 expressionNormal breast epitheliumTRAIL receptor expressionLigand receptor 1Apoptosis-inducing ligand receptor 1Adjuvant treatmentNode involvementNodal statusPathologic variablesTumor sizeCancer patientsClinical trialsPrognostic markerUsing a Xenograft Model of Human Breast Cancer Metastasis to Find Genes Associated with Clinically Aggressive Disease
Kluger HM, Lev D, Kluger Y, McCarthy MM, Kiriakova G, Camp RL, Rimm DL, Price JE. Using a Xenograft Model of Human Breast Cancer Metastasis to Find Genes Associated with Clinically Aggressive Disease. Cancer Research 2005, 65: 5578-5587. PMID: 15994930, DOI: 10.1158/0008-5472.can-05-0108.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBreast NeoplasmsCell AdhesionCell Growth ProcessesCell Line, TumorDisease Models, AnimalFemaleGene Expression ProfilingHumansImmunohistochemistryMiceMice, NudeMultivariate AnalysisNeoplasm InvasivenessNeoplasm MetastasisNeoplasm TransplantationOligonucleotide Array Sequence AnalysisPredictive Value of TestsReproducibility of ResultsTissue Array AnalysisTransplantation, HeterologousConceptsBreast cancerXenograft modelHuman breast cancer metastasisLymph node involvementLymph node metastasisChemokine ligand 1Human breast cancer cell linesBreast cancer metastasisLeukocyte protease inhibitorBreast cancer cell linesBreast cancer tissuesHSP-70 expressionHeat shock protein 70Cancer cell linesShock protein 70Identification of genesNode involvementNode metastasisAggressive diseaseClinicopathologic variablesPrimary tumorPrognostic markerNovel therapiesCDNA microarray analysisCancer tissues
2004
Expression Profiling Reveals Novel Pathways in the Transformation of Melanocytes to Melanomas
Hoek K, Rimm DL, Williams KR, Zhao H, Ariyan S, Lin A, Kluger HM, Berger AJ, Cheng E, Trombetta ES, Wu T, Niinobe M, Yoshikawa K, Hannigan GE, Halaban R. Expression Profiling Reveals Novel Pathways in the Transformation of Melanocytes to Melanomas. Cancer Research 2004, 64: 5270-5282. PMID: 15289333, DOI: 10.1158/0008-5472.can-04-0731.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBiomarkers, TumorCell Transformation, NeoplasticCohort StudiesDown-RegulationGene Expression ProfilingGene Expression Regulation, NeoplasticHumansLymphatic MetastasisMelanocytesMelanomaMiceNuclear ProteinsOligonucleotide Array Sequence AnalysisPrognosisSignal TransductionSkin NeoplasmsSurvival RateTranscription FactorsTransfectionTwist-Related Protein 1Ubiquitin ThiolesteraseConceptsGlobal differential gene expressionMembrane trafficking eventsNovel pathwayNormal melanocytesHelix protein TwistAdditional transcriptional regulatorsDifferential gene expressionMelanoma cellsTransformation of melanocytesCpG promoter methylationNormal human melanocytesTrafficking eventsTranscriptional regulatorsEmbryonic developmentGrowth suppressorChromosomal regionsExpression profilingGene expressionNotch pathwayOligonucleotide microarraysMelanoma tissue microarrayDifferential expressionGenesHuman melanocytesGrowth advantageHer2/neu is not a commonly expressed therapeutic target in melanoma – a large cohort tissue microarray study
Kluger HM, DiVito K, Berger AJ, Halaban R, Ariyan S, Camp RL, Rimm DL. Her2/neu is not a commonly expressed therapeutic target in melanoma – a large cohort tissue microarray study. Melanoma Research 2004, 14: 207-210. PMID: 15179190, DOI: 10.1097/01.cmr.0000130874.33504.2f.Peer-Reviewed Original ResearchMeSH KeywordsCohort StudiesFemaleGene Expression Regulation, NeoplasticHumansImmunohistochemistryMaleMelanomaNeoplasm StagingOligonucleotide Array Sequence AnalysisReceptor, ErbB-2ConceptsHER2/neu expressionHER2/neuNeu expressionMelanoma specimensNeu stainingMelanoma patientsLarge cohortPositive HER2/neu expressionChemotherapy-resistant malignancyPrimary cutaneous lesionNumerous new agentsTissue microarray studyMonoclonal antibody trastuzumabAdjuvant therapyCutaneous specimensTrastuzumab therapyMetastatic lesionsBreslow depthClark levelClinicopathological dataCutaneous lesionsPrimary lesionTumor stageMetastatic melanomaBreast cancercDNA microarray analysis of invasive and tumorigenic phenotypes in a breast cancer model
Kluger HM, Kluger Y, Gilmore-Hebert M, DiVito K, Chang JT, Rodov S, Mironenko O, Kacinski BM, Perkins AS, Sapi E. cDNA microarray analysis of invasive and tumorigenic phenotypes in a breast cancer model. Laboratory Investigation 2004, 84: 320-331. PMID: 14767486, DOI: 10.1038/labinvest.3700044.Peer-Reviewed Original ResearchConceptsAutophosphorylation sitesHC11 mammary epithelial cellsMAP kinase phosphatase-1SNARE protein Ykt6Macrophage colony-stimulating factor receptorK cDNA microarrayColony-stimulating factor receptorCDNA microarray analysisKinase phosphatase-1Effects of mutationsMammary epithelial cellsTransmembrane tyrosine kinase receptorTyrosine kinase receptorsPhosphatase 1HC11 cellsCDNA microarrayTumorigenic phenotypeChaperonin 10Gene expressionFms oncogeneMicroarray analysisInvasive phenotypeMetastatic competenceKinase receptorsVivo tumorigenesis