2017
Integrated MicroRNA–mRNA Profiling Identifies Oncostatin M as a Marker of Mesenchymal-Like ER-Negative/HER2-Negative Breast Cancer
Bottai G, Diao L, Baggerly KA, Paladini L, Győrffy B, Raschioni C, Pusztai L, Calin GA, Santarpia L. Integrated MicroRNA–mRNA Profiling Identifies Oncostatin M as a Marker of Mesenchymal-Like ER-Negative/HER2-Negative Breast Cancer. International Journal Of Molecular Sciences 2017, 18: 194. PMID: 28106823, PMCID: PMC5297825, DOI: 10.3390/ijms18010194.Peer-Reviewed Original ResearchConceptsEpidermal growth factorExpression profilesMessenger RNA (mRNA) expression profilesMiRNA-regulated pathwaysAvailable gene expression profilesOncostatin M signalingMesenchymal-like breast cancer cellsGene expression profilesRNA expression profilesImmune-related pathwaysPathway regulationGlobal miRNAOncogenic networksGene expressionSpecific miRNAsPathway analysisBreast cancer cellsHuman estrogen receptorTriple-negative breast cancerEMT pathwayMesenchymal transitionMiRNAMRNA dataOncostatin MCancer cells
2014
Combined analysis of gene expression, DNA copy number, and mutation profiling data to display biological process anomalies in individual breast cancers
Shi W, Balazs B, Györffy B, Jiang T, Symmans WF, Hatzis C, Pusztai L. Combined analysis of gene expression, DNA copy number, and mutation profiling data to display biological process anomalies in individual breast cancers. Breast Cancer Research And Treatment 2014, 144: 561-568. PMID: 24619174, DOI: 10.1007/s10549-014-2904-z.Peer-Reviewed Original ResearchConceptsDNA copy numberBiological processesIndividual molecular eventsCopy numberGene expressionMolecular eventsMulticellular organismal processGene Ontology databaseGO biological processesSignal transduction pathwaysOrganismal processesGO termsMolecular dataTransduction pathwaysSiRNA screenComplex genomic abnormalitiesIndividual cancersOntology databaseFunctional roleDriver eventsCell growthSequence abnormalitiesBreast cancer cell linesCancer cell linesGenomic abnormalitiesDifferences in Gene and Protein Expression and the Effects of Race/Ethnicity on Breast Cancer Subtypes
Chavez-MacGregor M, Liu S, De Melo-Gagliato D, Chen H, Do KA, Pusztai L, Symmans W, Nair L, Hortobagyi GN, Mills GB, Meric-Bernstam F, Gonzalez-Angulo AM. Differences in Gene and Protein Expression and the Effects of Race/Ethnicity on Breast Cancer Subtypes. Cancer Epidemiology Biomarkers & Prevention 2014, 23: 316-323. PMID: 24296856, PMCID: PMC3946290, DOI: 10.1158/1055-9965.epi-13-0929.Peer-Reviewed Original Research
2009
Building Networks with Microarray Data
Broom BM, Rinsurongkawong W, Pusztai L, Do KA. Building Networks with Microarray Data. Methods In Molecular Biology 2009, 620: 315-343. PMID: 20652510, DOI: 10.1007/978-1-60761-580-4_10.Peer-Reviewed Original ResearchConceptsDetailed differential equation modelsDifferential equation modelAvailable breast cancer dataMathematical detailsNetwork modelBayesian network modelCo-expression network analysisMicroarray dataGene expression data setsFalse interactionsBayesian networkGene interaction networksData setsNumber of samplesPlausible networksRobust networkBreast cancer dataExpression data setsMicroarray data setsGene clusterGene shavingGene interactionsInteraction networksPreliminary clusteringSubsequent biological experimentsMolecular Characterization of Breast Cancer with High-Resolution Oligonucleotide Comparative Genomic Hybridization Array
Andre F, Job B, Dessen P, Tordai A, Michiels S, Liedtke C, Richon C, Yan K, Wang B, Vassal G, Delaloge S, Hortobagyi GN, Symmans WF, Lazar V, Pusztai L. Molecular Characterization of Breast Cancer with High-Resolution Oligonucleotide Comparative Genomic Hybridization Array. Clinical Cancer Research 2009, 15: 441-451. PMID: 19147748, DOI: 10.1158/1078-0432.ccr-08-1791.Peer-Reviewed Original ResearchBiopsy, Fine-NeedleBreast NeoplasmsChromosome AberrationsCluster AnalysisFemaleGene AmplificationGene DosageGene Expression ProfilingGene Expression Regulation, NeoplasticHumansIn Situ Hybridization, FluorescenceNucleic Acid HybridizationOligonucleotide Array Sequence AnalysisOligonucleotidesReceptor, ErbB-2
2005
Breast Cancer Molecular Subtypes Respond Differently to Preoperative Chemotherapy
Rouzier R, Perou CM, Symmans WF, Ibrahim N, Cristofanilli M, Anderson K, Hess KR, Stec J, Ayers M, Wagner P, Morandi P, Fan C, Rabiul I, Ross JS, Hortobagyi GN, Pusztai L. Breast Cancer Molecular Subtypes Respond Differently to Preoperative Chemotherapy. Clinical Cancer Research 2005, 11: 5678-5685. PMID: 16115903, DOI: 10.1158/1078-0432.ccr-04-2421.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAntineoplastic Combined Chemotherapy ProtocolsBiopsy, NeedleBreastBreast NeoplasmsCluster AnalysisDoxorubicinFemaleFluorouracilGene Expression ProfilingGene Expression Regulation, NeoplasticHumansMiddle AgedMultivariate AnalysisOligonucleotide Array Sequence AnalysisPaclitaxelPredictive Value of TestsPreoperative CareReceptor, ErbB-2ConceptsPathologic complete responseComplete responsePreoperative chemotherapyBreast cancerEstrogen receptor-negative subtypesPathologic CR rateEstrogen receptor statusBasal-like groupDifferent molecular subtypesFine-needle aspirationAffymetrix U133A microarraysPreoperative paclitaxelCyclophosphamide chemotherapyReceptor statusCR rateLuminal tumorsDifferent prognosisNuclear gradeMolecular subtypesNeedle aspirationChemotherapy sensitivityChemotherapyCancerMolecular classificationHuman tumors
2003
Gene expression profiles obtained from fine-needle aspirations of breast cancer reliably identify routine prognostic markers and reveal large-scale molecular differences between estrogen-negative and estrogen-positive tumors.
Pusztai L, Ayers M, Stec J, Clark E, Hess K, Stivers D, Damokosh A, Sneige N, Buchholz TA, Esteva FJ, Arun B, Cristofanilli M, Booser D, Rosales M, Valero V, Adams C, Hortobagyi GN, Symmans WF. Gene expression profiles obtained from fine-needle aspirations of breast cancer reliably identify routine prognostic markers and reveal large-scale molecular differences between estrogen-negative and estrogen-positive tumors. Clinical Cancer Research 2003, 9: 2406-15. PMID: 12855612.Peer-Reviewed Original ResearchAdultAgedBiopsy, Fine-NeedleBreast NeoplasmsCluster AnalysisDNA, ComplementaryEstrogensFemaleGene Expression Regulation, NeoplasticHumansImmunohistochemistryIn Situ Hybridization, FluorescenceMiddle AgedOligonucleotide Array Sequence AnalysisPrognosisReceptor, ErbB-2Receptors, EstrogenRNARNA, MessengerSignal TransductionTime Factors
2002
Global Gene Expression Changes During Neoadjuvant Chemotherapy for Human Breast Cancer
Buchholz TA, Stivers DN, Stec J, Ayers M, Clark E, Bolt A, Sahin AA, Symmans WF, Hess KR, Kuerer HM, Valero V, Hortobagyi GN, Pusztai L. Global Gene Expression Changes During Neoadjuvant Chemotherapy for Human Breast Cancer. The Cancer Journal 2002, 8: 461-468. PMID: 12500855, DOI: 10.1097/00130404-200211000-00010.Peer-Reviewed Original ResearchConceptsCore biopsy specimensBiopsy specimensBreast cancerNeoadjuvant chemotherapyGlobal gene expression changesGene expression changesGood pathological responsePrimary breast cancerExpression changesHuman breast cancerHuman solid tumorsPoor respondersPosttreatment specimensPathological responseIndividual patientsChemotherapyPatientsSerial samplesSolid tumorsExpression profilesIndividual tumorsPretreatment samplesDifferent tumorsTumorsDifferent patients