2023
Race, Gene Expression Signatures, and Clinical Outcomes of Patients With High-Risk Early Breast Cancer
Kyalwazi B, Yau C, Campbell M, Yoshimatsu T, Chien A, Wallace A, Forero-Torres A, Pusztai L, Ellis E, Albain K, Blaes A, Haley B, Boughey J, Elias A, Clark A, Isaacs C, Nanda R, Han H, Yung R, Tripathy D, Edmiston K, Viscusi R, Northfelt D, Khan Q, Asare S, Wilson A, Hirst G, Lu R, Symmans W, Yee D, DeMichele A, van ’t Veer L, Esserman L, Olopade O. Race, Gene Expression Signatures, and Clinical Outcomes of Patients With High-Risk Early Breast Cancer. JAMA Network Open 2023, 6: e2349646. PMID: 38153734, PMCID: PMC10755617, DOI: 10.1001/jamanetworkopen.2023.49646.Peer-Reviewed Original ResearchConceptsDistant recurrence-free survivalPathologic complete responseErbB2-negative tumorsWorse distant recurrence-free survivalEarly breast cancerWhite patientsBreast cancerBlack patientsGene expression signaturesReceptor subtypesStage II/III breast cancerHigh-risk early breast cancerCox proportional hazards regression modelHigh-risk breast cancerClinical trial end pointsProportional hazards regression modelsTumor receptor subtypeRetrospective cohort studyPrimary tumor sizeRecurrence-free survivalTrial end pointsBreast cancer outcomesLong-term outcomesHazards regression modelsExpression signatures
2021
Targeted RNAseq assay incorporating unique molecular identifiers for improved quantification of gene expression signatures and transcribed mutation fraction in fixed tumor samples
Fu C, Marczyk M, Samuels M, Trevarton AJ, Qu J, Lau R, Du L, Pappas T, Sinn BV, Gould RE, Pusztai L, Hatzis C, Symmans WF. Targeted RNAseq assay incorporating unique molecular identifiers for improved quantification of gene expression signatures and transcribed mutation fraction in fixed tumor samples. BMC Cancer 2021, 21: 114. PMID: 33541297, PMCID: PMC7860187, DOI: 10.1186/s12885-021-07814-8.Peer-Reviewed Original ResearchConceptsPolymerase chain reactionParaffin-embedded tumor tissue samplesConcordance correlation coefficientFresh frozenFFPE samplesPrimary breast cancerMulti-gene signatureTumor tissue samplesActivating point mutationMutant allele fractionReverse transcriptionKey breast cancer genesGene expression signaturesBreast cancer genesPIK3CA mutationsBackgroundOur objectiveBreast cancerWhole transcriptome RNAseqTumor samplesLin's concordance correlation coefficientHormone receptorsFF samplesTissue samplesExpression signaturesChain reaction
2019
The impact of RNA extraction method on accurate RNA sequencing from formalin-fixed paraffin-embedded tissues
Marczyk M, Fu C, Lau R, Du L, Trevarton AJ, Sinn BV, Gould RE, Pusztai L, Hatzis C, Symmans WF. The impact of RNA extraction method on accurate RNA sequencing from formalin-fixed paraffin-embedded tissues. BMC Cancer 2019, 19: 1189. PMID: 31805884, PMCID: PMC6896723, DOI: 10.1186/s12885-019-6363-0.Peer-Reviewed Original ResearchConceptsBreast cancerFresh frozenParaffin-embedded tumor samplesFF samplesFFPE samplesConcordance correlation coefficientMixed-effects model analysisBreast cancer signaturesQiagen RNeasy kitWhole transcriptome RNA sequencingParaffin-embedded tissuesTranscriptome RNA sequencingLinear mixed-effects model analysisGene expression signaturesDifferent kitsClinical trialsGene signatureTumor samplesGene expressionTranslational researchCancerTissue samplesExpression signaturesArchival formalinSimilar concordance
2013
Genome-wide gene expression profiling to predict resistance to anthracyclines in breast cancer patients
Haibe-Kains B, Desmedt C, Di Leo A, Azambuja E, Larsimont D, Selleslags J, Delaloge S, Duhem C, Kains JP, Carly B, Maerevoet M, Vindevoghel A, Rouas G, Lallemand F, Durbecq V, Cardoso F, Salgado R, Rovere R, Bontempi G, Michiels S, Buyse M, Nogaret JM, Qi Y, Symmans F, Pusztai L, D'Hondt V, Piccart-Gebhart M, Sotiriou C. Genome-wide gene expression profiling to predict resistance to anthracyclines in breast cancer patients. Data In Brief 2013, 1: 7-10. PMID: 26484051, PMCID: PMC4608867, DOI: 10.1016/j.gdata.2013.09.001.Peer-Reviewed Original ResearchBreast cancer patientsResponse/resistanceAnthracycline monotherapyNeoadjuvant trialsGene expression signaturesNegative tumorsCancer patientsBreast cancerClinical dataEstrogen receptorClinical OncologyPredictive valuePatientsAnthracyclinesGene expressionII alphaExpression signaturesGenome-wide gene expressionMonotherapyExpressionTumorsCancerOncologyTrialsBiomarkers
2009
Correlation of PIK3CA mutation-associated gene expression signature (PIK3CA-GS) with deactivation of the PI3K pathway and with prognosis within the luminal-B ER+ breast cancers
Loi S, Haibe-Kains B, Lallemand F, Pusztai L, Bardelli A, Gillett C, Ellis P, Piccart-Gebhart M, Phillips W, McArthur G, Sotiriou C. Correlation of PIK3CA mutation-associated gene expression signature (PIK3CA-GS) with deactivation of the PI3K pathway and with prognosis within the luminal-B ER+ breast cancers. Journal Of Clinical Oncology 2009, 27: 533-533. DOI: 10.1200/jco.2009.27.15_suppl.533.Peer-Reviewed Original ResearchPI3K pathwayBreast cancerPIK3CA mutationsMutation statusGene expression signaturesK pathwayClinical outcomesLuminal B breast cancerLuminal BC subtypePIK3CA mutation statusBetter clinical outcomesIndependent prognostic informationB breast cancerExpression signaturesPI3K inhibitorsPI3K inhibitionBC cohortDistinct gene expression signaturesEndocrine therapyBC samplesBC subtypesPrognostic informationFavorable outcomeEstrogen receptorMutation carriers
2005
Gene expression profiling of primary breast cancer
Rouzier R, Wagner P, Morandi P, Pusztai L. Gene expression profiling of primary breast cancer. Current Oncology Reports 2005, 7: 38-44. PMID: 15610685, DOI: 10.1007/s11912-005-0024-y.Peer-Reviewed Original Research