2024
Image‐based multiplex immune profiling of cancer tissues: translational implications. A report of the International Immuno‐oncology Biomarker Working Group on Breast Cancer
Jahangir C, Page D, Broeckx G, Gonzalez C, Burke C, Murphy C, Reis‐Filho J, Ly A, Harms P, Gupta R, Vieth M, Hida A, Kahila M, Kos Z, van Diest P, Verbandt S, Thagaard J, Khiroya R, Abduljabbar K, Haab G, Acs B, Adams S, Almeida J, Alvarado‐Cabrero I, Azmoudeh‐Ardalan F, Badve S, Baharun N, Bellolio E, Bheemaraju V, Blenman K, Fujimoto L, Burgues O, Chardas A, Cheang M, Ciompi F, Cooper L, Coosemans A, Corredor G, Portela F, Deman F, Demaria S, Dudgeon S, Elghazawy M, Fernandez‐Martín C, Fineberg S, Fox S, Giltnane J, Gnjatic S, Gonzalez‐Ericsson P, Grigoriadis A, Halama N, Hanna M, Harbhajanka A, Hart S, Hartman J, Hewitt S, Horlings H, Husain Z, Irshad S, Janssen E, Kataoka T, Kawaguchi K, Khramtsov A, Kiraz U, Kirtani P, Kodach L, Korski K, Akturk G, Scott E, Kovács A, Lænkholm A, Lang‐Schwarz C, Larsimont D, Lennerz J, Lerousseau M, Li X, Madabhushi A, Maley S, Narasimhamurthy V, Marks D, McDonald E, Mehrotra R, Michiels S, Kharidehal D, Minhas F, Mittal S, Moore D, Mushtaq S, Nighat H, Papathomas T, Penault‐Llorca F, Perera R, Pinard C, Pinto‐Cardenas J, Pruneri G, Pusztai L, Rajpoot N, Rapoport B, Rau T, Ribeiro J, Rimm D, Vincent‐Salomon A, Saltz J, Sayed S, Hytopoulos E, Mahon S, Siziopikou K, Sotiriou C, Stenzinger A, Sughayer M, Sur D, Symmans F, Tanaka S, Taxter T, Tejpar S, Teuwen J, Thompson E, Tramm T, Tran W, van der Laak J, Verghese G, Viale G, Wahab N, Walter T, Waumans Y, Wen H, Yang W, Yuan Y, Bartlett J, Loibl S, Denkert C, Savas P, Loi S, Stovgaard E, Salgado R, Gallagher W, Rahman A. Image‐based multiplex immune profiling of cancer tissues: translational implications. A report of the International Immuno‐oncology Biomarker Working Group on Breast Cancer. The Journal Of Pathology 2024, 262: 271-288. PMID: 38230434, PMCID: PMC11288342, DOI: 10.1002/path.6238.Peer-Reviewed Original ResearchConceptsImmune profileInternational Immuno-Oncology Biomarker Working GroupIdentification of clinically relevant biomarkersField of immuno-oncologyBiomarker Working GroupManagement of cancer patientsImmune profiling of tumorsClinical trial perspectiveTranslational implicationsProfiling of tumorsIndividual tumor cellsPredicting disease prognosisClinically relevant biomarkersSubtypes of cancerImmuno-oncologyTumor microenvironmentMultiplex immunohistochemistryTreatment responseTumor cellsBreast cancerTumor samplesCancer patientsTreatment choiceDisease prognosisRelevant biomarkers
2023
Evaluation of the Sensitivity to Endocrine Therapy Index and 21-Gene Breast Recurrence Score in the SWOG S8814 Trial
Speers C, Symmans W, Barlow W, Trevarton A, The S, Du L, Rae J, Shak S, Baehner R, Sharma P, Pusztai L, Hortobagyi G, Hayes D, Albain K, Godwin A, Thompson A. Evaluation of the Sensitivity to Endocrine Therapy Index and 21-Gene Breast Recurrence Score in the SWOG S8814 Trial. Journal Of Clinical Oncology 2023, 41: 1841-1848. PMID: 36649570, PMCID: PMC10082279, DOI: 10.1200/jco.22.01499.Peer-Reviewed Original ResearchConceptsBreast Recurrence ScoreAnthracycline-based chemotherapyDisease-free survivalRecurrence scoreEndocrine therapyTherapy indexAdjuvant anthracycline-based chemotherapyNode-positive breast cancerAdjuvant endocrine therapyPrimary end pointSubset of patientsPostmenopausal patientsChemotherapy benefitTreatment armsPrognostic indexPrognostic informationBreast cancerPrognostic assessmentPrognostic performancePatientsEnd pointTumor samplesChemotherapyClinical validationProportional hazards assumption
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
2011
Consistent metagenes from cancer expression profiles yield agent specific predictors of chemotherapy response
Li Q, Eklund AC, Birkbak NJ, Desmedt C, Haibe-Kains B, Sotiriou C, Symmans WF, Pusztai L, Brunak S, Richardson AL, Szallasi Z. Consistent metagenes from cancer expression profiles yield agent specific predictors of chemotherapy response. BMC Bioinformatics 2011, 12: 310. PMID: 21798043, PMCID: PMC3155975, DOI: 10.1186/1471-2105-12-310.Peer-Reviewed Original ResearchConceptsEarly-stage lung cancerStage lung cancerNegative breast cancerCancer treatment decisionsHuman tumor samplesNeoadjuvant therapyChemotherapy responseLung cancerBreast cancerTreatment decisionsIndependent cohortPrognostic classifierAccurate biomarkersCancer expression profilesTumor typesPotential biomarkersTumor samplesConclusionsThese resultsSpecific predictorsStrong associationReliable predictorCohortCancerPredictorsBiomarkers
2010
Different gene expressions are associated with the different molecular subtypes of inflammatory breast cancer
Iwamoto T, Bianchini G, Qi Y, Cristofanilli M, Lucci A, Woodward WA, Reuben JM, Matsuoka J, Gong Y, Krishnamurthy S, Valero V, Hortobagyi GN, Robertson F, Symmans WF, Pusztai L, Ueno NT. Different gene expressions are associated with the different molecular subtypes of inflammatory breast cancer. Breast Cancer Research And Treatment 2010, 125: 785-795. PMID: 21153052, PMCID: PMC4109066, DOI: 10.1007/s10549-010-1280-6.Peer-Reviewed Original ResearchConceptsInflammatory breast cancerClinical subtypesBreast cancerNon-IBC patientsCase-control studyDistinct clinical subtypesDifferent molecular subtypesNon-IBC tumorsSignificant differencesNon-IBC specimensImmune system-related pathwaysLipid metabolism-related pathwaysHER2 statusReceptor phenotypeMetabolism-related pathwaysMolecular subtypesIBC tumorsSurvival curvesSubtypesTumor samplesHormone receptorsCancerPatientsT-testHER2
2009
From the Lab to the Clinic: Gene-Expression Profiles That Are Associated with Mek-Inhibitor Sensitivity In Vitro Are Coordinately Co-Expressed in Breast Cancer Biopsy Samples from the I-SPY Trial (CALGB 150007/150012, ACRIN 6657).
Wolf D, Das D, Lenburg M, Paquette J, Spellman P, Gray J, Gray J, Pusztai L, Symmans F, Hatzis C, Esserman L, van 't Veer L, I-SPY Investigators .. From the Lab to the Clinic: Gene-Expression Profiles That Are Associated with Mek-Inhibitor Sensitivity In Vitro Are Coordinately Co-Expressed in Breast Cancer Biopsy Samples from the I-SPY Trial (CALGB 150007/150012, ACRIN 6657). Cancer Research 2009, 69: 2042-2042. DOI: 10.1158/0008-5472.sabcs-09-2042.Peer-Reviewed Original ResearchSensitive cell linesCancer cell linesOutcome dataCell linesI-SPY 2 TRIALI-SPY 1 TRIALInitial tumor responseNeo-adjuvant chemotherapyPre-treatment biopsiesThird of patientsBreast cancer biopsy samplesDrug response predictorsBreast cancer therapyBreast cancer cell linesMEK inhibitor sensitivityExpression of genesTumor responseTherapeutic responseResponse predictorsPatientsBiopsy samplesTumor samplesPatient samplesCancer ResDrug sensitivityClinical evaluation of chemotherapy response predictors developed from breast cancer cell lines
Liedtke C, Wang J, Tordai A, Symmans WF, Hortobagyi GN, Kiesel L, Hess K, Baggerly KA, Coombes KR, Pusztai L. Clinical evaluation of chemotherapy response predictors developed from breast cancer cell lines. Breast Cancer Research And Treatment 2009, 121: 301-309. PMID: 19603265, DOI: 10.1007/s10549-009-0445-7.Peer-Reviewed Original ResearchMeSH KeywordsAntineoplastic Combined Chemotherapy ProtocolsBiomarkers, TumorBreast NeoplasmsCell Line, TumorCyclophosphamideDoxorubicinDrug Resistance, NeoplasmFemaleFluorouracilGene Expression ProfilingHumansNeoplasm StagingOligonucleotide Array Sequence AnalysisPaclitaxelPredictive Value of TestsTreatment OutcomeConceptsBreast cancer cell linesCancer cell linesResponse predictorsBaseline gene expression dataCell linesChemotherapy drugsHuman breast cancer cell linesStandard chemotherapy drugsFine-needle aspiration specimensNeedle aspiration specimensPathologic responseAffymetrix U133A gene chipsClinical evaluationBreast cancerPharmacogenomic predictorsSame drugStage IPredictive valueAspiration specimensMultigene predictorsTumor samplesPatientsResistant cellsPatient dataDrugs