2024
Comparative Analysis of Ficoll-Hypaque and CytoLyt® Techniques for Blood Removal in Breast Cancer Malignant Effusions: Effects on RNA Quality and Sequencing Outcomes
Sura G, Tran K, Trevarton A, Marczyk M, Fu C, Du L, Qu J, Lau R, Tasto A, Gould R, Tinnirello A, Sinn B, Pusztai L, Hatzis C, Symmans W. Comparative Analysis of Ficoll-Hypaque and CytoLyt® Techniques for Blood Removal in Breast Cancer Malignant Effusions: Effects on RNA Quality and Sequencing Outcomes. Journal Of The American Society Of Cytopathology 2024 DOI: 10.1016/j.jasc.2024.11.001.Peer-Reviewed Original ResearchRNA integrity numberRNA qualityRNA-seqMeasurement of gene expressionRNA-seq analysisMetastatic breast cancerFicoll-Hypaque methodDensity gradient enrichmentSequence dataRead-basedVariant detectionMalignant effusionsCytospin slidesFresh frozen samplesRNA fragmentsTranscript abundanceSequencing outcomesSequencing methodsBreast cancerRNA sequencingFicoll-HypaqueUMI-basedGene expressionRNAMalignant effusion specimens
2023
Evaluation of zero counts to better understand the discrepancies between bulk and single-cell RNA-Seq platforms
Zyla J, Papiez A, Zhao J, Qu R, Li X, Kluger Y, Polanska J, Hatzis C, Pusztai L, Marczyk M. Evaluation of zero counts to better understand the discrepancies between bulk and single-cell RNA-Seq platforms. Computational And Structural Biotechnology Journal 2023, 21: 4663-4674. PMID: 37841335, PMCID: PMC10568495, DOI: 10.1016/j.csbj.2023.09.035.Peer-Reviewed Original ResearchSingle-cell RNA-seq platformsSingle-cell RNA sequencingBulk RNA-seq dataRNA-seq platformsNumber of transcriptsLow-expression genesRNA-seq dataSingle-cell dataExpression levelsLow sequencing depthDiscordant genesRNA sequencingSequencing technologiesExpression shiftsPathway levelBiological pathwaysGene levelSequencing depthTranscriptomic platformsGenesIndividual cellsSingle cellsRNA integrityPathwayCellsAssessment of stained direct cytology smears of breast cancer for whole transcriptome and targeted messenger RNA sequencing
Marczyk M, Fu C, Lau R, Du L, Trevarton A, Sinn B, Gould R, Pusztai L, Hatzis C, Symmans W. Assessment of stained direct cytology smears of breast cancer for whole transcriptome and targeted messenger RNA sequencing. Cancer Cytopathology 2023, 131: 289-299. PMID: 36650408, PMCID: PMC10614161, DOI: 10.1002/cncy.22679.Peer-Reviewed Original ResearchConceptsCytology smearsBreast cancerConcordance correlation coefficientTumor tissue samplesParaffin-embedded sectionsClinical diagnostic proceduresSurgical resectionRNA sequencingTumor stromaCytologic specimensDiagnostic proceduresLin's concordance correlation coefficientPapanicolaou stainCancerTissue samplesDNA mutation testingSmearsSimilar concordanceTranscriptome RNA-SeqDiagnostic cytologyAllele fractionExpression levelsRNA-seqExpression of genesGene expression levels
2022
Investigating Sources of Zeros in 10× Single-Cell RNAseq Data
Slowik H, Zyla J, Marczyk M. Investigating Sources of Zeros in 10× Single-Cell RNAseq Data. Lecture Notes In Computer Science 2022, 13347: 71-80. DOI: 10.1007/978-3-031-07802-6_6.Peer-Reviewed Original ResearchSingle-cell levelSingle-cell RNA sequencingSingle-cell RNAseq dataNumber of transcriptsMulti-omics dataGene expression estimatesRibosomal genesRNA sequencingExpression profilingEnrichment analysisRNAseq dataBiological pathwaysSequencing platformsExpression dataGenesExpression estimatesIndividual cellsBreast cancer cell linesCancer cell linesCell linesSingle experimentLow mappabilityTranscriptsSequencingProfilingPredictive Markers of Response to Neoadjuvant Durvalumab with Nab-Paclitaxel and Dose-Dense Doxorubicin/Cyclophosphamide in Basal-Like Triple-Negative Breast Cancer.
Blenman KRM, Marczyk M, Karn T, Qing T, Li X, Gunasekharan V, Yaghoobi V, Bai Y, Ibrahim EY, Park T, Silber A, Wolf DM, Reisenbichler E, Denkert C, Sinn BV, Rozenblit M, Foldi J, Rimm DL, Loibl S, Pusztai L. Predictive Markers of Response to Neoadjuvant Durvalumab with Nab-Paclitaxel and Dose-Dense Doxorubicin/Cyclophosphamide in Basal-Like Triple-Negative Breast Cancer. Clinical Cancer Research 2022, 28: 2587-2597. PMID: 35377948, PMCID: PMC9464605, DOI: 10.1158/1078-0432.ccr-21-3215.Peer-Reviewed Original ResearchConceptsBasal-like triple-negative breast cancerPathologic complete responseResidual diseaseNeoadjuvant durvalumabDNA damage repairSomatic mutationsBreast cancerWnt/β-cateninHigh expressionTriple-negative breast cancerBasal-Like TripleDoxorubicin/cyclophosphamideDNA repairTumor mutation burdenRNA sequencingEpithelial-mesenchymal transitionFive-gene signatureB-cell markersCancer driversEnrichment analysisNegative breast cancerDamage repairGene expressionJAK-STATCell cycle
2021
Treatment scheduling effects on the evolution of drug resistance in heterogeneous cancer cell populations
Patwardhan GA, Marczyk M, Wali VB, Stern DF, Pusztai L, Hatzis C. Treatment scheduling effects on the evolution of drug resistance in heterogeneous cancer cell populations. Npj Breast Cancer 2021, 7: 60. PMID: 34040000, PMCID: PMC8154902, DOI: 10.1038/s41523-021-00270-4.Peer-Reviewed Original ResearchHeterogeneous cancer cell populationsCancer cell populationsTriple-negative breast cancerSingle-cell RNA sequencingCell populationsFitness advantageRNA sequencingMDA-MB-231 TNBC cellsDrug resistanceMechanisms of resistanceVitro screening assaysClonal dynamicsTNBC cellsScreening assaysResistant clonesPatterns of resistanceConcomitant treatmentTherapy combinationsBreast cancerClinical studiesTreatment doseTreatment scheduleBarcodesSequencingTreatment