2023
Short- and long-term effects of radiation exposure at low dose and low dose rate in normal human VH10 fibroblasts
Akuwudike P, López-Riego M, Marczyk M, Kocibalova Z, Brückner F, Polańska J, Wojcik A, Lundholm L. Short- and long-term effects of radiation exposure at low dose and low dose rate in normal human VH10 fibroblasts. Frontiers In Public Health 2023, 11: 1297942. PMID: 38162630, PMCID: PMC10755029, DOI: 10.3389/fpubh.2023.1297942.Peer-Reviewed Original ResearchConceptsLong-term effectsLow dosesDose-rate effectiveness factorLow dose rateSignificant early effectsColony forming assaysDays post irradiationEarly time pointsPooled cohortValidation cohortStrong cytotoxic effectEpidemiological dataLow doseGy/minCell growth curveSample cohortCohortThird cohortCell viability assaysRadiation exposureEarly effectsTime pointsCytotoxic effectsGene expression changesConsistent upregulationmiR-122 and miR-21 are Stable Components of miRNA Signatures of Early Lung Cancer after Validation in Three Independent Cohorts
Zyla J, Dziadziuszko R, Marczyk M, Sitkiewicz M, Szczepanowska M, Bottoni E, Veronesi G, Rzyman W, Polanska J, Widlak P. miR-122 and miR-21 are Stable Components of miRNA Signatures of Early Lung Cancer after Validation in Three Independent Cohorts. Journal Of Molecular Diagnostics 2023, 26: 37-48. PMID: 37865291, DOI: 10.1016/j.jmoldx.2023.09.010.Peer-Reviewed Original ResearchConceptsEarly lung cancerLung cancerLung cancer screening studyMiR-122MiR-21MiRNA signatureCancer screening studyLung cancer developmentPlasma miRNA signatureScreening studyIndependent cohortDiagnostic biomarkersPotential biomarkersCancer typesCohortCancer developmentCancerHealthy participantsMiR-144MiRNA panelDiagnostic potentialBiomarkersAdenocarcinomaDifferent cohortsMiRNAsPathological changes or technical artefacts? The problem of the heterogenous databases in COVID-19 CXR image analysis
Socha M, Prażuch W, Suwalska A, Foszner P, Tobiasz J, Jaroszewicz J, Gruszczynska K, Sliwinska M, Nowak M, Gizycka B, Zapolska G, Popiela T, Przybylski G, Fiedor P, Pawlowska M, Flisiak R, Simon K, Walecki J, Cieszanowski A, Szurowska E, Marczyk M, Polanska J, Polanska J, Marczyk M, Prazuch W, Suwalska A, Socha M, Foszner P, Tobiasz J, Nowak M, Fiedor P, Cieszanowski A, Oronowicz-Jaskowiak A, Golebiewski B, Simon K, Sliwinska M, Rataj M, Chmielarz P, Tur A, Drabik G, Popiela T, Kozub J, Przybylski G, Kozanecka A, Szurowska E, Hildebrandt S, Krutul-Walenciej K, Baron J, Gruszczynska K, Jaroszewicz J, Piotrowski D, Walecki J, Wasilewski P, Mazur S, Flisiak R, Zapolska G, Klaude K, Rataj K, Golebiewski B, Pawlowska M, Rabiko P, Rajewski P, Gizycka B, Blewaska P, Sznajder K, Plesniak R. Pathological changes or technical artefacts? The problem of the heterogenous databases in COVID-19 CXR image analysis. Computer Methods And Programs In Biomedicine 2023, 240: 107684. PMID: 37356354, PMCID: PMC10278898, DOI: 10.1016/j.cmpb.2023.107684.Peer-Reviewed Original ResearchConceptsChest X-ray imagesNeural networkClassification neural networkDeep neural networksSuper-resolution networkImage resolutionHeterogenous databasesDiagnostic algorithm developmentSet of artifactsX-ray imagesBias discoveryNetwork architecturePoor generalizationNetwork decisionsImage dataScientific research areasAI developmentTypes of dataAlgorithm developmentImage propertiesMedical imagingNetworkResearch areaImage analysisHigh accuracyPOLCOVID: a multicenter multiclass chest X-ray database (Poland, 2020–2021)
Suwalska A, Tobiasz J, Prazuch W, Socha M, Foszner P, Piotrowski D, Gruszczynska K, Sliwinska M, Walecki J, Popiela T, Przybylski G, Nowak M, Fiedor P, Pawlowska M, Flisiak R, Simon K, Zapolska G, Gizycka B, Szurowska E, Marczyk M, Cieszanowski A, Polanska J. POLCOVID: a multicenter multiclass chest X-ray database (Poland, 2020–2021). Scientific Data 2023, 10: 348. PMID: 37268643, PMCID: PMC10236395, DOI: 10.1038/s41597-023-02229-5.Peer-Reviewed Original ResearchConceptsLung maskChest X-ray databaseChest X-ray imagesArtificial intelligence toolsCOVID-19 detectionX-ray databaseImage collectionImage databaseX-ray imagesIntelligence toolsSegmentation solutionSegmentation modelDiagnosis methodOriginal radiographsDatasetImagesCOVID-19 diagnosisDatabaseHealthcare systemMaskMedical assistanceSmall numberLung areaSetToolAssessment 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
Molecular testing opportunities on cytology effusion specimens: the pre-analytic effects of various body fluid cytology preparation methods on RNA extraction quality and targeted sequencing
Sura G, Tran K, Fu C, Du L, Marczyk M, Martinez Y, Tinnirello A, Gould R, Lau R, Symmans W. Molecular testing opportunities on cytology effusion specimens: the pre-analytic effects of various body fluid cytology preparation methods on RNA extraction quality and targeted sequencing. Journal Of The American Society Of Cytopathology 2022, 12: 10-19. PMID: 36270909, PMCID: PMC10644714, DOI: 10.1016/j.jasc.2022.09.003.Peer-Reviewed Original ResearchConceptsCell blocksCarnoy's solutionDiff-QuikFF samplesCytology laboratoryFFPE cell blocksMultigene expression signaturesConcordance correlation coefficientCell block sectionsParaffin-embedded sectionsMalignant effusionsEffusion specimensMolecular subtypesSurePath samplesCytospin preparationsCytologic methodsCytologic samplesSurePath preparationsDiagnostic approachClinical researchRNA sequencing analysisExpression signaturesHigh concordanceBlock sectionsFrozen cell pelletsTreatment Efficacy Score—continuous residual cancer burden-based metric to compare neoadjuvant chemotherapy efficacy between randomized trial arms in breast cancer trials
Marczyk M, Mrukwa A, Yau C, Wolf D, Chen Y, Balassanian R, Nanda R, Parker B, Krings G, Sattar H, Zeck J, Albain K, Boughey J, Liu M, Elias A, Clark A, Venters S, Shad S, Basu A, Asare S, Buxton M, Asare A, Rugo H, Perlmutter J, DeMichele A, Yee D, Berry D, Veer L, Symmans W, Esserman L, Pusztai L, Consortium I. Treatment Efficacy Score—continuous residual cancer burden-based metric to compare neoadjuvant chemotherapy efficacy between randomized trial arms in breast cancer trials. Annals Of Oncology 2022, 33: 814-823. PMID: 35513244, DOI: 10.1016/j.annonc.2022.04.072.Peer-Reviewed Original ResearchConceptsTrial armsExperimental armSurvival differencesExact testPathologic complete response rateClinical trial armsI-SPY2 trialNeoadjuvant chemotherapy efficacyComplete response rateBreast cancer trialsCytotoxic efficacyFisher's exact testImpact of treatmentNeoadjuvant chemotherapyPCR ratePathologic responseResidual cancerControl cohortCancer trialsAssessed associationsChemotherapy efficacyEarly surrogateOlaparib armResponse rateHigher cytotoxic efficacyCancer Relevance of Human Genes
Qing T, Mohsen H, Cannataro VL, Marczyk M, Rozenblit M, Foldi J, Murray M, Townsend J, Kluger Y, Gerstein M, Pusztai L. Cancer Relevance of Human Genes. Journal Of The National Cancer Institute 2022, 114: 988-995. PMID: 35417011, PMCID: PMC9275765, DOI: 10.1093/jnci/djac068.Peer-Reviewed Original ResearchConceptsCore cancer genesHuman genesFunctional importanceSomatic mutation frequencySelection pressureGene/protein networksCancer genesHigher somatic mutation frequencyNegative selection pressureGene-gene interaction networksMutation frequencyProtein-truncating variantsGenomic contextCell viabilityGenes decreasesCancer Genome AtlasInteraction networksProtein networkCancer relevanceCancer cell viabilityCell survivalGenesCancer biologyGenome AtlasSearch toolsPredictive 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 cycleComprehensive Analysis of Metabolic Isozyme Targets in Cancer
Marczyk M, Gunasekharan V, Casadevall D, Qing T, Foldi J, Sehgal R, Shan NL, Blenman KRM, O'Meara TA, Umlauf S, Surovtseva YV, Muthusamy V, Rinehart J, Perry RJ, Kibbey R, Hatzis C, Pusztai L. Comprehensive Analysis of Metabolic Isozyme Targets in Cancer. Cancer Research 2022, 82: 1698-1711. PMID: 35247885, PMCID: PMC10883296, DOI: 10.1158/0008-5472.can-21-3983.Peer-Reviewed Original ResearchConceptsPotential therapeutic targetAcetyl-CoA carboxylase 1Therapeutic targetCancer typesCell linesBreast cancer viabilityPatient-derived xenograftsNovel metabolic targetsCorresponding cell linesExpression patternsDrug treatmentMatching normal tissuesRelated commentaryTumor growthMalignant transformationSmall molecule inhibitionCancer viabilityCancer Cell Line EncyclopediaNormal tissuesMetabolic vulnerabilitiesCarboxylase 1Anticancer therapyCellular changesCell proliferationMetabolic reprogramming
2021
Analysis of the Applicability of microRNAs in Peripheral Blood Leukocytes as Biomarkers of Sensitivity and Exposure to Fractionated Radiotherapy towards Breast Cancer
Marczyk M, Polańska J, Wojcik A, Lundholm L. Analysis of the Applicability of microRNAs in Peripheral Blood Leukocytes as Biomarkers of Sensitivity and Exposure to Fractionated Radiotherapy towards Breast Cancer. International Journal Of Molecular Sciences 2021, 22: 8705. PMID: 34445424, PMCID: PMC8395710, DOI: 10.3390/ijms22168705.Peer-Reviewed Original ResearchConceptsBreast cancer patientsExternal beam radiotherapyCourse of radiotherapyPeripheral blood leukocytesBiomarkers of sensitivityLogistic regression modelsMultinomial logistic regression modelsFractionated RadiotherapyInter-individual variabilityCancer patientsUnivariate analysisBreast cancerCombination of miRNAsBeam radiotherapyBlood leukocytesBlood samplesPromising biomarkerTotal doseSensitive biomarkerRadiotherapyPatientsStrong inter-individual variabilityBiomarkersDoseLeukocytesDiverse immune response of DNA damage repair-deficient tumors
Qing T, Jun T, Lindblad KE, Lujambio A, Marczyk M, Pusztai L, Huang KL. Diverse immune response of DNA damage repair-deficient tumors. Cell Reports Medicine 2021, 2: 100276. PMID: 34095878, PMCID: PMC8149377, DOI: 10.1016/j.xcrm.2021.100276.Peer-Reviewed Original ResearchConceptsCancer typesDDR-deficient tumorsImmune checkpoint inhibitorsHigh neoantigen loadDifferent immune phenotypesDiverse immune responsesAdaptive immune markersRepair-deficient tumorsDDR deficiencyCheckpoint inhibitorsImmunotherapy outcomesDNA damage repair deficiencyImmune infiltratesImmune markersNeoantigen loadSurvival outcomesImmune phenotypeTumor neoantigensImmune responseAnimal modelsGenomic biomarkersGermline mutationsPathway mutationsTumorsRepair deficiencyTargeted 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
2020
Technical Validity of a Customized Assay of Sensitivity to Endocrine Therapy Using Sections from Fixed Breast Cancer Tissue
Lau R, Du L, Chen E, Fu C, Gould R, Marczyk M, Sinn BV, Layman R, Bedrosian I, Valero V, Symmans WF. Technical Validity of a Customized Assay of Sensitivity to Endocrine Therapy Using Sections from Fixed Breast Cancer Tissue. Clinical Chemistry 2020, 66: 934-945. PMID: 32613237, DOI: 10.1093/clinchem/hvaa105.Peer-Reviewed Original ResearchConceptsQuantiGene PlexConcordance correlation coefficientBreast cancer tissuesParaffin-embedded tissue sectionsEndocrine therapyResection samplesBreast cancerTumor sectionsCancer tissuesStage IIParaffin blocksLin's concordance correlation coefficientTissue sectionsCustomized assayTherapyAnalytical sensitivityFFPE samplesNanoStringFFPE tissuesExpression indexWeekly testsAssaysTissueTechnical validityGermline variant burden in cancer genes correlates with age at diagnosis and somatic mutation burden
Qing T, Mohsen H, Marczyk M, Ye Y, O’Meara T, Zhao H, Townsend JP, Gerstein M, Hatzis C, Kluger Y, Pusztai L. Germline variant burden in cancer genes correlates with age at diagnosis and somatic mutation burden. Nature Communications 2020, 11: 2438. PMID: 32415133, PMCID: PMC7228928, DOI: 10.1038/s41467-020-16293-7.Peer-Reviewed Original ResearchConceptsAge groupsGermline variantsSomatic mutationsLate-onset cancerEarly-onset cancersCancer hallmark genesSomatic mutation burdenMutation burdenMalignant transformationCancer genesYounger ageGermline alterationsCancerVariant burdenBurdenAverage numberHallmark genesAgeNegative correlationStrong negative correlationMutationsPatientsGroup
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 concordanceLung cancer survival and comorbidities in lung cancer screening participants of the Gdańsk screening cohort
Ostrowski M, Marczyk M, Dziedzic R, Jelitto-Górska M, Marjański T, Pisiak S, Jędrzejczyk T, Polańska J, Zdrojewski T, Wojtyniak B, Rzyman W. Lung cancer survival and comorbidities in lung cancer screening participants of the Gdańsk screening cohort. European Journal Of Public Health 2019, 29: 1114-1117. PMID: 31004154, DOI: 10.1093/eurpub/ckz052.Peer-Reviewed Original ResearchConceptsChronic obstructive pulmonary diseaseLung cancer screening programsCancer screening programsCardiovascular diseaseDiabetes mellitusLung cancerScreening programLung cancer detection rateMedical eventsModifiable risk factorsLung cancer survivalObstructive pulmonary diseaseLung cancer patientsCancer detection rateHealth care providersHealth care systemWorld Health OrganizationScreening groupHeavy smokersPulmonary diseaseScreening cohortCancer patientsCancer survivalRisk factorsCare providersDefining Risk of Late Recurrence in Early-Stage Estrogen Receptor–Positive Breast Cancer: Clinical Versus Molecular Tools
Foldi J, O'Meara T, Marczyk M, Sanft T, Silber A, Pusztai L. Defining Risk of Late Recurrence in Early-Stage Estrogen Receptor–Positive Breast Cancer: Clinical Versus Molecular Tools. Journal Of Clinical Oncology 2019, 37: jco.18.01933. PMID: 30943126, DOI: 10.1200/jco.18.01933.Peer-Reviewed Original Research
2018
GaMRed—Adaptive Filtering of High-Throughput Biological Data
Marczyk M, Jaksik R, Polanski A, Polanska J. GaMRed—Adaptive Filtering of High-Throughput Biological Data. IEEE/ACM Transactions On Computational Biology And Bioinformatics 2018, 17: 149-157. PMID: 30040660, DOI: 10.1109/tcbb.2018.2858825.Peer-Reviewed Original Research
2017
Serum lipid profile discriminates patients with early lung cancer from healthy controls
Ros-Mazurczyk M, Jelonek K, Marczyk M, Binczyk F, Pietrowska M, Polanska J, Dziadziuszko R, Jassem J, Rzyman W, Widlak P. Serum lipid profile discriminates patients with early lung cancer from healthy controls. Lung Cancer 2017, 112: 69-74. PMID: 29191603, DOI: 10.1016/j.lungcan.2017.07.036.Peer-Reviewed Original ResearchConceptsEarly lung cancerSerum lipid profileLung cancerNegative predictive valuePredictive valueCancer patientsLipid profileComputed tomography lung cancer screeningLow-dose computed tomography (LDCT) lung cancer screeningTomography lung cancer screeningEarly-stage lung cancerHealthy participantsEarly lung cancer patientsLow-dose computed tomographyHigh-risk smokersLung cancer screeningLung cancer patientsStage lung cancerMaximum negative predictive valueBlood-based biomarkersPositive predictive valueSerum lipidomeCancer screeningHealthy controlsSerum signature