2023
Pan-cancer analysis of antibody-drug conjugate targets and putative predictors of treatment response
Bosi C, Bartha Á, Galbardi B, Notini G, Naldini M, Licata L, Viale G, Mariani M, Pistilli B, Ali H, André F, Piras M, Callari M, Barreca M, Locatelli A, Viganò L, Criscitiello C, Pusztai L, Curigliano G, Győrffy B, Dugo M, Bianchini G. Pan-cancer analysis of antibody-drug conjugate targets and putative predictors of treatment response. European Journal Of Cancer 2023, 195: 113379. PMID: 37913680, DOI: 10.1016/j.ejca.2023.113379.Peer-Reviewed Original ResearchConceptsGenotype-Tissue Expression (GTEx) databaseAntibody-drug conjugatesADC targetPan-cancer analysisCancer Genome AtlasExpression distributionGene expressionNew therapeutic opportunitiesTreatment responseExpression of determinantsPrimary tissuesGenome AtlasExpression levelsNormal tissuesPotential downstreamProtein expressionRelative expressionExpression databaseGenesTherapeutic opportunitiesExpressionTarget expressionMRNA levelsCancer typesInter-patient heterogeneity
2022
Cancer 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 tools
2020
Immunological Differences Between Immune-Rich Estrogen Receptor–Positive and Immune-Rich Triple-Negative Breast Cancers
O’Meara T, Marczyk M, Qing T, Yaghoobi V, Blenman K, Cole K, Pelekanou V, Rimm DL, Pusztai L. Immunological Differences Between Immune-Rich Estrogen Receptor–Positive and Immune-Rich Triple-Negative Breast Cancers. JCO Precision Oncology 2020, 4: po.19.00350. PMID: 32923897, PMCID: PMC7446500, DOI: 10.1200/po.19.00350.Peer-Reviewed Original ResearchER-positive breast cancerTriple-negative BCM2-like macrophagesTumor-infiltrating lymphocytesBreast cancerImmune-related genesEstrogen receptor-positive breast cancerImmuno-oncology therapeutic targetsRegulatory T cell markersReceptor-positive breast cancerTriple-negative breast cancerImmune activation markersT-cell markersImmune cell markersM1-like macrophagesDifferent immunotherapy strategiesBreast Cancer International ConsortiumNegative breast cancerImmuno-oncology trialsTGF-β pathwayAntitumor immunityCancer Genome AtlasImmunotherapy strategiesActivation markersImmune microenvironment
2017
Immune Gene Expression Is Associated with Genomic Aberrations in Breast Cancer
Safonov A, Jiang T, Bianchini G, Győrffy B, Karn T, Hatzis C, Pusztai L. Immune Gene Expression Is Associated with Genomic Aberrations in Breast Cancer. Cancer Research 2017, 77: 3317-3324. PMID: 28428277, DOI: 10.1158/0008-5472.can-16-3478.Peer-Reviewed Original ResearchConceptsTumor-infiltrating lymphocytesBreast cancer subtypesImmune infiltrationNeoantigen loadImmune surveillanceLower clonal heterogeneityCancer subtypesHigher immune gene expressionClonal heterogeneityImmune checkpoint inhibitorsMajor breast cancer subtypesFavorable prognostic factorTriple-negative cancersOverall mutation loadImmune gene expressionCheckpoint inhibitorsCancer Genome AtlasPrognostic factorsImmune metagenesBreast cancerCNV loadMutation loadGermline polymorphismsCancerCancer Res
2016
Predictors of Chemosensitivity in Triple Negative Breast Cancer: An Integrated Genomic Analysis
Jiang T, Shi W, Wali VB, Pongor L, Li C, Lau R, Győrffy B, Lifton RP, Symmans WF, Pusztai L, Hatzis C. Predictors of Chemosensitivity in Triple Negative Breast Cancer: An Integrated Genomic Analysis. PLOS Medicine 2016, 13: e1002193. PMID: 27959926, PMCID: PMC5154510, DOI: 10.1371/journal.pmed.1002193.Peer-Reviewed Original ResearchConceptsTriple-negative breast cancerPathologic complete responseMD Anderson Cancer CenterNegative breast cancerBreast cancerMutation burdenExtensive residual diseaseBetter survival outcomesBRCA deficiencyImmune cell activityAnderson Cancer CenterPredictor of chemosensitivityHigh mutation burdenWhole-exome sequencingACT chemotherapyMDACC cohortTNBC cohortNeoadjuvant chemotherapyCare chemotherapyTaxane chemotherapyCancer Genome AtlasComplete responseSuch patientsImproved survivalAggressive disease