2022
Clinical Efficacy and Whole-Exome Sequencing of Liquid Biopsies in a Phase IB/II Study of Bazedoxifene and Palbociclib in Advanced Hormone Receptor-Positive Breast Cancer.
Tsuji J, Li T, Grinshpun A, Coorens T, Russo D, Anderson L, Rees R, Nardone A, Patterson C, Lennon NJ, Cibulskis C, Leshchiner I, Tayob N, Tolaney SM, Tung N, McDonnell DP, Krop IE, Winer EP, Stewart C, Getz G, Jeselsohn R. Clinical Efficacy and Whole-Exome Sequencing of Liquid Biopsies in a Phase IB/II Study of Bazedoxifene and Palbociclib in Advanced Hormone Receptor-Positive Breast Cancer. Clinical Cancer Research 2022, 28: 5066-5078. PMID: 36215125, PMCID: PMC9722539, DOI: 10.1158/1078-0432.ccr-22-2305.Peer-Reviewed Original ResearchConceptsProgression-free survivalPhase Ib/II studyCombination of palbociclibBreast cancerWhole-exome sequencingESR1 mutationsII studyClinical efficacySafety profileHormone receptor-positive/HER2-negative advanced breast cancerAdvanced hormone receptor-positive breast cancerHER2-negative advanced breast cancerHormone receptor-positive breast cancerThird-generation selective estrogen receptor modulatorMedian progression-free survivalEndocrine-resistant breast cancerReceptor-positive breast cancerShorter progression-free survivalSelective estrogen receptor modulatorsClinical benefit rateAcceptable safety profileAdvanced breast cancerEstrogen receptor modulatorsSelective ER degraderDNA whole-exome sequencing
2020
Acquired FGFR and FGF Alterations Confer Resistance to Estrogen Receptor (ER) Targeted Therapy in ER+ Metastatic Breast Cancer
Mao P, Cohen O, Kowalski KJ, Kusiel JG, Buendia-Buendia JE, Cuoco MS, Exman P, Wander SA, Waks AG, Nayar U, Chung J, Freeman S, Rozenblatt-Rosen O, Miller VA, Piccioni F, Root DE, Regev A, Winer EP, Lin NU, Wagle N. Acquired FGFR and FGF Alterations Confer Resistance to Estrogen Receptor (ER) Targeted Therapy in ER+ Metastatic Breast Cancer. Clinical Cancer Research 2020, 26: 5974-5989. PMID: 32723837, DOI: 10.1158/1078-0432.ccr-19-3958.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedBreast NeoplasmsCell Line, TumorDrug Resistance, NeoplasmExome SequencingFemaleFibroblast Growth Factor 3FulvestrantGene Expression Regulation, NeoplasticHumansMCF-7 CellsMiddle AgedMutationNeoplasm MetastasisPiperazinesProtein Kinase InhibitorsPyridinesReceptor, Fibroblast Growth Factor, Type 1Receptor, Fibroblast Growth Factor, Type 2Receptors, EstrogenXenograft Model Antitumor AssaysConceptsMetastatic breast cancerEstrogen receptorBreast cancerFGFR pathwaySelective estrogen receptor degraderCDK4/6 inhibitor palbociclibBreast cancer cellsMAPK pathwayWhole-exome sequencingResistant cell linesMAPK pathway inhibitorsFulvestrant resistanceInhibitor palbociclibDrug combinationsFGFR inhibitorsTherapyPathway inhibitorMEK inhibitorsConfer resistanceCancer cellsCancerInsulin receptorGenes/pathwaysBiopsyCell linesThe Genomic Landscape of Intrinsic and Acquired Resistance to Cyclin-Dependent Kinase 4/6 Inhibitors in Patients with Hormone Receptor–Positive Metastatic Breast Cancer
Wander SA, Cohen O, Gong X, Johnson GN, Buendia-Buendia JE, Lloyd MR, Kim D, Luo F, Mao P, Helvie K, Kowalski KJ, Nayar U, Waks AG, Parsons SH, Martinez R, Litchfield LM, Ye XS, Yu C, Jansen VM, Stille JR, Smith PS, Oakley GJ, Chu QS, Batist G, Hughes ME, Kremer JD, Garraway LA, Winer EP, Tolaney SM, Lin NU, Buchanan SG, Wagle N. The Genomic Landscape of Intrinsic and Acquired Resistance to Cyclin-Dependent Kinase 4/6 Inhibitors in Patients with Hormone Receptor–Positive Metastatic Breast Cancer. Cancer Discovery 2020, 10: 1174-1193. PMID: 32404308, PMCID: PMC8815415, DOI: 10.1158/2159-8290.cd-19-1390.Peer-Reviewed Original ResearchMeSH KeywordsAntineoplastic AgentsBiopsyBreast NeoplasmsCell Cycle ProteinsCell Line, TumorCheckpoint Kinase 1Drug Resistance, NeoplasmExome SequencingFemaleGenomicsHumansProtein Kinase InhibitorsProto-Oncogene Proteins c-aktProto-Oncogene Proteins p21(ras)Receptors, SteroidRetinoblastoma Binding ProteinsUbiquitin-Protein LigasesConceptsCyclin-dependent kinase 4/6 inhibitorsMetastatic breast cancerBreast cancerResistant tumorsHormone receptor-positive metastatic breast cancerHormone receptor-positive breast cancerReceptor-positive breast cancerEstrogen receptor expressionCandidate resistance mechanismsWhole-exome sequencingPrecision-based approachesCDK4/6i resistanceMechanisms of resistanceReceptor expressionTherapeutic strategiesCDK4/6iTherapeutic opportunitiesPatient samplesTumorsIssue featurePatientsCancerAcquired ResistanceCancer cellsAlterationsPrevalence and mutational determinants of high tumor mutation burden in breast cancer
Barroso-Sousa R, Jain E, Cohen O, Kim D, Buendia-Buendia J, Winer E, Lin N, Tolaney S, Wagle N. Prevalence and mutational determinants of high tumor mutation burden in breast cancer. Annals Of Oncology 2020, 31: 387-394. PMID: 32067680, DOI: 10.1016/j.annonc.2019.11.010.Peer-Reviewed Original ResearchConceptsHigh tumor mutation burdenTumor mutation burdenPD-1 inhibitorsBreast cancerMutation burdenMedian tumor mutation burdenDifferent mutational signaturesPembrolizumab-based therapyMetastatic breast cancerSubset of patientsMut/MbMismatch repair deficiencyGenomic profilesMutational patternsAPOBEC activityGene panel sequencingMultiple tumor typesWhole-exome sequencingDe-identified dataDurable responsesMetastatic tumorsPrimary tumorTumor subtypesPatientsTumor types
2017
Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors
Adalsteinsson VA, Ha G, Freeman SS, Choudhury AD, Stover DG, Parsons HA, Gydush G, Reed SC, Rotem D, Rhoades J, Loginov D, Livitz D, Rosebrock D, Leshchiner I, Kim J, Stewart C, Rosenberg M, Francis JM, Zhang CZ, Cohen O, Oh C, Ding H, Polak P, Lloyd M, Mahmud S, Helvie K, Merrill MS, Santiago RA, O’Connor E, Jeong SH, Leeson R, Barry RM, Kramkowski JF, Zhang Z, Polacek L, Lohr JG, Schleicher M, Lipscomb E, Saltzman A, Oliver NM, Marini L, Waks AG, Harshman LC, Tolaney SM, Van Allen EM, Winer EP, Lin NU, Nakabayashi M, Taplin ME, Johannessen CM, Garraway LA, Golub TR, Boehm JS, Wagle N, Getz G, Love JC, Meyerson M. Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors. Nature Communications 2017, 8: 1324. PMID: 29109393, PMCID: PMC5673918, DOI: 10.1038/s41467-017-00965-y.Peer-Reviewed Original ResearchConceptsWhole-exome sequencingCell-free DNATumor biopsiesTumor whole-exome sequencingTumor contentHigh concordanceClonal somatic mutationsMetastatic tumorsBreast cancerMetastatic prostateBlood samplesPatientsTumor mutationsCfDNA profilingBiopsyMutational signaturesSomatic mutationsTumorsNumber alterationsConcordanceComprehensive profilingNeoantigensSequencingProstateCancer