2024
A multi-modal single-cell and spatial expression map of metastatic breast cancer biopsies across clinicopathological features
Klughammer J, Abravanel D, Segerstolpe Å, Blosser T, Goltsev Y, Cui Y, Goodwin D, Sinha A, Ashenberg O, Slyper M, Vigneau S, Jané‐Valbuena J, Alon S, Caraccio C, Chen J, Cohen O, Cullen N, DelloStritto L, Dionne D, Files J, Frangieh A, Helvie K, Hughes M, Inga S, Kanodia A, Lako A, MacKichan C, Mages S, Moriel N, Murray E, Napolitano S, Nguyen K, Nitzan M, Ortiz R, Patel M, Pfaff K, Porter C, Rotem A, Strauss S, Strasser R, Thorner A, Turner M, Wakiro I, Waldman J, Wu J, Gómez Tejeda Zañudo J, Zhang D, Lin N, Tolaney S, Winer E, Boyden E, Chen F, Nolan G, Rodig S, Zhuang X, Rozenblatt-Rosen O, Johnson B, Regev A, Wagle N. A multi-modal single-cell and spatial expression map of metastatic breast cancer biopsies across clinicopathological features. Nature Medicine 2024, 30: 3236-3249. PMID: 39478111, PMCID: PMC11564109, DOI: 10.1038/s41591-024-03215-z.Peer-Reviewed Original ResearchClinicopathological featuresLocal T cell infiltrationT cell infiltrationMetastatic breast cancerBreast cancer biopsiesCancer-related deathsEpithelial-to-mesenchymal transitionMetastatic diseaseClinically relevant discoveriesTumor biopsiesTumor microenvironmentCancer biopsiesBreast cancerAnatomical sitesMacrophage populationsSingle-nucleus RNA sequencingBiopsyH&E stainingConsecutive serial sectionsClinical annotationTumorSingle-cellSpatial expression characteristicsSerial sectionsCell type composition
2022
Perceptions of patients and medical oncologists toward biospecimen donation in the setting of abnormal breast imaging findings
Seah DS, Tayob N, Leone JP, Hu J, Yin J, Hughes M, Scott SM, Lederman RI, Frank E, Sohl JJ, Stadler ZK, Erick TK, Peppercorn J, Winer EP, Silverman SG, Come SE, Lin NU. Perceptions of patients and medical oncologists toward biospecimen donation in the setting of abnormal breast imaging findings. Breast Cancer Research And Treatment 2022, 192: 201-210. PMID: 35066788, DOI: 10.1007/s10549-021-06494-z.Peer-Reviewed Original ResearchConceptsAdditional biospecimensMedical oncologistsBreast biopsyBreast tissueBiopsy resultsSingle academic medical centerBreast medical oncologistsPain/discomfortPerceptions of patientsMost medical oncologistsAbnormal breastDiagnostic breast biopsyAcademic medical centerPercutaneous breast biopsyNational Cancer InstituteDonation of bloodCancer CenterDiagnostic biopsyPercutaneous biopsyMedical CenterBiopsyCancer InstitutePatientsOncologistsProcedure risk
2020
Perceptions of patients with early stage breast cancer toward research biopsies
Seah DS, Leone JP, Openshaw TH, Scott SM, Tayob N, Hu J, Lederman RI, Frank ES, Sohl JJ, Stadler ZK, Erick TK, Silverman SG, Peppercorn JM, Winer EP, Come SE, Lin NU. Perceptions of patients with early stage breast cancer toward research biopsies. Cancer 2020, 127: 1208-1219. PMID: 33320362, PMCID: PMC8247276, DOI: 10.1002/cncr.33371.Peer-Reviewed Original ResearchMeSH KeywordsAcademies and InstitutesAdultAgedAged, 80 and overAnalysis of VarianceAttitudeBiomedical ResearchBiopsyBlood DonorsBreastBreast NeoplasmsCancer Care FacilitiesFemaleHealth Services AccessibilityHumansMiddle AgedNeoplasm StagingSocioeconomic FactorsSurveys and QuestionnairesTissue and Organ ProcurementTissue DonorsConceptsEarly-stage breast cancerEarly breast cancerStage breast cancerResearch biopsiesBreast cancerMore patientsClinical trialsBreast biopsyMultivariate analysisProportion of patientsAcademic sitesCommunity oncology practicesPerceptions of patientsPerspectives of patientsCommunity-based sitesCommunity sitesMost patientsOncology sitesModifiable factorsPatients' willingnessUnivariate analysisOncology practiceBiopsyPatientsAcademic centersAcquired 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 lines
2018
Acquired HER2 mutations in ER+ metastatic breast cancer confer resistance to estrogen receptor–directed therapies
Nayar U, Cohen O, Kapstad C, Cuoco MS, Waks AG, Wander SA, Painter C, Freeman S, Persky NS, Marini L, Helvie K, Oliver N, Rozenblatt-Rosen O, Ma CX, Regev A, Winer EP, Lin NU, Wagle N. Acquired HER2 mutations in ER+ metastatic breast cancer confer resistance to estrogen receptor–directed therapies. Nature Genetics 2018, 51: 207-216. PMID: 30531871, DOI: 10.1038/s41588-018-0287-5.Peer-Reviewed Original ResearchConceptsHER2 mutationsEstrogen receptorBreast cancerClinical resistance mechanismsMainstay of treatmentMetastatic breast cancerReceptor-directed therapyCDK6 inhibitor palbociclibPre-existing mutationsMetastatic settingEstrogen independenceInhibitor palbociclibPrimary tumorMetastatic biopsiesInhibitor neratinibTherapyPatientsER mutationsCancerTamoxifenResistance mechanismsDistinct mechanismsMutationsConfer resistanceBiopsy
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
2016
A cancer precision medicine platform for multiple simultaneous genomic assays from metastatic biopsies (bx) in ER+ metastatic breast cancer.
Wagle N, Helvie K, Lloyd M, Marini L, Waks A, Cohen O, Oh C, Sougnez C, Oliver N, Quartey Q, Rotem A, Shah P, Lindeman N, Krop I, Garraway L, Winer E, Lin N. A cancer precision medicine platform for multiple simultaneous genomic assays from metastatic biopsies (bx) in ER+ metastatic breast cancer. Journal Of Clinical Oncology 2016, 34: 11513-11513. DOI: 10.1200/jco.2016.34.15_suppl.11513.Peer-Reviewed Original Research
2015
Variation in the Attitudes of Medical Oncologists Toward Research Biopsies in Patients With Metastatic Breast Cancer
Seah DS, Scott S, Guo H, Najita J, Lederman R, Frank E, Sohl J, Stadler Z, Silverman S, Peppercorn J, Winer E, Come S, Lin NU. Variation in the Attitudes of Medical Oncologists Toward Research Biopsies in Patients With Metastatic Breast Cancer. The Oncologist 2015, 20: 992-1000. PMID: 26240134, PMCID: PMC4571800, DOI: 10.1634/theoncologist.2015-0112.Peer-Reviewed Original ResearchConceptsMetastatic breast cancerBiopsy-related painResearch biopsiesMBC patientsMedical oncologistsOncologists' attitudesBreast cancerWillingness of patientsNational Cancer InstituteEligible respondersModifiable factorsAdditional biopsiesCancer CenterNCI centersPatients' willingnessCommon reasonBiopsyCancer InstitutePatientsSelf-administered surveyStandalone procedureTumor biologyAvailability of tissueElicit factorsPotential target
2013
Prospective clinical experience with research biopsies in breast cancer patients
Vaz-Luis I, Zeghibe CA, Frank ES, Sohl J, Washington KE, Silverman SG, Fonte JM, Mayer EL, Overmoyer BA, Richardson AL, Krop IE, Winer EP, Lin NU. Prospective clinical experience with research biopsies in breast cancer patients. Breast Cancer Research And Treatment 2013, 142: 203-209. PMID: 24113744, PMCID: PMC3825285, DOI: 10.1007/s10549-013-2717-5.Peer-Reviewed Original ResearchConceptsResearch biopsiesAdverse eventsDisease courseMetastatic samplesDana-Farber Cancer InstituteGrade 2 painGrade 3 painProspective clinical experiencePatient's disease courseSingle institution experienceBreast cancer patientsPerformance of biopsyHigh rateAnalytic cohortFirst recurrenceMetastatic diseaseMost patientsPerformance statusReceptor statusPrimary cancerProspective studyCancer patientsBreast cancerPatientsBiopsyAttitudes of patients with metastatic breast cancer toward research biopsies
Seah DS, Scott SM, Najita J, Openshaw T, Krag K, Frank E, Sohl J, Stadler ZK, Garrett M, Silverman SG, Peppercorn J, Winer EP, Come SE, Lin NU. Attitudes of patients with metastatic breast cancer toward research biopsies. Annals Of Oncology 2013, 24: 1853-1859. PMID: 23493137, DOI: 10.1093/annonc/mdt067.Peer-Reviewed Original Research
2011
Should a Sentinel Node Biopsy Be Performed in Patients with High‐Risk Breast Cancer?
Westover KD, Westover MB, Winer EP, Richardson AL, Iglehart JD, Punglia RS. Should a Sentinel Node Biopsy Be Performed in Patients with High‐Risk Breast Cancer? International Journal Of Breast Cancer 2011, 2011: 973245. PMID: 22295240, PMCID: PMC3262582, DOI: 10.4061/2011/973245.Peer-Reviewed Original ResearchAxillary diseaseSLN biopsyHigh riskNegative SLN biopsy resultsHigh-risk breast cancerNegative SLN biopsySLN biopsy resultsLymph node irradiationSentinel node biopsyBreast cancer patientsAxillary irradiationNode irradiationClinical characteristicsNodal biopsyNodal involvementNode biopsyAdditional surgeryBiopsy resultsCancer patientsBreast cancerBiopsyPatientsBayesian nomogramTest characteristicsDisease
2007
Sarcoidosis Mimicking Metastatic Breast Cancer
Tolaney SM, Colson YL, Gill RR, Schulte S, Duggan MM, Shulman LN, Winer EP. Sarcoidosis Mimicking Metastatic Breast Cancer. Clinical Breast Cancer 2007, 7: 804-810. PMID: 18021484, DOI: 10.3816/cbc.2007.n.044.Peer-Reviewed Original Research