2024
An algorithm for standardization of tumor Infiltrating lymphocyte evaluation in head and neck cancers
Xirou V, Moutafi M, Bai Y, Nwe Aung T, Burela S, Liu M, Kimple R, Shabbir Ahmed F, Schultz B, Flieder D, Connolly D, Psyrri A, Burtness B, Rimm D. An algorithm for standardization of tumor Infiltrating lymphocyte evaluation in head and neck cancers. Oral Oncology 2024, 152: 106750. PMID: 38547779, PMCID: PMC11060915, DOI: 10.1016/j.oraloncology.2024.106750.Peer-Reviewed Original ResearchConceptsTumor-infiltrating lymphocytesHead and neck cancerTILs evaluationHPV-positiveNeck cancerPrognostic valueHead and neck squamous cell cancer casesTIL variablesAssociated with favorable prognosisHPV-negative headHPV-negative populationHematoxylin-eosin-stained sectionsCox regression analysisPotential clinical implicationsInter-observer variabilityInfiltrating lymphocytesClinicopathological factorsFavorable prognosisValidation cohortTumor cellsCancer casesProspective settingQuPath softwareRetrospective collectionPredictive significance
2022
Quantitative measurement of HER2 expression to subclassify ERBB2 unamplified breast cancer.
Moutafi M, Robbins C, Yaghoobi V, Fernandez A, Martinez-Morilla S, Xirou V, Bai Y, Song Y, Gaule P, Krueger J, Bloom K, Hill S, Liebler D, Fulton R, Rimm D. Quantitative measurement of HER2 expression to subclassify ERBB2 unamplified breast cancer. Laboratory Investigation 2022, 102: 1101-1108. PMID: 36775350, DOI: 10.1038/s41374-022-00804-9.Peer-Reviewed Original ResearchConceptsHER2 expressionBreast cancerAttomol/HER2 proteinBreast cancer patientsBreast cancer casesOptimal patient careLevels of HER2Trastuzumab deruxtecanT-DXdCancer patientsLow HER2Cancer casesConventional assaysHER2Patient careAntibody concentrationsQuantitative immunofluorescenceAntibody drugsCancerCell linesAssaysExpressionHER2 detectionLower range
2021
An Open Source, Automated Tumor Infiltrating Lymphocyte Algorithm for Prognosis in Triple-Negative Breast Cancer
Bai Y, Cole K, Martinez-Morilla S, Ahmed FS, Zugazagoitia J, Staaf J, Bosch A, Ehinger A, Nimeus E, Hartman J, Acs B, Rimm DL. An Open Source, Automated Tumor Infiltrating Lymphocyte Algorithm for Prognosis in Triple-Negative Breast Cancer. Clinical Cancer Research 2021, 27: clincanres.0325.2021. PMID: 34088723, PMCID: PMC8530841, DOI: 10.1158/1078-0432.ccr-21-0325.Peer-Reviewed Original ResearchA new tool for technical standardization of the Ki67 immunohistochemical assay
Aung TN, Acs B, Warrell J, Bai Y, Gaule P, Martinez-Morilla S, Vathiotis I, Shafi S, Moutafi M, Gerstein M, Freiberg B, Fulton R, Rimm DL. A new tool for technical standardization of the Ki67 immunohistochemical assay. Modern Pathology 2021, 34: 1261-1270. PMID: 33536573, PMCID: PMC8222064, DOI: 10.1038/s41379-021-00745-6.Peer-Reviewed Original Research
2018
An international multicenter study to evaluate reproducibility of automated scoring for assessment of Ki67 in breast cancer
Rimm DL, Leung SCY, McShane LM, Bai Y, Bane AL, Bartlett JMS, Bayani J, Chang MC, Dean M, Denkert C, Enwere EK, Galderisi C, Gholap A, Hugh JC, Jadhav A, Kornaga EN, Laurinavicius A, Levenson R, Lima J, Miller K, Pantanowitz L, Piper T, Ruan J, Srinivasan M, Virk S, Wu Y, Yang H, Hayes DF, Nielsen TO, Dowsett M. An international multicenter study to evaluate reproducibility of automated scoring for assessment of Ki67 in breast cancer. Modern Pathology 2018, 32: 59-69. PMID: 30143750, DOI: 10.1038/s41379-018-0109-4.Peer-Reviewed Original ResearchConceptsIntraclass correlation coefficientBreast cancerBreast Cancer Working GroupAssessment of Ki67Pre-specified analysisCancer Working GroupInternational multicenter studyMulticenter studySubsequent clinical validationInternational Ki67Biopsy sectionsClinical valueBiomarker Ki67Breast tumorsKi67 immunohistochemistryEvaluation of reproducibilityKi67Clinical validationTumor cellsObserved intraclass correlation coefficientScoring methodCorrelation coefficientKi67 scoringMaximum scoreCancer
2017
Elevated T cell activation score is associated with improved survival of breast cancer
Lu L, Bai Y, Wang Z. Elevated T cell activation score is associated with improved survival of breast cancer. Breast Cancer Research And Treatment 2017, 164: 689-696. PMID: 28488141, DOI: 10.1007/s10549-017-4281-x.Peer-Reviewed Original ResearchConceptsT cell activation scoreBreast cancer patientsOverall survivalPatients' overall survivalCancer patientsImproved survivalPD-1Activation scoresBreast cancerCell death-1 receptorLow PD-1 expressionMultivariate Cox regression analysisT-lymphocyte antigen-4Kaplan-Meier survival curvesT cell activation statusDeath-1 receptorPD-1 expressionEffector T cellsImmune checkpoint blockadeCox regression analysisPoor overall survivalCox regression modelT cell functionActivation groupCell activation statusObjective, domain-specific HER2 measurement in uterine and ovarian serous carcinomas and its clinical significance
Carvajal-Hausdorf DE, Schalper KA, Bai Y, Black J, Santin AD, Rimm DL. Objective, domain-specific HER2 measurement in uterine and ovarian serous carcinomas and its clinical significance. Gynecologic Oncology 2017, 145: 154-158. PMID: 28196634, PMCID: PMC5941302, DOI: 10.1016/j.ygyno.2017.02.002.Peer-Reviewed Original ResearchMeSH KeywordsAdo-Trastuzumab EmtansineAfatinibAntibodies, Monoclonal, HumanizedAntineoplastic AgentsCohort StudiesExtracellular SpaceFemaleFluorescent Antibody TechniqueHumansIntracellular SpaceLapatinibMaytansineMiddle AgedNeoplasms, Cystic, Mucinous, and SerousOvarian NeoplasmsProtein DomainsQuinazolinesReceptor, ErbB-2Retrospective StudiesTissue Array AnalysisTrastuzumabUterine NeoplasmsConceptsUterine serous carcinomaOvarian serous carcinomaHER2 intracellular domainSerous carcinomaECD levelsECD statusTissue microarrayHER2 measurementQuantitative immunofluorescenceHER2 overexpression/amplificationClinico-pathologic characteristicsClinico-pathological featuresHER2-targeted agentsIntracellular domainOverexpression/amplificationHER2 extracellular domainExtracellular domainOSC patientsClinical trialsBreast cancerClinical significancePatientsHER2 assaysP95-HER2CarcinomaSpitz nevi and Spitzoid melanomas: exome sequencing and comparison with conventional melanocytic nevi and melanomas
Lazova R, Pornputtapong N, Halaban R, Bosenberg M, Bai Y, Chai H, Krauthammer M. Spitz nevi and Spitzoid melanomas: exome sequencing and comparison with conventional melanocytic nevi and melanomas. Modern Pathology 2017, 30: 640-649. PMID: 28186096, PMCID: PMC5413430, DOI: 10.1038/modpathol.2016.237.Peer-Reviewed Original Research
2016
Early and multiple origins of metastatic lineages within primary tumors
Zhao ZM, Zhao B, Bai Y, Iamarino A, Gaffney SG, Schlessinger J, Lifton RP, Rimm DL, Townsend JP. Early and multiple origins of metastatic lineages within primary tumors. Proceedings Of The National Academy Of Sciences Of The United States Of America 2016, 113: 2140-2145. PMID: 26858460, PMCID: PMC4776530, DOI: 10.1073/pnas.1525677113.Peer-Reviewed Original ResearchConceptsMetastatic lineagesGenetic changesEarly genetic divergenceMolecular evolutionary modelsSingle genetic changeDivergent lineagesTumor phylogeneticsDivergence timesAncestral stateGenetic divergenceCancer lineagesPhylogenetic analysisEvolutionary processesLineagesCancer evolutionMultiple originsDriver genesCancer biologyCancer progressionSomatic mutationsTumor developmentEvolutionary modelsDriver mutationsChronogramMutations
2014
Quantitative measurements of HER2 and phospho-HER2 expression: correlation with pathologic response to neoadjuvant chemotherapy and trastuzumab
Cheng H, Bai Y, Sikov W, Sinclair N, Bossuyt V, Abu-Khalaf MM, Harris LN, Rimm DL. Quantitative measurements of HER2 and phospho-HER2 expression: correlation with pathologic response to neoadjuvant chemotherapy and trastuzumab. BMC Cancer 2014, 14: 326. PMID: 24885187, PMCID: PMC4037428, DOI: 10.1186/1471-2407-14-326.Peer-Reviewed Original ResearchMeSH KeywordsAdenocarcinomaAlbuminsAntibodies, Monoclonal, HumanizedAntineoplastic Combined Chemotherapy ProtocolsBiomarkers, TumorBreast NeoplasmsCarboplatinChemotherapy, AdjuvantConnecticutFemaleFluorescent Antibody TechniqueHumansNeoadjuvant TherapyPaclitaxelPhosphorylationProteomicsReceptor, ErbB-2Rhode IslandTime FactorsTrastuzumabTreatment OutcomeConceptsLikelihood of responsePhospho-HER2Nab-paclitaxelPathologic responseHER2 levelsAdvanced HER2-positive breast cancerHER2-positive breast cancerCarboplatin combination therapyPreoperative clinical trialPre-surgical settingSingle-agent trastuzumabPathologic complete responseInitiation of treatmentWeeks of treatmentBreast cancer patientsTumor core biopsiesCore biopsy samplesMonoclonal antibody trastuzumabEvaluable patientsNeoadjuvant regimenNeoadjuvant chemotherapyNeoadjuvant therapyNeoadjuvant treatmentComplete responsePreoperative setting
2013
Comparison of HER2 and Phospho-HER2 Expression between Biopsy and Resected Breast Cancer Specimens Using a Quantitative Assessment Method
Bai Y, Cheng H, Bordeaux J, Neumeister V, Kumar S, Rimm DL, Stern DF. Comparison of HER2 and Phospho-HER2 Expression between Biopsy and Resected Breast Cancer Specimens Using a Quantitative Assessment Method. PLOS ONE 2013, 8: e79901. PMID: 24278211, PMCID: PMC3836903, DOI: 10.1371/journal.pone.0079901.Peer-Reviewed Original ResearchConceptsCore needle biopsyBreast cancer casesResection specimensCancer casesHER2/neu overexpressionPrediction of responsePre-analytic variablesNeu overexpressionTumor resectionNeedle biopsyBreast cancerHER2 immunoreactivityRetrospective collectionHER2Drug trastuzumabClinical implicationsHER2 proteinQuantitative immunofluorescenceResectionPHER2Good responseFurther studiesBiopsyTrastuzumabImmunoreactivity
2011
Optimal tumor sampling for immunostaining of biomarkers in breast carcinoma
Tolles J, Bai Y, Baquero M, Harris LN, Rimm DL, Molinaro AM. Optimal tumor sampling for immunostaining of biomarkers in breast carcinoma. Breast Cancer Research 2011, 13: r51. PMID: 21592345, PMCID: PMC3218938, DOI: 10.1186/bcr2882.Peer-Reviewed Original ResearchConceptsWhole tissue sectionsBreast carcinomaEstrogen receptorBiomarker expressionTumor biomarker expressionAmount of tumorTissue sectionsEvidence-based standardsHeterogeneous markersTherapeutic responseHER-2Optimal tumorBreast biopsyBreast tumorsClinical implicationsMAP-tauQuantitative immunofluorescenceClinical useLevel of expressionCarcinomaImmunostaining assaysBiomarkersTumorsTissue samplesBiomarker heterogeneityQuantitative assessment shows loss of antigenic epitopes as a function of pre-analytic variables
Bai Y, Tolles J, Cheng H, Siddiqui S, Gopinath A, Pectasides E, Camp RL, Rimm DL, Molinaro AM. Quantitative assessment shows loss of antigenic epitopes as a function of pre-analytic variables. Laboratory Investigation 2011, 91: 1253-1261. PMID: 21519325, PMCID: PMC3145004, DOI: 10.1038/labinvest.2011.75.Peer-Reviewed Original ResearchConceptsCore needle biopsyCold ischemic timePre-analytic variablesNeedle biopsyEstrogen receptorIschemic timeTumor resectionTumor resection specimensAntigenic lossResection specimensTissue biomarkersTotal AktBiopsyPhospho-AktQuantitative immunofluorescencePhospho-ERKPhospho-S6K1Antigenic epitopesTotal ERKResectionTotal proteinCytokeratinImmunological methodsAntigenicitySignificant changes