2021
Quantitative immunofluorescence and mRNA analysis of immune-related biomarker groups in matched paired tumor samples from OPHELIA window study in head and neck squamous cell carcinoma (HNSCC).
Psyrri A, Moutafi M, Koliou G, Papaxoinis G, Gavrielatou N, Economopoulou P, Kotsantis I, Gkotzamanidou M, Anastasiou M, Pectasides D, Fernandez A, Yaghoobi V, Shafi S, Vathiotis I, Aung T, Gkolfinopoulos S, Foukas P, Fountzilas G, Rimm D. Quantitative immunofluorescence and mRNA analysis of immune-related biomarker groups in matched paired tumor samples from OPHELIA window study in head and neck squamous cell carcinoma (HNSCC). Journal Of Clinical Oncology 2021, 39: 6064-6064. DOI: 10.1200/jco.2021.39.15_suppl.6064.Peer-Reviewed Original ResearchCombined positive scorePD-L1 expressionQuantitative immunofluorescencePD-L1Preclinical modelsCD8 T cell infiltrationNeck squamous cell carcinomaPhase II trialReal-time quantitative reverse transcription polymerase chain reactionT cell infiltrationPD-L1 upregulationSquamous cell carcinomaPD-L1 mRNAQuantitative reverse transcription polymerase chain reactionReverse transcription-polymerase chain reactionBiomarker groupsWindow studyTranscription-polymerase chain reactionSTING protein levelsPost-treatment samplesII trialAntitumor immunityImmune infiltratesPD-1Dual blockade
2020
A Static Self-Directed Method for Generating Brain Organoids from Human Embryonic Stem Cells.
Boisvert EM, Means RE, Michaud M, Thomson JJ, Madri JA, Katz SG. A Static Self-Directed Method for Generating Brain Organoids from Human Embryonic Stem Cells. Journal Of Visualized Experiments 2020 PMID: 32202516, PMCID: PMC7245934, DOI: 10.3791/60379.Peer-Reviewed Original ResearchConceptsEmbryonic stem cellsCell typesStem cellsIntrinsic developmental cuesHuman embryonic stem cellsHuman pluripotent stem cellsBrain organoidsBrain cell typesPluripotent stem cellsBasement membrane matrixMultiple cell typesDevelopmental cuesUse of organoidsExogenous growth factorsQuantitative reverse transcription polymerase chain reactionMultitude of diseasesHuman brain organoidsOrganoid growthSingle cellsReal-time quantitative reverse transcription polymerase chain reactionSpatial organizationOrganoidsGenetic disordersGrowth factorReverse transcription-polymerase chain reaction
2019
Closed system RT-qPCR as a potential companion diagnostic test for immunotherapy outcome in metastatic melanoma
Gupta S, McCann L, Chan YGY, Lai EW, Wei W, Wong PF, Smithy JW, Weidler J, Rhees B, Bates M, Kluger HM, Rimm DL. Closed system RT-qPCR as a potential companion diagnostic test for immunotherapy outcome in metastatic melanoma. Journal For ImmunoTherapy Of Cancer 2019, 7: 254. PMID: 31533832, PMCID: PMC6751819, DOI: 10.1186/s40425-019-0731-9.Peer-Reviewed Original ResearchMeSH KeywordsAgedAntineoplastic Agents, ImmunologicalB7-H1 AntigenBiomarkers, TumorCD8 AntigensFemaleFollow-Up StudiesGene Expression ProfilingHumansInterferon Regulatory Factor-1MaleMelanomaMiddle AgedMonitoring, ImmunologicPrognosisProgrammed Cell Death 1 Ligand 2 ProteinProgression-Free SurvivalReal-Time Polymerase Chain ReactionRetrospective StudiesReverse Transcriptase Polymerase Chain ReactionRNA, MessengerSkin NeoplasmsConceptsCompanion diagnostic testsImmunotherapy outcomesMelanoma patientsClinical benefitAnti-PD-1 therapyImmune checkpoint inhibitor therapyMRNA expressionQuantitative immunofluorescenceDiagnostic testsCheckpoint inhibitor therapyReal-time quantitative reverse transcription polymerase chain reactionMetastatic melanoma patientsQuantitative reverse transcription polymerase chain reactionReverse transcription-polymerase chain reactionTranscription-polymerase chain reactionYale Pathology archivesParaffin-embedded tissue sectionsAdjuvant settingICI therapyOS associationInhibitor therapyBaseline variablesMetastatic melanomaPredictive biomarkersPolymerase chain reactionQuantitative assessments and clinical outcomes in HER2 equivocal 2018 ASCO/CAP ISH group 4 breast cancer
Gupta S, Neumeister V, McGuire J, Song YS, Acs B, Ho K, Weidler J, Wong W, Rhees B, Bates M, Rimm DL, Bossuyt V. Quantitative assessments and clinical outcomes in HER2 equivocal 2018 ASCO/CAP ISH group 4 breast cancer. Npj Breast Cancer 2019, 5: 28. PMID: 31482108, PMCID: PMC6715641, DOI: 10.1038/s41523-019-0122-x.Peer-Reviewed Original ResearchBreast cancerQuantitative immunofluorescenceIHC 0/1Systemic treatmentRT-qPCRClinical Oncology/CollegeAdditional outcome informationProtein expressionReal-time quantitative reverse transcription polymerase chain reactionHER2 protein levelsQuantitative reverse transcription polymerase chain reactionReverse transcription-polymerase chain reactionTranscription-polymerase chain reactionASCO/CAP recommendationsRNA/protein expressionQIF scoresPatient characteristicsClinical outcomesTrastuzumab treatmentSurvival outcomesPolymerase chain reactionIHC 2Treatment decisionsCAP recommendationsPatients
2018
Sera From Children After Cardiopulmonary Bypass Reduces Permeability of Capillary Endothelial Cell Barriers
Pierce RW, Zahr RA, Kandil S, Faustino EVS, Pober JS. Sera From Children After Cardiopulmonary Bypass Reduces Permeability of Capillary Endothelial Cell Barriers. Pediatric Critical Care Medicine 2018, 19: 609-618. PMID: 29652749, PMCID: PMC6037548, DOI: 10.1097/pcc.0000000000001553.Peer-Reviewed Original ResearchConceptsTransendothelial electrical resistanceCardiopulmonary bypassCapillary endothelial cellsEndothelial cellsCapillary leakPatient seraClaudin-5Pulmonary capillary endothelial cellsBarrier functionPulmonary microvascular endothelial cellsReal-time quantitative reverse transcription polymerase chain reactionTertiary pediatric hospitalQuantitative reverse transcription polymerase chain reactionCardiopulmonary bypass circuitCongenital heart diseaseReverse transcription-polymerase chain reactionTranscription-polymerase chain reactionMicrovascular endothelial cellsEndothelial cell barrierCohort studyInflammatory mediatorsPediatric hospitalUnclear etiologyBarrier disruptionHeart disease
2017
High concordance of a closed-system, RT-qPCR breast cancer assay for HER2 mRNA, compared to clinically determined immunohistochemistry, fluorescence in situ hybridization, and quantitative immunofluorescence
Wasserman BE, Carvajal-Hausdorf DE, Ho K, Wong W, Wu N, Chu VC, Lai EW, Weidler JM, Bates M, Neumeister V, Rimm DL. High concordance of a closed-system, RT-qPCR breast cancer assay for HER2 mRNA, compared to clinically determined immunohistochemistry, fluorescence in situ hybridization, and quantitative immunofluorescence. Laboratory Investigation 2017, 97: 1521-1526. PMID: 28892092, PMCID: PMC5711560, DOI: 10.1038/labinvest.2017.93.Peer-Reviewed Original ResearchConceptsInvasive breast cancerBreast cancerQuantitative immunofluorescenceRT-qPCRFormalin-fixed paraffin-embedded tissue blocksRT-qPCR assaysEquivocal categoryReal-time quantitative reverse transcription polymerase chain reactionHER2 receptor statusQuantitative reverse transcription polymerase chain reactionParaffin-embedded tissue blocksReverse transcription-polymerase chain reactionTranscription-polymerase chain reactionIHC/FISHMRNA measurementsAssessment of HER2Low-resource settingsReceptor statusPolymerase chain reactionPathology reportsCT cutsSingle-use cartridgeResource settingsHER2 mRNATissue blocksInterleukin-13 receptor alpha 2 as a marker of poorer prognosis in high-grade astrocytomas.
Wanibuchi M, Kataoka-Sasaki Y, Sasaki M, Oka S, Otsuka Y, Yamaguchi M, Ohnishi H, Ohtaki S, Noshiro S, Ookawa S, Mikami T, Mikuni N, Honmou O. Interleukin-13 receptor alpha 2 as a marker of poorer prognosis in high-grade astrocytomas. Journal Of Neurosurgical Sciences 2017, 62: 239-244. PMID: 28079349, DOI: 10.23736/s0390-5616.16.03793-0.Peer-Reviewed Original ResearchConceptsHigh-grade astrocytomasInterleukin-13 receptor alpha 2Overall survivalMIB-1 indexReceptor alpha 2Median OSPoor prognosisPatient ageCox proportional hazards modelWorld Health Organization gradeMedian overall survivalMedian survival benefitAdvanced patient ageAlpha 2Real-time quantitative reverse transcription polymerase chain reactionLow expression groupQuantitative reverse transcription polymerase chain reactionReverse transcription-polymerase chain reactionProportional hazards modelTranscription-polymerase chain reactionExpression levelsSubset of casesParaffin-embedded glioma samplesHazard ratioSurvival benefit
2009
Gene Expression Profiles of Acute Exacerbations of Idiopathic Pulmonary Fibrosis
Konishi K, Gibson KF, Lindell KO, Richards TJ, Zhang Y, Dhir R, Bisceglia M, Gilbert S, Yousem SA, Song JW, Kim DS, Kaminski N. Gene Expression Profiles of Acute Exacerbations of Idiopathic Pulmonary Fibrosis. American Journal Of Respiratory And Critical Care Medicine 2009, 180: 167-175. PMID: 19363140, PMCID: PMC2714820, DOI: 10.1164/rccm.200810-1596oc.Peer-Reviewed Original ResearchConceptsIdiopathic pulmonary fibrosisStable idiopathic pulmonary fibrosisAcute exacerbationIPF lungsPulmonary fibrosisControl lungsPeripheral bloodReal-time quantitative reverse transcription polymerase chain reactionProtein levelsQuantitative reverse transcription polymerase chain reactionReverse transcription-polymerase chain reactionApoptosis of epitheliumTranscription-polymerase chain reactionDUTP nick-end labeling assayNick-end labeling assayGlobal gene expression signaturesAgilent gene expression microarraysEnd-labeling assayDEFA1-3Gene expression signaturesInflammatory etiologyEpithelial injuryControl subjectsExacerbationLung
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