2023
A Deep Learning Onion Peeling Approach to Measure Oral Epithelium Layer Number
Zhang X, Gleber-Netto F, Wang S, Jin K, Yang D, Gillenwater A, Myers J, Ferrarotto R, Pickering C, Xiao G. A Deep Learning Onion Peeling Approach to Measure Oral Epithelium Layer Number. Cancers 2023, 15: 3891. PMID: 37568707, PMCID: PMC10416878, DOI: 10.3390/cancers15153891.Peer-Reviewed Original ResearchOral epitheliumNeck squamous cell carcinomaSquamous cell carcinomaPatients' qualityCell carcinomaDysplasia severityEarly diagnosisPathologist's examinationOral cavityComplex cancersClinical relevanceDysplasia diagnosisSurvival analysisEpithelium layerDiagnostic potentialCell layerIntra-observer variationDiagnosisEpitheliumClose correlationPotential additionPrognosisCarcinomaCancer
2022
High enhancer activity is an epigenetic feature of HPV negative atypical head and neck squamous cell carcinoma
Callahan SC, Kochat V, Liu Z, Raman AT, Divenko M, Schulz J, Terranova CJ, Ghosh AK, Tang M, Johnson FM, Wang J, Skinner HD, Pickering CR, Myers JN, Rai K. High enhancer activity is an epigenetic feature of HPV negative atypical head and neck squamous cell carcinoma. Frontiers In Cell And Developmental Biology 2022, 10: 936168. PMID: 35927986, PMCID: PMC9343809, DOI: 10.3389/fcell.2022.936168.Peer-Reviewed Original ResearchNeck squamous cell carcinomaSquamous cell carcinomaCell carcinomaCell linesHNSCC cell linesAtypical headResistance pathwaysHNSCC subtypesFrequent recurrenceMolecular subtypesHeterogeneous diseaseLipid metabolismSubtypesSignificant mortalityCarcinomaMAPK signalingFuture targetsHigh enhancer activityDiseaseAtypicalsBromodomain inhibitorsTCGA tumorsEnhancer activityBasalMesenchymal
2019
Identification of novel diagnostic markers for sinonasal undifferentiated carcinoma
Takahashi Y, Gleber‐Netto F, Bell D, Roberts D, Xie T, Abdelmeguid AS, Pickering C, Myers JN, Hanna EY. Identification of novel diagnostic markers for sinonasal undifferentiated carcinoma. Head & Neck 2019, 41: 2688-2695. PMID: 30932264, DOI: 10.1002/hed.25748.Peer-Reviewed Original ResearchConceptsSinonasal squamous cell carcinomaSinonasal undifferentiated carcinomaUndifferentiated carcinomaDiagnostic markerNew diagnostic molecular markersSquamous cell carcinomaDistinct pathologic entityPotential therapeutic targetNovel diagnostic markerNew diagnostic markersSNSCC patientsNeuroendocrine featuresCell carcinomaHistopathologic markersSquamous lineagePathologic entityUndifferentiated tumorsAggressive cancerTumor specimensTherapeutic targetOncology panelUnsupervised cluster analysisCarcinomaPatientsMarkersPredicting Outcome in Head and Neck Cancer: miRNAs with Potentially Big Effects
Clump DA, Pickering CR, Skinner HD. Predicting Outcome in Head and Neck Cancer: miRNAs with Potentially Big Effects. Clinical Cancer Research 2019, 25: 1441-1442. PMID: 30413524, PMCID: PMC6415532, DOI: 10.1158/1078-0432.ccr-18-3078.Peer-Reviewed Original ResearchConceptsHigh-risk patient populationNeck squamous cell carcinomaFive-miRNA signatureSquamous cell carcinomaNovel miRNA signatureCell carcinomaClinical variablesHuman papillomavirusInferior outcomesPatient populationNeck cancerTreatment strategiesPredicting OutcomeMiRNA signatureNegative headOutcomesPatientsCarcinomaPapillomavirusCancerHead
2018
Mutation allele frequency threshold does not affect prognostic analysis using next-generation sequencing in oral squamous cell carcinoma
Ma J, Fu Y, Tu YY, Liu Y, Tan YR, Ju WT, Pickering CR, Myers JN, Zhang ZY, Zhong LP. Mutation allele frequency threshold does not affect prognostic analysis using next-generation sequencing in oral squamous cell carcinoma. BMC Cancer 2018, 18: 758. PMID: 30041611, PMCID: PMC6057048, DOI: 10.1186/s12885-018-4481-8.Peer-Reviewed Original ResearchConceptsOral squamous cell carcinomaSquamous cell carcinomaPrognostic analysisOSCC patientsCell carcinomaMethodsForty-six patientsClinical outcome analysisNext-generation sequencingAllele frequency thresholdWild-type genotypeParaffin-embedded tissuesNon-synonymous mutationsAllele frequenciesClinical outcomesOutcome analysisPatientsPanel of cancerType genotypeSignificant differencesCarcinomaFrequency thresholdNotch1CDKN2AMutationsCASP8
2017
APOBEC3A is an oral cancer prognostic biomarker in Taiwanese carriers of an APOBEC deletion polymorphism
Chen TW, Lee CC, Liu H, Wu CS, Pickering CR, Huang PJ, Wang J, Chang IY, Yeh YM, Chen CD, Li HP, Luo JD, Tan BC, Chan TEH, Hsueh C, Chu LJ, Chen YT, Zhang B, Yang CY, Wu CC, Hsu CW, See LC, Tang P, Yu JS, Liao WC, Chiang WF, Rodriguez H, Myers JN, Chang KP, Chang YS. APOBEC3A is an oral cancer prognostic biomarker in Taiwanese carriers of an APOBEC deletion polymorphism. Nature Communications 2017, 8: 465. PMID: 28878238, PMCID: PMC5587710, DOI: 10.1038/s41467-017-00493-9.Peer-Reviewed Original ResearchConceptsOral squamous cell carcinomaSquamous cell carcinomaCell carcinomaTaiwanese oral squamous cell carcinomasClinical prognostic relevanceBetter overall survivalCancer prognostic biomarkersExpression of APOBEC3AOverall survivalPrognostic relevanceTaiwanese patientsPrognostic biomarkerSecond cohortGermline polymorphismsCancer typesProminent cancerMutational profileDeletion polymorphismPatientsCarcinomaMutation signaturesExpressionPolymorphismCohortTumors
2015
Detection of somatic mutations and HPV in the saliva and plasma of patients with head and neck squamous cell carcinomas
Wang Y, Springer S, Mulvey CL, Silliman N, Schaefer J, Sausen M, James N, Rettig EM, Guo T, Pickering CR, Bishop JA, Chung CH, Califano JA, Eisele DW, Fakhry C, Gourin CG, Ha PK, Kang H, Kiess A, Koch WM, Myers JN, Quon H, Richmon JD, Sidransky D, Tufano RP, Westra WH, Bettegowda C, Diaz LA, Papadopoulos N, Kinzler KW, Vogelstein B, Agrawal N. Detection of somatic mutations and HPV in the saliva and plasma of patients with head and neck squamous cell carcinomas. Science Translational Medicine 2015, 7: 293ra104. PMID: 26109104, PMCID: PMC4587492, DOI: 10.1126/scitranslmed.aaa8507.Peer-Reviewed Original ResearchConceptsNeck squamous cell carcinomaOral cavity cancerSquamous cell carcinomaTumor DNACell carcinomaOral cavityDetection of HNSCCLate-stage diseaseFraction of patientsPlasma of patientsTumor-specific DNASomatic mutationsHNSCC patientsPatientsValuable biomarkerClinical diagnosisHuman papillomavirus genesCancerSalivaCarcinomaRecurrenceBiomarkersHPVOropharynxHNSCC
2014
Mutational Landscape of Aggressive Cutaneous Squamous Cell Carcinoma
Pickering CR, Zhou JH, Lee JJ, Drummond JA, Peng SA, Saade RE, Tsai KY, Curry JL, Tetzlaff MT, Lai SY, Yu J, Muzny DM, Doddapaneni H, Shinbrot E, Covington KR, Zhang J, Seth S, Caulin C, Clayman GL, El-Naggar AK, Gibbs RA, Weber RS, Myers JN, Wheeler DA, Frederick MJ. Mutational Landscape of Aggressive Cutaneous Squamous Cell Carcinoma. Clinical Cancer Research 2014, 20: 6582-6592. PMID: 25303977, PMCID: PMC4367811, DOI: 10.1158/1078-0432.ccr-14-1768.Peer-Reviewed Original ResearchConceptsAggressive cutaneous squamous cell carcinomaCutaneous squamous cell carcinomaSquamous cell carcinomaCell carcinomaCandidate tumor suppressorNeck squamous cell carcinomaNovel therapeutic targetNovel candidate tumor suppressorTumor suppressorWhole-exome sequencingBone invasionPoor outcomeTherapeutic targetLethal diseaseTumor suppressor geneCarcinomaKMT2C mutationsHigh mutational backgroundGene TP53Mutational landscapePutative linkDriver genesDiseaseMutational spectrumUV exposure
2011
Assembly and Initial Characterization of a Panel of 85 Genomically Validated Cell Lines from Diverse Head and Neck Tumor Sites
Zhao M, Sano D, Pickering CR, Jasser SA, Henderson YC, Clayman GL, Sturgis EM, Ow TJ, Lotan R, Carey TE, Sacks PG, Grandis JR, Sidransky D, Heldin NE, Myers JN. Assembly and Initial Characterization of a Panel of 85 Genomically Validated Cell Lines from Diverse Head and Neck Tumor Sites. Clinical Cancer Research 2011, 17: 7248-7264. PMID: 21868764, PMCID: PMC3229662, DOI: 10.1158/1078-0432.ccr-11-0690.Peer-Reviewed Original ResearchConceptsNeck cell linesSquamous cell carcinomaCell carcinomaCell linesTumor siteCutaneous squamous cell carcinomaNeck squamous cell carcinomaNeck tumor sitesHuman papillomavirus (HPV) statusPrimary tumor siteHPV-16 DNAOral leukoplakiaNeck cancerThyroid cancerCystic carcinomaMajor headPreclinical studiesNormal epitheliumDiverse headTissue sitesCarcinomaCancer research communityPrimary keratinocytesCancer therapyExome Sequencing of Head and Neck Squamous Cell Carcinoma Reveals Inactivating Mutations in NOTCH1
Agrawal N, Frederick MJ, Pickering CR, Bettegowda C, Chang K, Li RJ, Fakhry C, Xie TX, Zhang J, Wang J, Zhang N, El-Naggar AK, Jasser SA, Weinstein JN, Treviño L, Drummond JA, Muzny DM, Wu Y, Wood LD, Hruban RH, Westra WH, Koch WM, Califano JA, Gibbs RA, Sidransky D, Vogelstein B, Velculescu VE, Papadopoulos N, Wheeler DA, Kinzler KW, Myers JN. Exome Sequencing of Head and Neck Squamous Cell Carcinoma Reveals Inactivating Mutations in NOTCH1. Science 2011, 333: 1154-1157. PMID: 21798897, PMCID: PMC3162986, DOI: 10.1126/science.1206923.Peer-Reviewed Original ResearchMeSH KeywordsCarcinomaCarcinoma, Squamous CellCell Cycle ProteinsCodon, NonsenseExonsF-Box ProteinsF-Box-WD Repeat-Containing Protein 7Gene DosageGenes, p53Genes, Tumor SuppressorHead and Neck NeoplasmsHumansINDEL MutationMutationMutation, MissenseNeoplasms, Squamous CellOligonucleotide Array Sequence AnalysisOncogenesPapillomaviridaePapillomavirus InfectionsReceptor, Notch1Sequence Analysis, DNASmokingSquamous Cell Carcinoma of Head and NeckUbiquitin-Protein LigasesConceptsNeck squamous cell carcinomaSquamous cell carcinomaCell carcinomaHuman papillomavirusHPV-positive tumorsWhole-exome sequencingMore mutationsPrimary tumorCommon cancerMultiple tumorsTobacco useTumor typesTumorsTumor suppressor geneExome sequencingGene copy number analysisNotch1Copy number analysisPatientsCarcinomaInactivating mutationCancerSuppressor geneMutationsGenetic origin