2024
Immune infiltration at the primary tumor is associated with clinical outcome of patients with extranodal extension of lymph node metastasis in oral cancer
Michikawa C, Gleber-Netto F, Pickering C, Rao X, Wang J, Sikora A, Myers J, Frederick M. Immune infiltration at the primary tumor is associated with clinical outcome of patients with extranodal extension of lymph node metastasis in oral cancer. Oral Oncology 2024, 153: 106729. PMID: 38663156, DOI: 10.1016/j.oraloncology.2024.106729.Peer-Reviewed Original ResearchConceptsOral cavity squamous cell carcinomaAssociated with clinical outcomesExtranodal extensionLymph node metastasisImmune infiltrationImmune infiltration statusOverall survivalPrimary tumorNode metastasisOral cancerInfiltration statusClinical outcomes of OSCC patientsExtension of lymph node metastasesAssociated with clinical outcomes of patientsAssociated with OS rateLocally advanced oral cancerClinical outcomes of patientsOutcome of OSCC patientsAssociated with poor overall survivalImmune infiltration of tumorsLow immune infiltrationNode negative tumorsAdvanced oral cancerHuman papillomavirus-negativeInfiltration of tumors
2021
Whole-exome Sequencing in Penile Squamous Cell Carcinoma Uncovers Novel Prognostic Categorization and Drug Targets Similar to Head and Neck Squamous Cell CarcinomaClinical Implications of WES in Penile Squamous Carcinoma
Chahoud J, Gleber-Netto FO, McCormick BZ, Rao P, Lu X, Guo M, Morgan MB, Chu RA, Martinez-Ferrer M, Eterovic AK, Pickering CR, Pettaway CA. Whole-exome Sequencing in Penile Squamous Cell Carcinoma Uncovers Novel Prognostic Categorization and Drug Targets Similar to Head and Neck Squamous Cell CarcinomaClinical Implications of WES in Penile Squamous Carcinoma. Clinical Cancer Research 2021, 27: 2560-2570. PMID: 33441293, DOI: 10.1158/1078-0432.ccr-20-4004.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAged, 80 and overBiomarkers, TumorCase-Control StudiesComputational BiologyDisease ManagementDisease SusceptibilityExome SequencingHumansMaleMiddle AgedMolecular Targeted TherapyMutationNeoplasm GradingNeoplasm StagingPenile NeoplasmsPrognosisSquamous Cell Carcinoma of Head and NeckConceptsPenile squamous cell carcinomaSquamous cell carcinomaCell carcinomaHuman papilloma virus testingNeck squamous cell carcinomaNotch pathway alterationsMutation signaturesTumor mutation burdenWorse overall survivalLimited treatment optionsWhole-exome sequencing analysisPenile squamous carcinomaPotential clinical implicationsMutational signaturesDefective DNA mismatch repairCancer Genome Atlas studyWhole-exome sequencingNovel druggable targetsDistinct mutational signaturesNormal penile tissuesOverall survivalWorse survivalHigh TMBSquamous carcinomaPenile tissue
2020
The mutational landscape of early‐ and typical‐onset oral tongue squamous cell carcinoma
Campbell BR, Chen Z, Faden DL, Agrawal N, Li RJ, Hanna GJ, Iyer NG, Boot A, Rozen SG, Vettore AL, Panda B, Krishnan NM, Pickering CR, Myers JN, Guo X, Kuhs K. The mutational landscape of early‐ and typical‐onset oral tongue squamous cell carcinoma. Cancer 2020, 127: 544-553. PMID: 33146897, PMCID: PMC7891879, DOI: 10.1002/cncr.33309.Peer-Reviewed Original ResearchConceptsOral tongue squamous cell carcinomaTongue squamous cell carcinomaSquamous cell carcinomaTongue cancerYounger patientsCell carcinomaTobacco useDriver genesOral tongue cancerPatient-related factorsCancer driver genesTongue cancer specimensAge of onsetMutational landscapeSomatic mutationsMutation signaturesYounger birth cohortsSomatic mutational burdenOlder patientsCancer Genome AtlasSmoking ratesMutational burdenCancer specimensMulticenter consortiumBirth cohort
2019
Weekly paclitaxel, carboplatin, cetuximab, and cetuximab, docetaxel, cisplatin, and fluorouracil, followed by local therapy in previously untreated, locally advanced head and neck squamous cell carcinoma
Haddad RI, Massarelli E, Lee JJ, Lin HY, Hutcheson K, Lewis J, Garden AS, Blumenschein GR, William WN, Pharaon RR, Tishler RB, Glisson BS, Pickering C, Gold KA, Johnson FM, Rabinowits G, Ginsberg LE, Williams MD, Myers J, Kies MS, Papadimitrakopoulou V. Weekly paclitaxel, carboplatin, cetuximab, and cetuximab, docetaxel, cisplatin, and fluorouracil, followed by local therapy in previously untreated, locally advanced head and neck squamous cell carcinoma. Annals Of Oncology 2019, 30: 471-477. PMID: 30596812, PMCID: PMC7360148, DOI: 10.1093/annonc/mdy549.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAntineoplastic Combined Chemotherapy ProtocolsCarboplatinCetuximabCisplatinDocetaxelFemaleFluorouracilHumansInduction ChemotherapyMaleMiddle AgedNeoplasm Recurrence, LocalNeoplasm StagingPaclitaxelPapillomaviridaePapillomavirus InfectionsProgression-Free SurvivalSquamous Cell Carcinoma of Head and NeckConceptsProgression-free survivalSquamous cell carcinomaHigh-risk groupNeck squamous cell carcinomaPrimary end pointInduction chemotherapyLocal therapyCell carcinomaC-TPFAdvanced headT stageHistorical controlsEnd pointPhase II clinical trialHuman papillomavirus (HPV) statusLow-risk groupEligible patientsMedian followWeekly paclitaxelLocoregional treatmentT3-4P16 statusClinical trialsRisk groupsHPV
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 thresholdNotch1CDKN2AMutationsCASP8The Integrated Genomic Landscape of Thymic Epithelial Tumors
Radovich M, Pickering CR, Felau I, Ha G, Zhang H, Jo H, Hoadley KA, Anur P, Zhang J, McLellan M, Bowlby R, Matthew T, Danilova L, Hegde AM, Kim J, Leiserson MDM, Sethi G, Lu C, Ryan M, Su X, Cherniack AD, Robertson G, Akbani R, Spellman P, Weinstein JN, Hayes DN, Raphael B, Lichtenberg T, Leraas K, Zenklusen JC, Network T, Ally A, Appelbaum E, Auman J, Balasundaram M, Balu S, Behera M, Beroukhim R, Berrios M, Blandino G, Bodenheimer T, Bootwalla M, Bowen J, Brooks D, Carcano F, Carlsen R, Carvalho A, Castro P, Chalabreysse L, Chin L, Cho J, Choe G, Chuah E, Chudamani S, Cibulskis C, Cope L, Cordes M, Crain D, Curley E, Defreitas T, Demchok J, Detterbeck F, Dhalla N, Dienemann H, Edenfield W, Facciolo F, Ferguson M, Frazer S, Fronick C, Fulton L, Fulton R, Gabriel S, Gardner J, Gastier-Foster J, Gehlenborg N, Gerken M, Getz G, Heiman D, Hobensack S, Holbrook A, Holt R, Hoyle A, Hutter C, Ittmann M, Jefferys S, Jones C, Jones S, Kasaian K, Kim J, Kimes P, Lai P, Laird P, Lawrence M, Lin P, Liu J, Lolla L, Lu Y, Ma Y, Maglinte D, Mallery D, Mardis E, Marra M, Martin J, Mayo M, Meier S, Meister M, Meng S, Meyerson M, Mieczkowski P, Miller C, Mills G, Moore R, Morris S, Mose L, Muley T, Mungall A, Mungall K, Naresh R, Newton Y, Noble M, Owonikoko T, Parker J, Paulaskis J, Penny R, Perou C, Perrin C, Pihl T, Radenbaugh A, Ramalingam S, Ramirez N, Rieker R, Roach J, Sadeghi S, Saksena G, Schein J, Schmidt H, Schumacher S, Shelton C, Shelton T, Shi Y, Shih J, Sica G, Silveira H, Simons J, Sipahimalani P, Skelly T, Sofia H, Soloway M, Stuart J, Sun Q, Tam A, Tan D, Tarnuzzer R, Thiessen N, Van Den Berg D, Vasef M, Veluvolu U, Voet D, Walter V, Wan Y, Wang Z, Warth A, Weis C, Weisenberger D, Wilkerson M, Wise L, Wong T, Wu H, Wu Y, Yang L, Zhang J, Zmuda E, Fujimoto J, Scapulatempo-Neto C, Moreira A, Hwang D, Huang J, Marino M, Korst R, Giaccone G, Gokmen-Polar Y, Badve S, Rajan A, Ströbel P, Girard N, Tsao M, Marx A, Tsao A, Loehrer P. The Integrated Genomic Landscape of Thymic Epithelial Tumors. Cancer Cell 2018, 33: 244-258.e10. PMID: 29438696, PMCID: PMC5994906, DOI: 10.1016/j.ccell.2018.01.003.Peer-Reviewed Original ResearchConceptsThymic epithelial tumorsEpithelial tumorsWorld Health Organization (WHO) histological subtypeAutoimmune disease myasthenia gravisDisease myasthenia gravisMuscle autoantigensThymic carcinomaMyasthenia gravisAutoimmune diseasesHistological subtypesAdult malignanciesTumoral overexpressionMarked prevalenceTumorsThymomaSubtypesEnrichment of mutationsGenomic landscapeBiological effectsGenomic hallmarksMolecular linkUnique associationAssociationMulti-platform analysisGravis
2017
Distinct pattern of TP53 mutations in human immunodeficiency virus–related head and neck squamous cell carcinoma
Gleber‐Netto F, Zhao M, Trivedi S, Wang J, Jasser S, McDowell C, Kadara H, Zhang J, Wang J, William WN, Lee JJ, Nguyen ML, Pai SI, Walline HM, Shin DM, Ferris RL, Carey TE, Myers JN, Pickering CR, Consortium F. Distinct pattern of TP53 mutations in human immunodeficiency virus–related head and neck squamous cell carcinoma. Cancer 2017, 124: 84-94. PMID: 29053175, PMCID: PMC5785080, DOI: 10.1002/cncr.31063.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedCadherinsCarcinoma, Squamous CellCase-Control StudiesCaspase 8Class I Phosphatidylinositol 3-KinasesCyclin D1Cyclin-Dependent Kinase Inhibitor p16Cyclin-Dependent Kinase Inhibitor p18ErbB ReceptorsF-Box-WD Repeat-Containing Protein 7FemaleHead and Neck NeoplasmsHistone MethyltransferasesHistone-Lysine N-MethyltransferaseHIV InfectionsHLA-A AntigensHumansIn Situ HybridizationIntracellular Signaling Peptides and ProteinsKelch-Like ECH-Associated Protein 1LIM Domain ProteinsMaleMiddle AgedNF-E2-Related Factor 2Nuclear ProteinsPapillomaviridaePapillomavirus InfectionsProtein Serine-Threonine KinasesProto-Oncogene Proteins p21(ras)Receptor, Notch1Receptor, Notch2Receptor, Transforming Growth Factor-beta Type IIReceptors, Transforming Growth Factor betaSquamous Cell Carcinoma of Head and NeckTranscription FactorsTumor Suppressor Protein p53Tumor Suppressor ProteinsConceptsHuman immunodeficiency virus-infected individualsHuman immunodeficiency virus (HIV) infectionNeck squamous cell carcinomaHuman papillomavirus (HPV) statusImmunodeficiency virus infectionVirus-infected individualsSquamous cell carcinomaSample of HIVTP53 mutation frequencyHNSCC patientsCell carcinomaHistopathological differencesPolymerase chain reactionIon Reporter softwareP16 immunostainingDistinct biologyVirus infectionHigh incidenceHIVHNSCCMultiplex polymerase chain reactionDistinct patternsHIV virusTumor samplesTP53 geneAPOBEC3A 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 signaturesExpressionPolymorphismCohortTumorsPrevalence of promoter mutations in the TERT gene in oral cavity squamous cell carcinoma
Chang K, Wang C, Pickering CR, Huang Y, Tsai C, Tsang N, Kao H, Cheng M, Myers JN. Prevalence of promoter mutations in the TERT gene in oral cavity squamous cell carcinoma. Head & Neck 2017, 39: 1131-1137. PMID: 28230921, DOI: 10.1002/hed.24728.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAged, 80 and overCarcinoma, Squamous CellCohort StudiesDisease ProgressionDisease-Free SurvivalFemaleGene Expression Regulation, NeoplasticHumansKaplan-Meier EstimateMaleMiddle AgedMouth NeoplasmsMutationPrevalencePromoter Regions, GeneticReal-Time Polymerase Chain ReactionRetrospective StudiesRisk AssessmentStatistics, NonparametricSurvival AnalysisTaiwanTelomeraseConceptsOral cavity squamous cell carcinomaSquamous cell carcinomaTERT promoter mutationsAdjacent normal tissuesPromoter mutationsSomatic TERT promoter mutationsNormal tissuesC228T mutationTelomerase reverse transcriptase (TERT) promoterT mutationSCC tumor tissuesHuman telomerase reverse transcriptase (hTERT) promoterC250T mutationsReverse transcriptase promoterCell carcinomaSCC tumorsC228TTumor tissueTERT activityBetel nutTERT promoterTissuePresent studyMutationsSanger method
2015
Mechanisms for the Generation of Two Quadruplications Associated with Split‐Hand Malformation
Gu S, Posey JE, Yuan B, Carvalho CM, Luk HM, Erikson K, Lo IF, Leung GK, Pickering CR, Chung BH, Lupski JR. Mechanisms for the Generation of Two Quadruplications Associated with Split‐Hand Malformation. Human Mutation 2015, 37: 160-164. PMID: 26549411, PMCID: PMC4718869, DOI: 10.1002/humu.22929.Peer-Reviewed Original ResearchMeSH Keywords14-3-3 ProteinsAdultAgedAlu ElementsBase SequenceBasic Helix-Loop-Helix Transcription FactorsChromosome DuplicationChromosomes, Human, Pair 17DNA Copy Number VariationsFemaleGenetic LociGenome, HumanHand Deformities, CongenitalHumansInfantMaleMolecular Sequence DataPedigreeSequence AlignmentSequence Analysis, DNA
2014
Squamous Cell Carcinoma of the Oral Tongue in Young Non-Smokers Is Genomically Similar to Tumors in Older Smokers
Pickering CR, Zhang J, Neskey DM, Zhao M, Jasser SA, Wang J, Ward A, Tsai CJ, Alves M, Zhou JH, Drummond J, El-Naggar AK, Gibbs R, Weinstein JN, Wheeler DA, Wang J, Frederick MJ, Myers JN. Squamous Cell Carcinoma of the Oral Tongue in Young Non-Smokers Is Genomically Similar to Tumors in Older Smokers. Clinical Cancer Research 2014, 20: 3842-3848. PMID: 24874835, PMCID: PMC4102633, DOI: 10.1158/1078-0432.ccr-14-0565.Peer-Reviewed Original ResearchConceptsSquamous cell carcinomaOlder patientsOral tongueYounger patientsCell carcinomaWhole-exome sequencingOlder smokersSimilar patientsTongue tumorsNon smokersIncreasing incidenceEpidemiologic studiesIndependent cohortPatientsSCCOTSmokingTumorsCohortAlteration frequencyGenomic effectsTCGA dataCopy number analysisGene-specific mutationsOlder cohortTypes of mutations
2013
CT Imaging Correlates of Genomic Expression for Oral Cavity Squamous Cell Carcinoma
Pickering CR, Shah K, Ahmed S, Rao A, Frederick MJ, Zhang J, Unruh AK, Wang J, Ginsberg LE, Kumar AJ, Myers JN, Hamilton JD. CT Imaging Correlates of Genomic Expression for Oral Cavity Squamous Cell Carcinoma. American Journal Of Neuroradiology 2013, 34: 1818-1822. PMID: 23764725, PMCID: PMC7965627, DOI: 10.3174/ajnr.a3635.Peer-Reviewed Original ResearchConceptsOral cavity squamous cell carcinomaSquamous cell carcinomaEpidermal growth factor receptorGrowth factor receptorCell carcinomaGenomic biomarkersFactor receptorPrimary tumorImaging correlatesUntreated oral cavity squamous cell carcinomaRelevant genomic biomarkersVascular endothelial growth factor receptor 1Vascular endothelial growth factor receptorPrimary tumor sizeEndothelial growth factor receptorGrowth factor receptor 1Mass effectPreoperative CT imagingFactor receptor 1Untreated patientsAngiogenesis-related genesCT findingsPerineural invasionTumor sizePredictive biomarkersHigh intratumor genetic heterogeneity is related to worse outcome in patients with head and neck squamous cell carcinoma
Mroz EA, Tward AD, Pickering CR, Myers JN, Ferris RL, Rocco JW. High intratumor genetic heterogeneity is related to worse outcome in patients with head and neck squamous cell carcinoma. Cancer 2013, 119: 3034-3042. PMID: 23696076, PMCID: PMC3735618, DOI: 10.1002/cncr.28150.Peer-Reviewed Original ResearchConceptsMutant-allele tumor heterogeneityNeck squamous cell carcinomaSquamous cell carcinomaHigher mutant allele tumor heterogeneityClinical outcomesCell carcinomaWorse outcomesHigh-risk patientsWorse clinical outcomesOverall survival dataShorter overall survivalAdverse treatment outcomesTumor protein p53 (TP53) mutationsHigh genetic heterogeneityGenetic heterogeneityOverall survivalPrognostic valueAdverse outcomesHuman papillomavirusPatient cohortTreatment outcomesIndividual patientsHigh riskPatientsAdvanced stage