2022
A general calculus of fitness landscapes finds genes under selection in cancers
Hsu TK, Asmussen J, Koire A, Choi BK, Gadhikar M, Huh E, Lin CH, Konecki D, Kim YW, Pickering C, Kimmel M, Donehower L, Frederick M, Myers JN, Katsonis P, Lichtarge O. A general calculus of fitness landscapes finds genes under selection in cancers. Genome Research 2022, 32: gr.275811.121. PMID: 35301263, PMCID: PMC9104707, DOI: 10.1101/gr.275811.121.Peer-Reviewed Original ResearchConceptsEvolution of traitsFitness landscapeGenotype-phenotype relationshipsEvolutionary relationshipsComplex traitsPositive selectionGenomic searchSpecific traitsCancer InsightsGenesGenetic variantsFunctional impactTraitsExperimental supportLandscapeVariantsPhenotypeEvolutionSelectionGenotypesCancer cohort
2015
New DNA Methylation Markers and Global DNA Hypomethylation Are Associated with Oral Cancer Development
Foy JP, Pickering CR, Papadimitrakopoulou VA, Jelinek J, Lin SH, William WN, Frederick MJ, Wang J, Lang W, Feng L, Zhang L, Kim ES, Fan YH, Hong WK, El-Naggar AK, Lee JJ, Myers JN, Issa JP, Lippman SM, Mao L, Saintigny P. New DNA Methylation Markers and Global DNA Hypomethylation Are Associated with Oral Cancer Development. Cancer Prevention Research 2015, 8: 1027-1035. PMID: 26342026, PMCID: PMC4777304, DOI: 10.1158/1940-6207.capr-14-0179.Peer-Reviewed Original ResearchConceptsGlobal DNA hypomethylationOral squamous cell carcinomaOral premalignant lesionsDNA hypomethylationOral cancer-free survivalCancer-free survivalDNA methylation changesDNA methylation profilesPromoter methylationDNA promoter methylationGlobal DNA methylationTumor suppressor geneNew DNA methylation markersPromoter CpG sitesOSCC developmentDNA methylationMethylation changesMethylation profilesFoxi2Degree of methylationSuppressor geneCpG sitesMethylationDNA methylation markersGenes
2014
Sequencing HNC: Emergence of Notch Signaling
Pickering C, Ow T, Myers J. Sequencing HNC: Emergence of Notch Signaling. Current Cancer Research 2014, 303-323. DOI: 10.1007/978-1-4614-8815-6_15.ChaptersTumor suppressor geneSuppressor geneImportant tumor suppressor geneRecent sequencing studiesNeck cancer progressionIdentification of mutationsBiology of headSurprising new findingsNotch signalingGene Notch1Notch pathwaySequencing studiesCancer progressionGenomic abnormalitiesChromosomal alterationsMutationsGenesNotch1PathwayFrequent eventNew lightNeck cancerSignalingBiologyTP53 mutations
2013
Integrative Genomic Characterization of Oral Squamous Cell Carcinoma Identifies Frequent Somatic Drivers
Pickering CR, Zhang J, Yoo SY, Bengtsson L, Moorthy S, Neskey DM, Zhao M, Alves M, Chang K, Drummond J, Cortez E, Xie TX, Zhang D, Chung W, Issa JP, Zweidler-McKay PA, Wu X, El-Naggar AK, Weinstein JN, Wang J, Muzny DM, Gibbs RA, Wheeler DA, Myers JN, Frederick MJ. Integrative Genomic Characterization of Oral Squamous Cell Carcinoma Identifies Frequent Somatic Drivers. Cancer Discovery 2013, 3: 770-781. PMID: 23619168, PMCID: PMC3858325, DOI: 10.1158/2159-8290.cd-12-0537.Peer-Reviewed Original ResearchConceptsOral squamous cell carcinomaCaspase-8Integrative Genomic CharacterizationGenomic alterationsSquamous cell carcinomaComprehensive genomic analysisTumor suppressor geneCopy number changesSomatic driversKey genesGenomic analysisCell carcinomaGene expressionNotch pathwayGenomic characterizationSuppressor geneDriver pathwaysCopy numberPoint mutationsGenesSomatic eventsNumber changesSurvival of patientsOSCC cell linesSubset of head
2006
p16INK4a Modulates p53 in Primary Human Mammary Epithelial Cells
Zhang J, Pickering CR, Holst CR, Gauthier ML, Tlsty TD. p16INK4a Modulates p53 in Primary Human Mammary Epithelial Cells. Cancer Research 2006, 66: 10325-10331. PMID: 17079452, DOI: 10.1158/0008-5472.can-06-1594.Peer-Reviewed Original ResearchConceptsPrimary human mammary epithelial cellsHuman mammary epithelial cellsMammary epithelial cellsCell type-specific regulationTumor suppressor geneStabilization of p53Epithelial cellsP53 protein levelsE2F/Gene activityDownstream targetsCellular responsesSuppressor geneProteolytic degradationProtein levelsP53 proteinP16 proteinP53ProteinReduced levelsP53 statusPathwayCellsGenesRegulation