2025
Use of baseline plasma circulating tumor DNA (ctDNA) to predict duration of endocrine therapy (ET) and CDK4/6 inhibitor (CDK4/6i) therapy (tx) and to analyze intrinsic vs acquired endocrine resistance.
De Placido P, Hughes M, Weipert C, Sammons S, Morganti S, Parsons H, Abravanel D, Giordano A, Smith K, Patel A, Kirkner G, Stever C, Suggs G, Sendrick K, Snow C, Winer E, Tolaney S, Lin N, Jeselsohn R. Use of baseline plasma circulating tumor DNA (ctDNA) to predict duration of endocrine therapy (ET) and CDK4/6 inhibitor (CDK4/6i) therapy (tx) and to analyze intrinsic vs acquired endocrine resistance. Journal Of Clinical Oncology 2025, 43: 1075-1075. DOI: 10.1200/jco.2025.43.16_suppl.1075.Peer-Reviewed Original ResearchMetastatic breast cancerCirculating tumor DNACopy number lossHR+/HER2- metastatic breast cancerAcquired ResistanceEndocrine therapyLiver metastasesGenomic profilingCDKN2A copy number lossHormone receptor-positive/HER2-negativePlasma circulating tumor DNADuration of endocrine therapyPresence of liver metastasesIntrinsic resistanceCompare genomic profilesBaseline TFPlasma samplesAcquired endocrine resistanceMetastatic breast cancer diagnosisStandard-of-careCox regression modelsESR1 fusionsTumor sheddingSecond-lineMedian duration
2024
Targeted Dynamic Phospho-Proteogenomic Analysis of Gastric Cancer Cells Suggests Host Immunity Provides Survival Benefit
Kume K, Iida M, Iwaya T, Yashima-Abo A, Koizumi Y, Endo A, Wade K, Hiraki H, Calvert V, Wulfkuhle J, Espina V, Siwak D, Lu Y, Takemoto K, Suzuki Y, Sasaki Y, Tokino T, Petricoin E, Liotta L, Mills G, Nishizuka S. Targeted Dynamic Phospho-Proteogenomic Analysis of Gastric Cancer Cells Suggests Host Immunity Provides Survival Benefit. Molecular & Cellular Proteomics 2024, 23: 100870. PMID: 39461475, PMCID: PMC11621936, DOI: 10.1016/j.mcpro.2024.100870.Peer-Reviewed Original ResearchDNA-damaging drugsTotal lymphocyte countCell linesResistance to DNA damaging drugsPD-L1Adjuvant chemotherapyProtein dynamicsProtein-level regulationSurvival benefitCopy number lossExpression time courseGastric cancerRelapse-free survival rateGastric cancer cellsHost immunityAssociated with prolonged survivalIncreased STAT1 phosphorylationResistance to other drugsGlobal protein dynamicsImmune checkpoint blockadePD-L1 positivityPD-L1 expressionAdvanced gastric cancerExpression of STAT1Molecular targeted drugsIntegrated mutational landscape analysis of poorly differentiated high-grade neuroendocrine carcinoma of the uterine cervix
Bellone S, Jeong K, Halle M, Krakstad C, McNamara B, Greenman M, Mutlu L, Demirkiran C, Hartwich T, Yang-Hartwich Y, Zipponi M, Buza N, Hui P, Raspagliesi F, Lopez S, Paolini B, Milione M, Perrone E, Scambia G, Altwerger G, Ravaggi A, Bignotti E, Huang G, Andikyan V, Clark M, Ratner E, Azodi M, Schwartz P, Quick C, Angioli R, Terranova C, Zaidi S, Nandi S, Alexandrov L, Siegel E, Choi J, Schlessinger J, Santin A. Integrated mutational landscape analysis of poorly differentiated high-grade neuroendocrine carcinoma of the uterine cervix. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2321898121. PMID: 38625939, PMCID: PMC11046577, DOI: 10.1073/pnas.2321898121.Peer-Reviewed Original ResearchConceptsWhole-exome sequencingPatient-derived-xenograftsBase excision repairCopy number lossMultiregion whole-exome sequencingCopy number gainHigh-grade neuroendocrine carcinomaCNV analysisPhylogenetic analysisEvolutionary historyNeuroendocrine cervical cancerHuman papillomavirus DNAMutator phenotypeSensitivity to afatinibGenetic landscapeRecurrent mutationsRNA sequencingGene fusionsMutational landscape analysisExcision repairGenesMutationsPan-HERConsistent with deficiencyNeuroendocrine carcinoma
2021
Integrated mutational landscape analysis of uterine leiomyosarcomas
Choi J, Manzano A, Dong W, Bellone S, Bonazzoli E, Zammataro L, Yao X, Deshpande A, Zaidi S, Guglielmi A, Gnutti B, Nagarkatti N, Tymon-Rosario JR, Harold J, Mauricio D, Zeybek B, Menderes G, Altwerger G, Jeong K, Zhao S, Buza N, Hui P, Ravaggi A, Bignotti E, Romani C, Todeschini P, Zanotti L, Odicino F, Pecorelli S, Ardighieri L, Bilguvar K, Quick CM, Silasi DA, Huang GS, Andikyan V, Clark M, Ratner E, Azodi M, Imielinski M, Schwartz PE, Alexandrov LB, Lifton RP, Schlessinger J, Santin AD. Integrated mutational landscape analysis of uterine leiomyosarcomas. Proceedings Of The National Academy Of Sciences Of The United States Of America 2021, 118: e2025182118. PMID: 33876771, PMCID: PMC8053980, DOI: 10.1073/pnas.2025182118.Peer-Reviewed Original ResearchConceptsHomologous recombination DNA repair deficiencySequencing dataWhole-genome sequencing dataRNA sequencing dataTCGA samplesCopy number variation analysisATRX/DAXXCopy number lossNumber variation analysisDNA repair deficiencyWhole-exome sequencing dataRecurrent somatic mutationsCopy number gainsCancer Genome AtlasPatient-derived xenograftsTumor suppressorAkt geneGenetic landscapeHRD signaturesPTEN geneGenesMost fusionsC-MycMutational signaturesC-myc/
2020
Prevalence and tissue concordance of BRCA2 copy number loss evaluated by single-cell, shallow whole genome sequencing of circulating tumor cells (CTCs) in castration-resistant prostate cancer (CRPC).
Barnett E, Schonhoft J, Schultz N, Lee J, Zaidi S, Abida W, Carmichael T, Dago A, Solit D, Wenstrup R, Scher H. Prevalence and tissue concordance of BRCA2 copy number loss evaluated by single-cell, shallow whole genome sequencing of circulating tumor cells (CTCs) in castration-resistant prostate cancer (CRPC). Journal Of Clinical Oncology 2020, 38: 5531-5531. DOI: 10.1200/jco.2020.38.15_suppl.5531.Peer-Reviewed Original ResearchPoly ADP-ribose polymerase inhibitorsCirculating Tumor CellsCopy number variantsCastration-resistant prostate cancerCell-free DNACirculating tumor cell samplingInter-cellular heterogeneityDNA damage repairBRCA2 lossSource of genetic informationTumor cellsPoly ADP-ribose polymerase inhibitors therapyCopy number lossSource of tumor materialProstate cancer tissue specimensDetect circulating tumor cellsDNA damage repair deficiencyCTC-positive casesMetastatic CRPC patientsPre-treatment biopsiesCirculating tumor cell analysisGenome sequenceGenomic studiesCancer tissue specimensSequencing tissue
2018
CDKN2A Copy Number Loss Is an Independent Prognostic Factor in HPV-Negative Head and Neck Squamous Cell Carcinoma
Chen WS, Bindra RS, Mo A, Hayman T, Husain Z, Contessa JN, Gaffney SG, Townsend JP, Yu JB. CDKN2A Copy Number Loss Is an Independent Prognostic Factor in HPV-Negative Head and Neck Squamous Cell Carcinoma. Frontiers In Oncology 2018, 8: 95. PMID: 29670856, PMCID: PMC5893829, DOI: 10.3389/fonc.2018.00095.Peer-Reviewed Original ResearchDisease-free survivalNeck squamous cell carcinomaSquamous cell carcinomaOverall survivalHPV-negative HNSCCPrognostic factorsCell carcinomaPoor survivalLoss groupCDKN2A mRNAMedian disease-free survivalP16 expressionCopy number lossNumber lossMedian overall survivalReceipt of chemotherapyIndependent prognostic factorUseful prognostic factorHPV-negative headHigh p16 expressionProtein expression levelsHPV infectionCancer Genome AtlasBetter prognosisMultivariable analysisCDKN2A/p16 deletion in head and neck cancer cells is associated with Cdk2 activation, replication stress, and vulnerability to Chk1 inhibition
Gadhikar MA, Zhang J, Shen L, Rao X, Wang J, Zhao M, Kalu NN, Johnson FM, Byers LA, Heymach J, Hittelman WN, Udayakumar D, Pandita RK, Pandita TK, Pickering CR, Redwood AB, Piwnica-Worms H, Schlacher K, Frederick MJ, Myers JN. CDKN2A/p16 deletion in head and neck cancer cells is associated with Cdk2 activation, replication stress, and vulnerability to Chk1 inhibition. Cancer Research 2018, 78: canres.2802.2017. PMID: 29229598, PMCID: PMC5811346, DOI: 10.1158/0008-5472.can-17-2802.Peer-Reviewed Original ResearchMeSH KeywordsAntineoplastic AgentsApoptosisBiomarkers, TumorCarcinoma, Squamous CellCell ProliferationCheckpoint Kinase 1Cyclin-Dependent Kinase 2Cyclin-Dependent Kinase Inhibitor p16Cyclin-Dependent Kinase Inhibitor p18DNA ReplicationEnzyme ActivationEnzyme InhibitorsHead and Neck NeoplasmsHumansS PhaseSequence DeletionTumor Cells, CulturedConceptsBiomarker-driven strategiesHNSCC patientsS-phase arrestEarly S-phase arrestCDKN2A/Neck squamous cell carcinoma cell linesSquamous cell carcinoma cell linesSingle-agent activityCell carcinoma cell linesCell linesHypersensitive cellsCarcinoma cell linesCdk2 activationHNSCC cellsDrug dosesCertain tumorsCancer ResCopy number lossCausative factorsHypersensitivityCHK inhibitorsPanel medianMonotherapyDrug ICReplication stress
2017
(S032) Investigating CDKN2A Copy Number Loss in HPV- and HPV+ Head and Neck Cancer: A Demonstration of Integrated Genomic and Clinical Analyses Using TCGA
Chen W, Bindra R, Mo A, Hayman T, Husain Z, Contessa J, Yu J. (S032) Investigating CDKN2A Copy Number Loss in HPV- and HPV+ Head and Neck Cancer: A Demonstration of Integrated Genomic and Clinical Analyses Using TCGA. International Journal Of Radiation Oncology • Biology • Physics 2017, 98: e10. DOI: 10.1016/j.ijrobp.2017.02.068.Peer-Reviewed Original ResearchCDKN2A copy number loss in HPV- and HPV+ head and neck cancer to indicate poor prognosis: An integrated genomic and clinical TCGA analysis.
Chen W, Bindra R, Mo A, Hayman T, Husain Z, Contessa J, Gaffney S, Townsend J, Yu J. CDKN2A copy number loss in HPV- and HPV+ head and neck cancer to indicate poor prognosis: An integrated genomic and clinical TCGA analysis. Journal Of Clinical Oncology 2017, 35: 6060-6060. DOI: 10.1200/jco.2017.35.15_suppl.6060.Peer-Reviewed Original ResearchCopy number lossNumber lossP16 protein expression levelsDisease-free survivalTumor suppressor proteinMedian disease-free survivalMedian overall survivalOverall survivalGene transcriptionSuppressor proteinCDKN2A mRNAProtein expression levelsGenomic groupsCopy number ratioCancer Genome Atlas (TCGA) headGenomic measurementsHPV statusPoor prognosisNeck cancerExpression levelsLoss groupTCGA analysisProtein expressionP16 protein expressionCDKN2ANovel homozygous FANCL mutation and somatic heterozygous SETBP1 mutation in a Chinese girl with Fanconi Anemia
Wu W, Liu Y, Zhou Q, Wang Q, Luo F, Xu Z, Geng Q, Li P, Zhang HZ, Xie J. Novel homozygous FANCL mutation and somatic heterozygous SETBP1 mutation in a Chinese girl with Fanconi Anemia. European Journal Of Medical Genetics 2017, 60: 369-373. PMID: 28419882, DOI: 10.1016/j.ejmg.2017.04.008.Peer-Reviewed Original ResearchConceptsFanconi anemiaCopy number lossNovel homozygous mutation c.Copy number aberrationsDifferent genesMutant variantsSomatic gene mutationsGenotype-phenotype correlationBone marrow failureGenesGain of 3qNumber lossSETBP1 geneNumber aberrationsMutationsHomozygous mutation c.Genotype correlationMarrow failureMutation analysisMutation c.Gene mutationsFANCLChromosomal abnormalitiesHeterogeneous disorderSETBP1 mutations
2014
Recurrent chromosomal aberrations in intravenous leiomyomatosis of the uterus: high-resolution array comparative genomic hybridization study
Buza N, Xu F, Wu W, Carr RJ, Li P, Hui P. Recurrent chromosomal aberrations in intravenous leiomyomatosis of the uterus: high-resolution array comparative genomic hybridization study. Human Pathology 2014, 45: 1885-1892. PMID: 25033729, DOI: 10.1016/j.humpath.2014.05.010.Peer-Reviewed Original ResearchConceptsOligonucleotide array comparative genomic hybridizationArray comparative genomic hybridizationComparative genomic hybridizationGenome-wide investigationGenomic hybridizationChromosome 22qCopy number lossGene mappingChromosomal aberrationsComparative genomic hybridization studySuccinate dehydrogenase subunit BGenetic instabilityRecurrent chromosomal aberrationsRegions of lossSequencing analysisChromosome 12qNumber lossNumber variantsSubunit BChromosomal alterationsHybridization studies
2013
Landscape of somatic single-nucleotide and copy-number mutations in uterine serous carcinoma
Zhao S, Choi M, Overton JD, Bellone S, Roque DM, Cocco E, Guzzo F, English DP, Varughese J, Gasparrini S, Bortolomai I, Buza N, Hui P, Abu-Khalaf M, Ravaggi A, Bignotti E, Bandiera E, Romani C, Todeschini P, Tassi R, Zanotti L, Carrara L, Pecorelli S, Silasi DA, Ratner E, Azodi M, Schwartz PE, Rutherford TJ, Stiegler AL, Mane S, Boggon TJ, Schlessinger J, Lifton RP, Santin AD. Landscape of somatic single-nucleotide and copy-number mutations in uterine serous carcinoma. Proceedings Of The National Academy Of Sciences Of The United States Of America 2013, 110: 2916-2921. PMID: 23359684, PMCID: PMC3581983, DOI: 10.1073/pnas.1222577110.Peer-Reviewed Original ResearchConceptsNuRD chromatin-remodeling complexSomatic copy number variationsSomatic mutationsCell proliferation pathwaysCopy number mutationsDNA mismatch repairCopy number variationsCopy number lossChromatin remodelingTranscriptional machineryCopy number gainsChromosome segmentsFrequent mutationsChromosome 19Loss of TP53Cell cycleCancer genesWhole-exome sequencingBurden of mutationsMismatch repairProliferation pathwaysDNA damageMutational landscapeNormal DNAFrequent amplification
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