2025
A benchmarking study of copy number variation inference methods using single-cell RNA-sequencing data
Chen X, Fang L, Chen Z, Chen W, Wu H, Zhu B, Moos M, Farmer A, Zhang X, Xiong W, Gong S, Jones W, Mason C, Wu S, Xiao C, Wang C. A benchmarking study of copy number variation inference methods using single-cell RNA-sequencing data. Precision Clinical Medicine 2025, 8: pbaf011. PMID: 40584741, PMCID: PMC12204187, DOI: 10.1093/pcmedi/pbaf011.Peer-Reviewed Original ResearchScRNA-seq datasetsStudy genetic heterogeneityScRNA-seq dataCopy number variationsSingle-cell RNA sequencingRNA sequencing dataInference methodsRead lengthSequencing depthSingle-cell levelSequencing tissueScRNA-seqTranscriptome dataNumber variationsGenetic heterogeneityRNA sequencingBatch effectsHuman lung adenocarcinoma cell lineLung adenocarcinoma cell linesAdenocarcinoma cell lineCell linesInferCNVCancer researchSCCNVTumor heterogeneity
2023
Multi-omics profiling reveals cellular pathways and functions regulated by ALDH1B1 in colon cancer cells
Wang Y, Popovic Z, Charkoftaki G, Garcia-Milian R, Lam T, Thompson D, Chen Y, Vasiliou V. Multi-omics profiling reveals cellular pathways and functions regulated by ALDH1B1 in colon cancer cells. Chemico-Biological Interactions 2023, 384: 110714. PMID: 37716420, PMCID: PMC10807983, DOI: 10.1016/j.cbi.2023.110714.Peer-Reviewed Original ResearchColon cancer cellsCellular stress response pathwaysStress response pathwaysMulti-omics analysisCancer cellsSecond messenger signalingMulti-omics profilingNew molecular informationFunctional annotationCellular functionsResponse pathwaysKinase signalingCellular pathwaysColon adenocarcinoma cell lineHuman colon adenocarcinoma cell lineApoptosis signalingEnrichment analysisAldehyde dehydrogenase 1B1Molecular signaturesAdenocarcinoma cell lineMolecular informationSignalingNovel targetProtein expressionCell linesExportin 1 inhibition prevents neuroendocrine transformation through SOX2 down-regulation in lung and prostate cancers
Quintanal-Villalonga A, Durani V, Sabet A, Redin E, Kawasaki K, Shafer M, Karthaus W, Zaidi S, Zhan Y, Manoj P, Sridhar H, Shah N, Chow A, Bhanot U, Linkov I, Asher M, Yu H, Qiu J, de Stanchina E, Patel R, Morrissey C, Haffner M, Koche R, Sawyers C, Rudin C. Exportin 1 inhibition prevents neuroendocrine transformation through SOX2 down-regulation in lung and prostate cancers. Science Translational Medicine 2023, 15: eadf7006. PMID: 37531417, PMCID: PMC10777207, DOI: 10.1126/scitranslmed.adf7006.Peer-Reviewed Original ResearchConceptsPatient-derived xenograftsProstatic adenocarcinomaNE transformationXenograft modelExportin 1Associated with poor prognosisProstate adenocarcinoma cell lineInactivation of TP53Adenocarcinoma xenograft modelEctopic SOX2 expressionEGFR inhibitor osimertinibAdenocarcinoma cell lineNE phenotypeNeuroendocrine transformationSelinexor treatmentStandard cytotoxicsProstate cancerLineage plasticityPotential therapeutic targetNE featuresPoor prognosisProstateSOX2 expressionAdenocarcinomaLung
2022
RASGRF1 Fusions Activate Oncogenic RAS Signaling and Confer Sensitivity to MEK Inhibition.
Hunihan L, Zhao D, Lazowski H, Li M, Qian Y, Abriola L, Surovtseva YV, Muthusamy V, Tanoue LT, Rothberg BE, Schalper KA, Herbst RS, Wilson FH. RASGRF1 Fusions Activate Oncogenic RAS Signaling and Confer Sensitivity to MEK Inhibition. Clinical Cancer Research 2022, 28: 3091-3103. PMID: 35247929, PMCID: PMC9288503, DOI: 10.1158/1078-0432.ccr-21-4291.Peer-Reviewed Original ResearchConceptsLung adenocarcinomaSmoking historyPack-year smoking historyMinimal smoking historySubset of patientsPancreatic ductal adenocarcinoma cell linesPotential treatment strategyTight junction protein occludinJunction protein occludinWhole-exome sequencingAdenocarcinoma cell lineAdvanced malignanciesCancer Genome AtlasRaf-MEKAdvanced tumorsMultiple malignanciesTreatment strategiesKRAS mutationsTherapeutic strategiesTherapeutic targetOncogenic Ras signalingRelated commentaryOncogenic driversMEK inhibitionOncogenic alterations
2015
ALDH1B1 Is Crucial for Colon Tumorigenesis by Modulating Wnt/β-Catenin, Notch and PI3K/Akt Signaling Pathways
Singh S, Arcaroli J, Chen Y, Thompson DC, Messersmith W, Jimeno A, Vasiliou V. ALDH1B1 Is Crucial for Colon Tumorigenesis by Modulating Wnt/β-Catenin, Notch and PI3K/Akt Signaling Pathways. PLOS ONE 2015, 10: e0121648. PMID: 25950950, PMCID: PMC4423958, DOI: 10.1371/journal.pone.0121648.Peer-Reviewed Original ResearchMeSH KeywordsAldehyde DehydrogenaseAldehyde Dehydrogenase 1 FamilyAldehyde Dehydrogenase, MitochondrialAnimalsCell Line, TumorColonic NeoplasmsGene Expression Regulation, NeoplasticHCT116 CellsHT29 CellsHumansMiceNeoplasm TransplantationPhosphatidylinositol 3-KinasesProto-Oncogene Proteins c-aktReceptors, NotchRNA, Small InterferingSignal TransductionSpheroids, CellularWnt Signaling PathwayConceptsWnt/β-cateninPI3K/AktΒ-cateninSW-480 cellsColon cancer tumorigenesisWnt reporter activityPattern of expressionPI3K/Akt Signaling PathwayDual-luciferase reporterPI3K/Akt signal pathwayAkt Signaling PathwayTranscription factorsAkt signal pathwayNude mouse xenograft tumor modelColon tumorigenesisGene promoterColon adenocarcinoma cell lineMouse xenograft tumor modelALDH1B1 expressionAldehyde dehydrogenase 1B1Signaling pathwaysLuciferase reporterSize of spheroidsAdenocarcinoma cell lineXenograft tumor model
2013
CXCR2 Expression in Tumor Cells Is a Poor Prognostic Factor and Promotes Invasion and Metastasis in Lung Adenocarcinoma
Saintigny P, Massarelli E, Lin S, Ahn YH, Chen Y, Goswami S, Erez B, O'Reilly MS, Liu D, Lee JJ, Zhang L, Ping Y, Behrens C, Soto L, Heymach JV, Kim ES, Herbst RS, Lippman SM, Wistuba II, Hong WK, Kurie JM, Koo JS. CXCR2 Expression in Tumor Cells Is a Poor Prognostic Factor and Promotes Invasion and Metastasis in Lung Adenocarcinoma. Cancer Research 2013, 73: 571-582. PMID: 23204236, PMCID: PMC3548940, DOI: 10.1158/0008-5472.can-12-0263.Peer-Reviewed Original ResearchConceptsGene expression profilesNon-small cell lung cancerKnockdown clonesNSCLC cell linesHuman NSCLC cell linesExpression profilesCell linesStable knockdown clonesLung adenocarcinomaLung adenocarcinoma cell linesTumor cellsRAS pathway activationCXCR2 expressionPoor prognosisLung cancer cellsOrthotopic syngeneic mouse modelAdenocarcinoma cell linePromotes InvasionExpression of CXCL5Role of CXCR2Poor prognostic factorCell lung cancerPromoter methylationSyngeneic mouse modelProtein expression
2010
hI-con1, a factor VII-IgGFc chimeric protein targeting tissue factor for immunotherapy of uterine serous papillary carcinoma
Cocco E, Hu Z, Richter CE, Bellone S, Casagrande F, Bellone M, Todeschini P, Krikun G, Silasi DA, Azodi M, Schwartz PE, Rutherford TJ, Buza N, Pecorelli S, Lockwood CJ, Santin AD. hI-con1, a factor VII-IgGFc chimeric protein targeting tissue factor for immunotherapy of uterine serous papillary carcinoma. British Journal Of Cancer 2010, 103: 812-819. PMID: 20700124, PMCID: PMC2966612, DOI: 10.1038/sj.bjc.6605760.Peer-Reviewed Original ResearchConceptsUSPC cell linesInterleukin-2Tissue factorTF expressionReal-time PCRFactor VIILow HER2/neu expressionCell linesLow dosesPrimary USPC cell linesDependent cell-mediated cytotoxicityUterine serous papillary carcinomaHER2/neu expressionTargeting tissue factorSerous papillary adenocarcinomaStandard treatment modalityCell-mediated cytotoxicityTreatment of patientsNormal endometrial cellsSerous papillary carcinomaNovel therapeutic agentsType II receptorAdenocarcinoma cell lineEndometrial cancerAggressive variantVerification and Unmasking of Widely Used Human Esophageal Adenocarcinoma Cell Lines
Boonstra J, van Marion R, Beer D, Lin L, Chaves P, Ribeiro C, Pereira A, Roque L, Darnton S, Altorki N, Schrump D, Klimstra D, Tang L, Eshleman J, Alvarez H, Shimada Y, van Dekken H, Tilanus H, Dinjens W. Verification and Unmasking of Widely Used Human Esophageal Adenocarcinoma Cell Lines. Journal Of The National Cancer Institute 2010, 102: 271-274. PMID: 20075370, PMCID: PMC2902814, DOI: 10.1093/jnci/djp499.Peer-Reviewed Original ResearchMeSH KeywordsAdenocarcinomaAntineoplastic AgentsBenzenesulfonatesBiomedical ResearchCarcinomaCarcinoma, Large CellCell Line, TumorClinical Trials as TopicColorectal NeoplasmsDNA FingerprintingEsophageal NeoplasmsHumansLung NeoplasmsNational Institutes of Health (U.S.)NiacinamideOligonucleotidesOligopeptidesPhenylurea CompoundsProtein Kinase InhibitorsPyridinesSorafenibStomach NeoplasmsTandem Repeat SequencesTelomeraseUnited StatesConceptsEsophageal adenocarcinomaCell linesTumor typesHuman esophageal adenocarcinoma cell lineEsophageal adenocarcinoma cell linesEsophageal adenocarcinoma patientsDevelopment of treatment strategiesAdenocarcinoma cell lineBIC-1Treatment strategiesSEG-1Clinical trialsTumorCancer researchContaminated cell linesNational InstituteCellsExperimental cancer research
2009
WNT/TCF Signaling through LEF1 and HOXB9 Mediates Lung Adenocarcinoma Metastasis
Nguyen D, Chiang A, Zhang X, Kim J, Kris M, Ladanyi M, Gerald W, Massagué J. WNT/TCF Signaling through LEF1 and HOXB9 Mediates Lung Adenocarcinoma Metastasis. Journal Of End-to-End-testing 2009, 138: 51-62. DOI: 10.1016/s9999-9994(09)20363-1.Peer-Reviewed Original ResearchLung adenocarcinomaMultiple organsWnt/TCF pathwayMonths of diagnosisPrimary lung adenocarcinomaLung adenocarcinoma metastasisLung adenocarcinoma cell linesLung adenocarcinoma progressionLung adenocarcinoma cellsWnt/TCFAdenocarcinoma cell lineGene expression signaturesBone metastasesTCF pathwayAdenocarcinoma metastasisDeterminant of metastasisLung tumorsAdenocarcinoma progressionMetastatic subpopulationsTumor growthMetastasisMetastatic capacityAdenocarcinoma cellsChemotactic invasionExpression signatures
2005
High Expression of ErbB Family Members and Their Ligands in Lung Adenocarcinomas That Are Sensitive to Inhibition of Epidermal Growth Factor Receptor
Fujimoto N, Wislez M, Zhang J, Iwanaga K, Dackor J, Hanna AE, Kalyankrishna S, Cody DD, Price RE, Sato M, Shay JW, Minna JD, Peyton M, Tang X, Massarelli E, Herbst R, Threadgill DW, Wistuba II, Kurie JM. High Expression of ErbB Family Members and Their Ligands in Lung Adenocarcinomas That Are Sensitive to Inhibition of Epidermal Growth Factor Receptor. Cancer Research 2005, 65: 11478-11485. PMID: 16357156, DOI: 10.1158/0008-5472.can-05-1977.Peer-Reviewed Original ResearchMeSH KeywordsAdenocarcinomaAdenocarcinoma, Bronchiolo-AlveolarAnimalsAntineoplastic AgentsCarcinoma, Non-Small-Cell LungDrug Resistance, NeoplasmErbB ReceptorsGefitinibGenes, rasHumansLigandsLung NeoplasmsMiceMice, KnockoutMutationNeoplasms, Glandular and EpithelialPhosphorylationProto-Oncogene Proteins c-aktQuinazolinesReceptor, ErbB-2Receptor, ErbB-3Tumor Cells, CulturedTyrosineConceptsEpidermal growth factor receptorLung adenocarcinoma patientsLung adenocarcinoma cellsErbB family membersEGFR inhibitionGrowth factor receptorAdenocarcinoma patientsLung adenocarcinomaTumor biopsiesAdenocarcinoma cellsEpithelial neoplastic lesionsHigh expressionFactor receptorGenetic mutationsHuman lung adenocarcinoma cell lineLung adenocarcinoma cell linesAdenocarcinoma cell lineFamily membersNeoplastic lesionsOncogenic KrasErbB ligandsReceptorsAdenocarcinomaPatientsBiopsy
2004
A HOXA10 Estrogen Response Element (ERE) is Differentially Regulated by 17 Beta-estradiol and Diethylstilbestrol (DES)
Akbas GE, Song J, Taylor HS. A HOXA10 Estrogen Response Element (ERE) is Differentially Regulated by 17 Beta-estradiol and Diethylstilbestrol (DES). Journal Of Molecular Biology 2004, 340: 1013-1023. PMID: 15236964, DOI: 10.1016/j.jmb.2004.05.052.Peer-Reviewed Original ResearchMeSH KeywordsBase SequenceCell Line, TumorCell NucleusDiethylstilbestrolDNA-Binding ProteinsElectrophoretic Mobility Shift AssayEstradiolEstrogen Receptor alphaEstrogen Receptor betaGene Expression RegulationHomeobox A10 ProteinsHomeodomain ProteinsHumansLigandsProtein BindingReceptors, EstrogenResponse ElementsSubstrate SpecificityConceptsEstrogen response elementHOXA10 estrogen response elementConsensus estrogen response elementHox gene expressionHOXA10 geneEndometrial adenocarcinoma cell lineMolecular mechanismsSRC-1Ligand-specific activationGene expressionMüllerian duct differentiationReporter activityAdenocarcinoma cell lineFemale reproductive tractReporter expressionLigand specificityLuciferase reporter activityIshikawa cellsResponse elementEstrogen regulationEstrogen diethylstilbestrolHOXA10 expressionDevelopmental gene expressionDevelopmental anomaliesDuct differentiation
2000
A Vitamin D3 Analog Induces a G1-Phase Arrest in CaCo-2 Cells by Inhibiting Cdk2 and Cdk6: Roles of Cyclin E, p21Waf1, and p27Kip1**This work was supported by National Institutes of Health Grants DK-39573, CA-36745 (to T.A.B. and M.B.) and P30DK42086 (to T.A.B., Digestive Disease Research Core Center).
Scaglione-Sewell B, Bissonnette M, Skarosi S, Abraham C, Brasitus T. A Vitamin D3 Analog Induces a G1-Phase Arrest in CaCo-2 Cells by Inhibiting Cdk2 and Cdk6: Roles of Cyclin E, p21Waf1, and p27Kip1**This work was supported by National Institutes of Health Grants DK-39573, CA-36745 (to T.A.B. and M.B.) and P30DK42086 (to T.A.B., Digestive Disease Research Core Center). Endocrinology 2000, 141: 3931-3939. DOI: 10.1210/en.141.11.3931.Peer-Reviewed Original ResearchF6-D3Caco-2 cellsActivity of cyclin-dependent kinase 2Azoxymethane model of colon cancerCaco-2Colon cancerModel of colon cancerCyclin EChemopreventive actionTransforming growth factor-bCyclin-dependent kinase 2Human colon adenocarcinoma cell lineAntibody neutralization studiesColon adenocarcinoma cell lineDevelopment of colon adenocarcinomaVitamin D3 analogsHuman colonic epitheliumHuman colon cancerCyclin-dependent kinasesGrowth factor BRats treated with azoxymethaneExpression of cyclin EAdenocarcinoma cell lineAzoxymethane modelCell cycle arrest
1999
BRK/Sik expression in the gastrointestinal tract and in colon tumors.
Llor X, Serfas MS, Bie W, Vasioukhin V, Polonskaia M, Derry J, Abbott CM, Tyner AL. BRK/Sik expression in the gastrointestinal tract and in colon tumors. Clinical Cancer Research 1999, 5: 1767-77. PMID: 10430081.Peer-Reviewed Original ResearchConceptsNormal gastrointestinal tractGastrointestinal tractBrk expressionColon tumorsPrimary colon tumorsCell linesAdenocarcinoma cell lineNormal epithelial cellsBRK tyrosine kinaseColon adenocarcinoma cell lineEpithelial tumorsImmunohistochemical assaysColon tumor cell linesTumor cell linesTumor samplesTractTumorsEpithelial cellsColon tumor samplesIntestinal cDNA libraryRNase protection
1990
A Simple and Sensitive Microtiter Plate Estrogen Bioassay Based on Stimulation of Alkaline Phosphatase in Ishikawa Cells: Estrogenic Action of Δ5 Adrenal Steroids*
Littlefield BA, Gurpide E, Markiewicz L, McKinley B, Hochberg RB. A Simple and Sensitive Microtiter Plate Estrogen Bioassay Based on Stimulation of Alkaline Phosphatase in Ishikawa Cells: Estrogenic Action of Δ5 Adrenal Steroids*. Endocrinology 1990, 127: 2757-2762. PMID: 2249627, DOI: 10.1210/endo-127-6-2757.Peer-Reviewed Original ResearchConceptsEstrogenic actionIshikawa cellsHuman endometrial adenocarcinoma cell lineEndometrial adenocarcinoma cell lineAction of estradiolDelta 5Ishikawa human endometrial adenocarcinoma cell lineType of steroidAdenocarcinoma cell lineAdrenal steroidsEstrogen bioassayAdrenal delta 5Aromatase inhibitorsEstrogenC19 steroidsAlkPEstradiolSteroidsDelta 4StimulationAntiestrogensCell linesDehydrogenase inhibitorAlkaline phosphataseAlkaline phosphatase enzyme activity
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