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, 100870. PMID: 39461475, 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 drugs
2023
Computational Discovery and Validation of NAD+ Biosynthesis As Unique Vulnerability in B-Lymphoid Malignancies
Li Q, Robinson M, Leveille E, Zhang C, Sun R, Cheng Z, Kume K, Cosgun K, Kothari S, Khanduja D, Nakada D, Müschen M. Computational Discovery and Validation of NAD+ Biosynthesis As Unique Vulnerability in B-Lymphoid Malignancies. Blood 2023, 142: 418. DOI: 10.1182/blood-2023-190269.Peer-Reviewed Original ResearchSmall molecule inhibitorsDrug discovery toolNAMPT inhibitorsCompound screenCell type-specific targetsCell linesMolecule inhibitorsPurine/pyrimidine metabolismTumor cell linesEnergy metabolismSalvage biosynthesis pathwaySolid tumor cell linesB cell developmentCellular energy metabolismB cell signalingAmino acid metabolismCell cycle arrestDiscovery toolDepletion of metabolitesBiosynthesis pathwayCompetitive fitnessRate-limiting enzymeNAMPT deletionConditional mouse modelEnergy stress
2019
RPPAs for Cell Subpopulation Analysis
Kume K, Nishizuka SS. RPPAs for Cell Subpopulation Analysis. Advances In Experimental Medicine And Biology 2019, 1188: 227-237. PMID: 31820391, DOI: 10.1007/978-981-32-9755-5_12.ChaptersConceptsDrug-tolerant persistersStem cell-associated proteinsReverse phase protein arrayTolerant cell linesCell linesPhase protein arrayDifferent cell typesCell-associated proteinsGastric cancer cell linesCell biologyProteomic profilingProteomic profilesTolerant linesCellular heterogeneityClonal populationsCancer biologyPI3KCell typesCancer cell linesProtein arraysStem cellsIndividual subpopulationsProliferative conditionsBiologyProtein
2016
Downregulation of ST6GALNAC1 is associated with esophageal squamous cell carcinoma development
Iwaya T, Sawada G, Amano S, Kume K, Ito C, Endo F, Konosu M, Shioi Y, Akiyama Y, Takahara T, Otsuka K, Nitta H, Koeda K, Mizuno M, Nishizuka S, Sasaki A, Mimori K. Downregulation of ST6GALNAC1 is associated with esophageal squamous cell carcinoma development. International Journal Of Oncology 2016, 50: 441-447. PMID: 28035351, DOI: 10.3892/ijo.2016.3817.Peer-Reviewed Original ResearchMeSH KeywordsAgedCarcinogenesisCarcinoma, Squamous CellChromosomes, Human, Pair 17Down-RegulationEsophageal NeoplasmsEsophageal Squamous Cell CarcinomaFemaleGene Expression ProfilingGene Expression Regulation, NeoplasticHumansLoss of HeterozygosityMaleReal-Time Polymerase Chain ReactionSialyltransferasesTranscriptomeConceptsQuantitative real-time reverse transcription PCRSporadic esophageal squamous cell carcinomasResponsible geneRNA sequence analysisClinical ESCC samplesPutative tumor suppressor geneCell linesTumor suppressor geneChromosome 17q25.1Esophageal squamous cell carcinoma (ESCC) developmentReal-time reverse transcription PCREsophageal squamous cell carcinomaMultiple genesCandidate genesExpression patternsChromosome 17q25Reverse transcription-PCRSequence analysisSuppressor geneGenesMethylation analysisCorresponding normal tissuesST6GALNAC1Transcription-PCRESCC development
2014
A Compensatory Role of NF-κB to p53 in Response to 5-FU–Based Chemotherapy for Gastric Cancer Cell Lines
Endo F, Nishizuka SS, Kume K, Ishida K, Katagiri H, Ishida K, Sato K, Iwaya T, Koeda K, Wakabayashi G. A Compensatory Role of NF-κB to p53 in Response to 5-FU–Based Chemotherapy for Gastric Cancer Cell Lines. PLOS ONE 2014, 9: e90155. PMID: 24587255, PMCID: PMC3937424, DOI: 10.1371/journal.pone.0090155.Peer-Reviewed Original ResearchMeSH KeywordsAntimetabolites, AntineoplasticCell Line, TumorCodonDrug Resistance, NeoplasmFluorouracilGene Expression ProfilingGene Expression Regulation, NeoplasticGene Knockdown TechniquesHumansNF-kappa BProtein BindingProtein TransportStomach NeoplasmsTranscription Factor RelATumor Suppressor Protein p53ConceptsGastric cancer cell linesCancer cell linesNF-κBAdjuvant chemotherapyPrediction markersCell linesNF-κB-dependent mannerGastric cancer patientsKnockdown of RelANF-κB bindingArg homozygosityCurative resectionRelapse rateCancer patientsGastric cancerPrediction biomarkersChemotherapyP65 subunitTP53 knockdownChemotherapeutic efficacyProtein levelsCompensatory roleP53Target protein levelsTreatment
2012
Molecular Marker Identification for Relapse Prediction in 5-FU-Based Adjuvant Chemotherapy in Gastric and Colorectal Cancers
Ishida K, Nishizuka SS, Chiba T, Ikeda M, Kume K, Endo F, Katagiri H, Matsuo T, Noda H, Iwaya T, Yamada N, Fujiwara H, Takahashi M, Itabashi T, Uesugi N, Maesawa C, Tamura G, Sugai T, Otsuka K, Koeda K, Wakabayashi G. Molecular Marker Identification for Relapse Prediction in 5-FU-Based Adjuvant Chemotherapy in Gastric and Colorectal Cancers. PLOS ONE 2012, 7: e43236. PMID: 22905237, PMCID: PMC3419205, DOI: 10.1371/journal.pone.0043236.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAged, 80 and overAntimetabolites, AntineoplasticBiomarkers, TumorCell Line, TumorChemotherapy, AdjuvantCluster AnalysisColorectal NeoplasmsFluorouracilGene Expression Regulation, NeoplasticHumansImmunohistochemistryMAP Kinase Kinase 4Middle AgedPrognosisRecurrenceRNA, Small InterferingStomach NeoplasmsConceptsAdjuvant chemotherapyNF-κBCancer patientsTissue microarrayProtein expressionColorectal cancer patientsOverall survival rateGastrointestinal tract cancerGastric cancer patientsGastric cancer cell linesCell linesCancer cell linesJNK protein expressionR0 resectionTract cancerColorectal cancerImmunohistochemical examinationClinical significanceSurvival rateRelapse predictionBaseline expressionChemotherapyChemosensitivity markerPatientsGastric