2025
Hierarchical Multi‐Label Classification With Gene‐Environment Interactions in Disease Modeling
Li J, Zhang Q, Ma S, Fang K, Xu Y. Hierarchical Multi‐Label Classification With Gene‐Environment Interactions in Disease Modeling. Statistics In Medicine 2025, 44: e10330. PMID: 39865593, PMCID: PMC12201914, DOI: 10.1002/sim.10330.Peer-Reviewed Original ResearchConceptsHierarchical multi-label classificationMulti-label classificationGene-environment interaction analysisGene-environmentEfficient expectation-maximizationGene-environment interactionsSemi-supervised scenariosCancer Genome AtlasUnlabeled dataInteraction analysisExpectation-maximizationGenome AtlasSuperior performanceHierarchical responseDisease outcomeClassificationPenalized estimatorsPractice settingsDisease modelsBiomedical studiesAnalysis literatureE effects
2024
Expression and prognostic value of cell‐cycle‐associated genes in lung squamous cell carcinoma
Xu X, Jin K, Xu X, Yang Y, Zhou B. Expression and prognostic value of cell‐cycle‐associated genes in lung squamous cell carcinoma. The Journal Of Gene Medicine 2024, 26: e3735. PMID: 39171952, DOI: 10.1002/jgm.3735.Peer-Reviewed Original ResearchConceptsCell cycle-associated genesLung squamous carcinomaCell cycleMRNA expression dataGene expression profilesAssociated with positive prognosisCause of cancer-related deathExpression dataCancer Genome AtlasExpressed genesSquamous cell carcinomaLung squamous cell carcinomaTargeted therapy trialsGroup of patientsCancer-related deathsExpression of CDK4GenesExpression trendsExpression profilesMolecular studiesGenome AtlasSquamous carcinomaCell carcinomaPathological stagePrognostic value
2023
Pan-cancer analysis of antibody-drug conjugate targets and putative predictors of treatment response
Bosi C, Bartha Á, Galbardi B, Notini G, Naldini M, Licata L, Viale G, Mariani M, Pistilli B, Ali H, André F, Piras M, Callari M, Barreca M, Locatelli A, Viganò L, Criscitiello C, Pusztai L, Curigliano G, Győrffy B, Dugo M, Bianchini G. Pan-cancer analysis of antibody-drug conjugate targets and putative predictors of treatment response. European Journal Of Cancer 2023, 195: 113379. PMID: 37913680, DOI: 10.1016/j.ejca.2023.113379.Peer-Reviewed Original ResearchConceptsGenotype-Tissue Expression (GTEx) databaseAntibody-drug conjugatesADC targetPan-cancer analysisCancer Genome AtlasExpression distributionGene expressionNew therapeutic opportunitiesTreatment responseExpression of determinantsPrimary tissuesGenome AtlasExpression levelsNormal tissuesPotential downstreamProtein expressionRelative expressionExpression databaseGenesTherapeutic opportunitiesExpressionTarget expressionMRNA levelsCancer typesInter-patient heterogeneityIdentification of blood protein biomarkers associated with prostate cancer risk using genetic prediction models: analysis of over 140,000 subjects
Zhong H, Zhu J, Liu S, Ghoneim D, Surendran P, Liu T, Fahle S, Butterworth A, Alam A, Deng H, Yu H, Wu C, Wu L. Identification of blood protein biomarkers associated with prostate cancer risk using genetic prediction models: analysis of over 140,000 subjects. Human Molecular Genetics 2023, 32: 3181-3193. PMID: 37622920, PMCID: PMC10630250, DOI: 10.1093/hmg/ddad139.Peer-Reviewed Original ResearchConceptsPCa riskProstate cancerHuge public health burdenEtiology of PCaBlood protein biomarkersConventional epidemiologic studiesProstate cancer riskPublic health burdenConventional observational studiesCancer Genome AtlasPCa patientsHealth burdenProtein biomarker candidatesObservational studyEpidemiologic studiesCancer riskTherapeutic strategiesCancer-related pathwaysSignificant associationBiomarker candidatesGenome AtlasProtein levelsDrug repurposingRiskPositive associationIntegrated analysis of competitive endogenous RNA networks in elder patients with non-small cell lung cancer
Chen Z, Yu F, Zhu B, Li Q, Yu Y, Zong F, Liu W, Zhang M, Wu S. Integrated analysis of competitive endogenous RNA networks in elder patients with non-small cell lung cancer. Medicine 2023, 102: e33192. PMID: 36897674, PMCID: PMC9997791, DOI: 10.1097/md.0000000000033192.Peer-Reviewed Original ResearchConceptsMRNA ceRNA networkEndogenous RNA (ceRNA) networkCeRNA networkMessenger RNAsRNA networkLncRNA-miRNACompetitive endogenous RNA (ceRNA) networkLong non-coding RNAsPotential ceRNA networksNon-coding RNAsFunctions of DEmRNAsCancer-related processesCancer Genome AtlasGenome analysisGene OntologyKyoto EncyclopediaDevelopment of NSCLCGene Expression Omnibus (GEO) cohortNovel insightsGenome AtlasSurvival packageExpression levelsIntegrated analysisDEmRNAsMiRNAs
2022
Isotope tracing reveals distinct substrate preference in murine melanoma subtypes with differing anti-tumor immunity
Zhang X, Halberstam A, Zhu W, Leitner B, Thakral D, Bosenberg M, Perry R. Isotope tracing reveals distinct substrate preference in murine melanoma subtypes with differing anti-tumor immunity. Cancer & Metabolism 2022, 10: 21. PMID: 36457136, PMCID: PMC9714036, DOI: 10.1186/s40170-022-00296-7.Peer-Reviewed Original ResearchTumor microenvironmentAnti-tumor immunityPotential prognostic factorsObesity-associated cancersPotential prognostic predictorPatient RNA-seq dataSubset of studiesImmunogenic tumorsCancer Genome AtlasLymphocyte infiltrationMelanoma cell linesPrognostic factorsPrognostic predictorMetabolic therapyMelanoma subtypesMurine modelImmune functionMetabolic gene expressionMelanoma progressionMelanomaSubstrate metabolismMetabolic flux studiesGene expressionGenome AtlasCell linesCancer Relevance of Human Genes
Qing T, Mohsen H, Cannataro VL, Marczyk M, Rozenblit M, Foldi J, Murray M, Townsend J, Kluger Y, Gerstein M, Pusztai L. Cancer Relevance of Human Genes. Journal Of The National Cancer Institute 2022, 114: 988-995. PMID: 35417011, PMCID: PMC9275765, DOI: 10.1093/jnci/djac068.Peer-Reviewed Original ResearchConceptsCore cancer genesHuman genesFunctional importanceSomatic mutation frequencySelection pressureGene/protein networksCancer genesHigher somatic mutation frequencyNegative selection pressureGene-gene interaction networksMutation frequencyProtein-truncating variantsGenomic contextCell viabilityGenes decreasesCancer Genome AtlasInteraction networksProtein networkCancer relevanceCancer cell viabilityCell survivalGenesCancer biologyGenome AtlasSearch toolsProteogenomic and clinical implications of unique recurrent splice variants in clear cell renal cell carcinoma.
Chang A, Stewart P, Chakiryan N, Soupir A, Tian Y, Du D, Teer J, Kim Y, Spiess P, Chahoud J, Zhang Y, Koomen J, Berglund A, Wang L, Robinson T, Manley B. Proteogenomic and clinical implications of unique recurrent splice variants in clear cell renal cell carcinoma. Journal Of Clinical Oncology 2022, 40: 380-380. DOI: 10.1200/jco.2022.40.6_suppl.380.Peer-Reviewed Original ResearchGenotype-Tissue Expression (GTEx) projectRNA-seq dataClear cell renal cell carcinomaSplice variantsClinical Proteomic Tumor Analysis ConsortiumBulk RNA-seq dataCell renal cell carcinomaAlternative mRNA splicingAberrant splice variantsCancer Cell Line EncyclopediaProteomic diversityProteogenomic analysisCancer Genome AtlasMRNA splicingExpression projectPathway enrichmentSplicing processTumor suppressorNew pathogenic mechanismGenomic mutationsNovel pipelineAnalysis ConsortiumOncogenic pathwaysCancer-specific survivalGenome Atlas
2021
Molecular drivers of tumor progression in microsatellite stable APC mutation-negative colorectal cancers
Grant A, Xicola RM, Nguyen V, Lim J, Thorne C, Salhia B, Llor X, Ellis N, Padi M. Molecular drivers of tumor progression in microsatellite stable APC mutation-negative colorectal cancers. Scientific Reports 2021, 11: 23507. PMID: 34873211, PMCID: PMC8648784, DOI: 10.1038/s41598-021-02806-x.Peer-Reviewed Original ResearchMeSH KeywordsAdenomatous Polyposis ColiAdenomatous Polyposis Coli ProteinColorectal NeoplasmsDisease ProgressionDNA Copy Number VariationsDNA MethylationGenes, APCHumansMicrosatellite InstabilityMicrosatellite RepeatsMutationNeoplastic ProcessesPhenotypePromoter Regions, GeneticWnt Signaling PathwayConceptsAdenomatous polyposis coliMitochondrial activationDNA methylation profilesTumor suppressor gene adenomatous polyposis coliRNA expressionExpression of Axin2Cancer Genome AtlasIntracellular WntMethylation profilesAberrant regulationGene fusionsGenetic inactivationExtracellular WntNumber variationsGenome AtlasPolyposis coliSomatic mutationsAPC mutationsMutationsMolecular driversMutations of BRAFWntRSPO3Tumor progressionExpressionAssociation of 17q22 Amplicon Via Cell-Free DNA With Platinum Chemotherapy Response in Metastatic Triple-Negative Breast Cancer
Collier KA, Asad S, Tallman D, Jenison J, Rajkovic A, Mardis ER, Parsons HA, Tolaney SM, Winer EP, Lin NU, Ha G, Adalsteinsson VA, Stover DG. Association of 17q22 Amplicon Via Cell-Free DNA With Platinum Chemotherapy Response in Metastatic Triple-Negative Breast Cancer. JCO Precision Oncology 2021, 5: po.21.00104. PMID: 34849445, PMCID: PMC8624042, DOI: 10.1200/po.21.00104.Peer-Reviewed Original ResearchConceptsMetastatic triple-negative breast cancerProgression-free survivalTriple-negative breast cancerPlatinum chemotherapyCancer Genome AtlasBreast cancerBreast Cancer International Consortium data setLonger median progression-free survivalMedian progression-free survivalPlatinum-based chemotherapy regimenSomatic copy number alterationsCopy number alterationsCox proportional hazards modelPlatinum chemotherapy responseTriple negative breast cancer tumorsSpecific somatic copy number alterationsGenome AtlasBreast Cancer International ConsortiumProportional hazards modelBreast cancer tumorsWarrants further investigationCell-free DNAEvaluable patientsChemotherapy regimenMetastatic settingGenome-wide association analysis reveals regulation of at-risk loci by DNA methylation in prostate cancer
Liu Q, Liu G, Martin DT, Xing YT, Weiss RM, Qi J, Kang J. Genome-wide association analysis reveals regulation of at-risk loci by DNA methylation in prostate cancer. Asian Journal Of Andrology 2021, 23: 472-478. PMID: 33762478, PMCID: PMC8451484, DOI: 10.4103/aja.aja_20_21.Peer-Reviewed Original ResearchConceptsDNA methylationRisk lociGene expressionGenome-wide association analysisExpression quantitative trait loci (eQTL) analysisQuantitative trait locus (QTL) analysisMethylation-regulated genesEpigenetic association studiesSingle nucleotide polymorphism analysisNucleotide polymorphism analysisTranscript regulationGenomic regionsCancer Genome AtlasEpigenetic changesEpigenetic alterationsLocus analysisAssociation studiesAssociation analysisProgression of tumorsCpG sitesGenesLociMethylationGenome AtlasImportant locusMulti-omics analysis to identify susceptibility genes for colorectal cancer
Yuan Y, Bao J, Chen Z, Villanueva A, Wen W, Wang F, Zhao D, Fu X, Cai Q, Long J, Shu X, Zheng D, Moreno V, Zheng W, Lin W, Guo X. Multi-omics analysis to identify susceptibility genes for colorectal cancer. Human Molecular Genetics 2021, 30: 321-330. PMID: 33481017, PMCID: PMC8485221, DOI: 10.1093/hmg/ddab021.Peer-Reviewed Original ResearchMeSH KeywordsCarcinogenesisCell Line, TumorCell ProliferationColorectal NeoplasmsDNA MethylationGene Expression Regulation, NeoplasticGenetic Association StudiesGenetic Predisposition to DiseaseGenomeGenome-Wide Association StudyHumansNerve Tissue ProteinsPolymorphism, Single NucleotideRepressor ProteinsRisk FactorsTranscriptomeConceptsGenome-wide association studiesMulti-omics analysisSusceptibility genesTarget genesPutative target genesGWAS-identified variantsMost genetic variantsDNA methylation dataNovel susceptibility genesGenotype-Tissue ExpressionGenetic risk lociPutative susceptibility genesGene regulationIntergenic regionPathogenic dysregulationCancer Genome AtlasEpithelial-mesenchymal transitionRisk lociGene expressionMethylation dataAssociation studiesGenesCell behaviorGenetic variantsGenome Atlas
2020
Glycolytic expression in lower-grade glioma reveals an epigenetic association between IDH mutation status and PDL1/2 expression
Givechian K, Garner C, Benz S, Rabizadeh S, Soon-Shiong P. Glycolytic expression in lower-grade glioma reveals an epigenetic association between IDH mutation status and PDL1/2 expression. Neuro-Oncology Advances 2020, 3: vdaa162. PMID: 33532725, PMCID: PMC7837356, DOI: 10.1093/noajnl/vdaa162.Peer-Reviewed Original ResearchChIP-seq dataEpigenetic linkR132H/Promoter methylationPromoter methylation patternsPromoter H3K4me3Cancer Genome AtlasGenomic analysisDNA methylationRNA-seqImmortalized human astrocytesMethylation patternsMethylation dataEpigenetic associationsCheckpoint genesCell line dataMethylation levelsMethylationWild-type IDHHuman low-grade gliomasGenome AtlasExpression levelsExpression ratioGlycolysisGenesProfiling of gastric cancer cell-surface markers to achieve tumour–normal discrimination
Toh J, Hoppe M, Thakur T, Yang H, Tan K, Pang B, Ho S, Roy R, Ho K, Yeoh K, Tan P, Sundar R, Jeyasekharan A. Profiling of gastric cancer cell-surface markers to achieve tumour–normal discrimination. BMJ Open Gastroenterology 2020, 7: e000452. PMID: 32816956, PMCID: PMC7437876, DOI: 10.1136/bmjgast-2020-000452.Peer-Reviewed Original ResearchMeSH KeywordsAdenocarcinomaAntigens, CDAntigens, Tumor-Associated, CarbohydrateCA-19-9 AntigenCarcinoembryonic AntigenCell Adhesion MoleculesClaudin-4ClaudinsEpithelial Cell Adhesion MoleculeEvaluation Studies as TopicExome SequencingGenomicsGPI-Linked ProteinsHumansImmunohistochemistryMembrane ProteinsROC CurveSensitivity and SpecificitySingaporeStomach NeoplasmsUp-RegulationConceptsWhole-transcriptome sequencingCell surface markersMultispectral immunohistochemistryPutative cell surface proteinGastric cancerNormal tissuesMatched normal samplesCA72-4Cell surface proteinsTumor tissuesLive imaging approachesAnalysis of cell surface markersMolecular profiling of cancersHighest diagnostic validityIdentification of tumor tissueTranscriptome sequencingCancer Genome AtlasProfile of cancerProtein transcriptsCancer cell surface markersCA19-9Genome AtlasDifferentiated tumorsTissue microarrayTCGA dataDecreased copy‐neutral loss of heterozygosity in African American colorectal cancers
Augustus GJ, Xicola RM, Llor X, Ellis NA. Decreased copy‐neutral loss of heterozygosity in African American colorectal cancers. Genes Chromosomes And Cancer 2020, 59: 454-464. PMID: 32293075, PMCID: PMC8045478, DOI: 10.1002/gcc.22851.Peer-Reviewed Original ResearchLoss of Estrogen Receptors is Associated with Increased Tumor Aggression in Laryngeal Squamous Cell Carcinoma
Verma A, Schwartz N, Cohen DJ, Patel V, Nageris B, Bachar G, Boyan BD, Schwartz Z. Loss of Estrogen Receptors is Associated with Increased Tumor Aggression in Laryngeal Squamous Cell Carcinoma. Scientific Reports 2020, 10: 4227. PMID: 32144339, PMCID: PMC7060328, DOI: 10.1038/s41598-020-60675-2.Peer-Reviewed Original ResearchConceptsSquamous cell carcinomaERβ expressionCell carcinomaLaryngeal squamous cell carcinomaEstrogen receptor-dependent mechanismHigh ESR1 expressionClinical cancer stageCancer Genome AtlasImproved survivalTumor burdenPathological stageResponsive cancersCancer stageERα36 expressionHistopathological markersEstrogen receptorXenograft tumorsESR1 expressionTumor aggressionEpithelial samplesLSCCDependent mechanismGenome AtlasERα66CarcinomaAnalyses of non-coding somatic drivers in 2,658 cancer whole genomes
Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, Shuai S, Lanzós A, Herrmann C, Maruvka YE, Shen C, Amin SB, Bandopadhayay P, Bertl J, Boroevich KA, Busanovich J, Carlevaro-Fita J, Chakravarty D, Chan CWY, Craft D, Dhingra P, Diamanti K, Fonseca NA, Gonzalez-Perez A, Guo Q, Hamilton MP, Haradhvala NJ, Hong C, Isaev K, Johnson TA, Juul M, Kahles A, Kahraman A, Kim Y, Komorowski J, Kumar K, Kumar S, Lee D, Lehmann KV, Li Y, Liu EM, Lochovsky L, Park K, Pich O, Roberts ND, Saksena G, Schumacher SE, Sidiropoulos N, Sieverling L, Sinnott-Armstrong N, Stewart C, Tamborero D, Tubio JMC, Umer HM, Uusküla-Reimand L, Wadelius C, Wadi L, Yao X, Zhang CZ, Zhang J, Haber JE, Hobolth A, Imielinski M, Kellis M, Lawrence MS, von Mering C, Nakagawa H, Raphael BJ, Rubin MA, Sander C, Stein LD, Stuart JM, Tsunoda T, Wheeler DA, Johnson R, Reimand J, Gerstein M, Khurana E, Campbell PJ, López-Bigas N, Weischenfeldt J, Beroukhim R, Martincorena I, Pedersen J, Getz G. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature 2020, 578: 102-111. PMID: 32025015, PMCID: PMC7054214, DOI: 10.1038/s41586-020-1965-x.Peer-Reviewed Original ResearchConceptsInternational Cancer Genome ConsortiumStructural variantsPoint mutationsDriver discoveryProtein-coding genesNon-coding genesNon-coding regionsPan-cancer analysisDriver point mutationsSomatic driversCancer Genome AtlasRegulatory sequencesCancer genomesUntranslated regionGenome ConsortiumFocal deletionsGenesGenome AtlasGenomeNovel candidatesMutationsRecurrent breakpointsRegion of TP53DiscoveryVariantsGene Alterations of N6‐Methyladenosine (m6A) Regulators in Colorectal Cancer: A TCGA Database Study
Zhang Q, Cai Y, Kurbatov V, Khan SA, Lu L, Zhang Y, Johnson CH. Gene Alterations of N6‐Methyladenosine (m6A) Regulators in Colorectal Cancer: A TCGA Database Study. BioMed Research International 2020, 2020: 8826456. PMID: 33415160, PMCID: PMC7769650, DOI: 10.1155/2020/8826456.Peer-Reviewed Original ResearchMeSH KeywordsAdenosineAgedAlpha-Ketoglutarate-Dependent Dioxygenase FTOColorectal NeoplasmsDatabases, GeneticDisease-Free SurvivalDNA Copy Number VariationsFemaleGene Expression Regulation, NeoplasticGenes, NeoplasmHumansMaleMultivariate AnalysisMutationNerve Tissue ProteinsPrognosisProportional Hazards ModelsRNA Splicing FactorsRNA, MessengerConceptsDisease-free survivalImmune cell infiltrationM6A regulatorsCRC patientsCRC casesCell infiltrationMRNA expressionWorse overall survivalN6-methyladenosine regulatorsMicrosatellite instability statusMessenger RNA expressionCancer Genome AtlasOverall survivalColorectal cancerCRC tissuesDatabase studyImmune functionInstability statusColon tissuesRole of m6AGene alterationsRNA expressionCRCGenome AtlasGenetic mutations
2019
Histone-Related Genes Are Hypermethylated in Lung Cancer and Hypermethylated HIST1H4F Could Serve as a Pan-Cancer Biomarker
Dong S, Li W, Wang L, Hu J, Song Y, Zhang B, Ren X, Ji S, Li J, Xu P, Liang Y, Chen G, Lou J, Yu W. Histone-Related Genes Are Hypermethylated in Lung Cancer and Hypermethylated HIST1H4F Could Serve as a Pan-Cancer Biomarker. Cancer Research 2019, 79: 6101-6112. PMID: 31575549, DOI: 10.1158/0008-5472.can-19-1019.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAged, 80 and overBiomarkers, TumorBronchoalveolar Lavage FluidCell Line, TumorCpG IslandsDatasets as TopicDNA MethylationEarly Detection of CancerFemaleGene Expression Regulation, NeoplasticGenetic LociHistonesHumansLung NeoplasmsMaleMiddle AgedPromoter Regions, GeneticWhole Genome SequencingConceptsHistone-related genesWhole-genome DNA methylation analysisDNA methylation analysisHistone genesCancer Genome AtlasMethylation signaturesMethylation analysisGenesGenome AtlasPan-CancerBronchoalveolar lavage fluid samplesHypermethylationLavage fluid samplesEarly cancer diagnosisTCGA datasetPan-cancer biomarkerLung cancerTCGACancer-related deathsLung cancer cohortMethylationCancer cohortTumor typesTumorigenesisCancer diagnosisMulti-Institutional Validation of Deep Learning for Pretreatment Identification of Extranodal Extension in Head and Neck Squamous Cell Carcinoma.
Kann BH, Hicks DF, Payabvash S, Mahajan A, Du J, Gupta V, Park HS, Yu JB, Yarbrough WG, Burtness BA, Husain ZA, Aneja S. Multi-Institutional Validation of Deep Learning for Pretreatment Identification of Extranodal Extension in Head and Neck Squamous Cell Carcinoma. Journal Of Clinical Oncology 2019, 38: 1304-1311. PMID: 31815574, DOI: 10.1200/jco.19.02031.Peer-Reviewed Original ResearchConceptsNeck squamous cell carcinomaExtranodal extensionSquamous cell carcinomaLymph nodesCell carcinomaContrast-enhanced CT scanDiagnostic abilityBoard-certified neuroradiologistsTreatment escalationCancer Genome AtlasPathologic confirmationPretreatment identificationDiagnostic challengeExternal validation data setsPathology resultsPretreatment imagingPoor prognosticatorClinical utilityCT scanPatientsClinical decisionHNSCCDiagnostic accuracyInstitutional ValidationGenome Atlas
This site is protected by hCaptcha and its Privacy Policy and Terms of Service apply