2023
Machine learning-based cluster analysis of immune cell subtypes and breast cancer survival
Wang Z, Katsaros D, Wang J, Biglio N, Hernandez B, Fei P, Lu L, Risch H, Yu H. Machine learning-based cluster analysis of immune cell subtypes and breast cancer survival. Scientific Reports 2023, 13: 18962. PMID: 37923775, PMCID: PMC10624674, DOI: 10.1038/s41598-023-45932-4.Peer-Reviewed Original ResearchConceptsImmune cell clustersT cellsHost immunityImmune cellsUnsupervised hierarchical clusteringImmune responseCD8-positive T cellsMemory CD4 T cellsCox regression survival analysisRegulatory T cellsPositive T cellsCD4 T cellsDifferent immune cellsDistinct immune responsesBreast cancer survivalImmune cell subtypesMemory B cellsImmune cell typesRegression survival analysisCell clustersBreast cancer progressionT cell receptor signalingCytokine stormOverall survivalFavorable survivalElucidating the role of blood metabolites on pancreatic cancer risk using two‐sample Mendelian randomization analysis
Zhong H, Liu S, Zhu J, Xu T, Yu H, Wu L. Elucidating the role of blood metabolites on pancreatic cancer risk using two‐sample Mendelian randomization analysis. International Journal Of Cancer 2023, 154: 852-862. PMID: 37860916, PMCID: PMC10843029, DOI: 10.1002/ijc.34771.Peer-Reviewed Original ResearchConceptsPancreatic ductal adenocarcinomaPDAC riskBlood metabolitesGenetic instrumentsTwo-sample Mendelian randomization studyPancreatic Cancer Case-Control ConsortiumEPIC-Norfolk cohortPancreatic cancer riskEuropean ancestryPancreatic Cancer Cohort ConsortiumPotential side effectsCanadian Longitudinal StudyAssociations of metabolitesMendelian randomization studyTwo-sample Mendelian randomization (MR) analysisGenome-wide association studiesMendelian randomization analysisFatal malignancyDuctal adenocarcinomaCancer riskPDAC casesSide effectsAging CohortMetabolite biomarkersRandomization studyNight shift work, sleep duration and endometrial cancer risk: A pooled analysis from the Epidemiology of Endometrial Cancer Consortium (E2C2)
Frias-Gomez J, Alemany L, Benavente Y, Clarke M, de Francisco J, De Vivo I, Du M, Goodman M, Lacey J, Liao L, Lipworth L, Lu L, Merritt M, Michels K, O'Connell K, Paytubi S, Pelegrina B, Peremiquel-Trillas P, Petruzella S, Ponce J, Risch H, Setiawan V, Schouten L, Shu X, Trabert B, Van den Brandt P, Wentzensen N, Wilkens L, Yu H, Costas L. Night shift work, sleep duration and endometrial cancer risk: A pooled analysis from the Epidemiology of Endometrial Cancer Consortium (E2C2). Sleep Medicine Reviews 2023, 72: 101848. PMID: 37716022, PMCID: PMC10840870, DOI: 10.1016/j.smrv.2023.101848.Peer-Reviewed Original ResearchConceptsNight shift workEndometrial Cancer ConsortiumEndometrial cancer riskEndometrial cancerSleep durationShift workPostmenopausal womenPooled analysisInverse associationOdds ratioCancer riskCancer ConsortiumNon-significant inverse associationStudy-specific odds ratiosEndometrial cancer casesStrong risk factorConfidence intervalsLong sleep durationDaily sleep durationObese womenRisk factorsCancer casesLogistic regressionIndividual dataCancerIdentification 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 associationGenetic Susceptibility to Nonalcoholic Fatty Liver Disease and Risk for Pancreatic Cancer: Mendelian Randomization.
King S, Veliginti S, Brouwers M, Ren Z, Zheng W, Setiawan V, Wilkens L, Shu X, Arslan A, Beane Freeman L, Bracci P, Canzian F, Du M, Gallinger S, Giles G, Goodman P, Haiman C, Kogevinas M, Kooperberg C, LeMarchand L, Neale R, Visvanathan K, White E, Albanes D, Andreotti G, Babic A, Berndt S, Brais L, Brennan P, Buring J, Rabe K, Bamlet W, Chanock S, Fuchs C, Gaziano J, Giovannucci E, Hackert T, Hassan M, Katzke V, Kurtz R, Lee I, Malats N, Murphy N, Oberg A, Orlow I, Porta M, Real F, Rothman N, Sesso H, Silverman D, Thompson I, Wactawski-Wende J, Wang X, Wentzensen N, Yu H, Zeleniuch-Jacquotte A, Yu K, Wolpin B, Duell E, Li D, Hung R, Perdomo S, McCullough M, Freedman N, Patel A, Peters U, Riboli E, Sund M, Tjønneland A, Zhong J, Van Den Eeden S, Kraft P, Risch H, Amundadottir L, Klein A, Stolzenberg-Solomon R, Antwi S. Genetic Susceptibility to Nonalcoholic Fatty Liver Disease and Risk for Pancreatic Cancer: Mendelian Randomization. Cancer Epidemiology Biomarkers & Prevention 2023, 32: 1265-1269. PMID: 37351909, PMCID: PMC10529823, DOI: 10.1158/1055-9965.epi-23-0453.Peer-Reviewed Original ResearchConceptsNonalcoholic fatty liver diseasePancreatic cancer riskFatty liver diseasePancreatic cancerCancer riskLiver diseaseGenetic predispositionMendelian randomizationPancreatic Cancer Case-Control ConsortiumConfidence intervalsPancreatic Cancer Cohort ConsortiumPC risk factorsMR methodsRisk factorsGenome-wide association studiesGenetic susceptibilityLogistic regressionCancerMetabolic perturbationsMetabolic conditionsRiskDiseaseGenetic variantsAssociationPredispositionAssociation between use of antihypertensive drugs and the risk of cancer: a population-based cohort study in Shanghai
Wang S, Xie L, Zhuang J, Qian Y, Zhang G, Quan X, Li L, Yu H, Zhang W, Zhao W, Qian B. Association between use of antihypertensive drugs and the risk of cancer: a population-based cohort study in Shanghai. BMC Cancer 2023, 23: 425. PMID: 37165412, PMCID: PMC10173582, DOI: 10.1186/s12885-023-10849-8.Peer-Reviewed Original ResearchConceptsPopulation-based cohort studyTotal cancerAntihypertensive drugsHypertensive patientsCohort studyAntihypertensive medicinesThyroid cancerHigh riskPossible dose-response relationshipAntihypertensive drug administrationCommon antihypertensive drugsRisk of cancerCommunity healthcare centersDose-response relationshipMajor cancer typesAntihypertensive classesCancer casesMAIN OUTCOMECancer riskHealthcare centersDrug AdministrationPatientsSignificant associationCancerCancer typesMulti-omics profiling of papillary thyroid microcarcinoma reveals different somatic mutations and a unique transcriptomic signature
Li Q, Feng T, Zhu T, Zhang W, Qian Y, Zhang H, Zheng X, Li D, Yun X, Zhao J, Li Y, Yu H, Gao M, Qian B. Multi-omics profiling of papillary thyroid microcarcinoma reveals different somatic mutations and a unique transcriptomic signature. Journal Of Translational Medicine 2023, 21: 206. PMID: 36941725, PMCID: PMC10026500, DOI: 10.1186/s12967-023-04045-2.Peer-Reviewed Original ResearchConceptsTCGA patientsPositive thyroglobulin antibodiesPapillary thyroid microcarcinomaNew therapeutic hypothesesUnique transcriptomic signaturesImmune-related genesWhole-exome sequencingImmune interventionPeroxidase antibodiesThyroglobulin antibodiesEtiology of cancerRET fusionsThyroid microcarcinomaTCGA cohortBRAF mutationsPatientsDifferent somatic mutationsMulti-omics profilingLarger studyConclusionsOur findingsResultsIn additionExome sequencingTherapeutic hypothesesTranscriptomic signaturesMolecular landscapeGenetic variants of glucose metabolism and exposure to smoking in African American breast cancer.
Jung S, Papp J, Sobel E, Pellegrini M, Yu H. Genetic variants of glucose metabolism and exposure to smoking in African American breast cancer. Endocrine Related Cancer 2023, 30 PMID: 36705562, PMCID: PMC10095926, DOI: 10.1530/erc-22-0184.Peer-Reviewed Original ResearchConceptsInsulin resistanceBC riskLifestyle factorsSingle nucleotide polymorphismsAA womenRisk genotypesAfrican American postmenopausal womenAfrican-American breast cancerRisk of BCBreast cancer developmentDose-dependent mannerPostmenopausal womenPositive BCPredictive markerRisk factorsFemale hormonesBreast cancerGlucose metabolismMetabolic biomarkersGene-environment interaction analysisSmokingPreventive interventionsCancer developmentWhite womenIndividual single nucleotide polymorphismsAssociation of SNPs in the PAI1 Gene with Disease Recurrence and Clinical Outcome in Bladder Cancer
Murakami K, Furuya H, Hokutan K, Goodison S, Pagano I, Chen R, Shen C, Chan M, Ng C, Kobayashi T, Ogawa O, Miyake M, Thornquist M, Shimizu Y, Hayashi K, Wang Z, Yu H, Rosser C. Association of SNPs in the PAI1 Gene with Disease Recurrence and Clinical Outcome in Bladder Cancer. International Journal Of Molecular Sciences 2023, 24: 4943. PMID: 36902377, PMCID: PMC10003630, DOI: 10.3390/ijms24054943.Peer-Reviewed Original ResearchConceptsPlasminogen activator inhibitor-1Bladder cancerSingle nucleotide polymorphismsMutational statusWorse recurrence-free survivalUntranslated region (UTR) single nucleotide polymorphismRecurrence-free survivalBladder cancer developmentHuman bladder tumorsAssociation of SNPsCommon cancer typesActivator inhibitor-1Anti-apoptotic effectsOverall survivalDisease recurrenceClinical outcomesOverall incidenceBladder tumorsCaucasian patientsIndependent cohortCancer typesCancer developmentCancerInhibitor-1Cellular proliferation
2022
Dietary omega-3 fatty acids and endometrial cancer risk in the Epidemiology of Endometrial Cancer Consortium: An individual-participant meta-analysis
Brasky T, Hade E, Cohn D, Newton A, Petruzella S, O'Connell K, Bertrand K, Cook L, De Vivo I, Du M, Freudenheim J, Friedenreich C, Goodman M, Gorzelitz J, Ibiebele T, Krogh V, Liao L, Lipworth L, Lu L, McCann S, O'Mara T, Palmer J, Ponte J, Prizment A, Risch H, Sandin S, Schouten L, Setiawan V, Shu X, Trabert B, van den Brandt P, Webb P, Wentzensen N, Wilkens L, Wolk A, Yu H, Neuhouser M. Dietary omega-3 fatty acids and endometrial cancer risk in the Epidemiology of Endometrial Cancer Consortium: An individual-participant meta-analysis. Gynecologic Oncology 2022, 169: 137-146. PMID: 36934308, PMCID: PMC10025515, DOI: 10.1016/j.ygyno.2022.10.015.Peer-Reviewed Original ResearchConceptsEndometrial cancer riskEndometrial Cancer ConsortiumHigh dietary intakeCancer riskDietary intakeObese womenOdds ratioCancer ConsortiumDietary omega-3 fatty acidsOmega-3 fatty acidsEnergy-adjusted quartilesEndometrial cancer casesEndometrial cancer incidenceProspective cohort studyFood frequency questionnaireNormal-weight womenFatty acid intakeAdjusted odds ratioBody mass indexLong-chain omega-3Anti-inflammatory propertiesSubgroup of womenConfidence intervalsCase-control studyTwo-stage individual participant datad-Limonene inhibits the occurrence and progression of LUAD through suppressing lipid droplet accumulation induced by PM2.5 exposure in vivo and in vitro
Zhu T, Li Y, Feng T, Yang Y, Zhang K, Gao J, Quan X, Qian Y, Yu H, Qian B. d-Limonene inhibits the occurrence and progression of LUAD through suppressing lipid droplet accumulation induced by PM2.5 exposure in vivo and in vitro. Respiratory Research 2022, 23: 338. PMID: 36496421, PMCID: PMC9741803, DOI: 10.1186/s12931-022-02270-9.Peer-Reviewed Original ResearchConceptsLipid droplet accumulationHuman intervention trialsLung cancer patientsLung adenocarcinomaPM2.5 exposureProgression of LUADDroplet accumulationPulmonary fibrosisIntervention trialsCancer patientsMiR-195Trichrome stainingChinese Clinical Trial RegistrySerum miR-195Clinical Trials RegistryLipid metabolism disordersNormal lung epithelial cellsPotential preventive interventionsNormal lung tissuesDe novo lipogenesis pathwayMasson's trichrome stainingDevelopment of LUADOil red stainingLung epithelial cellsPotential intervention targets
2018
A G3BP1-interacting lncRNA promotes ferroptosis and apoptosis in cancer via nuclear sequestration of p53
Mao C, Wang X, Liu Y, Wang M, Yan B, Jiang Y, Shi Y, Shen Y, Liu X, Lai W, Yang R, Xiao D, Cheng Y, Liu S, Zhou H, Cao Y, Yu W, Muegge K, Yu H, Tao Y. A G3BP1-interacting lncRNA promotes ferroptosis and apoptosis in cancer via nuclear sequestration of p53. Cancer Research 2018, 78: canres.3454.2017. PMID: 29588351, PMCID: PMC8073197, DOI: 10.1158/0008-5472.can-17-3454.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsApoptosisBreast NeoplasmsCell Cycle CheckpointsCell NucleusCytoplasmDatasets as TopicDisease ProgressionDNA HelicasesDown-RegulationFemaleGene Expression Regulation, NeoplasticGenes, Tumor SuppressorHumansKaplan-Meier EstimateLung NeoplasmsMaleMiceMice, NudeMice, SCIDPoly-ADP-Ribose Binding ProteinsProtein BindingRNA HelicasesRNA Recognition MotifRNA Recognition Motif ProteinsRNA, Long NoncodingRNA, Small InterferingSignal TransductionTumor Suppressor Protein p53Xenograft Model Antitumor AssaysConceptsTumor suppressorCancer progressionProtein-binding protein 1Long noncoding RNACell cycle arrestLncRNA functionsRas GTPaseWild-type p53Interaction domainMetabolic genesNoncoding RNAsFunctional domainsP53 modulatorsNucleotides 1P53 pathwayProtein 1Precise roleTypes of cancerLncRNAsSuppressorFerroptosisApoptosisP53ExpressionCfp1
2016
Analysis of Microarray Data on Gene Expression and Methylation to Identify Long Non-coding RNAs in Non-small Cell Lung Cancer
Feng N, Ching T, Wang Y, Liu B, Lin H, Shi O, Zhang X, Zheng M, Zheng X, Gao M, Zheng Z, Yu H, Garmire L, Qian B. Analysis of Microarray Data on Gene Expression and Methylation to Identify Long Non-coding RNAs in Non-small Cell Lung Cancer. Scientific Reports 2016, 6: 37233. PMID: 27849024, PMCID: PMC5110979, DOI: 10.1038/srep37233.Peer-Reviewed Original ResearchMeSH KeywordsA549 CellsCarcinoma, Non-Small-Cell LungCell LineCell Line, TumorCell ProliferationDisease ProgressionDNA MethylationFemaleGene Expression ProfilingGene Expression Regulation, NeoplasticHEK293 CellsHumansLung NeoplasmsMaleOligonucleotide Array Sequence AnalysisRNA InterferenceRNA, Long NoncodingSurvival AnalysisConceptsDNA methylationGene expressionMicroarray dataGenome-wide expressionLong non-coding RNALong non-coding RNAsNon-coding RNANon-coding RNAsGene expression chipsNon-tumor tissuesAdditional tumor samplesCancer-related genesLOC146880Progression of NSCLCExpression chipsDifferential expressionLncRNA expressionMethylationTumor samplesLncRNAsAdjacent non-tumor tissuesTumor cellsCell proliferationRT-qPCRGenesComplement component 7 (C7), a potential tumor suppressor, is correlated with tumor progression and prognosis
Ying L, Zhang F, Pan X, Chen K, Zhang N, Jin J, Wu J, Feng J, Yu H, Jin H, Su D. Complement component 7 (C7), a potential tumor suppressor, is correlated with tumor progression and prognosis. Oncotarget 2016, 5: 86536-86546. PMID: 27852032, PMCID: PMC5349933, DOI: 10.18632/oncotarget.13294.Peer-Reviewed Original ResearchConceptsNon-small cell lung cancerComplement component 7NSCLC patientsPotential tumor suppressorOvarian cancerOvarian tissueMultivariate Cox regression analysisLow expressionZhejiang Cancer HospitalIndependent prognostic predictorCox regression analysisPrognosis of patientsAdvanced clinical stageCell lung cancerNormal ovarian tissuesExpression of C7Malignant ovarian tissuesTumor suppressorQuantitative polymerase chain reactionCancer HospitalClinical stagePrognostic predictorLung cancerPolymerase chain reactionPoor differentiation
2014
A Novel Model to Combine Clinical and Pathway-Based Transcriptomic Information for the Prognosis Prediction of Breast Cancer
Huang S, Yee C, Ching T, Yu H, Garmire L. A Novel Model to Combine Clinical and Pathway-Based Transcriptomic Information for the Prognosis Prediction of Breast Cancer. PLOS Computational Biology 2014, 10: e1003851. PMID: 25233347, PMCID: PMC4168973, DOI: 10.1371/journal.pcbi.1003851.Peer-Reviewed Original ResearchUp-regulation of microRNA-183-3p is a potent prognostic marker for lung adenocarcinoma of female non-smokers
Xu F, Zhang H, Su Y, Kong J, Yu H, Qian B. Up-regulation of microRNA-183-3p is a potent prognostic marker for lung adenocarcinoma of female non-smokers. Clinical And Translational Oncology 2014, 16: 980-985. PMID: 24805982, DOI: 10.1007/s12094-014-1183-9.Peer-Reviewed Original ResearchConceptsFemale lung adenocarcinomaLung adenocarcinomaLung tissueTianjin Medical University Cancer HospitalCorresponding normal lung tissuesCox proportional hazards modelMiR-183-3pProgression-free survivalLymph node metastasisLog-rank testNoncancerous lung tissuesPoor overall survivalLung cancer pathogenesisNormal lung tissuesLung cancer tissuesAdjacent noncancerous tissuesPotent prognostic markerPotential prognostic biomarkerProportional hazards modelT-testStudent's t-testBackgroundLung cancerOverall survivalNode metastasisClinicopathological characteristicsThe KRAS-Variant and miRNA Expression in RTOG Endometrial Cancer Clinical Trials 9708 and 9905
Lee LJ, Ratner E, Uduman M, Winter K, Boeke M, Greven KM, King S, Burke TW, Underhill K, Kim H, Boulware RJ, Yu H, Parkash V, Lu L, Gaffney D, Dicker AP, Weidhaas J. The KRAS-Variant and miRNA Expression in RTOG Endometrial Cancer Clinical Trials 9708 and 9905. PLOS ONE 2014, 9: e94167. PMID: 24732316, PMCID: PMC3986055, DOI: 10.1371/journal.pone.0094167.Peer-Reviewed Original ResearchConceptsEndometrial cancer riskType 2 endometrial cancerEndometrial cancerKRAS-variantCancer riskLymphovascular invasionSurvival outcomesTumor biologyType 1 endometrial cancerEndometrial cancer trialsOverall survival rateMiRNA expressionAge-matched controlsCase-control analysisFunctional germline variantsClinical characteristicsPatient ageTumor characteristicsCancer trialsTumor specimensSurvival rateType 1Germline variantsMiRNA expression levelsCancer
2013
Circulating MicroRNAs in Relation to EGFR Status and Survival of Lung Adenocarcinoma in Female Non-Smokers
Zhang H, Su Y, Xu F, Kong J, Yu H, Qian B. Circulating MicroRNAs in Relation to EGFR Status and Survival of Lung Adenocarcinoma in Female Non-Smokers. PLOS ONE 2013, 8: e81408. PMID: 24282590, PMCID: PMC3839880, DOI: 10.1371/journal.pone.0081408.Peer-Reviewed Original ResearchConceptsLung adenocarcinomaOverall survivalFemale patientsMiR-195MiR-122Survival outcomesPlasma levelsEGFR statusNon-smoking female patientsCox proportional hazards regressionKaplan-Meier survival analysisEGFR-mutant patientsProportional hazards regressionAdvanced disease stageEGFR mutation statusTime-dependent receiverMiR-122 expressionReal-time RT-PCRHazards regressionPoor prognosisPrognostic valueDisease stageNon smokersMutant patientsEGFR mutationsElucidating the Landscape of Aberrant DNA Methylation in Hepatocellular Carcinoma
Song M, Tiirikainen M, Kwee S, Okimoto G, Yu H, Wong L. Elucidating the Landscape of Aberrant DNA Methylation in Hepatocellular Carcinoma. PLOS ONE 2013, 8: e55761. PMID: 23437062, PMCID: PMC3577824, DOI: 10.1371/journal.pone.0055761.Peer-Reviewed Original ResearchConceptsDifferentially Methylated RegionsPromoter CpG islandsCpG islandsDNA methylationDifferential methylationMethylation changesGenome-wide methylation profilingDM locusGenome-wide levelDifferential methylation patternsAberrant DNA methylationPotential biological functionsSignificant differential methylationGene bodiesIllumina HumanMethylation450 BeadChipGenomic regionsIntergenic regionMethylated regionsMethylation patternsCellular developmentEpigenetic changesGene promoterGene listsMethylation profilingBiological functions
2012
PDCD6 is an independent predictor of progression free survival in epithelial ovarian cancer
Su D, Xu H, Feng J, Gao Y, Gu L, Ying L, Katsaros D, Yu H, Xu S, Qi M. PDCD6 is an independent predictor of progression free survival in epithelial ovarian cancer. Journal Of Translational Medicine 2012, 10: 31. PMID: 22369209, PMCID: PMC3305474, DOI: 10.1186/1479-5876-10-31.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAged, 80 and overApoptosisApoptosis Regulatory ProteinsBlotting, WesternCalcium-Binding ProteinsCarcinoma, Ovarian EpithelialCell CycleCell Line, TumorCell ProliferationDisease-Free SurvivalFemaleGene Expression Regulation, NeoplasticGene Knockdown TechniquesGene SilencingGenetic VectorsHumansKaplan-Meier EstimateLentivirusMiddle AgedNeoplasm InvasivenessNeoplasm MetastasisNeoplasms, Glandular and EpithelialOvarian NeoplasmsRNA, MessengerRNA, Small InterferingStatistics, NonparametricTransfectionConceptsEpithelial ovarian cancerProgression-free survivalOvarian cancer progressionOvarian cancer cellsOvarian cancerFree survivalOverall survivalIndependent predictorsKaplan-Meier survival analysisEpithelial ovarian cancer tissuesMetastatic ovarian cancer cellsCancer progressionPDCD6 expressionResidual tumor sizeClinical pathological factorsEpithelial ovarian cancer correlatesCancer cellsOvarian cancer correlatesOvarian cancer tissuesHistologic typeClinical progressionTumor sizeDisease stageTumor gradeCancer correlates