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 survivalNight 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 dataCancerGenetic 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 polymorphisms
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 data
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
2011
Genotypes and phenotypes of IGF-I and IGFBP-3 in breast tumors among Chinese women
Qian B, Zheng H, Yu H, Chen K. Genotypes and phenotypes of IGF-I and IGFBP-3 in breast tumors among Chinese women. Breast Cancer Research And Treatment 2011, 130: 217. PMID: 21562710, DOI: 10.1007/s10549-011-1552-9.Peer-Reviewed Original ResearchConceptsBreast cancer riskIGFBP-3 genotypesIGFBP-3 single nucleotide polymorphismsCancer riskChinese womenIGFBP-3Single nucleotide polymorphismsBreast cancerBreast tumorsTumor samplesLocal breast tissuesBreast cancer patientsIGF-I activityER-negative tumorsUnconditional logistic regressionCase-control studyFresh tumor samplesAge-matched controlsWilcoxon rank sum testRank sum testHigher peptide levelsIGFBP-3 geneIGF-I geneNegative tumorsCancer patientsRelationship of folate, vitamin B12 and methylation of insulin-like growth factor-II in maternal and cord blood
Ba Y, Yu H, Liu F, Geng X, Zhu C, Zhu Q, Zheng T, Ma S, Wang G, Li Z, Zhang Y. Relationship of folate, vitamin B12 and methylation of insulin-like growth factor-II in maternal and cord blood. European Journal Of Clinical Nutrition 2011, 65: 480-485. PMID: 21245875, PMCID: PMC3071883, DOI: 10.1038/ejcn.2010.294.Peer-Reviewed Original ResearchConceptsCord bloodMaternal bloodVitamin B12Serum levelsMother's bloodWeight gainMother's weight gainRelationship of folateInsulin-like growth factor IISerum folate levelsCross-sectional studyFetal origins hypothesisLevels of folateGrowth factor IIMultivariate linear regression modelPassive smokingInsulin-like growth factor 2 geneBreast cancerFolate levelsIGF2 P3Growth factor 2 geneFactor 2 genePercentage of methylationFactor IIBlood
2010
Association of genetic polymorphisms in DNA repair pathway genes with non-small cell lung cancer risk
Qian B, Zhang H, Zhang L, Zhou X, Yu H, Chen K. Association of genetic polymorphisms in DNA repair pathway genes with non-small cell lung cancer risk. Lung Cancer 2010, 73: 138-146. PMID: 21195504, DOI: 10.1016/j.lungcan.2010.11.018.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAged, 80 and overCarcinoma, Non-Small-Cell LungDNA RepairDNA Repair EnzymesDNA-Binding ProteinsFemaleGenetic Association StudiesGenetic Predisposition to DiseaseHumansLung NeoplasmsMaleMiddle AgedPolymorphism, GeneticRisk FactorsSmokingXeroderma Pigmentosum Group A ProteinXeroderma Pigmentosum Group D ProteinYoung AdultConceptsNon-small cell lung cancerLung cancer riskSquamous cell carcinomaLung cancerCancer riskCell carcinomaSingle nucleotide polymorphismsHigh riskGenetic polymorphismsNon-small cell lung cancer riskRisk of NSCLCCell lung cancer riskHigher lung cancer riskCell lung cancerVariant AA genotypeDominant risk factorNumerous epidemiological studiesLogistic regression modelsDNA repair pathway genesYoung smokersNSCLC casesSubgroup analysisRisk factorsHealthy controlsStratified analysisA KRAS-Variant in Ovarian Cancer Acts as a Genetic Marker of Cancer Risk
Ratner E, Lu L, Boeke M, Barnett R, Nallur S, Chin LJ, Pelletier C, Blitzblau R, Tassi R, Paranjape T, Hui P, Godwin AK, Yu H, Risch H, Rutherford T, Schwartz P, Santin A, Matloff E, Zelterman D, Slack FJ, Weidhaas JB. A KRAS-Variant in Ovarian Cancer Acts as a Genetic Marker of Cancer Risk. Cancer Research 2010, 70: 6509-6515. PMID: 20647319, PMCID: PMC2923587, DOI: 10.1158/0008-5472.can-10-0689.Peer-Reviewed Original ResearchConceptsOvarian cancerKRAS-variantOC patientsCancer riskRisk of OCIndependent case-control analysesCase-control studyOvarian cancer syndromeCase-control analysisFamily membersAdvanced diseaseWomen's cancersRisk factorsBRCA2 mutationsHBOC patientsOC casesIndependent cohortHBOC familiesHereditary breastSolid tumorsCancer syndromesKRAS oncogeneVariant allelesPatientsCancerABO Blood Group, Helicobacter pylori Seropositivity, and Risk of Pancreatic Cancer: A Case–Control Study
Risch HA, Yu H, Lu L, Kidd MS. ABO Blood Group, Helicobacter pylori Seropositivity, and Risk of Pancreatic Cancer: A Case–Control Study. Journal Of The National Cancer Institute 2010, 102: 502-505. PMID: 20181960, PMCID: PMC2902822, DOI: 10.1093/jnci/djq007.Peer-Reviewed Original ResearchMeSH KeywordsABO Blood-Group SystemAdultAgedAged, 80 and overAntibodies, BacterialAntigens, BacterialBacterial ProteinsCase-Control StudiesConfounding Factors, EpidemiologicConnecticutEnzyme-Linked Immunosorbent AssayFemaleHelicobacter InfectionsHelicobacter pyloriHumansIncidenceMaleMiddle AgedOdds RatioPancreatic NeoplasmsConceptsNon-O blood typeH pylori seropositivityCase-control studyPancreatic cancerPylori seropositivityABO blood groupEnzyme-linked immunosorbent assayBlood typeBlood groupPopulation-based case-control studyNon-O blood groupControl subjects frequencyH pylori colonizationVirulence protein CagAHelicobacter pylori seropositivityPancreatic cancer riskO blood typeRandom digit dialingCagA seropositivityCase patientsH pyloriControl subjectsRisk factorsPylori colonizationCancer riskRacial differences in the association between body mass index and serum IGF1, IGF2, and IGFBP3
Fowke JH, Matthews CE, Yu H, Cai Q, Cohen S, Buchowski MS, Zheng W, Blot WJ. Racial differences in the association between body mass index and serum IGF1, IGF2, and IGFBP3. Endocrine Related Cancer 2010, 17: 51-60. PMID: 19786462, PMCID: PMC2814999, DOI: 10.1677/erc-09-0023.Peer-Reviewed Original ResearchMeSH KeywordsAdultAge of OnsetAgedBlack or African AmericanBody Mass IndexBreast NeoplasmsCross-Sectional StudiesFemaleFollow-Up StudiesGenetic Predisposition to DiseaseHumansInsulin-Like Growth Factor Binding Protein 3Insulin-Like Growth Factor Binding ProteinsInsulin-Like Growth Factor IInsulin-Like Growth Factor IIMiddle AgedPostmenopausePremenopauseProspective StudiesSoutheastern United StatesWhite PeopleYoung AdultConceptsBody mass indexAge 21 yearsBreast cancer riskIGF1 levelsRace/ethnicityIGFBP3 levelsMass indexWhite womenAA womenCancer riskRacial differencesPremenopausal breast cancer riskAfrican American race/ethnicityLower body mass indexEffect of obesityHigher IGF1 levelsCross-sectional analysisFree IGF1Serum IGF1IGF levelsBMI rangeAge 40Wide BMI rangeProtein 3Women
2009
Genome-wide association study identifies variants in the ABO locus associated with susceptibility to pancreatic cancer
Amundadottir L, Kraft P, Stolzenberg-Solomon RZ, Fuchs CS, Petersen GM, Arslan AA, Bueno-de-Mesquita HB, Gross M, Helzlsouer K, Jacobs EJ, LaCroix A, Zheng W, Albanes D, Bamlet W, Berg CD, Berrino F, Bingham S, Buring JE, Bracci PM, Canzian F, Clavel-Chapelon F, Clipp S, Cotterchio M, de Andrade M, Duell EJ, Fox Jr J, Gallinger S, Gaziano JM, Giovannucci EL, Goggins M, González CA, Hallmans G, Hankinson SE, Hassan M, Holly EA, Hunter DJ, Hutchinson A, Jackson R, Jacobs KB, Jenab M, Kaaks R, Klein AP, Kooperberg C, Kurtz RC, Li D, Lynch SM, Mandelson M, McWilliams RR, Mendelsohn JB, Michaud DS, Olson SH, Overvad K, Patel AV, Peeters PH, Rajkovic A, Riboli E, Risch HA, Shu XO, Thomas G, Tobias GS, Trichopoulos D, Van Den Eeden SK, Virtamo J, Wactawski-Wende J, Wolpin BM, Yu H, Yu K, Zeleniuch-Jacquotte A, Chanock SJ, Hartge P, Hoover RN. Genome-wide association study identifies variants in the ABO locus associated with susceptibility to pancreatic cancer. Nature Genetics 2009, 41: 986-990. PMID: 19648918, PMCID: PMC2839871, DOI: 10.1038/ng.429.Peer-Reviewed Original ResearchMeSH KeywordsABO Blood-Group SystemAllelesCase-Control StudiesChromosomes, Human, Pair 9Cohort StudiesFemaleGene FrequencyGenetic Predisposition to DiseaseGenetic VariationGenome-Wide Association StudyGenotypeHaplotypesHumansIntronsLinkage DisequilibriumLogistic ModelsMaleOdds RatioPancreatic NeoplasmsPolymorphism, Single NucleotideProspective StudiesRisk FactorsUnited States