2017
Capture, amplification, and global profiling of microRNAs from low quantities of whole cell lysate
Wang N, Cheng J, Fan R, Lu J. Capture, amplification, and global profiling of microRNAs from low quantities of whole cell lysate. Analyst 2017, 142: 3203-3211. PMID: 28765841, PMCID: PMC5605290, DOI: 10.1039/c7an00670e.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsGene Expression ProfilingGene Knockout TechniquesGene LibraryMiceMicroRNAsNIH 3T3 CellsConceptsWhole cell lysatesSmall non-coding RNAsComplex regulatory networkMiRNA profilingCell lysatesPost-transcriptional levelIsogenic cell linesNon-coding RNAsAdaptor ligationLow quantity samplesGenome scaleRegulatory networksGlobal profilingMiRNA captureGene expressionExpression profilesHuman diseasesMiRNA expressionLibrary preparationMiRNA alterationsCell typesMiRNA releaseRNA purificationMulti-step purificationCell linesThe microRNA miR-31 inhibits CD8+ T cell function in chronic viral infection
Moffett HF, Cartwright ANR, Kim HJ, Godec J, Pyrdol J, Äijö T, Martinez GJ, Rao A, Lu J, Golub TR, Cantor H, Sharpe AH, Novina CD, Wucherpfennig KW. The microRNA miR-31 inhibits CD8+ T cell function in chronic viral infection. Nature Immunology 2017, 18: 791-799. PMID: 28530712, PMCID: PMC5753758, DOI: 10.1038/ni.3755.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAntibodies, ViralArenaviridae InfectionsCalciumCD8-Positive T-LymphocytesChromatin ImmunoprecipitationCytokinesDendritic CellsEnzyme-Linked Immunosorbent AssayFlow CytometryGene Expression ProfilingImmunoblottingInterferon Type ILymphocytic choriomeningitis virusMiceMice, KnockoutMicroRNAsNFATC Transcription FactorsReal-Time Polymerase Chain ReactionReceptors, Antigen, T-Cell
2016
Adenosine-to-inosine RNA editing by ADAR1 is essential for normal murine erythropoiesis
Liddicoat BJ, Hartner JC, Piskol R, Ramaswami G, Chalk AM, Kingsley PD, Sankaran VG, Wall M, Purton LE, Seeburg PH, Palis J, Orkin SH, Lu J, Li JB, Walkley CR. Adenosine-to-inosine RNA editing by ADAR1 is essential for normal murine erythropoiesis. Experimental Hematology 2016, 44: 947-963. PMID: 27373493, PMCID: PMC5035604, DOI: 10.1016/j.exphem.2016.06.250.Peer-Reviewed Original ResearchMeSH KeywordsAdenosineAdenosine DeaminaseAnimalsCluster AnalysisErythrocyte IndicesErythroid CellsErythropoiesisGene ExpressionGene Expression ProfilingGene Expression Regulation, DevelopmentalGene Knockout TechniquesGranulocytesHematopoietic Stem Cell TransplantationInosineInterferonsMiceMicroRNAsMyelopoiesisOrgan SpecificityPhenotypeReceptors, InterferonRetroelementsRNA EditingRNA-Binding ProteinsSignal TransductionTranscription, GeneticConceptsRNA editingErythroid cellsNormal erythropoiesisHematopoietic stem/progenitorsHematopoietic cell typesInnate immune signalingStem/progenitorsEditing eventsErythroid-specific transcriptsEssential functionsImmune signalingMurine erythropoiesisADAR1Cell deathCell typesMyeloid-restricted deletionEditingRNAMicroRNA levelsErythropoiesisCellsProfound activationTranscriptsSignalingAdenosine
2015
microRNA Expression Profiling: Technologies, Insights, and Prospects
Roden C, Mastriano S, Wang N, Lu J. microRNA Expression Profiling: Technologies, Insights, and Prospects. Advances In Experimental Medicine And Biology 2015, 888: 409-421. PMID: 26663195, DOI: 10.1007/978-3-319-22671-2_21.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceCell Line, TumorDisease Models, AnimalGene Expression ProfilingGene Expression Regulation, NeoplasticHigh-Throughput Nucleotide SequencingHumansMicroRNAsMolecular Sequence DataNeoplasmsReverse Transcriptase Polymerase Chain ReactionSequence Homology, Nucleic AcidSignal TransductionConceptsLong small noncoding RNAsExpression profilingMiRNA isoformsMiRNA expressionProfiling technologiesDiverse biological processesSingle-cell variabilitySmall noncoding RNAsMiRNA profiling technologiesGlobal miRNA expressionNext-generation sequencingNoncoding RNAsCell variabilitySingle-molecule measurementsBiological functionsBiological processesTumor suppressorMicroRNA researchQuantitative RT-PCRCareful experimental designMiRNAsIsoformsRT-PCRProfilingExpression
2014
A High-Throughput MicroRNA Expression Profiling System
Guo Y, Mastriano S, Lu J. A High-Throughput MicroRNA Expression Profiling System. Methods In Molecular Biology 2014, 1176: 33-44. PMID: 25030917, DOI: 10.1007/978-1-4939-0992-6_4.Peer-Reviewed Original ResearchMeSH KeywordsGene Expression ProfilingMicroRNAsOligonucleotide Array Sequence AnalysisRNA, Small UntranslatedConceptsHundreds of miRNAsSmall noncoding RNAsDiverse biological functionsMiRNA-related researchGlobal miRNA expressionTotal RNA samplesNoncoding RNAsBiological functionsHundreds of samplesMiRNA expressionRNA samplesMiRNA levelsBiochemical reactionsPathological processesRobust protocolBead-based detectionExpressionLarge numberMiRNAsMicroRNAsHigh detection specificityRNADetection specificityDeregulationHundreds
2013
MicroRNA-30c inhibits human breast tumour chemotherapy resistance by regulating TWF1 and IL-11
Bockhorn J, Dalton R, Nwachukwu C, Huang S, Prat A, Yee K, Chang YF, Huo D, Wen Y, Swanson KE, Qiu T, Lu J, Young Park S, Eileen Dolan M, Perou CM, Olopade OI, Clarke MF, Greene GL, Liu H. MicroRNA-30c inhibits human breast tumour chemotherapy resistance by regulating TWF1 and IL-11. Nature Communications 2013, 4: 1393. PMID: 23340433, PMCID: PMC3723106, DOI: 10.1038/ncomms2393.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBiomarkers, TumorBreast NeoplasmsCell Line, TumorCell SurvivalCluster AnalysisCytoskeletonDoxorubicinDrug Resistance, NeoplasmEpithelial-Mesenchymal TransitionFemaleGATA3 Transcription FactorGene Expression ProfilingGene Expression Regulation, NeoplasticHumansInterleukin-11MiceMicrofilament ProteinsMicroRNAsPrognosisProtein-Tyrosine KinasesReal-Time Polymerase Chain ReactionSuppression, GeneticXenograft Model Antitumor AssaysConceptsMicroRNA-30cChemotherapy resistanceBreast tumorsMesenchymal transitionRelapse-free survivalBreast cancer patientsPrimary breast tumorsTumor prognostic markersTumor chemotherapy resistanceNovel therapeutic strategiesInterleukin 11 expressionCancer patientsPrognostic markerBreast cancerTherapeutic strategiesTherapy resistanceTumor progressionIL-11Interleukin-11Direct targetingTwinfilin-1TumorsChemoresistanceFamily membersMolecular mechanisms
2012
An In Vivo Functional Screen Uncovers miR-150-Mediated Regulation of Hematopoietic Injury Response
Adams BD, Guo S, Bai H, Guo Y, Megyola CM, Cheng J, Heydari K, Xiao C, Reddy EP, Lu J. An In Vivo Functional Screen Uncovers miR-150-Mediated Regulation of Hematopoietic Injury Response. Cell Reports 2012, 2: 1048-1060. PMID: 23084747, PMCID: PMC3487471, DOI: 10.1016/j.celrep.2012.09.014.Peer-Reviewed Original ResearchConceptsMiR-150Injury responseBone marrow transplant modelCareful clinical managementHematopoietic suppressionTransplant modelPeripheral bloodHematopoietic recoveryRecipient miceClinical managementAssociated impairmentRole of microRNAsMyeloid cellsHeterozygous knockoutProgenitor cellsClonogenic potentialMajor blood lineagesNormal tissue physiologyHematopoietic stemTissue physiologyC-MybTreatmentMicroRNAsFunction screenCells
2011
MicroRNA Expression Profiling Identifies Activated B Cell Status in Chronic Lymphocytic Leukemia Cells
Li S, Moffett HF, Lu J, Werner L, Zhang H, Ritz J, Neuberg D, Wucherpfennig KW, Brown JR, Novina CD. MicroRNA Expression Profiling Identifies Activated B Cell Status in Chronic Lymphocytic Leukemia Cells. PLOS ONE 2011, 6: e16956. PMID: 21408091, PMCID: PMC3050979, DOI: 10.1371/journal.pone.0016956.Peer-Reviewed Original ResearchConceptsB cell statusChronic lymphocytic leukemiaCLL cellsB cellsCpG activationChronic lymphocytic leukemia cellsActivated B cellsLymphocytic leukemia cellsCell statusClinical courseFirst therapyExpression profiling identifiesLymphocytic leukemiaNormal donorsUnmutated statusMiR-155MiR-223MiR-181bMiR-29cMiR-181aLeukemia cellsMiR-103Untransformed B cellsRecent dataProfiling identifies
2009
MicroRNA dynamics in the stages of tumorigenesis correlate with hallmark capabilities of cancer
Olson P, Lu J, Zhang H, Shai A, Chun MG, Wang Y, Libutti SK, Nakakura EK, Golub TR, Hanahan D. MicroRNA dynamics in the stages of tumorigenesis correlate with hallmark capabilities of cancer. Genes & Development 2009, 23: 2152-2165. PMID: 19759263, PMCID: PMC2751988, DOI: 10.1101/gad.1820109.Peer-Reviewed Original ResearchConceptsPrimary tumorMouse modelHallmark capabilitiesPancreatic neuroendocrine tumorsAnti-angiogenic therapyTranscription factor ZEB1MiR changesMiR-200 familyMetastatic tumorsNeuroendocrine tumorsRare subsetEnhanced metastasisAngiogenesis inhibitorsMetastasisTumorsMiR signatureNeoplastic progressionHuman tumorsAltered expressionAdaptive resistanceExpression signaturesE-cadherinCancerMiRTherapy
2008
Distinct microRNA expression profiles in acute myeloid leukemia with common translocations
Li Z, Lu J, Sun M, Mi S, Zhang H, Luo RT, Chen P, Wang Y, Yan M, Qian Z, Neilly MB, Jin J, Zhang Y, Bohlander SK, Zhang DE, Larson RA, Le Beau MM, Thirman MJ, Golub TR, Rowley JD, Chen J. Distinct microRNA expression profiles in acute myeloid leukemia with common translocations. Proceedings Of The National Academy Of Sciences Of The United States Of America 2008, 105: 15535-15540. PMID: 18832181, PMCID: PMC2563085, DOI: 10.1073/pnas.0808266105.Peer-Reviewed Original ResearchConceptsPolo-like kinase 2Genome-wide miRNA expression analysisDistinct miRNA expression patternsMiRs-126/126Normal bone marrow progenitor cellsMiRNA expression patternsCommon translocationBone marrow progenitor cellsGenomic lociMiRNA expression analysisExpression analysisMarrow progenitor cellsAcute myeloid leukemia samplesExpression patternsSpecific miRNAsKinase 2Expression profilesTumor suppressorFunction experimentsGenetic rearrangementsPromoter demethylationColony-forming abilityImportant regulatorAML1-ETOExpression signaturesDicer-dependent pathways regulate chondrocyte proliferation and differentiation
Kobayashi T, Lu J, Cobb BS, Rodda SJ, McMahon AP, Schipani E, Merkenschlager M, Kronenberg HM. Dicer-dependent pathways regulate chondrocyte proliferation and differentiation. Proceedings Of The National Academy Of Sciences Of The United States Of America 2008, 105: 1949-1954. PMID: 18238902, PMCID: PMC2538863, DOI: 10.1073/pnas.0707900105.Peer-Reviewed Original ResearchConceptsDicer-dependent pathwaysSkeletal developmentBiogenesis of miRNAsMiRNA target genesMammalian skeletal developmentSmall noncoding RNAsSkeletal growth defectsChondrocyte proliferationSuppress gene expressionNormal skeletal developmentDiverse organismsCritical roleGrowth defectNoncoding RNAsRNA abundanceGene expressionExpression changesMicroarray analysisBiological processesSignaling systemMiRNAsBase pairingDistinct mechanismsIhh-PTHrPHypertrophic chondrocytes
2007
MicroRNA expression signatures accurately discriminate acute lymphoblastic leukemia from acute myeloid leukemia
Mi S, Lu J, Sun M, Li Z, Zhang H, Neilly MB, Wang Y, Qian Z, Jin J, Zhang Y, Bohlander SK, Le Beau MM, Larson RA, Golub TR, Rowley JD, Chen J. MicroRNA expression signatures accurately discriminate acute lymphoblastic leukemia from acute myeloid leukemia. Proceedings Of The National Academy Of Sciences Of The United States Of America 2007, 104: 19971-19976. PMID: 18056805, PMCID: PMC2148407, DOI: 10.1073/pnas.0709313104.Peer-Reviewed Original ResearchConceptsAcute myeloid leukemiaAcute lymphoblastic leukemiaLymphoblastic leukemiaAcute leukemiaMyeloid leukemiaExpression signaturesCommon acute leukemiaCommon childhood cancerCommon cytogenetic subtypeMicroRNA expression signatureNormal control samplesAcute leukemia samplesBetter prognosisChildhood cancerReal-time PCRCytogenetic subtypesMiR-223LeukemiaMiR-128aLeukemia samplesPromoter hypomethylationMiR-128MicroRNA expressionDiagnosisRegulation of expression
2005
MicroRNA expression profiles classify human cancers
Lu J, Getz G, Miska EA, Alvarez-Saavedra E, Lamb J, Peck D, Sweet-Cordero A, Ebert BL, Mak RH, Ferrando AA, Downing JR, Jacks T, Horvitz HR, Golub TR. MicroRNA expression profiles classify human cancers. Nature 2005, 435: 834-838. PMID: 15944708, DOI: 10.1038/nature03702.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsFlow CytometryGene Expression ProfilingGene Expression Regulation, NeoplasticHumansMicroRNAsNeoplasmsSensitivity and SpecificityConceptsCluster of microRNAsHuman cancersHuman chromosome 13Non-coding RNAsImportant transcription factorMicroRNA expression profileTranscription factorsExpression profilesGlobal downregulationRegulatory moleculesDifferentiation statePotential oncogeneMiR-17C-MycChromosome 13MicroRNAsHuman B-cell lymphomasMicroRNA profilesTumor formationVivo modelRNANucleotidesOncogeneDownregulationExpressionSystematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals
Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, Lindblad-Toh K, Lander ES, Kellis M. Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature 2005, 434: 338-345. PMID: 15735639, PMCID: PMC2923337, DOI: 10.1038/nature03441.Peer-Reviewed Original ResearchConceptsMiRNA genesRegulatory motifsNew miRNA genesHuman miRNA genesPost-transcriptional regulationCommon regulatory motifsLikely target genesMammalian genomesDog genomeGene regulationPromoter analysisHuman genomeHuman genesHuman promotersTarget genesUntranslated regionSystematic discoveryGenomeComprehensive identificationGenesNew motifMotifCandidate motifsFunctional elementsPromoter