2022
Protein and miRNA profile of circulating extracellular vesicles in patients with primary sclerosing cholangitis
Povero D, Tameda M, Eguchi A, Ren W, Kim J, Myers R, Goodman Z, Harrison S, Sanyal A, Bosch J, Ohno-Machado L, Feldstein A. Protein and miRNA profile of circulating extracellular vesicles in patients with primary sclerosing cholangitis. Scientific Reports 2022, 12: 3027. PMID: 35194091, PMCID: PMC8863778, DOI: 10.1038/s41598-022-06809-0.Peer-Reviewed Original ResearchConceptsSmall non-coding RNAsExtracellular vesiclesNon-coding RNAsNovel miRNAsControl subjectsFurther molecular characterizationMiRNA sequence analysisLiver-specific markersProtein profilingMiRNA cargoMolecular characterizationHuman diseasesCurrent serum markersNovel surrogate biomarkersPrimary sclerosing cholangitisCholestatic liver diseaseHealthy control subjectsMiRNA profilesProteinCell specificityDifferential centrifugationMiRNAsPSC patientsSclerosing cholangitisLiver disease
2020
Comprehensive characterization of hepatocyte-derived extracellular vesicles identifies direct miRNA-based regulation of hepatic stellate cells and DAMP-based hepatic macrophage IL-1β and IL-17 upregulation in alcoholic hepatitis mice
Eguchi A, Yan R, Pan S, Wu R, Kim J, Chen Y, Ansong C, Smith R, Tempaku M, Ohno-Machado L, Takei Y, Feldstein A, Tsukamoto H. Comprehensive characterization of hepatocyte-derived extracellular vesicles identifies direct miRNA-based regulation of hepatic stellate cells and DAMP-based hepatic macrophage IL-1β and IL-17 upregulation in alcoholic hepatitis mice. Journal Of Molecular Medicine 2020, 98: 1021-1034. PMID: 32556367, PMCID: PMC7810220, DOI: 10.1007/s00109-020-01926-7.Peer-Reviewed Original ResearchConceptsHepatic stellate cellsAlcoholic liver diseaseAlcoholic hepatitisAH miceIL-1βHepatic macrophagesStellate cellsExtracellular vesiclesPrimary hepatic stellate cellsIL-17 upregulationIL-17 productionUpregulated IL-1βHepatocyte-derived extracellular vesiclesNovel murine modelTLR9-dependent mannerMacrophage IL-1βHepatitis miceIL-17Liver diseaseControl miceCytokine productionLiver pathologyLiver fibrogenesisMurine modelΑ-SMA
2017
Extracellular vesicles released by hepatocytes from gastric infusion model of alcoholic liver disease contain a MicroRNA barcode that can be detected in blood
Eguchi A, Lazaro R, Wang J, Kim J, Povero D, Willliams B, Ho S, Stärkel P, Schnabl B, Ohno‐Machado L, Tsukamoto H, Feldstein A. Extracellular vesicles released by hepatocytes from gastric infusion model of alcoholic liver disease contain a MicroRNA barcode that can be detected in blood. Hepatology 2017, 65: 475-490. PMID: 27639178, PMCID: PMC5407075, DOI: 10.1002/hep.28838.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAnalysis of VarianceAnimalsBiopsy, NeedleCells, CulturedDisease Models, AnimalExtracellular VesiclesFatty Liver, AlcoholicHepatocytesHumansImmunoblottingImmunohistochemistryMiceMicroRNAsMiddle AgedRandom AllocationReal-Time Polymerase Chain ReactionSampling StudiesSeverity of Illness IndexStatistics, NonparametricYoung AdultConceptsBlood extracellular vesiclesLiver injuryExtracellular vesiclesNuclear factor kappa BAlcoholic liver diseaseChronic liver injuryWeeks of infusionBile duct ligationB-cell lymphoma 2Levels of EVsFactor kappa BSteatohepatitis developmentNonalcoholic steatohepatitisLiver diseaseObese miceHepatic macrophagesDuct ligationKappa BMiR-340Cell originLymphoma 2Intragastric infusionMiceMiRNA signatureTime pointsMiRIAD update: using alternative polyadenylation, protein interaction network analysis and additional species to enhance exploration of the role of intragenic miRNAs and their host genes
Hinske L, dos Santos F, Ohara D, Ohno-Machado L, Kreth S, Galante P. MiRIAD update: using alternative polyadenylation, protein interaction network analysis and additional species to enhance exploration of the role of intragenic miRNAs and their host genes. Database 2017, 2017: bax053. PMID: 29220447, PMCID: PMC5569676, DOI: 10.1093/database/bax053.Peer-Reviewed Original Research
2015
Alternative Polyadenylation Allows Differential Negative Feedback of Human miRNA miR-579 on Its Host Gene ZFR
Hinske L, Galante P, Limbeck E, Möhnle P, Parmigiani R, Ohno-Machado L, Camargo A, Kreth S. Alternative Polyadenylation Allows Differential Negative Feedback of Human miRNA miR-579 on Its Host Gene ZFR. PLOS ONE 2015, 10: e0121507. PMID: 25799583, PMCID: PMC4370670, DOI: 10.1371/journal.pone.0121507.Peer-Reviewed Original ResearchConceptsHost genesAlternative polyadenylationIntronic miRNAsMiR-579Protein-coding host genesPotential miRNA binding sitesHost gene expressionMiRNA binding sitesIntronic miRNAMiRNA genesNegative feedback loopRNA-seqPolyadenylation signalPolyadenylation sitesBioinformatics analysisCell line modelsGene expressionSilico analysisDifferential targetingPolyadenylationGenesMiRNAsZFRBinding sitesNegative feedback
2014
MAGI: a Node.js web service for fast microRNA-Seq analysis in a GPU infrastructure
Kim J, Levy E, Ferbrache A, Stepanowsky P, Farcas C, Wang S, Brunner S, Bath T, Wu Y, Ohno-Machado L. MAGI: a Node.js web service for fast microRNA-Seq analysis in a GPU infrastructure. Bioinformatics 2014, 30: 2826-2827. PMID: 24907367, PMCID: PMC4173015, DOI: 10.1093/bioinformatics/btu377.Peer-Reviewed Original ResearchConceptsWeb servicesWeb reportsLarge input filesNovel feature extractionEnd performance improvementsExploration of resultsGPU infrastructureInteractive visualizationJavaScript frameworkParallel computingGPU devicesHypertext PreprocessorCUDA CFeature extractionDrop operationInput filesPlot generationSalient featuresPerformance improvementInfrastructureNodesServicesData analysisComputingBrowserGAMUT: GPU accelerated microRNA analysis to uncover target genes through CUDA-miRanda
Wang S, Kim J, Jiang X, Brunner S, Ohno-Machado L. GAMUT: GPU accelerated microRNA analysis to uncover target genes through CUDA-miRanda. BMC Medical Genomics 2014, 7: s9. PMID: 25077821, PMCID: PMC4101446, DOI: 10.1186/1755-8794-7-s1-s9.Peer-Reviewed Original ResearchConceptsCompute Unified Device ArchitectureGraphics processing unitsHigh performance computeParallel computingNVIDIA Compute Unified Device ArchitectureUnified Device ArchitectureMultiple test datasetsGiga cell updatesTimes performance gainsSmith-Waterman algorithmGPU developersSW implementationSource codeExecution timeGHz CPUIntel XeonLong reference sequencesProcessing unitTarget identification algorithmCell updatesTest datasetProjects/Such large scalePerformance gainsBiomedical research communitymiRIAD—integrating microRNA inter- and intragenic data
Hinske L, França G, Torres H, Ohara D, Lopes-Ramos C, Heyn J, Reis L, Ohno-Machado L, Kreth S, Galante P. miRIAD—integrating microRNA inter- and intragenic data. Database 2014, 2014: bau099. PMID: 25288656, PMCID: PMC4186326, DOI: 10.1093/database/bau099.Peer-Reviewed Original ResearchConceptsProtein-coding genesIntragenic miRNAsHost genesGene expressionProtein-protein interaction dataSmall non-coding RNAsHost gene functionHost gene expressionMiRNA binding sitesNon-coding RNAsMajority of miRNAsGene functionGenomic contextFunctional annotationFunctional network analysisTarget mRNAsExpression correlationExonic regionsGenesMiRNAsDifferent tissuesInteraction dataBinding sitesGenomic classificationSilico validation
2013
Differential Expression of miR-145 in Children with Kawasaki Disease
Shimizu C, Kim J, Stepanowsky P, Trinh C, Lau H, Akers J, Chen C, Kanegaye J, Tremoulet A, Ohno-Machado L, Burns J. Differential Expression of miR-145 in Children with Kawasaki Disease. PLOS ONE 2013, 8: e58159. PMID: 23483985, PMCID: PMC3590129, DOI: 10.1371/journal.pone.0058159.Peer-Reviewed Original ResearchMeSH KeywordsArteriesBase SequenceChildChild, PreschoolCluster AnalysisGene Expression RegulationHumansInfantMicroRNAsModels, BiologicalMolecular Sequence DataMucocutaneous Lymph Node SyndromeReal-Time Polymerase Chain ReactionSequence AlignmentSequence Analysis, DNASignal TransductionTransforming Growth Factor betaConceptsTGF-β pathwayGene expressionMiR-145Small non-coding RNAsKawasaki disease pathogenesisExtracellular vesiclesSmall RNA speciesPost-transcriptional levelDiscovery of microRNAsKawasaki diseaseNon-coding RNAsExpression of genesDisease pathogenesisSmall extracellular vesiclesSmall RNAsRNA speciesTarget genesTop pathwaysVascular smooth muscle cellsPathway analysisDifferentiation of neutrophilsDifferential expressionMicroRNAsArterial wallGeneration of myofibroblasts
2012
Setting Up an Intronic miRNA Database
Hinske L, Heyn J, Galante P, Ohno-Machado L, Kreth S. Setting Up an Intronic miRNA Database. Methods In Molecular Biology 2012, 936: 69-76. PMID: 23007499, DOI: 10.1007/978-1-62703-083-0_5.Peer-Reviewed Original ResearchConceptsAvailable information resourcesWeb-based toolInformation resourcesGenome-wide analysisHost gene transcriptionAnalysis techniquesIntergenic miRNAsIntragenic microRNAsWide analysisUseful analysis techniqueHost genesMiRNA databaseGene transcriptionMiRNA dataDifferent analysis techniquesMiRNAsSignificant attentionTranscriptionDatabaseMore informationRecent pastBasic structureTechniqueUnique linkageGenes
2010
A potential role for intragenic miRNAs on their hosts' interactome
Hinske L, Galante P, Kuo W, Ohno-Machado L. A potential role for intragenic miRNAs on their hosts' interactome. BMC Genomics 2010, 11: 533. PMID: 20920310, PMCID: PMC3091682, DOI: 10.1186/1471-2164-11-533.Peer-Reviewed Original ResearchConceptsIntragenic miRNAsHost genesAdenylate/uridylate-rich elementsMiRNA targetsMRNA targetsHost interactomeGene cohortsMiRNA biogenesis pathwayNon-coding RNA moleculesHigh-confidence setMiRNA target genesProtein-coding regionsKEGG pathway analysisTight regulatory controlNegative feedback regulatorIntronic miRNAsMore intronsBiogenesis pathwayMiRNA genesNegative feedback loopUridylate-rich elementsCellular homeostasisTarget genesRNA moleculesInteractome