2015
Alterations in Gene Expression and DNA Methylation during Murine and Human Lung Alveolar Septation
Cuna A, Halloran B, Faye-Petersen O, Kelly D, Crossman DK, Cui X, Pandit K, Kaminski N, Bhattacharya S, Ahmad A, Mariani TJ, Ambalavanan N. Alterations in Gene Expression and DNA Methylation during Murine and Human Lung Alveolar Septation. American Journal Of Respiratory Cell And Molecular Biology 2015, 53: 60-73. PMID: 25387348, PMCID: PMC4566107, DOI: 10.1165/rcmb.2014-0160oc.Peer-Reviewed Original ResearchConceptsDNA methylationNormal septationGene expressionGenome-wide DNA methylation dataMajor epigenetic mechanismsLung developmentNumber of genesMouse lung developmentGene of interestDNA methylation dataGene expression dataMicroarray gene expression dataAlveolar septationCoordinated expressionEpigenetic mechanismsMethylated DNAMultiple genesMicroarray analysisMethylation dataExpression dataGenesMethylationExtracellular matrixAltered expressionAntioxidant defense
2014
Secreted Phosphoprotein 1 Is a Determinant of Lung Function Development in Mice
Ganguly K, Martin TM, Concel VJ, Upadhyay S, Bein K, Brant KA, George L, Mitra A, Thimraj TA, Fabisiak JP, Vuga LJ, Fattman C, Kaminski N, Schulz H, Leikauf GD. Secreted Phosphoprotein 1 Is a Determinant of Lung Function Development in Mice. American Journal Of Respiratory Cell And Molecular Biology 2014, 51: 637-651. PMID: 24816281, PMCID: PMC4224082, DOI: 10.1165/rcmb.2013-0471oc.Peer-Reviewed Original ResearchMeSH KeywordsAlveolar Epithelial CellsAnimalsAnimals, NewbornCore Binding Factor Alpha 1 SubunitFemaleGene Expression Regulation, DevelopmentalLung ComplianceMaleMice, Inbred C3HMice, Inbred C57BLMice, KnockoutOligonucleotide Array Sequence AnalysisOsteopontinPromoter Regions, GeneticPulmonary AlveoliPulmonary Disease, Chronic ObstructiveReceptor, Notch1ConceptsMicroarray analysisPhosphoprotein 1Quantitative trait lociLung functionQuantitative RT-PCR analysisDNA-protein bindingRunt-related transcription factor 2Transcription factor 2Developmental transcriptsLung developmentTrait lociNumerous genesSecreted Phosphoprotein 1Notch1 transcriptsRT-PCR analysisInsulin-like growth factor-1C3H/HeJ miceDiminished lung functionLung function developmentSPP1 promoterSPP1Growth factor-1Mean airspace chord lengthC3H/HeJGenetic variants
2013
Gene expression profiles reveal molecular mechanisms involved in the progression and resolution of bleomycin-induced lung fibrosis
Cabrera S, Selman M, Lonzano-Bolaños A, Konishi K, Richards TJ, Kaminski N, Pardo A. Gene expression profiles reveal molecular mechanisms involved in the progression and resolution of bleomycin-induced lung fibrosis. American Journal Of Physiology - Lung Cellular And Molecular Physiology 2013, 304: l593-l601. PMID: 23457188, PMCID: PMC4116413, DOI: 10.1152/ajplung.00320.2012.Peer-Reviewed Original ResearchConceptsLung fibrosisFibrotic responseResolution of bleomycinTranscriptional signatureGene expression profilesGene microarray analysisC57BL/6 miceProminent inflammationSingle doseExtracellular matrix-related genesInitial progressionControl animalsTIMP-1Normal architectureExpression profilesFibrosisMatrix metalloproteinasesHydroxyproline contentBleomycinMatrix-related genesSubsequent resolutionProgressionInflammationEqual volumeMicroarray analysis
2012
Matrix Metalloproteinase-19 Is a Key Regulator of Lung Fibrosis in Mice and Humans
Yu G, Kovkarova-Naumovski E, Jara P, Parwani A, Kass D, Ruiz V, Lopez-Otín C, Rosas IO, Gibson KF, Cabrera S, Ramírez R, Yousem SA, Richards TJ, Chensny LJ, Selman M, Kaminski N, Pardo A. Matrix Metalloproteinase-19 Is a Key Regulator of Lung Fibrosis in Mice and Humans. American Journal Of Respiratory And Critical Care Medicine 2012, 186: 752-762. PMID: 22859522, PMCID: PMC5450991, DOI: 10.1164/rccm.201202-0302oc.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBleomycinCells, CulturedCyclooxygenase 2Epithelial CellsGene Expression Regulation, EnzymologicHumansIdiopathic Pulmonary FibrosisLaser Capture MicrodissectionMatrix Metalloproteinases, SecretedMiceMice, KnockoutOligonucleotide Array Sequence AnalysisPulmonary AlveoliUp-RegulationConceptsIdiopathic pulmonary fibrosisHyperplastic epithelial cellsAlveolar epithelial cellsEpithelial cellsMMP-19IPF lungsWT miceLung fibrosisFibrotic responseHyperplastic alveolar epithelial cellsNovel mediatorLaser capture microscopeLung fibrotic responseDevelopment of fibrosisWild-type miceEpithelial phenotypic changesMatrix metalloproteinase-19Microarray analysisA549 epithelial cellsLung injuryBronchoalveolar lavagePulmonary fibrosisLung tissueSame lungFibrosis
2011
Genomic Differences Distinguish the Myofibroblast Phenotype of Distal Lung Fibroblasts from Airway Fibroblasts
Zhou X, Wu W, Hu H, Milosevic J, Konishi K, Kaminski N, Wenzel SE. Genomic Differences Distinguish the Myofibroblast Phenotype of Distal Lung Fibroblasts from Airway Fibroblasts. American Journal Of Respiratory Cell And Molecular Biology 2011, 45: 1256-1262. PMID: 21757679, PMCID: PMC3262668, DOI: 10.1165/rcmb.2011-0065oc.Peer-Reviewed Original ResearchConceptsGenomic differencesMicroarray analysisC-Jun N-terminal kinaseExtracellular matrix-associated moleculesMyofibroblast-like characteristicsDistinct genomic differencesN-terminal kinasePotential functional implicationsQuantitative real-time PCRMatrix-associated moleculesCytoskeletal organizationGene OntologyActin bindingLung fibroblastsReal-time PCRMyofibroblast phenotypeFunctional implicationsParenchymal fibroblastsAirway fibroblastsDifferentiated fibroblastsPathway activationDifferent phenotypesRegional fibroblastsFibroblastsPhenotype
2003
Overexpression of a set of genes, including WISP-1, common to pulmonary metastases of both mouse D122 Lewis lung carcinoma and B16-F10.9 melanoma cell lines
Margalit O, Eisenbach L, Amariglio N, Kaminski N, Harmelin A, Pfeffer R, Shohat M, Rechavi G, Berger R. Overexpression of a set of genes, including WISP-1, common to pulmonary metastases of both mouse D122 Lewis lung carcinoma and B16-F10.9 melanoma cell lines. British Journal Of Cancer 2003, 89: 314-319. PMID: 12865923, PMCID: PMC2394268, DOI: 10.1038/sj.bjc.6600977.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCarcinoma, Lewis LungCarrier ProteinsCCN Intercellular Signaling ProteinsFemaleGene Expression Regulation, NeoplasticGrowth SubstancesHumansIntracellular Signaling Peptides and ProteinsLung NeoplasmsMaleMelanomaMiceMice, Inbred C57BLNeoplasm MetastasisOligonucleotide Array Sequence AnalysisOncogene ProteinsPlasminogen Activator Inhibitor 2Polymerase Chain ReactionProto-Oncogene ProteinsTumor Cells, CulturedUteroglobinConceptsPlasminogen activator inhibitor-2Melanoma cell linesBrain natriuretic peptidePulmonary metastasesSet of genesLewis lung carcinomaWISP-1Cell linesSurfactant protein CMetastatic processReal-time quantitative PCRLung carcinomaOligonucleotide microarraysMicroarray analysisInhibitor 2GenesGenetic determinantsSpontaneous pulmonary metastasesIL-1 alphaMinimal residual diseaseProtein 1Cause of deathDevelopment of metastasesInterleukin-1 alphaQuantitative PCR
2002
Gene-microarray analysis of multiple sclerosis lesions yields new targets validated in autoimmune encephalomyelitis
Lock C, Hermans G, Pedotti R, Brendolan A, Schadt E, Garren H, Langer-Gould A, Strober S, Cannella B, Allard J, Klonowski P, Austin A, Lad N, Kaminski N, Galli SJ, Oksenberg JR, Raine CS, Heller R, Steinman L. Gene-microarray analysis of multiple sclerosis lesions yields new targets validated in autoimmune encephalomyelitis. Nature Medicine 2002, 8: 500-508. PMID: 11984595, DOI: 10.1038/nm0502-500.Peer-Reviewed Original ResearchMeSH KeywordsAcute DiseaseAnimalsAutopsyChronic DiseaseEncephalomyelitis, Autoimmune, ExperimentalFemaleGranulocyte Colony-Stimulating FactorHumansInflammationInterferon-gammaInterleukin-17Interleukin-6MiceMice, Inbred C57BLMultiple SclerosisOligonucleotide Array Sequence AnalysisReceptors, FcReproducibility of ResultsTranscription, GeneticConceptsExperimental autoimmune encephalomyelitisMultiple sclerosis lesionsMS lesionsAutoimmune encephalomyelitisSclerosis lesionsGranulocyte colony-stimulating factorCommon γ chainColony-stimulating factorGene microarray analysisAcute phaseInflammatory cytokinesInterleukin-6Chronic diseasesLesionsNew targetsEncephalomyelitisTherapyDownstream pathwaysMicroarray analysisΓ-chainMicroarray studiesInflammationChronicCytokinesInterferon
2001
DNA microarray analysis of genes involved in p53 mediated apoptosis: activation of Apaf-1
Kannan K, Kaminski N, Rechavi G, Jakob-Hirsch J, Amariglio N, Givol D. DNA microarray analysis of genes involved in p53 mediated apoptosis: activation of Apaf-1. Oncogene 2001, 20: 3449-3455. PMID: 11423996, DOI: 10.1038/sj.onc.1204446.Peer-Reviewed Original ResearchMeSH KeywordsApoptosisApoptotic Protease-Activating Factor 1Gene Expression ProfilingGene Expression Regulation, LeukemicGenesGenes, p53HumansLeukemia, MyeloidNeoplasm ProteinsOligonucleotide Array Sequence AnalysisProteinsRNA, MessengerRNA, NeoplasmTemperatureTranscription, GeneticTumor Cells, CulturedTumor Suppressor Protein p53ConceptsGene expression profilesGrowth arrestApaf-1Expression profilesMouse myeloid leukemic cell lineRegulated gene expression profilesP53-regulated genesDistinct transcriptional programsDNA microarray analysisCell linesTranscriptional programsCellular functionsSUMO-1Myeloid leukemic cell linesTemperature-sensitive p53MRNA speciesOligonucleotide microarraysProapoptotic genesMicroarray analysisLeukemic cell linesApoptotic processCellular responsesGenesP53 signalingStress conditions