2020
Gene coexpression networks reveal novel molecular endotypes in alpha-1 antitrypsin deficiency
Chu JH, Zang W, Vukmirovic M, Yan X, Adams T, DeIuliis G, Hu B, Mihaljinec A, Schupp JC, Becich MJ, Hochheiser H, Gibson KF, Chen ES, Morris A, Leader JK, Wisniewski SR, Zhang Y, Sciurba FC, Collman RG, Sandhaus R, Herzog EL, Patterson KC, Sauler M, Strange C, Kaminski N. Gene coexpression networks reveal novel molecular endotypes in alpha-1 antitrypsin deficiency. Thorax 2020, 76: 134-143. PMID: 33303696, PMCID: PMC10794043, DOI: 10.1136/thoraxjnl-2019-214301.Peer-Reviewed Original ResearchConceptsWeighted gene co-expression network analysisAlpha-1 antitrypsin deficiencyGene modulesGene co-expression network analysisDifferential gene expression analysisCo-expression network analysisPeripheral blood mononuclear cellsGene expression patternsPBMC gene expression patternsGene coexpression networksAATD individualsGene expression profilesGene expression analysisBronchoalveolar lavageAugmentation therapyClinical variablesAntitrypsin deficiencyGene expression assaysRNA-seqCoexpression networkGene validationExpression analysisExpression assaysWGCNA modulesExpression patterns
2019
Transcriptional regulatory model of fibrosis progression in the human lung
McDonough JE, Ahangari F, Li Q, Jain S, Verleden SE, Herazo-Maya J, Vukmirovic M, DeIuliis G, Tzouvelekis A, Tanabe N, Chu F, Yan X, Verschakelen J, Homer RJ, Manatakis DV, Zhang J, Ding J, Maes K, De Sadeleer L, Vos R, Neyrinck A, Benos PV, Bar-Joseph Z, Tantin D, Hogg JC, Vanaudenaerde BM, Wuyts WA, Kaminski N. Transcriptional regulatory model of fibrosis progression in the human lung. JCI Insight 2019, 4 PMID: 31600171, PMCID: PMC6948862, DOI: 10.1172/jci.insight.131597.Peer-Reviewed Original ResearchConceptsIdiopathic pulmonary fibrosisAdvanced fibrosisAlveolar surface densityFibrosis progressionLung fibrosisHuman lungDynamic Regulatory Events MinerExtent of fibrosisIPF lungsPulmonary fibrosisControl lungsIPF tissueB lymphocytesFibrosisLungLinear mixed-effects modelsMixed-effects modelsGene expression changesSystems biology modelsDifferential gene expression analysisGene expression analysisProgressionGene expression networksRNA sequencingBiology models
2011
High Throughput Determination of TGFβ1/SMAD3 Targets in A549 Lung Epithelial Cells
Zhang Y, Handley D, Kaplan T, Yu H, Bais AS, Richards T, Pandit KV, Zeng Q, Benos PV, Friedman N, Eickelberg O, Kaminski N. High Throughput Determination of TGFβ1/SMAD3 Targets in A549 Lung Epithelial Cells. PLOS ONE 2011, 6: e20319. PMID: 21625455, PMCID: PMC3098871, DOI: 10.1371/journal.pone.0020319.Peer-Reviewed Original ResearchMeSH KeywordsBase SequenceCell LineChromatin ImmunoprecipitationDNA PrimersElectrophoretic Mobility Shift AssayEpithelial CellsHumansLungOligonucleotide Array Sequence AnalysisPromoter Regions, GeneticProtein BindingReverse Transcriptase Polymerase Chain ReactionSmad3 ProteinTransforming Growth Factor beta1ConceptsGene expression microarraysLung epithelial cellsMolecular pathwaysTranscriptional regulationExpression microarraysGlobal transcriptional regulationTGFβ1/Smad3Epithelial cellsHuman promoter regionsSignal transduction cascadeTarget gene expressionEpithelial cell phenotypeGene expression analysisTranscription factor Smad3Primary lung epithelial cellsSmad3 targetsQuantitative real-time RT-PCRFOXA2 promoterHuman A549 alveolar epithelial cellsChromatin immunoprecipitationTransduction cascadeTarget genesA549 lung epithelial cellsExpression analysisGene expression
2009
Clara Cells Attenuate the Inflammatory Response through Regulation of Macrophage Behavior
Snyder JC, Reynolds SD, Hollingsworth JW, Li Z, Kaminski N, Stripp BR. Clara Cells Attenuate the Inflammatory Response through Regulation of Macrophage Behavior. American Journal Of Respiratory Cell And Molecular Biology 2009, 42: 161-171. PMID: 19423773, PMCID: PMC2822978, DOI: 10.1165/rcmb.2008-0353oc.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsChronic DiseaseFemaleIn Vitro TechniquesInterleukin-6LipopolysaccharidesLung DiseasesMacrophages, AlveolarMaleMiceMice, CongenicMice, Inbred C57BLMice, KnockoutNeutrophilsOligonucleotide Array Sequence AnalysisPneumoniaRNA, MessengerSignal TransductionToll-Like Receptor 4Tumor Necrosis Factor-alphaUteroglobinConceptsClara cell secretory proteinChronic lung diseaseCell secretory functionWild-type miceInflammatory responseClara cellsLung diseaseEpithelial remodelingGene expression analysisSecretory functionMacrophage behaviorTNF-alpha signalingLung inflammatory responsePolymorphonuclear leukocyte recruitmentTNF-alpha productionExpression analysisSecretory proteinsGenetic mouse modelsPseudomonas aeruginosa LPSPathway modelingCCSP deficiencyLung inflammationExcessive inflammationTNF-alphaAirway fluid
2007
Chromosomal aberrations and gene expression profiles in non-small cell lung cancer
Dehan E, Ben-Dor A, Liao W, Lipson D, Frimer H, Rienstein S, Simansky D, Krupsky M, Yaron P, Friedman E, Rechavi G, Perlman M, Aviram-Goldring A, Izraeli S, Bittner M, Yakhini Z, Kaminski N. Chromosomal aberrations and gene expression profiles in non-small cell lung cancer. Lung Cancer 2007, 56: 175-184. PMID: 17258348, DOI: 10.1016/j.lungcan.2006.12.010.Peer-Reviewed Original ResearchConceptsDNA replicationCopy numberWnt/beta-catenin pathwaySet of genesGene Ontology annotationsFunctional enrichment analysisExpression levelsAmplification of 3qGene expression profilesBeta-catenin pathwayGene expression analysisGene expression profilingArray CGHMatrix metalloproteasesGene expression levelsConcordant changesCopy number changesDNA copy numberActing genesArray comparative genomic hybridizationOntology annotationsComparative genomic hybridizationGenomic contentReal-time quantitative PCRExpression analysis
2004
Increase in p21 expression independent of the p53 pathway in bleomycin-induced lung fibrosis
Blundell R, Kaminski N, Harrison D. Increase in p21 expression independent of the p53 pathway in bleomycin-induced lung fibrosis. Experimental And Molecular Pathology 2004, 77: 231-237. PMID: 15507241, DOI: 10.1016/j.yexmp.2004.07.003.Peer-Reviewed Original ResearchConceptsP21 expressionLung fibrosisFibrotic lungsAnimal mouse modelsNuclear p21 expressionCytoplasmic p21 expressionExpression of p21Bleomycin injectionLung diseaseMouse modelAnimal modelsImmuno-histochemistryDay 14P27 expressionCell cycle regulatory genesBleomycin inductionFibrosisLungBleomycinP53 pathwayP53Gene expression analysisExpressionPCNAPathogenesisGene expression profiling of in vivo UVB‐irradiated human epidermis
Enk CD, Shahar I, Amariglio N, Rechavi G, Kaminski N, Hochberg M. Gene expression profiling of in vivo UVB‐irradiated human epidermis. Photodermatology Photoimmunology & Photomedicine 2004, 20: 129-137. PMID: 15144390, DOI: 10.1111/j.1600-0781.2004.00097.x.Peer-Reviewed Original ResearchConceptsGlobal gene expression analysisGene expression patternsGene expression analysisGene expression profilingIntact human epidermisOligonucleotide microarray technologyNumerous genesFunctional categoriesExpression analysisExpression profilingExpression patternsGene expressionBiological processesMicroarray profilingDifferential expressionDifferential regulationMicroarray technologyGenesMolecular pathwaysCultured cellsRNA samplesHuman epidermisUV-induced photodamageSemi-quantitative reverse transcriptase-polymerase chain reactionIntact tissueSil overexpression in lung cancer characterizes tumors with increased mitotic activity
Erez A, Perelman M, Hewitt SM, Cojacaru G, Goldberg I, Shahar I, Yaron P, Muler I, Campaner S, Amariglio N, Rechavi G, Kirsch IR, Krupsky M, Kaminski N, Izraeli S. Sil overexpression in lung cancer characterizes tumors with increased mitotic activity. Oncogene 2004, 23: 5371-5377. PMID: 15107824, DOI: 10.1038/sj.onc.1207685.Peer-Reviewed Original ResearchMeSH KeywordsAdenocarcinomaBlotting, WesternCell DifferentiationCell DivisionCell LineG1 PhaseGenes, Immediate-EarlyHeLa CellsHumansImmunohistochemistryIntracellular Signaling Peptides and ProteinsKinetochoresLung NeoplasmsMitosisNeoplasm MetastasisOligonucleotide Array Sequence AnalysisOncogene Proteins, FusionRNA, MessengerConceptsLung cancerT-cell acute lymphoblastic leukemiaMitotic activityAcute lymphoblastic leukemiaLung cancer samplesPrimary adenocarcinomaLymphoblastic leukemiaMetastatic spreadImmediate early genesMicroarray gene expression analysisTissue arraysPeak levelsCancer samplesProtein expressionTumorsCancerProtein levelsCell proliferationMitotic indexCommon chromosomal rearrangementsGene expression analysisSIL geneEarly genesOverexpressionRecent studies
2002
Gene expression analysis reveals matrilysin as a key regulator of pulmonary fibrosis in mice and humans
Zuo F, Kaminski N, Eugui E, Allard J, Yakhini Z, Ben-Dor A, Lollini L, Morris D, Kim Y, DeLustro B, Sheppard D, Pardo A, Selman M, Heller RA. Gene expression analysis reveals matrilysin as a key regulator of pulmonary fibrosis in mice and humans. Proceedings Of The National Academy Of Sciences Of The United States Of America 2002, 99: 6292-6297. PMID: 11983918, PMCID: PMC122942, DOI: 10.1073/pnas.092134099.Peer-Reviewed Original ResearchConceptsPulmonary fibrosisFibrotic lungsHuman pulmonary fibrosisPotential therapeutic targetGene expression analysisClinical diseaseSmooth muscleKnockout miceTherapeutic targetFibrosisHuman tissue samplesUntreatable groupLungTissue samplesMolecular pathwaysGlobal gene expression analysisExtracellular matrix formationMiceExpression analysisMatrilysinMolecular mechanismsKey regulatorGene expression patternsExpression patternsOligonucleotide microarrays