2021
Transcriptomics of bronchoalveolar lavage cells identifies new molecular endotypes of sarcoidosis
Vukmirovic M, Yan X, Gibson KF, Gulati M, Schupp JC, DeIuliis G, Adams TS, Hu B, Mihaljinec A, Woolard TN, Lynn H, Emeagwali N, Herzog EL, Chen ES, Morris A, Leader JK, Zhang Y, Garcia JGN, Maier LA, Collman RG, Drake WP, Becich MJ, Hochheiser H, Wisniewski SR, Benos PV, Moller DR, Prasse A, Koth LL, Kaminski N. Transcriptomics of bronchoalveolar lavage cells identifies new molecular endotypes of sarcoidosis. European Respiratory Journal 2021, 58: 2002950. PMID: 34083402, PMCID: PMC9759791, DOI: 10.1183/13993003.02950-2020.Peer-Reviewed Original ResearchConceptsWeighted gene co-expression network analysisGene co-expression network analysisCo-expression network analysisGene expression programsGene expression patternsDistinct transcriptional programsImmune response pathwaysIon Torrent ProtonMicroarray expression datasetsExpression programsTranscriptional programsPhenotypic traitsGene modulesResponse pathwaysRNA sequencingMolecular endotypesExpression patternsGene expressionHilar lymphadenopathyOrgan involvementGenomic researchMechanistic targetExpression datasetsT helper type 1T cell immune responses
2003
Global Expression Profiling of Fibroblast Responses to Transforming Growth Factor-β1 Reveals the Induction of Inhibitor of Differentiation-1 and Provides Evidence of Smooth Muscle Cell Phenotypic Switching
Chambers RC, Leoni P, Kaminski N, Laurent GJ, Heller RA. Global Expression Profiling of Fibroblast Responses to Transforming Growth Factor-β1 Reveals the Induction of Inhibitor of Differentiation-1 and Provides Evidence of Smooth Muscle Cell Phenotypic Switching. American Journal Of Pathology 2003, 162: 533-546. PMID: 12547711, PMCID: PMC1851161, DOI: 10.1016/s0002-9440(10)63847-3.Peer-Reviewed Original ResearchMeSH KeywordsCell DivisionCell LineCell SurvivalFetusFibroblastsGene Expression ProfilingHelix-Loop-Helix MotifsHumansImmunohistochemistryInhibitor of Differentiation Protein 1Inhibitor of Differentiation ProteinsLungMuscle, SmoothNeoplasm ProteinsPhenotypeRepressor ProteinsRNA, MessengerTranscription FactorsTranscription, GeneticTransforming Growth Factor betaTransforming Growth Factor beta1ConceptsMajor functional categoriesHelix transcription factorGlobal gene expressionNumber of genesCell lineage commitmentGlobal expression profilingDominant-negative antagonistSmooth muscle cell phenotypic switchingProtein levelsSmooth muscle myosin heavy chainInduction of inhibitorMuscle myosin heavy chainTransformation of fibroblastsImmediate early genesTranscriptional regulatorsTranscriptional programsExtracellular matrix protein depositionTranscriptional programmingProtein biosynthesisGene groupsLineage commitmentCytoskeletal reorganizationTranscription factorsFunctional categoriesCell signaling
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 conditionsDNA microarrays identification of primary and secondary target genes regulated by p53
Kannan K, Amariglio N, Rechavi G, Jakob-Hirsch J, Kela I, Kaminski N, Getz G, Domany E, Givol D. DNA microarrays identification of primary and secondary target genes regulated by p53. Oncogene 2001, 20: 2225-2234. PMID: 11402317, DOI: 10.1038/sj.onc.1204319.Peer-Reviewed Original ResearchConceptsSecondary target genesTarget genesCell linesTumor suppressor p53Primary targetP53 activatesPresence of cycloheximideSuch genesTranscriptional programsTranscriptional changesAdditional genesDNA repairAbsence of cycloheximideMurine p53Primary genesOligonucleotide microarraysCell cycleSuppressor p53GenesProtein synthesisCell adhesionLung cancer cell linesCancer cell linesCell phenotypeHuman lung cancer cell lines