2024
Dedifferentiated early postnatal lung myofibroblasts redifferentiate in adult disease
Chandran R, Adams T, Kabir I, Gallardo-Vara E, Kaminski N, Gomperts B, Greif D. Dedifferentiated early postnatal lung myofibroblasts redifferentiate in adult disease. Frontiers In Cell And Developmental Biology 2024, 12: 1335061. PMID: 38572485, PMCID: PMC10987733, DOI: 10.3389/fcell.2024.1335061.Peer-Reviewed Original ResearchRNA sequencing analysisSMA+ myofibroblastsGene expression profilesLung myofibroblastsAdult lungSequence analysisResponse to lung injurySingle cell RNA sequencing analysisTissue remodeling genesSmooth muscle cell markersLung to hypoxiaExpression profilesRemodeling genesMuscle cell markersResponse to injuryCell typesSMA cellsLineage tracingLung injuryCell markersLineagesGenesAdult diseaseDrug bleomycinLung surface area
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
2014
Pneumocystis jirovecii colonization is associated with enhanced Th1 inflammatory gene expression in lungs of humans with chronic obstructive pulmonary disease
Fitzpatrick ME, Tedrow JR, Hillenbrand ME, Lucht L, Richards T, Norris KA, Zhang Y, Sciurba FC, Kaminski N, Morris A. Pneumocystis jirovecii colonization is associated with enhanced Th1 inflammatory gene expression in lungs of humans with chronic obstructive pulmonary disease. Microbiology And Immunology 2014, 58: 202-211. PMID: 24438206, PMCID: PMC4106795, DOI: 10.1111/1348-0421.12135.Peer-Reviewed Original ResearchConceptsChronic obstructive pulmonary diseaseObstructive pulmonary diseaseLung Tissue Research ConsortiumPneumocystis colonizationPulmonary diseaseCOPD pathogenesisLung gene expression profilesChemokine ligands CXCL9Cognate receptor CXCR3Finding of upregulationLungs of humansInflammatory gene expressionLung tissue samplesPotential key pathwaysGene expression profilesPneumocystis jirovecii colonizationReceptor CXCR3Ligands CXCL9Lymphocyte traffickingT lymphocytesInflammatory genesPneumocystis jiroveciiDisease pathogenesisExpression profilesLigand expression
2013
Peripheral Blood Mononuclear Cell Gene Expression Profiles Predict Poor Outcome in Idiopathic Pulmonary Fibrosis
Herazo-Maya JD, Noth I, Duncan SR, Kim S, Ma SF, Tseng GC, Feingold E, Juan-Guardela BM, Richards TJ, Lussier Y, Huang Y, Vij R, Lindell KO, Xue J, Gibson KF, Shapiro SD, Garcia JG, Kaminski N. Peripheral Blood Mononuclear Cell Gene Expression Profiles Predict Poor Outcome in Idiopathic Pulmonary Fibrosis. Science Translational Medicine 2013, 5: 205ra136. PMID: 24089408, PMCID: PMC4175518, DOI: 10.1126/scitranslmed.3005964.Peer-Reviewed Original ResearchMeSH KeywordsBiomarkersCD28 AntigensCD4 AntigensCluster AnalysisCohort StudiesGene Expression ProfilingHumansIdiopathic Pulmonary FibrosisLeukocytes, MononuclearOligonucleotide Array Sequence AnalysisReproducibility of ResultsReverse Transcriptase Polymerase Chain ReactionSignal TransductionTreatment OutcomeConceptsTransplant-free survivalIdiopathic pulmonary fibrosisPeripheral blood mononuclear cell gene expression profilesReplication cohortCell gene expression profilesPoor outcomePulmonary fibrosisQuantitative reverse transcription polymerase chain reactionReverse transcription-polymerase chain reactionProportional hazards modelTranscription-polymerase chain reactionGene expression profilesPotential cellular sourcesT cell activationIPF patientsLung transplantationMicroarray cohortPatient ageOutcome biomarkerPatient groupVital capacityPolymerase chain reactionT cellsDiscovery cohortITK expressionGene 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
2010
Gene Expression Profiles Of Pulmonary Fibrosis Reveal Developmental Functions As Determinants That Distinguish NSIP And UIP In Interstitial Pneumonias
Konishi K, Richards T, Song J, Chensny L, Lindell K, Herazo J, Zhang Y, Gibson K, Kaminski N, Kim D. Gene Expression Profiles Of Pulmonary Fibrosis Reveal Developmental Functions As Determinants That Distinguish NSIP And UIP In Interstitial Pneumonias. 2010, a2492-a2492. DOI: 10.1164/ajrccm-conference.2010.181.1_meetingabstracts.a2492.Peer-Reviewed Original Research
2008
Network analysis of temporal effects of intermittent and sustained hypoxia on rat lungs
Wu W, Dave NB, Yu G, Strollo PJ, Kovkarova-Naumovski E, Ryter SW, Reeves SR, Dayyat E, Wang Y, Choi AM, Gozal D, Kaminski N. Network analysis of temporal effects of intermittent and sustained hypoxia on rat lungs. Physiological Genomics 2008, 36: 24-34. PMID: 18826996, PMCID: PMC2604785, DOI: 10.1152/physiolgenomics.00258.2007.Peer-Reviewed Original ResearchConceptsSystems biology approachEstrogen receptor 1Lung responseQuantitative real-time PCRRat lungBiology approachIntermittent hypoxiaExpression patternsSustained hypoxiaReal-time PCRDistinct gene expression patternsDifferent temporal expression patternsDownstream physiological effectsGene expression patternsTemporal expression patternsSteroid hormone receptor activityGene expression profilesTemporal expression changesRegulatory networksHormone receptor activityPulmonary hypertensionKey proteinsGene expressionMolecular networksExpression changesMolecular Staging of Epithelial Maturation Using Secretory Cell–Specific Genes as Markers
Zemke AC, Snyder JC, Brockway BL, Drake JA, Reynolds SD, Kaminski N, Stripp BR. Molecular Staging of Epithelial Maturation Using Secretory Cell–Specific Genes as Markers. American Journal Of Respiratory Cell And Molecular Biology 2008, 40: 340-348. PMID: 18757308, PMCID: PMC2645532, DOI: 10.1165/rcmb.2007-0380oc.Peer-Reviewed Original ResearchConceptsCell-specific genesCategories of genesUnique gene expression profileDevelopmental expression patternsSecretory cellsGene expression profilesCell marker genesExpression of FMO3Messenger RNA abundanceUnique developmental expression patternTransgenic approachesClara cell markerRNA abundanceMarker genesClara cellsExpression patternsExpression profilesMolecular markersEpithelial maturationPhenotypic changesFlavin monooxygenase 3GenesTemporal inductionBronchiolar Clara cellsEmbryonic day
2007
Pedigreed Primate Embryonic Stem Cells Express Homogeneous Familial Gene Profiles
Navara CS, Mich‐Basso J, Redinger CJ, Ben‐Yehudah A, Jacoby E, Kovkarova‐Naumovski E, Sukhwani M, Orwig K, Kaminski N, Castro CA, Simerly CR, Schatten G. Pedigreed Primate Embryonic Stem Cells Express Homogeneous Familial Gene Profiles. Stem Cells 2007, 25: 2695-2704. PMID: 17641389, PMCID: PMC4357318, DOI: 10.1634/stemcells.2007-0286.Peer-Reviewed Original ResearchConceptsHuman embryonic stem cellsEmbryonic stem cellsPrimate ESCsPrimate embryonic stem cellsExpression profilesStem cellsHeterogeneous gene expression profilesReliable expression profilesStable diploid karyotypeGene expression profilesMouse ESCsRhesus embryosHESC linesBiological limitationsPluripotency markersDiploid karyotypeGene profilesAnonymous originsBiomedical promiseBiological similaritiesESCHalf siblingsDisparate originsFull siblingsMouse strains331: Gene expression profiles in peripheral blood for the noninvasive diagnosis of chronic lung allograft rejection
Studer S, Richards T, Wu W, McCurry K, Kaminski N. 331: Gene expression profiles in peripheral blood for the noninvasive diagnosis of chronic lung allograft rejection. The Journal Of Heart And Lung Transplantation 2007, 26: s179. DOI: 10.1016/j.healun.2006.11.351.Peer-Reviewed Original ResearchChromosomal 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
Comprehensive gene expression profiles reveal pathways related to the pathogenesis of chronic obstructive pulmonary disease
Ning W, Li CJ, Kaminski N, Feghali-Bostwick CA, Alber SM, Di YP, Otterbein SL, Song R, Hayashi S, Zhou Z, Pinsky DJ, Watkins SC, Pilewski JM, Sciurba FC, Peters DG, Hogg JC, Choi AM. Comprehensive gene expression profiles reveal pathways related to the pathogenesis of chronic obstructive pulmonary disease. Proceedings Of The National Academy Of Sciences Of The United States Of America 2004, 101: 14895-14900. PMID: 15469929, PMCID: PMC522001, DOI: 10.1073/pnas.0401168101.Peer-Reviewed Original ResearchConceptsChronic obstructive pulmonary diseaseGene expressionObstructive pulmonary diseaseEgr-1 DNA-binding activityComprehensive gene expression profilesUnreported candidate genesMatrix metalloproteinase-2Gene expression patternsDNA-binding activityGene expression profilesEgr1-null miceExtracellular matrix proteinsEgr-1 protein expressionPulmonary diseaseEpithelial cellsGOLD 2Transcription factorsSAGE analysisPotential molecular targetsReal-time quantitative RT-PCRMolecular basisCandidate genesHuman lung fibroblast cellsRelated proteinsExpression patterns
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