2023
An integrated cell atlas of the lung in health and disease
Sikkema L, Ramírez-Suástegui C, Strobl D, Gillett T, Zappia L, Madissoon E, Markov N, Zaragosi L, Ji Y, Ansari M, Arguel M, Apperloo L, Banchero M, Bécavin C, Berg M, Chichelnitskiy E, Chung M, Collin A, Gay A, Gote-Schniering J, Hooshiar Kashani B, Inecik K, Jain M, Kapellos T, Kole T, Leroy S, Mayr C, Oliver A, von Papen M, Peter L, Taylor C, Walzthoeni T, Xu C, Bui L, De Donno C, Dony L, Faiz A, Guo M, Gutierrez A, Heumos L, Huang N, Ibarra I, Jackson N, Kadur Lakshminarasimha Murthy P, Lotfollahi M, Tabib T, Talavera-López C, Travaglini K, Wilbrey-Clark A, Worlock K, Yoshida M, van den Berge M, Bossé Y, Desai T, Eickelberg O, Kaminski N, Krasnow M, Lafyatis R, Nikolic M, Powell J, Rajagopal J, Rojas M, Rozenblatt-Rosen O, Seibold M, Sheppard D, Shepherd D, Sin D, Timens W, Tsankov A, Whitsett J, Xu Y, Banovich N, Barbry P, Duong T, Falk C, Meyer K, Kropski J, Pe’er D, Schiller H, Tata P, Schultze J, Teichmann S, Misharin A, Nawijn M, Luecken M, Theis F. An integrated cell atlas of the lung in health and disease. Nature Medicine 2023, 29: 1563-1577. PMID: 37291214, PMCID: PMC10287567, DOI: 10.1038/s41591-023-02327-2.Peer-Reviewed Original ResearchConceptsCell atlasGene modulesCell typesCell type definitionsHuman Cell AtlasSingle-cell technologiesSingle-cell datasetsUndescribed cell typeMultiple lung diseasesCell statesMarker genesMonocyte-derived macrophagesDistal axisStudy of diseasesHuman tissuesAnnotationAtlasGenesSPP1DiversityExpressionTreesLimited numberCellsNew data
2018
Characteristics of lung cancer among patients with idiopathic pulmonary fibrosis and interstitial lung disease – analysis of institutional and population data
Yoon JH, Nouraie M, Chen X, Zou RH, Sellares J, Veraldi KL, Chiarchiaro J, Lindell K, Wilson DO, Kaminski N, Burns T, Trejo Bittar H, Yousem S, Gibson K, Kass DJ. Characteristics of lung cancer among patients with idiopathic pulmonary fibrosis and interstitial lung disease – analysis of institutional and population data. Respiratory Research 2018, 19: 195. PMID: 30285867, PMCID: PMC6171146, DOI: 10.1186/s12931-018-0899-4.Peer-Reviewed Original ResearchConceptsIdiopathic pulmonary fibrosisSingle lung transplantInterstitial lung diseaseLung cancerIPF patientsPulmonary fibrosisIPF ILDNon-IPF ILD patientsLung Cancer RegistrySquamous cell histologySquamous cell carcinomaStandard incidence ratioBackgroundLung cancerCenter registryILD patientsLung transplantCell histologyClinical characteristicsInterstitial lungCancer RegistryIncidence ratiosWorse prognosisLower lobeCell carcinomaLung disease
2017
Lung Endothelial MicroRNA-1 Regulates Tumor Growth and Angiogenesis
Korde A, Jin L, Zhang JG, Ramaswamy A, Hu B, Kolahian S, Guardela BJ, Herazo-Maya J, Siegfried JM, Stabile L, Pisani MA, Herbst RS, Kaminski N, Elias JA, Puchalski JT, Takyar SS. Lung Endothelial MicroRNA-1 Regulates Tumor Growth and Angiogenesis. American Journal Of Respiratory And Critical Care Medicine 2017, 196: 1443-1455. PMID: 28853613, PMCID: PMC5736970, DOI: 10.1164/rccm.201610-2157oc.Peer-Reviewed Original ResearchConceptsNon-small cell lung cancerMiR-1 levelsLewis lung carcinoma xenograftsLung carcinoma xenograftsTransgenic miceEndothelial cellsNSCLC tumorsCarcinoma xenograftsLung endotheliumMiR-1Tumor growthTumor progressionVascular endothelial cadherin promoterMicroRNA-1Cohort of patientsTumor-bearing lungsCell lung cancerVascular endothelial growth factorCancer-free tissuesEndothelial growth factorInducible transgenic miceMiR-1 overexpressionKP miceOverall survivalTumor burden
2014
Matrix Metalloproteinase-19 Promotes Metastatic Behavior In Vitro and Is Associated with Increased Mortality in Non–Small Cell Lung Cancer
Yu G, Herazo-Maya JD, Nukui T, Romkes M, Parwani A, Juan-Guardela BM, Robertson J, Gauldie J, Siegfried JM, Kaminski N, Kass DJ. Matrix Metalloproteinase-19 Promotes Metastatic Behavior In Vitro and Is Associated with Increased Mortality in Non–Small Cell Lung Cancer. American Journal Of Respiratory And Critical Care Medicine 2014, 190: 780-790. PMID: 25250855, PMCID: PMC4299607, DOI: 10.1164/rccm.201310-1903oc.Peer-Reviewed Original ResearchConceptsNon-small cell lung cancerCell lung cancerLung cancerEpithelial-mesenchymal transitionLung tumorsMatrix metalloproteinasesProgression of NSCLCNormal lung tissuesHuman lung cancerNSCLC cell linesMultiple NSCLC cell linesLung cancer tumorsMMP19 expressionPoor prognosisCancer deathControl subjectsIncreased MortalityLung tissueNSCLC cellsMolecular pathogenesisPotential biomarkersDisease severityMetastatic behaviorCancerCancer tumorsBlockade of the Programmed Death-1 Pathway Restores Sarcoidosis CD4+ T-Cell Proliferative Capacity
Braun NA, Celada LJ, Herazo-Maya JD, Abraham S, Shaginurova G, Sevin CM, Grutters J, Culver DA, Dworski R, Sheller J, Massion PP, Polosukhin VV, Johnson JE, Kaminski N, Wilkes DS, Oswald-Richter KA, Drake WP. Blockade of the Programmed Death-1 Pathway Restores Sarcoidosis CD4+ T-Cell Proliferative Capacity. American Journal Of Respiratory And Critical Care Medicine 2014, 190: 560-571. PMID: 25073001, PMCID: PMC4214083, DOI: 10.1164/rccm.201401-0188oc.Peer-Reviewed Original ResearchConceptsPD-1 pathway blockadeT cell proliferative capacityPeripheral blood mononuclear cellsPD-L1 expressionPD-1 pathwayBlood mononuclear cellsT cell functionPathway blockadePD-L1Clinical outcomesLung diseaseMononuclear cellsControl subjectsProliferative capacityT cellsImmunohistochemistry analysisPD-1/PD-L1 expressionControl peripheral blood mononuclear cellsHealthy control peripheral blood mononuclear cellsHealthy control lungsIdiopathic lung diseaseSpontaneous clinical resolutionChronic lung diseaseHealthy control subjectsEffective therapeutic interventions
2012
Zyxin Is a Transforming Growth Factor-β (TGF-β)/Smad3 Target Gene That Regulates Lung Cancer Cell Motility via Integrin α5β1*
Mise N, Savai R, Yu H, Schwarz J, Kaminski N, Eickelberg O. Zyxin Is a Transforming Growth Factor-β (TGF-β)/Smad3 Target Gene That Regulates Lung Cancer Cell Motility via Integrin α5β1*. Journal Of Biological Chemistry 2012, 287: 31393-31405. PMID: 22778267, PMCID: PMC3438968, DOI: 10.1074/jbc.m112.357624.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell Adhesion MoleculesCell Line, TumorCell MovementFocal AdhesionsGene SilencingHumansIntegrin alpha5beta1Intercellular JunctionsLung NeoplasmsMiceMice, Mutant StrainsMicrofilament ProteinsPhosphoproteinsProto-Oncogene Proteins p21(ras)Signal TransductionSmad3 ProteinTransforming Growth Factor beta1ZyxinConceptsEpithelial-mesenchymal transitionCancer cell motilityCell motilityFocal adhesionsZyxin expressionCell-extracellular matrix adhesionLung cancer cellsFocal adhesion proteinsSingle cell motilityCell-cell junctionsCell adherens junctionsNovel functional targetSingle cell migrationLung cancer cell motilityCancer cellsNovel direct targetZyxin geneTGF-β signalingTumor suppressor effectActin cytoskeletonAdherens junctionsCytoskeletal organizationZyxinTarget genesAdhesion proteinsGlobal Methylation Patterns in Idiopathic Pulmonary Fibrosis
Rabinovich EI, Kapetanaki MG, Steinfeld I, Gibson KF, Pandit KV, Yu G, Yakhini Z, Kaminski N. Global Methylation Patterns in Idiopathic Pulmonary Fibrosis. PLOS ONE 2012, 7: e33770. PMID: 22506007, PMCID: PMC3323629, DOI: 10.1371/journal.pone.0033770.Peer-Reviewed Original ResearchConceptsCpG islandsMethylation patternsEpigenetic changesMethylation profilesHuman CpG island microarrayNuclear element-1 (LINE-1 or L1) retrotransposonsCellular biosynthetic processesCpG island microarrayGlobal methylation profilesRegulation of apoptosisGlobal methylation patternsLung phenotypeBRB-Array ToolsElement-1 (LINE-1 or L1) retrotransposonsCancer-specific changesBiosynthetic processesGlobal hypomethylationSpecific changesExtensive remodelingFalse discovery rateExtracellular matrix depositionArray resultsGenesHypomethylationLung cancer samples
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
Gene Expression Patterns, Prognostic and Diagnostic Markers, and Lung Cancer Biology
Kaminski N, Krupsky M. Gene Expression Patterns, Prognostic and Diagnostic Markers, and Lung Cancer Biology. CHEST Journal 2004, 125: 111s-115s. PMID: 15136452, DOI: 10.1378/chest.125.5_suppl.111s-a.Peer-Reviewed Original ResearchSil 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 studiesGene Expression Studies in Lung Development and Lung Stem Cell Biology
Mariani TJ, Kaminski N. Gene Expression Studies in Lung Development and Lung Stem Cell Biology. Current Topics In Developmental Biology 2004, 64: 57-71. PMID: 15563944, DOI: 10.1016/s0070-2153(04)64004-x.Peer-Reviewed Original Research
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
Transcriptional Profiling of Non-small Cell Lung Cancer Using Oligonucleotide Microarrays
Cojocaru G, Friedman N, Krupsky M, Yaron P, Simansky D, Yellin A, Rechavi G, Barash Y, Ben-Dor A, Yakhini Z, Kaminski N. Transcriptional Profiling of Non-small Cell Lung Cancer Using Oligonucleotide Microarrays. CHEST Journal 2002, 121: 44s. PMID: 11893681, DOI: 10.1378/chest.121.3_suppl.44s.Peer-Reviewed Original Research
2001
DNA 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