2020
Single-Cell Transcriptional Archetypes of Airway Inflammation in Cystic Fibrosis.
Schupp JC, Khanal S, Gomez JL, Sauler M, Adams TS, Chupp GL, Yan X, Poli S, Zhao Y, Montgomery RR, Rosas IO, Dela Cruz CS, Bruscia EM, Egan ME, Kaminski N, Britto CJ. Single-Cell Transcriptional Archetypes of Airway Inflammation in Cystic Fibrosis. American Journal Of Respiratory And Critical Care Medicine 2020, 202: 1419-1429. PMID: 32603604, PMCID: PMC7667912, DOI: 10.1164/rccm.202004-0991oc.Peer-Reviewed Original ResearchConceptsCF lung diseaseHealthy control subjectsImmune dysfunctionLung diseaseCystic fibrosisControl subjectsSputum cellsAbnormal chloride transportLung mononuclear phagocytesInnate immune dysfunctionDivergent clinical coursesImmune cell repertoireMonocyte-derived macrophagesCF monocytesAirway inflammationClinical courseProinflammatory featuresCell survival programInflammatory responseTissue injuryCell repertoireImmune functionTranscriptional profilesAlveolar macrophagesMononuclear phagocytes
2019
BAL Cell Gene Expression Is Indicative of Outcome and Airway Basal Cell Involvement in Idiopathic Pulmonary Fibrosis
Prasse A, Binder H, Schupp JC, Kayser G, Bargagli E, Jaeger B, Hess M, Rittinghausen S, Vuga L, Lynn H, Violette S, Jung B, Quast K, Vanaudenaerde B, Xu Y, Hohlfeld JM, Krug N, Herazo-Maya JD, Rottoli P, Wuyts WA, Kaminski N. BAL Cell Gene Expression Is Indicative of Outcome and Airway Basal Cell Involvement in Idiopathic Pulmonary Fibrosis. American Journal Of Respiratory And Critical Care Medicine 2019, 199: 622-630. PMID: 30141961, PMCID: PMC6396865, DOI: 10.1164/rccm.201712-2551oc.Peer-Reviewed Original ResearchConceptsIdiopathic pulmonary fibrosisAirway basal cellsChronic obstructive pulmonary diseaseObstructive pulmonary diseasePulmonary diseaseBAL cellsBasal cellsPulmonary fibrosisControl subjectsCell gene expressionIndependent IPF cohortsNine-gene signatureIPF cohortDerivation cohortClinical parametersRetrospective studyUnivariate analysisUnpredictable courseCell involvementDiscovery cohortGene expressionHealthy volunteersCox modelStage IIIFatal disease
2018
Gene correlation network analysis to identify regulatory factors in idiopathic pulmonary fibrosis
McDonough JE, Kaminski N, Thienpont B, Hogg JC, Vanaudenaerde BM, Wuyts WA. Gene correlation network analysis to identify regulatory factors in idiopathic pulmonary fibrosis. Thorax 2018, 74: 132. PMID: 30366970, PMCID: PMC6467239, DOI: 10.1136/thoraxjnl-2018-211929.Peer-Reviewed Original ResearchConceptsIdiopathic pulmonary fibrosisLung functionPulmonary fibrosisExtensive pathological changesSevere lung diseaseLung Tissue Research ConsortiumCorrelation network analysisIPF cohortIPF groupLung diseaseControl subjectsUpregulated modulesT cellsImmune responsePathological changesLeucocyte activationB cellsClinical relevanceSurfactant metabolismDisease pathologyInterferon responseFibrosisBlood vesselsPathological processesGene correlation network analysis
2017
Extracellular Mitochondrial DNA Is Generated by Fibroblasts and Predicts Death in Idiopathic Pulmonary Fibrosis
Ryu C, Sun H, Gulati M, Herazo-Maya J, Chen Y, Osafo-Addo A, Brandsdorfer C, Winkler J, Blaul C, Faunce J, Pan H, Woolard T, Tzouvelekis A, Antin-Ozerkis DE, Puchalski JT, Slade M, Gonzalez AL, Bogenhagen DF, Kirillov V, Feghali-Bostwick C, Gibson K, Lindell K, Herzog RI, Dela Cruz CS, Mehal W, Kaminski N, Herzog EL, Trujillo G. Extracellular Mitochondrial DNA Is Generated by Fibroblasts and Predicts Death in Idiopathic Pulmonary Fibrosis. American Journal Of Respiratory And Critical Care Medicine 2017, 196: 1571-1581. PMID: 28783377, PMCID: PMC5754440, DOI: 10.1164/rccm.201612-2480oc.Peer-Reviewed Original ResearchConceptsIdiopathic pulmonary fibrosisNormal human lung fibroblastsExtracellular mitochondrial DNABronchoalveolar lavageIPF fibroblastsPulmonary fibrosisInnate immune ligandsEvent-free survivalSmooth muscle actin expressionMtDNA concentrationsSmooth muscle actin-expressing myofibroblastsGrowth factor-β1Muscle actin expressionHuman lung fibroblastsTGF-β1 stimulationExtracellular mtDNAIPF cohortClinical outcomesControl subjectsDisease progressionGlycolytic reprogrammingSoluble mediatorsTGF-β1Factor-β1Immune ligands
2015
VCAM-1 is a TGF-β1 inducible gene upregulated in idiopathic pulmonary fibrosis
Agassandian M, Tedrow JR, Sembrat J, Kass DJ, Zhang Y, Goncharova EA, Kaminski N, Mallampalli RK, Vuga LJ. VCAM-1 is a TGF-β1 inducible gene upregulated in idiopathic pulmonary fibrosis. Cellular Signalling 2015, 27: 2467-2473. PMID: 26386411, PMCID: PMC4684430, DOI: 10.1016/j.cellsig.2015.09.003.Peer-Reviewed Original ResearchConceptsIdiopathic pulmonary fibrosisVCAM-1IPF subjectsPulmonary fibrosisVascular cell adhesion molecule-1Lethal interstitial lung diseaseVCAM-1 protein levelsCell adhesion molecule-1Interstitial lung diseaseLungs of subjectsProtein levelsHigher plasma levelsVCAM-1 mRNAAdhesion molecule-1Pulmonary diffusion capacityHuman lung fibroblastsIPF lungsLung functionFibrotic fociVital capacityLung diseaseUnknown etiologyControl subjectsPlasma levelsCell cycle arrestFK506-Binding Protein 10, a Potential Novel Drug Target for Idiopathic Pulmonary Fibrosis
Staab-Weijnitz CA, Fernandez IE, Knüppel L, Maul J, Heinzelmann K, Juan-Guardela BM, Hennen E, Preissler G, Winter H, Neurohr C, Hatz R, Lindner M, Behr J, Kaminski N, Eickelberg O. FK506-Binding Protein 10, a Potential Novel Drug Target for Idiopathic Pulmonary Fibrosis. American Journal Of Respiratory And Critical Care Medicine 2015, 192: 455-467. PMID: 26039104, PMCID: PMC4595665, DOI: 10.1164/rccm.201412-2233oc.Peer-Reviewed Original ResearchConceptsIdiopathic pulmonary fibrosisPrimary human lung fibroblastsGrowth factor-β1Endoplasmic reticulum stressPulmonary fibrosisFKBP10 expressionLung fibrosisNovel drug targetsControl subjectsFactor-β1Protein 10Immunofluorescent stainingReticulum stressReverse transcriptase-polymerase chain reactionQuantitative reverse transcriptase-polymerase chain reactionTranscriptase-polymerase chain reactionSmooth muscle actinPotential novel drug targetsHuman lung fibroblastsCollagen secretionDrug targetsWestern blot analysisProfibrotic mediatorsU.S. cohortGerman cohortA Novel Genomic Signature with Translational Significance for Human Idiopathic Pulmonary Fibrosis
Bauer Y, Tedrow J, de Bernard S, Birker-Robaczewska M, Gibson KF, Guardela BJ, Hess P, Klenk A, Lindell KO, Poirey S, Renault B, Rey M, Weber E, Nayler O, Kaminski N. A Novel Genomic Signature with Translational Significance for Human Idiopathic Pulmonary Fibrosis. American Journal Of Respiratory Cell And Molecular Biology 2015, 52: 217-231. PMID: 25029475, PMCID: PMC4370242, DOI: 10.1165/rcmb.2013-0310oc.Peer-Reviewed Original ResearchConceptsIdiopathic pulmonary fibrosisHuman idiopathic pulmonary fibrosisLung fibrosis modelGrowth factor-β1IPF lungsPulmonary fibrosisFibrosis modelFactor-β1Therapeutic interventionsDevastating lung diseasePrimary human lung fibroblastsLung Tissue Research ConsortiumGene marker setsPotential therapeutic interventionsHuman lung fibroblastsEpithelial A549 cellsHuman epithelial A549 cellsBleomycin instillationLung fibrosisControl lungsLung diseaseControl cohortControl subjectsTranslational significanceNovel treatments
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
2010
Characterization of Microrna Expression Profile In Platelets In Sickle Cell Disease
Jain S, Raghavachari N, Woodhouse K, Kaminski N, Gladwin M. Characterization of Microrna Expression Profile In Platelets In Sickle Cell Disease. Blood 2010, 116: 2030. DOI: 10.1182/blood.v116.21.2030.2030.Peer-Reviewed Original ResearchSickle cell diseasePulmonary hypertensionSCD patientsPathological platelet activationPlatelet activationCell diseaseRace-matched healthy controlsSickle cell disease patientsAfrican American control subjectsPittsburgh Medical CenterPlatelet-rich plasma samplesP-valueThromboembolic complicationsStudy enrollmentBlood InstitutePresent studyControl subjectsDisease patientsNational HeartIntravascular hemolysisHealthy controlsSCD groupSCD pathogenesisReal-time PCRIndividual patients
2009
Gene Expression Profiles of Acute Exacerbations of Idiopathic Pulmonary Fibrosis
Konishi K, Gibson KF, Lindell KO, Richards TJ, Zhang Y, Dhir R, Bisceglia M, Gilbert S, Yousem SA, Song JW, Kim DS, Kaminski N. Gene Expression Profiles of Acute Exacerbations of Idiopathic Pulmonary Fibrosis. American Journal Of Respiratory And Critical Care Medicine 2009, 180: 167-175. PMID: 19363140, PMCID: PMC2714820, DOI: 10.1164/rccm.200810-1596oc.Peer-Reviewed Original ResearchConceptsIdiopathic pulmonary fibrosisStable idiopathic pulmonary fibrosisAcute exacerbationIPF lungsPulmonary fibrosisControl lungsPeripheral bloodReal-time quantitative reverse transcription polymerase chain reactionProtein levelsQuantitative reverse transcription polymerase chain reactionReverse transcription-polymerase chain reactionApoptosis of epitheliumTranscription-polymerase chain reactionDUTP nick-end labeling assayNick-end labeling assayGlobal gene expression signaturesAgilent gene expression microarraysEnd-labeling assayDEFA1-3Gene expression signaturesInflammatory etiologyEpithelial injuryControl subjectsExacerbationLung
2007
Effects of exercise training on quadriceps muscle gene expression in chronic obstructive pulmonary disease
Radom-Aizik S, Kaminski N, Hayek S, Halkin H, Cooper DM, Ben-Dov I. Effects of exercise training on quadriceps muscle gene expression in chronic obstructive pulmonary disease. Journal Of Applied Physiology 2007, 102: 1976-1984. PMID: 17483440, DOI: 10.1152/japplphysiol.00577.2006.Peer-Reviewed Original ResearchMeSH KeywordsAgedCase-Control StudiesCluster AnalysisEnergy MetabolismExerciseGene ExpressionGene Expression ProfilingHumansMaleOligonucleotide Array Sequence AnalysisOxidative StressOxygen ConsumptionProteasome Endopeptidase ComplexPulmonary Disease, Chronic ObstructiveQuadriceps MuscleReproducibility of ResultsReverse Transcriptase Polymerase Chain ReactionRNA, MessengerUbiquitinConceptsChronic obstructive pulmonary diseaseObstructive pulmonary diseaseCOPD patientsPulmonary diseaseExercise trainingAge-matched healthy menMuscle gene expressionHigh expressionSkeletal muscle functionExercise capacityGene expressionWalk testHealthy menControl subjectsNeedle biopsyMuscle functionVastus lateralisPatientsOxidative stressTraining responseFunctional parametersDiseaseTissue stressExpressionGene pathways