2020
Assessment of viral RNA in idiopathic pulmonary fibrosis using RNA-seq
Yin Q, Strong MJ, Zhuang Y, Flemington EK, Kaminski N, de Andrade JA, Lasky JA. Assessment of viral RNA in idiopathic pulmonary fibrosis using RNA-seq. BMC Pulmonary Medicine 2020, 20: 81. PMID: 32245461, PMCID: PMC7119082, DOI: 10.1186/s12890-020-1114-1.Peer-Reviewed Original ResearchConceptsIdiopathic pulmonary fibrosisViral RNA expressionViral infectionPulmonary fibrosisPathogenesis of IPFLung biopsy samplesRNA expressionHerpes virus infectionLow-level evidenceReal-time RT-PCRAcute exacerbationControl lungsLung tissueVirus infectionBiopsy samplesSelect virusesPossible associationInfectionRT-PCRStatistical differenceNext-generation sequencingViral RNAFibrosisVirusRNA-seq results
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
2015
A 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
2013
Cartilage Oligomeric Matrix Protein in Idiopathic Pulmonary Fibrosis
Vuga LJ, Milosevic J, Pandit K, Ben-Yehudah A, Chu Y, Richards T, Sciurba J, Myerburg M, Zhang Y, Parwani AV, Gibson KF, Kaminski N. Cartilage Oligomeric Matrix Protein in Idiopathic Pulmonary Fibrosis. PLOS ONE 2013, 8: e83120. PMID: 24376648, PMCID: PMC3869779, DOI: 10.1371/journal.pone.0083120.Peer-Reviewed Original ResearchMeSH KeywordsAgedCartilage Oligomeric Matrix ProteinCells, CulturedCollagen Type ICollagen Type I, alpha 1 ChainExtracellular MatrixFemaleFibroblastsGene Expression RegulationHumansIdiopathic Pulmonary FibrosisLungMaleMiddle AgedPlasminogen Activator Inhibitor 1RNA, Small InterferingSignal TransductionSmad3 ProteinTransforming Growth Factor beta1VimentinConceptsIdiopathic pulmonary fibrosisCartilage oligomeric matrix proteinIPF lungsNormal human lung fibroblastsForce vital capacityHuman lung fibroblastsTGF-β1Oligomeric matrix proteinPulmonary fibrosisLung fibroblastsSerum COMP concentrationTGF-β1 activityEpithelial cell hyperplasiaMatrix proteinsLung restrictionWestern blot analysisExtracellular matrix depositionIPF patientsTime-dependent fashionDisease activityMedian survivalVital capacityCell hyperplasiaControl lungsBlood draw
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