2023
Somatic Mutations: The Next Frontier in Demystifying Chronic Obstructive Pulmonary Disease and Idiopathic Pulmonary Fibrosis?
Yan X, Kaminski N. Somatic Mutations: The Next Frontier in Demystifying Chronic Obstructive Pulmonary Disease and Idiopathic Pulmonary Fibrosis? American Journal Of Respiratory And Critical Care Medicine 2023, 208: 1150-1151. PMID: 37856835, PMCID: PMC10868359, DOI: 10.1164/rccm.202310-1774ed.Peer-Reviewed Original Research
2022
Bronchial epithelium epithelial-mesenchymal plasticity forms aberrant basaloid-like cells in vitro
Uthaya Kumar DB, Motakis E, Yurieva M, Kohar V, Martinek J, Wu TC, Khoury J, Grassmann J, Lu M, Palucka K, Kaminski N, Koff JL, Williams A. Bronchial epithelium epithelial-mesenchymal plasticity forms aberrant basaloid-like cells in vitro. American Journal Of Physiology - Lung Cellular And Molecular Physiology 2022, 322: l822-l841. PMID: 35438006, PMCID: PMC9142163, DOI: 10.1152/ajplung.00254.2021.Peer-Reviewed Original ResearchMeSH KeywordsEpithelial CellsEpithelial-Mesenchymal TransitionEpitheliumHumansLung DiseasesRespiratory MucosaRNA, Long NoncodingConceptsProtein codingEpithelial-mesenchymal transitionLncRNA genesEMT inductionSingle-cell RNA sequencingSingle-cell RNA-seq dataEpithelial-mesenchymal plasticityRNA-seq dataMechanisms of EMTSingle-cell levelEpithelial cell typesRole of EMTTranscriptional reprogrammingHuman bronchial epithelial cellsRNA genesEMT gene signatureTranscriptional changesTranscriptional differencesRNA sequencingSpecific lncRNAsBronchial epithelial cellsDifferential expressionMyofibroblast conversionCell typesGenes
2021
Chronic lung diseases are associated with gene expression programs favoring SARS-CoV-2 entry and severity
Bui LT, Winters NI, Chung MI, Joseph C, Gutierrez AJ, Habermann AC, Adams TS, Schupp JC, Poli S, Peter LM, Taylor CJ, Blackburn JB, Richmond BW, Nicholson AG, Rassl D, Wallace WA, Rosas IO, Jenkins RG, Kaminski N, Kropski JA, Banovich NE. Chronic lung diseases are associated with gene expression programs favoring SARS-CoV-2 entry and severity. Nature Communications 2021, 12: 4314. PMID: 34262047, PMCID: PMC8280215, DOI: 10.1038/s41467-021-24467-0.Peer-Reviewed Original ResearchConceptsChronic lung diseaseLung diseaseImmune responseSARS-CoV-2 entry factorsSevere coronavirus disease-19SARS-CoV-2 infectionWorse COVID-19 outcomesSARS-CoV-2 entryAdaptive immune responsesCoronavirus disease-19COVID-19 outcomesInnate immune responseInflammatory gene expression programSimilar cellular distributionPoor outcomePeripheral lungViral exposureDisease-19Inflammatory microenvironmentEntry factorsLung epitheliumLung cellsViral replicationAT2 cellsBasal differences
2019
The Human Lung Cell Atlas: A High-Resolution Reference Map of the Human Lung in Health and Disease
Schiller HB, Montoro DT, Simon LM, Rawlins EL, Meyer KB, Strunz M, Braga F, Timens W, Koppelman GH, Budinger GRS, Burgess JK, Waghray A, van den Berge M, Theis F, Regev A, Kaminski N, Rajagopal J, Teichmann S, Misharin A, Nawijn M. The Human Lung Cell Atlas: A High-Resolution Reference Map of the Human Lung in Health and Disease. American Journal Of Respiratory Cell And Molecular Biology 2019, 61: 31-41. PMID: 30995076, PMCID: PMC6604220, DOI: 10.1165/rcmb.2018-0416tr.Peer-Reviewed Original ResearchConceptsCell atlasHuman Cell Atlas consortiumCell typesCell-cell interactionsHigh-throughput techniquesFunction of geneticsLung cell typesTranscriptomic analysisDevelopmental processesIndividual cellsMolecular descriptionReference mapTissue microenvironmentDisease mechanismsCellular neighborhoodsHealthy human bodyMolecular profilePersonalized therapeutic regimensCellsLung diseaseTherapeutic regimensImmune cellsLung tissueRecent progressTissue matrixClimate change and lung health: presidential failure, professional responsibility
Hopkinson NS, Hart N, Jenkins G, Rosenfeld M, Smyth AR, Wilkinson AJK, Kaminski N. Climate change and lung health: presidential failure, professional responsibility. Thorax 2019, 74: 627-628. PMID: 31010935, DOI: 10.1136/thoraxjnl-2019-213184.Peer-Reviewed Original Research
2018
The aging lung: tissue telomere shortening in health and disease
Everaerts S, Lammertyn EJ, Martens DS, De Sadeleer LJ, Maes K, van Batenburg AA, Goldschmeding R, van Moorsel CHM, Dupont LJ, Wuyts WA, Vos R, Gayan-Ramirez G, Kaminski N, Hogg JC, Janssens W, Verleden GM, Nawrot TS, Verleden SE, McDonough JE, Vanaudenaerde BM. The aging lung: tissue telomere shortening in health and disease. Respiratory Research 2018, 19: 95. PMID: 29751799, PMCID: PMC5948770, DOI: 10.1186/s12931-018-0794-z.Peer-Reviewed Original ResearchMeSH KeywordsAdolescentAdultAgedChildFemaleHealth StatusHumansLungLung DiseasesMaleMiddle AgedTelomere ShorteningYoung AdultConceptsBronchiolitis obliterans syndromeRestrictive allograft syndromeRelative telomere lengthRegional disease severityShorter RTLNormal lungDisease severityLung agePrior transplantationLung tissueDiseased lungsChronic obstructive pulmonary diseaseChronic hypersensitivity pneumonitisObstructive pulmonary diseaseTelomere lengthNormal human lungPeripheral blood leucocytesDiseased lung tissueDistinct lung regionsAverage relative telomere lengthExplant lungsObliterans syndromeUnused donorPulmonary diseaseHypersensitivity pneumonitis
2017
Climate change and lung health: the challenge for a new president
Hopkinson NS, Hart N, Jenkins G, Kaminski N, Rosenfeld M, Smyth A, Wilkinson A. Climate change and lung health: the challenge for a new president. Thorax 2017, 72: 295. PMID: 28104829, DOI: 10.1136/thoraxjnl-2017-209978.Peer-Reviewed Original Research
2015
Integrative phenotyping framework (iPF): integrative clustering of multiple omics data identifies novel lung disease subphenotypes
Kim S, Herazo-Maya JD, Kang DD, Juan-Guardela BM, Tedrow J, Martinez FJ, Sciurba FC, Tseng GC, Kaminski N. Integrative phenotyping framework (iPF): integrative clustering of multiple omics data identifies novel lung disease subphenotypes. BMC Genomics 2015, 16: 924. PMID: 26560100, PMCID: PMC4642618, DOI: 10.1186/s12864-015-2170-4.Peer-Reviewed Original ResearchEpigenetics in idiopathic pulmonary fibrosis1
Tzouvelekis A, Kaminski N. Epigenetics in idiopathic pulmonary fibrosis1. Biochemistry And Cell Biology 2015, 93: 159-170. PMID: 25659821, DOI: 10.1139/bcb-2014-0126.Peer-Reviewed Original ResearchConceptsIdiopathic pulmonary fibrosisChronic lung disordersLung disordersDNA sequencesFibroproliferative lung disordersTranslational epigenetic studiesIndividual DNA sequencesEpithelial wound repairVariable disease phenotypesPulmonary fibrosisChronic inflammationLung cancerInjurious stimuliHeritable changesEffective treatmentGene functionEpigenetic modificationsEpigenomic alterationsEpigenetic studiesCurrent experimental evidenceDisease paradigmWound repairDisease phenotypeDisordersEnvironmental changes
2014
T-RECS: STABLE SELECTION OF DYNAMICALLY FORMED GROUPS OF FEATURES WITH APPLICATION TO PREDICTION OF CLINICAL OUTCOMES
Altman R, Dunker A, Hunter L, Ritchie M, Murray T, Klein T, HUANG G, TSAMARDINOS I, RAGHU V, KAMINSKI N, BENOS P. T-RECS: STABLE SELECTION OF DYNAMICALLY FORMED GROUPS OF FEATURES WITH APPLICATION TO PREDICTION OF CLINICAL OUTCOMES. Biocomputing 2014, 20: 431-42. PMID: 25592602, PMCID: PMC4299881, DOI: 10.1142/9789814644730_0041.Peer-Reviewed Original ResearchConceptsTraditional feature selection methodsFeature selection methodCohort of patientsPersonalized medicine strategiesReal expression dataFeature selectionClassification accuracyCluster selectionBiological datasetsClinical outcomesCluster featuresLung diseaseBreast cancerSelection methodPatient classificationStructured natureMedicine strategiesSurvival dataTarget variablesEfficient selectionCohortStable selectionImportant features
2010
Strategic Plan for Lung Vascular Research
Erzurum S, Rounds SI, Stevens T, Aldred M, Aliotta J, Archer SL, Asosingh K, Balaban R, Bauer N, Bhattacharya J, Bogaard H, Choudhary G, Dorn GW, Dweik R, Fagan K, Fallon M, Finkel T, Geraci M, Gladwin MT, Hassoun PM, Humbert M, Kaminski N, Kawut SM, Loscalzo J, McDonald D, McMurtry IF, Newman J, Nicolls M, Rabinovitch M, Shizuru J, Oka M, Polgar P, Rodman D, Schumacker P, Stenmark K, Tuder R, Voelkel N, Sullivan E, Weinshilboum R, Yoder MC, Zhao Y, Gail D, Moore TM. Strategic Plan for Lung Vascular Research. American Journal Of Respiratory And Critical Care Medicine 2010, 182: 1554-1562. PMID: 20833821, PMCID: PMC3029941, DOI: 10.1164/rccm.201006-0869ws.Peer-Reviewed Original ResearchConceptsPulmonary hypertensive diseasesSystemic vascular functionRight heart functionPulmonary vascular diseaseTranslational researchDisease-modifying therapiesCare of patientsHypertensive diseaseBlood InstituteLung diseaseVascular functionLung circulationLung vasculatureNational HeartVascular diseaseClinical studiesHeart functionTranslational findingsMultidisciplinary expertsDiseaseBiologic relationshipVascular biologyExtramural research programsVascular researchRegulatory signalingHave advanced research technologies made real impact on respiratory medicine?
Kjetil A, EICKELBERG O, GAULDIE J, KAMINSKI N, Martin K. Have advanced research technologies made real impact on respiratory medicine? Respirology 2010, 15: 876-880. PMID: 20646243, DOI: 10.1111/j.1440-1843.2010.01811.x.Peer-Reviewed Original ResearchConceptsGene array analysisGenetic manipulationGene expressionSystems biologyMolecular researchNovel pathwayArray analysisTremendous sophisticationDisease initiationPotential roleNovel toolAdvanced research technologiesLung diseaseRespiratory medicineHumans todayProteomicsUnique insightsGenesRNABiologyBioinformaticsProteinChronic lung diseaseTherapeutic interventionsPathwayFunctional Genomics of Chlorine-induced Acute Lung Injury in Mice
Leikauf GD, Pope-Varsalona H, Concel VJ, Liu P, Bein K, Brant KA, Dopico RA, Di YP, Jang AS, Dietsch M, Medvedovic M, Li Q, Vuga LJ, Kaminski N, You M, Prows DR. Functional Genomics of Chlorine-induced Acute Lung Injury in Mice. Annals Of The American Thoracic Society 2010, 7: 294-296. PMID: 20601635, PMCID: PMC3136967, DOI: 10.1513/pats.201001-005sm.Peer-Reviewed Original ResearchConceptsAcute lung injuryChlorine-induced acute lung injuryLung injuryMouse strainsMean survival timeGene-targeted miceSusceptibility candidate genesSupportive measuresSurvival timeDivergent strainsInjuryCandidate genesCritical candidate genesFunctional genomics approachMiceAdditional genetic analysesMolecular eventsFunctional significanceFunctional genomicsGenomic approachesChlorine exposureGenetic basisNovel insightsGenetic analysisHospitalization
2009
Chronic lung diseases
Wu W, Kaminski N. Chronic lung diseases. WIREs Mechanisms Of Disease 2009, 1: 298-308. PMID: 20835999, DOI: 10.1002/wsbm.23.Peer-Reviewed Original ResearchConceptsSystems biology approachBiology approachChronic lung diseaseComplex human diseasesHigh-throughput technologiesLung diseaseSystems biologyHuman diseasesTraditional experimental approachesComplex lung diseaseBiomedical researchExperimental approachSerious economic burdenHigh morbiditySerious threatHuman healthEconomic burdenMortality rateDiseaseBiologyMicroarrayPromising findingsClara Cells Attenuate the Inflammatory Response through Regulation of Macrophage Behavior
Snyder JC, Reynolds SD, Hollingsworth JW, Li Z, Kaminski N, Stripp BR. Clara Cells Attenuate the Inflammatory Response through Regulation of Macrophage Behavior. American Journal Of Respiratory Cell And Molecular Biology 2009, 42: 161-171. PMID: 19423773, PMCID: PMC2822978, DOI: 10.1165/rcmb.2008-0353oc.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsChronic DiseaseFemaleIn Vitro TechniquesInterleukin-6LipopolysaccharidesLung DiseasesMacrophages, AlveolarMaleMiceMice, CongenicMice, Inbred C57BLMice, KnockoutNeutrophilsOligonucleotide Array Sequence AnalysisPneumoniaRNA, MessengerSignal TransductionToll-Like Receptor 4Tumor Necrosis Factor-alphaUteroglobinConceptsClara cell secretory proteinChronic lung diseaseCell secretory functionWild-type miceInflammatory responseClara cellsLung diseaseEpithelial remodelingGene expression analysisSecretory functionMacrophage behaviorTNF-alpha signalingLung inflammatory responsePolymorphonuclear leukocyte recruitmentTNF-alpha productionExpression analysisSecretory proteinsGenetic mouse modelsPseudomonas aeruginosa LPSPathway modelingCCSP deficiencyLung inflammationExcessive inflammationTNF-alphaAirway fluid
2007
Genomics and proteomics of lung disease: conference summary
Raj JU, Aliferis C, Caprioli RM, Cowley AW, Davies PF, Duncan MW, Erle DJ, Erzurum SC, Finn PW, Ischiropoulos H, Kaminski N, Kleeberger SR, Leikauf GD, Loyd JE, Martin TR, Matalon S, Moore JH, Quackenbush J, Sabo-Attwood T, Shapiro SD, Schnitzer JE, Schwartz DA, Schwiebert LM, Sheppard D, Ware LB, Weiss ST, Whitsett JA, Wurfel MM, Matthay MA. Genomics and proteomics of lung disease: conference summary. American Journal Of Physiology - Lung Cellular And Molecular Physiology 2007, 293: l45-l51. PMID: 17468134, PMCID: PMC4212816, DOI: 10.1152/ajplung.00139.2007.Peer-Reviewed Original Research
2004
Functional Genomics of Lung Disease
Whitsett J, Bachurski C, Barnes K, Bunn P, Case L, Cook D, Crooks D, Duncan M, Dwyer-Nield L, Elston R, Fessler M, Franklin W, Friedman N, Garcia J, Geraci M, Glasgow C, Glasser S, Hardie W, Henning L, Johnson G, Kawkitinarong K, Keith R, Korfhagen T, Leikauf G, Liggett S, Malcolm K, Malkinson A, Mariani T, McDowell S, McGraw D, Medvedovic M, Moss J, Nogee L, Nonas S, Pacheco-Rodriguez G, Palmer L, Peters D, Prows D, Redline S, Regev A, Sartor M, Schwartz D, Silverman E, Steagall W, Stearman R, Taveira-DaSilva A, Tichelaar J, Tomlinson C, Tsukada K, Weaver T, Wert S, Wesselkamper S, Worthen G, Xu Y, Zerbe L, Zhang Y, Zhang Y, Choi A, Kaminski N. Functional Genomics of Lung Disease. American Journal Of Respiratory Cell And Molecular Biology 2004, 31: s1-s81. PMID: 15269003, DOI: 10.1165/rcmb.2004-0071su.Peer-Reviewed Original Research