2020
Retrograde signaling by a mtDNA-encoded non-coding RNA preserves mitochondrial bioenergetics
Blumental-Perry A, Jobava R, Bederman I, Degar A, Kenche H, Guan B, Pandit K, Perry N, Molyneaux N, Wu J, Prendergas E, Ye Z, Zhang J, Nelson C, Ahangari F, Krokowski D, Guttentag S, Linden P, Townsend D, Miron A, Kang M, Kaminski N, Perry Y, Hatzoglou M. Retrograde signaling by a mtDNA-encoded non-coding RNA preserves mitochondrial bioenergetics. Communications Biology 2020, 3: 626. PMID: 33127975, PMCID: PMC7603330, DOI: 10.1038/s42003-020-01322-4.Peer-Reviewed Original ResearchConceptsMitochondrial genomeNuclear-encoded genesCell type-specific mannerNon-coding RNASteady-state transcriptionMitochondrial energy metabolismControl regionPositive regulationMitochondrial bioenergeticsMitochondria stressMitochondrial functionSpecific mannerAlveolar epithelial type II cellsEnergy metabolismType II cellsEpithelial type II cellsGenomePhysiological stressRNAII cellsCellsMouse lungTranscriptionGenesMitochondria
2018
Spatial distribution of marker gene activity in the mouse lung during alveolarization
Ljungberg MC, Sadi M, Wang Y, Aronow BJ, Xu Y, Kao RJ, Liu Y, Gaddis N, Ardini-Poleske ME, Umrod T, Ambalavanan N, Nicola T, Kaminski N, Ahangari F, Sontag R, Corley RA, Ansong C, Carson JP. Spatial distribution of marker gene activity in the mouse lung during alveolarization. Data In Brief 2018, 22: 365-372. PMID: 30596133, PMCID: PMC6307338, DOI: 10.1016/j.dib.2018.10.150.Peer-Reviewed Original ResearchRNA-seq expression profilesMarker gene activityGene expression patternsLung developmentLung Development ProgramGene activityRNA-seqMolecular atlasCellular differentiationDifferent genesExpression patternsExpression profilesNormal lung developmentMouse lungMRNA transcriptsMammalian lungMRNA probesProbe sequencesAbnormal lung developmentCurated CollectionGenesSpatial distributionTranscriptsE16.5E18.5
2011
Integrative metabolome and transcriptome profiling reveals discordant energetic stress between mouse strains with differential sensitivity to acrolein‐induced acute lung injury
Fabisiak JP, Medvedovic M, Alexander DC, McDunn JE, Concel VJ, Bein K, Jang AS, Berndt A, Vuga LJ, Brant KA, Pope‐Varsalona H, Dopico RA, Ganguly K, Upadhyay S, Li Q, Hu Z, Kaminski N, Leikauf GD. Integrative metabolome and transcriptome profiling reveals discordant energetic stress between mouse strains with differential sensitivity to acrolein‐induced acute lung injury. Molecular Nutrition & Food Research 2011, 55: 1423-1434. PMID: 21823223, PMCID: PMC3482455, DOI: 10.1002/mnfr.201100291.Peer-Reviewed Original ResearchConceptsAcute lung injuryLung injuryAcrolein exposureMouse lungMouse strainsJ mouse lungEnvironmental tobacco smokeChain amino acid metabolismFatty acid β-oxidationLung metabolomeJ miceSM/J miceTobacco smokeAcrolein treatmentRespiratory irritantsAmino acid metabolismLungEnergetic stressInjuryAcid metabolismSM/JΒ-oxidationMiceIntegrative metabolomeHealth hazards
2008
Oxidative Stress Alters Syndecan-1 Distribution in Lungs with Pulmonary Fibrosis*
Kliment CR, Englert JM, Gochuico BR, Yu G, Kaminski N, Rosas I, Oury TD. Oxidative Stress Alters Syndecan-1 Distribution in Lungs with Pulmonary Fibrosis*. Journal Of Biological Chemistry 2008, 284: 3537-3545. PMID: 19073610, PMCID: PMC2635035, DOI: 10.1074/jbc.m807001200.Peer-Reviewed Original ResearchConceptsIdiopathic pulmonary fibrosisPulmonary fibrosisLavage fluidNeutrophil chemotaxisSyndecan-1EC-SODSyndecan-1 ectodomainWound healingMouse lungNull miceWestern blotOxidative stressInterstitial lung diseaseBronchoalveolar lavage fluidShed syndecan-1Aberrant wound healingAlveolar epithelial cellsHuman lung samplesHuman syndecan-1Extracellular superoxide dismutaseEpithelial wound healingIPF lungsProgressive fibrosisLung fibrosisAlveolar epithelial wound healing
2006
Gene expression profiling of target genes in ventilator-induced lung injury
Dolinay T, Kaminski N, Felgendreher M, Kim HP, Reynolds P, Watkins SC, Karp D, Uhlig S, Choi AM. Gene expression profiling of target genes in ventilator-induced lung injury. Physiological Genomics 2006, 26: 68-75. PMID: 16569776, DOI: 10.1152/physiolgenomics.00110.2005.Peer-Reviewed Original ResearchMeSH KeywordsA Kinase Anchor ProteinsAmphiregulinAnimalsCell Cycle ProteinsCluster AnalysisCysteine-Rich Protein 61DNA-Binding ProteinsEGF Family of ProteinsGene Expression ProfilingGene Expression RegulationGlycoproteinsImmediate-Early ProteinsImmunohistochemistryIntercellular Signaling Peptides and ProteinsInterleukin-11LipopolysaccharidesLungLung InjuryMaleMiceMice, Inbred BALB CNuclear Receptor Subfamily 4, Group A, Member 1Oligonucleotide Array Sequence AnalysisReceptors, Cytoplasmic and NuclearReceptors, SteroidReproducibility of ResultsRespiration, ArtificialRNA, MessengerTranscription FactorsConceptsVentilator-induced lung injuryLung injuryAcute respiratory distress syndromeHigh-pressure mechanical ventilationRespiratory distress syndromeHigh-pressure ventilationLow-pressure ventilationClassical inflammatory pathwaysGrowth factor-related genesDistress syndromeMechanical ventilationInflammatory pathwaysLPS treatmentInflammatory responseReal-time PCRMouse lungGene expression profilingProtein expressionImmunoblotting assaysMRNA expression patternsVentilationOverventilationLungNovel candidate genesInjury