2019
Integrating multiomics longitudinal data to reconstruct networks underlying lung development
Ding J, Ahangari F, Espinoza CR, Chhabra D, Nicola T, Yan X, Lal CV, Hagood JS, Kaminski N, Bar-Joseph Z, Ambalavanan N. Integrating multiomics longitudinal data to reconstruct networks underlying lung development. American Journal Of Physiology - Lung Cellular And Molecular Physiology 2019, 317: l556-l568. PMID: 31432713, PMCID: PMC6879899, DOI: 10.1152/ajplung.00554.2018.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAnimals, NewbornChildChild, PreschoolDNA MethylationEpigenesis, GeneticFemaleGene Expression ProfilingGene Expression Regulation, DevelopmentalGene Regulatory NetworksHigh-Throughput Nucleotide SequencingHumansImmunity, InnateInfantInfant, NewbornLungMaleMiceMice, Inbred C57BLMicroRNAsOrganogenesisProteomicsPulmonary AlveoliRNA, MessengerSingle-Cell AnalysisTranscriptomeConceptsSingle-cell RNA-seq dataLung developmentDynamic regulatory networksOmics data setsRNA-seq dataIndividual cell typesHuman lung developmentRegulatory networksDNA methylationLaser capture microdissectionEpigenetic changesExpression trajectoriesKey pathwaysCell typesActive pathwaysCapture microdissectionRegulatorKey eventsInnate immunityNew insightsSpecific key eventsPathwayComprehensive understandingProteomicsMethylation
2015
Alterations in Gene Expression and DNA Methylation during Murine and Human Lung Alveolar Septation
Cuna A, Halloran B, Faye-Petersen O, Kelly D, Crossman DK, Cui X, Pandit K, Kaminski N, Bhattacharya S, Ahmad A, Mariani TJ, Ambalavanan N. Alterations in Gene Expression and DNA Methylation during Murine and Human Lung Alveolar Septation. American Journal Of Respiratory Cell And Molecular Biology 2015, 53: 60-73. PMID: 25387348, PMCID: PMC4566107, DOI: 10.1165/rcmb.2014-0160oc.Peer-Reviewed Original ResearchConceptsDNA methylationNormal septationGene expressionGenome-wide DNA methylation dataMajor epigenetic mechanismsLung developmentNumber of genesMouse lung developmentGene of interestDNA methylation dataGene expression dataMicroarray gene expression dataAlveolar septationCoordinated expressionEpigenetic mechanismsMethylated DNAMultiple genesMicroarray analysisMethylation dataExpression dataGenesMethylationExtracellular matrixAltered expressionAntioxidant defenseEpigenetics 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 ResearchMeSH KeywordsAnimalsDNA MethylationEpigenesis, GeneticFibrosisHumansIdiopathic Pulmonary FibrosisLung DiseasesMiceRNA, Long NoncodingConceptsIdiopathic 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
Relationship of DNA Methylation and Gene Expression in Idiopathic Pulmonary Fibrosis
Yang IV, Pedersen BS, Rabinovich E, Hennessy CE, Davidson EJ, Murphy E, Guardela BJ, Tedrow JR, Zhang Y, Singh MK, Correll M, Schwarz MI, Geraci M, Sciurba FC, Quackenbush J, Spira A, Kaminski N, Schwartz DA. Relationship of DNA Methylation and Gene Expression in Idiopathic Pulmonary Fibrosis. American Journal Of Respiratory And Critical Care Medicine 2014, 190: 1263-1272. PMID: 25333685, PMCID: PMC4315819, DOI: 10.1164/rccm.201408-1452oc.Peer-Reviewed Original ResearchConceptsGene expressionDNA methylationMethylation marksMethylation changesQuantitative trait lociTrans-gene expressionIntegrative genomic analysisTrait lociEpigenetic mechanismsTranscriptional changesGenomic analysisTranscription factorsCASZ1 expressionTarget genesFunctional validationExpression relationshipsMethylationGenesDMRsExpressionEnvironmental factorsTargeted analysisPathogenesis of IPFComplex interactionsTranscriptome
2012
Global 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
2011
Evolving Genomic Approaches to Idiopathic Pulmonary Fibrosis: Moving Beyond Genes
Kass DJ, Kaminski N. Evolving Genomic Approaches to Idiopathic Pulmonary Fibrosis: Moving Beyond Genes. Clinical And Translational Science 2011, 4: 372-379. PMID: 22029812, PMCID: PMC3229869, DOI: 10.1111/j.1752-8062.2011.00287.x.Peer-Reviewed Original ResearchMeSH KeywordsEpigenesis, GeneticGenesGenomicsHumansIdiopathic Pulmonary FibrosisNational Institutes of Health (U.S.)United StatesConceptsGenomic technologiesIdiopathic pulmonary fibrosisPathogenesis of diseaseGenomic discoveriesSystems biology approachGene expression profilingContribution of microRNAsMost human diseasesGenomic approachesGene networksBiology approachHuman genomeEpigenetic researchGenomic dataExpression profilingHuman diseasesPulmonary fibrosisDiagnosis of IPFGenesLarge collaborative studiesProgressive scarringPeripheral bloodClinical severityLung parenchymaTherapeutic goals