2023
Examination of eQTL Polymorphisms Associated with Increased Risk of Progressive Complicated Sarcoidosis in European and African Descent Subjects.
Casanova N, Camp S, Gonzalez-Garay M, Batai K, Garman L, Montgomery C, Ellis N, Kittles R, Bime C, Hsu A, Holland S, Lussier Y, Karnes J, Sweiss N, Maier L, Koth L, Moller D, Kaminski N, Garcia J. Examination of eQTL Polymorphisms Associated with Increased Risk of Progressive Complicated Sarcoidosis in European and African Descent Subjects. European Journal Of Respiratory Medicine 2023, 5: 359-371. PMID: 38390497, PMCID: PMC10883688, DOI: 10.31488/ejrm.137.Peer-Reviewed Original ResearchExpression quantitative trait lociGenome-wide association studiesEQTL SNPsGenome-wide association study cohortsInnate immunityQuantitative trait lociAllograft rejection pathwayGWAS SNPsIndependent sarcoidosis cohortTrait lociAssociation studiesGenetic basisComplicated sarcoidosisSNPsHLA regionAfrican AmericansSarcoidosis riskSeverity of sarcoidosisGranulomatous inflammatory diseaseMHC class IISystemic granulomatous inflammatory diseaseEuropean AmericansSarcoidosis cohortVariants/genesPool
2015
eQTL of bronchial epithelial cells and bronchial alveolar lavage deciphers GWAS‐identified asthma genes
Li X, Hastie AT, Hawkins GA, Moore WC, Ampleford EJ, Milosevic J, Li H, Busse WW, Erzurum SC, Kaminski N, Wenzel SE, Meyers DA, Bleecker ER. eQTL of bronchial epithelial cells and bronchial alveolar lavage deciphers GWAS‐identified asthma genes. Allergy 2015, 70: 1309-1318. PMID: 26119467, PMCID: PMC4583797, DOI: 10.1111/all.12683.Peer-Reviewed Original ResearchMeSH KeywordsAllelesAsthmaBronchoalveolar Lavage FluidCase-Control StudiesChromosome MappingEpithelial CellsFemaleGenetic Association StudiesGenetic Predisposition to DiseaseGenome-Wide Association StudyHumansImmunoglobulin EMaleOrgan SpecificityPolymorphism, Single NucleotideQuantitative Trait LociRespiratory Function TestsRespiratory MucosaConceptsExpression quantitative trait lociGenome-wide association studiesSingle nucleotide polymorphismsAsthma genesQuantitative trait lociGenes/single-nucleotide polymorphismsCis-eQTL analysisFurther functional studiesDisease-relevant tissuesDecreased expressionTrait lociCausal genesTranscription analysisGene expressionPromoter regionAsthma-related genesAssociation studiesBronchial epithelial cellsProtein secretionGenesFunctional studiesNucleotide polymorphismsSpecific regulationExpression levelsExpression of IL33
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 interactionsTranscriptomeSecreted Phosphoprotein 1 Is a Determinant of Lung Function Development in Mice
Ganguly K, Martin TM, Concel VJ, Upadhyay S, Bein K, Brant KA, George L, Mitra A, Thimraj TA, Fabisiak JP, Vuga LJ, Fattman C, Kaminski N, Schulz H, Leikauf GD. Secreted Phosphoprotein 1 Is a Determinant of Lung Function Development in Mice. American Journal Of Respiratory Cell And Molecular Biology 2014, 51: 637-651. PMID: 24816281, PMCID: PMC4224082, DOI: 10.1165/rcmb.2013-0471oc.Peer-Reviewed Original ResearchMeSH KeywordsAlveolar Epithelial CellsAnimalsAnimals, NewbornCore Binding Factor Alpha 1 SubunitFemaleGene Expression Regulation, DevelopmentalLung ComplianceMaleMice, Inbred C3HMice, Inbred C57BLMice, KnockoutOligonucleotide Array Sequence AnalysisOsteopontinPromoter Regions, GeneticPulmonary AlveoliPulmonary Disease, Chronic ObstructiveReceptor, Notch1ConceptsMicroarray analysisPhosphoprotein 1Quantitative trait lociLung functionQuantitative RT-PCR analysisDNA-protein bindingRunt-related transcription factor 2Transcription factor 2Developmental transcriptsLung developmentTrait lociNumerous genesSecreted Phosphoprotein 1Notch1 transcriptsRT-PCR analysisInsulin-like growth factor-1C3H/HeJ miceDiminished lung functionLung function developmentSPP1 promoterSPP1Growth factor-1Mean airspace chord lengthC3H/HeJGenetic variants