2023
A statistical framework to identify cell types whose genetically regulated proportions are associated with complex diseases
Liu W, Deng W, Chen M, Dong Z, Zhu B, Yu Z, Tang D, Sauler M, Lin C, Wain L, Cho M, Kaminski N, Zhao H. A statistical framework to identify cell types whose genetically regulated proportions are associated with complex diseases. PLOS Genetics 2023, 19: e1010825. PMID: 37523391, PMCID: PMC10414598, DOI: 10.1371/journal.pgen.1010825.Peer-Reviewed Original ResearchMeSH KeywordsBreast NeoplasmsFemaleGene Expression ProfilingGenetic Predisposition to DiseaseGenome-Wide Association StudyHumansLungPolymorphism, Single NucleotidePulmonary Disease, Chronic ObstructiveConceptsCell typesDisease-associated tissuesWide association studyComplex diseasesCell type proportionsDisease-relevant tissuesReal GWAS dataFunctional genesTranscriptomic dataGWAS dataGenetic dataAssociation studiesNovel statistical frameworkChronic obstructive pulmonary diseaseStatistical frameworkObstructive pulmonary diseaseIdiopathic pulmonary fibrosisBreast cancer riskType proportionsBlood CD8Pulmonary diseasePulmonary fibrosisPredictive biomarkersLung tissueBreast cancer
2020
Genetic determinants of ammonia-induced acute lung injury in mice
Bein K, Ganguly K, Martin TM, Concel VJ, Brant KA, Di YPP, Upadhyay S, Fabisiak JP, Vuga LJ, Kaminski N, Kostem E, Eskin E, Prows DR, Jang AS, Leikauf GD. Genetic determinants of ammonia-induced acute lung injury in mice. American Journal Of Physiology - Lung Cellular And Molecular Physiology 2020, 320: l41-l62. PMID: 33050709, PMCID: PMC7847062, DOI: 10.1152/ajplung.00276.2020.Peer-Reviewed Original ResearchConceptsSNP associationsWide association mappingGenetic determinantsSignificant SNP associationsAcute lung injuryIntegrative functional approachAssociation mappingMolecular functionsTranscriptomic analysisCandidate genesFunctional domainsNonsynonymous SNPsPromoter regionLung injuryDiverse panelGenesSNPsMouse strainsPathophysiological roleAATFInjuryProteinLAMA3ExpressionAssemblyGenetic analyses identify GSDMB associated with asthma severity, exacerbations, and antiviral pathways
Li X, Christenson SA, Modena B, Li H, Busse WW, Castro M, Denlinger LC, Erzurum SC, Fahy JV, Gaston B, Hastie AT, Israel E, Jarjour NN, Levy BD, Moore WC, Woodruff PG, Kaminski N, Wenzel SE, Bleecker ER, Meyers DA, Program N. Genetic analyses identify GSDMB associated with asthma severity, exacerbations, and antiviral pathways. Journal Of Allergy And Clinical Immunology 2020, 147: 894-909. PMID: 32795586, PMCID: PMC7876167, DOI: 10.1016/j.jaci.2020.07.030.Peer-Reviewed Original ResearchConceptsExpression quantitative trait loci (eQTL) analysisQuantitative trait locus (QTL) analysisSingle nucleotide polymorphismsGasdermin BMultiple single nucleotide polymorphismsFunctional genesExpression levelsLocus analysisAntiviral pathwaysGenes/single-nucleotide polymorphismsWhole genome sequencesGene expression dataEpithelial cellsImmune system pathwaysHigh expression levelsHuman bronchial epithelial cellsIFN regulatory factorGPI attachmentGSDMB expressionAsthma susceptibilityGenetic analysisGene expressionPathway analysisBronchial epithelial cellsRegulatory factors
2016
Expression of asthma susceptibility genes in bronchial epithelial cells and bronchial alveolar lavage in the Severe Asthma Research Program (SARP) cohort
Li X, Hawkins GA, Moore WC, Hastie AT, Ampleford EJ, Milosevic J, Li H, Busse WW, Erzurum SC, Kaminski N, Wenzel SE, Bleecker ER, Meyers DA. Expression of asthma susceptibility genes in bronchial epithelial cells and bronchial alveolar lavage in the Severe Asthma Research Program (SARP) cohort. Journal Of Asthma 2016, 53: 775-782. PMID: 27050946, PMCID: PMC5137190, DOI: 10.3109/02770903.2016.1158268.Peer-Reviewed Original Research
2015
Solving the Conundrum: Immunogenetics of Sarcoidosis
Kaminski N, Drake WP. Solving the Conundrum: Immunogenetics of Sarcoidosis. American Journal Of Respiratory And Critical Care Medicine 2015, 192: 652-654. PMID: 26371809, PMCID: PMC4595685, DOI: 10.1164/rccm.201506-1235ed.Peer-Reviewed Original ResearchFemaleGenetic Predisposition to DiseaseGenome-Wide Association StudyHumansMalePolymorphism, Single NucleotideSarcoidosiseQTL 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
2013
Idiopathic Pulmonary Fibrosis: Time to Get Personal?
Noth I, Kaminski N. Idiopathic Pulmonary Fibrosis: Time to Get Personal? American Journal Of Respiratory And Critical Care Medicine 2013, 188: 1392-1394. PMID: 24328772, PMCID: PMC3917381, DOI: 10.1164/rccm.201311-1956ed.Peer-Reviewed Original ResearchAnimalsDisease ProgressionFemaleHumansIdiopathic Pulmonary FibrosisMalePolymorphism, Single NucleotideToll-Like Receptor 3Functional Genomic Assessment of Phosgene-Induced Acute Lung Injury in Mice
Leikauf GD, Concel VJ, Bein K, Liu P, Berndt A, Martin TM, Ganguly K, Jang AS, Brant KA, Dopico RA, Upadhyay S, Cario C, Di YP, Vuga LJ, Kostem E, Eskin E, You M, Kaminski N, Prows DR, Knoell DL, Fabisiak JP. Functional Genomic Assessment of Phosgene-Induced Acute Lung Injury in Mice. American Journal Of Respiratory Cell And Molecular Biology 2013, 49: 130522202035005. PMID: 23590305, PMCID: PMC3824050, DOI: 10.1165/rcmb.2012-0337oc.Peer-Reviewed Original ResearchMeSH KeywordsAcute Lung InjuryAllelesAnimalsChemical Warfare AgentsChromosome MappingElectrophoretic Mobility Shift AssayFemaleGene ExpressionGene Expression ProfilingGenomeGenome-Wide Association StudyGenomicsGenotypeIntegrinsLungMiceMice, Inbred StrainsOligonucleotide Array Sequence AnalysisPhosgenePolymorphism, Single NucleotidePromoter Regions, GeneticReelin ProteinSodium-Potassium-Exchanging ATPaseConceptsSignificant SNP associationsSNP associationsTranscriptomic analysisCompetitive electrophoretic mobility shift analysisGenome-wide association mappingFunctional genomic assessmentPutative transcription factorElectrophoretic mobility shift analysisMobility shift analysisAssociation mappingGenetic resolutionTranscription factorsCandidate genesFunctional domainsNonsynonymous SNPsGenomic assessmentPhenotypic differencesPhenotypic extremesDiverse panelGenesGenetic determinantsShift analysisPTPRTAllelesITGA9Genome-wide association study identifies multiple susceptibility loci for pulmonary fibrosis
Fingerlin TE, Murphy E, Zhang W, Peljto AL, Brown KK, Steele MP, Loyd JE, Cosgrove GP, Lynch D, Groshong S, Collard HR, Wolters PJ, Bradford WZ, Kossen K, Seiwert SD, du Bois RM, Garcia CK, Devine MS, Gudmundsson G, Isaksson HJ, Kaminski N, Zhang Y, Gibson KF, Lancaster LH, Cogan JD, Mason WR, Maher TM, Molyneaux PL, Wells AU, Moffatt MF, Selman M, Pardo A, Kim DS, Crapo JD, Make BJ, Regan EA, Walek DS, Daniel JJ, Kamatani Y, Zelenika D, Smith K, McKean D, Pedersen BS, Talbert J, Kidd RN, Markin CR, Beckman KB, Lathrop M, Schwarz MI, Schwartz DA. Genome-wide association study identifies multiple susceptibility loci for pulmonary fibrosis. Nature Genetics 2013, 45: 613-620. PMID: 23583980, PMCID: PMC3677861, DOI: 10.1038/ng.2609.Peer-Reviewed Original Research
2012
Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density
Coronnello C, Hartmaier R, Arora A, Huleihel L, Pandit KV, Bais AS, Butterworth M, Kaminski N, Stormo GD, Oesterreich S, Benos PV. Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density. PLOS Computational Biology 2012, 8: e1002830. PMID: 23284279, PMCID: PMC3527281, DOI: 10.1371/journal.pcbi.1002830.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAnimalsBone DensityDrosophilaHumansMicroRNAsModels, TheoreticalPolymorphism, Single NucleotidePersonalized medicine: applying omics to lung fibrosis
Herazo-Maya JD, Kaminski N. Personalized medicine: applying omics to lung fibrosis. Biomarkers In Medicine 2012, 6: 529-540. PMID: 22917154, PMCID: PMC3517740, DOI: 10.2217/bmm.12.38.Peer-Reviewed Original ResearchMeSH KeywordsBlood ProteinsDisease SusceptibilityGenomicsHumansMatrix Metalloproteinase 7Polymorphism, Single NucleotidePrecision MedicinePulmonary FibrosisTomography Scanners, X-Ray ComputedTumor Suppressor ProteinsConceptsIdiopathic pulmonary fibrosisFibrotic lung diseaseLung transplantPulmonary fibrosisLung fibrosisLung diseaseUnknown etiologyChronic diseasesSporadic formsHigh mortalityPatient careTreatment of diseasesDrug studiesCost-effective strategyDiseaseFibrosisDiagnosisPersonalized medicinePatientsTransplantEtiologyTherapyMortalityCarePreventionIntegrative Assessment of Chlorine-Induced Acute Lung Injury in Mice
Leikauf GD, Pope-Varsalona H, Concel VJ, Liu P, Bein K, Berndt A, Martin TM, Ganguly K, Jang AS, Brant KA, Dopico RA, Upadhyay S, Di YP, Li Q, Hu Z, Vuga LJ, Medvedovic M, Kaminski N, You M, Alexander DC, McDunn JE, Prows DR, Knoell DL, Fabisiak JP. Integrative Assessment of Chlorine-Induced Acute Lung Injury in Mice. American Journal Of Respiratory Cell And Molecular Biology 2012, 47: 234-244. PMID: 22447970, PMCID: PMC3423464, DOI: 10.1165/rcmb.2012-0026oc.Peer-Reviewed Original ResearchConceptsCandidate genesGenetic basisProtein catabolic processAcute lung injuryLung injuryHaplotype association mappingC57BLKS/JSingle nucleotide polymorphism associationsAssociation mappingMetabolomic profilingProtein transportCatabolic processTranscript levelsHaplotype mappingChromosome 1Chlorine-induced acute lung injuryAmino acid carrierSNP associationsReal-time PCRGenesGenetic associationMean survival timeRecognition sitesProfilingPromoter SNPs
2011
A Variant in the Promoter of MUC5B and Idiopathic Pulmonary Fibrosis
Zhang Y, Noth I, Garcia JG, Kaminski N. A Variant in the Promoter of MUC5B and Idiopathic Pulmonary Fibrosis. New England Journal Of Medicine 2011, 364: 1576-1577. PMID: 21506748, PMCID: PMC4327944, DOI: 10.1056/nejmc1013504.Peer-Reviewed Original ResearchMeSH KeywordsAgedCase-Control StudiesFemaleHumansIdiopathic Pulmonary FibrosisMaleMiddle AgedMucin-5BPolymorphism, Single NucleotideHaplotype Association Mapping of Acute Lung Injury in Mice Implicates Activin A Receptor, Type 1
Leikauf GD, Concel VJ, Liu P, Bein K, Berndt A, Ganguly K, Jang AS, Brant KA, Dietsch M, Pope-Varsalona H, Dopico RA, Di YP, Li Q, Vuga LJ, Medvedovic M, Kaminski N, You M, Prows DR. Haplotype Association Mapping of Acute Lung Injury in Mice Implicates Activin A Receptor, Type 1. American Journal Of Respiratory And Critical Care Medicine 2011, 183: 1499-1509. PMID: 21297076, PMCID: PMC3137140, DOI: 10.1164/rccm.201006-0912oc.Peer-Reviewed Original ResearchMeSH KeywordsAcroleinActivin Receptors, Type IAcute Lung InjuryAnimalsDisease Models, AnimalFemaleHaplotypesMiceMice, Inbred APolymorphism, Single NucleotideProtein Array AnalysisConceptsDNA-protein bindingHaplotype association mappingSingle nucleotide polymorphism associationsAssociation mappingSNP associationsGenome-wide strategiesPrevious genetic analysisAcute lung injuryAmino acid substitutionsGenomic approachesLung injuryTranscription factorsCell signalingEnriched pathwaysCandidate genesSequence differencesChromosome 1Genetic analysisAssociated variantsAcid substitutionsActivin A receptorsGenesFunctional consequencesPolymorphism associationPolar strains