2021
Inflamed Ulcerative Colitis Regions Associated With MRGPRX2-Mediated Mast Cell Degranulation and Cell Activation Modules, Defining a New Therapeutic Target
Chen E, Chuang LS, Giri M, Villaverde N, Hsu NY, Sabic K, Joshowitz S, Gettler K, Nayar S, Chai Z, Alter IL, Chasteau CC, Korie UM, Dzedzik S, Thin TH, Jain A, Moscati A, Bongers G, Duerr RH, Silverberg MS, Brant SR, Rioux JD, Peter I, Schumm LP, Haritunians T, McGovern DP, Itan Y, Cho JH. Inflamed Ulcerative Colitis Regions Associated With MRGPRX2-Mediated Mast Cell Degranulation and Cell Activation Modules, Defining a New Therapeutic Target. Gastroenterology 2021, 160: 1709-1724. PMID: 33421512, PMCID: PMC8494017, DOI: 10.1053/j.gastro.2020.12.076.Peer-Reviewed Original ResearchMeSH KeywordsAdrenomedullinAnimalsbeta-Arrestin 2Case-Control StudiesCell DegranulationCHO CellsColitis, UlcerativeColonCricetulusExtracellular Signal-Regulated MAP KinasesGenetic VariationHumansInositol PhosphatesLigandsMast CellsNerve Tissue ProteinsPhosphorylationReceptors, G-Protein-CoupledReceptors, NeuropeptideConceptsExtracellular signal-regulated kinaseSignal-regulated kinaseRNA sequencingArrestin recruitmentChinese hamster ovarySingle-cell RNA sequencingNew therapeutic targetsBulk RNA sequencingMast cell gene expressionCell gene expressionHuman ulcerative colitisKey upstream regulatorUlcerative colitisMast cell activationIP-1 accumulationSingle nucleotide polymorphismsTherapeutic targetCell activationCell-specific mediatorsUpstream regulatorGene expressionGenotype-dependent effectsG proteinsMast cellsIgE-independent mast cell activation
2019
BAL Cell Gene Expression in Severe Asthma Reveals Mechanisms of Severe Disease and Influences of Medications
Weathington N, O’Brien M, Radder J, Whisenant TC, Bleecker ER, Busse WW, Erzurum SC, Gaston B, Hastie A, Jarjour N, Meyers D, Milosevic J, Moore W, Tedrow J, Trudeau J, Wong H, Wu W, Kaminski N, Wenzel S, Modena B. BAL Cell Gene Expression in Severe Asthma Reveals Mechanisms of Severe Disease and Influences of Medications. American Journal Of Respiratory And Critical Care Medicine 2019, 200: 837-856. PMID: 31161938, PMCID: PMC6812436, DOI: 10.1164/rccm.201811-2221oc.Peer-Reviewed Original ResearchMeSH KeywordsAdrenergic beta-AgonistsAdultAsthmaBronchoalveolar Lavage FluidCase-Control StudiesCyclic AMPEosinophilsEpithelial CellsFemaleGene ExpressionHumansIn Vitro TechniquesLymphocytesMacrophages, AlveolarMaleNeutrophilsSequence Analysis, RNASeverity of Illness IndexSignal TransductionTHP-1 CellsConceptsCell gene expressionGene expressionAirway epithelial cell gene expressionEpithelial cell gene expressionGlobal gene expressionCellular gene expressionCell expression profilesAsthma susceptibility lociProtein levelsSystem-wide analysisExpression networksImportant disease mechanismCoexpression networkCellular milieuExpression changesExpression profilesSusceptibility lociCellular modelDisease mechanismsBiomolecular mechanismsNew targetsRobust upregulationSample traitsGenesExpressionPolycomb Repressive Complex 1 Controls Maintenance of Fungiform Papillae by Repressing Sonic Hedgehog Expression
Bar C, Cohen I, Zhao D, Pothula V, Litskevitch A, Koseki H, Zheng D, Ezhkova E. Polycomb Repressive Complex 1 Controls Maintenance of Fungiform Papillae by Repressing Sonic Hedgehog Expression. Cell Reports 2019, 28: 257-266.e5. PMID: 31269445, PMCID: PMC6921245, DOI: 10.1016/j.celrep.2019.06.011.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBody PatterningCell CycleChromatin ImmunoprecipitationChromatin Immunoprecipitation SequencingCyclin-Dependent Kinase Inhibitor p16Epigenesis, GeneticEpitheliumGene Expression Regulation, DevelopmentalGene OntologyHedgehog ProteinsMiceMice, KnockoutMicroscopy, Electron, ScanningPolycomb Repressive Complex 1Polycomb Repressive Complex 2RNA-SeqSignal TransductionTaste BudsTongueConceptsGene expressionPolycomb Repressive Complex 1Spatial gene expression patternsRepressive Complex 1Gene expression patternsCell gene expressionChromatin regulatorsTissue patterningSonic hedgehog expressionEpigenetic regulationNiche structureExpression patternsCell genesEpithelial progenitorsHedgehog expressionShhEctopic ShhTaste cellsPapilla structuresTissue patternsExpressionCellsPatterningProper maintenanceComplexes 1BAL Cell Gene Expression Is Indicative of Outcome and Airway Basal Cell Involvement in Idiopathic Pulmonary Fibrosis
Prasse A, Binder H, Schupp JC, Kayser G, Bargagli E, Jaeger B, Hess M, Rittinghausen S, Vuga L, Lynn H, Violette S, Jung B, Quast K, Vanaudenaerde B, Xu Y, Hohlfeld JM, Krug N, Herazo-Maya JD, Rottoli P, Wuyts WA, Kaminski N. BAL Cell Gene Expression Is Indicative of Outcome and Airway Basal Cell Involvement in Idiopathic Pulmonary Fibrosis. American Journal Of Respiratory And Critical Care Medicine 2019, 199: 622-630. PMID: 30141961, PMCID: PMC6396865, DOI: 10.1164/rccm.201712-2551oc.Peer-Reviewed Original ResearchConceptsIdiopathic pulmonary fibrosisAirway basal cellsChronic obstructive pulmonary diseaseObstructive pulmonary diseasePulmonary diseaseBAL cellsBasal cellsPulmonary fibrosisControl subjectsCell gene expressionIndependent IPF cohortsNine-gene signatureIPF cohortDerivation cohortClinical parametersRetrospective studyUnivariate analysisUnpredictable courseCell involvementDiscovery cohortGene expressionHealthy volunteersCox modelStage IIIFatal disease
2017
Profiling gene expression of antimony response genes in Leishmania (Viannia) panamensis and infected macrophages and its relationship with drug susceptibility
Barrera MC, Rojas LJ, Weiss A, Fernandez O, McMahon-Pratt D, Saravia NG, Gomez MA. Profiling gene expression of antimony response genes in Leishmania (Viannia) panamensis and infected macrophages and its relationship with drug susceptibility. Acta Tropica 2017, 176: 355-363. PMID: 28843396, PMCID: PMC5633519, DOI: 10.1016/j.actatropica.2017.08.017.Peer-Reviewed Original ResearchConceptsLeishmania resistanceDrug susceptibilityDrug resistanceHost cell gene expressionClinical strainsCell gene expressionExpression of ABCA2THP-1 cellsPrimary human macrophagesLeishmania susceptibilityGene expressionAntimonial drugsCutaneous leishmaniasisInfected macrophagesLeishmania panamensisIntracellular amastigotesHuman macrophagesResistant strainsSusceptible parasitesAntimonialsIntracellular parasitesLeishmania speciesMacrophagesL. panamensisAQP-9
2016
Gene Expression Correlated with Severe Asthma Characteristics Reveals Heterogeneous Mechanisms of Severe Disease
Modena BD, Bleecker ER, Busse WW, Erzurum SC, Gaston BM, Jarjour NN, Meyers DA, Milosevic J, Tedrow JR, Wu W, Kaminski N, Wenzel SE. Gene Expression Correlated with Severe Asthma Characteristics Reveals Heterogeneous Mechanisms of Severe Disease. American Journal Of Respiratory And Critical Care Medicine 2016, 195: 1449-1463. PMID: 27984699, PMCID: PMC5470748, DOI: 10.1164/rccm.201607-1407oc.Peer-Reviewed Original ResearchConceptsWeighted gene coexpression network analysisGene coexpression network analysisCoexpression network analysisGene expressionBiological processesAirway epithelial cell gene expressionEpithelial cell gene expressionNetwork of genesGene expression networksGene network modulesAsthma susceptibility lociT2 gene expressionCell gene expressionGene expression studiesNeuronal functionEpithelial growthMultiple molecular mechanismsExpression networksT2 genesGene networksUnderlying biological processesHub genesExpression studiesBiological insightsNetwork analysisGG-06 Single cell gene expression studies in lupus patient monocytes reveal novel patterns reflecting disease activity, interferon, and medical treatment
Jin Z, Fan W, Jensen M, Dorschner J, Vsetecka D, Amin S, Makol A, Ernste F, Osborn T, Moder K, Chowdhary V, Niewold T. GG-06 Single cell gene expression studies in lupus patient monocytes reveal novel patterns reflecting disease activity, interferon, and medical treatment. Lupus Science & Medicine 2016, 3: a30. DOI: 10.1136/lupus-2016-000179.58.Peer-Reviewed Original ResearchNon-classical monocytesSLE patientsDisease activityClassical monocytesPatients' monocytesCell gene expressionAnti-dsDNA titersHigh disease activityHigher IFN scoresSLE patient groupAnti-inflammatory genesMonocyte gene expressionPrednisone useGene expressionMedication useClinical featuresInterferon signatureC3 complementIFN scorePatient groupImmunologic characteristicsUnsupervised hierarchical clusteringMedical treatmentPatientsSingle Cell Gene Expression Studies in Lupus Monocytes Reveal a Unique Antii-Inflammatory Non-Classical Monocyte Population Associated with Clinical Quiescence
Jin Z, Jensen M, Dorschner J, Vsetecka D, Amin S, Makol A, Ernste F, Osborn T, Moder K, Chowdhary V, Niewold T, Fan W. Single Cell Gene Expression Studies in Lupus Monocytes Reveal a Unique Antii-Inflammatory Non-Classical Monocyte Population Associated with Clinical Quiescence. Journal Of Investigative Medicine 2016, 64: 977-977. DOI: 10.1136/jim-2016-000120.138.Peer-Reviewed Original Research
2014
Gene Expression in Relation to Exhaled Nitric Oxide Identifies Novel Asthma Phenotypes with Unique Biomolecular Pathways
Modena BD, Tedrow JR, Milosevic J, Bleecker ER, Meyers DA, Wu W, Bar-Joseph Z, Erzurum SC, Gaston BM, Busse WW, Jarjour NN, Kaminski N, Wenzel SE. Gene Expression in Relation to Exhaled Nitric Oxide Identifies Novel Asthma Phenotypes with Unique Biomolecular Pathways. American Journal Of Respiratory And Critical Care Medicine 2014, 190: 1363-1372. PMID: 25338189, PMCID: PMC4294630, DOI: 10.1164/rccm.201406-1099oc.Peer-Reviewed Original ResearchConceptsEpithelial cell gene expressionCell gene expressionGene expressionAirway epithelial cell gene expressionGene expression patternsSevere Asthma Research ProgramActin cytoskeletonGene clusterGenomic studiesGene transcriptionGene pathwaysMolecular basisExpression patternsAsthma phenotypesWnt pathwayMicroarray platformGenesNovel pathwayPhenotypeBiomolecular pathwaysNeuronal functionPathwayUnadjusted p-valuesExpressionBiological characteristics
2013
Cumulus and granulosa cell markers of oocyte and embryo quality
Uyar A, Torrealday S, Seli E. Cumulus and granulosa cell markers of oocyte and embryo quality. Fertility And Sterility 2013, 99: 979-997. PMID: 23498999, PMCID: PMC3866131, DOI: 10.1016/j.fertnstert.2013.01.129.Peer-Reviewed Original ResearchConceptsQuantitative reverse transcriptase-polymerase chain reactionGranulosa cell gene expressionRelevant outcome parametersReverse transcriptase-polymerase chain reactionTranscriptase-polymerase chain reactionMural granulosa cellsGranulosa cell markersBiomarkers of oocyteClinical benefitOutcome parametersWhole genome expression profilingGranulosa cellsOocyte qualityEmbryo qualityCell markersFollicular cellsNoninvasive meansCell gene expressionGenome expression profilingChain reactionEmbryo competenceMultitude of studiesOocytesTranscriptomic profilingExpression profiling
2009
FOG-1 Requires NuRD to Promote Hematopoiesis and Maintain Lineage Fidelity within the Megakaryocytic–Erythroid Compartment.
Gregory G, Miccio A, Bersenev A, Wang Y, Hong W, Zhang Z, Poncz M, Tong W, Blobel G. FOG-1 Requires NuRD to Promote Hematopoiesis and Maintain Lineage Fidelity within the Megakaryocytic–Erythroid Compartment. Blood 2009, 114: 702. DOI: 10.1182/blood.v114.22.702.702.Peer-Reviewed Original ResearchMegakaryocyte-erythroid progenitorsMast cell gene expressionCell gene expressionFOG-1Mast cell genesGATA-1Gene expressionLineage fidelityErythroid cellsCell genesGenome-wide transcriptome analysisTranscription factor GATA-1Epigenetic silencing mechanismsWide transcriptome analysisCofactor FOG-1Mast cell-specific genesStage-specific rolesCell-specific genesNuRD complexNucleosome remodelingGATA factorsSilencing mechanismNuRDTranscriptome analysisHematopoietic development
2008
The GATA-1 Cofactor FOG-1 Recruits NuRD to Promote Normal Erythroid and Megakaryocyte Development and Maintain Lineage Fidelity by Restricting Mast Cell Gene Expression.
Gregory G, Wang Y, Hong W, Miccio A, Bersenev A, Yu X, Wang H, Choi J, Shelat S, Tong W, Poncz M, Blobel G. The GATA-1 Cofactor FOG-1 Recruits NuRD to Promote Normal Erythroid and Megakaryocyte Development and Maintain Lineage Fidelity by Restricting Mast Cell Gene Expression. Blood 2008, 112: 1373. DOI: 10.1182/blood.v112.11.1373.1373.Peer-Reviewed Original ResearchGATA-1/FOGFOG-1Megakaryocytic-erythroid progenitorsMast cell gene expressionCell gene expressionErythroid cellsGene expressionMegakaryocyte developmentCell lineagesLineage-specific transcription factorsLevel of GATA2Mast cell fateTissue-specific nuclear factorsGATA-1 activityCo-repressor complexCofactor FOG-1Mast cell genesMast cell-specific genesCell-specific genesGene expression patternsMast cell lineageMature erythroid cellsNucleosome remodelingCell fateGATA-1Interaction of Campylobacter jejuni with Host Cells
Watson R, Galán J. Interaction of Campylobacter jejuni with Host Cells. 2008, 287-296. DOI: 10.1128/9781555815554.ch16.Peer-Reviewed Original ResearchHost cellsBacterial internalizationCell biologyHost cell gene expressionVesicular trafficking pathwaysPowerful genetic toolsCell gene expressionEndocytic machineryTrafficking pathwaysStrong phenotypeGenetic toolsCampylobacter jejuniJejuni mutantsGene expressionIntestinal epithelial cellsMicrobial pathogensInnate immune responseNonphagocytic cellsOwn uptakeBacterial determinantsSpecific adaptationsIntracellular pathogensMutantsPathogenic bacteriaCell interactions
2005
Early Transcriptional Response of Human Neutrophils to Anaplasma phagocytophilum Infection
Sukumaran B, Carlyon JA, Cai JL, Berliner N, Fikrig E. Early Transcriptional Response of Human Neutrophils to Anaplasma phagocytophilum Infection. Infection And Immunity 2005, 73: 8089-8099. PMID: 16299303, PMCID: PMC1307096, DOI: 10.1128/iai.73.12.8089-8099.2005.Peer-Reviewed Original ResearchConceptsEarly transcriptional responseTranscriptional responseGene expressionHost cell gene expressionComprehensive DNA microarray analysisA. phagocytophilum infectionDNA microarray analysisObligate intracellular pathogensCell gene expressionCFLAR geneTNFSF10 geneA. phagocytophilum-infected neutrophilsCytoskeletal remodelingVesicular transportTranscriptional profilesHost pathwaysMicroarray analysisAntiapoptotic genesPromyelocytic cell lineDifferential expressionPhagocytophilum infectionHost cellsGenesHuman neutrophilsIntracellular pathogens
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