2019
A Forward Chemical Genetic Screen Reveals Gut Microbiota Metabolites That Modulate Host Physiology
Chen H, Nwe PK, Yang Y, Rosen CE, Bielecka AA, Kuchroo M, Cline GW, Kruse AC, Ring AM, Crawford JM, Palm NW. A Forward Chemical Genetic Screen Reveals Gut Microbiota Metabolites That Modulate Host Physiology. Cell 2019, 177: 1217-1231.e18. PMID: 31006530, PMCID: PMC6536006, DOI: 10.1016/j.cell.2019.03.036.Peer-Reviewed Original ResearchConceptsHost physiologyBioactive microbial metabolitesHuman gut bacteriaHost sensingProlific producersG proteinsGut microbiota metabolitesBlood-brain barrierL-PheMicrobial metabolitesOrphan GPCRsGut bacteriaColonic motilityInhibitor administrationMicrobiota metabolitesIntestinal microbiotaSmall moleculesDietary histidineBacteriaPhysiologyMicrobiota metabolomeMetabolitesGPR97Orthogonal approachGPCRs
2013
Genome-Wide Association Study and Gene Expression Analysis Identifies CD84 as a Predictor of Response to Etanercept Therapy in Rheumatoid Arthritis
Cui J, Stahl EA, Saevarsdottir S, Miceli C, Diogo D, Trynka G, Raj T, Mirkov MU, Canhao H, Ikari K, Terao C, Okada Y, Wedrén S, Askling J, Yamanaka H, Momohara S, Taniguchi A, Ohmura K, Matsuda F, Mimori T, Gupta N, Kuchroo M, Morgan AW, Isaacs JD, Wilson AG, Hyrich KL, Herenius M, Doorenspleet ME, Tak PP, Crusius JB, van der Horst-Bruinsma IE, Wolbink GJ, van Riel PL, van de Laar M, Guchelaar HJ, Shadick NA, Allaart CF, Huizinga TW, Toes RE, Kimberly RP, Bridges SL, Criswell LA, Moreland LW, Fonseca JE, de Vries N, Stranger BE, De Jager PL, Raychaudhuri S, Weinblatt ME, Gregersen PK, Mariette X, Barton A, Padyukov L, Coenen MJ, Karlson EW, Plenge RM. Genome-Wide Association Study and Gene Expression Analysis Identifies CD84 as a Predictor of Response to Etanercept Therapy in Rheumatoid Arthritis. PLOS Genetics 2013, 9: e1003394. PMID: 23555300, PMCID: PMC3610685, DOI: 10.1371/journal.pgen.1003394.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAllelesAntigens, CDAntirheumatic AgentsArthritis, RheumatoidAsian PeopleBiomarkers, PharmacologicalEtanerceptFemaleGene Expression RegulationGenome-Wide Association StudyHumansImmunoglobulin GMaleMiddle AgedPolymorphism, Single NucleotideReceptors, Tumor Necrosis FactorSignaling Lymphocytic Activation Molecule FamilyTumor Necrosis Factor-alphaWhite PeopleConceptsGenome-wide association studiesGene expressionAssociation studiesAnti-TNF therapyRA patientsRheumatoid arthritisNon-significant trendGene expression dataEtanercept therapySite motifTranscription factorsImmune-related genesPeripheral blood mononuclear cellsExpression dataAnti-TNF medicationsDisease Activity ScoreBlood mononuclear cellsPredictors of responseCD84 expressionCommon variantsCD84European ancestryDisease activityBiologic therapyRefractory casesCommon Risk Alleles for Inflammatory Diseases Are Targets of Recent Positive Selection
Raj T, Kuchroo M, Replogle JM, Raychaudhuri S, Stranger BE, De Jager PL. Common Risk Alleles for Inflammatory Diseases Are Targets of Recent Positive Selection. American Journal Of Human Genetics 2013, 92: 517-529. PMID: 23522783, PMCID: PMC3617371, DOI: 10.1016/j.ajhg.2013.03.001.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesProtein-protein interaction networkRecent positive selectionPositive selectionInteraction networksExpression quantitative trait loci (eQTL) mapping studiesSelective pressureQuantitative trait locus (QTL) mapping studiesRecent positive natural selectionHundreds of lociPositive natural selectionFunctional genomics dataCis-regulatory effectsInflammatory disease susceptibilityHost resistanceSignificant selective pressureCommon risk allelesEvolutionary forcesMolecular functionsAssociated lociNatural selectionGenetic variationGenomic signaturesGenomic dataGene expression
2012
An RNA Profile Identifies Two Subsets of Multiple Sclerosis Patients Differing in Disease Activity
Ottoboni L, Keenan BT, Tamayo P, Kuchroo M, Mesirov JP, Buckle GJ, Khoury SJ, Hafler DA, Weiner HL, De Jager PL. An RNA Profile Identifies Two Subsets of Multiple Sclerosis Patients Differing in Disease Activity. Science Translational Medicine 2012, 4: 153ra131. PMID: 23019656, PMCID: PMC3753678, DOI: 10.1126/scitranslmed.3004186.Peer-Reviewed Original ResearchConceptsGlatiramer acetateDisease activityPatient populationFirst-line disease-modifying treatmentsMultiple sclerosis (MS) patient populationPeripheral blood mononuclear cellsMS patient populationDisease-modifying treatmentsMultiple sclerosis patientsBlood mononuclear cellsSubset of subjectsDisease courseSclerosis patientsMS subjectsMononuclear cellsInflammatory eventsTreatment responseUntreated subjectsAdditional groupHigh expressionTranscriptional signatureSubjectsRNA profilesTreatmentTranscriptional profiles