2024
Gene trajectory inference for single-cell data by optimal transport metrics
Qu R, Cheng X, Sefik E, Stanley III J, Landa B, Strino F, Platt S, Garritano J, Odell I, Coifman R, Flavell R, Myung P, Kluger Y. Gene trajectory inference for single-cell data by optimal transport metrics. Nature Biotechnology 2024, 43: 258-268. PMID: 38580861, PMCID: PMC11452571, DOI: 10.1038/s41587-024-02186-3.Peer-Reviewed Original ResearchGene dynamicsGene programTrajectory inferenceBiological processesCell-cell graphDynamics of genesCell trajectory inferenceSingle-cell RNA sequencingSingle-cell dataCell state transitionsMyeloid lineage maturationDynamics of biological processesGene distributionRNA sequencingPseudotemporal orderingGene processingTrajectories of cellsGenesActivity of biological processesTechnical noiseGroups of cellsLineage maturationCellsConstruct cellsSequence
2022
Epiregulin is a dendritic cell–derived EGFR ligand that maintains skin and lung fibrosis
Odell I, Steach H, Gauld S, Reinke-Breen L, Karman J, Carr T, Wetter J, Phillips L, Hinchcliff M, Flavell R. Epiregulin is a dendritic cell–derived EGFR ligand that maintains skin and lung fibrosis. Science Immunology 2022, 7: eabq6691. PMID: 36490328, PMCID: PMC9840167, DOI: 10.1126/sciimmunol.abq6691.Peer-Reviewed Original ResearchConceptsLung fibrosisDendritic cellsImmune cellsDiffuse cutaneous systemic sclerosisPersistence of fibrosisCutaneous systemic sclerosisExtent of fibrosisType I interferonSystemic sclerosisAutoimmune diseasesAntifibrotic targetsTherapeutic administrationMouse modelI interferonLung samplesLung explantsFibrosisFibrotic tissueImmune signalsEpiregulin expressionPatient's skinExtracellular matrix productionGenetic deficiencyEpiregulinEGFR ligandsInhibition of type 1 immunity with tofacitinib is associated with marked improvement in longstanding sarcoidosis
Damsky W, Wang A, Kim DJ, Young BD, Singh K, Murphy MJ, Daccache J, Clark A, Ayasun R, Ryu C, McGeary MK, Odell ID, Fazzone-Chettiar R, Pucar D, Homer R, Gulati M, Miller EJ, Bosenberg M, Flavell RA, King B. Inhibition of type 1 immunity with tofacitinib is associated with marked improvement in longstanding sarcoidosis. Nature Communications 2022, 13: 3140. PMID: 35668129, PMCID: PMC9170782, DOI: 10.1038/s41467-022-30615-x.Peer-Reviewed Original ResearchConceptsType 1 immunityInternal organ involvementOrgan involvementT cell-derived IFNIdiopathic inflammatory disorderOpen-label trialMonths of treatmentType 1 cytokinesJanus kinase inhibitorImmunologic changesLongstanding sarcoidosisSarcoidosis activitySarcoidosis symptomsClinical improvementCutaneous sarcoidosisSecondary outcomesComplete responsePrimary outcomeTofacitinib treatmentActivity scoreCytokine mediatorsIL-12IL-15IL-6Inflammatory disorders
2025
Engineering Mice to Study Human Immunity.
Sefik E, Xiao T, Chiorazzi M, Odell I, Zhang F, Agrawal K, Micevic G, Flavell R. Engineering Mice to Study Human Immunity. Annual Review Of Immunology 2025 PMID: 40020225, DOI: 10.1146/annurev-immunol-082523-124415.Peer-Reviewed Original ResearchHumanized miceHuman hematopoiesisImmune responseImmune systemHumanized mouse modelHuman hematopoietic stemImmunocompromised murine hostsResident immune cellsHuman immune responseStudy human immunityHuman immune systemIntegration of multi-omicsHematopoietic stemImmune cell growthImmune cellsEngineered miceProgenitor cellsMouse modelImmunological diseasesMurine hostCancer treatmentPreclinical drugsHuman immunityMiceModel disease
2023
IL-6 trans-signaling in a humanized mouse model of scleroderma
Odell I, Agrawal K, Sefik E, Odell A, Caves E, Kirkiles-Smith N, Horsley V, Hinchcliff M, Pober J, Kluger Y, Flavell R. IL-6 trans-signaling in a humanized mouse model of scleroderma. Proceedings Of The National Academy Of Sciences Of The United States Of America 2023, 120: e2306965120. PMID: 37669366, PMCID: PMC10500188, DOI: 10.1073/pnas.2306965120.Peer-Reviewed Original ResearchConceptsBone marrow-derived immune cellsIL-6Human hematopoietic stem cellsImmune cellsT cellsScleroderma skinSoluble IL-6 receptorCD8 T cellsHumanized mouse modelPathogenesis of sclerodermaMesenchymal cellsFibroblast-derived IL-6IL-6 receptorIL-6 signalingT cell activationHuman IL-6Human T cellsExpression of collagenFibrosis improvementPansclerotic morpheaHuman endothelial cellsHumanized miceReduced markersSkin graftsHuman CD4
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