2024
IL-10 constrains sphingolipid metabolism to limit inflammation
York A, Skadow M, Oh J, Qu R, Zhou Q, Hsieh W, Mowel W, Brewer J, Kaffe E, Williams K, Kluger Y, Smale S, Crawford J, Bensinger S, Flavell R. IL-10 constrains sphingolipid metabolism to limit inflammation. Nature 2024, 627: 628-635. PMID: 38383790, PMCID: PMC10954550, DOI: 10.1038/s41586-024-07098-5.Peer-Reviewed Original ResearchActivity of RelCeramide productionVery long chainFatty acid synthesis pathwayCeramide synthase 2Fatty acid homeostasisMetabolic fluxAvailable to cellsRegulatory nodesTranscription factorsCeramide accumulationSynthesis pathwayVLC ceramidesIL-10 deficiencyGene expressionSphingolipid metabolismAcid homeostasisAberrant activationIL-10Cell types1Innate immune cellsInflammatory gene expressionCeramideSignaling resultsGenetic deletion
2023
Spatial epigenome–transcriptome co-profiling of mammalian tissues
Zhang D, Deng Y, Kukanja P, Agirre E, Bartosovic M, Dong M, Ma C, Ma S, Su G, Bao S, Liu Y, Xiao Y, Rosoklija G, Dwork A, Mann J, Leong K, Boldrini M, Wang L, Haeussler M, Raphael B, Kluger Y, Castelo-Branco G, Fan R. Spatial epigenome–transcriptome co-profiling of mammalian tissues. Nature 2023, 616: 113-122. PMID: 36922587, PMCID: PMC10076218, DOI: 10.1038/s41586-023-05795-1.Peer-Reviewed Original ResearchConceptsGene expressionSingle-cell resolutionChromatin accessibilityJoint profilingHistone modificationsGene regulationCellular statesEpigenetic mechanismsCentral dogmaSpatial transcriptomeTranscriptional phenotypeCell statesOmics informationSpatial transcriptomicsEpigenetic primingMammalian tissuesEpigenomeMolecular biologyTissue architectureCell dynamicsMechanistic relationshipDifferential rolesNew insightsMouse brainProfilingIntegrated transcriptome and trajectory analysis of cutaneous T-cell lymphoma identifies putative precancer populations
Ren J, Qu R, Rahman N, Lewis J, King A, Liao X, Mirza F, Carlson K, Huang Y, Gigante S, Evans B, Rajendran B, Xu S, Wang G, Foss F, Damsky W, Kluger Y, Krishnaswamy S, Girardi M. Integrated transcriptome and trajectory analysis of cutaneous T-cell lymphoma identifies putative precancer populations. Blood Advances 2023, 7: 445-457. PMID: 35947128, PMCID: PMC9979716, DOI: 10.1182/bloodadvances.2022008168.Peer-Reviewed Original ResearchConceptsCutaneous T-cell lymphomaMalignant CTCL cellsDiverse transcriptomic profilesT cellsSingle-cell RNACTCL cellsDevelopment of CTCLIntegrated transcriptomeT-cell receptor sequencingT cell exhaustion phenotypeCommon antigenic stimulusPeripheral blood CD4Transcriptomic profilesGene expressionT-cell lymphomaIntegrative analysisPotential therapeutic targetProliferation advantageLimited diversityBlood CD4Blood involvementMutation levelsExhaustion phenotypeWorse prognosisAntigenic stimulus
2004
Lineage specificity of gene expression patterns
Kluger Y, Tuck DP, Chang JT, Nakayama Y, Poddar R, Kohya N, Lian Z, Nasr A, Halaban HR, Krause DS, Zhang X, Newburger PE, Weissman SM. Lineage specificity of gene expression patterns. Proceedings Of The National Academy Of Sciences Of The United States Of America 2004, 101: 6508-6513. PMID: 15096607, PMCID: PMC404075, DOI: 10.1073/pnas.0401136101.Peer-Reviewed Original ResearchConceptsGene expression patternsExpression patternsExpression dataGene Ontology databaseTree of relationshipsStem cellsBroad functional categoriesHematopoietic cell populationsMRNA expression dataHematopoietic programBioCarta databasesGenome databaseLineage choiceHematopoietic stem cellsKyoto EncyclopediaDifferent lineagesFunctional categoriesLineage developmentCell lineagesGene expressionLineage specificityOligonucleotide microarraysFunctional pathwaysLineage discriminationOntology database
2001
RNA expression patterns change dramatically in human neutrophils exposed to bacteria
Subrahmanyam Y, Yamaga S, Prashar Y, Lee H, Hoe N, Kluger Y, Gerstein M, Goguen J, Newburger P, Weissman S. RNA expression patterns change dramatically in human neutrophils exposed to bacteria. Blood 2001, 97: 2457-2468. PMID: 11290611, DOI: 10.1182/blood.v97.8.2457.Peer-Reviewed Original ResearchMeSH KeywordsCells, CulturedCytokinesDNA, ComplementaryEndopeptidasesEscherichia coliExpressed Sequence TagsGene Expression ProfilingGene Expression RegulationHumansInflammationNeutrophilsOxidoreductasesProtein KinasesReceptors, CytokineRNA, MessengerRNA, RibosomalSpecies SpecificitySubtraction TechniqueTranscription, GeneticTranscriptional ActivationVirulenceYersinia pestisConceptsMembrane trafficking regulatorsRNA expression patternsGene clusterTrafficking regulatorResponse genesGene inductionExpression patternsGene expressionNonpathogenic bacteriaCell typesVariety of stimuliMessenger RNA levelsYersinia pestisDifferent bacteriaVariety of cytokinesNeutrophil physiologyHuman neutrophilsBacteriaGenesActive regulationRNA levelsPestisMRNAActivation responseCellular inflammatory response