2024
Unraveling the Drivers of the Stress Granule Signature in Splicing Factor-Mutant Myeloid Malignancies
Biancon G, Busarello E, Cheng M, Sidoli S, VanOudenhove J, Bucciarelli G, Tebaldi T, Halene S. Unraveling the Drivers of the Stress Granule Signature in Splicing Factor-Mutant Myeloid Malignancies. Blood 2024, 144: 4117. DOI: 10.1182/blood-2024-211265.Peer-Reviewed Original ResearchRNA-binding proteinsStress granulesRNA-seqArsenite stressSF mutationsAcute myeloid leukemiaSplicing factorsSG proteinsStress responseClonal advantageSG coresMulti-OmicsDeregulated genesMyelodysplastic syndromeEnhances SG formationU2AF1 S34F mutationSingle-cell RNA-seqWT cellsMegakaryocyte-erythroid progenitorsRegulation of translationTranslation initiation factorsImprove cell fitnessRNA-seq analysisPost-translational modificationsU2AF1 mutationsSingle-cell RNA-seq analysis of cell-cell communications in human lung reveals a novel role of VEGF-D in acute lung injury
Yuan Y, Sharma L, Tang W, Raredon M, Ahangari F, Khoury J, Wu D, Niklason L, Kaminski N. Single-cell RNA-seq analysis of cell-cell communications in human lung reveals a novel role of VEGF-D in acute lung injury. Physiology 2024, 39: 1314. DOI: 10.1152/physiol.2024.39.s1.1314.Peer-Reviewed Original ResearchIdiopathic pulmonary fibrosisAcute lung injuryChronic obstructive pulmonary diseaseAcute respiratory distress syndromeAnalysis of cell-cell communicationVEGF-DMicrovascular nicheSingle-cell RNA-seqLung injury modelSingle-cell RNA-seq analysisLung injuryCell-cell communicationLigand-receptor pairsLPS-induced lung injury modelRNA-seqAdjacent cell typesPulmonary diseaseInjury modelHuman lung endothelial cellsBarrier functionImmune cell infiltrationTumor necrosis factor-aRespiratory distress syndromeLung vascular integrityGene expression
2023
Integrative analysis of transcriptome dynamics during human craniofacial development identifies candidate disease genes
Yankee T, Oh S, Winchester E, Wilderman A, Robinson K, Gordon T, Rosenfeld J, VanOudenhove J, Scott D, Leslie E, Cotney J. Integrative analysis of transcriptome dynamics during human craniofacial development identifies candidate disease genes. Nature Communications 2023, 14: 4623. PMID: 37532691, PMCID: PMC10397224, DOI: 10.1038/s41467-023-40363-1.Peer-Reviewed Original ResearchConceptsGene co-expression analysisSingle-cell RNA-seqCraniofacial disordersSet of genesCo-expression analysisTranscriptome dynamicsDevelopmental enhancersRegulatory hubEpigenomic dataCraniofacial developmentRNA-seqDe novo mutationsDisease genesGene expressionIntegrative analysisCraniofacial tissuesGenesNovo mutationsHuman tissuesMutationsDevelopment identifiesCommon congenital defectsWeeks post conceptionPost conceptionCraniofacial regionSingle‐Cell Transcriptomics of Bone Marrow Stromal Cells in Diversity Outbred Mice: A Model for Population‐Level scRNA‐Seq Studies
Dillard L, Rosenow W, Calabrese G, Mesner L, Al‐Barghouthi B, Abood A, Farber E, Onengut‐Gumuscu S, Tommasini S, Horowitz M, Rosen C, Yao L, Qin L, Farber C. Single‐Cell Transcriptomics of Bone Marrow Stromal Cells in Diversity Outbred Mice: A Model for Population‐Level scRNA‐Seq Studies. Journal Of Bone And Mineral Research 2023, 38: 1350-1363. PMID: 37436066, PMCID: PMC10528806, DOI: 10.1002/jbmr.4882.Peer-Reviewed Original ResearchConceptsGene regulatory networksMesenchymal lineage cellsBone marrow-derived stromal cellsGenome-wide association studiesOsteocyte-like cellsLineage cellsOsteogenic conditionsTranscriptomic profilesSingle-cell RNA-seqCell typesTranscriptomic data setsGenetics of osteoporosisDisease-Associated VariantsSingle-cell levelMarrow-derived stromal cellsTranscriptomic perspectiveRegulatory networksCausal genesRNA-seqTranscriptomic dataScRNA-seqMesenchymal progenitorsAssociation studiesGenetic studiesLineage precursors
2021
14-3-3 epsilon is an intracellular component of TNFbib2 receptor complex and its activation protects against osteoarthritis
Fu W, Hettinghouse A, Chen Y, Hu W, Ding X, Chen M, Ding Y, Mundra J, Song W, Liu R, Yi Y, Attur M, Samuels J, Strauss E, Leucht P, Schwarzkopf R, Liu C. 14-3-3 epsilon is an intracellular component of TNFbib2 receptor complex and its activation protects against osteoarthritis. Annals Of The Rheumatic Diseases 2021, 80: 1615-1627. PMID: 34226187, PMCID: PMC8595573, DOI: 10.1136/annrheumdis-2021-220000.Peer-Reviewed Original ResearchConceptsPathogenesis of osteoarthritisTNFR2 complexTherapeutic effectSingle-cell RNA-seqIntracellular componentsReceptor complexExtracellular signal-regulated kinaseNuclear factor kappa BSignal-regulated kinaseCommon joint diseaseFactor kappa BChondrocyte-specific deletionProteomic screenElk-1RNA-seqTranscription factorsCell-based assaysTNF signalingTNFR2 pathwayInducible componentJoint diseaseActivity screenTherapeutic targetKappa BOsteoarthritisBET proteolysis targeted chimera-based therapy of novel models of Richter Transformation-diffuse large B-cell lymphoma
Fiskus W, Mill CP, Perera D, Birdwell C, Deng Q, Yang H, Lara BH, Jain N, Burger J, Ferrajoli A, Davis JA, Saenz DT, Jin W, Coarfa C, Crews CM, Green MR, Khoury JD, Bhalla KN. BET proteolysis targeted chimera-based therapy of novel models of Richter Transformation-diffuse large B-cell lymphoma. Leukemia 2021, 35: 2621-2634. PMID: 33654205, PMCID: PMC8410602, DOI: 10.1038/s41375-021-01181-w.Peer-Reviewed Original ResearchMeSH KeywordsAdenineAnimalsAntineoplastic Combined Chemotherapy ProtocolsApoptosisBiomarkers, TumorBridged Bicyclo Compounds, HeterocyclicCell ProliferationCell Transformation, NeoplasticGene Expression Regulation, NeoplasticHumansLymphoma, Large B-Cell, DiffuseMicePiperidinesProteinsProteolysisSulfonamidesTumor Cells, CulturedXenograft Model Antitumor AssaysConceptsLarge B-cell lymphomaB-cell lymphomaRichter transformationBET protein inhibitorLymphoma burdenImproved survivalCombination therapyC-Myc levelsEffective therapyNovel therapiesCell lymphomaXenograft modelProtein inhibitorTherapyBET inhibitorsProtein expressionCLLGenetic alterationsLymphomaInhibitorsIRF4Single-cell RNA-seqHuman modelCRISPR knockoutCells
2020
Murine interfollicular epidermal differentiation is gradualistic with GRHL3 controlling progression from stem to transition cell states
Lin Z, Jin S, Chen J, Li Z, Lin Z, Tang L, Nie Q, Andersen B. Murine interfollicular epidermal differentiation is gradualistic with GRHL3 controlling progression from stem to transition cell states. Nature Communications 2020, 11: 5434. PMID: 33116143, PMCID: PMC7595230, DOI: 10.1038/s41467-020-19234-6.Peer-Reviewed Original ResearchConceptsCell statesRNA velocity analysisSingle-cell RNA-seqTerminal differentiation genesStem cell stateInterfollicular epidermisStem cellsInterfollicular epidermal differentiationStem cell expansionDifferentiation genesRNA-seqCommitment pointTerminal differentiationGRHL3Epidermal differentiationCell expansionDifferentiationCellsTransition cellsWntGenesHomeostasisApproaches for integrating heterogeneous RNA-seq data reveal cross-talk between microbes and genes in asthmatic patients
Spakowicz D, Lou S, Barron B, Gomez JL, Li T, Liu Q, Grant N, Yan X, Hoyd R, Weinstock G, Chupp GL, Gerstein M. Approaches for integrating heterogeneous RNA-seq data reveal cross-talk between microbes and genes in asthmatic patients. Genome Biology 2020, 21: 150. PMID: 32571363, PMCID: PMC7310008, DOI: 10.1186/s13059-020-02033-z.Peer-Reviewed Original ResearchSingle-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis
Adams TS, Schupp JC, Poli S, Ayaub EA, Neumark N, Ahangari F, Chu SG, Raby BA, DeIuliis G, Januszyk M, Duan Q, Arnett HA, Siddiqui A, Washko GR, Homer R, Yan X, Rosas IO, Kaminski N. Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis. Science Advances 2020, 6: eaba1983. PMID: 32832599, PMCID: PMC7439502, DOI: 10.1126/sciadv.aba1983.Peer-Reviewed Original ResearchConceptsIdiopathic pulmonary fibrosisVascular endothelial cellsIPF lungsPulmonary fibrosisChronic obstructive pulmonary disease (COPD) lungsFatal interstitial lung diseaseEndothelial cellsInterstitial lung diseaseCell populationsIPF myofibroblastsMyofibroblast fociNonsmoker controlsLung diseaseCOPD lungsBasaloid cellsSingle-cell atlasInvasive fibroblastsMacrophage populationsLungStromal cellsEpithelial cellsFibrosisCellular populationsDevelopmental markersSingle-cell RNA-seqIL-7 receptor alpha defines heterogeneity and signature of human effector memory CD8+ T cells in high dimensional analysis
Shin MS, Kim D, Yim K, Park HJ, You S, Dong X, Koumpouras F, Shaw AC, Fan R, Krishnaswamy S, Kang I. IL-7 receptor alpha defines heterogeneity and signature of human effector memory CD8+ T cells in high dimensional analysis. Cellular Immunology 2020, 355: 104155. PMID: 32619811, PMCID: PMC7415611, DOI: 10.1016/j.cellimm.2020.104155.Peer-Reviewed Original ResearchConceptsSingle-cell RNA-seqHuman effector memory CD8Effector memory CD8T cellsIL-7RαMemory CD8Gene regulationTranscription factorsRNA-seqPossible biological significanceDownstream eventsEM CD8Expression patternsExpressional relationshipDifferential expressionCytokine receptorsComprehensive landscapeHigh-dimensional cytometryBiological significanceIL-7 receptor alphaKey moleculesIL-7 receptor alpha chainReceptor alpha chainBiological implicationsHeterogeneous cell subsets
2019
Population and Single-Cell Analysis of Human Cardiogenesis Reveals Unique LGR5 Ventricular Progenitors in Embryonic Outflow Tract
Sahara M, Santoro F, Sohlmér J, Zhou C, Witman N, Leung CY, Mononen M, Bylund K, Gruber P, Chien KR. Population and Single-Cell Analysis of Human Cardiogenesis Reveals Unique LGR5 Ventricular Progenitors in Embryonic Outflow Tract. Developmental Cell 2019, 48: 475-490.e7. PMID: 30713072, DOI: 10.1016/j.devcel.2019.01.005.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell DifferentiationCell LineCells, CulturedEmbryonic Stem CellsEndothelial CellsHeart VentriclesHuman Embryonic Stem CellsHumansLIM-Homeodomain ProteinsMice, Inbred C57BLMultipotent Stem CellsMyocardiumMyocytes, CardiacOrganogenesisReceptors, G-Protein-CoupledSingle-Cell AnalysisConceptsCardiac stem/progenitor cellsMultipotent cardiac stem/progenitor cellsCardiac developmentMammalian cardiac developmentSingle-cell RNA-seqComprehensive gene expression profilesGene expression profilesHuman embryonic stemSingle-cell analysisStem/progenitor cellsMammalian cardiogenesisHuman cardiogenesisRNA-seqMorphogenetic processesProximal outflow tractEmbryonic stemEmbryonic outflow tractExpression profilesVentricular progenitorsPutative originHuman embryonic heartCardiac cellsEmbryonic heartProgenitor cellsCardiac derivativesMolecular signatures of multiple myeloma progression through single cell RNA-Seq
Jang J, Li Y, Mitra A, Bi L, Abyzov A, van Wijnen A, Baughn L, Van Ness B, Rajkumar V, Kumar S, Jen J. Molecular signatures of multiple myeloma progression through single cell RNA-Seq. Blood Cancer Journal 2019, 9: 2. PMID: 30607001, PMCID: PMC6318319, DOI: 10.1038/s41408-018-0160-x.Peer-Reviewed Original ResearchConceptsMM patientsMultiple myelomaPoor overall survivalCD138-positive cellsBone marrow aspirateMultiple myeloma progressionSingle-cell RNA-seqMGUS patientsGene expression signaturesOverall survivalMM progressionDisease progressionMyeloma progressionPatient prognosisTreatment stratificationMarrow aspiratesPlasma cellsPositive cellsPatientsL4 groupGene signatureLow expressionExpression signaturesMolecular pathwaysProgression
2018
iDREM: Interactive visualization of dynamic regulatory networks
Ding J, Hagood JS, Ambalavanan N, Kaminski N, Bar-Joseph Z. iDREM: Interactive visualization of dynamic regulatory networks. PLOS Computational Biology 2018, 14: e1006019. PMID: 29538379, PMCID: PMC5868853, DOI: 10.1371/journal.pcbi.1006019.Peer-Reviewed Original ResearchConceptsDynamic regulatory networksRegulatory networksHigh-throughput time series dataInteraction dataProtein-DNA interaction dataSingle-cell RNA-seqTime series gene expression dataStatic datasetsInteractive visualizationGene expression dataData typesRNA-seqTime series dataBiological processesExpression dataMiRNA expressionNetworkSeries dataImportant challengeNew versionDevelopmental dataNovel hypothesisUnified modelMultiple labsRecent years
2016
Zika Virus Disrupts Phospho-TBK1 Localization and Mitosis in Human Neuroepithelial Stem Cells and Radial Glia
Onorati M, Li Z, Liu F, Sousa AMM, Nakagawa N, Li M, Dell’Anno M, Gulden FO, Pochareddy S, Tebbenkamp AT, Han W, Pletikos M, Gao T, Zhu Y, Bichsel C, Varela L, Szigeti-Buck K, Lisgo S, Zhang Y, Testen A, Gao XB, Mlakar J, Popovic M, Flamand M, Strittmatter SM, Kaczmarek LK, Anton ES, Horvath TL, Lindenbach BD, Sestan N. Zika Virus Disrupts Phospho-TBK1 Localization and Mitosis in Human Neuroepithelial Stem Cells and Radial Glia. Cell Reports 2016, 16: 2576-2592. PMID: 27568284, PMCID: PMC5135012, DOI: 10.1016/j.celrep.2016.08.038.Peer-Reviewed Original ResearchMeSH KeywordsAxl Receptor Tyrosine KinaseBrainCell DeathCentrosomeFetusGene Expression ProfilingHumansImmunity, InnateMicrocephalyMitochondriaMitosisNeocortexNeural Stem CellsNeuroepithelial CellsNeurogliaNeuronsNeuroprotective AgentsNucleosidesPhosphorylationProtein Kinase InhibitorsProtein Serine-Threonine KinasesProto-Oncogene ProteinsReceptor Protein-Tyrosine KinasesSpinal CordTranscription, GeneticVirus ReplicationZika VirusZika Virus InfectionConceptsRadial glial cellsNES cellsNeuroepithelial stem cellsZIKV infectionFetal brain slicesStem cellsEarly human neurodevelopmentHuman neuroepithelial stem cellsHuman neural stem cellsCell deathSingle-cell RNA-seqNeural stem cellsNeurodevelopment defectsZIKV replicationGlial cellsBrain slicesPotential treatmentRadial gliaZika virusPhospho-TBK1Neurodevelopmental defectsRNA-seqSupernumerary centrosomesNucleoside analoguesHuman neurodevelopment
2015
Hierarchical deconstruction of mouse olfactory sensory neurons: from whole mucosa to single-cell RNA-seq
Saraiva L, Ibarra-Soria X, Khan M, Omura M, Scialdone A, Mombaerts P, Marioni J, Logan D. Hierarchical deconstruction of mouse olfactory sensory neurons: from whole mucosa to single-cell RNA-seq. Scientific Reports 2015, 5: 18178. PMID: 26670777, PMCID: PMC4680959, DOI: 10.1038/srep18178.Peer-Reviewed Original ResearchConceptsMature olfactory sensory neuronsOlfactory sensory neuronsRNA-seqOR genesGene expressionSingle-cell RNA-seqIntact OR genesOlfactory receptorsCell typesSingle-nucleotide polymorphismsOR-expressing OSNsOR gene expressionIntact olfactory receptorsNeuron-one receptor ruleCrude tissue samplesMonoallelic expressionNeuronal cell typesMouse olfactory mucosaMultiple cell typesChemosensory tissuesGenesCellular heterogeneityOlfactory mucosaSensory neuronsNon-neuronal
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