2024
Foxp3+ regulatory T cells reside within the corneal epithelium and co-localize with limbal stem cells
Tahvildari M, Me R, Setia M, Gao N, Suvas P, McClellan S, Suvas S. Foxp3+ regulatory T cells reside within the corneal epithelium and co-localize with limbal stem cells. Experimental Eye Research 2024, 249: 110123. PMID: 39396695, PMCID: PMC11622170, DOI: 10.1016/j.exer.2024.110123.Peer-Reviewed Original ResearchConceptsLimbal stem cellsRegulatory T cellsResident TregsT cellsFoxp3<sup>+</sup> regulatory T cellsLimbal stem cell functionMouse modelCorneal epithelial wound healingModel of mechanical injuryStem cellsDepletion of TregsCell functionEpithelial wound healingEpithelial cell functionWound healingStem cell functionMechanical injuryAnti-CD25Epithelial healingSubconjunctival injectionCorneal epitheliumCorneal stromaTregsCornealCorneaStem cells tightly regulate dead cell clearance to maintain tissue fitness
Stewart K, Abdusselamoglu M, Tierney M, Gola A, Hur Y, Gonzales K, Yuan S, Bonny A, Yang Y, Infarinato N, Cowley C, Levorse J, Pasolli H, Ghosh S, Rothlin C, Fuchs E. Stem cells tightly regulate dead cell clearance to maintain tissue fitness. Nature 2024, 633: 407-416. PMID: 39169186, PMCID: PMC11390485, DOI: 10.1038/s41586-024-07855-6.Peer-Reviewed Original ResearchStem cellsImmune-privileged nicheHair follicle stem cellsStem cell functionFollicle stem cellsTissue fitnessMesenchymal tissue cellsBillions of cellsDendritic cellsTissue stemProgenitor cellsPreserving tissue integrityDead cell clearanceClearance genesCell clearanceCell functionFunctional evidenceDying CellsHealthy counterpartsCell deathNon-motileTissue cellsHair cycleProfessional phagocytesApoptotic corpses
2023
EPIREGULIN creates a developmental niche for spatially organized human intestinal enteroids
Childs C, Holloway E, Sweet C, Tsai Y, Wu A, Vallie A, Eiken M, Capeling M, Zwick R, Palikuqi B, Trentesaux C, Wu J, Pellon-Cardenas O, Zhang C, Glass I, Loebel C, Yu Q, Camp J, Sexton J, Klein O, Verzi M, Spence J. EPIREGULIN creates a developmental niche for spatially organized human intestinal enteroids. JCI Insight 2023, 8: e165566. PMID: 36821371, PMCID: PMC10070114, DOI: 10.1172/jci.insight.165566.Peer-Reviewed Original ResearchConceptsHuman intestineHuman intestinal enteroidsEGF family membersIntestinal transcription factor CDX2Chromatin landscapeHuman cryptsTranscription factor CDX2Stem cell functionIntestinal enteroidsBiological discoveryCellular differentiationStandard culture conditionsNiche cuesEpithelial developmentEnteroidsEGFCrypt domainsOrgans in vitroPersonalized medicineCentral lumenCulture conditionsCell functionNiche in vitroSpatial organizationEGF in vitro
2021
Epigenome-Wide Association Study of Acute Lymphoblastic Leukemia in Children with Down Syndrome
Li S, Sok P, Xu K, Muskens I, Elliott N, Myint S, Pandey P, Hansen H, Morimoto L, Kang A, Metayer C, Ma X, Mueller B, Roy A, Roberts I, Rabin K, Brown A, Lupo P, Wiemels J, de Smith A. Epigenome-Wide Association Study of Acute Lymphoblastic Leukemia in Children with Down Syndrome. Blood 2021, 138: 214. DOI: 10.1182/blood-2021-151454.Peer-Reviewed Original ResearchEpigenome-wide association studiesB cell proportionsAcute lymphoblastic leukemiaNon-DS populationCell type proportionsDNA methylation dataSingle nucleotide polymorphismsDS-ALLCell proportionAssociation studiesDS controlBlood cell proportionsLymphoblastic leukemiaMethylation dataGenome-wide DNA methylation arraysGenome-wide SNP array dataB-cell acute lymphoblastic leukemiaGenome-wide association studiesLeukemic stem cell functionsDiscovery studiesStem cell functionRecent genome-wide association studiesDNA methylation arraysEpigenome-wide significanceNatural killer cellsLineages of embryonic stem cells show non-Markovian state transitions
Udomlumleart T, Hu S, Garg S. Lineages of embryonic stem cells show non-Markovian state transitions. IScience 2021, 24: 102879. PMID: 34401663, PMCID: PMC8353490, DOI: 10.1016/j.isci.2021.102879.Peer-Reviewed Original Research
2020
The Role of RNA Epigenetic Modification in Normal and Malignant Hematopoiesis
Vasic R, Gao Y, Liu C, Halene S. The Role of RNA Epigenetic Modification in Normal and Malignant Hematopoiesis. Current Stem Cell Reports 2020, 6: 144-155. PMID: 33777659, PMCID: PMC7992056, DOI: 10.1007/s40778-020-00178-y.Commentaries, Editorials and LettersHematopoietic stem cellsM6A machineryEpigenetic modificationsRNA modificationsStem cellsNormal hematopoietic stem cellsStem cell fate decisionsCell fate decisionsStem cell functionRNA epigenetic modificationRNA m6A modificationRecognition of RNAImmune cell developmentM6A RNA modificationEraser proteinsFate decisionsM6A readersVariety of functionsGene expressionMalignant hematopoiesisImmune signalingImmune system functionCritical regulatorCell developmentM6A modificationParacrine orchestration of intestinal tumorigenesis by a mesenchymal niche
Roulis M, Kaklamanos A, Schernthanner M, Bielecki P, Zhao J, Kaffe E, Frommelt LS, Qu R, Knapp MS, Henriques A, Chalkidi N, Koliaraki V, Jiao J, Brewer JR, Bacher M, Blackburn HN, Zhao X, Breyer RM, Aidinis V, Jain D, Su B, Herschman HR, Kluger Y, Kollias G, Flavell RA. Paracrine orchestration of intestinal tumorigenesis by a mesenchymal niche. Nature 2020, 580: 524-529. PMID: 32322056, PMCID: PMC7490650, DOI: 10.1038/s41586-020-2166-3.Peer-Reviewed Original ResearchMeSH KeywordsAdaptor Proteins, Signal TransducingAnimalsAntigens, LyArachidonic AcidCarcinogenesisCell Cycle ProteinsCell ProliferationColorectal NeoplasmsCyclooxygenase 2DinoprostoneFemaleFibroblastsHumansIntestinal MucosaIntestinesMaleMembrane ProteinsMesodermMiceNeoplastic Stem CellsOrganoidsParacrine CommunicationReceptors, Prostaglandin E, EP4 SubtypeSingle-Cell AnalysisStem Cell NicheYAP-Signaling ProteinsConceptsSingle-cell RNA-sequencing analysisTumor-initiating stem cellsRNA sequence analysisMesenchymal nicheStem cellsTumor initiationSca-1Hippo pathway effector YAPStem cell functionCell expansionPathway effector YAPMutant stem cellsEpithelial-specific ablationIntestinal stem cellsEarly tumor initiationProstaglandin E2Regenerative reprogrammingNormal epithelial stem cellsParacrine controlTumorigenic programsNiche modelsNuclear localizationTranscriptional activityYAP dephosphorylationEpithelial stem cells
2019
Functional Analysis of Human Hematopoietic Stem Cells In Vivo in Humanized Mice
Song Y, Gbyli R, Fu X, Halene S. Functional Analysis of Human Hematopoietic Stem Cells In Vivo in Humanized Mice. Methods In Molecular Biology 2019, 2097: 273-289. PMID: 31776933, DOI: 10.1007/978-1-0716-0203-4_18.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsHematopoietic stem cellsHematopoietic stem cell functionFunctional hematopoietic stem cellsStem cell functionStem cellsCell-intrinsic functionHuman hematopoietic stem cellsOrganismal contextFunctional analysisCell functionIntrinsic functionCell sourceCellular productsChimeric miceStem cell therapyCellsReprogrammingMouse modelMajor advancesCell therapyMiceVivoFunction
2016
Genome-Wide Analysis of Polyadenylation Events in Schmidtea mediterranea
Lakshmanan V, Bansal D, Kulkarni J, Poduval D, Krishna S, Sasidharan V, Anand P, Seshasayee A, Palakodeti D. Genome-Wide Analysis of Polyadenylation Events in Schmidtea mediterranea. G3: Genes, Genomes, Genetics 2016, 6: 3035-3048. PMID: 27489207, PMCID: PMC5068929, DOI: 10.1534/g3.116.031120.Peer-Reviewed Original ResearchMeSH Keywords3' Untranslated RegionsAnimalsComputational BiologyGenome, HelminthGenome-Wide Association StudyHigh-Throughput Nucleotide SequencingMicroRNAsMolecular Sequence AnnotationPlatyhelminthsPoly APolyadenylationReproducibility of ResultsRNA InterferenceRNA Processing, Post-TranscriptionalRNA, MessengerConceptsSchmidtea mediterraneaAdvent of next-generation sequencing technologiesNext-generation sequencing technologiesGene expressionTissue-specific expression patternsMiRNA mediated gene regulationGenome-wide scaleGenome-wide analysisPoly(A) sitePosttranscriptional gene expressionRegulate posttranscriptional gene expressionGene annotationInternal exonsPolyadenylated transcriptsTranscript isoformsPolyadenylation eventsDegradome sequencingProtein domainsSequencing technologiesPre-mRNAGene regulationCoding sequenceIdeal model systemStem cell functionFreshwater planarians
2015
Long Non-Coding RNAs Control Hematopoietic Stem Cell Function
Luo M, Jeong M, Sun D, Park H, Rodriguez B, Xia Z, Yang L, Zhang X, Sheng K, Darlington G, Li W, Goodell M. Long Non-Coding RNAs Control Hematopoietic Stem Cell Function. Cell Stem Cell 2015, 16: 426-438. PMID: 25772072, PMCID: PMC4388783, DOI: 10.1016/j.stem.2015.02.002.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBasic Helix-Loop-Helix Transcription FactorsBinding SitesBone Marrow CellsCell DifferentiationCell LineageCell Self RenewalCells, CulturedDNA (Cytosine-5-)-MethyltransferasesDNA MethylationDNA Methyltransferase 3AEpigenesis, GeneticGene Expression ProfilingGene Expression Regulation, DevelopmentalHematopoietic Stem CellsHigh-Throughput Nucleotide SequencingMiceMice, Inbred StrainsMice, KnockoutRNA, Long NoncodingRNA, Small InterferingConceptsHematopoietic stem cellsLong non-coding RNAsNon-coding RNAsLineage commitmentKey hematopoietic transcription factorsUnique gene expression programProtein-coding genesHematopoietic stem cell functionCell fate decisionsGene expression programsHematopoietic transcription factorsStem cell functionGenetic circuitryDifferentiated lineagesExpression programsFate decisionsLncRNA genesUnannotated lncRNAsDNA methylationEpigenetic featuresTranscription factorsHSC functionDeep sequencingGene expressionRegulated expression
2014
PIWI proteins and PIWI-interacting RNAs in the soma
Ross RJ, Weiner MM, Lin H. PIWI proteins and PIWI-interacting RNAs in the soma. Nature 2014, 505: 353-359. PMID: 24429634, PMCID: PMC4265809, DOI: 10.1038/nature12987.Peer-Reviewed Original ResearchConceptsPIWI-interacting RNAsPIWI proteinsPIWI-piRNA pathwayDiscovery of millionsWhole-body regenerationStem cell functionSomatic functionsDiverse organismsLower eukaryotesGenome rearrangementsSomatic cellsEpigenetic programmingBiological rolePathwayRNAProteinRecent studiesEukaryotesTransposonOrganismsBiologyUnanticipated dimensionsFunctionCellsRearrangement
2013
Improved regenerative myogenesis and muscular dystrophy in mice lacking Mkp5
Shi H, Verma M, Zhang L, Dong C, Flavell RA, Bennett AM. Improved regenerative myogenesis and muscular dystrophy in mice lacking Mkp5. Journal Of Clinical Investigation 2013, 123: 2064-2077. PMID: 23543058, PMCID: PMC3635719, DOI: 10.1172/jci64375.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell ProliferationCrosses, GeneticDual-Specificity PhosphatasesDystrophinFemaleMaleMAP Kinase Kinase 4MAP Kinase Signaling SystemMiceMice, Inbred C57BLMice, KnockoutMuscle, SkeletalMusclesMuscular Dystrophy, DuchenneMutationp38 Mitogen-Activated Protein KinasesRegenerationStem CellsConceptsMuscle stem cell functionMitogen-activated protein kinaseStem cell functionMKP-5MAPK phosphataseSkeletal muscle diseasesRegenerative myogenesisCell functionMuscle stem cell proliferationP38 mitogen-activated protein kinaseMuscle stem cellsDegenerative skeletal muscle diseaseStem cell proliferationEssential negative regulatorProtein kinaseMuscle diseaseNegative regulatorMAPK activityGenetic lossMKP5Muscle phenotypeDystrophic muscle phenotypeStem cellsMuscular dystrophyCell proliferation
2012
BCOR Is Involved in Myeloid Cell Growth Control by Regulating Hox Genes
Cao Q, Gery S, Shojaee S, Gearhart M, Bardwell V, Muschen M, Koeffler H. BCOR Is Involved in Myeloid Cell Growth Control by Regulating Hox Genes. Blood 2012, 120: 3445. DOI: 10.1182/blood.v120.21.3445.3445.Peer-Reviewed Original ResearchHox genesMyeloid cell differentiationCell differentiationCell linesIndividual Hox genesNormal hematopoiesisEssential developmental regulatorsStem cell stateOculofaciocardiodental syndromeEarly embryonic developmentCell growth controlStem cell functionTranscriptional repressive complexDownstream target genesTumor suppressor proteinGene expression profilesMesenchymal stem cell functionImmature hematopoietic cellsDevelopmental regulatorsPolycomb groupRepressive complexesHuman leukemic cell linesMost cell linesEmbryonic developmentSuppressor protein
2011
Adipocyte Lineage Cells Contribute to the Skin Stem Cell Niche to Drive Hair Cycling
Festa E, Fretz J, Berry R, Schmidt B, Rodeheffer M, Horowitz M, Horsley V. Adipocyte Lineage Cells Contribute to the Skin Stem Cell Niche to Drive Hair Cycling. Cell 2011, 146: 761-771. PMID: 21884937, PMCID: PMC3298746, DOI: 10.1016/j.cell.2011.07.019.Peer-Reviewed Original ResearchConceptsAdipocyte lineage cellsStem cell nicheStem cell activityLineage cellsCell nicheSkin stem cell nichesStem cell functionEpithelial stem cell nicheStem cell activationEpithelial stem cell functionSkin stem cellsTissue homeostasisNiche cellsFunctional analysisAdipogenic cellsSkin homeostasisMammalian skinTransplantation experimentsStem cellsPrecursor cellsHair cyclingCell functionAdipocyte cellsNicheFunctional tissue
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