2025
Spatiotemporal dynamics of fetal liver hematopoietic niches
Peixoto M, Soares-da-Silva F, Bonnet V, Zhou Y, Ronteix G, Santos R, Mailhe M, Nogueira G, Feng X, Pereira J, Azzoni E, Anselmi G, de Bruijn M, Perkins A, Baroud C, Pinto-do-Ó P, Cumano A. Spatiotemporal dynamics of fetal liver hematopoietic niches. Journal Of Experimental Medicine 2025, 222: e20240592. PMID: 39775824, PMCID: PMC11706214, DOI: 10.1084/jem.20240592.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsFemaleFetusHematopoiesisHematopoietic Stem CellsLiverMiceMice, Inbred C57BLStem Cell NicheStromal CellsConceptsFetal liverSource of hematopoietic growth factorsStromal cellsNon-hematopoietic stromal cellsHematopoietic growth factorsCytokine production patternsStromal cell populationsNeighboring stromal cellsEmbryonic hematopoietic cellsFetal hematopoiesisComplex cellular interactionsHematopoietic progenitorsHematopoietic cellsGrowth factorCell populationsFL developmentCellular interactionsCellsDevelopmental changesSignaling networks
2022
Dysregulated stem cell niches and altered lymphocyte recirculation cause B and T cell lymphopenia in WHIM syndrome
Zehentmeier S, Lim VY, Ma Y, Fossati J, Ito T, Jiang Y, Tumanov AV, Lee HJ, Dillinger L, Kim J, Csomos K, Walter JE, Choi J, Pereira JP. Dysregulated stem cell niches and altered lymphocyte recirculation cause B and T cell lymphopenia in WHIM syndrome. Science Immunology 2022, 7: eabo3170. PMID: 36149943, PMCID: PMC9614684, DOI: 10.1126/sciimmunol.abo3170.Peer-Reviewed Original ResearchConceptsSecondary lymphoid organsWHIM syndromeMesenchymal stem cellsInterleukin-7B lymphopeniaBone marrowBM mesenchymal stem cellsT cell numbersIL-7 productionT-cell lymphopeniaLymphotoxin beta receptorEarly progenitor stageLymphoid organsCell lymphopeniaMouse modelBeta receptorsB cellsB cell developmentLymphopeniaStromal cellsLeukocyte retentionSyndromeGOF mutationsLymphopoietic activityCritical pathways
2021
MAP3K2-regulated intestinal stromal cells define a distinct stem cell niche
Wu N, Sun H, Zhao X, Zhang Y, Tan J, Qi Y, Wang Q, Ng M, Liu Z, He L, Niu X, Chen L, Liu Z, Li HB, Zeng YA, Roulis M, Liu D, Cheng J, Zhou B, Ng LG, Zou D, Ye Y, Flavell RA, Ginhoux F, Su B. MAP3K2-regulated intestinal stromal cells define a distinct stem cell niche. Nature 2021, 592: 606-610. PMID: 33658717, DOI: 10.1038/s41586-021-03283-y.Peer-Reviewed Original ResearchConceptsStem cell nicheR-spondin 1Intestinal stromal cellsCell nicheDistinct stem cell nichesIntestinal stem cell nicheStromal cellsIntestinal stem cellsStromal cell populationsTissue homeostasisReactive oxygen speciesIntestinal stemMolecular mechanismsAcute intestinal damageSpecific functionsPrimary cellular sourceStem cellsColon cryptsOxygen speciesCell populationsIntestinal injuryIntestinal damageNicheCellular sourceCells
2020
Hedgehog Signaling Demarcates a Niche of Fibrogenic Peribiliary Mesenchymal Cells
Gupta V, Gupta I, Park J, Bram Y, Schwartz RE. Hedgehog Signaling Demarcates a Niche of Fibrogenic Peribiliary Mesenchymal Cells. Gastroenterology 2020, 159: 624-638.e9. PMID: 32289375, PMCID: PMC8204800, DOI: 10.1053/j.gastro.2020.03.075.Peer-Reviewed Original ResearchConceptsCholestatic injuryStellate cellsLiver tissueStromal cellsLiver diseaseBile ductBiliary treePortal tractsMesenchymal cellsPrimary sclerosing cholangitisAlcoholic liver diseaseEpithelial cellsMyofibroblast phenotypeQuantitative reverse transcription polymerase chain reactionBile duct ligationReverse transcription-polymerase chain reactionTranscription-polymerase chain reactionCanals of HeringControl liver tissueHedgehog signalingSclerosing cholangitisHepatic injuryHepatocellular injuryNonalcoholic steatohepatitisPortal fibroblastsParacrine 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
An intra-tumoral niche maintains and differentiates stem-like CD8 T cells
Jansen C, Prokhnevska N, Master V, Sanda M, Carlisle J, Bilen M, Cardenas M, Wilkinson S, Lake R, Sowalsky A, Valanparambil R, Hudson W, McGuire D, Melnick K, Khan A, Kim K, Chang Y, Kim A, Filson C, Alemozaffar M, Osunkoya A, Mullane P, Ellis C, Akondy R, Im S, Kamphorst A, Reyes A, Liu Y, Kissick H. An intra-tumoral niche maintains and differentiates stem-like CD8 T cells. Nature 2019, 576: 465-470. PMID: 31827286, PMCID: PMC7108171, DOI: 10.1038/s41586-019-1836-5.Peer-Reviewed Original ResearchConceptsCD8 T cellsStem-like CD8 T cellsT cellsStem-like T cellsCD8 T cell infiltrationCD8 T cell responsesMechanism of immune escapeTumor-infiltrating lymphocytesT cell infiltrationT cell responsesStem-like cellsSurvival benefitImmune nicheProgressive diseaseImmune escapeTumor typesTumorCD8Human cancersDifferentiation processLymphocytesPatientsCancerInfiltrationSurvivalMinimally Invasive Delivery of Microbeads with Encapsulated, Viable and Quiescent Neural Stem Cells to the Adult Subventricular Zone
Matta R, Lee S, Genet N, Hirschi KK, Thomas JL, Gonzalez AL. Minimally Invasive Delivery of Microbeads with Encapsulated, Viable and Quiescent Neural Stem Cells to the Adult Subventricular Zone. Scientific Reports 2019, 9: 17798. PMID: 31780709, PMCID: PMC6882840, DOI: 10.1038/s41598-019-54167-1.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell DifferentiationCell EncapsulationCell LineCell ProliferationCell SurvivalEndothelial CellsLateral VentriclesMaleMatrix MetalloproteinasesMiceMice, Inbred C57BLMicrospheresNeural Stem CellsNeuronsPolyethylene GlycolsRecovery of FunctionStem Cell NicheStem Cell TransplantationConceptsEndothelial cellsSubventricular zoneNSC quiescenceNon-injury modelQuiescent neural stem cellsAdult subventricular zoneNeuronal stem cellsStem cellsNeural stem cellsFunctional recoveryNeurological injuryInflammatory responseNeural stem cell maintenanceNSC deliveryNeural tissue repairNeurological diseasesMouse brainCell therapyNSC viabilityBrainTissue repairInjuryCo-encapsulated cellsSurvivalDeliveryMolecular Biology and Evolution of Cancer: From Discovery to Action
Somarelli JA, Gardner H, Cannataro VL, Gunady EF, Boddy AM, Johnson NA, Fisk J, Gaffney SG, Chuang JH, Li S, Ciccarelli FD, Panchenko AR, Megquier K, Kumar S, Dornburg A, DeGregori J, Townsend JP. Molecular Biology and Evolution of Cancer: From Discovery to Action. Molecular Biology And Evolution 2019, 37: 320-326. PMID: 31642480, PMCID: PMC6993850, DOI: 10.1093/molbev/msz242.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsMeSH KeywordsDisease ProgressionEvolution, MolecularGenetic FitnessGenomicsHumansNeoplasmsPhylogenyStem Cell NicheConceptsEvolutionary processesMolecular evolutionary processesEvolution of cancerCancer cell populationsEcological nichesNew therapeutic modesCancer evolutionEcological theoryMolecular biologyCancer biologyCancer progressionSuite of conceptsCell populationsBiologyNicheEvolutionCirculatory systemDeeper understandingDiscoveryCancerLymph vessels find a hairy niche
Kam CY, Greco V. Lymph vessels find a hairy niche. The EMBO Journal 2019, 38: embj2019103219. PMID: 31531872, PMCID: PMC6769378, DOI: 10.15252/embj.2019103219.Peer-Reviewed Original ResearchIdentification and transcriptome analysis of erythroblastic island macrophages
Li W, Wang Y, Zhao H, Zhang H, Xu Y, Wang S, Guo X, Huang Y, Zhang S, Han Y, Wu X, Rice CM, Huang G, Gallagher PG, Mendelson A, Yazdanbakhsh K, Liu J, Chen L, An X. Identification and transcriptome analysis of erythroblastic island macrophages. Blood 2019, 134: 480-491. PMID: 31101625, PMCID: PMC6676133, DOI: 10.1182/blood.2019000430.Peer-Reviewed Original ResearchConceptsErythroblastic islandsEBI macrophagesErythroid cellsErythroblastic island macrophagesGene expression profilesTranscriptome analysisNonerythroid cellsMacrophage functionHematopoietic nicheExpression profilesSpecialized functionsCentral macrophageKnockin mouse modelFlow cytometry analysisEpoRKey moleculesIron recyclingBone marrowCytometry analysisFetal liverNicheEfficient erythropoiesisErythropoiesisIron sourceImportant resourceRNA Profiling of the Human and Mouse Spinal Cord Stem Cell Niches Reveals an Embryonic-like Regionalization with MSX1+ Roof-Plate-Derived Cells
Ghazale H, Ripoll C, Leventoux N, Jacob L, Azar S, Mamaeva D, Glasson Y, Calvo CF, Thomas JL, Meneceur S, Lallemand Y, Rigau V, Perrin FE, Noristani HN, Rocamonde B, Huillard E, Bauchet L, Hugnot JP. RNA Profiling of the Human and Mouse Spinal Cord Stem Cell Niches Reveals an Embryonic-like Regionalization with MSX1+ Roof-Plate-Derived Cells. Stem Cell Reports 2019, 12: 1159-1177. PMID: 31031189, PMCID: PMC6524006, DOI: 10.1016/j.stemcr.2019.04.001.Peer-Reviewed Original ResearchConceptsTranscription factorsRNA profilingDevelopmental transcription factorsDorsal-ventral patternStem cell nicheEpendymal zoneMolecular resourcesMammalian lesionsConserved expressionCell nicheNeural stem cellsCell diversityPossible endogenous sourceQuiescent cellsGenesFloor plateStem cellsMsx1Endogenous sourcesTransgenic miceCellsProfilingSpinal cordCentral canalExpressionA highly efficient and faithful MDS patient-derived xenotransplantation model for pre-clinical studies
Song Y, Rongvaux A, Taylor A, Jiang T, Tebaldi T, Balasubramanian K, Bagale A, Terzi YK, Gbyli R, Wang X, Fu X, Gao Y, Zhao J, Podoltsev N, Xu M, Neparidze N, Wong E, Torres R, Bruscia EM, Kluger Y, Manz MG, Flavell RA, Halene S. A highly efficient and faithful MDS patient-derived xenotransplantation model for pre-clinical studies. Nature Communications 2019, 10: 366. PMID: 30664659, PMCID: PMC6341122, DOI: 10.1038/s41467-018-08166-x.Peer-Reviewed Original ResearchConceptsPatient-derived xenograftsMyelodysplastic syndromeXenotransplantation modelDysplastic morphologyImmunodeficient murine hostsPre-clinical studiesMDS stem cellsMDS subtypesComprehensive preclinical studiesPreclinical studiesTherapeutic efficacyMurine hostSerial transplantationDrug mechanismsMDS researchStem cell propagationStem cellsDifferentiation potentialHematopoietic stem cell nicheGenetic complexityNovel avenuesStem cell nicheCell propagationDisease representationsImmunodeficient
2018
Morphogenesis and Compartmentalization of the Intestinal Crypt
Sumigray KD, Terwilliger M, Lechler T. Morphogenesis and Compartmentalization of the Intestinal Crypt. Developmental Cell 2018, 45: 183-197.e5. PMID: 29689194, PMCID: PMC5987226, DOI: 10.1016/j.devcel.2018.03.024.Peer-Reviewed Original ResearchConceptsRac1 null miceAdult mammalian intestineCell shape changesProgenitor cellsStem cell nicheGene networksCrypt morphogenesisCrypt progenitor cellsEssential regulatorMammalian intestineCell nicheGenetic analysisUnexpected roleApical constrictionNiche formationHemidesmosomal adhesionCrypt developmentTissue architectureMouse cryptsMorphogenesisAbsorptive villiNull miceIntestinal cryptsQuantitative morphometricsShape changes
2017
Type-B ARABIDOPSIS RESPONSE REGULATORs Directly Activate WUSCHEL
Zhang F, May A, Irish VF. Type-B ARABIDOPSIS RESPONSE REGULATORs Directly Activate WUSCHEL. Trends In Plant Science 2017, 22: 815-817. PMID: 28886911, DOI: 10.1016/j.tplants.2017.08.007.Peer-Reviewed Original ResearchTregs Expand the Skin Stem Cell Niche
Horsley V, Naik S. Tregs Expand the Skin Stem Cell Niche. Developmental Cell 2017, 41: 455-456. PMID: 28586641, DOI: 10.1016/j.devcel.2017.05.020.Peer-Reviewed Original Research
2016
Hematopoietic Stem Cell Niches Produce Lineage-Instructive Signals to Control Multipotent Progenitor Differentiation
Gomes A, Hara T, Lim VY, Herndler-Brandstetter D, Nevius E, Sugiyama T, Tani-ichi S, Schlenner S, Richie E, Rodewald HR, Flavell RA, Nagasawa T, Ikuta K, Pereira JP. Hematopoietic Stem Cell Niches Produce Lineage-Instructive Signals to Control Multipotent Progenitor Differentiation. Immunity 2016, 45: 1219-1231. PMID: 27913094, PMCID: PMC5538583, DOI: 10.1016/j.immuni.2016.11.004.Peer-Reviewed Original ResearchConceptsCommon lymphoid progenitorsHematopoietic stem cellsMesenchymal progenitorsProgenitor differentiationHSC nicheCell lineage decisionsBone marrow nicheHSC maintenanceLineage decisionsDifferentiation signalsCytokines SCFEndothelial cellsSeparate nichesLymphoid progenitorsMultilineage differentiationMarrow nicheNicheChemokine receptor CXCR4Conditional deletionIL-7 receptorStem cellsProgenitorsDifferentiationIL-7DeletionLive imaging of stem cells: answering old questions and raising new ones
Park S, Greco V, Cockburn K. Live imaging of stem cells: answering old questions and raising new ones. Current Opinion In Cell Biology 2016, 43: 30-37. PMID: 27474806, PMCID: PMC5154884, DOI: 10.1016/j.ceb.2016.07.004.Peer-Reviewed Original ResearchMicroRNA-dependent roles of Drosha and Pasha in the Drosophila larval ovary morphogenesis
Yang H, Li M, Hu X, Xin T, Zhang S, Zhao G, Xuan T, Li M. MicroRNA-dependent roles of Drosha and Pasha in the Drosophila larval ovary morphogenesis. Developmental Biology 2016, 416: 312-323. PMID: 27339292, DOI: 10.1016/j.ydbio.2016.06.026.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell DifferentiationCytoskeletonDrosophila melanogasterDrosophila ProteinsEmbryonic Germ CellsFemaleGene Expression Regulation, DevelopmentalGene Knockdown TechniquesLarvaLuminescent ProteinsMicroRNAsMicroscopy, FluorescenceOrganogenesisOvaryRibonuclease IIIRNA InterferenceRNA-Binding ProteinsStem Cell NicheConceptsOvary morphogenesisPrimordial germ cellsLate third larval instarLoss of DroshaMiRNA pathway componentsCanonical miRNA pathwayGerm cell lineageMiRNA-mediated regulationGerm cell precursorsGenome-wide screeningTerminal filamentThird larval instarEarly larval stagesMiR-317Ovarian somaMiR-14MiR-8Argonaute 1Mutant phenotypeDicer-1MiRNA pathwayPGC differentiationGerm lineGSC nicheRegulatory networksThe Role of Adipocytes in Tissue Regeneration and Stem Cell Niches
Shook B, Rivera Gonzalez G, Ebmeier S, Grisotti G, Zwick R, Horsley V. The Role of Adipocytes in Tissue Regeneration and Stem Cell Niches. Annual Review Of Cell And Developmental Biology 2016, 32: 1-23. PMID: 27146311, PMCID: PMC5157158, DOI: 10.1146/annurev-cellbio-111315-125426.Peer-Reviewed Original ResearchMeSH KeywordsAdipocytesAnimalsDiseaseHumansModels, BiologicalOrganogenesisRegenerationStem Cell NicheConceptsStem cell nicheFunction of WATWhite adipose tissueTissue homeostasisCell nicheMetabolic regulationNovel roleMetabolic physiologyMajor regulatorMature adipocytesImmune tissuesVivo regulationEssential roleRole of adipocytesHomeostasisWhite adipocytesAdipocytesTissue regenerationRegulationEndocrine homeostasisRegenerationTissueNicheRegulatorRole
2015
Fetal liver hematopoietic stem cell niches associate with portal vessels
Khan J, Mendelson A, Kunisaki Y, Birbrair A, Kou Y, Arnal-Estapé A, Pinho S, Ciero P, Nakahara F, Ma'ayan A, Bergman A, Merad M, Frenette P. Fetal liver hematopoietic stem cell niches associate with portal vessels. Science 2015, 351: 176-180. PMID: 26634440, PMCID: PMC4706788, DOI: 10.1126/science.aad0084.Peer-Reviewed Original Research
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