2025
Acute inflammation induces acute megakaryopoiesis with impaired platelet production during fetal hematopoiesis.
Hu X, He Y, Li S, Jiang Y, Yu R, Wu Y, Fu X, Song Y, Lin C, Shi J, Li H, Gao Y. Acute inflammation induces acute megakaryopoiesis with impaired platelet production during fetal hematopoiesis. Development 2025, 152 PMID: 39817838, DOI: 10.1242/dev.204226.Peer-Reviewed Original ResearchFetal hematopoiesisMegakaryocyte-erythroid progenitorsAcute inflammationInterferon-stimulated genesDouble-stranded RNAMegakaryocyte maturationPlatelet productionImpaired platelet productionFormation of double-stranded RNADownstream interferon-stimulated genesCell fate determinationRNA m6A modificationPhosphorylation of STAT1Hematopoietic progenitorsMegakaryocyte progenitorsHematopoietic cellsM6A methyltransferase METTL3Hematopoietic developmentGene expression analysisImmune responseMegakaryopoiesisHematopoiesisInflammationFate determinationIGF1 expression
2024
Neuropeptide signalling orchestrates T cell differentiation
Hou Y, Sun L, LaFleur M, Huang L, Lambden C, Thakore P, Geiger-Schuller K, Kimura K, Yan L, Zang Y, Tang R, Shi J, Barilla R, Deng L, Subramanian A, Wallrapp A, Choi H, Kye Y, Ashenberg O, Schiebinger G, Doench J, Chiu I, Regev A, Sharpe A, Kuchroo V. Neuropeptide signalling orchestrates T cell differentiation. Nature 2024, 635: 444-452. PMID: 39415015, DOI: 10.1038/s41586-024-08049-w.Peer-Reviewed Original ResearchMeSH KeywordsActivating Transcription Factor 3AnimalsCalcitonin Gene-Related PeptideCalcitonin Receptor-Like ProteinCell DifferentiationCyclic AMP Response Element-Binding ProteinFemaleMaleMiceMice, Inbred C57BLReceptor Activity-Modifying Protein 3Signal TransductionSTAT1 Transcription FactorTh1 CellsTh2 CellsConceptsT helper type 1Acute viral infectionActivating transcription factor 3Th1 cell differentiationCAMP response element-binding proteinViral infectionCell differentiationNeuropeptide CGRPFate determinationT cellsCD8+ T cell responsesDifferentiation of Th2 cellsIn vitro polarizationT cell fate determinationT cell responsesTh1 cell responsesCell fate determinationIn vivo CRISPR screeningDownstream cAMP response element-binding proteinT cell differentiationT helper cell differentiationIn vivo differentiationResponse element-binding proteinElement-binding proteinNeuroimmune circuitsHox Genes
Duraiswamy A, Senkumar L, De Kumar B. Hox Genes. 2024 DOI: 10.1016/b978-0-12-822563-9.00196-7.Peer-Reviewed Original ResearchHox genesAberrant expression of HOX genesCell fate determinationExpression of Hox genesFate determinationTissue homeostasisMetastatic behavior of tumorsCell migrationGenesDevelopmental eventsDevelopmental defectsHoxCancer progressionAberrant expressionMetastatic behaviorBehavior of tumorsCellsDisease progressionDisease prognosisProteinHomeostasisOrganogenesisPrognosis
2023
KDM5 Lysine Demethylases in Pathogenesis, from Basic Science Discovery to the Clinic
Zhang S, Cao J, Yan Q. KDM5 Lysine Demethylases in Pathogenesis, from Basic Science Discovery to the Clinic. Advances In Experimental Medicine And Biology 2023, 1433: 113-137. PMID: 37751138, DOI: 10.1007/978-3-031-38176-8_6.ChaptersConceptsPlant homeodomainFamily proteinsKey epigenetic markCell fate determinationHistone methylation marksCancer type-dependent mannerKetoglutarate-dependent dioxygenasesSelective KDM5 inhibitorsTumor suppressive functionType-dependent mannerEpigenetic marksTumor suppressive roleFate determinationJumonji CLysine 4Active chromatinMethylation marksHistone H3Lysine demethylasesCatalytic coreKDM5 inhibitorsDrug targetsKDM5Cancer metastasisSuppressive role
2021
Integrative epigenomic and high-throughput functional enhancer profiling reveals determinants of enhancer heterogeneity in gastric cancer
Sheng T, Ho S, Ooi W, Xu C, Xing M, Padmanabhan N, Huang K, Ma L, Ray M, Guo Y, Sim N, Anene-Nzelu C, Chang M, Razavi-Mohseni M, Beer M, Foo R, Sundar R, Chan Y, Tan A, Ong X, Skanderup A, White K, Jha S, Tan P. Integrative epigenomic and high-throughput functional enhancer profiling reveals determinants of enhancer heterogeneity in gastric cancer. Genome Medicine 2021, 13: 158. PMID: 34635154, PMCID: PMC8504099, DOI: 10.1186/s13073-021-00970-3.Peer-Reviewed Original ResearchMeSH KeywordsAcetylationADP-Ribosylation FactorsCell Line, TumorCell ProliferationChromatinEnhancer Elements, GeneticEpigenomicsGene Expression Regulation, NeoplasticGenomicsHistonesHumansInhibitor of Growth Protein 1OncogenesPromoter Regions, GeneticRNA-SeqStomach NeoplasmsTranscriptomeWhole Genome SequencingConceptsSingle nucleotide polymorphismsActivity-by-contactEnhancer-promoter interactionsSomatic copy number alterationsGermline single nucleotide polymorphismsHistone modificationsDistal cis-regulatory elementsLow somatic mutation rateCell-specific gene expressionCis-regulatory elementsFunctional enhancer activityHistone modification profilesWhole-genome sequencingRegulatory region sequencingCell fate determinationSuper-enhancer regionsCopy number alterationsGenome copy numberEffect of histone acetylationSomatic mutation rateCancer-relevant genesFunctional assay dataEnhanced activityGC cell linesRegion sequences
2020
Genome-wide CRISPR screen identifies ZIC2 as an essential gene that controls the cell fate of early mesodermal precursors to human heart progenitors
Xu J, Zhou C, Foo K, Yang R, Xiao Y, Bylund K, Sahara M, Chien K. Genome-wide CRISPR screen identifies ZIC2 as an essential gene that controls the cell fate of early mesodermal precursors to human heart progenitors. Stem Cells 2020, 38: 741-755. PMID: 32129551, PMCID: PMC7891398, DOI: 10.1002/stem.3168.Peer-Reviewed Original ResearchConceptsHuman pluripotent stem cellsCRISPR knockout screensCell fateProgenitor formationEssential genesHuman cardiogenesisGenome-wide CRISPR knockout screenProgenitor cell fate determinationEarly mesodermal precursorsSingle-cell RNA-seq analysisMesoderm precursor cellsCell fate determinationDevelopmental signaling cascadesProgenitor cell fateRNA-seq analysisRNA-seq profilingMultiple gene setsPluripotent stem cellsMesoderm formationMesodermal precursorsHeart progenitorsCommitted stepMesodermal formationGene setsMaster regulator
2017
New Advances in Human X Chromosome Status from a Developmental and Stem Cell Biology
Patterson B, Tanaka Y, Park IH. New Advances in Human X Chromosome Status from a Developmental and Stem Cell Biology. Tissue Engineering And Regenerative Medicine 2017, 14: 643-652. PMID: 29276809, PMCID: PMC5738034, DOI: 10.1007/s13770-017-0096-4.Peer-Reviewed Original ResearchPluripotent stem cellsX chromosome statusStem cell biologyCell biologyX chromosome dosage compensationStem cellsDosage compensation processX-chromosome regulationChromosome dosage compensationHuman PSCsCell fate determinationActive X chromosomeChromosome statusEmbryonic stem cellsHuman pluripotent stem cellsHuman preimplantation embryosSpecific lincRNAsDosage compensationChromosome architectureChromosome regulationFate determinationImprinting statusEpigenetic dysregulationX chromosomePreimplantation embryosDevelopmentally regulated higher-order chromatin interactions orchestrate B cell fate commitment
Boya R, Yadavalli AD, Nikhat S, Kurukuti S, Palakodeti D, Pongubala JMR. Developmentally regulated higher-order chromatin interactions orchestrate B cell fate commitment. Nucleic Acids Research 2017, 45: 11070-11087. PMID: 28977418, PMCID: PMC5737614, DOI: 10.1093/nar/gkx722.Peer-Reviewed Original ResearchConceptsChromatin reorganizationHigher-order chromatin interactionsGenome-wide expression profilesCell fate choiceCell fate determinationCell fate commitmentHi-C analysisMulti-potent progenitorsB cell fate determinationGene expression patternsB cell fate choicesChromatin architectureGenome architectureGenome organizationChromatin interactionsTranscription regulationEpigenetic landscapeFate determinationGenomic lociFate commitmentB compartmentsCommitted stateDevelopmental switchInteraction landscapeExpression patternsAbstract 5020: A genome-scale ORF screen reveals an alternative splicing program that regulates mesenchymal and stem-like cell states in breast cancer
Li J, Choi P, Chaffer C, Labella K, Kim J, Doench J, Dai C, Giacomelli A, Ly S, Hwang J, Hong A, Ilic N, Gjoerup O, Meyerson M, Brooks A, Weinberg R, Hahn W. Abstract 5020: A genome-scale ORF screen reveals an alternative splicing program that regulates mesenchymal and stem-like cell states in breast cancer. Cancer Research 2017, 77: 5020-5020. DOI: 10.1158/1538-7445.am2017-5020.Peer-Reviewed Original ResearchAlternative splicing programFilamin BSplicing factorsGene set enrichment analysisAlternative splicingCell statesSplicing programCD44 cell surface markersRegulation of EMTShort isoformStem-like stateDownstream targetsStem cell fate determinationCell fate determinationRNA splicing factorsHuman mammary epithelial cellsBreast cancer patient samplesMammary epithelial cellsBreast cancer cell linesRNA sequencing analysisTumor formation in vivoAssociated with stem cell propertiesBasal-like breast cancerCancer patient samplesStem-like traitsChapter 15 Comparative Functions of miRNAs in Embryonic Neurogenesis and Neuronal Network Formation
Ristori E, Nicoli S. Chapter 15 Comparative Functions of miRNAs in Embryonic Neurogenesis and Neuronal Network Formation. 2017, 265-282. DOI: 10.1016/b978-0-12-804402-5.00015-7.Peer-Reviewed Original ResearchTarget mRNA degradationCell fate determinationGene regulatory pathwaysDynamic spatiotemporal expressionImportance of miRNAsSmall noncoding RNAsStem cell proliferationMulticellular organismsFate determinationMost miRNAsNeuronal network formationTranslational repressionModel organismsNeural stem cell proliferationMRNA degradationPosttranscriptional regulatorsNoncoding RNAsRegulatory pathwaysDevelopmental processesEmbryonic neurogenesisGene expressionSpatiotemporal expressionNovel roleNeuronal differentiationMiRNAs
2015
Choosing Cell Fate Through a Dynamic Cell Cycle
Chen X, Hartman A, Guo S. Choosing Cell Fate Through a Dynamic Cell Cycle. Current Stem Cell Reports 2015, 1: 129-138. PMID: 28725536, PMCID: PMC5487535, DOI: 10.1007/s40778-015-0018-0.Peer-Reviewed Original ResearchCell fate changesCell fateCell cycle dynamicsFate changesSomatic cellsDifferentiated somatic cell typesCell cycleCell fate specificationCell fate determinationInduction of pluripotencyTranscription factor concentrationsSomatic cell typesFate specificationFate determinationCell cycle accelerationCycle dynamicsTissue homeostasisDevelopmental systemsYamanaka factorsCell typesNormal developmentPluripotencyRecent discoveryReprogrammingFate
2011
Biochemical and Morphological Effects of Hypoxic Environment on Human Embryonic Stem Cells in Long-Term Culture and Differentiating Embryoid Bodies
Lim H, Han J, Woo D, Kim S, Kim S, Kang H, Kim J. Biochemical and Morphological Effects of Hypoxic Environment on Human Embryonic Stem Cells in Long-Term Culture and Differentiating Embryoid Bodies. Molecules And Cells 2011, 31: 123-132. PMID: 21347709, PMCID: PMC3932683, DOI: 10.1007/s10059-011-0016-8.Peer-Reviewed Original ResearchConceptsHuman embryonic stem cellsMild hypoxiaEmbryonic stem cellsEmbryoid bodiesLong-term cultureBrdU incorporationCell fate determinationDifferentiating embryoid bodiesExpression of markersCaspase-3 immunostainingStem cellsPercentage of cellsEmbryonic germ layersActive caspase-3Hematoxylineosin stainingMammalian reproductive tract
2008
Timing cell-fate determination during asymmetric cell divisions
Zhong W. Timing cell-fate determination during asymmetric cell divisions. Current Opinion In Neurobiology 2008, 18: 472-478. PMID: 18983918, PMCID: PMC2609754, DOI: 10.1016/j.conb.2008.10.005.Peer-Reviewed Original ResearchConceptsAsymmetric cell divisionCell divisionCell cycle progressionFate determinantsCell fate determinantsCell fate determinationCell fateDaughter cellsCellular organellesMolecular mechanismsCell cycleGolgi apparatusIntracellular signalingSubcellular distributionDifferent fatesCell typesNovel mechanismCell proliferationMolecular compositionMultiple roundsRecent findingsDivisionFateInvertebratesCentrosomesGATA4 mediates gene repression in the mature mouse small intestine through interactions with friend of GATA (FOG) cofactors
Beuling E, Bosse T, de Kerk D, Piaseckyj CM, Fujiwara Y, Katz SG, Orkin SH, Grand RJ, Krasinski SD. GATA4 mediates gene repression in the mature mouse small intestine through interactions with friend of GATA (FOG) cofactors. Developmental Biology 2008, 322: 179-189. PMID: 18692040, PMCID: PMC3031907, DOI: 10.1016/j.ydbio.2008.07.022.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBiomarkersCell DifferentiationCell ProliferationEnterocytesGATA4 Transcription FactorGene Expression RegulationIntestinal AbsorptionIntestinal MucosaIntestine, SmallMiceMice, TransgenicNuclear ProteinsOrgan SpecificityOrganic Anion Transporters, Sodium-DependentRNA, MessengerSymportersTranscription FactorsTranscriptional ActivationConceptsFriend of GATAGene repressionCell fate determinationFamily of cofactorsMammalian small intestineProximal-distal patternRepression functionGata (FOG) cofactorsFate determinationCell lineage markersFOG cofactorsGATA factorsGATA4 mutantsGene activationTranscription factorsGATA4 functionIntestinal epithelial cellsGATA4Multiple tissuesRepressionLineage markersMouse small intestineCofactorEpithelial cellsGenes
2004
GEFT, A Rho Family Guanine Nucleotide Exchange Factor, Regulates Neurite Outgrowth and Dendritic Spine Formation*
Bryan B, Kumar V, Stafford L, Cai Y, Wu G, Liu M. GEFT, A Rho Family Guanine Nucleotide Exchange Factor, Regulates Neurite Outgrowth and Dendritic Spine Formation*. Journal Of Biological Chemistry 2004, 279: 45824-45832. PMID: 15322108, DOI: 10.1074/jbc.m406216200.Peer-Reviewed Original ResearchMeSH KeywordsAnimalscdc42 GTP-Binding ProteinCells, CulturedGuanine Nucleotide Exchange FactorsHumansNeuritesNF-kappa Bp21-Activated KinasesProtein Serine-Threonine Kinasesrac1 GTP-Binding ProteinRatsRats, Sprague-DawleyRho Guanine Nucleotide Exchange FactorsTranscription Factor AP-1Transcriptional ActivationConceptsGuanine nucleotide exchange factorsNucleotide exchange factorsExchange factorRho family guanine nucleotide-exchange factorNeurite outgrowthState of Rac1Dendritic spine formationCell fate determinationActin cytoskeletal organizationExchange of GDPActivation of RacNormal cell growthRac1/Cdc42Spine formationFate determinationEukaryotic cellsGene regulationNeuroblastoma cellsSmall GTPasesActive GTPDbl familyRho familyCellular processesRho GTPasesCytoskeletal organization
2003
Diversifying Neural Cells through Order of Birth and Asymmetry of Division
Zhong W. Diversifying Neural Cells through Order of Birth and Asymmetry of Division. Neuron 2003, 37: 11-14. PMID: 12526768, DOI: 10.1016/s0896-6273(02)01178-9.Peer-Reviewed Original ResearchConceptsAsymmetry of divisionCell fate diversificationCell fate determinationAsymmetric cell divisionMature nervous systemFate diversificationDrosophila genesFate determinationCell divisionCell typesProgenitor cellsNeural cellsDevelopmental neurobiologyNervous systemCommon setCellsDivisionGenesDiversityDiversificationKey questions
2000
Plasma Membrane Compartmentalization in Yeast by Messenger RNA Transport and a Septin Diffusion Barrier
Takizawa P, DeRisi J, Wilhelm J, Vale R. Plasma Membrane Compartmentalization in Yeast by Messenger RNA Transport and a Septin Diffusion Barrier. Science 2000, 290: 341-344. PMID: 11030653, DOI: 10.1126/science.290.5490.341.Peer-Reviewed Original ResearchMeSH KeywordsActomyosinBiological TransportCell CompartmentationCell CycleCell Cycle ProteinsCell MembraneCytoskeletal ProteinsDiffusionDNA-Binding ProteinsFungal ProteinsMembrane ProteinsMutationMyosin Heavy ChainsMyosin Type VMyosinsOligonucleotide Array Sequence AnalysisRecombinant Fusion ProteinsRepressor ProteinsRNA, FungalRNA, MessengerSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsTemperatureTranscription FactorsConceptsPlasma membrane compartmentalizationCell fate determinationMembrane diffusion barrierMother-bud neckProtein-encoding mRNAsPlasma membrane compartmentMessenger RNA transportDNA microarray analysisCell polarityFate determinationMembrane compartmentalizationAsymmetric localizationBud tipMembrane compartmentsCellular processesRNA transportMother cellsMRNA localizationMicroarray analysisYeastEpithelial cellsProteinKey roleCellsLocalizationA carboxy-terminal deletion mutant of Notch1 accelerates lymphoid oncogenesis in E2A-PBX1 transgenic mice.
Feldman B, Hampton T, Cleary M. A carboxy-terminal deletion mutant of Notch1 accelerates lymphoid oncogenesis in E2A-PBX1 transgenic mice. Blood 2000, 96: 1906-13. PMID: 10961893, DOI: 10.1182/blood.v96.5.1906.h8001906_1906_1913.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsAnimals, NewbornBase SequenceFemaleGene DeletionGene Expression Regulation, NeoplasticHomeodomain ProteinsLymphoma, T-CellMaleMembrane ProteinsMiceMice, TransgenicMolecular Sequence DataMoloney murine leukemia virusMutationOncogene Proteins, FusionReceptor, Notch1Receptors, Cell SurfaceRetroviridae InfectionsSurvival AnalysisThymus NeoplasmsTranscription FactorsConceptsE2A-PBX1 transgenic miceTransgenic miceE2A-PBX1E2a-Pbx1 chimeric proteinsDevelopment of T-cell tumorsCarboxy-terminal deletion mutantsShortened latencyHox DNA binding partnersNegative regulatory sequencesDNA-binding partnerCell fate determinationCarboxy-terminal regionT-cell tumorsActivation of Notch1Region of Notch1E2A geneRegulatory sequencesBinding partnersFate determinationGenetic screeningChimeric proteinTruncating mutationsAcute leukemiaChromosomal translocationsRetroviral insertionA carboxy-terminal deletion mutant of Notch1accelerates lymphoid oncogenesis in E2A-PBX1transgenic mice
Feldman B, Hampton T, Cleary M. A carboxy-terminal deletion mutant of Notch1accelerates lymphoid oncogenesis in E2A-PBX1transgenic mice. Blood 2000, 96: 1906-1913. DOI: 10.1182/blood.v96.5.1906.Peer-Reviewed Original ResearchTransgenic miceE2A-PBX1E2a-Pbx1 chimeric proteinsShortened latencyDevelopment of T-cell tumorsE2A-PBX1 transgenic miceCarboxy-terminal deletion mutantsNegative regulatory sequencesHox DNA binding partnersDNA-binding partnerCell fate determinationT-cell tumorsE2A geneRegulatory sequencesBinding partnersAcute leukemiaFate determinationGenetic screeningChimeric proteinChromosomal translocationsTruncating mutationsTumor developmentNotch1 geneRetroviral infectionRetroviral insertionThe subcellular localization of OTX2 is cell-type specific and developmentally regulated in the mouse retina
Baas D, Bumsted KM, Martinez JA, Vaccarino FM, Wikler KC, Barnstable CJ. The subcellular localization of OTX2 is cell-type specific and developmentally regulated in the mouse retina. Brain Research 2000, 78: 26-37. PMID: 10891582, DOI: 10.1016/s0169-328x(00)00060-7.Peer-Reviewed Original ResearchMeSH Keywords3T3 CellsAnimalsAntibodiesBlotting, WesternCell NucleusCytoplasmGene Expression Regulation, DevelopmentalHomeodomain ProteinsHumansMiceMice, Inbred StrainsNerve Tissue ProteinsOtx Transcription FactorsPC12 CellsPigment Epithelium of EyeRabbitsRatsRetinal Ganglion CellsRetinal Rod Photoreceptor CellsTeratocarcinomaTrans-ActivatorsTransfectionTumor Cells, CulturedConceptsSubcellular localizationTranscription factorsHomeodomain-containing proteinCell fate determinationHomeodomain transcription factorCytoplasm of rodsFate determinationCell fateOtx2 proteinSubcellular distributionOtx2Retinal pigment epithelial cellsCell typesRod photoreceptorsPigment epithelial cellsRetinal developmentCytoplasmCell linesAdult eyesEpithelial cellsCentral nervous systemImmature rodsProteinCellsDifferential distribution
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