2023
Female naïve human pluripotent stem cells carry X chromosomes with Xa-like and Xi-like folding conformations
Patterson B, Yang B, Tanaka Y, Kim K, Cakir B, Xiang Y, Kim J, Wang S, Park I. Female naïve human pluripotent stem cells carry X chromosomes with Xa-like and Xi-like folding conformations. Science Advances 2023, 9: eadf2245. PMID: 37540754, PMCID: PMC10403202, DOI: 10.1126/sciadv.adf2245.Peer-Reviewed Original ResearchConceptsNaïve human pluripotent stem cellsHuman pluripotent stem cellsX-chromosome inactivationX chromosomePluripotent stem cellsStem cellsNaïve human embryonic stem cellsX chromosome stateX chromosome statusInactive X chromosomeActive X chromosomeHuman embryonic stem cellsEarly embryonic cellsEmbryonic stem cellsUnique epigenetic regulationChromatin compactionGenomic resolutionEpigenetic regulationChromosome inactivationChromosome stateSomatic cellsEmbryonic cellsChromosomesChromosome statusCells
2022
Getting the right cells
Cakir B, Park IH. Getting the right cells. ELife 2022, 11: e80373. PMID: 35770899, PMCID: PMC9246363, DOI: 10.7554/elife.80373.Peer-Reviewed Original Research
2021
Regeneration of infarcted mouse hearts by cardiovascular tissue formed via the direct reprogramming of mouse fibroblasts
Cho J, Kim S, Lee H, Rah W, Cho HC, Kim NK, Bae S, Shin DH, Lee MG, Park IH, Tanaka Y, Shin E, Yi H, Han JW, Hwang PTJ, Jun HW, Park HJ, Cho K, Lee SW, Jung JK, Levit RD, Sussman MA, Harvey RP, Yoon YS. Regeneration of infarcted mouse hearts by cardiovascular tissue formed via the direct reprogramming of mouse fibroblasts. Nature Biomedical Engineering 2021, 5: 880-896. PMID: 34426676, PMCID: PMC8809198, DOI: 10.1038/s41551-021-00783-0.Peer-Reviewed Original ResearchConceptsDirect reprogrammingMouse tail-tip fibroblastsBone morphogenetic protein 4Smooth muscle cellsTail-tip fibroblastsMuscle cellsSomatic cellsEndothelial cellsReprogrammingCell typesTissue-like structuresMouse fibroblastsProtein 4Gap junctionsCardiovascular tissuesVessel formationDisease modellingDrug discoveryImmature characteristicsFibroblastsCellsMouse heartsCardiomyocytesTissueHost cardiomyocytes
2020
Reprogramming progressive cells display low CAG promoter activity
Hu X, Wu Q, Zhang J, Kim J, Chen X, Hartman AA, Eastman AE, Park I, Guo S. Reprogramming progressive cells display low CAG promoter activity. Stem Cells 2020, 39: 43-54. PMID: 33075202, PMCID: PMC7821215, DOI: 10.1002/stem.3295.Peer-Reviewed Original Research
2019
Engineering of human brain organoids with a functional vascular-like system
Cakir B, Xiang Y, Tanaka Y, Kural MH, Parent M, Kang YJ, Chapeton K, Patterson B, Yuan Y, He CS, Raredon MSB, Dengelegi J, Kim KY, Sun P, Zhong M, Lee S, Patra P, Hyder F, Niklason LE, Lee SH, Yoon YS, Park IH. Engineering of human brain organoids with a functional vascular-like system. Nature Methods 2019, 16: 1169-1175. PMID: 31591580, PMCID: PMC6918722, DOI: 10.1038/s41592-019-0586-5.Peer-Reviewed Original ResearchConceptsHuman cortical organoidsBlood-brain barrier characteristicsTrans-endothelial electrical resistanceVasculature-like structuresHuman brain organoidsHuman brain developmentCortical organoidsFunctional maturationPrenatal brainBrain diseasesBrain developmentHuman embryonic stem cellsBlood vesselsBrain organoidsTight junctionsDiseaseStem cellsOrganoidsVariant 2Nutrient transportersNutrient deliveryCellsEndotheliumMicrovasculature
2016
Single cell transcriptomics reveals unanticipated features of early hematopoietic precursors
Yang J, Tanaka Y, Seay M, Li Z, Jin J, Garmire LX, Zhu X, Taylor A, Li W, Euskirchen G, Halene S, Kluger Y, Snyder MP, Park IH, Pan X, Weissman SM. Single cell transcriptomics reveals unanticipated features of early hematopoietic precursors. Nucleic Acids Research 2016, 45: 1281-1296. PMID: 28003475, PMCID: PMC5388401, DOI: 10.1093/nar/gkw1214.Peer-Reviewed Original ResearchConceptsHematopoietic stem cellsPrecursor cellsInduction of anemiaInterferon response genesG2/M phaseEarly precursor cellsHomeostatic cellsStages of differentiationTranscription factorsSurface markersCell cycle progressionLong-term hematopoietic stem cellsSpecific augmentationAnemic miceMarked increaseEarly hematopoietic precursorsHematopoietic precursorsStem cellsCycle progressionM phaseSingle-cell transcriptomicsCellsCell differentiationHematopoietic stressLineage-specific transcription factors
2015
Transcriptome Signature and Regulation in Human Somatic Cell Reprogramming
Tanaka Y, Hysolli E, Su J, Xiang Y, Kim KY, Zhong M, Li Y, Heydari K, Euskirchen G, Snyder MP, Pan X, Weissman SM, Park IH. Transcriptome Signature and Regulation in Human Somatic Cell Reprogramming. Stem Cell Reports 2015, 4: 1125-1139. PMID: 26004630, PMCID: PMC4471828, DOI: 10.1016/j.stemcr.2015.04.009.Peer-Reviewed Original ResearchMeSH KeywordsAlternative SplicingAnimalsBase SequenceCellular ReprogrammingCyclin EEmbryonic Stem CellsGene Expression RegulationHumansInduced Pluripotent Stem CellsKruppel-Like Factor 4Kruppel-Like Transcription FactorsMiceMolecular Sequence DataOctamer Transcription Factor-3Oncogene ProteinsPolymorphism, Single NucleotidePrincipal Component AnalysisProto-Oncogene Proteins c-mycRNASequence Analysis, RNASOXB1 Transcription FactorsTranscriptomeConceptsHuman somatic cell reprogrammingMonoallelic gene expressionSomatic cell reprogrammingPrevious transcriptome studiesHuman iPSC reprogrammingPluripotent stem cellsCell reprogrammingIPSC reprogrammingTranscriptome dataEarly reprogrammingTranscriptome studiesTranscriptome changesBiallelic expressionRNA-seqSomatic cellsExpression analysisGene expressionSpliced formsReprogrammingTranscriptome signaturesStem cellsInvaluable resourceCellular surface markersBiomedical researchCellsRole of Zscan4 in secondary murine iPSC derivation mediated by protein extracts of ESC or iPSC
Kwon YW, Paek JS, Cho HJ, Lee CS, Lee HJ, Park IH, Roh TY, Kang CM, Yang HM, Park YB, Kim HS. Role of Zscan4 in secondary murine iPSC derivation mediated by protein extracts of ESC or iPSC. Biomaterials 2015, 59: 102-115. PMID: 25956855, DOI: 10.1016/j.biomaterials.2015.03.031.Peer-Reviewed Original ResearchConceptsMES cellsSomatic cellsCell extractsProtein extractsGlobal gene expressionES-like cellsMouse iPS cellsPluripotent stem cellsCell-derived proteinsHistone modificationsFull reprogrammingEpigenetic statusDNA methylationZscan4Developmental potencyIPSC derivationGene expressionGenomic DNAIPS cellsAdult fibroblastsKey moleculesStem cellsProteinCellsColonies
2013
Trivalent Chromatin Marks the Way iN
Hysolli E, Park IH. Trivalent Chromatin Marks the Way iN. Cell Stem Cell 2013, 13: 510-512. PMID: 24209756, PMCID: PMC4665996, DOI: 10.1016/j.stem.2013.10.007.Peer-Reviewed Original ResearchInvestigation of Rett syndrome using pluripotent stem cells
Dajani R, Koo S, Sullivan GJ, Park I. Investigation of Rett syndrome using pluripotent stem cells. Journal Of Cellular Biochemistry 2013, 114: 2446-2453. PMID: 23744605, PMCID: PMC3773984, DOI: 10.1002/jcb.24597.Peer-Reviewed Original ResearchConceptsPluripotent stem cellsStem cellsRett syndromeFunction of MeCP2Pathophysiology of RTTEmbryonic stem cellsEpigenetic instabilityTranscription factorsDe novo mutationsRTT phenotypeCurrent iPSCHuman diseasesMeCP2Novo mutationsIPSCsCellsNeurodevelopmental disordersOverexpressionMutationsPhenotypeMurine modelRecapitulationMaintenanceIdentificationModelling human disease with pluripotent stem cells.
Siller R, Greenhough S, Park IH, Sullivan GJ. Modelling human disease with pluripotent stem cells. Current Gene Therapy 2013, 13: 99-110. PMID: 23444871, PMCID: PMC3785403, DOI: 10.2174/1566523211313020004.Peer-Reviewed Original ResearchConceptsPluripotent stem cellsStem cellsAffected cell typesCellular reprogrammingEndodermal lineagesPluripotent cellsHuman diseasesCell typesGenetic diseasesDisease phenotypeDisease mechanismsDisease modellingTissue of interestPatient tissuesCellsLimitless supplyReprogrammingLineagesRecent progressProgenyPhenotypeTissueTherapeutic interventionsHigh levelsCell technology
2012
Impact of Retrotransposons in Pluripotent Stem Cells
Tanaka Y, Chung L, Park IH. Impact of Retrotransposons in Pluripotent Stem Cells. Molecules And Cells 2012, 34: 509-516. PMID: 23135636, PMCID: PMC3784326, DOI: 10.1007/s10059-012-0242-8.Peer-Reviewed Original ResearchCellular reprogramming: a novel tool for investigating autism spectrum disorders
Kim KY, Jung YW, Sullivan GJ, Chung L, Park IH. Cellular reprogramming: a novel tool for investigating autism spectrum disorders. Trends In Molecular Medicine 2012, 18: 463-471. PMID: 22771169, PMCID: PMC3785941, DOI: 10.1016/j.molmed.2012.06.002.Peer-Reviewed Original ResearchConceptsInduced pluripotent stem cellsNovel ASD genesUse of iPSCsHuman disease modelsPluripotent stem cellsSomatic cellsGenomic technologiesAdvanced geneticsASD genesCellular modelStem cellsScreening platformSmall moleculesDisease modelsNovel toolNeurodevelopmental disordersUnprecedented opportunityCellsGenesGeneticsCell therapyAutism spectrum disorderMurine modelFuture perspectivesReciprocal social interactionReprogramming human somatic cells into induced pluripotent stem cells (iPSCs) using retroviral vector with GFP.
Kim KY, Hysolli E, Park IH. Reprogramming human somatic cells into induced pluripotent stem cells (iPSCs) using retroviral vector with GFP. Journal Of Visualized Experiments 2012 PMID: 22491226, PMCID: PMC3466658, DOI: 10.3791/3804.Peer-Reviewed Original ResearchConceptsHuman embryonic stem cellsInduced pluripotent stem cellsHuman somatic cellsHuman induced pluripotent stem cellsPluripotent stem cellsSomatic cellsIPSC coloniesStem cellsESC culture conditionsEmbryonic stem cellsPluripotency genesTranscription factorsRetroviral transgenesEctopic expressionGFP fluorescenceRetroviral vectorsHuman fibroblast cellsFibroblast cellsGFPCulture conditionsCellsAutologous cellsCellular sourceColoniesSurface markersReprogramming Human Somatic Cells into Induced Pluripotent Stem Cells (iPSCs) Using Retroviral Vector with GFP
Kim K, Hysolli E, Park I. Reprogramming Human Somatic Cells into Induced Pluripotent Stem Cells (iPSCs) Using Retroviral Vector with GFP. Journal Of Visualized Experiments 2012 DOI: 10.3791/3804-v.Peer-Reviewed Original ResearchThe lesser known story of X chromosome reactivation
Hysolli E, Tanaka Y, Kim K, Jung Y, Park IH. The lesser known story of X chromosome reactivation. Cell Cycle 2012, 11: 229-235. PMID: 22234239, PMCID: PMC3293375, DOI: 10.4161/cc.11.2.18998.Peer-Reviewed Original ResearchConceptsX chromosome reactivationX-chromosome inactivationInner cell massActive histone marksGerm cell formationX inactivation signalHistone marksActive chromosomeCellular reprogrammingInactivation signalGene poolPluripotent cellsKey regulatorFemale cellsGene expressionGerm layersCell formationXY cellsCell massImportant mechanismNatural occurrenceCellsReprogrammingChromosomesGenes
2011
Stage-specific signaling through TGFβ family members and WNT regulates patterning and pancreatic specification of human pluripotent stem cells
Nostro M, Sarangi F, Ogawa S, Holtzinger A, Corneo B, Li X, Micallef S, Park I, Basford C, Wheeler M, Daley G, Elefanty A, Stanley E, Keller G. Stage-specific signaling through TGFβ family members and WNT regulates patterning and pancreatic specification of human pluripotent stem cells. Development 2011, 138: 1445-1445. PMCID: PMC3264773, DOI: 10.1242/dev.065904.Peer-Reviewed Original ResearchStage-specific signaling through TGFβ family members and WNT regulates patterning and pancreatic specification of human pluripotent stem cells
Nostro M, Sarangi F, Ogawa S, Holtzinger A, Corneo B, Li X, Micallef S, Park I, Basford C, Wheeler M, Daley G, Elefanty A, Stanley E, Keller G. Stage-specific signaling through TGFβ family members and WNT regulates patterning and pancreatic specification of human pluripotent stem cells. Journal Of Cell Science 2011, 124: e1-e1. DOI: 10.1242/jcs.087957.Peer-Reviewed Original Research
2010
MicroRNA Profiling Reveals Two Distinct p53-Related Human Pluripotent Stem Cell States
Neveu P, Kye MJ, Qi S, Buchholz DE, Clegg DO, Sahin M, Park IH, Kim KS, Daley GQ, Kornblum HI, Shraiman BI, Kosik KS. MicroRNA Profiling Reveals Two Distinct p53-Related Human Pluripotent Stem Cell States. Cell Stem Cell 2010, 7: 671-681. PMID: 21112562, DOI: 10.1016/j.stem.2010.11.012.Peer-Reviewed Original ResearchConceptsInduced pluripotent stem cellsPluripotent stem cell stateEmbryonic stem cellsStem cell stateCell statesDifferentiated cellsStem cellsCell linesPluripotent stem cellsHuman cell linesGene setsMiRNA expression levelsMiR-92Cell line originMicroRNA profilingCancer cell linesLine originMiRNA profilesExpression levelsPluripotencyCancer cellsMiR-141CellsSubtle differencesHESCsLarge intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells
Loewer S, Cabili MN, Guttman M, Loh YH, Thomas K, Park IH, Garber M, Curran M, Onder T, Agarwal S, Manos PD, Datta S, Lander ES, Schlaeger TM, Daley GQ, Rinn JL. Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells. Nature Genetics 2010, 42: 1113-1117. PMID: 21057500, PMCID: PMC3040650, DOI: 10.1038/ng.710.Peer-Reviewed Original ResearchMeSH KeywordsCellular ReprogrammingCluster AnalysisEmbryonic Stem CellsFibroblastsGene Expression RegulationGene Knockdown TechniquesGenetic LociHumansInduced Pluripotent Stem CellsOpen Reading FramesReverse Transcriptase Polymerase Chain ReactionRNA, UntranslatedTranscription FactorsTranscription, Genetic