2019
Differential regulation of OCT4 targets facilitates reacquisition of pluripotency
Thakurela S, Sindhu C, Yurkovsky E, Riemenschneider C, Smith ZD, Nachman I, Meissner A. Differential regulation of OCT4 targets facilitates reacquisition of pluripotency. Nature Communications 2019, 10: 4444. PMID: 31570708, PMCID: PMC6768871, DOI: 10.1038/s41467-019-11741-5.Peer-Reviewed Original ResearchConceptsEctopic transcription factorsReacquisition of pluripotencySomatic cell reprogrammingCis-regulatory elementsTranscription factor expressionExact molecular mechanismsOCT4 targetsPluripotent stem cellsPluripotency inductionCell reprogrammingTranscription factorsSomatic cellsMolecular mechanismsDifferential regulationPluripotencyStem cellsVivo differentiationPrimary targetCellsFactor expressionFinal stepExperimental systemReprogrammingTargetDifferentiation
2016
Probabilistic Modeling of Reprogramming to Induced Pluripotent Stem Cells
Liu LL, Brumbaugh J, Bar-Nur O, Smith Z, Stadtfeld M, Meissner A, Hochedlinger K, Michor F. Probabilistic Modeling of Reprogramming to Induced Pluripotent Stem Cells. Cell Reports 2016, 17: 3395-3406. PMID: 28009305, PMCID: PMC5467646, DOI: 10.1016/j.celrep.2016.11.080.Peer-Reviewed Original ResearchCell DifferentiationCellular ReprogrammingComputer SimulationHumansInduced Pluripotent Stem CellsModels, StatisticalModels, Theoretical
2015
Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency
Cacchiarelli D, Trapnell C, Ziller MJ, Soumillon M, Cesana M, Karnik R, Donaghey J, Smith ZD, Ratanasirintrawoot S, Zhang X, Sui S, Wu Z, Akopian V, Gifford CA, Doench J, Rinn JL, Daley GQ, Meissner A, Lander ES, Mikkelsen TS. Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency. Cell 2015, 162: 412-424. PMID: 26186193, PMCID: PMC4511597, DOI: 10.1016/j.cell.2015.06.016.Peer-Reviewed Original ResearchMeSH KeywordsCellular ReprogrammingChromatinChromatin Assembly and DisassemblyEpigenesis, GeneticGene Expression ProfilingHistone DemethylasesHumansInduced Pluripotent Stem CellsConceptsInduced pluripotencyHuman cellsEmbryonic patterning genesComplementary functional analysesPre-implantation stagesPatterning genesDevelopmental regulatorsEpigenomic analysisMolecular principlesNovel regulatorFunctional analysisIntegrative analysisIntercellular heterogeneityMolecular underpinningsPluripotencyDisease modelingCell platformRegulatorCellsDistinct wavesDonor variabilityGenes
2011
Reference Maps of Human ES and iPS Cell Variation Enable High-Throughput Characterization of Pluripotent Cell Lines
Bock C, Kiskinis E, Verstappen G, Gu H, Boulting G, Smith ZD, Ziller M, Croft GF, Amoroso MW, Oakley DH, Gnirke A, Eggan K, Meissner A. Reference Maps of Human ES and iPS Cell Variation Enable High-Throughput Characterization of Pluripotent Cell Lines. Cell 2011, 144: 439-452. PMID: 21295703, PMCID: PMC3063454, DOI: 10.1016/j.cell.2010.12.032.Peer-Reviewed Original ResearchMeSH KeywordsCell DifferentiationCell LineDNA MethylationEmbryonic Stem CellsGene Expression ProfilingHumansInduced Pluripotent Stem CellsConceptsPluripotent cell linesEmbryonic stemPluripotent stem cellsCell linesDisease-relevant cell typesHuman iPS cell linesStem cellsReference mapHuman pluripotent stem cellsHuman embryonic stemIPS cell linesDifferentiation propensityDNA methylationIndividual cell linesHigh-throughput characterizationTranscriptional similarityGene expressionIPS cellsCell typesDifferentiation efficiencyDevelopmental potentialBiomedical researchComprehensive characterizationSpecific differencesCellsReprogramming Factor Expression Initiates Widespread Targeted Chromatin Remodeling
Koche RP, Smith ZD, Adli M, Gu H, Ku M, Gnirke A, Bernstein BE, Meissner A. Reprogramming Factor Expression Initiates Widespread Targeted Chromatin Remodeling. Cell Stem Cell 2011, 8: 96-105. PMID: 21211784, PMCID: PMC3220622, DOI: 10.1016/j.stem.2010.12.001.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCellular ReprogrammingChromatinChromatin Assembly and DisassemblyEpigenesis, GeneticFibroblastsHistonesInduced Pluripotent Stem CellsMethylationMiceTranscription FactorsTranscriptional ActivationConceptsPluripotent stem cell stateEuchromatic histone modificationsRepressive H3K27me3 modificationGenome-wide changesStem cell stateChromatin remodelingH3K4 methylationHistone modificationsH3K27me3 modificationEpigenetic responsesTranscriptional changesSomatic cellsRegulatory eventsGene promoterEpigenetic changesCell statesCorresponding lociSomatic identityMechanistic questionsFactor inductionEarly eventsLociH3K4me2ReprogrammingRapid progress
2010
Highly Efficient Reprogramming to Pluripotency and Directed Differentiation of Human Cells with Synthetic Modified mRNA
Warren L, Manos PD, Ahfeldt T, Loh YH, Li H, Lau F, Ebina W, Mandal PK, Smith ZD, Meissner A, Daley GQ, Brack AS, Collins JJ, Cowan C, Schlaeger TM, Rossi DJ. Highly Efficient Reprogramming to Pluripotency and Directed Differentiation of Human Cells with Synthetic Modified mRNA. Cell Stem Cell 2010, 7: 618-630. PMID: 20888316, PMCID: PMC3656821, DOI: 10.1016/j.stem.2010.08.012.Peer-Reviewed Original ResearchMeSH KeywordsCell DifferentiationCell LineageCells, CulturedCellular ReprogrammingHumansInduced Pluripotent Stem CellsRNA, MessengerConceptsInduced pluripotent stem cellsPluripotent stem cellsCell fateMultiple human cell typesSomatic cell reprogrammingCell typesUseful cell typesStem cellsHuman cell typesPatient-specific induced pluripotent stem cellsCell reprogrammingCellular reprogrammingInnate antiviral responseDirected DifferentiationIPSC derivationHuman cellsMyogenic cellsSynthetic mRNAAntiviral responseDisease modelingReprogrammingModified mRNARegenerative medicineFateMRNA