2021
Early developmental asymmetries in cell lineage trees in living individuals
Fasching L, Jang Y, Tomasi S, Schreiner J, Tomasini L, Brady MV, Bae T, Sarangi V, Vasmatzis N, Wang Y, Szekely A, Fernandez TV, Leckman JF, Abyzov A, Vaccarino FM. Early developmental asymmetries in cell lineage trees in living individuals. Science 2021, 371: 1245-1248. PMID: 33737484, PMCID: PMC8324008, DOI: 10.1126/science.abe0981.Peer-Reviewed Original ResearchCell-to-Cell Adhesion and Neurogenesis in Human Cortical Development: A Study Comparing 2D Monolayers with 3D Organoid Cultures
Scuderi S, Altobelli GG, Cimini V, Coppola G, Vaccarino FM. Cell-to-Cell Adhesion and Neurogenesis in Human Cortical Development: A Study Comparing 2D Monolayers with 3D Organoid Cultures. Stem Cell Reports 2021, 16: 264-280. PMID: 33513360, PMCID: PMC7878838, DOI: 10.1016/j.stemcr.2020.12.019.Peer-Reviewed Original Research
2020
SCELLECTOR: ranking amplification bias in single cells using shallow sequencing
Sarangi V, Jourdon A, Bae T, Panda A, Vaccarino F, Abyzov A. SCELLECTOR: ranking amplification bias in single cells using shallow sequencing. BMC Bioinformatics 2020, 21: 521. PMID: 33183232, PMCID: PMC7663899, DOI: 10.1186/s12859-020-03858-y.Peer-Reviewed Original ResearchConceptsMultiple displacement amplificationShallow sequencingSingle-cell platformsSingle-cell sequencingCoverage sequencing dataSingle cellsHuman neuronal cellsMosaic mutationsAmount of DNAAmplification qualityCell sequencingCoverage sequencingHigh-coverage dataSequencing dataHaplotype informationPhi29 polymeraseDNA damageIndividual cellsNeuronal cellsSequencingAmplification biasAllelic imbalancePresence of sitesMutationsFragment lengthCell Lineage Tracing and Cellular Diversity in Humans
Abyzov A, Vaccarino FM. Cell Lineage Tracing and Cellular Diversity in Humans. Annual Review Of Genomics And Human Genetics 2020, 21: 101-116. PMID: 32413272, DOI: 10.1146/annurev-genom-083118-015241.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsMeSH KeywordsCell DifferentiationCell LineageCell NucleusDevelopmental BiologyDNA MethylationDNA, MitochondrialEmbryo, MammalianHumansSingle-Cell AnalysisConceptsLineage tracingLineage mapCell lineage mapCell lineage tracingDNA methylation statusComplex biological processesMultiple cell typesMulticellular organismsCellular diversityMitochondrial DNALineage hierarchyCell lineagesBiological processesNatural variationCell typesMethylation statusLineagesNoncancerous cellsRecent studiesFetal developmentGeneral conceptual designCellsOrganismsHumansDNA
2019
Breakthrough Moments: Yoshiki Sasai’s Discoveries in the Third Dimension
Mariani J, Vaccarino FM. Breakthrough Moments: Yoshiki Sasai’s Discoveries in the Third Dimension. Cell Stem Cell 2019, 24: 837-838. PMID: 31173711, PMCID: PMC7085937, DOI: 10.1016/j.stem.2019.05.007.Commentaries, Editorials and Letters
2018
iPSC-derived neurons profiling reveals GABAergic circuit disruption and acetylated α-tubulin defect which improves after iHDAC6 treatment in Rett syndrome
Landucci E, Brindisi M, Bianciardi L, Catania LM, Daga S, Croci S, Frullanti E, Fallerini C, Butini S, Brogi S, Furini S, Melani R, Molinaro A, Lorenzetti FC, Imperatore V, Amabile S, Mariani J, Mari F, Ariani F, Pizzorusso T, Pinto AM, Vaccarino FM, Renieri A, Campiani G, Meloni I. iPSC-derived neurons profiling reveals GABAergic circuit disruption and acetylated α-tubulin defect which improves after iHDAC6 treatment in Rett syndrome. Experimental Cell Research 2018, 368: 225-235. PMID: 29730163, PMCID: PMC9410763, DOI: 10.1016/j.yexcr.2018.05.001.Peer-Reviewed Original ResearchMeSH KeywordsAcetylationCell DifferentiationFemaleGABAergic NeuronsHistone Deacetylase 6HumansInduced Pluripotent Stem CellsMaleRett SyndromeTubulinConceptsInduced pluripotent stem cellsRett syndromeCircuit disruptionΑ-tubulin deacetylaseNew therapeutic strategiesClassic Rett syndromeCommon neurodevelopmental disorderAcetylated α-tubulinEpileptic behaviorTherapeutic strategiesPathogenic mechanismsPluripotent stem cellsCytoskeleton dynamicsGenetic reprogrammingSyndromeTranscriptome changesRNA-seqNeurodevelopmental disordersSignificant decreaseNeuronsSelective inhibitorPatientsMECP2 geneΑ-tubulinTreatment
2013
Functional genomic screen of human stem cell differentiation reveals pathways involved in neurodevelopment and neurodegeneration
Zhang Y, Schulz VP, Reed BD, Wang Z, Pan X, Mariani J, Euskirchen G, Snyder MP, Vaccarino FM, Ivanova N, Weissman SM, Szekely AM. Functional genomic screen of human stem cell differentiation reveals pathways involved in neurodevelopment and neurodegeneration. Proceedings Of The National Academy Of Sciences Of The United States Of America 2013, 110: 12361-12366. PMID: 23836664, PMCID: PMC3725080, DOI: 10.1073/pnas.1309725110.Peer-Reviewed Original ResearchMeSH KeywordsAutistic DisorderCell DifferentiationGene SilencingGene TargetingGenome, HumanHumansIntellectual DisabilityNeuronsRNAStem CellsConceptsHuman embryonic stem cellsFunctional genomic screensGenomic screenUndifferentiated human embryonic stem cellsNeural lineage developmentSet of genesHuman stem cell differentiationProgenitor cell formationEmbryonic stem cellsStem cell differentiationRNA library screenNeuronal progenitor cellsLate-onset neurodegenerative disorderUnpredicted genesRNA granulesNext-generation sequencingSelf-renewal capacityLineage developmentComplex inheritanceShRNA libraryEarly neurogenesisLibrary screenParallel sequencingCell differentiationGenes
2012
Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells
Abyzov A, Mariani J, Palejev D, Zhang Y, Haney MS, Tomasini L, Ferrandino AF, Rosenberg Belmaker LA, Szekely A, Wilson M, Kocabas A, Calixto NE, Grigorenko EL, Huttner A, Chawarska K, Weissman S, Urban AE, Gerstein M, Vaccarino FM. Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells. Nature 2012, 492: 438-442. PMID: 23160490, PMCID: PMC3532053, DOI: 10.1038/nature11629.Peer-Reviewed Original ResearchOligodendrocyte Regeneration after Neonatal Hypoxia Requires FoxO1-Mediated p27Kip1 Expression
Jablonska B, Scafidi J, Aguirre A, Vaccarino F, Nguyen V, Borok E, Horvath TL, Rowitch DH, Gallo V. Oligodendrocyte Regeneration after Neonatal Hypoxia Requires FoxO1-Mediated p27Kip1 Expression. Journal Of Neuroscience 2012, 32: 14775-14793. PMID: 23077062, PMCID: PMC3517297, DOI: 10.1523/jneurosci.2060-12.2012.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAnimals, NewbornCell DifferentiationCells, CulturedCyclin-Dependent Kinase Inhibitor p27Forkhead Box Protein O1Forkhead Transcription FactorsGene Expression Regulation, DevelopmentalHumansHypoxia, BrainInfantInfant, NewbornMiceMice, 129 StrainMice, Inbred C57BLMice, KnockoutMice, TransgenicNerve RegenerationOligodendrogliaConceptsDiffuse white matter injuryNeonatal hypoxiaOligodendrocyte regenerationOligodendrocyte progenitor cell proliferationWhite matter injuryWhite matter lesionsPermanent neurodevelopmental disabilityCritical developmental time windowWhite matter developmentOverexpression of FoxO1Preterm infantsProgenitor cell proliferationDevelopmental time windowMatter lesionsOligodendrocyte deathAbnormal myelinationNeurodevelopmental disabilitiesMouse modelBiphasic effectP27Kip1 expressionNull miceOligodendrogenesisHypoxiaOligodendrocyte differentiationOligodendrocyte developmentNeurobiology meets genomic science: The promise of human-induced pluripotent stem cells
Stevens HE, Mariani J, Coppola G, Vaccarino FM. Neurobiology meets genomic science: The promise of human-induced pluripotent stem cells. Development And Psychopathology 2012, 24: 1443-1451. PMID: 23062309, PMCID: PMC3513939, DOI: 10.1017/s095457941200082x.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsMeSH KeywordsBrainCell DifferentiationEpigenesis, GeneticHuman DevelopmentHumansInduced Pluripotent Stem CellsModels, GeneticNeuronsConceptsHuman-induced pluripotent stem cellsPluripotent stem cellsStem cellsNeuronal cellsInduced pluripotent stem cell (iPSC) technologyPluripotent stem cell (iPSC) technologyNormal human brain developmentHuman genesSomatic cellsCell biologyStem cell technologyGene transcriptsHuman brain developmentAspects of developmentMessenger RNADevelopmental stepsGenomic scienceBiologySeries of eventsCellsBrain developmentGenesGeneticsHuman individualsTranscriptsEnvironmental Enrichment Increases the GFAP+ Stem Cell Pool and Reverses Hypoxia-Induced Cognitive Deficits in Juvenile Mice
Salmaso N, Silbereis J, Komitova M, Mitchell P, Chapman K, Ment LR, Schwartz ML, Vaccarino FM. Environmental Enrichment Increases the GFAP+ Stem Cell Pool and Reverses Hypoxia-Induced Cognitive Deficits in Juvenile Mice. Journal Of Neuroscience 2012, 32: 8930-8939. PMID: 22745493, PMCID: PMC3399175, DOI: 10.1523/jneurosci.1398-12.2012.Peer-Reviewed Original ResearchMeSH KeywordsAnalysis of VarianceAnimalsAnimals, NewbornBromodeoxyuridineCell CountCell DifferentiationCognition DisordersDeoxyuridineDisease Models, AnimalEnvironmentEstrogen AntagonistsFemaleGene Expression Regulation, DevelopmentalGlial Fibrillary Acidic ProteinGreen Fluorescent ProteinsHumansHypoxiaIdoxuridineKi-67 AntigenMaleMaze LearningMiceMice, Inbred C57BLMice, TransgenicNerve Tissue ProteinsNeurogenesisNeurogliaReceptors, EstrogenStem CellsTamoxifenConceptsHypoxic injuryBrain injuryAstroglial cellsChronic hypoxic injuryDevelopmental brain injuryLow birth weightCell poolEnvironmental enrichmentAdult brain injuryAbnormal lung developmentStem cell poolPerinatal hypoxic injuryFate-mapping modelsSocio-demographic factorsNeurobiological recoveryHippocampal neurogenesisVLBW cohortPremature childrenBirth weightCardiovascular abnormalitiesJuvenile miceAnimal modelsLung developmentInjuryCognitive deficits
2011
FGF Signaling Expands Embryonic Cortical Surface Area by Regulating Notch-Dependent Neurogenesis
Rash BG, Lim HD, Breunig JJ, Vaccarino FM. FGF Signaling Expands Embryonic Cortical Surface Area by Regulating Notch-Dependent Neurogenesis. Journal Of Neuroscience 2011, 31: 15604-15617. PMID: 22031906, PMCID: PMC3235689, DOI: 10.1523/jneurosci.4439-11.2011.Peer-Reviewed Original ResearchMeSH KeywordsAge FactorsAnalysis of VarianceAnimalsBrainBromodeoxyuridineCaspase 3Cell CountCell DifferentiationCells, CulturedCerebral CortexDNA-Binding ProteinsElectroporationEmbryo, MammalianEye ProteinsFatty Acid-Binding Protein 7Fatty Acid-Binding ProteinsFibroblast Growth FactorsGene Expression Regulation, DevelopmentalGreen Fluorescent ProteinsHomeodomain ProteinsKi-67 AntigenMiceMice, TransgenicMutationNerve Tissue ProteinsNeurogenesisNeuronsPaired Box Transcription FactorsPAX6 Transcription FactorReceptors, Fibroblast Growth FactorReceptors, NotchRepressor ProteinsSignal TransductionStem CellsT-Box Domain ProteinsTranscription FactorsConceptsCortical neurogenesisCortical surface area expansionCortical surface expansionCortical surface areaGrowth factor receptorEmbryonic day 12.5Fibroblast growth factor receptorFGFR mutantsNormal miceCortical layer structureCortical developmentNeurogenic stagesDominant negative FGFRLoss of functionRadial progenitorsNeurogenesisNotch pathway genesSevere deficitsFactor receptorDay 12.5Notch pathwayMiceSimultaneous activationGreater proportionFGFR activityCortical Glial Fibrillary Acidic Protein-Positive Cells Generate Neurons after Perinatal Hypoxic Injury
Bi B, Salmaso N, Komitova M, Simonini MV, Silbereis J, Cheng E, Kim J, Luft S, Ment LR, Horvath TL, Schwartz ML, Vaccarino FM. Cortical Glial Fibrillary Acidic Protein-Positive Cells Generate Neurons after Perinatal Hypoxic Injury. Journal Of Neuroscience 2011, 31: 9205-9221. PMID: 21697371, PMCID: PMC3142780, DOI: 10.1523/jneurosci.0518-11.2011.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAnimals, NewbornBrainCell DifferentiationCells, CulturedGlial Fibrillary Acidic ProteinHypoxia-Ischemia, BrainMiceMice, TransgenicNeuronsOxygenConceptsGlial fibrillary acidic protein-positive cellsCortical excitatory neuronsProtein-positive cellsPerinatal hypoxic injuryPostnatal hypoxiaGenetic fate mappingCortical astrogliaPremature childrenHypoxic injuryBrain injuryNew neuronsPreterm childrenNeurogenic nicheCognitive recoveryExcitatory neuronsGenerate neuronsNeuronal fateNeuronsHypoxiaCortical parenchymaInjuryParenchymaFate mappingCellsChildrenInduced pluripotent stem cells: A new tool to confront the challenge of neuropsychiatric disorders
Vaccarino FM, Stevens HE, Kocabas A, Palejev D, Szekely A, Grigorenko EL, Weissman S. Induced pluripotent stem cells: A new tool to confront the challenge of neuropsychiatric disorders. Neuropharmacology 2011, 60: 1355-1363. PMID: 21371482, PMCID: PMC3087494, DOI: 10.1016/j.neuropharm.2011.02.021.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsMeSH KeywordsCell DifferentiationHumansInduced Pluripotent Stem CellsMental DisordersNervous System DiseasesNeuronsConceptsInduced pluripotent stem cellsUse of iPSCsPluripotent stem cellsStem cellsEmbryonic stem cellsEarly developmental eventsMature somatic cellsEarly developmental stagesSomatic cellsGenetic variationGene productsDevelopmental eventsReprogramming strategiesNeural differentiationHuman brain developmentDevelopmental stagesIPSC technologyNeurodevelopmental pathwaysDevelopmental originsGenesPotential pharmacological interventionsNew toolGenetic deficitsCellsNeuropsychiatric disorders
2010
Pyramidal Neurons Are Generated from Oligodendroglial Progenitor Cells in Adult Piriform Cortex
Guo F, Maeda Y, Ma J, Xu J, Horiuchi M, Miers L, Vaccarino F, Pleasure D. Pyramidal Neurons Are Generated from Oligodendroglial Progenitor Cells in Adult Piriform Cortex. Journal Of Neuroscience 2010, 30: 12036-12049. PMID: 20826667, PMCID: PMC2940828, DOI: 10.1523/jneurosci.1360-10.2010.Peer-Reviewed Original ResearchMeSH KeywordsAdult Stem CellsAnimalsAntigensAntineoplastic Agents, HormonalBromodeoxyuridineCell CountCell DifferentiationCerebral CortexDoublecortin Domain ProteinsDrug Administration ScheduleEye ProteinsGene Expression RegulationGreen Fluorescent ProteinsHomeodomain ProteinsMiceMice, Inbred C57BLMice, TransgenicMicrotubule-Associated ProteinsMyelin Proteolipid ProteinNerve Tissue ProteinsNeuronsNeuropeptidesOligodendrogliaPaired Box Transcription FactorsPAX6 Transcription FactorProteoglycansPyramidal CellsReceptor, Platelet-Derived Growth Factor alphaReceptors, N-Methyl-D-AspartateRepressor ProteinsSOXB1 Transcription FactorsTamoxifenTime FactorsConceptsOligodendroglial progenitor cellsPyramidal glutamatergic neuronsPiriform cortexAdult piriform cortexGlutamatergic neuronsCortical glutamatergic neuronsProgenitor cellsNeural stem cell markersCortical neuronal networksStem cell markersTranscription factor characteristicImmature neuronsCerebral cortexPyramidal neuronsCell markersCortexNeuronsCre-loxP recombination systemNeuronal networksLines of evidenceMarkersLow levelsCellsPrevious studiesDoublecortin
2008
Decrease in excitatory neurons, astrocytes and proliferating progenitors in the cerebral cortex of mice lacking exon 3 from the Fgf2 gene
Chen K, Ohkubo Y, Shin D, Doetschman T, Sanford LP, Li H, Vaccarino FM. Decrease in excitatory neurons, astrocytes and proliferating progenitors in the cerebral cortex of mice lacking exon 3 from the Fgf2 gene. BMC Neuroscience 2008, 9: 94. PMID: 18826624, PMCID: PMC2577114, DOI: 10.1186/1471-2202-9-94.Peer-Reviewed Original Research
2007
Astroglial Cells in Development, Regeneration, and Repair
Vaccarino FM, Fagel DM, Ganat Y, Maragnoli ME, Ment LR, Ohkubo Y, Schwartz ML, Silbereis J, Smith KM. Astroglial Cells in Development, Regeneration, and Repair. The Neuroscientist 2007, 13: 173-185. PMID: 17404377, DOI: 10.1177/1073858406298336.Peer-Reviewed Original Research In PressConceptsFibroblast growth factor receptorAstroglial cellsGenetic fate mappingCell divisionLineage studiesGrowth factor receptorPostnatal CNSEmbryonic CNSMain cellular componentsFate mappingNeuronal differentiationCellular componentsCell typesInjury-induced increaseFactor receptorNeurogenic nichePerinatal injuryCerebral cortexYoung miceCellsOligodendrocytesNeuronsDifferent rolesCNSNiche
2006
Early Postnatal Astroglial Cells Produce Multilineage Precursors and Neural Stem Cells In Vivo
Ganat YM, Silbereis J, Cave C, Ngu H, Anderson GM, Ohkubo Y, Ment LR, Vaccarino FM. Early Postnatal Astroglial Cells Produce Multilineage Precursors and Neural Stem Cells In Vivo. Journal Of Neuroscience 2006, 26: 8609-8621. PMID: 16914687, PMCID: PMC6674357, DOI: 10.1523/jneurosci.2532-06.2006.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAnimals, NewbornAstrocytesBrainCell DifferentiationCell LineageCerebral VentriclesDoublecortin ProteinFemaleGlial Fibrillary Acidic ProteinHumansIntegrasesMaleMiceMice, TransgenicNeuronsOlfactory BulbOligodendrogliaPromoter Regions, GeneticRecombination, GeneticStem CellsTransgenesConceptsDentate gyrusHuman GFAP promoterCerebral cortexAstroglial cellsSubventricular zoneOlfactory bulbPostnatal brainNeural progenitor/stem cellsPostnatal day 5First postnatal weekProgenitor/stem cellsStem cellsInducible Cre recombinaseNeural stem cellsGenetic fate mappingMature neuronsPostnatal weekCNS regionsWhite matterDay 5GFAP promoterNeural precursorsCortexNeuronsCre recombinaseCortical neurogenesis enhanced by chronic perinatal hypoxia
Fagel DM, Ganat Y, Silbereis J, Ebbitt T, Stewart W, Zhang H, Ment LR, Vaccarino FM. Cortical neurogenesis enhanced by chronic perinatal hypoxia. Experimental Neurology 2006, 199: 77-91. PMID: 15916762, DOI: 10.1016/j.expneurol.2005.04.006.Peer-Reviewed Original ResearchConceptsChronic perinatal hypoxiaCerebral cortexPerinatal hypoxiaCortical neurogenesisCessation of hypoxiaInfant mouse brainSubcortical white matterLower cortical layersMature mammalian brainPostnatal day 3Forebrain subventricular zoneBrdU-positive cellsCortical neuron numberAstroglial cell proliferationNormoxic miceNeonatal injuryNeuronal lossBrain weightCortical neuronsNew neuronsCortical volumeNeuronal markersSubventricular zoneJuvenile micePutative neuroblasts
2005
Otx2 Regulates Subtype Specification and Neurogenesis in the Midbrain
Vernay B, Koch M, Vaccarino F, Briscoe J, Simeone A, Kageyama R, Ang SL. Otx2 Regulates Subtype Specification and Neurogenesis in the Midbrain. Journal Of Neuroscience 2005, 25: 4856-4867. PMID: 15888661, PMCID: PMC6724764, DOI: 10.1523/jneurosci.5158-04.2005.Peer-Reviewed Original ResearchMeSH KeywordsAge FactorsAnimalsAnimals, NewbornBasic Helix-Loop-Helix Transcription FactorsBody PatterningBromodeoxyuridineCell CountCell DifferentiationDopamineEmbryo, MammalianEmbryonic InductionFibroblast Growth Factor 8Gene Expression Regulation, DevelopmentalHomeobox Protein Nkx-2.2Homeodomain ProteinsImmunohistochemistryIn Situ HybridizationIn Situ Nick-End LabelingIntermediate Filament ProteinsIntracellular Signaling Peptides and ProteinsKruppel-Like Transcription FactorsMembrane ProteinsMesencephalonMiceMice, TransgenicNerve Tissue ProteinsNestinNeuronsOrganizers, EmbryonicOtx Transcription FactorsPatched ReceptorsReceptors, Cell SurfaceSerotoninTranscription FactorsWnt1 ProteinZebrafish ProteinsZinc Finger Protein GLI1ConceptsMid-hindbrain organizerFunction of Otx2Neuronal subtype identityTranscription factor Otx2Rostral brain developmentEmbryonic day 10.5Cre/loxP systemRole of Otx2Neuronal progenitor cellsMutant embryosProgenitor identityConditional mutantsE10.5 onwardOtx2 activityAnterior hindbrainEctopic expressionCerebellar-like structuresSubtype specificationSubtype identityTransgenic animalsNovel roleLater roleNovel mouse modelOtx2Otx2 expression