2024
Transgenerational transmission of post-zygotic mutations suggests symmetric contribution of first two blastomeres to human germline
Jang Y, Tomasini L, Bae T, Szekely A, Vaccarino F, Abyzov A. Transgenerational transmission of post-zygotic mutations suggests symmetric contribution of first two blastomeres to human germline. Nature Communications 2024, 15: 9117. PMID: 39438473, PMCID: PMC11496613, DOI: 10.1038/s41467-024-53485-x.Peer-Reviewed Original ResearchMassively parallel characterization of regulatory elements in the developing human cortex
Deng C, Whalen S, Steyert M, Ziffra R, Przytycki P, Inoue F, Pereira D, Capauto D, Norton S, Vaccarino F, Pollen A, Nowakowski T, Ahituv N, Pollard K, Akbarian S, Abyzov A, Ahituv N, Arasappan D, Almagro Armenteros J, Beliveau B, Bendl J, Berretta S, Bharadwaj R, Bhattacharya A, Bicks L, Brennand K, Capauto D, Champagne F, Chatterjee T, Chatzinakos C, Chen Y, Chen H, Cheng Y, Cheng L, Chess A, Chien J, Chu Z, Clarke D, Clement A, Collado-Torres L, Cooper G, Crawford G, Dai R, Daskalakis N, Davila-Velderrain J, Deep-Soboslay A, Deng C, DiPietro C, Dracheva S, Drusinsky S, Duan Z, Duong D, Dursun C, Eagles N, Edelstein J, Emani P, Fullard J, Galani K, Galeev T, Gandal M, Gaynor S, Gerstein M, Geschwind D, Girdhar K, Goes F, Greenleaf W, Grundman J, Guo H, Guo Q, Gupta C, Hadas Y, Hallmayer J, Han X, Haroutunian V, Hawken N, He C, Henry E, Hicks S, Ho M, Ho L, Hoffman G, Huang Y, Huuki-Myers L, Hwang A, Hyde T, Iatrou A, Inoue F, Jajoo A, Jensen M, Jiang L, Jin P, Jin T, Jops C, Jourdon A, Kawaguchi R, Kellis M, Khullar S, Kleinman J, Kleopoulos S, Kozlenkov A, Kriegstein A, Kundaje A, Kundu S, Lee C, Lee D, Li J, Li M, Lin X, Liu S, Liu J, Liu J, Liu C, Liu S, Lou S, Loupe J, Lu D, Ma S, Ma L, Margolis M, Mariani J, Martinowich K, Maynard K, Mazariegos S, Meng R, Myers R, Micallef C, Mikhailova T, Ming G, Mohammadi S, Monte E, Montgomery K, Moore J, Moran J, Mukamel E, Nairn A, Nemeroff C, Ni P, Norton S, Nowakowski T, Omberg L, Page S, Park S, Patowary A, Pattni R, Pertea G, Peters M, Phalke N, Pinto D, Pjanic M, Pochareddy S, Pollard K, Pollen A, Pratt H, Przytycki P, Purmann C, Qin Z, Qu P, Quintero D, Raj T, Rajagopalan A, Reach S, Reimonn T, Ressler K, Ross D, Roussos P, Rozowsky J, Ruth M, Ruzicka W, Sanders S, Schneider J, Scuderi S, Sebra R, Sestan N, Seyfried N, Shao Z, Shedd N, Shieh A, Shin J, Skarica M, Snijders C, Song H, State M, Stein J, Steyert M, Subburaju S, Sudhof T, Snyder M, Tao R, Therrien K, Tsai L, Urban A, Vaccarino F, van Bakel H, Vo D, Voloudakis G, Wamsley B, Wang T, Wang S, Wang D, Wang Y, Warrell J, Wei Y, Weimer A, Weinberger D, Wen C, Weng Z, Whalen S, White K, Willsey A, Won H, Wong W, Wu H, Wu F, Wuchty S, Wylie D, Xu S, Yap C, Zeng B, Zhang P, Zhang C, Zhang B, Zhang J, Zhang Y, Zhou X, Ziffra R, Zeier Z, Zintel T. Massively parallel characterization of regulatory elements in the developing human cortex. Science 2024, 384: eadh0559. PMID: 38781390, DOI: 10.1126/science.adh0559.Peer-Reviewed Original ResearchConceptsGene regulatory elementsRegulatory elementsRegulation of enhancer activityCharacterization of regulatory elementsCis-regulatory activityNeuronal developmentPrimary cellsEnhanced activityGene regulationHuman neuronal developmentNucleotide changesEnhancer sequencesSequence basisUpstream regulatorComprehensive catalogHuman cellsDeveloping cortexSequenceVariantsOrganoidsCellsCerebral organoidsCortexHuman cortexNucleotide
2023
Efficient reconstruction of cell lineage trees for cell ancestry and cancer
Jang Y, Fasching L, Bae T, Tomasini L, Schreiner J, Szekely A, Fernandez T, Leckman J, Vaccarino F, Abyzov A. Efficient reconstruction of cell lineage trees for cell ancestry and cancer. Nucleic Acids Research 2023, 51: e57-e57. PMID: 37026484, PMCID: PMC10250207, DOI: 10.1093/nar/gkad254.Peer-Reviewed Original ResearchConceptsLineage treesCell ancestryCell lineage treesFirst cell divisionStem cell linesPluripotent stem cell lineLineage reconstructionInduced pluripotent stem cell lineCell divisionCancer progressionLineage representationCell linesMosaic mutationsHuman skin fibroblastsTreesMutationsAncestrySkin fibroblastsMultiple cellsGenomeLineagesZygotesLinesFibroblastsCells
2020
Cell 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 StatementsConceptsLineage 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 designCellsOrganismsHumansDNAChapter 5 Induced pluripotent stem cells as models of human neurodevelopmental disorders
Jourdon A, Mariani J, Scuderi S, Amiri A, Wu F, Yuen E, Abyzov A, Vaccarino F. Chapter 5 Induced pluripotent stem cells as models of human neurodevelopmental disorders. 2020, 99-127. DOI: 10.1016/b978-0-12-814409-1.00005-7.ChaptersPluripotent stem cellsStem cellsStudy of speciesHuman neurodevelopmental disordersEpigenome analysisGene regulationIPSC fieldGenomic variationGene expressionGenetic backgroundDisease modelingStudies of neurodevelopmentIPSCsExperimental approachNeurodevelopmental disordersTranscriptomeGenomeCellsCell phenotypingSpeciesExperimental design issuesPhenotypeRegulationExpressionPhenotyping
2019
Approaches and Methods for Variant Analysis in the Genome of a Single Cell
Abyzov A, Vaccarino F, Urban A, Sarangi V. Approaches and Methods for Variant Analysis in the Genome of a Single Cell. Healthy Ageing And Longevity 2019, 10: 203-228. DOI: 10.1007/978-3-030-24970-0_14.Chapters
2017
Different mutational rates and mechanisms in human cells at pregastrulation and neurogenesis
Bae T, Tomasini L, Mariani J, Zhou B, Roychowdhury T, Franjic D, Pletikos M, Pattni R, Chen BJ, Venturini E, Riley-Gillis B, Sestan N, Urban AE, Abyzov A, Vaccarino FM. Different mutational rates and mechanisms in human cells at pregastrulation and neurogenesis. Science 2017, 359: 550-555. PMID: 29217587, PMCID: PMC6311130, DOI: 10.1126/science.aan8690.Peer-Reviewed Original ResearchConceptsSingle nucleotide variationsMutation rateCancer cell genomeClonal cell populationsCell genomeCell lineagesBackground mutagenesisHuman cellsMutational rateSomatic mosaicismSingle cellsOxidative damageGenomeMutagenesisCell populationsMutation spectrumNeurogenesisCellsHuman fetusesIndividual neuronsLineagesPregastrulationHuman brainBrainMutationsHuman induced pluripotent stem cells for modelling neurodevelopmental disorders
Ardhanareeswaran K, Mariani J, Coppola G, Abyzov A, Vaccarino FM. Human induced pluripotent stem cells for modelling neurodevelopmental disorders. Nature Reviews Neurology 2017, 13: 265-278. PMID: 28418023, PMCID: PMC5782822, DOI: 10.1038/nrneurol.2017.45.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsEmbryonic stem cellsNeurodevelopmental disordersPluripotent stem cellsBrain developmentStem cellsAbnormal brain developmentBrain cell typesDopaminergic neuronsCortical neuronsUnique genetic signatureEarly developmentKey PointsHumanHiPSC modelsSomatic cellsDisordersGenetic signaturesGenetic studiesAltered trajectoryCell typesAdult cellsNeuronsUnknown facetsCellsDrug discoveryHiPSCs
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 ResearchNeurobiology 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 StatementsConceptsHuman-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 individualsTranscriptsModeling human cortical development in vitro using induced pluripotent stem cells
Mariani J, Simonini MV, Palejev D, Tomasini L, Coppola G, Szekely AM, Horvath TL, Vaccarino FM. Modeling human cortical development in vitro using induced pluripotent stem cells. Proceedings Of The National Academy Of Sciences Of The United States Of America 2012, 109: 12770-12775. PMID: 22761314, PMCID: PMC3411972, DOI: 10.1073/pnas.1202944109.Peer-Reviewed Original ResearchConceptsHuman brain developmentHuman induced pluripotent stem cellsLayer-specific cortical neuronsBrain developmentHuman cerebral cortexHuman cortical developmentStem cellsPluripotent stem cellsCerebral cortexCortical neuronsCortical developmentCNS regionsRadial gliaCortical wallDorsal telencephalonEmbryonic telencephalonGene expression profilesInduced pluripotent stem cellsIntermediate progenitorsTelencephalic developmentTelencephalonExpression profilesTranscriptional programsCellsGlia
2011
Cortical 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 ResearchConceptsGlial 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 StatementsConceptsInduced 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
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
Midline radial glia translocation and corpus callosum formation require FGF signaling
Smith KM, Ohkubo Y, Maragnoli ME, Rašin M, Schwartz ML, Šestan N, Vaccarino FM. Midline radial glia translocation and corpus callosum formation require FGF signaling. Nature Neuroscience 2006, 9: 787-797. PMID: 16715082, DOI: 10.1038/nn1705.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAstrocytesCell MovementCell ShapeCerebral CortexCorpus CallosumDown-RegulationFemaleFibroblast Growth Factor 8Fibroblast Growth FactorsGrowth ConesMaleMiceMice, KnockoutMice, TransgenicNeurogliaReceptor, Fibroblast Growth Factor, Type 1Receptor, Fibroblast Growth Factor, Type 2RNA InterferenceSignal TransductionConceptsRadial glial cellsGlial cellsSomal translocationRadial gliaCorpus callosum formationReceptor 1 geneCallosal dysgenesisCerebral cortexFibroblast growth factor receptor 1 (FGFR1) geneIndusium griseumDorsomedial cortexDorsolateral cortexKnockout miceCortexAstrogliaApical endfeetFGFR1 geneAstrocytesGliaAxon guidanceDorsal midlinePrecise targetingCellsUnexpected roleFGF
2000
Stem Cells and Neuronal Progenitors and Their Diversity in the CNS: Are Time and Place Important?
Vaccarino F. Stem Cells and Neuronal Progenitors and Their Diversity in the CNS: Are Time and Place Important? The Neuroscientist 2000, 6: 338-352. DOI: 10.1177/107385840000600508.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsDifferent cell typesFibroblast growth factorStem cellsTranscription factorsEarly transcriptional regulatorCell typesHelix transcription factorHomeodomain transcription factorPattern of expressionMultilineage progenitor cellsTranscriptional regulatorsFounder cellsCellular repertoireExtracellular signalsProper assemblyNeuronal progenitorsPositional specificationBasic fibroblast growth factorBody axesImmediate progenyProgenitor cellsGrowth factorRegulatorCellsCNS domainsThe 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
1995
Basic Fibroblast Growth Factor Increases the Number of Excitatory Neurons Containing Glutamate in the Cerebral Cortex
Vaccarino F, Schwartz M, Hartigan D, Leckman J. Basic Fibroblast Growth Factor Increases the Number of Excitatory Neurons Containing Glutamate in the Cerebral Cortex. Cerebral Cortex 1995, 5: 64-78. PMID: 7719131, DOI: 10.1093/cercor/5.1.64.Peer-Reviewed Original ResearchConceptsBasic fibroblast growth factorNerve growth factorGlutamate-containing neuronsCerebral cortexFibroblast growth factorGrowth factorAspartate-containing neuronsDifferent neurotransmitter phenotypesNumber of GABARatio of glutamateStem cellsNeurotransmitter phenotypeExcitatory neuronsInhibitory neuronsRat telencephalonVentricular zoneBFGF mRNAGABANeuronsCortexGlutamateDiffusible factorsThreefold increaseCellsFactors
1985
gamma-Aminobutyric acid- and benzodiazepine-induced modulation of [35S]- t-butylbicyclophosphorothionate binding to cerebellar granule cells
Gallo V, Wise BC, Vaccarino F, Guidotti A. gamma-Aminobutyric acid- and benzodiazepine-induced modulation of [35S]- t-butylbicyclophosphorothionate binding to cerebellar granule cells. Journal Of Neuroscience 1985, 5: 2432-2438. PMID: 4032005, PMCID: PMC6565307, DOI: 10.1523/jneurosci.05-09-02432.1985.Peer-Reviewed Original ResearchConceptsGamma-aminobutyric acidIntact cerebellar granule cellsCerebellar granule cellsGranule cellsT-butylbicyclophosphorothionateEffects of muscimolDose-dependent fashionAbsence of diazepamNeuroblastoma cell linesBenzodiazepine receptor ligandsSpecific bindingMicroM diazepamConvulsant activityCerebellar astrocytesMuscimolDiazepamLocke's solutionTotal radioactivityPrimary culturesReceptor ligandsCell linesReceptor complexCarboxylic acid methylesterInhibitionCells