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 lengthOne for All: A Pooled Approach to Classify Functional Impacts of Multiple Mutations
Jourdon A, Vaccarino FM. One for All: A Pooled Approach to Classify Functional Impacts of Multiple Mutations. Cell Stem Cell 2020, 27: 1-3. PMID: 32619508, DOI: 10.1016/j.stem.2020.06.016.Commentaries, Editorials and Letters
2018
Transcriptome and epigenome landscape of human cortical development modeled in organoids
Amiri A, Coppola G, Scuderi S, Wu F, Roychowdhury T, Liu F, Pochareddy S, Shin Y, Safi A, Song L, Zhu Y, Sousa AMM, Gerstein M, Crawford G, Sestan N, Abyzov A, Vaccarino F, Akbarian S, An J, Armoskus C, Ashley-Koch A, Beach T, Belmont J, Bendl J, Borrman T, Brown L, Brown M, Brown M, Brunetti T, Bryois J, Burke E, Camarena A, Carlyle B, Chae Y, Charney A, Chen C, Cheng L, Cherskov A, Choi J, Clarke D, Collado-Torres L, Dai R, De La Torre Ubieta L, DelValle D, Devillers O, Dracheva S, Emani P, Evgrafov O, Farnham P, Fitzgerald D, Flatow E, Francoeur N, Fullard J, Gandal M, Gao T, Garrett M, Geschwind D, Giase G, Girdhar K, Giusti-Rodriguez P, Goes F, Goodman T, Grennan K, Gu M, Gürsoy G, Hadjimichael E, Hahn C, Haroutunian V, Hauberg M, Hoffman G, Huey J, Hyde T, Ivanov N, Jacobov R, Jaffe A, Jiang Y, Jiang Y, Johnson G, Kassim B, Kefi A, Kim Y, Kitchen R, Kleiman J, Knowles J, Kozlenkov A, Li M, Li Z, Lipska B, Liu C, Liu S, Mangravite L, Mariani J, Mattei E, Miller D, Moore J, Nairn A, Navarro F, Park R, Peters M, Pinto D, Pochareddy S, Polioudakis D, Pratt H, Price A, Purcaro M, Ray M, Reddy T, Rhie S, Roussos P, Sanders S, Santpere G, Schreiner S, Sheppard B, Shi X, Shieh A, Shin J, Skarica M, Song L, Sousa A, Spitsyna V, State M, Sullivan P, Swarup V, Szatkiewicz J, Szekely A, Tao R, van Bakel H, Wang Y, Wang D, Warrell J, Webster M, Weissman S, Weng Z, Werling D, White K, Willsey J, Wiseman J, Witt H, Won H, Wray G, Xia Y, Xu M, Yang Y, Yang M, Zandi P, Zhang J, Zharovsky E. Transcriptome and epigenome landscape of human cortical development modeled in organoids. Science 2018, 362 PMID: 30545853, PMCID: PMC6426303, DOI: 10.1126/science.aat6720.Peer-Reviewed Original ResearchiPSC-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
2017
Human 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 StatementsMeSH KeywordsBrainHumansInduced Pluripotent Stem CellsModels, BiologicalNerve NetNeurodevelopmental DisordersConceptsEmbryonic 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 discoveryHiPSCsOne thousand somatic SNVs per skin fibroblast cell set baseline of mosaic mutational load with patterns that suggest proliferative origin
Abyzov A, Tomasini L, Zhou B, Vasmatzis N, Coppola G, Amenduni M, Pattni R, Wilson M, Gerstein M, Weissman S, Urban AE, Vaccarino FM. One thousand somatic SNVs per skin fibroblast cell set baseline of mosaic mutational load with patterns that suggest proliferative origin. Genome Research 2017, 27: 512-523. PMID: 28235832, PMCID: PMC5378170, DOI: 10.1101/gr.215517.116.Peer-Reviewed Original ResearchMeSH KeywordsCell ProliferationCells, CulturedClonal EvolutionDNA Copy Number VariationsFibroblastsHumansInduced Pluripotent Stem CellsMosaicismMutation AccumulationSkinConceptsSomatic mosaicismFibroblast cellsSingle-cell whole-genome amplificationAllele frequenciesNumber of SNVsNormal cell proliferationCell proliferationWhole genome amplificationStem cell linesPluripotent stem cell lineHealthy human tissuesDe novo variantsCancer mutationsHigh-resolution analysisMutational loadPCR experimentsSkin fibroblast cellsMutational signaturesHiPSC linesDe novoGenomeNovo variantsFibroblast populationsCell linesSomatic SNVs
2015
Creating Patient-Specific Neural Cells for the In Vitro Study of Brain Disorders
Brennand KJ, Marchetto MC, Benvenisty N, Brüstle O, Ebert A, Belmonte J, Kaykas A, Lancaster MA, Livesey FJ, McConnell MJ, McKay RD, Morrow EM, Muotri AR, Panchision DM, Rubin LL, Sawa A, Soldner F, Song H, Studer L, Temple S, Vaccarino FM, Wu J, Vanderhaeghen P, Gage FH, Jaenisch R. Creating Patient-Specific Neural Cells for the In Vitro Study of Brain Disorders. Stem Cell Reports 2015, 5: 933-945. PMID: 26610635, PMCID: PMC4881284, DOI: 10.1016/j.stemcr.2015.10.011.Peer-Reviewed Original ResearchMeSH KeywordsBrainBrain DiseasesDrug DiscoveryHumansInduced Pluripotent Stem CellsMosaicismNeurogenesisPrecision MedicineImbalance of excitatory/inhibitory synaptic protein expression in iPSC-derived neurons from FOXG1+/− patients and in foxg1+/− mice
Patriarchi T, Amabile S, Frullanti E, Landucci E, Lo Rizzo C, Ariani F, Costa M, Olimpico F, W Hell J, M Vaccarino F, Renieri A, Meloni I. Imbalance of excitatory/inhibitory synaptic protein expression in iPSC-derived neurons from FOXG1+/− patients and in foxg1+/− mice. European Journal Of Human Genetics 2015, 24: 871-880. PMID: 26443267, PMCID: PMC4820038, DOI: 10.1038/ejhg.2015.216.Peer-Reviewed Original ResearchConceptsRett syndromeSynaptic markersInhibitory synapsesExcitatory/inhibitory balanceSynaptic protein expressionFetal mouse brainInhibitory synaptic markersPathogenesis of RTTExcitatory synaptic markersSevere neurodevelopmental disorderGlutamatergic markersInhibitory balanceAdult brainAdult micePrecise molecular mechanismsSynaptic differentiationPatientsMouse brainBrain synapsesPathological eventsNeuronsProtein expressionBrainGluD1Neurodevelopmental disordersFOXG1-Dependent Dysregulation of GABA/Glutamate Neuron Differentiation in Autism Spectrum Disorders
Mariani J, Coppola G, Zhang P, Abyzov A, Provini L, Tomasini L, Amenduni M, Szekely A, Palejev D, Wilson M, Gerstein M, Grigorenko EL, Chawarska K, Pelphrey KA, Howe JR, Vaccarino FM. FOXG1-Dependent Dysregulation of GABA/Glutamate Neuron Differentiation in Autism Spectrum Disorders. Cell 2015, 162: 375-390. PMID: 26186191, PMCID: PMC4519016, DOI: 10.1016/j.cell.2015.06.034.Peer-Reviewed Original ResearchConceptsInduced pluripotent stem cellsGene network analysisGene network modulesUpregulation of genesTranscription factor Foxg1Accelerated cell cyclePluripotent stem cellsRNA interferenceGenetic basisSynaptic assemblyCell cycleBrain developmentNeuron fateNeuron differentiationNeuronal differentiationGenomic mutationsHuman brain developmentIdiopathic autism spectrum disorderAltered expressionStem cellsCell proliferationFOXG1ASD pathophysiologyNetwork modulesNeural culturesThe use of stem cells to study autism spectrum disorder.
Ardhanareeswaran K, Coppola G, Vaccarino F. The use of stem cells to study autism spectrum disorder. The Yale Journal Of Biology And Medicine 2015, 88: 5-16. PMID: 25745370, PMCID: PMC4345539.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsMeSH KeywordsAnimalsAutism Spectrum DisorderHumansInduced Pluripotent Stem CellsModels, BiologicalNervous SystemStem Cell TransplantationConceptsHuman-induced pluripotent stem cellsStem cellsNeuronal developmentIdentification of hundredsEmbryonic stem cellsUnique genetic signaturePluripotent stem cellsCore symptomsASD patientsAutism spectrum disorderPost-mortem brain samplesGenome studiesGenetic signaturesAutism core symptomsNew therapeutic avenuesSerious developmental disabilitiesIdiopathic autism spectrum disorderSkin biopsiesHuman-specific behaviorsSpectrum disorderSingle drugDrug AdministrationTherapeutic avenuesBrain samplesDiagnostic tests
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 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 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 ResearchMeSH KeywordsCells, CulturedCerebral CortexGene Expression ProfilingHumansInduced Pluripotent Stem CellsModels, BiologicalNerve Tissue ProteinsNeuronsTranscription FactorsTranscriptomeConceptsHuman 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
Induced 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