2024
Evaluating performance and applications of sample-wise cell deconvolution methods on human brain transcriptomic data
Dai R, Chu T, Zhang M, Wang X, Jourdon A, Wu F, Mariani J, Vaccarino F, Lee D, Fullard J, Hoffman G, Roussos P, Wang Y, Wang X, Pinto D, Wang S, Zhang C, consortium P, Chen C, Liu C. Evaluating performance and applications of sample-wise cell deconvolution methods on human brain transcriptomic data. Science Advances 2024, 10: eadh2588. PMID: 38781336, PMCID: PMC11114236, DOI: 10.1126/sciadv.adh2588.Peer-Reviewed Original ResearchConceptsHuman brain transcriptome dataBrain transcriptomic dataRNA-seqTranscriptome dataCell-type gene expressionGene expressionCell-type proportionsSingle-cell dataMultiple brain disordersBrain cell typesCell deconvolution methodsPostmortem brainsRNA sequencingBrain disordersBrain developmentSchizophreniaEQTLAlzheimer's diseaseCell typesOrganoid samplesBrainBiological applicationsCharacterization of enhancer activity in early human neurodevelopment using Massively Parallel Reporter Assay (MPRA) and forebrain organoids
Capauto D, Wang Y, Wu F, Norton S, Mariani J, Inoue F, Crawford G, Ahituv N, Abyzov A, Vaccarino F. Characterization of enhancer activity in early human neurodevelopment using Massively Parallel Reporter Assay (MPRA) and forebrain organoids. Scientific Reports 2024, 14: 3936. PMID: 38365907, PMCID: PMC10873509, DOI: 10.1038/s41598-024-54302-7.Peer-Reviewed Original ResearchConceptsMassively parallel reporter assaysGene expressionRegulation of gene expressionForebrain organoidsHuman fetal tissuesHigh-throughput assayReporter assayFetal tissuesStem cellsNeurodevelopmentHuman neurodevelopmentActivation signalsEnhanced activityGenesOrganoidsForebrainBrain organoidsAssayBrain
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 brainBrainMutations
2015
Imbalance 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 disordersAltered expression of neuropeptides in FoxG1-null heterozygous mutant mice
Frullanti E, Amabile S, Lolli MG, Bartolini A, Livide G, Landucci E, Mari F, Vaccarino FM, Ariani F, Massimino L, Renieri A, Meloni I. Altered expression of neuropeptides in FoxG1-null heterozygous mutant mice. European Journal Of Human Genetics 2015, 24: 252-257. PMID: 25966633, PMCID: PMC4717204, DOI: 10.1038/ejhg.2015.79.Peer-Reviewed Original ResearchConceptsBasal gangliaAdult brainParvalbumin-positive GABAergic interneuronsNeonatal brain developmentWild-type littermatesGroup of neuropeptidesHeterozygous mutant miceHippocampal neurogenesisImpaired social interactionCalcium-dependent signalingTotal brainGABAergic interneuronsNeuronal excitabilityControl of movementHippocampal neuronsArginine vasopressinBehavioral impairmentsWhole brainMammalian forebrainHeterozygous miceMutant miceFOXG1 geneBrain developmentBrainAltered expression
2012
Age-related changes of gene expression in the neocortex: Preliminary data on RNA-Seq of the transcriptome in three functionally distinct cortical areas
Naumova OY, Palejev D, Vlasova NV, Lee M, Rychkov SY, Babich ON, Vaccarino F, Grigorenko EL. Age-related changes of gene expression in the neocortex: Preliminary data on RNA-Seq of the transcriptome in three functionally distinct cortical areas. Development And Psychopathology 2012, 24: 1427-1442. PMID: 23062308, PMCID: PMC3539811, DOI: 10.1017/s0954579412000818.Peer-Reviewed Original ResearchConceptsRNA-seqGene expressionAge-related transcriptional changesGene expression profilingCortical areasTranscriptional changesMolecular mechanismsTranscriptomeCentral nervous systemDistinct cortical areasAge-related changesDifferent cellsElderly individualsNervous systemExpressionAge-related variabilityNerve impulsesBrainPreliminary dataNeocortexHuman brainDevelopmental changesDifferent agesDistinct areasDifferentiation
2009
Modeling premature brain injury and recovery
Scafidi J, Fagel DM, Ment LR, Vaccarino FM. Modeling premature brain injury and recovery. International Journal Of Developmental Neuroscience 2009, 27: 863-871. PMID: 19482072, PMCID: PMC2783901, DOI: 10.1016/j.ijdevneu.2009.05.009.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsBrain injuryAnimal modelsSignificant public health problemPremature brain injuryPublic health problemRelevant animal modelsNeurodevelopmental sequelaePreterm brainPreterm infantsPremature birthPreclinical modelsHealth problemsInjuryBrain structuresCellular mechanismsBrainInfantsSchool ageNeuroanatomical structuresVariable degreesRecent insightsEpigenetic mechanismsSequelaeTherapyRecovery
1985
GABA‐Modulin: A Synaptosomal Basic Protein that Differs from Small Myelin Basic Protein of Rat Brain
Vaccarino F, Tronconi B, Panula P, Guidotti A, Costa E. GABA‐Modulin: A Synaptosomal Basic Protein that Differs from Small Myelin Basic Protein of Rat Brain. Journal Of Neurochemistry 1985, 44: 278-290. PMID: 3964832, DOI: 10.1111/j.1471-4159.1985.tb07142.x.Peer-Reviewed Original ResearchMeSH KeywordsAmino AcidsAnimalsBrain ChemistryCarrier ProteinsChromatography, High Pressure LiquidCyanogen BromideGABA Plasma Membrane Transport ProteinsMembrane ProteinsMembrane Transport ProteinsMuscimolMyelin ProteinsMyelin SheathNerve Tissue ProteinsOrganic Anion TransportersPeptide FragmentsRatsSubcellular FractionsSynaptosomesTissue DistributionConceptsGABA-modulinSmall myelin basic proteinMyelin basic proteinRat brainBasic proteinModulation of GABANeuronal membrane functionNeurotransmitter receptorsSynaptosomal fractionGABA bindingSynaptic membranesSynaptosomal membranesStaphylococcal V8 protease digestionSynaptosomal proteinsNeuronal specificityAcid compositionHigh potencyGABAHigh-affinity bindingBrainMyelinAmino acid compositionTotal synaptosomal proteinApparent molecular weightMembrane function