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 applications
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 ResearchMachine learning reveals bilateral distribution of somatic L1 insertions in human neurons and glia
Zhu X, Zhou B, Pattni R, Gleason K, Tan C, Kalinowski A, Sloan S, Fiston-Lavier AS, Mariani J, Petrov D, Barres BA, Duncan L, Abyzov A, Vogel H, Moran J, Vaccarino F, Tamminga C, Levinson D, Urban A. Machine learning reveals bilateral distribution of somatic L1 insertions in human neurons and glia. Nature Neuroscience 2021, 24: 186-196. PMID: 33432196, PMCID: PMC8806165, DOI: 10.1038/s41593-020-00767-4.Peer-Reviewed Original ResearchMeSH KeywordsAdaptor Proteins, Signal TransducingAdultCation Transport ProteinsEmbryonic DevelopmentFemaleGenomeHeLa CellsHigh-Throughput Nucleotide SequencingHumansLong Interspersed Nucleotide ElementsMachine LearningMental DisordersMutagenesis, InsertionalNeurogliaNeuronsPregnancyRetroelementsSchizophreniaConceptsBrain developmentPossible pathological effectsAnatomical distributionBilateral distributionHuman neuronsNervous systemHuman nervous systemNeuropsychiatric diseasesNeuropsychiatric disordersGliaPathological effectsNeuronsSomatic L1 insertionsWhole-genome sequencingHuman brainSomatic retrotranspositionFibroblast Growth Factor 2 Implicated in Childhood Anxiety and Depression Symptoms
Lebowitz ER, Orbach M, Marin CE, Salmaso N, Vaccarino FM, Silverman WK. Fibroblast Growth Factor 2 Implicated in Childhood Anxiety and Depression Symptoms. Journal Of Affective Disorders 2021, 282: 611-616. PMID: 33445083, PMCID: PMC7897422, DOI: 10.1016/j.jad.2020.12.055.Peer-Reviewed Original Research
2014
Transcriptome Analysis of the Human Striatum in Tourette Syndrome
Lennington JB, Coppola G, Kataoka-Sasaki Y, Fernandez TV, Palejev D, Li Y, Huttner A, Pletikos M, Sestan N, Leckman JF, Vaccarino FM. Transcriptome Analysis of the Human Striatum in Tourette Syndrome. Biological Psychiatry 2014, 79: 372-382. PMID: 25199956, PMCID: PMC4305353, DOI: 10.1016/j.biopsych.2014.07.018.Peer-Reviewed Original ResearchConceptsCopy number variantsGenome-wide association studiesGene coexpression modulesNumber variantsGene network analysisCommon genetic variantsCoexpression modulesUpregulated genesMetabolism modulesImmune-related genesNetwork analysisAssociation studiesDifferential expressionUpregulated modulesGenetic variantsGenesPatient's striatumTS individualsTranscriptomeVariantsMetabolic alterationsSame regionGamma-aminobutyric acidergic interneuronsTranscriptsRNA
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
2011
Annual Research Review: The promise of stem cell research for neuropsychiatric disorders
Vaccarino FM, Urban AE, Stevens HE, Szekely A, Abyzov A, Grigorenko EL, Gerstein M, Weissman S. Annual Research Review: The promise of stem cell research for neuropsychiatric disorders. Journal Of Child Psychology And Psychiatry 2011, 52: 504-516. PMID: 21204834, PMCID: PMC3124336, DOI: 10.1111/j.1469-7610.2010.02348.x.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsNervous systemNeuropsychiatric disordersPsychiatric disordersAdult-onset neuropsychiatric disordersEarly onset neuropsychiatric disordersHuman neural cellsAttention deficit hyperactivity disorderStem cellsNeural stem cellsDeficit hyperactivity disorderHuman brain developmentObsessive-compulsive disorderPharmacological interventionsFunctional neuronsBrain developmentUse of iPSCsNeural cellsHyperactivity disorderTime pointsDisordersCompulsive disorderPatientsNeural differentiationDevelopmental time pointsNeurodevelopmental conditions
2009
Decreased number of parvalbumin and cholinergic interneurons in the striatum of individuals with Tourette syndrome
Kataoka Y, Kalanithi PS, Grantz H, Schwartz ML, Saper C, Leckman JF, Vaccarino FM. Decreased number of parvalbumin and cholinergic interneurons in the striatum of individuals with Tourette syndrome. The Journal Of Comparative Neurology 2009, 518: 277-291. PMID: 19941350, PMCID: PMC2846837, DOI: 10.1002/cne.22206.Peer-Reviewed Original ResearchConceptsMedium spiny neuronsCholinergic interneuronsTourette syndromeNormal controlsCholinergic striatal interneuronsNumber of parvalbuminBrains of patientsCaudate nucleus volumeUnbiased stereological analysisStriatal interneuronsOngoing motor behaviorCholinergic cellsTotal neuronsCholine acetyltransferaseSpiny neuronsLimbic regionsStriatum of individualsTS patientsPostmortem brainsThalamic controlSensorimotor regionsInterneuronsCellular abnormalitiesNeuron firingTS subjects
2005
Altered parvalbumin-positive neuron distribution in basal ganglia of individuals with Tourette syndrome
Kalanithi PS, Zheng W, Kataoka Y, DiFiglia M, Grantz H, Saper CB, Schwartz ML, Leckman JF, Vaccarino FM. Altered parvalbumin-positive neuron distribution in basal ganglia of individuals with Tourette syndrome. Proceedings Of The National Academy Of Sciences Of The United States Of America 2005, 102: 13307-13312. PMID: 16131542, PMCID: PMC1201574, DOI: 10.1073/pnas.0502624102.Peer-Reviewed Original ResearchConceptsTourette syndromeNeuron distributionCalcium-binding protein parvalbuminNeuron numberT subjectsLower neuron numberGlobus pallidus pars externaParvalbumin-positive interneuronsTotal neuron numberUnbiased stereological techniquesChildhood neuropsychiatric disordersBasal ganglia tissueGABAergic neuronsGPi neuronsBasal gangliaCortico-striatoGlobus pallidusProtein parvalbuminThalamic circuitryGanglion tissueVocal ticsNormal controlsPutamen volumePars externaImaging studies