2021
Cell-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
Complex mosaic structural variations in human fetal brains
Sekar S, Tomasini L, Proukakis C, Bae T, Manlove L, Jang Y, Scuderi S, Zhou B, Kalyva M, Amiri A, Mariani J, Sedlazeck F, Urban AE, Vaccarino F, Abyzov A. Complex mosaic structural variations in human fetal brains. Genome Research 2020, 30: gr.262667.120. PMID: 33122304, PMCID: PMC7706730, DOI: 10.1101/gr.262667.120.Peer-Reviewed Original ResearchConceptsSingle nucleotide variantsCopy number variantsStructural variantsMegabase-scale copy number variantsHuman fetal brainFunctional consequencesMobile element insertionsSimilar functional consequencesFetal brainMosaic single-nucleotide variantsAdult brain neuronsStructural variationsPotential functional consequencesKilobase scaleDNA eventsGenomic fragmentDifferent chromosomesElement insertionsClonal approachHuman brain cellsFetal human brainNucleotide variantsReplication errorsHuman brainNumber variantsPsychENCODE and beyond: transcriptomics and epigenomics of brain development and organoids
Jourdon A, Scuderi S, Capauto D, Abyzov A, Vaccarino FM. PsychENCODE and beyond: transcriptomics and epigenomics of brain development and organoids. Neuropsychopharmacology 2020, 46: 70-85. PMID: 32659782, PMCID: PMC7689467, DOI: 10.1038/s41386-020-0763-3.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsRecent single-cell technologiesGene regulatory networksSingle-cell technologiesMulti-omics investigationsPluripotent stem cellsTranscriptional dynamicsBrain developmentCell fateEpigenomic datasetsRegulatory networksElement activityNeural lineagesStem cellsBrain organoidsOrganoidsBiological modelsFetal brainPsychENCODEBrain biologyMajor questionsEpigenomicsFetal tissuesTranscriptomicsLineagesBiologyThe role of somatic mosaicism in brain disease
Jourdon A, Fasching L, Scuderi S, Abyzov A, Vaccarino FM. The role of somatic mosaicism in brain disease. Current Opinion In Genetics & Development 2020, 65: 84-90. PMID: 32622340, PMCID: PMC7749073, DOI: 10.1016/j.gde.2020.05.002.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus Statements
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 Research
2015
The PsychENCODE project
Akbarian S, Liu C, Knowles JA, Vaccarino FM, Farnham PJ, Crawford GE, Jaffe AE, Pinto D, Dracheva S, Geschwind DH, Mill J, Nairn AC, Abyzov A, Pochareddy S, Prabhakar S, Weissman S, Sullivan PF, State MW, Weng Z, Peters MA, White KP, Gerstein MB, Amiri A, Armoskus C, Ashley-Koch AE, Bae T, Beckel-Mitchener A, Berman BP, Coetzee GA, Coppola G, Francoeur N, Fromer M, Gao R, Grennan K, Herstein J, Kavanagh DH, Ivanov NA, Jiang Y, Kitchen RR, Kozlenkov A, Kundakovic M, Li M, Li Z, Liu S, Mangravite LM, Mattei E, Markenscoff-Papadimitriou E, Navarro FC, North N, Omberg L, Panchision D, Parikshak N, Poschmann J, Price AJ, Purcaro M, Reddy TE, Roussos P, Schreiner S, Scuderi S, Sebra R, Shibata M, Shieh AW, Skarica M, Sun W, Swarup V, Thomas A, Tsuji J, van Bakel H, Wang D, Wang Y, Wang K, Werling DM, Willsey AJ, Witt H, Won H, Wong CC, Wray GA, Wu EY, Xu X, Yao L, Senthil G, Lehner T, Sklar P, Sestan N. The PsychENCODE project. Nature Neuroscience 2015, 18: 1707-1712. PMID: 26605881, PMCID: PMC4675669, DOI: 10.1038/nn.4156.Peer-Reviewed Original Research
2014
Alternative Splicing Generates Different Parkin Protein Isoforms: Evidences in Human, Rat, and Mouse Brain
Scuderi S, La Cognata V, Drago F, Cavallaro S, D′Agata V. Alternative Splicing Generates Different Parkin Protein Isoforms: Evidences in Human, Rat, and Mouse Brain. BioMed Research International 2014, 2014: 690796. PMID: 25136611, PMCID: PMC4124806, DOI: 10.1155/2014/690796.Peer-Reviewed Original ResearchConceptsExtensive alternative splicingParkinson protein 2Parkin isoformsAutosomal recessive early-onset Parkinson's diseaseTranscriptomic diversificationRecessive early-onset Parkinson's diseaseEncoded proteinsAlternative splicingPrimary transcriptGene mutationsExpression patternsGene transcriptsHuman pathologiesSplice variantsParkin deficiencyAmino acidsProtein 2Early-onset Parkinson's diseaseSporadic Parkinson's diseaseIsoformsElectrophoretic mobilityOnset Parkinson's diseaseTranscriptsProteinJuvenile Parkinson's disease
2012
Ameliorative effect of PACAP and VIP against increased permeability in a model of outer blood retinal barrier dysfunction
Scuderi S, D’Amico A, Castorina A, Imbesi R, Carnazza M, D’Agata V. Ameliorative effect of PACAP and VIP against increased permeability in a model of outer blood retinal barrier dysfunction. Peptides 2012, 39: 119-124. PMID: 23220033, DOI: 10.1016/j.peptides.2012.11.015.Peer-Reviewed Original ResearchMeSH KeywordsBlood-Retinal BarrierCapillary PermeabilityCell LineClaudin-1DextransDiabetes ComplicationsElectric ImpedanceFluorescein-5-isothiocyanateGene ExpressionGlucoseHumansInterleukin-1betaMacular EdemaOccludinPituitary Adenylate Cyclase-Activating PolypeptideRetinal Pigment EpitheliumTight JunctionsVasoactive Intestinal PeptideZonula Occludens-1 ProteinConceptsDiabetic macular edemaBlood-retinal barrierTransepithelial electrical resistanceBRB functionBlood-retinal barrier dysfunctionOuter blood-retinal barrierEffects of PACAPHuman retinal pigment epithelial cellsFITC-dextran diffusionRetinal pigment epithelial cellsZO-1 expressionTight junctionsPigment epithelial cellsMacular edemaMajor complicationsInflammatory aspectsRetinal barrierRetinal injuryBarrier dysfunctionIL-1βDiabetic retinopathyDiabetic milieuTJ-related proteinsOccludin expressionNormal glucose
2011
Epidermal growth factor receptor (EGFR) and neuregulin (Neu) activation in human airway epithelial cells exposed to nickel acetate
Giunta S, Castorina A, Scuderi S, Patti C, D’Agata V. Epidermal growth factor receptor (EGFR) and neuregulin (Neu) activation in human airway epithelial cells exposed to nickel acetate. Toxicology In Vitro 2011, 26: 280-287. PMID: 22210268, DOI: 10.1016/j.tiv.2011.12.012.Peer-Reviewed Original ResearchConceptsEpidermal growth factor receptorPhosphorylated proteinsGrowth factor receptorFactor receptorBcl-2Suppression of apoptosisAirway epithelial cellsEpithelial cellsReduced EGFRBax protein expressionApoptosis initiationEpithelial cell lineBEAS-2B cellsCell deathDNA fragmentationDNA damageAirway epithelial cell lineHuman airway epithelial cellsExpression levelsProteinApoptosisProtein expressionCell linesInitiation of carcinogenesisPotential involvement