2024
Noncoding variants and sulcal patterns in congenital heart disease: Machine learning to predict functional impact
Mondragon-Estrada E, Newburger J, DePalma S, Brueckner M, Cleveland J, Chung W, Gelb B, Goldmuntz E, Hagler D, Huang H, McQuillen P, Miller T, Panigrahy A, Porter G, Roberts A, Rollins C, Russell M, Tristani-Firouzi M, Grant P, Im K, Morton S. Noncoding variants and sulcal patterns in congenital heart disease: Machine learning to predict functional impact. IScience 2024, 28: 111707. PMID: 39877905, PMCID: PMC11772982, DOI: 10.1016/j.isci.2024.111707.Peer-Reviewed Original ResearchNoncoding variantsCongenital heart diseaseFunctions related to neuronal developmentGene regulatory signalsH3K9me2 modificationRegulatory signalsCongenital heart disease cohortsDevelopmental pathwaysNeuronal developmentFolding patternHeart diseaseFunctional impactGenetic factorsGenesVariantsBrain developmentPredictive impactSulcal patternsPhase separation of microtubule-binding proteins - implications for neuronal function and disease.
Duan D, Koleske A. Phase separation of microtubule-binding proteins - implications for neuronal function and disease. Journal Of Cell Science 2024, 137 PMID: 39679446, PMCID: PMC11795294, DOI: 10.1242/jcs.263470.Peer-Reviewed Original ResearchConceptsMT-binding proteinsLiquid-liquid phase separationRegulation of MT dynamicsProtein liquid-liquid phase separationNeuronal developmentTau neurofibrillary tanglesCytoskeletal regulationMT dynamicsNeurofibrillary tanglesBinding domainMT nucleationBiological functionsDisordered regionsAlzheimer's diseaseNeurodegenerative diseasesIn vivo studiesMaintains homeostasisMicrotubulesNeuronal functionMature neuronsProteinRegulationIn vitroFormation of aggregatesIn vitro studiesCollaborative Survival Analysis on Predicting Alzheimer’s Disease Progression
Xu W, Wang S, Shen L, Zhao Y. Collaborative Survival Analysis on Predicting Alzheimer’s Disease Progression. Statistics In Biosciences 2024, 1-24. DOI: 10.1007/s12561-024-09459-0.Peer-Reviewed Original ResearchAlzheimer's diseaseGenes associated with neuronal developmentAlzheimer's Disease Neuroimaging InitiativeGenetic dataAlzheimer's disease progressionGenetic variationPhenotypic varianceAD progressionGenetic featuresNeuronal developmentGenetic biomarkersAlzheimerADNI databaseMild cognitive impairmentSNPsCanonical correlation analysisGenesStructural MRI scansCombination of brain imagingBrain imagingGeneticsProgression of mild cognitive impairmentAD literatureTime-to-event outcomesTime-to-event predictionsRegulated circRNA nuclear export in neuronal differentiation
Li D, Huang Y. Regulated circRNA nuclear export in neuronal differentiation. Trends In Cell Biology 2024, 34: 620-621. PMID: 38964955, PMCID: PMC11316627, DOI: 10.1016/j.tcb.2024.06.005.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
DYRK1A promotes viral entry of highly pathogenic human coronaviruses in a kinase-independent manner
Strine M, Cai W, Wei J, Alfajaro M, Filler R, Biering S, Sarnik S, Chow R, Patil A, Cervantes K, Collings C, DeWeirdt P, Hanna R, Schofield K, Hulme C, Konermann S, Doench J, Hsu P, Kadoch C, Yan Q, Wilen C. DYRK1A promotes viral entry of highly pathogenic human coronaviruses in a kinase-independent manner. PLOS Biology 2023, 21: e3002097. PMID: 37310920, PMCID: PMC10263356, DOI: 10.1371/journal.pbio.3002097.Peer-Reviewed Original ResearchConceptsGenome-wide CRISPR/Cas9 screenCRISPR/Cas9 screenPathogenic human coronavirusesKinase-independent mannerRegulated kinase 1AProviral host factorNovel drug targetsMultiple cell typesDNA accessibilityHost factorsKinase functionHuman coronavirusesHost genesDistal enhancerNovel regulatorCas9 screenKinase 1AGene expressionNeuronal developmentDYRK1ADrug targetsDiverse coronavirusesProviral activityCell typesSevere acute respiratory syndrome coronavirus 2
2022
Dual in Utero Electroporation in Mice to Manipulate Two Specific Neuronal Populations in the Developing Cortex
Zhang L, Getz SA, Bordey A. Dual in Utero Electroporation in Mice to Manipulate Two Specific Neuronal Populations in the Developing Cortex. Frontiers In Bioengineering And Biotechnology 2022, 9: 814638. PMID: 35096799, PMCID: PMC8790278, DOI: 10.3389/fbioe.2021.814638.Peer-Reviewed Original Research
2021
Protein S-Nitrosylation in Neuronal Development
Nakamura T, Zhang X, Oh C, Lipton S. Protein S-Nitrosylation in Neuronal Development. 2021, 91-105. DOI: 10.1201/9781003204091-10.Peer-Reviewed Original ResearchPost-translational modificationsProtein S-nitrosylationS-nitrosylationReactive nitrogen speciesNeuronal developmentNeuronal differentiationTranscription factor MEF2Protein-protein interactionsIon channel activityProtein traffickingEnzymatic functionCysteine thiolsProtein conformationCellular mechanismsChannel activityNormal brain developmentNitrogen speciesSynaptic functionNitric oxide actsPathological processesBiological actionsProteinNeuronal survivalBiological systemsNeurogenesisCalcium Signaling Regulates Autophagy and Apoptosis
Sukumaran P, Da Conceicao V, Sun Y, Ahamad N, Saraiva L, Selvaraj S, Singh B. Calcium Signaling Regulates Autophagy and Apoptosis. Cells 2021, 10: 2125. PMID: 34440894, PMCID: PMC8394685, DOI: 10.3390/cells10082125.Peer-Reviewed Original ResearchConceptsCell survivalOpposing functionCell death processMaintenance of cellular functionDepletion of Ca<sup>2+</sup>Pathogenesis of neurodegenerative diseasesPromote cell survivalNon-excitable cellsCytosolic Ca<sup>2+</sup> levelsCellular homeostasisCellular functionsAutophagy machineryER storesHuntington's diseaseDiverse functionsDeath processNeuronal developmentFunctional significanceNeurodegenerative diseasesPhysiological functionsNeurodegenerative conditionsApoptosisCellsHomeostasisImmune regulationWhat is the role of synaptic protein TRIO's spectrin repeats?
Corcoran E, Bircher J, Koleske A. What is the role of synaptic protein TRIO's spectrin repeats? The FASEB Journal 2021, 35 DOI: 10.1096/fasebj.2021.35.s1.01837.Peer-Reviewed Original ResearchSpectrin repeatsProper neuronal developmentSpectrin repeat domainRare damaging variantsDisease-associated mutationsAccessory domainsCatalytic domainRepeat domainRegulatory proteinsRepeat functionDe novo missense mutationsSignaling mechanismDamaging mutationsNeuronal developmentDamaging variantsDisease mutationsBiochemical eventsNovo missense mutationNeurodevelopmental disordersMissense mutationsSpectrinRepeatsMutationsDomainTherapeutic strategiesAge-dependent ataxia and neurodegeneration caused by an αII spectrin mutation with impaired regulation of its calpain sensitivity
Miazek A, Zalas M, Skrzymowska J, Bogin BA, Grzymajło K, Goszczynski TM, Levine ZA, Morrow JS, Stankewich MC. Age-dependent ataxia and neurodegeneration caused by an αII spectrin mutation with impaired regulation of its calpain sensitivity. Scientific Reports 2021, 11: 7312. PMID: 33790315, PMCID: PMC8012654, DOI: 10.1038/s41598-021-86470-1.Peer-Reviewed Original ResearchConceptsSpectrin cleavageCalpain cleavage sitesCalcium-activated proteaseGlobal neurodegenerationTraumatic encephalopathyC57BL/6J miceDendritic integrityExcessive activationNeuronal integrityProgressive ataxiaImpaired regulationCalpain activationCalpain sensitivityPhysiologic significanceNeurodegenerative diseasesNeuronal developmentCalpain proteolysisCalpain proteasesCalcium-dependent bindingAtaxiaNeurodegenerationCalpainActivated calpainSubstrate-level regulationCaM affinitySmall Extracellular Vesicles Control Dendritic Spine Development through Regulation of HDAC2 Signaling
Zhang L, Lin TV, Yuan Q, Sadoul R, Lam TT, Bordey A. Small Extracellular Vesicles Control Dendritic Spine Development through Regulation of HDAC2 Signaling. Journal Of Neuroscience 2021, 41: 3799-3807. PMID: 33741723, PMCID: PMC8084316, DOI: 10.1523/jneurosci.0766-20.2021.Peer-Reviewed Original ResearchConceptsSmall extracellular vesiclesRegulation of HDAC2Extracellular vesiclesSpine developmentCell-cell signalingTranscriptional programsCortical neuronsSEV releaseTranscriptional decreaseDendritic spinesNeuronal developmentNeuron developmentDendritic spine developmentLines of evidenceHDAC2Paracrine communicationAge-dependent decreaseVesiclesPopulations of neuronsRegulationLC-MS/MSHDAC2 levelsSynaptic targetsExcitatory synapsesSpine growth
2020
Maternal antenatal depression and child mental health: Moderation by genomic risk for attention-deficit/hyperactivity disorder
Chen LM, Tollenaar MS, Dass S, Bouvette-Turcot AA, Pokhvisneva I, Gaudreau H, Parent C, Diorio J, McEwen LM, MacIsaac JL, Kobor MS, Beijers R, de Weerth C, Silveira PP, Karama S, Meaney MJ, O'Donnell KJ. Maternal antenatal depression and child mental health: Moderation by genomic risk for attention-deficit/hyperactivity disorder. Development And Psychopathology 2020, 32: 1810-1821. PMID: 33427178, DOI: 10.1017/s0954579420001418.Peer-Reviewed Original ResearchConceptsMaternal antenatal depressionAttention-deficit/hyperactivity disorderAntenatal depressionChild mental healthPolygenic risk scoresMental healthHyperactivity disorderChild mental health symptomsMental health symptomsConsiderable inter-individual variationConventional polygenic risk scoresMaternal depressionRisk scoreHealth symptomsReplication cohortSynaptic functionGenomic riskChild genetic variationInter-individual variationNeuronal developmentSimilar findingsDepressionSingle nucleotide polymorphismsDevelopmental originsBehavioral problemsCutting, Amplifying, and Aligning Microtubules with Severing Enzymes
Kuo YW, Howard J. Cutting, Amplifying, and Aligning Microtubules with Severing Enzymes. Trends In Cell Biology 2020, 31: 50-61. PMID: 33183955, PMCID: PMC7749064, DOI: 10.1016/j.tcb.2020.10.004.Peer-Reviewed Original ResearchConceptsAAA ATPasesTissue morphogenesisCellular processesMicrotubule cytoskeletonCell divisionGrowth promotionBiophysical advancesSevering enzymesMicrotubule networkMolecular mechanismsStrong promoterMicrotubule growthNeuronal developmentShort filamentsMicrotubulesSpastinEnzymeSeveringFidgetinKataninCytoskeletonMorphogenesisPromoterProteinRecent work
2019
Exploring the Regulatory Role of Circular RNAs in Neurodegenerative Disorders
D’Ambra E, Capauto D, Morlando M. Exploring the Regulatory Role of Circular RNAs in Neurodegenerative Disorders. International Journal Of Molecular Sciences 2019, 20: 5477. PMID: 31689888, PMCID: PMC6862314, DOI: 10.3390/ijms20215477.Peer-Reviewed Original ResearchConceptsCircular RNAsRegulatory non-coding RNAsNon-coding RNAsImportant regulatory functionsNeuronal specificationPathological conditionsCircRNAs expressionGene expressionCircRNAsNeuronal developmentRegulatory functionsExact functionRegulatory roleDifferent tissuesSynaptic plasticity inductionRNANervous systemNeurodegenerative diseasesNeurodegenerative disordersInnovative therapeutic approachesDynamic modulationRecent studiesExpressionDistinctive classCurrent advancesProhibitin promotes de-differentiation and is a potential therapeutic target in neuroblastoma
MacArthur I, Bei Y, Garcia H, Ortiz M, Toedling J, Klironomos F, Rolff J, Eggert A, Schulte J, Kentsis A, Henssen A. Prohibitin promotes de-differentiation and is a potential therapeutic target in neuroblastoma. JCI Insight 2019, 5 PMID: 30998507, PMCID: PMC6542629, DOI: 10.1172/jci.insight.127130.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsApoptosisCell Cycle CheckpointsCell DedifferentiationCell DifferentiationCell Line, TumorCell ProliferationChild, PreschoolChromosomes, Human, Pair 17HumansMAP Kinase Signaling SystemMiceNeuroblastomaProhibitinsProtein Kinase InhibitorsPyridonesPyrimidinonesRepressor ProteinsRNA-SeqRNA, MessengerSequence Analysis, RNAWhole Genome SequencingXenograft Model Antitumor AssaysConceptsLong arm of chromosome 17Neuroblastoma cellsSlow cell cycle progressionExpression of prohibitinImpaired ERK1/2 activationGene expression programsWhole genomeHigh-risk neuroblastomaChromosome 17Long armDe-differentiationPromote tumor cell proliferationTumor cell proliferationRNA sequencingAssociated with suppressionEctopic expressionProhibitinProliferation of neuroblastoma cellsCytogenetic hallmarkProhibitin expressionExpression programsAssociated with lossNeuronal developmentERK1/2 activationNeuroblastoma outcome
2018
Proteolytically released Lasso/teneurin-2 induces axonal attraction by interacting with latrophilin-1 on axonal growth cones
Vysokov NV, Silva JP, Lelianova VG, Suckling J, Cassidy J, Blackburn JK, Yankova N, Djamgoz MB, Kozlov SV, Tonevitsky AG, Ushkaryov YA. Proteolytically released Lasso/teneurin-2 induces axonal attraction by interacting with latrophilin-1 on axonal growth cones. ELife 2018, 7: e37935. PMID: 30457553, PMCID: PMC6245728, DOI: 10.7554/elife.37935.Peer-Reviewed Original ResearchConceptsLatrophilin-1Axonal growth conesAxonal attractionAdhesion G protein-coupled receptorsPostsynaptic transmembrane proteinsG protein-coupled receptorsGrowth conesTrans-synaptic interactionsGrowth cone steeringRegulated proteolysisTransmembrane proteinDownstream signalingAxonal pathfindingNeuronal developmentEnhanced exocytosisNovel mechanismSynapse formationNeurite outgrowthTeneurinsIntercellular spacesCytosolic calciumStable gradientSynaptogenesisExocytosisSignalingStriatin-1 is a B subunit of protein phosphatase PP2A that regulates dendritic arborization and spine development in striatal neurons
Li D, Musante V, Zhou W, Picciotto MR, Nairn AC. Striatin-1 is a B subunit of protein phosphatase PP2A that regulates dendritic arborization and spine development in striatal neurons. Journal Of Biological Chemistry 2018, 293: 11179-11194. PMID: 29802198, PMCID: PMC6052221, DOI: 10.1074/jbc.ra117.001519.Peer-Reviewed Original ResearchConceptsSerine/threonine phosphatase PP2AStriatin-interacting phosphataseRNA knockdown approachB subunitSTRIPAK complexPhosphatase PP2AProtein phosphataseMultiprotein complexesKnockdown approachStriatin familyMutant constructsStriatal neuronal culturesPP2ANeuronal developmentPrimary striatal neuronal culturesDendritic phenotypeKnockdown modelSynapse formationSubunitsSpine developmentSelective roleReduced expressionNeuron maturationNeuronal culturesStriatal neurons
2017
Patient-derived hiPSC neurons with heterozygous CNTNAP2 deletions display altered neuronal gene expression and network activity
Flaherty E, Deranieh R, Artimovich E, Lee I, Siegel A, Levy D, Nestor M, Brennand K. Patient-derived hiPSC neurons with heterozygous CNTNAP2 deletions display altered neuronal gene expression and network activity. Schizophrenia 2017, 3: 35. PMID: 28970473, PMCID: PMC5624885, DOI: 10.1038/s41537-017-0033-5.Peer-Reviewed Original ResearchNeural progenitor cellsGene expressionGlobal gene expressionNeuronal gene expressionPluripotent stem cellsNeuronal activityFamily triosCell adhesion moleculeNeurexin familyHiPSC neuronsMolecular mechanismsDeletion displayAxon guidanceNeuronal developmentGenetic backgroundStem cellsProgenitor cellsDeletionMultiple neuropsychiatric conditionsHeterozygous intragenic deletionDendritic arborizationGenesAnimal studiesAdhesion moleculesNeuropsychiatric conditionsIdentification of target genes downstream of semaphorin6A/PlexinA2 signaling in zebrafish
Emerson S, St. Clair R, Waldron A, Bruno S, Duong A, Driscoll H, Ballif B, McFarlane S, Ebert A. Identification of target genes downstream of semaphorin6A/PlexinA2 signaling in zebrafish. Developmental Dynamics 2017, 246: 539-549. PMID: 28440030, PMCID: PMC6322676, DOI: 10.1002/dvdy.24512.Peer-Reviewed Original ResearchConceptsSignaling pathwayTarget genesMicroarray analysisIdentification of target genesRegulate proliferationRetinal precursor cellsGuidance signaling pathwayGene expression changesTranscriptional regulationEarly eye developmentGenesDisrupted proliferationExpression changesEye developmentNeuronal developmentNeuronal positioningUp-regulatedZebrafish embryosMorphantsPLXNA2Downstream effectsRASL11BPathwayZebrafish eyeSema6A
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