Featured Publications
Neuron-specific signatures in the chromosomal connectome associated with schizophrenia risk
Rajarajan P, Borrman T, Liao W, Schrode N, Flaherty E, Casiño C, Powell S, Yashaswini C, LaMarca EA, Kassim B, Javidfar B, Espeso-Gil S, Li A, Won H, Geschwind DH, Ho SM, MacDonald M, Hoffman GE, Roussos P, Zhang B, Hahn CG, Weng Z, Brennand KJ, Akbarian S. Neuron-specific signatures in the chromosomal connectome associated with schizophrenia risk. Science 2018, 362 PMID: 30545851, PMCID: PMC6408958, DOI: 10.1126/science.aat4311.Peer-Reviewed Original ResearchMeSH KeywordsBrainCells, CulturedChromatinChromatin Assembly and DisassemblyChromosomes, HumanConnectomeEpigenesis, GeneticGene Expression Regulation, DevelopmentalGenetic Predisposition to DiseaseGenome, HumanGenome-Wide Association StudyHumansMaleNeural Stem CellsNeurogenesisNeurogliaNeuronsNucleic Acid ConformationProtein Interaction MapsProteomicsRiskSchizophreniaTranscription, GeneticTranscriptomeConceptsCoordinated transcriptional regulationThree-dimensional genomeSpatial genome organizationChromosomal contact mapsNeural progenitor cellsSchizophrenia risk variantsGenome organizationChromatin remodelingChromosomal conformationTranscriptional regulationProteomic interactionsDevelopmental remodelingHeritable riskGlial differentiationRisk variantsContact mapsProgenitor cellsVariant sequencesGenesConformation changeNeuronal connectivitySchizophrenia riskSequenceNeuropsychiatric diseasesDistal targets
2020
Transcriptional signatures of participant-derived neural progenitor cells and neurons implicate altered Wnt signaling in Phelan-McDermid syndrome and autism
Breen MS, Browne A, Hoffman GE, Stathopoulos S, Brennand K, Buxbaum JD, Drapeau E. Transcriptional signatures of participant-derived neural progenitor cells and neurons implicate altered Wnt signaling in Phelan-McDermid syndrome and autism. Molecular Autism 2020, 11: 53. PMID: 32560742, PMCID: PMC7304190, DOI: 10.1186/s13229-020-00355-0.Peer-Reviewed Original ResearchMeSH KeywordsAdolescentAdultAutistic DisorderChildChild, PreschoolChromosome DeletionChromosome DisordersChromosomes, Human, Pair 22FemaleGene Expression ProfilingGene Expression RegulationHumansInduced Pluripotent Stem CellsMaleNeural Stem CellsNeuronsReproducibility of ResultsWnt Signaling PathwayConceptsNeural progenitor cellsTranscriptional signatureGene co-expression network analysisHiPSC-NPCsCo-expression network analysisIndependent biological samplesHiPSC-derived neural cellsProgenitor cellsPostsynaptic density genesDistinct transcriptional signaturesGenetic risk lociHuman-induced pluripotent stem cellsPluripotent stem cellsPotassium channel activityProtein translationSpecific neurobiological pathwaysTranscriptional differencesEmbryonic developmentLoss of SHANK3Risk lociHiPSC neuronsMorphological phenotypesWnt pathwayGenesHiPSC clonesTranscriptional Signatures of Participant-Derived Neural Progenitor Cells and Neurons Implicate Altered WNT Signaling in Phelan-McDermid Syndrome and Autism
Breen M, Browne A, Hoffman G, Stathopoulous S, Brennand K, Buxbaum J, Drapeau E. Transcriptional Signatures of Participant-Derived Neural Progenitor Cells and Neurons Implicate Altered WNT Signaling in Phelan-McDermid Syndrome and Autism. Biological Psychiatry 2020, 87: s456-s457. DOI: 10.1016/j.biopsych.2020.02.1162.Peer-Reviewed Original ResearchASCL1- and DLX2-induced GABAergic neurons from hiPSC-derived NPCs
Barretto N, Zhang H, Powell SK, Fernando MB, Zhang S, Flaherty EK, Ho SM, Slesinger PA, Duan J, Brennand KJ. ASCL1- and DLX2-induced GABAergic neurons from hiPSC-derived NPCs. Journal Of Neuroscience Methods 2020, 334: 108548. PMID: 32065989, PMCID: PMC7426253, DOI: 10.1016/j.jneumeth.2019.108548.Peer-Reviewed Original ResearchNeural progenitor cellsHiPSC-NPCsSomatic cell reprogrammingGABAergic neuronsHiPSC-derived neural progenitor cellsDifferentiation of hiPSCsDistinct transcriptional profilesPluripotent stem cellsCell reprogrammingPatient-derived cellsElectrophysiological maturityFunctional GABAergic neuronsTranscriptional profilesNeuronal inductionStem cellsProgenitor cellsLentiviral overexpressionPure populationsDlx2Study of diseasesAscl1HiPSCsNeuronal populationsInduction protocolCell source
2018
Expression-based drug screening of neural progenitor cells from individuals with schizophrenia
Readhead B, Hartley BJ, Eastwood BJ, Collier DA, Evans D, Farias R, He C, Hoffman G, Sklar P, Dudley JT, Schadt EE, Savić R, Brennand KJ. Expression-based drug screening of neural progenitor cells from individuals with schizophrenia. Nature Communications 2018, 9: 4412. PMID: 30356048, PMCID: PMC6200740, DOI: 10.1038/s41467-018-06515-4.Peer-Reviewed Original ResearchConceptsNeural progenitor cellsHiPSC neural progenitor cellsCell typesCancer cell linesGene expression differencesProgenitor cellsDisease-associated genesPatient-specific platformPluripotent stem cellsTranscriptional responseExpression differencesTranscriptional signatureTranscriptomic signaturesStem cellsCell linesDependent mannerDrug discoveryDrug screeningCellsNeuropsychiatric disordersSchizophreniaBest treatmentDrugsDiscoveryGenes
2017
Transcriptional signatures of schizophrenia in hiPSC-derived NPCs and neurons are concordant with post-mortem adult brains
Hoffman GE, Hartley BJ, Flaherty E, Ladran I, Gochman P, Ruderfer DM, Stahl EA, Rapoport J, Sklar P, Brennand KJ. Transcriptional signatures of schizophrenia in hiPSC-derived NPCs and neurons are concordant with post-mortem adult brains. Nature Communications 2017, 8: 2225. PMID: 29263384, PMCID: PMC5738408, DOI: 10.1038/s41467-017-02330-5.Peer-Reviewed Original ResearchMeSH KeywordsAdolescentAdultAntigens, SurfaceAutopsyBrainCase-Control StudiesChildDNA Copy Number VariationsFemaleHumansInduced Pluripotent Stem CellsLinear ModelsMaleNanog Homeobox ProteinNestinNeural Stem CellsNeuronsOctamer Transcription Factor-3ProteoglycansRNA, MessengerSchizophreniaSequence Analysis, RNASOXB1 Transcription FactorsStage-Specific Embryonic AntigensSynapsinsTranscriptomeYoung AdultCerebral organoids reveal early cortical maldevelopment in schizophrenia—computational anatomy and genomics, role of FGFR1
Stachowiak E, Benson C, Narla S, Dimitri A, Chuye L, Dhiman S, Harikrishnan K, Elahi S, Freedman D, Brennand K, Sarder P, Stachowiak M. Cerebral organoids reveal early cortical maldevelopment in schizophrenia—computational anatomy and genomics, role of FGFR1. Translational Psychiatry 2017, 7: 6. PMID: 30446636, PMCID: PMC5802550, DOI: 10.1038/s41398-017-0054-x.Peer-Reviewed Original ResearchConceptsNeural progenitor cellsCerebral organoidsSchizophrenia patientsVentricular zoneInduced pluripotent stem cellsCortical neuronal maturationUtero brain developmentRole of FGFR1Stem cellsIntracortical connectivityFirst trimesterCortical maldevelopmentCortical malformationsPreventive treatmentCalretinin interneuronsNeuronal maturationSubcortical regionsControl individualsPioneer neuronsCortical zoneBrain developmentHuman embryonic stem cellsProgenitor cellsIntegrative nuclear FGFR1FGFR1 genePatient-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 conditionsEvaluating Synthetic Activation and Repression of Neuropsychiatric-Related Genes in hiPSC-Derived NPCs, Neurons, and Astrocytes
Ho S, Hartley B, Flaherty E, Rajarajan P, Abdelaal R, Obiorah I, Barretto N, Muhammad H, Phatnani H, Akbarian S, Brennand K. Evaluating Synthetic Activation and Repression of Neuropsychiatric-Related Genes in hiPSC-Derived NPCs, Neurons, and Astrocytes. Stem Cell Reports 2017, 9: 615-628. PMID: 28757163, PMCID: PMC5550013, DOI: 10.1016/j.stemcr.2017.06.012.Peer-Reviewed Original ResearchConceptsSynthetic activationRisk genesCell typesModulation of transcriptionNeuropsychiatric risk genesCommon single nucleotide variantsCas9 fusion proteinsEndogenous expression levelsNeural cell typesPluripotent stem cell-derived neural progenitor cellsRare copy number variationsCopy number variationsSingle nucleotide variantsNeural progenitor cellsGene functionFunctional annotationGenetic studiesGenesRisk variantsProgenitor cellsExpression levelsTranscriptionRepressionPositional effectsProteinHigh-Content Screening in hPSC-Neural Progenitors Identifies Drug Candidates that Inhibit Zika Virus Infection in Fetal-like Organoids and Adult Brain
Zhou T, Tan L, Cederquist G, Fan Y, Hartley B, Mukherjee S, Tomishima M, Brennand K, Zhang Q, Schwartz R, Evans T, Studer L, Chen S. High-Content Screening in hPSC-Neural Progenitors Identifies Drug Candidates that Inhibit Zika Virus Infection in Fetal-like Organoids and Adult Brain. Cell Stem Cell 2017, 21: 274-283.e5. PMID: 28736217, PMCID: PMC5553280, DOI: 10.1016/j.stem.2017.06.017.Peer-Reviewed Original ResearchConceptsZIKV infectionNeurological complicationsZika virusZIKV-infected patientsSerious neurological complicationsZika virus infectionCortical neural progenitor cellsForebrain organoidsAdult mouse brainHigh-content chemical screenDrug candidatesNeural progenitor cellsAdult patientsHuman forebrain organoidsVirus infectionMouse modelAdult brainAdult miceMouse brainTherapeutic potentialTherapeutic treatmentInfectionProgenitor cellsBrainComplications
2016
Spatial genome organization and cognition
Rajarajan P, Gil S, Brennand K, Akbarian S. Spatial genome organization and cognition. Nature Reviews Neuroscience 2016, 17: 681-691. PMID: 27708356, PMCID: PMC5503467, DOI: 10.1038/nrn.2016.124.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsPromoter-enhancer interactionsRegulatory sequencesGene transcription start siteSpatial genome organizationNon-coding DNACis-regulatory sequencesHundreds of kilobasesTranscription start siteCRISPR-Cas systemsChromosomal loopingGenome organizationTranscriptional activatorChromosomal conformationCohesin complexGenetic risk architectureTranscriptional regulationStart siteCandidate genesGene expressionStructural variantsDecoy modelsNeurodevelopmental diseasesCrucial layerEditing techniquesProgenitor cellsIdentification of small-molecule inhibitors of Zika virus infection and induced neural cell death via a drug repurposing screen
Xu M, Lee E, Wen Z, Cheng Y, Huang W, Qian X, TCW J, Kouznetsova J, Ogden S, Hammack C, Jacob F, Nguyen H, Itkin M, Hanna C, Shinn P, Allen C, Michael S, Simeonov A, Huang W, Christian K, Goate A, Brennand K, Huang R, Xia M, Ming G, Zheng W, Song H, Tang H. Identification of small-molecule inhibitors of Zika virus infection and induced neural cell death via a drug repurposing screen. Nature Medicine 2016, 22: 1101-1107. PMID: 27571349, PMCID: PMC5386783, DOI: 10.1038/nm.4184.Peer-Reviewed Original ResearchAltered proliferation and networks in neural cells derived from idiopathic autistic individuals
Marchetto M, Belinson H, Tian Y, Freitas B, Fu C, Vadodaria K, Beltrao-Braga P, Trujillo C, Mendes A, Padmanabhan K, Nunez Y, Ou J, Ghosh H, Wright R, Brennand K, Pierce K, Eichenfield L, Pramparo T, Eyler L, Barnes C, Courchesne E, Geschwind D, Gage F, Wynshaw-Boris A, Muotri A. Altered proliferation and networks in neural cells derived from idiopathic autistic individuals. Molecular Psychiatry 2016, 22: 820-835. PMID: 27378147, PMCID: PMC5215991, DOI: 10.1038/mp.2016.95.Peer-Reviewed Original ResearchConceptsNeural progenitor cellsInsulin growth factor-1Pluripotent stem cellsTranscriptional cascadeNeuronal networksAutism spectrum disorderGrowth factor-1Human cell modelsNormal brain sizeEarly brain overgrowthPotential cellular mechanismsMolecular mechanismsGenetic studiesClinical trialsIGF-1Therapeutic effectBrain pathologyAbnormal neurogenesisΒ-cateninCellular mechanismsStem cellsBrain overgrowthProgenitor cellsNeural cellsAltered proliferationDysregulation of miRNA-9 in a Subset of Schizophrenia Patient-Derived Neural Progenitor Cells
Topol A, Zhu S, Hartley B, English J, Hauberg M, Tran N, Rittenhouse C, Simone A, Ruderfer D, Johnson J, Readhead B, Hadas Y, Gochman P, Wang Y, Shah H, Cagney G, Rapoport J, Gage F, Dudley J, Sklar P, Mattheisen M, Cotter D, Fang G, Brennand K. Dysregulation of miRNA-9 in a Subset of Schizophrenia Patient-Derived Neural Progenitor Cells. Cell Reports 2016, 15: 1024-1036. PMID: 27117414, PMCID: PMC4856588, DOI: 10.1016/j.celrep.2016.03.090.Peer-Reviewed Original ResearchConceptsNeural progenitor cellsControl neural progenitor cellsMiR-9 targetsProgenitor cellsSubset of patientsMiR-9Levels/activitiesMiR-9 expressionSchizophrenia patientsMicroRNA-9Migration deficitsDisease riskNeural migrationAberrant levelsAberrant migrationPatientsMiRNA-9SchizophreniaMigration-associated genesRNA sequencingSZ riskRiskIndirect targetsSubsetCells
2015
Rapid Ngn2-induction of excitatory neurons from hiPSC-derived neural progenitor cells
Ho S, Hartley B, Julia T, Beaumont M, Stafford K, Slesinger P, Brennand K. Rapid Ngn2-induction of excitatory neurons from hiPSC-derived neural progenitor cells. Methods 2015, 101: 113-124. PMID: 26626326, PMCID: PMC4860098, DOI: 10.1016/j.ymeth.2015.11.019.Peer-Reviewed Original ResearchConceptsHuman induced pluripotent stem cellsNeural progenitor cellsHiPSC-derived neural progenitor cellsHigh-throughput drug screeningHiPSC neural progenitor cellsExogenous transcription factorsProgenitor cellsInduced pluripotent stem cellsPatient-specific platformPluripotent stem cellsPatient-derived neuronsSomatic reprogrammingTranscription factorsGenetic variationExcitatory neuronsDrug screeningNeurogenin 2Neuronal inductionFunctional neuronsThroughput drug screeningNeuronal phenotypeLentiviral transductionStem cellsStarting populationDisease etiologyIncreased abundance of translation machinery in stem cell–derived neural progenitor cells from four schizophrenia patients
Topol A, English J, Flaherty E, Rajarajan P, Hartley B, Gupta S, Desland F, Zhu S, Goff T, Friedman L, Rapoport J, Felsenfeld D, Cagney G, Mackay-Sim A, Savas J, Aronow B, Fang G, Zhang B, Cotter D, Brennand K. Increased abundance of translation machinery in stem cell–derived neural progenitor cells from four schizophrenia patients. Translational Psychiatry 2015, 5: e662-e662. PMID: 26485546, PMCID: PMC4930118, DOI: 10.1038/tp.2015.118.Peer-Reviewed Original ResearchConceptsHiPSC neural progenitor cellsNeural progenitor cellsNovel post-transcriptional mechanismProtein synthesisGlobal protein translationElongation factor proteinGlobal protein synthesisPost-transcriptional mechanismsProgenitor cellsHuman-induced pluripotent stem cellsPluripotent stem cellsMass spectrometry evidenceTranslation machineryTranslation initiationProtein translationEpigenetic factorsFactor proteinStem cellsProtein levelsTotal protein levelsCellsUnaffected controlsMachineryProteinAbundanceCharacterization of molecular and cellular phenotypes associated with a heterozygous CNTNAP2 deletion using patient-derived hiPSC neural cells
Lee I, Carvalho C, Douvaras P, Ho S, Hartley B, Zuccherato L, Ladran I, Siegel A, McCarthy S, Malhotra D, Sebat J, Rapoport J, Fossati V, Lupski J, Levy D, Brennand K. Characterization of molecular and cellular phenotypes associated with a heterozygous CNTNAP2 deletion using patient-derived hiPSC neural cells. Schizophrenia 2015, 1: 15019. PMID: 26985448, PMCID: PMC4789165, DOI: 10.1038/npjschz.2015.19.Peer-Reviewed Original ResearchClinical outcomesCNTNAP2 expressionHiPSC neural progenitor cellsDiscordant clinical outcomesHiPSC-derived neuronsOligodendrocyte precursor cellsNeural progenitor cellsContactin-associated proteinHuman neuronsAnimal modelsClinical settingGenetic deletionExpression patternsNeural cellsProgenitor cellsLarge heterozygous deletionsNeurodevelopmental disordersPrecursor cellsDisordersComplex disorderHeterozygous deletionSignificant differencesNeuronsStem cellsExon 14A guide to generating and using hiPSC derived NPCs for the study of neurological diseases.
Topol A, Tran N, Brennand K. A guide to generating and using hiPSC derived NPCs for the study of neurological diseases. Journal Of Visualized Experiments 2015, e52495. PMID: 25742222, PMCID: PMC4354663, DOI: 10.3791/52495.Peer-Reviewed Original ResearchConceptsNeural progenitor cellsHiPSC neural progenitor cellsRapid genetic screeningPluripotent stem cellsCellular phenotypesDevelopmental eventsMolecular consequencesGene expressionNeurological diseasesFunctional neuronsStem cellsProgenitor cellsOnset of symptomsMolecular factorsFurther differentiationPost-mortem studiesDisease initiationGenetic screeningOxidative stressSymptom onsetDisease progressionHealthy controlsDiseaseCellsPatientsAltered WNT Signaling in Human Induced Pluripotent Stem Cell Neural Progenitor Cells Derived from Four Schizophrenia Patients
Topol A, Zhu S, Tran N, Simone A, Fang G, Brennand K. Altered WNT Signaling in Human Induced Pluripotent Stem Cell Neural Progenitor Cells Derived from Four Schizophrenia Patients. Biological Psychiatry 2015, 78: e29-e34. PMID: 25708228, PMCID: PMC4520784, DOI: 10.1016/j.biopsych.2014.12.028.Peer-Reviewed Original Research
2014
Roles of Heat Shock Factor 1 in Neuronal Response to Fetal Environmental Risks and Its Relevance to Brain Disorders
Hashimoto-Torii K, Torii M, Fujimoto M, Nakai A, Fatimy R, Mezger V, Ju MJ, Ishii S, Chao SH, Brennand KJ, Gage FH, Rakic P. Roles of Heat Shock Factor 1 in Neuronal Response to Fetal Environmental Risks and Its Relevance to Brain Disorders. Neuron 2014, 82: 560-572. PMID: 24726381, PMCID: PMC4051437, DOI: 10.1016/j.neuron.2014.03.002.Peer-Reviewed Original ResearchConceptsCerebral cortical cellsHuman neural progenitor cellsNeural progenitor cellsHeat shock factor 1Maternal seizuresSeizure susceptibilityPrenatal exposureNeuropsychiatric dysfunctionShock factor 1Neuronal responsesBrain cellsSchizophrenia patientsBrain disordersLate onsetMouse cortexStructural abnormalitiesNeuropsychiatric disordersHSF1 deficiencyExposure of embryosProgenitor cellsSubthreshold levelsFactor 1Induced pluripotent stem cellsEnvironmental insultsCortical cells