2024
Transgenerational transmission of post-zygotic mutations suggests symmetric contribution of first two blastomeres to human germline
Jang Y, Tomasini L, Bae T, Szekely A, Vaccarino F, Abyzov A. Transgenerational transmission of post-zygotic mutations suggests symmetric contribution of first two blastomeres to human germline. Nature Communications 2024, 15: 9117. PMID: 39438473, PMCID: PMC11496613, DOI: 10.1038/s41467-024-53485-x.Peer-Reviewed Original Research
2023
Efficient reconstruction of cell lineage trees for cell ancestry and cancer
Jang Y, Fasching L, Bae T, Tomasini L, Schreiner J, Szekely A, Fernandez T, Leckman J, Vaccarino F, Abyzov A. Efficient reconstruction of cell lineage trees for cell ancestry and cancer. Nucleic Acids Research 2023, 51: e57-e57. PMID: 37026484, PMCID: PMC10250207, DOI: 10.1093/nar/gkad254.Peer-Reviewed Original ResearchConceptsLineage treesCell ancestryCell lineage treesFirst cell divisionStem cell linesPluripotent stem cell lineLineage reconstructionInduced pluripotent stem cell lineCell divisionCancer progressionLineage representationCell linesMosaic mutationsHuman skin fibroblastsTreesMutationsAncestrySkin fibroblastsMultiple cellsGenomeLineagesZygotesLinesFibroblastsCellsClonally Selected Lines After CRISPR-Cas Editing Are Not Isogenic
Panda A, Suvakov M, Mariani J, Drucker K, Park Y, Jang Y, Kollmeyer T, Sarkar G, Bae T, Kim J, Yoon W, Jenkins R, Vaccarino F, Abyzov A. Clonally Selected Lines After CRISPR-Cas Editing Are Not Isogenic. The CRISPR Journal 2023, 6: 176-182. PMID: 37071670, PMCID: PMC10123805, DOI: 10.1089/crispr.2022.0050.Peer-Reviewed Original ResearchConceptsCopy number alterationsSeparate genomic lociSingle nucleotide mutationsApplication of CRISPRCRISPR-Cas editingOff-target editsScreening of clonesGenomic divergenceWhole-genome sequencingGenomic lociSelection of clonesGenome sequencingNucleotide mutationsTarget editsCultured cellsClonal linesNumber alterationsCell cloningClonesMutationsCloningCRISPR
2022
Analysis of somatic mutations in 131 human brains reveals aging-associated hypermutability
Bae T, Fasching L, Wang Y, Shin JH, Suvakov M, Jang Y, Norton S, Dias C, Mariani J, Jourdon A, Wu F, Panda A, Pattni R, Chahine Y, Yeh R, Roberts RC, Huttner A, Kleinman JE, Hyde TM, Straub RE, Walsh CA, Urban A, Leckman J, Weinberger D, Vaccarino F, Abyzov A, Walsh C, Park P, Sestan N, Weinberger D, Moran J, Gage F, Vaccarino F, Gleeson J, Mathern G, Courchesne E, Roy S, Chess A, Akbarian S, Bizzotto S, Coulter M, Dias C, D’Gama A, Ganz J, Hill R, Huang A, Khoshkhoo S, Kim S, Lee A, Lodato M, Maury E, Miller M, Borges-Monroy R, Rodin R, Zhou Z, Bohrson C, Chu C, Cortes-Ciriano I, Dou Y, Galor A, Gulhan D, Kwon M, Luquette J, Sherman M, Viswanadham V, Jones A, Rosenbluh C, Cho S, Langmead B, Thorpe J, Erwin J, Jaffe A, McConnell M, Narurkar R, Paquola A, Shin J, Straub R, Abyzov A, Bae T, Jang Y, Wang Y, Molitor C, Peters M, Linker S, Reed P, Wang M, Urban A, Zhou B, Zhu X, Pattni R, Serres Amero A, Juan D, Lobon I, Marques-Bonet T, Solis Moruno M, Garcia Perez R, Povolotskaya I, Soriano E, Antaki D, Averbuj D, Ball L, Breuss M, Yang X, Chung C, Emery S, Flasch D, Kidd J, Kopera H, Kwan K, Mills R, Moldovan J, Sun C, Zhao X, Zhou W, Frisbie T, Cherskov A, Fasching L, Jourdon A, Pochareddy S, Scuderi S. Analysis of somatic mutations in 131 human brains reveals aging-associated hypermutability. Science 2022, 377: 511-517. PMID: 35901164, PMCID: PMC9420557, DOI: 10.1126/science.abm6222.Peer-Reviewed Original ResearchConceptsTranscription factorsSomatic mutationsPutative transcription factorEnhancer-like regionSingle nucleotide mutationsWhole-genome sequencingGene regulationSomatic duplicationGenome sequencingDamaging mutationsBackground mutagenesisMutationsHypermutabilityClonal expansionMotifDiseased brainPotential linkVivo clonal expansionMutagenesisGenesDuplicationSequencingRegulationAll2: A tool for selecting mosaic mutations from comprehensive multi-cell comparisons
Sarangi V, Jang Y, Suvakov M, Bae T, Fasching L, Sekar S, Tomasini L, Mariani J, Vaccarino FM, Abyzov A. All2: A tool for selecting mosaic mutations from comprehensive multi-cell comparisons. PLOS Computational Biology 2022, 18: e1009487. PMID: 35442945, PMCID: PMC9060341, DOI: 10.1371/journal.pcbi.1009487.Peer-Reviewed Original Research
2020
One for All: A Pooled Approach to Classify Functional Impacts of Multiple Mutations
Jourdon A, Vaccarino FM. One for All: A Pooled Approach to Classify Functional Impacts of Multiple Mutations. Cell Stem Cell 2020, 27: 1-3. PMID: 32619508, DOI: 10.1016/j.stem.2020.06.016.Commentaries, Editorials and Letters
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
2016
Kv3.3 Channels Bind Hax-1 and Arp2/3 to Assemble a Stable Local Actin Network that Regulates Channel Gating
Zhang Y, Zhang XF, Fleming MR, Amiri A, El-Hassar L, Surguchev AA, Hyland C, Jenkins DP, Desai R, Brown MR, Gazula VR, Waters MF, Large CH, Horvath TL, Navaratnam D, Vaccarino FM, Forscher P, Kaczmarek LK. Kv3.3 Channels Bind Hax-1 and Arp2/3 to Assemble a Stable Local Actin Network that Regulates Channel Gating. Cell 2016, 165: 434-448. PMID: 26997484, PMCID: PMC4826296, DOI: 10.1016/j.cell.2016.02.009.Peer-Reviewed Original ResearchMeSH KeywordsActin CytoskeletonActin-Related Protein 2Actin-Related Protein 2-3 ComplexActin-Related Protein 3Adaptor Proteins, Signal TransducingAmino Acid SequenceCell MembraneMolecular Sequence DataMutationNeuronsPluripotent Stem CellsRac GTP-Binding ProteinsShaw Potassium ChannelsSignal TransductionSpinocerebellar AtaxiasConceptsCytoplasmic C-terminusProline-rich domainPlasma membraneHAX-1Actin nucleationC-terminusCortical actin filament networkLocal actin networkStem cell-derived neuronsActin filament networkCell-derived neuronsAnti-apoptotic proteinsActin cytoskeletonKv3.3 potassium channelActin assemblyActin structuresActin networkArp2/3Channel gatingFilament networkGrowth conesCerebellar neurodegenerationKv3.3TerminusPotassium channels
2014
Fgfr1 Inactivation in the Mouse Telencephalon Results in Impaired Maturation of Interneurons Expressing Parvalbumin
Smith KM, Maragnoli ME, Phull PM, Tran KM, Choubey L, Vaccarino FM. Fgfr1 Inactivation in the Mouse Telencephalon Results in Impaired Maturation of Interneurons Expressing Parvalbumin. PLOS ONE 2014, 9: e103696. PMID: 25116473, PMCID: PMC4130531, DOI: 10.1371/journal.pone.0103696.Peer-Reviewed Original ResearchConceptsGanglionic eminenceSoma sizeCortical interneuronsAstrocytes of miceCortex of adultCortical GABAergic neuronsParvalbumin-positive cortical interneuronsRadial glial cellsSmaller soma sizeMedial ganglionic eminenceFibroblast growth factorDeficient astrocytesLocomotor hyperactivityGABAergic cellsGABAergic neuronsInterneuron maturationGlial cellsCortical astrocytesPostnatal periodAdult CNSPostnatal brainInterneuron markersInterneuronsImmunopositive interneuronsAstrocytes
2011
FGF Signaling Expands Embryonic Cortical Surface Area by Regulating Notch-Dependent Neurogenesis
Rash BG, Lim HD, Breunig JJ, Vaccarino FM. FGF Signaling Expands Embryonic Cortical Surface Area by Regulating Notch-Dependent Neurogenesis. Journal Of Neuroscience 2011, 31: 15604-15617. PMID: 22031906, PMCID: PMC3235689, DOI: 10.1523/jneurosci.4439-11.2011.Peer-Reviewed Original ResearchMeSH KeywordsAge FactorsAnalysis of VarianceAnimalsBrainBromodeoxyuridineCaspase 3Cell CountCell DifferentiationCells, CulturedCerebral CortexDNA-Binding ProteinsElectroporationEmbryo, MammalianEye ProteinsFatty Acid-Binding Protein 7Fatty Acid-Binding ProteinsFibroblast Growth FactorsGene Expression Regulation, DevelopmentalGreen Fluorescent ProteinsHomeodomain ProteinsKi-67 AntigenMiceMice, TransgenicMutationNerve Tissue ProteinsNeurogenesisNeuronsPaired Box Transcription FactorsPAX6 Transcription FactorReceptors, Fibroblast Growth FactorReceptors, NotchRepressor ProteinsSignal TransductionStem CellsT-Box Domain ProteinsTranscription FactorsConceptsCortical neurogenesisCortical surface area expansionCortical surface expansionCortical surface areaGrowth factor receptorEmbryonic day 12.5Fibroblast growth factor receptorFGFR mutantsNormal miceCortical layer structureCortical developmentNeurogenic stagesDominant negative FGFRLoss of functionRadial progenitorsNeurogenesisNotch pathway genesSevere deficitsFactor receptorDay 12.5Notch pathwayMiceSimultaneous activationGreater proportionFGFR activity
2009
Increased Brain Size in Autism—What It Will Take to Solve a Mystery
Vaccarino FM, Smith KM. Increased Brain Size in Autism—What It Will Take to Solve a Mystery. Biological Psychiatry 2009, 66: 313-315. PMID: 19643218, PMCID: PMC2803090, DOI: 10.1016/j.biopsych.2009.06.013.Commentaries, Editorials and Letters