oFlowSeq: a quantitative approach to identify protein coding mutations affecting cell type enrichment using mosaic CRISPR-Cas9 edited cerebral organoids
Murray, Liam F
Olson, Meagan N
Barton, Nathaniel J
Church, George M
Lim, Elaine T
UMass Chan AffiliationsMolecular, Cell and Cancer Biology
Program in Bioinformatics and Integrative Biology
Document TypeJournal Article
MetadataShow full item record
AbstractCerebral organoids are comprised of diverse cell types found in the developing human brain, and can be leveraged in the identification of critical cell types perturbed by genetic risk variants in common, neuropsychiatric disorders. There is great interest in developing high-throughput technologies to associate genetic variants with cell types. Here, we describe a high-throughput, quantitative approach (oFlowSeq) by utilizing CRISPR-Cas9, FACS sorting, and next-generation sequencing. Using oFlowSeq, we found that deleterious mutations in autism-associated gene KCTD13 resulted in increased proportions of Nestin+ cells and decreased proportions of TRA-1-60+ cells within mosaic cerebral organoids. We further identified that a locus-wide CRISPR-Cas9 survey of another 18 genes in the 16p11.2 locus resulted in most genes with > 2% maximum editing efficiencies for short and long indels, suggesting a high feasibility for an unbiased, locus-wide experiment using oFlowSeq. Our approach presents a novel method to identify genotype-to-cell type imbalances in an unbiased, high-throughput, quantitative manner.
SourceDawes P, Murray LF, Olson MN, Barton NJ, Smullen M, Suresh M, Yan G, Zhang Y, Fernandez-Fontaine A, English J, Uddin M, Pak C, Church GM, Chan Y, Lim ET. oFlowSeq: a quantitative approach to identify protein coding mutations affecting cell type enrichment using mosaic CRISPR-Cas9 edited cerebral organoids. Hum Genet. 2023 Mar 6. doi: 10.1007/s00439-023-02534-4. Epub ahead of print. PMID: 36877372.
Permanent Link to this Itemhttp://hdl.handle.net/20.500.14038/51964
Rights© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.