Title | Massively parallel in vivo Perturb-seq reveals cell-type-specific transcriptional networks in cortical development. |
Publication Type | Journal Article |
Year of Publication | 2024 |
Authors | Zheng X, Wu B, Liu Y, Simmons SK, Kim K, Clarke GS, Ashiq A, Park J, Li J, Wang Z, Tong L, Wang Q, Rajamani KT, Muñoz-Castañeda R, Mu S, Qi T, Zhang Y, Ngiam ZChao, Ohte N, Hanashima C, Wu Z, Xu X, Levin JZ, Jin X |
Journal | Cell |
Volume | 187 |
Issue | 13 |
Pagination | 3236-3248.e21 |
Date Published | 2024 Jun 20 |
ISSN | 1097-4172 |
Keywords | Animals, Cell Line, Cerebral Cortex, CRISPR-Cas Systems, Dependovirus, Female, Forkhead Transcription Factors, Gene Regulatory Networks, Genetic Vectors, Humans, Mice, Mice, Inbred C57BL, Nerve Tissue Proteins, Neurons, Single-Cell Analysis, Transcription, Genetic, Transcriptome |
Abstract | Leveraging AAVs' versatile tropism and labeling capacity, we expanded the scale of in vivo CRISPR screening with single-cell transcriptomic phenotyping across embryonic to adult brains and peripheral nervous systems. Through extensive tests of 86 vectors across AAV serotypes combined with a transposon system, we substantially amplified labeling efficacy and accelerated in vivo gene delivery from weeks to days. Our proof-of-principle in utero screen identified the pleiotropic effects of Foxg1, highlighting its tight regulation of distinct networks essential for cell fate specification of Layer 6 corticothalamic neurons. Notably, our platform can label >6% of cerebral cells, surpassing the current state-of-the-art efficacy at <0.1% by lentivirus, to achieve analysis of over 30,000 cells in one experiment and enable massively parallel in vivo Perturb-seq. Compatible with various phenotypic measurements (single-cell or spatial multi-omics), it presents a flexible approach to interrogate gene function across cell types in vivo, translating gene variants to their causal function. |
DOI | 10.1016/j.cell.2024.04.050 |
Alternate Journal | Cell |
PubMed ID | 38772369 |
PubMed Central ID | PMC11193654 |
Grant List | R01 HG012819 / HG / NHGRI NIH HHS / United States |