Massively parallel in vivo Perturb-seq reveals cell-type-specific transcriptional networks in cortical development.

TitleMassively parallel in vivo Perturb-seq reveals cell-type-specific transcriptional networks in cortical development.
Publication TypeJournal Article
Year of Publication2024
AuthorsZheng 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
JournalCell
Volume187
Issue13
Pagination3236-3248.e21
Date Published2024 Jun 20
ISSN1097-4172
KeywordsAnimals, 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.

DOI10.1016/j.cell.2024.04.050
Alternate JournalCell
PubMed ID38772369
PubMed Central IDPMC11193654
Grant ListR01 HG012819 / HG / NHGRI NIH HHS / United States