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

Cell, Journal Year: 2024, Volume and Issue: 187(13), P. 3236 - 3248.e21

Published: May 20, 2024

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 peripheral nervous systems. Through extensive tests 86 vectors AAV serotypes combined a transposon system, substantially amplified efficacy accelerated gene delivery from weeks days. Our proof-of-principle utero screen identified pleiotropic effects Foxg1, highlighting its tight regulation distinct networks essential for cell fate specification Layer 6 corticothalamic neurons. Notably, our platform can label >6% cerebral cells, surpassing current state-of-the-art at <0.1% by lentivirus, achieve analysis over 30,000 cells one experiment enable massively parallel Perturb-seq. Compatible various phenotypic measurements (single-cell or spatial multi-omics), it presents flexible approach interrogate function types vivo, translating variants their causal function.

Language: Английский

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Toward a foundation model of causal cell and tissue biology with a Perturbation Cell and Tissue Atlas

Cell, Journal Year: 2024, Volume and Issue: 187(17), P. 4520 - 4545

Published: Aug. 1, 2024

Language: Английский

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Empowering biomedical discovery with AI agents

Cell, Journal Year: 2024, Volume and Issue: 187(22), P. 6125 - 6151

Published: Oct. 1, 2024

We envision "AI scientists" as systems capable of skeptical learning and reasoning that empower biomedical research through collaborative agents integrate AI models tools with experimental platforms. Rather than taking humans out the discovery process, combine human creativity expertise AI's ability to analyze large datasets, navigate hypothesis spaces, execute repetitive tasks. are poised be proficient in various tasks, planning workflows performing self-assessment identify mitigate gaps their knowledge. These use language generative feature structured memory for continual machine incorporate scientific knowledge, biological principles, theories. can impact areas ranging from virtual cell simulation, programmable control phenotypes, design cellular circuits developing new therapies.

Language: Английский

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Multiplexed, image-based pooled screens in primary cells and tissues with PerturbView

Nature Biotechnology, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 7, 2024

Language: Английский

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Massively parallel in vivo Perturb-seq screening

Nature Protocols, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 12, 2025

Language: Английский

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The Current Situation and Development Prospect of Whole-Genome Screening

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(1), P. 658 - 658

Published: Jan. 4, 2024

High-throughput genetic screening is useful for discovering critical genes or gene sequences that trigger specific cell functions and/or phenotypes. Loss-of-function mainly achieved through RNA interference (RNAi), CRISPR knock-out (CRISPRko), and (CRISPRi) technologies. Gain-of-function depends on the overexpression of a cDNA library activation (CRISPRa). Base editing can perform both gain- loss-of-function screening. This review discusses techniques based Cas9 nuclease, including Cas9-mediated genome dCas9-based interference. We compare these methods with previous RNAi propose future prospects applications

Language: Английский

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Spatial omics advances for in situ RNA biology

Molecular Cell, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 1, 2024

Language: Английский

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CellFIE: Integrating Pathway Discovery With Pooled Profiling of Perturbations Uncovers Pathways of Huntington's Disease, Including Genetic Modifiers of Neuronal Development and Morphology

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 20, 2025

Abstract Genomic screens and GWAS are powerful tools for identifying disease-modifying genes, but it is often challenging to understand the pathways by which these genes function. Here, we take an integrated approach that combines network analysis imaging-based pooled genetic perturbation study examine modifiers of Huntington’s disease (HD). The computational highlighted several in a subnetwork enriched neuronal development morphology. To test functional roles developed experimental pipeline allows CRISPRi KD 21 human iPSC-derived neurons followed optical genotypes, arborization, multiplexed pathway activity morphological fingerprint readout. This recovered known involved morphology confirmed unexpected links from between HD Our overcomes challenges measurement function health could be adapted other phenotypes neurological diseases.

Language: Английский

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Sequencing-free whole genome spatial transcriptomics at molecular resolution in intact tissue

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: March 11, 2025

Recent breakthroughs in spatial transcriptomics technologies have enhanced our understanding of diverse cellular identities, compositions, interactions, organizations, and functions. Yet existing tools are still limited either transcriptomic coverage or resolution. Leading spatial-capture spatial-tagging techniques that rely on in-vitro sequencing offer whole-transcriptome coverage, principle, but at the cost lower resolution compared to image-based techniques. In contrast, high-performance techniques, which situ hybridization sequencing, achieve single-molecule retain sub-cellular morphologies, by probe libraries target only a subset transcriptome, typically covering several hundred few thousand transcript species. Together, these limitations hinder unbiased, hypothesis-free analyses high Here we develop new technology termed Reverse-padlock Amplicon Encoding FISH (RAEFISH) with whole-genome level while retaining intact tissues. We demonstrate targeting 23,000 human species 22,000 mouse species, including nearly entire protein-coding transcriptome long-noncoding RNAs, single cells cultures tissue sections. Our reveal differential subcellular localizations transcripts, cell-type-specific cell-type-invariant zonation dependent gene expression programs underlying preferential cell-cell interactions. Finally, further for direct readout gRNAs an high-content CRISPR screen. Overall, developments provide research community broadly applicable enables high-coverage, high-resolution profiling both long short, native engineered RNA many biomedical contexts.

Language: Английский

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Transcriptome-wide analysis of differential expression in perturbation atlases

Nature Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: April 21, 2025

Language: Английский

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