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Updated: May 22, 2025
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Pooled CRISPR-Based Genetic Screens in Mammalian Cells
Published on: September 4, 2019
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Simultaneous CRISPR screening and spatial transcriptomics reveal intracellular, intercellular, and functional
Loϊc Binan1, Aiping Jiang2, Serwah A Danquah3
1Spatial Technology Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Cell
|March 13, 2025
Summary
Perturb-FISH combines imaging and transcriptomics to reveal gene functions in cells. This powerful method uncovers how genes regulate cellular behavior and interactions in complex biological systems.
Area of Science:
- Molecular Biology
- Genomics
- Cell Biology
Background:
- Pooled optical screens offer large-scale cellular analysis but lack high-plex transcriptomic insights.
- Current methods struggle to link spatial and functional cellular data with molecular pathways at single-cell resolution.
Purpose of the Study:
- To develop a novel method integrating spatial transcriptomics with guide RNA detection for functional genomics.
- To investigate gene regulatory networks in cellular responses and disease models.
Main Methods:
- Developed Perturb-FISH, combining imaging spatial transcriptomics with in situ amplified guide RNA detection.
- Applied Perturb-FISH to study lipopolysaccharide response in monocytes, 3D xenograft tumor models, and autism spectrum disorder risk genes in hIPSC astrocytes.
Main Results:
- Perturb-FISH accurately captures intracellular perturbation effects, similar to Perturb-seq.
- Identified intercellular and density-dependent regulation of innate immune responses.
- Revealed tumor-immune interactions affected by genetic knockout and identified genetic interactions and pathways in hIPSC astrocytes related to autism spectrum disorder.
Conclusions:
- Perturb-FISH is a versatile method for dissecting genetic and molecular underpinnings of spatial and functional biology at single-cell resolution.
- Enables large-scale functional genomics by linking genotype to spatial and functional cellular phenotypes.
