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Droplet-based functional CRISPR screening of cell-cell interactions by SPEAC-seq
Camilo Faust Akl1, Mathias Linnerbauer1, Zhaorong Li1
1Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
Nature Protocols
|September 26, 2024
Summary
We developed a new method, SPEAC-seq, for high-throughput genetic screening of cell-cell interaction regulators. This technique enables unbiased discovery of key molecules controlling intercellular communication in various biological contexts.
Area of Science:
- Cell Biology
- Genetics
- Neuroscience
Background:
- Cell-cell interactions are crucial for tissue function and regulation.
- Traditional methods for studying cell communication are limited, often requiring prior knowledge and lacking functional readouts.
Purpose of the Study:
- To introduce a novel high-throughput platform for unbiased genetic screening of cell-cell interaction regulators.
- To overcome limitations of existing methods for characterizing cell-cell communication.
Main Methods:
- Systematic Perturbation of Encapsulated Associated Cells followed by Sequencing (SPEAC-seq) combines genome-wide CRISPR libraries with microfluidics.
- Cells are cocultured in droplets, sorted based on functional readouts from fluorescent reporter circuits.
- Demonstrated application in studying neuroinflammation between microglia and astrocytes using NF-κB activation reporters.
Main Results:
- Discovered thousands of microglial regulators of astrocyte NF-κB activation, crucial for central nervous system inflammation control.
- SPEAC-seq enables large-scale investigation of cell-cell interactions.
- Genome-wide screening is achievable in under two weeks with microfluidics.
Conclusions:
- SPEAC-seq is a versatile platform for unbiased discovery of cell interaction regulators.
- The method can be adapted to various cell types, functions, and physiological contexts.
- This technology significantly advances the study of intercellular communication.
