Spatial CRISPR genomics identifies regulators of the tumor microenvironment

Area of Science:

• Genomics
• Cancer Biology
• Immunology

Background:

• CRISPR screens are effective for cell-intrinsic gene functions but limited for extracellular and tissue-level analyses.
• Understanding gene function within the complex tumor microenvironment (TME) is crucial for cancer research.

Purpose of the Study:

• To develop and apply a novel spatial functional genomics approach, Perturb-map, for dissecting extracellular gene functions within the tissue context.
• To investigate the impact of gene knockouts on tumor growth, histopathology, and immune composition in a mouse lung cancer model.

Main Methods:

• Development of Perturb-map, a spatial functional genomics technique.
• Application of Perturb-map to perform parallel gene knockouts in a mouse lung cancer model.
• Integration of Perturb-map with spatial transcriptomics for comprehensive analysis of CRISPR-edited tumors.

Main Results:

• Perturb-map enabled simultaneous assessment of gene knockout effects on tumor growth, histopathology, and immune cell infiltration.
• In Tgfbr2 knockout tumors, a fibro-mucinous TME phenotype was observed with T cell exclusion.
• Upregulated TGFβ signaling and fibroblast activation were noted, indicating increased TGFβ bioavailability and immunosuppression.

Conclusions:

• Perturb-map is established as a powerful tool for single-cell resolution functional genomics in tissues while preserving spatial architecture.
• Cancer cell TGFβ-receptor responsiveness significantly influences the TME, impacting immune cell interactions and tumor progression.