Cell. 2022 Mar 10. pii: S0092-8674(22)00195-7. [Epub ahead of print]
Maxime Dhainaut,
Samuel A Rose,
Guray Akturk,
Aleksandra Wroblewska,
Sebastian R Nielsen,
Eun Sook Park,
Mark Buckup,
Vladimir Roudko,
Luisanna Pia,
Robert Sweeney,
Jessica Le Berichel,
C Matthias Wilk,
Anela Bektesevic,
Brian H Lee,
Nina Bhardwaj,
Adeeb H Rahman,
Alessia Baccarini,
Sacha Gnjatic,
Dana Pe'er,
Miriam Merad,
Brian D Brown.
While CRISPR screens are helping uncover genes regulating many cell-intrinsic processes, existing approaches are suboptimal for identifying extracellular gene functions, particularly in the tissue context. Here, we developed an approach for spatial functional genomics called Perturb-map. We applied Perturb-map to knock out dozens of genes in parallel in a mouse model of lung cancer and simultaneously assessed how each knockout influenced tumor growth, histopathology, and immune composition. Moreover, we paired Perturb-map and spatial transcriptomics for unbiased analysis of CRISPR-edited tumors. We found that in Tgfbr2 knockout tumors, the tumor microenvironment (TME) was converted to a fibro-mucinous state, and T cells excluded, concomitant with upregulated TGFβ and TGFβ-mediated fibroblast activation, indicating that TGFβ-receptor loss on cancer cells increased TGFβ bioavailability and its immunosuppressive effects on the TME. These studies establish Perturb-map for functional genomics within the tissue at single-cell resolution with spatial architecture preserved and provide insight into how TGFβ responsiveness of cancer cells can affect the TME.
Keywords: CRISPR screens; Socs1; TGF beta; cancer immunology; interferon gamma; lung cancer; spatial genomics; spatial transcriptomics; tumor clonality; tumor microenvironment