RT Journal Article
SR Electronic
T1 Perturb-map enables CRISPR genomics with spatial resolution and identifies regulators of tumor immune composition
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.07.13.451021
DO 10.1101/2021.07.13.451021
A1 Maxime Dhainaut
A1 Samuel A Rose
A1 Guray Akturk
A1 Aleksandra Wroblewska
A1 Eun Sook Park
A1 Sebastian R Nielsen
A1 Mark Buckup
A1 Vladimir Roudko
A1 Luisanna Pia
A1 Jessica Le Berichel
A1 Anela Bektesevic
A1 Brian H Lee
A1 Alessia Baccarini
A1 Nina Bhardwaj
A1 Adeeb H Rahman
A1 Sacha Gnjatic
A1 Dana Pe’er
A1 Miriam Merad
A1 Brian D Brown
YR 2021
UL http://biorxiv.org/content/early/2021/07/14/2021.07.13.451021.abstract
AB The cellular architecture of a tumor, particularly immune composition, has a major impact on cancer outcome, and thus there is an interest in identifying genes that control the tumor microenvironment (TME). While CRISPR screens are helping uncover genes regulating many cell-intrinsic processes, existing approaches are suboptimal for identifying gene functions operating extracellularly or within a tissue context. To address this, we developed an approach for spatial functional genomics called Perturb-map, which utilizes protein barcodes (Pro-Code) to enable spatial detection of barcoded cells within tissue. We show >120 Pro-Codes can be imaged within a tumor, facilitating spatial mapping of 100s of cancer clones. We applied Perturb-map to knockout 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. Additionally, we paired Perturb-map and spatial transcriptomics for unbiased molecular analysis of Pro-Code/CRISPR lesions. Our studies found in Tgfbr2 knockout lesions, the TME was converted to a mucinous state and T-cells excluded, which was concomitant with increased TGFβ expression and pathway activation, suggesting Tgfbr2 loss on lung cancer cells enhanced suppressive effects of TGFβ on the TME. These studies establish Perturb-map for functional genomics within a tissue at single cell-resolution with spatial architecture preserved.Competing Interest StatementThe authors have declared no competing interest.