Perturb-map Enables Identification of Genetic Regulators of the TME

Current techniques for evaluating genes that control the tumor microenvironment (TME) are suboptimal, with these approaches generally not preserving tissue architecture. Dhainaut, Rose, and colleagues thus descri be the “Perturb-map” approach, which uses a protein barcode system (Pro-Code) that allows for spatial and functional genomics in vivo. Using lung and breast cancer cell lines expressing these Pro-Codes, multiplex imaging was able to detect Pro-Code–expressing populations, allowing the spatial resolution of up to 120 different Pro-Codes in these tumor models. Initial visualization of these Pro-Codes within these tumor cells indicated clonality of the different tumor types in both primary and metastatic samples. Additionally, Perturb-map and Pro-Codes were shown to be able to resolve CRISPR screens, and functionally found that CRISPR knockout of Cd274 and Cd47 impaired Kras^G12D, p53^−/− lung cancer cell growth, while loss of B2m promoted tumor growth. Furthermore, tumors lacking Tgfbr2 were among the largest tumors and were demonstrated to be more fibromucinous in nature and also had a remodeled stroma. Moreover, analyses into how gene alterations affected immune cell recruitment were performed using Perturb-map, with tissue sections stained for both Pro-Codes and different immune cell markers showing that immune infiltration occurred in specific patterns when different genes were altered, for example, loss of Tgfbr2 led to CD4⁺ and CD8⁺ T-cell exclusion, and spatial distribution of immune cells was shown to be altered with a majority of immune cells on the outer areas of the tumor, supporting the ability of Perturb-map to quantify immune infiltration and provide spatial distribution information. Use of Perturb-map further revealed gene expression signatures correlated with different gene perturbations and spatial locations, such as Tgfbr2 knockout tumors having an induction of collagen-coding and TGFβ signaling genes. This developed resource can therefore support the resolution of CRISPR screens through multiplex imaging and spatial transcriptomics as well as define how genetic changes, like those to TGFβ, can alter surrounding cells within the TME.

Dhainaut M, Rose SA, Akturk G, Wroblewska A, Nielsen SR, Park ES, et al. Spatial CRISPR genomics identifies regulators of the tumor microenvironment. Cell 2022;185:1223–39.e20.

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