空间 CRISPR 基因组学识别肿瘤微环境的调节因子

SCI

16 April 2022

Spatial CRISPR genomics identifies regulators of the tumor microenvironment

（Cell IF：41.582）

• Dhainaut Maxime,Rose Samuel A,Akturk Guray et al. Spatial CRISPR genomics identifies regulators of the tumor microenvironment.[J] .Cell, 2022, 185: 1223-1239.e20.

Abstract 摘要

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.

虽然CRISPR筛查有助于发现调控许多细胞内在过程的基因，但现有的方法在识别细胞外基因功能方面并不理想，特别是在组织背景下。在这里，我们开发了一种空间功能基因组学方法，称为Perturb-map。我们应用Perturb-map在肺癌的小鼠模型中并行敲除了数十个基因，同时评估了每个敲除如何影响肿瘤生长、组织病理学和免疫成分。此外，我们将Perturb-map和空间转录组配对，以对CRISPR编辑的肿瘤进行无偏分析。

我们发现，在TGFBR2基因敲除肿瘤中，肿瘤微环境转变为纤维粘液状态，T细胞被排除在外，伴随着转化生长因子β和转化生长因子β介导的成纤维细胞的激活，表明肿瘤细胞上转化生长因子β受体的缺失增加了转化生长因子β的生物利用度及其对转化生长因子β的免疫抑制作用。这些研究为组织内单细胞分辨率的功能基因组学建立了Perturb-map，并保留了空间结构，并提供了对癌细胞转化生长因子β反应如何影响全肺微环境的洞察。

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