Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Cell. 2022 Mar 31;185(7):1223-1239.e20. doi: 10.1016/j.cell.2022.02.015. Epub 2022 Mar 14.
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 筛选正在帮助揭示调节许多细胞内在过程的基因，但现有的方法对于识别细胞外基因功能并不理想，特别是在组织背景下。在这里，我们开发了一种称为 Perturb-map 的空间功能基因组学方法。我们在肺癌的小鼠模型中同时敲除了数十个基因，并同时评估了每个敲除如何影响肿瘤生长、组织病理学和免疫组成。此外，我们将 Perturb-map 与空间转录组学配对，用于对 CRISPR 编辑肿瘤进行无偏分析。我们发现，在 Tgfbr2 敲除肿瘤中，肿瘤微环境 (TME) 转化为纤维粘液状态，T 细胞被排除，同时 TGFβ 上调和 TGFβ 介导的成纤维细胞激活，表明癌细胞上 TGFβ 受体的丧失增加了 TGFβ 的生物利用度及其对 TME 的免疫抑制作用。这些研究建立了 Perturb-map，用于在保留空间结构的情况下以单细胞分辨率进行组织内的功能基因组学研究，并深入了解癌细胞对 TGFβ 的反应如何影响 TME。
