In vivosingle-cell CRISPR uncovers distinct TNF-α programs in clonal expansion and tumorigenesis

• DOI: 10.1101/2023.07.13.548697
• Publication Date: 2023-07-14T19:35:11Z
• Authors: Peter F. Renz; Umesh Ghoshdastider; Simona Baghai Sain; Fabiola Valdivia-...; Ameya Khandekar; Mark Ormiston; Martino Bernasconi; Jonas A. Kretz; Minkyoung Lee; Katie Hyams; Merima Forny; Marcel Pohly; Xenia Ficht; Stephanie J. Ellis; Andreas E. Moor; Ataman Sendoel

The tumor evolution model posits that malignant transformation is preceded by randomly distributed driver mutations in cancer genes, which cause clonal expansions phenotypically normal tissues. Although occur frequently human epithelia and can remodel almost entire tissues, the mechanisms behind why only a small number of clones transform into tumors remain enigmatic. Here, we develop an vivo single-cell CRISPR strategy to systematically investigate tissue-wide dynamics 150 most mutated squamous cell carcinoma genes. We couple ultrasound-guided utero lentiviral microinjections, RNA sequencing, guide capture spatial transcriptomics longitudinally monitor type-specific expansions, document their underlying gene programs contrast from initiation. uncover TNF-α signaling module acts as generalizable epithelial Conversely, during tumorigenesis, downregulated, instead, identify subpopulation invasive cells switch autocrine program. By analyzing clonally expanded perturbations frequency tumors, demonstrate program associated with epithelial-mesenchymal transition (EMT) preexistent epidermal stem cells, contributing predisposition for Finally, provide evidence sufficient mediate properties show signature correlates shorter overall survival patients. Collectively, our study demonstrates power applying screening mammalian tissues unveils distinct evolution. Understanding biology governing will development novel strategies early detection therapy.