Circular RNAs impinge on non-cell-autonomous mechanisms to regulate tumorigenesis. [scRNA-Seq]

The functional contribution of many circular RNAs (circRNAs) to cancer is poorly understood. Here, we report that knockdown in sarcoma cells of the endogenous circRNA, circCsnk1g3, modulates changes in immune cell proportions and expression profiles in the tumor lung microenvironment. Overall design: Single-cell transcriptomic profiling subcutaneous mouse sarcomas, with or without expression of circCsnk1g3. Soft-tissue sarcoma cells were generated as transformed mouse mesenchymal stem cells (p53-/-Ccne1+) which formed subcutaneous tumors when transplanted in mice,. To examine the effect of tumor circRNA expression on the microenvironment, tumor cells were additionally transduced with an shRNA to knock down circCsnk1g3, or with a nontargeting shRNA (shSCR). Tumors were transplanted into mice seeded on polyurethane scaffolds. Tumors were harvested, digested, and enriched for CD45+ immune cells. Immune cells from each mouse were individually hashtagged with sequenceable oligos, and then pooled and captured with the 10X Chromium 3' Single-Cell workflow. Each sample represents pooled immune-enriched cells isolated from two groups of mouse tumors (n=4 mice per group): Mouse sarcoma (p53-/-Ccne1+) bearing a non-targeting control shRNA (shSCR). Mouse sarcoma (p53-/-Ccne1+) bearing an shRNA to knock down circCsnk1g3 expression (shcircCsnk1g3).