Tumor-derived RAC1A159V mutation promotes an immunosuppressive tumor microenvironment that represses response to immune checkpoint inhibitor [scRNA-seq]
Immune checkpoint inhibitors that activate cytotoxic T lymphocytes to kill cancer cells have seen great success in therapies against various tumor types. However, the overall response rate in patients remains unacceptable at ~15%.  RAC1, a member of Rho GTPase family, regulates multiple cellular processes in cancer, including vesicle trafficking, glycolysis, and exocytosis/endocytosis, which may contribute to tumor immune microenvironment modulation. RAC1A159V is a hotspot mutation found in several cancer types including colon cancer and is associated with poor prognosis. In this study, we have generated MC38 RAC1A159V cells by using CRISPR/Cas9 and confirmed that RAC1A159V results in upregulated RAC1 activity and downstream PAK1 and mTOR signaling.  We have found the RAC1A159V tumors grow at a similar rate as RAC1WT tumors in immunodeficient NSG mice but faster than RAC1WT tumors in syngeneic immunoproficient mice, and the RAC1A159V tumors are highly resistant to anti-PD1 treatment. Flow cytometry and scRNA-seq analyses reveal that RAC1A159V cells form “cold” tumors with an immunosuppressive microenvironment and suppressed tumor-immune cell interactions. Mechanistically, we show RAC1A159V upregulates glycosphingolipid biosynthesis to activate mTORC1 signaling in tumor cells, which in turn increases glycolysis, impairs key chemokine production, and decreases IFNGR1 expression of the tumor cells. mTORC1 inhibition re-sensitizes the RAC1A159V tumors to anti-PD1 treatment by reversing effects by RAC1A159V mutation on tumor cell glycolysis, chemokine production, and IFNGR1 expression. Our results demonstrate that RAC1A159V in tumors drives immune evasion via mTOR mediated glycolysis, chemotaxis, and IFN-? response, and further suggest an approach of combining targeting of RAC1-mTOR signaling with immune checkpoint inhibitors for the treatment of immune-cold RAC1A159V tumors. Overall design: MC38 tumor cells both wild-type and containing the RAC1A159V mutation were treated with IgG (control) and aPD1 (treatment) and subjected to single cell RNA-seq.