Novel metastasis suppressor PI3KC2β is mediated by mTORC1 signalling in breast cancer

Abstract HER2 amplification or mutation accounts for 25% of breast cancer patients that can advance to metastatic disease. Therefore, it is important to identify novel genes which mediate metastasis in HER2+ breast cancer. Here, we describe a new metastatic suppressor gene, Class II phosphatidylinositol 3-kinases (Pik3c2b), by in vivo CRISPR-Cas9 library screening of a custom designed library targeting genes implicated in autophagy using murine HER2+ breast cancer (N418) cells. We further showed that PI3KC2β KO N418 cells increased their migration and invasion in vitro, and lung metastasis in both spontaneous and experimental metastasis assays in vivo. Analysis of breast cancer patient database and tissue samples correlated lower expression of PI3KC2β with decreased metastasis, overall and relapse-free survival. Further, PI3KC2β deletion induced activation of mTORC1 signalling, independent of affecting its kinase activity. Mechanistically, we found that PI3KC2β forms a complex with ITSN1 and raptor that could decreasing stability of raptor, and deletion of either PI3KC2β or ITSN1 led to increased raptor levels and mTORC1 signalling. Lastly, rapamycin treatment reduced migration and invasion of PI3KC2β KO tumor cells in vitro and their lung metastasis in vivo, supporting an important role of mTORC1 pathway. Together, our results identify PI3KC2β as a suppressor for HER2+ breast cancer metastasis by negatively regulating mTORC1 signalling by affecting its complex formation with ITSN1 and raptor. Implications: Our findings revealed PI3KC2β as a new metastasis suppressor for HER2+ breast cancer, which might serve as a potential diagnostic and therapeutic target for the disease.