Genomic alterations in PIK3CA-mutated breast cancer result in mTORC1 activation and limit the sensitivity to PI3Ka inhibitors

PI3Ka inhibitors have shown clinical activity in PIK3CAmutated estrogen receptor-positive (ER^þ) patients with breast cancer. Using whole genome CRISPR/Cas9 sgRNA knockout screens, we identified and validated several negative regulators of mTORC1 whose loss confers resistance to PI3Ka inhibition. Among the top candidates were TSC1, TSC2, TBC1D7, AKT1S1, STK11, MARK2, PDE7A, DEPDC5, NPRL2, NPRL3, C12orf66, SZT2, and ITFG2. Loss of these genes invariably results in sustained mTOR signaling under pharmacologic inhibition of the PI3K–AKT pathway. Moreover, resistance could be prevented or overcome by mTOR inhibition, confirming the causative role of sustained mTOR activity in limiting the sensitivity to PI3Ka inhibition. Cumulatively, genomic alterations affecting these genes are identified in about 15% of PIK3CAmutated breast tumors and appear to be mutually exclusive. This study improves our understanding of the role of mTOR signaling restoration in leading to resistance to PI3Ka inhibition and proposes therapeutic strategies to prevent or revert this resistance.