Hormone-receptor-positive breast cancer is the most common subtype in women diagnosed with early-stage breast cancer. In estrogen receptor-positive (ER+) breast cancer, mutations are often found in the subunits of the SWI/SNF chromatin remodeling complexes, with ARID1A being the most frequently mutated subunit gene. Most cancer-associated mutations in ARID1A result in loss of function. Furthermore, mutations in ARID1A are linked to tumor relapse, and their co-occurrence with PIK3CA mutations in various types of cancer suggests potential cooperativity. However, the precise role of these mutations in ER+ breast cancer remains unclear. Therefore, our main goal is to reveal the role of co-occurring ARID1A and PIK3CA mutations in breast cancer progression and therapy resistance.

We utilized MCF-7 and MCF10A cell lines to establish ARID1A knockout models through the CRISPR-Cas9 system. To explore the correlation between ARID1A loss and additional genomic alterations, including PIK3CA mutations and ER loss, we evaluated their effects on cancer aggressiveness and therapy resistance. This was achieved through a series of assays, including colony formation, flow cytometry, spheroid formation, migration, and luciferase reporter assays. Mechanistic insights were examined through western blot and reverse phase protein array assays.

We interrogated the Foundation Medicine database and found that mutations in PIK3CA exhibit co-occurrence with ARID1A mutations. Laboratory functional studies demonstrated that co-occurring PIK3CA mutations and ARID1A loss enhance cell proliferation, spheroid formation, and migration, particularly in cells with baseline downregulation of ER and MAPK-ERK pathways. Mechanistically, the aggressive cellular phenotypes appear to be driven by the activation of the MAPK-ERK, PI3K/AKT, and the non-canonical ER pathways. Therapeutically, ARID1A knockout in PIK3CA mutated cells displayed relative resistance to PIK3CA inhibition. We overcame this resistance by targeting both PIK3CA and MEK (ERK kinase), or by inhibiting mTORC1, a downstream effector of both the AKT and ERK pathways. These findings suggest that breast cancers harboring PIK3CA and ARID1A mutations may benefit from combinatorial treatment strategies. Identifying patients with these genomic alterations could lead to more personalized therapies.

Our current results indicate that PIK3CA mutations and ARID1A loss co-occurrence promote breast cancer aggressiveness and drug resistance via enhanced activation of the PI3K and ERK pathways. These insights highlight the need for tailored therapeutic strategies and may help optimize treatment approaches for specific patient populations.