Abstract 3006: Genomic determinants of PIK3CA mutation driven breast cancer initiation

Abstract PIK3CA is the second most mutated and/or amplified gene in breast cancer after p53. The PIK3CA-specific inhibitor Alpelisib is an FDA approved treatment for breast cancer. Toxicity and rapid development of resistance limit its clinical utility. Mutations in PIK3CA are found in many normal organs including the breast suggesting that additional genomic aberrations are needed for mutant PIK3CA to initiate breast cancer, and those aberrations can be exploited for therapy. Consistent with this possibility, our previous studies have demonstrated that immortalized breast epithelial cells derived from BRCA1/2 mutation carriers are susceptible to transformation by the PIK3CA mutant, whereas transformation of immortalized breast epithelial cells from healthy donors required combinations of mutant PIK3CA and SV40-T/t antigens. These results suggest that transformation of breast epithelial cells by PIK3CA mutants requires additional genomic aberrations like those induced by SV40-T/t antigens or BRCA1/2 mutations. To decipher genomic aberrations required for PIK3CA mutant driven breast epithelial transformation, we used model system of immortalized breast luminal epithelial cell lines from healthy donors. We show that mutations that activate MEK/ERK pathway such as NF-1 mutation in parallel with PIK3CA mutations initiate ductal carcinoma- in situ (DCIS)-like breast tumors with accompanying reduction in BRCA2 protein, whereas mutant PIK3CA plus SV40-T/t antigens generate invasive ductal adenocarcinoma (IDC). DCIS and IDC cells differed significantly in the expression of extracellular matrix components including reduced expression of LAMC2 and COL17A1 and upregulation of drivers of aneuploidy in IDC cells. Consistent with the possibility of mutant PIK3CA and MEK/ERK pathway collaboration in breast cancer initiation, Estrogen Receptor-positive/PIK3CA mutation-positive breast tumors contained higher levels of activated ERK compared to Estrogen Receptor-positive/PIK3CA-wild type breast cancers. Significance: To our knowledge, this is the first study to generate DCIS like lesions from breast epithelial cells from healthy women using combinations of breast cancer-enriched genomic aberrations and without the use of viral proteins such as SV40-T/t antigens or HPV E6. In this process, we have developed an isogenic DCIS and IDC model to study breast cancer progression. These results also suggest that mutant PIK3CA is a weaker oncogene and the effective therapy for mutant PIK3CA driven breast cancers needs to include inhibitors of PIK3CA as well as drugs that target genomic aberrations that cooperate with mutant PIK3CA. ​ Citation Format: Snehal B. Bhandare, Ruizhong Wang, Poornima Bhat-Nakshatri, Stephanie Adama, Sarah R. Spivak, Farzaneh Behzadnia, Cihat Erdogan, Hongyu Gao, Yunlong Liu, Lylah H. Hutson, Xin Dauterman, George Sandusky, Harikrishna Nakshatri. Genomic determinants of PIK3CA mutation driven breast cancer initiation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 3006.