Abstract 4329: Developing oncogenic mutant-selective antisense oligonucleotide to treat PIK3CA-mutated cancers

Abstract Phosphatidylinositol 3-kinases are heterodimers consisting of a p110 catalytic domain and a p85 regulatory domain. PIK3CA, which encodes the p110α catalytic subunit, is frequently mutated in human cancer. The FDA approved a WT p110-specific inhibitor, alpelisib, to treat PIK3CA-mutant breast cancer patients a few years ago. However, alpelisib and other WT p110α inhibitors could cause severe hyperglycemia in patients because WT p110α inhibitors block the intracellular action of insulin on the liver and skeletal muscle, thereby creating a transient state of insulin resistance. Most PIK3CA/p110α oncogenic mutations occur at two hot spot regions, one in the helical domain and the other in the kinase domain. Recently, a couple of PIK3CA/p110α kinase domain mutant-specific inhibitors have been developed. Early-phase clinical trials showed that the kinase domain mutant-specific inhibitors did not cause severe hyperglycemia in patients. Half of all p110α mutations are in the helical domain, and the E545K is the most frequent recurrent helical domain mutation. However, developing small molecule inhibitors against the PIK3CA/p110α helical domain mutations remains challenging. To this end, we have developed antisense oligonucleotides (ASOs) that preferentially degrade PIK3CA/p110α helical domain mutant mRNAs. In a cell-based assay, our lead ASO (ASO18) potently and preferentially degraded the PIK3CA E545K mutant allele at low nM concentrations. In multiple subcutaneous xenograft models, intra-tumor injection of ASO18 significantly inhibits the growth of tumors that harbor a PIK3CA E545K mutation but not a PIK3CA WT tumor. Based on our previous findings that p85β dissociates from PIK3CA/p110α E545K mutant protein and translocates into the nucleus to stabilize EZH2, we further demonstrated that a combination of ASO18 with an EZH2 inhibitor tazemetostat synergistically suppress xenograft growth of tumors harboring a PIK3CA E545K mutation. To deliver the ASO systematically, we used an FDA-approved D-Lin-MC3-DMA lipid nanoparticle (LNP) formulation to load the ASO, showing that ASO capsulated efficiently (over 95%). Moreover, the dose of LNP-ASO in the nanomolar range could achieve the same potency as the micromolar level of free ASO in tissue culture cells. Experiments assessing the efficacy of the LNP-ASO in xenograft models are ongoing. To our knowledge, our study represents the first mutant-selective ASO against an oncogenic mutation, which may lead to the development of a mutant-selective ASO to treat patients whose tumors harbor a PIK3CA E545K mutation. Citation Format: Peng Ning, Yamu Li, Clemens Burda, Zhenghe Wang. Developing oncogenic mutant-selective antisense oligonucleotide to treat PIK3CA-mutated cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 4329.