Abstract 1952: Co-alterations in PIK3CA and ARID1A lead to enhanced sensitivity to PI3K inhibition

Abstract Background: There is increasing interest in developing precision medicine strategies for cancers with PIK3CA mutations. Co-alterations in PIK3CA and ARID1A (AD) occur in ~1% of all cancers. Previously, patients with co-alterations in PIK3CA and AD have shown both an improved objective response rate and improved progression free survival following copanlisib (cop) treatment compared to cancers with PIK3CA mutations and wild-type AD. Here we evaluate potential mechanisms for this enhanced clinical benefit. Methods: AD was knocked out in SW48 and SW48PIK3CA-H1047R (SW48PK) human 2D colorectal cancer cell lines using CRISPR (SW48AD; SW48PKAD). Knockouts were confirmed using PCR genotyping, amplicon sequencing, and western blot (WB). A cell proliferation assay (WST-1) was performed at increasing doses of cop for 48hrs to determine cell viability. WBs were performed at 6hrs and 24hrs after cop treatment to determine levels of phosphorylation of AKT, S6, and 4EBP1 and levels of apoptosis-related proteins (MCL-1, BCL-xL, BCL-2, PARP). Athymic nude mice were flank injected with SW48PK and SW48PKAD and treated with cop (10mg/kg in PEG400/acidified water (0.1N HCl, pH 3.5; 20/80, v/v) or vehicle for 25 days or until moribund. Results: WST-1 assay showed highest sensitivity to cop in SW48PKAD cells compared to SW48, SW48PK and SW48AD. At 10nM (p=0.01), there was a significant difference in cell viability between SW48PK and SW48PKAD. No significant difference was seen in the phosphorylation (p) of AKT, S6, or 4EBP1 between SW48PK and SW48PKAD. Expression of MCL-1 protein decreased in SW48PKAD compared to SW48PK. No difference was seen in levels of BCL-xL and BCL-2. On treatment with cop, there was a greater reduction in pS6 in SW48PKAD at 24 hours compared to SW48PK, but no significant difference in pAKT and p4EBP1. There was a gradual increase in MCL-1, BCL-xL, and cleaved PARP in SW48PKAD overtime following cop treatment compared to SW48PK. In vivo, untreated SW48PKAD tumors grew more quickly than the SW48PK tumors (8-fold increase in tumor size in SW48PKAD compared to 5-fold increase in SW48PK by day 25, p=0.06). SW48PKAD mice had significant tumor reduction (p=0.002) on cop treatment by day 25; however, SW48PK mice did not. Conclusions: ARID1A loss along with PIK3CA mutation leads to greater PI3K inhibition response most likely due to enhanced induction of apoptosis. Further confirmation of this enhanced sensitivity is required with better in vitro models such as patient-derived cancer organoids. Citation Format: Shirsa Udgata, Jordan N. Stoecker, Anna L. Lippert, Cheri A. Pasch, Dustin A. Deming. Co-alterations in PIK3CA and ARID1A lead to enhanced sensitivity to PI3K inhibition [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1952.