Abstract 4316: Co-alterations in <i>PIK3CA</i> and <i>ARID1A</i> lead to greater sensitivity to PI3K pathway inhibition
Authors: Xingqi Shen, Shirsa Udgata, Jordan N. Stoecker, Cheri A. Pasch, Dustin A. Deming
Journal: Cancer Research (2025)

Abstract Introduction: Co-alterations in PIK3CA (PK) and ARID1A (AD) occur in ∼1% of all cancers. Previously we have shown that patients with mutations in both genes are more sensitive to copanlisib (cop) treatment than those with just PIK3CA(PK) mutation. Here we evaluate the efficacy of PI3K/AKT and PI3K/mTOR dual inhibitors, compared to that of cop using PKAD patient-derived cancer organoids (PDCOs). Methods: RSEM files from NCI repository were obtained for endometrial cancer (EC) PDCOs with PK, AD, PKAD and wild type for PK and AD. Expression data in RSEM format were processed using the tximport package in RStudio to import data into data frames. The DESeq2 package was used to create differential gene expression (DGE) files. Additionally, bulk-RNA sequencing was done by UW Bioinformatics Research Core on 2D colorectal cancer (CRC) cell lines, SW48 and SW48PIK3CA-H1047R (SW48PK), from which AD was deleted with CRISPR (SW48AD; SW48PKAD). Gene Set Enrichment Analysis was run to identify hallmark pathway alterations (| -log10(FDR q-val) | &amp;gt;= 1). PDCOs were obtained following surgery with consent and following UW IRB protocol. PDCOs were generated as described previously. AD was deleted from a CRC PDCO line, with a PIK3CAH1047R mutation (CRC-PK) using CRISPR (CRC-PKAD). PDCO lines were treated with PI3K inhibitors (alpelisib (alp), pictilisib (pict), cop, capivasertib (cap), sapanisertib (sap) and everolimus (eve)). Relative change in diameter (ΔD) was measured at day 0 and day 2 using ImageJ. Normalized ΔD (nΔD) was calculated as the ratio of median ΔD of treatment and control. Results: Bulk-RNA-seq analysis of EC PDCO samples showed significant downregulation in immune signature pathways like epithelial-mesenchymal-transition, Interferon-γ, and IL6-JAK9-STAT3 signaling, along with a significant upregulation in the WNT-beta catenin signaling pathway when comparing PKAD and PK. Comparison between PKAD and AD showed upregulation in p53, apoptosis, and WNT-beta catenin signaling pathways. RNA-seq of 2D CRCs showed significant downregulation of the p53 (-log10FDR = 10), MYC target v2 (2.366), and apoptosis (1.826) pathways when comparing SW48PKAD and SW48PK. PKAD CRC PDCO lines had greater sensitivity to cop treatment than those with PK alterations alone (PK: nΔD=0.175; PKAD: nΔD =-0.12; p &amp;lt; 0.005). An enhanced response was observed with some other PI3K inhibitors, including sapanisertib (PK=0.13; PKAD=0.014; p &amp;lt; 0.005) everolimus (PK=0.66, PKAD=0.36; p &amp;lt; 0.005) and capivasertib (PK=0.85; PKAD=0.47; p &amp;lt; 0.05). An enhanced response was not observed with alpelisib (PK=0.54; PKAD=0.61; p = 0.77) nor pictilisib (PK=0.64, PKAD=0.76; p &amp;lt; 0.005). Conclusions: Cancers with PK and AD alterations have enhanced efficacy to PI3K pathway inhibition, especially those inhibitors with downstream activity against AKT or MTOR. Further mechanistic and in vivo studies are warranted in addition to further clinical validation. Citation Format: Xingqi Shen, Shirsa Udgata, Jordan N. Stoecker, Cheri A. Pasch, Dustin A. Deming. Co-alterations in PIK3CA and ARID1A lead to greater sensitivity to PI3K pathway inhibition [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 4316.