Abstract 6053: Down-regulation of interferon gamma response and other immune-related pathways in <i>PIK3CA</i> mutant colorectal cancer
Authors: Alec B. Cornelio, Alexa E. Schmitz, Xingqi Shen, Shirsa Udgata, Cheri A. Pasch, Dustin A. Deming
Journal: Cancer Research (2025)

Abstract Background: The PIK3CA gene, encoding the p110α protein, is commonly mutated across different cancer types, including colorectal cancer (CRC). As 18% of CRCs have a PIK3CA mutation, a more comprehensive understanding of its influence on immune processes is needed. Here we sought to isolate and characterize the RNA expression signature of PIK3CA mutant CRC at both the tumor and patient-derived cancer organoid (PDCO) level. Methods: Patient/Originator Specimen (tumor) and Organoid Culture (PDCO) RNA sequencing data of CRC patients with and without PIK3CA mutations were sampled from the National Cancer Institute’s Patient-Derived Models Repository (NCI PDMR) Database. After filtering out patients with coexisting BRAF, KRAS, and NRAS mutations, patients were separated into two groups: wild-type (WT) and PIK3CA mutant (PK). The PDCO dataset contained 15 patients (nine WT vs six PK), and the tumor dataset contained eight patients (four WT vs four PK). Gene Set Enrichment Analysis (GSEA) was performed on the differential expression results comparing these two groups. A cutoff of |log10 false discovery rate (FDR)| ≥ 1.3 was used to determine significance for pathways. Data analysis was performed in R with the following packages: DESeq2, tximport, tximportData, dplyr, readr, magrittr, and ggplot. Results: In the PDCO data set, two immune pathways were significantly up-regulated in WT compared to PK: interferon alpha (IFNα, FDR q-value &amp;lt; 0.001) and interferon gamma (IFN-γ, 0.018). In the tumor data set, more immune pathways were significantly down-regulated in PK compared to WT. PK had a down-regulation in pathways involved in T cell activation and function like IL6 JAK STAT3 signaling (q = 0.009) and IL2 STAT5 signaling (q = 0.003). Interestingly, in the tumor data set, PK had multiple inflammatory pathways down-regulated compared to WT: TNFA signaling via NFKB, allograft rejection, inflammatory response, complement (all q &amp;lt; 0.001), IFN-γ response (q = 0.004). IFN-γ response was investigated further due to it being significantly down-regulated in PK in both PDCO and tumor data sets. Significant enrichment was seen in common genes for both groups as follows: PDE4B (organoid log2FC = -1.24 and tumor log2FC = -3.97), IRF5 (-1.11 and -3.05), BTG1 (-0.753 and -2.72), TNFAIP2 (-0.5 and -2.69), and CD40 (-0.405 and -2.09). IRF5 has been implicated in M1 macrophage polarization, CD40 in CD8 T cell activation, PDE4B and TNFAIP2 in inflammation, and BTG1 in B cell regulation. Downregulation of these genes hints at PK possibly inhibiting important immune cell markers and the possible mechanisms through which PK is acting. Conclusions: These analyses indicate mutated PIK3CA may play a role in suppressing the immune response in CRC, which can be seen even in PDCOs. Further investigation is needed to determine the mechanisms by which PIK3CA is suppressing the IFN-γ response and other immune-related pathways. Citation Format: Alec B. Cornelio, Alexa E. Schmitz, Xingqi Shen, Shirsa Udgata, Cheri A. Pasch, Dustin A. Deming. Down-regulation of interferon gamma response and other immune-related pathways in PIK3CA mutant colorectal cancer [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 6053.