Abstract 4595: Transcriptomic and tumor microenvironment alterations in microsatellite stable rectal tumors: Comparison between neoadjuvant-treated and treatment-naive patients

Abstract Neoadjuvant therapy (NAT) for rectal cancer has markedly improved survival rates and the likelihood of complete therapeutic response. However, recurrence after curative intent therapy and resistance to primary oncological therapy remain, shortening the survival. The modulation of transcriptomic profiles by NAT and its association with therapeutic response remain unclear. Methods: The preliminary analyses of observational study of 680 colorectal cancer (CRC) patients focused on a sub-cohort of 233 primary rectal cancer patients, of whom 95 received NAT (chemoradiotherapy, radiation therapy with immediate surgery or wait period, or chemotherapy) and 138 were treatment-naive. Pathological responses varied from minimal to excellent. Transcriptomic, genomic, and immunohistochemical (IHC) profiling were performed on surgical resection samples. Mutation statuses of non-synonymous variants in CRC driver genes were compared between groups. Gene expression profiles were classified into consensus molecular subtypes (CMS) and intrinsic CMS (iCMS), with differentially expressed genes analyzed for hallmark pathway enrichment. Results: Transcriptomic analysis revealed a significant shift in molecular subtypes, with 66% of NAT tumors classified as iCMS3 (CMS4), compared to 63% of treatment-naive tumors classified as iCMS2. Pathway enrichment analysis of 4, 817 differentially expressed genes showed significantly higher expression of hallmark pathways, particularly epithelial-to-mesenchymal transition and p53 signaling, in NAT tumors. Treatment-naive samples classified as iCMS3 (27%) displayed expression patterns similar to NAT iCMS3 tumors. The fraction of epithelial cells was significantly lower in NAT compared to treatment-naive, as determined by IHC. No significant differences in the overall mutation statuses of key CRC driver genes were observed between groups. Although, mutations in APC and TP53 were less frequent in the NAT tumors. Notably, KRAS mutations were mutually exclusive with TP53 in treatment-naive samples (36/95), whereas TP53 mutations co-occurred with APC in NAT tumors (48/22). Conclusion: NAT potentially induces a shift in gene expression from iCMS2 to iCMS3 in left-sided MSS rectal tumors, accompanied by increased epithelial-to-mesenchymal transition and altered driver gene interactions. Further investigations are needed to confirm whether NAT drives this gene expression shift, to elucidate its effects on tumor microenvironment modulation with available IHC data of T-cell, TMA, and CAF panels and to assess their impact on therapeutic outcomes and potential to inform adjuvant therapy strategies. Citation Format: Emmi K. Hämäläinen, Kalle Ojala, Mikael Marttinen, Matti Nykter, Toni Seppälä. Transcriptomic and tumor microenvironment alterations in microsatellite stable rectal tumors: Comparison between neoadjuvant-treated and treatment-naive patients [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 4595.