Abstract 1248: Single-cell RNAseq revealed multiple resistance mechanisms in patient-derived xenograft model of rectal cancer during treatment
Authors: Yuwei song, Regina K. Irwin, Karin M. Hardiman, Zechen Chong
Journal: Cancer Research (2025)

Abstract Background: Colorectal cancer (CRC) is the third leading cause of cancer-related deaths in the US, with rectal cancer (RC) accounting for one-third of cases. Only 20% of RC patients have a complete response to chemoradiation therapy (CRT) and may be able to avoid surgery, therefore, therapeutic resistance remains a major barrier to improving outcomes. The genetic and cellular heterogeneity of RC, particularly in treatment-resistant sub-clones, suggests that this diversity could be a harbinger of adverse outcomes. A detailed characterization of treatment responses at the subclonal level is critical to advancing targeted therapeutic strategies. Methods: Patient-derived xenograft (PDX) models and single-cell RNA sequencing were employed to investigate the cellular and molecular landscape of RC tumors. Two PDX models were established from the primary tumors of pre-treatment RC patients. Mice bearing tumors were subjected to a standard CRT regimen, consisting of 2 Gy daily radiation and 100mg/kg capecitabine daily for two weeks, followed by a week-long rest period. Tumor tissues were collected at baseline and at various post-treatment intervals for sequencing. Results: Our scRNA-seq analysis of one PDX model identified five distinct tumor clusters with varying responses to treatment. Two clusters demonstrated initial sensitivity to CRT, followed by a resurgence, indicating potential therapy resistance. Pathway analysis revealed cluster-specific activation of critical oncogenic pathways, including HIF-1, p53, and FoxO signaling pathways. These pathways are implicated in tumor progression and therapeutic resistance, and the associated marker genes present potential targets for intervention. Lineage tracing of tumor cells uncovered two differentiation trajectories, with one showing increased resistance. Cell-cell communication analysis highlighted extensive interactions among tumor sub-populations, particularly mediated by CLDN3-CLDN3 adhesion, which may contribute to therapeutic resistance. Additionally, our investigation into copy number variations identified alterations in the chr6p21.31-p21.1 region, which harbors several oncogenes with copy number changes directly implicated in tumor progression. In the second PDX model, scRNA-seq identified two therapy-resistant tumor clusters among five detected clusters. The resistant tumor clusters exhibited enrichment of HIF-1, Hippo, and p53 signaling pathways, similar to the first PDX model but also unique activation of pathways like TGF-β and Hippo signaling. Conclusion: Our study highlights the dynamic, heterogeneity of RC tumors to CRT, identifying both shared and patient-specific resistance mechanisms in two PDX models. These findings underscore the complexity of RC tumor biology and offer a foundation for developing precision therapies targeting treatment-resistant subclones. Citation Format: Yuwei song, Regina K. Irwin, Karin M. Hardiman, Zechen Chong. Single-cell RNAseq revealed multiple resistance mechanisms in patient-derived xenograft model of rectal cancer during treatment [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 1248.