Transcriptomic Analyses and Novel Organoid and Xenograft Modeling Reveals Potential Drug Sensitivities in a KRAS G12V-Mutant Colorectal Cancer Brain Metastasis

Brain metastases (BM) occur in 2.3% of patients with colorectal cancer (CRC), which is the second leading cause of cancer deaths globally. Despite aggressive treatment like surgery and chemo-irradiation, median survival for patients with BM originating from CRC (CRC-BM) remains poor at 5.3 months, highlighting the need for improved therapies. Next-generation sequencing has identified KRAS mutations in approximately 40% of metastatic CRC cases. Therapies targeting mutant KRAS and downstream MAPK pathway components exist, but their effectiveness is often limited by therapy resistance, underscoring the need for novel drug targets beyond the MAPK pathway. Additionally, there is a lack of accurate preclinical models for CRC-BM. In this study, we generated a patient-derived organoid model (PDO) from a KRAS G12V mutant CRC-BM surgical sample. PDO consistently formed intracranial tumors in both male and female mice, indicative of their stable malignant potential. Both the PDO and PDO-derived xenografts (PDoX) retained the KRAS G12V mutation and key epithelial and mesenchymal markers, closely resembling the original BM. Spatial transcriptome analysis of the patient BM revealed six distinct functional tumor epithelial cells, with features such as enhanced MAPK signaling and upregulated ER-stress. Bulk RNA sequencing analyses showed differences between PDO and PDoX, which reflected in vitro growth conditions. PDO, PDoX, and patient BM shared pathways including ER-stress and unfolded protein response (UPR) pathway. DNA methylation profiling revealed a varying number of differentially methylated regions between samples derived from primary CRC and BM, and comparable numbers of these regions between PDO and PDoX. Proof-of-concept was demonstrated by pharmacologically inhibiting RAS-RAF-MAPK signaling, and more effectively key molecules in the ER-stress sensor/UPR pathways. In conclusion, we developed a patient-derived organoid (PDO) model from a KRAS G12V mutant CRC-BM, closely mirroring the tumor’s clinical characteristics. Targeting the MAPK and ER/UPR pathways significantly reduced PDO viability, revealing key therapeutic vulnerabilities.