A KRAS G12V-mutant patient-derived organoid model of brain metastasis as a target discovery platform

Brain metastasis (BM) is the most common brain tumor, with annual incidence rates ranging from 8 - 14 cases per 100,000 people. In the past decade, eligibility criteria have broadened, advancing treatments for BM with molecular targeted therapies and immune checkpoint inhibitors. Unfortunately, this progress has not yet reached patients with rare forms of BM, such as those originating from colorectal cancer (CRC), which is the second leading cause of cancer death worldwide. BM from CRC (BM-CRC) have the poorest prognosis amongst metastatic CRCs, due to their inherent resistance to chemotherapy and radiation, underscoring the need for new therapeutic approaches. Drug development faces in oncology faces significant challenges and has a high attrition rate, largely due to tumor diversity and the limitation of traditional models, such as 2D cell cultures and animal testing, which often fail to replicate human tumor behavior. Additionally, the small patient cohorts for BM-CRC impede molecular studies necessary for development of evidence-based therapies and clinical guidelines We recently identified elevated levels of transcriptomic signatures for unfolded protein response (UPR) in BM-CRC, by analyses of a public dataset of single cell RNA sequencing data from 8 patients with BM-CRC. CellChat performed with these single cell data revealed interaction between tumor and tumor microenvironment (TME), which underlined the dependency of the tumor on specific components of the TME. We confirmed that the UPR, activated by endoplasmatic reticulum (ER) stress in cancer cells, is upregulated in BM-CRC compared to parental CRC, using multi-omic analyses. To investigate the UPR as a potential therapeutic vulnerability in patients, we generated a novel patient-derived organoid (PDO) from a therapy-resistant KRAS G12V mutant BM-CRC. PDOs reliably forms intracranial tumors in xenografts models and mirror the phenotypic and genetic features of the original malignant tumor reliably BM-CRC. Our preclinical data showed that pharmacologic inhibition of an ER stress-related pathway more effectively reduced PDO viability than MAPK inhibition alone. We furthermore conducted molecular analyses how the upregulation of the UPR influences cell states of BM-CRC, correlating with their poor prognosis. Taken together, our new PDO model was generated as a platform for drug discovery and to evaluate targeted therapies for treatment-refractory BM-CRC. Our preclinical and multi-omics data puts forward UPR as a therapeutic vulnerability.