Impact of treatment history on drug resistance of metastatic colorectal cancer organoids

The treatment of metastatic colorectal cancer (mCRC) is impeded by drug resistance. We investigated how prior chemotherapy affects tumor genotype, phenotype, and resistance mechanisms by comparing 35 patient-derived metastatic organoids (PDOs) from pretreated and chemonaive patients with mCRC. Combining PDO drug sensitivity assessments with RNA and whole genome sequencing, we found PDOs from pretreated patients exhibited higher mutational load and more structural variants. Chemotherapy-related mutational signatures correlated with previous exposure. PDOs from oxaliplatin-resistant patients maintained this resistance, showing the upregulation of <i>ZNF300</i>, <i>TGM2</i>, and Hedgehog pathway enrichment. Acquired resistance to 5-FU and irinotecan was only partially captured, with irinotecan resistance linked to specific mutational signatures and deep deletions in common fragile sites, associated with distinct gene expression profiles. Our findings reveal that PDOs capture chemotherapy-induced genomic and phenotypic changes differently depending on the drug, suggesting varied mechanisms of acquired resistance involving both tumor cell-intrinsic properties and dynamic tumor cell states.