Single cell analysis of colorectal cancer identifies mitogen-activated protein kinase as a key driver of tumor cell plasticity

Abstract In colorectal cancer, oncogenic mutations transform a hierarchically organized and homeostatic epithelium into invasive cancer tissue lacking visible organization. We sought to identify differences in cellular composition between normal colon and colorectal cancer, and to define signals controlling cancer cell development. We used single cell RNA and protein profiling to analyze tumors and matched normal tissues of twelve colorectal cancer patients. RNA metabolic labelling followed by single cell RNA sequencing in patient-derived normal colon and colorectal cancer organoids was employed to define colorectal cancer cell developmental trajectories. We find that colorectal cancer tissues exhibited consistent changes in cellular composition in the epithelial, immune and stromal compartments across patients compared to normal colon. Tumor epithelial cells displayed patient-specific gene expression often correlating with somatic copy number alterations, but mainly organized into patient-overarching clusters. These clusters were defined by cell type-specific transcriptional programs related to stem, transient-amplifying and immature goblet cells, and showed differential expression for signatures of oncogenic traits such as replication stress. Patient-derived colorectal cancer organoids exhibited developmental trajectories forming along a gradient of mitogen-activated protein kinase activity that were Wnt-independent. Likewise, colorectal cancer cell types of patient samples were organized by mitogen-activated protein kinase activity. Our single-cell analyses provide a subtyping system for colorectal cancer cells based on transcriptional readout of morphogenetic signals and oncogenic traits. We provide evidence that mitogen-activated protein kinase signaling, a key pathway for targeted therapy, is a main driver of colorectal cancer cell plasticity.