A Single-cell Perturbation Landscape of Colonic Stem Cell Polarisation

Cancer cells are regulated by oncogenic mutations and microenvironmental signals, yet these processes are often studied separately. To functionally map how cell-intrinsic and cell-extrinsic cues co-regulate cell-fate in colorectal cancer (CRC), we performed a systematic single-cell analysis of 1,107 colonic organoid cultures regulated by 1) CRC oncogenic mutations, 2) microenvironmental fibroblasts and macrophages, 3) stromal ligands, and 4) signalling inhibitors. Multiplexed single-cell analysis revealed a stepwise epithelial differentiation landscape dictated by combinations of oncogenes and stromal ligands, spanning from fibroblast-induced Clusterin (CLU)+ revival colonic stem cells (revCSC) to oncogene-driven LRIG1+ hyper-proliferative CSC (proCSC). The transition from revCSC to proCSC is regulated by decreasing WNT3A and TGF-β-driven YAP signalling and increasing KRASG12D or stromal EGF/Epiregulin-activated MAPK/PI3K flux. We find APC-loss and KRASG12D collaboratively limit access to revCSC and disrupt stromal-epithelial communication -- trapping epithelia in the proCSC fate. These results reveal that oncogenic mutations dominate homeostatic differentiation by obstructing cell-extrinsic regulation of cell-fate plasticity.Grants: - "Cell-Cell Communication Analysis of Cancer Organoids Using Multimodal Single-Cell PTM and RNA Profiling" (Grant ID MR/T028270/1, UKRI Medical Research Council) - "BRC Cancer Theme Start-Up Funding" (Grant ID BRC422, UCLH Biomedical Research Centre) - "Connecting Single-Cell Ligands, Receptors, and Signals in Tumour Microenvironment Organoids" (Grant ID C7893/A26233, Cancer Research UK City of London Centre) - "Heterocellular APC Signalling in Colorectal Cancer" (Grant ID C60693/A23783, Cancer Research UK