Modelling cell competition in colorectal cancer A game of clones

Clonal dynamics, the spatiotemporal changes in the distribution, composition, and behavior of genetically distinct cell populations within tissues, play a central role in tumor initiation, progression, and therapeutic resistance. In colorectal cancer (CRC), clonal competition and spatial organization generate intratumoral heterogeneity that critically impacts treatment response. Understanding how these processes govern disease progression and therapeutic vulnerability represents an important challenge in cancer biology. This thesis presents methodological and conceptual advances that improve our understanding of clonal dynamics in CRC through the integration of fluorescent optical labeling, advanced imaging, and quantitative computational modeling.
We first review the molecular mechanisms governing cell competition during development, homeostasis, aging, and cancer, with emphasis on in vitro models. Building on this, we develop a picoliter-scale droplet deposition framework to generate fluorescently labeled multiclonal colonies, enabling quantitative analysis of clonal heterogeneity, competition, and spatial intermixing. We further combine a custom image analysis pipeline, multi-color clonal tracing, with an agent-based computational model to explore how local cell density influences colony growth. We additionally introduce LeGO-CSA, an improved clonogenic survival assay integrating fluorescent barcoding with imaging-based readouts for high-throughput, high-content analysis of cell growth. Finally, we quantify clonal dispersal across multiple in vitro and in vivo CRC models, showing that dispersal is cell line-specific and largely independent of proliferation, and derive a dispersal-associated gene signature predictive of poor prognosis and recurrence in CRC patients. Together, this thesis advances our understanding of clonal dynamics and provide a foundation for developing strategies to monitor and potentially target these processes in CRC.