3 Clonal dynamics of colon carcinoma progression

Abstract

IntroductionCancer formation is initiated by a single cell that acquires sequential mutations, eventually resulting in a metastasizing carcinoma. Throughout this process numerous clones arise, each with their own unique genetic composition. All these clones have slightly different fitnesses and compete with each other; this process of competition (clonal dynamics) plays an important role in cancer progression and determines the genetic composition of the tumour as a whole.Material and methodsTo understand these clonal dynamics we have developed a viral lineage tracing system, which allows us to simultaneously track the clonal dynamics of thousands of unique clones. We applied this system to an organoid model of colon carcinoma progression, which consists of WT, APC-/- (A), APC-/- P53-/- (AP), APC-/- P53-/- KRASG12D (APK) and APC-/- P53-/- KRASG12D SMAD4-/- (APKS) organoid lines, which mimics colon carcinoma progression in patients.Results and discussionsWe found that clonal dynamics change dramatically throughout progression from A/AP to APK/APKS, where there is fast and stringent selection in A/AP organoid lines and slower selection in APK/APKS organoids lines. Furthermore Whole Genome Sequencing (WGS) of the organoids revealed that Copy Number Variation (CNV) patterns are deterministic in the A/AP organoids, with a strong preference for losses of chromosome 4 and chromosome 18, and much more varied in APK/APKS organoids. Finally, through single cell whole genome sequencing it was possible to identify the sequence of CNV events through which unique genetic clones arise in the APKS mutant organoids.ConclusionIn this study, we find reproducible differences in clonal dynamics between adenoma and carcinoma like organoids. These differences in clonal dynamics are in line with current views on colon carcinoma progression, where early in the progression of the tumour several large-scale clonal expansions occur, while late in progression clonal dynamics are less extreme.