Genomic Instability Profiles at the Single Cell Level in Mouse Colorectal Cancers of Defined Genotypes

SIMPLE SUMMARY: Colorectal cancer (CRC) is one of the leading causes of cancer mortality; it typically originates as adenomas that progress over time to carcinomas. We decided to investigate the accumulation of numerous genomic alterations during tumour progression by using a mouse model with three different targetable alleles that can be found in human colorectal cancers. We conclude that the rate of accumulation of SNSs is higher in transformed compared to non-transformed cells, and that it is unaffected by the number of cancer-driver genes that are active in the tumour. ABSTRACT: The genomes of many human CRCs have been sequenced, revealing a large number of genetic alterations. However, the molecular mechanisms underlying the accumulation of these alterations are still being debated. In this study, we examined colorectal tumours that developed in mice with Apc(lox/lox), LSL-Kras(G12D), and Tp53(lox/lox) targetable alleles. Organoids were derived from single cells and the spectrum of mutations was determined by exome sequencing. The number of single nucleotide substitutions (SNSs) correlated with the age of the tumour, but was unaffected by the number of targeted cancer-driver genes. Thus, tumours that expressed mutant Apc, Kras, and Tp53 alleles had as many SNSs as tumours that expressed only mutant Apc. In contrast, the presence of large-scale (>10 Mb) copy number alterations (CNAs) correlated strongly with Tp53 inactivation. Comparison of the SNSs and CNAs present in organoids derived from the same tumour revealed intratumoural heterogeneity consistent with genomic lesions accumulating at significantly higher rates in tumour cells compared to normal cells. The rate of acquisition of SNSs increased from the early stages of cancer development, whereas large-scale CNAs accumulated later, after Tp53 inactivation. Thus, a significant fraction of the genomic instability present in cancer cells cannot be explained by aging processes occurring in normal cells before oncogenic transformation.