Extensive subclonal mutational diversity in human colorectal cancer and its significance
Menée à l'aide d'échantillons tumoraux prélevés sur 5 patients atteints d'un cancer colorectal, d'une méthode de séquençage et d'un modèle mathématique, cette étude estime la fréquence de mutations sous-clonales au niveau des gènes codant pour les ADN polymérases et des gènes fréquemment mutés dans les tumeurs colorectales, puis modélise l'évolution du taux de mutations sous-clonales en fonction de l'évolution du nombre de cellules tumorales
Cancers evolve many mutations. Clonal driver mutations are selected early. Subsequent evolution occurs in a branching fashion, possibly without selection (“neutral evolution”). Rarer mutations occur later on smaller branches of the evolutionary tree. Using a DNA-sequencing method, duplex sequencing, with unprecedented accuracy and sensitivity, we quantified rare unique subclonal mutations in diagnostic specimens from 5 human colorectal cancers. Rarer subclones probe later evolutionary time points than previously possible. We confirm neutral evolution at later times and find many more subclonal mutations than expected. A theoretical method allowed us to extrapolate further forward in time to diagnosis. At diagnosis, every DNA base is mutated in at least one cancer cell. In particular, any therapy resistance mutation would be present.Human colorectal cancers (CRCs) contain both clonal and subclonal mutations. Clonal driver mutations are positively selected, present in most cells, and drive malignant progression. Subclonal mutations are randomly dispersed throughout the genome, providing a vast reservoir of mutant cells that can expand, repopulate the tumor, and result in the rapid emergence of resistance, as well as being a major contributor to tumor heterogeneity. Here, we apply (DS) methodology to quantify subclonal mutations in CRC tumor with unprecedented depth (104) and accuracy (<10−7). We measured mutation frequencies in genes encoding replicative DNA polymerases and in genes frequently mutated in CRC, and found an unexpectedly high effective mutation rate, 7.1 × 10−7. The curve of subclonal mutation accumulation as a function of sequencing depth, using DNA obtained from 5 different tumors, is in accord with a neutral model of tumor evolution. We present a theoretical approach to model neutral evolution independent of the infinite-sites assumption (which states that a particular mutation arises only in one tumor cell at any given time). Our analysis indicates that the infinite-sites assumption is not applicable once the number of tumor cells exceeds the reciprocal of the mutation rate, a circumstance relevant to even the smallest clinically diagnosable tumor. Our methods allow accurate estimation of the total mutation burden in clinical cancers. Our results indicate that no DNA locus is wild type in every malignant cell within a tumor at the time of diagnosis (probability of all cells being wild type, 10−308).
Proceedings of the National Academy of Sciences , article en libre accès, 2018