Single-crypt evolutionary trajectories of human sporadic and hereditary colorectal precancers

Abstract

Our understanding of the earliest genomic processes and evolutionary trajectories that distinguish sporadic from hereditary human cancers remains limited, impeding early diagnosis and risk stratification. Here, we performed whole-genome sequencing of 319 single crypts dissected from normal colorectal mucosa, premalignant polyps and malignant colorectal cancers (CRCs) from five sporadic patients and three familial adenomatous polyposis (FAP) patients. We found 66% of premalignant crypts from sporadic polyps did not harbor APC mutations, but frequently accumulated non-canonical but positively selected driver mutations including KMT2C, CACNA1A and FBLN2. In contrast, most premalignant crypts (71%) in FAP indeed acquired one or more somatic APC mutations or 5q loss of heterogeneity (LOH). Sporadic polyps were dominated by clock-like mutational processes at single-crypt level. In contrast, FAP crypts evolved more diverse genomics processes, including reactive oxygen species-associated damages, APOBEC-associated mutagenesis and pks+ Escherichia coli-associated mutagenesis. Premalignant crypts in FAP also exhibited a 2-fold higher burden of LINE-1 retrotranspositions than sporadic ones, despite arising at a substantially younger age. Phylogenetic timing estimations showed that the first somatic APC mutation in FAP often occurs prenatally. Phylogeographic analysis further revealed spatial lineage segregation in early polyclonal polyps, followed by Big-Bang lineage intermixing in later monoclonal ones. Together, these data demonstrate that early colorectal tumorigenesis does not obey a universal APC-first model, where sporadic and hereditary precancers follow distinct evolutionary trajectories. Our study also highlights that polyclonal-to-monoclonal transition in premalignant stages represents the Big-Bang growth of colorectal tumors, offering crucial insight into early diagnosis and risk stratification.