Tracing clonal evolution of the human colon from development through aging to understand colorectal cancer initiation

Despite extensive research on colorectal cancer, the transition from normal tissue to precancerous states-and which precancerous lesions ultimately progress to cancer-remains poorly understood. This gap largely reflects limited knowledge of the normal colon and early precancerous stages. Understanding how the colon changes throughout development, growth, and aging, and how precancerous lesions diverge from normal tissue, is therefore essential for elucidating colorectal cancer initiation. Somatic mutations accumulated from development across the lifespan can serve as molecular barcodes to reconstruct lineage relationships among colonic cells. Here, we performed whole-genome sequencing of 1,098 single colonic crypts from 14 donors, obtained using laser capture microdissection or organoid culture. Among these, we conducted an in-depth analysis of 732 crypts sampled extensively across the colon from two donors, enabling high-resolution reconstruction of colonic development, growth, and aging. Through this approach, we defined the number of stem cells that give rise to the human colon, characterized the clonal territories maintained by individual stem cells, and demonstrated that stem cell diversity is stably preserved throughout colon growth and aging. We further analyzed adenomas and serrated lesions to define how these precancerous states differ from normal tissue and cancer, and to elucidate how the polypogenesis of these two lesion types differs, as they are known to arise through distinct molecular pathways. Placing these lesions within a lineage-resolved framework of normal colonic biology revealed fundamental differences in their evolutionary trajectories. Additionally, by tracing crypt fission dynamics during colon growth, we were able to precisely infer the timing of mutagenic exposure responsible for the SBS89 mutational signature. These findings provide insights into how environmental factors, including the microbiome, may influence the normal colon and contribute to colorectal cancer development. Together, our study establishes a comprehensive framework linking normal colonic development and aging to the emergence of precancerous and cancerous states. By bridging this critical gap, our work provides a foundation for understanding the origins of colorectal cancer and related diseases.