Clonal evolution and mutational trajectories of metastatic colorectal cancer shaped by anticancer therapies

The evolutionary dynamics of cancer genomes at single-cell resolution under therapeutic pressure remain elusive. Hence, we perform whole-genome sequencing of 58 single-cell-derived tumoroids and 18 matched bulk tumors from six patients with metastatic colorectal cancer. High-resolution phylogenies reveal the clonal evolution of cancer with quantitative and qualitative profiling of therapy-associated mutations at the single-cell level. We uncover pronounced inter- and intra-patient heterogeneity in burden and spectrum of chemotherapy-induced mutations, with preferential enrichment in more proliferative lineages, highlighting differential mutagenic effects across co-existing cancer cell populations. Late-stage mutational trajectories uncover strikingly dynamic genomic alterations, including complex structural variants, extrachromosomal DNA amplifications, and LINE-1 retrotranspositions, often involving alterations in cancer driver genes. Together, we show the clonal architecture and mutational landscapes of advanced cancers under therapeutic pressure, providing an important foundation for future studies of late-stage cancer evolution under therapies.