Clonal evolution from primary to locally recurrent rectal cancer reveals recurrence-acquired potentially actionable alterations in treatment-naïve tumors.

Locally recurrent rectal cancer (LRRC) occurs in 6-10% of patients after curative surgery. It is often regarded as a simple residual disease, yet accumulating evidence suggests that LRRC is biologically distinct from primary tumors. Clonal evolution in matched primary-recurrence pairs not exposed to preoperative therapy has not been systematically investigated. We analyzed formalin-fixed paraffin-embedded tumor specimens from 15 matched pairs of primary and locally recurrent rectal cancers not exposed to preoperative therapy using targeted next-generation sequencing of 22 colorectal cancer-related genes, including TP53, KRAS, PIK3CA, MET, and FGFR family members.

Tumor areas were selectively collected to ensure high tumor purity. Mutations were classified as shared or unique, and variant allele frequencies (VAFs) and clonality (VAF > 30%) were evaluated. Among 415 pathogenic mutations, 12/15 pairs (80%) harbored shared driver alterations, with TP53 shared in 11 (73%). Shared mutations showed higher VAFs in recurrences than in primaries (median 57.1% vs 47.6%; p = 0.003).

Unique mutations were modestly higher in recurrences (median 5.4% vs 4.8%; p = 0.048). Clonal mutations exhibited greater VAFs at recurrence (median 86.4% vs 49.8%; p = 0.048), while the numbers of clonal mutations were comparable (32 vs 32). Potentially actionable alterations involving MET and FGFR family genes were observed in recurrent lesions in a subset of cases, including some detected at clonal levels. LRRC is not merely residual disease but an evolutionarily progressed tumor entity characterized by persistence and dominance of truncal drivers with acquisition of clinically relevant alterations.

Profiling recurrent lesions may guide therapy as primary tumor profiling alone may miss potentially actionable alterations present in recurrent lesions.