The Evolving Genomic Landscape of Esophageal Squamous Cell Carcinoma Under Chemoradiotherapy

Esophageal squamous cell carcinoma (ESCC) often recurs after chemoradiotherapy (CRT), and the prognosis of ESCC after CRT has not improved over the past few decades. The mutation process in CRT-resistant clones and the functional relevance of genetic alterations remain unclear. To address these problems, we performed whole-exome sequencing of 52 tumor samples from 33 ESCC patients who received radiotherapy combined with 5-fluorouracil/platinum. In multi-region analyses of pretreatment and locally recurrent lesions from five cases, most driver gene-altered clones remained under CRT selection pressure, while few driver gene alterations were acquired at recurrence. The mutation signatures of recurrent ESCC, including increased deletion frequency and platinum dose-dependent base substitution signatures, were substantially different from those of primary ESCC and reflected the iatrogenic impacts of CRT. Single-region analysis of 28 pretreatment tumors indicated that focal copy number gain at the MYC locus was significantly associated with poor progression-free survival and overall survival after CRT. MYC gain remained throughout the CRT course and potentially contributes to intrinsic resistance to CRT. Consistent with these findings, MYC copy number and mRNA and protein levels in ESCC cell lines correlated positively with resistance to radiotherapy, and MYC knockdown improved sensitivity to radiotherapy. Overall, these data characterize the clonal evolution process induced by CRT and clinically relevant associations for genetic alterations in ESCC. These findings increase our understanding of therapeutic resistance and support the rationale for precision CRT.