KRAS-extrachromosomal DNA drives intratumoral heterogeneity in gastric cancer

Extrachromosomal DNA (ecDNA), autonomously replicating circular DNA outside the chromosomes, exists as critical oncogene driver in approximately 20% of all tumors. Massive ecDNA amplification and its asymmetric segregation during mitotic drive high level oncogene amplification and contribute to tumor heterogeneity. Gastric cancer exhibits a high frequency of ecDNA occurrence. KRAS, a key oncogene in multiple cancers, is frequently amplified in gastric cancer; however, its functional implications via ecDNA remain largely understudied. In this study, we performed whole-genome sequencing and single-cell RNA sequencing on a gastric cancer sample to identify genomic amplification and transcription driven by ecDNA. We identified KRAS-ecDNA in gastric cancer, which exhibited significantly elevated KRAS expression and pronounced transcriptional heterogeneity. Functionally, ecDNA_High cells showed enhanced ribosome biogenesis, upregulated DNA repair pathways, differential activation of transcription factors,and reduced MHC-II signaling, indicating potential immune evasion. Drug response predictions suggested that KRAS-ecDNA_High cells are sensitive to MAPK inhibitors and upstream receptor inhibitors, despite showing broad resistance to conventional chemotherapies. Our study uncovers the critical role of KRAS-ecDNA in gastric cancer. These findings provide a rationale for targeting ecDNA-driven oncogenic programs and offer targeted strategies to combat ecDNA-mediated oncogenic evolution.