IDDF2024-ABS-0202 Multi-omics profiling reveals characteristics and associations of gastric cancer with extrachromosomal DNA (ecDNA) and drug resistance

Background

Extrachromosomal DNA (ecDNA), circular DNA about 1 Mb in size, is a recent hallmark of various tumors. Its distinct traits, like uneven distribution during cell division and high oncogene copy numbers, have led to increased interest in its role in drug resistance. However, the precise mechanism remains unclear. This study uses multi-omics strategies to understand ecDNA in gastric cancer models and its association with drug resistance, comparing wild-type and drug-resistant cell lines.

Methods

Whole-genome sequencing (WGS) data from gastric cancer cell lines were anaylzed using the AmpliconArchitect (AA) algorithm to identify ecDNA-harboring cells and to reconstruct ecDNA structures. Moreover, whole-exome sequencing (WES) and RNA sequencing were conducted on gastric cancer patients, with ecDNA presence evaluated using the GCAP algorithm and its correlation with patient survival analyzed through Kaplan-Meier curves. Additionally, GSEA enrichment analysis was performed to predict signaling pathways potentially influenced by ecDNA.

Results

We conducted WGS analysis on 23 gastric cancer cell lines, identifying ecDNA in 14 of them, including SNU216 and trastuzumab-resistant SNU216 cell lines. In our patient cohort of 93 gastric cancer patients, ecDNA was detected in 26 patients (28.0%), associated with poorer survival outcomes. ERBB2 (HER-2) was commonly carried by ecDNA in both cell lines and patients. Interestingly, while SNU216 and SNU216-TR shared ecDNA carrying HER-2, SNU216-TR also had a distinct ecDNA lacking known prominent oncogenes. GSEA analysis revealed upregulation of DNA damage-related pathways and downregulation of immune-related pathways in ecDNA-positive gastric cancer (p < 0.05).

Conclusions

ecDNA appears prevalent in gastric cancer, influencing DNA damage and immune-related pathways. The discovery in SNU216 and SNU216-TR suggests that the new ecDNA in SNU216-TRmay contribute to drug resistance through non-coding sequences rather than solely increasing drug-resistant gene copies. This implies a necessity for therapies targeting ecDNA to enhance treatment outcomes in HER-2-positive gastric cancer patients.