Genomic characterization between HER2‐positive and negative gastric cancer patients in a prospective trial

Abstract Background We aimed to clarify the genomic characteristics of HER2‐positive and negative gastric cancer cases that potentially affect tumor progression and treatment response in a prospective trial. Methods We collected 80 formalin‐fixed paraffin‐embedded (FFPE) samples (49 HER2+ and 31 HER2‐) from gastric cancer patients who participated in the TROX‐A1 trial (UMIN000036865). We queried a 435‐gene panel (CANCERPLEX‐JP) to generate comprehensive genomic profiling data, including the tumor mutation burden, somatic mutations, and copy number variations. In addition, the genomic differences between HER2+ and HER2‐ gastric cancer patients were analyzed. Results Mutational analyses showed that TP53 was the most frequently mutated gene regardless of HER2 status. ARID1A mutation was significantly enriched in HER2‐negative patients. The number of total mutations in HER2‐negative patients with ARID1A mutation was remarkably higher than that in HER2‐positive patients. Next, copy number variation analyses showed that the number of amplified genes (such as CCNE1 , PGAP3 , and CDK12 ) in HER2‐positive cases was significantly higher than that in HER2‐negative cases. Moreover, PTEN deletion was more common in HER2‐positive cases. Finally, we found that, compared with HER2‐positive patients, HER2‐negative patients tended to have a higher tumor mutation burden, particularly in patients with ARID1A mutation. Pathway analyses of the gene alterations showed an enrichment of several immune‐related pathways in HER2‐negative patients. Conclusions According to the genomic profiling of HER2‐positive and negative gastric cancer, several gene alterations in the HER2 pathway may be the potential mechanism underlying trastuzumab resistance. Relative to HER2‐positive gastric cancer, HER2‐negative gastric tumors with ARID1A mutation may be sensitive to immune checkpoint inhibitors.