The comprehensive genomic profiling and PD-L1 expression of primary lymphoepithelioma-like carcinoma of the stomach.
Authors: Li Zhi , Cui Qian , Wu Hongmei , Zeng Wenrong , Xiao Zebin , Chen Chunxiang , Du Haiwei , Li Min 
Published: June 2021

e16279

Background: Lymphoepithelioma-like carcinoma (LELC) of the stomach is a rare histological type of gastric cancer (GC) with an incidence of 1-4% all GCs, characterized by Epstein-Barr virus infection (EBV+). There is no established agent for patients with LELC of the stomach due to the lack of the genomic data. In this work, we performed the comprehensive genomic profiling and PD-L1 expression of primary LELC of the stomach to investigate the molecular mechanism of tumorigenesis. Methods: Capture-based targeted sequencing was performed on tumor tissue samples collected from 20 patients with LELC of the stomach and 8 patients with LELC of the parotid gland using a panel consisting of 520 cancer-related genes. Tumor tissues were stained by immunohistochemistry for PD-L1 and CD8. PD-L1 expression level was determined by combined positive score (CPS). Tumor mutation burden (TMB) was calculated as a ratio of the total nonsynonymous mutations per total coding region of the panel, excluding copy number variations and fusions. Results: Total of 217 somatic mutations in 127 genes were identified from 18 patients with LELC of the stomach. The most frequently mutated genes included PIK3CA, ARID1A, SMAD4 and KMT2D, occurring in 65% (13/20), 55% (11/20), 30% (6/20), and 25% (5/20) of patients with LELC of the stomach. For LELC of the parotid gland, 13 somatic mutations in 8 genes were identified from 7 patients. All patients with LELC of the stomach/parotid gland were EBV positive and microsatellite-stable. Patients with LELC of the stomach had a significantly higher mutation frequency in PIK3CA (65% vs. 0%, p < 0.01) and ARID1A (55% vs. 0%, p < 0.01) than patients with LELC of the parotid gland. Patients with LELC of the stomach also had a significantly higher mutation frequency in mTOR (70 vs. 0%, p < 0.001) and VEGF signaling pathway (70% vs. 0%, p < 0.001) than patients with LELC of the parotid gland. Compared to LELC of the parotid gland, LELC of the stomach showed a significantly increased TMB (5.0 vs. 1.0 muts/Mb, p < 0.001) and a decreased CPS (47.5 vs. 100.0, p < 0.01). Tumor-infiltrating CD8+ T cell densities in LELC of the stomach and LELC of the parotid gland were comparable. Next, we compared mutational profiling of LELC of the stomach from our cohort to mutational landscape of EBV+ gastric adenocarcinoma obtained from The Cancer Genome Atlas. Patients with LELC of the stomach had a significantly higher mutation frequency in PIK3CA than patients with EBV+ gastric adenocarcinoma (65% vs. 0%, p < 0.001). The mutation frequencies of ARID1A, SMAD4 and KMT2D between patients with LELC of the stomach and EBV+ gastric adenocarcinoma were comparable. Conclusions: This study is the first to elucidate the comprehensive genomic profiling of LELC of the stomach in the Chinese population. Our work demonstrated that genomic landscape of LELC of the stomach is distinctive to LELC of the parotid gland and EBV+ gastric adenocarcinoma.