Somatic mutational profiles of stage II and III gastric cancer according to tumor microenvironment immune type

• Published in: Genes chromosomes & cancer 2019-01, Vol.58 (1), p.12-22
• Main Authors: Koh, Jiwon, Nam, Soo Kyung, Roh, Hanseong, Kim, Jonghyuk, Lee, Byung‐Chul, Kim, Jin Won, Ahn, Sang‐Hoon, Park, Do Joong, Kim, Hyung‐Ho, Park, Kyoung Un, Chung, Jin Haeng, Kim, Woo Ho, Lee, Hye Seung
• Format: Article
• Language: English
• Subjects: BRCA2 protein; Breast cancer; Cancer; cancer microenvironment; CD8 antigen; Cell death; Fibroblast growth factor receptor 2; Fibroblast growth factor receptors; Gastric cancer; Genes; Genetics; high‐throughput nucleotide sequencing; Lymphocytes; Mutation; p53 Protein; PD-L1 protein; programmed cell death 1 ligand 1; Runx1 protein; tumor‐infiltrating lymphocytes
• ISSN: 1045-2257; 1098-2264
• DOI: 10.1002/gcc.22683

We aimed to determine somatic mutational profiles of stage II/III gastric cancers (GCs) according to their tumor microenvironment immune types (TMITs), which classify cancer based on co‐assessment of PD‐L1 expression and CD8+ tumor infiltrating lymphocytes. Eighty patients with stage II/III GC were classified as follows: TMIT I (PD‐L1+/CD8High), TMIT II (PD‐L1−/CD8Low), TMIT III (PD‐L1+/CD8Low), and TMIT IV (PD‐L1−/CD8High). Deep targeted sequencing using a panel of 170 cancer‐related genes was performed on an Illumina HiSeq‐2500 system. Most frequently mutated genes included GNAQ (41.3%), TP53 (38.8%), CREBBP (35.0%), and MAP3K1 (35.0%). PIK3CA mutations were observed more frequently in TMIT I (45.8%) and III (66.7%), than in II (12.0%) and IV (8.0%). Other genes with enriched mutations within TMIT I included ATM (33.3%), BRCA2 (33.3%), MAP3K4 (29.2%), and FLT4 (25.0%). FGFR3, MAP3K1, and RUNX1 mutations were more frequently found in TMIT II. TMIT III had a unique somatic mutation profile harboring enriched mutations of histone modifiers including CREBBP and KMT2A, and we found FGFR2 amplification exclusively within TMIT IV. Fuzzy clustering analysis based on somatic mutation frequencies identified a hypermutated group (cluster 1) and a hypomutated group (cluster 2). Cluster 1 had significant associations with TMIT I, EBV+ GCs, and MSI‐H GCs (P = .023, .014, and .004), and had better overall survival (P = .057) than Cluster 2. TMIT I, EBV+, and MSI‐H GCs were estimated to have greater tumor mutational burden (P = .023, .003, and .015). By analyzing somatic mutation profiles according to TMIT classification, we identified TMIT‐specific genetic alterations that provide clues for biological linkage between GC genetics and microenvironment.