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

Genes Chromosomes Cancer. 2019 Jan;58(1):12-22. doi: 10.1002/gcc.22683. Epub 2018 Oct 16.


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.

Keywords: cancer microenvironment; gastric cancer; high-throughput nucleotide sequencing; programmed cell death 1 ligand 1; tumor-infiltrating lymphocytes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aged
  • B7-H1 Antigen / immunology
  • Female
  • Gene Expression Regulation, Neoplastic
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Lymphocytes, Tumor-Infiltrating / immunology*
  • Male
  • Microsatellite Instability
  • Middle Aged
  • Mutation
  • Neoplasm Proteins / genetics*
  • Neoplasm Staging
  • Stomach Neoplasms / classification
  • Stomach Neoplasms / genetics*
  • Stomach Neoplasms / immunology
  • Stomach Neoplasms / pathology
  • Tumor Microenvironment / genetics
  • Tumor Microenvironment / immunology*


  • B7-H1 Antigen
  • CD274 protein, human
  • Neoplasm Proteins