Development of a streamlined NGS-based TCGA classification scheme for gastric cancer and its implications for personalized therapy

Background: The Cancer Genome Atlas (TCGA) has identified four distinct molecular subtypes of gastric cancer (GC) with prognostic significance: Epstein-Barr virus (EBV)-positive, microsatellite instability (MSI)-high, genomically stable (GS), and chromosomal instability (CIN). Unfortunately, the complex analysis required for TCGA classification limits its practical use in clinical settings. Our study sought to devise a next-generation sequencing (NGS)-based method to classify GC more efficiently, serving as a promising biomarker for prognosis and immunotherapy efficacy.

Methods: This study was a retrospective observation study, and we employed 2 independent GC cohorts. The 3DMed cohort (n=765), comprising data on 733 cancer-related genes along with 4 EBV-encoded genes, was utilized to develop the new NGS classification. Additionally, the secondary Korean cohort (n=55), which includes both genomic data and information on immune checkpoint inhibitor (ICI) treatment, was employed to establish a correlation between NGS subtypes and ICI responsiveness.

Results: In the 3DMed cohort, we identified 5.2% EBV, 4.6% MSI, 30.6% GS, and 59.6% CIN subtypes. The MSI subtype exhibited the highest number of mutation events, along with the highest tumor mutational burden (TMB) and strong programmed cell death ligand 1 (PD-L1) expression. CIN tumors showed extensive copy number variations (CNVs) and genomic heterogeneity. The EBV subtype presented recurrent ARID1A and PIK3CA mutations and fewer TP53 mutations. GS tumors exhibited specific mutations in CDH1 and ARID1A. In the Korean cohort, ICIs were most effective in MSI and EBV cases, showing disease control rates of 100%, compared to 62.9% in GS and 12.5% in CIN subtypes.

Conclusions: The NGS method successfully maps the mutational landscape of GC, providing a practical TCGA classification surrogate to optimize patient-specific treatment strategies.