Identification of Immune&Driver Molecular Subtypes Optimizes Immunotherapy Strategies for Gastric Cancer

TL;DR

This study identifies two molecular subtypes of gastric cancer that respond differently to immunotherapy and chemotherapy, helping to optimize treatment strategies.

Contribution

The novel contribution is the integration of immune and driver gene data to define subtypes with distinct immunotherapy and chemotherapy sensitivities.

Findings

CS1 subtype is associated with better prognosis and sensitivity to chemotherapy.

CS2 subtype shows higher immune activity and better response to immunotherapy.

A prediction model for immunotherapy response achieved high accuracy in gastric cancer and melanoma datasets.

Abstract

Immunotherapy has become a promising treatment for gastric cancer. However, its effectiveness varies significantly across subtypes because of heterogeneous immune microenvironments and genomic alterations. Here, we established Immune&Driver molecular subtypes CS1 and CS2 by systematically integrating multi-omics data for immune-related and driver genes. CS1 was linked to a better prognosis, while CS2 represented a poorer prognostic phenotype. CS1 displayed enhanced genomic instability, marked by higher mutation frequency and chromosomal alterations. In contrast, CS2 exhibited higher immune activity, with a higher density of immune cell infiltration and increased expression of chemokines and immune checkpoint genes. Among FDA-approved anti-cancer agents included in a pan-cancer drug sensitivity prediction framework, CS1 was predicted to be more sensitive to conventional chemotherapeutic agents, whereas CS2 was predicted to be more responsive to immune-related agents. In melanoma datasets, a CS2-like transcriptomic pattern was associated with improved response to anti-PD-1 therapy, with the combination of anti-PD-1 and anti-CTLA-4 showing more favorable response patterns compared to anti-PD-1 monotherapy. Additionally, we developed an immunotherapy response prediction model using PCA-based logistic regression according to the transcriptional expression of CS biomarkers. The model was trained in melanoma immunotherapy cohorts and validated across independent melanoma datasets, and it further achieved a higher AUC in an external gastric cancer cohort treated with anti-PD-1 therapy. Collectively, this study highlights immune and genomic heterogeneity in gastric cancer and provides a hypothesis-generating framework for exploring immunotherapy response.

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