Macrophages in tertiary lymphoid structures promote apoptosis of ATF4-positive gastric cancer cells via IL18.

BACKGROUND: Gastric cancer (GC) is a globally prevalent and highly fatal malignancy of the digestive system. Despite its transformative role in gastric cancer, immunotherapy’s efficacy is limited by the complexity and incomplete understanding of the heterogeneous tumor microenvironment, necessitating a deeper analysis to uncover mechanisms of resistance. METHOD: We analyzed the immune response status of GC patients and generated a single-cell transcriptome landscape of GC patients under various immunotherapy regimens. Dynamic changes in prognosis, biological functions, developmental trajectories, transcription factors, and intercellular communication among different cell subpopulations were assessed. To complement our computational exploration and provide histological validation, we also collected gastric cancer tissues from two patients who responded to immunotherapy. Hematoxylin and eosin staining and immunofluorescence experiments were performed on these tissues to confirm the pathological features and the spatial distribution of key immune cells identified in our single-cell analysis. RESULTS: Our study highlighted that PDIA6 in APOA1 + PDIA6 + GC activated the PPAR signaling pathway by increasing APOA1 expression through RNA-binding protein (RBP) action. Given the established role of the PPAR pathway in promoting lipid metabolism and cell proliferation, this activation likely provides a survival and growth advantage to this GC subpopulation. CYP3A5 + GC exhibited a unique metabolic pattern supporting tumor survival and resistance to immunotherapy. In clinical samples with effective immunotherapy, tertiary lymphoid structures showed expression of CD68 and IL18. IL18 + macrophages potentially influenced ATF4 + GC cells via the cytokine signaling axis, promoting immune infiltration. Apoptotic tumor cells were more enriched in the immune-responsive group compared to the immune-unresponsive subgroup. Furthermore, cancer-associated fibroblasts reprogrammed the tumor microenvironment by targeting endothelial cells with CTGF-ITGA5 and immune cells with CTGF-ITGB2. Within the XCL1 + NR4A2 + effector CD8 + T cell subpopulation, NR4A2 transcriptionally regulated the expression of XCL1 and effector genes through negative feedback loop, consequently inhibiting inflammatory pathways and the body’s antitumor immune response. CONCLUSION: Our findings delineate the cellular composition of the tumor microenvironment in GC patients based on GSE183904, significantly advancing the analysis of distinct immune responses in these patients. This study contributes to a comprehensive understanding of immunotherapy efficacy and proposes novel biomarker-driven strategies for patient stratification and targeted therapy in GC. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-025-07559-z.