Helicobacter pylori -driven T cell stress in tumors as a mediator of resistance to immune checkpoint blockade in gastric cancer

The influence of microbiota residing within tumors on patient response to immunotherapies for gastric cancer (GC) is not yet fully understood. We aim to define the characteristics and functional role of tumor-resident microbiota in the context of immune checkpoint inhibitor (ICI) efficacy in GC. A comprehensive multi-omics analysis was performed on samples from 137 GC patients, all of whom were treatment-naïve regarding chemo- or antibiotics. This extensive dataset included both metagenomes and host transcriptomes, with single-cell RNA sequencing data. To achieve accurate quantification, we developed a novel tumor-resident microbial index (TM index) that compared taxon-level load between tumor tissue and matched normal tissue. Treatment responses were subsequently validated using syngeneic mouse models with a cancer-bacteria co-culture platform. Abundance analyses consistently highlighted Helicobacter pylori as the only species significantly decreased in tumor tissue compared to paired normal tissue. Metagenome-assembled genomes showed patient-specific H. pylori strains, maintaining over 99% genomic identity across the paired samples. The TM HP index indicated that high levels of H. pylori were predominantly found in the genomically stable (GS) subtype, characterized by a partially preserved normal physiology. Single-cell RNA sequencing data showed that H. pylori -infected cells exhibit a signature of elevated T cell stress, correlating with the overexpression of HSPA1A . Critically, H. pylori significantly compromised the therapeutic effectiveness of anti-PD-L1 by reducing the infiltration of T cells in mouse models. However, a negative effect was not observed with standard 5-fluorouracil or oxaliplatin treatments. Our findings implicate H. pylori as a mediator of immunotherapy resistance and a therapeutically actionable target for overcoming ICI resistance in GC.