Prior antibiotic administration disrupts anti-PD-1 responses in advanced gastric cancer by altering the gut microbiome and systemic immune response

Abstract

Evidence on whether prior antibiotic (pATB) administration modulates outcomes of programmed cell death protein-1 (PD-1) inhibitors in advanced gastric cancer (AGC) is scarce. In this study, we find that pATB administration is consistently associated with poor progression-free survival (PFS) and overall survival (OS) in multiple cohorts consisting of patients with AGC treated with PD-1 inhibitors. In contrast, pATB does not affect outcomes among patients treated with irinotecan. Multivariable analysis of the overall patients treated with PD-1 inhibitors confirms that pATB administration independently predicts worse PFS and OS. Administration of pATBs is associated with diminished gut microbiome diversity, reduced abundance of Lactobacillus gasseri, and disproportional enrichment of circulating exhaustive CD8⁺ T cells, all of which are associated with worse outcomes. Considering the inferior treatment response and poor survival outcomes by pATB administration followed by PD-1 blockade, ATBs should be prescribed with caution in patients with AGC who are planning to receive PD-1 inhibitors.

Keywords: PD-1 inhibitor; advanced gastric cancer; antibiotics; chemotherapy; gut microbiome; systemic immune response.

Graphical abstract

Figure 1

Schematic description of each cohort

Figure 2

Survival outcomes according to the administration of pATBs within 28 days prior to the start of treatment (A and B) PFS (A) and OS (B) in the retrospective exploratory cohort treated with PD-1 inhibitors according to the administration of pATBs. (C and D) PFS (C) and OS (D) in the chemotherapy cohort treated with irinotecan according to the administration of pATBs. (E and F) PFS (E) and OS (F) in the retrospective validation cohort treated with PD-1 inhibitors according to the administration of pATBs. (G and H) PFS (G) and OS (H) in the prospective validation cohort treated with PD-1 inhibitors according to the administration of pATBs. PD-1, programmed death-1; HR, hazard ratio; CI, confidence interval; pATBs, prior antibiotics; PFS, progression-free survival; OS, overall survival.

Figure 3

Comparison of gut microbiome composition according to the administration of pATBs within 28 days prior to the start of treatment (A and B) PFS (A) and OS (B) in the experimental stool/blood analysis cohort treated with PD-1 inhibitors according to the administration of pATBs. (C) PC analysis of gut microbiota based on unweighted UniFrac distances. PERMANOVA was performed to compare the differences of gut microbial community according to the administration of pATBs. (D) Diversity of gut microbiota based on Shannon index according to the administration of pATBs. (E and F) PFS (E) and OS (F) according to the diversity of gut microbiota based on Shannon index. The median Shannon index value was used to define the “Shannon index^high” and “Shannon index^low” subgroups. (G) Heatmap showing the significantly different 26 amplicon sequence variants according to the administration of pATBs. The heatmap was constructed by hierarchical clustering using the unweighted pair group method with an arithmetic mean. The color pattern on heatmap represents column Z score. Asterisks indicate amplicon sequence variants with survival implication (Lactobacillus gasseri). (H and I) PFS (H) and OS (I) according to the abundance of Lactobacillus gasseri. The median abundance of Lactobacillus gasseri was used to define the “Lactobacillus gasseri^high” and “Lactobacillus gasseri^low” subgroups. HR, hazard ratio; CI, confidence interval; pATBs, prior antibiotics; PFS, progression-free survival; OS, overall survival; PC, principal coordinate; PERMANOVA, permutational multivariate analysis of variance; PD-1, programmed death-1.

Figure 4

Single-cell transcriptomes of circulating immune cells from 24 patients treated with PD-1 blockade (A) UMAP of total 59,485 cells from peripheral blood, colored to show annotated cell types. (B) Thirteen different cell types and their specific marker gene expression levels, where brightness indicates log-normalized average expression. (C) UMAP of 16,592 mononuclear phagocytes from peripheral blood, colored to show annotated cell types. (D) UMAP of 35,760 NK and T lymphocytes from peripheral blood, colored to show annotated cell types. (E) The heatmap showing the relative abundance of each subclusters. Color pattern on heatmap represents column Z score. Asterisks indicate subclusters with survival implication (exhaustive CD8 T). (F) Dot plot showing the differences of each subclusters and statistical significance according to the administration of pATBs. (G and H) PFS (G) and OS (H) according to the ratio between exhaustive CD8 T and effector CD8 T subclusters. The median value of the ratio between exhaustive CD8 T and effector CD8 T subclusters was used to define the “(exhaustive CD8 T/effector CD8 T)^high” and “(exhaustive CD8 T/effector CD8 T)^low” subgroups. UMAP, uniform manifold approximation and projection; pATBs, prior antibiotics; HR, hazard ratio; CI, confidence interval; PFS, progression-free survival: OS, overall survival.