Background & aims:
The gut microbiota is closely related to cancer patient response to immune checkpoint inhibitors (ICI). However, there are inconsistencies in species affecting ICI efficacy, whilst the role of non-bacterial microbes in immunotherapy remains elusive. Here, we evaluated the association of trans-kingdom microbes with ICI by multi-cohort pan-cancer analyses.

Methods:
We retrieved fecal metagenomes from 1,359 ICI recipients (601 responders, 758 non-responders) with four different cancers (metastatic melanoma (MM), non-small cell lung carcinoma (NSCLC), renal cell cancer (RCC), hepatocellular carcinoma) from 12 published datasets. Trans-kingdom microbiota composition and microbial interaction were analyzed. The performance of microbial biomarkers to predict ICI response was assessed by logistic regression and random forest. Signature responder-associated microbial species were functionally examined in vitro and in mice.

Results:
Multi-cohort analysis revealed that the composition of trans-kingdom gut microbiota (bacteria, eukaryotes, virus, and archaea) was significantly different between ICI responders and non-responders in pan-cancer. We identified microbes consistently enriched, including bacteria (Faecalibacterium prausnitzii, Coprococcus comes) and eukaryotes (Nemania serpens, Hyphopichia pseudoburtonii) or depleted bacterium Hungatella hathewayi in responders of ≥ 2 cancer types or from ≥ 3 cohorts. Responder-associated species in each cancer type were also revealed, such as F. prausnitzii for patients with MM and 6 microbial species in NSCLC (e.g., bacterium Candidatus Gastranaerophilales bacterium MH-37, eukaryote Aspergillus tamarii, virus crAssphage cr127-1), of which their abundances were correlated with better survival of patients. Functional validation confirmed that these signature species influenced ICI efficacy by modulating CD8⁺ T cell activity in vitro and in mice. Moreover, panels of trans-kingdom microbial biomarkers (bacteria and eukaryotes) showed great performance in predicting ICI response in patients from the discovery and two validation cohorts (MM: AUROC = 72.27-80.19%; NSCLC: AUROC = 72.70-87.98%; RCC: AUROC = 83.33-89.58%).

Conclusion:
This study identified trans-kingdom microbial signatures associated with ICI in pan-cancer and in specific cancer types, which were further confirmed in vitro and in mice. Trans-kingdom microbial biomarkers are potential predictors of ICI response in cancer patients.

Danyu Chen

Appearances