Immune checkpoint inhibitor (ICI) therapy response in cancer patients can be heavily influenced by the composition of the gut microbiome. Recent studies have revealed bacterial species associated with ICI therapy response. However, mechanistic understanding behind these observations is lacking. In this study we investigated the gut microbiome of >200 ICI treated cancer patients on a metagenomic and functional level to reveal the underlying molecular mechanisms by which the gut microbiome influences ICI therapy efficacy and toxicity in cancer patients.

Over 400 fecal samples from cancer patients were collected before and during ICI therapy through the UNICIT biobank study and analyzed using metagenomic and functional analyses. Next generation IgA-SEQ was used to identify immunostimulatory bacteria, bridging the gap between the gut microbiome composition, immunity and ICI-therapy response. The inflammatory potential of the gut microbiome was further assessed through metagenomic CAzyme (Carbohydrate-Active enzymes) and functional mucus degradation analyses. Innate immune activating potential by bacterial-derived inflammatory products (e.g. flagellin, NOD1/2 ligands and ALPK1) was assessed through NFκB reporter assays. Lastly, host inflammatory biomarkers (e.g. IgA and calprotectin) were assessed to generate a complete understanding of the inflammatory potential of the gut microbiome in ICI-treated cancer patients.

This study revealed that excessive inflammatory potential of the gut microbiome at the start of therapy reduced the efficacy of ICI therapy, as shown by e.g. elevated innate immune activation and mucus degradation in non-responders compared to responders. Patients who developed colitis, one of the most common immune-related adverse events (irAEs) during ICI therapy, showed a diminished mucus degrading potential at the start of therapy compared to people who do not develop irAEs. This decrease became even more pronounced during the toxic event itself. Additionally, during colitis we observed an increase in secretory IgA, IgA-coated bacteria, and innate immune activation. Excessive innate immune activation gradually increased over the course of treatment in patients who develop colitis, whereas this remained stable in patients without irAEs.

This study combined functional and metagenomic data derived from a large cohort of ICI treated cancer patients to uncover the underlying molecular mechanisms by which the gut microbiome influences ICI therapy response. Our data shows distinctive metagenomic and functional gut microbiome profiles for ICI therapy efficacy and toxicity. This will enhance the development of novel microbiome-inspired biomarkers and therapeutic interventions.

The authors thank the UNICIT consortium, participating patients, Emma van Dijk, Ona Traveria Sánchez, Kirsten van der Kooij, Ignacio Montero Ordóñez and David Rios-Covián.