Cross-cohort gut microbiome associations with immune checkpoint inhibitor response in advanced melanoma

• Published in: Nature medicine Vol. 28; no. 3; pp. 535 - 544
• Main Authors: Lee, Karla A., Thomas, Andrew Maltez, Bolte, Laura A., Björk, Johannes R., de Ruijter, Laura Kist, Armanini, Federica, Asnicar, Francesco, Blanco-Miguez, Aitor, Board, Ruth, Calbet-Llopart, Neus, Derosa, Lisa, Dhomen, Nathalie, Brooks, Kelly, Harland, Mark, Harries, Mark, Leeming, Emily R., Lorigan, Paul, Manghi, Paolo, Marais, Richard, Newton-Bishop, Julia, Nezi, Luigi, Pinto, Federica, Potrony, Miriam, Puig, Susana, Serra-Bellver, Patricio, Shaw, Heather M., Tamburini, Sabrina, Valpione, Sara, Vijay, Amrita, Waldron, Levi, Zitvogel, Laurence, Zolfo, Moreno, de Vries, Elisabeth G. E., Nathan, Paul, Fehrmann, Rudolf S. N., Bataille, Véronique, Hospers, Geke A. P., Spector, Tim D., Weersma, Rinse K., Segata, Nicola
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.03.2022; Nature Publishing Group
• Subjects: 631/326/2565/2142; 692/53/2422; Biomarkers; Biomedical and Life Sciences; Biomedicine; Cancer Research; Digestive system; Gastrointestinal Microbiome - genetics; Humans; Immune checkpoint inhibitors; Immune Checkpoint Inhibitors - therapeutic use; Infectious Diseases; Inhibitors; Intestinal microflora; Machine learning; Melanoma; Melanoma - drug therapy; Melanoma - genetics; Metabolic Diseases; Metagenomics; Microbiomes; Microbiota; Microorganisms; Molecular Medicine; Neurosciences; Patients; Reproducibility of Results; Skin Neoplasms - drug therapy; Skin Neoplasms - genetics; Species
• ISSN: 1078-8956; 1546-170X; 1546-170X
• DOI: 10.1038/s41591-022-01695-5

The composition of the gut microbiome has been associated with clinical responses to immune checkpoint inhibitor (ICI) treatment, but there is limited consensus on the specific microbiome characteristics linked to the clinical benefits of ICIs. We performed shotgun metagenomic sequencing of stool samples collected before ICI initiation from five observational cohorts recruiting ICI-naive patients with advanced cutaneous melanoma ( n  = 165). Integrating the dataset with 147 metagenomic samples from previously published studies, we found that the gut microbiome has a relevant, but cohort-dependent, association with the response to ICIs. A machine learning analysis confirmed the link between the microbiome and overall response rates (ORRs) and progression-free survival (PFS) with ICIs but also revealed limited reproducibility of microbiome-based signatures across cohorts. Accordingly, a panel of species, including Bifidobacterium pseudocatenulatum , Roseburia spp. and Akkermansia muciniphila , associated with responders was identified, but no single species could be regarded as a fully consistent biomarker across studies. Overall, the role of the human gut microbiome in ICI response appears more complex than previously thought, extending beyond differing microbial species simply present or absent in responders and nonresponders. Future studies should adopt larger sample sizes and take into account the complex interplay of clinical factors with the gut microbiome over the treatment course. An analysis of metagenomic sequencing of stool samples from multiple cohorts of patients with melanoma treated with immune checkpoint blockade uncovers microbiome correlates of response to therapy and also reveals widespread variability across populations.