Custom scoring based on ecological topology of gut microbiota associated with cancer immunotherapy outcome.

The gut microbiota influences the clinical responses of cancer patients to immunecheckpoint inhibitors (ICIs). However, there is no consensus definition of detrimental dysbiosis. Based on metagenomics (MG) sequencing of 245 non-small cell lung cancer (NSCLC) patient feces, we constructed species-level co-abundance networks that were clustered into species-interacting groups (SIGs) correlating with overall survival. Thirty-seven and forty-five MG species (MGSs) were associated with resistance (SIG1) and response (SIG2) to ICIs, respectively. When combined with the quantification of Akkermansia species, this procedure allowed a person-based calculation of a topological score (TOPOSCORE) that was validated in an additional 254 NSCLC patients and in 216 genitourinary cancer patients. Finally, this TOPOSCORE was translated into a 21-bacterial probe set-based qPCR scoring that was validated in a prospective cohort of NSCLC patients as well as in colorectal and melanoma patients. This approach could represent a dynamic diagnosis tool for intestinal dysbiosis to guide personalized microbiota-centered interventions.

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Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.

Déclaration de conflit d'intérêts

Declaration of interests L. Zitvogel is founder of everImmune and its SAB President. L.D. is an everImmune SAB member. R.D. is a scientific co-founder of everImmune. L. Zitvogel received a research contract from Kaleido, 9 meters/Innovate Pharma, and is currently sponsored by Pileje. G.Z. received a research grant from Fondation Roche; received fees from Roche, MSD, BMS, and Astra Zeneca; and is a consultant for Da Volterra & Inventiva. E.D. reports grants and personal fees from Roche Genentech, grants from Boehringer, grants from AstraZeneca, grants and personal fees from Merck Serono, grants from BMS, and grants from MSD. E.D. is founder of Graegis/Alys. M.L.I., L.B., and A.F. are employees and shareholders of Bio-Me. P.D. had consulting and advisory roles for AstraZeneca, Bristol-Myers Squibb, Boehringer Ingelheim, Celgene, Daiichi Sankyo, Eli Lilly, Merck, Novartis, Pfizer, prIME Oncology, Peer CME, Roche, and Samsung, as well as honoraria from AstraZeneca, Bristol-Myers Squibb, Boehringer Ingelheim, Celgene, Eli Lilly, Merck, Novartis, Pfizer, prIME Oncology, Peer CME, Roche, and Samsung. P.D. ran clinical trials as principal or co-investigator for AstraZeneca, Bristol-Myers Squibb, Boehringer Ingelheim, Eli Lilly, Merck, Novartis, Pfizer, Roche, MedImmune, Sanofi-Aventis, Taiho Pharma, Novocure, and Daiichi Sankyo and received travel, accommodation, and expenses from AstraZeneca, Roche, Novartis, prIME Oncology, and Pfizer. M.F. and R.K.W. were supported by the Seerave Foundation. R.K.W. received unrestricted research grants from Takeda, J&J, Ferring, and Tramedico; speaker’s fee from AbbVie, MSD., and Boston Scientific; and has acted as consultant for Takeda Pharmaceuticals. C.C. reported personal fees from Amgen, Bayer, Merck Serono, MSD, Nordic Pharma, Roche, Pierre Fabre, Servier, and Takeda and research grants from Bayer, Merck Serono, Pierre Fabre, Seagen, Servier, and Tempus. F.G. received honoraria from Amgen, Sanofi, Merk Serono, MSD, BMS, and Astra Zeneca; had a consultancy or advisory role for Roche and Enterome; and received direct research fundings from Roche, Enterome, Astra Zeneca, and Servier and traveling supports from Servier, Amgen, and Roche. L. Zaho is cofounder of Notitia Biotechnologies. F.B. institutional interest AbbVie, ACEA, Amgen, Astra Zeneca, Bayer, Bristol-Myers Squibb, Boehringer Ingelheim, EISAI, Eli Lilly Oncology, F. Hoffmann–La Roche Ltd, Genentech, Ipsen, Ignyta, Innate Pharma, Loxo, Novartis, MedImmune, Merck, Mirati, MSD, Pierre Fabre, Pfizer, Sanofi-Aventis, and Takeda.art