Abstract 3813: Multipronged approach identifying new hallmarks of antibiotics-mediated immunosuppression in a prospective trial of cancer immunotherapy
Authors: Carolina Alves Costa Silva, Giacomo Vitali, Yasmine Hassani, Estelle Menu, Adele Bonato, Deborah Suissa, Lorenzo Belluomini, Anna Reni, Valerio Iebba, Roxanne Birebent, Sylvère Durand, Guillermo Hernandez, Marie Xiberras, Caroline Flament, Anne-Laure Mallard de La Varende, Simon Thomas, Stéphane Ranque, Pierre Edouard Fournier, Joel Doré, Guido Kroemer, Damien Drubay, Laurence Zitvogel, Lisa Derosa
Journal: Cancer Research (2025)

Abstract Antibiotics (ATB) compromise the efficacy of immunotherapy regimens such as immune checkpoint inhibition (ICI) and CAR-T cell in patients with solid and hematological malignancies. However, prospective clinical and translational studies addressing the specific ATB types and biological mechanisms underlying their harmful effects remain deficient. Using a multi-omics approach to evaluate the local and systemic effects of ATB, we demonstrated that broad-spectrum (but not narrow) ATB adversely affect clinical outcomes across two cohorts composed of 481 (retrospective) and 145 (prospective) patients with lung, bladder, and kidney cancers (ONCOBIOTICS, NCT04567446). ATB use disrupted intestinal interkingdom microbial communities, reducing the diversity of bacterial and fungal species. Within 90 days of ATB exposure, stool metagenomics revealed a bacterial taxonomic shift with an overrepresentation of the immunosuppressive Enterocloster genus and a loss of Methanomethylophilaceae archaea. Moreover, fungal stool culturomics were more likely to be positive with a predominance of ethanol-producing fungi such as Candida spp. and C. cladosporioides. Using a dendritic cell / T cell test on isolated fungal species, patients were not defective in fungal-specific recall responses (positive in 90% versus 60% of HV), mostly Th1 and/or Th17. Blood metabolomics demonstrated that ATB significantly disrupted microbiota-derived metabolites, particularly bile acid metabolism, and the intestinal regulation of lymphocyte migration through the gut immune checkpoint mucosal addressin cell-adhesion molecule-1 (MAdCAM-1). ATB use was associated with the downregulation of the MAdCAM-1, and the recirculation of enterotropic α4β7 central memory CD4+ T cells, conventional monocytes, immature NK cells, and IgA+ CD27+ memory B cells, while promoting CD8+ T cell exhaustion. The recovery of the gut microbiota composition shift and the downregulation of MAdCAM-1 took at least 90 days after ATB stop, reinforcing the need for microbiota-centered interventions to accelerate recovery. Intriguingly, microbiota-metabolic markers such as Methanomethylophilaceaearchaea, Geotrichum candidum, and taurocholic acid identified a subset of ATB users with favorable prognosis. These findings reveal new hallmarks of ATB-associated dysbiosis that merit further investigation. Citation Format: Carolina Alves Costa Silva, Giacomo Vitali, Yasmine Hassani, Estelle Menu, Adele Bonato, Deborah Suissa, Lorenzo Belluomini, Anna Reni, Valerio Iebba, Roxanne Birebent, Sylvère Durand, Guillermo Hernandez, Marie Xiberras, Caroline Flament, Anne-Laure Mallard de La Varende, Simon Thomas, Milieu Intérieur Consortium, ONCOBIOTICS network, Stéphane Ranque, Pierre Edouard Fournier, Joel Doré, Guido Kroemer, Damien Drubay, Laurence Zitvogel, Lisa Derosa. Multipronged approach identifying new hallmarks of antibiotics-mediated immunosuppression in a prospective trial of cancer immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 3813.