Lisa Derosa1, Bertrand Routy2, Marine Fidelle3, Valerio Iebba4, Laurie Alla5, Edoardo Pasolli6, Nicola Segata7, Aude Desnoyer8, Filippo Pietrantonio9, Gladys Ferrere4, Jean-Eudes Fahrner10, Emmanuelle Le Chatellier5, Nicolas Pons5, Nathalie Galleron5, Hugo Roume5, Connie P M Duong4, Laura Mondragón11, Kristina Iribarren12, Mélodie Bonvalet4, Safae Terrisse13, Conrad Rauber14, Anne-Gaëlle Goubet14, Romain Daillère12, Fabien Lemaitre12, Anna Reni4, Beatrice Casu4, Maryam Tidjani Alou4, Carolina Alves Costa Silva4, Didier Raoult15, Karim Fizazi16, Bernard Escudier16, Guido Kroemer17, Laurence Albiges18, Laurence Zitvogel19. 1. Gustave Roussy Cancer Campus (GRCC), Villejuif, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Équipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France; Faculté de Médecine Kremlin-Bicêtre, Université Paris Sud, Université Paris Saclay, France; Department of Medical Oncology, Gustave Roussy Cancer Campus (GRCC), Villejuif, France. Electronic address: deros.lisa@gmail.com. 2. Hematology-Oncology Division, Department of Medicine, Centre Hospitalier de l'Université de Montréal (CHUM), Montréal, QC, Canada; Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal l, Canada CHUM, Montréal, QC, Canada. 3. Gustave Roussy Cancer Campus (GRCC), Villejuif, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Équipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France; Faculté de Médecine Kremlin-Bicêtre, Université Paris Sud, Université Paris Saclay, France; Center of Clinical Investigations in Biotherapies of Cancer (CICBT) 1428, Villejuif, France; Faculté de Pharmacie, University Paris-Saclay, Chatenay-Malabry, France. 4. Gustave Roussy Cancer Campus (GRCC), Villejuif, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Équipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France. 5. Université Paris-Saclay, INRAE MetaGenoPolis, Jouy-en-Josas, France. 6. Department of Agricultural Sciences, University of Naples Federico II, Napoli, Italy. 7. Department CIBIO, University of Trento, Trento, Italy; Istituto Europeo di Oncologie, Milan, Italy. 8. Gustave Roussy Cancer Campus (GRCC), Villejuif, France; Faculté de Pharmacie, University Paris-Saclay, Chatenay-Malabry, France; Gustave Roussy Cancer Campus, Laboratory of Immunomonitoring in Oncology, CNRS-UMS 3655 and INSERM-US23, Villejuif, France. 9. IRCCS Istituto Nazionale dei Tumori Foundation, Milan, Italy. 10. Gustave Roussy Cancer Campus (GRCC), Villejuif, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Équipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France; Faculté de Médecine Kremlin-Bicêtre, Université Paris Sud, Université Paris Saclay, France; Transgene S.A., Illkirch-Graffenstaden, France. 11. Faculté de Médecine Kremlin-Bicêtre, Université Paris Sud, Université Paris Saclay, France; Cell Biology and Metabolomics Platforms, Gustave Roussy Cancer Campus, Villejuif, France; Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, INSERM U1138, Centre de Recherche des Cordeliers, Paris, France. 12. EverImmune, GRCC, Villejuif, France. 13. Gustave Roussy Cancer Campus (GRCC), Villejuif, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Équipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France; Faculté de Médecine Kremlin-Bicêtre, Université Paris Sud, Université Paris Saclay, France; Department of Medical Oncology, Gustave Roussy Cancer Campus (GRCC), Villejuif, France. 14. Gustave Roussy Cancer Campus (GRCC), Villejuif, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Équipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France; Faculté de Médecine Kremlin-Bicêtre, Université Paris Sud, Université Paris Saclay, France. 15. Aix-Marseille Université, MEPHI, IRD, IHU Méditerranée Infection, Marseille, France. 16. Gustave Roussy Cancer Campus (GRCC), Villejuif, France; Department of Medical Oncology, Gustave Roussy Cancer Campus (GRCC), Villejuif, France. 17. Cell Biology and Metabolomics Platforms, Gustave Roussy Cancer Campus, Villejuif, France; Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, INSERM U1138, Centre de Recherche des Cordeliers, Paris, France; EverImmune, GRCC, Villejuif, France; Aix-Marseille Université, MEPHI, IRD, IHU Méditerranée Infection, Marseille, France; Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, Paris, France; Suzhou Institute for Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, China; Department of Women's and Children's Health, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden. 18. Gustave Roussy Cancer Campus (GRCC), Villejuif, France; Faculté de Médecine Kremlin-Bicêtre, Université Paris Sud, Université Paris Saclay, France; Department of Medical Oncology, Gustave Roussy Cancer Campus (GRCC), Villejuif, France. 19. Gustave Roussy Cancer Campus (GRCC), Villejuif, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Équipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France; Faculté de Médecine Kremlin-Bicêtre, Université Paris Sud, Université Paris Saclay, France; Department of Medical Oncology, Gustave Roussy Cancer Campus (GRCC), Villejuif, France; Center of Clinical Investigations in Biotherapies of Cancer (CICBT) 1428, Villejuif, France; EverImmune, GRCC, Villejuif, France; Suzhou Institute for Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, China. Electronic address: laurence.zitvogel@gustaveroussy.fr.
Abstract
BACKGROUND: The development of immune checkpoint blockade (ICB) has revolutionized the clinical outcome of renal cell carcinoma (RCC). Nevertheless, improvement of durability and prediction of responses remain unmet medical needs. While it has been recognized that antibiotics (ATBs) decrease the clinical activity of ICB across various malignancies, little is known about the direct impact of distinct intestinal nonpathogenic bacteria (commensals) on therapeutic outcomes of ICB in RCC. OBJECTIVE: To evaluate the predictive value of stool bacteria composition for ICB efficacy in a cohort of advanced RCC patients. DESIGN, SETTING, AND PARTICIPANTS: We prospectively collected fecal samples from 69 advanced RCC patients treated with nivolumab and enrolled in the GETUG-AFU 26 NIVOREN microbiota translational substudy phase 2 trial (NCT03013335) at Gustave Roussy. We recorded patient characteristics including ATB use, prior systemic therapies, and response criteria. We analyzed 2994 samples of feces from healthy volunteers (HVs). In parallel, preclinical studies performed in RCC-bearing mice that received fecal transplant (FMT) from RCC patients resistant to ICB (NR-FMT) allowed us to draw a cause-effect relationship between gut bacteria composition and clinical outcomes for ICB. The influence of tyrosine kinase inhibitors (TKIs) taken before starting nivolumab on the microbiota composition has also been assessed. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: Metagenomic data (MG) from whole genome sequencing (WGS) were analyzed by multivariate and pairwise comparisons/fold ratio to identify bacterial fingerprints related to ATB or prior TKI exposure and patients' therapeutic response (overall response and progression-free survival), and compared with the data from cancer-free donors. RESULTS AND LIMITATIONS: Recent ATB use (n = 11; 16%) reduced objective response rates (from 28% to 9%, p < 0.03) and markedly affected the composition of the microbiota, facilitating the dominance of distinct species such as Clostridium hathewayi, which were also preferentially over-represented in stools from RCC patients compared with HVs. Importantly, TKIs taken prior to nivolumab had implications in shifting the microbiota composition. To establish a cause-effect relationship between gut bacteria composition and ICB efficacy, NR-FMT mice were successfully compensated with either FMT from responding RCC patients or beneficial commensals identified by WGS-MG (Akkermansia muciniphila and Bacteroides salyersiae). CONCLUSIONS: The composition of the microbiota is influenced by TKIs and ATBs, and impacts the success of immunotherapy. Future studies will help sharpen the role of these specific bacteria and their potential as new biomarkers. PATIENT SUMMARY: We used quantitative shotgun DNA sequencing of fecal microbes as well as preclinical models of fecal or bacterial transfer to study the association between stool composition and (pre)clinical outcome to immune checkpoint blockade. Novel insights into the pathophysiological relevance of intestinal dysbiosis in the prognosis of kidney cancer may lead to innovative therapeutic solutions, such as supplementation with probiotics to prevent primary resistance to therapy.
BACKGROUND: The development of immune checkpoint blockade (ICB) has revolutionized the clinical outcome of renal cell carcinoma (RCC). Nevertheless, improvement of durability and prediction of responses remain unmet medical needs. While it has been recognized that antibiotics (ATBs) decrease the clinical activity of ICB across various malignancies, little is known about the direct impact of distinct intestinal nonpathogenic bacteria (commensals) on therapeutic outcomes of ICB in RCC. OBJECTIVE: To evaluate the predictive value of stool bacteria composition for ICB efficacy in a cohort of advanced RCCpatients. DESIGN, SETTING, AND PARTICIPANTS: We prospectively collected fecal samples from 69 advanced RCCpatients treated with nivolumab and enrolled in the GETUG-AFU 26 NIVOREN microbiota translational substudy phase 2 trial (NCT03013335) at Gustave Roussy. We recorded patient characteristics including ATB use, prior systemic therapies, and response criteria. We analyzed 2994 samples of feces from healthy volunteers (HVs). In parallel, preclinical studies performed in RCC-bearing mice that received fecal transplant (FMT) from RCCpatients resistant to ICB (NR-FMT) allowed us to draw a cause-effect relationship between gut bacteria composition and clinical outcomes for ICB. The influence of tyrosine kinase inhibitors (TKIs) taken before starting nivolumab on the microbiota composition has also been assessed. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: Metagenomic data (MG) from whole genome sequencing (WGS) were analyzed by multivariate and pairwise comparisons/fold ratio to identify bacterial fingerprints related to ATB or prior TKI exposure and patients' therapeutic response (overall response and progression-free survival), and compared with the data from cancer-free donors. RESULTS AND LIMITATIONS: Recent ATB use (n = 11; 16%) reduced objective response rates (from 28% to 9%, p < 0.03) and markedly affected the composition of the microbiota, facilitating the dominance of distinct species such as Clostridium hathewayi, which were also preferentially over-represented in stools from RCCpatients compared with HVs. Importantly, TKIs taken prior to nivolumab had implications in shifting the microbiota composition. To establish a cause-effect relationship between gut bacteria composition and ICB efficacy, NR-FMT mice were successfully compensated with either FMT from responding RCCpatients or beneficial commensals identified by WGS-MG (Akkermansia muciniphila and Bacteroides salyersiae). CONCLUSIONS: The composition of the microbiota is influenced by TKIs and ATBs, and impacts the success of immunotherapy. Future studies will help sharpen the role of these specific bacteria and their potential as new biomarkers. PATIENT SUMMARY: We used quantitative shotgun DNA sequencing of fecal microbes as well as preclinical models of fecal or bacterial transfer to study the association between stool composition and (pre)clinical outcome to immune checkpoint blockade. Novel insights into the pathophysiological relevance of intestinal dysbiosis in the prognosis of kidney cancer may lead to innovative therapeutic solutions, such as supplementation with probiotics to prevent primary resistance to therapy.