Together, these data have important implications. We show that dietary fiber and probiotic use, factors known to affect the gut microbiome, are associated with differential outcomes to ICB. Although causality cannot be addressed from the observational human cohort, where unmeasured confounders may exist, our preclinical models support the hypothesis that dietary fiber and probiotics modulate the microbiome and that antitumor immunity is impaired in mice receiving a low-fiber diet and in those receiving probiotics—with suppression of intratumoral IFN-γ T cell responses in both cases.
Some analyses in the current cohort were not adequately powered to assess the full effect of these factors, and further validation is needed in independent cohorts with more in-depth and detailed assessment of dietary intake and the use of specific probiotic supplements, along with further mechanistic studies in preclinical models. Nonetheless, these notable (and perhaps unexpected) findings from studies in this observational patient cohort are corroborated by parallel studies in preclinical models with preliminary mechanistic insights. In light of these collective results, dietary habits and probiotic supplement use should be considered in patients receiving ICB and in efforts to modulate the gut microbiota. These factors should be more thoughtfully evaluated in strategies to improve cancer outcomes.
Acknowledgments
C.N.S. acknowledges the Parker Institute for Cancer Immunotherapy for funding time devoted to continued analysis of this project. She also acknowledges M. D. Swartz, L. B. Piller, and X. Du at UTSPH for their participation on her thesis committee. J.L.M. acknowledges the Transdisciplinary Research in Energetics and Cancer Research Training Workshop R25CA203650. J.L.M. and C.R.D. acknowledge the MDACC Center for Energy Balance in Cancer Prevention and Survivorship. C.R.D. acknowledges the MDACC Bionutrition Core. We thank our collaborators and personnel at the LICI, NCI Microbiome and Genetics Core Facility, and NCI Mouse Gnotobiotic Core Facility, The Alkek Center for Metagenomics and Microbiome Research (CMMR) at Baylor College of Medicine (including S. J. Javornik Cregeen for her role in microbiome data processing), and CosmosID for their high quality and timely microbiome data generation services. We also wish to acknowledge MD Anderson’s Program for Innovative Microbiome and Translational Research (PRIME-TR) for supporting the analysis and interpretation of the microbiome results presented herein (J.A.W. and N.J.A. are the program director and executive scientific director for PRIME-TR, respectively). Most importantly, the study team wishes to thank all patients who contributed their time, samples, and data to this research.
Funding: This study received support from National Institute of Health grant 1R01 CA219896-01A1 (J.A.W.); US-Israel Binational Science Foundation grant 201332 (J.A.W.); the Melanoma Research Alliance grant 4022024 (J.A.W.); American Association for Cancer Research Stand Up to Cancer grant SU2C-AACR-IRG-19-17 (J.A.W.); the Andrew Sabin Family Fellows Program (J.A.W. and C.R.D.); MD Anderson Cancer Center’s Melanoma Moon Shots Program (J.A.W., J.L.M., C.R.D., M.A.D., H.A.T., J.E.G., and E.M.B.); and the Melanoma Research Alliance grant 564449 (L.C., J.A.W., and J.L.M.). The authors additionally received support from Department of Defense grant W81XWH 16 1 0121 (J.A.W.); the MD Anderson Cancer Center Multidisciplinary Research Program grant (J.A.W.); the Parker Institute for Cancer Immunotherapy at MD Anderson Cancer Center (J.A.W., H.A.T., P.S., and J.P.A.); American Society of Clinical Oncology and Conquer Cancer Foundation Career Development award AWD0000627 (J.L.M.); the Elkins Foundation (J.L.M.); the Seerave Foundation (J.L.M.); Rising Tide Foundation grant AWD00004505 (J.L.M.); the Mark Foundation grant AWD00004538 (J.L.M.); the Longenbaugh-Torian Fund (J.L.M.); the MD Anderson Cancer Center SPORE in Melanoma P50CA221703 (M.A.D., H.A.T., I.C.G., J.A.W., S.P.P., J.E.L., J.E.G., A.J.L., and J.L.M.); the MD Anderson Physician Scientist Program (J.L.M.); the Cancer Research Institute Irvington Fellowship Program (M.V.); Cancer Prevention and Research Institute of Texas Research Training Program RP170067 (A.P.C., J.T., and J.Z.); Cancer Prevention and Research Institute of Texas Research Training Program RP210028 (L.M.K.); the US Department of State, Bureau of Educational and Cultural Affairs (A.P.C.); the Fulbright Franco–Américaine Commission (A.P.C.); Cancer Prevention and Research Institute of Texas Research Training Program RP160097 (X.Z.); National Health and Medical Research Council of Australia CJ Martin Early Career Fellowship grant 1148680 (M.C.A.); National Institutes of Health T32 CA 009599 (M.G.W. and B.A.H.); the MD Anderson NCI Cancer Center Support grant P30 CA016672 (M.G.W., B.A.H., C.R.D., K.C.-D., and C.B.P.); National Institute of Health grant 1F32CA260769-01 (G.Mo.); the Charles A. King Trust Postdoctoral Research Fellowship (Y.Y. and C.H.); the John M. Skibber Endowed Professorship (J.E.G.); the Michael and Patricia Melanoma Research Endowment (J.E.G.); National Institute of Health grant R0AI143886 (J.H.); Columbia University Health Sciences NCI Cancer Center Support grant P30 CA013696 (J.H.); National Institute of Health grant R01HL124112 (R.R.J.); Cancer Prevention and Research Institute of Texas grant RR160089 (R.R.J.); National Institute of Health grant R01AI109294 (S.S.W.); National Institute of Health grant R01AI133822 (S.S.W.); the Richard E. Haynes Distinguished Professor in Clinical Cancer Prevention (L.C.); American Cancer Society grant RSG-17-049-01-NEC (C.R.D.); the National Institute of Health Intramural Research Program (E.P.-G., C.-P.D., and G.Me.); FLEX Synergy Award from the National Cancer Institute Center for Cancer Research (E.P.-G., C.-P.D., and G.Me.); the National Cancer Institute Intramural Research Program (J.A.M., M.V., J.H.B., R.R.R., and G.T.); the Dr. Miriam and Sheldon G. Adelson Medical Research Foundation (M.A.D.); American Cancer Society/Melanoma Research Alliance grant 134148-MRAT-19-168-01 (M.A.D.); the AIM at Melanoma Foundation (M.A.D.); the National Institute of Health/National Cancer Institute grant 1 P50 CA221703-02 (M.A.D.); the National Institute of Health/National Cancer Institute grant 1U54CA224070-03 (M.A.D.); Cancer Fighters of Houston (M.A.D.); and the Anne and John Mendelsohn Chair for Cancer Research (M.A.D.).
Author contributions: Project conceptualization: C.N.S., J.L.M., C.H., M.V., N.J.A., G.T., L.C., W.S.G., C.R.D., S.S.W., J.A.W., M.I.R., Y.S., and M.A.W.K. Methodology: C.N.S., J.L.M., N.J.A., V.G., C.H., M.V., J.C.M., G.T., L.C., C.R.D., J.A.W., K.L.H., J.A.M., C.B.P., J.H., A.J.L., and M.A.W.K. Software: C.N.S., V.G., M.A.W.K., J.Z., X.Z., K.L.H., J.F.P., J.R., N.J.A., M.C.W., L.E.H., Y.Y., C.H., J.A.M., J.H.B., R.R.R., and A.M. Validation: M.V., J.A.M., C.N.S., V.G., M.A.W.K., J.Z., X.Z., A.P.C., S.S.W., Y.Z., Y.B.M., S.J., L.N., S.J., and H.A.T. Formal analysis: C.N.S., V.G., A.P.C., M.A.W.K., J.Z., X.Z., K.L.H., J.R., N.J.A., Y.Y., C.H., J.A.M., R.R.R., A.M., C.B.P., J.H., C.R.D., L.W., L.N., and N.-A.A.S.A. Investigation: C.N.S., J.L.M., B.A.H., A.P.C., P.-O.G., C.W.H., K.W., S.S.W., Y.Z., Y.B.M., M.V., Y.S.K., E.P.-G., I.C.G., R.N.A., H.A.T., A.D., M.K.W., S.P.P., S.E.W., M.A.D., M.I.R., J.E.G., J.E.L., P.H., V.J., K.C.N., A.J.L., M.T.T., L.M.K., A.L.H., M.A.J., E.N.B., B.P., B.S.L., K.C.-D., T.C., S.S., N.-A.A.S.A., J.T., V.J., C.M.Z., M.A.W.K., and J.A.W. Resources: J.A.W., J.P.A., P.S., S.S.W., R.R.J., C.H., G.T., J.F.P., P.A.F., G.Me., E.P.-G., C.-P.D., A.J.L., B.S.L., and H.A.T. Data curation: M.W., N.J.A., J.A.M., R.R.R., A.M., C.N.S., J.L.M., C.R.D., E.S., E.P., L.E.H., J.C.M., T.R., E.N.B., R.A.S.-S., J.A., C.M.Z., L.W., M.C.W., M.C.A., N.-A.A.S.A., and B.S.L. Writing - original draft: C.N.S., J.L.M., V.G., J.A.M., M.V., A.P.C., M.A.W.K., N.J.A., L.N., S.S.W., L.C., G.T., C.R.D., J.A.W., J.H., J.P.A., and P.S. Writing - review and editing: C.N.S., J.L.M., V.G., J.A.M., M.V., A.P.C., M.A.W.K., X.Z., M.G.W., C.B.P., M.C.W., G.Me., T.R., J.H.B., B.A.H., M.C.A., R.R.R., A.M., Y.S.K., J.R., K.L.H., J.Z., Y.Z., Y.B.M., L.M.K., S.J., C.W.H., K.W., P.-O.G., A.L.H., M.A.J., E.N.B., E.P.-G., C.-P.D., G.Mo., B.P., B.S.L., R.A.S.-S., R.A., J.A., C.M.Z., E.P., E.S., J.S., L.E.H., E.M.B., L.W., M.D., K.C.-D., S.S., T.C., N.-A.A.S.A., S.D., J.T., J.C.M., I.C.G., R.N.A., H.A.T., A.D., M.K.W., S.P.P., S.E.W., M.A.D., M.I.R., J.E.G., J.E.L., P.H., V.J., Y.S., R.S., N.J.A., K.C.N., L.N., J.F.P., P.A.F., A.J.L., J.H., R.R.J., R.R.R., Y.Y., W.S.G., C.H., P.S., S.S.W., J.P.A., L.C., G.T., C.R.D., and J.A.W. Visualization: C.N.S., J.L.M., V.G., J.A.M., M.V., A.P.C., M.A.W.K., X.Z., N.J.A., R.R.R., A.M., C.B.P., J.H., C.R.D., J.A.W., G.T., Y.Y., C.H., K.C.-D., and M.I.R. Supervision: C.N.S., J.L.M., V.G., L.C., M.V., G.T., C.H., C.R.D., J.A.W., and P.A.F. Project administration: C.N.S., J.L.M., M.G.W., S.D., E.M.B., J.S., L.E.H., C.R.D., J.A.W., M.V., G.T., and G.Me. Funding acquisition: J.L.M., C.R.D., L.C., J.A.W., E.M.B., G.T., M.A.D., C.H., and Y.S.
Competing interests: J.A.W., V.G., and M.C.A. are inventors on patent WO2020106983A1 submitted by the Board of Regents, The University of Texas System, and Institut Gustav Roussy that covers methods and compositions for treating cancer and for predicting a subject’s response to combination checkpoint inhibitor therapy. J.A.W. and V.G. are inventors and C.N.S. is a collaborator on a US patent application (PCT/US17/53.717) submitted by the University of Texas MD Anderson Cancer Center that covers methods to enhance ICB responses by modulating the microbiome. J.A.W. and R.R.J. are inventors on patent WO2020150429A1 submitted by the Board of Regents, The University of Texas System, that covers methods and compositions for treating immune checkpoint inhibitor (ICI)–associated colitis in a subject through the administration of fecal matter from a healthy donor to the subject. R.R.J. is an inventor on patent WO2016086161A1 submitted by the Memorial Sloan Kettering Cancer Center that covers compositions and methods for increasing the abundance of commensal bacteria belonging to the order Clostridiales that are associated with reduced lethal graft-versus-host disease and improved overall survival after bone marrow or hematopoietic stem cell transplant. R.R.J. is an inventor on patent WO2017041039A1 submitted by Memorial Sloan Kettering Cancer Center that covers methods and compositions for reducing the risk of cancer relapse in a subject who has received cancer treatment. J.A.W. reports compensation for speaker’s bureau and honoraria from Imedex, Dava Oncology, Omniprex, Illumina, Gilead, PeerView, Physician Education Resource, MedImmune, and Bristol-Myers Squibb and serves as a consultant and/or advisory board member for Roche/Genentech, Novartis, AstraZeneca, GlaxoSmithKline, Bristol-Myers Squibb, Merck, Biothera Pharmaceuticals, Microbiome DX, and Micronoma. J.A.W. also receives research support from GlaxoSmithKline, Roche/Genentech, Bristol-Myers Squibb, and Novartis. V.G. reports honoraria from ExpertConnect and Kansas Society of Clinical Oncology. J.L.M. reports advisory board participation and honoraria from Bristol-Myers Squibb, Merck, and Roche/Genentech. M.C.A. reports advisory board participation, honoraria, and research funding to their institution from MSD Australia, outside the submitted work, and contract research for BMS Australia, outside the current work. A.P.C. is an employee and equity holder at Immunai. A.P.C. serves as an advisory member and holds equity in Vastbiome. G.Mo. is a coinventor on US patents (PCT/US2019/022194, PCT/US2020/029556, and PCT/US2020/046050) not related to the content of this paper. M.I.R. reports paid consultant position for AMGEN and paid consultant and advisory board membership for MERCK. I.C.G. reports research support from Bristol-Myers Squibb and Merck. I.C.G. serves as a consultant for Bristol-Myers Squibb, Array, and Novartis. R.N.A. receives research funding from Merck, Bristol-Myers Squibb, Genentech, Novartis, and Iovance. J.E.G. is a consultant and/or is on the advisory board for Merck, Regeneron, Syndex, Novartis, and Bristol-Myers Squibb, unrelated to the content of this work. R.R.J. is an advisor and holds equity in Seres Therapeutics and Kaleido Biosciences; serves on the advisory board of MaaT Pharma, LISCure Biosciences, and Prolacta Biosciences; and consults for Davolterra, Merck, Microbiome DX, and Karius. C.H. is on the scientific advisory board for Seres Therapeutics and Empress Therapeutics. M.K.W. is on the advisory boards of Merck, Pfizer, Bristol Myers Squibb, Regeneron, EMD-Serono, ExiCure, Castle Biosciences, and Adagene. H.A.T. is a consultant for BMS, Merck, Novartis, Genentech, Eisai, Iovance, Karyopharm, and Pfizer and reports research funding to institution from BMS, Merck, Novartis, Genentech, GSK, and Dragonfly. A.D. serves as a consultant for Nektar, MultiVir, Idera, Array, and Bristol-Myers Squibb. P.S. reports consulting or stock ownership or advisory board for Achelois, Adaptive Biotechnologies, Affini-T, Apricity, BioAtla, BioNTech, Candel Therapeutics, Catalio, Codiak, Constellation, Dragonfly, Earli, Enable Medicine, Glympse, Hummingbird, ImaginAb, Infinity Pharma, Jounce, JSL Health, Lava Therapeutics, Lytix, Marker, Oncolytics, PBM Capital, Phenomic AI, Polaris Pharma, Sporos, Time Bioventures, Trained Therapeutix, Two Bear Capital, and Venn Biosciences. J.P.A. reports consulting, stock ownership, or advisory board membership for Achelois, Adaptive Biotechnologies, Apricity, BioAtla, BioNTech, Candel Therapeutics, Codiak, Dragonfly, Earli, Enable Medicine, Hummingbird, ImaginAb, Jounce, Lava Therapeutics, Lytix, Marker, PBM Capital, Phenomic AI, Polaris Pharma, Time Bioventures, Trained Therapeutix, Two Bear Capital, and Venn Biosciences. M.A.D. has been a consultant to Roche/Genentech, Array, Pfizer, Novartis, BMS, GSK, Sanofi-Aventis, Vaccinex, Apexigen, Eisai, and ABM Therapeutics, and he has been the principal investigator of research grants to MD Anderson from Roche/Genentech, GSK, Sanofi-Aventis, Merck, Myriad, and Oncothyreon. P.H. is on the scientific advisory board for Dragonfly and Immatics. M.I.R. is on the melanoma advisory board for Merck and is a paid consultant for AMGEN and Merck. S.P.P. reports institutional clinical trial support from NCI, Merck, and Bristol Myers Squibb during the conduct of the study; institutional clinical trial support from Reata Pharmaceuticals, Novartis, Deciphera, Provectus Biopharmaceuticals, Foghorn Therapeutics, TriSalus Life Sciences, and Seattle Genetics; advisory board honoraria from Castle Biosciences and TriSalus Life Sciences; honoraria as Peer Discussion Group Leader for Merck; and honoraria for service as Chair of International Data Monitoring Committee for Immunocore, outside the submitted work.
Data and materials availability: Raw sequencing data and all relevant human data necessary for reproducing results are available in the NCBI Sequence Read Archive under BioProject ID PRJNA770295. All analyzed sequencing data are available in the supplementary materials.