Data availability
Data can be retrieved from the corresponding authors upon reasonable request.
Code availability
The MATLAB codes will become available online upon acceptance of the manuscript.
Acknowledgments
This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no 863955) to T.S., grants R01CA247441, R21EB031982 and 5U01CA2618425 to L.L.M, grants R01-CA259253, R01-CA208205, R01-NS118929, U01-CA261842, and U01-CA 224348, Outstanding Investigator Award R35-CA197743 and grants from the National Foundation for Cancer Research, Jane’s Trust Foundation, Niles Albright Research Foundation and Harvard Ludwig Cancer Center to R.K.J. J.A.W. is supported by the National Institute of Health (R01CA219896) and G.M. is also supported by the National Institute of Health (F32CA260769).
Author contributions
Conceptualization: R.K.J., J.A.W., Methodology: R.K.J., T.S., L.L.M., A.H., C.H., A.K.M., G.M., N.J.A., Software, Validation, Formal Analysis: A.H., C.H., A.K.M., Investigation, Resources, Data Curation: R.K.J., T.S., L.L.M., A.H., C.H., A.K.M., G.M., N.J.A., Writing-Original Draft: T.S., A.H., C.H., A.K.M., G.M., Writing-Review & Editing: all authors, Supervision: R.K.J., T.S., L.L.M., N.J.A., J.A.W., Funding Acquisition: R.K.J., T.S., L.L.M., G.M., J.A.W.
Declaration of interests
R.K.J. received consultant fees from Cur, DynamiCure, Elpis, Innocoll, Merck, SynDevRx; owns equity in Accurius, Enlight, SynDevRx; and served on the Boards of Trustees of Tekla Healthcare Investors, Tekla Life Sciences Investors, Tekla Healthcare Opportunities Fund, Tekla World Healthcare Fund; and received grants from Boehringer Ingelheim and Sanofi. J.A.W. is an inventor of a US patent application (PCT/US17/53.717) submitted by the University of Texas MD Anderson Cancer Center, which covers methods to enhance immune checkpoint blockade responses by modulating the microbiome; reports compensation for the speaker’s bureau and honoraria from Imedex, Dava Oncology, Omniprex, Illumina, Gilead, PeerView, Physician Education Resource, MedImmune, Exelixis and Bristol Myers Squibb; and has served as a consultant/advisory board member for Roche/Genentech, Novartis, AstraZeneca, GlaxoSmithKline, Bristol Myers Squibb, Micronoma, OSE therapeutics, Merck, and Everimmune. J.A.W. receives stock options from Micronoma and OSE therapeutics. L.L.M receives equity from Bayer and is a consultant for SimBiosys. Neither any reagent nor any funding from all the above organizations was used in this study. Other co-authors have no conflict of interests to declare.