Abstract
Current methods for biomarker discovery and target identification in immuno-oncology rely on static snapshots of tumor immunity. To thoroughly characterize the temporal nature of antitumor immune responses, we developed a 34-parameter spectral flow cytometry panel and performed high-throughput analyses in critical contexts. We leveraged two distinct preclinical models that recapitulate cancer immunoediting (NPK-C1) and immune checkpoint blockade (ICB) response (MC38), respectively, and profiled multiple relevant tissues at and around key inflection points of immune surveillance and escape and/or ICB response. Machine learning-driven data analysis revealed a pattern of KLRG1 expression that uniquely identified intratumoral effector CD4 T cell populations that constitutively associate with tumor burden across tumor models, and are lost in tumors undergoing regression in response to ICB. Similarly, a Helios-KLRG1 + subset of tumor-infiltrating regulatory T cells (Tregs) was associated with tumor progression from immune equilibrium to escape, and were also lost in tumors responding to ICB. Validation studies confirmed KLRG1 signatures in human tumorinfiltrating CD4 T cells associate with disease progression in renal cancer. These findings nominate KLRG1+ CD4 T cell populations as subsets for further investigation in cancer immunity and demonstrate the utility of longitudinal spectral flow profiling as an engine of dynamic biomarker and/or target discovery.
Competing Interest Statement
B.I. has received consulting fees from Volastra Therapeutics Inc, Merck, AstraZeneca and Janssen Pharmaceuticals and has received research funding to Columbia University from Alkermes, Arcus Biosciences, Checkmate Pharmaceuticals, Compugen, Immunocore, and Synthekine. C.G.D. is a co-inventor on patents licensed from JHU to BMS and Janssen, has served as a paid consultant to AZ Medimmune, BMS, Pfizer, Roche, Sanofi Aventis, Genentech, Merck, and Janssen, has received sponsored research funding to his institution from BMS IIoN and Janssen, and is a current employee of Janssen.
Footnotes
Funding: C.R.A. was supported by the NIH grants UL1TR001873 and TL1TR001875. B.I. received support from NIH, National Cancer Institute (NCI) grants R37CA258829, R01CA266446, R21CA263381, an American Cancer Society Research Scholar Grant, a Burroughs Wellcome Fund Career Award for Medical Scientists, a Velocity Fellows Award, the Louis V. Gerstner, Jr. Scholars Program and a Young Investigator Award by the Melanoma Research Alliance. This research was funded in part through the NIH/NCI Cancer Center Support Grant P30CA013696, a Prostate Cancer Foundation Challenge Award (C.G.D./M.C.D.).
Conflicts of Interest: B.I. has received consulting fees from Volastra Therapeutics Inc, Merck, AstraZeneca and Janssen Pharmaceuticals and has received research funding to Columbia University from Alkermes, Arcus Biosciences, Checkmate Pharmaceuticals, Compugen, Immunocore, and Synthekine. C.G.D. is a co-inventor on patents licensed from JHU to BMS and Janssen, has served as a paid consultant to AZ Medimmune, BMS, Pfizer, Roche, Sanofi Aventis, Genentech, Merck, and Janssen, has received sponsored research funding to his institution from BMS IIoN and Janssen, and is a current employee of Janssen.