Cystatin C is a glucocorticoid response gene predictive of cancer immunotherapy failure Sam O Kleeman 1 , Miriam Ferrer 1 , Breanna Demestichas 1 , Sean Bankier 2,3 , Hassal Lee 1 , Todd Heywood 1 , Arno Ruusalepp 4 , Johan L. M. Bjorkegren 5 , Brian R Walker 2,6 , Hannah V Meyer 1,+ , and Tobias Janowitz 1,7,+,* 1 Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA 2 BHF Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, UK 3 Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway 4 Department of Cardiac Surgery, Tartu University Hospital, Tartu, Estonia 5 Department of Genetics & Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA 6 Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK 7 Cancer Institute, Northwell Health, New York, USA + These authors jointly supervised this work * Correspondence to janowitz@cshl.edu Abstract The secreted protein Cystatin C (CyC) is a cysteine protease inhibitor of incompletely characterized biomedical function, used clinically for estimation of glomerular filtration rate. Plasma CyC is elevated in many patients, especially when they receive glucocorticoid (GC) treatment. Here we empirically connect GCs with systemic regulation of CyC. First, we leveraged genome-wide association and structural equation modeling to determine the genetics of the latent trait CyC production in UK Biobank. Using multi-modal genomic, transcriptional, and experimental approaches, we demonstrated that CyC is a direct target of GC receptor, with GC- responsive CyC secretion exhibited by macrophages and cancer cells in vitro. Elevated serum CyC levels were positively correlated with GC levels in a murine model of cancer progression. Consistent with the coupling of CyC levels to GC signaling in a disease relevant manner, CyC predicted elevated all-cause and cancer-specific mortality in humans. These associations were orthogonally confirmed by a polygenic score (PGS) capturing germline predisposition to CyC production. This PGS predicted checkpoint immunotherapy failure in a combined clinical trial cohort of 685 metastatic cancer patients, with available germline exome sequencing. Taken together, our results demonstrate that CyC captures biomedically-relevant variations in endogenous GC activity, raising the possibility that CyC may be a direct effector of GC-induced immunosuppression and therefore a target for combination cancer immunotherapy. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) The copyright holder for this preprint this version posted August 20, 2021. ; https://doi.org/10.1101/2021.08.17.21261668 doi: medRxiv preprint NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice.