High-Throughput Screening and Proteomic Characterization of Compounds Targeting Myeloid-Derived Suppressor Cells

Myeloid-derived suppressor cells (MDSC) are a heterogeneous cell population of incompletely differentiated immune cells. They are known to suppress T cell activity and are implicated in multiple chronic diseases, which make them an attractive cell population for drug discovery. Here, we characterized the baseline proteomes and phospho-proteomes of mouse MDSC differentiated from a progenitor cell line to a depth of 7000 proteins and phosphorylation sites. We also validated the cellular system for drug discovery by recapitulating and identifying known and novel molecular responses to the well-studied MDSC drugs entinostat and mocetinostat. We established a high-throughput drug screening platform using a MDSC/T cell coculture system and assessed the effects of ∼21,000 small molecule compounds on T cell proliferation and IFN-γ secretion to identify novel MDSC modulator. The most promising candidates were validated in a human MDSC system, and subsequent proteomic experiments showed significant upregulation of several proteins associated with the reduction of reactive oxygen species (ROS). Proteome-wide solvent-induced protein stability assays identified Acyp1 and Cd74 as potential targets, and the ROS-reducing drug phenotype was validated by measuring ROS levels in cells in response to compound, suggesting a potential mode of action. We anticipate that the data and chemical tools developed in this study will be valuable for further research on MDSC and related drug discovery. [Display omitted] •(Phospho-)proteome profiling of differentiated myeloid-derived suppressor cells.•Phenotypic screen of 21,000 small molecules to identify novel MDSC modulators.•Reduction of reactive oxygen species identified as potential mode of action.•Chemical proteomics reveals Acyp1 and Cd74 as potential target proteins. Myeloid-derived suppressor cells (MDSCs) counteract the immune system when fighting cancer. Krumm et al. screened 21,000 compounds in T-cell coculture system in search for modulators of MDSC. They identified Acyp1 and Cd74 as potential targets of the most interesting compound by chemical proteomics. Characterization of the cellular response by (phospho-)proteomics and functional assays revealed upregulation of cellular reactive oxygen species metabolism as a likely mode of action of this MDSC modulator.