Proteomic profiling of the neuroblastoma secretome identifies extracellular vesicles as drivers of T cell suppression

Abstract

Immunosuppressive tumor microenvironments in solid tumors hamper the efficacy of immunotherapies, including CAR T-cell therapy. To identify immunosuppressive secreted factors in high-risk neuroblastoma, a childhood solid tumor with a 5-year overall survival of below 60%, we mapped secreted factors of 16 genetically diverse patient-derived neuroblastoma tumoroids by LC-MS. The secretomes suppressed T cell activation, proliferation and cytotoxicity to varying extents, suggesting that this panel constituted a valuable discovery foundation to identify clinically relevant immunosuppressive factors. 29 proteins were significantly enriched in highly suppressive secretomes, of which Neuropeptide Y (NPY) had the highest correlation with functionally-determined immunosuppression. No direct or indirect effect of NPY on (CAR) T cell activation could be validated. Instead, NPY proved to be a biomarker for extracellular vesicle (EV) secretion. Finally, we demonstrated that neuroblastoma-derived EVs potently suppress T cell activation. Altogether, this study provides an atlas of the neuroblastoma secretome and reveals immunosuppressive effects of EVs on T cells. These insights contribute to the understanding of the immunosuppressive neuroblastoma TME.