BAP1 Loss Promotes Suppressive Tumor Immune Microenvironment via Upregulation of PROS1 in Class 2 Uveal Melanomas

SIMPLE SUMMARY: Uveal melanoma is a highly metastatic cancer of the eye which is notoriously resistant to therapy. Elucidating the mechanisms of metastasis in order to devise effective therapies has been a major challenge. The strongest genetic risk factor for metastasis in uveal melanoma is the mutational inactivation of the BAP1 tumor-suppressor gene. However, it remains unknown how BAP1 loss promotes tumor progression. Here, we show that BAP1 loss leads to increased expression of PROS1 in uveal melanocytes and melanoma cells, which in turn leads to phosphorylation and activation of the receptor tyrosine kinase MERTK on adjacent macrophages, driving them into a suppressive M2-polarized state. This mechanism could help explain the suppressive tumor immune microenvironment that is characteristic of BAP1-mutant uveal melanomas, and it suggests that BAP1 loss may lead to metastasis at least in part by facilitating immune escape. These findings provide new insights into the role of BAP1 in uveal melanoma, and they nominate new strategies for increasing the efficacy of immunotherapy in this cancer. ABSTRACT: Uveal melanoma (UM) is the most common primary cancer of the eye and is associated with a high rate of metastatic death. UM can be stratified into two main classes based on metastatic risk, with class 1 UM having a low metastatic risk and class 2 UM having a high metastatic risk. Class 2 UM have a distinctive genomic, transcriptomic, histopathologic, and clinical phenotype characterized by biallelic inactivation of the BAP1 tumor-suppressor gene, an immune-suppressive microenvironment enriched for M2-polarized macrophages, and poor response to checkpoint-inhibitor immunotherapy. To identify potential mechanistic links between BAP1 loss and immune suppression in class 2 UM, we performed an integrated analysis of UM samples, as well as genetically engineered UM cell lines and uveal melanocytes (UMC). Using RNA sequencing (RNA-seq), we found that the most highly upregulated gene associated with BAP1 loss across these datasets was PROS1, which encodes a ligand that triggers phosphorylation and activation of the immunosuppressive macrophage receptor MERTK. The inverse association between BAP1 and PROS1 in class 2 UM was confirmed by single-cell RNA-seq, which also revealed that MERTK was upregulated in CD163+ macrophages in class 2 UM. Using ChIP-seq, BAP1 knockdown in UM cells resulted in an accumulation of H3K27ac at the PROS1 locus, suggesting epigenetic regulation of PROS1 by BAP1. Phosphorylation of MERTK in RAW 264.7 monocyte–macrophage cells was increased upon coculture with BAP1(−/−) UMCs, and this phosphorylation was blocked by depletion of PROS1 in the UMCs. These findings were corroborated by multicolor immunohistochemistry, where class 2/BAP1-mutant UMs demonstrated increased PROS1 expression in tumor cells and increased MERTK phosphorylation in CD163+ macrophages compared with class 1/BAP1-wildtype UMs. Taken together, these findings provide a mechanistic link between BAP1 loss and the suppression of the tumor immune microenvironment in class 2 UMs, and they implicate the PROS1–MERTK pathway as a potential target for immunotherapy in UM.