Loss of BAP1 expression is associated with an immunosuppressive microenvironment in uveal melanoma, with implications for immunotherapy development

Abstract

Immunotherapy using immune checkpoint inhibitors (ICIs) induces durable responses in many metastatic cancers. Metastatic uveal melanoma (mUM), typically occurring in the liver, is one of the most refractory tumours to ICIs and has dismal outcomes. Monosomy 3 (M3), polysomy 8q, and BAP1 loss in primary uveal melanoma (pUM) are associated with poor prognoses. The presence of tumour‐infiltrating lymphocytes (TILs) within pUM and surrounding mUM – and some evidence of clinical responses to adoptive TIL transfer – strongly suggests that UMs are indeed immunogenic despite their low mutational burden. The mechanisms that suppress TILs in pUM and mUM are unknown. We show that BAP1 loss is correlated with upregulation of several genes associated with suppressive immune responses, some of which build an immune suppressive axis, including HLA‐DR, CD38, and CD74. Further, single‐cell analysis of pUM by mass cytometry confirmed the expression of these and other markers revealing important functions of infiltrating immune cells in UM, most being regulatory CD8+ T lymphocytes and tumour‐associated macrophages (TAMs). Transcriptomic analysis of hepatic mUM revealed similar immune profiles to pUM with BAP1 loss, including the expression of IDO1. At the protein level, we observed TAMs and TILs entrapped within peritumoural fibrotic areas surrounding mUM, with increased expression of IDO1, PD‐L1, and β‐catenin (CTNNB1), suggesting tumour‐driven immune exclusion and hence the immunotherapy resistance. These findings aid the understanding of how the immune response is organised in BAP1 − mUM, which will further enable functional validation of detected biomarkers and the development of focused immunotherapeutic approaches. © 2020 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.

Transcriptome Profiling Reveals New Insights into the Immune Microenvironment and Upregulation of Novel Biomarkers in Metastatic Uveal Melanoma

“…With respect to the immune profile of the mUM, we confirm our previous results [ 25 , 26 ] that the main “reactive inflammatory” cell within these metastatic tumours is the M2 macrophage with an expression of CD68, CD163, and CD4. Although considered to be bystander cells, these TAMs are likely to actively contribute to the immunosuppressive environment within the mUM.…”

“…Any tumour infiltrating lymphocytes (TILs) present in mUM were CD8+ T-cells with low expression of cytotoxic markers, such as Granzyme B, and they were typically “excluded” from the tumour core [ 25 ]. These results, which were supported by others and suggest CD8+ T-cell exhaustion [ 27 , 28 ], were corroborated by our earlier study using NanoString analyses of six hepatic mUM by Figueiredo et al 2020 [ 26 ]. We showed that within mUM, conventional immune checkpoint regulators (CTLA-4, PD1 and PD-L1) were low and that immune suppressive genes (e.g., HLA-DRA , CD38 , CD74 , LGALS3 ) were increased [ 26 ].…”

“…Intriguingly, UM has relatively low immunogenicity in both the eye and its metastatic sites. The underlying characteristics of the tumour microenvironment (TME) of mUM resulting in its ability for “immune escape” are poorly understood, but have become the subject of intensive investigation [ 25 , 26 ].…”

Molecular Insights and Emerging Strategies for Treatment of Metastatic Uveal Melanoma

“…The presence of this monosomy is associated with a five-year survival rate of 39%, whereas a 90% five-year survival rate is observed for UM without monosomy 3 [ 58 ]. Interestingly, BRCA1-associated protein-1 (BAP1) is a tumor-suppressor gene placed on chromosome 3, and it is mutated in 47% of primary UM and up to 91% of metastatic UM [ 59 , 60 , 61 , 62 , 63 , 64 ]. The splicing factor 3B subunit 1 (SF3B1) is consistent with disomy 3 and shows more favorable prognosis, although an association with delayed metastases has been reported [ 65 , 66 , 67 ].…”

“…Furthermore, a clear prevalence of proangiogenic and protumorigenic M2 phenotype macrophages has been demonstrated within hepatic mUM in late stages of the disease [ 127 , 131 ]. Interestingly, BAP1 loss has recently been correlated with upregulation of several genes associated with suppressive immune responses and, at the protein level, with entrapment of infiltrating immune cells within peritumoural fibrotic areas surrounding mUM [ 62 ]. There is evidence suggesting that dormant cells express mutant neoantigens, which can occur naturally or rather derive from treatment [ 133 , 134 ].…”