Unraveling the single cell spatial landscapes of melanoma brain metastases

The cellular composition that defines the tumor ecosystem plays a crucial role in determining the responsiveness of tumors to immune checkpoint inhibitors (ICi) and pharmacological blockade of BRAF (BRAFi). However, the compositional changes that likely shape the ecosystems of primary melanomas for metastasis to the brain on the one hand and the progression of brain metastases on the other remain unclear. In this study, we resolved the spatial landscapes of progressive melanoma brain metastases (MBM) by profiling 13 regions from 8 distinct metastases, together with one matched primary tumor spanning various stages of tumor development and therapeutic intervention. Single cell resolved spatial transcriptomics-based profiling uncovered distinct and common patterns of MBM progression. Our approach revealed remarkable cellular and spatial heterogeneity and identified key tumor subsets of MET or NGFR expressing cell populations. Moreover, spatial profiling of tumors which have progressed under ICi or BRAFi identified BZW2+ tumor cells contributing to an immune-suppressive microenvironment, preventing immune cell infiltration and dispersion within the tumor. Elevated BZW2 expression was associated with resistance to ICi therapy and is inversely correlated with the antigen transporter TAP1. Spatially-aware automated profiling of immune cell-enriched areas revealed "hot" niches characterized by tumor cell expression of TAP1, PD-L2, HLA-DRA whereas "cold" niches featured high levels of particularly BZW2 and SOX4. The latter suppressor of translation and transcriptional regulator was co-localized with the clinically targetable MET receptor in a subset of tumor cells that exhibit immune evasion features. In summary, we provide for the first time, spatially resolved landscapes of MBM that reveal insights into the cellular heterogeneity of tumors and the mechanisms underlying immune escape.