TMIC-74 - Spatial landscape of melanoma brain metastases with and without pre-surgical immune checkpoint blockade

We recently characterized the immune populations of brain metastases samples with or without immune checkpoint blockade (ICB) treatment. In that study, we utilized single cell RNAseq (scRNAseq) and multiplex immunofluorescence (mIF) to demonstrate that ICB induced T cell infiltration and the migration of a unique MRC1+ macrophage subset from the perivascular space into the tumor parenchyma. However, scRNAseq’s tissue dissociation step loses spatial information of cells while mIF has low dimensionality, covering only a few markers for each tissue section. Thus, we applied sequencing-based Visium spatial transcriptomics (ST) to study the spatial architecture of melanoma brain metastases with/without ICB treatment and developed a pipeline that leverages public scRNAseq data as a reference to resolve fine-grained cell types on each Visium spot. ICB was associated with an increased CXCL13⁺ terminally exhausted T cell subset in close spatial proximity to tumor cells, suggestive of tumor specificity. ICB also reduced multiple MRC1⁺ macrophage subtypes in the blood vessel regions, supporting our mIF observation. Furthermore, we discovered that MRC1⁺ macrophages in close proximity to blood vessels expressed elevated TIMP1. TIMP1 is a known inhibitor of MMP9 that prevents ECM degradation and blood vessel damage, thus limiting T cell extravasation. In contrast, MRC1⁺ macrophages that migrated into the tumor had higher interferon activation and expressed CXCL9 and CXCL12 chemokines, which could recruit T cells via CXCR3 and CXCR4. Such findings could explain the increased T cell infiltration with ICB even in metastatic brain tumors. However, these MRC1⁺ macrophages also had an M2 signature and expressed multiple immune checkpoint ligands. Such data suggest these cells might also increase immunosuppressive interactions with T cells. In summary, our study reveals how ICB affects the spatial architecture and crosstalk of different cell types within melanoma brain metastases and will provide insights into new therapeutic strategies for brain metastases patients.