Spatially-resolved single-cell imaging of melanoma brain metastases identifies localized immune patterns predictive of immune checkpoint blockade response

BACKGROUND: A subset of patients with advanced-stage melanoma with brain metastases responds intracranially to immune-checkpoint inhibitors (ICIs). We reasoned that features of the spatial architecture of the tumor microenvironment correlate with treatment responses. METHODS: We used highly multiplexed single-cell imaging to characterize the TME in 44 samples of MBM patients; both treatment naïve subjects and subjects who had received ICI were included in the cohort. Samples were stained with a 42-plex metal-isotope tagged antibody panel and subsequently imaged using imaging mass cytometry. Downstream analysis focused on phenotypic and spatial characteristics of the tumor microenvironments of ICI responders and non-responders and on correlations of protein expression with overall and local progression-free survival. RESULTS: Single-cell phenotyping identified more than 1.1 million cells, predominantly tumor (67%) and immune cells (29%). ICI responders exhibited higher baseline proportions of B cells, IDO+ macrophages, and specific T cell subsets (regulatory and exhausted/activated CD8+). Conversely, neutrophil infiltration was negatively associated with intracranial response and survival. Spatial analysis revealed that responders possess a more localized, clustered immune cell pattern compared to the dispersed patterns seen in non-responders. Modeling CD8+ T cell distribution showed that localized infiltration was positively associated with overall and local progression-free survival, while dispersed patterns correlated with poorer outcomes. Furthermore, ICI-pretreated samples showed higher immune-tumor co-localization than treatment-naïve samples. CONCLUSIONS: Our single-cell, spatially resolved characterization of the tumor microenvironment of human melanoma brain metastases demonstrated distinct phenotypic and spatial infiltration patterns of various immune cells that are associated with ICI response and survival outcomes.