GSE174401
Single cell characterization of the immune microenvironment of melanoma brain and leptomeningeal metastases
Melanoma brain metastases (MBM) and leptomeningeal metastases (LMM) are two manifestations of melanoma CNS metastasis with vastly different survival outcomes. Using single cell RNA-Seq analysis we uncovered a unique, immune-suppressed T-cell landscape in the LMM microenvironment distinct from that of brain and skin metastases. An LMM patient with an unusually long survival demonstrated an immune repertoire that was distinct from those of poor survivors and more similar to CSF from non-LMM patients. Upon response to PD-1 therapy, this extreme responder showed increased levels of T-cells and dendritic cells in their CSF, whereas poor survivors showed little improvement in their T-cell responses. In MBM patients, systemic therapy was associated with increased immune infiltrate, with similar T-cell transcriptional diversity noted between skin metastases and MBM - suggestive of immune cell trafficking into the brain. A correlation analysis across the entire immune landscape identified the presence of a rare population of dendritic cells (DC3s) that correlated with increased overall survival and positively regulated the immune environment through modulation of activated T-cells and MHC expression. Our study provides the first atlas of two distinct sites of melanoma CNS metastases and identifies rare populations of cells that underlie the biology of this devastating disease. Overall design: Single cell rnaseq of immune microenvironment of cutatneous melanoma, and brain, leptomeningeal metastases.