Immunogenomics and spatial proteomic mapping highlight distinct neuro-immune architectures in melanoma vs. non-melanoma-derived brain metastasis

Brain metastases (BrMs) are a devastating complication of solid tumors with challenging clinical management. In this study, immunogenomic and digital spatial analyses were applied to interrogate the peripheral blood and tumor specimens derived from 53 unique patients with metastatic brain tumors originating from different solid tumors including melanoma, breast cancer, lung cancer and renal cell carcinoma. In the peripheral blood, lower levels of neutrophil -lymphocytes ratio (NLR) were detected at time of craniotomy in patients with melanoma-derived brain metastasis (MBM) vs. non-melanoma- derived brain metastasis (non-MBM). Independently from the primary tumor of derivation, patients with BrMs and increased NLR levels were characterized by shorter overall survival (OS) following craniotomy. In the tumor microenvironment (TME), molecular evaluations performed on FFPEs revealed higher expression of genes and mRNA signatures identifying NK cells, CD8 cells and B cells in MBM (n=13) vs. non-MBM brain metastasis (n=41). Focusing on CD8 cells, higher infiltration of CD8+ cells were observed in patients with MBM with longer OS following craniotomy. Spatial proteomic analysis further highlighted the infiltration of CD8+ cells, antigen presenting cells- (HLA-DR+, CD11c+, B2M+), agonists of T cell activity (CD137+, CD40+) and B cells (CD20+) enriched in MBM vs non-MBM. On the contrary, an increased expression of genes associated with neuro-development, cell- cell adhesion, neutrophil enrichment together with the increased infiltrations of cells promoting neuro-differentiation (Neun+, S100+), immune regulatory functions (CD25+, CD127+), and granulocytes aggregation (CD66b+) were observed in non-MBM vs. MBM. These findings highlight that the TME of BrMs plays a pivotal role in the pathogenesis and therapeutic resistance of BrMs derived from different solid tumors. Our results also suggest that distinct neuro-immune interplay may contribute to treatment resistance in BrMs. To comprehensively examine the immune landscape of the tumor microenvironment of metastases derived from different solid tumors, we analyzed a set of surgically resected BrMs originated from different solid tumors including melanoma, lung cancer, breast cancer and renal cell carcinoma (RCC), using whole gene expression profile, digital spatial proteomics (DSP), immunohistochemistry (IHC), multiplex immunofluorescence (mIF), and spectral flow cytometry. Formalin-fixed, paraffin embedded (FFPE) tumor biposies were derived from 13 MBM and 41 non-MBM [18 lung cancer-derived brain metastasis (LBM), 18 breast cancer-derived brain metastasis (BBM) and 5 renal cancer-derived brain metastasis (RCM) biopsies. Three BBM specimens (BREBRM45-B, BREBRM46-B, BREBRM47-B) derived from the same patient (patient 26) and four LBM specimens derived from two different pts (2 specimens/each: LUNBRM14-B and LUNBRM44-B specimens from patient 34, and LUNBRM18-B and LUNBRM36-B from patient 37). RNA was isolated from the tumor regions of the 54 FFPEs specimens derived from 50 unique patients with brain metastasis and subjected to whole gene expression profiling by RNA-seq.