Characterization, immune cell phenotyping and differential gene expression analysis of brain metastases and primary breast cancer samples

Tumor heterogeneity in breast cancer is well recognized, but research has largely focused on primary tumors, while metastatic lesions, particularly brain metastases (BM), remain understudied. With the rising incidence of BM in metastatic breast cancer (MBC) and their poor prognosis, a deeper understanding of the molecular mechanisms driving BM formation, progression, and immune evasion is crucial for developing better therapeutic strategies. We performed an integrated analysis of BM and matched primary breast tumors using immunohistochemistry, in-situ hybridization, tumor-infiltrating lymphocyte (TIL) quantification, and bulk RNA sequencing. Tumor receptor status, gene expression profiles, immune cell composition, and pathway alterations were analyzed in ten patients with paired samples. Changes in receptor status were observed between primary tumors and BM, including alterations in estrogen receptor and HER2 expression. RNA sequencing revealed differentially expressed genes and pathways, with an apparent downregulation of immune-related genes in BM. Immune profiling suggested a shift in the tumor microenvironment, with BM showing lower B- and CD8 + T-cell infiltration and a relative increase in M2 macrophages and follicular helper T-cells. While these findings are descriptive and limited by sample size, they point towards a potentially more immunosuppressive milieu in BM that may contribute to immune evasion and reduced responsiveness to checkpoint inhibitor therapy. Our study highlights molecular and immunological differences between primary breast tumors and BM. The altered immune landscape in BM, characterized by diminished TIL infiltration and an increase in immunosuppressive cells, warrants further investigation in larger, more homogeneous cohorts.