Single cell and spatial sequencing analysis of cancer associated fibroblasts in the brain metastasis tumor microenvironment

Brain metastasis (BM) remains largely incurable. Cancer-associated fibroblasts (CAFs) can either support or inhibit tumor growth in the tumor microenvironment (TME), yet their role in BM is not well described. In this study we define four transcriptionally distinct CAF subpopulations using single-cell and spatial sequencing of human BM tissues. The four CAF subpopulations we describe are termed extracellular matrix (ECM), immune, contractile, or neural CAFs, and each subpopulation shows distinct spatial distributions within the BM TME. Further analyses reveal that BM CAFs engage extensively in cell-cell communication and adopt distinct cell states, including an ECM CAF cell state marked by high levels of immunoglobulin superfamily containing leucine rich repeat expression (ISLR-CAFs). Functionally, ISLR-CAFs reduce BM tumor cell viability in vitro, consistent with a tumor-inhibitory role. These findings highlight the heterogeneity of CAFs in BM, emphasizing the importance of understanding stromal contributions in the underlying biology of BM. Cancer associated fibroblast subpopulations are identified by single cell and spatial sequencing as relevant components of the brain metastasis tumor microenvironment, where they participate in the tissue architecture and intercellular communication.