ccRCC lung metastases harbor cancer associated fibroblast lymphocyte exclusion sites that form a confined TME as revealed by single cell and spatial multi-omics

Tumor progression and metastasis is driven by interplays between cancer cells and their surrounding tumor microenvironment (TME). Investigating the spatiotemporal transcriptomic and proteomic profile of primary and metastatic tumors sheds light on how differences in spatial architecture shape the TME and promote tumor metastasis. Here, we profiled six primary clear cell renal cell carcinoma (ccRCC) specimens and their lung metastases using three different spatial transcriptomic and proteomic platforms: CosMx, Xenium and CODEX. After cell segmentation and annotation, we incorporated the cellular context and spatial information to identify niches by identifying spatial regions with similar cell type composition. This revealed 12 distinctive niches including cancer, stroma, alveolar, and tertiary lymphoid structure (TLS) niches, formed by 25 different cell types. Furthermore, we analyzed cell-cell communication and architecture were analyzed to understand the intercellular interplay and spatial organization in primary and metastatic ccRCC. The architecture analysis showed that the metastatic lesion has a distinct architecture compared to the primary tumor which we refer to as Cancer Associated fibroblaST Lymphocyte Exclusion Sites (CASTLES). The key characteristic of CASTLES is that malignant cells surrounded by cancer associated fibroblasts (CAFs), endothelial cells as well as tumor associated macrophages (TAMs), constituting a physical barrier. In contrast, primary ccRCC cells were accessible to tumor infiltrating leukocytes (TILs). This difference in spatial organization supports the aggressive characteristics of metastatic cancer cells. Our results show the impact of spatial architecture on primary and metastatic ccRCC, as well as the relation between spatial organization of the cellular context and cell-cell communication. In addition, it suggests that cancer-associated fibroblasts (CAFs) and immune cells are essential components of the ccRCC TME. Their interaction constitutes a major factor not only for tumor progression but also limiting therapy response in metastatic ccRCC.