Spatial multi-omics reveals a cancer-associated fibroblast-T cell niche sustaining tissue-resident immunity in clear-cell renal cell carcinoma

Clear-cell renal cell carcinoma (ccRCC) has a lot of immune cells in it, but the performance of the body's immune system against ccRCC and the outcome for patients who have ccRCC vary greatly. Recent studies indicate that not only how many immune cells are present, but also the state of those cells and how they are arranged within the tumor microenvironment (TME) contribute to how well an individual's immune system can eliminate ccRCC. Therefore, this study aimed to systematically characterize the spatial organization and functional interactions of immune and stromal cells in ccRCC using integrated single-cell and spatial multi-omics approaches.

To better understand ccRCC through this multi-omics analysis, we utilized two cohort studies of single-cell RNA sequencing (scRNA-seq) data combined with spatial transcriptomics (sRNA-seq) data to make a multi-omics atlas of ccRCC. We performed in-depth functional enrichment analysis, survival analysis, modeling of cell-to-cell communication, as well as spatial validation of these analyses, to identify the heterogeneous nature of cell-cell interactions in vivo within the ccRCC TME and determine how they correlate and contribute to prognostic outcomes for ccRCC patients.

We identified various epithelial, immune, and mesenchymal cell states in ccRCC, showing distinct differences in their prognostic values: CD4 Trm, iCAFs, PDGFRB⁺ mesenchymal cells, and proximal tubule-like epithelial programs had positive prognostic associations, while resident CD8 T cells and ascending thin limb-like epithelial cell programs had negative prognostic associations. Spatial and computational analyses of these results showed the presence of a secure iCAF-CD4 Trm cell niche, with fibronectin-integrin α5β1 signaling as an anchor for CD4 Trm residency, located at the tumor-stroma interface.

These results demonstrate that the prognosis of ccRCC is determined by the spatial organization of the immune-stromal cell niche rather than just by the number of immune cells present. The iCAF-CD4 Trm axes may provide opportunities for precision immunomodulatory therapy.