Single-cell resolution spatial analysis of antigen-presenting cancer-associated fibroblast niches [Xenium PM]

One of the most common origins of Peritoneal metastasis (PM) is colon cancer, which occurs in about 20% of colon cancer patients. Given the cancer cell heterogeneity in PM, we first tried to dissect the spatial distribution of CAF and the associated niches at a single cell resolution, we exploited the Xenium In Situ high-plex spatial imaging platform. We performed the Xenium assays with 8 human PM samples of colon origin including one PM-adjacent tissue. Among the 8 PM samples, 3 samples carried a distinct iCMS3 epithelial signature (PM1, PM2, PM3), 2 carried iCMS2 signature (PM6, PM7), while the other 2 samples had a mix of both iCMS2 and iCMS3 signatures (PM4, PM5). We found that the presence of iCMS3 cancer cells was associated with an increase infiltration of lymphocytes and the formation of tertiary lymphoid structures (TLS). We designed a custom gene panel comprising 480 genes for cell type recognition and gene functional analysis. Tissue sections were prepared according to the Xenium In Situ for FFPE-Tissue Preparation Guide protocol. FFPE sections were cut to 5 μm and placed in the designated sample area on a Xenium slide.