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

To explore the CAF niches in pancreatic ductal adenocarcinoma (PDAC), we performed Xenium assays in 3 treatment-naïve and 3 chemoradiotherapy-treated human PDAC samples. We found that after the chemoradiotherapy treatment, tissues became more desmoplastic with a larger CAF proportion. And interestingly, we found there was a reduction of cancer cell 1 in the chemoradiotherapy group while the ratio of cancer cell 2 remained similar, suggesting cancer cell 2 was the chemoradiotherapy-resistant cancer cell population. Through differential gene analysis, we found cancer 2 was marked by a high level of SPP1 expression. 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.