Identification of DEGs
Differential gene expression analysis was performed using the FindMarkers function in the Seurat v.4.1 R package separately in responders (>6 months survival) and nonresponders (<6 months survival) for pre- versus on-treatment specimens. Since epithelial cell numbers per specimen were very variable, we randomly downsampled the cells in specimens with large cell numbers to the median cell count of 557 per specimen. The volcano plots call out all genes with Bonferroni corrected 