Fig. 3

Volcano plots showing differential protein expression. Expression was considered statistically significant if changes were ≥  ± two fold (≥ ± one fold in Log2 scale, red dashed vertical lines) with a p value ≤ 0.05 (≥ 1.3 in-Log10 scale, green dashed horizontal line). A paired t-test was used for these analyses. A Comparison of baseline (pre-treatment) expression between epithelial and immune cells. B Comparison of expression in epithelial cell before and after treatment. C Comparison of expression in immune cells before and after treatment. An excel file is provided for all volcano plots in supplementary Tables 2–4. D Representative images used for pre-treatment GeoMx analysis. E Representative images used for pre-treatment GeoMx analyses (all images are available in Supplementary Fig. 3A and B). The time elapsed between pre and post treatment analyses was dictated by surgical reaction scheduling and varied between 4–10 days