Fig. 5: Paired spatial resolved proteomics confirm the antigen presenting role of C1QC⁺ RTMs in immunotherapy.

a The potential biological functions and relevant signaling pathways of MSS/MSI_R and NR CRC patients were evaluated by the GO analyses. The hypergeometric test for over-representation was adopted to evaluate the statistical significance with multiple tests corrections. b Gene set enrichment analysis (GSEA) enrichment for APC and C1QC⁺ RTMs in MSS_NR and MSS_R samples. NES, normalize enrichment score. The Kolmogorov-Smirnov test was adopted to evaluate the statistical significance with multiple tests corrections. c Fast gene set enrichment analysis (FGSEA) enrichment for top 10 upregulated pathways and top 10 downregulated pathways comparing MSS_NR and MSS_R according to the hallmark gene sets. d Heatmap showing different immunotherapy-related pathways enriched in the integrated MSS/MSI_R and NR groups by gene set variation analysis (GSVA) analysis, colored by z-score transformed mean GSVA scores. e Boxplot illustrating the C1QC⁺ RTM scores, calculated using the C1QC⁺ RTM signature, in spatial proteomics analyses. The one-way ANOVA test was adopted to evaluate the statistical significance. f Scatter plots showing Pearson’s correlation between C1QC⁺ RTM and MHC-I score, calculated using the C1QC⁺ RTM signature and MHC-I signature, in spatial proteomics analyses. g, h Scatter plots depicting the Pearson’s correlation between C1QC⁺ RTM and MHC-II scores, as determined through spatial proteomics analyses and further validated through bulk proteomics. The Pearson Coefficient Test was adopted to evaluate the statistical significance.