Fig. 2: Consensus molecular subtyping of our set of CRC samples, characterization of their TME and spatially resolved mapping of their histological and molecular features.

a–e Cell type proportions per sample as estimated by the results of the deconvolution. The number of spots containing an abundance of at least 20% of the specified cell types is also displayed. NK natural killers, Mac Macrophages, cDCs conventional dendritic cells. f Enrichment/depletion assessment of selected cell types (x-axis) in CMS2 and mixed CMS1-CMS2 tumors in the different tissue compartments defined by the pathologist’s spot classification (y-axis). IC immune cells. g–j Spatial mapping of the predicted abundance of CMS2 and CMS3 tumor cells and the module scores of the iCMS2-upregulated and the gastric metaplasia signatures overlaid with the pathologist’s tissue annotation in the S5_Rec_Rep1 sample. k Per spot Pearson’s cross-correlation across all the samples between TF activities and CMS cell abundances. For visualization purposes, the 10 most highly correlated TFs in absolute value per CMS are shown. l Per spot Pearson’s cross-correlation across all the samples between pathway activities and CMS cell abundances. m–o Spatial mapping of the predicted abundance of the CMS1 cells, the JAK-STAT pathway activity and the MAPK pathway activity overlaid with the pathologist’s tissue annotation in the S3_Col_R sample. p–r Spatial mapping of the predicted abundance of the CMS2 cells, the WNT pathway activity and the VEGF pathway activity overlaid with the pathologist’s tissue annotation in the S2_Col_R_Rep1 sample. s, t Spatial mapping of the predicted transcriptional activity of the MYC and E2F4 TFs overlaid with the pathologist’s tissue annotation in the S5_Rec_Rep1 sample. Note the colocalization with CMS2 tumor cell abundance (Fig. 2g).