Fig. 3: Cell type composition changes in the ‘omental metastasis’ cohort, with immune cells converting into regulatory, exhausted, anti-adipogenic, and protumorigenic phenotypes.

A Bubble plot for merged non-metastasized samples and ‘omental metastasis’ tissue samples comprising distant, peritumoral, and tumor core. Estimated effects of ‘Tissue Region’ on cell type composition based on GLM. The color gradient indicates the log2-transformed odds ratio (red, enrichment; blue, depletion), and bubble sizes indicate the Bonferroni-corrected –log10(P value). B UMAP visualization of the ‘omental metastasis’ cohort by tissue region. C UMAP visualization for lymphoid cells. D Matching cluster composition barplots by tissue region for lymphoid cells. E Stacked plot showing expression of gene signatures related to intratumoral CD8⁺ T cells states, including central memory (CM), effector memory (EM), terminally differentiated (TEMRA), progenitor exhausted (TPEX), exhausted (TEX) and naïve in non-metastasized samples and omental metastasis tissue samples using scRNA-seq. F Experimental design for flow cytometry analyses of phenotypic properties of CD8⁺ T cells in omental deposits of SO1 experimental syngeneic mouse models. Created in BioRender. Jacob, F. (2025) https://BioRender.com/hh1ags0. G Box plot showing percentage of TCF1⁺PD1⁺CD8⁺, TIM3⁺PD1⁺CD8⁺ and TIM3^-PD1⁺CD8⁺ T cells in omental tumor samples of SO1 experimental models (nine mice per group). Box plot: lower quartile, median, upper quartile; whiskers, minimum and maximum. Statistical significance was calculated by a two-sided Mann-Whitney test. P-values are indicated. H UMAP visualization for myeloid cells. I Matching cluster composition barplots by tissue region for myeloid cells. J Neutrophil extracellular trap detection in omentum tissue distant to the tumor core. Myeloid UMAP plot showing activation marker ARG1 and NET marker PADI4 expression. K Confocal immunofluorescence stainings of matched distant tissue derived from FFPE blocks (‘omental metastasis’ subcohort) confirm neutrophil and NET presence in the omentum distant to the tumor core. Stainings were performed on two consecutive sections and yielded consistent results. Representative of n = 3 technical images obtained from n = 3 independent patient samples. MPO myeloperoxidase, CIT citrullinated histone H3, CK7 cytokeratin 7. See also Supplementary Figs. 3–5. Source data are provided as a Source Data file.