Fig. 4

scRNA-seq reveals distinct immunosuppressive T-cell subtypes in Apc^Min/+; p16^cis/cis colon tumors during development and progression. A UMAP plot showing major cell populations identified from tumors and adjacent normal colon mucosa by canonical cell markers. B A bar plot of the proportion of each cell type in individual tumor tissues and adjacent normal colon mucosa. Individual tumors are ordered by diameter and binned into small or large tumors (T). C Sub-clustering analysis of CD3⁺ T cells. UMAP plot showing transcriptionally distinct T-cell, subtypes identified in both normal and tumor tissues. For individual normal and tumor samples, the cellular composition of T-cell subtypes is shown by a bar plot. D Violin plots showing expression levels of marker genes identifying CD8⁺ cells in each sub-cluster. Compared to the normal CD8⁺ T cells (CD8 + _N), tumor-associated CD8⁺ T cells (CD8 + _T) show decreased expression of the cytotoxic genes (Gzma and Gzmb) and increased expression of the exhaustion marker gene (Tcf7), indicating a dysfunctional state. E Violin plots showing expression levels of the marker genes for γδT17 cells. F GO analysis using ClusterProfiler of DEGs in γδT17 cells for early- vs. late-stage tumors for DEGs with a log-fold change ≥ 0.25. Correction for multiple testing in the Wilcoxon Rank Sum test and MAST was performed with the Benjamini–Hochberg method. G Category net (CNET) plot showing the top pathways and associated DEGs in γδT17 cells during tumor progression. The color of the dots represents the fold change in gene expression, and the size of the dots is proportional to the number of genes enriched with the GO term