Figure 4.

Peripheral CD4⁺ and DN T cells reveal a shift from naive toward effector phenotypes

(A) UMAP visualization of 15 CD4⁺ and DN (double-negative) T cell subclusters. The inset shows the projection of these cells onto the T/NK cell UMAP (Level 2).

(B) UMAP visualization of 11 CD4⁺ and 4 DN annotated T cell populations.

(C) Dot plot shows canonical marker gene expression and proportions in CD4⁺ & DN T cell subclusters (LOC611565: antigen WC1.1-like).

(D) Bar plot depicts the proportion of cells across CanL clinical stages, colored by CD4⁺/DN cell population. See also Table S2.

(E) Trajectory analysis of CD4⁺ T cell populations performed on a UMAP reduction of a CD4⁺ T cell population subset.

(F) Heatmap visualization of the top 50 differentially expressed genes (DEGs) of each subcluster. Showing DEGs and subclusters arranged by hierarchical clustering. Highlighted DEGs correspond to those visualized in Figure 4G. See also Table S4.

(G) Dot plots show expression and proportions within specific cell populations across CanL clinical stage, showing representative DEGs of the subcluster’s DEG signature.

(H) Line graphs of individual subclusters summarizing signature Z-scores across CanL clinical stages.

The visualizations show the mean (dark burgundy line) and standard deviation (light burgundy ribbon) of Z-scores from the subcluster's DEG signature (Top 50 DEGs), alongside a control (gray ribbon) of upper and lower confidence intervals from bootstrapping (n = 100,000) non-signature genes. See also Figure S4 and Table S4.