Figure 3. scRNA-Seq of tumor-infiltrating CD4 Tconvs.

CD45⁺ cells isolated ex vivo from 4 head and neck cancer specimens were subjected to scRNA-Seq. (A) t-SNE plot of 2060 CD4 Tconvs color-coded by their associated cluster. (B) Results of differential expression analysis of scRNA-Seq data from ENTPD1⁺ versus ENTPD1^– CD4 Tconvs are shown in a volcano plot. Genes significantly upregulated in ENTPD1⁺ cells are shown in red and those significantly downregulated are shown in orange. (C) Violin plots showing the expression of CTLA4, HAVCR2, and LAG3 in ENTPD1^– and ENTPD1⁺ cells (left) and t-SNE plots color-coded by levels of expression (gray to red) of ENTPD1, CTLA4, HAVCR2, and LAG3 (right). (D) t-SNE plots showing analysis of TOX exhaustion gene sets (left,ref. 15, and right, ref. 12) using Single-Cell Signature Explorer Viewer. Tconvs, conventional FOXP3^- CD4 T cells; TILs, tumor-infiltrating lymphocytes.