Epi-immunotherapy inhibits tumor-promoting and immunosuppressive IL21⁺ Th cells. (A) Heat map showing the abundance of clusters in pretreatment and on-treatment tumors from responders (R; treated by CDP) and nonresponders (NR; treated by DP). Color for the average of z score–scaled abundance. The abundance in responders is compared with nonresponders by negative binomial-generalized linear models for pretreatment and on-treatment samples separately. Only CD4⁺ T cells exhibiting significant abundance differences (nominal P < .05) are shown. The clusters exhibited significant abundance change between pretreatment and on-treatment samples are highlighted in red (see supplemental Figure 10A). ∗∗adjusted P < .01; ∗adjusted P < .05; †nominal P < .05. (B) The expression pattern of representative signature genes in CD4⁺ T-cell clusters. ∗adjusted P < .01; and log₂ fold change > 0.15; †adjusted P < .01; and log₂ fold change > 0; test by limma analysis. (C-D) Scatterplots illustrating TCR clone frequencies in pretreatment and on-treatment samples from patients treated by DP (C) and CDP (D). Only large clones (with sizes ≥5 either in pretreatment or on-treatment samples) are shown. Color for categories of T-cell expansion/contraction; size for clone frequencies in patients. (E) Pie charts showing the cell state compositions of expanded/contracted clones in treatment group DP and CDP. Toth indicates other T cells besides IL21⁺ Th. (F) Sankey plots showing the dominant-state dynamics of large clones. Cells of the same clone in a paired pretreatment and on-treatment sample are connected. Color for the dominant transcriptomic state. Clones dominated by IL21⁺ Th cluster are plotted. (G) Dot plots showing the expression of ligand/receptor genes. The left panel is for receptor genes on HRS-like cells, and cognate ligand genes on IL21⁺ Th cells; the right panel is for receptor genes on IL21⁺ Th cells and cognate ligand genes on HRS-like cells. Paired ligand-receptors are labeled in the same color and number. (H) Heat map showing top-ranked ligands predicted to have high regulatory potentials on IL21⁺ Th cells by the NicheNet analysis. Genes were ranked by corrected AUPR. (I-J) Chord diagrams illustrating representative interactions of high specificity between CD30⁺ HRS-like cells (I) or IL21⁺ Th cells (J) and CD8⁺ T cells/NK cells. Width of the chord for interaction strength. AUPR, area under the precision-recall curve.