Epi-immunotherapy promotes the antitumor response mediated by diverse CD8⁺ tumor-reactive T cells. (A) Box plots showing normalized counts of total CD8⁺ and NK cells for paired pretreatment (Pre) and on-treatment (On) samples. Adjusted P values and fold change values by negative binomial-generalized linear models were also shown. Box middle lines, median; box limits, upper and lower quartiles; box whiskers, 1.5× the interquartile range. (B) The expression pattern of representative genes related to exhaustion, costimulation, cytotoxicity, chemokine, adhesion, and transcription factor in CD8⁺ T-cell clusters. ∗adjusted P value < .01 and log₂ fold change > 0.15; †adjusted P value < .01 and log₂ fold change > 0; test by limma analysis. (C) Scatterplots showing CD8⁺ T-cell clusters’ clonality measured by Shannon entropy–based index, the proportion of clonal cells (clone size ≥ 5). Size for proliferation activity indicated by MKI67⁺ cell proportion. (D) Box plots comparing clonality between pretreatment (Pre) and on-treatment (On) samples. Tests by paired t tests. (E) Box plots comparing the fractions of expanded clones between treatment groups. Fraction is the number of expanded clones in a patient divided by the total number of clones in that patient. (F) Pie charts showing the cell state compositions of expanded/contracted clones in the 2 treatment groups. Toth indicates other T cells besides exhausted T cells (Tex). (G) Heat map showing TCR sharing strength between cluster HAVCR2⁺ Tex and other CD8⁺ clusters in the 2 treatment groups. Top clusters with the highest sharing strength with HAVCR2⁺ Tex are highlighted in bold. (H-I) 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 HAVCR2⁺ Tex or CXCR5⁺ Tex are plotted. (H) clones in DP-treated patients, (I) clones in CDP-treated patients. (J) 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 CD8⁺ T clusters exhibiting significant abundance differences (nominal P < .05) are shown. The orange bar next to the left side annotates clusters having significant abundance differences in the pretreatment samples, and the red bar next to the left side annotates other clusters. The clusters exhibited significant abundance change between pretreatment and on-treatment samples are highlighted in red (see supplemental Figure 8F). ∗∗adjusted P < .01; ∗adjusted P < .05; †nominal P < .05.