Extended Data Fig. 3: Translatome landscapes of tumor-specific and in vitro chronically stimulated CD8⁺ T cells profiled by RPLace-seq.

(a) Bar plot showing the gene count of mRNAs (TPM > 0.5) identified by RPLace-seq in TdLNs T_PEX and Tumor T_EX cells. (b and c) Scatter plot comparing normalized expression (rlog) of mRNAs between RPLace-seq replicates in TdLNs T_PEX cells (b) and Tumor T_EX cells (c). Pearson correlation was used to assess agreement, and the coefficient of determination(R²), P-values (two-sided), and the line of best fit are indicated. (d) Volcano plot showing the differential analysis of RPF abundance between TdLNs T_PEX and Tumor T_EX cells. Genes with significantly differential RPF abundance were defined by threshold |log₂FC | > 1 and P-value < 0.05. P-values were calculated with the two-sided Wald test. Numbers of up- or down-regulated genes are indicated. (e and f) Volcano plot showing the differential analysis of RPF abundance between d4 T_EX and d0 T_N (e), and between d8 T_EX and d4 T_EX (f). Genes with significantly differential RPF abundance were defined by threshold |log₂FC | > 1 and P-value < 0.05. P-values were calculated with the two-sided Wald test. Numbers of up- or down-regulated genes are indicated. (g) Scatter plot comparing log₂FC of mRNA levels and RPF abundance between Tumor T_EX cells and TdLNs T_PEX cells. Pearson correlation was used to assess agreement, and the coefficient of determination (R²) and p-value (two-sided) are indicated. (h) Scatter plot comparing log₂FC of mRNA levels and RPF abundance between Tumor T_EX cells and TdLNs T_PEX cells. The genes with significantly differential RPF abundance were highlighted and are further divided into three groups based on the log₂FC of mRNA levels: (i) less than −0.5, (ii) between −0.5 and 0.5, or (iii) greater than 0.5. The mRNA numbers in each group are indicated. (i) Scatter plot showing the log₂FC of TE and mean RPF abundance in Tumor T_EX cells and TdLNs T_PEX cells. OXPHOS mRNAs are highlighted in red (log₂FC TE > 0) or blue (log₂FC TE < 0). The mRNA numbers in each group are indicated. (j) Heatmap showing the relative levels of mRNA, RPF, and TE across indicated gene sets in Tumor T_EX cells and TdLNs T_PEX cells. (k) Box plots showing the mRNA levels, RPF abundance, and TE for indicated genes in Tumor T_EX cells and TdLNs T_PEX cells (n = 2).