Extended Data Fig. 10: MYB regulates the expression of multiple genes that are critical to exhausted T cell function and maintenance.

(a, b) Congenically marked Myb^fl/flCd4^Cre (Myb-cKO, CD45.2⁺) and Cd4^Cre (Ctrl, CD45.2⁺ or CD45.2⁺CD45.1⁺) P14 T cells were adoptively transferred into separate naive recipient (CD45.1) mice, which were then infected with LCMV-Docile. Splenic P14 T_PEX cells were sorted at day 7 post-infection and processed for bulk RNA-seq. (a) Schematic of the experimental set-up. (b) Gene set enrichment analysis showing loss of CD62L⁺ T_PEX transcriptional signature in Myb-cKO T_PEX cells compared to control T_PEX cells. (c) Volcano plots highlighting genes differentially expressed (FDR < 0.15) between control CD62L⁺ T_PEX and CD62L⁻ T_PEX cells. (d–e) Mixed bone marrow chimeric mice containing congenically marked Myb-cKO and control CD8⁺ T cells were infected with LCMV-Docile. Flow cytometry plots (d) and quantification (e) showing the frequencies of the entire antigen-responsive PD-1⁺ cell compartment among Myb-cKO and control CD8⁺ T cells in the spleen and lymph nodes at day 70 post-infection. (f, g) Congenically marked Myb-cKO and Ctrl P14 T cells were adoptively transferred into separate naive recipient mice, which were then infected with LCMV-Docile. Splenic P14 T_PEX cells were analysed at day 8 post-infection. (f) Schematic of the experimental set-up. (g) Quantification showing the abundances of the indicated P14 subsets per spleen. (h) Heat map depicting genes differentially expressed (FDR < 0.15, FC > 1) between control CD62L⁺ T_PEX and CD62L⁻ T_PEX cell or Myb-cKO and control T_PEX and T_EX cells, with genes of interest annotated. (i) Gene set enrichment analysis showing loss of CX3CR1⁺ T_EX transcriptional signature in P14 Myb-cKO T_EX cells compared to control T_EX cells. (j) Volcano plot highlighting genes differentially expressed (FDR < 0.15) between control and Myb-cKO T_EX cells with genes of interested annotated. (k) Flow cytometry plots and quantification show the frequencies of CX3CR1⁺ cells among control and Myb-cKO T_EX P14 T cells at day 8 post LCMV-Docile infection. (l) Flow cytometry plots and quantifications showing CX3CR1 and CD101 expression in Myb-cKO and control T_EX cells at the indicated time points after infection. Dots in graph represent individual mice; box plots indicate range, interquartile and median. Symbols and error bars in (l) represent mean and s.e.m., respectively Data are representative of two independent experiments (e, g, k, l). P values are from two-tailed unpaired t-tests; P > 0.05, not significant (n.s.).

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