Eomes identifies thymic precursors of self-specific memory-phenotype CD8+ T cells

Unprimed mice harbor a substantial population of "memory-phenotype" CD8+ T cells (CD8-MP cells) that exhibit hallmarks of activation and innate-like functional properties. Due to the lack of faithful markers to distinguish CD8-MP cells from bona fide CD8+ memory T cells, the developmental origins and antigen specificities of CD8-MP cells remain incompletely defined. Using deep T cell receptor (TCR) sequencing, we found that the TCRs expressed by CD8-MP cells are highly recurrent and distinct from the TCRs expressed by naive-phenotype CD8+ T cells. CD8-MP clones exhibited reactivity to widely expressed self-ligands. T cell precursors expressing CD8-MP TCRs upregulated the transcription factor Eomes during maturation in the thymus, prior to induction of the full memory phenotype, suggestive of a unique program triggered by recognition of self-ligands. Moreover, CD8-MP cells infiltrate oncogene-driven prostate tumors and express high densities of PD-1, suggesting a potential role in anti-tumor immunity and response to immunotherapy. TCRalpha chains were sequenced from FACS-purified CD8-Naïve (CD8+ CD44lo CD122neg) and CD8-MP (CD8+ CD44hi CD122+) T cells from the pooled spleen and lymph nodes of mice expressing a fixed transgenic TCRbeta. Cells were purified from five different 9-week-old male mice on the C57BL/6J (B6) background. In addition, TCRalpha chains were sequenced from FACS-purified CD8+ T cells from the prostate tumors of five 27-week-old TRAMP+/- males expressing the fixed TCRbeta chain.