TCR signaling regulated T cell exhaustion in response to chronic viral infection - Summary Although it is becoming increasingly clear that CD8+ T cells responding to chronic infection are phenotypically and functionally diverse, little is known about how to overcome T cell exhaustion to treat infectious diseases. Using single cell RNA sequencing (scRNA-seq), the investigator’s team has confirmed the presence of previously identified TCF-1hi progenitor and PD-1hi exhausted T subsets. Surprisingly, they also found a CX3CR1+ effector subset at the late phase of chronic infection. More importantly, they have shown that CX3CR1+ effector cell formation is critically dependent on IL-21-producing CD4+ helper T cells. The discovery of this potent antiviral effector subset provides new opportunities for therapeutic interventions to treat infectious diseases. To better understand the genesis of CX3CR1+ effector cells, the investigator’s team proposes to use the newly developed technology of paired single-cell RNA and TCR sequencing (scTCR-seq) to “lineage trace” back to the ancestors (progenitors) of effector and exhausted cells. Their preliminary data suggest that TCR signaling strengths positively correlate with exhausted T cell subset differentiation, but negatively correlate with effector T cell differentiation. In parallel, they also provide evidence that CX3CR1+ effector cell formation depends on cross- presenting dendritic cells (DCs), especially Batf3+ XCR1+ cDC1s. These cDC1 cells are likely subjected to CD40- mediated CD4 helper T cell licensing, which is unexpected in the context of persistent infection and possibly occurs within specialized cellular structures. Taken together, the investigator hypothesizes that progenitor CD8+ T cells need to be primed and activated by the cDC1s again at the late phase of chronic infection to enter into a proliferative burst as a transitory differentiation state, and then bifurcate into two terminally differentiated subsets: CX3CR1+ effector and PD-1hi exhausted CD8+ T cells. Mechanistically, CD4+ T cells need to provide signals to license DCs for their antigen-presentation, and TCR signaling strength dictates the threshold of progenitor cell activation and influences the effector versus exhausted cell fate choice. Harnessing this knowledge, they intend to alter the course of T cell differentiation by changing TCR signaling strength through identification and validation of TCR signaling regulators (TSRs) that can be exploited to favor the formation of CX3CR1+ effector T cells for improved viral control. The investigator’s team will test these hypotheses in the following three aims. First, they will use paired scRNA- and scTCR- seq and associated computational tools and biological validations to delineate virus-specific CD8+ T cell differentiation trajectories and dissect how TCR signaling strength affects cell fate decisions. Second, they will use genetic models to delineate the mechanisms by which DCs are licensed by CD4+ helper T cells for CD8+ T cell priming and differentiation. Third, they will employ high-throughput targeted CRISPR screen and gene editing to test if manipulating TCR signaling strength can redirect CD8+ T cells toward effector differentiation and overcome exhaustion to treat chronic infection and cancer.
