Preprint Club
A cross-institutional Journal Club Initiative

Keywords

• Single cell RNA and TCR Sequencing

• T cell exhaustion

• T cell memory

• Immune checkpoint blockade

Main Findings

Memory T cells form after the clearance of acute infection or vaccination to rapidly proliferate and protect against re-exposure to the same pathogen. In contrast to T cell memory, T cell exhaustion occurs after chronic antigen exposure, and it is characterized by decreased proliferation and differentiation. Previous studies have linked the decreased functional capabilities of exhausted T cells to epigenetic profiles characterized by decreased accessibility of effector gene loci and increased accessibility of co-stimulatory molecules and transcription factors encoding for exhaustion (i.e. Tox, Lag3, Pdcd1). Since these studies have been performed on aggregate T cell populations rather than individual clones, it is unclear whether individual clones of exhausted T cells can develop the phenotypic and functional capabilities of memory T cells after the clearance of chronic LCMV infection.

By combining single cell RNA/TCR, ATAC and bulk TCR sequencing, Raposo et al., identify a subset of exhausted T cells that exhibit transcriptional, epigenetic, and functional similarity to bona fide central memory T cells that arise after acute LCMV infection. They identified this subset by comparing single cell RNA/TCR and bulk TCR sequencing on gp33+ CD8+ T cells isolated from mice that had either cleared acute LCMV Armstrong (Tcm) or chronic LCMV C-13 (cTcm) infection. The authors found very few differentially expressed genes between both Tcm populations and validated that both Tcm populations were phenotypically similar by flow cytometry. Additionally, they performed ATAC sequencing and although most exhausted T cell clones exhibit “epigenetic scars” associated with exhaustion, cTcmcells do not exhibit these scars and instead have similar epigenetic profiles to bona fide Tcm cells. Lastly, the authors showed that cTcm cells are functionally similar to bona fide Tcm by performing a rechallenge experiment with LCMV in mice lacking endogenous CD4+ and CD8+ T cells.

To understand how these cTcm cells arise after the clearance of chronic LCMV infection, the authors performed longitudinal TCR tracking between blood samples obtained during chronic infection at 21 days post infection (dpi) and after peripheral viral clearance at 100 dpi. They also performed an adoptive transfer of Tex P14 T cells into an infection free mouse and found that cTcm cells arose from progenitor exhausted (Tcf-1+ PD-1+) biased T cell clones. Lastly, since immune checkpoint blockade is known to expand progenitor exhausted T cells, and cTcm cells are expanded from Tex-prog  biased clones, the authors tested how blocking the PD-1 pathway using anti PD-L1 therapy impacted the population of cTcm T cells. They assessed the clonal trajectories using the cyclone analytical framework and found that anti PD-L1 therapy may drive the proliferation and differentiation of previously unexpanded T cell clones that contribute to the cTcm pool after antigen clearance.

Limitations

The authors did a good job using multiple orthogonal techniques to characterize the newly identified population of cTcm cells, however future experiments to address these outstanding questions would improve upon their findings:

1.  Do these findings translate to other models of chronic antigen stimulation (i.e. cancer?)

Although LCMV infection is a commonly used model to study T cell exhaustion, it is unclear at this time whether the findings can apply to other settings of chronic antigen stimulation such as cancer. In chronic LCMV infection, the cTcmcells were identified after clearance of the viral infection. However, in cancer the tumour is not cleared without additional intervention, which begs the question if cTcm cells are present only when the infection is controlled and thus may not be present at baseline in cancer.

2.  What factors underlie whether Tex-prog clones become Tcm cells or not?

The authors do not address the factors that determine whether Tex-prog cells become cTcm T cells, but they hypothesize that factors that promote the generation of Tex-prog cells will result in an increase in cTcm cells. To build on these findings, future studies investigating their hypothesis that niches of low antigen density may impact the generation of cTcm cells will strengthen our understanding of the environmental determinants that result in the generation of T cell memory.

Significance/Novelty

This study identifies a novel developmental pathway for the generation of central memory T cells from exhausted clones and identifies a therapeutic intervention (anti PD-L1) therapy that expands these cTcm cells. These findings better inform our understanding of the intersection between T cell memory and T cell exhaustion and illustrate the plasticity of certain subsets of exhausted T cells. By conducting future studies to understand if these findings apply to other pathologies such as cancer, this work will provide more clarity on how immunotherapy alters T cell memory in cancer.

Credit

Reviewed by Annette Wu as part of a cross-institutional journal club between the Icahn School of Medicine at Mount Sinai, the University of Oxford, the Karolinska Institute, the University of Texas MD Anderson Cancer Center and the University of Toronto.