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Longitudinal single cell transcriptional and epigenetic mapping of effector, memory, and exhausted CD8 T cells reveals shared biological circuits across distinct cell fates

Giles J.R. et al. (BioRxiv) DOI: 10.1101/2022.03.27.485974

Longitudinal single cell transcriptional and epigenetic mapping of effector, memory, and exhausted CD8 T cells reveals shared biological circuits across distinct cell fates


  • CD8 T cell exhaustion

  • CD8 T cell differentiation

  • scRNAseq

  • scATACseq

  • Chronic infection

  • Acute infection

  • Btg1

Main Findings

T cells enter a hypofunctional state of T cell exhaustion during persistent antigen stimulation in chronic infections, cancer, and autoimmunity. Exhausted CD8 T cells are heterogeneous and composed of distinct subsets of progenitor exhausted (Exh-Pre), effector-like or transitory exhausted and terminally exhausted CD8 Tcells1, 2. However, the developmental relationships, and transcriptional and epigenetic mechanisms governing the differentiation of these subsets is largely unknown.

Giles et al, describe both transcriptional (scRNAseq) and epigenetically (scATACseq) defined subset heterogeneity and the underlying molecular mechanisms governing CD8 T cell differentiation using mouse models of acutely resolved infection (LCMV Armstrong) and persistent chronic viral infection (LCMV cl13) of Lymphocytic choriomeningitis virus (LCMV). They compared Single Cell–Assay for Transposase -Accessible Chromatin Sequencing (scATACseq) and Single Cell RNA sequencing (scRNAseq) of LCMV-specific P14CD8T cells (Transgenic CD8 T cells recognizing the LCMV derived gp33-41peptide) collected on days 8, 15 and 30 post infection and revealed further heterogeneity among effector-like CD8 T cells and terminal exhausted CD8 T cells in chronic infection. Among effector-like exhausted cells, the authors uncovered a subset expressing NK-associated genes (Exh-KLR)with high expression of genes associated with cytotoxicity(Gzma, Gzmb) suggesting that they are more cytotoxic than other CD8 exhausted subsets. They next show that although these NK receptor-expressing CD8 T cells were found in both acute and chronic infection, they were distinct from Teff and Tmem CD8 T cells found in acute infections and indicates their functional utility in multiple disease contexts. Next, the authors show that PD1blockade accelerated differentiation of Exh-pre to Exh-intermediate. They also show that over time, there are multiple epigenetically distinct populations of TCF-1+antigen-experienced CD8 T cells, suggesting that TCF1 expression alone cannot be used to define stem/progenitor populations in non-naïve CD8 T cells. Finally, the authors identified transcriptional factors involved in T cell exhaustion and identify stress regulator Btg1as a novel regulator of TEX differentiation. They show that Btg1 was necessary for sustaining Exh-pre and effector-like CD8T cells early in chronic infection and further show that Btg1 knockdown results insignificantly fewer TEX.


  • It is unclear if these additional TEX subsets differ in functionality or is a representation of differentiation/transition into different exhausted fates.

  • It is also unclear if these additional subsets are also found in other chronic infection instances like cancer.

  • Btg1is an anti-proliferative gene, regulates growth and differentiation 3. Btg1 knock-down (KD) results are promising, but more elaborate experiments are needed to establish the role of Btg1 as a regulator of T cell exhaustion. It would be valuable to recapitulate the finding in an acute infection and cancer. Further phenotypic analysis after Btg1 KD would give further insight to develop future immunotherapy strategies.


  • A major finding of this study is the description of a population of Exhausted CD8 T cells expressing NK-associated genes, this cell population had been previously described as Transitory effector like cells.

  • The Authors here are comparing the different states of CD8 T cell exhaustion in chronic and acutely resolved infections and describe the heterogeneity found in this pool of exhausted cells. They describe several developmental relationships and transcriptional and underlying epigenetic mechanisms that regulate the differentiation of T cell exhaustion subtypes. Dataset and analysis described in this preprint can serve as a great resource and provide further insight to develop improved strategies to improve CD8 T cell responses in chronic infections and cancer.


1. Hashimoto, M. et al. CD8 T Cell Exhaustion in Chronic Infection and Cancer: Opportunities for Interventions. Annu Rev Med 69,301-318 (2018).

2.Utzschneider, D.T. et al. T Cell Factor 1-Expressing Memory-like CD8(+) T Cells Sustain the Immune Response to Chronic Viral Infections. Immunity 45,415-427 (2016).

3.Yuniati, L., Scheijen, B., van der Meer, L.T. & van Leeuwen, F.N.  Tumor suppressors BTG1 and BTG2: Beyond growth control. J Cell Physiol 234,5379-5389 (2019).


Reviewed by Abishek Vaidya as part of the cross-institutional journal club of the Immunology Institute of the Icahn School of Medicine, Mount Sinai, and the Kennedy Institute of Rheumatology, University of Oxford.

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