Molecular and cellular insights into T cell exhaustion

Abstract

In chronic infections and cancer, T cells are exposed to persistent antigen and/or inflammatory signals. This scenario is often associated with the deterioration of T cell function: a state called 'exhaustion'. Exhausted T cells lose robust effector functions, express multiple inhibitory receptors and are defined by an altered transcriptional programme. T cell exhaustion is often associated with inefficient control of persisting infections and tumours, but revitalization of exhausted T cells can reinvigorate immunity. Here, we review recent advances that provide a clearer molecular understanding of T cell exhaustion and reveal new therapeutic targets for persisting infections and cancer.

Figure 1. Progressive development of T cell exhaustion

Upon infection, naive T cells are activated by antigen, co-stimulation and inflammation, and they exponentially proliferate to form effector populations^,. Whereas the majority of effector CD8⁺ T cells that express killer cell lectin-like receptor subfamily G member 1 (KLRG1) die during the contraction phase, a population of effector CD8⁺ T cells that retains CD127 expression can give rise to memory or exhausted CD8⁺ T cells. In the setting of acute infection, where antigen and/or inflammation is cleared, effector CD8⁺ T cells further differentiate into functional memory CD8⁺ T cells that can produce multiple cytokines (such as interferon-γ (IFNγ), tumour necrosis factor (TNF) and interleukin-2 (IL-2)) and mount robust recall responses upon secondary infection^,. These memory T cells are also maintained efficiently long term without antigen via IL-7- and IL-15-driven homeostatic self-renewal. By contrast, during chronic infection, antigen and inflammation persist after the effector phase. As infection progresses and T cell stimulation continues, T cells lose effector functions in a hierarchical manner and become exhausted. Typically, functions such as IL-2 production and cytokine polyfunctionality, as well as high proliferative capacity, are lost early; this is followed by defects in the production of IFNγ, TNF and chemokines, as well as in degranulation. T cell exhaustion is also accompanied by a progressive increase in the amount and diversity of inhibitory receptors that are expressed, including programmed cell death protein 1 (PD1), lymphocyte activation gene 3 protein (LAG3), 2B4, CD160 and T cell immunoreceptor with immunoglobulin and ITIM domains (TIGIT). Ultimately, if the severity or duration of the infection is high or prolonged, virus-specific T cells can be lost (‘deletion’). Variables — such as the level and number of inhibitory receptors expressed, strength of antigen stimulation, availability of CD4⁺ T cell help and the duration of infection — can all influence the severity of exhaustion. Exhausted T cell populations are heterogeneous, and subsets of T-bet^hi PD1^mid and EOMES^hi PD1^hi CD8⁺ exhausted T cells exist. Only the T-bet^hi PD1^mid subset is responsive to reinvigoration by blockade of the PD1 pathway. CXCR3, CXC-chemokine receptor 3; PDL1, PD1 ligand 1.

Figure 2. Overview of mechanisms of T cell exhaustion

Pathways implicated in regulating T cell exhaustion can be classified into three general categories (centre and inner circle): cell-to-cell signals including prolonged T cell receptor (TCR) engagement (signal 1) and co-stimulatory and/or co-inhibitory signals (signal 2); soluble factors such as excessive levels of inflammatory cytokines (for example, type I interferons (IFNs)) and suppressive cytokines including interleukin-10 (IL-10) and transforming growth factor-β (TGFβ); and tissue and microenvironmental influences driven by changes in the expression levels of chemokine receptors, adhesion molecules and nutrient receptors. This last class of influences may include altered tissue distribution and/or migratory patterns and lead to changes in pathways sensing oxygen tension (the von Hippel–Lindau tumour suppressor (VHL) and/or hypoxia-inducible factor (HIF) pathways), pH and nutrient levels. Tissue destruction and altered lymphoid organization may have a major role. Other immune cell types and stromal cells could be the source of many of these changes (outer circle). Cell types such as antigen-presenting cells (APCs), CD4⁺ T cells, natural killer (NK) cells, B cells and regulatory cells (for example, myeloid-derived suppressor cells (MDSCs) and regulatory T (T_Reg) cells) have been implicated in CD8⁺ T cell exhaustion. Overall, during chronic infections, cell-intrinsic and cell-extrinsic signals are probably integrated and thereby negatively influence T cell differentiation and promote exhaustion. The precise balance of these signals may determine the severity and/or qualitative aspects of T cell exhaustion in different disease settings. CTLA4, cytotoxic T lymphocyte antigen 4; DC, dendritic cell; FOXP3, forkhead box P3; LAG3, lymphocyte activation gene 3 protein; PD1, programmed cell death protein 1; T_H cell, T helper cell.

Figure 3. Molecular pathways of inhibitory receptors associated with T cell exhaustion

Ligand and receptor pairs for inhibitory pathways are depicted, showing the intracellular domains of receptors that contribute to T cell exhaustion. Many inhibitory receptors have immunoreceptor tyrosine-based inhibitory motifs (ITIMs) and/or immunoreceptor tyrosine-based switch motifs (ITSMs) in their intracellular domains; however, some receptors have specific motifs, such as YVKM for cytotoxic T lymphocyte antigen 4 (CTLA4) and KIEELE for lymphocyte activation gene 3 protein (LAG3). The molecular mechanisms of inhibitory receptor signalling are also illustrated and can be classified as: ectodomain competition (inhibitory receptors sequester target receptors or ligands); modulation of intracellular mediators (local and transient intracellular attenuation of positive signals from activating receptors such as T cell receptors and co-stimulatory receptors); and induction of inhibitory genes. Multiple inhibitory receptors are responsible for these three mechanisms. AP-1, activator protein 1; BAT3, HLA-B-associated transcript 3 (also known as BAG6); BTLA, B and T lymphocyte attenuator; CEACAM1, carcinoembryonic antigen-related cell adhesion molecule 1; GRB2, growth factor receptor-bound protein 2; HVEM, herpes virus entry mediator (also known as TNFRSF14); NFAT, nuclear factor of activated T cells; NF-κB, nuclear factor-κB; PD1, programmed cell death protein 1; PDL1, PD1 ligand 1; PI3K, phosphoinositide 3-kinase; PLCγ, phospholipase Cγ; TIGIT, T cell immunoreceptor with immunoglobulin and ITIM domains; TIM3, T cell immunoglobulin and mucin domain-containing protein 3.

Figure 4. Transcriptional and epigenetic mechanisms of T cell exhaustion

Altered usage of key transcription factors is associated with the altered transcriptional and developmental programme of T cell exhaustion. Several potential mechanisms exist. a | Different use of transcription factor binding partners is one potential mechanism for distinct context-dependent transcription factor activity. In the example shown, transcription factor B is closely associated with memory-related genes in the context of acute infection where transcription factor A is abundant (top panel). However, the same transcription factor B is linked with exhaustion-related genes in chronic infection (lower panel). Post-translational modifications of transcription factors and/or their subcellular localization may also be important in this setting. b | The dosage or concentration of a transcription factor could also provide a mechanism for context-dependent transcriptional function. Here, a transcription factor binds only at specific high-affinity binding sites if the amount of the factor is low (top panel). By contrast, at high transcription factor concentrations binding can occur more broadly (that is, occurring also at lower affinity sites), which leads to different transcriptional activity (lower panel). c | DNA methylation, histone modifications and the ‘chromatin landscape’ resulting from overall epigenetic regulation could provide a mechanism for context-specific transcription factor function in exhausted T cells (transcription factor X in this example). The enhancer landscape of a cell may determine how different transcription factors function.