From thymus to tissues and tumors: A review of T-cell biology

Abstract

T cells are critical orchestrators of the adaptive immune response that optimally eliminate a specific pathogen. Aberrant T-cell development and function are implicated in a broad range of human disease including immunodeficiencies, autoimmune diseases, and allergic diseases. Accordingly, therapies targeting T cells and their effector cytokines have markedly improved the care of patients with immune dysregulatory diseases. Newer discoveries concerning T-cell-mediated antitumor immunity and T-cell exhaustion have further prompted development of highly effective and novel treatment modalities for malignancies, including checkpoint inhibitors and antigen-reactive T cells. Recent discoveries are also uncovering the depth and variability of T-cell phenotypes: while T cells have long been described using a subset-based classification system, next-generation sequencing technologies suggest an astounding degree of complexity and heterogeneity at the single-cell level.

Keywords: CD4; CD8; T cells; adaptive immunity.

Figure 1:. T cell development.

T cell progenitors, or precursor cells, arrive in the thymus from the bone marrow. They lose multipotent potential and commit to the T cell lineage under control of Notch signaling and Bcl11b, Gata3, and TCF-1. These committed thymocytes subsequently recombine their T cell receptors (TCRs) under the control of RAG enzymes and DNA repair machinery to generate a diverse TCR repertoire. TCR recombination is followed by positive selection of T cells that recognize self-MHC:peptide complexes; this occurs in the thymic cortex and is mediated by thymic cortical epithelial cells. The thymocytes then migrate to the medulla where they are tested for reactivity against self-peptides-by medullary thymic epithelial cells; self-reactive T cells are negatively selected and deleted. Next, developing thymocytes differentiate into CD4⁺ vs. CD8⁺ T cells under the control of Runx3 (CD8⁺) or Gata3 and ThPOK (CD4⁺). A subset of CD4⁺ T cells develop in to FOXP3⁺ regulatory T cells (Treg), whereas the others mature into naïve T cells.

Figure 2.. T cell activation.

The T cell receptor (TCR) is a multi-protein complex in which αβ chains are noncovalently attached to CD3 proteins, whose cytoplasmic tails contain immunoreceptor tyrosine activation motifs (ITAMs). When TCRs are activated by peptide:MHC, a complex series of phosphorylation events ensues. First, CD4 and CD8 molecules recruit Lck, a kinase that phosphorylates the ITAMs on CD3 and TCRζ. This allows the ITAMs to recruit Zap70 kinase, which is also phosphorylated by Lck. Phosphorylated Zap70 then phosphorylates the adaptor protein LAT, which recruits various downstream signaling molecules.

Figure 3:. CD4⁺ subsets and heterogeneity.

The classical view of CD4⁺ differentiation holds that naïve T cells differentiate into distinct subsets under the control of subset-specific environmental signals and downstream transcription factors. In this view, T helper 1 (Th1) cells express T-bet and produce interferon gamma (IFN-γ) whereas Th2 cells express Gata3 produce IL-4, IL-5, and IL-13. Th17 cells express RORγt and produce IL-17-family cytokines, Th9 cells express PU.1 and produce IL-9, and Th22 cells produce IL-22. Peripherally derived regulatory T cells promote immune tolerance, whereas T follicular helper (Tfh) cells are critical for B cell responses. In many cases subsets can by identified by the expression of specific cell surface markers; for example, CXCR3 marks Th1 cells while CCR6 marks Th17 cells. However, single cell technologies reveal that there is substantial overlap and heterogeneity between these different subsets in vivo.

Figure 4.. CD8⁺ subsets and heterogeneity.

CD8⁺ cells comprise several subsets. These include effector memory CD8⁺ T cells, which promote early immune responses; long-lived central memory CD8⁺ cells, which prevent reinfection; and resident memory CD8⁺ T cells, which reside in mucosal tissues and prevent influx of pathogens. Effector memory T cells are described to have several of their own subgroups, analogous to CD4⁺ helper subsets. Tc1 are analogous to Th1 and produce IFN-γ, Tc2 are analogous to Th2 and produce type 2 cytokines, Tc9 are analogous to Th9 and produce IL-9, Tc17 are analogous to Th17 and produce IL-17A, and Tc22 are analogous to Th22 and produce IL-22. In vivo, CD8⁺ T cells are characterized by a large amount of heterogeneity and overlap between these various subsets, with specific clones potentially co-expressing elements of multiple different subsets. This complexity is illustrated by single cell transcriptomic analyses.

Figure 5.. T cell metabolism.

Naïve T cells have relatively low metabolic demands and primarily rely on oxidative phosphorylation, whereas activated and proliferating T cells depend upon glycolysis and glutaminolysis. These metabolic shifts are accompanied by mitochondrial remodeling, which also plays a role in T cell exhaustion and antitumor immunity. Metabolic pathways are extensively targeted by disease-modifying drugs to treat immune-dysregulatory disease. Rapamycin (sirolimus) targets mechanistic Target of Rapamycin (mTOR), which is activated ty T cell receptor (TCR) stimulation and proliferation-inducing cytokines like IL (interleukin) −2 and IL-7. In environments with limited glucose availability, AMP protein kinase (AMPK) inhibits mTOR, pushing T cells towards quiescence and a memory phenotype

Figure 6.. T cell epigenetics.

Chromatin remodeling is a major requirement for regulation of gene expression and involves the architectural transition from an inactive/repressed state to an open/accessible state. Within accessible areas of chromatin, genes can be found in association with noncoding regulatory elements (REs) including promoters – located in proximity to the transcriptional start site (TSS) – and enhancers, which are distal to the TSS. Enhancers can directly interact with target genes by forming transcriptionally active loops, can recruit transcriptional modifiers, or can be transcribed to noncoding regulatory RNAs that have various regulatory roles. As an example, the extended type 2 locus is shown. This includes the Il4, Il13, Rad50, and Il5 genes as well as multiple noncoding regulatory elements that are open/accessible when the genes are open/poised for transcription.