Transcriptional and post-transcriptional control of T cell function

Transcriptional regulatory mechanisms

Differentiation of naïve CD4+ T cells into different helper subtypes allows tailoring of the immune response to different pathogens and to cancer. However, abnormal patterns of T cell polarization can lead to autoimmune and inflammatory diseases or allergies, and T cell dysfunction limits the immune response to cancer. 

Th1 and Th2 cells represent the archetypal CD4+ T cell lineages and their differentiation is determined by the transcription factors T-bet and GATA3, respectively. T-bet directly activates the Th1 signature cytokine interferon gamma (IFNG) and represses the Th2 cytokines IL4, IL5 and IL13, while GATA3 displays the opposite functionality. We have extended this knowledge of T-bet and GATA3 function across the genome by showing that the proteins bind cis-regulatory regions at a key set of immune regulatory genes (Kanhere et al., 2012; Gokmen et al., 2013; Henderson et al., 2021). We have also found that T-bet binding to its target genes is disrupted by genetic variants that are associated with inflammatory disease suggesting that alterations in T-bet function may be a causative factor in these cases (Soderquest et al., 2017).

We are also investigating the mechanisms through which T-bet activates Th1 gene expression. We have found that T-bet activates genes through recruitment of the elongation factor P-TEFb (Hertweck et al., 2016; Figure 1), that CDK9 inhibitors that block P-TEFb function abrogate Th1-mediated inflammatory disease (Hertweck et al., 2016; Omer et al., 2022), and that T-bet represses the alternative Th2 cell fate by redistributing GATA3 from Th2 genes to T-bet binding sites. These studies provide new opportunities to direct T cell fate in disease treatment.

Post-transcriptional regulatory mechanisms

We have extended our studies on the regulation of T cell effector function to tumour-infiltrating T cells. T cells in tumours are often dysfunctional due to chronic stimulation and an immunosuppressive environment. Treatments that enhance anti-tumour immunity, including checkpoint inhibitors and adoptive cell therapies, have revolutionised cancer therapy but unfortunately many patients do not respond. Cytotoxic CD4+ T cells hold promise as a therapeutic modality but how their activity is regulated remains poorly understood. 

We have found that the anti-tumour activity of cytotoxic CD4+ T cells is primarily controlled at the post-transcriptional level. In untreated tumours, cytotoxic T cells exist in a poised but inactive state that is characterised by the presence of granzyme B (GzmB) mRNA but not protein. We’ve further shown that this post-transcriptional regulatory checkpoint is mediated by the RNA binding proteins ZFP36 and ZFP36L1. ZFP36L1 downregulation is necessary for the induction of GzmB protein production and control of tumour growth that is driven by checkpoint inhibitor therapies. Reciprocally, knockout of Zfp36 and Zfp36l1 is sufficient to induce GzmB protein production by T cells in tumours and extends mouse survival. Our work demonstrates the key role played by post-transcriptional processes in the regulation of tumour immunity and highlights the potential therapeutic utility of targeting these mechanisms for the treatment of cancer.

A two-step model for acquisition of cytotoxic activity by tumor-infiltrating CD4+ T cells.

In untreated tumors CD4+ TEFF acquire a cytotoxic gene expression program, which is regulated by the Blimp-1-Bcl6 axis in response to type-I IFN signals. However, GzmB protein production is blocked by ZFP36 and ZFP36L1. Anti-CTLA-4-mediated TREG depletion or LAG-3/PD-1 blockade downregulate Zfp36l1, releasing the block to GzmB protein production and reduces tumor growth.