How RNA binding proteins control effector T cell responses

T cell responses rely on the T cell receptor (TCR) for antigen specificity, CD28 for a second signal, and a cadre of additional signals including cytokines and certain TNF superfamily costimulatory receptors. The latter includes CD134 (OX40) and CD137 (4-1BB), which provide a powerful boost to clonal expansion of effector

CD8 T cells, robust cytokine production, metabolic fitness, and many other attributes including potent anti- tumor cytotoxicity. The molecular mechanism of costimulation-based programming in effector T cells is largely unknown. In particular, a unique gene signature for this process, beyond generalized factors such as NFKB

and NFAT, is unclear suggesting that other critical processes have gone undetected. Our recent published data showed only a small number of transcriptional changes after costimulation, which could not explain the power behind costimulation. A major increase, however, in the spliceosome pathway was evident, but whether

this process could have a specific impact on effector T cells was unknown. Analysis showed that the spliceosome pathway contained a group of RNA binding proteins involved in alternative RNA splicing, which should not be confused with steady state core intron splicing factors. Alternative RNA splicing can mediate

exon skipping, intron retention and other processes that generate multiple mRNA isoforms from a single gene, and thereby greatly expand the proteome of cells. We demonstrated that the RNA binding protein Tardbp played a key role in effector T cell function. These changes in T cell function correlated with Tardbp-dependent

exon skipping in the IL-2 repressor IKAROS (Ikzf1) mRNA, and a series of other RNA splicing events that remain to be studied. Aim 1 will examine how Tardbp programs effector CD8 T cell function by addressing effector activities that include target cell cytotoxicity, responses to infection, and a role for specific

costimulators. Our results will be integrated with the identification of the direct mRNA isoforms generated by Tardbp, and their potential function. Aim 2 will examine a second RNA binding protein, Tra2b, for its novel role in controlling T cell responses through the action of an ultra-conserved ‘poison exon’ contained within the

Tra2b transcript. Using a combination of innovative approaches, we will test if Tra2b’s poison exon impacts TCR sensitivity in CD8 and CD4 T cells during tumor immunity. For Aim 3, the RNA binding protein network in exhausted T cells will be edited to optimize function and translatability. Our proposal uses a combination

of in silico and cutting-edge methods that will break new ground in understanding how alternative splicing through the action of RNA binding proteins can control effector T cell programming. In sum, a new understanding of effector T cells and their potential in clinical translation will be gained from this research.