RNA Metabolism in T Lymphocytes

Abstract

RNA metabolism plays a central role in regulating of T cell-mediated immunity. RNA processing, modifications, and regulations of RNA decay influence the tight and rapid regulation of gene expression during T cell phase transition. Thymic selection, quiescence maintenance, activation, differentiation, and effector functions of T cells are dependent on selective RNA modulations. Recent technical improvements have unveiled the complex crosstalk between RNAs and T cells. Moreover, resting T cells contain large amounts of untranslated mRNAs, implying that the regulation of RNA metabolism might be a key step in controlling gene expression. Considering the immunological significance of T cells for disease treatment, an understanding of RNA metabolism in T cells could provide new directions in harnessing T cells for therapeutic implications.

Keywords: Cellular; Immunity; RNA; RNA metabolism; T-lymphocytes.

Figure 1. The life cycle of conventional T cells. T cells are produced in the bone marrow and mature into thymocytes in the thymus. In the early stage of T cell development, which is called the DN stage, they lack CD4 and CD8 coreceptors. This stage is divided into 4 sub-phases (DN1, DN2, DN3, and DN4) according to the surface expression of CD44 and CD25. During the DN3 phase, thymocytes undergo TCRβ rearrangement, known as ‘β-selection.’ As they express both CD4 and CD8, they become DP thymocytes. Positive selection occurs in the DP stage, which selectively removes thymocytes that are incapable of binding to MHC molecules. Thymocytes differentiate into CD4 or CD8 SP thymocytes depending on the recognition of peptides presented on MHC-I or MHC-II molecules. Subsequently, SP thymocytes undergo negative selection, leading to apoptosis upon strong interaction with self-antigens. Thymocytes that pass through these processes become naive T cells and circulate in the body. Upon cognate antigen stimulation and various cytokine signals, they are activated and differentiate into effector T cells. CD4 T cells differentiate into T_FH, Th1, Th2, Th17, and T_reg cells with expression of their master transcription factors, Bcl-6, T-bet, GATA-3, Rorγt, and Foxp3, respectively. Activated CD8 T cells have a cytotoxic effect and induce apoptosis in virus-infected or cancer cells. After playing an effector function, most effector T cells undergo apoptotic death, but a few survive and become memory T cells, responsible for the secondary immune response.

Figure 2. Imbalance between transcription and translation in quiescence and activation. During the transition between quiescence and activation, activated T cells become highly proliferative and increase in both size and internal mass. These processes require many proteins to support cell growth. During the early stage of T cell activation, the increase in transcription rates and corresponding RNA copy numbers are insufficient to explain such massive protein synthesis. The quantity of available ribosomal machinery is similar in quiescent and activated T cells, indicating translational preparedness in resting T cells in the presence of idling ribosomes. Imbalanced transcriptional and translational processes suggest that RNA level regulation might be a rate-limiting step for gene expression in the early stages of T cell activation, highlighting the significant role of RNA metabolism.

Figure 3. Dynamics of RNA metabolism in T cells. RNA metabolism affects T cell function throughout their life cycle. During the developmental phase, several genes, such as such as Lef-1, Il27ra, and Irf7, which play a critical role in thymocyte maturation, are processed by splicing factors, CELF2, SRSF1, and FOXA1/2. p53 mRNA stabilized by ELAVL1 supports thymocyte proliferation, whereas ZFP36L1/2 mediated Notch-1 mRNA decay secures thymocyte selection by limiting uncontrolled proliferation. The CNOT complex, which has de-adenylase activity, degrades mRNAs by shortening poly(A) tails at the 3'-end. BTG1 and BTG2 cooperate with the CNOT complex to maintain quiescence of resting (naive) T cells by degrading global mRNAs, leading to a poised status. Distinct splicing patterns in resting T cells, which contain LINE1 in mRNAs, suppress the corresponding gene expression. T cell activation affects the exon skipping or inclusion processes driven by CELF2 or HNRNP U, which generates binding sites containing MKK7 or full-length MALT1A. m⁶A modification of inhibitory Socs family mRNAs by the m⁶A writer, METTL3, facilitates mRNA decay by enhancing IL-7R/JAK/STAT5 signaling. In contrast, ALKBH5, an m⁶A eraser, inhibits the degradation of Ifng and Cxcl2 mRNAs by removing m⁶A marks upon T cell activation. Splicing factor U2AF2 is involved in the optimal expression of CD62L and CD25. A low degree of TCR signaling stimulates the splicing factor HNRNP L/A1, forming a CD3ζ variant that lacks one of the ITAMs. ELAVL1 enhances the mRNA stability of various effector molecules such as IL-4, IL-13, IL-17, CD25, and OX40. Excessive effector functions are inhibited by selective mRNA decay. ZFP36L1/2 and ROQUIN recruit the CNOT complex and degrades Ifng and Icos mRNA, respectively. Endonuclease activity by REGNASE-1 also contributes to controlling the abundance of mRNAs from inflammatory genes.

ITAM, immunoreceptor tyrosine-based activation motif.