N⁶-adenosine methylation (m⁶A) is involved in the life and death decisions of T cells

N⁶-adenosine methylation (m⁶A) is the most abundant modification observed in mRNA transcripts. It is a dynamic modification that is performed by members of the so-called writer complex (including Wtap, Virma and Mettl3) and that can be removed by so-called eraser proteins [1]. In addition, m⁶A is recognized by reader proteins (including Ythdf2) that can exert a response. Readers and m⁶A can modify virtually all mRNA processes, including RNA splicing, secondary structures, nuclear export and transcript stability [1]. The functional relevance of m⁶A-mediated regulation in specific cell types and treatment conditions remains only partly understood. In T cells, earlier studies have demonstrated a relevant role for m⁶A in T effector (T_eff), T follicular helper (T_FH) and T regulatory (T_reg) cells through manipulation of m⁶A pathway genes in mice [2–6]. In these studies, disruption of m⁶A resulted in dysregulation of gene expression patterns and caused colitis and systemic autoinflammatory disease. In a recent study by Ito-Kureha et al., the authors set out to further understand how m⁶A signaling affects T-cell functions by manipulating Wtap in select T cells with a murine knockout model [7]. They found that m⁶A signaling controls many aspects of T-cell immunobiology: activation, proliferation, life, and death.

The researchers first assessed the role of Wtap in T cells. Therefore, Ito-Kureha et al. developed an elegant Cre-conditional Wtap knockout mouse model. In this model, Wtap was knocked out in either (nearly) all T cells (CD4-Cre) or in T_reg cells specifically (Foxp3-Cre) [7]. The Wtap knockout in all T cells resulted in a colitis phenotype in line with earlier observations [5]. T_reg-specific knockout showed increased expression of RORgt and IL-17a in T_reg cells and associated systemic inflammation. Several experiments have shown that Wtap is involved in TCR signaling and the response to activation. In Wtap^−/− T cells, the authors reported altered thymocyte differentiation patterns and T_reg induction, a reduced proliferative response to lymphopenia, and increased activation and cell death after CD3/CD28 stimulation. These results indicate a regulatory role for Wtap in TCR signaling, as well as a role in regulating cell death in activated proliferating T cells.

The effects of Wtap deficiency were shown to be similar in the Virma and Mettl3 knockout models, indicating that they were the result of changes in m⁶A signaling and not the m⁶A-independent effect of Wtap. To unravel at the transcriptomic level what function Wtap has in T cells, Ito-Kureha et al. examined differential gene expression in Wtap^−/− T cells followed by gene network analysis. Only upregulated gene networks were observed, consistent with the general destabilizing effect of m⁶A on mRNA through degradation by YTHDF1-3 reader proteins [8]. However, indirect effects were possible, and not every m⁶A was recognized by YTHDF1-3; therefore, CLIP analyses were performed to pinpoint transcripts that were both N⁶-adenosine methylated (m⁶A) and recognized by YTHDF2. Among the differentially expressed gene transcripts that had m⁶A positions and that were YTHDF2 recognized, Orai1 and Ripk1 were selected for validation and follow-up because of their proapoptotic functions. Wtap was shown to control the downregulation of Orai1 and Ripk1 and to be important for decreased cell death in combination with TCR signaling in T cells.

Overall, Ito-Kureha et al. have shown that m⁶A signaling plays an important role in the immunobiology of T cells. m⁶A signaling affects differentiation, TCR and Ca²⁺ signaling, proliferation, and survival. Even though their study focuses on Wtap, for which they developed the elegant Cre-conditional knockout mouse model, the importance of m⁶A signaling underlies the Wtap^−/− associated phenotypes and was phenocopied in knockout models of other m⁶A pathway genes. To precisely determine how processes such as TCR signaling, proliferation and cell death are regulated by m⁶A signaling remains difficult to elucidate, as such processes affect each other. Another outstanding question is whether Wtap and m⁶A signaling play a similar role in human T cells and in the event of T-cell activation. Precise spatiotemporal measurements of m⁶A signaling could shed light on these questions. Novel techniques to probe m⁶A-edited positions with single-cell or single-molecule resolution, such as DART-seq [9] or third-generation RNA sequencing [10], could prove important to advance the field in this direction. In addition, the regulation of immune processes in other immune cell types by m6A will be of great interest. The precise understanding of m⁶A signaling in immunobiology could open up new avenues for clinical intervention in immune-related diseases or for immunotherapy.

Competing interests

The authors declare no competing interests.