Deciphering the developmental trajectory of tissue-resident Foxp3+ regulatory T cells

Abstract

Foxp3⁺ T_REG cells have been at the focus of intense investigation for their recognized roles in preventing autoimmunity, facilitating tissue recuperation following injury, and orchestrating a tolerance to innocuous non-self-antigens. To perform these critical tasks, T_REG cells undergo deep epigenetic, transcriptional, and post-transcriptional changes that allow them to adapt to conditions found in tissues both at steady-state and during inflammation. The path leading T_REG cells to express these tissue-specialized phenotypes begins during thymic development, and is further driven by epigenetic and transcriptional modifications following TCR engagement and polarizing signals in the periphery. However, this process is highly regulated and requires T_REG cells to adopt strategies to avoid losing their regulatory program altogether. Here, we review the origins of tissue-resident T_REG cells, from their thymic and peripheral development to the transcriptional regulators involved in their tissue residency program. In addition, we discuss the distinct signalling pathways that engage the inflammatory adaptation of tissue-resident T_REG cells, and how they relate to their ability to recognize tissue and pathogen-derived danger signals.

Keywords: Foxp3 + eTREG cells; TREG development; inflammation; mucosal immunity; polarization; tissue residency; transcriptional adaptation.

Figure 1

The developmental trajectory of tissue-resident T_REG cells involves a series of events starting from thymic selection to peripheral TCR engagement. In this figure, the trajectory of peripheral regulatory T (T_REG) cells is depicted, as currently defined by recent multi-omics approaches conducted in various lymphoid and non-lymphoid tissues. During thymic selection, precursor regulatory T cells (T_REGP) expressing self-reactive T-cell receptors (TCR) give rise to a pool of naive CD45RA⁺CCR7^hi regulatory T cells (T_REG). Once in circulation, these T_REG cells encounter their specific antigen, triggering an activation cascade that results in a metabolic shift and chromatin remodeling. Subsequently, CD45RO⁺CD69^hi effector regulatory T cells (eT_REG) can either stay in lymph nodes as central memory (cmT_REG) or migrate to tissues, where they become tissue-resident (TR-T_REG) or effector memory regulatory T cells (emT_REG). While thymic-derived TR-T_REG cells comprise a large portion of T_REG cells in tissues, T_REG located in the gut, for example, include peripherally-induced regulatory T cells (pT_REG). The absence of clear markers poses a challenge in distinguishing between these two populations in situ. In addition, while TR-T_REG cells isolated from various tissues typically display a conserved phenotype marked by the expression of ICOS, ST2, Helios, and GATA3, a significant portion of T_REG cells in the gut exhibit a distinctive RORγT-driven phenotype. Interestingly, there is cumulating evidence that T_REG cells lacking Helios expression may be more driven to express RORγT, suggesting a possible segregation between TR-T_REG cells derived from the thymus or induced in the periphery.

Figure 2

The acquisition of a tissue-resident program requires a series of epigenetic and transcriptional changes that involve modulation of Foxp3 expression or activity. After thymic egress into the periphery, T_REG cells are TCR-activated by self or non-self-antigens, and undergo a series of epigenetic and transcriptional changes that guide their maturation into TR-T_REG cells. While not entirely understood, this process seems to happen in a step-wise manner. First, TCR-engaged T_REG cells upregulate key transcriptional programs in part driven by the transcription factor BATF, which, in conjunction with Foxp3, promotes the accessibility of Foxp3 and expression of BATF-driven genes including Ctla4, Icos, Gata3, Irf4. Key to the stability of their epigenetic landscape, T_REG cells require Dnmt1 and its partner Uhrf1 to promote the methylation of CpG-rich regions and control the accessibility to inflammatory genes, including Ifng, Il6, Il12, Il17a, Il22, Ccr1, Cxcr6, Runx2 and Stat3. Finally, Foxp3 partners with Lef1 to promote the expression of genes involved in its core program, including Foxp3, Il2ra and Tgfb1, and also with TCF1 to suppress the expression of genes associated with inflammation like Il6ra, Ifngr2 and Stat3. Importantly, BATF and IRF4 can, in turn, suppress Foxp3 expression, a process that, while not fully understood, may enable the temporal accessibility of genes normally repressed by FoxP3. Once in the tissue, BATF enables the continued suppression of genes like Rorc (RORγT), Il6ra and Stat3. GATA3 promotes the transcription of Foxp3, but may be further involved in the expression of other GATA3-associated genes, like Il1rl1(ST2). IRF4 is also required for the expression of core TR-T_REG genes, including Icos, Il1rl1 and Il10. Moreover, there is evidence that Lef1 and Tcf7 (TCF1) mRNA expression are significantly decreased in TR-T_REG cells, suggesting they are no longer required. Finally, BLIMP-1 expression is increased, and can actively inhibit the action of Dnmt3a, promoting the accessibility of key genes in T_REG cells such as Foxp3. Consistently, murine models with Foxp3-conditional deletion of BATF, GATA3, IRF4, TCF1 and BLIMP-1 reveal how critical these regulators are for the function of TR-T_REG cells.

Figure 3

Specific inflammatory signals alter the trajectory of T_REG cells in non-lymphoid sites by engaging specialized programs prior and during their migration to inflamed tissues. During active inflammation, the presence of cytokines such as IFNγ, IL-2, IL-6, and TGF-β can divert the differentiation of T_REG cells to adopt helper-like phenotypes, allowing them to migrate to specific sites of inflammation alongside conventional T cells. Importantly, by acquiring these master transcription factors, effector T_REG cells (eT_REG) become responsive to signals provided by IL-12, IL-4 or IL-23. While these cytokines further promote the transcriptional program engaged by these specialized T_REG cells, they can ultimately diminish their suppressive functions and allow them them to contribute to inflammation as exT_REG cells. Importantly, it remains to be determined if the resulting population of emT_REG cells in the tissue after inflammation acquire a residency program that lead them to form part of the TR-T_REG cell population.