A multiply redundant genetic switch ‘ locks in ’ the transcriptional signature of regulatory T cells

Regulatory T cells (Treg cells) have a key role in immunological homeo­ stasis, control autoimmune deviation, prevent runaway responses to microbes or allergens and regulate certain nonimmunological functions1,2. Most Treg cells differentiate in the thymus as a rescue pathway for cells that express a self­reactive T cell antigen receptor (TCR)3, but some also differentiate in peripheral organs in response to chronic challenges such as commensal bacteria4. Phenotypic stability is an important consideration for Treg cells, as the self­reactivity of their TCRs makes it important for their suppressive phenotype to be stable, lest they convert into aggressive effector cells. Support for the idea of Treg cell instability, and for the proposal that Treg cells turned into aggressive effector cells by the loss of the Forkhead­family tran­ scription factor Foxp3 have a role in autoimmune diseases, stemmed from results obtained by transfer of Treg cells into alymphoid hosts5–7 and from lineage­tracing experiments that relied on continuously active Foxp3­driven transgenes encoding Cre recombinase8. However, those results have been largely refuted by the observation that Treg cells transferred into normal hosts are stable for long periods of time and by lineage­tracing experiments done in pulse­chase mode with a tamoxifen­controlled Cre recombinase system9. Thus, with the excep­ tion of effector cells that transiently express Foxp3 after activation10, the phenotype of committed Treg cells seems very stable over time9. Treg cell function is underwritten by a canonical ‘Treg cell signa­ ture’, a set of transcripts that are over­ or underexpressed in Treg cells relative to their expression in the CD4+ conventional T cell (Tconv cell) counterparts of the Treg cells11,12. This signature is estab­ lished very early during Treg cell differentiation11, and the genes encode proteins with a range of cellular locations and several molecular medi­ ators of Treg cell action13. Foxp3 is essential for the specification and maintenance of Treg cells, as shown by the lethal lymphoproliferation and multiorgan autoimmunity that develop in its absence in scurfy mutant mice or in patients with the immunological disorder IPEX syndrome (immune dysregulation, polyendocrinopathy, enteropathy, X­linked)14, and plays an important part in determining the Treg cell signature11,15,16. Foxp3 was initially considered the ‘master regula­ tor’ of Treg cells, but a more nuanced view has since emerged. Cells with many Treg cell characteristics, including a transcriptionally active Foxp3 locus (Treg cell–like cells), can differentiate in the absence of Foxp3, albeit in lower numbers and with less stability17,18, and per­ haps some patients with IPEX19. A segment of the Treg cell signature can also be elicited in transforming growth factor­β (TGF­β)­induced Treg cells derived from CD4+ T cells of scurfy mice11. Conversely, the transduction of FOXP3 or its induction by TGF­β are not sufficient to elicit the full Treg cell signature11,20. Many other transcription factors have been reported to interact with Foxp3 and to promote Treg cell function. These include factors from a variety of families, and physical or functional interactions have been demonstrated for Runx1, NFAT, Eos, phosphorylated STAT3,