DNA demethylation in the human <i>FOXP3</i> locus discriminates regulatory T cells from activated FOXP3⁺ conventional T cells

TLDR

FOXP3 is essential for regulatory T cell development and function, its abundance protects against autoimmunity and allergy while serving as a negative prognostic marker in solid tumors, yet transient FOXP3 expression also occurs in activated conventional T cells. The study aimed to determine whether a broader set of genes is epigenetically imprinted in the Treg lineage. To address this, the authors performed a genome‑wide differential methylation hybridization analysis. They found that DNA demethylation of the FOXP3 locus occurs exclusively in Treg, is absent in activated conventional CD4⁺ T cells and TGF‑β‑treated cells, persists in stable Treg after expansion, and that no other gene showed Treg‑specific demethylation, establishing FOXP3 DNA demethylation as the most reliable marker for natural Treg.

Abstract

Abstract The transcription factor FOXP3 is critical for development and function of regulatory T cells (Treg). Their number and functioning appears to be crucial in the prevention of autoimmunity and allergy, but also to be a negative prognostic marker for various solid tumors. Although expression of the transcription factor FOXP3 currently constitutes the best‐known marker for Treg, in humans, transient expression is also observed in activated non‐Treg. Extending our recent findings for the murine foxp3 locus, we observed epigenetic modification of several regions in the human FOXP3 locus exclusively occurring in Treg. Importantly, activated conventional CD4 + T cells and TGF‐β‐treated cells displayed no FOXP3 DNA demethylation despite expression of FOXP3, whereas subsets of Treg stable even upon extended in vitro expansion remained demethylated. To investigate whether a whole set of genes might be epigenetically imprinted in the Treg lineage, we conducted a genome‐wide differential methylation hybridization analysis. Several genes were found displaying differential methylation between Treg and conventional T cells, but none beside FOXP3 turned out to be entirely specific to Treg when tested on a broad panel of cells and tissues. We conclude that FOXP3 DNA demethylation constitutes the most reliable criterion for natural Treg available at present.