Transcriptional and epigenetic basis of Treg cell development and function: its genetic anomalies or variations in autoimmune diseases

Abstract

Naturally arising regulatory CD4⁺ T (Treg) cells, which specifically express the transcription factor FoxP3 in the nucleus and CD25 and CTLA-4 on the cell surface, are a T-cell subpopulation specialized for immune suppression, playing a key role in maintaining immunological self-tolerance and homeostasis. FoxP3 is required for Treg function, especially for its suppressive activity. However, FoxP3 expression per se is not necessary for Treg cell lineage commitment in the thymus and insufficient for full Treg-type gene expression in mature Treg cells. It is Treg-specific epigenetic changes such as CpG demethylation and histone modification that can confer a stable and heritable pattern of Treg type gene expression on developing Treg cells in a FoxP3-independent manner. Anomalies in the formation of Treg-specific epigenome, in particular, Treg-specific super-enhancers, which largely include Treg-specific DNA demethylated regions, are indeed able to cause autoimmune diseases in rodents. Furthermore, in humans, single nucleotide polymorphisms in Treg-specific DNA demethylated regions associated with Treg signature genes, such as IL2RA (CD25) and CTLA4, can affect the development and function of naïve Treg cells rather than effector T cells. Such genetic variations are therefore causative of polygenic common autoimmune diseases including type 1 diabetes and rheumatoid arthritis via affecting endogenous natural Treg cells. These findings on the transcription factor network with FoxP3 at a key position as well as Treg-specific epigenetic landscape facilitate our understanding of Treg cell development and function, and can be exploited to prepare functionally stable FoxP3-expressing Treg cells from antigen-specific conventional T cells to treat autoimmune diseases.

Fig. 1. Expression of Treg-associated genes along Treg differentiation in the thymus.

a Schematic representation of the developmental paths of Treg cells. DN: double negative T cells, DP: double positive T cells, imCD4SP: immature CD4 single positive T cells, Prec: Treg precursor cells, tTreg: thymic Treg cells, Tconv: conventional T cells. b The gene expression profile of the Treg-associated genes based on the deposited RNA-seq data. Relative expression level of each gene at each developmental stage is shown.

Fig. 2. Treg-specific super-enhancers controlling Treg-specific transcription and epigenetic changes.

a Super enhancers (SEs) defined as genomic regions with dense clustering of highly active enhancers accompanying strong activation-linked histone modification (such H3K27ac), promoted open chromatin states, strong binding of multiple transcription factors, and increased DNA demethylation. They contribute to the cell-type specific gene expression and cell lineage determination. b Treg-specific SEs are associated with Treg signature genes.

Fig. 3. Establishment of Treg-specific super-enhancers along Treg differentiation in the thymus.

a Developmental events in the genome along tTreg differentiation. Satb1: Satb1 expression, Histone modif: Treg-type histone modifications, SE: Treg-specific super-enhancers, DNAdemethyl: Treg-specific DNA demethylation, FoxP3 exp: FoxP3 expression. b Developmental changes in Satb1-binding and H3K27ac modification. The super-enhancer region at the Foxp3 gene locus is indicated by bar.

Fig. 4. Treg-SEs control Treg-specific gene transcription and epigenetic changes in developing Treg cells.

Treg cell development requires both the induction of Treg-specific epigenome and the establishment of Treg-type transcription networks including FoxP3 at a key position.

Fig. 5. Location of autoimmune SNPs at Treg-DRs specific for naïve Treg cells.

Characterization of specific demethylated regions in the genome of naïve or activated Treg or Tconv cells reveals that SNPs associated with autoimmune disease (e.g., SNPs found at IL2RA or CTLA4 gene loci) are predominantly present at naïve Treg-specific DRs. Black and white circles represent methylated and demethylated CpGs, respectively.