The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia;
Blood. 2013 Oct 17;122(16):2823-36. doi: 10.1182/blood-2013-02-481788. Epub 2013 Aug 23.
Regulatory T cells (Treg) prevent the emergence of autoimmune disease. Prototypic natural Treg (nTreg) can be reliably identified by demethylation at the Forkhead-box P3 (FOXP3) locus. To explore the methylation landscape of nTreg, we analyzed genome-wide methylation in human naive nTreg (rTreg) and conventional naive CD4(+) T cells (Naive). We detected 2315 differentially methylated cytosine-guanosine dinucleotides (CpGs) between these 2 cell types, many of which clustered into 127 regions of differential methylation (RDMs). Activation changed the methylation status of 466 CpGs and 18 RDMs in Naive but did not alter DNA methylation in rTreg. Gene-set testing of the 127 RDMs showed that promoter methylation and gene expression were reciprocally related. RDMs were enriched for putative FOXP3-binding motifs. Moreover, CpGs within known FOXP3-binding regions in the genome were hypomethylated. In support of the view that methylation limits access of FOXP3 to its DNA targets, we showed that increased expression of the immune suppressive receptor T-cell immunoglobulin and immunoreceptor tyrosine-based inhibitory motif domain (TIGIT), which delineated Treg from activated effector T cells, was associated with hypomethylation and FOXP3 binding at the TIGIT locus. Differential methylation analysis provides insight into previously undefined human Treg signature genes and their mode of regulation.
调节性 T 细胞（Treg）可预防自身免疫性疾病的发生。典型的天然调节性 T 细胞（nTreg）可以通过 Forkhead-box P3（FOXP3）基因座的去甲基化来可靠识别。为了探索 nTreg 的甲基化图谱，我们分析了人类幼稚 nTreg（rTreg）和常规幼稚 CD4（+）T 细胞（Naive）的全基因组甲基化。我们在这 2 种细胞类型之间检测到 2315 个差异甲基化的胞嘧啶-鸟嘌呤二核苷酸（CpG），其中许多聚集在 127 个差异甲基化区域（RDMs）中。激活改变了 Naive 中的 466 个 CpG 和 18 个 RDM 的甲基化状态，但没有改变 rTreg 中的 DNA 甲基化。对 127 个 RDM 的基因集测试表明，启动子甲基化和基因表达呈相互关联。RDMs 富含潜在的 FOXP3 结合基序。此外，基因组中已知 FOXP3 结合区域内的 CpG 被低甲基化。为了支持甲基化限制 FOXP3 与其 DNA 靶标结合的观点，我们表明，免疫抑制受体 T 细胞免疫球蛋白和免疫受体酪氨酸基抑制基序域（TIGIT）的表达增加，将 Treg 与激活的效应 T 细胞区分开来，与 TIGIT 基因座的低甲基化和 FOXP3 结合相关。差异甲基化分析为以前未定义的人类 Treg 特征基因及其调控模式提供了深入了解。
