Maintenance DNA methylation is essential for regulatory T cell development and stability of suppressive function
Kathryn A. Helmin, … , Samuel E. Weinberg, Benjamin D. Singer
Kathryn A. Helmin, … , Samuel E. Weinberg, Benjamin D. Singer
Published September 8, 2020
Citation Information: J Clin Invest. 2020;130(12):6571-6587. https://doi.org/10.1172/JCI137712.
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Research Article Autoimmunity Immunology

Maintenance DNA methylation is essential for regulatory T cell development and stability of suppressive function

Abstract

Tregs require Foxp3 expression and induction of a specific DNA hypomethylation signature during development, after which Tregs persist as a self-renewing population that regulates immune system activation. Whether maintenance DNA methylation is required for Treg lineage development and stability and how methylation patterns are maintained during lineage self-renewal remain unclear. Here, we demonstrate that the epigenetic regulator ubiquitin-like with plant homeodomain and RING finger domains 1 (Uhrf1) is essential for maintenance of methyl-DNA marks that stabilize Treg cellular identity by repressing effector T cell transcriptional programs. Constitutive and induced deficiency of Uhrf1 within Foxp3+ cells resulted in global yet nonuniform loss of DNA methylation, derepression of inflammatory transcriptional programs, destabilization of the Treg lineage, and spontaneous inflammation. These findings support a paradigm in which maintenance DNA methylation is required in distinct regions of the Treg genome for both lineage establishment and stability of identity and suppressive function.

Authors

Kathryn A. Helmin, Luisa Morales-Nebreda, Manuel A. Torres Acosta, Kishore R. Anekalla, Shang-Yang Chen, Hiam Abdala-Valencia, Yuliya Politanska, Paul Cheresh, Mahzad Akbarpour, Elizabeth M. Steinert, Samuel E. Weinberg, Benjamin D. Singer

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Figure 7

Altered DNA methylation patterns explain the transcriptional reprogramming of Uhrf1-deficient Treg and ex-Foxp3 cells.

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Altered DNA methylation patterns explain the transcriptional reprogrammi...
(A) Principal component analysis of 202,525 differentially methylated CpGs with an FDR q < 0.05. Ellipses represent normal contour lines with 1 SD probability. (B) Cumulative distribution function plot of differentially methylated CpGs. (C) CpG methylation at 17,249 DMRs within 5 kb of gene bodies (inclusive). (D) Venn diagram of genes associated with DMR and differentially expressed genes. (E) K-means clustering of 545 DMRs with a difference of more than 25% between any groups and an FDR q < 0.05 that were grouped and then averaged by unique gene association. β Scores are scaled across rows. (F and G) Scatter plots comparing DMRs within Foxp3-GFP+tdTomato+ cells versus ex-Foxp3 cells from iUhrf1+/+ mice (F) and iUhrf1fl/fl mice (G). Interior axis ticks (rug plots) represent positions of DMRs on each axis. Colored points represent greater than 25% difference between ex-Foxp3 cells (pink) and Foxp3-GFP+tdTomato+ cells (blue) with the number of DMRs in each such subset shown. (H) Difference-difference plot comparing the difference in DMR methylation status between ex-Foxp3 and Foxp3-GFP+tdTomato+ cells in iUhrf1+/+ mice and iUhrf1fl/fl mice. Colored points represent greater than 25% difference between iUhrf1+/+ mice (green) and iUhrf1fl/fl mice (purple) with the number of DMRs in each such subset shown. (I) Metagene analysis of CpG methylation across the start (S) through the end (E) of Treg-specific super-enhancer elements (Treg-SE) as defined previously (20). Violin plots show median and quartiles. n = 4 mice per cell type for both genotypes. A hypergeometric P value is shown in D. ‡q < 0.0001; NS, not significant by a mixed-effects analysis with the 2-stage linear step-up procedure of Benjamini, Krieger, and Yekutieli with Q = 5% (C); exact q values are in Supplemental Data.