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 6

Induction of Uhrf1 deficiency generates ex-Foxp3 cells with distinct inflammatory transcriptional programs.

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Induction of Uhrf1 deficiency generates ex-Foxp3 cells with distinct inf...
(A) Schematic of the pulse-chase experimental design. (B) Representative contour plots of splenic live CD3ε+CD4+ cell subsets (see Supplemental Figure 6D for summary data). (C) Principal component analysis of 1270 differentially expressed genes identified from a generalized linear model and ANOVA-like testing with FDR q < 0.05. Ellipses represent normal contour lines with 1 SD probability. (D) K-means clustering of 1270 genes with an FDR q < 0.05 comparing the cell populations from C scaled as Z-score across rows. (E and F) Fold-change–fold-change plots for iUhrf1+/+ (E) and iUhrf1fl/fl (F) mice of Foxp3-GFP+tdTomato+ versus Foxp3-GFP+tdTomato– and ex-Foxp3 versus Foxp3-GFP+tdTomato– highlighting genes exhibiting an increase (q < 0.05) in Foxp3-GFP+tdTomato+ versus ex-Foxp3 (blue dots) and ex-Foxp3 versus Foxp3-GFP+tdTomato+ (pink dots). Numbers of differentially expressed genes are indicated. (G) Cumulative distribution function plots comparing Foxp3-GFP+tdTomato+ cells from iUhrf1+/+ versus iUhrf1fl/fl mice with each population normalized to the Foxp3-GFP+tdTomato– population sorted from their respective genotypes. The cumulative proportion of all genes (black), a Treg-defining gene set (43) (orange), and the GSE22045_TREG_VS_TCONV_UP gene set (48) (red) are shown. (H) Cumulative distribution function plots as in G comparing the ex-Foxp3 cells from iUhrf1+/+ versus iUhrf1fl/fl mice. n = 5 (iUhrf1+/+); n = 6 (iUhrf1fl/fl). P values resulting from Kolmogorov-Smirnov tests for cumulative distributions comparing all genes against either gene set are shown in G and H.