T cell receptor signaling induces expression of lysine demethylase KDM6B to maintain Treg homeostasis
Minghong He, Beisi Xu, Pria G. Bose, Morgan J. McCullough, Rani S. Sellers, Xinying Zong, Wenjie Qi, Brianna L. Banten, Miriya K. Tune, Matthew P. Zimmerman, Genevieve Mullins, Brian C. Miller, J. Justin Milner, Jason K. Whitmire, Ageliki Tsagaratou, Karl B. Shpargel, Claire M. Doerschuk, Yong-Dong Wang, Jacob A. Steele, Shondra M. Pruett-Miller, Yongqiang Feng, Jason R. Mock
Minghong He, Beisi Xu, Pria G. Bose, Morgan J. McCullough, Rani S. Sellers, Xinying Zong, Wenjie Qi, Brianna L. Banten, Miriya K. Tune, Matthew P. Zimmerman, Genevieve Mullins, Brian C. Miller, J. Justin Milner, Jason K. Whitmire, Ageliki Tsagaratou, Karl B. Shpargel, Claire M. Doerschuk, Yong-Dong Wang, Jacob A. Steele, Shondra M. Pruett-Miller, Yongqiang Feng, Jason R. Mock
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Research Article Immunology Pulmonology

T cell receptor signaling induces expression of lysine demethylase KDM6B to maintain Treg homeostasis

Abstract

Tregs expressing forkhead box P3 (FOXP3) play crucial roles in maintaining immune tolerance and tissue integrity. EZH2, a histone H3 lysine 27 (H3K27) methyltransferase, is known as a key regulator of Treg identity and suppressive function upon activation. Here, we demonstrate that the H3K27 lysine demethylase KDM6B, which catalyzes the opposing reaction to EZH2, is also required for Treg identity and function after activation. Treg-specific deletion of Kdm6b impaired tissue Treg fate and function. KDM6B was upregulated after T cell antigen receptor signaling in Tregs and contributed to the regulation of Treg-associated gene expression through both direct and indirect mechanisms. A subset of Treg functional genes were direct targets of KDM6B and were co-occupied by FOXP3 at cis-regulatory regions, where KDM6B recruitment limited H3K27me3 accumulation. More broadly, KDM6B-dependent H3K27 demethylation facilitated Treg gene expression programs that supported tissue Treg homeostasis.

Authors

Minghong He, Beisi Xu, Pria G. Bose, Morgan J. McCullough, Rani S. Sellers, Xinying Zong, Wenjie Qi, Brianna L. Banten, Miriya K. Tune, Matthew P. Zimmerman, Genevieve Mullins, Brian C. Miller, J. Justin Milner, Jason K. Whitmire, Ageliki Tsagaratou, Karl B. Shpargel, Claire M. Doerschuk, Yong-Dong Wang, Jacob A. Steele, Shondra M. Pruett-Miller, Yongqiang Feng, Jason R. Mock

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Figure 4

KDM6B coordinates with FOXP3 to regulate Treg functional genes.

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KDM6B coordinates with FOXP3 to regulate Treg functional genes. (A) A he...
(A) A heatmap of FOXP3 and KDM6B CUT&RUN showing binding at 3 different FOXP3 binding regions in aTreg and rTregs: increased (Up) (P < 0.05), constitutive (Cons) (P > 0.5; 0.95 < fold change [FC] < 1.05), and decreased (Down) (P < 0.05). Two replicates per condition were combined for analysis. FOXP3 CUT&RUN data were adapted from He et al. (28). (B) Average density signal of KDM6B binding at the 3 different FOXP3 binding regions in A. (C) Number of peaks (top) and genes (bottom) linked to the overlapped regions between FOXP3 (all reproducible peaks) and KDM6B binding peaks. (D) DNA sequence motifs of transcription factors enriched at KDM6B binding sites. (E) FOXP3 and KDM6B binding peaks at the Tnf gene region. (F) Principal component (PC) analysis of RNA-Seq results. RNA-Seq was performed in rTregs from lymphoid organs of Foxp3YFP-Cre or Kdm6bΔTreg mice stimulated with plate-bound anti-CD3 and anti-CD28 antibodies (TCR) for 3 hours. Two replicates per condition were combined for analysis. (G) A heatmap showing expression patterns of genes in rTregs indicated in F. (H) Functional annotation of genes in clusters C1–C4. (I) Effect of Kdm6b deficiency on the expression of genes linked to aTreg program or effector T cell program. (J and K) Number of genes regulated by FOXP3 (sgNC- versus sgFoxp3-transduced Tregs) (28) and KDM6B. (L) Frequency of TNF-α expression Tregs in the spleen of Foxp3YFP-Cre or Kdm6bΔTreg mice (n = 5 mice/strain, representative of 2 separate experiments). **P < 0.01 by 2-tailed t test. CDF, cumulative distribution function; Chemok, chemokine; cytok, cytokine; Reg, regulation.