Kdm6b's Role in Regulating Immune Cells in the Intestine

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Summary

The authors of this article mainly demonstrated that Kdm6b could regulate the development and function of small intestinal IELs in an intracellular manner. The authors first established a mouse model (Kdm6b^F/F-CD4Cre) that conditionally knocked out Kdm6b in T cells. Single-cell transcriptome and V(D)J sequencing revealed that loss of Kdm6b led to a decrease in the proportion of TCRαβ+ cells in IELs, reduced TCR diversity, and differences in TCR V-J gene rearrangements, indicating a pivotal role for Kdm6b in maintaining IEL homeostasis in the small intestine. Subsequently, it was confirmed by flow cytometry that loss of Kdm6b disrupted the homeostasis and migration of IELPs in thymic progenitors and promoted apoptosis of TCRαβ+CD8αα+ IELs, resulting in a decrease in the number of TCRαβ+CD8αα+ in the intestine. Through bulk RNA-seq, ChIP-qPCR, and CUT&Tag-seq, it was shown that Kdm6b could promote TCRαβ+CD8αα+ IELs anti-apoptotic gene Bcl2 and cytotoxicity gene Gzmb, and the expression of Fasl can promote the maturation of TCRαβ+CD8αα+ IELs, and Kdm6b can also regulate the expression of intestinal homing molecule CCR9 by reducing the level of H3K27Me3 on the promoter. Taken together, the above results suggest an essential role for Kdm6b in the maturation and cytotoxicity of TCRαβ+CD8αα+ intestinal intraepithelial lymphocytes.

Research Criteria

The first line of immune defense is provided by IELs, which are found in the intestine. They primarily consist of non-classical CD8+ T cells and classical CD4+ and CD8+ T cells. Although t-bet, Runx3, and other transcription factors are essential for the growth and operation of IELs, it is still unclear how their epigenetic regulation works.

Kdm6b is an enzyme that encourages histone H3 (H3K27Me3) to be demethylated, which controls how genes are expressed. Although the mechanism is largely unknown, it is thought to play a role in maintaining Th17 cell differentiation, the lineage of natural killer T cells, and the development of intestinal intraepithelial lymphocytes (IELs). The author aims to examine how Kdm6b affects different IEL subsets, particularly TCR+CD8+.

Sample Type

Intestinal epithelial lymphocytes (IELs) from mouse small intestine

Result—Single-Cell Transcriptome And V(D)J Sequencing Reveal that Kdm6b Controls the Heterogeneity and TCR Diversity of Small Intestinal IELs

First, the authors analyzed the expression of Kdm6a and Kdm6b of the Kdm6 family in different T cell subsets and found that Kdm6b was higher than that of Kdm6a in different IEL subsets. The authors then constructed a T cell-specific conditional knockout Kdm6b mouse model (normal group Kdm6bF/F and knockout group Kdm6bF/F-CD4Cre). Using single-cell transcriptome and V(D)J sequencing technology to analyze CD45+ small intestinal IELs, a total of 5880 Kdm6bF/F mouse cells and 6488 Kdm6bF/F-CD4Cre mouse cells were captured. After dimensionality reduction clustering, it was divided into 8 clusters, and the proportions of clusters 1, 3, 5, 6, and 7 in the two groups were very different, indicating that the loss of Kdm6b in T cells changed the heterogeneity of small intestinal IELs). Except for cluster 8, which was identified as DC, the rest were T cells. The proportion of cluster 6 cells decreased the most; its top marker gene was Trav3-3. By analyzing TCR expression, it was found that in Kdm6b-deficient mice, the proportion of TCRαβ+ cells (including clusters 3, 5, 6) decreased, the proportion of TCRγδ+ cells (including clusters 1 and 7) increased, and TCR diversity decreased. At the same time, the loss of Kdm6b may also lead to differences in the rearrangement of TCR V-J genes. For example, in IELs with normal Kdm6b, Trbv13-3-Trbj1-1 is the major V-J gene combination, whereas, in Kdm6b-deficient IELs, the major V-J gene combination becomes Trbv5-Trbj1-4. These results suggest a critical role for Kdm6b in maintaining the homeostasis of small intestinal IELs.

Fig.1 Deficiency of Kdm6b in T cells alters the heterogeneity and TCR repertoire of small intestinal IELs. (Zhang, 2022)

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Reference

1. Zhang, H.; et al. The histone demethylase Kdm6b regulates the maturation and cytotoxicity of TCRαβ+CD8αα+ intestinal intraepithelial. Cell Death & Differentiation. 2022, 29: 1349-1363.