Epigenetic basis for aberrant upregulation of autoantigen genes in humans with ANCA vasculitis
Dominic J. Ciavatta, JiaJin Yang, Gloria A. Preston, Anshul K. Badhwar, Hong Xiao, Peter Hewins, Carla M. Nester, William F. Pendergraft III, Terry R. Magnuson, J. Charles Jennette, Ronald J. Falk
Dominic J. Ciavatta, JiaJin Yang, Gloria A. Preston, Anshul K. Badhwar, Hong Xiao, Peter Hewins, Carla M. Nester, William F. Pendergraft III, Terry R. Magnuson, J. Charles Jennette, Ronald J. Falk
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Research Article Autoimmunity

Epigenetic basis for aberrant upregulation of autoantigen genes in humans with ANCA vasculitis

Abstract

Antineutrophil cytoplasmic autoantibody (ANCA) causes vascular injury that leads to small-vessel vasculitis. Patients with ANCA aberrantly express neutrophil granule–encoding genes, including 2 that encode autoantigens: proteinase 3 (PR3) and myeloperoxidase (MPO). To uncover a potential transcriptional regulatory mechanism for PR3 and MPO disrupted in patients with ANCA vasculitis, we examined the PR3 and MPO loci in neutrophils from ANCA patients and healthy control individuals for epigenetic modifications associated with gene silencing. We found that levels of the chromatin modification H3K27me3, which is associated with gene silencing, were depleted at PR3 and MPO loci in ANCA patients compared with healthy controls. Interestingly, in both patients and controls, DNA was unmethylated at a CpG island in PR3, whereas in healthy controls, DNA was methylated at a CpG island in MPO. Consistent with decreased levels of H3K27me3, JMJD3, the demethylase specific for H3K27me3, was preferentially expressed in ANCA patients versus healthy controls. In addition, we describe a mechanism for recruiting the H3K27 methyltransferase enhancer of zeste homolog 2 (EZH2) to PR3 and MPO loci mediated by RUNX3. RUNX3 message was decreased in patients compared with healthy controls, and may also be under epigenetic control. DNA methylation was increased at the RUNX3 promoter in ANCA patients. These data indicate that epigenetic modifications associated with gene silencing are perturbed at ANCA autoantigen–encoding genes, potentially contributing to inappropriate expression of PR3 and MPO in ANCA patients.

Authors

Dominic J. Ciavatta, JiaJin Yang, Gloria A. Preston, Anshul K. Badhwar, Hong Xiao, Peter Hewins, Carla M. Nester, William F. Pendergraft III, Terry R. Magnuson, J. Charles Jennette, Ronald J. Falk

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Figure 9

Model for PR3 and MPO gene silencing in normal neutrophils and disruption in ANCA vasculitis patients, highlighting the role of the H3K27me3 modification and enzymes that regulate this histone mark.

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Model for PR3 and MPO gene silencing in normal neutrophils and disruptio...
(A) Granulocyte genes are silenced in normal mature circulating neutrophils. We hypothesize that maintenance of a transcriptionally silent state is a dynamic process. Inflammatory cytokines can induce JMJD3 (26). Our present demonstration of an interaction between RUNX3 and PRC2 subunits suggests RUNX3 can recruit EZH2 and reestablish H3K27me3. This epigenetic modification would maintain the transcriptionally silent state. (B) In neutrophils of ANCA vasculitis patients, H3K27me3 is depleted at PR3 and MPO because of an unknown process, perhaps during neutrophil development. An alternative, but not mutually exclusive, possibility is that increased JMJD3 in ANCA patients reverses the silent state at PR3 and MPO by erasing the histone mark necessary for PcG-mediated silencing. Low levels of RUNX3 fail to recruit the EZH2 necessary to reestablish H3K27me3 and maintain transcriptional silence. Furthermore, DNA methylation at MPO may also contribute to maintaining the transcriptionally silent state (not shown). An intriguing possibility is that PR3 and MPO are in a transcriptionally poised state marked by both H3K27me3 and H3K4me3 (59) in neutrophils of healthy individuals. In neutrophils of patients with ANCA vasculitis, depletion of H3K27me3 allows transcription of PR3 and MPO.