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 2

PR3 and MPO genes are depleted for H3K27me3 in neutrophils of ANCA vasculitis patients.

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PR3 and MPO genes are depleted for H3K27me3 in neutrophils of ANCA vasc...
(A–C) Quantitative ChIP analysis for H3K27me3 enrichment on chromatin isolated from neutrophils of healthy controls (white circles; n = 23) and ANCA vasculitis patients (black diamonds; n = 15) is shown for PR3 (A), MPO (B), and MYO-D (C). Levels of H3K27me3 immunoprecipitated chromatin are reported as percent of input DNA. 4 of 5 ANCA patients were clinically in remission (dashed ellipse); and 9 of the remaining 10 had active disease (Supplemental Table 1 and Supplemental Figure 3). (D) Pearson correlation analysis of logarithmically transformed H3K27me3 levels at PR3 promoter versus logarithmically transformed PR3 expression levels among ANCA patients (black diamonds, active; gray diamonds, remission) and healthy controls (white circles) showed a modest inverse correlation (r = –0.494; P = 0.0019). (E) Pearson correlation analysis of logarithmically transformed H3K27me3 levels at MPO promoter versus logarithmically transformed MPO expression levels among ANCA patients and healthy controls (symbols as in D) trended toward an inverse correlation, but was not statistically significant (r = –0.189; P = 0.264). Only 4 ANCA patients in remission are shown because expression data for PR3 and MPO were not obtained for ANCA patient no. 1 (Supplemental Table 1).