Objectives To identify novel DNA methylation sites significant for rheumatoid arthritis (RA) and comprehensively understand their underlying pathological mechanism.
Methods We performed (1) genome-wide DNA methylation and mRNA expression profiling in peripheral blood mononuclear cells from RA patients and health controls; (2) correlation analysis and causal inference tests for DNA methylation and mRNA expression data; (3) differential methylation genes regulatory network construction; (4) validation tests of 10 differential methylation positions (DMPs) of interest and corresponding gene expressions; (5) correlation between PARP9 methylation and its mRNA expression level in Jurkat cells and T cells from patients with RA; (6) testing the pathological functions of PARP9 in Jurkat cells.
Results A total of 1046 DNA methylation positions were associated with RA. The identified DMPs have regulatory effects on mRNA expressions. Causal inference tests identified six DNA methylation–mRNA–RA regulatory chains (eg, cg00959259-PARP9-RA). The identified DMPs and genes formed an interferon-inducible gene interaction network (eg, MX1, IFI44L, DTX3L and PARP9). Key DMPs and corresponding genes were validated their differences in additional samples. Methylation of PARP9 was correlated with mRNA level in Jurkat cells and T lymphocytes isolated from patients with RA. The PARP9 gene exerted significant effects on Jurkat cells (eg, cell cycle, cell proliferation, cell activation and expression of inflammatory factor IL-2).
Conclusions This multistage study identified an interferon-inducible gene interaction network associated with RA and highlighted the importance of PARP9 gene in RA pathogenesis. The results enhanced our understanding of the important role of DNA methylation in pathology of RA.
- rheumatoid arthritis
- t cells
- autoimmune diseases
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HZ and L-FW contributed equally.
Handling editor Josef S Smolen
Contributors HZ participated in study design, recruiting patients with RA, data analysis, molecular testing, drafted and revised the manuscript. LFW participated in molecular testing, data analysis and revised the manuscript. XBM participated in data interpretation and revised the manuscript. XL coordinated the sample collection. HT participated in sample collection, data analysis. XWZ participated in sample collection, cell culture, molecular testing and revised the manuscript. WX participated in cell culture, molecular testing, data interpretation and revised the manuscript. YFG, MJW, KQZ and JW participated in recruiting patients with RA, data analysis and revised the manuscript. YHQ and XL participated in recruiting patients with RA, gene expression data acquisition, data analysis and revised the manuscript. YHZ participated in study design and revised the manuscript. YZL and NJY participated in revising the manuscript. SFL and FYD conceived the study, participated in study design, coordinated the sample collection, revised and finalised the manuscript. All authors read and approved the final manuscript.
Funding The study was supported by Natural Science Foundation of China (81401343, 81473046,81872681, 81373010, 81502868, 31401079, 81541068), the Natural Science Foundation ofJiangsu Province (BK20150346), the Natural Science Research Project of Jiangsu Provincial Higher Education (16KJA330001), the Startup Fund from Soochow University (Q413900112,Q413900712) and a Project of the Priority Academic Program Development of Jiangsu Higher Education Institutions.
Competing interests None declared.
Patient consent Obtained.
Ethics approval The ethical committee of Soochow University.
Provenance and peer review Not commissioned; externally peer reviewed.
Data sharing statement The microarray data for methylation have been submitted to the GEO database with accession number GSE111942.