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Genome-scale case-control analysis of CD4+ T-cell DNA methylation in juvenile idiopathic arthritis reveals potential targets involved in disease

Justine A Ellis18*, Jane E Munro23, Raul A Chavez1, Lavinia Gordon4, Jihoon E Joo56, Jonathan D Akikusa23, Roger C Allen23, Anne-Louise Ponsonby7, Jeffrey M Craig5 and Richard Saffery6

Author Affiliations

1 Genes, Environment & Complex Disease, Murdoch Childrens Research Institute, 50 Flemington Rd, Parkville, Vic, Australia

2 Rheumatology, Department of General Medicine, Royal Children’s Hospital, Parkville, Vic, Australia

3 Arthritis & Rheumatology, Murdoch Childrens Research Institute, Parkville, Vic, Australia

4 Bioinformatics Unit, Murdoch Childrens Research Institute, Parkville, Vic, Australia

5 Early Life Epigenetics, Murdoch Childrens Research Institute, Parkville, Vic, Australia

6 Cancer, Disease and Developmental Epigenetics, Murdoch Childrens Research Institute, Parkville, Vic, Australia

7 Environmental & Genetic Epidemiology Research, Murdoch Childrens Research Institute, Parkville, Vic, Australia

8 Department of Physiology, The University of Melbourne, Melbourne, Vic, Australia

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Clinical Epigenetics 2012, 4:20  doi:10.1186/1868-7083-4-20

Published: 13 November 2012



Juvenile Idiopathic Arthritis (JIA) is a complex autoimmune rheumatic disease of largely unknown cause. Evidence is growing that epigenetic variation, particularly DNA methylation, is associated with autoimmune disease. However, nothing is currently known about the potential role of aberrant DNA methylation in JIA. As a first step to addressing this knowledge gap, we have profiled DNA methylation in purified CD4+ T cells from JIA subjects and controls. Genomic DNA was isolated from peripheral blood CD4+ T cells from 14 oligoarticular and polyarticular JIA cases with active disease, and healthy age- and sex-matched controls. Genome-scale methylation analysis was carried out using the Illumina Infinium HumanMethylation27 BeadChip. Methylation data at >25,000 CpGs was compared in a case-control study design.


Methylation levels were significantly different (FDR adjusted p<0.1) at 145 loci. Removal of four samples exposed to methotrexate had a striking impact on the outcome of the analysis, reducing the number of differentially methylated loci to 11. The methotrexate-naive analysis identified reduced methylation at the gene encoding the pro-inflammatory cytokine IL32, which was subsequently replicated using a second analysis platform and a second set of case-control pairs.


Our data suggests that differential T cell DNA methylation may be a feature of JIA, and that reduced methylation at IL32 is associated with this disease. Further work in larger prospective and longitudinal sample collections is required to confirm these findings, assess whether the identified differences are causal or consequential of disease, and further investigate the epigenetic modifying properties of therapeutic regimens.

Epigenetics; Juvenile idiopathic arthritis; DNA methylation; Autoimmunity; Methylome; Methotrexate