DNA methylation differences within INS, PTPN22 and IL2RA promoters in lymphocyte subsets in children with type 1 diabetes and controls

Abstract

We elucidated the effect of four known T1D-susceptibility associated single nucleotide polymorphism (SNP) markers in three genes (rs12722495 and rs2104286 in IL2RA, rs689 in INS and rs2476601 in PTPN22) on CpG site methylation of their proximal promoters in different lymphocyte subsets using pyrosequencing. The study cohort comprised 25 children with newly diagnosed T1D and 25 matched healthy controls. The rs689 SNP was associated with methylation at four CpG sites in INS promoter: −234, −206, −102 and −69. At all four CpG sites, the susceptibility genotype AA was associated with a higher methylation level compared to the other genotypes. We also found an association between rs12722495 and methylation at CpG sites −373 and −356 in IL2RA promoter in B cells, where the risk genotype AA was associated with lower methylation level compared to the AG genotype. The other SNPs analyzed did not demonstrate significant associations with CpG site methylation in the examined genes. Additionally, we compared the methylation between children with T1D and controls, and found statistically significant methylation differences at CpG −135 in INS in CD8+ T cells (p = 0.034), where T1D patients had a slightly higher methylation compared to controls (87.3 ± 7.2 vs. 78.8 ± 8.9). At the other CpG sites analyzed, the methylation was similar. Our results not only confirm the association between INS methylation and rs689 discovered in earlier studies but also report this association in sorted immune cells. We also report an association between rs12722495 and IL2RA promoter methylation in B cells. These results suggest that at least part of the genetic effect of rs689 and rs12722495 on T1D pathogenesis may be conveyed by DNA methylation.

Keywords:

• Type 1 diabetes
• DNA methylation
• INS
• IL2RA
• PTPN22

Acknowledgements

The authors thank Lovisa Reinius (Karolinska Institutet) and Marjo Haanperä (National Institute for Health and Welfare, THL) for their expertise and assistance with pyrosequencing. We are grateful to Anne Suominen (University of Turku) for her skillful technical assistance. We also give special thanks to Antti-Pekka Laine for assistance with the statistical analysis.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

The datasets used and/or analyzed in the present study are not readily available due to data privacy regulations. Requests to access the datasets should be directed to DIPP Steering Committee, [email protected].

Additional information

Funding

This work was funded by the Sigrid Jusélius Foundation, the Finnish Medical Foundation, and the Päivikki and Sakari Sohlberg –Foundation.