Background/Purpose: Sjögren’s Syndrome (SS) is a chronic, multisystem autoimmune disease characterized by progressive destruction of the exocrine glands, with subsequent mucosal and conjunctival dryness. Increasing evidence supports a role for DNA methylation status in autoimmune disease risk and severity. Our goal was to characterize methylation profiles in SS subjects and healthy controls across multiple cell and tissue types to identify similarities and differences relevant to disease status and pathogenesis. 

Methods: We generated genome-wide DNA methylation profiles using Illumina HumanMethylation450 BeadChips in minor salivary gland biopsy tissue, fresh and banked peripheral blood mononuclear cells (PBMC), CD14+ monocytes, CD19+ B cells, and CD4+ T cells in ten participants (five cases and five controls) from the Sjögren’s International Collaborative Clinical Alliance (SICCA; http://sicca.ucsf.edu/; N01 DE32636) repository. Sorting of freshly collected blood samples was performed using MACS®technology. DNA yields for all cell and tissue types were high; all samples were background subtracted and normalized with beta-mixture quantile dilation (BMIQ). After removing SNPS and sites with beta-value detection p-values <0.05, 473,864 CpGs remained in our final data set.

Results: Methylation of individual CpG sites was stable across the six cell types for ~240,000 CpGs (variance< 0.001); however, variance was less than 0.0001 for ~94,000 CpGs and exceeded 0.10 for ~900 CpGs. Mean methylation was calculated within each cell and tissue type for all CpGs in the final data set. Mean methylation was moderately to highly correlated between all cell and tissue types in cases, controls, and in a combined data set (r²: 0.82 – 0.99) with the lowest correlation between salivary gland tissue and CD14+ monocytes and the highest correlation between fresh and banked PBMCs. Methylation levels within 16 putative SS genes were similar between cases and controls. However, median levels of methylation in individual CpGs within IL10 and TNFSF4 were 12% and 26% decreased in CD14+ T cells, and CD19+ B cells in cases compared to controls, respectively. Median levels of methylation in individual CpGs within TNFAIP3 and KLHL24 were hyper-methylated by 10%, 27%, and 19% in CD4+ T cells, CD19+ B cells and gland tissue biopsy samples in cases compared to controls, respectively. Data visualization of methylation profiles using Multi-Dimensional Scaling applied to several different subsets of CpG revealed distinct separation between cell types in addition to separation based on SS case status. The greatest separation by case status was visible in CD19+ B cells and salivary gland tissue samples.

Conclusion: Our results emphasize the cell and tissue specificity of DNA methylation in addition to differences in methylation based on case status for some cell types. Additional research, including studies of gene expression for regions associated with disease risk or severity, will be required to fully define the role of DNA methylation in SS.

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ACR Meeting Abstracts - https://acrabstracts.org/abstract/dna-methylation-in-six-cell-and-tissue-types-in-sjogrens-syndrome-reveals-distinct-patterns-across-samples-and-clustering-based-on-disease-status/