Background/Purpose: Increasing evidence supports a role for epigenetic factors, including DNA methylation status, in autoimmune disease risk and severity. Our goal is to characterize DNA methylation profiles in SS, including multiple cell and tissue types relevant to disease.

Methods: We generated genome-wide DNA methylation profiles using Illumina HumanMethylation450 bead chips in minor salivary gland biopsy tissue, parotid saliva, PBMCs, and the following cell subpopulations: CD14+ monocytes, CD19+ B cells, and CD4+ T cells in a subset of participants from the Sjögren’s International Collaborative Clinical Alliance (SICCA) repository (http:/sicca.ucsf.edu/). All subjects were Caucasian females. SS cases (n=5) had severe disease, meeting all 3 of the ACR classification criteria for SS (Arth Care & Res 2012; 64:475), including focal lymphocytic sialadenitis on minor salivary gland biopsy, keratoconjunctiva sicca based on ocular staining pattern (ocular staining score ≥ 3), and presence of SSA and/or SSB autoantibodies. A single control individual with no evidence of SS based on the aforementioned and other objective tests was also studied. Sorting of freshly collected blood samples was performed using MACS® technology. Labial salivary gland biopsy tissue, parotid saliva and PBMCs were collected at entry to the SICCA repository, and a second blood sample was collected from each subject for isolation of the aforementioned cell subpopulations an average of 4.4 years following the baseline visit. Genome-wide DNA methylation profiles (450k sites) were compared across the 7 cell and tissue types within the 6 study subjects to characterize cell and tissue differences in DNA methylation status.  

Results: DNA yields for all cell and tissue types were high, with the exception of parotid saliva, which yielded between 0.75 – 1.07 µg DNA but was still sufficient for whole genome methylation profiling. Assessments of purity for sorted cell subpopulations ranged from a mean of 59% (for CD4+ T cells) to 80% (for CD14+ monocytes).  Within-individual comparisons of tissue-specific genome wide DNA methylation profiles revealed striking differences, with r²ranging from 0.105 (for saliva vs. B cells) to 0.998 (baseline vs. followup PBMCs).   

Conclusion: These preliminary results emphasize the cell and tissue specificity of DNA methylation status, which is an important epigenetic process with potential to influence patterns of gene expression in health and disease. Additional work, including detailed analysis of site-specific DNA methylation differences in larger samples of SS case and control individuals, followed by 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/differences-in-genome-wide-dna-methylation-profiles-across-multiple-cell-and-tissue-types-in-sjogrens-syndrome-ss/