Background/Purpose: Cutaneous lupus erythematous (CLE) is a disfiguring manifestation of systemic LE (SLE), and the pathogenesis remains unclear. However, epidermal regulation of skin inflammation and cell death contribute, potentially in a female-biased manner. Differential DNA methylation is important in the organ-specific manifestations of SLE but has not been studied in the skin. Thus, we explored the genome-wide DNA methylation changes in keratinocytes (KC) to investigate the functional relevance in CLE.

Methods: Eight SLE skin biopsy samples were taken from non-sun-exposed, unaffected skin from participants of the Michigan Lupus Cohort as well as age (+/- 6 years), sex, and ethnicity-matched healthy control subjects. Freshly cultured KC (at passage 2) were used to isolate DNA using DNeasy Blood and Tissue Kit. DNA was bisulfite converted for DNA methylation studies using the EZ DNA Methylation Kit. Genome-wide DNA methylation analysis was performed using the Infinium HumanMethylation450 BeadChip Kit. Differentially methylated loci were mapped to genes or gene regions and subject to gene ontology and pathway analysis using the Database for Annotation, Visualization, and Integrated Discovery (DAVID).

Results: We identified 1443 differentially methylated sites with 924 hypomethylated genes and 519 hypermethylated genes in lupus KC compared to controls. Pathway analysis revealed Hippo signaling as the top canonical pathway associated with the DNA methylation profile of primary lupus KCs. TEA Domain Transcription Factor 1 (TEAD1), a key transcription factor in the Hippo pathway, was significantly hypomethylated in lupus compared to control (Δβ =-0.17, P= 4.36 X 10^-9). Further, methylation of LATS1/2, which contributes to inactivation of Hippo pathway effector proteins TAZ and YAP, was significantly increased (Δβ= 0.11, P= 3.82 X 10^-4). YAP and TAZ were both hypermethylated (Δβ= 0.11 (P= 1.53 X 10^-3) and 0.12 (P= 2.20 X 10^-4), respectively), thereby increasing TEAD1 activity.

Conclusion: SLE KCs display methylation changes in the Hippo pathway that may contribute to dysregulated apoptosis, a known feature that contributes to photosensitivity in CLE.  Vestigial like family member 3 (VGLL3) has recently been identified as a putative transcription factor and master orchestrator of sex bias in autoimmune diseases, including SLE and CLE. Importantly, studies have shown VGLL3 operates through TEAD1 in other cell types and may be a key upstream regulator in the skin. Overall, these results suggest that differential methylation in KC may underlie dysregulated apoptosis and female bias of CLE.

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ACR Meeting Abstracts - https://acrabstracts.org/abstract/genome-wide-dna-methylation-analysis-in-lupus-keratinocytes-identifies-differential-methylation-of-genes-that-regulate-apoptosis/