Background/Purpose: Risk factors are known for many diseases, but the etiologies of most autoimmune diseases remain unknown and are idiopathic. Pathogenesis of disease likely involves complex interplay between genetic and environmental risk factors. Specifically, Epstein Barr virus (EBV) has suggestive associations with many autoimmune diseases, and EBV infection is nearly ubiquitous in adults. The molecular mechanisms underlying these associations, however, remain unclear.

Methods: We tested the hypothesis that some autoimmune variants might act by altering the binding of the EBV-encoded transcription factor Zta, consequently resulting in downstream changes in gene expression. To this end, we comprehensively characterized the DNA binding of Zta to both methylated and unmethylated DNA sequences using protein binding microarrays (PBMs). Based on these data, we identified plausible causal variants for multiple sclerosis (MS), systemic lupus erythematosus (SLE), and juvenile idiopathic arthritic (JIA) predicted to alter Zta binding. From among these, we identified variants located within likely regulatory regions in EBV-infected B cells using publically available functional genomic datasets. We screened these candidate variants using electrophoretic mobility shift assays (EMSAs) to identify general differential binding of nuclear factors, and validated differential Zta binding using EMSA-supershift and DNA Affinity Precipitation Assays coupled with Western blots (DAPA-Westerns).

Results: These experiments revealed three genetic variants, associated with MS, SLE, and JIA, respectively, exhibiting stronger Zta binding to the risk allele. We provide data showing that each of these variants is associated with genotype-dependent expression in EBV-transformed B cell lines. Using luciferase reporter assays, we further demonstrate that the MS risk allele in the RGS14 promoter results in greater promoter activity, and that this activity is significantly diminished in cell lines lacking EBV.

Conclusion: Collectively, these data demonstrate for the first time that differential binding of a viral protein to a disease-associated genetic variant can result in altered levels of host gene expression in ways that are predicted to influence autoimmune disease. Since Zta is a viral protein, and is expressed throughout human life subsequent to EBV infection, but only in virally infected cells, these results offer a potential therapeutic target for multiple autoimmune diseases.

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ACR Meeting Abstracts - https://acrabstracts.org/abstract/allele-dependent-binding-of-a-viral-protein-to-autoimmune-disease-associated-genetic-variants-2/