AUTHOR=Pasula Satish , Gopalakrishnan Jaanam , Fu Yao , Tessneer Kandice L. , Wiley Mandi M. , Pelikan Richard C. , Kelly Jennifer A. , Gaffney Patrick M. 

TITLE=Systemic lupus erythematosus variants modulate the function of an enhancer upstream of TNFAIP3

JOURNAL=Frontiers in Genetics

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2022.1011965

DOI=10.3389/fgene.2022.1011965

ISSN=1664-8021

ABSTRACT=<p><italic>TNFAIP3</italic>/A20 is a prominent autoimmune disease risk locus that is correlated with hypomorphic <italic>TNFAIP3</italic> expression and exhibits complex chromatin architecture with over 30 predicted enhancers. This study aimed to functionally characterize an enhancer ∼55 kb upstream of the <italic>TNFAIP3</italic> promoter marked by the systemic lupus erythematosus (SLE) risk haplotype index SNP, rs10499197. Allele effects of rs10499197, rs58905141, and rs9494868 were tested by EMSA and/or luciferase reporter assays in immune cell types. Co-immunoprecipitation, ChIP-qPCR, and 3C-qPCR were performed on patient-derived EBV B cells homozygous for the non-risk or SLE risk <italic>TNFAIP3</italic> haplotype to assess haplotype-specific effects on transcription factor binding and chromatin regulation at the <italic>TNFAIP3</italic> locus. This study found that the <italic>TNFAIP3</italic> locus has a complex chromatin regulatory network that spans ∼1M bp from the promoter region of <italic>IL20RA</italic> to the 3′ untranslated region of <italic>TNFAIP3</italic>. Functional dissection of the enhancer demonstrated co-dependency of the RelA/p65 and CEBPB binding motifs that, together, increase <italic>IL20RA</italic> and <italic>IFNGR1</italic> expression and decreased <italic>TNFAIP3</italic> expression in the context of the <italic>TNFAIP3</italic> SLE risk haplotype through dynamic long-range interactions up- and downstream. Examination of SNPs in linkage disequilibrium (<italic>D’</italic> = 1.0) with rs10499197 identified rs9494868 as a functional SNP with risk allele-specific increase in nuclear factor binding and enhancer activation <italic>in vitro</italic>. In summary, this study demonstrates that SNPs carried on the ∼109 kb SLE risk haplotype facilitate hypermorphic <italic>IL20RA</italic> and <italic>IFNGR1</italic> expression, while suppressing <italic>TNFAIP3</italic> expression, adding to the mechanistic potency of this critically important locus in autoimmune disease pathology.</p>