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

TNFAIP3/A20 is a prominent autoimmune disease risk locus that is correlated with hypomorphic TNFAIP3 expression and exhibits complex chromatin architecture with over 30 predicted enhancers. This study aimed to functionally characterize an enhancer ∼55 kb upstream of the TNFAIP3 promoter marked by th...

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Autores principales: Pasula, Satish, Gopalakrishnan, Jaanam, Fu, Yao, Tessneer, Kandice L., Wiley, Mandi M., Pelikan, Richard C., Kelly, Jennifer A., Gaffney, Patrick M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9527318/
https://www.ncbi.nlm.nih.gov/pubmed/36199584
http://dx.doi.org/10.3389/fgene.2022.1011965
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author Pasula, Satish
Gopalakrishnan, Jaanam
Fu, Yao
Tessneer, Kandice L.
Wiley, Mandi M.
Pelikan, Richard C.
Kelly, Jennifer A.
Gaffney, Patrick M.
author_facet Pasula, Satish
Gopalakrishnan, Jaanam
Fu, Yao
Tessneer, Kandice L.
Wiley, Mandi M.
Pelikan, Richard C.
Kelly, Jennifer A.
Gaffney, Patrick M.
author_sort Pasula, Satish
collection PubMed
description TNFAIP3/A20 is a prominent autoimmune disease risk locus that is correlated with hypomorphic TNFAIP3 expression and exhibits complex chromatin architecture with over 30 predicted enhancers. This study aimed to functionally characterize an enhancer ∼55 kb upstream of the TNFAIP3 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 TNFAIP3 haplotype to assess haplotype-specific effects on transcription factor binding and chromatin regulation at the TNFAIP3 locus. This study found that the TNFAIP3 locus has a complex chromatin regulatory network that spans ∼1M bp from the promoter region of IL20RA to the 3′ untranslated region of TNFAIP3. Functional dissection of the enhancer demonstrated co-dependency of the RelA/p65 and CEBPB binding motifs that, together, increase IL20RA and IFNGR1 expression and decreased TNFAIP3 expression in the context of the TNFAIP3 SLE risk haplotype through dynamic long-range interactions up- and downstream. Examination of SNPs in linkage disequilibrium (D’ = 1.0) with rs10499197 identified rs9494868 as a functional SNP with risk allele-specific increase in nuclear factor binding and enhancer activation in vitro. In summary, this study demonstrates that SNPs carried on the ∼109 kb SLE risk haplotype facilitate hypermorphic IL20RA and IFNGR1 expression, while suppressing TNFAIP3 expression, adding to the mechanistic potency of this critically important locus in autoimmune disease pathology.
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spelling pubmed-95273182022-10-04 Systemic lupus erythematosus variants modulate the function of an enhancer upstream of TNFAIP3 Pasula, Satish Gopalakrishnan, Jaanam Fu, Yao Tessneer, Kandice L. Wiley, Mandi M. Pelikan, Richard C. Kelly, Jennifer A. Gaffney, Patrick M. Front Genet Genetics TNFAIP3/A20 is a prominent autoimmune disease risk locus that is correlated with hypomorphic TNFAIP3 expression and exhibits complex chromatin architecture with over 30 predicted enhancers. This study aimed to functionally characterize an enhancer ∼55 kb upstream of the TNFAIP3 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 TNFAIP3 haplotype to assess haplotype-specific effects on transcription factor binding and chromatin regulation at the TNFAIP3 locus. This study found that the TNFAIP3 locus has a complex chromatin regulatory network that spans ∼1M bp from the promoter region of IL20RA to the 3′ untranslated region of TNFAIP3. Functional dissection of the enhancer demonstrated co-dependency of the RelA/p65 and CEBPB binding motifs that, together, increase IL20RA and IFNGR1 expression and decreased TNFAIP3 expression in the context of the TNFAIP3 SLE risk haplotype through dynamic long-range interactions up- and downstream. Examination of SNPs in linkage disequilibrium (D’ = 1.0) with rs10499197 identified rs9494868 as a functional SNP with risk allele-specific increase in nuclear factor binding and enhancer activation in vitro. In summary, this study demonstrates that SNPs carried on the ∼109 kb SLE risk haplotype facilitate hypermorphic IL20RA and IFNGR1 expression, while suppressing TNFAIP3 expression, adding to the mechanistic potency of this critically important locus in autoimmune disease pathology. Frontiers Media S.A. 2022-09-19 /pmc/articles/PMC9527318/ /pubmed/36199584 http://dx.doi.org/10.3389/fgene.2022.1011965 Text en Copyright © 2022 Pasula, Gopalakrishnan, Fu, Tessneer, Wiley, Pelikan, Kelly and Gaffney. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Pasula, Satish
Gopalakrishnan, Jaanam
Fu, Yao
Tessneer, Kandice L.
Wiley, Mandi M.
Pelikan, Richard C.
Kelly, Jennifer A.
Gaffney, Patrick M.
Systemic lupus erythematosus variants modulate the function of an enhancer upstream of TNFAIP3
title Systemic lupus erythematosus variants modulate the function of an enhancer upstream of TNFAIP3
title_full Systemic lupus erythematosus variants modulate the function of an enhancer upstream of TNFAIP3
title_fullStr Systemic lupus erythematosus variants modulate the function of an enhancer upstream of TNFAIP3
title_full_unstemmed Systemic lupus erythematosus variants modulate the function of an enhancer upstream of TNFAIP3
title_short Systemic lupus erythematosus variants modulate the function of an enhancer upstream of TNFAIP3
title_sort systemic lupus erythematosus variants modulate the function of an enhancer upstream of tnfaip3
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9527318/
https://www.ncbi.nlm.nih.gov/pubmed/36199584
http://dx.doi.org/10.3389/fgene.2022.1011965
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