Fine Mapping of the Sjögren’s Disease and Systemic Lupus Erythematosus DDX6-CXCR5 Risk Interval Reveals Common SNPs with Functional Significance in Immune and Salivary Gland Cells

Mandi Wiley¹, Bhuwan Khatri¹, Kandice Tessneer¹, Michelle Joachims¹, Anna Stolarczyk¹, Anna Nagel¹, Astrid Rasmussen¹, Professor Simon Bowman², Lida Radfar³, Roald Omdal⁴, Marie Wahren-Herlenius⁵, Blake Warner⁶, Torsten Witte⁷, Roland Jonsson⁸, Maureen Rischmueller⁹, Patrick Gaffney¹, Judith James¹, Lars Ronnblom¹⁰, Hal Scofield¹, Xavier Mariette¹¹, Fai Ng¹², Gunnel Nordmark¹⁰, Betty Tsao¹³ and Christopher Lessard¹, ¹Oklahoma Medical Research Foundation, Oklahoma City, OK, ²University Hospitals Birmingham, Birmingham, United Kingdom, ³University of Oklahoma Health Sciences Center, Oklahoma City, OK, ⁴Stavanger University, Stavanger, Norway, ⁵Karolinska Institutet, Stockholm, Sweden, ⁶National Institutes of Health, Bethesda, MD, ⁷MH-Hannover, Hannover, Germany, ⁸University of Bergen, Bergen, Norway, ⁹RheumatologySA, Adelaide, Australia, ¹⁰Uppsala University, Uppsala, Sweden, ¹¹Paris-Saclay University, Rueil Malmaison, Ile-de-France, France, ¹²Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom, ¹³Medical University of South Carolina, Charleston, SC

Meeting: ACR Convergence 2022

Keywords: Bioinformatics, Epigenetics, genetics, Sjögren's syndrome, Systemic lupus erythematosus (SLE)

Session Information

Date: Monday, November 14, 2022

Title: Sjögren's Syndrome – Basic and Clinical Science Poster

Session Type: Poster Session D

Session Time: 1:00PM-3:00PM

Background/Purpose: Sjögren’s Disease (SjD) and Systemic Lupus Erythematosus (SLE) share several characteristics and have similar genome-wide significant associations in the DDX6-CXCR5 locus. Fine mapping of the DDX6-CXCR5 risk locus will refine the association signals and identify the most likely functional SNPs common across the two diseases.

Methods: ImmunoChip data from European ancestry (3785 SLE; 1916 SjD; 6893 controls) were imputed and SNP-trait associations tested. Bayesian statistics defined a credible SNP set. Allele-specific SNP function were tested by electrophoretic mobility shift assays and luciferase expression assays in EBV transformed B (EBV B), Daudi B, Jurkat T, THP1 monocytes, and A253 salivary gland cell lines. Chromosome conformation capture with quantitative PCR (3C-qPCR) tested chromatin interactions.

Results: Fine mapping and bioinformatic analyses identified 5 common SNPs on the SjD and SLE DDX6-CXCR5 risk association with strong functional evidence in immune cell types: rs57494551 in the first intron of DDX6, and rs4938572, rs4936443, rs7117261, and rs4938573 in the promoter/enhancer region of DDX6 and CXCR5. The rs57494551 risk allele increased enhancer activity in B cells (EBV B, Daudi: p< 0.0004) and A253 cells (p< 0.0001), but decreased promoter activity in T cells (p< 0.0001), monocytes (p=0.0148), and A253 cells (p=0.0085). SNP rs4938572 is an eQTL of DDX6 in T cells, the risk allele significantly increased protein binding (p=0.0042), and promoter (p=0.0018) and enhancer (p=0.003) activity in T cells. Risk allele of rs4938572 also increased promoter activity in A253 cells (p=0.0007), but showed no effect on promoter or enhancer activity in B cells. Risk allele of rs4936443 showed significant promoter (p< 0.002) and enhancer (p< 0.007) activity in THP1 monocytes and A253 cells. Risk allele of rs7117261 decreased enhancer activity in EBV B cells (p=0.0184), T cells (p=0.0252), and A253 cells (p=0.0007). Risk allele of rs4938573 decreased promoter activity in EBV B cells (p=0.0237), T cells (p< 0.0001), and A253 cells (p=0.0031), but increased enhancer activity in A253 cells (p< 0.0001). Overall, A253 cells had more significant allelic-specific changes in promoter and enhancer activity across the five SNPs than immune cells. 3C-qPCR in EBV B, T, and A253 cells showed similar genomic architecture across the interval with two regulatory regions carrying rs4938572 or rs57494551; both interacted with a region upstream of DDX6 that includes the long non-coding (lnc)RNA, AP002954. However, no cell type- or allele-specific changes in chromosome-chromosome interactions were observed.

Conclusion: Functional characterization of the five prioritized SNPs from the DDX6-CXCR5 association of SjD and SLE implicate the risk alleles as modulators of promoter and/or enhancer activities that regulate cell type-specific expression of DDX6, CXCR5, AP002954, among others. Further, these findings emphasize the importance of exploring the functional significance of SNPs in the context of complex chromatin architecture in disease-relevant cell types and tissues.

Disclosures: M. Wiley, None; B. Khatri, None; K. Tessneer, None; M. Joachims, None; A. Stolarczyk, None; A. Nagel, None; A. Rasmussen, None; P. Bowman, Novartis, AstraZeneca, AbbVie/Abbott, Galapagos; L. Radfar, None; R. Omdal, None; M. Wahren-Herlenius, None; B. Warner, Pfizer, Astellas Bio; T. Witte, AbbVie, Amgen, Bristol-Myers Squibb, Celgene, Chugai, Janssen, Lilly, MSD, Mylan, Novartis, Pfizer, Roche, UCB, Galapagos; R. Jonsson, None; M. Rischmueller, None; P. Gaffney, None; J. James, Bristol-Myers Squibb(BMS), AstraZeneca, Novartis, Progentec Biosciences; L. Ronnblom, None; H. Scofield, None; X. Mariette, AstraZeneca, Bristol Myers Squibb, Galapagos, GSK, Novartis, Pfizer; F. Ng, None; G. Nordmark, None; B. Tsao, None; C. Lessard, Janssen.

To cite this abstract in AMA style:

Wiley M, Khatri B, Tessneer K, Joachims M, Stolarczyk A, Nagel A, Rasmussen A, Bowman P, Radfar L, Omdal R, Wahren-Herlenius M, Warner B, Witte T, Jonsson R, Rischmueller M, Gaffney P, James J, Ronnblom L, Scofield H, Mariette X, Ng F, Nordmark G, Tsao B, Lessard C. Fine Mapping of the Sjögren’s Disease and Systemic Lupus Erythematosus DDX6-CXCR5 Risk Interval Reveals Common SNPs with Functional Significance in Immune and Salivary Gland Cells [abstract]. Arthritis Rheumatol. 2022; 74 (suppl 9). https://acrabstracts.org/abstract/fine-mapping-of-the-sjogrens-disease-and-systemic-lupus-erythematosus-ddx6-cxcr5-risk-interval-reveals-common-snps-with-functional-significance-in-immune-and-salivary-gland-cells/. Accessed .

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