2019: 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

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.