Authors: Mandi Wiley, Marcin Radziszewski, Bhuwan Khatri, Michelle Joachims, Kandice Tessneer, Anna Stolarczyk, Songyuan Yao, James Li, Cherilyn Pritchett Frazee, Audrey Johnston, Astrid Rasmussen, Juan-manuel Anaya, Lara Aqrawi, Sang-cheol Bae, Eva Baecklund, Albin Björk, Johan Brun, Sara Bucher, Nick Dand, Maija-leena Eloranta, Fiona Engelke, Helena Forsblad D'elia, Cecilia Fugmann, Stuart Glenn, Chen Gong, Jacques-eric Gottenberg, Daniel Hammenfors, Juliana Imgenberg Kreuz, Janicke Jensen, Svein Joar Johnsen, Malin Jonsson, Jennifer Kelly, Sharmily Khanam, Kwangwoo Kim, Marika Kvarnström, Thomas Mandl, Javier Martín, David Morris, Gaetane Nocturne, Katrine Norheim, Peter Olsson, Øyvind Palm, Jacques-olivier Pers, Nelson Rhodus, Christopher Sjöwall, Kathrine Skarstein, Kimberly Taylor, Phil Tombleson, Gudny Thorlacius, Swamy Venuturupalli, Edward Vital, Daniel Wallace, Lida Radfar, Michael Brennan, Judith James, R Scofield, Patrick Gaffney, Lindsey Criswell, Roland Jonsson, Silke Appel, Per Eriksson, Simon Bowman, Roald Omdal, Lars Rönnblom, Blake Warner, Maureen Rischmueller, Torsten Witte, A Farris, Xavier Mariette, Caroline Shiboski, Marta Alarcón Riquelme, Wan-fai Ng, Joel Guthridge, Timothy Vyse, Betty Tsao, Gunnel Nordmark, Christopher Lessard
Description:Objective: Sjögren's disease (SjD) and systemic lupus erythematosus (SLE) share genetic risk at the DDX6-CXCR5 locus (11q23.3). Identifying and functionally characterising shared SNPs spanning this locus can provide new insights into common genetic mechanisms of autoimmunity.
Methods: Transdisease meta-analyses, fine-mapping, and bioinformatic analyses prioritised shared likely functional single nucleotide polymorphisms (SNPs) for allele-specific and cell type-specific functional interrogation using electromobility shift, luciferase reporter, and quantitative chromatin conformation capture assays and clustered regularly interspaced short palindromic repeat (CRISPR) gene regulation.
Results: Five shared SNPs were identified as likely functional in primary human immune cells, salivary gland and kidney tissues: rs57494551, rs4936443, rs4938572, rs7117261, and rs4938573. All 5 SNPs exhibited cell type-specific and allele-specific effects on nuclear protein binding affinity and enhancer/promoter regulatory activity in immune, salivary gland epithelial, and kidney epithelial cell models. Mapping of chromatin-chromatin interactions revealed a chromatin regulatory network that expanded beyond DDX6 and CXCR5 to include PHLDB1, lnc-PHLDB1-1, BCL9L, TRAPPC4, among others. Coalescence of functional assays and multiomic data analyses indicated that these SNPs likely modulate the activity of 3 regulatory regions: intronic rs57494551 regulatory region, intergenic SNP haplotype (rs4938572, rs4936443, and rs7117261) regulatory region, and rs4938573 regulatory region upstream of the CXCR5 promoter.
Conclusions: Shared genetic susceptibly at the DDX6-CXCR5 locus in SjD and SLE likely alters common mechanisms of autoimmunity, including interferon signalling (DDX6), autophagy (TRAPPC4), and lymphocytic infiltration of disease-target tissues (CXCR5). Further, using multiomic data from patients with SjD, combined with bioinformatic and in vitro functional studies, can provide mechanistic insights into how genetic risk influences the biological pathways that drive complex autoimmunity.