A Comprehensive Analysis of Shared Loci between Systemic Lupus Erythematosus (SLE) and Sixteen Autoimmune Diseases Reveals Limited Genetic Overlap
PLOS GENETICS
Authors: Ramos, Paula S.; Criswell, Lindsey A.; Moser, Kathy L.; Comeau, Mary E.; Williams, Adrienne H.; Pajewski, Nicholas M.; Chung, Sharon A.; Graham, Robert R.; Zidovetzki, Raphael; Kelly, Jennifer A.; Kaufman, Kenneth M.; Jacob, Chaim O.; Vyse, Timothy J.; Tsao, Betty P.; Kimberly, Robert P.; Gaffney, Patrick M.; Alarcon-Riquelme, Marta E.; Harley, John B.; Langefeld, Carl D.
Abstract
In spite of the well-known clustering of multiple autoimmune disorders in families, analyses of specific shared genes and polymorphisms between systemic lupus erythematosus (SLE) and other autoimmune diseases (ADs) have been limited. Therefore, we comprehensively tested autoimmune variants for association with SLE, aiming to identify pleiotropic genetic associations between these diseases. We compiled a list of 446 non-Major Histocompatibility Complex (MHC) variants identified in genome-wide association studies (GWAS) of populations of European ancestry across 17 ADs. We then tested these variants in our combined Caucasian SLE cohorts of 1,500 cases and 5,706 controls. We tested a subset of these polymorphisms in an independent Caucasian replication cohort of 2,085 SLE cases and 2,854 controls, allowing the computation of a meta-analysis between all cohorts. We have uncovered novel shared SLE loci that passed multiple comparisons adjustment, including the VTCN1 (rs12046117, P = 2.02610(-06)) region. We observed that the loci shared among the most ADs include IL23R, OLIG3/TNFAIP3, and IL2RA. Given the lack of a universal autoimmune risk locus outside of the MHC and variable specificities for different diseases, our data suggests partial pleiotropy among ADs. Hierarchical clustering of ADs suggested that the most genetically related ADs appear to be type 1 diabetes with rheumatoid arthritis and Crohn's disease with ulcerative colitis. These findings support a relatively distinct genetic susceptibility for SLE. For many of the shared GWAS autoimmune loci, we found no evidence for association with SLE, including IL23R. Also, several established SLE loci are apparently not associated with other ADs, including the ITGAM-ITGAX and TNFSF4 regions. This study represents the most comprehensive evaluation of shared autoimmune loci to date, supports a relatively distinct non-MHC genetic susceptibility for SLE, provides further evidence for previously and newly identified shared genes in SLE, and highlights the value of studies of potentially pleiotropic genes in autoimmune diseases.
Gene-gene interaction of BLK, TNFSF4, TRAF1, TNFAIP3, and REL in systemic lupus erythematosus
ARTHRITIS AND RHEUMATISM
Authors: Zhou, Xu-jie; Lu, Xiao-lan; Nath, Swapan K.; Lv, Ji-cheng; Zhu, Sai-nan; Yang, Hai-zhen; Qin, Lian-xiang; Zhao, Ming-hui; Su, Yin; Shen, Nan; Li, Zhan-guo; Zhang, Hong
Abstract
Objective Although the number of convincingly established genetic associations with systemic lupus erythematosus (SLE) has increased sharply over the last few years, refinement of these associations is required, and their potential roles in genegene interactions need to be further investigated. Recent genome-wide association studies (GWAS) in SLE have produced renewed interest in B cell/T cell responses and the NF-?B signaling pathway. The aim of this study was to search for possible genegene interactions based on identified single-nucleotide polymorphisms (SNPs), in using an approach based on the role of signaling pathways. Methods. The SNPs in BLK, TNFSF4, TRAF1, TNFAIP3, and REL were replicated in order to evaluate genetic associations with SLE. TaqMan genotyping was conducted in 804 Chinese patients with SLE and 722 matched control subjects. A multiple logistic regression model was used to estimate the multiplicative interaction effect of the SNPs, and additive interactions were analyzed by 2 x 2 factorial designs. Data from a previously published GWAS conducted by the International Consortium on the Genetics of Systemic Lupus Erythematosus were derived for comparison and validation. Results. Single-marker analysis validated the association of BLK rs2736340 (P = 4.25 x 10(-6)) as well as TNFSF4 rs2205960 (P = 2.82 x 10(-5)) and TNFAIP3 rs5029939 (P = 1.92 x 10(-3)) with SLE susceptibility in Chinese. Multiplicative interaction analysis indicated that BLK had an interactive effect with TNFSF4 in Chinese patients with SLE (P = 6.57 x 10(-4)). Additive interaction analysis revealed interactions between TRAF1 and TNFAIP3 in both Chinese (P = 2.18 x 10(-3)) and Caucasians (P = 2.86 x 10(-4)). In addition, multiple tendencies toward interactions were observed, and an additive effect was observed as the number of risk genotypes increased. Conclusion. The results of this study provide evidence of the possible gene-gene interactions of BLK, TNFSF4, TRAF1, TNFAIP3, and REL in SLE, which may represent a synergic effect of T cells and B cells through the NF-kappa B pathway in determining immunologic aberration.