Variation in the ICAM1-ICAM4-ICAM5 locus is associated with systemic lupus erythematosus susceptibility in multiple ancestries.

Kim, Kwangwoo,Brown, Elizabeth E,Choi, Chan-Bum,Alarc?n-Riquelme, Marta E,Kelly, Jennifer A,Glenn, Stuart B,Ojwang, Joshua O,Adler, Adam,Lee, Hye-Soon,Boackle, Susan A,Criswell, Lindsey A,Alarc?n, Gra British Medical Association 2012 Annals of the Rheumatic Diseases Vol.71 No.11

<P>Systemic lupus erythematosus (SLE; OMIM 152700) is a chronic autoimmune disease for which the aetiology includes genetic and environmental factors. ITGAM, integrin α(M) (complement component 3 receptor 3 subunit) encoding a ligand for intracellular adhesion molecule (ICAM) proteins, is an established SLE susceptibility locus. This study aimed to evaluate the independent and joint effects of genetic variations in the genes that encode ITGAM and ICAM.</P>

Evaluation of <i>TRAF6</i> in a large multiancestral lupus cohort

Namjou, Bahram,Choi, Chan‐,Bum,Harley, Isaac T. W.,Alarcó,n‐,Riquelme, Marta E.,Kelly, Jennifer A.,Glenn, Stuart B.,Ojwang, Joshua O.,Adler, Adam,Kim, Kwangwoo,Gallant, Caroline J.,B Wiley Subscription Services, Inc., A Wiley Company 2012 Vol.64 No.6

<P><B>Abstract</B></P><P><B>Objective</B></P><P>Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease with significant immune system aberrations resulting from complex heritable genetics as well as environmental factors. We undertook to study the role of <I>TRAF6</I> as a candidate gene for SLE, since it plays a major role in several signaling pathways that are important for immunity and organ development.</P><P><B>Methods</B></P><P>Fifteen single‐nucleotide polymorphisms (SNPs) across <I>TRAF6</I> were evaluated in 7,490 SLE patients and 6,780 control subjects from different ancestries. Population‐based case–control association analyses and meta‐analyses were performed. <I>P</I> values, false discovery rate q values, and odds ratios (ORs) with 95% confidence intervals (95% CIs) were calculated.</P><P><B>Results</B></P><P>Evidence of associations was detected in multiple SNPs. The best overall <I>P</I> values were obtained for SNPs rs5030437 and rs4755453 (<I>P</I> = 7.85 × 10<SUP>−5</SUP> and <I>P</I> = 4.73 × 10<SUP>−5</SUP>, respectively) without significant heterogeneity among populations (<I>P</I> = 0.67 and <I>P</I> = 0.50, respectively, in Q statistic). In addition, SNP rs540386, which was previously reported to be associated with rheumatoid arthritis (RA), was found to be in linkage disequilibrium with these 2 SNPs (r<SUP>2</SUP> = 0.95) and demonstrated evidence of association with SLE in the same direction (meta‐analysis <I>P</I> = 9.15 × 10<SUP>−4</SUP>, OR 0.89 [95% CI 0.83–0.95]). The presence of thrombocytopenia improved the overall results in different populations (meta‐analysis <I>P</I> = 1.99 × 10<SUP>−6</SUP>, OR 0.57 [95% CI 0.45–0.72], for rs5030470). Finally, evidence of family‐based association in 34 African American pedigrees with the presence of thrombocytopenia was detected in 1 available SNP (rs5030437) with a Z score magnitude of 2.28 (<I>P</I> = 0.02) under a dominant model.</P><P><B>Conclusion</B></P><P>Our data indicate the presence of association of <I>TRAF6</I> with SLE, consistent with the previous report of association with RA. These data provide further support for the involvement of <I>TRAF6</I> in the pathogenesis of autoimmunity.</P>

Association of a functional variant downstream of TNFAIP3 with systemic lupus erythematosus

Adrianto, Indra,Wen, Feng,Templeton, Amanda,Wiley, Graham,King, Jarrod B,Lessard, Christopher J,Bates, Jared S,Hu, Yanqing,Kelly, Jennifer A,Kaufman, Kenneth M,Guthridge, Joel M,Alarc처n-Riquelme, Mart Nature Publishing Group, a division of Macmillan P 2011 Nature genetics Vol.43 No.3

Systemic lupus erythematosus (SLE, MIM152700) is an autoimmune disease characterized by self-reactive antibodies resulting in systemic inflammation and organ failure. TNFAIP3, encoding the ubiquitin-modifying enzyme A20, is an established susceptibility locus for SLE. By fine mapping and genomic re-sequencing in ethnically diverse populations, we fully characterized the TNFAIP3 risk haplotype and identified a TT>A polymorphic dinucleotide (deletion T followed by a T to A transversion) associated with SLE in subjects of European (P = 1.58 ? 10<SUP>??8</SUP>, odds ratio = 1.70) and Korean (P = 8.33 ? 10<SUP>??10</SUP>, odds ratio = 2.54) ancestry. This variant, located in a region of high conservation and regulatory potential, bound a nuclear protein complex composed of NF-觀B subunits with reduced avidity. Further, compared with the non-risk haplotype, the haplotype carrying this variant resulted in reduced TNFAIP3 mRNA and A20 protein expression. These results establish this TT>A variant as the most likely functional polymorphism responsible for the association between TNFAIP3 and SLE.

Preferential Binding to Elk-1 by SLE-Associated <i>IL10</i> Risk Allele Upregulates <i>IL10</i> Expression

Sakurai, Daisuke,Zhao, Jian,Deng, Yun,Kelly, Jennifer A.,Brown, Elizabeth E.,Harley, John B.,Bae, Sang-Cheol,Alarcό,n-Riquelme, Marta E.,Edberg, Jeffrey C.,Kimberly, Robert P.,Ramsey-Goldman, Ros Public Library of Science 2013 PLoS genetics Vol.9 No.10

<▼1><P>Immunoregulatory cytokine interleukin-10 (IL-10) is elevated in sera from patients with systemic lupus erythematosus (SLE) correlating with disease activity. The established association of <I>IL10</I> with SLE and other autoimmune diseases led us to fine map causal variant(s) and to explore underlying mechanisms. We assessed 19 tag SNPs, covering the <I>IL10</I> gene cluster including <I>IL19</I>, <I>IL20</I> and <I>IL24</I>, for association with SLE in 15,533 case and control subjects from four ancestries. The previously reported <I>IL10</I> variant, rs3024505 located at 1 kb downstream of <I>IL10</I>, exhibited the strongest association signal and was confirmed for association with SLE in European American (EA) (<I>P</I> = 2.7×10<SUP>−8</SUP>, OR = 1.30), but not in non-EA ancestries. SNP imputation conducted in EA dataset identified three additional SLE-associated SNPs tagged by rs3024505 (rs3122605, rs3024493 and rs3024495 located at 9.2 kb upstream, intron 3 and 4 of <I>IL10</I>, respectively), and SLE-risk alleles of these SNPs were dose-dependently associated with elevated levels of <I>IL10</I> mRNA in PBMCs and circulating IL-10 protein in SLE patients and controls. Using nuclear extracts of peripheral blood cells from SLE patients for electrophoretic mobility shift assays, we identified specific binding of transcription factor Elk-1 to oligodeoxynucleotides containing the risk (G) allele of rs3122605, suggesting rs3122605 as the most likely causal variant regulating <I>IL10</I> expression. Elk-1 is known to be activated by phosphorylation and nuclear localization to induce transcription. Of interest, phosphorylated Elk-1 (p-Elk-1) detected only in nuclear extracts of SLE PBMCs appeared to increase with disease activity. Co-expression levels of p-Elk-1 and IL-10 were elevated in SLE T, B cells and monocytes, associated with increased disease activity in SLE B cells, and were best downregulated by ERK inhibitor. Taken together, our data suggest that preferential binding of activated Elk-1 to the <I>IL10</I> rs3122605-G allele upregulates <I>IL10</I> expression and confers increased risk for SLE in European Americans.</P></▼1><▼2><P><B>Author Summary</B></P><P>Systemic lupus erythematosus (SLE), a debilitating autoimmune disease characterized by the production of pathogenic autoantibodies, has a strong genetic basis. Variants of the <I>IL10</I> gene, which encodes cytokine interleukin-10 (IL-10) with known function of promoting B cell hyperactivity and autoantibody production, are associated with SLE and other autoimmune diseases, and serum IL-10 levels are elevated in SLE patients correlating with increased disease activity. In this study, to discover SLE-predisposing causal variant(s), we assessed variants within the genomic region containing <I>IL10</I> and its gene family member <I>IL19</I>, <I>IL20</I> and <I>IL24</I> for association with SLE in case and control subjects from diverse ancestries. We identified SLE-associated SNP rs3122605 located at 9.2 kb upstream of <I>IL10</I> as the most likely causal variant in subjects of European ancestry. The SLE-risk allele of rs3122605 was dose-dependently associated with elevated <I>IL10</I> expression at both mRNA and protein levels in peripheral blood samples from SLE patients and controls, which could be explained, at least in part, by its preferential binding to Elk-1, a transcription factor activated in B cells during active disease of SLE patients. Elk-1-mediated IL-10 overexpression could be downregulated by inhibiting activation of mitogen-activated protein kinases, suggesting a potential therapeutic target for SLE.</P></▼2>

Decreased <i>SMG7</i> expression associates with lupus-risk variants and elevated antinuclear antibody production

Deng, Yun,Zhao, Jian,Sakurai, Daisuke,Sestak, Andrea L,Osadchiy, Vadim,Langefeld, Carl D,Kaufman, Kenneth M,Kelly, Jennifer A,James, Judith A,Petri, Michelle A,Bae, Sang-Cheol,Alarcó,n-Riquelme, H. K. Lewis 2016 Annals of the rheumatic diseases Vol.75 No.11

<B>Objectives</B><P>Following up the systemic lupus erythematosus (SLE) genome-wide association studies (GWAS) identification of <I>NMNAT2</I> at rs2022013, we fine-mapped its 150 kb flanking regions containing <I>NMNAT2</I> and <I>SMG7</I> in a 15 292 case-control multi-ancestry population and tested functions of identified variants.</P><B>Methods</B><P>We performed genotyping using custom array, imputation by IMPUTE 2.1.2 and allele specific functions using quantitative real-time PCR and luciferase reporter transfections. SLE peripheral blood mononuclear cells (PBMCs) were cultured with small interfering RNAs to measure antinuclear antibody (ANA) and cyto/chemokine levels in supernatants using ELISA.</P><B>Results</B><P>We confirmed association at <I>NMNAT2</I> in European American (EA) and Amerindian/Hispanic ancestries, and identified independent signal at <I>SMG7</I> tagged by rs2702178 in EA only (p=2.4×10<SUP>−8</SUP>, OR=1.23 (95% CI 1.14 to 1.32)). In complete linkage disequilibrium with rs2702178, rs2275675 in the promoter region robustly associated with <I>SMG7</I> mRNA levels in multiple expression quantitative trait locus (eQTL) datasets. Its risk allele was dose-dependently associated with decreased <I>SMG7</I> mRNA levels in PBMCs of 86 patients with SLE and 119 controls (p=1.1×10<SUP>−3</SUP> and 6.8×10<SUP>−8</SUP>, respectively) and conferred reduced transcription activity in transfected HEK-293 (human embryonic kidney cell line) and Raji cells (p=0.0035 and 0.0037, respectively). As a critical component in the nonsense-mediated mRNA decay pathway, SMG7 could regulate autoantigens including ribonucleoprotein (RNP) and Smith (Sm). We showed <I>SMG7</I> mRNA levels in PBMCs correlated inversely with ANA titres of patients with SLE (r=−0.31, p=0.01), and <I>SMG7</I> knockdown increased levels of ANA IgG and chemokine (C-C motif) ligand 19 in SLE PBMCs (p=2.0×10<SUP>−5</SUP> and 2.0×10<SUP>−4</SUP>, respectively).</P><B>Conclusion</B><P>We confirmed <I>NMNAT2</I> and identified independent <I>SMG7</I> association with SLE. The inverse relationship between levels of the risk allele-associated <I>SMG7</I> mRNAs and ANA suggested the novel contribution of mRNA surveillance pathway to SLE pathogenesis.</P>