Transcriptomic network analysis reveals key drivers of response to anti-TNF biologics in patients with rheumatoid arthritis.

OBJECTIVE: Anti-TNF biologics have been widely used to ameliorate disease activity in patients with rheumatoid arthritis (RA). However, a large fraction of patients show a poor response to these agents. Moreover, no clinically applicable predictive biomarkers have been established. This study aimed to identify response-associated biomarkers using longitudinal transcriptomic data in two independent RA cohorts. METHODS: RNA sequencing data from peripheral blood cell samples of Korean and Caucasian RA cohorts before and after initial treatment with anti-TNF biologics were analyzed to assess treatment-induced expression changes that differed between highly reliable excellent and null responders. Weighted correlation network, immune cell composition, and key driver analyses were performed to understand response-associated transcriptomic networks and cell types and their correlation with disease activity indices. RESULTS: In total, 305 response-associated genes showed significantly different treatment-induced expression changes between excellent and null responders. Co-expression network construction and subsequent key driver analysis revealed that 41 response-associated genes played a crucial role as key drivers of transcriptomic alteration in four response-associated networks involved in various immune pathways: type I interferon signalling, myeloid leucocyte activation, B cell activation, and NK cell/lymphocyte-mediated cytotoxicity. Transcriptomic response scores that we developed to estimate the individual-level degree of expression changes in the response-associated key driver genes were significantly correlated with the changes in clinical indices in independent patients with moderate or ambiguous response outcomes. CONCLUSIONS: This study provides response-specific treatment-induced transcriptomic signatures by comparing the transcriptomic landscape between patients with excellent and null responses to anti-TNF drugs at both gene and network levels.

Pregnancy Outcomes Associated With Biologic Agent Exposure in Patients With Several Rheumatic Diseases and Inflammatory Bowel Diseases.

BACKGROUND: This study aimed to analyze pregnancy outcomes based on biologic agents use in women using the nationwide population-based database. METHODS: The study used the claims database to identify women of childbearing age with several rheumatic (rheumatoid arthritis, juvenile idiopathic arthritis, ankylosing spondylitis, psoriatic arthritis) and inflammatory bowel diseases (Crohn's disease and ulcerative colitis) who had pregnancy-related codes between January 2010 and December 2019. We analyzed live births and adverse pregnancy outcomes based on the previous use of biologics. We also stratified the patients according to duration of biologic agent exposure before pregnancy and the use of biologics during pregnancy to analyze the pregnancy outcomes by subgroups. RESULTS: We identified 4,787 patients with pregnancy events. Among them, 1,034 (21.6%) used biologics before pregnancy. Live birth rate was not different between the biologics group and biologics naïve group (75.0% vs. 75.2%). Multivariate analyses showed that biologics use was associated with higher risk of intrauterine growth retardation (odds ratio [OR], 1.780) and lower risk of gestational diabetes mellitus (OR, 0.776) compared with biologics naïve. Biologics use during pregnancy was associated with higher risk of preterm delivery (OR, 1.859), preeclampsia/eclampsia (OR, 1.762), intrauterine growth retardation (OR, 3.487), and cesarean section (OR, 1.831), but lower risk of fetal loss (OR, 0.274) compared with biologics naïve. CONCLUSIONS: Although there was no difference in live birth rate between the biologics group and biologics naïve group, biologics use seems to be associated with several adverse pregnancy outcomes, especially in patients with biologics during pregnancy. Therefore, patients with biologics during pregnancy need to be carefully observed for adverse pregnancy outcomes.

Novel classification of axial spondyloarthritis to predict radiographic progression using machine learning.

OBJECTIVES: Prediction and determination of drug efficacy for radiographic progression is limited by the heterogeneity inherent in axial spondyloarthritis (axSpA). We investigated whether unbiased clustering analysis of phenotypic data can lead to coherent subgroups of axSpA patients with a distinct risk of radiographic progression. METHODS: A group of 412 patients with axSpA was clustered in an unbiased way using a agglomerative hierarchical clustering method, based on their phenotype mapping. We used a generalised linear model, naïve Bayes, Decision Trees, K-Nearest-Neighbors, and Support Vector Machines to construct a consensus classification method. Radiographic progression over 2 years was assessed using the modified Stoke Ankylosing Spondylitis Spine Score (mSASSS). RESULTS: axSpA patients were classified into three distinct subgroups with distinct clinical characteristics. Sex, smoking, HLA-B27, baseline mSASSS, uveitis, and peripheral arthritis were the key features that were found to stratifying the phenogroups. The three phenogroups showed distinct differences in radiographic progression rate (p<0.05) and the proportion of progressors (p<0.001). Phenogroup 2, consisting of male smokers, had the worst radiographic progression, while phenogroup 3, exclusively suffering from uveitis, showed the least radiographic progression. The axSpA phenogroup classification, including its ability to stratify risk, was successfully replicated in an independent validation group. CONCLUSIONS: Phenotype mapping results in a clinically relevant classification of axSpA that is applicable for risk stratification. Novel coupling between phenotypic features and radiographic progression can provide a glimpse into the mechanisms underlying divergent and shared features of axSpA.

Association of influenza infection with hospitalisation-related systemic lupus erythematosus flares: a time series analysis.

OBJECTIVES: This study aimed to investigate whether the influenza annual outbreak in Korea is related to hospitalisation-related flares in systemic lupus erythematosus (SLE) patients. METHODS: The weekly frequency of hospitalisation-related SLE flares (2012-2015) was collected from the Korean National Health Insurance claim database. The weekly laboratory-confirmed detection rate of influenza infection was obtained from the Korea Centers for Disease Control and Prevention database. A generalised linear model was used to examine the relative risks (RRs) of hospitalisation-related SLE flares associated with influenza infection, after adjusting for time trends and meteorological data. RESULTS: A total of 2,223 hospitalisation-related SLE flares were analysed. An interquartile range (24.5%) increase in influenza infection was associated with a 14.0% increase in hospitalisation-related SLE flares (RR, 1.14; 95% confidence interval [CI]: 1.04-1.25; p=0.006). In addition, influenza infections at lag 0-1 (over 2 weeks including concurrent and 1 previous week) and lag 0-2 (over 3 weeks including concurrent and 2 previous weeks) were associated with increase in hospitalisation-related SLE flares (RR, 1.14; 95% confidence interval [CI]: 1.03-1.26; p=0.014 and RR, 1.13; 95% CI: 1.02-1.26; p=0.023). Significant associations were especially observed in women (RR, 1.15; 95% CI: 1.15-1.16; p=0.006) and immunosuppressant (RR, 1.26; 95% CI: 1.26-1.27; p<0.001) or glucocorticoid recipients (RR, 1.17, 95% CI: 1.16-1.17; p=0.004). CONCLUSIONS: This study shows a significant association between seasonal influenza infection and flares in SLE patients, which suggests influenza can be a novel environmental risk factor for SLE flares.

Lupus Risk Variant Increases pSTAT1 Binding and Decreases ETS1 Expression.

Genetic variants at chromosomal region 11q23.3, near the gene ETS1, have been associated with systemic lupus erythematosus (SLE), or lupus, in independent cohorts of Asian ancestry. Several recent studies have implicated ETS1 as a critical driver of immune cell function and differentiation, and mice deficient in ETS1 develop an SLE-like autoimmunity. We performed a fine-mapping study of 14,551 subjects from multi-ancestral cohorts by starting with genotyped variants and imputing to all common variants spanning ETS1. By constructing genetic models via frequentist and Bayesian association methods, we identified 16 variants that are statistically likely to be causal. We functionally assessed each of these variants on the basis of their likelihood of affecting transcription factor binding, miRNA binding, or chromatin state. Of the four variants that we experimentally examined, only rs6590330 differentially binds lysate from B cells. Using mass spectrometry, we found more binding of the transcription factor signal transducer and activator of transcription 1 (STAT1) to DNA near the risk allele of rs6590330 than near the non-risk allele. Immunoblot analysis and chromatin immunoprecipitation of pSTAT1 in B cells heterozygous for rs6590330 confirmed that the risk allele increased binding to the active form of STAT1. Analysis with expression quantitative trait loci indicated that the risk allele of rs6590330 is associated with decreased ETS1 expression in Han Chinese, but not other ancestral cohorts. We propose a model in which the risk allele of rs6590330 is associated with decreased ETS1 expression and increases SLE risk by enhancing the binding of pSTAT1.

Two functional lupus-associated BLK promoter variants control cell-type- and developmental-stage-specific transcription.

Efforts to identify lupus-associated causal variants in the FAM167A/BLK locus on 8p21 are hampered by highly associated noncausal variants. In this report, we used a trans-population mapping and sequencing strategy to identify a common variant (rs922483) in the proximal BLK promoter and a tri-allelic variant (rs1382568) in the upstream alternative BLK promoter as putative causal variants for association with systemic lupus erythematosus. The risk allele (T) at rs922483 reduced proximal promoter activity and modulated alternative promoter usage. Allelic differences at rs1382568 resulted in altered promoter activity in B progenitor cell lines. Thus, our results demonstrated that both lupus-associated functional variants contribute to the autoimmune disease association by modulating transcription of BLK in B cells and thus potentially altering immune responses.

Digital tomosynthesis as a new diagnostic tool for evaluation of spine damage in patients with ankylosing spondylitis.

We aimed to compare digital tomosynthesis (DTS) with radiographs for the assessment of spinal bone damage in patients with ankylosing spondylitis (AS). The study comprised 68 patients with AS who underwent both DTS and radiographs of the cervical and lumbar spine on the same day. Spinal bone damage was assessed using the modified Stoke Ankylosing Spondylitis Spinal Score (mSASSS) and the presence of facet joint damage. The Wilcoxon signed-rank test and McNemar's test were used to compare spinal bone damage between the two modalities. In 68 AS patients with mean 4.5 years of disease duration, the mean mSASSS was 11.7 ± 11.3 with radiographs and 13.1 ± 11.5 with DTS (p = 0.001). A grade 1 (erosion, sclerosis, or squaring) score in the mSASSS system was higher with DTS than with radiographs (p = 0.001), but grade 2 (syndesmophyte) and grade 3 (bridge) scores (p > 0.005 each) were not. In particular, the grade 1 score was higher with DTS than with radiographs at the cervicothoracic (p < 0.001) and thoracolumbar (p = 0.003) junctions. With regard to facet joint damage, erosion/sclerosis of facet joints was better depicted by DTS than by radiographs in the cervical (54.4 vs. 22.1%, p < 0.001) and lumbar spine (72.1 vs. 11.8%, p < 0.001). DTS depicted more subtle damage of spinal vertebrae in patients with AS than radiographs did. Moreover, erosion/sclerosis of facet joints was better detected with DTS than with radiographs.

Medial Synovial Fold of the Posterior Cruciate Ligament on Knee Magnetic Resonance Imaging and Arthroscopy: Retrospective Investigation of Impingement.

OBJECTIVE: The purpose of this study was to classify the types of medial synovial fold of the posterior cruciate ligament (PCL) on magnetic resonance imaging (MRI) and to identify the relationships between fold type and impingement of the PCL on arthroscopy. SUBJECTS AND METHODS: Ninety-nine patients who underwent knee MRI and arthroscopy were included. All MRIs were retrospectively and independently assessed by 2 radiologists. Medial synovial folds of the PCL on MRI were categorized into 3 types. Type A showed no medial synovial fold. Type B showed a small synovial protrusion that did not extend beyond an imaginary line drawn from the medial tibial spine to the lateral aspect of the medial femoral condyle. Type C had a long enough fold to extend beyond the imaginary line. The presence of a tear in the anterior cruciate ligament, PCL, or menisci and impingement of the PCL were obtained from arthroscopic records. RESULTS: Intraobserver agreement in the classification of medial synovial folds was nearly perfect (κ = 0.850). Interobserver agreement was substantial (κ = 0.759). Of 99 cases, 34 were type A, 41 were type B, and 24 were type C folds on MRI. Thirty-nine impingements of the PCL (39.4%) were identified on arthroscopy. Multivariable analysis revealed that type C folds were 40.60 times more likely to have impingement than type A folds (odds ratio, 40.60; 95% confidence interval, 8.73-188.93; P < 0.001). CONCLUSIONS: Of the 3 types of medial synovial folds, type C was significantly associated with impingement of the PCL on arthroscopy. Therefore, type C folds may be a cause of internal derangement of the knee.

Loss of anterior concavity of the first sacrum can predict spinal involvement in ankylosing spondylitis.

In this study, we evaluated the frequency of squaring of the first sacrum (S1), defined as the loss of anterior concavity, in patients with ankylosing spondylitis (AS). We also determined the interobserver reliability in the assessment of S1 squaring and the relationships of S1 squaring with MRI findings and the modified Stoke Ankylosing Spondylitis Spinal Score (mSASSS). To this end, we performed a retrospective study of 100 patients with AS (mean age 33.2 years; range 19-57 years) and 100 control patients (mean age 35.6 years; range 19-50 years). Four experienced radiologists independently assessed the presence of S1 squaring in the AS and control groups. The frequencies of S1 squaring as scored by the four observers were 47, 48, 46, and 42 in the AS group and 3, 6, 4, and 6 in the control group. The interobserver agreement among the four observers with respect to S1 squaring was excellent (κ value 0.80) in the AS group and fair to good (κ value 0.61) in the control group. In patients with AS, the presence of S1 squaring showed fair to good agreement with the MRI changes (κ value 0.74). Moreover, the mSASSSs of patients with versus without S1 squaring were significantly different (mean 23.9 vs 7.0, p < 0.001). In conclusion, S1 squaring is relatively common in patients with AS. Moreover, S1 squaring is closely correlated with MRI changes and significantly associated with the mSASSS. Assessment of S1 squaring could be a simple method that is potentially useful for predicting early spinal structural involvement in patients with AS.

Direct medical costs and their predictors in South Korean patients with systemic lupus erythematosus.

We aimed to estimate the annual direct medical costs of South Korean systemic lupus erythematosus (SLE) patients, and their predictors. The 2010 annual direct medical costs of SLE patients in the Hanyang BAE Lupus cohort in South Korea were assessed. The information was taken directly from the hospital database and medical records, and included clinical characteristics, disease activity, organ damage, and healthcare utilization. Cost predictors were estimated with a multivariate linear regression model. A total of 749 SLE patients (92.7 % female, mean age 35.7 ± 11.3 years, mean disease duration 9.6 ± 4.9 years) were studied. Their mean annual direct medical costs amounted to USD 3305. The largest component of these costs was the cost of medication (USD 1269, 38.4 %), followed by those of diagnostic procedures and tests (USD 1177, 35.6 %). Regression analysis showed that adjusted mean SLE disease activity index score (p < 0.0001), systemic damage index (p < 0.0001), and renal (p = 0.0039) and hematologic (p = 0.0353) involvement were associated with increased direct medical costs, whereas longer disease duration was associated with lower direct medical costs. Greater disease activity and greater organ damage predict higher costs for South Korean SLE patients. Major organ involvement such as renal disorder and hematologic involvement also predicts higher costs, whereas longer duration of disease predicts lower costs.

Prevalence, incidence, and associated factors of avascular necrosis in Korean patients with systemic lupus erythematosus: a nationwide epidemiologic study.

Avascular necrosis (AVN) is one of the most frequent types of organ damage in systemic lupus erythematosus (SLE). However, little is currently known about the epidemiology of AVN in SLE patients. The aim of this study was to estimate the prevalence and incidence of AVN in Korean patients with SLE based on National Health Insurance (NHI) claims data and to determine the risk factors for AVN among SLE patients. This study was conducted using the 2006-2010 data of 25,358 SLE patients from the NHI program. AVN cases were defined as those with at least one diagnosis of AVN. The prevalence was calculated by dividing the number of AVN cases by the number of SLE cases in the same year. The annual incidence was calculated by dividing the number of incident AVN cases by the number of SLE-prevalent cases not previously diagnosed with AVN. Patients who developed AVN in 2008-2010 were compared with SLE patients who did not develop AVN to identify any risk factors. The prevalence of AVN among SLE patients (2006-2010) was 31.5-34.2 per 1,000 persons and was similar in all the years studied. The incidence per 1,000 persons of AVN among SLE patients was 8.6 [95 % confidence interval (95 % CI) 6.9-10.3] in 2008, 9.8 (95 % CI 8.0-11.6) in 2009, and 8.4 (95 % CI 6.8-10.0) in 2010. Regression analysis indicated that taking an oral corticosteroid [odds ratio (OR) 2.12, 95 % CI 1.39-3.23] or an intravenous corticosteroid (OR 1.5, 95 % CI 1.2-1.89) was significantly associated with AVN. In addition, AVN was associated with use of immunosuppressive agents (OR 2.12, 95 % CI 1.66-2.72), hydroxychloroquine (OR 1.4, 95 % CI 1.09-1.81), and lipid-lowering agents (OR 1.78, 95 % CI 1.24-2.57) among the prescribed medications, and with hypertension (OR 1.39, 95 % CI 1.08-1.79) among the comorbidities. The prevalence and incidence of AVN among SLE patients, which were 31.5-34.2 and 8.4-9.8 per 1,000 persons, respectively, may be representative of the entire population of symptomatic AVN patients with SLE in Korea. AVN is associated with the use of corticosteroids, immunosuppressants, hydroxychloroquine, lipid-lowering agents, and with hypertension. Studies of large, prospective cohorts are needed to confirm these results.

Association of an activity-enhancing variant of IRAK1 and an MECP2-IRAK1 haplotype with increased susceptibility to rheumatoid arthritis.

OBJECTIVE: To investigate whether a human X chromosome locus of IRAK1 and MECP2 is associated with susceptibility to rheumatoid arthritis (RA), an autoimmune disease that predominantly affects women. METHODS: A total of 2,334 unrelated Korean participants (including 1,318 patients with RA) were genotyped for 5 tag single-nucleotide polymorphisms (SNPs) and 3 additional SNPs in an Xq28 region harboring MECP2 and IRAK1. Twenty-nine additional neighboring SNPs were imputed using the Korean HapMap Project data. All 37 SNPs were statistically tested for association with RA susceptibility, and 2 SNPs associated with RA were examined for their functional effects. RESULTS: RA susceptibility was associated with multiple SNPs in a 79-kb linkage disequilibrium block harboring both MECP2 and IRAK1. The most significant association was for MECP2 SNP rs1734792 (P = 0.00089), but 2 nonsynonymous IRAK1 SNPs, rs1059702 (P = 0.0034) and rs1059703 (P = 0.0042), which were in strong linkage disequilibrium with the MECP2 SNP (D' = 0.87 and 0.91, respectively) affected IRAK1 protein activity. The major haplotype of the 2 nonsynonymous SNPs was associated with a 1.7-fold increase in RA susceptibility versus the minor haplotype (P = 0.0082), and with increased IRAK1 activity, which was demonstrated by a 1.7-fold increase in the intracellular activity of transcription factor NF-κB. CONCLUSION: Our findings indicate that RA susceptibility is associated with multiple SNPs in MECP2 and IRAK1, but high linkage disequilibrium between them does not allow for further localization. Therefore, both genes remain candidates. Nevertheless, the major haplotype of the 2 nonsynonymous IRAK1 SNPs encoding for pPhe196Ser and pSer532Leu confers enhanced IRAK1 activity and, consequently, enhanced susceptibility to RA, as compared to the minor haplotype.

Prevalence and incidence of systemic lupus erythematosus in South Korea.

The aim of this study was to estimate the nationwide prevalence and incidence of systemic lupus erythematosus (SLE) in South Korea. National Health Insurance claims data covering almost all Koreans (~50 million) during 2006-2010 were analyzed. Individuals with SLE were identified if (1) they had experienced at least one hospitalization for SLE (International Classification of Diseases, 10th revision code M32), (2) they had taken at least one concomitant prescription of immunosuppressant and hydroxychloroquine, or (3) they had taken anti-dsDNA antibody (≥2) or complement tests (≥2) during each calendar year. Incident cases were defined only if they had not been SLE prevalent for the preceding 2 years and had been SLE prevalent for 2 years consecutively thereafter. The annual prevalence (per 100,000) increased slightly from 20.6 [95% confidence interval (95% CI) 20.2-21.0] in 2006 to 26.5 (95% CI 26.0-27.0) in 2010, and the incidence (per 100,000) ranged between 2.5 (95% CI 2.4-2.6) in 2008 and 2.8 (95% CI 2.7-2.9) in 2009. The number of SLE-prevalent female patients outnumbered SLE-prevalent male patients by approximately sixfold, with a female-to-male incidence ratio of ~9:1. The prevalence and incidence of SLE increased significantly with age, regardless of sex, to a peak the age of 30-39 years. However, while both of them significantly decreased thereafter in females, this tendency was not observed in males.

Associations of upper respiratory mucosa microbiota with Rheumatoid arthritis, autoantibodies, and disease activity.

The lung is recognized as a site for initiating the formation of self-antigen and autoimmune responses in rheumatoid arthritis (RA). We aimed to investigate the association of upper respiratory microbiota with RA, autoantibody production, and disease activity. Forty-six patients with RA and 17 controls were examined. Nasopharyngeal swab samples were sequenced for microbiome profiling using the V3-V4 region of the 16S rRNA gene. The microbial diversity and relative abundance were compared between RA patients and controls. Correlation analyses were conducted to evaluate the relationship between microbial abundance and clinical markers such as autoantibodies and disease activity. Microbial diversity analysis revealed no major differences between RA patients and healthy controls. However, beta diversity analysis indicated a subtle distinction in microbial composition (unweighted UniFrac distance) between the two groups (P = 0.03), hinting at a minor subset of microbiota associated with disease status. Differential abundance analysis uncovered specific taxa at various taxonomic levels, including Saccharibacteria (TM7) [O-1] (PFDR = 2.53 × 10-2), TM7 [F-1] (PFDR = 5.20 × 10-3), Microbacterium (PFDR = 3.37 × 10-4), and Stenotrophomonas (PFDR = 2.57 × 10-3). The relative abundance of ten genera correlated significantly with anti-cyclic citrullinated peptide (anti-CCP) antibody levels (PFDR < 0.05) and 11 genera were significantly associated with disease activity markers, including ESR, CRP, DAS28-ESR, and DAS-CRP (PFDR < 0.05). In particular, Saccharibacteria TM7 [G-3] and Peptostreptococcaceae [XI] [G-1] were correlated with all disease activity biomarkers. Dysbiosis in the upper respiratory mucosa is associated with RA, anti-CCP antibody levels, and disease activity.

Correction: Associations of upper respiratory mucosa microbiota with Rheumatoid arthritis, autoantibodies, and disease activity.

[This corrects the article DOI: 10.1371/journal.pone.0308010.].

Association of HLA-DRB1 locus with treatment response to abatacept or TNF inhibitors in patients with seropositive rheumatoid arthritis.

The strongest genetic risk factor for rheumatoid arthritis (RA) has been known as HLA-DRB1 based on amino acid positions 11, 71, and 74. This study analyzed the association between specific HLA-DRB1 locus and treatment response to abatacept or TNF inhibitors (TNFi) in patients with seropositive RA. A total of 374 Korean RA patients were treated with abatacept (n = 110) or TNFi (n = 264). Associations between HLA-DRB1 and treatment response after 6 months were analyzed using multivariable logistic regression. Seropositive RA patients with HLA-DRB1 shared epitope (SE) had a favorable response to abatacept (OR = 3.67, P = 0.067) and an inversely associated response to TNFi (OR 0.57, P = 0.058) based on EULAR response criteria, but the difference was not statistically significant in comparison to those without SE. In analyses using amino acid positions of HLA-DRB1, a significant association was found between valine at amino acid position 11 of SE and good response to abatacept (OR = 6.46, P = 5.4 × 10-3). The VRA haplotype also showed a good response to abatacept (OR = 4.56, P = 0.013), but not to TNFi. Our results suggest that treatment response to abatacept or TNFi may differ depending on HLA-DRB1 locus in seropositive RA, providing valuable insights for selecting optimal therapy.

Association of genetic polymorphisms in CD40 with susceptibility to SLE in the Korean population.

OBJECTIVE: The aim of this study was to examine the association of CD40 polymorphisms with the risk of SLE in the Korean population. METHODS: A total of 601 Korean SLE patients and 984 healthy controls were enrolled. We selected seven CD40 gene SNPs based on previous results of CD40 gene sequencing in the Korean population. Statistical analysis was carried out by logistic regression, controlling for age and sex as covariates. Odds ratios (ORs) and P-values in co-dominant, dominant and recessive models were also calculated. RESULTS: SNP rs3765456 showed significant association with risk of SLE (OR = 1.34, P = 0.007, Pcorr = 0.03) in the dominant model. SNPs rs1883832 and rs4810485, and haplotype 2 (GTTCTAA) were also associated with the risk of SLE in the dominant model, but statistical significance disappeared after correction for multiple testing. Haplotype 2 had a protective effect on LN (OR = 0.47, P = 0.01, Pcorr = 0.05) in the recessive model while rs73115010, rs6074028 and haplotype 3 (ACGTCGG) resulted in increased risk of arthritis in the recessive model (OR = 2.87, 2.76 and 2.46, P = 0.002, 0.004 and 0.01, Pcorr = 0.009, 0.02 and 0.05, respectively). CONCLUSION: CD40 gene polymorphisms are possible risk factors for SLE development, especially rs3765456 in the dominant model. CD40 polymorphisms are also associated with SLE clinical manifestation, mainly nephritis and arthritis. Further replication with larger numbers, and populations of different ethnicities, are needed to confirm our findings.

Association of two independent functional risk haplotypes in TNIP1 with systemic lupus erythematosus.

OBJECTIVE: Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by autoantibody production and altered type I interferon expression. Genetic surveys and genome-wide association studies have identified >30 SLE susceptibility genes. One of these genes, TNIP1, encodes the ABIN1 protein. ABIN1 functions in the immune system by restricting NF-κB signaling. The present study was undertaken to investigate the genetic factors that influence association with SLE in genes that regulate the NF-κB pathway. METHODS: We analyzed a dense set of genetic markers spanning TNIP1 and TAX1BP1, as well as the TNIP1 homolog TNIP2, in case-control populations of diverse ethnic origins. TNIP1, TNIP2, and TAX1BP1 were fine-mapped in a total of 8,372 SLE cases and 7,492 healthy controls from European-ancestry, African American, Hispanic, East Asian, and African American Gullah populations. Levels of TNIP1 messenger RNA (mRNA) and ABIN1 protein in Epstein-Barr virus-transformed human B cell lines were analyzed by quantitative reverse transcription-polymerase chain reaction and Western blotting, respectively. RESULTS: We found significant associations between SLE and genetic variants within TNIP1, but not in TNIP2 or TAX1BP1. After resequencing and imputation, we identified 2 independent risk haplotypes within TNIP1 in individuals of European ancestry that were also present in African American and Hispanic populations. Levels of TNIP1 mRNA and ABIN1 protein were reduced among subjects with these haplotypes, suggesting that they harbor hypomorphic functional variants that influence susceptibility to SLE by restricting ABIN1 expression. CONCLUSION: Our results confirm the association signals between SLE and TNIP1 variants in multiple populations and provide new insight into the mechanism by which TNIP1 variants may contribute to SLE pathogenesis.