[Show abstract][Hide abstract]ABSTRACT: Genome wide association studies have identified variants in PXK that confer risk for humoral autoimmune diseases, including systemic lupus erythematosus (SLE or lupus), rheumatoid arthritis and more recently systemic sclerosis. While PXK is involved in trafficking of epidermal growth factor Receptor (EGFR) in COS-7 cells, mechanisms linking PXK to lupus pathophysiology have remained undefined. In an effort to uncover the mechanism at this locus that increases lupus-risk, we undertook a fine-mapping analysis in a large multi-ancestral study of lupus patients and controls. We define a large (257kb) common haplotype marking a single causal variant that confers lupus risk detected only in European ancestral populations and spans the promoter through the 3' UTR of PXK. The strongest association was found at rs6445972 with P < 4.62 × 10(-10), OR 0.81 (0.75-0.86). Using stepwise logistic regression analysis, we demonstrate that one signal drives the genetic association in the region. Bayesian analysis confirms our results, identifying a 95% credible set consisting of 172 variants spanning 202 kb. Functionally, we found that PXK operates on the B-cell antigen receptor (BCR); we confirmed that PXK influenced the rate of BCR internalization. Furthermore, we demonstrate that individuals carrying the risk haplotype exhibited a decreased rate of BCR internalization, a process known to impact B cell survival and cell fate. Taken together, these data define a new candidate mechanism for the genetic association of variants around PXK with lupus risk and highlight the regulation of intracellular trafficking as a genetically regulated pathway mediating human autoimmunity.
Full-text · Article · Jan 2014 · Frontiers in Genetics
[Show abstract][Hide abstract]ABSTRACT: Recent reports have associated NCF2, encoding a core component of the multi-protein NADPH oxidase (NADPHO), with systemic lupus erythematosus (SLE) susceptibility in individuals of European ancestry. To identify ethnicity-specific and -robust variants within NCF2, we assessed 145 SNPs in and around the NCF2 gene in 5325 cases and 21 866 controls of European-American (EA), African-American (AA), Hispanic (HS) and Korean (KR) ancestry. Subsequent imputation, conditional, haplotype and bioinformatic analyses identified seven potentially functional SLE-predisposing variants. Association with non-synonymous rs17849502, previously reported in EA, was detected in EA, HS and AA (PEA = 1.01 × 10-54, PHS = 3.68 × 10-10, PAA = 0.03); synonymous rs17849501 was similarly significant. These SNPs were monomorphic in KR. Novel associations were detected with coding variants at rs35937854 in AA (PAA = 1.49 × 10-9), and rs13306575 in HS and KR (PHS = 7.04 × 10-7, PKR = 3.30 × 10-3). In KR, a 3-SNP haplotype was significantly associated (P = 4.20 × 10-7), implying that SLE predisposing variants were tagged. Significant SNP-SNP interaction (P = 0.02) was detected between rs13306575 and rs17849502 in HS, and a dramatically increased risk (OR = 6.55) with a risk allele at each locus. Molecular modeling predicts that these non-synonymous mutations could disrupt NADPHO complex assembly. The risk allele of rs17849501, located in a conserved transcriptional regulatory region, increased reporter gene activity, suggesting in vivo enhancer function. Our results not only establish allelic heterogeneity within NCF2 associated with SLE, but also emphasize the utility of multi-ethnic cohorts to identify predisposing variants explaining additional phenotypic variance ('missing heritability') of complex diseases like SLE.
Full-text · Article · Nov 2013 · Human Molecular Genetics
[Show abstract][Hide abstract]ABSTRACT: Comparison of recombination at TNFSF4 in African-American TNFSF4risk and TNFSF4non-risk individuals. Phased chromosomes from African-American SLE individuals homozygous for TNFSF4risk (n = 10) and TNFSF4non-risk(n = 10) were tested for recombination using Rhomap from the LDHAT2.0 package. A fine-scale map of recombination rate (4Ner/kb) across 250 kb of chromosome 1q25 which encompassed TNFSF4 and extended 5′ and 3′ regions was inferred. Individuals were identified as homozygous for TNFSF4risk or TNFSF4non-risk. We ran Rhomap for a total of 1,100,000 rjMCMC iterations including a burn-in of 100000 iterations, sampling the chain after every 100. Grey diamonds indicate the location to scale of SNPs significantly associated with risk of SLE in this cohort, the TNFSF4 gene is also located to scale under the graph. (EPS)
[Show abstract][Hide abstract]ABSTRACT: Left, Principal component (PC) 1 versus PC2 analyses of four Hapmap III African (yellow) and two Hapmap III European (red) populations and our African-American SLE-control cohort (black). Right. Population stratification between African-American cases (red) and controls (black) was minimised by principal components analysis using 367 major ancestry informative markers. This figure depicts the most profound ancestry differences along continuous axis of variation between cases and controls after QC filtering of the AA cohort. (EPS)
[Show abstract][Hide abstract]ABSTRACT: We previously established an 80 kb haplotype upstream of TNFSF4 as a susceptibility locus in the autoimmune disease SLE. SLE-associated alleles at this locus are associated with inflammatory disorders, including atherosclerosis and ischaemic stroke. In Europeans, the TNFSF4 causal variants have remained elusive due to strong linkage disequilibrium exhibited by alleles spanning the region. Using a trans-ancestral approach to fine-map the locus, utilising 17,900 SLE and control subjects including Amerindian/Hispanics (1348 cases, 717 controls), African-Americans (AA) (1529, 2048) and better powered cohorts of Europeans and East Asians, we find strong association of risk alleles in all ethnicities; the AA association replicates in African-American Gullah (152,122). The best evidence of association comes from two adjacent markers: rs2205960-T (P = 1.71×10(-34) , OR = 1.43[1.26-1.60]) and rs1234317-T (P = 1.16×10(-28) , OR = 1.38[1.24-1.54]). Inference of fine-scale recombination rates for all populations tested finds the 80 kb risk and non-risk haplotypes in all except African-Americans. In this population the decay of recombination equates to an 11 kb risk haplotype, anchored in the 5' region proximal to TNFSF4 and tagged by rs2205960-T after 1000 Genomes phase 1 (v3) imputation. Conditional regression analyses delineate the 5' risk signal to rs2205960-T and the independent non-risk signal to rs1234314-C. Our case-only and SLE-control cohorts demonstrate robust association of rs2205960-T with autoantibody production. The rs2205960-T is predicted to form part of a decameric motif which binds NF-κBp65 with increased affinity compared to rs2205960-G. ChIP-seq data also indicate NF-κB interaction with the DNA sequence at this position in LCL cells. Our research suggests association of rs2205960-T with SLE across multiple groups and an independent non-risk signal at rs1234314-C. rs2205960-T is associated with autoantibody production and lymphopenia. Our data confirm a global signal at TNFSF4 and a role for the expressed product at multiple stages of lymphocyte dysregulation during SLE pathogenesis. We confirm the validity of trans-ancestral mapping in a complex trait.
[Show abstract][Hide abstract]ABSTRACT: We used the Immunochip array to analyze 2,816 individuals with juvenile idiopathic arthritis (JIA), comprising the most common subtypes (oligoarticular and rheumatoid factor-negative polyarticular JIA), and 13,056 controls. We confirmed association of 3 known JIA risk loci (the human leukocyte antigen (HLA) region, PTPN22 and PTPN2) and identified 14 loci reaching genome-wide significance (P < 5 x 10(-8)) for the first time. Eleven additional new regions showed suggestive evidence of association with JIA (P < 1 x 10(-6)). Dense mapping of loci along with bioinformatics analysis refined the associations to one gene in each of eight regions, highlighting crucial pathways, including the interleukin (IL)-2 pathway, in JIA disease pathogenesis. The entire Immunochip content, the HLA region and the top 27 loci (P < 1 x 10(-6)) explain an estimated 18, 13 and 6% of the risk of JIA, respectively. In summary, this is the largest collection of JIA cases investigated so far and provides new insight into the genetic basis of this childhood autoimmune disease.
[Show abstract][Hide abstract]ABSTRACT: Objective:
Little is known about the genetic etiology of systemic lupus erythematosus (SLE) in individuals of African ancestry, despite its higher prevalence and greater disease severity. Overproduction of nitric oxide (NO) and reactive oxygen species are implicated in the pathogenesis and severity of SLE, making NO synthases and other reactive intermediate-related genes biological candidates for disease susceptibility. We analyzed variation in reactive intermediate genes for association with SLE in 2 populations with African ancestry.
A total of 244 single-nucleotide polymorphisms (SNP) from 53 regions were analyzed in non-Gullah African Americans (AA; 1432 cases and 1687 controls) and the genetically more homogeneous Gullah of the Sea Islands of South Carolina (133 cases and 112 controls). Single-marker, haplotype, and 2-locus interaction tests were computed for these populations.
The glutathione reductase gene GSR (rs2253409; p = 0.0014, OR 1.26, 95% CI 1.09-1.44) was the most significant single SNP association in AA. In the Gullah, the NADH dehydrogenase NDUFS4 (rs381575; p = 0.0065, OR 2.10, 95% CI 1.23-3.59) and NO synthase gene NOS1 (rs561712; p = 0.0072, OR 0.62, 95% CI 0.44-0.88) were most strongly associated with SLE. When both populations were analyzed together, GSR remained the most significant effect (rs2253409; p = 0.00072, OR 1.26, 95% CI 1.10-1.44). Haplotype and 2-locus interaction analyses also uncovered different loci in each population.
These results suggest distinct patterns of association with SLE in African-derived populations; specific loci may be more strongly associated within select population groups.
No preview · Article · May 2013 · The Journal of Rheumatology
[Show abstract][Hide abstract]ABSTRACT: Follow-up case-control association results. Case-control association results for the follow-up study at selected candidate genes from the strongest admixture peak (2q22–q24) using 1525 cases and 1810 controls from CCAA and 3968 cases and 3542 controls from CCEA pinpoint IFIH1 as a candidate gene for SLE. * Allele frequencies given correspond to the A1 allele. Local ancestry correction is labeled as Pc, whereas P-value refers to the uncorrected value.
[Show abstract][Hide abstract]ABSTRACT: Geographical distribution of allele frequencies for our 3 independently associated SNPs in IFIH1. Allele frequency differences between populations of the Human Genome Diversity Project for our three independent SNPs of interest show a south-to-north gradient of increase in allele frequency of derived (risk) alleles. Source HGDP Selection browser (http://hgdp.uchicago.edu/cgi-bin/gbrowse/HGDP/) (accessed January 2012).
[Show abstract][Hide abstract]ABSTRACT: Genetic models of association of IFIH1 with SLE. Genetic models at each independent SNP for African-Americans (AA) and European-Americans (EA) show that the best model for rs1990760 and rs130233890 are allelic, and dominant for rs10930046. The best model was chosen using the Akaike information criterion (AIC).
[Show abstract][Hide abstract]ABSTRACT: Risk allele frequencies and Fst values between populations for three IFIH1 SNPs. Local ancestry at three SNPs in IFIH1 was estimated for AA. Individuals whose ancestral state was European (N = 129) and African (N = 2124) were selected, and their risk allele (“A”) frequency compared with allele frequencies in CEPH and YRI. FST was calculated between these groups.
[Show abstract][Hide abstract]ABSTRACT: Overview of study design, samples sizes, ethnicity and demographics. Our study comprised admixture mapping on African Americans (AA), followed by a case-control study on AA and individuals of European Ancestry (EA). Data sources: Oklahoma Medical Research Foundation (OMRF); Dallas Heart Study (DHS); University of Alabama at Birmingham (UAB); Study of Addiction Gene x Environment (SAGE); Health ABC (HABC); Wellcome Trust Consortium Case Control Study (WTCC). CCAA and CCEA are cases and controls from AA and EA samples genotyped at OMRF.
[Show abstract][Hide abstract]ABSTRACT: Rationale for selecting 20 candidate genes at 2q22–24. In order to follow-up the peak at 2q22–24, we chose 20 genes to target on the basis of previous information about their function and reported clinical associations related with SLE. Positions based on genome build 36.