Nicolas Dominguez

Genetic associations of LYN with systemic lupus erythematosus.

We targeted LYN, a src-tyosine kinase involved in B-cell activation, in case–control association studies using populations of European-American, African-American and Korean subjects. Our combined European-derived population, consisting of 2463 independent cases and 3131 unrelated controls, shows significant association with rs6983130 in a female-only analysis with 2254 cases and 2228 controls (P=1.1 × 10−4, odds ratio (OR)=0.81 (95% confidence interval: 0.73–0.90)). This single nucleotide polymorphism (SNP) is located in the 5′ untranslated region within the first intron near the transcription initiation site of LYN. In addition, SNPs upstream of the first exon also show weak and sporadic association in subsets of the total European-American population. Multivariate logistic regression analysis implicates rs6983130 as a protective factor for systemic lupus erythematosus (SLE) susceptibility when anti-dsDNA, anti-chromatin, anti-52 kDa Ro or anti-Sm autoantibody status were used as covariates. Subset analysis of the European-American female cases by American College of Rheumatology classification criteria shows a reduction in the risk of hematological disorder with rs6983130 compared with cases without hematological disorders (P=1.5 × 10−3, OR=0.75 (95% CI: 0.62−0.89)). None of the 90 SNPs tested show significant association with SLE in the African American or Korean populations. These results support an association of LYN with European-derived individuals with SLE, especially within autoantibody or clinical subsets.

Genetic and physical interaction of the B-cell systemic lupus erythematosus-associated genes BANK1 and BLK

Objectives Altered signalling in B cells is a predominant feature of systemic lupus erythematosus (SLE). The genes BANK1 and BLK were recently described as associated with SLE. BANK1 codes for a B-cell-specific cytoplasmic protein involved in B-cell receptor signalling and BLK codes for an Src tyrosine kinase with important roles in B-cell development. To characterise the role of BANK1 and BLK in SLE, a genetic interaction analysis was performed hypothesising that genetic interactions could reveal functional pathways relevant to disease pathogenesis. Methods The GPAT16 method was used to analyse the gene–gene interactions of BANK1 and BLK. Confocal microscopy was used to investigate co-localisation, and immunoprecipitation was used to verify the physical interaction of BANK1 and BLK. Results Epistatic interactions between BANK1 and BLK polymorphisms associated with SLE were observed in a discovery set of 279 patients and 515 controls from northern Europe. A meta-analysis with 4399 European individuals confirmed the genetic interactions between BANK1 and BLK. As BANK1 was identified as a binding partner of the Src tyrosine kinase LYN, the possibility that BANK1 and BLK could also show a protein–protein interaction was tested. The co-immunoprecipitation and co-localisation of BLK and BANK1 were demonstrated. In a Daudi cell line and primary naive B cells endogenous binding was enhanced upon B-cell receptor stimulation using anti-IgM antibodies. Conclusion This study shows a genetic interaction between BANK1 and BLK, and demonstrates that these molecules interact physically. The results have important consequences for the understanding of SLE and other autoimmune diseases and identify a potential new signalling pathway.

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.

Replication of the BANK1 genetic association with systemic lupus erythematosus in a European-Derived Population

Systemic lupus erythematosus (SLE) is an autoimmune disease with highly variable clinical presentation. Patients suffer from immunological abnormalities that target T-cell, B-cell and accessory cell functions. B cells are hyperactive in SLE patients. An adapter protein expressed in B cells called BANK1 (B-cell scaffold protein with ankyrin repeats) was reported in a previous study to be associated with SLE in a European population. The objective of this study was to assess the BANK1 genotype–phenotype association in an independent replication sample. We genotyped 38 single nucleotide polymorphisms (SNPs) in BANK1 on 1892 European-derived SLE patients and 2652 European-derived controls. The strongest associations with SLE and BANK1 were at rs17266594 (corrected P-value=1.97 × 10−5, odds ratio (OR)=1.22, 95% CI 1.12–1.34) and rs10516487 (corrected P-value=2.59 × 10−5, OR=1.22, 95% CI 1.11–1.34). Our findings suggest that the association is explained by these two SNPs, confirming previous reports that these polymorphisms contribute to the risk of developing lupus. Analysis of patient subsets enriched for hematological, immunological and renal ACR criteria or the levels of autoantibodies, such as anti-RNP A and anti-SmRNP, uncovers additional BANK1 associations. Our results suggest that BANK1 polymorphisms alter immune system development and function to increase the risk for developing lupus.

Growing and starving Dictyostelium cells produce distinct density-sensing factors

Prestarvation factor (PSF) and conditioned medium factor (CMF) are two autocrine factors produced by Dictyostelium cells. Although secreted at different times in the Dictyostelium life cycle (PSF by growing cells and CMF by starving cells), both factors are glycoproteins that are used by cells to measure their own density, and both are important in cell aggregation. To examine the relationship between PSF and CMF, a CMF antisense transformant was tested for the production of PSF during growth. Although this transformant produced extremely low levels of CMF, its production of PSF was essentially normal. We conclude that these two factors are not products of the same gene.

B-Cell and Monocyte Contribution to Systemic Lupus Erythematosus Identified by Cell-Type-Specific Differential Expression Analysis in RNA-Seq Data

Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by complex interplay among immune cell types. SLE activity is experimentally assessed by several blood tests, including gene expression profiling of heterogeneous populations of cells in peripheral blood. To better understand the contribution of different cell types in SLE pathogenesis, we applied the two methods in cell-type-specific differential expression analysis, csSAM and DSection, to identify cell-type-specific gene expression differences in heterogeneous gene expression measures obtained using RNA-seq technology. We identified B-cell-, monocyte-, and neutrophil-specific gene expression differences. Immunoglobulin-coding gene expression was altered in B-cells, while a ribosomal signature was prominent in monocytes. On the contrary, genes differentially expressed in the heterogeneous mixture of cells did not show any functional enrichment. Our results identify antigen binding and structural constituents of ribosomes as functions altered by B-cell- and monocyte-specific gene expression differences, respectively. Finally, these results position both csSAM and DSection methods as viable techniques for cell-type-specific differential expression analysis, which may help uncover pathogenic, cell-type-specific processes in SLE.

Effects of IRF5 Lupus Risk Haplotype on Pathways Predicted to Influence B Cell Functions

Both genetic and environmental interactions affect systemic lupus erythematosus (SLE) development and pathogenesis. One known genetic factor associated with lupus is a haplotype of the interferon regulatory factor 5 (IRF5) gene. Analysis of global gene expression microarray data using gene set enrichment analysis identified multiple interferon- and inflammation-related gene sets significantly overrepresented in cells with the risk haplotype. Pathway analysis using expressed genes from the significant gene sets impacted by the IRF5 risk haplotype confirmed significant correlation with the interferon pathway, Toll-like receptor pathway, and the B-cell receptor pathway. SLE patients with the IRF5 risk haplotype have a heightened interferon signature, even in an unstimulated state (P = 0.011), while patients with the IRF5 protective haplotype have a B cell interferon signature similar to that of controls. These results identify multiple genes in functionally significant pathways which are affected by IRF5 genotype. They also establish the IRF5 risk haplotype as a key determinant of not only the interferon response, but also other B-cell pathways involved in SLE.

Evidence of Dynamically Dysregulated Gene Expression Pathways in Hyperresponsive B Cells from African American Lupus Patients

Recent application of gene expression profiling to the immune system has shown a great potential for characterization of complex regulatory processes. It is becoming increasingly important to characterize functional systems through multigene interactions to provide valuable insights into differences between healthy controls and autoimmune patients. Here we apply an original systematic approach to the analysis of changes in regulatory gene interconnections between in Epstein-Barr virus transformed hyperresponsive B cells from SLE patients and normal control B cells. Both traditional analysis of differential gene expression and analysis of the dynamics of gene expression variations were performed in combination to establish model networks of functional gene expression. This Pathway Dysregulation Analysis identified known transcription factors and transcriptional regulators activated uniquely in stimulated B cells from SLE patients.

Erratum: Genetic associations of LYN with systemic lupus erythematosus (Genes and Immunity (2009) 10 (397-403) DOI: 10.1038/gene.2009.19)

R Lu, GS Vidal, JA Kelly, AM Delgado-Vega, XK Howard, SR Macwana, N Dominguez, W Klein, C Burrell, IT Harley, KM Kaufman, GR Bruner, KL Moser, PM Gaffney, GS Gilkeson, EK Wakeland, Q-Z Li, CD Langefeld, MC Marion, J Divers, GS Alarcón, EE Brown, RP Kimberly, JC Edberg, R Ramsey-Goldman, JD Reveille, G McGwin Jr, LM Vilá, MA Petri, S-C Bae, S-K Cho, S-Y Bang, I Kim, CB Choi, J Martin, TJ Vyse, JT Merrill, JB Harley, ME Alarcón-Riquelme, SK Nath, JA James and JM Guthridge, for the BIOLUPUS and GENLES Multicenter Collaborations

35 GENE EXPRESSION ANALYSIS OF EUROPEAN-AMERICAN LUPUS PATIENTS WITH THYROID DISEASE COMPARED TO MATCHED CONTROLS

Purpose We have studied gene expression in Epstein-Barr virus transformed B cell lines to define differences between SLE patients and matched controls. We used this design to remove, to the extent possible, environmental influences and the secondary changes in gene expression caused by lupus and found in peripheral blood cells from patients who are ill. In the present study, we have focused on gene expression analysis of cell lines derived from European-American lupus patients who also present evidence of thyroid disease compared to unrelated matched controls. Methods 12 European-American SLE patients were selected according to American College of Rheumatology (ACR) criteria for SLE and their contribution to the 5q14 (lupus affected with autoimmune thyroid disease) genetic linkage. 12 controls were matched by age, sex, race, and state of residence. Human genome U133 plus 2.0 arrays (Affymetrix) were used for each subject. Gene expression differences were evaluated for genes with p < .05 for the paired t-test, p < .0001 for the associative t-test, and an apparent ratio of expression of > 2.0 or < 0.5. Results The affecteds from pedigrees linked at 5q14 differently expressed 191 genes when compared to controls (59 up-regulated, 54 down-regulated, 19 only in lupus patients, and 59 only in matched controls). Two of the differentially expressed genes were located in 5q14 intervals. The differentially expressed genes include members of signal transduction pathways, thyroid hormone receptor, small nuclear ribonucleotide proteins and immune response related genes. Conclusions We identified genes by differential gene expression analysis of cell lines derived from European-American lupus patients with thyroid disease. Two of these genes come from within the genetic linkage interval identified in other studies of this subset of lupus patients.