Fuencisla Matesanz

Interferon regulatory factor 5 (IRF5) gene variants are associated with multiple sclerosis in three distinct populations

Background: IRF5 is a transcription factor involved both in the type I interferon and the toll-like receptor signalling pathways. Previously, IRF5 has been found to be associated with systemic lupus erythematosus, rheumatoid arthritis and inflammatory bowel diseases. Here we investigated whether polymorphisms in the IRF5 gene would be associated with yet another disease with features of autoimmunity, multiple sclerosis (MS). Methods: We genotyped nine single nucleotide polymorphisms and one insertion-deletion polymorphism in the IRF5 gene in a collection of 2337 patients with MS and 2813 controls from three populations: two case–control cohorts from Spain and Sweden, and a set of MS trio families from Finland. Results: Two single nucleotide polymorphism (SNPs) (rs4728142, rs3807306), and a 5 bp insertion-deletion polymorphism located in the promoter and first intron of the IRF5 gene, showed association signals with values of p<0.001 when the data from all cohorts were combined. The predisposing alleles were present on the same common haplotype in all populations. Using electrophoretic mobility shift assays we observed allele specific differences in protein binding for the SNP rs4728142 and the 5 bp indel, and by a proximity ligation assay we demonstrated increased binding of the transcription factor SP1 to the risk allele of the 5 bp indel. Conclusion: These findings add IRF5 to the short list of genes shown to be associated with MS in more than one population. Our study adds to the evidence that there might be genes or pathways that are common in multiple autoimmune diseases, and that the type I interferon system is likely to be involved in the development of these diseases.

Effects of the multiple sclerosis associated −330 promoter polymorphism in IL2 allelic expression

The -330 IL2 gene promoter polymorphism has been associated with multiple sclerosis (MS) [J. Neuroimmunol. 119 (2001) 101], but the basis underlying this association remains unknown to date. In the present work, we have found that IL2 promoter-luciferase constructs, transfected in Jurkat cell line, showed twofold higher levels of gene expression in the -330 G allele. However, the transcriptional effect of this polymorphism in lymphocytes showed that the G allele was related to lower expression of IL2. This difference increased in the patient group. Divergence between in vivo and in vitro influence of the -330 IL2 promoter polymorphic site suggests the existence of additional unknown polymorphisms affecting gene regulation. Our data show an increased IL2 expression among GT and TT genotypes previously associated with susceptibility to MS.

IFNAR1 and IFNAR2 polymorphisms confer susceptibility to multiple sclerosis but not to interferon-beta treatment response.

We investigated the role of three polymorphisms in the IFNAR1 (SNPs 18417 and -408) and IFNAR2 (SNP 11876) genes in multiple sclerosis (MS) susceptibility and in the IFNbeta treatment response in a group of 147 patients and 210 controls undergoing interferon therapy during the last 2 years. Only the 18417 and the 11876 SNPs showed an association with disease susceptibility (p=0.001 and 0.035, respectively) although no differential genotype distribution were observed between interferon responders and non-responder MS patients. No alteration of the expression level of IFNAR-1 was observed with respect to the -408 genotypes or to interferon treatment response. These data suggest a role for the IFNAR pathway in susceptibility to MS.

IL2RA/CD25 Gene Polymorphisms: Uneven Association with Multiple Sclerosis (MS) and Type 1 Diabetes (T1D)

Background IL-2 receptor (IL2R) alpha is the specific component of the high affinity IL2R system involved in the immune response and in the control of autoimmunity. Methods and Results Here we perform a replication and fine mapping of the IL2RA gene region analyzing 3 SNPs previously associated with multiple sclerosis (MS) and 5 SNPs associated with type 1 diabetes (T1D) in a collection of 798 MS patients and 927 matched Caucasian controls from the south of Spain. We observed association with MS in 6 of 8 SNPs. The rs1570538, at the 3′- UTR extreme of the gene, previously reported to have a weak association with MS, is replicated here (P = 0.032). The most associated T1D SNP (rs41295061) was not associated with MS in the present study. However, the rs35285258, belonging to another independent group of SNPs associated with T1D, showed the maximal association in this study but different risk allele. We replicated the association of only one (rs2104286) of the two IL2RA SNPs identified in the recently performed genome-wide association study of MS. Conclusions These findings confirm and extend the association of this gene with MS and reveal a genetic heterogeneity of the associated polymorphisms and risk alleles between MS and T1D suggesting different immunopathological roles of IL2RA in these two diseases.

Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes

Many genomic alterations associated with human diseases localize in noncoding regulatory elements located far from the promoters they regulate, making it challenging to link noncoding mutations or risk-associated variants with target genes. The range of action of a given set of enhancers is thought to be defined by insulator elements bound by the 11 zinc-finger nuclear factor CCCTC-binding protein (CTCF). Here we analyzed the genomic distribution of CTCF in various human, mouse and chicken cell types, demonstrating the existence of evolutionarily conserved CTCF-bound sites beyond mammals. These sites preferentially flank transcription factor–encoding genes, often associated with human diseases, and function as enhancer blockers in vivo, suggesting that they act as evolutionarily invariant gene boundaries. We then applied this concept to predict and functionally demonstrate that the polymorphic variants associated with multiple sclerosis located within the EVI5 gene impinge on the adjacent gene GFI1.

The autoimmune disease-associated KIF5A, CD226 and SH2B3 gene variants confer susceptibility for multiple sclerosis.

Genome-wide association studies (GWAS) have revealed that different diseases share susceptibility variants. Twelve single-nucleotide polymorphisms (SNPs) previously associated with different immune-mediated diseases in GWAS were genotyped in a Caucasian Spanish population of 2864 multiple sclerosis (MS) patients and 2930 controls. Three SNPs were found to be associated with MS: rs1678542 in KIF5A (P=0.001, odds ratio (OR)=1.13, 95% confidence interval (CI)=1.05–1.23); rs3184504 in SH2B3 (P=0.00001, OR=1.19, 95% CI=1.10–1.27) and rs763361 in CD226 (P=0.00007, OR=1.16, 95%CI=1.08–1.25). These variants have previously been associated with rheumatoid arthritis and type 1 diabetes. The SH2B3 polymorphism has additionally been associated with systemic lupus erythematosus. Our results, in addition to validating some of these loci as risk factors for MS, are consistent with shared genetic mechanisms underlying different immune-mediated diseases. These data may help to shape the contribution of each pathway to different disorders.

Allelic expression and interleukin-2 polymorphisms in multiple sclerosis.

We have investigated the association of two single nucleotide polymorphisms (SNPs) at positions -384 and 114 in the human interleukin-2 (hIL-2) with multiple sclerosis (MS). For two of the -384 genotypes (G/T, T/T), we observed an association with the susceptibility to secondary progressive (SP) course of MS (P=0.005 and P=0.013, respectively). Expression level differences of the IL-2 alleles (between one- and three-fold) were not attributable to the -384 promoter polymorphism. These data indicate for the first time the relevance of the il-2 gene locus in human MS and its possible involvement in other autoimmune diseases.

Protein tyrosine phosphatase gene (PTPN22) polymorphism in multiple sclerosis.

Sirs: Multiple sclerosis (MS) is a common inflammatory disease of the central nervous system (CNS) with a complex pathogenesis involving multiple genetic and environmental contributions. Alterations in the signalling pathway that regulate T-cell tyrosine phosphorylation play an important role in MS [6]. Tyrosine phosphorylation is regulated by the equal and balanced action of protein tyrosine kinases (PTKs) and protein tyrosine phosphatases (PTPs) [1]. The lymphoid-specific phosphatase (LYP), encoded by the PTPN22 gene, is important in negative control of T-cell activation and in T-cell development. A functional polymorphism at nucleotide 1858 in codon 620 (Arg620Trp) in the PTPN22 gene has been associated with type 1 diabetes mellitus (T1D), rheumatoid arthritis (RA), and systemic lupus erythematosus (SLE) in humans [3, 4, 7, 8]. In the present study, we tested the possible role of the 1858C→T variant of the PTPN22 gene in MS predisposition. We examined the distribution frequency of the PTPN22 1858C→T polymorphism of 120 patients with clinically defined MS and 200 healthy controls by a TaqMan 5’ allelic discrimination [8]. The frequencies of 1858C/C, 1858C/T and 1858T/T genotypes were 87.5 %%, 12 % and 0.5 % respectively in controls and 83.3 %, 15.8 % and 0.9 % in the patient group. The allele and genotype distribution frequencies were similar in MS patients and controls and were in Hardy-Weinberg equilibrium. Indeed, stratification of MS patients according to their clinical phenotypes (RR and SP) and genus revealed no significant differences (data not shown). This lack of association of the PTPN22 1858C→T polymorphism with MS should be interpreted cautiously. Because of the relatively small sample size, slight effects may be not uncovered and therefore these results do not completely rule out the possibility of an association with MS. The association of RA, T1D and SLE susceptibility with the PTPN22 1858C→T polymorphism suggests that the PTPN22 1858T allele predisposes individuals to developing autoimmune diseases. However, the PTPN22 1858C→T polymorphism seems not to be a critical point in the susceptibility to MS. Given the expression of this molecule in many immunological relevant cell types, our data support the hypothesis that PTPN22 may act in different ways in different autoimmune diseases. It is possible that different genetic backgrounds could condition the effect of the PTPN22 polymorphism, but this seems not to be the reason since the PTPN22 polymorphism confers susceptibility to other autoimmune diseases such as RA and SLE with the same genetic background [8]. Furthermore, there are no significant differences between 1858C→T genotype distribution of control groups from North America, where an association of the PTPN22 1858C→T polymorphism with RA and SLE has been described [3, 7], and South Spain populations. It is worth mentioning that the Sardinia population has a high MS prevalence (150/100,000) [10]). However, they have the lowest proportion of 1858 T allele which is associated with susceptibility to autoimmune diseases [4]. This is in concordance with the absence of PTPN22 1858 T polymorphism association with MS. Similar contradictory findings have been reported concerning the influence of CTLA-4 gene in autoimmunity. While the CTLA-4CT60 marker has been associated with a range of autoimmune diseases, such as T1D, Graves’ disease, thyroiditis and SLE [5, 11], no linkage was observed with RA [9, 2] These findings support the notion that common susceptibility alleles are not shared among all autoimmune diseases, but rather among groups of these conditions. In conclusion, our data suggest that the PTPN22 1858 SNP has no, or only a negligible effect on MS susceptibility in the Spanish population. However, a minor effect of the PTPN22 SNP cannot be ruled out, and this may only be verifiable in an extremely large data set.

Multiple Sclerosis Risk Variant HLA-DRB1*1501 Associates with High Expression of DRB1 Gene in Different Human Populations

The human leukocyte antigen (HLA) DRB1*1501 has been consistently associated with multiple sclerosis (MS) in nearly all populations tested. This points to a specific antigen presentation as the pathogenic mechanism though this does not fully explain the disease association. The identification of expression quantitative trait loci (eQTL) for genes in the HLA locus poses the question of the role of gene expression in MS susceptibility. We analyzed the eQTLs in the HLA region with respect to MS-associated HLA-variants obtained from genome-wide association studies (GWAS). We found that the Tag of DRB1*1501, rs3135388 A allele, correlated with high expression of DRB1, DRB5 and DQB1 genes in a Caucasian population. In quantitative terms, the MS-risk AA genotype carriers of rs3135388 were associated with 15.7-, 5.2- and 8.3-fold higher expression of DQB1, DRB5 and DRB1, respectively, than the non-risk GG carriers. The haplotype analysis of expression-associated variants in a Spanish MS cohort revealed that high expression of DRB1 and DQB1 alone did not contribute to the disease. However, in Caucasian, Asian and African American populations, the DRB1*1501 allele was always highly expressed. In other immune related diseases such as type 1 diabetes, inflammatory bowel disease, ulcerative colitis, asthma and IgA deficiency, the best GWAS-associated HLA SNPs were also eQTLs for different HLA Class II genes. Our data suggest that the DR/DQ expression levels, together with specific structural properties of alleles, seem to be the causal effect in MS and in other immunopathologies rather than specific antigen presentation alone.

IL2RA/CD25 polymorphisms contribute to multiple sclerosis susceptibility

Received in revised form: 28 June 2006 Sirs: Multiple sclerosis (MS) is a neurodegenerative disease of the central nervous system (CNS) whose primary mechanism of injury is by inflammatory/autoimmune demyelination and, to a variable degree, axonal damage. Epidemiological studies, genome screenings and case-control studies suggest that multiple genetic factors influence susceptibility to multiple sclerosis (MS) [