Variation in the IL7RA and IL2RA genes in German multiple sclerosis patients

MSGD: a manually curated database of genomic, transcriptomic, proteomic and drug information for multiple sclerosis

Multiple sclerosis (MS) is the most common inflammatory demyelinating disease of the central nervous system. 'Omics' technologies (genomics, transcriptomics, proteomics) and associated drug information have begun reshaping our understanding of multiple sclerosis. However, these data are scattered across numerous references, making them challenging to fully utilize. We manually mined and compiled these data within the Multiple Sclerosis Gene Database (MSGD) database, intending to continue updating it in the future. We screened 5485 publications and constructed the current version of MSGD. MSGD comprises 6255 entries, including 3274 variant entries, 1175 RNA entries, 418 protein entries, 313 knockout entries, 612 drug entries and 463 high-throughput entries. Each entry contains detailed information, such as species, disease type, detailed gene descriptions (such as official gene symbols), and original references. MSGD is freely accessible and provides a user-friendly web interface. Users can easily search for genes of interest, view their expression patterns and detailed information, manage gene sets and submit new MS-gene associations through the platform. The primary principle behind MSGD's design is to provide an exploratory platform, aiming to minimize filtration and interpretation barriers while ensuring highly accessible presentation of data. This initiative is expected to significantly assist researchers in deciphering gene mechanisms and improving the prevention, diagnosis and treatment of MS. Database URL: http://bio-bigdata.hrbmu.edu.cn/MSGD.

Soluble IL-7Rα/sCD127 in Health, Disease, and Its Potential Role as a Therapeutic Agent

Soluble cytokine receptors can influence immune responses by modulating the biological functions of their respective ligands. These effects can be either agonistic or antagonistic and a number of soluble cytokine receptors have been shown to play critical roles in both maintenance of health and disease pathogenesis. Soluble IL-7Ra (sCD127) is one such example. With its impact on the IL-7/CD127 pathway, which is fundamental for the development and homeostasis of T cells, the role of sCD127 in health and disease has been extensively studied in recent years. Within this review, the role of sCD127 in maintaining host immune function is presented. Next, by addressing genetic factors affecting sCD127 expression and the associated levels of sCD127 production, the roles of sCD127 in autoimmune disease, infections and cancer are described. Finally, advances in the field of soluble cytokine therapy and the potential for sCD127 as a biomarker and therapeutic agent are discussed.

Association between IL7 Receptor Alpha (Il7ra) gene rs6897932 polymorphism and the risk of Multiple Sclerosis: A meta-regression and meta-analysis

BACKGROUND

In this systematic review and meta-analysis, we aimed to find a consistent conclusion for the association between the interleukin 7 receptor alpha (IL7RA) gene rs6897932 single nucleotide polymorphism (SNP) and multiple sclerosis (MS) risk.

METHODS

Here, we performed a comprehensive systematic search in PubMed, Scopus, and Web of Science to find relevant studies published before November 2020 investigating the association between rs6897932 SNP and MS risk. In the pooled analysis, we determined the odds ratio (OR) and the corresponding 95% confidence interval (CI) for the association level between rs6897932 SNP and the risk of MS.

RESULTS

In the current meta-analysis 33 case-control studies (30 articles) containing 19351 patients and 21005 healthy controls certify the inclusion criteria. According to the pooled analysis, a statistically significant association of IL7RA gene rs6897932 SNP with MS risk was found across recessive model (OR= 0.84, 95% CI= 0.77-0.92, P< 0.001, FEM), allelic model (OR= 0.91, 95% CI= 0.85-0.99, P= 0. 02, REM), TT vs. CC model (OR= 0.79, 95% CI= 0.67-0.93, P= 0.005, REM). Moreover, the subgroup analysis based on the ethnicity indicated a negative significant association in Europeans; dominant model (OR= 0.88, 95% CI= 0.78-1.01, P= 0.06, REM), recessive model (OR= 0.79, 95% CI= 0.71-0.88, P< 0.001, REM), allelic model (OR= 0.88, 95% CI= 0.81-0.96, P= 0.003, REM), TT vs. CC model (OR= 0.74, 95% CI= 0.61-0.88, P<0.001, REM) models. Nonetheless, no significant association was detected in Asians and Americans.

CONCLUSIONS

IL7RA gene rs6897932 SNP decreases MS susceptibility in overall population and Europeans.

The association of genetic variants IL2RA rs2104286, IFI30 rs11554159 and IKZF3 rs12946510 with multiple sclerosis onset and severity in patients from Serbia

An algorithm Probabilistic Identification of Causal SNPs, identified 434 causal variants for multiple sclerosis (MS) including IL2RA rs2104286, IFI30 rs11554159 and IKZF3 rs12946510. Analysis of individual and combined effects of these variants in the Serbian population identified that Il2RA rs2104286 G allele carriers had a lower risk for developing MS (gender adjusted OR = 0.63, p = .003). With regard to the IFI30 rs11554159 recessive genetic model, among HLA-DRB1*15:01 positive patients, the AA homozygote had a significantly higher MSSS compared to the G allele carriers (p = .003). This study confirms role of IL2RA rs2104286 in MS and suggest the role of IFI30 rs11554159 in disease severity, which needs validation.

Epigenetic aspects of multiple sclerosis and future therapeutic options

Multiple sclerosis (MS) is a chronic inflammatory and neurodegenerative disease accompanied by demyelination of neurons in the central nervous system that mostly affects young adults, especially women. This disease has two phases including relapsing-remitting form (RR-MS) by episodes of relapse and periods of clinical remission and secondary-progressive form (SP-MS), which causes more disability. The inheritance pattern of MS is not exactly identified and there is an agreement that it has a complex pattern with an interplay among environmental, genetic and epigenetic alternations. Epigenetic mechanisms that are identified for MS pathogenesis are DNA methylation, histone modification and some microRNAs' alternations. Several cellular processes including apoptosis, differentiation and evolution can be modified along with epigenetic changes. Some alternations are associated with epigenetic mechanisms in MS patients and these changes can become key points for MS therapy. Therefore, the aim of this review was to discuss epigenetic mechanisms that are associated with MS pathogenesis and future therapeutic approaches.

IL7RA genetic variants differentially affect IL-7Rα expression and alternative splicing: a role in autoimmune and infectious diseases?

Interleukin-7 receptor α chain (IL-7Rα) single nucleotide polymorphisms (SNPs) are associated with susceptibility to immunopathologies like autoimmune and inflammatory diseases. The current hypothesis about underlying mechanisms is based on the regulation of IL-7 availability for self-reactive T cells by influencing the generation of a soluble (s)IL-7Rα variant. This assumption was mainly predicated on the well-defined IL7RA SNP rs6897932, which affects alternative splicing and causes aberrant generation of the sIL-7Rα variant with potential effects on the IL-7 serum reservoir. However, more recent studies shed light on novel functions of autoimmunity risk-associated IL7RA SNPs and characterized the largely neglected effect of rs6897932 on membrane (m)IL-7Rα expression. These findings as well as a described role of impaired mIL-7Rα expression and IL7RA SNP influence on chronic infectious diseases necessitates the reevaluation of previous findings on the role of IL7RA SNPs in immunopathology.

Association of interleukin 6, interleukin 7 receptor alpha, and interleukin 12B gene polymorphisms with multiple sclerosis

Pro-inflammatory and anti-inflammatory cytokines have been shown to play a crucial role in the pathophysiology of multiple sclerosis (MS). We investigated the association between interleukin (IL) IL6-174 G/C (rs1800795), IL7RA C/T (rs6897932), and IL-12B A1188C (rs3212227) gene polymorphisms (SNPs) and MS. The study consisted of 297 unrelated MS patients and 135 healthy individuals. In IL6-174G/C (rs1800795), a significant association between the C allele and MS risk [OR 1.41, 95% CI (1.05-1.92); P = 0.025] was found. Carriage of genotypes CC and CG were more common in MS patients [OR 1.58, 95% CI (1.04-2.39); P = 0.031] and also in female MS patients [OR 1.68, 95% CI (1.02-2.79); P = 0.043]. However, after applying Bonferroni's correction the differences did not remain significant. No significant association between the IL7RA C/T (rs6897932) and IL12B A1188C (rs3212227) gene polymorphisms and MS susceptibility was observed. Regarding IL-12B A1188C (rs3212227), a significant association between the CC genotype and MS progression, expressed as MSSS, was demonstrated in the female MS group. Our results indicate that the distribution of IL6-174G/C (rs1800795) SNP was marginally associated with MS susceptibility. We also showed that IL-12B A1188C (rs3212227) can contribute to the progression of the disease in the Czech population.

Investigating the exon 6 sequence changes of interleukin 7 receptor A (IL7RA) gene in patients with relapsing-remitting multiple sclerosis

BACKGROUND

Interleukin 7 receptor alpha (IL7RA) gene that encodes a subunit of IL7 receptor has been reported to be associated with different immunologic disease.

OBJECTIVE

Multiple Sclerosis (MS) patients have shown an aberrant blood level of soluble form of IL7R protein. The genomic changes in the sequence of this gene have been suggested to be correlated with its altered splicing specially, variants in the exon 6 of the gene have been reported to influence the maintenance or skipping of this exon and control the soluble or insoluble form of the final product. In order to evaluate this changes in the IL7RA gene and to determine a possible correlation between these changes and the MS susceptibility the whole sequence of the exon 6 and 7 and their flanking sequences were analyzed.

METHODS

In this regard, we investigate the sequence changes of the exon 6 and 7 of the IL7RA gene in 75 relapsing-remitting MS patients and compare the results with 75 healthy control using sequence analyzing.

RESULTS

The results of the sequence analysis were used in two aspects. The allelic and genotypic estimated frequencies of a reported risk variant rs6897932 in patients and controls in our population confirmed its association with the disease (P= 0.009, OR = 6.273, for TT genotype). Also, we report a possible hazardous cutoff for changes in a potential exon splicing silencer element (ESS (nt. 20-24)) and its correlation with rs6897932 to confer the risk of developing MS.

CONCLUSION

In conclusion our results confirm the association between IL7RA exon 6 sequence changes and increased susceptibility for multiple sclerosis.

Variants in the IL7RA gene confer susceptibility to multiple sclerosis in Caucasians: evidence based on 9734 cases and 10436 controls

Recently, numerous genome wide association studies (GWAS) and other case-control association studies examining the relationship between interleukin-7 receptor α chain (IL7RA) gene rs3194051, rs987107, rs11567686, and rs11567685 variants and multiple sclerosis (MS) risk have been conducted, but the conclusions have been inconsistent. The main objective of this meta-analysis was to more precisely explore the association of these four IL7RA variants with MS development. Twenty-seven eligible studies involving 9734 cases and 10436 controls were included in the present meta-analysis. Power calculation, publication bias, sensitivity analysis and cumulative meta-analysis were performed to derive a reliable conclusion. Our study indicated three IL7RA loci were significantly associated with increasing MS risk (rs3194051: recessive model: OR = 1.22, 95% CI 1.08–1.38; rs987107: recessive model: OR = 1.44, 95% CI 1.22–1.69; and rs11567686: dominant model: OR = 1.18, 95% CI 1.01–1.37). Additionally, IL7RA rs11567685 variants might not be related to MS development. In all, IL7RA locus polymorphisms could play an important role in the predisposition to MS, which could contribute to a better understanding the pathogenesis of multiple sclerosis.

The single nucleotide variant rs12722489 determines differential estrogen receptor binding and enhancer properties of an IL2RA intronic region

We studied functional effect of rs12722489 single nucleotide polymorphism located in the first intron of human IL2RA gene on transcriptional regulation. This polymorphism is associated with multiple autoimmune conditions (rheumatoid arthritis, multiple sclerosis, Crohn's disease, and ulcerative colitis). Analysis in silico suggested significant difference in the affinity of estrogen receptor (ER) binding site between alternative allelic variants, with stronger predicted affinity for the risk (G) allele. Electrophoretic mobility shift assay showed that purified human ERα bound only G variant of a 32-bp genomic sequence containing rs12722489. Chromatin immunoprecipitation demonstrated that endogenous human ERα interacted with rs12722489 genomic region in vivo and DNA pull-down assay confirmed differential allelic binding of amplified 189-bp genomic fragments containing rs12722489 with endogenous human ERα. In a luciferase reporter assay, a kilobase-long genomic segment containing G but not A allele of rs12722489 demonstrated enhancer properties in MT-2 cell line, an HTLV-1 transformed human cell line with a regulatory T cell phenotype.

The expression of lnc-IL-7R long non-coding RNA dramatically correlated with soluble and membrane-bound isoforms of IL-7Ra gene in multiple sclerosis patients

BACKGROUND AND PURPOSE

Multiple sclerosis (MS) is a neurological disease of the central nervous system (CNS) that causes physical and cognitive impairments. IL-7Ra is a key non-MHC gene associated with MS. IL-7Ra is a likely functional candidate for this complex disease because it is involved in the development, maturation, and homeostasis of T and B cells. Our aim was to evaluate the expression level and controlling role of lnc-IL-7R in the expression of two variants of IL-7Ra in MS patients versus healthy controls and their correlation with certain clinical features.

METHODS

Using the real-time PCR method, we analyzed the expression levels of membrane-bound (IL-7RB) and soluble (IL-7RS) isoforms of IL-7R gene and lnc-IL-7R in 36 MS patients versus 30 healthy controls.

RESULTS

Our results revealed no significant difference between the expression levels of IL-7RB and IL-7RS isoforms of IL-7R gene and lnc-IL-7R in MS patients versus healthy controls (p=0.7, p=0.6 and p=0.8, respectively). Moreover, we found a significant correlation between the expression levels of IL-7RB with lnc-IL-7R, IL-7RS with lnc-IL-7R and IL-7RB with IL-7RS in both patient and control groups.

CONCLUSIONS

We have probably uncovered new evidence for the controlling role of long non-coding RNAs in the expression level of genes and their roles in MS.

Epigenetic Modifications and Therapy in Multiple Sclerosis

Breakthroughs in genetic studies, like whole human genome sequencing and genome-wide association studies (GWAS), have richened our knowledge of etiopathology of autoimmune diseases (AID) through discovery of genetic patterns. Nonetheless, the precise etiology of autoimmune diseases remains largely unknown. The lack of complete concordance of autoimmune disease in identical twins suggests that non-genetic factors also play a major role in determining disease susceptibility. Although there is no certain definition, epigenetics has been known as heritable alterations in gene function without changes in the nucleotide sequence. DNA methylation, histone modifications, and microRNA-associated gene expression suppression are the central mechanisms for epigenetic regulations. Multiple sclerosis (MS) is a disorder of the central nervous system (CNS), characterized by both inflammatory and neurodegenerative features. Although studies on epigenetic alterations in MS only began in the past decade, a mounting number of surveys suggest that epigenetic changes may be involved in the initiation and development of MS, probably through bridging the effects of environmental risk factors to genetics. Arming with clear understanding of epigenetic dysregulations underpins development of epigenetic therapies. Identifying agents inhibiting the enzymes controlling epigenetic modifications, particularly DNA methyltransferases and histone deacetylases, will be promising therapeutic tool toward MS. In the article underway, it is aimed to go through the recent progresses, attempting to disclose how epigenetics associates with the pathogenesis of MS and how can be used as therapeutic approach.

Interleukin 7 receptor polymorphisms and the risk of multiple sclerosis: A meta-analysis

BACKGROUND

Multiple sclerosis (MS) is considered as the most common chronic inflammatory neurologic disorder diagnosed in young adults. Both environmental and genetic factors may influence risk of MS development. Interleukin 7 receptor (IL7R) is one of the most studied gene polymorphism on MS that may play a possible role in MS development. The most studied polymorphism of IL7R gene is "rs6897932" polymorphism on IL7Rα gene (IL7RA).

METHODS

PubMed, Scopus, and Google scholar databases were searched for all of related studies on the association of IL7RA polymorphism with single nucleotide polymorphism (SNP) ID of "rs6897932" and the risk of MS through August 07, 2015. After exclusion of irrelevant articles, 11 eligible studies were selected, which were analyzed to determine an association between the MS and IL7R T244I polymorphism (rs6897932). For identification of this association, odds ratios (ORs) and 95% confidence interval (95% CI) were calculated. Four models of allelic (T vs. C), co-dominant genotype (TT vs. CC), dominant (TT+CT vs. CC), and recessive genotypes (TT vs. CT+CC) were considered to check the possible role of rs6897932 polymorphism in MS. A sensitivity analysis was conducted to find the reliability of this study. Furthermore, funnel plots were used to evaluate publication bias.

RESULTS

A total of 11 case-control studies were identified through this meta-analysis, which containing 6752 cases and 7349 controls. In overall, the frequency of the C allele was found to be higher in patients with MS compared to healthy controls (75.66% vs. 72.19%). T allele was significantly associated with the decreased risk of MS in a random effect model (T vs. C: OR=0.84, 95% CI=0.77-0.92, P-value <0.001). In the co-dominant, dominant, and recessive genotypes models, a significant association between the IL7R T244I polymorphism and MS risk was demonstrated (TT vs. CC: OR=0.70, 95% CI=0.61-0.80, P-value <0.001; TT+CT vs. CC: OR=0.82, 95% CI=0.73-0.92, P-value <0.001; TT vs. CT+CC: OR=0.76, 95% CI=0.66-0.87, P-value <0.001). Sensitivity analysis revealed that this study is reliable. There was no evidence of publication bias.

CONCLUSION

It was demonstrated that the IL7R T244I polymorphism was associated with susceptibility to MS. However, more well-designed studies with large sample size are needed to validate this association between this single nucleotide polymorphism and MS.

Genetic variants in IL2RA and IL7R affect multiple sclerosis disease risk and progression

Multiple sclerosis (MS) is a common demyelinating neurodegenerative disease with a strong genetic component. Previous studies have associated genetic variants in IL2RA and IL7R in the pathophysiology of the disease. In this study, we describe the association between IL2RA (rs2104286) and IL7R (rs6897932) in the Canadian population. Genotyping 1,978 MS patients and 830 controls failed to identify any significant association between these variants and disease risk. However, stratified analysis for family history of disease and disease course identified a trend towards association for IL2RA in patients without a family history (p = 0.05; odds ratio = 0.77) and a significant association between IL7R and patients who developed progressive MS (PrMS) (p = 0.002; odds ratio = 0.73). Although not statistically significant, the effect of IL2RA (rs2104286) in patients without a family history of MS indicates that the genetic components for familial and sporadic disease are perhaps distinct. This data suggests that the onset of sporadic disease is likely determined by a large number of variants of small effect, whereas MS in patients with a family history of disease is caused by a few deleterious variants. In addition, the significant association between PrMS and rs6897932 indicates that IL7R may not be disease-causing but a determinant of disease course. Further characterization of the effect of IL2RA and IL7R genetic variants in defined MS subtypes is warranted to evaluate the effect of these genes on specific clinical outcomes and to further elucidate the mechanisms of disease onset and progression.

Multiple sclerosis: individualized disease susceptibility and therapy response

Multiple sclerosis (MS) is a heterogeneous disease in which diverse genetic, pathological and clinical backgrounds lead to variable therapy response. Accordingly, MS care should be tailored to address disease traits unique to each person. At the core of personalized management is the emergence of new knowledge, enabling optimized treatment and disease-modifying therapies. This overview analyzes the promise of genetic and nongenetic biomarkers in advancing decision-making algorithms to assist diagnosis or in predicting the disease course and therapy response in any given MS patient.

Single nucleotide polymorphisms in multiple sclerosis: disease susceptibility and treatment response biomarkers

Multiple sclerosis (MS) is a chronic inflammatory demyelinating and neurodegenerative disease of the central nervous system characterized by unpredictable and variable clinical course. Etiology of MS involves both genetic and environmental factors. New technologies identified genetic polymorphisms associated with MS susceptibility among which immunologically relevant genes are significantly overrepresented. Although individual genes contribute only a small part to MS susceptibility, they might be used as biomarkers, thus helping to identify accurate diagnosis, predict clinical disease course and response to therapy. This review focuses on recent progress in research on MS genetics with special emphasis on the possibility to use single nucleotide polymorphism of candidate genes as biomarkers of susceptibility to disease and response to therapy.

The human IL-7 receptor gene: deletions, polymorphisms and mutations

Most T cell subsets depend on IL-7 for survival. IL-7 binds to IL-7Rα and γc, initiating the signaling cascade. Deletion of IL-7Ra in humans has, for some time, been known to cause severe combined immunodeficiency. More recently, polymorphisms in IL-7R have been shown be a risk factor for a number of diseases that are autoimmune or involve excess immune and inflammatory responses including multiple sclerosis, type 1 diabetes, rheumatoid arthritis, primary biliary cirrhosis, inflammatory bowel disease, atopic dermatitis, inhalation allergy, sarcoidosis and graft-versus host disease. The polymorphism that affects risk to most of these immunopathologies is T244I at the border of the extracellular domain and the transmembrane region. The same region has recently been shown to harbor gain-of-function mutations in acute lymphoblastic leukemia. These studies have suggested new therapies that target the IL-7 pathway.

[New gene map for multiple sclerosis]

BACKGROUND

Multiple sclerosis (MS) is a demyelinating, inflammatory disease of the central nervous system which affects young adults with a relapsing or progressive disease course. The etiology of the disease is unknown, but both environmental and genetic factors contribute to the risk of developing MS.

MATERIAL AND METHODS

We give an overview of new knowledge of the genetic risk factors for MS, based on our own work as well as on literature in this field.

RESULTS

Through genome-wide association studies and subsequent replication studies a series of novel MS genes have recently been identified, in addition to the HLA association previously described. The International MS Genetics Consortium in collaboration with the Wellcome Trust Case Control Consortium recently published a genome-wide study of 9,722 MS patients and 17,376 controls. Genome-wide significant association (p < 10-8) was observed for 29 new as well as 23 previously identified gene regions, in addition to the HLA-DRB1 and -A loci .The majority of these MS-associated regions encode immune-related molecules.

CONCLUSION

Genetic studies of large patient and control samples obtained through international and national collaborations have identified a list of more than 50 MS risk-gene regions, in addition to HLA-DRB1 and -A loci. The risk associated with each of these loci is low, however, they collectively point to the importance of immune-related pathways in the etiology of MS.

Interleukin 2 Receptor α Gene Polymorphism and Risk of Multiple Sclerosis: A Meta-Analysis

This meta-analysis studied the association between interleukin 2 receptor a (IL2RA) gene polymorphisms rs2104286 and rs12722489 and susceptibility to multiple sclerosis (MS). Case-control genetic association studies published before January 2011 were retrieved from the PubMed and EMBASE databases and the Cochrane Library. Eight studies comprising 13 569 patients and 23 435 controls met the selection criteria for meta-analysis of the IL2RA rs2104286 polymorphism. Using a fixed-effects model, the T allele and the TT and TT + TC genotypes of the IL2RA rs2104286 polymorphism were found to be associated with MS. Five studies comprising 5643 patients and 6415 controls met the selection criteria for meta-analysis of the IL2RA rs12722489 polymorphism. Using a fixed-effects model, the C allele and the CC genotype of the IL2RA rs12722489 polymorphism were found to be associated with MS but the CC + CT genotype was not. It was concluded that both of the IL2RA gene polymorphisms, rs2104286 and rs12722489, were associated with increased susceptibility to MS.

A knowledge-driven interaction analysis reveals potential neurodegenerative mechanism of multiple sclerosis susceptibility

Gene-gene interactions are proposed as an important component of the genetic architecture of complex diseases, and are just beginning to be evaluated in the context of genome-wide association studies (GWAS). In addition to detecting epistasis, a benefit to interaction analysis is that it also increases power to detect weak main effects. We conducted a knowledge-driven interaction analysis of a GWAS of 931 multiple sclerosis (MS) trios to discover gene-gene interactions within established biological contexts. We identify heterogeneous signals, including a gene-gene interaction between CHRM3 (muscarinic cholinergic receptor 3) and MYLK (myosin light-chain kinase) (joint P=0.0002), an interaction between two phospholipase C-β isoforms, PLCβ1 and PLCβ4 (joint P=0.0098), and a modest interaction between ACTN1 (actinin alpha 1) and MYH9 (myosin heavy chain 9) (joint P=0.0326), all localized to calcium-signaled cytoskeletal regulation. Furthermore, we discover a main effect (joint P=5.2E-5) previously unidentified by single-locus analysis within another related gene, SCIN (scinderin), a calcium-binding cytoskeleton regulatory protein. This work illustrates that knowledge-driven interaction analysis of GWAS data is a feasible approach to identify new genetic effects. The results of this study are among the first gene-gene interactions and non-immune susceptibility loci for MS. Further, the implicated genes cluster within inter-related biological mechanisms that suggest a neurodegenerative component to MS.

Environmental pathways to autoimmune diseases: the cases of primary biliary cirrhosis and multiple sclerosis

The pathways leading to autoimmunity remain enigmatic despite numerous lines of experimental inquiry and epidemiological evidence. The mechanisms leading to the initiation and perpetuation of specific diseases such as primary biliary cirrhosis (PBC) or multiple sclerosis (MS) remain largely enigmatic, although it is established that a combination of genetic predisposition and environmental stimulation is required. The growing number of genome-wide association studies and the largely incomplete concordance for autoimmune diseases in monozygotic twins concur to support the role of the environment (including infectious agents and chemicals) in the breakdown of tolerance leading to autoimmunity through different mechanisms. In the present article we illustrate the current hypotheses related to an environmental impact on the onset of PBC and MS as two representative conditions investigated with complementary approaches. Indeed, while a role of post-translational antigen modifications has been proposed for MS, this field remain unexplored in PBC where, conversely, most evidence is gathered from geoepidemiology and experimental data on xenobiotics or infectious agents.

Relevance of IL7R genotype and mRNA expression in Dutch patients with multiple sclerosis

Background: The interleukin 7 receptor (IL7R) has been recognized as a susceptibility gene for Multiple Sclerosis (MS). Analysis of rs6897932 (the most strongly MS-associated single nucleotide polymorphism (SNP)), showed effects of genotype on the relative expression of membrane-bound to total amount of IL7R mRNA.

Objective: We assessed the relevance of IL7R on MS phenotype (including clinical and magnetic resonance imaging (MRI) parameters) at DNA and mRNA level in Dutch patients with MS.

Methods: The genotype of rs6897932 was analyzed in 697 patients with MS and 174 healthy controls. The relevance of genotype and carriership of the C allele on MS phenotype (disease activity and severity, using clinical and MRI parameters) was assessed. In addition, relative gene expression of membrane-bound to total IL7R mRNA was analyzed with respect to disease phenotype in a subgroup of 95 patients with early relapsing MS.

Results: In particular, homozygosity for the risk allele is a risk factor for MS in our population (ORCC vs CT and TT = 1.65 (95% CI: 1.18–2.30), two-sided p = 0.004). However, no effect of genotype or the relative expression of membrane-bound IL7R (presence of exon 6–7) to total amount of IL7R mRNA (presence of exon 4–5) was found on MS phenotype.

Discussion: Homozygosity for the IL7R exon 6 rs6897932 C allele is associated with a higher risk for MS in our Dutch population. No effect was found of genotype or mRNA expression on disease phenotype.

The epigenetics of autoimmunity

The etiology of autoimmune diseases remains largely unknown. Concordance rates in monozygotic twins are lower than 50% while genome-wide association studies propose numerous significant associations representing only a minority of patients. These lines of evidence strongly support other complementary mechanisms involved in the regulation of genes expression ultimately causing overt autoimmunity. Alterations in the post-translational modification of histones and DNA methylation are the two major epigenetic mechanisms that may potentially cause a breakdown of immune tolerance and the perpetuation of autoimmune diseases. In recent years, several studies both in clinical settings and experimental models proposed that the epigenome may hold the key to a better understanding of autoimmunity initiation and perpetuation. More specifically, data support the impact of epigenetic changes in systemic lupus erythematosus, rheumatoid arthritis, multiple sclerosis and other autoimmune diseases, in some cases based on mechanistical observations. We herein discuss what we currently know and what we expect will come in the next future. Ultimately, epigenetic treatments already being used in oncology may soon prove beneficial also in autoimmune diseases.

Association of IL2RA polymorphisms with susceptibility to multiple sclerosis is not explained by missense mutations in IL2RA

Genome-wide association studies have identified an association between two intronic single nucleotide polymorphisms (SNPs), rs12722489 and rs2104286, in the interleukin-2 receptor alpha-chain gene (IL2RA) and susceptibility to multiple sclerosis (MS). We studied these SNPs in association with susceptibility to and severity of MS in a population-based cohort of 220 patients from Olmsted County, Minnesota, compared with 442 matched controls. We sequenced the exons, splice sites and 5' and 3' untranslated regions in 27 randomly selected MS patients (powered for allele frequency≥0.04) to search for mutations. No novel missense mutation was identified. Two patients (7.5%) had an exon 2 SNP (rs4308625) and two patients had an exon 4 SNP (rs2228149), both synonymous.

Association between the IL7R T244I polymorphism and multiple sclerosis: a meta-analysis

Previously published analyses of the association between the interleukin 7 receptor (IL7R) T244I polymorphism (rs6897932) and multiple sclerosis (MS) have yielded conflicting results. We performed a meta-analysis to assess whether the combined data showed this association, and to investigate its effect size. We analyzed 10 studies identified from PubMed (12,185 MS patients and 15,855 controls) and calculated the odds ratios (ORs) and 95% confidence intervals (CIs) for the C-allele, the C/C genotype (recessive effect) and the C/C + C/T (dominant effect) genotype. Heterogeneity within and between studies was observed: allele C: Q = 30.86, P = 0.002; genotype C/C: Q = 30.28, P = 0.003. Using a random-effects model, the C-allele and the C/C genotype were associated with MS (OR = 1.11, 95% CI = 1.04-1.19, P = 0.001 for the C-allele; OR = 1.15, 95% CI = 1.06-1.24, P = 0.0009 for the C/C genotype). The C/C + C/T genotype was also associated with MS using a fixed-effects model (OR = 1.15, 95% CI = 1.05-1.26, P = 0.003). There was no significant publication bias among the selected studies according to the funnel plot. We also performed the analysis on a European subgroup. This revealed an association between IL7R T244I and MS (P < 0.00001 for the C-allele and the C/C genotype; P = 0.0004 for the C/C + C/T genotype), no heterogeneity was observed (allele C: P = 0.07; genotype C/C: P = 0.10). In conclusion, the meta-analysis demonstrated that the IL7R T244I polymorphism was associated with susceptibility to MS.

A transcription factor map as revealed by a genome-wide gene expression analysis of whole-blood mRNA transcriptome in multiple sclerosis

Background

Several lines of evidence suggest that transcription factors are involved in the pathogenesis of Multiple Sclerosis (MS) but complete mapping of the whole network has been elusive. One of the reasons is that there are several clinical subtypes of MS and transcription factors that may be involved in one subtype may not be in others. We investigate the possibility that this network could be mapped using microarray technologies and contemporary bioinformatics methods on a dataset derived from whole blood in 99 untreated MS patients (36 Relapse Remitting MS, 43 Primary Progressive MS, and 20 Secondary Progressive MS) and 45 age-matched healthy controls.

Methodology/Principal Findings

We have used two different analytical methodologies: a non-standard differential expression analysis and a differential co-expression analysis, which have converged on a significant number of regulatory motifs that are statistically overrepresented in genes that are either differentially expressed (or differentially co-expressed) in cases and controls (e.g., V$KROX_Q6, p-value <3.31E-6; V$CREBP1_Q2, p-value <9.93E-6, V$YY1_02, p-value <1.65E-5).

Conclusions/Significance

Our analysis uncovered a network of transcription factors that potentially dysregulate several genes in MS or one or more of its disease subtypes. The most significant transcription factor motifs were for the Early Growth Response EGR/KROX family, ATF2, YY1 (Yin and Yang 1), E2F-1/DP-1 and E2F-4/DP-2 heterodimers, SOX5, and CREB and ATF families. These transcription factors are involved in early T-lymphocyte specification and commitment as well as in oligodendrocyte dedifferentiation and development, both pathways that have significant biological plausibility in MS causation.

IL-7Rα confers susceptibility to experimental autoimmune encephalomyelitis

Multiple sclerosis (MS) is a neurological disorder that causes paralysis in young adults and affects women more frequently than men. The etiology of MS is not known, but it is generally viewed as an autoimmune disease of the central nervous system (CNS), influenced by genetic and environmental factors. Recent studies have identified interleukin-7 receptor α (IL-7Rα) as a risk factor for MS. But the role of IL-7Rα in experimental autoimmune encephalomyelitis (EAE) model of MS is not known. In this study we demonstrate that IL-7Rα-deficient (IL-7Rα(-/-)) mice remain resistant to MOGp35-55-induced EAE. When compared with C57BL/6 wild-type mice, IL-7Rα(-/-) mice showed less severe inflammation and demyelination in the CNS. The attenuation of EAE in IL-7Rα(-/-) mice was associated with a decrease in T-helper (Th) 1 and Th17 responses in the CNS and lymphoid organs. IL-7Rα(-/-) mice also showed an increase in Th2 response and CD4(+)Foxp3(+) regulatory T cells. These findings highlight that IL-7Rα confers susceptibility by influencing autoimmune Th1/Th17 responses in EAE model of MS.

Overexpression of glia maturation factor reinstates susceptibility to myelin oligodendrocyte glycoprotein-induced experimental autoimmune encephalomyelitis in glia maturation factor deficient mice

Glia maturation factor (GMF), a primarily CNS localized protein was discovered and characterized in our laboratory. We previously demonstrated that GMF is the upstream regulator for excessive production and release of proinflammatory cytokines/chemokines in brain cells leading to the destruction of oligodendrocytes, the myelin forming cells, and neurons. We also reported that mice lacking endogenous GMF (GMF-deficient, GMF-KO) were resistant to myelin oligodendrocyte glycoprotein peptide 35-55 (MOG(35-55)) induced EAE, since immunization induced only delayed EAE with diminished severity. In the present study we show that a replication-defective adenovirus-GMF construct caused expression of GMF in CNS of GMF-KO mice and reinstated MOG(35-55) induced early and severe EAE. Our results show that MOG(35-55) immunization caused only a muted EAE and inflammation/demyelination in mice lacking endogenous GMF. The diminished incidence of EAE in GMF-KO mice was consistent with the significantly reduced expressions of cytokines/chemokines. The muted severity of EAE in GMF-KO mice was restored to full blown levels upon reintroduction of GMF using an adeno-GMF-virus (Adv-GMF) vector. Consistent with the clinical findings, histological examination of the CNS of mice with EAE revealed profound differences between wild type (Wt), GMF-KO, and GMF-KO mice with re-introduced GMF (GMF-KO+Adv-GMF). Spinal cord sections from mice with EAE were analyzed for the infiltration of mononuclear cells (inflammation) and myelin loss (demyelination). In Wt mice, 40% of spinal cord quadrants were positive for demyelination and 45% of spinal cord quadrants were positive for inflammation at the peak of EAE. Drastically reduced infiltrates (15%) and demyelination (10%) were found in GMF-KO mice that developed reduced severity of EAE. Upon GMF reintroduction in GMF-KO mice, MOG(35-55) immunization caused extensive monocytes infiltration (48%) and demyelination (46%), similar to that observed in the immunized Wt mice. The levels of cytokine/chemokine in the spinal cords of mice at three time points, corresponding to the onset, peak severity and recovery period of EAE, show a distinct pattern of very large increases in IFN-γ, TNF-α, GM-CSF and MCP-1 in Wt and GMF-KO+Adv-GMF mice compared to GMF-KO and GMF-KO+Adv-LacZ mice.

Interleukin 7 receptor alpha polymorphism rs6897932 and susceptibility to multiple sclerosis in the Western Balkans

The interleukin 7 receptor alpha single nucleotide polymorphism rs6897932 was identified as a multiple sclerosis susceptibility-modifying polymorphism in genome-wide and gene scan studies, mainly in populations in western countries.

The aim of this study was to investigate the association of interleukin 7 receptor alpha rs6897932 with multiple sclerosis in populations from the Western Balkans: Serbia, Croatia, and Slovenia.

A total of 678 unrelated white patients and 597 unrelated, ethnically matched healthy controls were included in the study. Genotyping was performed by real-time polymerase chain reaction.

We found no significant difference in genotype or allele frequencies between controls and patients with multiple sclerosis either separately in Serbian, Croatian, and Slovenian populations or in the whole sample from the Western Balkans. The odds ratio for multiple sclerosis in this study was 1.04 (0.86—1.25) for the C allele.

It is known that demographic as well as environmental factors have a substantial role in multiple sclerosis development, as well as population genetic background. The results of this study indicate that other types of genome variants should be required for the development and/or progression of multiple sclerosis, which may vary among populations.

Serum inflammatory cytokines, complement components, and soluble interleukin 2 receptor in primary biliary cirrhosis

Primary biliary cirrhosis (PBC) is a chronic cholestatic autoimmune liver disease characterized by selective destruction of the intrahepatic bile ducts and highly specific serum anti-mitochondrial autoantibodies (AMA). Several studies have attempted to determine the cytokine pattern characterizing PBC, yet no definitive data have been gathered. The present study was designed to evaluate pro-inflammatory cytokines (IL-1beta, IL-6, TNFalpha), soluble IL-2 receptor (sIL-2R, e.g. soluble CD25), and complement components (C1q, C3, factor B, properdin) levels in sera from 84 patients with PBC and 41 controls. PBC was characterized by significantly higher levels of all pro-inflammatory cytokines when compared to controls; these included IL-1beta (433.3 +/- 13.2 vs. 316.6 +/- 14.7 pg/ml, P < 0.001), IL-6 (701 +/- 17.4 vs. 158 +/- 22.5 pg/ml, P < 0.001), TNFalpha (3.38 +/- 0.6 pg/ml vs. undetectable, P = 0.001), and sIL-2R (1527.1 +/- 106 vs. 566.4 +/- 28.7 U/ml, P < 0.001). Similarly, all complement components were also significantly higher in PBC compared to control sera. In conclusion, PBC sera manifest higher levels of sIL-2R and complement components and this may reflect a perpetuated immune activation. As expected, we also report that all major pro-inflammatory cytokine levels are enhanced in PBC. Further longitudinal analyses could demonstrate a correlation between these markers and disease stage or inflammatory activity, to predict histological staging, disease activity, and response to treatment.