GWAS-identified multiple sclerosis risk loci involved in immune response: validation in Russians

Association of CD58 rs12044852 and rs2300747 polymorphisms with the risk of multiple sclerosis: A systematic review and meta-analysis

OBJECTIVE

Multiple sclerosis is a serious neurodegenerative disorder that causes disability in young adults. Genetic predisposition of multiple sclerosis is well documented and several single nucleotide polymorphisms (SNPs) of the CD58 were found to be associated with this disease. This systematic review and meta-analysis were done with the aim of finding the association between CD58 gene SNPs (rs12044852 and rs2300747) and the risk of multiple sclerosis (MS).

METHOD

A comprehensive search was done in PubMed, Google Scholar, Embase, and MSGene.org to find the relevant data. Our search yielded 13 relevant publications which were included for meta-analysis consisting of 5194 cases and 5766 controls. All the statistical analysis was conducted using meta and metafor packages in R studio. The odds ratio (OR) along with 95 % confidence intervals and p values were determined using the fixed effects and random effects model. The I2 test was done to measure heterogeneity. Subgroup analysis was performed along with analysis for publication bias.

RESULTS

We found significant association for both rs12044852 (allelic, dominant, over-dominant, heterozygous, and homozygous models) and rs2300747 (allelic, dominant, over-dominant, heterozygous models) with multiple sclerosis. Both the SNPs provided a protective effect for multiple sclerosis. Subgroup analysis indicated that rs12044852 polymorphism provided a protective effect in both Asians and Caucasians. However, for rs2300747, the Asian population showed no statistically significant association with the risk of MS.

CONCLUSION

Polymorphism of rs12044852 and rs2300747 of the CD58 gene provided a protective effect for multiple sclerosis. The protective effect is more prominent in Caucasian populations compared to Asians.

Analysis of herpesvirus infection and genome single nucleotide polymorphism risk factors in multiple sclerosis, Volga federal district, Russia

Multiple sclerosis (MS) is a heterogeneous disease where herpesvirus infection and genetic predisposition are identified as the most consistent risk factors. Serum and blood samples were collected from 151 MS and 70 controls and used to analyze circulating antibodies for, and DNA of, Epstein Barr virus (EBV), human cytomegalovirus (HCMV), human herpes virus 6 (HHV6), and varicella zoster virus (VZV). The frequency of selected single nucleotide polymorphisms (SNPs) in MS and controls were studied. Herpesvirus DNA in blood samples were analyzed using qPCR. Anti-herpesvirus antibodies were detected by ELISA. SNPs were analyzed by the allele-specific PCR. For statistical analysis, Fisher exact test, odds ratio and Kruskall-Wallis test were used; p<0.05 values were considered as significant. We have found an association between circulating anti-HHV6 antibodies and MS diagnosis. We also confirmed higher frequency of A and C alleles in rs2300747 and rs12044852 of CD58 gene and G allele in rs929230 of CD6 gene in MS as compared to controls. Fatigue symptom was linked to AC and AA genotype in rs12044852 of CD58 gene. An interesting observation was finding higher frequency of GG genotype in rs12722489 of IL2RA and T allele in rs1535045 of CD40 genes in patient having anti-HHV6 antibodies. A link was found between having anti-VZV antibodies in MS and CC genotype in rs1883832 of CD40 gene.

Lupus enhancer risk variant causes dysregulation of IRF8 through cooperative lncRNA and DNA methylation machinery

Despite strong evidence that human genetic variants affect the expression of many key transcription factors involved in autoimmune diseases, establishing biological links between non-coding risk variants and the gene targets they regulate remains a considerable challenge. Here, we combine genetic, epigenomic, and CRISPR activation approaches to screen for functional variants that regulate IRF8 expression. We demonstrate that the locus containing rs2280381 is a cell-type-specific enhancer for IRF8 that spatially interacts with the IRF8 promoter. Further, rs2280381 mediates IRF8 expression through enhancer RNA AC092723.1, which recruits TET1 to the IRF8 promoter regulating IRF8 expression by affecting methylation levels. The alleles of rs2280381 modulate PU.1 binding and chromatin state to regulate AC092723.1 and IRF8 expression differentially. Our work illustrates an integrative strategy to define functional genetic variants that regulate the expression of critical genes in autoimmune diseases and decipher the mechanisms underlying the dysregulation of IRF8 expression mediated by lupus risk variants.

CD58 Immunobiology at a Glance

The glycoprotein CD58, also known as lymphocyte-function antigen 3 (LFA-3), is a costimulatory receptor distributed on a broad range of human tissue cells. Its natural ligand CD2 is primarily expressed on the surface of T/NK cells. The CD2-CD58 interaction is an important component of the immunological synapse (IS) that induces activation and proliferation of T/NK cells and triggers a series of intracellular signaling in T/NK cells and target cells, respectively, in addition to promoting cell adhesion and recognition. Furthermore, a soluble form of CD58 (sCD58) is also present in cellular supernatant in vitro and in local tissues in vivo. The sCD58 is involved in T/NK cell-mediated immune responses as an immunosuppressive factor by affecting CD2-CD58 interaction. Altered accumulation of sCD58 may lead to immunosuppression of T/NK cells in the tumor microenvironment, allowing sCD58 as a novel immunotherapeutic target. Recently, the crucial roles of costimulatory molecule CD58 in immunomodulation seem to be reattracting the interests of investigators. In particular, the CD2-CD58 interaction is involved in the regulation of antiviral responses, inflammatory responses in autoimmune diseases, immune rejection of transplantation, and immune evasion of tumor cells. In this review, we provide a comprehensive summary of CD58 immunobiology.

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.

Pattern Recognition Receptors in Multiple Sclerosis and Its Animal Models

Pattern recognition receptors (PRRs) coordinate the innate immune response and have a significant role in the development of multiple sclerosis (MS). Accumulating evidence has identified both pathogenic and protective functions of PRR signaling in MS and its animal model, experimental autoimmune encephalomyelitis (EAE). Additionally, evidence for PRR signaling in non-immune cells and PRR responses to host-derived endogenous ligands has also revealed new pathways controlling the development of CNS autoimmunity. Many PRRs remain uncharacterized in MS and EAE, and understanding the distinct triggers and functions of PRR signaling in CNS autoimmunity requires further investigation. In this brief review, we discuss the diverse pathogenic and protective functions of PRRs in MS and EAE, and highlight major avenues for future research.

Analysis of chosen SNVs in GPC5, CD58 and IRF8 genes in multiple sclerosis patients

PURPOSE

Multiple sclerosis (MS) is an autoimmune disease of the central nervous system with a neurodegenerative compound. Heterogenetic background of autoimmunity pathway components has been suggested in the MS pathogenesis. The main aim of our study was to evaluate the association between selected polymorphisms of theCD58, IRF8 and GPC5 genes and treatment effectiveness in a group of relapsing-remitting MS patients. This is the first study of MS patients from Podlaskie Region in the Polish population.

MATERIALS AND METHODS

The study group comprised 174 relapsing-remitting MS patients diagnosed under 40 years of age. Genotyping was performed using ready to use TaqMan assays.

RESULTS

We demonstrate a strong association of the polymorphisms with sex, age of onset and response to the treatment applied. A significant correlation was observed in the presence of allele T of rs10492503 polymorphism inGPC5 gene with sex and age of MS onset. Logistic regression analysis revealed an increased risk of the interaction of rs17445836 in IRF8 gene with male sex and the type of treatment (OR = 3.80, p < 0.05), and a decreased risk in the interaction of female sex with disease progress according to the EDSS scale (OR=-2.33, p < 0.05).

CONCLUSIONS

The analysis of the correlation between different alleles, genotypes and clinical status confirmed the interaction between the genetic factors of age of onset and response to therapy. The study suggests that genetic variants inGPC5, CD58 and IRF8 genes may be of clinical interest in MS as predictors of age of onset and response to therapy.

Genetic variants in SLC22A3 contribute to the susceptibility to colorectal cancer

Previous a genome‐wide association study (GWAS) of colorectal cancer in Japanese population has identified a risk region at the chromosome 6q26‐q27 associated with colorectal cancer risk. However, the causal gene at this locus remained unclear. In our study, we enrolled a total of 14 candidate functional single nucleotide polymorphisms (SNPs) at 6q26‐q27 (318 kb), and then genotyped them by TaqMan method in a Chinese population including 1,147 colorectal cancer cases and 1,203 controls. Among that, 5 SNPs were identified statistical association with colorectal cancer risk by logistic regression analysis. Of which, SNP rs420038 G > A in SLC22A3 was related to decreased risk of colorectal cancer (adjusted odds ratio (OR) = 0.79, 95% confidence interval (CI) = 0.67–0.94, p = 0.007), and also associated with lower expression of SLC22A3 (p = 0.040) using expression quantitative trait loci (eQTL) analysis. Moreover, by the luciferase assays, we found that compared to the G allele of rs420038, the A allele could suppress the activity of the promoter in SLC22A3. Furthermore, the expression of SLC22A3 was significantly higher in colorectal cancer tissues than that in paired normal tissues (p < 0.001). Meanwhile, the phenotypes of proliferation, migration, invasion, cell cycle and apoptosis of colorectal cancer cell were significantly affected by SLC22A3 in vitro. Our results revealed a novel susceptible locus, rs420038 in SLC22A3, which may be involved in colorectal cancer development and progression.

What's new?

The identification of genes or loci associated with colorectal cancer (CRC) susceptibility can facilitate the discovery of molecular pathways underlying CRC development and progression. Here, the authors investigated a risk region at chromosome 6q26‐q27, which previously was linked to CRC susceptibility in a Japanese population. Analyses of candidate functional single nucleotide polymorphisms (SNPs) at 6q26‐q27 revealed a novel functional SNP, rs420038 G>A, in the SLC22A3 gene. While expression of SLC22A3 was elevated in CRC tissues, the novel SNP was associated with decreased CRC risk in a Chinese population. The A allele of rs420038 significantly suppressed SLC22A3 promoter activity.

[Association analysis of cytokine receptors' genes polymorphisms with clinical features of multiple sclerosis]

AIM

To study the association of polymorphisms in the IL2RA and TNFRSF1A genes with severity and early clinical manifestations of remitted multiple sclerosis (MS).

MATERIAL AND METHODS

Five hundred and eight patients of Russian ethnicity with bout-onset MS were genotyped for IL7RA (rs6897932), IL2RA (rs2104286) and TNFRSF1A (rs1800693) polymorphisms. Association analysis of the gene variants with disease severity, variants of MS manifestation, and first remission duration was performed.

RESULTS AND CONCLUSION

Dividing the MS patients by disease severity, estimated with the MSSS, we found a significant increase in the TNFRSF1A*T/T genotype carriage in patients with milder MS course (MSSS≤3), and, respectively, in the TNFRSF1A*C allele carriage in patients with moderate to severe MS (MSSS> 3). Dividing the MS patients into two groups according to their MS manifestation variants, we revealed a significant increase in the TNFRSF1A*T allele carriage in patients with favorable variants of MS manifestation (optic neuritis or sensory disturbances), and of the TNFRSF1A*C/C genotype in patients with unfavorable variants (motor disorders, brain stem disorders, impaired coordination, pelvic disorders, mental disorders or polysymptomatic onset). No associations with first remission duration were observed. Multi-locus analysis to search for allelic combinations associated with the studied clinical features of MS was applied. In this analysis, a polymorphic variant of CTLA4 gene (rs231775), for which we have previously reported the association of the CTLA4*G allele with short first remission (less than 1 year), was also included. The carriage of biallelic combination (CTLA4*G + TNFRSF1A*C) was associated with short first remission more significantly than the carriage of CTLA4*G by itself. One more biallelic combination associated with short first remission (CTLA4*G/G + IL7RA*T), was identified. No other biallelic combinations significantly associated with the clinical features studied were observed.

TNFRSF1A polymorphisms and their role in multiple sclerosis susceptibility and severity in the Slovak population

Tumour necrosis factor (TNF)-mediated signalling plays a key role in inflammatory and neurodegenerative processes leading to the development of multiple sclerosis (MS). Recent studies have highlighted the role of tumour necrosis factor receptor superfamily member 1A (TNFRSF1A) gene encoding the type 1 TNF receptor in the genetic predisposition to MS. This study aimed to validate the association of TNFRSF1A rs1800693 and rs4149584 polymorphisms with susceptibility to MS in the Slovak population and analyse their influence on age at disease onset, severity, and disability progression. Polymerase chain reaction-restriction fragment length polymorphism method was used to genotype both TNFRSF1A polymorphisms in 541 MS patients and 724 healthy controls. Logistic regression analysis revealed a significantly increased risk of developing MS for the carriers of rs1800693 C allele (TC + CC vs. TT: pcorr = 0.005; OR = 1.61; 95% CI = 1.23-2.12), irrespective of sex and carriage of the major MS risk allele HLA-DRB1*15:01. On the other hand, no association could be found between rs4149584 and MS risk (GA + AA vs. GG: pcorr = 1.00; OR = 1.25; 95% CI = 0.71-2.21). Moreover, neither polymorphism was significantly associated with age at disease onset, MS Severity Score (MSSS) or MS Progression Index (PI) in any of the inheritance models. In conclusion, our results provide support for a sex- and HLA-DRB1*15:01-independent association of TNFRSF1A rs1800693 SNP with MS susceptibility, but not with age at disease onset, severity or rate of disability accumulation.

Protective C allele of the single-nucleotide polymorphism rs1335532 is associated with strong binding of Ascl2 transcription factor and elevated CD58 expression in B-cells

CD58 is expressed on the surface of antigen-presenting cells, including B-cells, and provides co-stimulation to regulatory T-cells (Treg) through CD2 receptor binding. Tregs appear to be essential suppressors of tissue-specific autoimmune responses. Thereby, CD58 plays protective role in multiple sclerosis (MS) and CD58 was identified among several loci associated with MS susceptibility. Minor (C) variant of the single-nucleotide polymorphism (SNP) rs1335532 is associated with lower MS risk according to genome-wide association studies (GWAS) and its presence correlates with higher CD58 mRNA levels in MS patients. We found that genomic region containing rs1335532 has enhancer properties and can significantly boost the CD58 promoter activity in lymphoblast cells. Using bioinformatics and pull-down assay we found that the protective (C) rs1335532 allele created functional binding site for ASCL2 transcription factor, a target of the Wnt signaling pathway. Both in B-lymphoblastoid cell lines and in primary B-cells, as well as in a monocytic cell line, activation of Wnt signaling resulted in an increased CD58 promoter activity in the presence of the protective but not the risk allele of rs1335532, whereas ASCL2 knockdown abrogated this effect. In summary, our results suggest that ASCL2 mediates the protective function of rs1335532 minor (C) allele in MS.

Meta-analysis of the association of IL2RA polymorphisms rs2104286 and rs12722489 with multiple sclerosis risk

BACKGROUND

The interleukin-2 receptor alpha (IL2RA) gene polymorphisms may be implicated in the genetic susceptibility to multiple sclerosis (MS). This meta-analysis aims to evaluate the relationship of the IL2RA polymorphisms rs2104286 and rs12722489 with MS risk in different populations.

METHODS

Eligible association studies were identified through search in Pubmed, Medline, Web of Science, and Scopus (end of search: August 2017). Summary odds ratios (ORs) with 95% confidence intervals (CIs) were calculated using random-effects or fixed-effects models. All statistical analyses were two-sided.

RESULTS

Eleven studies including 8608 cases and 9061 controls evaluated rs2104286. The results demonstrated that the A allele of rs2104286 was associated with increased risk of MS in Caucasians (OR = 1.19, 95%CI: 1.13-1.25, p < 0.001) and Asians (OR = 1.25, 95%CI: 1.01-1.55, p = 0.041), respectively. Concerning rs12722489, six studies with 4259 cases and 5420 controls were eligible. We found that the C allele of rs12722489 was associated with elevated MS risk in Caucasians (OR = 1.20, 95% CI: 1.12-1.29, p < 0.001) but not in Asians (OR = 1.10, 95%CI: 0.75-1.63, p = 0.629). Statistical evidence from the Egger and Begg tests showed absence of publication bias. Sensitivity analysis showed that the results were stable.

CONCLUSION

Our meta-analysis suggests that the rs2104286 A allele is associated with increased MS risk in both Caucasians and Asians, whereas the rs12722489 C allele is associated with elevated MS risk in Caucasians but not in Asians.

Single-nucleotide polymorphism rs948854 in human galanin gene and multiple sclerosis: a gender-specific risk factor

We performed comparative analyses of the genotype distribution and allelic frequencies of the rs948854 polymorphism (G/A) in the galanin gene's promoter in patients with multiple sclerosis (MS) and in healthy matched controls. In total 111 patients and 115 control subjects were included. The analyses revealed that the presence of the minor allele (G) increased susceptibility to MS in men (OR = 2.49, P = 0.008) but not in women. The presence of the G allele in men was also significantly associated with the late onset of MS. Furthermore, rs948854 polymorphism affected the rate of MS progression depending on the sex of the patients. In woman (typically slowly progressing), the percentage of patients with the slow (<0.5 EDSS score per year) progression rate was significantly reduced (χ²  = 5.7, P = 0.017) in the minor allele carriers group (52.6%), in comparison with the wild-type carriers (83.9%). In men (typically quickly progressing), the number of patients with fast progression rate (≥0.75 EDSS score per year) tended to increase in the minor allele carriers group (50%) compared with number of patients with the wild-type carriers (31.3%). These data demonstrate for the first time an association between rs948854 polymorphism and multiple sclerosis and, further, that this association is sex specific. They also point to diagnostic and prognostic benefits of genetic screening of patients with multiple sclerosis. © 2016 Wiley Periodicals, Inc.

Pharmacogenetics of glatiramer acetate therapy for multiple sclerosis: the impact of genome-wide association studies identified disease risk loci

AIM

Association analysis of genome-wide association studies (GWAS) identified multiple sclerosis (MS) risk genetic variants with glatiramer acetate (GA) treatment efficacy.

PATIENTS & METHODS

SNPs in 17 GWAS-identified immune response loci were analyzed in 296 Russian MS patients as possible markers of optimal GA treatment response for at least 2 years.

RESULTS

Alleles/genotypes of EOMES, CLEC16A, IL22RA2, PVT1 and HLA-DRB1 were associated by themselves with event-free phenotype during GA treatment for at least 2 years (p _f  = 0.032 - 0.00092). The biallelic combinations including EOMES, CLEC16A, IL22RA2, PVT1, TYK2, CD6, IL7RA and IRF8 genes were associated with response to GA with increased significance level (p _f  = 0.0060 - 1.1 × 10^-5). The epistasic interactions or additive effects were observed between the components of the identified biallelic combinations.

CONCLUSION

We pinpointed the involvement of several GWAS-identified MS risk loci in GA therapy efficacy. These findings may be aggregated to predict the optimal GA response in MS patients.

[Polymorphic variants of the immune response genes as risk factors for primary progressive multiple sclerosis]

AIM

To analyze the involvement of immune response genes in the pathogenesis of primary progressive multiple sclerosis (PPMS).

MATERIAL AND METHODS

This multicenter study included 111 patients with PPMS from the Russian ethnic group. The association of PPMS with genes of immune system was analyzed by the study of polymorphic variants of genes of cytokines and genes of antigen-presenting cells.

RESULTS AND CONCLUSION

The genotypes of IL-4 (rs2243250)*C/C and CLEC16A (rs6498169)*G/G were associated with PPMS in Russians. The association between the HLA-DRB1*15 and PPMS found out in other populations was confirmed in Russians.

Association of EVI5 rs11808092, CD58 rs2300747, and CIITA rs3087456 polymorphisms with multiple sclerosis risk: A meta-analysis

Purpose

Multiple sclerosis (MS) is a major demyelinating disease of the central nervous system with a strong genetic component. Previous studies have reported that the association of EVI5 rs11808092, CD58 rs2300747, and CIITA rs3087456 polymorphisms with the susceptibility to MS. However, the results were inconsistent. Thus, we conducted this meta-analysis to provide a more accurate estimation of the association between any of these polymorphisms and MS risk.

Methods

The PubMed, Embase, Chinese National Knowledge Infrastructure, Wan Fang databases and MSGene were used to search all potentially relevant studies. The odds ratio (OR) with 95% confidence interval (CI) was used to investigate the associations between these three polymorphisms and MS risk.

Results

16 independent case–control studies from 12 publications were finally included into this meta-analysis. The results showed that EVI5 rs11808092 polymorphism was related with increasing the development of MS under five genetic models (allelic: OR = 1.17, 95% CI = 1.10–1.24, P < 0.01; homozygous: OR = 1.37, 95% CI = 1.18–1.59, P < 0.01; heterozygous: OR = 1.16, 95% CI = 1.07–1.26, P < 0.01; recessive: OR = 1.28, 95% CI = 1.11–1.48, P < 0.01; and dominant: OR = 1.19, 95% CI = 1.11–1.48, P < 0.01). CD58 rs2300747 polymorphism was found to be associated with decreasing MS risk in three genetic models (allelic: OR = 0.86, 95% CI = 0.78–0.94, P < 0.01; heterozygous: OR = 0.85, 95% CI = 0.76–0.94, P < 0.01, and dominant: OR = 0.84, 95% CI = 0.76–0.93, P < 0.01). However, this meta-analysis indicated that CIITA rs3087456 polymorphism was not related to multiple sclerosis.

Conclusions

The mutant alleles of EVI5 rs11808092 polymorphism may increase the susceptibility to MS while those of CD58 rs2300747 polymorphism may decrease MS risk. In addition, CIITA rs3087456 polymorphism might not be associated with MS.