Genomic regulation of CTLA4 and multiple sclerosis

The cytotoxic T lymphocyte antigen 4 gene (CTLA4) is a critical regulator of T-cell activation and it is an important therapeutic target for cancer and autoimmune diseases. Here, we analyzed the genomic regulation of CTLA4 gene expression in order to identify single nucleotide polymorphisms (SNPs) that affect its expression and splicing, and to assess their association with Multiple Sclerosis (MS). We analyzed 152 healthy subjects and 146 patients with MS, of which 52 controls and 51 patients were used for gene expression analysis. We genotyped 17 SNPs in the CTLA4 gene using the SNaPshot Multiplex Kit, and in addition gene expression of the soluble (sCTLA4) and full length (flCTLA4) isoforms was quantified by real-time PCR, while protein levels of sCTLA4 were measured by ELISA. We found that the SNPs at -1577, +6230, +10242, +10717 and +12310 influence CTLA4 expression and the combination of the -1577 GG and +6230 GG genotypes provokes the strongest decrease in CTLA4 gene expression. We found that the SNP at -658 only acted as a regulatory SNP in patients with MS, suggesting the existence of epigenetic changes due to this disease. We also identified a decrease in CTLA4 gene expression levels in patients receiving chemotherapy, although no association was observed between MS and any of the polymorphisms studied. In conclusion, we have identified several SNPs in the CTLA4 gene and studied their influence on its genetic regulation. The involvement of CTLA4 in the pathogenesis of MS may be subtle and related to the functional changes in its pathway rather than predisposing genetic polymorphisms.     

Genetic association between polymorphisms in the ADAMTS14 gene and multiple sclerosis

ADAMTS14 is a novel member of the ADAMTS (a disintegrin-like and metalloproteinase domain with thrombospondin type 1 modules) metalloproteinase family which processes extracellular matrix proteins. In the present study we performed a comprehensive investigation of the ADAMTS14 as a candidate gene for susceptibility to multiple sclerosis (MS). Eight single nucleotide polymorphisms (SNPs) were analyzed in a case-control study of 287 patients with MS [192 with relapsing-remitting MS (RRMS) and 95 with primary-progressive MS (PPMS)], and 285 age- and sex-matched controls. Allele and genotype frequencies were compared between controls and the MS subgroups, and gene-based haplotypes were reconstructed by computational procedures. Pairwise linkage disequilibrium values (D') suggested that three locus pairs (SNPs 3 through 5) had alleles in strong disequilibrium and constituted a haplotype block spanning 14 kb. Overall comparisons of allele and genotype frequencies showed association for SNPs 3 and 6 with MS. Stratification of MS patients according to major clinical forms revealed an increased frequency of both allele C (p = 0.006) and CC homozygosity (p = 0.008) at SNP6 in RRMS patients compared with controls. PPMS was associated with allele A at SNP2 compared with RRMS (p = 0.003) and controls (p = 0.009), and with CG heterozygosity at SNP3 compared with controls (p = 0.005). Haplotype frequency comparisons showed significant association between PPMS and the AGGGC haplotype compared with controls (p = 0.0004), and negative association between RRMS and the GGAGT haplotype compared with controls (p = 0.0026). No association was detected between different genotypes and disease severity measured by the Multiple Sclerosis Severity Score (MSSS). These findings suggest a potentially important role for the ADAMTS14 gene in predisposition to MS.     

Association analysis of the LAG3 and CD4 genes in multiple sclerosis in two independent populations

We have investigated the genetic involvement of the CD4 and the LAG3 genes, two appealing candidates for MS due to their suggested role in MS pathology. We genotyped a Swedish case–control material consisting of 920 MS patients and 778 controls in an initial study of CD4, three SNPs showed a significant association with MS. An independent material consisting of 1720 Nordic MS patients and 1416 controls were used for confirmation of associated markers in CD4 and to do a confirmative study of the LAG3 gene from previous findings. The result, including a total of 2640 MS patients and 2194 controls shows no significant association with CD4 and LAG3 and MS. We conclude that these genes are of minor importance in regard of genetic predisposition to the MS.     

ITGA4 polymorphisms and susceptibility to multiple sclerosis

In multiple sclerosis (MS), alpha(4)beta(1) integrin, also known as Very Late Antigen 4 (VLA4), facilitates migration of leukocytes across the blood brain barrier. Several studies suggest that expression of alpha(4) integrin may be increased in MS patients compared to controls, and down-regulation or antagonism of alpha(4) integrin may be associated with immunomodulatory treatment success. We analysed association of 13 single nucleotide polymorphisms (SNPs) in the gene encoding alpha(4) integrin (ITGA4) with susceptibility to MS in two distinct populations comprising cases and controls from the Basque Country in northern Spain (352 patients; 235 controls) and Nordic countries (1119 patients; 1235 controls). Carriage of the C allele of the ITGA4 promoter SNP rs1449263 was independently and weakly increased in MS patients from each population compared to respective controls (P = 0.037 in Basque; and P = 0.042 in Nordic cohorts), though these associations were lost upon application of permutation correction. Meta-analysis of rs1449263*C carriage revealed a Mantel-Haenszel common OR of 1.26 (95% CI 1.06-1.49; P = 0.0069). Though our data only modestly argue for a role of ITGA4 in determining susceptibility to MS, we suggest that further examination of this gene, particularly the promoter region, is warranted.     

Analysis of the IL28RA locus as genetic risk factor for multiple sclerosis

Recently, we reported an association between a SNP in IL28RA and MS. Here, we performed a fine-mapping of the IL28RA locus by genotyping 10 haplotype-tagging SNPs in a Basque-Spanish population. In addition, based on shared genetic risk loci between autoimmune diseases, a psoriasis-associated SNP located at this locus, rs4649203, was genotyped in four independent populations, comprising a total of 2582 cases and 2614 controls. We did not find any consistent association between IL28RA and MS in these populations, suggesting that, although it may play a role in other autoimmune diseases, this gene is unlikely of general relevance to MS pathogenesis.     

The neuropeptide genes TAC1, TAC3, TAC4, VIP and PACAP(ADCYAP1), and susceptibility to multiple sclerosis

The related immunomodulatory neuropeptides vasoactive intestinal peptide (VIP) and pituitary adenylyl cyclase activating peptide (PACAP; gene symbol ADCYAP1) have recently been proposed as novel therapeutics for the treatment of multiple sclerosis (MS). These neuropeptides, as well as those belonging to the tachykinin family exert pleiotropic effects, many of which are of relevance to central nervous system inflammation. In the present study, we have analysed 14 single nucleotide polymorphisms (SNPs) and 4 microsatellite markers in the VIP, ADCYAP1, TAC3 and TAC4 genes for susceptibility to MS in a case-control collection from Northern Ireland. Following correction for multiple comparisons, we did not find any significant associations between single polymorphic markers or multiple-marker haplotypes and susceptibility to MS. Furthermore, we analysed 2 SNPs in the TAC1 gene in a set of Sardinian trio MS families, based on our previous observation of association of these SNPs with MS in the Northern Irish (Genes Immun. 2005, 6, 265-270). Analysis of these SNPs in the Sardinians was not significant though a similar trend to that originally observed in the Northern Irish was present. Meta-analysis of the Sardinian and Northern Irish TAC1 SNP genotype data revealed a Mantel-Haenszel Common OR Estimate for the TAC1 intron 1 SNP rs2072100 of 0.76 (95% CI 0.63-0.92; P=0.005; A allele) and for the TAC1 promoter SNP rs7793277 of 0.76 (95% CI 0.615-0.95; P=0.014; C allele). Our data advocate a need for further exploration of the TAC1 gene region in MS.     

Investigation of <Emphasis Type="Italic">TGFB2</Emphasis> as a candidate gene in multiple sclerosis and Parkinson’s disease

Given the known roles of TGFbeta2 in both regulating the immune system and promoting the survival of dopaminergic neurons, it is feasible that genetic variations in TGFB2 might play an aetiological role in neurological diseases such as Multiple Sclerosis (MS) and Parkinson's disease (PD). Hence we performed an indirect association analysis of TGFB2 using 8 haplotype-tagging SNPs in a population of 937 MS patients, 538 PD cases and 2022 controls. We found no evidence for association with susceptibility or progression of MS, but have demonstrated a trend towards association of the 5' region of the gene with susceptibility to PD. Further analysis of TGFB2 is warranted in other PD cohorts.     

The Promoter SNP,but not the Alternative Splicing SNP,is Linked to Multiple Sclerosis Among Jordanian Patients

Multiple sclerosis is a chronic inflammatory autoimmune disease of the human central nervous system. A number of studies with compelling evidence have provided correlation between single nucleotide polymorphisms in interleukin-7 receptor alpha and multiple sclerosis (MS) in several populations. One such variation, rs6897932, is located within the coding region and results in the generation of a soluble receptor, whereas another one, rs11567685, is located in the promoter region and affects gene expression. In this study, we investigated the frequencies of these two SNPs and their association to MS in 200 healthy controls and 200 MS patients based on a simple PCR-RFLP strategy not reported previously. The frequencies of the high risk alleles for both SNPs were in a high range among healthy and MS subjects relative to previous studies. In addition, whereas no association was found between the alternative splicing SNP, rs6897932, and MS, a significant link was found between the promoter SNP, rs11567685, and MS. These results are in contrast to other studies and may have important implications as to the molecular contribution of IL-7Rα in multiple sclerosis.     

Association analysis of the LAG3 and CD4 genes in multiple sclerosis in two independent populations

We have investigated the genetic involvement of the CD4 and the LAG3 genes, two appealing candidates for MS due to their suggested role in MS pathology. We genotyped a Swedish case–control material consisting of 920 MS patients and 778 controls in an initial study of CD4, three SNPs showed a significant association with MS. An independent material consisting of 1720 Nordic MS patients and 1416 controls were used for confirmation of associated markers in CD4 and to do a confirmative study of the LAG3 gene from previous findings. The result, including a total of 2640 MS patients and 2194 controls shows no significant association with CD4 and LAG3 and MS. We conclude that these genes are of minor importance in regard of genetic predisposition to the MS.     

Melatonin pathway genes are associated with progressive subtypes and disability status in multiple sclerosis among Finnish patients

In this study we investigated the relationship between melatonin pathway and multiple sclerosis (MS) in a high-risk Finnish population by studying the single nucleotide polymorphisms (SNPs) in the genes coding for critical enzymes and receptors involved in the melatonin pathway. A total of 590 subjects (193 MS patients and 397 healthy controls) were genotyped for seven SNPs in four genes including tryptophan hydroxylases (TPH)1 and 2, arylalkylamine N-acetyltransferase (AANAT) and melatonin receptor 1B (MTNR1B). An overrepresentation of T allele carriers of a functional polymorphism (G-703T, rs4570625) in the promoter region of TPH2 gene was observed in the progressive MS subtypes. The haplotype rs4570625-rs10506645TT of TPH2 gene was associated with the risk of severe disability in primary progressive MS (PPMS), while haplotype rs4570625-rs10506645TC appeared to be protective against disability in secondary progressive MS (SPMS). In the MTNR1B gene, the haplotype rs10830963-rs4753426GC was associated with the risk of SPMS, whereas another haplotype rs10830963-rs4753426GT showed an association with the risk of PPMS. These data showing the association of polymorphisms in the TPH2 and MTNR1B genes with the progressive subtypes of MS and disability suggest dysregulation in melatonin pathway. Melatonin pathway seems to be involved in disease progression, and therefore its potential effects in overcoming MS-related neurodegeneration may be worth evaluating in future clinical trials.     

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.     

Pharmacogenetics of MXA SNPs in interferon-beta treated multiple sclerosis patients

The myxovirus resistance A (MXA) mRNA has been extensively investigated for assessing the biologic responses of multiple sclerosis (MS) patients to interferon-beta (IFN-beta) therapy. The objective of this study was to evaluate the associations between two MXA promoter region single nucleotide polymorphisms (rs2071430 and rs17000900) and the gene expression responses, clinical and MRI phenotypes in IFN-beta treated MS patients. The rs2071430 and rs17000900 SNPs, which are located in or near an interferon-stimulated response element (ISRE), were genotyped in 179 relapsing MS patients. Quantitative MRI measurements were available for 101 patients on IFN-beta monotherapy. Gene expression was assessed in 22 anti-interferon-beta neutralizing antibody negative patients. No significant association was found between the MXA genotype at these two SNPs and clinical, MRI and MXA gene expression in MS patients treated with IFN-beta therapy.     

Association study of the DISC1/TRAX locus with schizophrenia in a Japanese population

Disrupted-in-Schizophrenia-1 (DISC1), identified by cytogenetic approaches in a pedigree with familial psychosis, is considered a candidate susceptibility gene for schizophrenia in some populations. In the pedigree, the TRAX gene, located adjacent to DISC1 on the disrupted chromosome 1, may also contribute to the pathophysiology of the familial schizophrenia. We studied association of the DISC1 and TRAX genes with schizophrenia in 338 Japanese by analyzing 15 single nucleotide polymorphisms (SNPs), including 12 SNPs in DISC1 and three in TRAX, respectively. No significant difference was observed between the patients and controls in allelic frequencies or genotypic distributions of 15 SNPs. A weak trend for the association in genotypic distribution of one SNP in TRAX (major homo/hetero/minor homo: 0.324/0.431/0.245 vs. 0.293/0.526/0.181 for patients vs controls, p = 0.039 in the 2 x 3 comparison) turned out to be insignificant after Bonferroni correction. Haplotype analysis did not support the association between the patients and controls. The present study suggests that the DISC1/TRAX locus may not have a major role in Japanese schizophrenia.     

Coding region polymorphisms in T cell signal transduction genes. Prevalence and association to development of multiple sclerosis

We systematically assessed 53 genes involved in T cell signaling, among which 72 SNPs in 32 genes were reported in databases as causing non-synonymous amino acid substitutions. Screening of 41 of these SNPs in DNA pools from 4000 Norwegian controls showed that only 12 SNPs (29%) were polymorphic. These were tested for association to MS in DNA pools from 364 Norwegian MS patients. To eliminate sources of variance introduced by DNA pooling, the SNPs in the best-ranked PLCG1 as well as the PTPN22 gene were thereafter genotyped in individual MS and control samples, however, without finding evidence for association to MS.     

No genetic association between polymorphisms in the kainate-type glutamate receptor gene, GRIK4, and schizophrenia in the Chinese population

BACKGROUND: Schizophrenia is a chronic psychiatric disorder with a strong genetic component. Several studies have suggested that dysfunctions in the glutamatergic transmission are linked to the pathogenesis of schizophrenia, and that the kainate ionotropic glutamate receptors are involved in this mechanism. A recent study provides cytogenetic and genetic evidence to support a role for the kainate-type glutamate receptor gene (GRIK4), in schizophrenia. A systematic case-control association study of GRIK4 involving a Scottish population found that three SNPs, rs4935752, rs6589846 and rs4430518, were associated with schizophrenia. METHODS: Here, we investigated rs4935752, rs6589846, rs4430518 and other 2 SNPs within the GRIK4 gene in an association study of the Chinese population. Our sample consisted of 288 schizophrenia and 288 control subjects. All recruits were Han Chinese drawn from the city of Shanghai. RESULTS: No individual SNP nor any haplotype was associated with schizophrenia in our study. CONCLUSION: These results suggest that the five SNPs within the GRIK4 gene are unlikely to play a major role in the susceptibility to schizophrenia in the Chinese population.     

NOS2A as a candidate gene in Relapsing-Remitting Multiple Sclerosis: a haplotype study using selected subsets of single nucleotide polymorphisms

As with other autoimmune diseases, susceptibility to multiple sclerosis (MS) is believed to result from the complex interaction of a number of genes, each with modest effect. Several genome-wide screens have implicated the nitric oxide synthase 2A gene (NOS2A), which encodes the inducible form of nitric oxide synthase, as being potentially associated with MS. To determine whether genetic variants within this gene may constitute a risk factor for causing MS, we investigated 13 single nucleotide polymorphisms in the NOS2A gene, in a case-control group of 214 Italian patients with MS and 121 controls. All these single nucleotide polymorphisms (SNPs) were analyzed using the SNPlex? Genotyping System (Applied Biosystems). Data were analyzed using Genemapper 4.0 and Haploview 4.1. No significant association between cases and controls (P>0.05) was observed for the alleles of the SNPs. Defining the haplotype blocks also failed to detect any associated haplotypes. Our results suggest that polymorphic variation within the NOS2A gene does not influence the susceptibility to MS in patients of Italian origin.     

IL28B polymorphisms are not associated with the response to interferon-β in multiple sclerosis

Recent studies have revealed an association between interleukin 28B (IL28B) and response to IFN-alpha treatment in hepatitis C patients. Here we investigated the influence of IL28B polymorphisms in the response to interferon-beta (IFNβ) in multiple sclerosis (MS) patients. We genotyped two SNPs of the IL28B gene (rs8099917 and rs12979860) in 588 MS patients classified into responders (n=281) and non-responders (n=307) to IFNβ. Combined analysis of the study cohorts showed no significant associations between SNPs rs8099917 and rs12979860 and the response to treatment. These findings do not support a role of IL28B polymorphisms in the response to IFNβ in MS patients.     

Association between the oxytocin receptor (OXTR) gene and autism: relationship to Vineland Adaptive Behavior Scales and cognition

Evidence both from animal and human studies suggests that common polymorphisms in the oxytocin receptor (OXTR) gene are likely candidates to confer risk for autism spectrum disorders (ASD). In lower mammals, oxytocin is important in a wide range of social behaviors, and recent human studies have shown that administration of oxytocin modulates behavior in both clinical and non-clinical groups. Additionally, two linkage studies and two recent association investigations also underscore a possible role for the OXTR gene in predisposing to ASD. We undertook a comprehensive study of all 18 tagged SNPs across the entire OXTR gene region identified using HapMap data and the Haploview algorithm. Altogether 152 subjects diagnosed with ASDs (that is, DSM IV autistic disorder or pervasive developmental disorder--NOS) from 133 families were genotyped (parents and affected siblings). Both individual SNPs and haplotypes were tested for association using family-based association tests as provided in the UNPHASED set of programs. Significant association with single SNPs and haplotypes (global P-values <0.05, following permutation test adjustment) were observed with ASD. Association was also observed with IQ and the Vineland Adaptive Behavior Scales (VABS). In particular, a five-locus haplotype block (rs237897-rs13316193-rs237889-rs2254298-rs2268494) was significantly associated with ASD (nominal global P=0.000019; adjusted global P=0.009) and a single haplotype (carried by 7% of the population) within that block showed highly significant association (P=0.00005). This is the third association study, in a third ethnic group, showing that SNPs and haplotypes in the OXTR gene confer risk for ASD. The current investigation also shows association with IQ and total VABS scores (as well as the communication, daily living skills and socialization subdomains), suggesting that this gene shapes both cognition and daily living skills that may cross diagnostic boundaries.     

Interleukin-10 polymorphisms in Spanish multiple sclerosis patients

Interleukin-10 (IL-10) is an anti-inflammatory cytokine that may be an important regulator in multiple sclerosis (MS) pathogenesis. IL-10 gene contains three single nucleotide polymorphisms (SNPs) and two polymorphic microsatellites in the 5'-flanking region. Our aim was to ascertain if any of these polymorphic markers is associated or linked to MS among Spanish patients. We have genotyped 300 patients and 357 ethnically matched controls for the microsatellites, and most of them also for the promoter SNPs. We included in this study the parents of 63 patients in order to perform a TDT analysis as well. IL-10G12 allele was significantly increased in MS patients (17% versus 11% in controls; p=0.004; p(c)<0.05). No other allele showed a significant difference between patients and controls, and the TDT analysis yielded negative results. The data indicate that IL-10 is not a major susceptibility locus in MS, but in our population it might, however, have a minor role.     

RGS4 is not a susceptibility gene for schizophrenia in Japanese: association study in a large case-control population

The regulator of the G-protein signaling 4 (RGS4) has been implicated in the susceptibility to schizophrenia. RGS4 interacts with ErbB3 that acts as receptors for neuregulin 1 and these proteins may play a role in the pathogenesis of schizophrenia via glutamatergic dysfunction. Recently, two meta-analysis studies provided different interpretations for the genetic association between RGS4 and schizophrenia. We attempted to confirm this association in a case-control study of 1918 Japanese patients with schizophrenia and 1909 Japanese control subjects. Four widely studied single nucleotide polymorphisms (SNPs) were genotyped, and none showed association with schizophrenia. SNP 1 (rs10917670), p=0.92; SNP 4 (rs951436), p=0.91; SNP 7 (rs951439), p=0.27; and SNP 18 (rs2661319), p=0.43. A haplotype block constructed by these SNPs spans the 5' flanking region to the 5' mid-region of the RGS4 gene. Previous meta-analysis showed that both two major haplotypes of this block were risk haplotypes. The two common haplotypes were observed in the Japanese population. However, neither haplotype was significantly associated with schizophrenia. We conclude that the common haplotypes and SNPs of the RGS4 gene identified thus far are unlikely to contribute to the genetic susceptibility to schizophrenia in the Japanese population.