Tag-SNP analysis of the GFI1-EVI5-RPL5-FAM69 risk locus for multiple sclerosis

A recent genome-wide association study conducted by the International Multiple Sclerosis Genetic Consortium (IMSGC) identified, among others, a number of putative multiple sclerosis (MS) susceptibility variants at position 1p22. Twenty-one SNPs positively associated with MS were located at the GFI-EVI5-RPL5-FAM69A locus. In this study, we performed an analysis and fine mapping of this locus, genotyping eight Tag-SNPs in 732 MS patients and 974 controls from Spain. We observed an association with MS in three of eight Tag-SNPs: rs11804321 (P=0.008, OR=1.29; 95% CI1.08-1.54), rs11808092 (P=0.048, OR=1.19; 95% CI1.03-1.39) and rs6680578 (P=0.0082, OR=1.23; 95% CI1.07-1.41). After correcting for multiple comparisons and using logistic regression analysis to test the addition of each SNP to the most associated SNPs, we observed that rs11804321 alone was sufficient to model the association. This Tag-SNP captures two SNPs in complete linkage disequilibrium (r2= 1), both located within the 17th intron of the EVI5 gene. Our findings agree with the corresponding data of the recent IMSGC study and present new genetic evidence that points to EVI5 as a factor of susceptibility to MS. © 2010 Macmillan Publishers Limited All rights reserved.Financial support for the study was provided by the Ministerio de Ciencia e Innovación-Fondos Feder (Grant SAF2009–11491) and Junta de Andalucía (P07-CVI-02551) to A. Alcina, and by Fondo de Investigación Sanitaria (PI081636) to F. Matesanz. María Fedetz is a holder of a fellowship from Fundación IMABIS. Dorothy Ndagire is a holder of AECI-Ministerio de Asuntos Exteriores fellowship.Peer Reviewe

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

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

High ACSL5 Transcript Levels Associate with Systemic Lupus Erythematosus and Apoptosis in Jurkat T Lymphocytes and Peripheral Blood Cells

Systemic lupus erythematosus (SLE) is a prototypical autoimmune disease in which increased apoptosis and decreased apoptotic cells removal has been described as most relevant in the pathogenesis. Long-chain acyl-coenzyme A synthetases (ACSLs) have been involved in the immunological dysfunction of mouse models of lupus-like autoimmunity and apoptosis in different in vitro cell systems. The aim of this work was to assess among the ACSL isoforms the involvement of ACSL2, ACSL4 and ACSL5 in SLE pathogenesis. Findings With this end, we determined the ACSL2, ACSL4 and ACSL5 transcript levels in peripheral blood mononuclear cells (PBMCs) of 45 SLE patients and 49 healthy controls by quantitative real time-PCR (q-PCR). We found that patients with SLE had higher ACSL5 transcript levels than healthy controls [median (range), healthy controls = 16.5 (12.3–18.0) vs. SLE = 26.5 (17.8–41.7), P = 3.9×10 E-5] but no differences were found for ACSL2 and ACSL4. In in vitro experiments, ACSL5 mRNA expression was greatly increased when inducing apoptosis in Jurkat T cells and PBMCs by Phorbol-Myristate-Acetate plus Ionomycin (PMA+Io). On the other hand, short interference RNA (siRNA)-mediated silencing of ACSL5 decreased induced apoptosis in Jurkat T cells up to the control levels as well as decreased mRNA expression of FAS, FASLG and TNF. Conclusions These findings indicate that ACSL5 may play a role in the apoptosis that takes place in SLE. Our results point to ACSL5 as a potential novel functional marker of pathogenesis and a possible therapeutic target in SLE.Financial support for the study was provided by the Ministerio de Ciencia e Innovación-Fondos Feder (PN-SAF2009-11491) and Junta de Andalucía (P07-CVI-02551) to A. Alcina and Fondo de Investigación Sanitaria (FIS PI081636, CP10/00526) to F. Matesanz. M. Fedetz and D. Ndagire are holders of a fellowship from Fundación Española de Esclerosis Múltiple (FEDEM). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewe

Conditional logistic regression analysis of the MS associated variants.

<p>F_A, Frequency of affected; F_U, Frequency of unaffected; NA, not applicable; <i>P</i> cond, <i>P</i>-value of logistic regression analysis conditioned on the respective SNP; <i>OR</i>, odds ratio; <i>SNP</i>, single-nucleotide polymorphism. The data from African American are from McElroy et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029819#pone.0029819-McElroy2" target="_blank">[7]</a>.</p

Association of HapMap III SNPs from the HLA region with expression levels of the HLA <i>DRB1</i> gene.

<p>The figure shows the strength of association between SNPs and gene expression levels, plotted as −log <i>P</i>-values. Coordinates are in NCBI Build 36. Shown are the CEU, YRI, LWK, MEX, GHI, CHB and JPT HapMap populations <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029819#pone.0029819-International1" target="_blank">[26]</a>.</p

LD plots of the GWAS- SNPs associated with different immune related disease.

<p>Data are from HapMap III CEU population. (<b>A</b>) Linkage disequilibrium by r². (<b>B</b>) Linkage disequilibrium by D′. Disease abbreviations: Type 1 diabetes (T1D), inflammatory bowel disease (IBD), ulcerative colitis (UC), systemic lupus erythematosus (SLE), asthma and IgA deficiency.</p

Association of the MS-risk variant rs9271100 with <i>DRB1</i> gene expression levels.

<p>In all plots, expression levels are represented for the three genotype groups. (<b>A</b>) Box plots of expression data from normalized results of ILMN_1715169 (<i>DRB1</i>) probe generated by Illumina Human-6 v2 Expression BeadChip (EMBL-EBI database (<a href="http://www.ebi.ac.uk/arrayexpress/" target="_blank">http://www.ebi.ac.uk/arrayexpress/</a>) ID projects E-MTAB-198). (<b>B</b>) Box plot of expression data from the NM_002124 (<i>DRB1</i>) transcript of 41 CEU individuals obtained from RNA-Seq <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029819#pone.0029819-Cheung1" target="_blank">[19]</a>. P-values are calculated by Kruskal Wallis Test.</p

Association of risk-variants for different immune-related diseases with expression levels of HLA genes.

<p>Expression data are from CEU individuals obtained from RNA-Seq <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029819#pone.0029819-Caballero1" target="_blank">[9]</a>. The data are from the transcripts <i>DQB1</i> NM_002123, <i>DQA1</i> NM_002122, <i>DRB1</i> NM_002124, <i>DQA2</i> NM_020056 and <i>DRB5</i> NM_002125. Underlined are marked the risk alleles.</p

A splice variant in the ACSL5 gene relates migraine with fatty acid activation in mitochondria

This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/4.0/Genome-wide association studies (GWAS) in migraine are providing the molecular basis of this heterogeneous disease, but the understanding of its aetiology is still incomplete. Although some biomarkers have currently been accepted for migraine, large amount of studies for identifying new ones is needed. The migraine-associated variant rs12355831:A>G (P = 2x10(-6)), described in a GWAS of the International Headache Genetic Consortium, is localized in a non-coding sequence with unknown function. We sought to identify the causal variant and the genetic mechanism involved in the migraine risk. To this end, we integrated data of RNA sequences from the Genetic European Variation in Health and Disease (GEUVADIS) and genotypes from 1000 GENOMES of 344 lymphoblastoid cell lines (LCLs), to determine the expression quantitative trait loci (eQTLs) in the region. We found that the migraine-associated variant belongs to a linkage disequilibrium block associated with the expression of an acyl-coenzyme A synthetase 5 (ACSL5) transcript lacking exon 20 (ACSL5-Delta 20). We showed by exon-skipping assay a direct causality of rs2256368-G in the exon 20 skipping of approximately 20 to 40% of ACSL5 RNA molecules. In conclusion, we identified the functional variant (rs2256368:A>G) affecting ACSL5 exon 20 skipping, as a causal factor linked to the migraine-associated rs12355831:A>G, suggesting that the activation of long-chain fatty acids by the spliced ACSL5-Delta 20 molecules, a mitochondrial located enzyme, is involved in migraine pathology.We thank the GEUVADIS Consortium for the RNA-Seq data and 1000 Genomes consortium for accessibility that permitted the analysis of our data. We thank Dr LR Desviat for kindly provide us the pSPL3 plasmid and suggestions. This work was supported by Fondo de Investigacion Sanitaria (FIS) Instituto de Salud Carlos III(ISCIII) Fondos Europeos de Desarrollo Regional (FEDER), Union Europea (grant numbers P12/00555 and PI13/01527) and Junta de Andalucia (JA)- Fondos Europeos de Desarrollo Regional (FEDER) (grant number CTS2704).Peer reviewe