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BACKGROUND/OBJECTIVES Immune-mediated inflammatory diseases (IMIDs) are prevalent diseases. There is, however, a lack of understanding of the link between diet and IMIDs, how much dietary patterns vary between them and if there are food groups associated with a worsening of the disease. SUBJECTS/METHODS To answer these questions we analyzed a nation-wide cohort of n = 11,308 patients from six prevalent IMIDs and 2050 healthy controls. We compared their weekly intake of the major food categories, and used a Mendelian randomization approach to determine which dietary changes are caused by disease. Within each IMID, we analyzed the association between food frequency and disease severity. RESULTS After quality control, n = 11,230 recruited individuals were used in this study. We found that diet is profoundly altered in all IMIDs: at least three food categories are significantly altered in each disease (P

Crohn's disease (CD) is a complex and multifactorial illness. There are still considerable gaps in our knowledge regarding its pathophysiology. A transcriptomic approach could shed some light on little-known biological alterations of the disease. We therefore aimed to explore the ileal transcriptome to gain knowledge about CD. We performed whole transcriptome gene expression analysis on ileocecal resections from CD patients and inflammatory bowel disease-free controls, as well as on a CD-independent cohort to replicate selected results. Normalized data were hierarchically clustered, and gene ontology and the molecular network were studied. Cell cultures and molecular methods were used for further evaluations. Genome-wide expression data analysis identified a robust transmembrane immunoglobulin domain-containing 1 (TMIGD1) gene underexpression in CD tissue, which was even more marked in inflamed ileum, and which was replicated in the validation cohort. Immunofluorescence showed TMIGD1 to be located in the apical microvilli of well-differentiated enterocytes but not in intestinal crypt. This apical TMIGD1 was lower in the noninflamed tissue and almost disappeared in the inflamed mucosa of surgical resections. In vitro studies showed hypoxic-dependent TMIGDI decreased its expression in enterocyte-like cells. The gene enrichment analysis linked TMIGD1 with cell recovery and tissue remodeling in CD settings. involving guanylate cyclase activities. Transcriptomics may be useful for finding new targets that facilitate studies of the CD pathology. This is how TMIGD1 was identified in CD patients, which was related to multiciliate ileal epithelial cell differentiation. NEW & NOTEWORTHY This is a single-center translational research study that aimed to look for key targets involved in Crohn's disease and define molecular pathways through different functional analysis strategies. With this approach, we have identified and described a novel target, the almost unknown TMIGD1 gene, which may be key in the recovery of injured mucosa involving intestinal epithelial cell differentiation.

The production of antibodies to anti-tumor necrosis factor alpha (TNF) agents is one of the main causes of treatment failure in Crohn’s disease (CD). To date, however, the contribution of genetics to anti-TNF immunogenicity in CD is still unknown. The objective of the present study was to identify genetic variation associated with anti-TNF immunogenicity in CD. We performed a two-stage genome-wide association study in a cohort of 96 and 123 adalimumab-treated patients, respectively. In the discovery stage, we identified a genome-wide significant association between the CD96 locus and the production of antibodies to anti-TNF treatment (P = 1.88e–09). This association was validated in the replication stage (P

Rheumatoid arthritis (RA) is an immune-mediated inflammatory disease characterized by a defective adaptive immune receptor repertoire (AIRR) that fails to distinguish self from non-self antigens. The AIRR is vast, encompassing four T cell receptor (TCR) and three B cell receptor (BCR) chains, each of which displays an extraordinary amino acid sequence variability in the antigen-binding site. How the concerted action of T and B cell clones is associated with the development and clinical evolution of immune-mediated diseases is still not known. Using a new immunosequencing technology that allows the unbiased amplification of the seven receptor chains, we conducted an in-depth quantitative analysis of the seven-receptor chain variability in RA. Compared to healthy controls, the AIRR in RA was found to be characterized by a lower BCR diversity, the depletion of highly similar BCR clones, an isotype-specific signature as well as a skewed IGL chain and gene segment usage. A predictor based on quantitative multi-chain AIRR information was able to accurately predict disease, including the elusive seronegative subset of RA patients. AIRR features of the seven immune receptor chains were also different between patients with distinct clinically relevant phenotypes. Incorporating HLA variation data, we were able to identify the TCR clones that are specifically associated with the main disease risk variants. The longitudinal analysis of the AIRR revealed that treatment with Tumor Necrosis Factor (TNF) inhibitors selectively restores the diversity of B cell clones in RA patients by reducing the frequency of clones with a similar biochemical profile. The biochemical properties of the TNFi-modulated clones were also found to differ between responders and non-responders, supporting a different antigenic reactivity in the B cell compartment of these two groups of RA patients. Our comprehensive analysis of the TCR and BCR repertoire reveals a complex T and B cell architecture in RA, and provides the basis for precision medicine strategies based on the highly informative features of the adaptive immune response.

Background Crohn’s disease (CD) is a chronic inflammatory bowel disease that normally requires bowel surgical resection due to intra-abdominal inflammatory complications such as fistulae and stenosis. However, 90% of patients that underwent surgery and did not receive prophylaxis, suffer from postsurgical endoscopic recurrence within one year. Methods The objective of this study is to understand the de novo postsurgical lesion formation in order to stablish a potential mechanism of action and its derived predictive signals to devise preventive strategies. To achieve it, transcriptome analyses of the inflamed and macroscopically unaffected zone of the ileocecal resection from 20 patients from a hospital cohort and 10 controls were performed. Patients were classified for early postsurgical recurrence by means of Rutgeerts index (i0 Results The transcriptome results showed there were no differences neither between i0, i1 and i2a (anastomotic lesions) nor when comparing i2b (non-anastomotic lesions) vs ≥i3. However, when comparing i0+i1+i2a vs. i2b+i3+i4 there were differently expressed genes highlighting ADIPOQ in the inflamed zone and the FXR/FGF19 axis in the unaffected zone. When replicating the results in the corroborative cohort, we identified FXR and other xenobiotic nuclear receptors as the genes differentially expressed in i2a vs i2b, i3 and/or i4, mainly in the macroscopically unaffected zone. Specifically, the differentially expressed genes were: MOGAT2, PXR, FXR and AHR (i2a vs i4), PPARα and FXR (i2a vs i3), TMIGD1, PPARα, FXR and AHR (i2a vs i3+i4) and FXR (i2a vs i2b+i3+i4). Conclusion Nuclear receptor FXR is activated in the ileum by bile acids action and it is key in the lipid metabolism regulation and in the bile acids production by means of FGF19. Moreover, ileal FXR, as well as other xenobiotic nuclear receptors, actively participates in the enhancement of the intestinal barrier function and in the innate immunity regulation. In conclusion, the results obtained in this study suggest a link between bowel xenobiotic metabolism and the de novo lesion formation in previously unaffected areas in the postsurgical recurrence in CD.

ObjectivePsoriatic arthritis (PsA) is a chronic inflammatory arthritis affecting up to 30% of patients with psoriasis (Ps). To date, most of the known risk loci for PsA are shared with Ps, and identifying disease-specific variation has proven very challenging. The objective of the present study was to identify genetic variation specific for PsA.MethodsWe performed a genome-wide association study in a cohort of 835 patients with PsA and 1558 controls from Spain. Genetic association was tested at the single marker level and at the pathway level. Meta-analysis was performed with a case–control cohort of 2847 individuals from North America. To confirm the specificity of the genetic associations with PsA, we tested the associated variation using a purely cutaneous psoriasis cohort (PsC, n=614) and a rheumatoid arthritis cohort (RA, n=1191). Using network and drug-repurposing analyses, we further investigated the potential of the PsA-specific associations to guide the development of new drugs in PsA.ResultsWe identified a new PsA risk single-nucleotide polymorphism at B3GNT2 locus (p=1.10e-08). At the pathway level, we found 14 genetic pathways significantly associated with PsA (pFDRConclusionThese findings provide insights into the biological mechanisms that are specific for PsA and could contribute to develop more effective therapies.

Background Tumour Necrosis Factor (TNF) inhibitors have improved the management of many patients with rheumatoid arthritis (RA). However,~30% of anti-TNF treated patients do not show a significant clinical improvement. To date, little is known on the biological mechanisms underlying the differential response to anti-TNF agents. Objectives We sought to identify genetic variation associated with the anti-TNF response in RA using a sequential multi-omics approach. Methods First, we aimed to identify gene coexpression modules (GCMs) associated with anti-TNF response. For this objective, we extracted the RNA from synovial biopsies of 13 RA patients starting anti-TNF therapy and determined the expression profiles using Illumina microarrays. GCMs were identified using the WGCNA approach. The association between GCMs and anti-TNF response was performed using the eigengene of each GCM. Clinical response was defined using the EULAR criteria at week 14. To analyse the association of GCMs with anti-TNF response at the genetic level, we used 348 anti-TNF treated RA patients from Spain. The statistical analysis was performed using GWAS data and the set-based test in PLINK. The GCMs that were significantly associated with anti-TNF response were subsequently tested for validation in an independent cohort of 2706 anti-TNF treated RA patients. The functional implication of the validated GCMs was studied via pathway and cell type epigenetic enrichment analyses. Results We identified 148 GCMs in the RA synovium. From these, 15 GCMs were found to be associated with anti-TNF response (p Conclusions Our study shows the existence of a drug-specific genetic basis for the anti-TNF response. Therefore, this molecular diversity should be considered for biomarker research in RA. Disclosure of Interest None declared

Background: Systemic lupus erythematosus (SLE) is a genetically complex rheumatic disease characterized by heterogeneous clinical manifestations of unknown etiology. Recent studies have suggested the existence of a genetic basis for SLE heterogeneity. The objective of the present study was to identify new genetic variation associated with the clinically relevant phenotypes in SLE. Methods: A two-stage pathway-based approach was used to identify the genetic variation associated with the main clinical phenotypes in SLE. In the discovery stage, 482 SLE patients were genotyped using Illumina Human Quad610 microarrays. Association between 798 reference genetic pathways from the Molecular Signatures Database and 11 SLE phenotypes was tested using the set-based method implemented in PLINK software. Pathways significantly associated after multiple test correction were subsequently tested for replication in an independent cohort of 425 SLE patients. Using an in silico approach, we analyzed the functional effects of common SLE therapies on the replicated genetic pathways. The association of known SLE risk variants with the development of the clinical phenotypes was also analyzed. Results: In the discovery stage, we found a significant association between the vascular endothelial growth factor (VEGF) pathway and oral ulceration (P value for false discovery rate (P FDR ) < 0.05), and between the negative regulation signaling pathway of retinoic acid inducible gene-I/melanoma differentiation associated gene 5 and the production of antinuclear antibodies (P FDR < 0.05). In the replication stage, we validated the association between the VEGF pathway and oral ulceration. Therapies commonly used to treat mucocutaneous phenotypes in SLE were found to strongly influence VEGF pathway gene expression (P = 4.60e-4 to 5.38e-14). Analysis of known SLE risk loci identified a strong association between PTPN22 and the risk of hematologic disorder and with the development of antinuclear antibodies. Conclusions: The present study has identified VEGF genetic pathway association with the risk of oral ulceration in SLE. New therapies targeting the VEGF pathway could be more effective in reducing the severity of this phenotype. These findings represent a first step towards the understanding of the genetic basis of phenotype heterogeneity in SLE, This study was funded by the Spanish Ministry of Economy and Competitiveness (grant numbers: PSE-010000-2006-6 and IPT-010000-2010-36 and by the “Agència de Gestió d’Ajuts Universitaris i de Recerca” (AGAUR, Generalitat de Catalunya, FI-DGR 2016, grant number: 00587)

Background Recent genome-wide association studies (GWAS) have identified more than 50 loci associated with systemic lupus erythematosus but they explain less than 30% of the heritability of the disease. Meta-analysis including new populations can contribute to identify additional genetic risk factors. Objectives The aim of the presents study was to identify additional genetic risk loci for SLE. Methods We performed a meta-analysis using data from a recent large scale GWAS from 4,036 cases and 6,959 controls from Caucasian European ancestry [1] and a newly genotyped cohort of 907 SLE patients and 1,524healthy controls from Spain. Genetic association was tested at the single-marker level using linear regression and at the pathway-level using Fisher9s modified method. Results Combining the two cohorts we identified genome-wide significant association (P Conclusions In conclusion, we have identified five new risk loci for SLE through a meta-analysis including a new GWAS. References Bentham J, Morris DL et al. Nature Genetics 2015. Acknowledgements We would like to thank the clinical researchers and patients participating in the IMID Consortium for their collaboration. We would also like to thank the international SLE consortium for access to the data. Disclosure of Interest None declared

Background PsA has a higher heritability than PsV, indicating the existence of additional PsA-specific genetic factors. To date, however, the specific genetic basis underlying PsA is poorly understood. Objectives The objective the present study was to identify new genetic variation specifically associated with PsA risk. Methods In order to characterize the genetic basis of PsA, we performed a GWAS meta-analysis at the single-marker level as well as at the pathway level (GWPA). A cohort of 835 PsA patients and 1,558 controls from the Spanish population was genotyped for >550,000 SNPs. GWAS data from a second cohort of 1,430 PsA patients and 1,417 controls from the North American population was also used. In order to confirm the specificity of the new genetic variation associated with PsA risk, we analyzed the association with purely cutaneous psoriasis (PsC, n=614) and rheumatoid arthritis (RA, n=1,191). We performed a pharmacogenetic analysis to investigate the new PsA-specific pathways as a source for drug discovery in PsA. Results GWAS meta-analysis identified a new association between B3GNT2 gene and PsA (P Conclusions The present study represents an important step towards the characterization of the genetic factors specific to PsA risk. Disclosure of Interest None declared

Background Autoimmune diseases are highly disabling chronic disorders characterized by the activation of multiple immune and inflammatory pathways against self-components. Clinical studies have demonstrated that autoimmune diseases have a higher prevalence of cardiovascular events compared to the general population. Understanding the genetic and biological mechanisms underlying cardiovascular disease (CVD) risk in autoimmunity could therefore be fundamental to develop more efficient preventive and therapeutic strategies. Objectives The objective of this study was to characterize the genetic basis of CVD risk in autoimmune diseases. Methods A total of 6,485 patients from the six autoimmune diseases RA, PA, SLE, PS, CD and UC were recruited by the Spanish biomedical consortium IMID Consortium. All patients were Caucasian European from the Spain. CVD patients were defined as having ≥1 out of the 3 most frequent cardiovascular phenotypes: (i) ischemic heart disease (ii) cerebrovascular accident and (iii) peripheral arterial disease. In order to characterize the genetic basis of CVD risk in autoimmune diseases, we used genome-wide genotyping data from all autoimmune disease patients included in the study. First, we tested the association of established CVD risk variants within each autoimmune disease. Second, we analyzed the association of autoimmune disease risk variants with an increase in CVD risk. Finally, we used the cross-phenotype meta-analysis approach (CPMA) to perform a genome-wide meta-analysis and identify global genetic patterns associated with CVD risk in autoimmune diseases. Results A total of 17 loci previously associated with CVD risk in the general population were significantly associated with CVD risk in the autoimmune patient cohorts ( P P CFLAR-CASP8 . The CPMA identified a total of 10 genetic patterns significantly associated with CVD risk across all autoimmune diseases. Two of these patterns showed a highly significant association with CVD risk in RA, PsA and SLE. The functional analysis of these two genetic patterns revealed a significant enrichment in key pathways related to the etiology of rheumatic diseases like TNFα ( FDR (FDR Conclusions The results of the present study represent an important step towards the characterization of the genetic basis of CVD in autoimmune diseases. These findings contribute to explain the higher prevalence of cardiovascular events observed in patients with autoimmune diseases compared to the general population. Disclosure of Interest None declared

Supplementary information is available in the online Supplementary Material file. (PDF 13965 kb)

Psoriasis is a chronic inflammatory disease with a complex genetic architecture. To date, the psoriasis heritability is only partially explained. However, there is increasing evidence that the missing heritability in psoriasis could be explained by multiple genetic variants of low effect size from common genetic pathways. The objective of this study was to identify new genetic variation associated with psoriasis risk at the pathway level. We genotyped 598,258 single nucleotide polymorphisms in a discovery cohort of 2,281 case-control individuals from Spain. We performed a genome-wide pathway analysis using 1,053 reference biological pathways. A total of 14 genetic pathways (PFDR ≤ 2.55 × 10(-2)) were found to be significantly associated with psoriasis risk. Using an independent validation cohort of 7,353 individuals from the UK, a total of 6 genetic pathways were significantly replicated (PFDR ≤ 3.46 × 10(-2)). We found genetic pathways that had not been previously associated with psoriasis risk such as retinol metabolism (Pcombined = 1.84 × 10(-4)), the transport of inorganic ions and amino acids (Pcombined = 1.57 × 10(-7)), and post-translational protein modification (Pcombined = 1.57 × 10(-7)). In the latter pathway, MGAT5 showed a strong network centrality, and its association with psoriasis risk was further validated in an additional case-control cohort of 3,429 individuals (P < 0.05). These findings provide insights into the biological mechanisms associated with psoriasis susceptibility. This study was funded by of the Spanish Ministry of Economy and Competitiveness, grant numbers: PSE-010000-2006-6 and IPT-010000-2010-36

Journal Article; Research Support, Non-U.S. Gov't; OBJECTIVE Anti-TNF therapies have been highly efficacious in the management of rheumatoid arthritis (RA), but 25-30% of patients do not show a significant clinical response. There is increasing evidence that genetic variation at the Fc receptor FCGR2A is associated with the response to anti-TNF therapy. We aimed to validate this genetic association in a patient cohort from the Spanish population, and also to identify new genes functionally related to FCGR2A that are also associated with anti-TNF response. METHODS A total of 348 RA patients treated with an anti-TNF therapy were included and genotyped for FCGR2A polymorphism rs1081274. Response to therapy was determined at 12 weeks, and was tested for association globally and independently for each anti-TNF drug (infliximab, etanercept and adalimumab). Using gene expression profiles from macrophages obtained from synovial fluid of RA patients, we searched for genes highly correlated with FCGR2A expression. Tag SNPs were selected from each candidate gene and tested for association with the response to therapy. RESULTS We found a significant association between FCGR2A and the response to adalimumab (P=0.022). Analyzing the subset of anti-CCP positive RA patients (78%), we also found a significant association between FCGR2A and the response to infliximab (P=0.035). DHX32 and RGS12 were the most consistently correlated genes with FCGR2A expression in RA synovial fluid macrophages (P

Background Systemic lupus erythematosus (SLE) is a genetically complex rheumatic disease with heterogeneous clinical manifestations. Recent studies have suggested the existence of a genetic basis for the diverse SLE clinical phenotypes. Also, there is increasing evidence indicating that a substantial part of the genetic variation associated with complex diseases is explained by small-effect genes from common genetic pathways. Objectives The objective of the present study was to identify new genetic variation associated with SLE phenotypes using a genome-wide association study at the pathway level. Methods A total of 598,258 SNPs were genotyped in a discovery cohort of n=482 SLE patients of southern European ancestry using the Illumina platform Quad610. After quality control analysis, including ancestry estimation using principal-component analysis, genome-wide pathway analysis was performed. A total of 14 clinically relevant SLE phenotypes were tested for association with n>700 reference genetic pathways. Significantly associated pathways (corrected P-value in silico analysis on cell types of relevance in SLE pathogenesis. Results In the discovery stage, two genetic pathways were significantly associated with the presence of oral ulcers and antinuclear antibodies in SLE ( P FDR VEGF ) genetic pathway ( P =1.3e-2). Analyzing the transcriptional effect of the topical immunotherapies used for the treatment of oral ulcers in SLE, we found a significant differential expression of VEGF pathway genes ( P Conclusions In this work we have performed the first genome-wide association study for clinically relevant SLE phenotype using a pathway-based approach. With this new approach, we have identified and validated the association of VEGF genetic pathway with oral ulcers in SLE. These findings represent an important step towards the characterization of the genetic basis of phenotype heterogeneity in SLE. Disclosure of Interest None declared

Background Immune mediated and inflammatory diseases (IMIDs) such a rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), psoriasis (Ps), and psoriatic arthritis (PsA), are associated with higher rates of cardiovascular (CV) morbidity and mortality, mostly due to accelerated atherosclerosis. Classic CV risk factors do not fully account for the gap observed in the prevalence and incidence of CV disease, when compared to that of the general population. Objectives To analyze the influence of different demographic and clinical variables in the prevalence of CV disease in subjects affected with RA, PsA, Ps, SLE, or inflammatory bowel disease. Additionally, we compared the adjusted prevalence of CV disease among these conditions. Methods Subjects included in this cross-sectional study were collected as part of the Immune-Mediated Inflammatory Disease Consortium (IMIDC) between 2007 and 2010. Demographic, disease and cardiovascular related clinical data was collected using a standard protocol of questionnaires, after a clinical interview with close questions and review of medical records. Bivariate and multivariate logistic and mixed-effects logistic regression models were performed for each condition, and the overall IMIDC, respectively. Standardize prevalence (SP) for each IMID was calculated using marginal analysis. Results 9951 patients were included. When analyzed separately, traditional CV risk factors had a different contribution to CV disease in each IMID. Overall, when analyzed all subjects, older age at study, longer elapsed time from IMID diagnosis to study, presence of traditional CV risk factors (arterial hypertension, type2 diabetes mellitus, dyslipidemia, obesity) and male gender were independently associated with a higher CV disease risk. After adjusting by demographic and traditional CV risk factors, SLE exhibited the highest SP, followed by RA and Ps/Crohn9s disease. Conclusions Cardiovascular disease is related to immune-mediated inflammatory diseases. A different impact is shown dependent of particular disease directly affecting the burden of disease. Acknowledgements We would like to thank all the patients and physicians for their collaboration. Disclosure of Interest None declared

Rheumatoid arthritis (RA) is the most frequent autoimmune chronic inflammatory disease of the joints and it is characterized by the inflammation of the synovial membrane and the subsequent destruction of the joints. In RA, CD4+ T cells are the main drivers of disease initiation and the perpetuation of the damaging inflammatory process. To date, however, the genetic regulatory mechanisms of CD4+ T cells associated with RA etiology are poorly understood. The genome-wide analysis of expression quantitative trait loci (eQTL) in disease-relevant cell types is a recent genomic integration approach that is providing significant insights into the genetic regulatory mechanisms of many human pathologies. The objective of the present study was to analyze, for the first time, the genome-wide genetic regulatory mechanisms associated with the gene expression of CD4+ T cells in RA. Whole genome gene expression profiling of CD4+ T cells and the genome-wide genotyping (598,258 SNPs) of 29 RA patients with an active disease were performed. In order to avoid the excessive burden of multiple testing associated with genome-wide trans-eQTL analysis, we developed and implemented a novel systems genetics approach. Finally, we compared the genomic regulation pattern of CD4+ T cells in RA with the genomic regulation observed in reference lymphoblastoid cell lines (LCLs). We identified a genome-wide significant cis-eQTL associated with the expression of FAM66C gene (P = 6.51e−9). Using our new systems genetics approach we identified six statistically significant trans-eQTLs associated with the expression of KIAA0101 (P