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OBJECTIVES The idiopathic inflammatory myopathies (IIM) are heterogeneous diseases, thought to be initiated by immune activation in genetically predisposed individuals. In this study we imputed variants from the Immunochip array using a large reference panel to fine-map associations and identify novel associations in IIM. METHODS We analysed 2,565 Caucasian IIM samples collected through the Myositis Genetics Consortium (MYOGEN) and 10,260 ethnically-matched controls. We imputed 1,648,116 variants from the Immunochip array using the Haplotype Reference Consortium panel and conducted association analysis on IIM, and clinical and serological subgroups. RESULTS The human leukocyte antigen (HLA) locus was consistently the most significantly associated region. Four non-HLA regions reached genome-wide significance, three in the whole IIM cohort (SDK2 and LINC00924 - both novel, and STAT4), with evidence of independent variants in STAT4, and NAB1 in the polymyositis (PM) subgroup. We also found suggestive evidence of association with loci previously associated with other autoimmune rheumatic diseases (TEC and LTBR). We identified more significant associations than those previously reported in IIM, for STAT4 and DGKQ in the total cohort, for NAB1 and FAM167A-BLK loci in PM, and CCR5 in inclusion body myositis. We found enrichment of variants among DNase I hypersensitivity sites and histone marks associated with active transcription within blood cells. CONCLUSIONS We report novel and strong associations in IIM and PM, and localise signals to single genes and immune cell types. This article is protected by copyright. All rights reserved.

Objectives: The idiopathic inflammatory myopathies (IIM) are heterogeneous diseases, thought to be initiated by immune activation in genetically predisposed individuals. In this study we imputed variants from the Immunochip array using a large reference panel to fine-map associations and identify novel associations in IIM. Methods: We analysed 2,565 Caucasian IIM samples collected through the Myositis Genetics Consortium (MYOGEN) and 10,260 ethnically-matched controls. We imputed 1,648,116 variants from the Immunochip array using the Haplotype Reference Consortium panel and conducted association analysis on IIM, and clinical and serological subgroups. Results: The human leukocyte antigen (HLA) locus was consistently the most significantly associated region. Four non-HLA regions reached genome-wide significance, three in the whole IIM cohort (SDK2 and LINC00924 - both novel, and STAT4), with evidence of independent variants in STAT4, and NAB1 in the polymyositis (PM) subgroup. We also found suggestive evidence of association with loci previously associated with other autoimmune rheumatic diseases (TEC and LTBR). We identified more significant associations than those previously reported in IIM, for STAT4 and DGKQ in the total cohort, for NAB1 and FAM167A-BLK loci in PM, and CCR5 in inclusion body myositis. We found enrichment of variants among DNase I hypersensitivity sites and histone marks associated with active transcription within blood cells.Conclusions: We report novel and strong associations in IIM and PM, and localise signals to single genes and immune cell types.

Additional file 6: Table S1. Assays used in RTqPCR experiments The assay IDs for the TaqMan® Advanced miRNA assays and gene expression assays used to assess reference genes (‘Reference selection’), for validation of microRNA (‘miRNA validation’) and targets (‘mRNA validation’) found to be dysregulated in RNA sequencing of whole blood from idiopathic inflammatory myopathy patients compared to controls and used to assess expression in human skeletal muscle cells transfected with miRNA mimic compared to cells transfected with negative control miRNA mimic (‘Transfection’). Table S2. RTqPCR to validate microRNA identified in RNA sequencing in idiopathic inflammatory myopathy patients versus controls PM Polymyositis, DM Dermatomyositis, IBM Inclusion body myositis, Anti-Jo1 Subset of PM and DM with anti-Jo1 autoantibodies, IIM Idiopathic inflammatory myopathy, DE Differentially expressed RTqPCR was performed on total RNA from 6 PM and 5 DM (including 5 anti-Jo-1), 4 IBM, and 4 control whole blood samples. The RTqPCR results are presented next to the RNA sequencing results for these microRNA for comparison. Expression fold change was calculated using the 2-∆∆Ct method and then converted to Log2 fold change values. P-values were calculated using an independent T-test on delta Ct values from each sample (Experimental Ct-Reference Ct) in the subgroups. Table S3. RTqPCR results for skeletal muscle cells transfected with miR-96-5p mimic compared to controls RTqPCR assays for the expression of predicted miR-96-5p mRNA targets were performed on total RNA extracted from human skeletal muscle cells transfected with miR-96-5p miRNA mimic (n = 5) and cells transfected with negative control miRNA mimic (n = 3). Expression fold change was calculated using the 2-∆∆Ct method and then converted to Log2 fold change values. P-values were calculated using an independent T-test on delta Ct values from each sample (Experimental Ct-Reference Ct).

Additional file 1. Supplementary Methods and Results

Objectives To characterise the 10 year relationship between anti-transcriptional intermediary factor 1 antibody (anti-TIF1-Ab) positivity and cancer onset in a large UK-based adult dermatomyositis (DM) cohort. Methods Data from anti-TIF1-Ab positive/negative adults with verified diagnoses of DM from UKMYONET were analysed. Each patient was followed up until they developed cancer. Kaplan-Meier methods and Cox-proportional hazard modelling were employed to estimate cumulative cancer incidence. Results Data from 263 DM cases were analysed, with a total of 3,252 person-years and a median 11 years follow-up; 55 (21%) of DM cases were anti-TIF1-Ab positive. After 10 years of follow up, a higher proportion of anti-TIF1-Ab positive cases developed cancer, compared with anti-TIF1-Ab negative cases: 38% vs 15% (hazard ratio 3.4 [95% CI 2.2, 5.4]). All the detected malignancy cases in the anti-TIF1-Ab positive cohort occurred between 3 years prior to and 2.5 years after DM onset. No cancer cases were detected within the following 7.5 years in this group, whereas cancers were detected during this period in the anti-TIF1-Ab negative cases. Ovarian cancer was more common in the anti-TIF1-Ab positive vs negative cohort – 19% versus 2% respectively (p-value

ObjectiveImmune-mediated inflammatory diseases (IMIDs) are heterogeneous and complex conditions with overlapping clinical symptoms and elevated familial aggregation, which suggests the existence of a shared genetic component. In order to identify this genetic background in a systematic fashion, we performed the first cross-disease genome-wide meta-analysis in systemic seropositive rheumatic diseases, namely, systemic sclerosis, systemic lupus erythematosus, rheumatoid arthritis and idiopathic inflammatory myopathies.MethodsWe meta-analysed ~6.5 million single nucleotide polymorphisms in 11 678 cases and 19 704 non-affected controls of European descent populations. The functional roles of the associated variants were interrogated using publicly available databases.ResultsOur analysis revealed five shared genome-wide significant independent loci that had not been previously associated with these diseases: NAB1, KPNA4-ARL14, DGQK, LIMK1 and PRR12. All of these loci are related with immune processes such as interferon and epidermal growth factor signalling, response to methotrexate, cytoskeleton dynamics and coagulation cascade. Remarkably, several of the associated loci are known key players in autoimmunity, which supports the validity of our results. All the associated variants showed significant functional enrichment in DNase hypersensitivity sites, chromatin states and histone marks in relevant immune cells, including shared expression quantitative trait loci. Additionally, our results were significantly enriched in drugs that are being tested for the treatment of the diseases under study.ConclusionsWe have identified shared new risk loci with functional value across diseases and pinpoint new potential candidate loci that could be further investigated. Our results highlight the potential of drug repositioning among related systemic seropositive rheumatic IMIDs.

Objectives To characterize the 10 year relationship between anti-transcriptional intermediary factor 1 antibody (anti-TIF1-Ab) positivity and cancer onset in a large UK-based adult DM cohort. Methods Data from anti-TIF1-Ab-positive/-negative adults with verified diagnoses of DM from the UK Myositis Network register were analysed. Each patient was followed up until they developed cancer. Kaplan–Meier methods and Cox proportional hazard modelling were employed to estimate the cumulative cancer incidence. Results Data from 263 DM cases were analysed, with a total of 3252 person-years and a median 11 years of follow-up; 55 (21%) DM cases were anti-TIF1-Ab positive. After 10 years of follow-up, a higher proportion of anti-TIF1-Ab-positive cases developed cancer compared with anti-TIF1-Ab-negative cases: 38% vs 15% [hazard ratio 3.4 (95% CI 2.2, 5.4)]. All the detected malignancy cases in the anti-TIF1-Ab-positive cohort occurred between 3 years prior to and 2.5 years after DM onset. No cancer cases were detected within the following 7.5 years in this group, whereas cancers were detected during this period in the anti-TIF1-Ab-negative cases. Ovarian cancer was more common in the anti-TIF1-Ab-positive vs -negative cohort: 19% vs 2%, respectively (P < 0.05). No anti-TIF1-Ab-positive case

Figure S1. Radio-immunoprecipitation of NSCLC samples and positive controls. A Autoradiograph of a 10% SDS-PAGE, loaded with immunoprecipitates using either serum containing known autoantibodies (Lane 1: Healthy Control/Normal Serum (NS), Lane 2: anti-Jo-1 and anti-U1RNP/Sm, Lane 3: anti-PMScl, anti-Ro60 and anti-La, Lane 4: anti-Mitrochondrial autoantibodies (AMAs), Lane 5; anti-Ku and anti-Mi-2), or NSCLC samples screened as part of this study (lanes 6â 14). The sample loaded into lane 11 (NSCLC269, marker with *) contains anti-EJ autoantibodies. B Autoradiograph of a 10% SDS-PAGE, loaded with immunoprecipitates using serum known to contain anti-EJ autoantibodies (lanes 1â 4) or NSCLC269 identified as containing anti-EJ. (PPTX 309 kb)

Aims:The EuroMyositis Registry facilitates collaboration across the idiopathic inflammatory myopathy (IIM) research community. This inaugural report examines pooled Registry data.Methods: Cross-sectional analysis of IIM cases from 11 countries was performed. Associations between clinical subtypes, extramuscular involvement, environmental exposures, and medications were investigated.Results: Of 3,067 IIM cases, 69% were female. The most common IIM subtype was dermatomyositis (DM) (31%). Smoking was more frequent in connective tissue disease overlap cases (45%, odds ratio [OR] 1.44, 95% confidence interval 1.09-1.90, p=0.012). Smoking was associated with ILD (1.32, 1.06-1.65, p=0.013), dysphagia (1.43, 1.16-1.77, p=0.001), malignancy ever (1.78, 1.36-2.33, p

Background The prevalence of dermatomyositis (DM) versus DM and polymyositis (PM) combined has been shown to be negatively associated with latitude. This observation has been attributed to increasing exposure to ultraviolet (UV) light towards the equator. This study investigated whether differing genetic background in populations could contribute to this distribution of DM. Methods Case data from the MYOGEN Immunochip study (n=1,769) were used to model the association of DM prevalence and DM-specific autoantibodies with latitude. Control data (n=9,911) were used to model the relationship of HLA associated with DM autoantibodies and DM or PM SNPs (suggestive significance in the Immunochip project p

Table S1. Immunochip study data included in analyses. Assigned latitude and numbers of PM, DM and controls at each centre included in the study. (DOCX 25Â kb)

Purpose of review: To review the advances in our understanding of the genetics of inclusion body myositis (IBM) in the past year.Recent findings: One large genetic association study focusing on immune-related genes in IBM has refined the association within the HLA region to HLA-DRB1 alleles, and identified certain amino acid positions in HLA-DRB1 that may explain this risk. A suggestive association with CCR5 may indicate genetic overlap with other autoimmune diseases. Sequencing studies of candidate genes involved in related neuromuscular or neurodegenerative diseases have identified rare variants in VCP and SQSTM1. Proteomic studies of rimmed vacuoles in IBM and subsequent genetic analyses of candidate genes identified rare missense variants in FYCO1. Complex, large scale mitochondrial deletions in Cytochrome c oxidase (COX)-deficient muscle fibres expand our understanding of mitochondrial abnormalities in IBM.Summary: The pathogenesis of IBM is likely multifactorial, including inflammatory and degenerative changes, and mitochondrial abnormalities. There has been considerable progress in our understanding of the genetic architecture of IBM, using complementary genetic approaches to investigate these different pathways.

Section One – Copy of the Service Evaluation Questionnaire. Section Two – Draft standard of care statements and initial feedback. Section Three – Modified Delphi process. Section Four – Subsequent changes to statements. Section Five – Suggested Audit Standards. (DOCX 50 kb)

Aims T he EuroMyositis Registry facilitates collaboration across the idiopathic inflammatory myopathy (IIM) research community. This inaugural report examines pooled Registry data. Methods Cross-sectional analysis of IIM cases from 11 countries was performed. Associations between clinical subtypes, extramuscular involvement, environmental exposures and medications were investigated. Results O f 3067 IIM cases, 69% were female. The most common IIM subtype was dermatomyositis (DM) (31%). Smoking was more frequent in connective tissue disease overlap cases (45%, OR 1.44, 95% CI 1.09 to 1.90, p=0.012). Smoking was associated with interstitial lung disease (ILD) (OR 1.32, 95% CI 1.06 to 1.65, p=0.013), dysphagia (OR 1.43, 95% CI 1.16 to 1.77, p=0.001), malignancy ever (OR 1.78, 95% CI 1.36 to 2.33, p

OBJECTIVE: Inclusion body myositis (IBM) is characterized by a combination of inflammatory and degenerative changes affecting muscle. While the primary cause of IBM is unknown, genetic factors may influence disease susceptibility. To determine genetic factors contributing to the etiology of IBM, we conducted the largest genetic association study of the disease to date, investigating immune-related genes using the Immunochip. METHODS: A total of 252 Caucasian patients with IBM were recruited from 11 countries through the Myositis Genetics Consortium and compared with 1,008 ethnically matched controls. Classic HLA alleles and amino acids were imputed using SNP2HLA. RESULTS: The HLA region was confirmed as the most strongly associated region in IBM (P = 3.58 × 10(-33) ). HLA imputation identified 3 independent associations (with HLA-DRB1*03:01, DRB1*01:01, and DRB1*13:01), although the strongest association was with amino acid positions 26 and 11 of the HLA-DRB1 molecule. No association with anti-cytosolic 5'-nucleotidase 1A-positive status was found independent of HLA-DRB1*03:01. There was no association of HLA genotypes with age at onset of IBM. Three non-HLA regions reached suggestive significance, including the chromosome 3 p21.31 region, an established risk locus for autoimmune disease, where a frameshift mutation in CCR5 is thought to be the causal variant. CONCLUSION: This is the largest, most comprehensive genetic association study to date in IBM. The data confirm that HLA is the most strongly associated region and identifies novel amino acid associations that may explain the risk in this locus. These amino acid associations differentiate IBM from polymyositis and dermatomyositis and may determine properties of the peptide-binding groove, allowing it to preferentially bind autoantigenic peptides. A novel suggestive association within the chromosome 3 p21.31 region suggests a role for CCR5.

Genetic factors have been suggested to be involved in the pathogenesis of sporadic inclusion body myositis (sIBM). Sequestosome 1 (SQSTM1) and valosin-containing protein (VCP) are 2 key genes associated with several neurodegenerative disorders but have yet to be thoroughly investigated in sIBM. A candidate gene analysis was conducted using whole-exome sequencing data from 181 sIBM patients, and whole-transcriptome expression analysis was performed in patients with genetic variants of interest. We identified 6 rare missense variants in the SQSTM1 and VCP in 7 sIBM patients (4.0%). Two variants, the SQSTM1 p.G194R and the VCP p.R159C, were significantly overrepresented in this sIBM cohort compared with controls. Five of these variants had been previously reported in patients with degenerative diseases. The messenger RNA levels of major histocompatibility complex genes were upregulated, this elevation being more pronounced in SQSTM1 patient group. We report for the first time potentially pathogenic SQSTM1 variants and expand the spectrum of VCP variants in sIBM. These data suggest that defects in neurodegenerative pathways may confer genetic susceptibility to sIBM and reinforce the mechanistic overlap in these neurodegenerative disorders.