275 results on '"Siminovitch, KA"'
Search Results
52. 14-3-3η Autoantibodies: Diagnostic Use in Early Rheumatoid Arthritis.
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Maksymowych WP, Boire G, van Schaardenburg D, Wichuk S, Turk S, Boers M, Siminovitch KA, Bykerk V, Keystone E, Tak PP, van Kuijk AW, Landewé R, van der Heijde D, Murphy M, and Marotta A
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- Adult, Aged, Arthritis, Rheumatoid blood, Arthritis, Rheumatoid immunology, Biomarkers blood, Disease Progression, Female, Humans, Male, Middle Aged, Osteoarthritis blood, Osteoarthritis immunology, Sensitivity and Specificity, 14-3-3 Proteins immunology, Arthritis, Rheumatoid diagnosis, Autoantibodies blood
- Abstract
Objective: To describe the expression and diagnostic use of 14-3-3η autoantibodies in early rheumatoid arthritis (RA)., Methods: 14-3-3η autoantibody levels were measured using an electrochemiluminescent multiplexed assay in 500 subjects (114 disease-modifying antirheumatic drug-naive patients with early RA, 135 with established RA, 55 healthy, 70 autoimmune, and 126 other non-RA arthropathy controls). 14-3-3η protein levels were determined in an earlier analysis. Two-tailed Student t tests and Mann-Whitney U tests compared differences among groups. Receiver-operator characteristic (ROC) curves were generated and diagnostic performance was estimated by area under the curve (AUC), as well as specificity, sensitivity, and likelihood ratios (LR) for optimal cutoffs., Results: Median serum 14-3-3η autoantibody concentrations were significantly higher (p < 0.0001) in patients with early RA (525 U/ml) when compared with healthy controls (235 U/ml), disease controls (274 U/ml), autoimmune disease controls (274 U/ml), patients with osteoarthritis (259 U/ml), and all controls (265 U/ml). ROC curve analysis comparing early RA with healthy controls demonstrated a significant (p < 0.0001) AUC of 0.90 (95% CI 0.85-0.95). At an optimal cutoff of ≥ 380 U/ml, the ROC curve yielded a sensitivity of 73%, a specificity of 91%, and a positive LR of 8.0. Adding 14-3-3η autoantibodies to 14-3-3η protein positivity enhanced the identification of patients with early RA from 59% to 90%; addition of 14-3-3η autoantibodies to anticitrullinated protein antibodies (ACPA) and/or rheumatoid factor (RF) increased identification from 72% to 92%. Seventy-two percent of RF- and ACPA-seronegative patients were positive for 14-3-3η autoantibodies., Conclusion: 14-3-3η autoantibodies, alone and in combination with the 14-3-3η protein, RF, and/or ACPA identified most patients with early RA.
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- 2015
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53. Genetics in PBC: what do the "risk genes" teach us?
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Hirschfield GM and Siminovitch KA
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- Autoimmune Diseases genetics, Autoimmune Diseases immunology, Genome-Wide Association Study, HLA Antigens genetics, HLA Antigens immunology, Humans, Liver Cirrhosis, Biliary immunology, Risk Factors, Genetic Predisposition to Disease, Liver Cirrhosis, Biliary genetics
- Abstract
Primary biliary cirrhosis is characterised by a progressive and destructive lymphocytic cholangitis, targeting small intra-hepatic bile ducts. In association with the histologic liver injury, patients characteristically express highly specific auto-antibodies that recognise a conserved epitope of the pyruvate dehydrogenase complex found on the inner membrane of the mitochondria. Family studies demonstrate a clear increased incidence and prevalence of associated autoimmune diseases; and historically, a clear HLA association with disease has been evident. With the use of a high-throughput whole-genome array technology, significant insights into the non-HLA loci associated with risk for disease development have been made. These studies, which have primarily incorporated genome-wide association screens and targeted analysis of immune genes, have highlighted the integral roles for immune cell development and function in disease risk. This has revealed the IL-12/JAK-STAT signalling pathway as a key etiologic factor. In conjunction with a better understanding of environmental triggers, such work lays the foundation for better disease insights mechanistically and, hopefully, therapeutically. Obstacles to uncovering all the associated genetic risk and the correlation between genotype and phenotype remain to be circumvented, as do better appreciation of the processes that underpin not only disease initiation but also presentation and outcome.
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- 2015
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54. A role for noncoding variation in schizophrenia.
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Roussos P, Mitchell AC, Voloudakis G, Fullard JF, Pothula VM, Tsang J, Stahl EA, Georgakopoulos A, Ruderfer DM, Charney A, Okada Y, Siminovitch KA, Worthington J, Padyukov L, Klareskog L, Gregersen PK, Plenge RM, Raychaudhuri S, Fromer M, Purcell SM, Brennand KJ, Robakis NK, Schadt EE, Akbarian S, and Sklar P
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- Arthritis, Rheumatoid genetics, Calcium Channels, L-Type genetics, Databases, Genetic, Enhancer Elements, Genetic genetics, Gene Expression Regulation, Genetic Loci, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Molecular Sequence Annotation, Organ Specificity genetics, Promoter Regions, Genetic, Protein Binding genetics, Risk Factors, DNA, Intergenic genetics, Polymorphism, Single Nucleotide genetics, Schizophrenia genetics
- Abstract
A large portion of common variant loci associated with genetic risk for schizophrenia reside within noncoding sequence of unknown function. Here, we demonstrate promoter and enhancer enrichment in schizophrenia variants associated with expression quantitative trait loci (eQTL). The enrichment is greater when functional annotations derived from the human brain are used relative to peripheral tissues. Regulatory trait concordance analysis ranked genes within schizophrenia genome-wide significant loci for a potential functional role, based on colocalization of a risk SNP, eQTL, and regulatory element sequence. We identified potential physical interactions of noncontiguous proximal and distal regulatory elements. This was verified in prefrontal cortex and -induced pluripotent stem cell-derived neurons for the L-type calcium channel (CACNA1C) risk locus. Our findings point to a functional link between schizophrenia-associated noncoding SNPs and 3D genome architecture associated with chromosomal loopings and transcriptional regulation in the brain., (Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.)
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- 2014
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55. Serum 14-3-3η is a novel marker that complements current serological measurements to enhance detection of patients with rheumatoid arthritis.
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Maksymowych WP, Naides SJ, Bykerk V, Siminovitch KA, van Schaardenburg D, Boers M, Landewé R, van der Heijde D, Tak PP, Genovese MC, Weinblatt ME, Keystone EC, Zhukov OS, Abolhosn RW, Popov JM, Britsemmer K, van Kuijk AW, and Marotta A
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- Adult, Area Under Curve, Biomarkers blood, Canada, Case-Control Studies, Cohort Studies, Disease Progression, Enzyme-Linked Immunosorbent Assay methods, Female, Humans, Male, Middle Aged, Monitoring, Physiologic, Prognosis, ROC Curve, Reference Values, Rheumatoid Factor blood, Sensitivity and Specificity, Severity of Illness Index, Statistics, Nonparametric, 14-3-3 Proteins blood, Arthritis, Rheumatoid blood, Arthritis, Rheumatoid physiopathology
- Abstract
Objective: Serum 14-3-3η is a novel joint-derived proinflammatory mediator implicated in the pathogenesis of rheumatoid arthritis (RA). In our study, we assessed the diagnostic utility of 14-3-3η and its association with standard clinical and serological measures., Methods: A quantitative ELISA was used to assess 14-3-3η levels. Early (n=99) and established patients with RA (n=135) were compared to all controls (n=385), including healthy subjects (n=189). The sensitivity, specificity, positive and negative predictive values of 14-3-3η, and the likelihood ratios (LR) for RA were determined through receiver-operator curve analysis. The incremental value of adding 14-3-3η to anticitrullinated protein antibody (ACPA) and rheumatoid factor (RF) in diagnosing early and established RA was assessed., Results: Serum 14-3-3η differentiated established patients with RA from healthy individuals and all controls (p<0.0001). A serum 14-3-3η cutoff of ≥0.19 ng/ml delivered a sensitivity and specificity of 77% and 93%, respectively, with corresponding LR positivity of 10.4. At this cutoff in early RA, 64% of patients with early RA were positive for 14-3-3η, with a corresponding specificity of 93% (LR+ of 8.6), while 59% and 57% were positive for ACPA or RF, respectively. When ACPA, RF, and 14-3-3η positivity were used in combination, 77 of the 99 patients (78%) with early RA were positive for any 1 of the 3 markers. Serum 14-3-3η did not correlate with C-reactive protein, erythrocyte sedimentation rate, or Disease Activity Score, but patients who were 14-3-3η-positive had significantly worse disease., Conclusion: Serum 14-3-3η is a novel RA mechanistic marker that is highly specific, associated with worse disease, and complements current markers, enabling a more accurate diagnosis of RA.
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- 2014
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56. Efficient production of sTNFRII-gAD fusion protein in large quantity by use of the modified CHO-S cell expression system.
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Cai Q, Zhao A, Yuting Yin, Ma L, Jiao Z, Zhi H, Lai S, Cheng S, Yang H, Lu Y, Siminovitch KA, and Gao J
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- Animals, Biological Assay, CHO Cells, Cricetinae, Cricetulus, Culture Media chemistry, DNA Restriction Enzymes, Gene Expression Profiling, Humans, Plasmids, Protein Multimerization, Protein Structure, Tertiary, Signal Transduction, Surface Plasmon Resonance, Tumor Necrosis Factor-alpha antagonists & inhibitors, Adiponectin biosynthesis, Receptors, Tumor Necrosis Factor, Type II biosynthesis, Recombinant Fusion Proteins biosynthesis
- Abstract
TNFα is one of the initial and important mediators to activate downstream signaling pathways by binding to trimerized TNFα receptors (TNFR), and thus is an ideal drug target for cancer therapy. Taking advantage of intrinsic homotimerization of the globular domain of adiponectin (gAD), we have developed a novel TNFα antagonist, the trimerized fusion protein named sTNFRII-gAD. However, our previously-used CHO expression system yielded less than 10 mg/L of sTNFRII-gAD. To produce large quantities of sTNFRII-gAD efficiently, we used a modified CHO-S cell expression system, which is based on a pMH3 vector with non-coding GC-rich DNA fragments for high-level gene expression. We obtained stable clones that produced 75 mg/L of sTNFRII-gAD in the 96-well plate, adapted the clones to 40 ml suspension serum-free batch culture, then optimized the culturing conditions to scale up the fed-batch culture in a 3 L shake-flask and finally in a 5 L AP30 bioreactor. We achieved a final yield of 52 mg/L of sTNFRII-gAD. The trimerized sTNFRII-gAD exhibited the higher affinity to TNFα with a dissociation constant (Kd) of 5.63 nM than the dimerized sTNFRII-Fc with a Kd of 13.4 nM, and further displayed the higher TNFα-neutralizing activity than sTNFRII-Fc (p<0.05) in a L929 cytotoxicity assay. Therefore, the strategy employed in this study may provide an efficient avenue for large-scale production of other recombinant proteins by use of the modified CHO-S cell expression system.
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- 2014
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57. RFC1 80G>A is a genetic determinant of methotrexate efficacy in rheumatoid arthritis: a human genome epidemiologic review and meta-analysis of observational studies.
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Kung TN, Dennis J, Ma Y, Xie G, Bykerk V, Pope J, Thorne C, Keystone E, Siminovitch KA, and Gagnon F
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- Antirheumatic Agents therapeutic use, Humans, Observational Studies as Topic, Pharmacogenetics, Polymorphism, Single Nucleotide genetics, Treatment Outcome, Arthritis, Rheumatoid drug therapy, Genetic Determinism, Methotrexate therapeutic use, Reduced Folate Carrier Protein genetics
- Abstract
Objective: Associations have been reported between candidate genes and the response to methotrexate (MTX) in rheumatoid arthritis (RA) patients, but most of the studies have been small and have yielded conflicting results. This study was undertaken to provide a systematic review of all genetic variant associations with MTX efficacy and toxicity, and to conduct a meta-analysis evaluating the most commonly studied single-nucleotide polymorphism for which prior cumulative analysis has been lacking., Methods: A systematic review and meta-analysis were performed to identify genetic variant associations with MTX efficacy and toxicity. Studies were identified from the Medline, EMBase, HuGENet Navigator, and Cochrane Library databases through December 2012, and from the 2009-2011 abstracts of the American College of Rheumatology and the European League Against Rheumatism annual meeting proceedings. Additional unpublished genotype data from a Canadian cohort of patients with early RA were also included., Results: Among the 87 identified studies examining genetic associations with MTX efficacy and toxicity, the reduced folate carrier 1 gene (RFC1) variant 80G>A (Arg(27) His, rs1051266) was selected for random-effects meta-analysis. RFC1 80G>A was associated with MTX efficacy in both the recessive model (odds ratio [OR] 1.42, 95% confidence interval [95% CI] 1.04-1.93) and the additive model (OR 1.28, 95% CI 1.10-1.49). Restriction of the sensitivity analyses to studies that involved Caucasian subjects only and that used similar outcome measures (MTX failure versus nonfailure) maintained and improved the associations in both models. No significant association between RFC1 80G>A and MTX toxicity was detected., Conclusion: In these analyses of available data from observational studies, RFC1 80G>A was found to be associated with MTX efficacy, but not toxicity, in RA patients. This variant merits further prospective analysis as a potential predictor of MTX efficacy. Variability in the definitions of response in pharmacogenetic studies is a source of data heterogeneity that should be addressed., (Copyright © 2014 by the American College of Rheumatology.)
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- 2014
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58. Reply: To PMID 23740775.
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Farrer LA, Sherva R, Merkel PA, and Siminovitch KA
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- Female, Humans, Male, Genetic Predisposition to Disease, Granulomatosis with Polyangiitis genetics, HLA-DP beta-Chains genetics, Polymorphism, Single Nucleotide, Semaphorins genetics
- Published
- 2014
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59. Hepatocyte-specific Ptpn6 deletion promotes hepatic lipid accretion, but reduces NAFLD in diet-induced obesity: potential role of PPARγ.
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Xu E, Forest MP, Schwab M, Avramoglu RK, St-Amand E, Caron AZ, Bellmann K, Shum M, Voisin G, Paquet M, Montoudis A, Lévy E, Siminovitch KA, Neel BG, Beauchemin N, and Marette A
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- Animals, Diet, High-Fat, Fatty Acids metabolism, Insulin Resistance, Lipogenesis, Mice, Mice, Inbred C57BL, Non-alcoholic Fatty Liver Disease, Fatty Liver etiology, Liver metabolism, Obesity complications, PPAR gamma physiology, Protein Tyrosine Phosphatase, Non-Receptor Type 6 physiology
- Abstract
Unlabelled: Hepatocyte-specific Shp1 knockout mice (Ptpn6(H-KO)) are protected from hepatic insulin resistance evoked by high-fat diet (HFD) feeding for 8 weeks. Unexpectedly, we report herein that Ptpn6(H-KO) mice fed an HFD for up to 16 weeks are still protected from insulin resistance, but are more prone to hepatic steatosis, as compared with their HFD-fed Ptpn6(f/f) counterparts. The livers from HFD-fed Ptpn6(H-KO) mice displayed 1) augmented lipogenesis, marked by increased expression of several hepatic genes involved in fatty acid biosynthesis, 2) elevated postprandial fatty acid uptake, and 3) significantly reduced lipid export with enhanced degradation of apolipoprotein B (ApoB). Despite more extensive hepatic steatosis, the inflammatory profile of the HFD-fed Ptpn6(H-KO) liver was similar (8 weeks) or even improved (16 weeks) as compared to their HFD-fed Ptpn6(f/f) littermates, along with reduced hepatocellular damage as revealed by serum levels of hepatic enzymes. Interestingly, comparative microarray analysis revealed a significant up-regulation of peroxisome proliferator-activated receptor gamma (PPARγ) gene expression, confirmed by quantitative polymerase chain reaction. Elevated PPARγ nuclear activity also was observed and found to be directly regulated by Shp1 in a cell-autonomous manner., Conclusion: These findings highlight a novel role for hepatocyte Shp1 in the regulation of PPARγ and hepatic lipid metabolism. Shp1 deficiency prevents the development of severe hepatic inflammation and hepatocellular damage in steatotic livers, presenting hepatocyte Shp1 as a potential novel mediator of nonalcoholic fatty liver diseases in obesity., (© 2014 by the American Association for the Study of Liver Diseases.)
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- 2014
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60. Genetics of rheumatoid arthritis contributes to biology and drug discovery.
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Okada Y, Wu D, Trynka G, Raj T, Terao C, Ikari K, Kochi Y, Ohmura K, Suzuki A, Yoshida S, Graham RR, Manoharan A, Ortmann W, Bhangale T, Denny JC, Carroll RJ, Eyler AE, Greenberg JD, Kremer JM, Pappas DA, Jiang L, Yin J, Ye L, Su DF, Yang J, Xie G, Keystone E, Westra HJ, Esko T, Metspalu A, Zhou X, Gupta N, Mirel D, Stahl EA, Diogo D, Cui J, Liao K, Guo MH, Myouzen K, Kawaguchi T, Coenen MJ, van Riel PL, van de Laar MA, Guchelaar HJ, Huizinga TW, Dieudé P, Mariette X, Bridges SL Jr, Zhernakova A, Toes RE, Tak PP, Miceli-Richard C, Bang SY, Lee HS, Martin J, Gonzalez-Gay MA, Rodriguez-Rodriguez L, Rantapää-Dahlqvist S, Arlestig L, Choi HK, Kamatani Y, Galan P, Lathrop M, Eyre S, Bowes J, Barton A, de Vries N, Moreland LW, Criswell LA, Karlson EW, Taniguchi A, Yamada R, Kubo M, Liu JS, Bae SC, Worthington J, Padyukov L, Klareskog L, Gregersen PK, Raychaudhuri S, Stranger BE, De Jager PL, Franke L, Visscher PM, Brown MA, Yamanaka H, Mimori T, Takahashi A, Xu H, Behrens TW, Siminovitch KA, Momohara S, Matsuda F, Yamamoto K, and Plenge RM
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- Alleles, Animals, Arthritis, Rheumatoid metabolism, Arthritis, Rheumatoid pathology, Asian People genetics, Case-Control Studies, Computational Biology, Drug Repositioning, Female, Genome-Wide Association Study, Hematologic Neoplasms genetics, Hematologic Neoplasms metabolism, Humans, Male, Mice, Mice, Knockout, Polymorphism, Single Nucleotide genetics, White People genetics, Arthritis, Rheumatoid drug therapy, Arthritis, Rheumatoid genetics, Drug Discovery, Genetic Predisposition to Disease genetics, Molecular Targeted Therapy
- Abstract
A major challenge in human genetics is to devise a systematic strategy to integrate disease-associated variants with diverse genomic and biological data sets to provide insight into disease pathogenesis and guide drug discovery for complex traits such as rheumatoid arthritis (RA). Here we performed a genome-wide association study meta-analysis in a total of >100,000 subjects of European and Asian ancestries (29,880 RA cases and 73,758 controls), by evaluating ∼10 million single-nucleotide polymorphisms. We discovered 42 novel RA risk loci at a genome-wide level of significance, bringing the total to 101 (refs 2 - 4). We devised an in silico pipeline using established bioinformatics methods based on functional annotation, cis-acting expression quantitative trait loci and pathway analyses--as well as novel methods based on genetic overlap with human primary immunodeficiency, haematological cancer somatic mutations and knockout mouse phenotypes--to identify 98 biological candidate genes at these 101 risk loci. We demonstrate that these genes are the targets of approved therapies for RA, and further suggest that drugs approved for other indications may be repurposed for the treatment of RA. Together, this comprehensive genetic study sheds light on fundamental genes, pathways and cell types that contribute to RA pathogenesis, and provides empirical evidence that the genetics of RA can provide important information for drug discovery.
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- 2014
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61. Integration of sequence data from a Consanguineous family with genetic data from an outbred population identifies PLB1 as a candidate rheumatoid arthritis risk gene.
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Okada Y, Diogo D, Greenberg JD, Mouassess F, Achkar WA, Fulton RS, Denny JC, Gupta N, Mirel D, Gabriel S, Li G, Kremer JM, Pappas DA, Carroll RJ, Eyler AE, Trynka G, Stahl EA, Cui J, Saxena R, Coenen MJ, Guchelaar HJ, Huizinga TW, Dieudé P, Mariette X, Barton A, Canhão H, Fonseca JE, de Vries N, Tak PP, Moreland LW, Bridges SL Jr, Miceli-Richard C, Choi HK, Kamatani Y, Galan P, Lathrop M, Raj T, De Jager PL, Raychaudhuri S, Worthington J, Padyukov L, Klareskog L, Siminovitch KA, Gregersen PK, Mardis ER, Arayssi T, Kazkaz LA, and Plenge RM
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- Base Sequence, Cohort Studies, Exome genetics, Exons genetics, Female, Genetic Loci genetics, Genotyping Techniques, High-Throughput Nucleotide Sequencing, Humans, Male, Meta-Analysis as Topic, Mutation genetics, Pedigree, Polymorphism, Single Nucleotide genetics, Reproducibility of Results, Risk Factors, White People genetics, Arthritis, Rheumatoid enzymology, Arthritis, Rheumatoid genetics, Consanguinity, Genetic Predisposition to Disease, Genome-Wide Association Study, Lysophospholipase genetics
- Abstract
Integrating genetic data from families with highly penetrant forms of disease together with genetic data from outbred populations represents a promising strategy to uncover the complete frequency spectrum of risk alleles for complex traits such as rheumatoid arthritis (RA). Here, we demonstrate that rare, low-frequency and common alleles at one gene locus, phospholipase B1 (PLB1), might contribute to risk of RA in a 4-generation consanguineous pedigree (Middle Eastern ancestry) and also in unrelated individuals from the general population (European ancestry). Through identity-by-descent (IBD) mapping and whole-exome sequencing, we identified a non-synonymous c.2263G>C (p.G755R) mutation at the PLB1 gene on 2q23, which significantly co-segregated with RA in family members with a dominant mode of inheritance (P = 0.009). We further evaluated PLB1 variants and risk of RA using a GWAS meta-analysis of 8,875 RA cases and 29,367 controls of European ancestry. We identified significant contributions of two independent non-coding variants near PLB1 with risk of RA (rs116018341 [MAF = 0.042] and rs116541814 [MAF = 0.021], combined P = 3.2 × 10(-6)). Finally, we performed deep exon sequencing of PLB1 in 1,088 RA cases and 1,088 controls (European ancestry), and identified suggestive dispersion of rare protein-coding variant frequencies between cases and controls (P = 0.049 for C-alpha test and P = 0.055 for SKAT). Together, these data suggest that PLB1 is a candidate risk gene for RA. Future studies to characterize the full spectrum of genetic risk in the PLB1 genetic locus are warranted.
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- 2014
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62. Pharmacogenetics of the G protein-coupled receptors.
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Thompson MD, Cole DE, Capra V, Siminovitch KA, Rovati GE, Burnham WM, and Rana BK
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- Databases, Genetic, Genetic Association Studies, Humans, Mutation, Polymorphism, Genetic, Precision Medicine, Receptors, G-Protein-Coupled agonists, Receptors, G-Protein-Coupled antagonists & inhibitors, Receptors, G-Protein-Coupled metabolism, Pharmacogenetics, Receptors, G-Protein-Coupled genetics
- Abstract
Pharmacogenetics investigates the influence of genetic variants on physiological phenotypes related to drug response and disease, while pharmacogenomics takes a genome-wide approach to advancing this knowledge. Both play an important role in identifying responders and nonresponders to medication, avoiding adverse drug reactions, and optimizing drug dose for the individual. G protein-coupled receptors (GPCRs) are the primary target of therapeutic drugs and have been the focus of these studies. With the advance of genomic technologies, there has been a substantial increase in the inventory of naturally occurring rare and common GPCR variants. These variants include single-nucleotide polymorphisms and insertion or deletions that have potential to alter GPCR expression of function. In vivo and in vitro studies have determined functional roles for many GPCR variants, but genetic association studies that define the physiological impact of the majority of these common variants are still limited. Despite the breadth of pharmacogenetic data available, GPCR variants have not been included in drug labeling and are only occasionally considered in optimizing clinical use of GPCR-targeted agents. In this chapter, pharmacogenetic and genomic studies on GPCR variants are reviewed with respect to a subset of GPCR systems, including the adrenergic, calcium sensing, cysteinyl leukotriene, cannabinoid CB1 and CB2 receptors, and the de-orphanized receptors such as GPR55. The nature of the disruption to receptor function is discussed with respect to regulation of gene expression, expression on the cell surface (affected by receptor trafficking, dimerization, desensitization/downregulation), or perturbation of receptor function (altered ligand binding, G protein coupling, constitutive activity). The large body of experimental data generated on structure and function relationships and receptor-ligand interactions are being harnessed for the in silico functional prediction of naturally occurring GPCR variants. We provide information on online resources dedicated to GPCRs and present applications of publically available computational tools for pharmacogenetic studies of GPCRs. As the breadth of GPCR pharmacogenomic data becomes clearer, the opportunity for routine assessment of GPCR variants to predict disease risk, drug response, and potential adverse drug effects will become possible.
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- 2014
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63. Mammalian diaphanous-related formin 1 regulates GSK3β-dependent microtubule dynamics required for T cell migratory polarization.
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Dong B, Zhang SS, Gao W, Su H, Chen J, Jin F, Bhargava A, Chen X, Jorgensen L, Alberts AS, Zhang J, and Siminovitch KA
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- Adenomatous Polyposis Coli Protein, Animals, Carrier Proteins genetics, Cell Polarity genetics, Cell Polarity immunology, Enzyme Activation, Formins, Glycogen Synthase Kinase 3 beta, Intercellular Adhesion Molecule-1 metabolism, Lymphocyte Activation immunology, Lymphocyte Function-Associated Antigen-1 genetics, Lymphocyte Function-Associated Antigen-1 metabolism, Mice, Mice, Knockout, Phosphorylation, Protein Binding, T-Lymphocytes immunology, Carrier Proteins metabolism, Cell Movement genetics, Cell Movement immunology, Glycogen Synthase Kinase 3 metabolism, Microtubules metabolism, T-Lymphocytes metabolism
- Abstract
The mammalian diaphanous-related formin (mDia1), a Rho-regulated cytoskeletal modulator, has been shown to promote T lymphocyte chemotaxis and interaction with antigen presenting cells, but the mechanisms underpinning mDia1 roles in these processes have not been defined. Here we show that mDia1(-/-) T cells exhibit impaired lymphocyte function-associated antigen 1 (LFA-1)-mediated T cell adhesion, migration and in vivo trafficking. These defects are associated with impaired microtubule (MT) polarization and stabilization, altered MT dynamics and reduced peripheral clustering of the MT plus-end-protein, adenomatous polyposis coli (APC) in migrating T cells following LFA-1-engagement. Loss of mDia1 also leads to impaired inducible inactivation of the glycogen synthase kinase (GSK) 3β as well as hyperphosphorylation and reduced levels of APC in migrating T cells. These findings identify essential roles for the mDia1 formin in modulating GSK3β-dependent MT contributions to induction of T-cell polarity, adhesion and motility.
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- 2013
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64. Deep basal inferoseptal crypts occur more commonly in patients with hypertrophic cardiomyopathy due to disease-causing myofilament mutations.
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Deva DP, Williams LK, Care M, Siminovitch KA, Moshonov H, Wintersperger BJ, Rakowski H, and Crean AM
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- Cardiomyopathy, Hypertrophic epidemiology, Female, Humans, Male, Middle Aged, Ontario epidemiology, Polymorphism, Single Nucleotide genetics, Prevalence, Risk Factors, Cardiac Myosins genetics, Cardiomyopathy, Hypertrophic genetics, Cardiomyopathy, Hypertrophic pathology, Genetic Predisposition to Disease epidemiology, Genetic Predisposition to Disease genetics, Heart Septum pathology, Magnetic Resonance Imaging statistics & numerical data, Myosin Heavy Chains genetics
- Abstract
Purpose: To determine the relationship between deep basal inferoseptal crypts and disease-causing gene mutations in hypertrophic cardiomyopathy (HCM)., Materials and Methods: Institutional research and ethics board approval was obtained for this retrospective study, and the requirement to obtain informed consent was waived. Two readers, who were blinded to genetic status, independently assessed cardiac magnetic resonance (MR) images obtained in 300 consecutive unrelated genetically tested patients with HCM. Readers documented the morphologic phenotype, the presence of deep basal inferoseptal crypts, and the imaging plane in which crypts were first convincingly visualized. The Student t test, the Fisher exact test, and multivariate logistic regression were used for comparisons and to evaluate the relationship between these crypts and the detection of disease-causing mutations., Results: The frequency of deep basal inferoseptal crypts was significantly higher in patients with disease-causing mutations than in those without disease-causing mutations (36% and 4%, respectively; P < .001). The presence of crypts was a stronger predictor of disease-causing mutations than was reverse septal curvature (P = .025). Patients with these crypts had a higher likelihood of having disease-causing mutations than non-disease-causing mutations (P < .001). Thirty-one of the 34 patients with both deep basal inferoseptal crypts and reverse septal curvature (91%) had disease-causing mutations (sensitivity, 26%; specificity, 98%). The presence of deep basal inferoseptal crypts (odds ratio: 6.64; 95% confidence interval: 2.631, 16.755; P < .001) and reverse septal curvature (odds ratio: 4.8; 95% confidence interval: 2.552, 9.083; P < .001) were predictive of disease-causing mutations. Both observers required additional imaging planes to identify approximately half of all crypts., Conclusion: Deep basal inferoseptal crypts occur more commonly in patients with HCM with disease-causing mutations than in those with genotype-negative HCM., (© RSNA, 2013.)
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- 2013
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65. Association of granulomatosis with polyangiitis (Wegener's) with HLA-DPB1*04 and SEMA6A gene variants: evidence from genome-wide analysis.
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Xie G, Roshandel D, Sherva R, Monach PA, Lu EY, Kung T, Carrington K, Zhang SS, Pulit SL, Ripke S, Carette S, Dellaripa PF, Edberg JC, Hoffman GS, Khalidi N, Langford CA, Mahr AD, St Clair EW, Seo P, Specks U, Spiera RF, Stone JH, Ytterberg SR, Raychaudhuri S, de Bakker PI, Farrer LA, Amos CI, Merkel PA, and Siminovitch KA
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- Adult, Alleles, Female, Gene Frequency, Genetic Association Studies, Genome-Wide Association Study, Genotype, Granulomatosis with Polyangiitis immunology, Haplotypes, Humans, Major Histocompatibility Complex, Male, Genetic Predisposition to Disease, Granulomatosis with Polyangiitis genetics, HLA-DP beta-Chains genetics, Polymorphism, Single Nucleotide, Semaphorins genetics
- Abstract
Objective: To identify genetic determinants of granulomatosis with polyangiitis (Wegener's) (GPA)., Methods: We carried out a genome-wide association study (GWAS) of 492 GPA cases and 1,506 healthy controls (white subjects of European descent), followed by replication analysis of the most strongly associated signals in an independent cohort of 528 GPA cases and 1,228 controls., Results: Genome-wide significant associations were identified in 32 single-nucleotide polymorphic (SNP) markers across the HLA region, the majority of which were located in the HLA-DPB1 and HLA-DPA1 genes encoding the class II major histocompatibility complex (MHC) DPβ chain 1 and DPα chain 1 proteins, respectively. Peak association signals in these 2 genes, emanating from SNPs rs9277554 (for DPβ chain 1) and rs9277341 (DPα chain 1) were strongly replicated in an independent cohort (in the combined analysis of the initial cohort and the replication cohort, P = 1.92 × 10(-50) and 2.18 × 10(-39) , respectively). Imputation of classic HLA alleles and conditional analyses revealed that the SNP association signal was fully accounted for by the classic HLA-DPB1*04 allele. An independent single SNP, rs26595, near SEMA6A (the gene for semaphorin 6A) on chromosome 5, was also associated with GPA, reaching genome-wide significance in a combined analysis of the GWAS and replication cohorts (P = 2.09 × 10(-8) )., Conclusion: We identified the SEMA6A and HLA-DP loci as significant contributors to risk for GPA, with the HLA-DPB1*04 allele almost completely accounting for the MHC association. These two associations confirm the critical role of immunogenetic factors in the development of GPA., (Copyright © 2013 by the American College of Rheumatology.)
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- 2013
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66. Identification of the NF-κB activating protein-like locus as a risk locus for rheumatoid arthritis.
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Xie G, Lu Y, Sun Y, Zhang SS, Keystone EC, Gregersen PK, Plenge RM, Amos CI, and Siminovitch KA
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- Alleles, Canada, Case-Control Studies, Female, Genetic Predisposition to Disease, Genotype, Haplotypes, Humans, Logistic Models, Male, Polymorphism, Single Nucleotide, United States, Arthritis, Rheumatoid genetics, Co-Repressor Proteins genetics, Nuclear Proteins genetics
- Abstract
Objective: To fine-map the NF-κB activating protein-like (NKAPL) locus identified in a prior genome-wide study as a possible rheumatoid arthritis (RA) risk locus and thereby delineate additional variants with stronger and/or independent disease association., Methods: Genotypes for 101 SNPs across the NKAPL locus on chromosome 6p22.1 were obtained on 1368 Canadian RA cases and 1471 controls. Single marker associations were examined using logistic regression and the most strongly associated NKAPL locus SNPs then typed in another Canadian and a US-based RA case/control cohort., Results: Fine-mapping analyses identified six NKAPL locus variants in a single haplotype block showing association with p≤5.6×10(-8) in the combined Canadian cohort. Among these SNPs, rs35656932 in the zinc finger 193 gene and rs13208096 in the NKAPL gene remained significant after conditional logistic regression, contributed independently to risk for disease, and were replicated in the US cohort (Pcomb=4.24×10(-10) and 2.44×10(-9), respectively). These associations remained significant after conditioning on SNPs tagging the HLA-shared epitope (SE) DRB1*0401 allele and were significantly stronger in the HLA-SE negative versus positive subgroup, with a significant negative interaction apparent between HLA-DRB1 SE and NKAPL risk alleles., Conclusions: By illuminating additional NKAPL variants with highly significant effects on risk that are distinct from, but interactive with those arising from the HLA-DRB1 locus, our data conclusively identify NKAPL as an RA susceptibility locus.
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- 2013
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67. Human genetics in rheumatoid arthritis guides a high-throughput drug screen of the CD40 signaling pathway.
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Li G, Diogo D, Wu D, Spoonamore J, Dancik V, Franke L, Kurreeman F, Rossin EJ, Duclos G, Hartland C, Zhou X, Li K, Liu J, De Jager PL, Siminovitch KA, Zhernakova A, Raychaudhuri S, Bowes J, Eyre S, Padyukov L, Gregersen PK, Worthington J, Gupta N, Clemons PA, Stahl E, Tolliday N, and Plenge RM
- Subjects
- Alleles, Animals, Antigens, CD19 genetics, Arthritis, Rheumatoid pathology, B-Lymphocytes cytology, B-Lymphocytes metabolism, CD40 Antigens metabolism, Genetic Predisposition to Disease, Genome-Wide Association Study, High-Throughput Screening Assays, Humans, Mice, NF-kappa B genetics, NF-kappa B metabolism, Quantitative Trait Loci genetics, Signal Transduction, Small Molecule Libraries chemistry, Small Molecule Libraries pharmacology, Arthritis, Rheumatoid drug therapy, Arthritis, Rheumatoid genetics, CD40 Antigens antagonists & inhibitors, CD40 Antigens genetics, Drug Evaluation, Preclinical
- Abstract
Although genetic and non-genetic studies in mouse and human implicate the CD40 pathway in rheumatoid arthritis (RA), there are no approved drugs that inhibit CD40 signaling for clinical care in RA or any other disease. Here, we sought to understand the biological consequences of a CD40 risk variant in RA discovered by a previous genome-wide association study (GWAS) and to perform a high-throughput drug screen for modulators of CD40 signaling based on human genetic findings. First, we fine-map the CD40 risk locus in 7,222 seropositive RA patients and 15,870 controls, together with deep sequencing of CD40 coding exons in 500 RA cases and 650 controls, to identify a single SNP that explains the entire signal of association (rs4810485, P = 1.4×10(-9)). Second, we demonstrate that subjects homozygous for the RA risk allele have ∼33% more CD40 on the surface of primary human CD19+ B lymphocytes than subjects homozygous for the non-risk allele (P = 10(-9)), a finding corroborated by expression quantitative trait loci (eQTL) analysis in peripheral blood mononuclear cells from 1,469 healthy control individuals. Third, we use retroviral shRNA infection to perturb the amount of CD40 on the surface of a human B lymphocyte cell line (BL2) and observe a direct correlation between amount of CD40 protein and phosphorylation of RelA (p65), a subunit of the NF-κB transcription factor. Finally, we develop a high-throughput NF-κB luciferase reporter assay in BL2 cells activated with trimerized CD40 ligand (tCD40L) and conduct an HTS of 1,982 chemical compounds and FDA-approved drugs. After a series of counter-screens and testing in primary human CD19+ B cells, we identify 2 novel chemical inhibitors not previously implicated in inflammation or CD40-mediated NF-κB signaling. Our study demonstrates proof-of-concept that human genetics can be used to guide the development of phenotype-based, high-throughput small-molecule screens to identify potential novel therapies in complex traits such as RA., Competing Interests: The authors have declared that no competing interests exist.
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- 2013
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68. Pathway-based analysis of primary biliary cirrhosis genome-wide association studies.
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Kar SP, Seldin MF, Chen W, Lu E, Hirschfield GM, Invernizzi P, Heathcote J, Cusi D, Gershwin ME, Siminovitch KA, and Amos CI
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- Algorithms, Canada, Cohort Studies, Databases, Genetic, Female, Gene Frequency, Genotype, Humans, Italy, Linkage Disequilibrium, Male, Meta-Analysis as Topic, Middle Aged, Polymorphism, Single Nucleotide, Genetic Predisposition to Disease genetics, Genome-Wide Association Study methods, Liver Cirrhosis, Biliary genetics, Signal Transduction genetics
- Abstract
Genome-wide association studies (GWAS) have successfully identified several loci associated with primary biliary cirrhosis (PBC) risk. Pathway analysis complements conventional GWAS analysis. We applied the recently developed linear combination test for pathways to datasets drawn from independent PBC GWAS in Italian and Canadian subjects. Of the Kyoto Encyclopedia of Genes and Genomes and BioCarta pathways tested, 25 pathways in the Italian dataset (449 cases, 940 controls) and 26 pathways in the Canadian dataset (530 cases, 398 controls) were associated with PBC susceptibility (P<0.05). After correcting for multiple comparisons, only the eight most significant pathways in the Italian dataset had FDR <0.25 with tumor necrosis factor/stress-related signaling emerging as the top pathway (P=7.38 × 10⁻⁴, FDR=0.18). Two pathways, phosphatidylinositol signaling and hedgehog signaling, were replicated in both datasets (P<0.05), and subjected to two additional complementary pathway tests. Both pathway signals remained significant in the Italian dataset on modified gene set enrichment analysis (P<0.05). In both GWAS, variants nominally associated with PBC were significantly overrepresented in the phosphatidylinositol pathway (Fisher exact P<0.05). These results point to established and novel pathway-level associations with inherited predisposition to PBC that, on further independent replication and functional validation, may provide fresh insights into PBC etiology.
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- 2013
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69. Ras-guanine-nucleotide-releasing factors 1 and 2 interact with PLCγ at focal adhesions to enable IL-1-induced Ca(2+) signalling, ERK activation and MMP-3 expression.
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Wang Q, Siminovitch KA, Downey GP, and McCulloch CA
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- Animals, Calcium Signaling drug effects, Interleukin-1 pharmacology, MAP Kinase Signaling System drug effects, Mice, NIH 3T3 Cells, Phospholipase C gamma antagonists & inhibitors, Phospholipase C gamma genetics, Phosphorylation, RNA, Small Interfering genetics, Focal Adhesions metabolism, Matrix Metalloproteinase 3 metabolism, Phospholipase C gamma metabolism, ras Guanine Nucleotide Exchange Factors metabolism, ras-GRF1 metabolism
- Abstract
IL (interleukin)-1 signalling in anchorage-dependent cells involves focal-adhesion-restricted and Ca2+-dependent Ras and ERK (extracellular-signal-regulated kinase) activation that leads to MMP (matrix metalloproteinase) release and extracellular matrix remodelling. Ras activity is regulated, in part, by the Ca2+-responsive Ras GRFs (guanine-nucleotide-releasing factors) 1 and 2, but the mechanisms that link and localize IL-1-induced Ca2+ signalling to focal adhesions are not defined. In the present study we characterized the role of Ras-GRF1/2 in Ca2+ and Ras→ERK signalling after IL-1 stimulation. By immunoprecipitation we found that Ras-GRF1/2 associates with PLCγ1 (phospholipase Cγ1). This association enables PLCγ1 recruitment to focal adhesions and is required for Ras signalling, ERK activation and MMP-3 release downstream of IL-1 stimulation. Depletion of PLCγ1 by siRNA (small interfering RNA) abolished IL-1-induced Ras activation and MMP-3 expression. Buffering of cytosolic Ca2+ reduced Ras interactions with Ras-GRF1/2 and blocked MMP-3 release. The results of the present study show that, in addition to their functions as Ras-exchange factors, Ras-GRF1 and -GRF2 may act as adaptors that bind PLCγ1 and restrict Ca2+ signalling to the vicinity of focal adhesions, indicating a new role for these GRFs that is required for IL-1 induction of the Ras→ERK pathway and MMP-3 expression.
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- 2013
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70. Rare, low-frequency, and common variants in the protein-coding sequence of biological candidate genes from GWASs contribute to risk of rheumatoid arthritis.
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Diogo D, Kurreeman F, Stahl EA, Liao KP, Gupta N, Greenberg JD, Rivas MA, Hickey B, Flannick J, Thomson B, Guiducci C, Ripke S, Adzhubey I, Barton A, Kremer JM, Alfredsson L, Sunyaev S, Martin J, Zhernakova A, Bowes J, Eyre S, Siminovitch KA, Gregersen PK, Worthington J, Klareskog L, Padyukov L, Raychaudhuri S, and Plenge RM
- Subjects
- Exons, Genome-Wide Association Study, Humans, Risk Factors, Arthritis, Rheumatoid genetics, Gene Frequency, Genetic Predisposition to Disease, Genetic Variation, Polymorphism, Single Nucleotide
- Abstract
The extent to which variants in the protein-coding sequence of genes contribute to risk of rheumatoid arthritis (RA) is unknown. In this study, we addressed this issue by deep exon sequencing and large-scale genotyping of 25 biological candidate genes located within RA risk loci discovered by genome-wide association studies (GWASs). First, we assessed the contribution of rare coding variants in the 25 genes to the risk of RA in a pooled sequencing study of 500 RA cases and 650 controls of European ancestry. We observed an accumulation of rare nonsynonymous variants exclusive to RA cases in IL2RA and IL2RB (burden test: p = 0.007 and p = 0.018, respectively). Next, we assessed the aggregate contribution of low-frequency and common coding variants to the risk of RA by dense genotyping of the 25 gene loci in 10,609 RA cases and 35,605 controls. We observed a strong enrichment of coding variants with a nominal signal of association with RA (p < 0.05) after adjusting for the best signal of association at the loci (p(enrichment) = 6.4 × 10(-4)). For one locus containing CD2, we found that a missense variant, rs699738 (c.798C>A [p.His266Gln]), and a noncoding variant, rs624988, reside on distinct haplotypes and independently contribute to the risk of RA (p = 4.6 × 10(-6)). Overall, our results indicate that variants (distributed across the allele-frequency spectrum) within the protein-coding portion of a subset of biological candidate genes identified by GWASs contribute to the risk of RA. Further, we have demonstrated that very large sample sizes will be required for comprehensively identifying the independent alleles contributing to the missing heritability of RA., (Copyright © 2013 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.)
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- 2013
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71. Meta-analysis of genetic polymorphisms in granulomatosis with polyangiitis (Wegener's) reveals shared susceptibility loci with rheumatoid arthritis.
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Chung SA, Xie G, Roshandel D, Sherva R, Edberg JC, Kravitz M, Dellaripa PF, Hoffman GS, Mahr AD, Seo P, Specks U, Spiera RF, St Clair EW, Stone JH, Plenge RM, Siminovitch KA, Merkel PA, and Monach PA
- Subjects
- Adolescent, Adult, Aged, Aged, 80 and over, Arthritis, Rheumatoid immunology, Female, Genetic Predisposition to Disease, Genotype, Granulomatosis with Polyangiitis immunology, Humans, Male, Middle Aged, Risk Factors, Arthritis, Rheumatoid genetics, Genetic Loci, Granulomatosis with Polyangiitis genetics, Polymorphism, Genetic
- Abstract
Objective: To examine the association of previously identified autoimmune disease susceptibility loci with granulomatosis with polyangiitis (Wegener's) (GPA), and to determine whether the genetic susceptibility profiles of other autoimmune diseases are associated with those of GPA., Methods: Genetic data from 2 cohorts were meta-analyzed. Genotypes for 168 previously identified single-nucleotide polymorphisms (SNPs) associated with susceptibility to different autoimmune diseases were ascertained in a total of 880 patients with GPA and 1,969 control subjects of European descent. Single-marker associations were identified using additive logistic regression models. Associations of multiple SNPs with GPA were assessed using genetic risk scores based on susceptibility loci for Crohn's disease, type 1 diabetes, systemic lupus erythematosus, rheumatoid arthritis (RA), celiac disease, and ulcerative colitis. Adjustment for population substructure was performed in all analyses, using ancestry-informative markers and principal components analysis., Results: Genetic polymorphisms in CTLA4 were significantly associated with GPA in the single-marker meta-analysis (odds ratio [OR] 0.79, 95% confidence interval [95% CI] 0.70-0.89, P = 9.8 × 10(-5) ). The genetic risk score for RA susceptibility markers was significantly associated with GPA (OR 1.05 per 1-unit increase in genetic risk score, 95% CI 1.02-1.08, P = 5.1 × 10(-5) )., Conclusion: RA and GPA may arise from a similar genetic predisposition. Aside from CTLA4, other loci previously found to be associated with common autoimmune diseases were not statistically significantly associated with GPA in this study., (Copyright © 2012 by the American College of Rheumatology.)
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- 2012
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72. Vitamin D receptor polymorphism rs2228570 (Fok1) is associated with rheumatoid arthritis in North American natives.
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Hitchon CA, Sun Y, Robinson DB, Peschken CA, Bernstein CN, Siminovitch KA, and El-Gabalawy HS
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- Adult, Aged, Alleles, Arthritis, Rheumatoid ethnology, Female, Gene Frequency, Genetic Association Studies, Genotype, Humans, Male, Middle Aged, Arthritis, Rheumatoid genetics, Genetic Predisposition to Disease, Indians, North American genetics, Polymorphism, Single Nucleotide, Receptors, Calcitriol genetics
- Abstract
Objective: Vitamin D (VitD) has immunomodulatory activity relevant to rheumatoid arthritis (RA) and acts by binding nuclear receptors that regulate gene transcription. VitD receptor polymorphisms have been variably associated with RA. Because North American Native (NAN) populations have a high prevalence of RA with a strong genetic contribution, we studied potential associations of the rs2228570 (Fok1) VitD receptor polymorphism in a Canadian NAN population., Methods: The single-nucleotide polymorphism (SNP) Fok1 was tested by sequencing NAN patients with RA (n=448) and unrelated NAN controls (n=704). Associations were tested using genotypic, dominant, and recessive models., Results: The minor allele frequency (F/C) in the NAN control population was 0.44 and lower than reported in white subjects of the same geographical area. The Fok1 VitD receptor SNP was significantly associated with RA. Comparing patients with RA to unaffected NAN controls, the Fok1 SNP was associated with RA using both genotypic [FF vs Ff vs ff: RA 20%, 54%, 26% vs control 22%, 44%, 34% (chi-square 13.35, p=0.003)] and dominant models [FF/Ff vs ff: RA 74% vs 26% control 66% vs 34% (OR 1.5, 95% CI 1.16-1.96, p=0.003)]. This association was strongest in shared-epitope-positive RA., Conclusion: VitD receptor polymorphisms may contribute to the high prevalence of RA in NAN populations.
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- 2012
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73. Classical HLA-DRB1 and DPB1 alleles account for HLA associations with primary biliary cirrhosis.
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Invernizzi P, Ransom M, Raychaudhuri S, Kosoy R, Lleo A, Shigeta R, Franke A, Bossa F, Amos CI, Gregersen PK, Siminovitch KA, Cusi D, de Bakker PI, Podda M, Gershwin ME, and Seldin MF
- Subjects
- Case-Control Studies, Gene Frequency, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Italy, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide, Risk Factors, White People genetics, HLA-DP beta-Chains genetics, HLA-DRB1 Chains genetics, Liver Cirrhosis, Biliary genetics, Liver Cirrhosis, Biliary immunology
- Abstract
Susceptibility to primary biliary cirrhosis (PBC) is strongly associated with human leukocyte antigen (HLA)-region polymorphisms. To determine if associations can be explained by classical HLA determinants, we studied Italian, 676 cases and 1440 controls, genotyped with dense single-nucleotide polymorphisms (SNPs) for which classical HLA alleles and amino acids were imputed. Although previous genome-wide association studies and our results show stronger SNP associations near DQB1, we demonstrate that the HLA signals can be attributed to classical DRB1 and DPB1 genes. Strong support for the predominant role of DRB1 is provided by our conditional analyses. We also demonstrate an independent association of DPB1. Specific HLA-DRB1 genes (*08, *11 and *14) account for most of the DRB1 association signal. Consistent with previous studies, DRB1*08 (P=1.59 × 10(-11)) was the strongest predisposing allele, whereas DRB1*11 (P=1.42 × 10(-10)) was protective. Additionally, DRB1*14 and the DPB1 association (DPB1*03:01; P=9.18 × 10(-7)) were predisposing risk alleles. No signal was observed in the HLA class 1 or class 3 regions. These findings better define the association of PBC with HLA and specifically support the role of classical HLA-DRB1 and DPB1 genes and alleles in susceptibility to PBC.
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- 2012
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74. Hepatocyte-specific Ptpn6 deletion protects from obesity-linked hepatic insulin resistance.
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Xu E, Charbonneau A, Rolland Y, Bellmann K, Pao L, Siminovitch KA, Neel BG, Beauchemin N, and Marette A
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- Animals, Blood Glucose metabolism, Diet, High-Fat, Gene Deletion, Insulin metabolism, Mice, Obesity metabolism, Insulin Resistance physiology, Liver metabolism, Obesity physiopathology, Protein Tyrosine Phosphatase, Non-Receptor Type 6 deficiency
- Abstract
The protein-tyrosine phosphatase Shp1 negatively regulates insulin action on glucose homeostasis in liver and muscle, but its potential role in obesity-linked insulin resistance has not been examined. To investigate the role of Shp1 in hepatic insulin resistance, we generated hepatocyte-specific Shp1 knockout mice (Ptpn6(H-KO)), which were subjected to extensive metabolic monitoring throughout an 8-week standard chow diet (SD) or high-fat diet (HFD) feeding. We report for the first time that Shp1 expression is upregulated in metabolic tissues of HFD-fed obese mice. When compared with their Shp1-expressing Ptpn6(f/f) littermates, Ptpn6(H-KO) mice exhibited significantly lowered fasting glycemia and heightened hepatic insulin sensitivity. After HFD feeding, Ptpn6(H-KO) mice developed comparable levels of obesity as Ptpn6(f/f) mice, but they were remarkably protected from liver insulin resistance, as revealed by euglycemic clamps and hepatic insulin signaling determinations. Although Ptpn6(H-KO) mice still acquired diet-induced peripheral insulin resistance, they were less hyperinsulinemic during a glucose tolerance test because of reduced insulin secretion. Ptpn6(H-KO) mice also exhibited increased insulin clearance in line with enhanced CC1 tyrosine phosphorylation in liver. These results show that hepatocyte Shp1 plays a critical role in the development of hepatic insulin resistance and represents a novel therapeutic target for obesity-linked diabetes.
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- 2012
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75. Association of primary biliary cirrhosis with variants in the CLEC16A, SOCS1, SPIB and SIAE immunomodulatory genes.
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Hirschfield GM, Xie G, Lu E, Sun Y, Juran BD, Chellappa V, Coltescu C, Mason AL, Milkiewicz P, Myers RP, Odin JA, Luketic VA, Bacon B, Bodenheimer H, Liakina V, Vincent C, Levy C, Pillai S, Lazaridis KN, Amos CI, and Siminovitch KA
- Subjects
- Acetylesterase metabolism, Alleles, Case-Control Studies, Chromosome Mapping methods, DNA-Binding Proteins metabolism, Enzyme Assays, Genetic Loci, Genetic Predisposition to Disease, Haplotypes, Humans, Lectins, C-Type metabolism, Liver Cirrhosis, Biliary immunology, Liver Cirrhosis, Biliary metabolism, Logistic Models, Monosaccharide Transport Proteins metabolism, Polymorphism, Single Nucleotide, Risk Factors, Suppressor of Cytokine Signaling 1 Protein, Suppressor of Cytokine Signaling Proteins metabolism, Transcription Factors metabolism, Acetylesterase genetics, DNA-Binding Proteins genetics, Lectins, C-Type genetics, Liver Cirrhosis, Biliary genetics, Monosaccharide Transport Proteins genetics, Suppressor of Cytokine Signaling Proteins genetics, Transcription Factors genetics
- Abstract
We fine mapped two primary biliary cirrhosis (PBC) risk loci, CLEC16A (C-type lectin domain family 16 member A)-suppressor of cytokine signaling 1 (SOCS1) and Spi-B protein (SPIB) and sequenced a locus, sialic acid acetylesterase (SIAE), proposed to harbor autoimmunity-associated mutations. In all, 1450 PBC cases and 2957 healthy controls were genotyped for 84 single-nucleotide polymorphisms (SNPs) across the CLEC16A-SOCS1 and SPIB loci. All 10 exons of the SIAE gene were resequenced in 381 cases and point substitutions of unknown significance assayed for activity and secretion. Fine mapping identified 26 SNPs across the CLEC16A-SOCS1 and 11 SNPs across the SPIB locus with significant association to PBC, the strongest signals at the CLEC16A-SOCS1 locus emanating from a SOCS1 intergenic SNP (rs243325; P=9.91 × 10(-9)) and at the SPIB locus from a SPIB intronic SNP (rs34944112; P=3.65 × 10(-9)). Among the associated SNPs at the CLEC16A-SOCS1 locus, two within the CLEC16A gene as well as one SOCS1 SNP (rs243325) remained significant after conditional logistic regression and contributed independently to risk. Sequencing of the SIAE gene and functional assays of newly identified variants revealed six patients with functional non-synonymous SIAE mutations (Fisher's P=9 × 10(-4) vs controls) We demonstrate independent effects on risk of PBC for CLEC16A, SOCS1 and SPIB variants, while identifying functionally defective SIAE variants as potential factors in risk for PBC.
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- 2012
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76. Meta-analysis identifies nine new loci associated with rheumatoid arthritis in the Japanese population.
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Okada Y, Terao C, Ikari K, Kochi Y, Ohmura K, Suzuki A, Kawaguchi T, Stahl EA, Kurreeman FA, Nishida N, Ohmiya H, Myouzen K, Takahashi M, Sawada T, Nishioka Y, Yukioka M, Matsubara T, Wakitani S, Teshima R, Tohma S, Takasugi K, Shimada K, Murasawa A, Honjo S, Matsuo K, Tanaka H, Tajima K, Suzuki T, Iwamoto T, Kawamura Y, Tanii H, Okazaki Y, Sasaki T, Gregersen PK, Padyukov L, Worthington J, Siminovitch KA, Lathrop M, Taniguchi A, Takahashi A, Tokunaga K, Kubo M, Nakamura Y, Kamatani N, Mimori T, Plenge RM, Yamanaka H, Momohara S, Yamada R, Matsuda F, and Yamamoto K
- Subjects
- Case-Control Studies, Humans, Japan epidemiology, Arthritis, Rheumatoid epidemiology, Arthritis, Rheumatoid genetics, Genetic Loci, Genetic Markers, Genetic Predisposition to Disease, Genome-Wide Association Study, Polymorphism, Single Nucleotide genetics
- Abstract
Rheumatoid arthritis is a common autoimmune disease characterized by chronic inflammation. We report a meta-analysis of genome-wide association studies (GWAS) in a Japanese population including 4,074 individuals with rheumatoid arthritis (cases) and 16,891 controls, followed by a replication in 5,277 rheumatoid arthritis cases and 21,684 controls. Our study identified nine loci newly associated with rheumatoid arthritis at a threshold of P < 5.0 × 10(-8), including B3GNT2, ANXA3, CSF2, CD83, NFKBIE, ARID5B, PDE2A-ARAP1, PLD4 and PTPN2. ANXA3 was also associated with susceptibility to systemic lupus erythematosus (P = 0.0040), and B3GNT2 and ARID5B were associated with Graves' disease (P = 3.5 × 10(-4) and 2.9 × 10(-4), respectively). We conducted a multi-ancestry comparative analysis with a previous meta-analysis in individuals of European descent (5,539 rheumatoid arthritis cases and 20,169 controls). This provided evidence of shared genetic risks of rheumatoid arthritis between the populations.
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- 2012
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77. The human OCTN1 (SLC22A4) reconstituted in liposomes catalyzes acetylcholine transport which is defective in the mutant L503F associated to the Crohn's disease.
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Pochini L, Scalise M, Galluccio M, Pani G, Siminovitch KA, and Indiveri C
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- Acetylcarnitine chemistry, Acetylcarnitine pharmacology, Acetylcholine genetics, Acetylcholine metabolism, Adenosine Triphosphate chemistry, Adenosine Triphosphate metabolism, Betaine analogs & derivatives, Betaine chemistry, Betaine pharmacology, Biological Transport, Active genetics, Carnitine chemistry, Carnitine pharmacology, Catalysis, Humans, Kinetics, Liposomes metabolism, Nootropic Agents chemistry, Nootropic Agents pharmacology, Organic Cation Transport Proteins antagonists & inhibitors, Organic Cation Transport Proteins genetics, Organic Cation Transport Proteins metabolism, Potassium Channel Blockers chemistry, Potassium Channel Blockers pharmacology, Symporters, Tetraethylammonium chemistry, Tetraethylammonium pharmacology, Acetylcholine chemistry, Amino Acid Substitution, Crohn Disease, Liposomes chemistry, Mutation, Missense, Organic Cation Transport Proteins chemistry
- Abstract
The organic cation transporter (OCTN1) plays key roles in transport of selected organic cations, but understanding of its biological functions remains limited by restricted knowledge of its substrate targets. Here we show capacity of human OCTN1-reconstituted proteoliposomes to mediate uptake and efflux of [(3)H]acetylcholine, the Km of transport being 1.0mM with V(max) of 160nmol⋅mg(-1)protein⋅min(-1). OCTN1-mediated transport of this neurotransmitter was time-dependent and was stimulated by intraliposomal ATP. The transporter operates as uniporter but translocates acetylcholine in both directions. [(3)H]acetylcholine uptake was competitively inhibited by tetraethylammonium, γ-butyrobetaine and acetylcarnitine, and was also inhibited by various polyamines. Decreasing intraliposomal ATP concentrations increased OCTN Km for acetylcholine, but V(max) was unaffected. Evaluation of the acetylcholine transporter properties of a variant form of OCTN1, the Crohn's disease-associated 503F variant, revealed time course, Km and V(max) for acetylcholine uptake to be comparable to that of wild-type OCTN1. Km for acetylcholine efflux was also comparable for both OCTN1 species, but V(max) of OCTN1 503F-mediated acetylcholine efflux (1.9nmol⋅mg(-1)protein⋅min(-1)) was significantly lower than that of wild-type OCTN1 (14nmol⋅mg(-1)protein⋅min(-1)). These data identify a new transport role for OCTN1 and raise the possibility that its involvement in the non-neuronal acetylcholine system may be relevant to the pathogenesis of Crohn's disease., (Copyright © 2011 Elsevier B.V. All rights reserved.)
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- 2012
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78. Five amino acids in three HLA proteins explain most of the association between MHC and seropositive rheumatoid arthritis.
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Raychaudhuri S, Sandor C, Stahl EA, Freudenberg J, Lee HS, Jia X, Alfredsson L, Padyukov L, Klareskog L, Worthington J, Siminovitch KA, Bae SC, Plenge RM, Gregersen PK, and de Bakker PI
- Subjects
- Case-Control Studies, Genome-Wide Association Study, Haplotypes genetics, Humans, Polymorphism, Single Nucleotide genetics, Amino Acid Substitution genetics, Arthritis, Rheumatoid genetics, HLA-B Antigens genetics, HLA-DP beta-Chains genetics, HLA-DRB1 Chains genetics, Major Histocompatibility Complex genetics, Models, Molecular
- Abstract
The genetic association of the major histocompatibility complex (MHC) to rheumatoid arthritis risk has commonly been attributed to alleles in HLA-DRB1. However, debate persists about the identity of the causal variants in HLA-DRB1 and the presence of independent effects elsewhere in the MHC. Using existing genome-wide SNP data in 5,018 individuals with seropositive rheumatoid arthritis (cases) and 14,974 unaffected controls, we imputed and tested classical alleles and amino acid polymorphisms in HLA-A, HLA-B, HLA-C, HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQB1 and HLA-DRB1, as well as 3,117 SNPs across the MHC. Conditional and haplotype analyses identified that three amino acid positions (11, 71 and 74) in HLA-DRβ1 and single-amino-acid polymorphisms in HLA-B (at position 9) and HLA-DPβ1 (at position 9), which are all located in peptide-binding grooves, almost completely explain the MHC association to rheumatoid arthritis risk. This study shows how imputation of functional variation from large reference panels can help fine map association signals in the MHC.
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- 2012
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79. Non-HLA genes modulate the risk of rheumatoid arthritis associated with HLA-DRB1 in a susceptible North American Native population.
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El-Gabalawy HS, Robinson DB, Daha NA, Oen KG, Smolik I, Elias B, Hart D, Bernstein CN, Sun Y, Lu Y, Houwing-Duistermaat JJ, and Siminovitch KA
- Subjects
- Alleles, Arthritis, Rheumatoid ethnology, Female, Gene Frequency, Genotype, Humans, Male, Models, Genetic, Neprilysin genetics, Polymorphism, Single Nucleotide, Receptors, Tumor Necrosis Factor, Member 14 genetics, TNF Receptor-Associated Factor 1 genetics, Arthritis, Rheumatoid genetics, Genetic Predisposition to Disease, HLA-DRB1 Chains genetics, Indians, North American genetics
- Abstract
Most of the genetic risk for rheumatoid arthritis (RA) is conferred by 'shared epitope' (SE), encoding alleles of HLA-DRB1. Specific North American Native (NAN) populations have RA prevalence rates of 2-5%, representing some of the highest rates estimated worldwide. As many NAN populations also demonstrate a high background frequency of SE, we sought to determine whether other genetic factors contribute to disease risk in this predisposed population. RA patients (n=333) and controls (n=490) from the Cree/Ojibway NAN population in Central Canada were HLA-DRB1 typed and tested for 21 single-nucleotide polymorphisms (SNPs) that have previously been associated with RA, including PTPN22, TRAF1-C5, CTLA4, PADI4, STAT4, FCRL3, CCL21, MMEL1-TNFRSF14, CDK6, PRKCQ, KIF5A-PIP4K2C, IL2RB, TNFAIP3, IL10-1082G/A and REL. Our findings indicate that SE is prevalent and represents a major genetic risk factor for RA in this population (82% cases versus 68% controls, odds ratio=2.2, 95% confidence interval 1.6-3.1, P<0.001). We also demonstrate that in the presence of SE, the minor allele of MMEL1-TNFRSF14 significantly reduces RA risk in a dominant manner, whereas TRAF1-C5 increases the risk. These findings point to the importance of non-HLA genes in determining RA risk in a population with a high frequency of disease predisposing HLA-DRB1 alleles.
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- 2011
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80. The autoimmune disease-associated PTPN22 variant promotes calpain-mediated Lyp/Pep degradation associated with lymphocyte and dendritic cell hyperresponsiveness.
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Zhang J, Zahir N, Jiang Q, Miliotis H, Heyraud S, Meng X, Dong B, Xie G, Qiu F, Hao Z, McCulloch CA, Keystone EC, Peterson AC, and Siminovitch KA
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- Animals, Autoimmune Diseases pathology, B-Lymphocytes immunology, Calpain metabolism, Isoenzymes genetics, Isoenzymes metabolism, Male, Mice, Mice, Mutant Strains, Organ Size, Spleen immunology, Spleen pathology, T-Lymphocytes immunology, Thymus Gland immunology, Thymus Gland pathology, Autoimmune Diseases genetics, Autoimmune Diseases immunology, Dendritic Cells immunology, Lymphocyte Activation, Protein Tyrosine Phosphatase, Non-Receptor Type 22 genetics, Protein Tyrosine Phosphatase, Non-Receptor Type 22 metabolism
- Abstract
A variant of the PTPN22-encoded Lyp phosphatase (Lyp620W) confers risk for autoimmune disease, but the mechanisms underlying this association remain unclear. We show here that mice expressing the Lyp variant homolog Pep619W manifest thymic and splenic enlargement accompanied by increases in T-cell number, activation and positive selection and in dendritic- and B-cell activation. Although Ptpn22 (Pep) transcript levels were comparable in Pep619W and wild-type Pep619R mice, Pep protein levels were dramatically reduced in the mutant mice, with Pep619W protein being more rapidly degraded and showing greater association with and in vitro cleavage by calpain 1 than Pep619R. Similarly, levels of the Lyp620W variant were decreased in human T and B cells, and its calpain binding and cleavage were increased relative to wild-type Lyp620R. Thus, calpain-mediated degradation with consequently reduced Lyp/Pep expression and lymphocyte and dendritic cell hyperresponsiveness represents a mechanism whereby Lyp620W may increase risk for autoimmune disease.
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- 2011
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81. Pervasive sharing of genetic effects in autoimmune disease.
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Cotsapas C, Voight BF, Rossin E, Lage K, Neale BM, Wallace C, Abecasis GR, Barrett JC, Behrens T, Cho J, De Jager PL, Elder JT, Graham RR, Gregersen P, Klareskog L, Siminovitch KA, van Heel DA, Wijmenga C, Worthington J, Todd JA, Hafler DA, Rich SS, and Daly MJ
- Subjects
- Cluster Analysis, Comorbidity, Genetic Loci, Genome-Wide Association Study, Humans, Phenotype, Polymorphism, Single Nucleotide, Protein Interaction Maps, Autoimmune Diseases genetics
- Abstract
Genome-wide association (GWA) studies have identified numerous, replicable, genetic associations between common single nucleotide polymorphisms (SNPs) and risk of common autoimmune and inflammatory (immune-mediated) diseases, some of which are shared between two diseases. Along with epidemiological and clinical evidence, this suggests that some genetic risk factors may be shared across diseases-as is the case with alleles in the Major Histocompatibility Locus. In this work we evaluate the extent of this sharing for 107 immune disease-risk SNPs in seven diseases: celiac disease, Crohn's disease, multiple sclerosis, psoriasis, rheumatoid arthritis, systemic lupus erythematosus, and type 1 diabetes. We have developed a novel statistic for Cross Phenotype Meta-Analysis (CPMA) which detects association of a SNP to multiple, but not necessarily all, phenotypes. With it, we find evidence that 47/107 (44%) immune-mediated disease risk SNPs are associated to multiple-but not all-immune-mediated diseases (SNP-wise P(CPMA)<0.01). We also show that distinct groups of interacting proteins are encoded near SNPs which predispose to the same subsets of diseases; we propose these as the mechanistic basis of shared disease risk. We are thus able to leverage genetic data across diseases to construct biological hypotheses about the underlying mechanism of pathogenesis., Competing Interests: The authors have declared that no competing interests exist.
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- 2011
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82. Fine mapping the TAGAP risk locus in rheumatoid arthritis.
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Chen R, Stahl EA, Kurreeman FA, Gregersen PK, Siminovitch KA, Worthington J, Padyukov L, Raychaudhuri S, and Plenge RM
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- Case-Control Studies, Genetic Loci, Genome-Wide Association Study, Humans, Polymorphism, Single Nucleotide, Risk Factors, Arthritis, Rheumatoid genetics, GTPase-Activating Proteins genetics
- Abstract
A common allele at the TAGAP gene locus demonstrates a suggestive, but not conclusive association with risk of rheumatoid arthritis (RA). To fine map the locus, we conducted comprehensive imputation of CEU HapMap single-nucleotide polymorphisms (SNPs) in a genome-wide association study (GWAS) of 5,500 RA cases and 22,621 controls (all of European ancestry). After controlling for population stratification with principal components analysis, the strongest signal of association was to an imputed SNP, rs212389 (P=3.9 × 10(-8), odds ratio=0.87). This SNP remained highly significant upon conditioning on the previous RA risk variant (rs394581, P=2.2 × 10(-5)) or on a SNP previously associated with celiac disease and type I diabetes (rs1738074, P=1.7 × 10(-4)). Our study has refined the TAGAP signal of association to a single haplotype in RA, and in doing so provides conclusive statistical evidence that the TAGAP locus is associated with RA risk. Our study also underscores the utility of comprehensive imputation in large GWAS data sets to fine map disease risk alleles.
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- 2011
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83. Compartmentalized CDK2 is connected with SHP-1 and β-catenin and regulates insulin internalization.
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Fiset A, Xu E, Bergeron S, Marette A, Pelletier G, Siminovitch KA, Olivier M, Beauchemin N, and Faure RL
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- Amino Acid Sequence, Antigens, CD metabolism, Cell Adhesion Molecules metabolism, Cell Line, Cell Membrane metabolism, Cyclin-Dependent Kinase 2 genetics, Detergents chemistry, Endosomes enzymology, Endosomes metabolism, Humans, Molecular Sequence Data, Phosphorylation, Protein Binding, RNA Interference, RNA, Small Interfering metabolism, Cyclin-Dependent Kinase 2 metabolism, Insulin metabolism, Protein Tyrosine Phosphatase, Non-Receptor Type 6 metabolism, beta Catenin metabolism
- Abstract
The cyclin-dependant kinase Cdk2 is compartmentalized in endosomes but its role is poorly understood. Here we show that Cdk2 present in hepatic endosome fractions is strictly located in a Triton X-100-resistant environment. The endosomal Cdk2 was found to be associated with the protein tyrosine phosphatase SHP-1, a regulator of insulin clearance, and the actin anchor β-catenin, a known substrate for both Cdk2 and SHP-1. In the plasma membranes and endosome fractions, β-catenin is associated with CEACAM1, also known as regulator of insulin clearance. We show that β-catenin, not CEACAM1, is a substrate for Cdk2. Partial down-modulation of Cdk2 in HEK293 cells increased the rate of insulin internalization. These findings reveal that Cdk2 functions, at least in part, via a Cdk2/SHP-1/β-catenin/CEACAM1 axis, and show for the first time that Cdk2 has the capacity to regulate insulin internalization., (Copyright © 2011 Elsevier Inc. All rights reserved.)
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- 2011
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84. N-WASp is required for Schwann cell cytoskeletal dynamics, normal myelin gene expression and peripheral nerve myelination.
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Jin F, Dong B, Georgiou J, Jiang Q, Zhang J, Bharioke A, Qiu F, Lommel S, Feltri ML, Wrabetz L, Roder JC, Eyer J, Chen X, Peterson AC, and Siminovitch KA
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- Animals, Axons metabolism, Blotting, Western, Cells, Cultured, Cytoskeleton genetics, Fluorescent Antibody Technique, Gait genetics, Gene Expression, Mice, Mice, Knockout, Myelin Sheath genetics, Reverse Transcriptase Polymerase Chain Reaction, Wiskott-Aldrich Syndrome Protein, Neuronal genetics, Cytoskeleton metabolism, Myelin Sheath metabolism, Peripheral Nerves metabolism, Schwann Cells metabolism, Wiskott-Aldrich Syndrome Protein, Neuronal metabolism
- Abstract
Schwann cells elaborate myelin sheaths around axons by spirally wrapping and compacting their plasma membranes. Although actin remodeling plays a crucial role in this process, the effectors that modulate the Schwann cell cytoskeleton are poorly defined. Here, we show that the actin cytoskeletal regulator, neural Wiskott-Aldrich syndrome protein (N-WASp), is upregulated in myelinating Schwann cells coincident with myelin elaboration. When N-WASp is conditionally deleted in Schwann cells at the onset of myelination, the cells continue to ensheath axons but fail to extend processes circumferentially to elaborate myelin. Myelin-related gene expression is also severely reduced in the N-WASp-deficient cells and in vitro process and lamellipodia formation are disrupted. Although affected mice demonstrate obvious motor deficits these do not appear to progress, the mutant animals achieving normal body weights and living to advanced age. Our observations demonstrate that N-WASp plays an essential role in Schwann cell maturation and myelin formation.
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- 2011
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85. Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci.
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Zhernakova A, Stahl EA, Trynka G, Raychaudhuri S, Festen EA, Franke L, Westra HJ, Fehrmann RS, Kurreeman FA, Thomson B, Gupta N, Romanos J, McManus R, Ryan AW, Turner G, Brouwer E, Posthumus MD, Remmers EF, Tucci F, Toes R, Grandone E, Mazzilli MC, Rybak A, Cukrowska B, Coenen MJ, Radstake TR, van Riel PL, Li Y, de Bakker PI, Gregersen PK, Worthington J, Siminovitch KA, Klareskog L, Huizinga TW, Wijmenga C, and Plenge RM
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- Alleles, Arthritis, Rheumatoid immunology, Celiac Disease immunology, Genetic Loci, Genome-Wide Association Study, Histocompatibility Antigens genetics, Lymphocyte Activation, Polymorphism, Single Nucleotide, Selection, Genetic, T-Lymphocytes immunology, T-Lymphocytes metabolism, Arthritis, Rheumatoid genetics, Celiac Disease genetics
- Abstract
Epidemiology and candidate gene studies indicate a shared genetic basis for celiac disease (CD) and rheumatoid arthritis (RA), but the extent of this sharing has not been systematically explored. Previous studies demonstrate that 6 of the established non-HLA CD and RA risk loci (out of 26 loci for each disease) are shared between both diseases. We hypothesized that there are additional shared risk alleles and that combining genome-wide association study (GWAS) data from each disease would increase power to identify these shared risk alleles. We performed a meta-analysis of two published GWAS on CD (4,533 cases and 10,750 controls) and RA (5,539 cases and 17,231 controls). After genotyping the top associated SNPs in 2,169 CD cases and 2,255 controls, and 2,845 RA cases and 4,944 controls, 8 additional SNPs demonstrated P<5 × 10(-8) in a combined analysis of all 50,266 samples, including four SNPs that have not been previously confirmed in either disease: rs10892279 near the DDX6 gene (P(combined) = 1.2 × 10(-12)), rs864537 near CD247 (P(combined) = 2.2 × 10(-11)), rs2298428 near UBE2L3 (P(combined) = 2.5 × 10(-10)), and rs11203203 near UBASH3A (P(combined) = 1.1 × 10(-8)). We also confirmed that 4 gene loci previously established in either CD or RA are associated with the other autoimmune disease at combined P<5 × 10(-8) (SH2B3, 8q24, STAT4, and TRAF1-C5). From the 14 shared gene loci, 7 SNPs showed a genome-wide significant effect on expression of one or more transcripts in the linkage disequilibrium (LD) block around the SNP. These associations implicate antigen presentation and T-cell activation as a shared mechanism of disease pathogenesis and underscore the utility of cross-disease meta-analysis for identification of genetic risk factors with pleiotropic effects between two clinically distinct diseases., Competing Interests: YL has employment and stock interest in Celera.
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- 2011
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86. Genetics and the environment converge to dysregulate N-glycosylation in multiple sclerosis.
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Mkhikian H, Grigorian A, Li CF, Chen HL, Newton B, Zhou RW, Beeton C, Torossian S, Tatarian GG, Lee SU, Lau K, Walker E, Siminovitch KA, Chandy KG, Yu Z, Dennis JW, and Demetriou M
- Subjects
- Animals, Antigens, CD genetics, CTLA-4 Antigen, Case-Control Studies, Cholecalciferol metabolism, Cohort Studies, Down-Regulation, Female, Genetic Variation, Glycosylation, Haplotypes, Humans, Male, Mice, Mice, Inbred Strains, Multiple Sclerosis metabolism, N-Acetylglucosaminyltransferases genetics, N-Acetylglucosaminyltransferases metabolism, Receptors, Interleukin-2 genetics, Receptors, Interleukin-7 genetics, Risk Factors, Signal Transduction, Sunlight, Multiple Sclerosis genetics
- Abstract
How environmental factors combine with genetic risk at the molecular level to promote complex trait diseases such as multiple sclerosis (MS) is largely unknown. In mice, N-glycan branching by the Golgi enzymes Mgat1 and/or Mgat5 prevents T cell hyperactivity, cytotoxic T-lymphocyte antigen 4 (CTLA-4) endocytosis, spontaneous inflammatory demyelination and neurodegeneration, the latter pathologies characteristic of MS. Here we show that MS risk modulators converge to alter N-glycosylation and/or CTLA-4 surface retention conditional on metabolism and vitamin D(3), including genetic variants in interleukin-7 receptor-α (IL7RA*C), interleukin-2 receptor-α (IL2RA*T), MGAT1 (IV(A)V(T-T)) and CTLA-4 (Thr17Ala). Downregulation of Mgat1 by IL7RA*C and IL2RA*T is opposed by MGAT1 (IV(A)V(T-T)) and vitamin D(3), optimizing branching and mitigating MS risk when combined with enhanced CTLA-4 N-glycosylation by CTLA-4 Thr17. Our data suggest a molecular mechanism in MS whereby multiple environmental and genetic inputs lead to dysregulation of a final common pathway, namely N-glycosylation.
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- 2011
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87. Locus category based analysis of a large genome-wide association study of rheumatoid arthritis.
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Freudenberg J, Lee AT, Siminovitch KA, Amos CI, Ballard D, Li W, and Gregersen PK
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- Animals, Arthritis, Rheumatoid immunology, Humans, Immune System, Linkage Disequilibrium genetics, Mice, Polymorphism, Single Nucleotide genetics, Arthritis, Rheumatoid genetics, Genetic Loci genetics, Genome, Human genetics, Genome-Wide Association Study
- Abstract
To pinpoint true positive single-nucleotide polymorphism (SNP) associations in a genome-wide association study (GWAS) of rheumatoid arthritis (RA), we categorize genetic loci by external knowledge. We test both the 'enrichment of associated loci' in a locus category and the 'combined association' of a locus category. The former is quantified by the odds ratio for the presence of SNP associations at the loci of a category, whereas the latter is quantified by the number of loci in a category that have SNP associations. These measures are compared with their expected values as obtained from the permutation of the affection status. To account for linkage disequilibrium (LD) among SNPs, we view each LD block as a genetic locus. Positional candidates were defined as loci implicated by earlier GWAS results, whereas functional candidates were defined by annotations regarding the molecular roles of genes, such as gene ontology categories. As expected, immune-related categories show the largest enrichment signal, although it is not very strong. The intersection of positional and functional candidate information predicts novel RA loci near the genes TEC/TXK, MBL2 and PIK3R1/CD180. Notably, a combined association signal is not only produced by immune-related categories, but also by most other categories and even randomly defined categories. The unspecific quality of these signals limits the possible conclusions from combined association tests. It also reduces the magnitude of enrichment test results. These unspecific signals might result from common variants of small effect and hardly concentrated in candidate categories, or an inflated size of associated regions from weak LD with infrequent mutations.
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- 2010
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88. Biochemical and genetic evidence for a SAP-PKC-theta interaction contributing to IL-4 regulation.
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Cannons JL, Wu JZ, Gomez-Rodriguez J, Zhang J, Dong B, Liu Y, Shaw S, Siminovitch KA, and Schwartzberg PL
- Subjects
- Animals, CD4-Positive T-Lymphocytes immunology, CD4-Positive T-Lymphocytes metabolism, Cell Line, Gene Expression Regulation immunology, Humans, Interleukin-4 deficiency, Interleukin-4 genetics, Isoenzymes deficiency, Jurkat Cells, Lymphocyte Activation genetics, Lymphocyte Activation immunology, Mice, Mice, Inbred C57BL, Mice, Knockout, Mice, Transgenic, Protein Kinase C deficiency, Protein Kinase C-theta, Protein Transport genetics, Protein Transport immunology, Receptors, Cell Surface deficiency, Signal Transduction genetics, Signal Transduction immunology, Signaling Lymphocytic Activation Molecule Family Member 1, Up-Regulation genetics, Up-Regulation immunology, Antigens, CD genetics, Antigens, CD metabolism, Interleukin-4 biosynthesis, Isoenzymes genetics, Isoenzymes metabolism, Protein Kinase C genetics, Protein Kinase C metabolism, Receptors, Cell Surface genetics, Receptors, Cell Surface metabolism
- Abstract
Signaling lymphocytic activation molecule-associated protein (SAP), an adaptor molecule that recruits Fyn to the signaling lymphocytic activation molecule (SLAM) family of immunomodulatory receptors, is mutated in X-linked lymphoproliferative disease. CD4(+) T cells from SAP-deficient mice have defective TCR-induced and follicular Th cell IL-4 production and impaired T cell-mediated help for germinal center formation; however, the downstream intermediates contributing to these defects remain unclear. We previously found that SAP-deficient CD4(+) T cells exhibit decreased protein kinase C (PKC)-theta recruitment upon TCR stimulation. We demonstrate in this paper using GST pulldowns and coimmunoprecipitation studies that SAP constitutively associates with PKC- in T cells. SAP-PKC-theta interactions required R78 of SAP, a residue previously implicated in Fyn recruitment, yet SAP's interactions with PKC-theta occurred independent of phosphotyrosine binding and Fyn. Overexpression of SAP in T cells increased and sustained PKC-theta recruitment to the immune synapse and elevated IL-4 production in response to TCR plus SLAM-mediated stimulation. Moreover, PKC-theta, like SAP, was required for SLAM-mediated increases in IL-4 production, and, conversely, membrane-targeted PKC-theta mutants rescued IL-4 expression in SAP(-/-) CD4(+) T cells, providing genetic evidence that PKC-theta is a critical component of SLAM/SAP-mediated pathways that influence TCR-driven IL-4 production.
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- 2010
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89. Elucidation of the integrin LFA-1-mediated signaling pathway of actin polarization in natural killer cells.
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Mace EM, Zhang J, Siminovitch KA, and Takei F
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- Actin-Related Protein 2 metabolism, Animals, Blotting, Western, Embryonic Stem Cells metabolism, Female, Immunoprecipitation, Intercellular Adhesion Molecule-1 metabolism, Mice, Mice, Inbred C57BL, Mice, Knockout, Phosphatidylinositol 4,5-Diphosphate metabolism, Phosphotransferases (Alcohol Group Acceptor) metabolism, Stromal Cells metabolism, Talin physiology, Vinculin metabolism, Wiskott-Aldrich Syndrome Protein physiology, Actins metabolism, Killer Cells, Natural metabolism, Lymphocyte Function-Associated Antigen-1 metabolism, Signal Transduction physiology
- Abstract
The leukocyte integrin LFA-1 is critical for natural killer (NK) cell cytotoxicity as it mediates NK-cell adhesion to target cells and generates activating signals that lead to polarization of the actin cytoskeleton. However, the LFA-1-mediated signaling pathway is not fully understood. Here, we examined the subcellular localization of actin-associated proteins in wild-type, talin-deficient, and Wiskott-Aldrich Syndrome protein (WASP)-deficient NK cells bound to beads coated with the LFA-1 ligand intercellular adhesion molecule-1 (ICAM-1). In addition, we carried out coimmunoprecipitation analyses and also used a pharmacologic reagent to reduce the level of phosphatidylinositol-4,5-bisphosphate (PIP(2)). The results revealed the following signaling pathways. Upon ICAM-1 binding to LFA-1, talin redistributes to the site of LFA-1 ligation and initiates 2 signaling pathways. First, talin recruits the actin nucleating protein complex Arp2/3 via constitutive association of vinculin with talin and Arp2/3. Second, talin also associates with type I phosphatidylinositol 4-phosphate 5-kinase (PIPKI) and binding of LFA-1 to ICAM-1 results in localized increase in PIP(2). This increase in PIP(2) recruits WASP to the site of LFA-1 ligation where WASP promotes Arp2/3-mediated actin polymerization. These processes are critical for the initiation of NK cell-mediated cytotoxicity.
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- 2010
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90. Genome-wide meta-analyses identify three loci associated with primary biliary cirrhosis.
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Liu X, Invernizzi P, Lu Y, Kosoy R, Lu Y, Bianchi I, Podda M, Xu C, Xie G, Macciardi F, Selmi C, Lupoli S, Shigeta R, Ransom M, Lleo A, Lee AT, Mason AL, Myers RP, Peltekian KM, Ghent CN, Bernuzzi F, Zuin M, Rosina F, Borghesio E, Floreani A, Lazzari R, Niro G, Andriulli A, Muratori L, Muratori P, Almasio PL, Andreone P, Margotti M, Brunetto M, Coco B, Alvaro D, Bragazzi MC, Marra F, Pisano A, Rigamonti C, Colombo M, Marzioni M, Benedetti A, Fabris L, Strazzabosco M, Portincasa P, Palmieri VO, Tiribelli C, Croce L, Bruno S, Rossi S, Vinci M, Prisco C, Mattalia A, Toniutto P, Picciotto A, Galli A, Ferrari C, Colombo S, Casella G, Morini L, Caporaso N, Colli A, Spinzi G, Montanari R, Gregersen PK, Heathcote EJ, Hirschfield GM, Siminovitch KA, Amos CI, Gershwin ME, and Seldin MF
- Subjects
- Canada, Genome, Genome-Wide Association Study, Humans, Interferon Regulatory Factors, Liver Cirrhosis, Biliary, Meta-Analysis as Topic, Odds Ratio, Alleles, White People genetics
- Abstract
A genome-wide association screen for primary biliary cirrhosis risk alleles was performed in an Italian cohort. The results from the Italian cohort replicated IL12A and IL12RB associations, and a combined meta-analysis using a Canadian dataset identified newly associated loci at SPIB (P = 7.9 x 10(-11), odds ratio (OR) = 1.46), IRF5-TNPO3 (P = 2.8 x 10(-10), OR = 1.63) and 17q12-21 (P = 1.7 x 10(-10), OR = 1.38).
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- 2010
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91. Variants at IRF5-TNPO3, 17q12-21 and MMEL1 are associated with primary biliary cirrhosis.
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Hirschfield GM, Liu X, Han Y, Gorlov IP, Lu Y, Xu C, Lu Y, Chen W, Juran BD, Coltescu C, Mason AL, Milkiewicz P, Myers RP, Odin JA, Luketic VA, Speiciene D, Vincent C, Levy C, Gregersen PK, Zhang J, Heathcote EJ, Lazaridis KN, Amos CI, and Siminovitch KA
- Subjects
- Case-Control Studies, Genes, Genome-Wide Association Study, Genotype, Humans, Risk Factors, Liver Cirrhosis, Biliary genetics
- Abstract
We genotyped individuals with primary biliary cirrhosis and unaffected controls for suggestive risk loci (genome-wide association P < 1 x 10(-4)) identified in a previous genome-wide association study. Combined analysis of the genome-wide association and replication datasets identified IRF5-TNPO3 (combined P = 8.66 x 10(-13)), 17q12-21 (combined P = 3.50 x 10(-13)) and MMEL1 (combined P = 3.15 x 10(-8)) as new primary biliary cirrhosis susceptibility loci. Fine-mapping studies showed that a single variant accounts for the IRF5-TNPO3 association. As these loci are implicated in other autoimmune conditions, these findings confirm genetic overlap among such diseases.
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- 2010
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92. Carriage of a tumor necrosis factor polymorphism amplifies the cytotoxic T-lymphocyte antigen 4 attributed risk of primary biliary cirrhosis: evidence for a gene-gene interaction.
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Juran BD, Atkinson EJ, Larson JJ, Schlicht EM, Liu X, Heathcote EJ, Hirschfield GM, Siminovitch KA, and Lazaridis KN
- Subjects
- Adult, Aged, Aged, 80 and over, CTLA-4 Antigen, Female, Humans, Male, Middle Aged, Polymorphism, Single Nucleotide, Risk, Antigens, CD genetics, Liver Cirrhosis, Biliary genetics, Tumor Necrosis Factor-alpha genetics
- Abstract
Unlabelled: Common genetic variants significantly influence complex diseases such as primary biliary cirrhosis (PBC). We recently reported an association between PBC and a single nucleotide polymorphism (rs231725) of the immunoreceptor gene cytotoxic T-lymphocyte antigen 4 (CTLA4). We hypothesized that PBC risk attributed to this polymorphism might be increased by propensity to an overly robust inflammatory response. Thus, we examined its potential interaction with the commonly studied -308AG promoter polymorphism (rs1800629) of the tumor necrosis factor (TNF) gene for which the variant TNF2A allele causes increased TNF production. The polymorphisms were genotyped in 866 PBC patients and 761 controls from independent US and Canadian registries; the effects of individual single nucleotide polymorphisms (SNPs) and their interaction on PBC risk was assessed by logistic regression. The reported association of PBC with the CTLA4 "A/A" genotype was replicated in the Canadian cohort and significant for PBC risk in the combined data (odds ratio [OR], 1.68; P = 0.0005). TNF2A allele frequency was elevated in PBC patients, but only reached borderline significance using the combined data (OR, 1.21; P = 0.042). Analysis showed that TNF2A carriage was significantly increased in CTLA4 "A/A" PBC patients compared with CTLA4 "A/A" controls (39.7% versus 16.5%, P = 0.0004); no apparent increase of TNF2A carriage was noted in CTLA4 "A/G" or "G/G" individuals. Finally, interaction under a logistic model was highly significant, as TNF2A carriage in combination with the CTLA4 "A/A" genotype was present in 6.5% of PBC patients, compared with 1.7% of controls (OR, 3.98; P < 0.0001)., Conclusion: TNF2A amplifies the CTLA4 rs231725 "A/A" genotype risk for PBC. Although the mechanisms remain unclear, the premise that deficiency in T-cell regulation resulting in an increased risk of PBC is amplified by overexpression of an important proinflammatory cytokine provides a basis for future functional studies.
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- 2010
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93. Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci.
- Author
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Stahl EA, Raychaudhuri S, Remmers EF, Xie G, Eyre S, Thomson BP, Li Y, Kurreeman FA, Zhernakova A, Hinks A, Guiducci C, Chen R, Alfredsson L, Amos CI, Ardlie KG, Barton A, Bowes J, Brouwer E, Burtt NP, Catanese JJ, Coblyn J, Coenen MJ, Costenbader KH, Criswell LA, Crusius JB, Cui J, de Bakker PI, De Jager PL, Ding B, Emery P, Flynn E, Harrison P, Hocking LJ, Huizinga TW, Kastner DL, Ke X, Lee AT, Liu X, Martin P, Morgan AW, Padyukov L, Posthumus MD, Radstake TR, Reid DM, Seielstad M, Seldin MF, Shadick NA, Steer S, Tak PP, Thomson W, van der Helm-van Mil AH, van der Horst-Bruinsma IE, van der Schoot CE, van Riel PL, Weinblatt ME, Wilson AG, Wolbink GJ, Wordsworth BP, Wijmenga C, Karlson EW, Toes RE, de Vries N, Begovich AB, Worthington J, Siminovitch KA, Gregersen PK, Klareskog L, and Plenge RM
- Subjects
- Autoantibodies administration & dosage, Genome-Wide Association Study, Humans, Polymorphism, Single Nucleotide, Risk Factors, Arthritis, Rheumatoid genetics, Genetic Loci, Genetic Predisposition to Disease
- Abstract
To identify new genetic risk factors for rheumatoid arthritis, we conducted a genome-wide association study meta-analysis of 5,539 autoantibody-positive individuals with rheumatoid arthritis (cases) and 20,169 controls of European descent, followed by replication in an independent set of 6,768 rheumatoid arthritis cases and 8,806 controls. Of 34 SNPs selected for replication, 7 new rheumatoid arthritis risk alleles were identified at genome-wide significance (P < 5 x 10(-8)) in an analysis of all 41,282 samples. The associated SNPs are near genes of known immune function, including IL6ST, SPRED2, RBPJ, CCR6, IRF5 and PXK. We also refined associations at two established rheumatoid arthritis risk loci (IL2RA and CCL21) and confirmed the association at AFF3. These new associations bring the total number of confirmed rheumatoid arthritis risk loci to 31 among individuals of European ancestry. An additional 11 SNPs replicated at P < 0.05, many of which are validated autoimmune risk alleles, suggesting that most represent genuine rheumatoid arthritis risk alleles.
- Published
- 2010
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94. Navigating the road to personalized medicine: can we believe?
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Hirschfield GM, Amos CI, and Siminovitch KA
- Subjects
- Genetic Variation, Genotype, Humans, Nod2 Signaling Adaptor Protein genetics, Crohn Disease genetics, Genetic Predisposition to Disease, Precision Medicine
- Published
- 2010
- Full Text
- View/download PDF
95. Uptake of apoptotic DC converts immature DC into tolerogenic DC that induce differentiation of Foxp3+ Treg.
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Kushwah R, Wu J, Oliver JR, Jiang G, Zhang J, Siminovitch KA, and Hu J
- Subjects
- Animals, B7-2 Antigen biosynthesis, B7-2 Antigen genetics, CD4-Positive T-Lymphocytes cytology, CD4-Positive T-Lymphocytes immunology, Coculture Techniques, Dendritic Cells cytology, Dendritic Cells drug effects, Dendritic Cells metabolism, Dendritic Cells radiation effects, Interleukin-12 biosynthesis, Interleukin-12 genetics, Intracellular Signaling Peptides and Proteins physiology, Lipopolysaccharides pharmacology, Lymphopoiesis, Mice, Mice, Inbred C57BL, Necrosis, Protein Biosynthesis, Protein Serine-Threonine Kinases physiology, Spleen cytology, Spleen immunology, T-Lymphocytes, Regulatory cytology, TOR Serine-Threonine Kinases, Transforming Growth Factor beta1 metabolism, Apoptosis drug effects, Apoptosis radiation effects, Dendritic Cells immunology, Forkhead Transcription Factors analysis, Immune Tolerance immunology, Phagocytosis immunology, T-Lymphocytes, Regulatory immunology
- Abstract
DC apoptosis has been observed in patients with cancer and sepsis, and defects in DC apoptosis have been implicated in the development of autoimmune diseases. However, the mechanisms of how DC apoptosis affects immune responses, are unclear. In this study, we showed that immature viable DC have the ability to uptake apoptotic DC as well as necrotic DC without it being recognized as an inflammatory event by immature viable DC. However, the specific uptake of apoptotic DC converted immature viable DC into tolerogenic DC, which were resistant to LPS-induced maturation. These tolerogenic DC secreted increased levels of TGF-beta1, which induced differentiation of naïve T cells into Foxp3(+) Treg. Furthermore, induction of Treg differentiation only occurred upon uptake of apoptotic DC and not apoptotic splenocytes by viable DC, indicating that it is specifically the uptake of apoptotic DC that gives viable immature DC the potential to induce Foxp3(+) Treg. Taken together, these findings identify uptake of apoptotic DC by viable immature DC as an immunologically tolerogenic event.
- Published
- 2010
- Full Text
- View/download PDF
96. Fibrocyte activation in rheumatoid arthritis.
- Author
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Galligan CL, Siminovitch KA, Keystone EC, Bykerk V, Perez OD, and Fish EN
- Subjects
- Adult, Animals, Arthritis, Rheumatoid blood, Arthritis, Rheumatoid immunology, Cells, Cultured, Connective Tissue Cells immunology, Connective Tissue Cells metabolism, Female, Fibroblasts immunology, Flow Cytometry, Humans, Male, Mice, Mice, Inbred DBA, Middle Aged, Signal Transduction, Synovial Membrane cytology, Synovial Membrane immunology, Synovial Membrane metabolism, Arthritis, Rheumatoid metabolism, Fibroblasts metabolism
- Abstract
Objectives: RA is a common, relapsing autoimmune disease primarily affecting the joints. Fibroblast-like synovial (FLS) cells are thought to be responsible for pannus formation and secretion of factors that recruit leucocytes to affected joints, thereby promoting bone and cartilage destruction. Fibrocytes are multipotent circulating stem cells that may have a role in RA pathogenesis, perhaps as the precursors of the FLS cells, or by regulating FLS cell function., Methods: We utilized multidimensional phospho-specific flow cytometry to characterize the activation status of peripheral blood (PB) fibrocytes derived from human RA patients at different stages of disease and from mice with CIA., Results: Human PB fibrocytes from RA patients exhibited phosporylation activation of the p44/42 and p38 MAP kinases (MAPKs), and STAT3 (signal transducer and activator of transcription) and STAT-5 early in disease, within the first year of diagnosis. Similarly, in murine CIA, an increase in the total number of PB phosphoSTAT5-positive fibrocytes was observed at early time points in disease. Notably, in the affected paws of mice with CIA, we identified an increased number of fibrocytes, in contrast to the paws of control mice., Conclusions: These data suggest that activated fibrocytes may influence the disease process in RA and may serve as surrogate markers for disease in the PB of affected patients.
- Published
- 2010
- Full Text
- View/download PDF
97. Glucagon-like peptide-1 receptor signalling selectively regulates murine lymphocyte proliferation and maintenance of peripheral regulatory T cells.
- Author
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Hadjiyanni I, Siminovitch KA, Danska JS, and Drucker DJ
- Subjects
- Animals, Cell Division, Cell Movement, Cyclic AMP metabolism, Diabetes Mellitus, Type 1 physiopathology, Female, Flow Cytometry, Glucagon-Like Peptide-1 Receptor, Humans, Lymph Nodes cytology, Lymph Nodes immunology, Male, Mice, Mice, Knockout, Organ Specificity, Receptors, Glucagon deficiency, Receptors, Glucagon genetics, Signal Transduction, T-Lymphocyte Subsets cytology, T-Lymphocyte Subsets immunology, T-Lymphocytes, Regulatory cytology, Lymphocyte Activation immunology, Mice, Inbred NOD immunology, Receptors, Glucagon immunology, T-Lymphocytes, Regulatory immunology
- Abstract
Aims/hypothesis: Glucagon-like peptide-1 receptor (GLP-1R) agonists improve glucose control in animals and humans with type 1 diabetes. However, there is little information on the role of the GLP-1R in the immune system. We studied the role of the GLP-1R in immune function in wild-type (WT) and nonobese diabetic (NOD) and Glp1r-/- mice., Methods: Glp1r mRNA expression was examined in sorted immune subpopulations by RT-PCR. The effects of GLP-1R activation were assessed on cAMP production and proliferation, migration and survival of primary immune cells from WT and NOD mice. The ability of primary cells from Glp1r-/- mice to proliferate, migrate or survive apoptosis was determined. Immunophenotyping studies were performed to assess the frequency of immune subpopulations in Glp1r-/- mice., Results: Ex vivo activation of the GLP-1R resulted in a modest but significant elevation of cAMP in primary thymocytes and splenocytes from both WT and NOD mice. GLP-1R activation did not increase proliferation of primary thymocytes, splenocytes or peripheral lymph node cells. In contrast, Glp1r-/- thymocytes exhibited a hypoproliferative response, whilst peripheral Glp1r-/- lymphocytes were hyperproliferative in response to mitogenic stimulation. Activation or loss of GLP-1R signalling did not modify apoptosis or chemotaxis in primary lymphocytes. Male Glp1r-/- mice exhibited a significantly lower percentage of peripheral regulatory T cells, although no differences were observed in the numbers of CD4+ and CD8+ T cells and B cells in the spleen and lymph nodes of Glp1r-/- mice., Conclusions/interpretation: These studies establish that GLP-1R signalling may regulate lymphocyte proliferation and maintenance of peripheral regulatory T cells.
- Published
- 2010
- Full Text
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98. Genetic variants at CD28, PRDM1 and CD2/CD58 are associated with rheumatoid arthritis risk.
- Author
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Raychaudhuri S, Thomson BP, Remmers EF, Eyre S, Hinks A, Guiducci C, Catanese JJ, Xie G, Stahl EA, Chen R, Alfredsson L, Amos CI, Ardlie KG, Barton A, Bowes J, Burtt NP, Chang M, Coblyn J, Costenbader KH, Criswell LA, Crusius JB, Cui J, De Jager PL, Ding B, Emery P, Flynn E, Harrison P, Hocking LJ, Huizinga TW, Kastner DL, Ke X, Kurreeman FA, Lee AT, Liu X, Li Y, Martin P, Morgan AW, Padyukov L, Reid DM, Seielstad M, Seldin MF, Shadick NA, Steer S, Tak PP, Thomson W, van der Helm-van Mil AH, van der Horst-Bruinsma IE, Weinblatt ME, Wilson AG, Wolbink GJ, Wordsworth P, Altshuler D, Karlson EW, Toes RE, de Vries N, Begovich AB, Siminovitch KA, Worthington J, Klareskog L, Gregersen PK, Daly MJ, and Plenge RM
- Subjects
- Case-Control Studies, Genetic Predisposition to Disease, Genotype, Humans, Polymorphism, Single Nucleotide, Positive Regulatory Domain I-Binding Factor 1, Risk Factors, Arthritis, Rheumatoid genetics, CD2 Antigens genetics, CD28 Antigens genetics, CD58 Antigens genetics, Genetic Variation, Repressor Proteins genetics
- Abstract
To discover new rheumatoid arthritis (RA) risk loci, we systematically examined 370 SNPs from 179 independent loci with P < 0.001 in a published meta-analysis of RA genome-wide association studies (GWAS) of 3,393 cases and 12,462 controls. We used Gene Relationships Across Implicated Loci (GRAIL), a computational method that applies statistical text mining to PubMed abstracts, to score these 179 loci for functional relationships to genes in 16 established RA disease loci. We identified 22 loci with a significant degree of functional connectivity. We genotyped 22 representative SNPs in an independent set of 7,957 cases and 11,958 matched controls. Three were convincingly validated: CD2-CD58 (rs11586238, P = 1 x 10(-6) replication, P = 1 x 10(-9) overall), CD28 (rs1980422, P = 5 x 10(-6) replication, P = 1 x 10(-9) overall) and PRDM1 (rs548234, P = 1 x 10(-5) replication, P = 2 x 10(-8) overall). An additional four were replicated (P < 0.0023): TAGAP (rs394581, P = 0.0002 replication, P = 4 x 10(-7) overall), PTPRC (rs10919563, P = 0.0003 replication, P = 7 x 10(-7) overall), TRAF6-RAG1 (rs540386, P = 0.0008 replication, P = 4 x 10(-6) overall) and FCGR2A (rs12746613, P = 0.0022 replication, P = 2 x 10(-5) overall). Many of these loci are also associated to other immunologic diseases.
- Published
- 2009
- Full Text
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99. Apoptotic dendritic cells induce tolerance in mice through suppression of dendritic cell maturation and induction of antigen-specific regulatory T cells.
- Author
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Kushwah R, Oliver JR, Zhang J, Siminovitch KA, and Hu J
- Subjects
- Adjuvants, Immunologic pharmacology, Animals, Cell Differentiation immunology, Dendritic Cells cytology, Enzyme-Linked Immunosorbent Assay, Mice, Mice, Inbred C57BL, Mice, Transgenic, Ovalbumin immunology, Ovalbumin pharmacology, Transforming Growth Factor beta1 biosynthesis, Transforming Growth Factor beta1 immunology, Apoptosis immunology, Dendritic Cells immunology, Immune Tolerance immunology, Lymphocyte Activation immunology, T-Lymphocytes, Regulatory immunology
- Abstract
Dendritic cell (DC) apoptosis has been shown to play a role in maintaining a balance between tolerance and immunity. However, the mechanisms of how DC apoptosis affects the immune response are unclear. We have shown that in vitro culture of apoptotic DCs with immature DCs, results in their uptake by immature DCs, which subsequently turn into tolerogenic DCs, which then secrete TGF-beta1 and induce Foxp3(+) regulatory T cells (T(regs)). In this study we looked at the effects of apoptotic DCs in vivo. Here we show that apoptotic DCs are taken up by viable DCs in vivo, which suppresses the ability of viable DCs to undergo maturation and subsequent migration to the lymph nodes in response to LPS. Additionally, delivery of apoptotic DCs to LPS inflamed lungs results in resolution of inflammation, which is mediated by the ability of apoptotic DCs to suppress response of viable DCs to LPS. Additionally, apoptotic DCs also induce TGF-beta1 secretion in the mediastinal lymph nodes, which results in expansion of Foxp3(+) T(regs). Most importantly, we show that delivery of apoptotic DCs followed by OVA in CFA to mice suppresses T cell response to OVA and instead induces de novo generation of OVA-specific T(regs). Furthermore, delivery of apoptotic DCs followed by OVA in CFA results in expansion of T(regs) in TCR transgenic (OT-II) mice. These findings demonstrate that apoptotic DCs are taken up by viable DCs in vivo, which promotes tolerance through suppression of DC maturation and induction of T(regs).
- Published
- 2009
- Full Text
- View/download PDF
100. Contributions of Wiskott-Aldrich syndrome family cytoskeletal regulatory adapters to immune regulation.
- Author
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Zhang J, Dong B, and Siminovitch KA
- Subjects
- Animals, Cytoskeletal Proteins immunology, Humans, Lymphocyte Activation, Protein Multimerization immunology, Signal Transduction, T-Lymphocytes immunology, T-Lymphocytes pathology, Wiskott-Aldrich Syndrome pathology, Wiskott-Aldrich Syndrome Protein Family immunology, Cytoskeletal Proteins metabolism, Immunomodulation, T-Lymphocytes metabolism, Wiskott-Aldrich Syndrome immunology, Wiskott-Aldrich Syndrome Protein Family metabolism
- Abstract
Cytoskeletal structure and dynamic rearrangement are integrally involved in coupling external stimuli to the orchestrated network of molecular interactions and cellular responses required for T-cell effector function. Members of the Wiskott-Aldrich syndrome protein (WASp) family are now widely recognized as cytoskeletal scaffolding adapters that coordinate the transmission of stimulatory signals to downstream induction of actin remodeling and cytoskeletal-dependent T-cell responses. In this review, we discuss the structural and functional properties of the WASp family members, with an emphasis on the roles of these proteins in the molecular pathways underpinning T-cell activation. The contributions of WASp family proteins and the cytoskeletal reorganization they evoke to expression of specific T-cell effector functions and the implications of such activity to normal immune responses and to the immunologic deficits manifested by Wiskott-Aldrich syndrome patients are also described.
- Published
- 2009
- Full Text
- View/download PDF
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